plain text manual pages for MOPAC 6
MOPAC MANUAL
(Sixth Edition)
by
James J. P. Stewart,
Frank J. Seiler Research Laboratory
United States Air Force Academy
CO 80840
October 1990
CONTENTS
1 FORWARD BY PROF. MICHAEL J. S. DEWAR . . . . . . . . i
2 PREFACE TO SIXTH EDITION, VERSION 6.00 . . . . . . iii
3 UPDATES FROM VERSION 5.00 . . . . . . . . . . . . iii
4 ACKNOWLEDGEMENTS . . . . . . . . . . . . . . . . . vi
CHAPTER 1 DESCRIPTION OF MOPAC
1.1 SUMMARY OF MOPAC CAPABILITIES . . . . . . . . . . 1-2
1.2 COPYRIGHT STATUS OF MOPAC . . . . . . . . . . . . 1-3
1.3 PORTING MOPAC TO OTHER MACHINES . . . . . . . . . 1-3
1.4 RELATIONSHIP OF AMPAC AND MOPAC . . . . . . . . . 1-3
1.5 PROGRAMS RECOMMENDED FOR USE WITH MOPAC . . . . . 1-5
1.6 THE DATA-FILE . . . . . . . . . . . . . . . . . . 1-6
1.6.1 Example Of Data For Ethylene . . . . . . . . . . 1-6
1.6.2 Example Of Data For Polytetrahydrofuran . . . . 1-8
CHAPTER 2 KEYWORDS
2.1 SPECIFICATION OF KEYWORDS . . . . . . . . . . . . 2-1
2.2 FULL LIST OF KEYWORDS USED IN MOPAC . . . . . . . 2-2
2.3 DEFINITIONS OF KEYWORDS . . . . . . . . . . . . . 2-5
2.4 KEYWORDS THAT GO TOGETHER . . . . . . . . . . . 2-41
CHAPTER 3 GEOMETRY SPECIFICATION
3.1 INTERNAL COORDINATE DEFINITION . . . . . . . . . . 3-1
3.1.1 Constraints . . . . . . . . . . . . . . . . . . 3-2
3.2 GAUSSIAN Z-MATRICES . . . . . . . . . . . . . . . 3-2
3.3 CARTESIAN COORDINATE DEFINITION . . . . . . . . . 3-4
3.4 CONVERSION BETWEEN VARIOUS FORMATS . . . . . . . . 3-4
3.5 DEFINITION OF ELEMENTS AND ISOTOPES . . . . . . . 3-5
3.6 EXAMPLES OF COORDINATE DEFINITIONS. . . . . . . . 3-8
CHAPTER 4 EXAMPLES
4.1 MNRSD1 TEST DATA FILE FOR FORMALDEHYDE . . . . . . 4-1
4.2 MOPAC OUTPUT FOR TEST-DATA FILE MNRSD1 . . . . . . 4-2
CHAPTER 5 TESTDATA
5.1 DATA FILE FOR A FORCE CALCULATION . . . . . . . . 5-2
5.2 RESULTS FILE FOR THE FORCE CALCULATION . . . . . . 5-2
5.3 EXAMPLE OF REACTION PATH WITH SYMMETRY . . . . . 5-11
CHAPTER 6 BACKGROUND
6.1 INTRODUCTION . . . . . . . . . . . . . . . . . . . 6-1
Page 2
6.2 AIDER . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3 CORRECTION TO THE PEPTIDE LINKAGE . . . . . . . . 6-2
6.4 LEVEL OF PRECISION WITHIN MOPAC . . . . . . . . . 6-4
6.5 CONVERGENCE TESTS IN SUBROUTINE ITER . . . . . . . 6-6
6.6 CONVERGENCE IN SCF CALCULATION . . . . . . . . . . 6-6
6.7 CAUSES OF FAILURE TO ACHIEVE AN SCF . . . . . . . 6-8
6.8 TORSION OR DIHEDRAL ANGLE COHERENCY . . . . . . . 6-8
6.9 VIBRATIONAL ANALYSIS . . . . . . . . . . . . . . . 6-9
6.10 A NOTE ON THERMOCHEMISTRY . . . . . . . . . . . . 6-9
6.11 REACTION COORDINATES . . . . . . . . . . . . . . 6-17
6.12 SPARKLES . . . . . . . . . . . . . . . . . . . . 6-31
6.13 MECHANISM OF THE FRAME IN THE FORCE CALCULATION 6-32
6.14 CONFIGURATION INTERACTION . . . . . . . . . . . 6-33
6.15 REDUCED MASSES IN A FORCE CALCULATION . . . . . 6-40
6.16 USE OF SADDLE CALCULATION . . . . . . . . . . . 6-40
6.17 HOW TO ESCAPE FROM A HILLTOP . . . . . . . . . . 6-42
6.18 POLARIZABILITY CALCULATION . . . . . . . . . . . 6-44
6.19 SOLID STATE CAPABILITY . . . . . . . . . . . . . 6-46
CHAPTER 7 PROGRAM
7.1 MAIN GEOMETRIC SEQUENCE . . . . . . . . . . . . . 7-2
7.2 MAIN ELECTRONIC FLOW . . . . . . . . . . . . . . . 7-3
7.3 CONTROL WITHIN MOPAC . . . . . . . . . . . . . . . 7-4
CHAPTER 8 ERROR MESSAGES PRODUCED BY MOPAC
CHAPTER 9 CRITERIA
9.1 SCF CRITERION . . . . . . . . . . . . . . . . . . 9-1
9.2 GEOMETRIC OPTIMIZATION CRITERIA . . . . . . . . . 9-2
CHAPTER 10 DEBUGGING
10.1 DEBUGGING KEYWORDS . . . . . . . . . . . . . . . 10-1
CHAPTER 11 INSTALLING MOPAC
11.1 ESP CALCULATION. . . . . . . . . . . . . . . . . 11-6
APPENDIX A FORTRAN FILES
APPENDIX B SUBROUTINE CALLS IN MOPAC
Page 3
APPENDIX C DESCRIPTION OF SUBROUTINES IN MOPAC
APPENDIX D HEATS OF FORMATION OF SOME MNDO, PM3 AND AM1 COMPOUNDS
APPENDIX E REFERENCES
1 FORWARD BY PROF. MICHAEL J. S. DEWAR
"MOPAC is the present culmination of a
continuing project that started twenty years ago,
directed to the development of quantum mechanical
procedures simple enough, and accurate enough, to
be useful to chemists as an aid in their own
research. A historical account of this
development, with references, has appeared [1].
The first really effective treatment was MINDO/3
[2], which is still useful in various areas of
hydrocarbon chemistry but ran into problems with
heteroatoms. This was succeeded by MNDO [3] and
more recently by AM1 [4] which seems to have
overcome most of the deficiencies of its
predecessors at no cost in computing time.
Our computer programs steadily evolved with
the development of new algorithms. In addition to
the basic programs for the SCF calculations and
geometry optimization, programs were developed for
calculating vibration frequencies [5],
thermodynamic parameters [6], kinetic isotope
effects [7], linear polymers [8], polarizabilities
and hyperpolarizabilities [9,10], and SCF-CI
calculations [11]. While this disjointed
collection of programs served its purpose, it was
inconvenient and time consuming to use. A major
step was the integration [12] of most of these
into a single unified program [MOPAC] with a
greatly simplified input. The individual programs
were also rewritten in a more efficient form so
that the computing time reported for most
calculations has now been halved. In its present
form MOPAC is impressively easy to use and it
contains options for nearly all the applications
where our procedures have been found useful."
Michael J.S. Dewar, January 1987
i
REFERENCES
(1) Dewar, M.J.S., J. Mol. Struct., 100, 41 (1983).
(2) Dewar, M.J.S.; Bingham, R.C.; Lo, D.H., J. Am. Chem. Soc., 97,
1285 (1975).
(3) Dewar, M.J.S.; Thiel, W., J. Am. Chem. Soc., 99, 4899 (1977).
(4) Dewar, M.J.S.; Zoebisch, E.G.; Healy, E.F.; Stewart, J.J.P.,
J. Am. Chem. Soc.; 107, 3902 (1985).
(5) Dewar, M.J.S.; Ford, G.P., J. Am. Chem. Soc., 99, 1685 (1977);
Dewar, M.J.S.; Ford, G.; McKee, M.; Rzepa, H.S.; Yamaguchi, Y.,
J. Mol. Struct., 43, 135 (1978).
(6) Dewar, M.J.S.; Ford, G., J. Am. Chem. Soc., 99, 7822 (1977).
(7) Dewar, M.J.S.; Brown, S.B.; Ford, G.P.; Nelson, D.J.;
Rzepa, H.S., J. Am. Chem. Soc., 100, 7832 (1978).
(8) Dewar, M.J.S.; Yamaguchi, Y.; Suck, S.H.,
Chem. Phys. Lett., 50,175,279 (1977).
(9) Dewar, M.J.S.; Bergman, J.G.; Suck, S.H.; Weiner, P.K.,
Chem. Phys. Lett., 38,226,(1976); Dewar, M.J.S.; Yamaguchi, Y.;
Suck, S.H., Chem. Phys. Lett., 59, 541 (1978).
(10) Dewar, M.J.S.; Stewart, J.J.P., Chem. Phys. Lett.,
111,416 (1984).
(11) Dewar, M.J.S.; Doubleday, C., J. Am. Chem. Soc.,
100, 4935 (1978).
(12) Stewart, J.J.P. QCPE # 455.
ii
2 PREFACE TO SIXTH EDITION, VERSION 6.00
As indicated at the time of release of MOPAC 5.00, there has
been a gap of two years' duration. It is likely that a second gap
of two years' duration will follow this release.
The main change from a user's point of view (who else matters?)
in MOPAC 6.00 has been that MOPAC now runs faster than before. In
addition, the range of PM3 and AM1 elements is increased. Finally,
some bells and whistles have been added, such as Gaussian Z-matrix
input and output, polymer electronic and phonon band structures and
densities of states. Experienced users should refer to the 'update
release notes' for a concise description of all modifications.
3 UPDATES FROM VERSION 5.00
Except for MOPAC 5.00, MOPAC has been updated once a year.
This is the best compromise between staying current and asking users
to continuously change their software. Updates may be obtained from
QCPE at the same cost as the original, or from sites that have a
current copy. All VAX versions of MOPAC have the same QCPE number -
455; they are distinguished by version numbers. Users are
recommended to update their programs at least once every two years,
and preferably every year.
New Features of Version 6.0
1. PM3 has been extended to include Be, Mg, Zn, Ga, Ge, As, Se, Cd,
In, Sn, Sb, Te, Hg, Tl, Pb, and Bi.
2. Changes to the IRC/DRC
1. The amount of output has been reduced. The 'missing' output
can be printed by using appropriate keywords.
2. Half-lives are now accurately generated. Earlier versions
had a small error due to calculation start-up. Both
positive and negative half-lives are now accurate.
3. The energy partition output has been rewritten so that all terms
having to do with each diatomic pair are now printed on one
line.
4. A LOG file will normally be generated. This is intended to be
read while the calculation is running. The LOG file can be
suppressed by the user.
5. Elements can be labeled with up to six alphanumeric characters.
iii
6. Gaussian Z-matrices can be input and printed (in the ARC file).
7. Multiple data-sets can be run in one job.
8. Up to three lines of keywords can be specified.
9. The DEBUG, 1SCF, and C.I. keywords have been re-defined.
10. An Eigenvector Following option has been added.
11. Polymer electronic band structure and density of states added.
12. Polymer phonon band structure and density of states added.
13. The GRID option has been rewritten.
14. The PATH option has been extended.
KEYWORDS ADDED IN VERSION 6.00
In going to Version 6.00, many keywords were added. These are
defined fully later on. The complete set of new or modified
keywords follows:
& + AIDER AIGIN AIGOUT
DIPOLE DIPX DIPZ DIPZ DMAX=n.n
EF EIGINV ESP ESPRST HESS=n
IUPD=n K=(n.nn,n) MODE=n MS=n NOANCI
NODIIS NOLOG NONR NOTHIEL NSURF
OLDGEO ORIDE POINT POINT1=n POINT2=n
POTWRT RECALC=n SCALE SCFCRT= SCINCR
SETUP SETUP=name SLOPE STEP SYMAVG
STO3G TS WILLIAMS
KEYWORDS DROPPED FROM VERSION 5.00
FULSCF Reason: Line searches now always involve full SCF
calculations. The frozen density matrix option is no longer
supported.
CYCLES=n Reason: The maximum number of cycles is now not defined.
Users should control jobs via " t=n.nn".
ERRORS CORRECTED IN VERSION 5.0
1. Force constants and frequencies calculated using non-variationally
optimized wavefunctions were faulty.
2. A full keyword line (no extra spaces) would be corrupted if the first
character was not a space.
iv
3. PRECISE FORCE calculations on triatomics had spuriously large trivial
vibrations.
4. FORCE calculations with many more hydrogen atoms than MAXLIT would
fail to generate force constants or normal coordinates.
5. The EXTERNAL option was limited to AM1.
6. Vibrational transition dipoles were in error by about 30%.
7. The reformation of the density matrix when a non-variationally
optimized wavefunction was used was incomplete.
Help with MOPAC
-------------------------------------------------
Telephone and mail support is given by the
Frank J. Seiler Research Laboratory on a time
permitting basis. If you need help, call
the Seiler MOPAC Consultant at
(719) 472-2655
Similarly, mail should be addressed to
MOPAC Consultant
FJSRL/NC
U.S. Air Force Academy CO 80840-6528
-------------------------------------------------
v
4 ACKNOWLEDGEMENTS
Acknowledgements
For her unflagging patience in checking the manual for clarity
of expression, and for drawing to my attention innumerable spelling
and grammatical errors, I thank my wife, Anna.
Over the years a large amount of advice, ideas and code has
been contributed by various people in order to improve MOPAC. The
following incomplete list recognises various contributors:
Prof. Santiago Olivella: Critical analysis of Versions 1 to 3.
Prof. Tsuneo Hirano: Rewrite of the Energy Partition.
Prof. Peter Pulay: Designing the rapid pseudodiagonalization.
Prof. Mark Gordon: Critical comments on the IRC.
Prof. Henry Kurtz: Writing the polarizability and
hyperpolarizability.
Prof. Henry Rzepa: Providing the code for the BFGS optimizer.
Dr. Yoshihisa Inoue: Many suggestions for improving readability.
Major Donn Storch and Lt. Col. Skip Dieter: Critical review of
versions
3-5.
Lt. Cols. Larry Davis and Larry Burggraf: Designed the form
of the DRC and IRC.
Dr. John McKelvey: Numerous suggestions for improving output.
Dr. Erich Wimmer: Suggestions for imcreasing the speed of
calculation.
Dr. James Friedheim: Testing of Versions 1 and 2.
Dr. Eamonn Healy: Critical evaluation of Versions 1-4.
This list does not include the large number of people who
developed methods which are used in MOPAC. The more important
contributions are given in the References at the end of this Manual
I wish to thank Prof. Michael J. S. Dewar for providing the
facilities and funds during the initial development of the MOPAC program,
the staff of the Frank J. Seiler Research Laboratory and the Chemistry
Department at the Air Force Academy for their support.
vi
CHAPTER 1
DESCRIPTION OF MOPAC
MOPAC is a general-purpose semi-empirical molecular orbital package
for the study of chemical structures and reactions. The semi-empirical
Hamiltonians MNDO, MINDO/3, AM1, and PM3 are used in the electronic part
of the calculation to obtain molecular orbitals, the heat of formation
and its derivative with respect to molecular geometry. Using these
results MOPAC calculates the vibrational spectra, thermodynamic
quantities, isotopic substitution effects and force constants for
molecules, radicals, ions, and polymers. For studying chemical
reactions, a transition-state location routine and two transition state
optimizing routines are available. For users to get the most out of the
program, they must understand how the program works, how to enter data,
how to interpret the results, and what to do when things go wrong.
While MOPAC calls upon many concepts in quantum theory and
thermodynamics and uses some fairly advanced mathematics, the user need
not be familiar with these specialized topics. MOPAC is written with the
non-theoretician in mind. The input data are kept as simple as possible
so users can give their attention to the chemistry involved and not
concern themselves with quantum and thermodynamic exotica.
The simplest description of how MOPAC works is that the user creates
a data-file which describes a molecular system and specifies what kind of
calculations and output are desired. The user then commands MOPAC to
carry out the calculation using that data-file. Finally the user
extracts the desired output on the system from the output files created
by MOPAC.
NOTES (1) This is the "sixth edition". MOPAC has undergone a steady
expansion since its first release, and users of the earlier editions are
recommended to familiarize themselves with the changes which are
described in this manual. If any errors are found, or if MOPAC does not
perform as described, please contact Dr. James J. P. Stewart,
Frank J. Seiler Research Laboratory, U.S. Air Force Academy, Colorado
Springs, CO 80840-6528. (2) MOPAC runs successfully on normal CDC, Data
General, Gould, and Digital computers, and also on the CDC 205 and
CRAY-XMP "supercomputers". The CRAY version has been partly optimized to
take advantage of the CRAY architecture. Several versions exist for
microcomputers such as the IBM PC-AT and XT, Zenith, etc.
1-1
DESCRIPTION OF MOPAC Page 1-2
1.1 SUMMARY OF MOPAC CAPABILITIES
1. MNDO, MINDO/3, AM1, and PM3 Hamiltonians.
2. Restricted Hartree-Fock (RHF) and Unrestricted Hartree-Fock
(UHF) methods.
3. Extensive Configuration Interaction
1. 100 configurations
2. Singlets, Doublets, Triplets, Quartets, Quintets, and
Sextets
3. Excited states
4. Geometry optimizations, etc., on specified states
4. Single SCF calculation
5. Geometry optimization
6. Gradient minimization
7. Transition state location
8. Reaction path coordinate calculation
9. Force constant calculation
10. Normal coordinate analysis
11. Transition dipole calculation
12. Thermodynamic properties calculation
13. Localized orbitals
14. Covalent bond orders
15. Bond analysis into sigma and pi contributions
16. One dimensional polymer calculation
17. Dynamic Reaction Coordinate calculation
18. Intrinsic Reaction Coordinate calculation
- 2 -
DESCRIPTION OF MOPAC Page 1-3
1.2 COPYRIGHT STATUS OF MOPAC
At the request of the Air Force Academy Law Department the following
notice has been placed in MOPAC.
Notice of Public Domain nature of MOPAC
'This computer program is a work of the United States
Government and as such is not subject to protection by
copyright (17 U.S.C. # 105.) Any person who fraudulently
places a copyright notice or does any other act contrary
to the provisions of 17 U.S. Code 506(c) shall be subject
to the penalties provided therein. This notice shall not
be altered or removed from this software and is to be on
all reproductions.'
I recommend that a user obtain a copy by either copying it from an
existing site or ordering an 'official' copy from the Quantum Chemistry
Program Exchange, (QCPE), Department of Chemistry, Indiana University,
Bloomington, Indiana, 47405. The cost covers handling only. Contact the
Editor, Richard Counts, at (812) 855-4784 for further details.
1.3 PORTING MOPAC TO OTHER MACHINES
MOPAC is written for the DIGITAL VAX computer. However, the program
has been written with the idea that it will be ported to other machines.
After such a port has been done, the new program should be given the
version number 6.10, or, if two or more versions are generated, 6.20,
6.30, etc. To validate the new copy, QCPE has a test-suite of
calculations. If all tests are passed, within the tolerances given in
the tests, then the new program can be called a valid version of MOPAC 6.
Insofar as is practical, the mode of submission of a MOPAC job should be
preserved, e.g.,
(prompt) MOPAC <data-set> [<queue-options>...]
Any changes which do not violate the FORTRAN-77 conventions, and
which users believe would be generally desirable, can be sent to the
author.
1.4 RELATIONSHIP OF AMPAC AND MOPAC
In 1985 MOPAC 3.0 and AMPAC 1.0 were submitted to QCPE for
distribution. At that time, AMPAC differed from MOPAC in that it had the
AM1 algorithm. Additionally, changes in some MNDO parameters in AMPAC
made AMPAC results incompatable with MOPAC Versions 1-3. Subsequent
- 3 -
DESCRIPTION OF MOPAC Page 1-4
versions of MOPAC, in addition to being more highly debugged than Version
3.0, also had the AM1 method. Such versions were compatable with AMPAC
and with versions 1-3 of MOPAC.
In order to avoid confusion, all versions of MOPAC after 3.0 include
journal references so that the user knows unambiguously which parameter
sets were used in any given job.
Since 1985 AMPAC and MOPAC have evolved along different lines. In
MOPAC I have endeavoured to provide a highly robust program, one with
only a few new features, but which is easily portable and which can be
relied upon to give precise, if not very exciting, answers. At Austin,
the functionality of AMPAC has been enhanced by the research work of
Prof. Dewar's group. The new AMPAC 2.1 thus has functionalities not
present in MOPAC. In publications, users should cite not only the
program name but also the version number.
Commercial concerns have optimized both MOPAC and AMPAC for use on
supercomputers. The quality of optimization and the degree to which the
parent algorithm has been preserved differs between MOPAC and AMPAC and
also between some machine specific versions. Different users may prefer
one program to the other, based on considerations such as speed. Some
modifications of AMPAC run faster than some modifications of MOPAC, and
vice versa, but if these are modified versions of MOPAC 3.0 or AMPAC 1.0,
they represent the programming prowess of the companies doing the
conversion, and not any intrinsic difference between the two programs.
Testing of these large algorithms is difficult, and several times
users have reported bugs in MOPAC or AMPAC which were introduced after
they were supplied by QCPE.
Cooperative Development of MOPAC
MOPAC has developed, and hopefully will continue to develop, by the
addition of contributed code. As a policy, any supplied code which is
incorporated into MOPAC will be described in the next release of the
Manual, and the author or supplier acknowledged. In the following
release only journal references will be retained. The objective is to
produce a good program. This is obviously not a one-person undertaking;
if it was, then the product would be poor indeed. Instead, as we are in
a time of rapid change in computational chemistry, a time characterized
by a very free exchange of ideas and code, MOPAC has been evolving by
accretion. The unstinting and generous donation of intellectual effort
speaks highly of the donors. However, with the rapid commercialization
of computational chemistry software in the past few years, it is
unfortunate but it seems unlikely that this idyllic state will continue.
- 4 -
DESCRIPTION OF MOPAC Page 1-5
1.5 PROGRAMS RECOMMENDED FOR USE WITH MOPAC
MOPAC is the core program of a series of programs for the theoretical
study of chemical phenomena. This version is the sixth in an on-going
development, and efforts are being made to continue its further
evolution. In order to make using MOPAC easier, five other programs have
also been written. Users of MOPAC are recommended to use all four
programs. Efforts will be made to continue the development of these
programs.
HELP
HELP is a stand-alone program which mimics the VAX HELP function.
It is intended for users on UNIX computers. HELP comes with the basic
MOPAC 6.00, and is recommended for general use.
DRAW
DRAW, written by Maj. Donn Storch, USAF, and available through QCPE,
is a powerful editing program specifically written to interface with
MOPAC. Among the various facilities it offers are:
1. The on-line editing and analysis of a data file, starting from
scratch or from an existing data file, an archive file, or from
a results file.
2. The option of continuous graphical representation of the system
being studied. Several types of terminals are supported,
including DIGITAL, TEKTRONIX, and TERAK terminals.
3. The drawing of electron density contour maps generated by
DENSITY on graphical devices.
4. The drawing of solid-state band structures generated by MOSOL.
5. The sketching of molecular vibrations, generated by a normal
coordinate analysis.
DENSITY
DENSITY, written by Dr. James J. P. Stewart, and available through
QCPE, is an electron-density plotting program. It accepts data-files
directly from MOPAC, and is intended to be used for the graphical
representation of electron density distribution, individual M.O.'s, and
difference maps.
MOHELP
MOHELP, also available through QCPE, is an on-line help facility,
written by Maj. Donn Storch and Dr. James J. P. Stewart, to allow non-VAX
users access to the VAX HELP libraries for MOPAC, DRAW, and DENSITY.
- 5 -
DESCRIPTION OF MOPAC Page 1-6
MOSOL
MOSOL (Distributed by QCPE) is a full solid-state MNDO program
written by Dr. James J. P. Stewart. In comparison with MOPAC, MOSOL is
extremely slow. As a result, while geometry optimization, force
constants, and other functions can be carried out by MOSOL, these slow
calculations are best done using the solid-state facility within MOPAC.
MOSOL should be used for two or three dimensional solids only, a task
that MOPAC cannot perform.
1.6 THE DATA-FILE
This section is aimed at the complete novice -- someone who knows
nothing at all about the structure of a MOPAC data-file.
First of all, there are at most four possible types of data-files
for MOPAC, but the simplest data-file is the most commonly used. Rather
than define it, two examples are shown below. An explanation of the
geometry definitions shown in the examples is given in the chapter
"GEOMETRY SPECIFICATION".
1.6.1 Example Of Data For Ethylene
Line 1 : UHF PULAY MINDO3 VECTORS DENSITY LOCAL T=300
Line 2 : EXAMPLE OF DATA FOR MOPAC
Line 3 : MINDO/3 UHF CLOSED-SHELL D2D ETHYLENE
Line 4a: C
Line 4b: C 1.400118 1
Line 4c: H 1.098326 1 123.572063 1
Line 4d: H 1.098326 1 123.572063 1 180.000000 0 2 1 3
Line 4e: H 1.098326 1 123.572063 1 90.000000 0 1 2 3
Line 4f: H 1.098326 1 123.572063 1 270.000000 0 1 2 3
Line 5 :
As can be seen, the first three lines are textual. The first line
consists of keywords (here seven keywords are shown). These control the
calculation. The next two lines are comments or titles. The user might
want to put the name of the molecule and why it is being run on these two
lines.
These three lines are obligatory. If no name or comment is wanted,
leave blank lines. If no keywords are specified, leave a blank line. A
common error is to have a blank line before the keyword line: this error
is quite tricky to find, so be careful not to have four lines before the
start of the geometric data (lines 4a-4f in the example). Whatever is
decided, the three lines, blank or otherwise, are obligatory.
- 6 -
DESCRIPTION OF MOPAC Page 1-7
In the example given, one line of keywords and two of documentation
are shown. By use of keywords, these defaults can be changed. Modifying
keywords are +, &, and SETUP. These are defined in the KEYWORDS chapter.
The following table illustrates the allowed combinations:
Line 1 Line 2 Line 3 Line 4 Line 5 Setup used
Keys Text Text Z-matrix Z-matrix not used
Keys + Keys Text Text Z-matrix not used
Keys + Keys + Keys Text Text not used
Keys & Keys Text Z-matrix Z-matrix not used
Keys & Keys & Keys Z-matrix Z-matrix not used
Keys SETUP Text Text Z-matrix Z-matrix 1 or 2 lines used
Keys + Keys SETUP Text Text Z-matrix 1 line used
Keys & Keys SETUP Text Z-matrix Z-matrix 1 line used
No other combinations are allowed.
The proposed use of the SETUP option is to allow a frequently
used set of keywords to be defined by a single keyword. For
example, if the default criteria are not suitable, SETUP might
contain
" SCFCRT=1.D-8 SHIFT=30 ITRY=600 GNORM=0.02 ANALYT "
" "
The order of usage of a keyword is Line 1 > Line 2 > Line 3. Line 1
> SETUP. Line 2 > SETUP. SETUP > built in default values.
The next set of lines defines the geometry. In the example,
the numbers are all neatly lined up; this is not necessary, but does
make it easier when looking for errors in the data. The geometry is
defined in lines 4a to 4f; line 5 terminates both the geometry and
the data-file. Any additional data, for example symmetry data,
would follow line 5.
Summarizing, then, the structure for a MOPAC data-file is:
Line 1: Keywords. (See chapter 2 on definitions of keywords)
Line 2: Title of the calculation, e.g. the name of the
molecule or ion.
Line 3: Other information describing the calculation.
Lines 4: Internal or cartesian coordinates (See chapter on
specification of geometry)
Line 5: Blank line to terminate the geometry definition.
Other layouts for data-files involve additions to the simple
layout. These additions occur at the end of the data-file, after
line 5. The three most common additions are:
(a) Symmetry data: This follows the geometric data, and is
ended by a blank line.
- 7 -
DESCRIPTION OF MOPAC Page 1-8
(b) Reaction path: After all geometry and symmetry data (if
any) are read in, points on the reaction coordinate are defined.
(c) Saddle data: A complete second geometry is input. The
second geometry follows the first geometry and symmetry data (if
any).
1.6.2 Example Of Data For Polytetrahydrofuran
The following example illustrates the data file for a four hour
polytetrahydrofuran calculation. As you can see the layout of the
data is almost the same as that for a molecule, the main difference
is in the presence of the translation vector atom "Tv".
Line 1 :T=4H
Line 2 : POLY-TETRAHYDROFURAN (C4 H8 O)2
Line 3 :
Line 4a: C 0.000000 0 0.000000 0 0.000000 0 0 0 0
Line 4b: C 1.551261 1 0.000000 0 0.000000 0 1 0 0
Line 4c: O 1.401861 1 108.919034 1 0.000000 0 2 1 0
Line 4d: C 1.401958 1 119.302489 1 -179.392581 1 3 2 1
Line 4e: C 1.551074 1 108.956238 1 179.014664 1 4 3 2
Line 4f: C 1.541928 1 113.074843 1 179.724877 1 5 4 3
Line 4g: C 1.551502 1 113.039652 1 179.525806 1 6 5 4
Line 4h: O 1.402677 1 108.663575 1 179.855864 1 7 6 5
Line 4i: C 1.402671 1 119.250433 1 -179.637345 1 8 7 6
Line 4j: C 1.552020 1 108.665746 1 -179.161900 1 9 8 7
Line 4k: XX 1.552507 1 112.659354 1 -178.914985 1 10 9 8
Line 4l: XX 1.547723 1 113.375266 1 -179.924995 1 11 10 9
Line 4m: H 1.114250 1 89.824605 1 126.911018 1 1 3 2
Line 4n: H 1.114708 1 89.909148 1 -126.650667 1 1 3 2
Line 4o: H 1.123297 1 93.602831 1 127.182594 1 2 4 3
Line 4p: H 1.123640 1 93.853406 1 -126.320187 1 2 4 3
Line 4q: H 1.123549 1 90.682924 1 126.763659 1 4 6 5
Line 4r: H 1.123417 1 90.679889 1 -127.033695 1 4 6 5
Line 4s: H 1.114352 1 90.239157 1 126.447043 1 5 7 6
Line 4t: H 1.114462 1 89.842852 1 -127.140168 1 5 7 6
Line 4u: H 1.114340 1 89.831790 1 126.653999 1 6 8 7
Line 4v: H 1.114433 1 89.753913 1 -126.926618 1 6 8 7
Line 4w: H 1.123126 1 93.644744 1 127.030541 1 7 9 8
Line 4x: H 1.123225 1 93.880969 1 -126.380511 1 7 9 8
Line 4y: H 1.123328 1 90.261019 1 127.815464 1 9 11 10
Line 4z: H 1.123227 1 91.051403 1 -125.914234 1 9 11 10
Line 4A: H 1.113970 1 90.374545 1 126.799259 1 10 12 11
Line 4B: H 1.114347 1 90.255788 1 -126.709810 1 10 12 11
Line 4C: Tv 12.299490 1 0.000000 0 0.000000 0 1 11 10
Line 5 : 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Polytetrahydrofuran has a repeat unit of (C4 H8 O)2; i.e.,
twice the monomer unit. This is necessary in order to allow the
lattice to repeat after a translation through 12.3 Angstroms. See
the section on Solid State Capability for further details.
- 8 -
DESCRIPTION OF MOPAC Page 1-9
Note the two dummy atoms on lines 4k and 4l. These are useful,
but not essential, for defining the geometry. The atoms on lines 4y
to 4B use these dummy atoms, as does the translation vector on line
4C. The translation vector has only the length marked for
optimization. The reason for this is also explained in the
Background chapter.
- 9 -
CHAPTER 2
KEYWORDS
2.1 SPECIFICATION OF KEYWORDS
All control data are entered in the form of keywords, which form the
first line of a data-file. A description of what each keyword does is
given in Section 2-3. The order in which keywords appear is not
important although they must be separated by a space. Some keywords can
be abbreviated, allowed abbreviations are noted in Section 2-3 (for
example 1ELECTRON can be entered as 1ELECT). However the full keyword is
preferred in order to more clearly document the calculation and to
obviate the possibility that an abbreviated keyword might not be
recognized. If there is insufficient space in the first line for all the
keywords needed, then consider abbreviating the longer words. One type
of keyword, those with an equal sign, such as, BAR=0.05, may not be
abbreviated, and the full word needs to be supplied.
Most keywords which involve an equal sign, such as SCFCRT=1.D-12
can, at the user's discretion, be written with spaces before and after
the equal sign. Thus all permutations of SCFCRT=1.D-12, such as
SCFCRT =1.D-12, SCFCRT = 1.D-12, SCFCRT= 1.D-12, SCFCRT = 1.D-12, etc.
are allowed. Exceptions to this are T=, T-PRIORITY=, H-PRIORITY=,
X-PRIORITY=, IRC=, DRC= and TRANS=. ' T=' cannot be abbreviated to ' T '
as many keywords start or end with a 'T'; for the other keywords the
associated abbreviated keywords have specific meanings.
If two keywords which are incompatible, like UHF and C.I., are
supplied, or a keyword which is incompatible with the species supplied,
for instance TRIPLET and a methyl radical, then error trapping will
normally occur, and an error message will be printed. This usually takes
an insignificant time, so data are quickly checked for obvious errors.
- 10 -
KEYWORDS Page 2-2
2.2 FULL LIST OF KEYWORDS USED IN MOPAC
& - TURN NEXT LINE INTO KEYWORDS
+ - ADD ANOTHER LINE OF KEYWORDS
0SCF - READ IN DATA, THEN STOP
1ELECTRON- PRINT FINAL ONE-ELECTRON MATRIX
1SCF - DO ONE SCF AND THEN STOP
AIDER - READ IN AB INITIO DERIVATIVES
AIGIN - GEOMETRY MUST BE IN GAUSSIAN FORMAT
AIGOUT - IN ARC FILE, INCLUDE AB-INITIO GEOMETRY
ANALYT - USE ANALYTICAL DERIVATIVES OF ENERGY W.R.T. GEOMETRY
AM1 - USE THE AM1 HAMILTONIAN
BAR=n.n - REDUCE BAR LENGTH BY A MAXIMUM OF n.n
BIRADICAL- SYSTEM HAS TWO UNPAIRED ELECTRONS
BONDS - PRINT FINAL BOND-ORDER MATRIX
C.I. - A MULTI-ELECTRON CONFIGURATION INTERACTION SPECIFIED
CHARGE=n - CHARGE ON SYSTEM = n (e.g. NH4 => CHARGE=1)
COMPFG - PRINT HEAT OF FORMATION CALCULATED IN COMPFG
CONNOLLY - USE CONNOLLY SURFACE
DEBUG - DEBUG OPTION TURNED ON
DENOUT - DENSITY MATRIX OUTPUT (CHANNEL 10)
DENSITY - PRINT FINAL DENSITY MATRIX
DEP - GENERATE FORTRAN CODE FOR PARAMETERS FOR NEW ELEMENTS
DEPVAR=n - TRANSLATION VECTOR IS A MULTIPLE OF BOND-LENGTH
DERIV - PRINT PART OF WORKING IN DERIV
DFORCE - FORCE CALCULATION SPECIFIED, ALSO PRINT FORCE MATRIX.
DFP - USE DAVIDON-FLETCHER-POWELL METHOD TO OPTIMIZE GEOMETRIES
DIPOLE - FIT THE ESP TO THE CALCULATED DIPOLE
DIPX - X COMPONENT OF DIPOLE TO BE FITTED
DIPY - Y COMPONENT OF DIPOLE TO BE FITTED
DIPZ - Z COMPONENT OF DIPOLE TO BE FITTED
DMAX - MAXIMUM STEPSIZE IN EIGENVECTOR FOLLOWING
DOUBLET - DOUBLET STATE REQUIRED
DRC - DYNAMIC REACTION COORDINATE CALCULATION
DUMP=n - WRITE RESTART FILES EVERY n SECONDS
ECHO - DATA ARE ECHOED BACK BEFORE CALCULATION STARTS
EF - USE EF ROUTINE FOR MINIMUM SEARCH
EIGINV -
EIGS - PRINT ALL EIGENVALUES IN ITER
ENPART - PARTITION ENERGY INTO COMPONENTS
ESP - ELECTROSTATIC POTENTIAL CALCULATION
ESPRST - RESTART OF ELECTROSTATIC POTENTIAL
ESR - CALCULATE RHF UNPAIRED SPIN DENSITY
EXCITED - OPTIMIZE FIRST EXCITED SINGLET STATE
EXTERNAL - READ PARAMETERS OFF DISK
FILL=n - IN RHF OPEN AND CLOSED SHELL, FORCE M.O. n
TO BE FILLED
FLEPO - PRINT DETAILS OF GEOMETRY OPTIMIZATION
FMAT - PRINT DETAILS OF WORKING IN FMAT
FOCK - PRINT LAST FOCK MATRIX
FORCE - FORCE CALCULATION SPECIFIED
GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK
- 11 -
KEYWORDS Page 2-3
GNORM=n.n- EXIT WHEN GRADIENT NORM DROPS BELOW n.n
GRADIENTS- PRINT ALL GRADIENTS
GRAPH - GENERATE FILE FOR GRAPHICS
HCORE - PRINT DETAILS OF WORKING IN HCORE
HESS=N - OPTIONS FOR CALCULATING HESSIAN MATRICES IN EF
H-PRIO - HEAT OF FORMATION TAKES PRIORITY IN DRC
HYPERFINE- HYPERFINE COUPLING CONSTANTS TO BE CALCULATED
IRC - INTRINSIC REACTION COORDINATE CALCULATION
ISOTOPE - FORCE MATRIX WRITTEN TO DISK (CHANNEL 9 )
ITER - PRINT DETAILS OF WORKING IN ITER
ITRY=N - SET LIMIT OF NUMBER OF SCF ITERATIONS TO N.
IUPD - MODE OF HESSIAN UPDATE IN EIGENVECTOR FOLLOWING
K=(N,N) - BRILLOUIN ZONE STRUCTURE TO BE CALCULATED
KINETIC - EXCESS KINETIC ENERGY ADDED TO DRC CALCULATION
LINMIN - PRINT DETAILS OF LINE MINIMIZATION
LARGE - PRINT EXPANDED OUTPUT
LET - OVERRIDE CERTAIN SAFETY CHECKS
LOCALIZE - PRINT LOCALIZED ORBITALS
MAX - PRINTS MAXIMUM GRID SIZE (23*23)
MECI - PRINT DETAILS OF MECI CALCULATION
MICROS - USE SPECIFIC MICROSTATES IN THE C.I.
MINDO/3 - USE THE MINDO/3 HAMILTONIAN
MMOK - USE MOLECULAR MECHANICS CORRECTION TO CONH BONDS
MODE=N - IN EF, FOLLOW HESSIAN MODE NO. N
MOLDAT - PRINT DETAILS OF WORKING IN MOLDAT
MS=N - IN MECI, MAGNETIC COMPONENT OF SPIN
MULLIK - PRINT THE MULLIKEN POPULATION ANALYSIS
NLLSQ - MINIMIZE GRADIENTS USING NLLSQ
NOANCI - DO NOT USE ANALYTICAL C.I. DERIVATIVES
NODIIS - DO NOT USE DIIS GEOMETRY OPTIMIZER
NOINTER - DO NOT PRINT INTERATOMIC DISTANCES
NOLOG - SUPPRESS LOG FILE TRAIL, WHERE POSSIBLE
NOMM - DO NOT USE MOLECULAR MECHANICS CORRECTION TO CONH BONDS
NONR -
NOTHIEL - DO NOT USE THIEL'S FSTMIN TECHNIQUE
NSURF=N - NUMBER OF SURFACES IN AN ESP CALCULATION
NOXYZ - DO NOT PRINT CARTESIAN COORDINATES
NSURF - NUMBER OF LAYERS USED IN ELECTROSTATIC POTENTIAL
OLDENS - READ INITIAL DENSITY MATRIX OFF DISK
OLDGEO - PREVIOUS GEOMETRY TO BE USED
OPEN - OPEN-SHELL RHF CALCULATION REQUESTED
ORIDE -
PARASOK - IN AM1 CALCULATIONS SOME MNDO PARAMETERS ARE TO BE USED
PI - RESOLVE DENSITY MATRIX INTO SIGMA AND PI BONDS
PL - MONITOR CONVERGENCE OF DENSITY MATRIX IN ITER
PM3 - USE THE MNDO-PM3 HAMILTONIAN
POINT=N - NUMBER OF POINTS IN REACTION PATH
POINT1=N - NUMBER OF POINTS IN FIRST DIRECTION IN GRID CALCULATION
POINT2=N - NUMBER OF POINTS IN SECOND DIRECTION IN GRID CALCULATION
POLAR - CALCULATE FIRST, SECOND AND THIRD ORDER POLARIZABILITIES
POTWRT - IN ESP, WRITE OUT ELECTROSTATIC POTENTIAL TO UNIT 21
POWSQ - PRINT DETAILS OF WORKING IN POWSQ
PRECISE - CRITERIA TO BE INCREASED BY 100 TIMES
PULAY - USE PULAY'S CONVERGER TO OBTAIN A SCF
QUARTET - QUARTET STATE REQUIRED
- 12 -
KEYWORDS Page 2-4
QUINTET - QUINTET STATE REQUIRED
RECALC=N - IN EF, RECALCULATE HESSIAN EVERY N STEPS
RESTART - CALCULATION RESTARTED
ROOT=n - ROOT n TO BE OPTIMIZED IN A C.I. CALCULATION
ROT=n - THE SYMMETRY NUMBER OF THE SYSTEM IS n.
SADDLE - OPTIMIZE TRANSITION STATE
SCALE - SCALING FACTOR FOR VAN DER WAALS DISTANCE IN ESP
SCFCRT=n - DEFAULT SCF CRITERION REPLACED BY THE VALUE SUPPLIED
SCINCR - INCREMENT BETWEEN LAYERS IN ESP
SETUP - EXTRA KEYWORDS TO BE READ OF SETUP FILE
SEXTET - SEXTET STATE REQUIRED
SHIFT=n - A DAMPING FACTOR OF n DEFINED TO START SCF
SIGMA - MINIMIZE GRADIENTS USING SIGMA
SINGLET - SINGLET STATE REQUIRED
SLOPE - MULTIPLIER USED TO SCALE MNDO CHARGES
SPIN - PRINT FINAL UHF SPIN MATRIX
STEP - STEP SIZE IN PATH
STEP1=n - STEP SIZE n FOR FIRST COORDINATE IN GRID CALCULATION
STEP2=n - STEP SIZE n FOR SECOND COORDINATE IN GRID CALCULATION
STO-3G - DEORTHOGONALIZE ORBITALS IN STO-3G BASIS
SYMAVG - AVERAGE SYMMETRY EQUIVALENT ESP CHARGES
SYMMETRY - IMPOSE SYMMETRY CONDITIONS
T=n - A TIME OF n SECONDS REQUESTED
THERMO - PERFORM A THERMODYNAMICS CALCULATION
TIMES - PRINT TIMES OF VARIOUS STAGES
T-PRIO - TIME TAKES PRIORITY IN DRC
TRANS - THE SYSTEM IS A TRANSITION STATE
(USED IN THERMODYNAMICS CALCULATION)
TRIPLET - TRIPLET STATE REQUIRED
TS - USING EF ROUTINE FOR TS SEARCH
UHF - UNRESTRICTED HARTREE-FOCK CALCULATION
VECTORS - PRINT FINAL EIGENVECTORS
VELOCITY - SUPPLY THE INITIAL VELOCITY VECTOR IN A DRC CALCULATION
WILLIAMS - USE WILLIAMS SURFACE
X-PRIO - GEOMETRY CHANGES TAKE PRIORITY IN DRC
XYZ - DO ALL GEOMETRIC OPERATIONS IN CARTESIAN COORDINATES.
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KEYWORDS Page 2-5
2.3 DEFINITIONS OF KEYWORDS
The definitions below are given with some technical expressions
which are not further defined. Interested users are referred to Appendix
E of this manual to locate appropriate references which will provide
further clarification.
There are three classes of keywords: (1) those which CONTROL
substantial aspects of the calculation, i.e., those which affect the
final heat of formation, (2) those which determine which OUTPUT will be
calculated and printed, and (3) those which dictate the WORKING of the
calculation, but which do not affect the heat of formation. The
assignment to one of these classes is designated by a (C), (O) or (W),
respectively, following each keyword in the list below.
& (C)
An ' &' means 'turn the next line into keywords'. Note the space
_ _
before the '' sign. Since '' is a keyword, it must be preceeded by a
space. A ' &' on line 1 would mean that a second line of keywords should
be read in. If that second line contained a ' &', then a third line of
keywords would be read in. If the first line has a ' &' then the first
description line is omitted, if the second line has a ' &', then both
description lines are omitted.
Examples
Use of one '&'
VECTORS DENSITY RESTART & NLLSQ T=1H SCFCRT=1.D-8 DUMP=30M ITRY=300
PM3 FOCK OPEN(2,2) ROOT=3 SINGLET SHIFT=30
Test on a totally weird system
Use of two '&'s
LARGE=-10 & DRC=4.0 T=1H SCFCRT=1.D-8 DUMP=30M ITRY=300 SHIFT=30
PM3 OPEN(2,2) ROOT=3 SINGLET NOANCI ANALYT T-PRIORITY=0.5 &
LET GEO-OK VELOCITY KINETIC=5.0
+ (C)
A ' +' sign means 'read another line of keywords'. Note the space
before the '+' sign. Since '+' is a keyword, it must be preceeded by a
space. A ' +' on line 1 would mean that a second line of keywords should
be read in. If that second line contains a ' +', then a third line of
keywords will be read in. Regardless of whether a second or a third line
of keywords is read in, the next two lines would be description lines.
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KEYWORDS Page 2-6
Example of ' +' option
RESTART T=4D FORCE OPEN(2,2) SHIFT=20 PM3 +
SCFCRT=1.D-8 DEBUG + ISOTOPE FMAT ECHO singlet ROOT=3
THERMO(300,400,1) ROT=3
Example of data set with three lines of keywords. NOTE: There
are two lines of description, this and the previous line.
0SCF (O)
The data can be read in and output, but no actual calculation is
performed when this keyword is used. This is useful as a check on the
input data. All obvious errors are trapped, and warning messages
printed.
A second use is to convert from one format to another. The input
geometry is printed in various formats at the end of a 0SCF calculation.
If NOINTER is absent, cartesian coordinates are printed.
Unconditionally, MOPAC Z-matrix internal coordinates are printed, and if
AIGOUT is present, Gaussian Z-matrix internal coordinates are printed.
0SCF should now be used in place of DDUM.
1ELECTRON (O)
The final one-electron matrix is printed out. This matrix is
composed of atomic orbitals; the array element between orbitals i and j
on different atoms is given by
H(i,j) = 0.5 x (beta(i) +beta(j)) x overlap(i,j)
The matrix elements between orbitals i and j on the same atom are
calculated from the electron-nuclear attraction energy, and also from the
U(i) value if i=j.
The one-electron matrix is unaffected by (a) the charge and (b) the
electron density. It is only a function of the geometry. Abbreviation:
1ELEC.
1SCF (C)
When users want to examine the results of a single SCF calculation
of a geometry, 1SCF should be used. 1SCF can be used in conjunction with
RESTART, in which case a single SCF calculation will be done, and the
results printed.
When 1SCF is used on its own (that is, RESTART is not also used)
then derivatives will only be calculated if GRAD is also specified.
1SCF is helpful in a learning situation. MOPAC normally performs
many SCF calculations, and in order to minimize output when following the
working of the SCF calculation, 1SCF is very useful.
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KEYWORDS Page 2-7
AIDER (C)
AIDER allows MOPAC to optimize an ab-initio geometry. To use it,
calculate the ab-initio gradients using, e.g., Gaussian. Supply MOPAC
with these gradients, after converting them into kcal/mol. The geometry
resulting from a MOPAC run will be nearer to the optimized ab-initio
geometry than if the geometry optimizer in Gaussian had been used.
AIGIN (C)
If the geometry (Z-matrix) is specified using the Gaussian-8X, then
normally this will be read in without difficulty. In the event that it
is mistaken for a normal MOPAC-type Z-matrix, the keyword AIGIN is
provided. AIGIN will force the data-set to be read in assuming Gaussian
format. This is necessary if more than one system is being studied in
one run.
AIGOUT (O)
The ARCHIVE file contains a data-set suitable for submission to
MOPAC. If, in addition to this data-set, the Z-matrix for Gaussian input
is wanted, then AIGOUT (ab initio geometry output), should be used.
The Z-matrix is in full Gaussian form. Symmetry, where present,
will be correctly defined. Names of symbolics will be those used if the
original geometry was in Gaussian format, otherwise 'logical' names will
be used. Logical names are of form <t><a><b>[<c>][<d>] where <t> is 'r'
for bond length, 'a' for angle, or 'd' for dihedral, <a> is the atom
number, <b> is the atom to which <a> is related, <c>, if present, is the
atom number to which <a> makes an angle, and <d>, if present, is the atom
number to which <a> makes a dihedral.
ANALYT (W)
By default, finite difference derivatives of energy with respect to
geometry are used. If ANALYT is specified, then analytical derivatives
are used instead. Since the analytical derivatives are over Gaussian
functions -- a STO-6G basis set is used -- the overlaps are also over
Gaussian functions. This will result in a very small (less than 0.1
Kcal/mole) change in heat of formation. Use analytical derivatives (a)
when the mantissa used is less than about 51-53 bits, or (b) when
comparison with finite difference is desired. Finite difference
derivatives are still used when non-variationally optimized wavefunctions
are present.
AM1 (C)
The AM1 method is to be used. By default MNDO is run.
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KEYWORDS Page 2-8
BAR=n.nn (W)
In the SADDLE calculation the distance between the two geometries is
steadily reduced until the transition state is located. Sometimes,
however, the user may want to alter the maximum rate at which the
distance between the two geometries reduces. BAR is a ratio, normally
0.15, or 15 percent. This represents a maximum rate of reduction of the
bar of 15 percent per step. Alternative values that might be considered
are BAR=0.05 or BAR=0.10, although other values may be used. See also
SADDLE.
If CPU time is not a major consideration, use BAR=0.03.
BIRADICAL (C)
NOTE: BIRADICAL is a redundant keyword, and represents a particular
configuration interaction calculation. Experienced users of MECI (q.v.)
can duplicate the effect of the keyword BIRADICAL by using the MECI
keywords OPEN(2,2) and SINGLET.
For molecules which are believed to have biradicaloid character the
option exists to optimize the lowest singlet energy state which results
from the mixing of three states. These states are, in order, (1) the
(micro)state arising from a one electron excitation from the HOMO to the
LUMO, which is combined with the microstate resulting from the
time-reversal operator acting on the parent microstate, the result being
a full singlet state; (2) the state resulting from de-excitation from the
formal LUMO to the HOMO; and (3) the state resulting from the single
electron in the formal HOMO being excited into the LUMO.
Microstate 1 Microstate 2 Microstate 3
Alpha Beta Alpha Beta Alpha Beta Alpha Beta
LUMO * * * *
--- --- --- --- --- --- --- ---
+
HOMO * * * *
--- --- --- --- --- --- --- ---
A configuration interaction calculation is involved here. A biradical
calculation done without C.I. at the RHF level would be meaningless.
Either rotational invariance would be lost, as in the D2d form of
ethylene, or very artificial barriers to rotations would be found, such
as in a methane molecule "orbiting" a D2d ethylene. In both cases the
inclusion of limited configuration interaction corrects the error.
BIRADICAL should not be used if either the HOMO or LUMO is degenerate; in
this case, the full manifold of HOMO x LUMO should be included in the
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KEYWORDS Page 2-9
C.I., using MECI options. The user should be aware of this situation.
When the biradical calculation is performed correctly, the result is
normally a net stabilization. However, if the first singlet excited
state is much higher in energy than the closed-shell ground state,
BIRADICAL can lead to a destabilization. Abbreviation: BIRAD. See also
MECI, C.I., OPEN, SINGLET.
BONDS (O)
The rotationally invariant bond order between all pairs of atoms is
printed. In this context a bond is defined as the sum of the squares of
the density matrix elements connecting any two atoms. For ethane,
ethylene, and acetylene the carbon-carbon bond orders are roughly 1.00,
2.00, and 3.00 respectively. The diagonal terms are the valencies
calculated from the atomic terms only and are defined as the sum of the
bonds the atom makes with other atoms. In UHF and non-variationally
optimized wavefunctions the calculated valency will be incorrect, the
degree of error being proportional to the non-duodempotency of the
density matrix. For an RHF wavefunction the square of the density matrix
is equal to twice the density matrix.
The bonding contributions of all M.O.'s in the system are printed
immediately before the bonds matrix. The idea of molecular orbital
valency was developed by Gopinathan, Siddarth, and Ravimohan. Just as an
atomic orbital has a 'valency', so has a molecular orbital. This leads
to the following relations: The sum of the bonding contributions of all
occupied M.O.'s is the same as the sum of all valencies which, in turn is
equal to two times the sum of all bonds. The sum of the bonding
contributions of all M.O.'s is zero.
C.I.=n (C)
Normally configuration interaction is invoked if any of the keywords
which imply a C.I. calculation are used, such as BIRADICAL, TRIPLET or
QUARTET. Note that ROOT= does not imply a C.I. calculation: ROOT= is
only used when a C.I. calculation is done. However, as these implied
C.I.'s involve the minimum number of configurations practical, the user
may want to define a larger than minimum C.I., in which case the keyword
C.I.=n can be used. When C.I.=n is specified, the n M.O.'s which
"bracket" the occupied- virtual energy levels will be used. Thus, C.I.=2
will include both the HOMO and the LUMO, while C.I.=1 (implied for
odd-electron systems) will only include the HOMO (This will do nothing
for a closed-shell system, and leads to Dewar's half-electron correction
for odd-electron systems). Users should be aware of the rapid increase
in the size of the C.I. with increasing numbers of M.O.'s being used.
Numbers of microstates implied by the use of the keyword C.I.=n on its
own are as follows:
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KEYWORDS Page 2-10
Keyword Even-electron systems Odd-electron systems
No. of electrons, configs No. of electrons, configs
Alpha Beta Alpha Beta
C.I.=1 1 1 1 1 0 1
C.I.=2 1 1 4 1 0 2
C.I.=3 2 2 9 2 1 9
C.I.=4 2 2 36 2 1 24
C.I.=5 3 3 100 3 2 100
C.I.=6 3 3 400 3 2 300
C.I.=7 4 4 1225 4 3 1225
C.I.=8 (Do not use unless other keywords also used, see below)
If a change of spin is defined, then larger numbers of M.O.'s can be
used up to a maximum of 10. The C.I. matrix is of size 100 x 100. For
calculations involving up to 100 configurations, the spin-states are
exact eigenstates of the spin operators. For systems with more than 100
configurations, the 100 configurations of lowest energy are used. See
also MICROS and the keywords defining spin-states.
Note that for any system, use of C.I.=5 or higher normally implies
the diagonalization of a 100 by 100 matrix. As a geometry optimization
using a C.I. requires the derivatives to be calculated using derivatives
of the C.I. matrix, geometry optimization with large C.I.'s will require
more time than smaller C.I.'s.
Associated keywords: MECI, ROOT=, MICROS, SINGLET, DOUBLET, etc.
C.I.=(n,m)
In addition to specifying the number of M.O.'s in the active space,
the number of electrons can also be defined. In C.I.=(n,m), n is the
number of M.O.s in the active space, and m is the number of doubly filled
levels to be used.
EXAMPLES
Keywords Number of M.O.s No. Electrons
C.I.=2 2 2 (1)
C.I.=(2,1) 2 2 (3)
C.I.=(3,1) 3 2 (3)
C.I.=(3,2) 3 4 (5)
C.I.=(3,0) OPEN(2,3) 3 2 (N/A)
C.I.=(3,1) OPEN(2,2) 3 4 (N/A)
C.I.=(3,1) OPEN(1,2) 3 N/A (3)
Odd electron systems given in parentheses.
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CHARGE=n (C)
When the system being studied is an ion, the charge, n, on the ion
must be supplied by CHARGE=n. For cations n can be 1 or 2 or 3, etc, for
anions -1 or -2 or -3, etc.
EXAMPLES
ION KEYWORD ION KEYWORD
NH4(+) CHARGE=1 CH3COO(-) CHARGE=-1
C2H5(+) CHARGE=1 (COO)(=) CHARGE=-2
SO4(=) CHARGE=-2 PO4(3-) CHARGE=-3
HSO4(-) CHARGE=-1 H2PO4(-) CHARGE=-1
DCART (O)
The cartesian derivatives which are calculated in DCART for
variationally optimized systems are printed if the keyword DCART is
present. The derivatives are in units of kcals/Angstrom, and the
coordinates are displacements in x, y, and z.
DEBUG (O)
Certain keywords have specific output control meanings, such as
FOCK, VECTORS and DENSITY. If they are used, only the final arrays of
the relevant type are printed. If DEBUG is supplied, then all arrays are
printed. This is useful in debugging ITER. DEBUG can also increase the
amount of output produced when certain output keywords are used, e.g.
COMPFG.
DENOUT (O)
The density matrix at the end of the calculation is to be output in
a form suitable for input in another job. If an automatic dump due to
the time being exceeded occurs during the current run then DENOUT is
invoked automatically. (see RESTART)
DENSITY (O)
At the end of a job, when the results are being printed, the density
matrix is also printed. For RHF the normal density matrix is printed.
For UHF the sum of the alpha and beta density matrices is printed.
If density is not requested, then the diagonal of the density
matrix, i.e., the electron density on the atomic orbitals, will be
printed.
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DEP (O)
For use only with EXTERNAL=. When new parameters are published,
they can be entered at run-time by using EXTERNAL=, but as this is
somewhat clumsy, a permanent change can be made by use of DEP.
If DEP is invoked, a complete block of FORTRAN code will be
generated, and this can be inserted directly into the BLOCK DATA file.
Note that the output is designed for use with PM3. By modifying the
names, the output can be used with MNDO or AM1.
DEPVAR=n.nn (C)
In polymers the translation vector is frequently a multiple of some
internal distance. For example, in polythene it is the C1-C3 distance.
If a cluster unit cell of C6H12 is used, then symmetry can be used to tie
together all the carbon atom coordinates and the translation vector
distance. In this example DEPVAR=3.0 would be suitable.
DFP (W)
By default the Broyden-Fletcher-Goldfarb-Shanno method will be used
to optimize geometries. The older Davidon-Fletcher-Powell method can be
invoked by specifying DFP. This is intended to be used for comparison of
the two methods.
DIPOLE (C)
Used in the ESP calculation, DIPOLE will constrain the calculated
charges to reproduce the cartesian dipole moment components calculated
from the density matrix and nuclear charges.
DIPX (C)
Similar to DIPOLE, except the fit will be for the X-component only.
DIPY (C)
Similar to DIPOLE, except the fit will be for the Y-component only.
DIPZ (C)
Similar to DIPOLE, except the fit will be for the Z-component only.
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DMAX=n.nn (W)
In the EF routine, the maximum step-size is 0.2 (Angstroms or
radians), by default. This can be changed by specifying DMAX=n.nn.
Increasing DMAX can lead to faster convergence but can also make the
optimization go bad very fast. Furthermore, the Hessian updating may
deteriorate when using large stepsizes. Reducing the stepsize to 0.10 or
0.05 is recommended when encountering convergence problems.
DOUBLET (C)
When a configuration interaction calculation is done, all spin
states are calculated simultaneously, either for component of spin = 0 or
1/2. When only doublet states are of interest, then DOUBLET can be
specified, and all other spin states, while calculated, are ignored in
the choice of root to be used.
Note that while almost every odd-electron system will have a doublet
ground state, DOUBLET should still be specified if the desired state must
be a doublet.
DOUBLET has no meaning in a UHF calculation.
DRC (C)
A Dynamic Reaction Coordinate calculation is to be run. By default,
total energy is conserved, so that as the "reaction" proceeds in time,
energy is transferred between kinetic and potential forms.
DRC=n.nnn (C)
In a DRC calculation, the "half-life" for loss of kinetic energy is
defined as n.nnn femtoseconds. If n.nnn is set to zero, infinite damping
simulating a very condensed phase is obtained.
This keyword cannot be written with spaces around the '=' sign.
DUMP (W)
Restart files are written automatically at one hour cpu time
intervals to allow a long job to be restarted if the job is terminated
catastrophically. To change the frequency of dump, set DUMP=nn to
request a dump every nn seconds. Alternative forms, DUMP=nnM, DUMP=nnH,
DUMP=nnD for a dump every nn minutes, hours, or days, respectively. DUMP
only works with geometry optimization, gradient minimization, path, and
FORCE calculations. It does not (yet) work with a SADDLE calculation.
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ECHO (O)
Data are echoed back if ECHO is specified. Only useful if data are
suspected to be corrupt.
EF (C)
The Eigenvector Following routine is an alternative to the BFGS, and
appears to be much faster. To invoke the Eigenvector Following routine,
specify EF. EF is particularly good in the end-game, when the gradient
is small. See also HESS, DMAX, EIGINV.
EIGINV (W)
Not recommended for normal use. Used with the EF routine. See
source code for more details.
ENPART (O)
This is a very useful tool for analyzing the energy terms within a
system. The total energy, in eV, obtained by the addition of the
electronic and nuclear terms, is partitioned into mono- and bi-centric
contributions, and these contributions in turn are divided into nuclear
and one- and two-electron terms.
ESP (C)
This is the ElectroStatic Potential calculation of K. M. Merz and
B. H. Besler. ESP calculates the expectation values of the electrostatic
potential of a molecule on a uniform distribution of points. The
resultant ESP surface is then fitted to atom centered charges that best
reproduce the distribution, in a least squares sense.
ESPRST (W)
ESPRST restarts a stopped ESP calculation. Do not use with RESTART.
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ESR (O)
The unpaired spin density arising from an odd-electron system can be
calculated both RHF and UHF. In a UHF calculation the alpha and beta
M.O.'s have different spatial forms, so unpaired spin density can
naturally be present on in-plane hydrogen atoms such as in the phenoxy
radical.
In the RHF formalism a MECI calculation is performed. If the
keywords OPEN and C.I.= are both absent then only a single state is
calculated. The unpaired spin density is then calculated from the state
function. In order to have unpaired spin density on the hydrogens in,
for example, the phenoxy radical, several states should be mixed.
EXCITED (C)
The state to be calculated is the first excited open-shell singlet
state. If the ground state is a singlet, then the state calculated will
be S(1); if the ground state is a triplet, then S(2). This state would
normally be the state resulting from a one-electron excitation from the
HOMO to the LUMO. Exceptions would be if the lowest singlet state were a
biradical, in which case the EXCITED state could be a closed shell.
The EXCITED state will be calculated from a BIRADICAL calculation in
which the second root of the C.I. matrix is selected. Note that the
eigenvector of the C.I. matrix is not used in the current formalism.
Abbreviation: EXCI.
NOTE: EXCITED is a redundant keyword, and represents a particular
configuration interaction calculation. Experienced users of MECI can
duplicate the effect of the keyword EXCITED by using the MECI keywords
OPEN(2,2), SINGLET, and ROOT=2.
EXTERNAL=name (C)
Normally, PM3, AM1 and MNDO parameters are taken from the BLOCK DATA
files within MOPAC. When the supplied parameters are not suitable, as in
an element recently parameterized, and the parameters have not yet
installed in the user's copy of MOPAC, then the new parameters can be
inserted at run time by use of EXTERNAL=<filename>, where <filename> is
the name of the file which contains the new parameters.
<filename> consists of a series of parameter definitions in the
format
<Parameter> <Element> <Value of parameter>
where the possible parameters are USS, UPP, UDD, ZS, ZP, ZD, BETAS,
BETAP, BETAD, GSS, GSP, GPP, GP2, HSP, ALP, FNnm, n=1,2, or 3, and m=1 to
10, and the elements are defined by their chemical symbols, such as Si or
SI.
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KEYWORDS Page 2-16
When new parameters for elements are published, they can be typed in
as shown. This file is ended by a blank line, the word END or nothing,
i.e., no end-of-file delimiter. An example of a parameter data file
would be:
Start of line (Put at least 2 spaces before and after parameter name)
Line 1: USS Si -34.08201495
Line 2: UPP Si -28.03211675
Line 3: BETAS Si -5.01104521
Line 4: BETAP Si -2.23153969
Line 5: ZS Si 1.28184511
Line 6: ZP Si 1.84073175
Line 7: ALP Si 2.18688712
Line 8: GSS Si 9.82
Line 9: GPP Si 7.31
Line 10: GSP Si 8.36
Line 11: GP2 Si 6.54
Line 12: HSP Si 1.32
Derived parameters do no need to be entered; they will be calculated
from the optimized parameters. All "constants" such as the experimental
heat of atomization are already inserted for all elements.
NOTE: EXTERNAL can only be used to input parameters for MNDO, AM1,
or PM3. It is unlikely, however, that any more MINDO/3 parameters will
be published.
See also DEP to make a permanent change.
FILL=n (C)
The n'th M.O. in an RHF calculation is constrained to be filled.
It has no effect on a UHF calculation. After the first iteration (NOTE:
not after the first SCF calculation, but after the first iteration within
the first SCF calculation) the n'th M.O. is stored, and, if occupied, no
further action is taken at that time. If unoccupied, then the HOMO and
the n'th M.O.'s are swapped around, so that the n'th M.O. is now filled.
On all subsequent iterations the M.O. nearest in character to the stored
M.O. is forced to be filled, and the stored M.O. replaced by that M.O.
This is necessitated by the fact that in a reaction a particular M.O.
may change its character considerably. A useful procedure is to run 1SCF
and DENOUT first, in order to identify the M.O.'s; the complete job is
then run with OLDENS and FILL=nn, so that the eigenvectors at the first
iteration are fully known. As FILL is known to give difficulty at times,
consider also using C.I.=n and ROOT=m.
FLEPO (O)
The predicted and actual changes in the geometry, the derivatives,
and search direction for each geometry optimization cycle are printed.
This is useful if there is any question regarding the efficiency of the
geometry optimizer.
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KEYWORDS Page 2-17
FMAT
Details of the construction of the Hessian matrix for the force
calculation are to be printed.
FORCE (C)
A force-calculation is to be run. The Hessian, that is the matrix
(in millidynes per Angstrom) of second derivatives of the energy with
respect to displacements of all pairs of atoms in x, y, and z directions,
is calculated. On diagonalization this gives the force constants for the
molecule. The force matrix, weighted for isotopic masses, is then used
for calculating the vibrational frequencies. The system can be
characterized as a ground state or a transition state by the presence of
five (for a linear system) or six eigenvalues which are very small (less
than about 30 reciprocal centimeters). A transition state is further
characterized by one, and exactly one, negative force constant.
A FORCE calculation is a prerequisite for a THERMO calculation.
Before a FORCE calculation is started, a check is made to ensure
that a stationary point is being used. This check involves calculating
the gradient norm (GNORM) and if it is significant, the GNORM will be
reduced using BFGS. All internal coordinates are optimized, and any
symmetry constraints are ignored at this point. An implication of this
is that if the specification of the geometry relies on any angles being
exactly 180 or zero degrees, the calculation may fail.
The geometric definition supplied to FORCE should not rely on angles
or dihedrals assuming exact values. (The test of exact linearity is
sufficiently slack that most molecules that are linear, such as acetylene
and but-2-yne, should not be stopped.) See also THERMO, LET, TRANS,
ISOTOPE.
In a FORCE calculation, PRECISE will eliminate quartic contamination
(part of the anharmonicity). This is normally not important, therefore
PRECISE should not routinely be used. In a FORCE calculation, the SCF
criterion is automatically made more stringent; this is the main cause of
the SCF failing in a FORCE calculation.
GEO-OK (W)
Normally the program will stop with a warning message if two atoms
are within 0.8 Angstroms of each other, or, more rarely, the BFGS routine
has difficulty optimizing the geometry. GEO-OK will over-ride the job
termination sequence, and allow the calculation to proceed. In practice,
most jobs that terminate due to these checks contain errors in data, so
caution should be exercised if GEO-OK is used. An important exception to
this warning is when the system contains, or may give rise to, a Hydrogen
molecule. GEO-OK will override other geometric safety checks such as the
unstable gradient in a geometry optimization preventing reliable
optimization.
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KEYWORDS Page 2-18
See also the message "GRADIENTS OF OLD GEOMETRY, GNORM= nn.nnnn"
GNORM=n.nn (W)
The geometry optimization termination criteria in both gradient
minimization and energy minimization can be over-ridden by specifying a
gradient norm requirement. For example, GNORM=20 would allow the
geometry optimization to exit as soon as the gradient norm dropped below
20.0, the default being 1.0.
For high-precision work, GNORM=0.0 is recommended. Unless LET is
also used, the GNORM will be set to the larger of 0.01 and the specified
GNORM. Results from GNORM=0.01 are easily good enough for all
high-precision work.
GRADIENTS (O)
In a 1SCF calculation gradients are not calculated by default: in
non-variationally optimized systems this would take an excessive time.
GRADIENTS allows the gradients to be calculated. Normally, gradients
will not be printed if the gradient norm is less than 2.0. However, if
GRADIENTS is present, then the gradient norm and the gradients will
unconditionally be printed. Abbreviation: GRAD.
GRAPH (O)
Information needed to generate electron density contour maps can be
written to a file by calling GRAPH. GRAPH first calls MULLIK in order to
generate the inverse-square-root of the overlap matrix, which is required
for the re-normalization of the eigenvectors. All data essential for the
graphics package DENSITY are then output.
HESS=n (W)
When the Eigenvector Following routine is used for geometry
optimization, it frequently works faster if the Hessian is constructed
first. If HESS=1 is specified, the Hessian matrix will be constructed
before the geometry is optimized. There are other, less common, options,
e.g. HESS=2. See comments in subroutine EF for details.
H-PRIORITY (O)
In a DRC calculation, results will be printed whenever the
calculated heat of formation changes by 0.1 Kcal/mole. Abbreviation:
H-PRIO.
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KEYWORDS Page 2-19
H-PRIORITY=n.nn (O)
In a DRC calculation, results will be printed whenever the
calculated heat of formation changes by n.nn Kcal/mole.
IRC (C)
An Intrinsic Reaction Coordinate calculation is to be run. All
kinetic energy is shed at every point in the calculation. See
Background.
IRC=n (C)
An Intrinsic Reaction Coordinate calculation to be run; an initial
perturbation in the direction of normal coordinate n to be applied. If n
is negative, then perturbation is reversed, i.e., initial motion is in
the opposite direction to the normal coordinate. This keyword cannot be
written with spaces around the '=' sign.
ISOTOPE (O)
Generation of the FORCE matrix is very time-consuming, and in
isotopic substitution studies several vibrational calculations may be
needed. To allow the frequencies to be calculated from the (constant)
force matrix, ISOTOPE is used. When a FORCE calculation is completed,
ISOTOPE will cause the force matrix to be stored, regardless of whether
or not any intervening restarts have been made. To re-calculate the
frequencies, etc. starting at the end of the force matrix calculation,
specify RESTART.
The two keywords RESTART and ISOTOPE can be used together. For
example, if a normal FORCE calculation runs for a long time, the user may
want to divide it up into stages and save the final force matrix. Once
ISOTOPE has been used, it does not need to be used on subsequent RESTART
runs.
ISOTOPE can also be used with FORCE to set up a RESTART file for an
IRC=n calculation.
ITRY=NN (W)
The default maximum number of SCF iterations is 200. When this
limit presents difficulty, ITRY=nn can be used to re-define it. For
example, if ITRY=400 is used, the maximum number of iterations will be
set to 400. ITRY should normally not be changed until all other means of
obtaining a SCF have been exhausted, e.g. PULAY CAMP-KING etc.
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KEYWORDS Page 2-20
IUPD=n (W)
IUPD is used only in the EF routine. IUPD should very rarely be
touched. IUPD=1 can be used in minimum searches if the the message
"HEREDITARY POSITIVE DEFINITENESS ENDANGERED. UPDATE SKIPPED THIS CYCLE"
occurs every cycle for 10-20 iterations. Never use IUPD=2 for a TS
search! For more information, read the comments in subroutine EF.
K=(n.nn,n) (C)
Used in band-structure calculations, K=(n.nn,n) specifies the
step-size in the Brillouin zone, and the number of atoms in the monomeric
unit. Two band-structure calculations are supported: electronic and
phonon. Both require a polymer to be used. If FORCE is used, a phonon
spectrum is assumed, otherwise an electronic band structure is assumed.
For both calculations, a density of states is also done. The band
structure calculation is very fast, so a small step-size will not use
much time.
The output is designed to be fed into a graphics package, and is not
'elegant'. For polyethylene, a suitable keyword would be K=(0.01,6).
KINETIC=n.nnn (C)
In a DRC calculation n.nnn Kcals/mole of excess kinetic energy is
added to the system as soon as the kinetic energy builds up to 0.2
Kcal/mole. The excess energy is added to the velocity vector, without
change of direction.
LARGE (O)
Most of the time the output invoked by keywords is sufficient.
LARGE will cause less-commonly wanted, but still useful, output to be
printed.
1. To save space, DRC and IRC outputs will, by default, only print the
line with the percent sign. Other output can be obtained by use of the
keyword LARGE, according to the following rules:
Keyword Effect
LARGE Print all internal and cartesian coordinates
and cartesian velocities.
LARGE=1 Print all internal coordinates.
LARGE=-1 Print all internal and cartesian coordinates
and cartesian velocities.
LARGE=n Print every n'th set of internal coordinates.
LARGE=-n Print every n'th set of internal and cartesian
coordinates and cartesian velocities.
If LARGE=1 is used, the output will be the same as that of Version
5.0, when LARGE was not used. If LARGE is used, the output will be the
same as that of Version 5.0, when LARGE was used. To save disk space, do
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KEYWORDS Page 2-21
not use LARGE.
LINMIN (O)
There are two line-minimization routines in MOPAC, an energy
minimization and a gradient norm minimization. LINMIN will output
details of the line minimization used in a given job.
LET (W)
As MOPAC evolves, the meaning of LET is changing.
Now LET means essentially "I know what I'm doing, override safety
checks".
Currently, LET has the following meanings
1. In a FORCE calculation, it means that the supplied geometry is
to be used, even if the gradients are large.
2. In a geometry optimization, the specified GNORM is to be used,
even if it is less than 0.01.
3. In a POLAR calculation, the molecule is to be orientated along
its principal moments of inertia before the calculation starts.
LET will prevent this step being done.
LOCALIZE (O)
The occupied eigenvectors are transformed into a localized set of
M.O.'s by a series of 2 by 2 rotations which maximize <psi**4>. The
value of 1/<psi**4> is a direct measure of the number of centers involved
in the M.O.. Thus the value of 1/<psi**4> is 2.0 for H2, 3.0 for a
three-center bond and 1.0 for a lone pair. Higher degeneracies than
allowed by point group theory are readily obtained. For example, benzene
would give rise to a 6-fold degenerate C-H bond, a 6-fold degenerate C-C
sigma bond and a three-fold degenerate C-C pi bond. In principle, there
is no single step method to unambiguously obtain the most localized set
of M.O.'s in systems where several canonical structures are possible,
just as no simple method exists for finding the most stable conformer of
some large compound. However, the localized bonds generated will
normally be quite acceptable for routine applications. Abbreviation:
LOCAL.
MAX
In a grid calculation, the maximum number of points (23) in each
direction is to be used. The default is 11. The number of points in
each direction can be set with POINTS1 and POINTS2.
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KEYWORDS Page 2-22
MECI (O)
At the end of the calculation details of the Multi Electron
Configuration Interaction calculation are printed if MECI is specified.
The state vectors can be printed by specifying VECTORS. The MECI
calculation is either invoked automatically, or explicitly invoked by the
use of the C.I.=n keyword.
MICROS=n (C)
The microstates used by MECI are normally generated by use of a
permutation operator. When individually defined microstates are desired,
then MICROS=n can be used, where n defines the number of microstates to
be read in.
Format for Microstates
After the geometry data plus any symmetry data are read in, data
defining each microstate is read in, using format 20I1, one microstate
per line. The microstate data is preceded by the word "MICROS" on a line
by itself. There is at present no mechanism for using MICROS with a
reaction path.
For a system with n M.O.'s in the C.I. (use OPEN=(n1,n) or C.I.=n to
do this), the populations of the n alpha M.O.'s are defined, followed by
the n beta M.O.'s. Allowed occupancies are zero and one. For n=6 the
closed-shell ground state would be defined as 111000111000, meaning one
electron in each of the first three alpha M.O.'s, and one electron in
each of the first three beta M.O.'s.
Users are warned that they are responsible for completing any spin
manifolds. Thus while the state 111100110000 is a triplet state with
component of spin = 1, the state 111000110100, while having a component
of spin = 0 is neither a singlet nor a triplet. In order to complete the
spin manifold the microstate 110100111000 must also be included.
If a manifold of spin states is not complete, then the eigenstates
of the spin operator will not be quantized. When and only when 100 or
fewer microstates are supplied, can spin quantization be conserved.
There are two other limitations on possible microstates. First, the
number of electrons in every microstate should be the same. If they
differ, a warning message will be printed, and the calculation continued
(but the results will almost certainly be nonsense). Second, the
component of spin for every microstate must be the same, except for
teaching purposes. Two microstates of different components of spin will
have a zero matrix element connecting them. No warning will be given as
this is a reasonable operation in a teaching situation. For example, if
all states arising from two electrons in two levels are to be calculated,
say for teaching Russel-Saunders coupling, then the following microstates
would be used:
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KEYWORDS Page 2-23
Microstate No. of alpha, beta electrons Ms State
1100 2 0 1 Triplet
1010 1 1 0 Singlet
1001 1 1 0 Mixed
0110 1 1 0 Mixed
0101 1 1 0 Singlet
0011 0 2 -1 Triplet
Constraints on the space manifold are just as rigorous, but much
easier to satisfy. If the energy levels are degenerate, then all
components of a manifold of degenerate M.O.'s should be either included
or excluded. If only some, but not all, components are used, the
required degeneracy of the states will be missing.
As an example, for the tetrahedral methane cation, if the user
supplies the microstates corresponding to a component of spin = 3/2,
neglecting Jahn-Teller distortion, the minimum number of states that can
be supplied is 90 = (6!/(1!*5!))*(6!/(4!*2!)).
While the total number of electrons should be the same for all
microstates, this number does not need to be the same as the number of
electrons supplied to the C.I.; thus in the example above, a cationic
state could be 110000111000.
The format is defined as 20I1 so that spaces can be used for empty
M.O.'s.
MINDO/3 (C)
The default Hamiltonian within MOPAC is MNDO, with the alternatives
of AM1 and MINDO/3. To use the MINDO/3 Hamiltonian the keyword MINDO/3
should be used. Acceptable alternatives to the keyword MINDO/3 are MINDO
and MINDO3.
MMOK (C)
If the system contains a peptide linkage, then MMOK will allow a
molecular mechanics correction to be applied so that the barrier to
rotation is increased (to 14.00 Kcal/mole in N-methyl acetamide).
MODE (C)
MODE is used in the EF routine. Normally the default MODE=1 is used
to locate a transition state, but if this is incorrect, explicitly define
the vector to be followed by using MODE=n. (MODE is not a recommended
keyword). If you use the FORCE option when deciding which mode to
follow, set all isotopic masses to 1.0. The normal modes from FORCE are
normally mass-weighted; this can mislead. Alternatively, use LARGE with
FORCE: this gives the force constants and vectors in addition to the
mass-weighted normal modes. Only the mass-weighted modes can be drawn
with DRAW.
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KEYWORDS Page 2-24
MS=n
Useful for checking the MECI calculation and for teaching. MS=n
overrides the normal choice of magnetic component of spin. Normally, if
a triplet is requested, an MS of 1 will be used; this excludes all
singlets. If MS=0 is also given, then singlets will also be calculated.
The use of MS should not affect the values of the results at all.
MULLIK (O)
A full Mulliken Population analysis is to be done on the final RHF
wavefunction. This involves the following steps:
(1) The eigenvector matrix is divided by the square root
of the overlap matrix, S.
(2) The Coulson-type density matrix, P, is formed.
(3) The overlap population is formed from P(i,j)*S(i,j).
(4) Half the off-diagonals are added onto the diagonals.
NLLSQ (C)
The gradient norm is to be minimized by Bartel's method. This is a
Non-Linear Least Squares gradient minimization routine. Gradient
minimization will locate one of three possible points:
(a) A minimum in the energy surface. The gradient norm will go to
zero, and the lowest five or six eigenvalues resulting from a FORCE
calculation will be approximately zero.
(b) A transition state. The gradient norm will vanish, as in (a),
but in this case the system is characterized by one, and only one,
negative force constant.
(c) A local minimum in the gradient norm space. In this (normally
unwanted) case the gradient norm is minimized, but does not go to zero.
A FORCE calculation will not give the five or six zero eigenvalues
characteristic of a stationary point. While normally undesirable, this
is sometimes the only way to obtain a geometry. For instance, if a
system is formed which cannot be characterized as an intermediate, and at
the same time is not a transition state, but nonetheless has some
chemical significance, then that state can be refined using NLLSQ.
NOANCI (W)
RHF open-shell derivatives are normally calculated using Liotard's
analytical C.I. method. If this method is NOT to be used, specify NOANCI
(NO ANalytical Configuration Interaction derivatives).
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NODIIS (W)
In the event that the G-DIIS option is not wanted, NODIIS can be
used. The G-DIIS normally accelerates the geometry optimization, but
there is no guarantee that it will do so. If the heat of formation rises
unexpectedly (i.e., rises during a geometry optimization while the GNORM
is larger than about 0.3), then try NODIIS.
NOINTER (O)
The interatomic distances are printed by default. If you do not
want them to be printed, specify NOINTER. For big jobs this reduces the
output file considerably.
NOLOG (O)
Normally a copy of the archive file will be directed to the LOG
file, along with a synopsis of the job. If this is not wanted, it can be
suppressed completely by NOLOG.
NOMM (C)
All four semi-empirical methods underestimate the barrier to
rotation of a peptide bond. A Molecular Mechanics correction has been
added which increases the barrier in N-methyl acetamide to 14 Kcal/mole.
If you do not want this correction, specify NOMM (NO Molecular
Mechanics).
NONR (W)
Not recommended for normal use. Used with the EF routine. See
source code for more details.
NOTHIEL (W)
In a normal geometry optimization using the BFGS routine, Thiel's
FSTMIN technique is used. If normal line-searches are wanted, specify
NOTHIEL.
NOXYZ (O)
The cartesian coordinates are printed by default. If you do not
want them to be printed, specify NOXYZ. For big jobs this reduces the
output file considerably.
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KEYWORDS Page 2-26
NSURF (C)
In an ESP calculation, NSURF=n specifies the number of surface
layers for the Connolly surface.
OLDENS (W)
A density matrix produced by an earlier run of MOPAC is to be used
to start the current calculation. This can be used in attempts to obtain
an SCF when a previous calculation ended successfully but a subsequent
run failed to go SCF.
OLDGEO (C)
If multiple geometries are to be run, and the final geometry from
one calculation is to be used to start the next calculation, OLDGEO
should be specified. Example: If a MNDO, AM1, and PM3 calculation were
to be done on one system, for which only a rough geometry was available,
then after the MNDO calculation, the AM1 calculation could be done using
the optimized MNDO geometry as the starting geometry, by specifying
OLDGEO.
OPEN(n1,n2) (C)
The M.O. occupancy during the SCF calculation can be defined in
terms of doubly occupied, empty, and fractionally occupied M.O.'s. The
fractionally occupied M.O.'s are defined by OPEN(n1,n2), where n1 =
number of electrons in the open-shell manifold, and n2 = number of
open-shell M.O.'s; n1/n2 must be in the range 0 to 2. OPEN(1,1) will be
assumed for odd-electron systems unless an OPEN keyword is used. Errors
introduced by use of fractional occupancy are automatically corrected in
a MECI calculation when OPEN(n1,n2) is used.
ORIDE (W)
Do not use this keyword until you have read Simons' article. ORIDE
is part of the EF routine, and means "Use whatever Lamdas are produced
even if they would normally be 'unacceptable'."
J. Simons, P. Jorgensen, H. Taylor, J. Ozment, J. Phys. Chem. 87,
2745 (1983).
PARASOK (W)
USE THIS KEYWORD WITH EXTREME CAUTION!! The AM1 method has been
parameterized for only a few elements, less than the number available to
MNDO or PM3. If any elements which are not parameterized at the AM1
level are specified, the MNDO parameters, if available, will be used.
The resulting mixture of methods, AM1 with MNDO, has not been studied to
see how good the results are, and users are strictly on their own as far
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KEYWORDS Page 2-27
as accuracy and compatibility with other methods is concerned. In
particular, while all parameter sets are referenced in the output, other
programs may not cite the parameter sets used and thus compatibility with
other MNDO programs is not guaranteed.
PI (O)
The normal density matrix is composed of atomic orbitals, that is s,
px, py and pz. PI allows the user to see how each atom-atom interaction
is split into sigma and pi bonds. The resulting "density matrix" is
composed of the following basis-functions:- s-sigma, p-sigma, p-pi,
d-sigma, d-pi, d-dell. The on-diagonal terms give the hybridization
state, so that an sp2 hybridized system would be represented as s-sigma
1.0, p-sigma 2.0, p-pi 1.0
PM3 (C)
The PM3 method is to be used.
POINT=n (C)
The number of points to be calculated on a reaction path is
specified by POINT=n. Used only with STEP in a path calculation.
POINT1=n (C)
In a grid calculation, the number of points to be calculated in the
first direction is given by POINT1=n. 'n' should be less than 24;
default: 11.
POINT2=n (C)
In a grid calculation, the number of points to be calculated in the
second direction is given by POINT2=n. 'n' should be less than 24,
default: 11;
POTWRT (W)
In an ESP calculation, write out surface points and electrostatic
potential values to UNIT 21.
POLAR (C)
The polarizability and first and second hyperpolarizabilities are to
be calculated. At present this calculation does not work for polymers,
but should work for all other systems.
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KEYWORDS Page 2-28
By default, an electric field gradient of 0.001 is used. This can
be modified by specifying POLAR=n.nnnnn, where n.nnnnn is the new field.
POLAR calculates the polarizabilities from the heat of formation and
from the dipole. The degree to which they agree is a measure of the
precision (not the accuracy) of the calculation. The results from the
heat of formation calculation are more trustworthy than those from the
dipole.
Users should note that the hyperpolarizabilities obtained have to be
divided by 2.0 for beta and 6.0 for gamma to conform with experimental
convention.
Two sets of results are printed: a set (labeled E4) derived from
the effect of the applied electric field on the heat of formation, and a
set (labeled DIP) derived from the value of the dipole in various
electric fields.
POWSQ (C)
Details of the working of POWSQ are printed out. This is only
useful in debugging.
PRECISE (W)
The criteria for terminating all optimizations, electronic and
geometric, are to be increased by a factor, normally, 100. This can be
used where more precise results are wanted. If the results are going to
be used in a FORCE calculation, where the geometry needs to be known
quite precisely, then PRECISE is recommended; for small systems the extra
cost in CPU time is minimal. PRECISE is not recommended for experienced
users, instead GNORM=n.nn and SCFCRT=n.nn are suggested. PRECISE should
only very rarely be necessary in a FORCE calculation: all it does is
remove quartic contamination, which only affects the trivial modes
significantly, and is very expensive in CPU time.
PULAY (W)
The default converger in the SCF calculation is to be replaced by
Pulay's procedure as soon as the density matrix is sufficiently stable.
A considerable improvement in speed can be achieved by the use of PULAY.
If a large number of SCF calculations are envisaged, a sample calculation
using 1SCF and PULAY should be compared with using 1SCF on its own, and
if a saving in time results, then PULAY should be used in the full
calculation. PULAY should be used with care in that its use will prevent
the combined package of convergers (SHIFT, PULAY and the CAMP-KING
convergers) from automatically being used in the event that the system
fails to go SCF in (ITRY-10) iterations.
The combined set of convergers very seldom fails.
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KEYWORDS Page 2-29
QUARTET (C)
RHF interpretation: The desired spin-state is a quartet, i.e., the
state with component of spin = 1/2 and spin = 3/2. When a configuration
interaction calculation is done, all spin states of spin equal to, or
greater than 1/2 are calculated simultaneously, for component of spin =
1/2. From these states the quartet states are selected when QUARTET is
specified, and all other spin states, while calculated, are ignored in
the choice of root to be used. If QUARTET is used on its own, then a
single state, corresponding to an alpha electron in each of three M.O.'s
is calculated.
UHF interpretation: The system will have three more alpha electrons
than beta electrons.
QUINTET (C)
RHF interpretation: The desired spin-state is a quintet, that is,
the state with component of spin = 0 and spin = 2. When a configuration
interaction calculation is done, all spin states of spin equal to, or
greater than 0 are calculated simultaneously, for component of spin = 0.
From these states the quintet states are selected when QUINTET is
specified, and the septet states, while calculated, will be ignored in
the choice of root to be used. If QUINTET is used on its own, then a
single state, corresponding to an alpha electron in each of four M.O.'s
is calculated.
UHF interpretation: The system will have three more alpha electrons
than beta electrons.
RECALC=n
RECALC=n calculates the Hessian every n steps in the EF
optimization. For small n this is costly but is also very effective in
terms of convergence. RECALC=10 and DMAX=0.10 can be useful for
difficult cases. In extreme cases RECALC=1 and DMAX=0.05 will always
find a stationary point, if it exists.
RESTART (W)
When a job has been stopped, for whatever reason, and intermediate
results have been stored, then the calculation can be restarted at the
point where it stopped by specifying RESTART. The most common cause of a
job stopping before completion is its exceeding the time allocated. A
saddle-point calculation has no restart, but the output file contains
information which can easily be used to start the calculation from a
point near to where it stopped.
It is not necessary to change the geometric data to reflect the new
geometry. As a result, the geometry printed at the start of a restarted
job will be that of the original data, not that of the restarted file.
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KEYWORDS Page 2-30
A convenient way to monitor a long run is to specify 1SCF and
RESTART; this will give a normal output file at very little cost.
NOTE 1: In the FORCE calculation two restarts are possible. These
are (a) a restart in FLEPO if the geometry was not optimized fully before
FORCE was called, and (b) the normal restart in the construction of the
force matrix. If the restart is in FLEPO within FORCE then the keyword
FORCE should be deleted, and the keyword RESTART used on its own.
Forgetting this point is a frequent cause of failed jobs.
NOTE 2: Two restarts also exist in the IRC calculation. If an IRC
calculation stops while in the FORCE calculation, then a normal restart
can be done. If the job stops while doing the IRC calculation itself
then the keyword IRC=n should be changed to IRC, or it can be omitted if
DRC is also specified. The absence of the string "IRC=" is used to
indicate that the FORCE calculation was completed before the restart
files were written.
ROOT=n (C)
The n'th root of a C.I. calculation is to be used in the
calculation. If a keyword specifying the spin-state is also present,
e.g. SINGLET or TRIPLET, then the n'th root of that state will be
selected. Thus ROOT=3 and SINGLET will select the third singlet root.
If ROOT=3 is used on its own, then the third root will be used, which may
be a triplet, the third singlet, or the second singlet (the second root
might be a triplet). In normal use, this keyword would not be used. It
is retained for educational and research purposes. Unusual care should
be exercised when ROOT= is specified.
ROT=n (C)
In the calculation of the rotational contributions to the
thermodynamic quantities the symmetry number of the molecule must be
supplied. The symmetry number of a point group is the number of
equivalent positions attainable by pure rotations. No reflections or
improper rotations are allowed. This number cannot be assumed by
default, and may be affected by subtle modifications to the molecule,
such as isotopic substitution. A list of the most important symmetry
numbers follows:
---- TABLE OF SYMMETRY NUMBERS ----
C1 CI CS 1 D2 D2D D2H 4 C(INF)V 1
C2 C2V C2H 2 D3 D3D D3H 6 D(INF)H 2
C3 C3V C3H 3 D4 D4D D4H 8 T TD 12
C4 C4V C4H 4 D6 D6D D6H 12 OH 24
C6 C6V C6H 6 S6 3
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KEYWORDS Page 2-31
SADDLE (C)
The transition state in a simple chemical reaction is to be
optimized. Extra data are required. After the first geometry,
specifying the reactants, and any symmetry functions have been defined,
the second geometry, specifying the products, is defined, using the same
format as that of the first geometry.
SADDLE often fails to work successfully. Frequently this is due to
equivalent dihedral angles in the reactant and product differing by about
360 degrees rather than zero degrees. As the choice of dihedral can be
difficult, users should consider running this calculation with the
keyword XYZ. There is normally no ambiguity in the definition of
cartesian coordinates. See also BAR=.
Many of the bugs in SADDLE have been removed in this version. Use
of the XYZ option is strongly recommended.
SCALE (C)
SCALE=n.n specifies the scaling factor for Van der Waals' radii for
the initial layer of the Connolly surface in the ESP calculation.
SCFCRT=n.nn (W)
The default SCF criterion is to be replaced by that defined by
SCFCRT=.
The SCF criterion is the change in energy in kcal/mol on two
successive iterations. Other minor criteria may make the requirements
for an SCF slightly more stringent. The SCF criterion can be varied from
about 0.001 to 1.D-25, although numbers in the range 0.0001 to 1.D-9 will
suffice for most applications.
An overly tight criterion can lead to failure to achieve a SCF, and
consequent failure of the run.
SCINCR=n.nn
In an ESP calculation, SCINCR=n.nn specifies the increment between
layers of the surface in the Connolly surface. (default: 0.20)
SETUP (C)
If, on the keyword line, the word 'SETUP' is specified, then one or
two lines of keywords will be read from a file with the logical name
SETUP. The logical file SETUP must exist, and must contain at least one
line. If the second line is defined by the first line as a keyword line,
and the second line contains the word SETUP, then one line of keywords
will be read from a file with the logical name SETUP.
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KEYWORDS Page 2-32
SETUP=name (C)
Same as SETUP, only the logical or actual name of the SETUP file is
'name'.
SEXTET (C)
RHF interpretation: The desired spin-state is a sextet: the state
with component of spin = 1/2 and spin = 5/2.
The sextet states are the highest spin states normally calculable
using MOPAC in its unmodified form. If SEXTET is used on its own, then a
single state, corresponding to one alpha electron in each of five M.O.'s,
is calculated. If several sextets are to be calculated, say the second
or third, then OPEN(n1,n2) should be used.
UHF interpretation: The system will have five more alpha electrons
than beta electrons.
SHIFT=n.nn (W)
In an attempt to obtain an SCF by damping oscillations which slow
down the convergence or prevent an SCF being achieved, the virtual M.O.
energy levels are shifted up or down in energy by a shift technique. The
principle is that if the virtual M.O.'s are changed in energy relative to
the occupied set, then the polarizability of the occupied M.O.'s will
change pro rata. Normally, oscillations are due to autoregenerative
charge fluctuations.
The SHIFT method has been re-written so that the value of SHIFT
changes automatically to give a critically-damped system. This can
result in a positive or negative shift of the virtual M.O. energy
levels. If a non-zero SHIFT is specified, it will be used to start the
SHIFT technique, rather than the default 15eV. If SHIFT=0 is specified,
the SHIFT technique will not be used unless normal convergence techniques
fail and the automatic "ALL CONVERGERS..." message is produced.
SIGMA (C)
The McIver-Komornicki gradient norm minimization routines, POWSQ and
SEARCH are to be used. These are very rapid routines, but do not work
for all species. If the gradient norm is low, i.e., less than about 5
units, then SIGMA will probably work; in most cases, NLLSQ is
recommended. SIGMA first calculates a quite accurate Hessian matrix, a
slow step, then works out the direction of fastest decent, and searches
along that direction until the gradient norm is minimized. The Hessian
is then partially updated in light of the new gradients, and a fresh
search direction found. Clearly, if the Hessian changes markedly as a
result of the line-search, the update done will be inaccurate, and the
new search direction will be faulty.
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KEYWORDS Page 2-33
SIGMA should be avoided if at all possible when non-variationally
optimized calculations are being done.
If the Hessian is suspected to be corrupt within SIGMA it will be
automatically recalculated. This frequently speeds up the rate at which
the transition state is located. If you do not want the Hessian to be
reinitialized -- it is costly in CPU time -- specify LET on the keyword
line.
SINGLET (C)
When a configuration interaction calculation is done, all spin
states are calculated simultaneously, either for component of spin = 0 or
1/2. When only singlet states are of interest, then SINGLET can be
specified, and all other spin states, while calculated, are ignored in
the choice of root to be used.
Note that while almost every even-electron system will have a
singlet ground state, SINGLET should still be specified if the desired
state must be a singlet.
SINGLET has no meaning in a UHF calculation, but see also TRIPLET.
SLOPE (C)
In an ESP calculation, SLOPE=n.nn specifies the scale factor for
MNDO charges. (default=1.422)
SPIN (O)
The spin matrix, defined as the difference between the alpha and
beta density matrices, is to be printed. If the system has a
closed-shell ground state, e.g. methane run UHF, the spin matrix will be
null.
If SPIN is not requested in a UHF calculation, then the diagonal of
the spin matrix, that is the spin density on the atomic orbitals, will be
printed.
STEP (C)
In a reaction path, if the path step is constant, STEP can be used
instead of explicitly specifying each point. The number of steps is
given by POINT. If the reaction coordinate is an interatomic distance,
only positive STEPs are allowed.
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KEYWORDS Page 2-34
STEP1=n.nnn (C)
In a grid calculation the step size in degrees or Angstroms for the
first of the two parameters is given by n.nnn. By default, an 11 by 11
grid is generated. See POINT1 and POINT2 on how to adjust this number.
The first point calculated is the supplied geometry, and is in the upper
left hand corner. This is a change from Version 5.00, where the supplied
geometry was the central point.
STEP2=n.nnn (C)
In a grid calculation the step size in degrees or Angstroms for the
second of the two parameters is given by n.nnn.
STO3G (W)
In an ESP calculation STO3G means "Use the STO-3G basis set to
de-orthogonalize the semiempirical orbitals".
SYMAVG (W)
Used by the ESP, SYMAVG will average charges which should have the
same value by symmetry.
SYMMETRY (C)
Symmetry data defining related bond lengths, angles and dihedrals
can be included by supplying additional data after the geometry has been
entered. If there are any other data, such as values for the reaction
coordinates, or a second geometry, as required by SADDLE, then it would
follow the symmetry data. Symmetry data are terminated by one blank
line. For non-variationally optimized systems symmetry constraints can
save a lot of time because many derivatives do not need to be calculated.
At the same time, there is a risk that the geometry may be wrongly
specified, e.g. if methane radical cation is defined as being
tetrahedral, no indication that this is faulty will be given until a
FORCE calculation is run. (This system undergoes spontaneous Jahn-Teller
distortion.)
Usually a lower heat of formation can be obtained when SYMMETRY is
specified. To see why, consider the geometry of benzene. If no
assumptions are made regarding the geometry, then all the C-C bond
lengths will be very slightly different, and the angles will be almost,
but not quite 120 degrees. Fixing all angles at 120 degrees, dihedrals
at 180 or 0 degrees, and only optimizing one C-C and one C-H bond-length
will result in a 2-D optimization, and exact D6h symmetry. Any
deformation from this symmetry must involve error, so by imposing
symmetry some error is removed.
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KEYWORDS Page 2-35
The layout of the symmetry data is:
<defining atom> <symmetry relation> <defined atom> <defined atom>,...
where the numerical code for <symmetry relation> is given in the table of
SYMMETRY FUNCTIONS below.
For example, ethane, with three independent variables, can be
defined as
SYMMETRY
ETHANE, D3D NA NB NC
C
C 1.528853 1 1
H 1.105161 1 110.240079 1 2 1
H 1.105161 0 110.240079 0 120.000000 0 2 1 3
H 1.105161 0 110.240079 0 240.000000 0 2 1 3
H 1.105161 0 110.240079 0 60.000000 0 1 2 3
H 1.105161 0 110.240079 0 180.000000 0 1 2 3
H 1.105161 0 110.240079 0 300.000000 0 1 2 3
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
3, 1, 4, 5, 6, 7, 8,
3, 2, 4, 5, 6, 7, 8,
Here atom 3, a hydrogen, is used to define the bond lengths
(symmetry relation 1) of atoms 4,5,6,7 and 8 with the atoms they are
specified to bond with in the NA column of the data file; similarly, its
angle (symmetry relation 2) is used to define the bond-angle of atoms
4,5,6,7 and 8 with the two atoms specified in the NA and NB columns of
the data file. The other angles are point-group symmetry defined as a
multiple of 60 degrees.
Spaces, tabs or commas can be used to separate data. Note that only
three parameters are marked to be optimized. The symmetry data can be
the last line of the data file unless more data follows, in which case a
blank line must be inserted after the symmetry data.
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KEYWORDS Page 2-36
The full list of available symmetry relations is as follows:
SYMMETRY FUNCTIONS
<Symmetry
relation>
1 BOND LENGTH IS SET EQUAL TO THE REFERENCE BOND LENGTH
2 BOND ANGLE IS SET EQUAL TO THE REFERENCE BOND ANGLE
3 DIHEDRAL ANGLE IS SET EQUAL TO THE REFERENCE DIHEDRAL ANGLE
4 DIHEDRAL ANGLE VARIES AS 90 DEGREES - REFERENCE DIHEDRAL
5 DIHEDRAL ANGLE VARIES AS 90 DEGREES + REFERENCE DIHEDRAL
6 DIHEDRAL ANGLE VARIES AS 120 DEGREES - REFERENCE DIHEDRAL
7 DIHEDRAL ANGLE VARIES AS 120 DEGREES + REFERENCE DIHEDRAL
8 DIHEDRAL ANGLE VARIES AS 180 DEGREES - REFERENCE DIHEDRAL
9 DIHEDRAL ANGLE VARIES AS 180 DEGREES + REFERENCE DIHEDRAL
10 DIHEDRAL ANGLE VARIES AS 240 DEGREES - REFERENCE DIHEDRAL
11 DIHEDRAL ANGLE VARIES AS 240 DEGREES + REFERENCE DIHEDRAL
12 DIHEDRAL ANGLE VARIES AS 270 DEGREES - REFERENCE DIHEDRAL
13 DIHEDRAL ANGLE VARIES AS 270 DEGREES + REFERENCE DIHEDRAL
14 DIHEDRAL ANGLE VARIES AS THE NEGATIVE OF THE REFERENCE
DIHEDRAL
15 BOND LENGTH VARIES AS HALF THE REFERENCE BOND LENGTH
16 BOND ANGLE VARIES AS HALF THE REFERENCE BOND ANGLE
17 BOND ANGLE VARIES AS 180 DEGREES - REFERENCE BOND ANGLE
18 BOND LENGTH IS A MULTIPLE OF REFERENCE BOND-LENGTH
Function 18 is intended for use in polymers, in which the
translation vector may be a multiple of some bond-length. 1,2,3 and 14
are most commonly used. Abbreviation: SYM.
SYMMETRY is not available for use with cartesian coordinates.
T= (W)
This is a facility to allow the program to shut down in an orderly
manner on computers with execution time C.P.U. limits.
The total C.P.U. time allowed for the current job is limited to
nn.nn seconds; by default this is one hour, i.e., 3600 seconds. If the
next cycle of the calculation cannot be completed without running a risk
of exceeding the assigned time the calculation will write a restart file
and then stop. The safety margin is 100 percent; that is, to do another
cycle, enough time to do at least two full cycles must remain.
Alternative specifications of the time are T=nn.nnM, this defines
the time in minutes, T=nn.nnH, in hours, and T=nn.nnD, in days, for very
long jobs. This keyword cannot be written with spaces around the '='
sign.
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KEYWORDS Page 2-37
THERMO (O)
The thermodynamic quantities, internal energy, heat capacity,
partition function, and entropy can be calculated for translation,
rotation and vibrational degrees of freedom for a single temperature, or
a range of temperatures. Special situations such as linear systems and
transition states are accommodated. The approximations used in the
THERMO calculation are invalid below 100K, and checking of the lower
bound of the temperature range is done to prevent temperatures of less
than 100K being used.
Another limitation, for which no checking is done, is that there
should be no internal rotations. If any exist, they will not be
recognized as such, and the calculated quantities will be too low as a
result.
In order to use THERMO the keyword FORCE must also be specified, as
well as the value for the symmetry number; this is given by ROT=n.
If THERMO is specified on its own, then the default values of the
temperature range are assumed. This starts at 200K and increases in
steps of 10 degrees to 400K. Three options exist for overriding the
default temperature range. These are:
THERMO(nnn) (O)
The thermodynamic quantities for a 200 degree range of temperatures,
starting at nnnK and with an interval of 10 degrees are to be calculated.
THERMO(nnn,mmm) (O)
The thermodynamic quantities for the temperature range limited by a
lower bound of nnn Kelvin and an upper bound of mmm Kelvin, the step size
being calculated in order to give approximately 20 points, and a
reasonable value for the step. The size of the step in Kelvin degrees
will be 1, 2, or 5, or a power of 10 times these numbers.
THERMO(nnn,mmm,lll) (O)
Same as for THERMO(nnn,mmm), only now the user can explicitly define
the step size. The step size cannot be less than 1K.
T-PRIORITY (O)
In a DRC calculation, results will be printed whenever the
calculated time changes by 0.1 femtoseconds. Abbreviation, T-PRIO.
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KEYWORDS Page 2-38
T-PRIORITY=n.nn (O)
In a DRC calculation, results will be printed whenever the
calculated time changes by n.nn femtoseconds.
TRANS (C)
The imaginary frequency due to the reaction vector in a transition
state calculation must not be included in the thermochemical calculation.
The number of genuine vibrations considered can be:
3N-5 for a linear ground state system,
3N-6 for a non-linear ground state system, or
3N-6 for a linear transition-state complex,
3N-7 for a non-linear transition-state complex.
This keyword must be used in conjunction with THERMO if a transition
state is being calculated.
TRANS=n (C)
The facility exists to allow the THERMO calculation to handle
systems with internal rotations. TRANS=n will remove the n lowest
vibrations. Note that TRANS=1 is equivalent to TRANS on its own. For
xylene, for example, TRANS=2 would be suitable.
This keyword cannot be written with spaces around the '=' sign.
TRIPLET (C)
The triplet state is defined. If the system has an odd number of
electrons, an error message will be printed.
UHF interpretation.
The number of alpha electrons exceeds that of the beta electrons by
2. If TRIPLET is not specified, then the numbers of alpha and beta
electrons are set equal. This does not necessarily correspond to a
singlet.
RHF interpretation.
An RHF MECI calculation is performed to calculate the triplet state.
If no other C.I. keywords are used, then only one state is calculated by
default. The occupancy of the M.O.'s in the SCF calculation is defined
as (...2,1,1,0,..), that is, one electron is put in each of the two
highest occupied M.O.'s.
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KEYWORDS Page 2-39
See keywords C.I.=n and OPEN(n1,n2).
TS (C)
Within the Eigenvector Following routine, the option exists to
optimize a transition state. To do this, use TS. Preliminary
indications are that the TS method is much faster and more reliable than
either SIGMA or NLLSQ.
TS appears to work well with cartesian coordinates.
In the event that TS does not converge on a stationary point, try
adding RECALC=5 to the keyword line.
UHF (C)
The unrestricted Hartree-Fock Hamiltonian is to be used.
VECTORS (O)
The eigenvectors are to be printed. In UHF calculations both alpha
and beta eigenvectors are printed; in all cases the full set, occupied
and virtual, are output. The eigenvectors are normalized to unity, that
is the sum of the squares of the coefficients is exactly one. If DEBUG
is specified, then ALL eigenvectors on every iteration of every SCF
calculation will be printed. This is useful in a learning context, but
would normally be very undesirable.
VELOCITY (C)
The user can supply the initial velocity vector to start a DRC
calculation. Limitations have to be imposed on the geometry in order for
this keyword to work. These are (a) the input geometry must be in
cartesian coordinates, (b) the first three atoms must not be coaxial, (c)
triatomic systems are not allowed (See geometry specification - triatomic
systems are in internal coordinates, by definition.)
Put the velocity vector after the geometry as three data per line,
representing the x, y, and z components of velocity for each atom. The
units of velocity are centimeters per second.
The velocity vector will be rotated so as to suit the final
cartesian coordinate orientation of the molecule.
If KINETIC=n.n is also specified, the velocity vector will be scaled
to equal the velocity corresponding to n.n kcal/mole. This allows the
user to define the direction of the velocity vector; the magnitude is
given by KINETIC=n.n.
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KEYWORDS Page 2-40
WILLIAMS (C)
Within the ESP calculation, the Connolly surface is used as the
default. If the surface generation procedure of Donald Williams is
wanted, the keyword WILLIAMS should be used.
X-PRIORITY (O)
In a DRC calculation, results will be printed whenever the
calculated geometry changes by 0.05 Angstroms. The geometry change is
defined as the linear sum of the translation vectors of motion for all
atoms in the system. Abbreviation, X-PRIO.
X-PRIORITY=n.nn (O)
In a DRC calculation, results will be printed whenever the
calculated geometry changes by n.nn Angstroms.
XYZ (W)
The SADDLE calculation quite often fails due to faulty definition of
the second geometry because the dihedrals give a lot of difficulty. To
make this option easier to use, XYZ was developed. A calculation using
XYZ runs entirely in cartesian coordinates, thus eliminating the problems
associated with dihedrals. The connectivity of the two systems can be
different, but the numbering must be the same. Dummy atoms can be used;
these will be removed at the start of the run. A new numbering system
will be generated by the program, when necessary.
XYZ is also useful for removing dummy atoms from an internal
coordinate file; use XYZ and 0SCF.
If a large ring system is being optimized, sometimes the closure is
difficult, in which case XYZ will normally work.
Except for SADDLE, do not use XYZ by default: use it only when
something goes wrong!
In order for XYZ to be used, the supplied geometry must either be in
cartesian coordinates or, if internal coordinates are used, symmetry must
not be used, and all coordinates must be flagged for optimization. If
dummy atoms are present, only 3N-6 coordinates need to be flagged for
optimization.
If at all possible, the first 3 atoms should be real. Except in
SADDLE, XYZ will still work if one or more dummy atoms occur before the
fourth real atom, in which case more than 3N-6 coordinates will be
flagged for optimization. This could cause difficulties with the EF
method, which is why dummy atoms at the start of the geometry
specification should be avoided. The coordinates to be optimized depend
on the internal coordinate definition of real atoms 1, 2, and 3. If the
position of any of these atoms depends on dummy atoms, then the
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KEYWORDS Page 2-41
optimization flags will be different from the case where the first three
atoms defined are all real. The geometry is first converted to cartesian
coordinates and dummy atoms excluded. The cartesian coordinates to be
optimized are:
Atoms R R R R R X R X R X R R R X X X R X X X R X X X
X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z X Y Z
Atom 1
2 + + + + + + + + + + + + + + + + +
3 + + + + + + + + + + + + + + + + + + + + + + +
4 on + + + + + + + + + + + + + + + + + + + + + + + +
Where R and X apply to real and dummy atoms in the internal coordinate
Z-matrix, and atoms 1, 2, 3, and 4 are the real atoms in cartesian
coordinates. A '+' means that the relevant coordinate is flagged for
optimization. Note that the number of flagged coordinates varies from
3N-6 to 3N-3, atom 1 is never optimized.
2.4 KEYWORDS THAT GO TOGETHER
Normally only a subset of keywords are used in any given piece of
research. Keywords which are related to each other in this way are:
1. In getting an SCF: SHIFT, PULAY, ITRY, CAMP, SCFCRT, 1SCF, PL.
2. In C.I. work: SINGLET, DOUBLET, etc., OPEN(n,m), C.I.=(n,m),
LARGE, MECI, MS=n, VECTORS, ESR, ROOT=n, MICROS.
3. In excited states: UHF with (TRIPLET, QUARTET, etc.), C.I.=n,
C.I.=(n,m).
4. In geometry optimization:
1. Using BFGS: GNORM=n.n, XYZ, PRECISE.
2. Using EF: GNORM=n.n, XYZ, PRECISE
3. Using NLLSQ: GNORM=n.n, XYZ, PRECISE
4. Using SIGMA: GNORM=n.n, XYZ, PRECISE
5. In Gaussian work: AIGIN, AIGOUT, AIDER.
6. In SADDLE: XYZ, BAR=n.n
- 50 -
CHAPTER 3
GEOMETRY SPECIFICATION
FORMAT: The geometry is read in using essentially "Free-Format" of
FORTRAN-77. In fact, a character input is used in order to accommodate
the chemical symbols, but the numeric data can be regarded as
"free-format". This means that integers and real numbers can be
interspersed, numbers can be separated by one or more spaces, a tab
and/or by one comma. If a number is not specified, its value is set to
zero.
The geometry can be defined in terms of either internal or cartesian
coordinates.
3.1 INTERNAL COORDINATE DEFINITION
For any one atom (i) this consists of an interatomic distance in
Angstroms from an already-defined atom (j), an interatomic angle in
degrees between atoms i and j and an already defined k, (k and j must be
different atoms), and finally a torsional angle in degrees between atoms
i, j, k, and an already defined atom l (l cannot be the same as k or j).
See also dihedral angle coherency.
Exceptions:
1. Atom 1 has no coordinates at all: this is the origin.
2. Atom 2 must be connected to atom 1 by an interatomic distance
only.
3. Atom 3 can be connected to atom 1 or 2, and must make an angle
with atom 2 or 1 (thus - 3-2-1 or 3-1-2); no dihedral is
possible for atom 3. By default, atom 3 is connected to atom 2.
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GEOMETRY SPECIFICATION Page 3-2
3.1.1 Constraints
1. Interatomic distances must be greater than zero. Zero Angstroms
is acceptable only if the parameter is symmetry-related to
another atom, and is the dependent function.
2. Angles must be in the range 0.0 to 180.0, inclusive. This
constraint is for the benefit of the user only; negative angles
are the result of errors in the construction of the geometry,
and angles greater than 180 degrees are fruitful sources of
errors in the dihedrals.
3. Dihedrals angles must be definable. If atom i makes a dihedral
with atoms j, k, and l, and the three atoms j, k, and l are in a
straight line, then the dihedral has no definable angle. During
the calculation this constraint is checked continuously, and if
atoms j, k, and l lie within 0.02 Angstroms of a straight line,
the calculation will output an error message and then stop. Two
exceptions to this constraint are:
(a) if the angle is zero or 180 degrees, in which case the
dihedral is not used.
(b) if atoms j, k, and l lie in an exactly straight line
(usually the result of a symmetry constraint), as in acetylene,
acetonitrile, but-2-yne, etc.
If the exceptions are used, care must be taken to ensure that the
program does not violate these constraints during any optimizations or
during any calculations of derivatives - see also FORCE.
Conversion to Cartesian Coordinates
By definition, atom 1 is at the origin of cartesian coordinate space
-- be careful, however, if atom 1 is a dummy atom. Atom 2 is defined as
lying on the positive X axis -- for atom 2, Y=0 and Z=0. Atom 3 is in
the X-Y plane unless the angle 3-2-1 is exactly 0 or 180 degrees. Atom
4, 5, 6, etc. can lie anywhere in 3-D space.
3.2 GAUSSIAN Z-MATRICES
With certain limitations, geometries can now be specified within
MOPAC using the Gaussian Z-matrix format.
Exceptions to the full Gaussian standard
1. The option of defining an atom's position by one distance and
two angles is not allowed. In other words, the N4 variable
described in the Gaussian manual must either be zero or not
specified. MOPAC requires the geometry of atoms to be defined
- 52 -
GEOMETRY SPECIFICATION Page 3-3
in terms of, at most, one distance, one angle, and one dihedral.
2. Gaussian cartesian coordinates are not supported.
3. Chemical symbols must not be followed by an integer identifying
the atom. Numbers after a symbol are used by MOPAC to indicate
isotopic mass. If labels are desired, they should be enclosed
in parentheses, thus "Cl(on C5)34.96885".
4. The connectivity (N1, N2, N3) must be integers. Labels are not
allowed.
Specification of Gaussian Z-matrices.
The information contained in the Gaussian Z-matrix is identical to
that in a MOPAC Z-matrix. The order of presentation is different. Atom
N, (real or dummy) is specified in the format:
Element N1 Length N2 Alpha N3 Beta
where Element is the same as for the MOPAC Z-matrix. N1, N2, and N3 are
the connectivity, the same as the MOPAC Z-matrix NA, NB, and NC: bond
lengths are between N and N1, angles are between N, N1 and N2, and
dihedrals are between N, N1, N2, and N3. The same rules apply to N1, N2,
and N3 as to NA, NB, and NC.
Length, Alpha, and Beta are the bond lengths, the angle, and
dihedral. They can be 'real', e.g. 1.45, 109.4, 180.0, or 'symbolic'.
A symbolic is an alphanumeric string of up to 8 characters, e.g. R51,
A512, D5213, CH, CHO, CHOC, etc. Two or more symbolics can be the same.
Dihedral symbolics can optionally be preceeded by a minus sign, in which
case the value of the dihedral is the negative of the value of the
symbolic. This is the equivalent of the normal MOPAC SYMMETRY operations
1, 2, 3, and 14.
If an internal coordinate is real, it will not be optimized. This
is the equivalent of the MOPAC optimization flag "0". If an internal
coordinate is symbolic, it can be optimized.
The Z-matrix is terminated by a blank line, after which comes the
starting values of the symbolics, one per line. If there is a blank line
in this set, then all symbolics after the blank line are considered
fixed; that is, they will not be optimized. The set before the blank
line will be optimized.
- 53 -
GEOMETRY SPECIFICATION Page 3-4
Example of Gaussian Z-matrix geometry specification
Line 1 AM1
Line 2 Ethane
Line 3
Line 4 C
Line 5 C 1 r21
Line 6 H 2 r32 1 a321
Line 7 H 2 r32 1 a321 3 d4213
Line 8 H 2 r32 1 a321 3 -d4213
Line 9 H 1 r32 2 a321 3 60.
Line 10 H 1 r32 2 a321 3 180.
Line 11 H 1 r32 2 a321 3 d300
Line 12
Line 13 r21 1.5
Line 14 r32 1.1
Line 15 a321 109.5
Line 16 d4313 120.0
Line 17
Line 18 d300 300.0
Line 19
3.3 CARTESIAN COORDINATE DEFINITION
A definition of geometry in cartesian coordinates consists of the
chemical symbol or atomic number, followed by the cartesian coordinates
and optimization flags but no connectivity.
MOPAC uses the lack of connectivity to indicate that cartesian
coordinates are to be used. A unique case is the triatomics for which
only internal coordinates are allowed. This is to avoid conflict of
definitions: the user does not need to define the connectivity of atom
2, and can elect to use the default connectivity for atom 3. As a
result, a triatomic may have no explicit connectivity defined, the user
thus taking advantage of the default connectivity. Since internal
coordinates are more commonly used than cartesian, the above choice was
made.
If the keyword XYZ is absent every coordinate must be marked for
optimization. If any coordinates are not to be optimized, the keyword
XYZ must be present. The coordinates of all atoms, including atoms 1, 2
and 3 can be optimized. Dummy atoms should not be used, for obvious
reasons.
3.4 CONVERSION BETWEEN VARIOUS FORMATS
MOPAC can accept any of the following formats: cartesian, MOPAC
internal coordinates, and Gaussian internal coordinates. Both MOPAC and
Gaussian Z-matrices can also contain dummy atoms. Internally, MOPAC
- 54 -
GEOMETRY SPECIFICATION Page 3-5
works with either a cartesian coordinate set (if XYZ is specified) or
internal coordinates (the default). If the 0SCF option is requested, the
geometry defined on input will be printed in MOPAC Z-matrix format, along
with other optional formats.
The type(s) of geometry printed at the end of a 0SCF calculation
depend only on the keywords XYZ, AIGOUT, and NOXYZ. The geometry printed
is independent of the type of input geometry, and therefore makes a
convenient conversion mechanism.
If XYZ is present, all dummy atoms are removed and the internal
coordinate definition remade. All symmetry relations are lost if XYZ is
used.
If NOXYZ is present, cartesian coordinates will not be printed.
If AIGOUT is present, a data set using Gaussian Z-matrix format is
printed.
Note: (1) Only if the keyword XYZ is absent and the keyword
SYMMETRY present in a MOPAC internal coordinate geometry, or two or more
internal coordinates in a Gaussian Z-matrix have the same symbolic will
symmetry be present in the MOPAC or Gaussian geometries output. (2) This
expanded use of 0SCF replaces the program DDUM, supplied with earlier
copies of MOPAC.
3.5 DEFINITION OF ELEMENTS AND ISOTOPES
Elements are defined in terms of their atomic numbers or their
chemical symbols, case insensitive. Thus, chlorine could be specified as
17, or Cl. In Version 6, only main-group elements and transition metals
for which the 'd' shell is full are available.
Acceptable symbols for MNDO are:
Elements Dummy atom, sparkles and
Translation Vector
H
Li * B C N O F
Na' * Al Si P S Cl + o
K' * ... Zn * Ge * * Br XX Cb ++ + -- - Tv
Rb' * ... * * Sn * * I 99 102 103 104 105 106 107
* * ... Hg * Pb *
' These symbols refer to elements which lack a basis set.
+ This is the dummy atom for assisting with geometry specification.
* Element not parameterized.
o This is the translation vector for use with polymers.
Old parameters for some elements are available. These are provided
to allow compatibility with earlier copies of MOPAC. To use these older
parameters, use a keyword composed of the chemical symbol followed by the
- 55 -
GEOMETRY SPECIFICATION Page 3-6
year of publication of the parameters. Keywords currently available:
Si1978 S1978.
For AM1, acceptable symbols are:
Elements Dummy atom, sparkles and
Translation Vector
H
* * B C N O F
Na' * Al Si P S Cl + o
K' * ... Zn * Ge * * Br XX Cb ++ + -- - Tv
Rb' * ... * * Sn * * I 99 102 103 104 105 106 107
* * ... Hg * * *
If users need to use other elements, such as beryllium or lead, they
can be specified, in which case MNDO-type atoms will be used. As the
behavior of such systems is not well investigated, users are cautioned to
exercise unusual care. To alert users to this situation, the keyword
PARASOK is defined.
For PM3, acceptable symbols are:
Elements Dummy atom, sparkles and
Translation Vector
H
* Be * C N O F
Na' Mg Al Si P S Cl + o
K' * ... Zn Ga Ge As Se Br XX Cb ++ + -- - Tv
Rb' * ... Cd In Sn Sb Te I 99 102 103 104 105 106 107
* * ... Hg Tl Pb Bi
Diatomics Parameterized within the MINDO/3 Formalism
H B C N O F Si P S Cl A star (*) indicates
----------------------------------------- that the atom-pair is
H * * * * * * * * * * parameterized within
B * * * * * * MINDO/3.
C * * * * * * * * * *
N * * * * * * * *
O * * * * * * * *
F * * * * * * *
Si * * *
P * * * * * *
S * * * * * *
Cl * * * * * *
Note: MINDO/3 should now be regarded as being of historical
interest only. MOPAC contains the original parameters. These do not
reproduce the original reported results in the case of P, Si, or S. The
original work was faulty, see G. Frenking, H. Goetz, and F. Marschner,
J.A.C.S., 100, 5295 (1978). Re-optimized parameters for P-C and P-Cl
were derived later which gave better results. These are:
- 56 -
GEOMETRY SPECIFICATION Page 3-7
Alpha(P-C): 0.8700 G. Frenking, H. Goetz, F. Marschner,
Beta(P-C): 0.5000 J.A.C.S., 100, 5295-5296 (1978).
Alpha(P-Cl): 1.5400 G. Frenking, F. Marschner, H. Goetz,
Beta(P-Cl): 0.2800 Phosphorus and Sulfur, 8, 337-342 (1980).
Although better than the original parameters, these have not been
adopted within MOPAC because to do so at this time would prevent earlier
calculations from being duplicated. Parameters for P-O and P-F have been
added: these were abstracted from Frenking's 1980 paper. No
inconsistency is involved as MINDO/3 historically did not have P-O or P-F
parameters.
Extra entities available to MNDO, MINDO/3, AM1 and PM3
+ A 100% ionic alkali metal.
++ A 100% ionic alkaline earth metal.
- A 100% ionic halogen-like atom
-- A 100% ionic group VI-like atom.
Cb A special type of monovalent atom
Elements 103, 104, 105, and 106 are the sparkles; elements 11 and 19
are sparkles tailored to look like the alkaline metal ions; Tv is the
translation vector for polymer calculations. See "Full description of
sparkles".
Element 102, symbol Cb, is designed to satisfy valency requirements
of atoms for which some bonds are not completed. Thus in "solid" diamond
the usual way to complete the normal valency in a cluster model is to use
hydrogen atoms. This approach has the defect that the electronegativity
of hydrogen is different from that of carbon. The "Capped bond" atom,
Cb, is designed to satisfy these valency requirements without acquiring a
net charge.
Cb behaves like a monovalent atom, with the exception that it can
alter its electronegativity to achieve an exactly zero charge in whatever
environment it finds itself. It is thus all things to all atoms. On
bonding to hydrogen it behaves similar to a hydrogen atom. On bonding to
fluorine it behaves like a very electronegative atom. If several capped
bond atoms are used, each will behave independently. Thus if the two
hydrogen atoms in formic acid were replaced by Cb's then each Cb would
independently become electroneutral.
Capped bonds internal coordinates should not be optimized. A fixed
bond-length of 1.7 Angstroms is recommended, if two Cb are on one atom, a
contained angle of 109.471221 degrees is suggested, and if three Cb are
on one atom, a contained dihedral of -120 degrees (note sign) should be
used.
Element 99, X, or XX is known as a dummy atom, and is used in the
definition of the geometry; it is deleted automatically from any
cartesian coordinate geometry files. Dummy atoms are pure mathematic
points, and are useful in defining geometries; for example, in ammonia
the definition of C3v symmetry is facilitated by using one dummy atom and
symmetry relating the three hydrogens to it.
- 57 -
GEOMETRY SPECIFICATION Page 3-8
Output normally only gives chemical symbols.
Isotopes are used in conjunction with chemical symbols. If no
isotope is specified, the average isotopic mass is used, thus chlorine is
35.453. This is different from some earlier versions of MOPAC, in which
the most abundant isotope was used by default. This change was justified
by the removal of any ambiguity in the choice of isotope. Also, the
experimental vibrational spectra involve a mixture of isotopes. If a
user wishes to specify any specific isotope it should immediately follow
the chemical symbol (no space), e.g., H2, H2.0140, C(meta)13, or
C13.00335.
The sparkles ++, +, --, and - have no mass; if they are to be used
in a force calculation, then appropriate masses should be used.
Each internal coordinate is followed by an integer, to indicate the
action to be taken.
Integer Action
1 Optimize the internal coordinate.
0 Do not optimize the internal coordinate.
-1 Reaction coordinate, or grid index.
Remarks:
Only one reaction coordinate is allowed, but this can be made more
versatile by the use of SYMMETRY. If a reaction coordinate is used, the
values of the reaction coordinate should follow immediately after the
geometry and any symmetry data. No terminator is required, and
free-format-type input is acceptable.
If two "reaction coordinates" are used, then MOPAC assumes that the
two-dimensional space in the region of the supplied geometry is to be
mapped. The two dimensions to be mapped are in the plane defined by the
"-1" labels. Step sizes in the two directions must be supplied using
STEP1 and STEP2 on the keyword line.
Using internal coordinates, the first atom has three unoptimizable
coordinates, the second atom two, (the bond-length can be optimized) and
the third atom has one unoptimizable coordinate. None of these six
unoptimizable coordinates at the start of the geometry should be marked
for optimization. If any are so marked, a warning is given, but the
calculation will continue.
In cartesian coordinates all parameters can be optimized.
3.6 EXAMPLES OF COORDINATE DEFINITIONS.
Two examples will be given. The first is formic acid, HCOOH, and is
presented in the normal style with internal coordinates. This is
followed by formaldehyde, presented in such a manner as to demonstrate as
- 58 -
GEOMETRY SPECIFICATION Page 3-9
many different features of the geometry definition as possible.
MINDO/3
Formic acid
Example of normal geometry definition
O Atom 1 needs no coordinates.
C 1.20 1 Atom 2 bonds to atom 1.
O 1.32 1 116.8 1 2 1 Atom 3 bonds to atom 2 and
makes an angle with atom 1.
H 0.98 1 123.9 1 0.0 0 3 2 1 Atom 4 has a dihedral of 0.0
with atoms 3, 2 and 1.
H 1.11 1 127.3 1 180.0 0 2 1 3
0 0.00 0 0.0 0 0.0 0 0 0 0
Atom 2, a carbon, is bonded to oxygen by a bond-length of 1.20
Angstroms, and to atom 3, an oxygen, by a bond-length of 1.32 Angstroms.
The O-C-O angle is 116.8 degrees. The first hydrogen is bonded to the
hydroxyl oxygen and the second hydrogen is bonded to the carbon atom.
The H-C-O-O dihedral angle is 180 degrees.
MOPAC can generate data-files, both in the Archive files, and at
the end of the normal output file, when a job ends prematurely due to
time restrictions. Note that the data are all neatly lined up. This
is, of course, characteristic of machine-generated data, but is useful
when checking for errors.
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GEOMETRY SPECIFICATION Page 3-10
Format of internal coordinates in ARCHIVE file
O 0.000000 0 0.000000 0 0.000000 0 0 0 0
C 1.209615 1 0.000000 0 0.000000 0 1 0 0
O 1.313679 1 116.886168 1 0.000000 0 2 1 0
H 0.964468 1 115.553316 1 0.000000 0 3 2 1
H 1.108040 1 128.726078 1 180.000000 0 2 1 3
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Polymers are defined by the presence of a translation vector. In
the following example, polyethylene, the translation vector spans three
monomeric units, and is 7.7 Angstroms long. Note in this example the
presence of two dummy atoms. These not only make the geometry
definition easier but also allow the translation vector to be specified
in terms of distance only, rather than both distance and angles.
Example of polymer coordinates from ARCHIVE file
T=20000
POLYETHYLENE, CLUSTER UNIT : C6H12
C 0.000000 0 0.000000 0 0.000000 0 0 0 0
C 1.540714 1 0.000000 0 0.000000 0 1 0 0
C 1.542585 1 113.532306 1 0.000000 0 2 1 0
C 1.542988 1 113.373490 1 179.823613 1 3 2 1
C 1.545151 1 113.447508 1 179.811764 1 4 3 2
C 1.541777 1 113.859804 1 -179.862648 1 5 4 3
XX 1.542344 1 108.897076 1 -179.732346 1 6 5 4
XX 1.540749 1 108.360151 1 -178.950271 1 7 6 5
H 1.114786 1 90.070026 1 126.747447 1 1 3 2
H 1.114512 1 90.053136 1 -127.134856 1 1 3 2
H 1.114687 1 90.032722 1 126.717889 1 2 4 3
H 1.114748 1 89.975504 1 -127.034513 1 2 4 3
H 1.114474 1 90.063308 1 126.681098 1 3 5 4
H 1.114433 1 89.915262 1 -126.931090 1 3 5 4
H 1.114308 1 90.028131 1 127.007845 1 4 6 5
H 1.114434 1 90.189506 1 -126.759550 1 4 6 5
H 1.114534 1 88.522263 1 127.041363 1 5 7 6
H 1.114557 1 88.707407 1 -126.716355 1 5 7 6
H 1.114734 1 90.638631 1 127.793055 1 6 8 7
H 1.115150 1 91.747016 1 -126.187496 1 6 8 7
Tv 7.746928 1 0.000000 0 0.000000 0 1 7 8
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
- 60 -
CHAPTER 4
EXAMPLES
In this chapter various examples of data-files are described. With
MOPAC comes two sets of data for running calculations. One of these is
called MNRSD1.DAT, and this will now be described.
4.1 MNRSD1 TEST DATA FILE FOR FORMALDEHYDE
The following file is suitable for generating the results described
in the next section, and would be suitable for debugging data.
Line 1: SYMMETRY
Line 2: Formaldehyde, for Demonstration Purposes
Line 3:
Line 4: O
Line 5: C 1.2 1
Line 6: H 1.1 1 120 1
Line 7: H 1.1 0 120 0 180 0 2 1 3
Line 8:
Line 9: 3 1 4
Line 10: 3 2 4
Line 11:
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EXAMPLES Page 4-2
These data could be more neatly written as
Line 1: SYMMETRY
Line 2: Formaldehyde, for Demonstration Purposes
Line 3:
Line 4: O
Line 5: C 1.20 1 1
Line 6: H 1.10 1 120.00 1 2 1
Line 7: H 1.10 0 120.00 0 180.00 0 2 1 3
Line 8:
Line 9: 3, 1, 4,
Line 10: 3, 2, 4,
Line 11:
These two data-files will produce identical results files.
In all geometric specifications, care must be taken in defining the
internal coordinates to ensure that no three atoms being used to define
a fourth atom's dihedral angle ever fall into a straight line. This can
happen in the course of a geometry optimization, in a SADDLE calculation
or in following a reaction coordinate. If such a condition should
develop, then the position of the dependent atom would become
ill-defined.
4.2 MOPAC OUTPUT FOR TEST-DATA FILE MNRSD1
****************************************************************************
** FRANK J. SEILER RES. LAB., U.S. AIR FORCE ACADEMY, COLO. SPGS., CO.
80840
****************************************************************************
MNDO CALCULATION RESULTS Note
1
****************************************************************************
* MOPAC: VERSION 6.00 CALC'D. 4-OCT-90 Note
2
* SYMMETRY - SYMMETRY CONDITIONS TO BE IMPOSED
* T= - A TIME OF 3600.0 SECONDS REQUESTED
* DUMP=N - RESTART FILE WRITTEN EVERY 3600.0 SECONDS
********************************************************************043BY043
PARAMETER DEPENDENCE DATA
REFERENCE ATOM FUNCTION NO. DEPENDENT ATOM(S)
3 1 4
3 2 4
- 62 -
EXAMPLES Page 4-3
DESCRIPTIONS OF THE FUNCTIONS USED
1 BOND LENGTH IS SET EQUAL TO THE REFERENCE BOND LENGTH
2 BOND ANGLE IS SET EQUAL TO THE REFERENCE BOND ANGLE
SYMMETRY Note
3
Formaldehyde, for Demonstration Purposes
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 O Note
4
2 C 1.20000 * 1
3 H 1.10000 * 120.00000 * 2 1
4 H 1.10000 120.00000 180.00000 2 1
3
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 O 0.0000 0.0000 0.0000
2 C 1.2000 0.0000 0.0000 Note
5
3 H 1.7500 0.9526 0.0000
4 H 1.7500 -0.9526 0.0000
H: (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
C: (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
O: (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 6
INTERATOMIC DISTANCES
O 1 C 2 H 3 H 4
------------------------------------------------------
O 1 0.000000
C 2 1.200000 0.000000
H 3 1.992486 1.100000 0.000000 Note
6
H 4 1.992486 1.100000 1.905256 0.000000
CYCLE: 1 TIME: 0.75 TIME LEFT: 3598.2 GRAD.: 6.349 HEAT:-
32.840147
CYCLE: 2 TIME: 0.37 TIME LEFT: 3597.8 GRAD.: 2.541 HEAT:-
32.880103
HEAT OF FORMATION TEST SATISFIED Note
7
PETERS TEST SATISFIED Note
8
-------------------------------------------------------------------------
--
SYMMETRY Note
9
Formaldehyde, for Demonstration Purposes Note
10
PETERS TEST WAS SATISFIED IN BFGS OPTIMIZATION Note
11
SCF FIELD WAS ACHIEVED Note
12
- 63 -
EXAMPLES Page 4-4
MNDO CALCULATION Note
13
VERSION 6.00
4-OCT-90
FINAL HEAT OF FORMATION = -32.88176 KCAL Note
14
TOTAL ENERGY = -478.11917 EV
ELECTRONIC ENERGY = -870.69649 EV
CORE-CORE REPULSION = 392.57733 EV
IONIZATION POTENTIAL = 11.04198
NO. OF FILLED LEVELS = 6
MOLECULAR WEIGHT = 30.026
SCF CALCULATIONS = 15
COMPUTATION TIME = 2.740 SECONDS Note
15
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB
NC
1 O
2 C 1.21678 * 1 Note
16
3 H 1.10590 * 123.50259 * 2 1
4 H 1.10590 123.50259 180.00000 2 1
3
INTERATOMIC DISTANCES
O 1 C 2 H 3 H 4
------------------------------------------------------
O 1 0.000000
C 2 1.216777 0.000000
H 3 2.046722 1.105900 0.000000
H 4 2.046722 1.105900 1.844333 0.000000
- 64 -
EXAMPLES Page 4-5
EIGENVALUES
-42.98352 -25.12201 -16.95327 -16.29819 -14.17549 -11.04198 0.85804
3.6768
3.84990 7.12408 Note
17
NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY
1 O -0.2903 6.2903
2 C 0.2921 3.7079 Note
18
3 H -0.0009 1.0009
4 H -0.0009 1.0009
DIPOLE X Y Z TOTAL
POINT-CHG. 1.692 0.000 0.000 1.692
HYBRID 0.475 0.000 0.000 0.475 Note
19
SUM 2.166 0.000 0.000 2.166
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 O 0.0000 0.0000 0.0000
2 C 1.2168 0.0000 0.0000
3 H 1.8272 0.9222 0.0000
4 H 1.8272 -0.9222 0.0000
ATOMIC ORBITAL ELECTRON POPULATIONS
1.88270 1.21586 1.89126 1.30050 1.25532 0.86217 0.89095
0.69950
1.00087 1.00087 Note
20
TOTAL CPU TIME: 3.11 SECONDS
== MOPAC DONE ==
NOTES ON RESULTS FILE
NOTE 1: The banner indicates whether the calculation uses a MNDO,
MINDO/3, AM1 or PM3 Hamiltonian; here, the default MNDO Hamiltonian is
used.
NOTE 2: The Version number is a constant for any release of MOPAC,
and refers to the program, not to the Hamiltonians used. The version
number should be cited in any correspondence regarding MOPAC. Users'
own in-house modified versions of MOPAC will have a final digit
different from zero, e.g. 6.01.
All the keywords used, along with a brief explanation, should be
printed at this time. If a keyword is not printed, it has not been
recognized by the program. Keywords can be in upper or lower case
- 65 -
EXAMPLES Page 4-6
letters, or any mixture. The cryptic message at the right end of the
lower line of asterisks indicates the number of heavy and light atoms
this version of MOPAC is configured for.
NOTE 3: Symmetry information is output to allow the user to verify
that the requested symmetry functions have in fact been recognized and
used.
NOTE 4: The data for this example used a mixture of atomic numbers
and chemical symbols, but the internal coordinate output is consistently
in chemical symbols.
The atoms in the system are, in order:
Atom 1, an oxygen atom; this is defined as being at the
origin.
Atom 2, the carbon atom. Defined as being 1.2 Angstroms
from the oxygen atom, it is located in the +x direction. This
distance is marked for optimization.
Atom 3, a hydrogen atom. It is defined as being 1.1
Angstroms from the carbon atom, and making an angle of 120
degrees with the oxygen atom. The asterisks indicate that the
bond length and angle are both to be optimized.
Atom 4, a hydrogen atom. The bond length supplied has been
overwritten with the symmetry-defined C-H bond length. Atom 4 is
defined as being 1.1 Angstroms from atom 2, making a bond-angle
of 120 degrees with atom 1, and a dihedral angle of 180 degrees
with atom 3.
None of the coordinates of atom 4 are marked for
optimization. The bond-length and angle are symmetry-defined by
atom 3, and the dihedral is group-theory symmetry-defined as
being 180 degrees. (The molecule is flat.)
NOTE 5: The cartesian coordinates are calculated as follows:
Stage 1: The coordinate of the first atom is defined as
being at the origin of cartesian space, while the coordinate of
the second atom is defined as being displaced by its defined bond
length along the positive x-axis. The coordinate of the third
atom is defined as being displaced by its bond length in the x-y
plane, from either atom 1 or 2 as defined in the data, or from
atom 2 if no numbering is given. The angle it makes with atoms 1
and 2 is that given by its bond angle.
The dihedral, which first appears in the fourth atom, is
defined according to the I.U.P.A.C. convention. NOTE: This is
different from previous versions of MNDO and MINDO/3, where the
dihedral had the opposite chirality to that defined by the
I.U.P.A.C. convention.
- 66 -
EXAMPLES Page 4-7
Stage 2: Any dummy atoms are removed. As this particular
system contains no dummy atoms, nothing is done.
NOTE 6: The interatomic distances are output for the user's
advice, and a simple check made to insure that the smallest interatomic
distance is greater than 0.8 Angstroms.
NOTE 7: The geometry is optimized in a series of cycles, each
cycle consisting of a line search and calculation of the gradients. The
time given is the C.P.U. time for the cycle; time left is the total
time requested (here 100 seconds) less the C.P.U. time since the start
of the calculation (which is earlier than the start of the first
cycle!). These times can vary slightly from cycle to cycle due to
different options being used, for example whether or not two or more SCF
calculations need to be done to ensure that the heat of formation is
lowered. The gradient is the scalar length in kcal/mole/Angstrom of the
gradient vector.
NOTE 8: At the end of the BFGS geometry optimization a message is
given which indicates how the optimization ended. All "normal"
termination messages contain the word "satisfied"; other terminations
may give acceptable results, but more care should be taken, particularly
regarding the gradient vector.
NOTE 9 and 10: The keywords used, titles and comments are
reproduced here to remind the user of the name of the calculation.
NOTES 11 and 12: Two messages are given here. The first is a
reminder of how the geometry was obtained, whether from the
Broyden-Fletcher-Goldfarb-Shanno, Eigenvector Following, Bartel's or the
McIver-Komornicki methods. For any further results to be printed the
second message must be as shown; when no SCF is obtained no results will
be printed.
NOTE 13: Again, the results are headed with either MNDO or MINDO/3
banners, and the version number. The date has been moved to below the
version number for convenience.
NOTE 14: The total energy of the system is the addition of the
electronic and nuclear terms. The heat of formation is relative to the
elements in their standard state. The I.P. is the negative of the
energy level of the highest occupied, or highest partially occupied
molecular orbital (in accordance with Koopmans' theorem).
NOTE 15: Advice on time required for the calculation. This is
obviously useful in estimating the times required for other systems.
NOTE 16: The fully optimized geometry is printed here. If a
parameter is not marked for optimization, it will not be changed unless
it is a symmetry-related parameter.
NOTE 17: The roots are the eigenvalues or energy levels in
electron volts of the molecular orbitals. There are six filled levels,
therefore the HOMO has an energy of -11.041eV; analysis of the
corresponding eigenvector (not given here) shows that it is mainly
- 67 -
EXAMPLES Page 4-8
lone-pair on oxygen. The eigenvectors form an orthonormal set.
NOTE 18: The charge on an atom is the sum of the positive core
charge; for hydrogen, carbon, and oxygen these numbers are 1.0, 4.0, and
6.0, respectively, and the negative of the number of valence electrons,
or atom electron density on the atom, here 1.0010, 3.7079, and 6.2902
respectively.
NOTE 19: The dipole is the scalar of the dipole vector in
cartesian coordinates. The components of the vector coefficients are
the point-charge dipole and the hybridization dipole. In formaldehyde
there is no z-dipole since the molecule is flat.
NOTE 20: MNDO AM1, PM3, and MINDO/3 all use the Coulson density
matrix. Only the diagonal elements of the matrix, representing the
valence orbital electron populations, will be printed, unless the
keyword DENSITY is specified.
Two extra lines are added as a result of user requests:
(1) The total CPU time for the job, excluding loading of the
executable, is printed.
(2) In order to know that MOPAC has ended, the message
== MOPAC DONE == is printed.
- 68 -
CHAPTER 5
TESTDATA
TESTDATA.DAT, supplied with MOPAC 6.00, is a single large job
consisting of several small systems, which are run one after the other.
In order, the calculations run are
1. A FORCE calculation on formaldehyde. The extra keywords at the
start are to be used later when TESTDATA.DAT acts as a SETUP
file. This unusual usage of a data set was made necessary by
the need to ensure that a SETUP file existed. If the first two
lines are removed, the data set used in the example given below
is generated.
2. The vibrational frequencies of a highly excited dication of
methane are calculated. A non-degenerate state was selected in
order to preserve tetrahedral symmetry (to avoid the
Jahn-Teller effects).
3. Illustration of the use of the '&' in the keyword line, and of
the new optional definition of atoms 2 and 3
4. Illustration of Gaussian Z-matrix input.
5. An example of Eigenvector Following, to locate a transition
state.
6. Use of SETUP. Normally, SETUP would point to a special file
which would contain keywords only. Here, the only file we can
guarantee exists, is the file being run, so that is the one
used.
7. Example of labelling atoms.
8. This part of the test writes the density matrix to disk, for
later use.
9. A simple calculation on water.
- 69 -
TESTDATA Page 5-2
10. The previous, optimized, geometry is to be used to start this
calculation.
11. The density matrix written out earlier is now used as input to
start an SCF.
This example is taken from the first data-file in TESTDATA.DAT, and
illustrates the working of a FORCE calculation.
5.1 DATA FILE FOR A FORCE CALCULATION
Line 1 nointer noxyz + mndo dump=8
Line 2 t=2000 + thermo(298,298) force isotope
Line 3 ROT=2
Line 4 DEMONSTRATION OF MOPAC - FORCE AND THERMODYNAMICS CALCULATION
Line 5 FORMALDEHYDE, MNDO ENERGY = -32.8819 See Manual.
Line 6 O
Line 7 C 1.216487 1 1 0 0
Line 8 H 1.106109 1 123.513310 1 2 1 0
Line 9 H 1.106109 1 123.513310 1 180.000000 1 2 1 3
Line 10 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
5.2 RESULTS FILE FOR THE FORCE CALCULATION
****************************************************************************
** FRANK J. SEILER RES. LAB., U.S. AIR FORCE ACADEMY, COLO. SPGS., CO.
80840
****************************************************************************
MNDO CALCULATION RESULTS
***************************************************************************
* MOPAC: VERSION 6.00 CALC'D. 12-OCT-90
* T= - A TIME OF 2000.0 SECONDS REQUESTED
* DUMP=N - RESTART FILE WRITTEN EVERY 8.0 SECONDS
* FORCE - FORCE CALCULATION SPECIFIED
* PRECISE - CRITERIA TO BE INCREASED BY 100 TIMES
* NOINTER - INTERATOMIC DISTANCES NOT TO BE PRINTED Note 1
* ISOTOPE - FORCE MATRIX WRITTEN TO DISK (CHAN. 9 )
* NOXYZ - CARTESIAN COORDINATES NOT TO BE PRINTED
* THERMO - THERMODYNAMIC QUANTITIES TO BE CALCULATED
* ROT - SYMMETRY NUMBER OF 2 SPECIFIED
*******************************************************************040BY040
- 70 -
TESTDATA Page 5-3
NOINTER NOXYZ + MNDO DUMP=8
T=2000 + THERMO(298,298) FORCE ISOTOPE
ROT=2 PRECISE
DEMONSTRATION OF MOPAC - FORCE AND THERMODYNAMICS CALCULATION
FORMALDEHYDE, MNDO ENERGY = -32.8819 See Manual.
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
1 O
2 C 1.21649 * 1
3 H 1.10611 * 123.51331 * 2 1
4 H 1.10611 * 123.51331 * 180.00000 * 2 1 3
H: (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
C: (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
O: (MNDO): M.J.S. DEWAR, W. THIEL, J. AM. CHEM. SOC., 99, 4899, (1977)
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 6
HEAT OF FORMATION = -32.881900 KCALS/MOLE
INTERNAL COORDINATE DERIVATIVES
ATOM AT. NO. BOND ANGLE DIHEDRAL
1 O
2 C 0.000604
3 H 0.000110 -0.000054
4 H 0.000110 -0.000054 0.000000
GRADIENT NORM = 0.00063 Note 2
TIME FOR SCF CALCULATION = 0.45
TIME FOR DERIVATIVES = 0.32 Note 3
MOLECULAR WEIGHT = 30.03
- 71 -
TESTDATA Page 5-4
PRINCIPAL MOMENTS OF INERTIA IN CM(-1)
A = 9.832732 B = 1.261998 C = 1.118449
PRINCIPAL MOMENTS OF INERTIA IN UNITS OF 10**(-40)*GRAM-CM**2
A = 2.846883 B = 22.181200 C = 25.028083
ORIENTATION OF MOLECULE IN FORCE CALCULATION
NO. ATOM X Y Z
1 8 -0.6093 0.0000 0.0000
2 6 0.6072 0.0000 0.0000
3 1 1.2179 0.9222 0.0000
4 1 1.2179 -0.9222 0.0000
FIRST DERIVATIVES WILL BE USED IN THE CALCULATION OF SECOND
DERIVATIVES
ESTIMATED TIME TO COMPLETE CALCULATION = 36.96 SECONDS
STEP: 1 TIME = 2.15 SECS, INTEGRAL = 2.15 TIME LEFT: 1997.08
STEP: 2 TIME = 2.49 SECS, INTEGRAL = 4.64 TIME LEFT: 1994.59
STEP: 3 TIME = 2.53 SECS, INTEGRAL = 7.17 TIME LEFT: 1992.06
STEP: 4 TIME = 2.31 SECS, INTEGRAL = 9.48 TIME LEFT: 1989.75
STEP: 5 RESTART FILE WRITTEN, INTEGRAL = 11.97 TIME LEFT: 1987.26
STEP: 6 TIME = 2.43 SECS, INTEGRAL = 14.40 TIME LEFT: 1984.83
STEP: 7 TIME = 2.32 SECS, INTEGRAL = 16.72 TIME LEFT: 1982.51
STEP: 8 TIME = 2.30 SECS, INTEGRAL = 19.02 TIME LEFT: 1980.21
STEP: 9 RESTART FILE WRITTEN, INTEGRAL = 22.17 TIME LEFT: 1977.06
STEP: 10 TIME = 2.52 SECS, INTEGRAL = 24.69 TIME LEFT: 1974.54
STEP: 11 TIME = 2.25 SECS, INTEGRAL = 26.94 TIME LEFT: 1972.29
STEP: 12 TIME = 3.15 SECS, INTEGRAL = 30.09 TIME LEFT: 1969.14
FORCE MATRIX IN MILLIDYNES/ANGSTROM
0
O 1 C 2 H 3 H 4
------------------------------------------------------
O 1 9.557495
C 2 8.682982 11.426823
H 3 0.598857 2.553336 3.034881
H 4 0.598862 2.553344 0.304463 3.034886
HEAT OF FORMATION = -32.881900 KCALS/MOLE
ZERO POINT ENERGY 18.002 KILOCALORIES PER MOLE Note 4
- 72 -
TESTDATA Page 5-5
THE LAST 6 VIBRATIONS ARE THE TRANSLATION AND ROTATION MODES
THE FIRST THREE OF THESE BEING TRANSLATIONS IN X, Y, AND Z,
RESPECTIVELY
NORMAL COORDINATE ANALYSIS
Note 5
ROOT NO. 1 2 3 4 5 6
1209.90331 1214.67040 1490.52685 2114.53841 3255.93651
3302.12319
1 0.00000 0.00000 -0.04158 -0.25182 0.00000
0.00067
2 0.06810 0.00001 0.00000 0.00000 0.00409
0.00000
3 0.00000 -0.03807 0.00000 0.00000 0.00000
0.00000
4 0.00000 0.00000 -0.03819 0.32052 0.00000 -
0.06298
5 -0.13631 -0.00002 0.00000 0.00000 0.08457
0.00000
6 -0.00002 0.15172 0.00000 0.00000 0.00000
0.00000
7 -0.53308 -0.00005 0.55756 0.08893 -0.39806
0.36994
8 0.27166 0.00003 -0.38524 0.15510 -0.53641
0.57206
9 0.00007 -0.60187 0.00001 0.00000 0.00000
0.00000
10 0.53307 0.00006 0.55757 0.08893 0.39803
0.36997
11 0.27165 0.00003 0.38524 -0.15509 -0.53637 -
0.57209
12 0.00007 -0.60187 0.00001 0.00000 0.00000
0.00000
ROOT NO. 7 8 9 10 11 12
-0.00019 -0.00044 -0.00016 3.38368 2.03661 -
0.76725
1 0.25401 0.00000 0.00000 0.00000 0.00000
0.00000
2 0.00000 -0.25401 0.00000 0.00000 0.00000 -
0.17792
3 0.00000 0.00000 -0.25401 0.00000 -0.19832
0.00000
4 0.25401 0.00000 0.00000 0.00000 0.00000
0.00000
5 0.00000 -0.25401 0.00000 0.00000 0.00000
0.17731
6 0.00000 0.00000 -0.25401 0.00000 0.19764
0.00000
7 0.25401 0.00000 0.00000 0.00000 0.00000 -
0.26930
8 0.00000 -0.25401 0.00000 0.00000 0.00000
0.35565
9 0.00000 0.00000 -0.25401 0.70572 0.39642
0.00000
10 0.25401 0.00000 0.00000 0.00000 0.00000
0.26930
11 0.00000 -0.25401 0.00000 0.00000 0.00000
0.35565
12 0.00000 0.00000 -0.25401 -0.70572 0.39642
0.00000
- 73 -
TESTDATA Page 5-6
MASS-WEIGHTED COORDINATE ANALYSIS
Note 6
ROOT NO. 1 2 3 4 5 6
1209.90331 1214.67040 1490.52685 2114.53841 3255.93651
3302.12319
1 0.00000 0.00000 -0.16877 -0.66231 0.00000
0.00271
2 0.26985 0.00003 0.00000 0.00000 0.01649
0.00000
3 0.00002 -0.15005 0.00000 0.00000 0.00000
0.00000
4 0.00000 0.00000 -0.13432 0.73040 0.00001 -
0.22013
5 -0.46798 -0.00005 0.00000 0.00000 0.29524
0.00001
6 -0.00006 0.51814 0.00000 0.00000 0.00000
0.00000
7 -0.53018 -0.00005 0.56805 0.05871 -0.40255
0.37455
8 0.27018 0.00003 -0.39249 0.10238 -0.54246
0.57918
9 0.00007 -0.59541 0.00001 0.00000 0.00000
0.00000
10 0.53018 0.00006 0.56806 0.05871 0.40252
0.37457
11 0.27018 0.00003 0.39249 -0.10238 -0.54242 -
0.57922
12 0.00007 -0.59541 0.00001 0.00000 0.00000
0.00000
Note 7
ROOT NO. 7 8 9 10 11 12
-0.00025 -0.00022 -0.00047 3.38368 2.03661 -
0.76725
1 0.72996 0.00000 0.00000 0.00000 0.00000
0.00000
2 0.00000 -0.72996 0.00000 0.00000 0.00000 -
0.62774
3 0.00000 0.00000 -0.72996 0.00000 -0.66681
0.00000
4 0.63247 0.00000 0.00000 0.00000 0.00000
0.00000
5 0.00000 -0.63247 0.00000 0.00000 0.00000
0.54204
6 0.00000 0.00000 -0.63247 0.00000 0.57578
0.00000
7 0.18321 0.00000 0.00000 0.00000 0.00000 -
0.23848
8 0.00000 -0.18321 0.00000 0.00000 0.00000
0.31495
9 0.00000 0.00000 -0.18321 0.70711 0.33455
0.00000
10 0.18321 0.00000 0.00000 0.00000 0.00000
0.23848
11 0.00000 -0.18321 0.00000 0.00000 0.00000
0.31495
12 0.00000 0.00000 -0.18321 -0.70711 0.33455
0.00000
- 74 -
TESTDATA Page 5-7
DESCRIPTION OF VIBRATIONS
VIBRATION 1 ATOM PAIR ENERGY CONTRIBUTION
RADIAL
FREQ. 1209.90 C 2 -- H 3 42.7% ( 79.4%)
12.6%
T-DIPOLE 0.8545 C 2 -- H 4 42.7%
12.6%
TRAVEL 0.1199 O 1 -- C 2 14.6%
0.0%
RED. MASS 1.9377
VIBRATION 2 ATOM PAIR ENERGY CONTRIBUTION
RADIAL
FREQ. 1214.67 C 2 -- H 3 45.1% ( 62.3%)
0.0%
T-DIPOLE 0.1275 C 2 -- H 4 45.1%
0.0%
TRAVEL 0.1360 O 1 -- C 2 9.8%
0.0%
RED. MASS 1.5004
VIBRATION 3 ATOM PAIR ENERGY CONTRIBUTION
RADIAL
FREQ. 1490.53 C 2 -- H 4 49.6% ( 61.5%)
0.6%
T-DIPOLE 0.3445 C 2 -- H 3 49.6%
0.6%
TRAVEL 0.1846 O 1 -- C 2 0.9%
100.0%
RED. MASS 0.6639
VIBRATION 4 ATOM PAIR ENERGY CONTRIBUTION
RADIAL
FREQ. 2114.54 O 1 -- C 2 60.1% (100.5%)
100.0%
T-DIPOLE 3.3662 C 2 -- H 4 20.0%
17.7%
TRAVEL 0.0484 C 2 -- H 3 20.0%
17.7%
RED. MASS 6.7922
VIBRATION 5 ATOM PAIR ENERGY CONTRIBUTION
RADIAL
FREQ. 3255.94 C 2 -- H 3 49.5% ( 72.2%)
98.1%
T-DIPOLE 0.7829 C 2 -- H 4 49.5%
98.1%
TRAVEL 0.1174 O 1 -- C 2 1.0%
0.0%
RED. MASS 0.7508
VIBRATION 6 ATOM PAIR ENERGY CONTRIBUTION
RADIAL
FREQ. 3302.12 C 2 -- H 4 49.3% ( 69.8%)
95.5%
T-DIPOLE 0.3478 C 2 -- H 3 49.3%
95.5%
TRAVEL 0.1240 O 1 -- C 2 1.4%
100.0%
RED. MASS 0.6644
SYSTEM IS A GROUND STATE
FORMALDEHYDE, MNDO ENERGY = -32.8819 See Manual.
DEMONSTRATION OF MOPAC - FORCE AND THERMODYNAMICS CALCULATION
MOLECULE IS NOT LINEAR
THERE ARE 6 GENUINE VIBRATIONS IN THIS SYSTEM
THIS THERMODYNAMICS CALCULATION IS LIMITED TO
MOLECULES WHICH HAVE NO INTERNAL ROTATIONS
- 75 -
TESTDATA Page 5-8
Note 8
CALCULATED THERMODYNAMIC PROPERTIES
*
TEMP. (K) PARTITION FUNCTION H.O.F. ENTHALPY HEAT CAPACITY
ENTROPY
KCAL/MOL CAL/MOLE CAL/K/MOL
CAL/K/MOL
298 VIB. 1.007 23.39484 0.47839 0.09151
ROT. 709. 888.305 2.981 16.026
INT. 714. 911.700 3.459 16.117
TRA. 0.159E+27 1480.509 4.968 36.113
TOT. -32.882 2392.2088 8.4274 52.2300
* NOTE: HEATS OF FORMATION ARE RELATIVE TO THE
ELEMENTS IN THEIR STANDARD STATE AT 298K
TOTAL CPU TIME: 32.26 SECONDS
== MOPAC DONE ==
NOTE 1: All three words, ROT, FORCE, and THERMO are necessary in
order to obtain thermodynamic properties. In order to obtain results
for only one temperature, THERMO has the first and second arguments
identical. The symmetry number for the C2v point-group is 2.
NOTE 2: Internal coordinate derivatives are in Kcal/Angstrom or
Kcal/radian. Values of less than about 0.2 are quite acceptable.
NOTE 3: In larger calculations, the time estimates are useful. In
practice they are pessimistic, and only about 70% of the time estimated
will be used, usually. The principal moments of inertia can be directly
related to the microwave spectrum of the molecule. They are simple
functions of the geometry of the system, and are usually predicted with
very high accuracy.
NOTE 4: Zero point energy is already factored into the MNDO
parameterization. Force constant data are not printed by default. If
you want this output, specify LARGE in the keywords.
NOTE 5: Normal coordinate analysis has been extensively changed.
The first set of eigenvectors represent the 'normalized' motions of the
atoms. The sum of the speeds (not the velocities) of the atoms adds to
unity. This is verified by looking at the motion in the 'z' direction
of the atoms in vibration 2. Simple addition of these terms, unsigned,
adds to 1.0, whereas to get the same result for mode 1 the scalar of the
motion of each atom needs to be calculated first.
Users might be concerned about reproducibility. As can be seen
from the vibrational frequencies from Version 3.00 to 6.00 given below,
the main difference over earlier FORCE calculations is in the trivial
frequencies.
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Real Frequencies of Formaldehyde
Version 3.00 1209.96 1214.96 1490.60 2114.57 3255.36 3301.57
Version 3.10 1209.99 1215.04 1490.59 2114.57 3255.36 3301.58
Version 4.00 1209.88 1214.67 1490.52 2114.52 3255.92 3302.10
Version 5.00 1209.89 1214.69 1490.53 2114.53 3255.93 3302.10
Version 6.00 1209.90 1214.67 1490.53 2114.54 3255.94 3302.12
Trivial Frequencies of Formaldehyde
T(x) T(y) T(z) R(x) R(y) R(z)
Version 3.00 -0.00517 -0.00054 -0.00285 57.31498 11.59518 9.01619
Version 3.10 -0.00557 0.00049 -0.00194 87.02506 11.18157 10.65295
Version 4.00 -0.00044 -0.00052 -0.00041 12.99014 -3.08110 -3.15427
Version 5.00 0.00040 -0.00044 -0.00062 21.05654 2.80744 3.83712
Version 6.00 -0.00025 -0.00022 -0.00047 3.38368 2.03661 -0.76725
NOTE 6: Normal modes are not of much use in assigning relative
importance to atoms in a mode. Thus in iodomethane it is not obvious
from an examination of the normal modes which mode represents the C-I
stretch. A more useful description is provided by the energy or
mass-weighted coordinate analysis. Each set of three coefficients now
represents the relative energy carried by an atom. (This is not
strictly accurate as a definition, but is believed (by JJPS) to be more
useful than the stricter definition.)
NOTE 7: The following description of the coordinate analysis is
given without rigorous justification. Again, the analysis, although
difficult to understand, has been found to be more useful than previous
descriptions.
On the left-hand side are printed the frequencies and transition
dipoles. Underneath these are the reduced masses and idealized
distances traveled which represent the simple harmonic motion of the
vibration. The mass is assumed to be attached by a spring to an
infinite mass. Its displacement is the travel.
The next column is a list of all pairs of atoms that contribute
significantly to the energy of the mode. Across from each pair (next
column) is the percentage energy contribution of the pair to the mode,
calculated according to the formula described below.
FORMULA FOR ENERGY CONTRIBUTION
The total vibrational energy, T, carried by all pairs of bonded
atoms in a molecule is first calculated. For any given pair of atoms, A
and B, the relative contribution, R.C.(A,B), as a percentage, is given
by the energy of the pair, P(A,B), times 100 divided by T, i.e.,
R.C.(A,B) = 100P(A,B)/T
As an example, for formaldehyde the energy carried by the pair of
atoms (C,O) is added to the energy of the two (C,H) pairs to give a
total, T. Note that this total cannot be related to anything which is
physically meaningful (there is obvious double-counting), but it is a
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TESTDATA Page 5-10
convenient artifice. For mode 4, the C=O stretch, the relative
contribution of the carbon-oxygen pair is 60.1%. It might be expected
to be about 100% (after all, we envision the C=O bond as absorbing the
photon); however, the fact that the carbon atom is vibrating implies
that it is changing its position relative to the two hydrogen atoms. If
the total vibrational energy, Ev (the actual energy of the absorbed
photon, as distinct from T), were carried equally by the carbon and
oxygen atoms, then the relative contributions to the mode would be C=O,
50% ; C-H, 25% ; C-H, 25%, respectively. This leads to the next entry,
which is given in parentheses.
For the pair with the highest relative contribution (in mode 4, the
C=O stretch), the energy of that pair divided by the total energy of the
mode, Ev, is calculated as a percentage. This is the absolute
contribution, A.C. as a percentage, to the total energy of the mode.
A.C.(A,B) = 100P(A,B)/Ev
Now the C=O is seen to contribute 100.5 percent of the energy. For this
sort of partitioning only the sum of all A.C.'s must add to 100%, each
pair can contribute more or less than 100%. In the case of a free
rotator, e.g. ethane, the A.C. of any specific bonded pair to the
total energy can be very high (several hundred percent).
It may be easier to view P/Ev as a contribution to the total energy
of the mode, Ev. In this case the fact that P/Ev can be greater than
unity can be explained by the fact that there are other relative motions
within the molecule which make a negative contribution to Ev.
From the R.C.'s an idea can be obtained of where the energy of the
mode is going; from the A.C. value the significance of the highest
contribution can be inferred. Thus, in mode 4 all three bonds are
excited, but because the C=O bond carries about 100% of the energy, it
is clear that this is really a C=O bond stretch mode, and that the
hydrogens are only going along for the ride.
In the last column the percentage radial motion is printed. This
is useful in assigning the mode as stretching or bending. Any
non-radial motion is de-facto tangential or bending.
To summarize: The new analysis is more difficult to understand,
but is considered by the author (JJPS) to be the easiest way of
describing what are often complicated vibrations.
NOTE 8: In order, the thermodynamic quantities calculated are:
(1) The vibrational contribution,
(2) The rotational contribution,
(3) The sum of (1) and (2), this gives the internal contribution,
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(4) The translational contribution.
For partition functions the various contributions are multiplied
together.
A new quantity is the heat of formation at the defined temperature.
This is intended for use in calculating heats of reaction. Because of a
limitation in the data available, the H.o.F. at T Kelvin is defined as
"The heat of formation of the compound at T Kelvin from it's elements in
their standard state at 298 Kelvin". Obviously, this definition of heat
of formation is incorrect, but should be useful in calculating heats of
reaction, where the elements in their standard state at 298 Kelvin drop
out.
5.3 EXAMPLE OF REACTION PATH WITH SYMMETRY
In this example, one methyl group in ethane is rotated relative to
the other and the geometry is optimized at each point. As the reaction
coordinate involves three hydrogen atoms moving, symmetry is imposed to
ensure equivalence of all hydrogens.
Line 1: SYMMETRY T=600
Line 2: ROTATION OF METHYL GROUP IN ETHANE
Line 3: EXAMPLE OF A REACTION PATH CALCULATION
Line 4: C
Line 5: C 1.479146 1
Line 6: H 1.109475 1 111.328433 1
Line 7: H 1.109470 0 111.753160 0 120.000000 0 2 1 3
Line 8: H 1.109843 0 110.103163 0 240.000000 0 2 1 3
Line 9: H 1.082055 0 121.214083 0 60.000000 -1 1 2 3
Line 10: H 1.081797 0 121.521232 0 180.000000 0 1 2 3
Line 11: H 1.081797 0 121.521232 0 -60.000000 0 1 2 3
Line 12: 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Line 13: 3 1 4 5 6 7 8
Line 14: 3 2 4 5 6 7 8
Line 15: 6 7 7
Line 16: 6 11 8
Line 17:
Line 18: 70 80 90 100 110 120 130 140 150
Points to note:
(1) The dihedrals of the second and third hydrogens are not marked
for optimization: the dihedrals follow from point-group symmetry.
(2) All six C-H bond lengths and H-C-C angles are related by
symmetry: see lines 13 and 14.
(3) The dihedral on line 9 is the reaction coordinate, while the
dihedrals on lines 10 and 11 are related to it by symmetry functions on
lines 15 and 16. The symmetry functions are defined by the second
number on lines 13 to 16 (see SYMMETRY for definitions of functions 1,
2, 7, and 11).
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(4) Symmetry data are ended by a blank line.
(5) The reaction coordinate data are ended by the end of file.
Several lines of data are allowed.
(6) Whenever symmetry is used in addition to other data below the
geometry definition it will always follow the "blank line" immediately
following the geometry definition. The other data will always follow
the symmetry data.
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CHAPTER 6
BACKGROUND
6.1 INTRODUCTION
While all the theory used in MOPAC is in the literature, so that in
principle one could read and understand the algorithm, many parts of the
code involve programming concepts or constructions which, while not of
sufficient importance to warrant publication, are described here in
order to facilitate understanding.
6.2 AIDER
AIDER will allow gradients to be defined for a system. MOPAC will
calculate gradients, as usual, and will then use the supplied gradients
to form an error function. This error function is: (supplied gradients
- initial calculated gradients), which is then added to the computed
gradients, so that for the initial SCF, the apparent gradients will
equal the supplied gradients.
A typical data-set using AIDER would look like this:
PM3 AIDER AIGOUT GNORM=0.01 EF
Cyclohexane
X
X 1 1.0
C 1 CX 2 CXX
C 1 CX 2 CXX 3 120.000000
C 1 CX 2 CXX 3 -120.000000
X 1 1.0 2 90.0 3 0.000000
X 1 1.0 6 90.0 2 180.000000
C 1 CX 7 CXX 3 180.000000
C 1 CX 7 CXX 3 60.000000
C 1 CX 7 CXX 3 -60.000000
H 3 H1C 1 H1CX 2 0.000000
H 4 H1C 1 H1CX 2 0.000000
H 5 H1C 1 H1CX 2 0.000000
H 8 H1C 1 H1CX 2 180.000000
H 9 H1C 1 H1CX 2 180.000000
H 10 H1C 1 H1CX 2 180.000000
H 3 H2C 1 H2CX 2 180.000000
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H 4 H2C 1 H2CX 2 180.000000
H 5 H2C 1 H2CX 2 180.000000
H 8 H2C 1 H2CX 2 0.000000
H 9 H2C 1 H2CX 2 0.000000
H 10 H2C 1 H2CX 2 0.000000
CX 1.46613
H1C 1.10826
H2C 1.10684
CXX 80.83255
H1CX 103.17316
H2CX 150.96100
AIDER
0.0000
13.7589 -1.7383
13.7589 -1.7383 0.0000
13.7589 -1.7383 0.0000
0.0000 0.0000 0.0000
0.0000 0.0000 0.0000
13.7589 -1.7383 0.0000
13.7589 -1.7383 0.0000
13.7589 -1.7383 0.0000
-17.8599 -2.1083 0.0000
-17.8599 -2.1083 0.0000
-17.8599 -2.1083 0.0000
-17.8599 -2.1083 0.0000
-17.8599 -2.1083 0.0000
-17.8599 -2.1083 0.0000
-17.5612 -0.6001 0.0000
-17.5612 -0.6001 0.0000
-17.5612 -0.6001 0.0000
-17.5612 -0.6001 0.0000
-17.5612 -0.6001 0.0000
-17.5612 -0.6001 0.0000
Each supplied gradient goes with the corresponding internal
coordinate. In the example given, the gradients came from a 3-21G
calculation on the geometry shown. Symmetry will be taken into account
automatically. Gaussian prints out gradients in atomic units; these
need to be converted into kcal/mol/Angstrom or kcal/mol/radian for MOPAC
to use. The resulting geometry from the MOPAC run will be nearer to the
optimized 3-21G geometry than if the normal geometry optimizers in
Gaussian had been used.
6.3 CORRECTION TO THE PEPTIDE LINKAGE
The residues in peptides are joined together by peptide linkages,
-HNCO-. These linkages are almost flat, and normally adopt a trans
configuration; the hydrogen and oxygen atoms being on opposite sides of
the C-N bond. Experimentally, the barrier to interconversion in
N-methyl acetamide is about 14 Kcal/mole, but all four methods within
MOPAC predict a significantly lower barrier, PM3 giving the lowest
value.
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The low barrier can be traced to the tendency of semiempirical
methods to give pyramidal nitrogens. The degree to which
pyramidalization of the nitrogen atom is preferred can be seen in the
following series of compounds.
Compound MINDO/3 MNDO AM1 PM3 Exp
Ammonia Py Py Py Py Py
Aniline Py Py Py Py Py
Formamide Py Py Flat Py Py
Acetamide Flat Py Flat Py Flat
N-methyl formamide Flat Py Flat Py Flat
N-methyl acetamide Flat Flat Flat Py Flat
To correct this, a molecular-mechanics correction has been applied.
This consists of identifying the -R-HNCO- unit, and adding a torsion
potential of form
2
Const*Sin(Theta)
where Theta is the X-N-C-O angle, X=R or H, and Const varies from method
to method. This has two effects: there is a force constraining the
nitrogen to be planar, and HNCO barrier in N-methyl acetamide is raised
to 14.00 Kcal/mole. When the MM correction is in place, the nitrogen
atom for all methods for the last three compounds shown above is planar.
The correction should be user-transparent
Cautions
1. This correction will lead to errors of 0.5 - 1.5 Kcal/mole if
the peptide linkage is made or broken in a reaction
calculation.
2. If the correction is applied to formamide the nitrogen will be
flat, contrary to experiment.
3. When calculating rotation barriers, take into account the rapid
rehybridization which occurs. When the dihedral is 0 or 180
degrees the nitrogen will be planar (sp2), but at 90 degrees
the nitrogen should be pyramidal, as the partial double bond is
broken. At that geometry the true transition state involves
motion of the nitrogen substituent so that the nitrogen in the
transition state is more nearly sp2. In other words, a simple
rotation of the HNCO dihedral will not yield the activation
barrier, however it will be within 2 Kcal/mole of the correct
answer. The 14 Kcal barrier mentioned earlier refers to the
true transition state.
4. Any job involving a CONH group will require either the keyword
NOMM or MMOK. If you do not want the correction to be applied,
use the keyword "NOMM" (NO Molecular Mechanics).
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6.4 LEVEL OF PRECISION WITHIN MOPAC
Several users have criticised the tolerances within MOPAC. The
point made is that significantly different results have been obtained
when different starting conditions have been used, even when the same
conformer should have resulted. Of course, different results must be
expected -- there will always be small differences -- nonetheless any
differences should be small, e.g. heats of formation (H.o.F.)
differences should be less than about 0.1 kcal/mole. MOPAC has been
modified to allow users to specify a much higher precision than the
default when circumstances warrant it.
Reasons for low precision
There are several reasons for obtaining low quality results. The
most obvious cause of such errors is that for general work the default
criteria will result in a difference in H.o.F. of less than 0.1
Kcal/mole. This is only true for fairly rigid systems, e.g.
formaldehyde and benzene. For systems with low barriers to rotation or
flat potential surfaces, e.g. aniline or water dimer, quite large
H.o.F. errors can result.
Various Precision Levels
In normal (non-publication quality) work the default precision of
MOPAC is recommended. This will allow reasonably precise results to be
obtained in a reasonable time. Unless this precision proves
unsatisfactory, use this default for all routine work.
The best way of controlling the precision of the geometry
optimization and gradient minimization is by specifying a gradient norm
which must be satisfied. This is done via the keyword GNORM=. Altering
the GNORM automatically disables the other termination tests resulting
in the gradient norm dominating the calculation. This works both ways:
a GNORM of 20 will give a very crude optimization while a GNORM of 0.01
will give a very precise optimization. The default GNORM is 1.0.
When the highest precision is needed, such as in exacting geometry
work, or when you want results which cannot be improved, then use the
combination keywords GNORM=0.0 and SCFCRT=1.D-NN; NN should be in the
range 2-15. Increasing the SCF criterion (the default is SCFCRT=1.D-4)
helps the line search routines by increasing the precision of the heat
of formation calculation; however, it can lead to excessive run times,
so take care. Also, there is an increased chance of not achieving an
SCF when the SCF criterion is excessively increased.
Superficially, requesting a GNORM of zero might seem excessively
stringent, but as soon as the run starts, it will be cut back to 0.01.
Even that might seem too stringent. The geometry optimization will
continue to lower the energy, and hopefully the GNORM, but frequently it
will not prove possible to lower the GNORM to 0.01. If, after 10
cycles, the energy does not drop then the job will be stopped. At this
point you have the best geometry that MOPAC, in its current form, can
give.
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If a slightly less than highest precision is needed, such as for
normal publication quality work, set the GNORM to the limit wanted. For
example, for a flexible system, a GNORM of 0.1 to 0.5 will normally be
good enough for all but the most demanding work.
If higher than the default, but still not very high precision is
wanted, then use the keyword PRECISE. This will tighten up various
criteria so that higher than routine precision will be given.
If high precision is used, so that the printed GNORM is 0.000, and
the resulting geometry resubmitted for one SCF and gradients
calculation, then normally a GNORM higher than 0.000 will result. This
is NOT an error in MOPAC: the geometry printed is only precise to six
figures after the decimal point. Geometries need to be specified to
more than six decimals in order to drive the GNORM to less than 0.000.
If you want to test MOPAC, or use it for teaching purposes, the
GNORM lower limit of 0.01 can be overridden by specifying LET, in which
case you can specify any limit for GNORM. However, if it is too low the
job may finish due to an irreducible minimum in the heat of formation
being encountered. If this happens, the "STATIONARY POINT" message will
be printed.
Finally there is a full analytical derivative function within
MOPAC. These use STO-6G Gaussian wavefunctions because the derivatives
of the overlap integral are easier to calculate in Gaussians than in
STO's. Consequently, there will be a small difference in the calculated
H.o.F.s when analytical derivatives are used. If there is any doubt
about the accuracy of the finite derivatives, try using the analytical
derivatives. They are a bit slower than finite derivatives but are more
precise (a rough estimate is 12 figures for finite difference, 14 for
analytical).
Some calculations, mainly open shell RHF or closed shell RHF with
C.I. have untracked errors which prevent very high precision. For these
systems GNORM should be in the range 1.0 to 0.1.
How Large can a Gradient Be and
Still Be Acceptable?
A common source of confusion is the limit to which the GNORM should
be reduced in order to obtain acceptable results. There is no easy
answer, however a few guidelines can be given.
First of all reducing the GNORM to an arbitarily small number is
not sensible. If the keywords GNORM=0.000001, LET, and EF are used, a
geometry con be obtained which is precise to about 0.000001 Angstroms.
If ANALYT is also used, the results obtained will be slightly different.
Chemically, this change is meaningless, and no significance should be
attached to such numbers. In addition, any minor change to the
algorithm, such as porting it to a new machine, will give rise to small
changes in the optimized geometry. Even the small changes involved in
going from MOPAC 5.00 to MOPAC 6.00 caused small changes in the
optimized geometry of test molecules.
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As a guide, a GNORM of 0.1 is sufficient for all heat-of-formation
work, and a GNORM of 0.01 for most geometry work. If the system is
large, you may need to settle for a GNORM of 1.0 - 0.5.
This whole topic was raised by Dr. Donald B. Boyd of Lilly
Research Laboratories, who provided unequivocal evidence for a failure
of MOPAC and convinced me of the importance of increasing precision in
certain circumstances.
6.5 CONVERGENCE TESTS IN SUBROUTINE ITER
Self-Consistency Test
The SCF iterations are stopped when two tests are satisfied. These
are (1) when the difference in electronic energy, in eV, between any two
consecutive iterations drops below the adjustable parameter, SELCON, and
the difference between any three consecutive iterations drops below ten
times SELCON, and (2) the difference in density matrix elements on two
successive iterations falls below a preset limit, which is a multiple of
SELCON.
SELCON is set initially to 0.0001 kcal/mole; this can be made 100
times smaller by specifying PRECISE or FORCE. It can be over-ridden by
explicitly defining the SCF criterion via SCFCRT=1.D-12.
SELCON is further modified by the value of the gradient norm, if
known. If GNORM is large, then a more lax SCF criterion is acceptable,
and SCFCRT can be relaxed up to 50 times it's default value. As the
gradient norm drops, the SCF criterion returns to its default value.
The SCF test is performed using the energy calculated from the Fock
matrix which arises from a density matrix, and not from the density
matrix which arises from a Fock. In the limit, the two energies would
be identical, but the first converges faster than the second, without
loss of precision.
6.6 CONVERGENCE IN SCF CALCULATION
A brief description of the convergence techniques used in
subroutine ITER follows.
ITER, the SCF calculation, employs six methods to achieve a
self-consistent field. In order of usage, these are:
(a) Intrinsic convergence by virtue of the way the calculation is
carried out. Thus a trial Fock gives rise to a trial density matrix,
which in turn is used to generate a better Fock matrix.
This is normally convergent, but many exceptions are known. The
main situations when the intrinsic convergence does not work are:
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(1) A bad starting density matrix. This normally occurs
when the default starting density matrix is used. This is a very
crude approximation, and is only used to get the calculation
started. A large charge is generated on an atom in the first
iteration, the second iteration overcompensates, and an
oscillation is generated.
(2) The equations are only very slowly convergent. This can
be due to a long-lived oscillation or to a slow transfer of
charge.
(b) Oscillation damping. If, on any two consecutive iterations, a
density matrix element changes by more than 0.05, then the density
matrix element is set equal to the old element shifted by 0.05 in the
direction of the calculated element. Thus, if on iterations 3 and 4 a
certain density matrix element was 0.55 and 0.78, respectively, then the
element would be set to 0.60 (=0.55+0.05) on iteration 4. The density
matrix from iteration 4 would then be used in the construction of the
next Fock matrix. The arrays which hold the old density matrices are
not filled until after iteration 2. For this reason they are not used
in the damping before iteration 3.
(c) Three-point interpolation of the density matrix. Subroutine
CNVG monitors the number of iterations, and if this is exactly divisible
by three, and certain other conditions relating to the density matrices
are satisfied, a three-point interpolation is performed. This is the
default converger, and is very effective with normally convergent
calculations. It fails in certain systems, usually those where
significant charge build-up is present.
(d) Energy-level shift technique. The virtual M.O. energy levels
are normally shifted to more positive energy. This has the effect of
damping oscillations, and intrinsically divergent equations can often be
changed to intrinsically convergent form. With slowly-convergent
systems the virtual M.O. energy levels can be moved to a more negative
value.
The precise value of the shift used depends on the behavior of the
iteration energy. If it is dropping, then the HOMO-LUMO gap is reduced,
if the iteration energy rises, the gap is increased rapidly.
(e) Pulay's method. If requested, when the largest change in
density matrix elements on two consecutive iterations has dropped below
0.1, then routine CNVG is abandoned in favor of a multi-Fock matrix
interpolation. This relies on the fact that the eigenvectors of the
density and Fock matrices are identical at self-consistency, so [P.F]=0
at SCF. The extent to which this condition does not occur is a measure
of the deviance from self-consistency. Pulay's method uses this
relationship to calculate that linear combination of Fock matrices which
minimize [P.F]. This new Fock matrix is then used in the SCF
calculation.
Under certain circumstances, Pulay's method can cause very slow
convergence, but sometimes it is the only way to achieve a
self-consistent field. At other times the procedure gives a ten-fold
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increase in speed, so care must be exercised in its use. (invoked by
the keyword PULAY)
(f) The Camp-King converger. If all else fails, the Camp-King
converger is just about guaranteed to work every time. However, it is
time-consuming, and therefore should only be invoked as a last resort.
It evaluates that linear combination of old and current
eigenvectors which minimize the total energy. One of its strengths is
that systems which otherwise oscillate due to charge surges, e.g.
CHO-H, the C-H distance being very large, will converge using this very
sophisticated converger.
6.7 CAUSES OF FAILURE TO ACHIEVE AN SCF
In a system where a biradical can form, such as ethane decomposing
into two CH3 units, the normal RHF procedure can fail to go
self-consistent. If the system has marked biradicaloid character, then
BIRADICAL or UHF and TRIPLET can often prove successful. These options
rely on the assumption that two unpaired electrons can represent the
open shell part of the wave-function.
Consider H-Cl, with the interatomic distance being steadily
increased. At first the covalent bond will be strong, and a
self-consistent field is readily obtained. Gradually the bond will
become more ionic, and eventually the charge on chlorine will become
very large. The hydrogen, meanwhile, will become very electropositive,
and there will be an increased energy advantage to any one electron to
transfer from chlorine to hydrogen. If this in fact occurred, the
hydrogen would suddenly become very electron-rich and would, on the next
iteration, lose its extra electron to the chlorine. A sustained
oscillation would then be initiated. To prevent this, if BIRADICAL is
specified, exactly one electron will end up on hydrogen. A similar
result can be obtained by specifying TRIPLET in a UHF calculation.
6.8 TORSION OR DIHEDRAL ANGLE COHERENCY
MOPAC calculations do not distinguish between enantiomers,
consequently the sign of the dihedrals can be multiplied by -1 and the
calculations will be unaffected. However, if chirality is important, a
user should be aware of the sign convention used.
The dihedral angle convention used in MOPAC is that defined by
Klyne and Prelog in Experientia 16, 521 (1960). In this convention,
four atoms, AXYB, with a dihedral angle of 90 degrees, will have atom B
rotated by 90 degrees clockwise relative to A when X and Y are lined up
in the direction of sight, X being nearer to the eye. In their words,
"To distinguish between enantiomeric types the angle 'tau' is considered
as positive when it is measured clockwise from the front substituent A
to the rear substituent B, and negative when it is measured
anticlockwise." The alternative convention was used in all earlier
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programs, including QCPE 353.
6.9 VIBRATIONAL ANALYSIS
Analyzing normal coordinates is very tedious. Users are normally
familiar with the internal coordinates of the system they are studying,
but not familiar with the cartesian coordinates. To help characterize
the normal coordinates, a very simple analysis is done automatically,
and users are strongly encouraged to use this analysis first, and then
to look at the normal coordinate eigenvectors.
In the analysis, each pair of bonded atoms is examined to see if
there is a large relative motion between them. By bonded is meant
within the Van der Waals' distance. If there is such a motion, the
indices of the atoms, the relative distance in Angstroms, and the
percentage radial motion are printed. Radial plus tangential motion
adds to 100%, but as there are two orthogonal tangential motions and
only one radial, the radial component is printed.
6.10 A NOTE ON THERMOCHEMISTRY
By
Tsuneo Hirano
Department of Synthetic Chemistry
Faculty of Engineering
University of Tokyo
Hongo, Bunkyo-ku, Tokyo, Japan
1) Basic Physical Constants
"Quantities, Units and Symbols in Physical Chemistry,"
Blackwell Scientific Publications Ltd, Oxford OX2 0EL, UK, 1987
(IUPAC, based on CODATA of ICSU, 1986). pp 81-82.
Speed of light c = 2.997 92458 D10 cm/s (Definition)
Boltzmann constant k = R/Na
= 1.380 658 D-23 J/K
= 1.380 658 D-16 erg/K
Planck constant h = 6.626 0755 D-34 J s
= 6.626 0755 D-27 erg s
Gas constant R = 8.314 510 J/mol/K
= 1.987 216 cal/mol/K
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Avogadro number Na = 6.022 1367 D23 /mol
Volume of 1 mol of gas V0 = 22.414 10 l/mol (at 1 atm, 25 C)
1 J = 1.D7 erg
1 kcal = 4.184 kJ (Definition)
1 eV = 23.060 6 kcal/mol
1 a.u. = 27.211 35 eV/mol = 627.509 6 kcal/mol
1 cm-1 = 2.859 144 cal/mol (= Na h c / 4.184D7)
1 atm = 1.013 25 D5 Pa = 1.013 25 D6 dyn/cm**2 (Definition)
* * * * * *
Moment of inertia: I
1 amu angstrom**2 = 1.660 540 D-40 g cm**2
Rotational constants: A, B, and C (e.g. A = h/(8*pi*pi*I))
A(in MHz) = 5.053 791 D5 / I(in amu angstrom**2)
A(in cm-1) = 5.053 791 D5/ c/ I(in amu angstrom**2)
= 16.857 63 / I(in amu angstrom**2)
2) Thermochemistry from ab initio MO methods.
Ab initio MO methods provide total energies, Eeq, as the sum of
electronic and nuclear-nuclear repulsion energies for molecules,
isolated in vacuum, without vibration at 0 K.
Eeq = Eel + Enuclear-nuclear (1)
From the 0 K-potential surface and using the harmonic oscillator
approximation, we can calculate the vibrational frequencies, vi, of the
normal modes of vibration. Using these, we can calculate vibrational,
rotational and translational contributions to the thermodynamic
quantities such as the partition function and heat capacity which arise
from heating the system from 0 to T K.
Q: partition function
E: energy
S: entropy
C: heat capacity
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[Vibration]
Qvib = sum over i { 1/(1 - exp(-hvi/kT))} (2)
Evib, for a molecule at the temperature T as
Evib = sum over i {(1/2)hvi + hvi*exp(-hvi/kT)/(1 - exp(-hvi/kT))}
(3)
where h is the Planck constant, vi the i-th normal vibration frequency,
and k the Boltzmann constant. For 1 mole of molecules, Evib should be
multiplied by the Avogadro number Na(= gas constant R/k). Thus,
Evib = Na * sum over i {(1/2)hvi
+ hvi*exp(-hvi/kT)/(1-exp(-hvi/kT))} (4)
Note that the first term in Eq. 4 is the Zero-point vibration
energy. Hence, the second term in Eq. 4 is the additional vibrational
contribution due to the temperature increase from 0 K to T K. Namely,
Evib = Ezero + Evib(0-->T) (5)
Ezero = Na * sum over i {(1/2)hvi}, (6)
Evib(0-->T) = Na * sum over i {hvi*exp(-hvi/kT)/(1 - exp(-
hvi/kT))}.
(7)
The value of Evib from GAUSSIAN 82 and 86 includes Ezero as defined by
Eqs. 4 - 7.
Svib = R sum over i {(hvi/kT)*exp(-hvi/kT)/(1 - exp(-hvi/kT))
- ln(1 - exp(-hvi/kT))} (8)
Cviv = R sum over i {((hvi/kT)**2) exp(-hvi/kT)/
(1 - exp(-hvi/kT))**2} (9)
At temperature T (>0 K), a molecule rotates about the x, y, and
z-axes and translates in x, y, and z-directions. By assuming the
equipartition of energy, energies for rotation and translation, Erot and
Etr, are calculated.
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[Rotation]
(sym) is symmetry number.
I is moment of inertia.
IA, IB, and IC are moments of inertia about A, B, and C axes.
<linear molecule>
Qrot = (1/(sym))[8(pi**2) I kT/ h**2] (10)
Erot = (2/2)RT (11)
Srot = R ln + R (43)
Crot = (2/2)R (44)
<non-linear molecule>
Qrot = [ pi / (A B C C1**3)]**(1/2) / (sym) (45)
Erot = (3/2)RT (46)
Srot = (R/2) ln { (1/(sym)**2) (1/A) (1/B) (1/C) (pi) (kT/hc)**3 }
+ (3/2)R
= 0.5R { 3 ln (kT/hc) - 2 ln (sym) + ln (pi/(A B C)) + 3}
(47)
= 0.5R { -3 ln C1 -2 ln (sym) + ln (pi/(A B C)) + 3}
Crot = (3/2)R (48)
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[Translation]
Qtra = [ ( 2 pi (M/Na) kT)**(1/2) / h]**3
= [ (2 pi M k T * 1.660540D-24)**(1/2) /h]**3 (49)
Etra = (3/2)RT (50)
Htra = (3/2)RT + pV = (5/2)RT (cf. pV = RT) (51)
Stra = (R/2) [ 5 ln T + 3 ln M ] - 2.31482 (cf. p = 1 atm)
= 0.993608 [ 5 ln T + 3 ln M] - 2.31482 (52)
In MOPAC,
Hvib = Evib(0-->T) (53)
(Note: Ezero is <not> included in Hvib.
Wi is not derived from force-constants at 0 K)
and
HT = [Hvib + Hrot + Htra] for T. (54)
H298 = [Hvib + Hrot + Htra] for T = 298.15. (55)
Note that HT (and H298) is equivalent to
(56)
except that the normal frequencies are those obtained from force
constants at 25 degree C, or at least not at 0 K.
Thus, Standard Enthalpy of Formation, Delta-H, can be calculated
according to Eqs. 25, 26 and 29, as shown in Eq. 30;
Delta-H = Escf + (HT - H298) (57)
Note that Ezero is already counted in Escf (see Eq. 29).
By using Eq. 27, Standard Internal Energy of Formation, Delta-U,
can be calculated as
Delta-U = Delta-H - R(T - 298.15). (58)
Standard Gibbs Free-Energy of Formation, Delta-G, can be calculated
by taking the difference from that for the isomer or that at different
temperature,
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Delta-G = [Delta-H - T*S] for the state under consideration
- [Delta-H - T*S] for reference state. (59)
Taking the difference is necessary to cancel the unknown values of
standard entropy of formation for the constituent elements.
6.11 REACTION COORDINATES
The Intrinsic Reaction Coordinate method pioneered and developed by
Mark Gordon has been incorporated in a modified form into MOPAC. As
this facility is quite complicated all the keywords associated with the
IRC have been grouped together in this section.
Definitions of Terms
DRC
The Dynamic Reaction Coordinate is the path followed by all the
atoms in a system assuming conservation of energy, i.e., as the
potential energy changes the kinetic energy of the system changes in
exactly the opposite way so that the total energy (kinetic plus
potential) is a constant. If started at a ground state geometry, no
significant motion should be seen. Similarly, starting at a transition
state geometry should not produce any motion - after all it is a
stationary point and during the lifetime of a calculation it is unlikely
to accumulate enough momentum to travel far from the starting position.
In order to calculate the DRC path from a transition state, either
an initial deflection is necessary or some initial momentum must be
supplied.
Because of the time-dependent nature of the DRC the time elapsed
since the start of the reaction is meaningful, and is printed.
Description
The course of a molecular vibration can be followed by calculating
the potential and kinetic energy at various times. Two extreme
conditions can be identified: (a) gas phase, in which the total energy
is a constant through time, there being no damping of the kinetic energy
allowed, and (b) liquid phase, in which kinetic energy is always set to
zero, the motion of the atoms being infinitely damped.
All possible degrees of damping are allowed. In addition, the
facility exists to dump energy into the system, appearing as kinetic
energy. As kinetic energy is a function of velocity, a vector quantity,
the energy appears as energy of motion in the direction in which the
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molecule would naturally move. If the system is a transition state,
then the excess kinetic energy is added after the intrinsic kinetic
energy has built up to at least 0.2Kcal/mole.
For ground-state systems, the excess energy sometimes may not be
added; if the intrinsic kinetic energy never rises above 0.2kcal/mole
then the excess energy will not be added.
Equations Used
Force acting on any atom
g(i) + g'(i)t + g"(i)t**2 = dE/dx(i) + d**2E/dx(i)**2 +d**3E/dx(i)**3
Acceleration due to force acting on each atom
a(i) = (g(i)+g'(i)t+g"(i)t**2)/M(i)
New velocity
V(o)+Dt*g(i)/M(i)+1/2*Dt**2*g'(i)/M(i)+/3*Dt**3*g"(i)/M(i)
or
V(i) = V(i) + V'(i)t + V''(i)t**2 + V'''(i)t**3
That is, the change in velocity is equal to the integral over the
time interval of the acceleration.
New position of atoms
X(i) = X(o) + V(o)t + 1/2*V't**2 + 1/3*V''t**3 + 1/4*V'''t**4
That is, the change in position is equal to the integral over the
time interval of the velocity.
The velocity vector is accurate to the extent that it takes into
account the previous velocity, the current acceleration, the predicted
acceleration, and the change in predicted acceleration over the time
interval. Very little error is introduced due to higher order
contributions to the velocity; those that do occur are absorbed in a
re-normalization of the magnitude of the velocity vector after each time
interval.
The magnitude of Dt, the time interval, is determined mainly by the
factor needed to re-normalize the velocity vector. If it is
significantly different from unity, Dt will be reduced; if it is very
close to unity, Dt will be increased.
Even with all this, errors creep in and a system, started at the
transition state, is unlikely to return precisely to the transition
state unless an excess kinetic energy is supplied, for example
0.2Kcal/mole.
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The calculation is carried out in cartesian coordinates, and
converted into internal coordinates for display. All cartesian
coordinates must be allowed to vary, in order to conserve angular and
translational momentum.
IRC
The Intrinsic Reaction Coordinate is the path followed by all the
atoms in a system assuming all kinetic energy is completely lost at
every point, i.e., as the potential energy changes the kinetic energy
generated is annihilated so that the total energy (kinetic plus
potential) is always equal to the potential energy only.
The IRC is intended for use starting with the transition state
geometry. A normal coordinate is chosen, usually the reaction
coordinate, and the system is displaced in either the positive or
negative direction along this coordinate. The internal modes are
obtained by calculating the mass-weighted Hessian matrix in a force
calculation and translating the resulting cartesian normal mode
eigenvectors to conserve momentum. That is, the initial cartesian
coordinates are displaced by a small amount proportional to the
eigenvector coefficients plus a translational constant; the constant is
required to ensure that the total translational momentum of the system
is conserved as zero. At the present time there may be small residual
rotational components which are not annihilated; these are considered
unimportant.
General Description of the DRC and IRC.
As the IRC usually requires a normal coordinate, a force constant
calculation normally has to be done first. If IRC is specified on its
own a normal coordinate is not used and the IRC calculation is performed
on the supplied geometry.
A recommended sequence of operations to start an IRC calculation is
as follows:
1. Calculate the transition state geometry. If the T/S is not
first optimized, then the IRC calculation may give very
misleading results. For example, if NH3 inversion is defined
as the planar system but without the N-H bond length being
optimized the first normal coordinate might be for N-H stretch
rather than inversion. In that case the IRC will relax the
geometry to the optimized planar structure.
2. Do a normal FORCE calculation, specifying ISOTOPE in order to
save the FORCE matrices. Do not attempt to run the IRC
directly unless you have confidence that the FORCE calculation
will work as expected. If the IRC calculation is run directly,
specify ISOTOPE anyway: that will save the FORCE matrix and if
the calculation has to be re-done then RESTART will work
correctly.
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3. Using IRC=n and RESTART run the IRC calculation. If RESTART is
specified with IRC=n then the restart is assumed to be from the
FORCE calculation. If RESTART is specified without IRC=n, say
with IRC on its own, then the restart is assumed to be from an
earlier IRC calculation that was shut down before going to
completion.
A DRC calculation is simpler in that a force calculation is not a
prerequisite; however, most calculations of interest normally involve
use of an internal coordinate. For this reason IRC=n can be combined
with DRC to give a calculation in which the initial motion (0.3Kcal
worth of kinetic energy) is supplied by the IRC, and all subsequent
motion obeys conservation of energy. The DRC motion can be modified in
three ways:
1. It is possible to calculate the reaction path followed by a
system in which the generated kinetic energy decays with a
finite half-life. This can be defined by DRC=n.nnn, where
n.nnn is the half-life in femtoseconds. If n.nn is 0.0 this
corresponds to infinite damping simulating the IRC. A
limitation of the program is that time only has meaning when
DRC is specified without a half-life.
2. Excess kinetic energy can be added to the calculation by use of
KINETIC=n.nn. After the kinetic energy has built up to
0.2Kcal/mole or if IRC=n is used then n.nn Kcal/mole of kinetic
energy is added to the system. The excess kinetic energy
appears as a velocity vector in the same direction as the
initial motion.
3. The RESTART file <filename>.RES can be edited to allow the user
to modify the velocity vector or starting geometry. This file
is formatted.
Frequently DRC leads to a periodic, repeating orbit. One special
type - the orbit in which the direction of motion is reversed so that
the system retraces its own path - is sensed for and if detected the
calculation is stopped after exactly one cycle. If the calculation is
to be continued, the keyword GEO-OK will allow this check to be
by-passed.
Due to the potentially very large output files that the DRC can
generate extra keywords are provided to allow selected points to be
printed. After the system has changed by a preset amount the following
keywords can be used to invoke a print of the geometry.
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KeyWord Default User Specification
X-PRIO 0.05 Angstroms X-PRIORITY=n.nn
T-PRIO 0.10 Femtoseconds T-PRIORITY=n.nn
H-PRIO 0.10 Kcal/mole H-PRIORITY=n.nn
Option to allow only extrema to be output
In the geometry specification, if an internal coordinate is marked
for optimization then when that internal coordinate passes through an
extremum a message will be printed and the geometry output.
Difficulties can arise from the way internal coordinates are
processed. The internal coordinates are generated from the cartesian
coordinates, so an internal coordinate supplied may have an entirely
different meaning on output. In particular the connectivity may have
changed. For obvious reasons dummy atoms should not be used in the
supplied geometry specification. If there is any doubt about the
internal coordinates or if the starting geometry contains dummy atoms
then run a 1SCF calculation specifying XYZ. This will produce an ARC
file with the "ideal" numbering - the internal numbering system used by
MOPAC. Use this ARC file to construct a data file suitable for the DRC
or IRC.
Notes
1. Any coordinates marked for optimization will result in only
extrema being printed.
2. If extrema are being printed then kinetic energy extrema will
also be printed.
Keywords for use with the IRC and DRC
1. Setting up the transition state: NLLSQ SIGMA TS.
2. Constructing the FORCE matrix: FORCE or IRC=n, ISOTOPE, LET.
3. Starting an IRC: RESTART and IRC=n, T-PRIO, X-PRIO, H-PRIO.
4. Starting a DRC: DRC or DRC=n.nn, KINETIC=n.nn.
5. Starting a DRC from a transition state: (DRC or DRC=n) and
IRC=n, KINETIC=n.
6. Restarting an IRC: RESTART and IRC.
7. Restarting a DRC: RESTART and (DRC or DRC=n.nn).
8. Restarting a DRC starting from a transition state: RESTART and
(DRC or DRC=n.nn).
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Other keywords, such as T=nnn or GEO-OK can be used anytime.
Examples of DRC/IRC data
Use of the IRC/DRC facility is quite complicated. In the following
examples various "reasonable" options are illustrated for a calculation
on water.
It is assumed that an optimized transition-state geometry is
available.
Example 1: A Dynamic Reaction Coordinate, starting at the
transition state for water inverting, initial motion opposite to the
transition normal mode, with 6kcal of excess kinetic energy added in.
Every point calculated is to be printed (Note all coordinates are marked
with a zero, and T-PRIO, H-PRIO and X-PRIO are all absent). The results
of an earlier calculation using the same keywords is assumed to exist.
The earlier calculation would have constructed the force matrix. While
the total cpu time is specified, it is in fact redundant in that the
calculation will run to completion in less than 600 seconds.
KINETIC=6 RESTART IRC=-1 DRC T=600
WATER
H 0.000000 0 0.000000 0 0.000000 0 0 0 0
O 0.911574 0 0.000000 0 0.000000 0 1 0 0
H 0.911574 0 180.000000 0 0.000000 0 2 1 0
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Example 2: An Intrinsic Reaction Coordinate calculation. Here the
restart is from a previous IRC calculation which was stopped before the
minimum was reached. Recall that RESTART with IRC=n implies a restart
from the FORCE calculation. Since this is a restart from within an IRC
calculation the keyword IRC=n has been replaced by IRC. IRC on its own
(without the "=n") implies an IRC calculation from the starting position
- here the RESTART position - without initial displacement.
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RESTART IRC T=600
WATER
H 0.000000 0 0.000000 0 0.000000 0 0 0 0
O 0.911574 0 0.000000 0 0.000000 0 1 0 0
H 0.911574 0 180.000000 0 0.000000 0 2 1 0
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Output Format for IRC and DRC
The IRC and DRC can produce several different forms of output.
Because of the large size of these outputs, users are recommended to use
search functions to extract information. To facilitate this, specific
lines have specific characters. Thus, a search for the "%" symbol will
summarize the energy profile while a search for "AA" will yield the
coordinates of atom 1, whenever it is printed. The main flags to use in
searches are:
SEARCH FOR YIELDS
'% ' Energies for all points calculated,
excluding extrema
'%M' Energies for all turning points
'%MAX' Energies for all maxima
'%MIN' Energies for all minima
'%' Energies for all points calculated
'AA*' Internal coordinates for atom 1 for every point
'AE*' Internal coordinates for atom 5 for every point
'123AB*' Internal coordinates for atom 5 for point 123
As the keywords for the IRC/DRC are interdependent, the following
list of keywords illustrates various options.
Keyword Resulting Action
DRC The Dynamic Reaction Coordinate is calculated.
Energy is conserved, and no initial impetus.
DRC=0.5 In the DRC kinetic energy is lost with a half-
life of 0.5 femtoseconds.
DRC=-1.0 Energy is put into a DRC with an half-life of
-1.0 femtoseconds, i.e., the system gains
energy.
IRC The Intrinsic Reaction Coordinate is
calculated. No initial impetus is given.
Energy not conserved.
IRC=-4 The IRC is run starting with an impetus in the
negative of the 4th normal mode direction. The
impetus is one quantum of vibrational energy.
IRC=1 KINETIC=1 The first normal mode is used in an IRC, with
the initial impetus being 1.0Kcal/mole.
DRC KINETIC=5 In a DRC, after the velocity is defined, 5 Kcal
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of kinetic energy is added in the direction of
the initial velocity.
IRC=1 DRC KINETIC=4 After starting with a 4 kcal impetus in the
direction of the first normal mode, energy is
conserved.
DRC VELOCITY KINETIC=10 Follow a DRC trajectory which starts with an
initial velocity read in, normalized to a
kinetic energy of 10 kcal/mol.
Instead of every point being printed, the option exists to print
specific points determined by the keywords T-PRIORITY, X-PRIORITY and
H-PRIORITY. If any one of these words is specified, then the calculated
points are used to define quadratics in time for all variables normally
printed. In addition, if the flag for the first atom is set to T then
all kinetic energy turning points are printed. If the flag for any
other internal coordinate is set to T then, when that coordinate passes
through an extremum, that point will be printed. As with the PRIORITYs,
the point will be calculated via a quadratic to minimize non-linear
errors.
N.b.: Quadratics are unstable in the regions of inflection points,
in these circumstances linear interpolation will be used. A result of
this is that points printed in the region of an inflection may not
correspond exactly to those requested. This is not an error and should
not affect the quality of the results.
Test of DRC - Verification of Trajectory Path
Introduction: Unlike a single-geometry calculation or even a
geometry optimization, verification of a DRC trajectory is not a simple
task. In this section a rigorous proof of the DRC trajectory is
presented; it can be used both as a test of the DRC algorithm and as a
teaching exercise. Users of the DRC are asked to follow through this
proof in order to convince themselves that the DRC works as it should.
Part 1: The Nitrogen Molecule
For the nitrogen molecule and using MNDO, the equilibrium distance
is 1.103802 Angstroms, the heat of formation is 8.276655 Kcal/mole and
the vibrational frequency is 2739.6 cm(-1). For small displacements,
the energy curve versus distance is parabolic and the gradient curve is
approximately linear, as is shown in the following table. A nitrogen
molecule is thus a good approximation to a harmonic oscillator.
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STRETCHING CURVE FOR NITROGEN MOLECULE
N-N DIST H.O.F. GRADIENT
(Angstroms) (Kcal/mole) (Kcal/mole/Angstrom)
1.1180 8.714564 60.909301
1.1170 8.655723 56.770564
1.1160 8.601031 52.609237
1.1150 8.550512 48.425249
1.1140 8.504188 44.218525
1.1130 8.462082 39.988986
1.1120 8.424218 35.736557
1.1110 8.390617 31.461161
1.1100 8.361303 27.162720
1.1090 8.336299 22.841156
1.1080 8.315628 18.496393
1.1070 8.299314 14.128353
1.1060 8.287379 9.736959
1.1050 8.279848 5.322132
1.1040 8.276743 0.883795
1.1030 8.278088 -3.578130
1.1020 8.283907 -8.063720
1.1010 8.294224 -12.573055
1.1000 8.309061 -17.106213
1.0990 8.328444 -21.663271
1.0980 8.352396 -26.244309
1.0970 8.380941 -30.849404
1.0960 8.414103 -35.478636
1.0950 8.451906 -40.132083
1.0940 8.494375 -44.809824
1.0930 8.541534 -49.511939
1.0920 8.593407 -54.238505
1.0910 8.650019 -58.989621
1.0900 8.711394 -63.765330
Period of Vibration.
The period of vibration (time taken for the oscillator to undertake
one complete vibration, returning to its original position and velocity)
can be calculated in three ways. Most direct is the calculation from
the energy curve; using the gradient constitutes a faster, albeit less
direct, method, while calculating it from the vibrational frequency is
very fast but assumes that the vibrational spectrum has already been
calculated.
(1) From the energy curve.
For a simple harmonic oscillator the period 'r' is given by
r = 2*pi*sqrt(m/k)
where m = reduced mass and k = force-constant. The reduced mass (in
AMU) of a nitrogen molecule is 14.0067/2 = 7.00335, and the
force-constant can be calculated from
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2
E - c = 1/2*k(R-Ro).
Given Ro = 1.1038, R = 1.092, c = 8.276655 and E = 8.593407Kcal/mol
then
2
k = 4548.2 Kcal/mole/A
3 7 8 8 2
= 4545 * 4.184 * 10 * 10 * 10 * 10 ergs/cm
30 2
= 1.9029 * 10 ergs/cm
30
Therefore, r = 2 * 3.14159 * sqrt(7.0035/(1.9029*10 )) seconds
-15
= 12.054 * 10 seconds
= 12.054 fS (Femtoseconds)
(2) From the gradient curve.
The force constant is the derivative of the gradient W.R.T.
distance
k = dG/dx
Since we are using discrete points, the force constant is best
obtained from finite differences:
k = (G2-G1)/(x2-x1)
For x2 = 1.1100, G2 = 27.163 and for x1 = 1.0980, G1 = -26.244,
giving rise to k = 4450 kcal/mole/A/A and a period of 12.186 fS.
(3) From the vibrational frequency.
Given a "frequency" of vibration of N2 of v=2739.6 cm(-1) the
period of oscillation is given directly by
r = 1/(v*c)
10
= 1/(2739.6 * 2.998 * 10 ) seconds
= 12.175 fS
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Summarizing, by three different methods the period of oscillation
of N2 is calculated to be 12.054, 12.186 and 12.175 fS, average
12.138fS.
Initial Dynamics of N2 Molecule with N-N distance = 1.094 Angstroms
A useful check on the dynamics of N2 is to calculate the initial
acceleration of the two nitrogen atoms after releasing them from a
starting interatomic separation of 1.094 Angstroms.
At R(N-N) = 1.094 Angstroms,
G = -44.810 Kcal/mole/Angstrom
19
= -18.749 * 10 ergs/cm
19
Therefore acceleration f = -18.749 * 10 /14.0067 cm/sec/sec
18
= -13.386 * 10 cm/sec/sec
15
= -13.386 * 10 * Earth surface gravity!
Distance from equilibrium = 0.00980 Angstroms.
-15 18
After 0.1 fS velocity = 0.1 * 10 * (-13.386 * 10 ) cm/sec
= 1338.6 cm/sec
In the DRC the time-interval between points calculated is a
complicated function of the curvature of the local surface. By default,
the first time-interval is 0.105fS, so the calculated velocity at this
time should be 0.105 * 1338.6 = 1405.6cm/sec, in the DRC calculation the
predicted velocity is 1405.6cm/sec.
The option is provided to allow sampling of the system at constant
time-intervals, the default being 0.1fS. For the first few points the
calculated velocities are as follows.
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TIME CALCULATED LINEAR DIFF.
VELOCITY VELOCITY VELOCITY
0.000 0.0 0.0 0.0
0.100 1338.6 1338.6 0.0
0.200 2673.9 2677.2 -3.3
0.300 4001.0 4015.8 -14.8
0.400 5317.3 5354.4 -37.1
0.500 6618.5 6693.0 -74.5
0.600 7900.8 8031.6 -130.8
As the calculated velocity is a fourth-order polynomial of the
acceleration, and the acceleration, its first, second and third
derivatives, are all changing, the predicted velocity rapidly becomes a
poor guide to future velocities.
For simple harmonic motion the velocity at any time is given by
v = v0 * sin(2*pi*t/r)
By fitting the computed velocities to simple harmonic motion, a much
better fit is obtained
Calculated Simple Harmonic Diff
Time Velocity 25316.Sin(0.529t)
0.000 0.0 0.0 0.0
0.100 1338.6 1338.6 0.0
0.200 2673.9 2673.4 +0.5
0.300 4001.0 4000.8 +0.2
0.400 5317.3 5317.0 +0.3
0.500 6618.5 6618.3 +0.2
0.600 7900.8 7901.0 -0.2
The repeat-time required for this motion is 11.88 fS, in good
agreement with the three values calculated using static models. The
repeat time should not be calculated from the time required to go from a
minimum to a maximum and then back to a minimum -- only half a cycle.
For all real systems the potential energy is a skewed parabola, so that
the potential energy slopes are different for both sides; a compression
(as in this case) normally leads to a higher force-constant, and shorter
apparent repeat time (as in this case). Only the addition of the two
half-cycles is meaningful.
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Conservation of Normal Coordinate
So far this analysis has only considered a homonuclear diatomic. A
detailed analysis of a large polyatomic is impractical, and for
simplicity a molecule of formaldehyde will be studied.
In polyatomics, energy can transfer between modes. This is a
result of the non-parabolic nature of the potential surface. For small
displacements the surface can be considered as parabolic. This means
that for small displacements interconversion between modes should occur
only very slowly. Of the six normal modes, mode 1, at 1204.5 cm(-1),
the in-plane C-H asymmetric bend, is the most unsymmetric vibration, and
is chosen to demonstrate conservation of vibrational purity.
Mode 1 has a frequency corresponding to 3.44 Kcal/mole and a
predicted vibrational time of 27.69fS. By direct calculation, using the
DRC, the cycle time is 27.55fS. The rate of decay of this mode has an
estimated half-life of a few thousands femtoseconds.
Rate of Decay of Starting Mode
For trajectories initiated by an IRC=n calculation, whenever the
potential energy is a minimum the current velocity is compared with the
supplied velocity. The square of the cosine of the angle between the
two velocity vectors is a measure of the intensity of the original mode
in the current vibration.
Half-Life for Decay of Initial Mode
Vibrational purity is assumed to decay according to zero'th order
kinetics. The half-life is thus -0.6931472*t/log(psi2) fS, where psi2
is the square of the overlap integral of the original vibration with the
current vibration. Due to the very slow rate of decay of the starting
mode, several half-life calculations should be examined. Only when
successive half-lives are similar should any confidence be placed in
their value.
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DRC Print Options
The amount of output in the DRC is controlled by three sets of
options. These sets are:
(a) Equivalent Keywords H-PRIORITY, T-PRIORITY, and X-PRIORITY
(b) Potential Energy Turning Point option.
(c) Geometry Maxima Turning Point options.
If T-PRIORITY is used then turning points cannot be monitored.
Currently H-PRIORITY and X-PRIORITY are not implemented, but will be as
soon as practical.
To monitor geometry turning points, put a "T" in place of the
geometry optimization flag for the relevant geometric variable.
To monitor the potential energy turning points, put a "T" for the
flag for atom 1 bond length (Do not forget to put in a bond-length (zero
will do)!).
The effect of these flags together is as follows.
1. No options: All calculated points will be printed. No turning
points will be calculated.
2. Atom 1 bond length flagged with a "T": If T-PRIO, etc. are
NOT specified, then potential energy turning points will be
printed.
3. Internal coordinate flags set to "T": If T-PRIO, etc. are NOT
specified, then geometry extrema will be printed. If only one
coordinate is flagged, then the turning point will be displayed
in chronologic order; if several are flagged then all turning
points occuring in a given time-interval will be printed as
they are detected. In other words, some may be out of
chronologic order. Note that each coordinate flagged will give
rise to a different geometry: minimize flagged coordinates to
minimize output.
4. Potential and geometric flags set: The effect is equivalent to
the sum of the first two options.
5. T-PRIO set: No turning points will be printed, but constant
time-slices (by default 0.1fS) will be used to control the
print.
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6.12 SPARKLES
Four extra "elements" have been put into MOPAC. These represent
pure ionic charges, roughly equivalent to the following chemical
entities:
Chemical Symbol Equivalent to
+ Tetramethyl ammonium radical, Potassium
atom or Cesium atom.
++ Barium atom.
- Borohydride radical, Halogen, or
Nitrate radical
-- Sulfate, oxalate.
For the purposes of discussion these entities are called
"sparkles": the name arises from consideration of their behavior.
Behavior of sparkles in MOPAC.
Sparkles have the following properties:
1. Their nuclear charge is integer, and is +1, +2, -1, or -2;
there are an equivalent number of electrons to maintain
electroneutrality, 1, 2, -1, and -2 respectively. For example,
a '+' sparkle consists of a unipositive nucleus and an
electron. The electron is donated to the quantum mechanics
calculation.
2. They all have an ionic radius of 0.7 Angstroms. Any two
sparkles of opposite sign will form an ion-pair with a
interatomic separation of 1.4A.
3. They have a zero heat of atomization, no orbitals, and no
ionization potential.
They can be regarded as unpolarizable ions of diameter 1.4A. They
do not contribute to the orbital count, and cannot accept or donate
electrons.
Since they appear as uncharged species which immediately ionize,
attention should be given to the charge on the whole system. For
example, if the alkaline metal salt of formic acid was run, the formula
would be:
HCOO+ where + is the unipositive sparkle. The charge on the system
would then be zero.
A water molecule polarized by a positive sparkle would have the
formula H2O+, and the charge on the system would be +1
At first sight, a sparkle would appear to be too ionic to be a
point charge and would combine with the first charge of opposite sign it
encountered.
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This representation is faulty, and a better description would be of
an ion, of diameter 1.4A, and the charge delocalized over its surface.
Computationally, a sparkle is an integer charge at the center of a
repulsion sphere of form exp(-alpha*r). The hardness of the sphere is
such that other atoms or sparkles can approach within about 2 Angstroms
quite easily, but only with great difficulty come closer than 1.4A.
Uses of Sparkles
1. They can be used as counterions, e.g. for acid anions or for
cations. Thus, if the ionic form of an acid is wanted, then
the moieties H.X, H.-, and +.X could be examined.
2. Two sparkles of equal and opposite sign can form a dipole for
mimicking solvation effects. Thus water could be surrounded by
six dipoles to simulate the solvent cage. A dipole of value D
can be made by using the two sparkles + and -, or using ++ and
--. If + and - are used, the inter-sparkle separation would be
D/4.803 Angstroms. If ++ and -- are used, the separation would
be D/9.606 Angstroms. If the inter-sparkle separation is less
than 1.0 Angstroms (a situation that cannot occur naturally)
then the energy due to the dipole on its own is subtracted from
the total energy.
3. They can operate as polarization functions. A controlled,
shaped electric field can easily be made from two or more
sparkles. The polarizability in cubic Angstroms of a molecule
in any particular orientation can then easily be calculated.
6.13 MECHANISM OF THE FRAME IN THE FORCE CALCULATION
The FORCE calculation uses cartesian coordinates, and all 3N modes
are calculated, where N is the number of atoms in the system. Clearly,
there will be 5 or 6 "trivial" vibrations, which represent the three
translations and two or three rotations. If the molecule is exactly at
a stationary point, then these "vibrations" will have a force constant
and frequency of precisely zero. If the force calculation was done
correctly, and the molecule was not exactly at a stationary point, then
the three translations should be exactly zero, but the rotations would
be non-zero. The extent to which the rotations are non-zero is a
measure of the error in the geometry.
If the distortions are non-zero, the trivial vibrations can
interact with the low-lying genuine vibrations or rotations, and with
the transition vibration if present.
To prevent this the analytic form of the rotations and vibrations
is calculated, and arbitrary eigenvalues assigned; these are 500, 600,
700, 800, 900, and 1000 millidynes/angstrom for Tx, Ty, Tz, Rx, Ry and
Rz (if present), respectively. The rotations are about the principal
axes of inertia for the system, taking into account isotopic masses.
The "force matrix" for these trivial vibrations is determined, and added
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on to the calculated force matrix. After diagonalization the arbitrary
eigenvalues are subtracted off the trivial vibrations, and the resulting
numbers are the "true" values. Interference with genuine vibrations is
thus avoided.
6.14 CONFIGURATION INTERACTION
MOPAC contains a very large Multi-Electron Configuration
Interaction calculation, MECI, which allows almost any configuration
interaction calculation to be performed. Because of its complexity, two
distinct levels of input are supported; the default values will be of
use to the novice while an expert has available an exhaustive set of
keywords from which a specific C.I. can be tailored.
A MECI calculation involves the interaction of microstates
representing specific permutations of electrons in a set of M.O.'s.
Starting with a set electronic configuration, either closed shell or
open shell, but unconditionally restricted Hartree-Fock, the first step
in a MECI calculation is the removal from the M.O.'s of the electrons to
be used in the C.I.
Each microstate is then constructed from these empty M.O.'s by
adding in electrons according to a prescription. The energy of the
configuration is evaluated, as is the energy of interaction with all
previously-defined configurations. Diagonalization then results in
state functions. From the eigenvectors the expectation value of s**2 is
calculated, and the spin-states of the state functions calculated.
General Overview of Keywords
Keywords associated with the operations of MECI are:
SINGLET DOUBLET EXCITED
TRIPLET QUARTET BIRADICAL
QUINTET SEXTET ESR
OPEN(n1,n2) C.I.=n MECI
ROOT=n
Each keyword may imply others; thus TRIPLET implies an open-shell
system, therefore OPEN(2,2), and C.I.=2 are implied, if not user
specified.
Starting Electronic Configuration
MECI is restricted to RHF calculations, but with that single
restriction any starting configuration will be supported. Examples of
starting configurations would be
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System KeyWords used Starting Configuration
Methane <none> 2.00 2.00 2.00 2.00 2.00
Methyl Radical <none> 2.00 2.00 2.00 2.00 1.00
Twisted Ethylene TRIPLET 2.00 2.00 2.00 1.00 1.00
Twisted Ethylene OPEN(2,2) 2.00 2.00 2.00 1.00 1.00
Twisted Ethylene Cation OPEN(1,2) 2.00 2.00 2.00 0.50 0.50
Methane Cation CHARGE=1 OPEN(5,3) 2.00 2.00 1.67 1.67 1.67
Choice of starting configuration is important. For example, if
twisted ethylene, a ground-state triplet, is not defined using TRIPLET
or OPEN(2,2), then the closed-shell ground-state structure will be
calculated. Obviously, this configuration is a legitimate microstate,
but from the symmetry of the system a better choice would be to define
one electron in each of the two formally degenerate pi-type M.O.'s. The
initial SCF calculation does not distinguish between OPEN(2,2) and
TRIPLET since both keywords define the same starting configuration.
This can be verified by monitoring the convergence using PL, for which
both keywords give the same SCF energy.
Removal of Electrons from Starting Configuration
For a starting configuration of alpha M.O. occupancies O(i), O(i)
being in the range 0.0 to 1.0, the energies of the M.O.'s involved in
the MECI can be calculated from
E(i) = Sum(j)(2J(i,j)-K(i,j))O(j)
where J(i,j) and K(i,j) are the coulomb and exchange integrals between
M.O.'s i and j. The M.O. index j runs over those M.O.'s involved in
the MECI only. Most MECI calculations will involve between 1 and 5
M.O.'s, so a system with about 30 filled or partly filled M.O.'s could
have M.O.'s 25-30 involved. The resulting eigenvalues correspond to
those of the cationic system resulting from removal of n electrons,
where n is twice the sum of the orbital occupancies of those M.O.'s
involved in the C.I.
The arbitrary zero of energy in a MECI calculation is the starting
ground state, without any correction for errors introduced by the use of
fractional occupancies. In order to calculate the energy of the various
configurations, the energy of the vacuum state (i.e., the state
resulting from removal of the electrons used in the C.I.) needs to be
evaluated. This energy is defined by
GSE = Sum(i)[ E(i)O(i) + J(i,i) * O(i)*O(i)
+ Sum(j<i)( 2(2J(i,j) - K(i,j) ) * O(i)*O(j) ) ]
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Formation of Microstate Configuration
Microstates are particular electron configurations. Thus if there
are 5 electrons in 5 levels, then various microstates could be as
follows:
Microstates for 5 electrons in 5 M.O.'s
Electron Configuration Electron Configuration
Alpha Beta M(s) Alpha Beta
M(s)
1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5
1 1,1,1,0,0 1,1,0,0,0 1/2 4 1,1,1,1,1 0,0,0,0,0 5/2
2 1,1,0,0,0 1,1,1,0,0 -1/2 5 1,1,0,1,0 1,1,0,0,0 1/2
3 1,1,1,0,0 0,0,0,1,1 1/2 6 1,1,0,1,0 1,0,1,0,0 1/2
For 5 electrons in 5 M.O.'s there are 252 microstates
(10!/(5!*5!)), but as states of different spin do not mix, we can use a
smaller number. If doublet states are needed then 100 states
(5!/(2!*3!)*(5!/3!*2!) are needed. If only quartet states are of
interest then 25 states (5!/(1!*4!)*(5!/4!*1!) are needed and if the
sextet state is required, then only one state is calculated.
In the microstates listed, state 1 is the ground-state
configuration. This can be written as (2,2,1,0,0), meaning that M.O.'s
1 and 2 are doubly occupied, M.O. 3 is singly occupied by an alpha
electron, and M.O.'s 4 and 5 are empty. Microstate 1 has a component of
spin of 1/2, and is a pure doublet. By Kramer's degeneracy - sometimes
called time-inversion symmetry - microstate 2 is also a doublet, and has
a spin of 1/2 and a component of spin of -1/2.
Microstate 3, while it has a component of spin of 1/2, is not a
doublet, but is in fact a component of a doublet, a quartet and a
sextet. The coefficients of these states can be calculated from the
Clebsch-Gordon 3-J symbol. For example, the coefficient in the sextet
is 1/Sqrt(5).
Microstate 4 is a pure sextet. If all 100 microstates of component
of spin = 1/2 were used in a C.I., one of the resulting states would
have the same energy as the state resulting from microstate 4.
Microstate 5 is an excited doublet, and microstate 6 is an excited
state of the system, but not a pure spin-state.
By default, if n M.O.'s are included in the MECI, then all possible
microstates which give rise to a component of spin = 0 for even electron
systems, or 1/2 for odd electron systems, will be used.
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Permutations of Electrons among Molecular Orbitals
(0,1) = 0 (2,4) = 1100 (3,5) = 11100 (2,5) = 11000
1010 11010 10100
(1,1) = 1 1001 11001 10010
0110 10110 10001
(0,2) = 0 0101 10101 01100
0011 10011 01010
(1,2) = 10 01110 01001
01 (1,4) = 1000 01101 00110
0100 01011 00101
(1,3) = 100 0010 00111 00011
010 0001
001
(2,3) = 110
101
011
Sets of Microstates for Various MECI Calculations
Odd Electron Systems Even Electron Systems
Alpha Beta No. of Alpha Beta No. of
Configs. Configs.
C.I.=1 (1,1) * (0,1) = 1 (1,1) * (1,1) = 1
2 (1,2) * (0,2) = 2 (1,2) * (1,2) = 4
3 (2,3) * (1,3) = 9 (2,3) * (2,3) = 9
4 (2,4) * (1,4) = 24 (2,4) * (2,4) = 36
5 (3,5) * (2,5) = 100 (3,5) * (3,5) = 100
Multi Electron Configuration Interaction
The numbering of the M.O.'s used in the MECI is standard, and
follows the Aufbau principle. The order of filling is in order of
energy, and alpha before beta. This point is critically important in
deciding the sign of matrix elements. For a 5 M.O. system, then, the
order of filling is.
_ _ _ _ _
(1)(1)(2)(2)(3)(3)(4)(4)(5)(5)
A triplet state arising from two microstates, each with a component
of spin = 0, will thus be the positive combination.
_ _
(1)(2) + (1)(2)
This is in variance with the sign convention used in earlier
programs for running MNDO. This standard sign convention was chosen in
order to allow the signs of the microstate coefficients to conform to
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those resulting from the spin step-down operator.
Matrix elements between all pairs of microstates are calculated in
order to form the secular determinant. Many elements will be
identically zero, due to the interacting determinants differing by more
than two M.O.'s. For the remaining interactions the following types can
be identified.
1. The two determinants are identical:
No permutations are necessary in order to calculate the
sign of the matrix element. E(p,p) is given simply by
E(p,p)=Sum(i)Oa(i,p)*[Eig(i) + Sum(1/2(<iijj>-<ijij>)*Oa(j,p)
+ <iijj> *Ob(j,p))
+ Sum(i)Ob(i,p)*[Eig(i) + Sum(1/2(<iijj>-<ijij>)*Ob(j,p))
Oa(i,p) = Occupancy of alpha M.O. i in Microstate p
Ob(i,p) = Occupancy of beta M.O. i in Microstate p
2. Determinants differing by exactly one M.O.:
The differing M.O. can be of type alpha or beta. It is
sufficient to evaluate the case in which both M.O.'s are of
alpha type, the beta form is obtained in like manner.
E(p,q) = Sum(k) [ <ijkk> - <ikjk> ) * (Occa(k) - Occg(k))
+ <ijkk> * (Occb(k) - Occg(k)]
E(p,q) may need to be multiplied by -1, if the number of
two electron permutations required to bring M.O.'s i and j
into coincidence is odd.
Where Occa(k) is the alpha molecular orbital occupancy in
the configuration interaction.
3. Determinants differing by exactly two M.O.'s:
The two M.O.'s can have the same or opposite spins. Three
cases can be identified:
1. Both M.O.'s have alpha spin:
For the first microstate having M.O.'s i and j, and
the second microstate having M.O.'s k and l, the matrix
element connecting the two microstates is given by
Q(p,q) = <ikjl> - <iljk>
E(p,q) may need to be multiplied by -1, if the number of
two electron permutations required to bring M.O. i into
coincidence with M.O. k and M.O. j into coincidence with
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M.O. l is odd.
2. Both M.O.'s have beta spin:
The matrix element is calculated in the same manner as
in the previous case.
3. One M.O. has alpha spin, and one beta spin:
For the first microstate having M.O.'s alpha(i) and
beta(j), and the second microstate having M.O.'s alpha(k)
and beta(l), the matrix element connecting the two
microstates is given by
Q(p,q) = <ikjl>
E(p,q) may need to be multiplied by -1, if the number of
two electron permutations required to bring M.O. i into
coincidence with M.O. k and M.O. j into coincidence with
M.O. l is odd.
States Arising from Various Calculations
Each MECI calculation invoked by use of the keyword C.I.=n normally
gives rise to states of quantized spins. When C.I. is used without any
other modifying keywords, the following states will be obtained.
No. of M.O.'s States Arising States Arising From
From Odd Electron Systems Even Electron Systems
in MECI Doublets Singlets Triplets
1 1 1
2 2 3 1
3 8 1 6 3
4 20 4 20 15 1
5 75 24 1 50 45 5
These numbers of spin states will be obtained irrespective of the
chemical nature of the system.
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Calculation of Spin-States
In order to calculate the spin-state, the expectation value of S2
is calculated.
S2 = S(S+1) = Sz**2 + 2*S(+)S(-)
= Ne -
Sum(i) [C(i,k)*C(i,k)*(1/4*(Na(i)-Nb(i))**2
+ Sum(l) Oa(l,i)*Ob(l,i))
+Sum(j) 2[C(i,k)*C(j,k)*(Kronekerdelta(C(i,k)( S(+)S(-) )C(j,k)]]
Where Ne = No. of electrons in C.I.
C(i,k) = Coefficient of Microstate i in State k
Na(i) = Number of alpha electrons in Microstate i
Nb(i) = Number of beta electrons in Microstate i
Oa(l,k) = Occupancy of alpha M.O. l in Microstate k
Ob(l,k) = Occupancy of beta M.O. l in Microstate k
S(+) = Spin shift up or step up operator
S(-) = Spin shift down or step down operator
The Kronekerdelta is 1 if the two terms in brackets following it
are identical.
The spin state is calculated from S = 1/2 ( Sqrt(1+4*S2) - 1 )
In practice, S is calculated to be exactly integer, or half
integer. That is, there is insignificant error due to approximations
used. This does not mean, however, that the method is accurate. The
spin calculation is completely precise, in the group theoretic sense,
but the accuracy of the calculation is limited by the Hamiltonian used,
a space-dependent function.
Choice of State to be Optimized
MECI can calculate a large number of states of various total spin.
Two schemes are provided to allow a given state to be selected. First,
ROOT=n will, when used on its own, select the n'th state, irrespective
of its total spin. By default n=1. If ROOT=n is used in conjunction
with a keyword from the set SINGLET, DOUBLET, TRIPLET, QUARTET, QUINTET,
or SEXTET, then the n'th root of that spin-state will be used. For
example, ROOT=4 and SINGLET will select the 4th singlet state. If there
are two triplet states below the fourth singlet state then this will
mean that the sixth state will be selected.
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Calculation of Unpaired Spin Density
Starting with the state functions as linear combinations of
configurations, the unpaired spin density, corresponding to the alpha
spin density minus the beta spin density, will be calculated for the
first few states. This calculation is straightforward for diagonal
terms, and only those terms are used.
6.15 REDUCED MASSES IN A FORCE CALCULATION
Reduced masses for a diatomic are given by
(mass1) * (mass2)
_________________
(mass1) + (mass2)
For a Hydrogen molecule the reduced mass is thus 0.5; for heavily
hydrogenated systems, e.g. methane, the reduced mass can be very low.
A vibration involving only heavy atoms , e.g. a C-N in cyanide, should
give a large reduced mass.
For the "trivial" vibrations the reduced mass is ill-defined, and
where this happens the reduced mass is set to zero.
6.16 USE OF SADDLE CALCULATION
A SADDLE calculation uses two complete geometries, as shown on the
following data file for the ethyl radical hydrogen migration from one
methyl group to the other.
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Line 1: UHF SADDLE
Line 2: ETHYL RADICAL HYDROGEN MIGRATION
Line 3:
Line 4: C 0.000000 0 0.000000 0 0.000000 0 0 0 0
Line 5: C 1.479146 1 0.000000 0 0.000000 0 1 0 0
Line 6: H 1.109475 1 111.328433 1 0.000000 0 2 1 0
Line 7: H 1.109470 1 111.753160 1 120.288410 1 2 1 3
Line 8: H 1.109843 1 110.103163 1 240.205278 1 2 1 3
Line 9: H 1.082055 1 121.214083 1 38.110989 1 1 2 3
Line 10: H 1.081797 1 121.521232 1 217.450268 1 1 2 3
Line 11: 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Line 12: C 0.000000 0 0.000000 0 0.000000 0 0 0 0
Line 13: C 1.479146 1 0.000000 0 0.000000 0 1 0 0
Line 14: H 1.109475 1 111.328433 1 0.000000 0 2 1 0
Line 15: H 1.109470 1 111.753160 1 120.288410 1 2 1 3
Line 16: H 2.109843 1 30.103163 1 240.205278 1 2 1 3
Line 17: H 1.082055 1 121.214083 1 38.110989 1 1 2 3
Line 18: H 1.081797 1 121.521232 1 217.450268 1 1 2 3
Line 19: 0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Line 20:
Details of the mathematics of SADDLE appeared in print in 1984,
(M. J. S. Dewar, E. F. Healy, J. J. P. Stewart, J. Chem. Soc. Faraday
Trans. II, 3, 227, (1984)) so only a superficial description will be
given here.
The main steps in the saddle calculation are as follows:
1. The heats of formation of both systems are calculated.
2. A vector R of length 3N-6 defining the difference between the
two geometries is calculated.
3. The scalar P of the difference vector is reduced by some
fraction, normally about 5 to 15 percent.
4. Identify the geometry of lower energy; call this G.
5. Optimize G, subject to the constraint that it maintains a
constant distance P from the other geometry.
6. If the newly-optimized geometry is higher in energy then the
other geometry, then go to 1. If it is higher, and the last
two steps involved the same geometry moving, make the other
geometry G without modifying P, and go to 5.
7. Otherwise go back to 2.
The mechanism of 5 involves the coordinates of the moving geometry
being perturbed by an amount equal to the product of the discrepancy
between the calculated and required P and the vector R.
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As the specification of the geometries is quite difficult, in that
the difference vector depends on angles (which are, of necessity
ill-defined by 360 degrees) SADDLE can be made to run in cartesian
coordinates using the keyword XYZ. If this option is chosen then the
initial steps of the calculation are as follows:
1. Both geometries are converted into cartesian coordinates.
2. Both geometries are centered about the origin of cartesian
space.
3. One geometry is rotated until the difference vector is a
minimum - this minimum is within 1 degree of the absolute
bottom.
4. The SADDLE calculation then proceeds as described above.
LIMITATIONS:
The two geometries must be related by a continuous deformation of
the coordinates. By default, internal coordinates are used in
specifying geometries, and while bond lengths and bond angles are
unambiguously defined (being both positive), the dihedral angles can be
positive or negative. Clearly 300 degrees could equally well be
specified as -60 degrees. A wrong choice of dihedral would mean that
instead of the desired reaction vector being used, a completely
incorrect vector was used, with disastrous results.
To correct this, ensure that one geometry can be obtained from the
other by a continuous deformation, or use the XYZ option.
6.17 HOW TO ESCAPE FROM A HILLTOP
A particularly irritating phenomenon sometimes occurs when a
transition state is being refined. A rough estimate of the geometry of
the transition state has been obtained by either a SADDLE or reaction
path or by good guesswork. This geometry is then refined by SIGMA or by
NLLSQ, and the system characterized by a force calculation. It is at
this point that things often go wrong. Instead of only one negative
force constant, two or more are found. In the past, the recommendation
has been to abandon the work and to go on to something less masochistic.
It is possible, however, to systematically progress from a multiple
maximum to the desired transition state. The technique used will now be
described.
If a multiple maximum is identified, most likely one negative force
constant corresponds to the reaction coordinate, in which case the
objective is to render the other force constants positive. The
associated normal mode eigenvalues are complex, but in the output are
printed as negative frequencies, and for the sake of simplicity will be
described as negative vibrations. Use DRAW-2 to display the negative
vibrations, and identify which mode corresponds to the reaction
coordinate. This is the one we need to retain.
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BACKGROUND Page 6-43
Hitherto, simple motion in the direction of the other modes has
proved difficult. However the DRC provides a convenient mechanism for
automatically following a normal coordinate. Pick the largest of the
negative modes to be annihilated, and run the DRC along that mode until
a minimum is reached. At that point, refine the geometry once more
using SIGMA and repeat the procedure until only one negative mode
exists.
To be on the safe side, after each DRC+SIGMA sequence do the
DRC+SIGMA operation again, but use the negative of the initial normal
coordinate to start the trajectory. After both stationary points are
reached, choose the lower point as the starting point for the next
elimination. The lower point is chosen because the transition state
wanted is the highest point on the lowest energy path connecting
reactants to products. Sometimes the two points will have equal energy:
this is normally a consequence of both trajectories leading to the same
point or symmetry equivalent points.
After all spurious negative modes have been eliminated, the
remaining normal mode corresponds to the reaction coordinate, and the
transition state has been located.
This technique is relatively rapid, and relies on starting from a
stationary point to begin each trajectory. If any other point is used,
the trajectory will not be even roughly simple harmonic. If, by
mistake, the reaction coordinate is selected, then the potential energy
will drop to that of either the reactants or products, which,
incidentally, forms a handy criterion for selecting the spurious modes:
if the potential energy only drops by a small amount, and the time
evolution is roughly simple harmonic, then the mode is one of the
spurious modes. If there is any doubt as to whether a minimum is in the
vicinity of a stationary point, allow the trajectory to continue until
one complete cycle is executed. At that point the geometry should be
near to the initial geometry.
Superficially, a line-search might appear more attractive than the
relatively expensive DRC. However, a line-search in cartesian space
will normally not locate the minimum in a mode. An obvious example is
the mode corresponding to a methyl rotation.
Keyword Sequences to be Used
1. To locate the starting stationary point given an approximate
transition state:-
SIGMA
2. To define the normal modes:-
FORCE ISOTOPE
At this point, copy all the files to a second filename, for use
later.
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BACKGROUND Page 6-44
3. Given vibrational frequencies of -654, -123, 234, and 456,
identify via DRAW-2 the normal coordinate mode, let's say that
is the -654 mode. Eliminate the second mode by:
IRC=2 DRC T=30M RESTART LARGE
Use is made of the FORCE restart file.
4. Identify the minimum in the potential energy surface by
inspection or using the VAX SEARCH command, of form:
SEARCH <Filename>.OUT %
5. Edit out of the output file the data file corresponding to the
lowest point, and refine the geometry using:
SIGMA
6. Repeat the last three steps but for the negative of the normal
mode, using the copied files. The keywords for the first of
the two jobs are:
IRC=-2 DRC T=30M RESTART LARGE
7. Repeat the last four steps as often as there are spurious
modes.
8. Finally, carry out a DRC to confirm that the transition state
does, in fact, connect the reactants and products. The drop in
potential energy should be monotonic. If you are unsure
whether this last operation will work successfully, do it at
any time you have a stationary point. If it fails at the very
start, then we are back where we were last year -- give up and
go home!!
6.18 POLARIZABILITY CALCULATION
If the electrons in a molecule are easily moved as the result of a
stimulus, then the molecule is easily polarizable. Thus, if an applied
electric field can easily induce a dipole, then the polarizability is
large. Any induced dipole will lower the energy of the system, but this
stabilization might be masked by the presence of a permanent dipole. To
avoid this, use is made of an alternating electric field. If the
molecule has an intrinsic dipole, then the molecule will be stabilized
in one direction. When the field is reversed, the molecule will be
destabilized, but, on averaging the two effects, the result is a net
stabilization due only to the induced dipole.
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BACKGROUND Page 6-45
Originally, MOPAC calculated the polarizability of molecules,
radicals, and ions by use of a shaped electric field.
In the current version of MOPAC the polarizability and
hyperpolarizability are calculated by direct perturbation of the
Hamiltonian matrix elements. This technique was developed by
Dr. Henry A. Kurtz of Memphis State University while on a USAF-UES
Summer Faculty Research Program. The following discussion assumes that
a homogeneous electric field gradient exists across the molecule.
The heat of formation of the molecule in this field is then
calculated. This quantity can be expressed as a series sum.
Heat = H.o.F - V*E(Charge) - dV/dx*E(Dipole)
- d2V/dx2*E(polarizability)
That is, the heat of formation in the field is the sum of the basic
heat of formation, less the electric potential times any charge, any
dipole times the electric field gradient, and any polarizability times
the square of the electric field gradient.
We are interested in the polarizability, P.
P = (2/23.061)*d**2H/dE**2
The second derivative of H with respect to E is given by
d**2H/dE**2 = (H(E)+H(-E)-2*H(0))/(2*E),
H(E) being the heat of formation in the electric field.
The polarizability volume, Vol, is calculated from the
polarizability by
Vol=P/(E*4*pi*E(o)) = 2/(E*23.061*4*pi*E(o)) * d**2H/dE**2
Substituting for E we have
Vol=2*l**4*pi*E(o)/(23.061*Q*Q*C*C*(1-1/2**(-1/3))**2) * d**2H/dE**2.
It is a simple matter to evaluate the value of this second-rank tensor
by calculating the heats of formation of the molecule subject to four
different electric field gradients. For the tensor component V(i,j),
i=x or y or z, j=x or y or z, the directions of the four different
fields are defined by.
Field 1 +i, +j Field 2 +i, -j
Field 2 -i, -j Field 4 -i, +j.
Thus if i=x and j=x the four fields are
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BACKGROUND Page 6-46
Field 1 +x
Field 2 0
Field 3 -x
Field 4 0
Using these four heats of formation, in Kcal/mole, the
polarizability can be calculated in units of cubic angstroms via
Vol = (Heat(2)+Heat(4)-Heat(1)-Heat(3))*(l*l*l*l)*2*pi*Eo
23.061 * (1-a) * (1-a) * Q * Q * C * C
1eV is 1.60219 * 10-19 Joules
Eo is 8.854188 * 10-12 Joules**(-1).C**2.M**(-1)
or 8.854188 * 10-22 Joules**(-1).C**2.Angstroms**(-1)
Vol = (eV * l**4 * J**(-1) * C**2 * M**(-1))
C**2
Vol = 2 * 3.1415926 * 8.854188*10-22 / (23.061 * 1.60219*10-19)
=(Heat(2)+Heat(4)-Heat(1)-Heat(3))*0.0015056931*(l*l*l*l)
(1-a)*(1-a)*Q*Q
Monopolar and dipolar terms are eliminated in this treatment.
Finally, monatomic additive terms are included when MNDO is used.
A polarization matrix of size 3 * 3 is constructed and
diagonalized, and the resulting eigenvalues are the calculated
independent polarization volumes in cubic Angstroms; the vectors are the
independent polarization vectors.
6.19 SOLID STATE CAPABILITY
Currently MOPAC can only handle up to one-dimensional extended
systems. As the solid-state method used is unusual, details are given
at this point.
If a polymer unit cell is large enough, then a single point in
k-space, the Gamma point, is sufficient to specify the entire Brillouin
zone. The secular determinant for this point can be constructed by
adding together the Fock matrix for the central unit cell plus those for
the adjacent unit cells. The Born-von Karman cyclic boundary conditions
are satisfied, and diagonalization yields the correct density matrix for
the Gamma point.
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BACKGROUND Page 6-47
At this point in the calculation, conventionally, the density
matrix for each unit cell is constructed. Instead, the Gamma-point
density and one-electron density matrices are combined with a
"Gamma-point-like" Coulomb and exchange integral strings to produce a
new Fock matrix. The calculation can be visualized as being done
entirely in reciprocal space, at the Gamma point.
Most solid-state calculations take a very long time. These
calculations, called "Cluster" calculations after the original
publication, require between 1.3 and 2 times the equivalent molecular
calculation.
A minor "fudge" is necessary to make this method work. The
contribution to the Fock matrix element arising from the exchange
integral between an atomic orbital and its equivalent in the adjacent
unit cells is ignored. This is necessitated by the fact that the
density matrix element involved is invariably large.
The unit cell must be large enough that an atomic orbital in the
center of the unit cell has an insignificant overlap with the atomic
orbitals at the ends of the unit cell. In practice, a translation
vector of more that about 7 or 8 Angstroms is sufficient. For one rare
group of compounds a larger translation vector is needed. Polymers with
delocalized pi-systems, and polymers with very small band-gaps will
require a larger translation vector, in order to accurately sample
k-space. For these systems, a translation vector in the order of 15-20
Angstroms is needed.
- 127 -
CHAPTER 7
PROGRAM
The logic within MOPAC is best understood by use of flow-diagrams.
There are two main sequences, geometric and electronic. These join
only at one common subroutine COMPFG. It is possible, therefore, to
understand the geometric or electronic sections in isolation, without
having studied the other section.
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PROGRAM Page 7-2
7.1 MAIN GEOMETRIC SEQUENCE
______
MAIN
______
___________________________________________________
______ _________ ______
______
IRC/DRC FORCE REACT1 PATHS
or
EF __________ __________ _______
or
POLAR
_______ __ _______________
______ _____ ______
NLLSQ ____________
and FMAT FLEPO
POWSQ
_______ ______ _______
_______ _______
SEARCH
or LINMIN
LOCMIN
________ ________
___________________________________________
_______
COMPFG (See ELECTRONIC SEQUENCE)
________
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PROGRAM Page 7-3
7.2 MAIN ELECTRONIC FLOW
________
COMPFG (See GEOMETRIC SEQUENCE)
________
___________________________________
______ ______ _______
HCORE _______ DERIV ____ GMETRY
_______ _______ SYMTRY
______ ________
DCART
_______ ______ _______
____ ____ _________
DHC ____ ITER ____ RSP
_____ ______ _________
___ __ ________
______ _____ ______ DENSIT
ROTATE FOCK1 CNVG
PULAY
H1ELEC FOCK2 ________
________ _______ _____
_____ MECI
DIAT ______
______
___
SS
____
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PROGRAM Page 7-4
7.3 CONTROL WITHIN MOPAC
Almost all the control information is passed via the single datum
"KEYWRD", a string of 80 characters, which is read in at the start of
the job.
Each subroutine is made independent, as far as possible, even at
the expense of extra code or calculation. Thus, for example, the SCF
criterion is set in subroutine ITER, and nowhere else. Similarly,
subroutine DERIV has exclusive control of the step size in the
finite-difference calculation of the energy derivatives. If the default
values are to be reset, then the new value is supplied in KEYWRD, and
extracted via INDEX and READA. The flow of control is decided by the
presence of various keywords in KEYWRD.
When a subroutine is called, it assumes that all data required for
its operation are available in either common blocks or arguments.
Normally no check is made as to the validity of the data received. All
data are "owned" by one, and only one, subroutine. Ownership means the
implied permission and ability to change the data. Thus MOLDAT "owns"
the number of atomic orbitals, in that it calculates this number, and
stores it in the variable NORBS. Many subroutines use NORBS, but none
of them is allowed to change it. For obvious reasons no exceptions
should be made to this rule. To illustrate the usefulness of this
convention, consider the eigenvectors, C and CBETA. These are owned by
ITER. Before ITER is called, C and CBETA are not calculated, after ITER
has been called C and CBETA are known, so any subroutine which needs to
use the eigenvectors can do so in the certain knowledge that they exist.
Any variables which are only used within a subroutine are not
passed outside the subroutine unless an overriding reason exists. This
is found in PULAY and CNVG, among others where arrays used to hold
spin-dependent data are used, and these cannot conveniently be defined
within the subroutines. In these examples, the relevant arrays are
"owned" by ITER.
A general subroutine, of which ITER is a good example, handles
three kinds of data: First, data which the subroutine is going to work
on, for example the one and two electron matrices; second, data
necessary to manipulate the first set of data, such as the number of
atomic orbitals; third, the calculated quantities, here the electronic
energy, and the density and Fock matrices.
Reference data are entered into a subroutine by way of the common
blocks. This is to emphasize their peripheral role. Thus the number of
orbitals, while essential to ITER, is not central to the task it has to
perform, and is passed through a common block.
Data the subroutine is going to work on are passed via the argument
list. Thus the one and two electron matrices, which are the main reason
for ITER's existence, are entered as two of the four arguments. As ITER
does not own these matrices it can use them but may not change their
contents. The other argument is EE, the electronic energy. EE is owned
by ITER even though it first appears before ITER is called.
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PROGRAM Page 7-5
Sometimes common block data should more correctly appear in an
argument list. This is usually not done in order to prevent obscuring
the main role the subroutine has to perform. Thus ITER calculates the
density and Fock matrices, but these are not represented in the argument
list as the calling subroutine never needs to know them; instead, they
are stored in common.
SUBROUTINE GMETRY: Description for programmers.
GMETRY has two arguments, GEO and COORD. On input GEO contains
either (a) internal coordinates or (b) cartesian coordinates. On exit
COORD contains the cartesian coordinates.
The normal mode of usage is to supply the internal coordinates, in
which case the connectivity relations are found in common block GEOKST.
If the contents of NA(1) is zero, as required for any normal
system, then the normal internal to cartesian conversion is carried out.
If the contents of NA(1) is 99, then the coordinates found in GEO
are assumed to be cartesian, and no conversion is made. This is the
situation in a FORCE calculation.
A further option exists within the internal to cartesian
conversion. If STEP, stored in common block REACTN, is non-zero, then a
reaction path is assumed, and the internal coordinates are adjusted
radially in order that the "distance" in internal coordinate space from
the geometry specified in GEO is STEPP away from the geometry stored in
GEOA, stored in REACTN.
During the internal to cartesian conversion, the angle between the
three atoms used in defining a fourth atom is checked to ensure that it
is not near to 0 or 180 degrees. If it is near to these angles, then
there is a high probability that a faulty geometry will be generated and
to prevent this the calculation is stopped and an error message printed.
NOTE 1: If the angle is exactly 0 or 180 degrees, then the
calculation is not terminated: This is the normal situation in a
high-symmetry molecule such as propyne.
NOTE 2: The check is only made if the fourth atom has a bond angle
which is not zero or 180 degrees.
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CHAPTER 8
ERROR MESSAGES PRODUCED BY MOPAC
MOPAC produces several hundred messages, all of which are intended
to be self-explanatory. However, when an error occurs it is useful to
have more information than is given in the standard messages.
The following alphabetical list gives more complete definitions of
the messages printed.
AN UNOPTIMIZABLE GEOMETRIC PARAMETER....
When internal coordinates are supplied, six coordinates cannot be
optimized. These are the three coordinates of atom 1, the angle and
dihedral on atom 2 and the dihedral on atom 3. An attempt has been made
to optimize one of these. This is usually indicative of a typographic
error, but might simply be an oversight. Either way, the error will be
corrected and the calculation will not be stopped here.
ATOM NUMBER nn IS ILLDEFINED
The rules for definition of atom connectivity are:
1. Atom 2 must be connected to atom 1 (default - no override)
2. Atom 3 must be connected to atom 1 or 2, and make an angle with
2 or 1.
3. All other atoms must be defined in terms of already-defined
atoms: these atoms must all be different. Thus atom 9 might
be connected to atom 5, make an angle with atom 6, and have a
dihedral with atom 7. If the dihedral was with atom 5, then
the geometry definition would be faulty.
If any of these rules is broken, a fatal error message is printed,
and the calculation stopped.
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ERROR MESSAGES PRODUCED BY MOPAC Page 8-2
ATOMIC NUMBER nn IS NOT AVAILABLE ...
An element has been used for which parameters are not available.
Only if a typographic error has been made can this be rectified. This
check is not exhaustive, in that even if the elements are acceptable
there are some combinations of elements within MINDO/3 that are not
allowed. This is a fatal error message.
ATOMIC NUMBER OF nn ?
An atom has been specified with a negative or zero atomic number.
This is normally caused by forgetting to specify an atomic number or
symbol. This is a fatal error message.
ATOMS nn AND nn ARE SEPARATED BY nn.nnnn ANGSTROMS.
Two genuine atoms (not dummies) are separated by a very small
distance. This can occur when a complicated geometry is being
optimized, in which case the user may wish to continue. This can be
done by using the keyword GEO-OK. More often, however, this message
indicates a mistake, and the calculation is, by default, stopped.
ATTEMPT TO GO DOWNHILL IS UNSUCCESSFUL...
A quite rare message, produced by Bartel's gradient norm
minimization. Bartel's method attempts to minimize the gradient norm by
searching the gradient space for a minimum. Apparently a minimum has
been found, but not recognized as such. The program has searched in all
(3N-6) directions, and found no way down, but the criteria for a minimum
have not been satisfied. No advice is available for getting round this
error.
BOTH SYSTEMS ARE ON THE SAME SIDE...
A non-fatal message, but still cause for concern. During a SADDLE
calculation the two geometries involved are on opposite sides of the
transition state. This situation is verified at every point by
calculating the cosine of the angle between the two gradient vectors.
For as long as it is negative, then the two geometries are on opposite
sides of the T/S. If, however, the cosine becomes positive, then the
assumption is made that one moiety has fallen over the T/S and is now
below the other geometry. That is, it is now further from the T/S than
the other, temporarily fixed, geometry. To correct this, identify
geometries corresponding to points on each side of the T/S. (Two
geometries on the output separated by the message "SWAPPING...") and
make up a new data-file using these geometries. This corresponds to
points on the reaction path near to the T/S. Run a new job using these
two geometries, but with BAR set to a third or a quarter of its original
value, e.g. BAR=0.05. This normally allows the T/S to be located.
- 134 -
ERROR MESSAGES PRODUCED BY MOPAC Page 8-3
C.I. NOT ALLOWED WITH UHF
There is no UHF configuration interaction calculation in MOPAC.
Either remove the keyword that implies C.I. or the word UHF.
CALCULATION ABANDONED AT THIS POINT
A particularly annoying message! In order to define an atom's
position, the three atoms used in the connectivity table must not
accidentally fall into a straight line. This can happen during a
geometry optimization or gradient minimization. If they do, and if the
angle made by the atom being defined is not zero or 180 degrees, then
its position becomes ill-defined. This is not desirable, and the
calculation will stop in order to allow corrective action to be taken.
Note that if the three atoms are in an exactly straight line, this
message will not be triggered. The good news is that the criterion used
to trigger this message was set too coarsely. The criterion has been
tightened so that this message now does not often appear. Geometric
integrity does not appear to be compromized.
CARTESIAN COORDINATES READ IN, AND CALCULATION...
If cartesian coordinates are read in, but the calculation is to be
carried out using internal coordinates, then either all possible
geometric variables must be optimized, or none can be optimized. If
only some are marked for optimization then ambiguity exists. For
example, if the "X" coordinate of atom 6 is marked for optimization, but
the "Y" is not, then when the conversion to internal coordinates takes
place, the first coordinate becomes a bond-length, and the second an
angle. These bear no relationship to the "X" or "Y" coordinates. This
is a fatal error.
CARTESIAN COORDINATES READ IN, AND SYMMETRY...
If cartesian coordinates are read in, but the calculation is to be
carried out using internal coordinates, then any symmetry relationships
between the cartesian coordinates will not be reflected in the internal
coordinates. For example, if the "Y" coordinates of atoms 5 and 6 are
equal, it does not follow that the internal coordinate angles these
atoms make are equal. This is a fatal error.
ELEMENT NOT FOUND
When an external file is used to redefine MNDO, AM1, or PM3
parameters, the chemical symbols used must correspond to known elements.
Any that do not will trigger this fatal message.
- 135 -
ERROR MESSAGES PRODUCED BY MOPAC Page 8-4
ERROR DURING READ AT ATOM NUMBER ....
Something is wrong with the geometry data. In order to help find
the error, the geometry already read in is printed. The error lies
either on the last line of the geometry printed, or on the next
(unprinted) line. This is a fatal error.
FAILED IN SEARCH, SEARCH CONTINUING
Not a fatal error. The McIver-Komornicki gradient minimization
involves use of a line-search to find the lowest gradient. This message
is merely advice. However, if SIGMA takes a long time, consider doing
something else, such as using NLLSQ, or refining the geometry a bit
before resubmitting it to SIGMA.
<<<<----**** FAILED TO ACHIEVE SCF. ****---->>>>
The SCF calculation failed to go to completion; an unwanted and
depressing message that unfortunately appears every so often.
To date three unconditional convergers have appeared in the
literature: the SHIFT technique, Pulay's method, and the Camp-King
converger. It would not be fair to the authors to condemn their
methods. In MOPAC all sorts of weird and wonderful systems are
calculated, systems the authors of the convergers never dreamed of.
MOPAC uses a combination of all three convergers at times. Normally
only a quadratic damper is used.
If this message appears, suspect first that the calculation might
be faulty, then, if you feel confident, use PL to monitor a single SCF.
Based on the SCF results either increase the number of allowed
iterations, default: 200, or use PULAY, or Camp-King, or a mixture.
If nothing works, then consider slackening the SCF criterion. This
will allow heats of formation to be calculated with reasonable
precision, but the gradients are likely to be imprecise.
GEOMETRY TOO UNSTABLE FOR EXTRAPOLATION..
In a reaction path calculation the initial geometry for a point is
calculated by quadratic extrapolation using the previous three points.
If a quadratic fit is likely to lead to an inferior geometry, then
the geometry of the last point calculated will be used. The total
effect is to slow down the calculation, but no user action is
recommended.
- 136 -
ERROR MESSAGES PRODUCED BY MOPAC Page 8-5
** GRADIENT IS TOO LARGE TO ALLOW...
Before a FORCE calculation can be performed the gradient norm must
be so small that the third and higher order components of energy in the
force field are negligible. If, in the system under examination, the
gradient norm is too large, the gradient norm will first be reduced
using FLEPO, unless LET has been specified. In some cases the FORCE
calculation may be run only to decide if a state is a ground state or a
transition state, in which case the results have only two
interpretations. Under these circumstances, LET may be warranted.
GRADIENT IS VERY LARGE...
In a calculation of the thermodynamic properties of the system, if
the rotation and translation vibrations are non-zero, as would be the
case if the gradient norm was significant, then these "vibrations" would
interfere with the low-lying genuine vibrations. The criteria for
THERMO are much more stringent than for a vibrational frequency
calculation, as it is the lowest few genuine vibrations that determine
the internal vibrational energy, entropy, etc.
ILLEGAL ATOMIC NUMBER
An element has been specified by an atomic number which is not in
the range 1 to 107. Check the data: the first datum on one of the
lines is faulty. Most likely line 4 is faulty.
IMPOSSIBLE NUMBER OF OPEN SHELL ELECTRONS
The keyword OPEN(n1,n2) has been used, but for an even-electron
system n1 was specified as odd or for an odd-electron system n1 was
specified as even. Either way, there is a conflict which the user must
resolve.
IMPOSSIBLE OPTION REQUESTED
A general catch-all. This message will be printed if two
incompatible options are used, such as both MINDO/3 and AM1 being
specified. Check the keywords, and resolve the conflict.
INTERNAL COORDINATES READ IN, AND CALCULATION...
If internal coordinates are read in, but the calculation is to be
carried out using cartesian coordinates, then either all possible
geometric variables must be optimized, or none can be optimized. If
only some are marked for optimization, then ambiguity exists. For
example, if the bond-length of atom 6 is marked for optimization, but
the angle is not, then when the conversion to cartesian coordinates
takes place, the first coordinate becomes the "X" coordinate and the
second the "Y" coordinate. These bear no relationship to the bond
length or angle. This is a fatal error.
- 137 -
ERROR MESSAGES PRODUCED BY MOPAC Page 8-6
INTERNAL COORDINATES READ IN, AND SYMMETRY...
If internal coordinates are read in, but the calculation is to be
carried out using cartesian coordinates, then any symmetry relationships
between the internal coordinates will not be reflected in the cartesian
coordinates. For example, if the bond-lengths of atoms 5 and 6 are
equal, it does not follow that these atoms have equal values for their
"X" coordinates. This is a fatal error.
JOB STOPPED BY OPERATOR
Any MOPAC calculation, for which the SHUTDOWN command works, can be
stopped by a user who issues the command "$SHUT <filename>, from the
directory which contains <filename>.DAT
MOPAC will then stop the calculation at the first convenient point,
usually after the current cycle has finished. A restart file will be
written and the job ended. The message will be printed as soon as it is
detected, which would be the next time the timer routine is accessed.
**** MAX. NUMBER OF ATOMS ALLOWED:....
At compile time the maximum sizes of the arrays in MOPAC are fixed.
The system being run exceeds the maximum number of atoms allowed. To
rectify this, modify the file DIMSIZES.DAT to increase the number of
heavy and light atoms allowed. If DIMSIZES.DAT is altered, then the
whole of MOPAC should be re-compiled and re-linked.
**** MAX. NUMBER OF ORBITALS:....
At compile time the maximum sizes of the arrays in MOPAC are fixed.
The system being run exceeds the maximum number of orbitals allowed. To
rectify this, modify the file DIMSIZES.DAT to change the number of heavy
and light atoms allowed. If DIMSIZES.DAT is altered, then the whole of
MOPAC should be re-compiled and re-linked.
**** MAX. NUMBER OF TWO ELECTRON INTEGRALS..
At compile time the maximum sizes of the arrays in MOPAC are fixed.
The system being run exceeds the maximum number of two-electron
integrals allowed. To rectify this, modify the file DIMSIZES.DAT to
modify the number of heavy and light atoms allowed. If DIMSIZES.DAT is
altered, then the whole of MOPAC should be re-compiled and re-linked.
NAME NOT FOUND
Various atomic parameters can be modified in MOPAC by use of
EXTERNAL=. These comprise
Uss Betas Gp2 GSD
Upp Betap Hsp GPD
Udd Betad AM1 GDD
Zs Gss Expc FN1
Zp Gsp Gaus FN2
Zd Gpp Alp FN3
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ERROR MESSAGES PRODUCED BY MOPAC Page 8-7
Thus to change the Uss of hydrogen to -13.6 the line
USS H -13.6
could be used. If an attempt is made to modify any other parameters,
then an error message is printed, and the calculation terminated.
NUMBER OF PARTICLES, nn GREATER THAN...
When user-defined microstates are not used, the MECI will calculate
all possible microstates that satisfy the space and spin constraints
imposed. This is done in PERM, which permutes N electrons in M levels.
If N is greater than M, then no possible permutation is valid. This is
not a fatal error - the program will continue to run, but no C.I. will
be done.
NUMBER OF PERMUTATIONS TOO GREAT, LIMIT 60
The number of permutations of alpha or beta microstates is limited
to 60. Thus if 3 alpha electrons are permuted among 5 M.O.'s, that will
generate 10 = 5!/(3!*2!) alpha microstates, which is an allowed number.
However if 4 alpha electrons are permuted among 8 M.O.'s, then 70 alpha
microstates result and the arrays defined will be insufficient. Note
that 60 alpha and 60 beta microstates will permit 3600 microstates in
all, which should be more than sufficient for most purposes. (An
exception would be for excited radical icosohedral systems.)
SYMMETRY SPECIFIED, BUT CANNOT BE USED IN DRC
This is self explanatory. The DRC requires all geometric
constraints to be lifted. Any symmetry constraints will first be
applied, to symmetrize the geometry, and then removed to allow the
calculation to proceed.
SYSTEM DOES NOT APPEAR TO BE OPTIMIZABLE
This is a gradient norm minimization message. These routines will
only work if the nearest minimum to the supplied geometry in
gradient-norm space is a transition state or a ground state. Gradient
norm space can be visualized as the space of the scalar of the
derivative of the energy space with respect to geometry. To a first
approximation, there are twice as many minima in gradient norm space as
there are in energy space.
It is unlikely that there exists any simple way to refine a
geometry that results in this message. While it is appreciated that a
large amount of effort has probably already been expended in getting to
this point, users should steel themselves to writing off the whole
geometry. It is not recommended that a minor change be made to the
geometry and the job re-submitted.
Try using SIGMA instead of POWSQ.
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ERROR MESSAGES PRODUCED BY MOPAC Page 8-8
TEMPERATURE RANGE STARTS TOO LOW,...
The thermodynamics calculation assumes that the statistical
summations can be replaced by integrals. This assumption is only valid
above 100K, so the lower temperature bound is set to 100, and the
calculation continued.
THERE IS A RISK OF INFINITE LOOPING...
The SCF criterion has been reset by the user, and the new value is
so small that the SCF test may never be satisfied. This is a case of
user beware!
THIS MESSAGE SHOULD NEVER APPEAR, CONSULT A PROGRAMMER!
This message should never appear; a fault has been introduced into
MOPAC, most probably as a result of a programming error. If this
message appears in the vanilla version of MOPAC (a version ending in
00), please contact JJPS as I would be most interested in how this was
achieved.
THREE ATOMS BEING USED TO DEFINE....
If the cartesian coordinates of an atom depend on the dihedral
angle it makes with three other atoms, and those three atoms fall in an
almost straight line, then a small change in the cartesian coordinates
of one of those three atoms can cause a large change in its position.
This is a potential source of trouble, and the data should be changed to
make the geometric specification of the atom in question less ambiguous.
This message can appear at any time, particularly in reaction path
and saddle-point calculations.
An exception to this rule is if the three atoms fall into an
exactly straight line. For example, if, in propyne, the hydrogens are
defined in terms of the three carbon atoms, then no error will be
flagged. In such a system the three atoms in the straight line must not
have the angle between them optimized, as the finite step in the
derivative calculation would displace one atom off the straight line and
the error-trap would take effect.
Correction involves re-defining the connectivity. LET and GEO-OK
will not allow the calculation to proceed.
- - - - - - - TIME UP - - - - - - -
The time defined on the keywords line or 3,600 seconds, if no time
was specified, is likely to be exceeded if another cycle of calculation
were to be performed. A controlled termination of the run would follow
this message. The job may terminate earlier than expected: this is
ordinarily due to one of the recently completed cycles taking unusually
long, and the safety margin has been increased to allow for the
possibility that the next cycle might also run for much longer than
expected.
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ERROR MESSAGES PRODUCED BY MOPAC Page 8-9
TRIPLET SPECIFIED WITH ODD NUMBER OF ELECTRONS.
If TRIPLET has been specified the number of electrons must be even.
Check the charge on the system, the empirical formula, and whether
TRIPLET was intended.
""""""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCY
See the error-message:
<<<<----**** FAILED TO ACHIEVE SCF. ****---->>>>
UNDEFINED SYMMETRY FUNCTION USED
Symmetry operations are restricted to those defined, i.e., in the
range 1-18. Any other symmetry operations will trip this fatal message.
UNRECOGNIZED ELEMENT NAME
In the geometric specification a chemical symbol which does not
correspond to any known element has been used. The error lies in the
first datum on a line of geometric data.
**** WARNING ****
Don't pay too much attention to this message. Thermodynamics
calculations require a higher precision than vibrational frequency
calculations. In particular, the gradient norm should be very small.
However, it is frequently not practical to reduce the gradient norm
further, and to date no-one has determined just how slack the gradient
criterion can be before unacceptable errors appear in the thermodynamic
quantities. The 0.4 gradient norm is only a suggestion.
WARNING: INTERNAL COORDINATES...
Triatomics are, by definition, defined in terms of internal
coordinates. This warning is only a reminder. For diatomics, cartesian
and internal coordinates are the same. For tetra-atomics and higher,
the presence or absence of a connectivity table distinguishes internal
and cartesian coordinates, but for triatomics there is an ambiguity. To
resolve this, cartesian coordinates are not allowed for the data input
for triatomics.
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CHAPTER 9
CRITERIA
MOPAC uses various criteria which control the precision of its
stages. These criteria are chosen as the best compromise between speed
and acceptable errors in the results. The user can override the default
settings by use of keywords; however, care should be exercised as
increasing a criterion can introduce the potential for infinite loops,
and decreasing a criterion can result in unacceptably imprecise results.
These are usually characterized by 'noise' in a reaction path, or large
values for the trivial vibrations in a force calculation.
9.1 SCF CRITERION
Name: SCFCRT.
Defined in ITER.
Default value 0.0001 kcal/mole
Basic Test Change in energy in kcal/mole on successive
iterations is less than SCFCRT.
Exceptions: If PRECISE is specified, SCFCRT=0.000001
If a polarization calculation SCFCRT=1.D-11
If a FORCE calculation SCFCRT=0.0000001
If SCFCRT=n.nnn is specified SCFCRT=n.nnn
If a BFGS optimization, SCFCRT becomes a function
of the difference between the current energy and
the lowest energy of previous SCFs.
Secondary tests: (1) Change in density matrix elements on two
successive iterations must be less than 0.001
(2) Change in energy in eV on three successive
iterations must be less than 10 x SCFCRT.
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CRITERIA Page 9-2
9.2 GEOMETRIC OPTIMIZATION CRITERIA
Name: TOLERX "Test on X Satisfied"
Defined in FLEPO
Default value 0.0001 Angstroms
Basic Test The projected change in geometry is less than
TOLERX Angstroms.
Exceptions If GNORM is specified, the TOLERX test is not used.
Name: DELHOF "Herbert's Test Satisfied"
Defined in FLEPO
Default value 0.001
Basic Test The projected decrease in energy is less than
DELHOF Kcals/mole.
Exceptions If GNORM is specified, the DELHOF test is not used.
Name: TOLERG "Test on Gradient Satisfied"
Defined in FLEPO
Default value 1.0
Basic Test The gradient norm in Kcals/mole/Angstrom is less
than TOLERG multiplied by the square root of the
number of coordinates to be optimized.
Exceptions If GNORM=n.nnn is specified, TOLERG=n.nnn divided
by the square root of the number of coordinates
to be optimized, and the secondary tests are not
done. If LET is not specified, n.nnn is reset to
0.01, if it was smaller than 0.01.
If PRECISE is specified, TOLERG=0.2
If a SADDLE calculation, TOLERG is made a function
of the last gradient norm.
Name: TOLERF "Heat of Formation Test Satisfied"
Defined in FLEPO
Default value 0.002 Kcal/mole
Basic Test The calculated heats of formation on two successive
cycles differ by less than TOLERF.
Exceptions If GNORM is specified, the TOLERF test is not used.
Secondary Tests For the TOLERG, TOLERF, and TOLERX tests, a
second test in which no individual component of the
gradient should be larger than TOLERG must be
satisfied.
Other Tests If, after the TOLERG, TOLERF, or TOLERX test has been
satisfied three consecutive times the heat of
formation has dropped by less than 0.3Kcal/mole, then
the optimization is stopped.
Exceptions If GNORM is specified, then this test is not performed.
Name: TOL2
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CRITERIA Page 9-3
Defined in POWSQ
Default value 0.4
Basic Test The absolute value of the largest component of the
gradient is less than TOL2
Exceptions If PRECISE is specified, TOL2=0.01
If GNORM=n.nn is specified, TOL2=n.nn
If LET is not specified, TOL2 is reset to
0.01, if n.nn was smaller than 0.01.
Name: TOLS1
Defined in NLLSQ
Default Value 0.000 000 000 001
Basic Test The square of the ratio of the projected change in the
geometry to the actual geometry is less than TOLS1.
Name: <none>
Defined in NLLSQ
Default Value 0.2
Basic Test Every component of the gradient is less than 0.2.
- 144 -
CHAPTER 10
DEBUGGING
There are three potential sources of difficulty in using MOPAC,
each of which requires special attention. There can be problems with
data, due to errors in the data, or MOPAC may be called upon to do
calculations for which it was not designed. There are intrinsic errors
in MOPAC which extensive testing has not yet revealed, but which a
user's novel calculation uncovers. Finally there can be bugs introduced
by the user modifying MOPAC, either to make it compatible with the host
computer, or to implement local features.
For whatever reason, the user may need to have access to more
information than the normal keywords can provide, and a second set,
specifically for debugging, is provided. These keywords give
information about the working of individual subroutines, and do not
affect the course of the calculation.
10.1 DEBUGGING KEYWORDS
FULL LIST OF KEYWORDS FOR DEBUGGING SUBROUTINES
INFORMATION PRINTED
1ELEC the one-electron matrix. Note 1
COMPFG Heat of Formation.
DCART Cartesian derivatives.
DEBUG Note 2
DEBUGPULAY Pulay matrix, vector, and error-function. Note 3
DENSITY Every density matrix. Note 1
DERI1 Details of DERI1 calculation
DERI2 Details of DERI2 calculation
DERITR Details of DERITR calculation
DERIV All gradients, and other data in DERIV.
DERNVO Details of DERNVO calculation
DFORCE Print Force Matrix.
DIIS Details of DIIS calculation
EIGS All eigenvalues.
FLEPO Details of BFGS minimization.
FMAT
FOCK Every Fock matrix Note 1
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DEBUGGING Page 10-2
HCORE The one electron matrix, and two electron integrals.
ITER Values of variables and constants in ITER.
LARGE Increases amount of output generated by other keywords.
LINMIN Details of line minimization (LINMIN, LOCMIN, SEARCH)
MOLDAT Molecular data, number of orbitals, "U" values, etc.
MECI C.I. matrices, M.O. indices, etc.
PL Differences between density matrix elements Note 4
in ITER.
LINMIN Function values, step sizes at all points in the
line minimization (LINMIN or SEARCH).
TIMES Times of stages within ITER.
VECTORS All eigenvectors on every iteration. Note 1
NOTES
1. These keywords are activated by the keyword DEBUG. Thus if
DEBUG and FOCK are both specified, every Fock matrix on every
iteration will be printed.
2. DEBUG is not intended to increase the output, but does allow
other keywords to have a special meaning.
3. PULAY is already a keyword, so DEBUGPULAY was an obvious
alternative.
4. PL initiates the output of the value of the largest difference
between any two density matrix elements on two consecutive
iterations. This is very useful when investigating options for
increasing the rate of convergence of the SCF calculation.
SUGGESTED PROCEDURE FOR LOCATING BUGS
Users are supplied with the source code for MOPAC, and, while the
original code is fairly bug-free, after it has been modified there is a
possibility that bugs may have been introduced. In these circumstances
the author of the changes is obviously responsible for removing the
offending bug, and the following ideas might prove useful in this
context.
First of all, and most important, before any modifications are done
a back-up copy of the standard MOPAC should be made. This will prove
invaluable in pinpointing deviations from the standard working. This
point cannot be over-emphasized - MAKE A BACK-UP BEFORE MODIFYING
MOPAC!!!!
Clearly, a bug can occur almost anywhere, and a logical search
sequence is necessary in order to minimize the time taken to locate it.
If possible, perform the debugging with a small molecule, in order
to save time (debugging is, of necessity, time consuming) and to
minimize output.
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DEBUGGING Page 10-3
The two sets of subroutines in MOPAC, those involved with the
electronics and those involved in the geometrics, are kept strictly
separate, so the first question to be answered is which set contains the
bug. If the heats of formation, derivatives, I.P.s, and charges, etc.,
are correct, the bug lies in the geometrics; if faulty, in the
electronics.
Bug in the Electronics Subroutines.
Use formaldehyde for this test. The supplied data-file MNRSD1.DAT
could be used as a template for this operation. Use keywords 1SCF,
DEBUG, and any others necessary.
The main steps are:
(1) Check the starting one-electron matrix and two-electron
integral string, using the keyword HCORE. It is normally sufficient to
verify that the two hydrogen atoms are equivalent, and that the pi
system involves only pz on oxygen and carbon. Note that numerical
values are not checked, but only relative values.
If an error is found, use MOLDAT to verify the orbital character,
etc.
If faulty the error lies in READ, GETGEO or MOLDAT.
Otherwise the error lies in HCORE, H1ELEC or ROTATE.
If the starting matrices are correct, go on to step (2).
(2) Check the density or Fock matrix on every iteration, with the
words FOCK or DENSITY. Check the equivalence of the two hydrogen atoms,
and the pi system, as in (1).
If an error is found, check the first Fock matrix. If faulty, the
bug lies in ITER, probably in the Fock subroutines FOCK1 or FOCK2. or
in the (guessed) density matrix (MOLDAT). An exception is in the UHF
closed-shell calculation, where a small asymmetry is introduced to
initiate the separation of the alpha and beta UHF wavefunctions.
If no error is found, check the second Fock matrix. If faulty, the
error lies in the density matrix DENSIT, or the diagonalization RSP.
If the Fock matrix is acceptable, check all the Fock matrices. If
the error starts in iterations 2 to 4, the error probably lies in CNVG,
if after that, in PULAY, if used.
If SCF is achieved, and the heat of formation is faulty, check
HELECT. If C.I. was used check MECI.
If the derivatives are faulty, use DCART to verify the cartesian
derivatives. If these are faulty, check DCART and DHC. If they are
correct, or not calculated, check the DERIV finite difference
calculation. If the wavefunction is non-variationally optimized, check
DERNVO.
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DEBUGGING Page 10-4
If the geometric calculation is faulty, use FLEPO to monitor the
optimization, DERIV may also be useful here.
For the FORCE calculation, DCART or DERIV are useful for
variationally optimized functions, COMPFG for non-variationally
optimized functions.
For reaction paths, verify that FLEPO is working correctly; if so,
then PATHS is faulty.
For saddle-point calculations, verify that FLEPO is working
correctly; if so, then REACT1 is faulty.
Keep in mind the fact that MOPAC is a large calculation, and while
intended to be versatile, many combinations of options have not been
tested. If a bug is found in the original code, please communicate
details to the Academy, to Dr. James J. P. Stewart, Frank J. Seiler
Research Laboratory, U.S. Air Force Academy, Colorado Springs, CO
80840-6528.
- 148 -
CHAPTER 11
INSTALLING MOPAC
MOPAC is distributed on a magnetic tape as a set of FORTRAN-77
files, along with ancillary documents such as command, help, data and
results files. The format of the tape is that of DIGITAL'S VAX
computers. The following instructions apply only to users with VAX
computers: users with other machines should use the following
instructions as a guide to getting MOPAC up and running.
1. Put the magnetic tape on the tape drive, write protected.
2. Allocate the tape drive with a command such as $ALLOCATE MTA0:
3. Go into an empty directory which is to hold MOPAC
4. Mount the magnetic tape with the command $MOUNT MTA0: MOPAC
5. Copy all the files from the tape with the command
$COPY MTA0:*.* *
A useful operation after this would be to make a hard copy of the
directory. You should now have the following sets of files in the
directory:
1. A file, AAAINVOICE.TXT, summarizing this list.
2. A set of FORTRAN-77 files, see Appendix 1.
3. The command files COMPILE, MOPACCOM, MOPAC, RMOPAC, and SHUT.
4. A file, MOPAC.OPT, which lists all the object modules used by
MOPAC.
5. Help files MOPAC.HLP and HELP.FOR
6. A text file MOPAC.MAN.
7. A manual summarizing the updates, called UPDATE.MAN.
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INSTALLING MOPAC Page 11-2
8. Two test-data files: TESTDATA.DAT and MNRSD1.DAT, and
corresponding results files, TESTDATA.OUT and MNRSD1.OUT.
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INSTALLING MOPAC Page 11-3
STRUCTURE OF COMMAND FILES
COMPILE
The parameter file DIMSIZES.DAT should be read and, if necessary,
modified before COMPILE is run.
DO NOT RUN COMPILE AT THIS TIME!!
COMPILE should be run once only. It assigns DIMSIZES.DAT, the
block of FORTRAN which contains the PARAMETERS for the dimension sizes
to the logical name "SIZES". This is a temporary assignment, but the
user is strongly recommended to make it permanent by suitably modifying
LOGIN file(s). COMPILE is a modified version of Maj Donn Storch's
COMPILE for DRAW-2.
All the FORTRAN files are then compiled, using the array sizes
given in DIMSIZES.DAT: these should be modified before COMPILE is run.
If, for whatever reason, DIMSIZES.DAT needs to be changed, then COMPILE
should be re-run, as modules compiled with different DIMSIZES.DAT will
be incompatible.
The parameters within DIMSIZES.DAT that the user can modify are
MAXLIT, MAXHEV, MAXTIM and MAXDMP. MAXLIT is assigned a value equal to
the largest number of hydrogen atoms that a MOPAC job is expected to
run, MAXHEV is assigned the corresponding number of heavy (non-hydrogen)
atoms. The ratio of light to heavy atoms should not be less than 1/2.
Do not set MAXHEV or MAXLIT less than 7. If you do, some subroutines
will not compile correctly. Some molecular orbital eigenvector arrays
are overlapped with Hessian arrays, and to prevent compilation time
error messages, the number of allowed A.O.'s must be greater than, or
equal to three times the number of allowed real atoms. MAXTIM is the
default maximum time in seconds a job is allowed to run before either
completion or a restart file being written. MAXDMP is the default time
in seconds for the automatic writing of the restart files. If your
computer is very reliable, and disk space is at a premium, you might
want to set MAXDMP as MAXDMP=999999.
If SYBYL output is wanted, set ISYBYL to 1, otherwise set it to
zero.
If you want, NMECI can be changed. Setting it to 1 will save some
space, but will prevent all C.I. calculations except simple radicals.
If you want, NPULAY can be set to 1. This saves memory, but also
disables the PULAY converger.
If you want, MESP can be varied. This is only meaningful if ESP is
installed.
Compile MOPAC. This operation takes about 7 minutes, and should be
run "on-line", as a question and answer session is involved.
When everything is successfully compiled, the object files will
then be assembled into an executable image called MOPAC.EXE. Once the
image exists, there is no reason to keep the object files, and if space
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INSTALLING MOPAC Page 11-4
is at a premium these can be deleted at this time.
If you need to make any changes to any of the files, COMPILE
followed by the names of the changed files will reconstruct MOPAC,
provided all the other OBJ files exist. For example, if you change the
version number in DIMSIZES.DAT, then READ.FOR and WRITE.FOR are affected
and will need to be recompiled. This can be done using the command
@COMPILE WRITE,READ
In the unlikely event that you want to link only, use the command
@COMPILE LINK
Sometimes the link stage will fail, and give the message
"%LINK-E-INSVIRMEM, insufficient virtual memory for 2614711. pages
-LINK-E-NOIMGFIL, image file not created",
or your MOPAC will not run due to the size of the image. In these cases
you should ask the system manager to alter your PGFLQUO and WSEXTENT
limits. Possibly the system limits, VIRTUALPAGECNT CURRENT and MAX will
need to be changed. As an example, on a Microvax 3600 with 16Mb of
memory, PGFLQUO=50000, WSEXTENT=16000, VIRTUALPAGECNT CURRENT=40768,
VIRTUALPAGECNT MAX=600000 are sufficient for the default MOPAC values of
43 heavy and 43 light atoms.
In order for users to have access to MOPAC they must insert in
their individual LOGIN.COM files the line
$@ <Mopac-directory>MOPACCOM
where <Mopac-directory> is the name of the disk and directory which
holds all the MOPAC files. For example, DRA0:[MOPAC], thus
$@ DRA0:[MOPAC]MOPAC
MOPACCOM.COM should be modified once to accommodate local
definitions of the directory which is to hold MOPAC. This change must
also be made to RMOPAC.COM and to MOPAC.COM.
MOPAC
This command file submits a MOPAC job to a queue. Before use,
MOPAC.COM should be modified to suit local conditions. The user's VAX
is assumed to run three queues, called QUEUE3, QUEUE2, and QUEUE1. The
user should substitute the actual names of the VAX queues for these
symbolic names. Thus, for example, if the local names of the queues are
"TWELVEHOUR", for jobs of length up to 12 hours, "ONEHOUR", for jobs of
less than one hour, and "30MINS" for quick jobs, then in place of
"QUEUE3", "QUEUE2", and "QUEUE1" the words "TWELVEHOUR", "ONEHOUR", and
"30MINS" should be inserted.
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INSTALLING MOPAC Page 11-5
RMOPAC
RMOPAC is the command file for running MOPAC. It assigns all the
data files that MOPAC uses to the channels. If the user wants to use
other file-name endings than those supplied, the modifications should be
made to RMOPAC.
When a long job ends, RMOPAC will also send a mail message to the
user giving a brief description of the job. You may want to change the
default definition of "a long job"; currently it is 12 hours. This
feature was written by Dr. James Petts of Kodak Ltd Research Labs.
A recommended sequence of operations to get MOPAC up and running
would be:
1. Modify the file DIMSIZES.DAT. The default sizes are 40 heavy
atoms and 40 light atoms. Do not make the size less than 7 by
7.
2. Read through the COMMAND files to familiarize yourself with
what is being done.
3. Edit the file MOPAC.COM to use the local queue names.
4. Edit the file RMOPAC.COM if the default file-names are not
acceptable.
5. Edit MOPACCOM.COM to assign MOPACDIRECTORY to the disk and
directory which will hold MOPAC.
6. Edit the individual LOGIN.COM files to insert the following
line
$@ <Mopac-directory>MOPACCOM
Note that MOPACDIRECTORY cannot be used, as the definition
of MOPACDIRECTORY is made in MOPACCOM.COM
7. Execute the modified LOGIN command so that the new commands are
effective.
8. Run COMPILE.COM. This takes about 8 minutes to execute.
9. Enter the command
$MOPAC
You will receive the message
"What file? :"
to which the reply should be the actual data-file name. For
example, "MNRSD1", the file is assumed to end in .DAT,
e.g. MNRSD1.DAT.
You will then be prompted for the queue:
"What queue? :"
Any queue defined in MOPAC.COM will suffice:
"SYS$BATCH"
Finally, the priority will be requested:
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INSTALLING MOPAC Page 11-6
"What priority? [5]:"
To which any value between 1 and 5 will suffice. Note that
the
maximum priority is limited by the system (manager).
11.1 ESP CALCULATION.
As supplied, MOPAC will not do the ESP calculation because of the
large memory requirement of the ESP. To install the ESP, make the
following changes:
1. Rename ESP.ROF to ESP.FOR
2. Add to the first line of MOPAC.OPT the string " ESP, " (without
the quotation marks).
3. Edit MNDO.FOR to uncomment the line "C# CALL ESP".
4. Compile ESP and MNDO, and relink MOPAC using, e.g. "@COMPILE
ESP,MNDO".
5. If the resulting executable is too large, modify DIMSIZES.DAT
to reduce MAXHEV and MAXLIT, then recompile everything and
relink MOPAC with "@COMPILE".
To familiarize yourself with the system, the following operations
might be useful.
1. Run the (supplied) test molecules, and verify that MOPAC is
producing "acceptable" results.
2. Make some simple modifications to the datafiles supplied in
order to test your understanding of the data format
3. When satisfied that MOPAC is working, and that data files can
be made, begin production runs.
Working of SHUTDOWN command
If, for whatever reason, a run needs to be stopped prematurely, the
command $SHUT <jobname> can be issued. This will execute a small
command-language file, which copies the data-file to form a new file
called <filename>.END
The next time MOPAC calls function SECOND, the presence of a
readable file called SHUTDOWN, logically identified with <filename>.END,
is checked for, and if it exists, the apparent elapsed CPU time is
increased by 1,000,000 seconds, and a warning message issued. No
further action is taken until the elapsed time is checked to see if
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INSTALLING MOPAC Page 11-7
enough time remains to do another cycle. Since an apparently very long
time has been used, there is not enough time left to do another cycle,
and the restart files are generated and the run stopped.
SHUTDOWN is completely machine - independent.
Specific instructions for mounting MOPAC on other computers have
been left out due to limitations of space in the Manual; however, the
following points may prove useful:
1. Function SECOND is machine-specific. SECOND is
double-precision, and should return the CPU time in seconds,
from an arbitary zero of time. If the SHUT command has been
issued, the value returned by SECOND should be increased by
1,000,000.
2. On UNIX-based and other machines, on-line help can be provided
by using help.f. Documentation on help.f is in help.f.
3. OPEN and CLOSE statements are a fruitful source of problems.
If MOPAC does not work, most likely the trouble lies in these
statements.
4. RMOPAC.COM should be read to see what files are attached to
what logical channel.
How to use MOPAC
The COM file to run the MOPAC can be accessed using the command
"MOPAC" followed by none, one, two or three arguments. Possible options
are:
MOPAC MYDATAFILE 120 4
MOPAC MYDATAFILE 120
MOPAC MYDATAFILE
In the latter case it is assumed that the shortest queue will be
adequate. The COM file to run the MOPAC can be accessed using the
command "MOPAC" followed by none, one or two arguments. Possible
options are:
MOPAC MYDATAFILE 120
MOPAC MYDATAFILE
In the latter case it is assumed that the default time (15 seconds) will
be adequate.
MOPAC
In this case you will be prompted for the datafile, and then for
the queue. Restarts should be user transparent. If MOPAC does make any
restart files, do not change them (It would be hard to do anyhow, as
they're in machine code), as they will be used when you run a RESTART
job. The files used by MOPAC are:
- 155 -
INSTALLING MOPAC Page 11-8
File Description Logical name
<filename>.DAT Data FOR005
<filename>.OUT Results FOR006
<filename>.RES Restart FOR009
<filename>.DEN Density matrix (in binary) FOR010
SYS$OUTPUT LOG file FOR011
<filename>.ARC Archive or summary FOR012
<filename>.GPT Data for program DENSITY FOR013
<filename>.SYB SYBYL data FOR016
SETUP.DAT SETUP data SETUP
- 156 -
INSTALLING MOPAC Page 11-9
SHORT VERSION
For various reasons it might not be practical to assemble the
entire MOPAC program. For example, your computer may have memory
limitations, or you may have very large systems to be run, or some
options may never be wanted. For whatever reason, if using the entire
program is undesirable, an abbreviated version, which lacks the full
range of options of the whole program, can be specified at compile time.
At the bottom of the DIMSIZES.DAT file the programmer is asked for
various options to be used in compiling. These options allow arrays of
MECI, PULAY, and ESP to assume their correct size.
As long as no attempt is made to use the reduced subroutines, the
program will function normally. If an attempt is made to use an option
which has been excluded then the program will error.
- 157 -
INSTALLING MOPAC Page 11-10
Size of MOPAC
The amount of storage required by MOPAC depends mainly on the
number of heavy and light atoms. As it is useful for programmers to
have an idea of how large various MOPACs are, the following data are
presented as a guide.
Sizes of various MOPAC Version 6.00 executables in which the number
of heavy atoms is equal to the number of light atoms, assembled on
a VAX computer, are:
No. of heavy atoms Size of Executable (Kbytes)
MOPAC 5.00 MOPAC 6.00 (AMPAC 2.00)
10 1,653 2,054 N/A
20 3,442 4,689 4,590
30 6,356 8,990 9,150
40 10,400 14,955 15,588
50 15,572 22,586 23,944
60 21,872 31,880 34,145
100 58,361 87,519
200 228,602 336.867
300 511,723 754,540
The size of any given MOPAC executable may be estimated from
MOPAC 5.00 Size = 9939 + N* 9.57 + N*N*5.64 Kbytes
MOPAC 6.00 Size = 1091 + N*13.40 + N*N*8.33 Kbytes
The large increase in size of MOPAC was caused mainly by the inclusion
of the analytical C.I. derivatives. Because they are so much more
efficient and accurate than finite differences, and because computer
memory is becoming more available, this increase was accepted as the
lesser of two evils.
The size of MOPAC executables will vary from machine to machine,
due to the different sizes of the code. For a VAX, this amounts
to approximately 0.1Mb. Most machines use a 64 bit or 8 byte
double precision real number, so the multipliers of N and N*N
should apply to them. For large jobs, 0.1Mb is negligable, therefore
the above expression should be applicable to most computers.
No. of lines in program in
Version 5.00 = 22,084 = 17,718 code + 4,366 comment.
Version 6.00 = 31,857 = 22,526 code + 9,331 comment.
- 158 -
APPENDIX A
FORTRAN FILES
NAMES OF FORTRAN-77 FILES
AABABC ANALYT ANAVIB AXIS BLOCK BONDS BRLZON
CALPAR CAPCOR CDIAG CHRGE CNVG COMPFG DATIN
DCART DELMOL DELRI DENROT DENSIT DEPVAR DERI0
DERI1 DERI2 DERI21 DERI22 DERI23 DERITR DERIV
DERNVO DERS DFOCK2 DFPSAV DIAG DIAT DIAT2
DIIS DIJKL1 DIJKL2 DIPIND DIPOLE DOFS DOT
DRC DRCOUT EF ENPART EXCHNG FFHPOL FLEPO
FMAT FOCK1 FOCK2 FORCE FORMXY FORSAV FRAME
FREQCY GEOUT GEOUTG GETGEG GETGEO GETSYM GETTXT
GMETRY GOVER GRID H1ELEC HADDON HCORE HELECT
HQRII IJKL INTERP ITER JCARIN LINMIN LOCAL
LOCMIN MAMULT MATOUT MATPAK MECI MECID MECIH
MECIP MNDO MOLDAT MOLVAL MULLIK MULT NLLSQ
NUCHAR PARSAV PARTXY PATHK PATHS PERM POLAR
POWSAV POWSQ PRTDRC QUADR REACT1 READ READA
REFER REPP ROTAT ROTATE RSP SEARCH SECOND
SETUPG SOLROT SWAP SYMTRY THERMO TIMER UPDATE
VECPRT WRITE WRTKEY WRTTXT XYZINT
- 159 -
APPENDIX B
SUBROUTINE CALLS IN MOPAC
A list of the program segments which call various subroutines.
SUBROUTINE CALLS
AABABC
AABACD
AABBCD
AINTGS
ANALYT DERS DELRI DELMOL
ANAVIB
AXIS RSP
BABBBC
BABBCD
BANGLE
BFN
BINTGS
BKRSAV GEOUT
BONDS VECPRT MPCBDS
BRLZON CDIAG DOFS
CALPAR
CAPCOR
CDIAG ME08A EC08C SORT
CHRGE
CNVG
COE
COMPFG SETUPG SYMTRY GMETRY TIMER HCORE ITER
DIHED DERIV MECIP
DANG
DATIN UPDATE MOLDAT CALPAR
DCART ANALYT DHC DIHED
DELMOL ROTAT
DELRI
DENROT GMETRY COE
DENSIT
DEPVAR
DERI0
DERI1 TIMER DHCORE SCOPY DFOCK2 SUPDOT MTXM MXM
DIJKL1 MECID MECIH SUPDOT TIMER
- 160 -
SUBROUTINE CALLS IN MOPAC Page B-2
DERI2 DERI21 DERI22 MXM OSINV MTXM SCOPY DERI23
DIJKL2 MECID MECIH SUPDOT
DERI21 MTXMC HQRII MXM
DERI22 MXM MXMT FOCK2 FOCK1 SUPDOT
DERI23 SCOPY
DERITR SYMTRY GMETRY HCORE ITER DERIV DERNVO DCART
JCARIN MXM GEOUT DERITR
DERNVO DERI0 DERI1 DERI2
DERS
DFOCK2 JAB KAB
DFPSAV XYZINT GEOUT
DHC H1ELEC ROTATE SOLROT FOCK2
DHCORE H1ELEC ROTATE
DIAG EPSETA
DIAGI
DIAT COE GOVER DIAT2
DIAT2 SET
DIHED DANG
DIIS SPACE VECPRT MINV
DIJKL1 FORMXY
DIJKL2
DIPIND CHRGE GMETRY
DIPOLE
DOFS
DRC GMETRY COMPFG PRTDRC
DRCOUT
EA08C EA09C
EA09C
EC08C EA08C
EF BKRSAV COMPFG BKRSAV UPDHES HQRII FORMD SYMTRY
ENPART
EPSETA
EXCHNG
FFHPOL COMPFG DIPIND VECPRT RSP MATOUT
FLEPO DFPSAV COMPFG SCOPY GEOUT SUPDOT LINMIN DIIS
FMAT FORSAV COMPFG CHRGE
FOCK2 JAB KAB
FOCK2D
FORCE GMETRY COMPFG NLLSQ FLEPO WRITE XYZINT AXIS
FMAT VECPRT FRAME RSP MATOUT FREQCY MATOUT
DRC ANAVIB THERMO
FORMD OVERLP
FORMXY
FORSAV
FRAME AXIS
FREQCY BRLZON FRAME RSP
GEOUT XYZINT WRTTXT CHRGE
GEOUTG XXX
GETDAT
GETGEG GETVAL GETVAL GETVAL
GETGEO GEOUT NUCHAR XYZINT
GETSYM
GETTXT UPCASE
GMETRY GEOUT
GOVER
- 161 -
SUBROUTINE CALLS IN MOPAC Page B-3
GRID DFPSAV FLEPO GEOUT WRTTXT
H1ELEC DIAT
HADDON DEPVAR
HCORE H1ELEC ROTATE SOLROT VECPRT
HELECT
HQRII
IJKL PARTXY
INTERP HQRII SCHMIT SCHMIB SPLINE
ITER EPSETA VECPRT FOCK2 FOCK1 WRITE INTERP PULAY
HQRII DIAG MATOUT SWAP DENSIT CNVG
JAB
JCARIN SYMTRY GMETRY
KAB
LINMIN COMPFG EXCHNG
LOCAL MATOUT
LOCMIN COMPFG EXCHNG
MNDO GETDAT READ MOLDAT DATIN REACT1 GRID PATHS
PATHK FORCE DRC NLLSQ COMPFG POWSQ EF
FLEPO WRITE POLAR
MAMULT
MATOUT
ME08A ME08B
ME08B
MECI IJKL PERM MECIH VECPRT HQRII MATOUT
MECIH
MECIP MXM
MINV
MOLDAT REFER GMETRY VECPRT
MOLVAL
MPCBDS
MPCPOP
MPCSYB
MTXM
MTXMC MXM
MULLIK RSP GMETRY MULT DENSIT VECPRT
MULT
MXM
MXMT
NLLSQ PARSAV COMPFG GEOUT LOCMIN PARSAV
NUCHAR
OSINV
OVERLP
PARSAV XYZINT GEOUT
PARTXY FORMXY
PATHK DFPSAV FLEPO GEOUT WRTTXT
PATHS DFPSAV FLEPO WRITE
PERM
POLAR GMETRY AXIS COMPFG FFHPOL
POWSAV XYZINT GEOUT
POWSQ POWSAV COMPFG VECPRT RSP SEARCH
PRTDRC CHRGE XYZINT QUADR
PULAY MAMULT OSINV
QUADR
REACT1 GETGEO SYMTRY GEOUT GMETRY FLEPO COMPFG WRITE
- 162 -
SUBROUTINE CALLS IN MOPAC Page B-4
READ GETTXT GETGEG GETGEO DATE GEOUT WRTKEY GETSYM
SYMTRY NUCHAR WRTTXT GMETRY
REFER
REPP
ROTAT
ROTATE REPP
RSP EPSETA TRED3 TQLRAT TQL2 TRBAK3
SAXPY
SCHMIB
SCHMIT
SCOPY
SEARCH COMPFG
SECOND
SET AINTGS BINTGS
SETUPG
SOLROT ROTATE
SORT
SPACE
SPLINE BFN
SUPDOT
SWAP
SYMTRY HADDON
THERMO
TIMCLK
TIMER
TIMOUT
TQL2
TQLRAT
TRBAK3
TRED3
UPCASE
UPDATE
UPDHES
VECPRT
WRITE DATE WRTTXT GEOUT DERIV TIMOUT SYMTRY GMETRY GEOUT
VECPRT MATOUT CHRGE BRLZON MPCSYB DENROT MOLVAL BONDS
LOCAL ENPART MULLIK MPCPOP GEOUTG
WRTKEY
WRTTXT
XXX
XYZGEO BANGLE DIHED
XYZINT DIHED BANGLE XYZGEO
- 163 -
SUBROUTINE CALLS IN MOPAC Page B-5
A list of subroutines called by various segments (the inverse of the
first list)
Subroutine Called by
AABABC MECIH
AABACD MECIH
AABBCD MECIH
AINTGS SET
ANALYT DCART
ANAVIB FORCE
AXIS FORCE FRAME POLAR
BABBBC MECIH
BABBCD MECIH
BANGLE XYZGEO XYZINT
BFN SPLINE
BINTGS SET
BKRSAV EF
BONDS WRITE
BRLZON FREQCY WRITE
CALPAR DATIN
CAPCOR ITER
CDIAG BRLZON
CHRGE DIPIND FMAT GEOUT PRTDRC WRITE
CNVG ITER
COE DENROT DIAT
COMPFG DRC EF FFHPOL FLEPO FMAT
FORCE LINMIN LOCMIN MNDO NLLSQ
POLAR POWSQ REACT1 SEARCH
DANG DIHED
DATIN MNDO
DCART DERITR
DELMOL ANALYT
DELRI ANALYT
DENROT WRITE
DENSIT ITER MULLIK
DEPVAR HADDON
DERI0 DERNVO
DERI1 DERNVO
DERI2 DERI2 DERNVO
DERI21 DERI2
DERI22 DERI2
DERI23 DERI2
DERITR DERITR
DERNVO DERITR
DERS ANALYT
DFOCK2 DERI1
DFPSAV FLEPO GRID PATHK PATHS
DHC DCART DERI1
DHCORE DERI1
DIAG DERI21 ITER
DIAGI DERI21
DIAT DIAT H1ELEC
DIAT2 DIAT
DIHED COMPFG DCART XYZGEO XYZINT
DIIS FLEPO
DIJKL1 DERI1
- 164 -
SUBROUTINE CALLS IN MOPAC Page B-6
DIJKL2 DERI2
DIPIND FFHPOL
DIPOLE FMAT WRITE
DOFS BRLZON
DRC FORCE MNDO
DRCOUT PRTDRC
EA08C EC08C
EA09C EA08C
EC08C CDIAG
EF MNDO
ENPART WRITE
EPSETA DIAG ITER RSP
EXCHNG LINMIN LOCMIN
FFHPOL POLAR
FLEPO FORCE GRID MNDO PATHK PATHS
REACT1
FMAT FORCE
FOCK2 DERI22 DHC ITER
FORCE MNDO
FORMD EF
FORMXY DIJKL1 PARTXY
FORSAV FMAT
FRAME FORCE FREQCY
FREQCY FORCE
GEOUT BKRSAV DERITR DFPSAV FLEPO GETGEO
GMETRY GRID NLLSQ PARSAV PATHK
POWSAV REACT1 READ
WRITE WRITE
GEOUTG WRITE
GETDAT MNDO
GETGEG READ
GETGEO REACT1 READ
GETSYM READ
GETTXT READ
GMETRY COMPFG DENROT DERITR DIPIND DRC
FORCE JCARIN MOLDAT MULLIK POLAR
REACT1 READ WRITE
GOVER DIAT
GRID MNDO
H1ELEC DHC DHCORE HCORE
HADDON SYMTRY
HCORE COMPFG DERITR
HELECT DCART DERI2 ITER
HQRII EF INTERP ITER MECI
IJKL MECI
INTERP ITER
ITER COMPFG DERITR
JAB DFOCK2 FOCK2
JCARIN DERITR
KAB DFOCK2 FOCK2
LINMIN FLEPO
LOCAL WRITE
LOCMIN NLLSQ
MNDO (main segment)
MAMULT PULAY
- 165 -
SUBROUTINE CALLS IN MOPAC Page B-7
MATOUT FFHPOL FORCE ITER LOCAL MECI
WRITE
ME08A CDIAG
ME08B ME08A
MECI COMPFG DERI1 DERI2 MECI
MECIH DERI1 DERI2 MECI
MECIP COMPFG
MINV DIIS
MOLDAT DATIN MNDO
MOLVAL WRITE
MPCBDS BONDS
MPCPOP WRITE
MPCSYB WRITE
MTXM DERI1 DERI2 DERI21
MTXMC DERI21
MULLIK WRITE
MULT MULLIK
MXM DERI1 DERI2 DERI21 DERI22 DERITR
MECIP MTXMC
MXMT DERI22
NLLSQ FORCE MNDO
NUCHAR GETGEO READ
OSINV DERI2 PULAY
OVERLP FORMD
PARSAV NLLSQ
PARTXY IJKL
PATHK MNDO
PATHS MNDO
PERM MECI
POLAR MNDO
POWSAV POWSQ
POWSQ MNDO
PRTDRC DRC
PULAY ITER
QUADR PRTDRC
REACT1 MNDO
READ MNDO
REFER MOLDAT
REPP ROTATE
ROTAT DELMOL DHC DHCORE HCORE SOLROT
ROTATE DHC DHCORE HCORE SOLROT
RSP AXIS FFHPOL FORCE FREQCY MULLIK
POWSQ
SCHMIB INTERP
SCHMIT INTERP
SCOPY DERI1 DERI2 DERI23 FLEPO
SEARCH POWSQ
SECOND DERI2 DRC EF ESP FLEPO
FMAT FORCE GRID ITER MNDO
NLLSQ PATHK PATHS POWSQ REACT1
TIMER WRITE
SET COMPFG DIAT2
SETUPG COMPFG
SOLROT DHC HCORE
SORT CDIAG
- 166 -
SUBROUTINE CALLS IN MOPAC Page B-8
SPACE DIIS
SPLINE INTERP
SUPDOT DERI1 DERI1 DERI2 DERI22 FLEPO
SWAP ITER
SYMTRY COMPFG DERITR EF JCARIN REACT1
READ WRITE
THERMO FORCE
TIMCLK SECOND
TIMER COMPFG DERI1 DERI1
TIMOUT WRITE
TQL2 RSP
TQLRAT RSP
TRBAK3 RSP
TRED3 RSP
UPCASE GETTXT
UPDATE DATIN
UPDHES EF
VECPRT BONDS DIIS FFHPOL FORCE HCORE
ITER MECI MOLDAT MULLIK POWSQ
WRITE
WRITE FORCE ITER MNDO PATHS REACT1
WRTKEY READ
WRTTXT GEOUT GRID PATHK READ WRITE
XXX GEOUTG
XYZGEO XYZINT
XYZINT DFPSAV FORCE GEOUT GETGEO PARSAV
POWSAV PRTDRC
- 167 -
APPENDIX C
DESCRIPTION OF SUBROUTINES IN MOPAC
AABABC Utility: Calculates the configuration interaction matrix
element between two configurations differing by exactly
one alpha M.O. Called by MECI only.
AABACD Utility: Calculates the configuration interaction matrix
element between two configurations differing by exactly
two alpha M.O.'s. Called by MECI only.
AABBCD Utility: Calculates the configuration interaction matrix
element between two configurations differing by exactly
two M.O.'s; one configuration has alpha M.O. "A" and beta
M.O. "C" while the other configuration has alpha M.O. "B"
and beta M.O. "D". Called by MECI only.
AINTGS Utility: Within the overlap integrals, calculates the
A-integrals. Dedicated to function SS within DIAT.
ANALYT Main Sequence: Calculates the analytical derivatives
of the energy with respect to cartesian coordinates for all
atoms. Use only if the mantissa is short (less than 52 bits)
or out of interest. Should not be used for routine work
on a VAX.
ANAVIB Utility: Gives a brief interpretation of the modes of
vibration of the molecule. The principal pairs of atoms
involved in each vibration are identified, and the mode
of motion (tangential or radial) is output.
AXIS Utility: Works out the three principal moments of inertia
of a molecule. If the system is linear, one moment of inertia
is zero. Prints moments in units of cm**(-1) and
10**(-40) gram-cm-cm.
BABBBC Utility: Calculates the configuration interaction matrix
element between two configurations differing by exactly
one beta M.O. Called by MECI only.
BABBCD Utility: Calculates the configuration interaction matrix
element between two configurations differing by exactly
- 168 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-2
two beta M.O.'s. Called by MECI only.
BANGLE Utility: Given a set of coordinates, BANGLE will calculate the
angle between any three atoms.
BFN Utility: Calculates the B-functions in the Slater overlap.
BINTGS Utility: Calculates the B-functions in the Slater overlap.
BKRSAV Utility: Saves and restores data used by the eigenvector
following subroutine. Called by EF only.
BONDS Utility: Evaluates and prints the valencies of atoms and
bond-orders between atoms. Main argument: density matrix.
No results are passed to the calculation, and no data
are changed. Called by WRITE only.
BRLZON Main Sequence: BRLZON generates a band structure, or phonon
structure, for high polymers. Called by WRITE and FREQCY.
CALPAR Utility: When external parameters are read in via EXTERNAL=,
the derived parameters are worked out using CALPAR. Note that
all derived parameters are calculated for all parameterized
elements at the same time.
CAPCOR Utility: Capping atoms, of type Cb, should not contribute to
the energy of a system. CAPCOR calculates the energy
contribution due to the Cb and subtracts it from the
electronic energy.
CDIAG Utility: Complex diagonalization. Used in generating
eigenvalues
of complex Hermitian secular determinant for band structures.
Called by BRLZON only.
CHRGE Utility: Calculates the total number of valence electrons
on each atom. Main arguments: density matrix, array of
atom charges (empty on input). Called by ITER only.
CNVG Utility: Used in SCF cycle. CNVG does a three-point
interpolation of the last three density matrices.
Arguments: Last three density matrices, Number of iterations,
measure of self-consistency (empty on input). Called by ITER
only.
COE Utility: Within the general overlap routine COE calculates
the angular coefficients for the s, p and d real atomic
orbitals given the axis and returns the rotation matrix.
COMPFG Main Sequence: Evaluates the total heat of formation of the
supplied geometry, and the derivatives, if requested. This
is the nodal point connecting the electronic and geometric
parts of the program. Main arguments: on input: geometry,
on output: heat of formation, gradients.
DANG Utility: Called by XYZINT, DANG computes the angle between a
- 169 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-3
point, the origin, and a second point.
DATIN Utility: Reads in external parameters for use within
MOPAC. Originally used for the testing of new parameters,
DATIN is now a general purpose reader for parameters.
Invoked by the keyword EXTERNAL.
DCART Utility: Called by DERIV, DCART sets up a list of cartesian
derivatives of the energy W.R.T. coordinates which DERIV can
then use to construct the internal coordinate derivatives.
DELMOL Utility: Part of analytical derivates. Two-electron.
DELRI Utility: Part of analytical derivates. Two-electron.
DENROT Utility: Converts the ordinary density matrix into
a condensed density matrix over basis functions s (sigma),
p (sigma) and p (pi), i.e., three basis functions. Useful
in hybridization studies. Has capability to handling "d"
functions, if present.
DENSIT Utility: Constructs the Coulson electron density matrix from
the eigenvectors. Main arguments: Eigenvectors, No. of singly
and doubly occupied levels, density matrix (empty on input)
Called by ITER.
DEPVAR Utility: A symmetry-defined "bond length" is related to
another bond length by a multiple. This special symmetry
function is intended for use in Cluster calculations.
Called by HADDON.
DERI0 Utility: Part of the analytical C.I. derivative package.
Calculates the diagonal dominant part of the super-matrix.
DERI1 Utility: Part of the analytical C.I. derivative package.
Calculates the frozen density contribution to the derivative of
the energy w.r.t. cartesian coordinates, and the derivatives of
the frozen Fock matrix in M.O. basis. It's partner is DERI2.
DERI2 Utility: Part of the analytical C.I. derivative package.
Calculates the relaxing density contribution to the derivative
of the energy w.r.t. cartesian coordinates. Uses the results of
DERI1.
DERI21 Utility: Part of the analytical C.I. derivative package.
Called by DERI2 only.
DERI22 Utility: Part of the analytical C.I. derivative package.
Called by DERI2 only.
DERI23 Utility: Part of the analytical C.I. derivative package.
Called by DERI2 only.
DERITR Utility: Calculates derivatives of the energy w.r.t. internal
coordinates using full SCF's. Used as a foolproof way of
- 170 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-4
calculating derivatives. Not recommended for normal use.
DERIV Main Sequence: Calculates the derivatives of the energy with
respect to the geometric variables. This is done either by
using initially cartesian derivatives (normal mode), by
analytical C.I. RHF derivatives, or by full SCF calculations
(NOANCI in half-electron and C.I. mode). Arguments: on
input: geometry, on output: derivatives. Called by COMPFG.
DERNVO Analytical C.I. Derivative main subroutine. Calculates the
derivative of the energy w.r.t. geometry for a non-variationally
optimized wavefunction (a SCF-CI wavefunction).
DERS Utility: Called by ANALYT, DERS calculates the analytical
derivatives of the overlap matrix within the molecular frame.
DEX2 Utility: A function called by ESP.
DFOCK2 Utility: Part of the analytical C.I. derivative package. Called
by DERI1, DFOCK2 calculates the frozen density contribution to
the derivative of the energy w.r.t. cartesian coordinates.
DFPSAV Utility: Saves and restores data used by the
BFGS geometry optimization. Main arguments:
parameters being optimized, gradients of parameters, last heat
of formation, integer and real control data. Called by FLEPO.
DHC Utility: Called by DCART and calculates the energy of a pair
of atoms using the SCF density matrix. Used in the finite
difference derivatve calculation.
DHCORE Utility: Part of the analytical C.I. derivative package. Called
by DERI1, DHCORE calculates the derivatives of the 1 and 2
electron integrals w.r.t. cartesian coordinates.
DIAG Utility: Rapid pseudo-diagonalization. Given a set of vectors
which almost block-diagonalize a secular determinant, DIAG
modifies the vectors so that the block-diagonalization is more
exact. Main arguments: Old vectors, Secular Determinant,
New vectors (on output). Called by ITER.
DIAGI Utility: Calculates the electronic energy arising from
a given configuration. Called by MECI.
DIAT Utility: Calculates overlap integrals between two atoms in
general cartesian space. Principal quantum numbers up to 6, and
angular quantum numbers up to 2 are allowed. Main arguments:
Atomic numbers and cartesian coordinates in Angstroms of the
two atoms, Diatomic overlaps (on exit). Called by H1ELEC.
DIAT2 Utility: Calculates reduced overlap integrals between atoms
of principal quantum numbers 1, 2, and 3, for s and p orbitals.
Faster than the SS in DIAT. This is a dedicated subroutine, and
is unable to stand alone without considerable backup. Called
by DIAT.
- 171 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-5
DIGIT Utility: Part of READA. DIGIT assembles numbers given a
character string.
DIHED Utility: Calculates the dihedral angle between four atoms.
Used in converting from cartesian to internal coordinates.
DIIS Utility: Pulay's Geometric Direct Inversion of the Iterative
Subspace (G-DIIS) accelerates the rate at which the BFGS
locates an energy minimum. (In MOPAC 6.00, the DIIS is only
partially installed - several capabilities of the DIIS are not
used)
DIJKL1 Utility: Part of the analytical C.I. derivative package. Called
by DERI1, DIJKL1 calculates the two-electron integrals over
M.O. bases, e.g. <i,j (1/r) k,l>.
DIJKL2 Utility: Part of the analytical C.I. derivative package. Called
by DERI2, DIJKL2 calculates the derivatives of the two-electron
integrals over M.O. bases, e.g. <i,j (1/r) k,l>, w.r.t.
cartesian coordinates.
DIPIND Utility: Similar to DIPOLE, but used by the POLAR calculation
only.
DIPOLE Utility: Evaluates and, if requested, prints dipole components
and dipole for the molecule or ion. Arguments: Density matrix,
Charges on every atom, coordinates, dipoles (on exit).
Called by WRITE and FMAT.
DIST2 Utility: Called by ESP only, DIST2 works out the distance
between two points in 3D space.
DOFS Main Sequence: Calculates the density of states within a
Brillouin zone. Used in polymer work only.
DOT Utility: Given two vectors, X and Y, of length N, function DOT
returns with the dot product X.Y. I.e., if X=Y, then DOT = the
square of X. Called by FLEPO.
DRC Main Sequence: The dynamic and intrinsic reaction coordinates
are calculated by following the mass-weighted trajectories.
DRCOUT Utility: Sets up DRC and IRC data in quadratic form
preparatory to being printed.
EA08C Part of the diagonalizer RSP.
EA09C Part of the diagonalizer RSP.
EC08C Part of the diagonalizer RSP.
EF Main Sequence: EF is the Eigenvector Following routine.
EF implements the keywords EF and TS.
ELESP Utility: Within the ESP, ELESP calculates the electronic
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DESCRIPTION OF SUBROUTINES IN MOPAC Page C-6
contribution to the electrostatic potential.
ENPART Utility: Partitions the energy of a molecule into its monatomic
and diatomic components. Called by WRITE when the keyword
ENPART is specified. No data are changed by this call.
EPSETA Utility: Calculates the machine precision and dynamic range
for use by the two diagonalizers.
ESP Main Sequence: ESP is not present in the default copy of MOPAC.
ESP calculates the atomic charges which would reproduce the
electrostatic potential of the nuclii and electronic
wavefunction.
ESPBLO Block Data: Used by the ESP calculation, ESPBLO fills two small
arrays!
ESPFIT Utility: Part of the ESP. ESP fits the quantum mechanical
potential to a classical point charge model
EXCHNG Utility: Dedicated procedure for storing 3 parameters and one
array in a store. Used by SEARCH.
FFHPOL Utility: Part of the POLAR calculation. Evaluates the
effect of an electric field on a molecule.
FLEPO Main Sequence: Optimizes a geometry by minimizing the energy.
Makes use of the first and estimated second derivatives to
achieve this end. Arguments: Parameters to be optimized,
(overwritten on exit with the optimized parameters), Number of
parameters, final optimized heat of formation. Called by MAIN,
REACT1, and FORCE.
FM06AS Utility: Part of CDIAG.
FM06BS Utility: part of CDIAG.
FMAT Main sequence: Calculates the exact Hessian matrix for a system
This is done by either using differences of first derivatives
(normal mode) or by four full SCF calculations (half electron
or C.I. mode). Called by FORCE.
FOCK1 Utility: Adds on to Fock matrix the one-center two electron
terms. Called by ITER only.
FOCK2 Utility: Adds on to Fock matrix the two-center two electron
terms. Called by ITER and DERIV. In ITER the entire Fock matrix
is filled; in DERIV, only diatomic Fock matrices are
constructed.
FOCK2D Written out of MOPAC 6.00.
FORCE Main sequence: Performs a force-constant and vibrational
frequency calculation on a given system. If the starting
gradients are large, the geometry is optimized to reduce the
gradient norm, unless LET is specified in the keywords.
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DESCRIPTION OF SUBROUTINES IN MOPAC Page C-7
Isotopic substitution is allowed. Thermochemical quantities
are calculated. Called by MAIN.
FORMD Main Sequence: Called by EF. FORMD constructs the next step
in the geometry optimization or transition state location.
FORMXY Utility: Part of DIJKL1. FORMXY constructs part of the two-
electron integral over M.O.'s.
FORSAV Utility: Saves and restores data used in FMAT in FORCE
calculation. Called by FMAT.
FRAME Utility: Applies a very rigid constraint on the translations
and rotations of the system. Used to separate the trivial
vibrations in a FORCE calculation.
FREQCY Main sequence: Final stage of a FORCE calculation. Evaluates
and prints the vibrational frequencies and modes.
FSUB Utility: Part of ESP.
GENUN Utility: Part of ESP. Generates unit vectors over a sphere.
called by SURFAC only.
GEOUT Utility: Prints out the current geometry. Can be called at
any time. Does not change any data.
GEOUTG Utility: Prints out the current geometry in Gaussian Z-matrix
format.
GETDAT Utility: Reads in all the data, and puts it in a scratch file
on channel 5.
GETGEG Utility: Reads in Gaussian Z-matrix geometry. Equivalent to
GETGEO and GETSYM combined.
GETGEO Utility: Reads in geometry in character mode from specified
channel, and stores parameters in arrays. Some error-checking
is done. Called by READ and REACT1.
GETSYM Utility: Reads in symmetry data. Used by READ.
GETTXT Utility: Reads in KEYWRD, KOMENT and TITLE.
GETVAL Utility: Called by GETGEG, GETVAL either gets an internal
coordinate or a logical name for that coordinate.
GMETRY Utility: Fills the cartesian coordinates array. Data are
supplied from the array GEO, GEO can be (a) in internal
coordinates, or (b) in cartesian coordinates. If STEP is
non-zero, then the coordinates are modified in light of the
other geometry and STEP. Called by HCORE, DERIV, READ, WRITE,
MOLDAT, etc.
GOVER Utility: Calculates the overlap of two Slater orbitals which
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DESCRIPTION OF SUBROUTINES IN MOPAC Page C-8
have been expanded into six gaussians. Calculates the
STP-6G overlap integrals.
GRID Main Sequence: Calculates a grid of points for a 2-D search
in coordinate space. Useful when more information is needed
about a reaction surface.
H1ELEC Utility: Given any two atoms in cartesian space, H1ELEC
calculates the one-electron energies of the off-diagonal
elements of the atomic orbital matrix.
H(i,j) = -S(i,j)*(beta(i)+beta(j))/2.
Called by HCORE and DERIV.
HADDON Utility: The symmetry operation subroutine, HADDON relates two
geometric variables by making one a dependent function of the
other. Called by SYMTRY only.
HCORE Main sequence: Sets up the energy terms used in calculating the
SCF heat of formation. Calculates the one and two electron
matrices, and the nuclear energy.
Called by COMPFG.
HELECT Utility: Given the density matrix, and the one electron and
Fock matrices, calculates the electronic energy. No data are
changed by a call of HELECT. Called by ITER and DERIV.
HQRII Utility: Rapid diagonalization routine. Accepts a secular
determinant, and produces a set of eigenvectors and
eigenvalues. The secular determinant is destroyed.
IJKL Utility: Fills the large two-electron array over a M.O.
basis set. Called by MECI.
INTERP Utility: Runs the Camp-King converger. q.v.
ITER Main sequence: Given the one and two electron matrices, ITER
calculates the Fock and density matrices, and the electronic
energy. Called by COMPFG.
JAB Utility: Calculates the coulomb contribution to the Fock matrix
in NDDO formalism. Called by FOCK2.
JCARIN Utility: Calculates the difference vector in cartesian
coordinates
corresponding to a small change in internal coordinates.
KAB Utility: Calculates the exchange contribution to the Fock matrix
in NDDO formalism. Called by FOCK2.
LINMIN Main sequence: Called by the BFGS geometry optimized FLEPO,
LINMIN takes a step in the search-direction and if the energy
drops, returns. Otherwise it takes more steps until if finds
one which causes the energy to drop.
LOCAL Utility: Given a set of occupied eigenvectors, produces a
canonical set of localized bonding orbitals, by a series of
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DESCRIPTION OF SUBROUTINES IN MOPAC Page C-9
2 x 2 rotations which maximize <psi**4>. Called
by WRITE.
LOCMIN Main sequence: In a gradient minimization, LOCMIN does a line-
search to find the gradient norm minimum. Main arguments:
current geometry, search direction, step, current gradient
norm; on exit: optimized geometry, gradient norm.
MAMULT Utility: Matrix multiplication. Two matrices, stored as lower
half triangular packed arrays, are multiplied together, and the
result stored in a third array as the lower half triangular
array. Called from PULAY.
MATOUT Utility: Matrix printer. Prints a square matrix, and a
row-vector, usually eigenvectors and eigenvalues. The indices
printed depend on the size of the matrix: they can be either
over orbitals, atoms, or simply numbers, thus M.O.'s are over
orbitals, vibrational modes are over numbers. Called by WRITE,
FORCE.
ME08A Utilities: Part of the complex diagonalizer, and called by
ME08B CDIAG.
MECI Main sequence: Main function for Configuration Interaction,
MECI constructs the appropriate C.I. matrix, and evaluates the
roots, which correspond to the electronic energy of the states
of the system. The appropriate root is then returned.
Called by ITER only.
MECID Utility: Constructs the differential C.I. secular determinant.
MECIH Utility: Constructs the normal C.I. secular determinant.
MECIP Utility: Reforms the density matrix after a MECI calculation.
MINV Utility: Called by DIIS. MINV inverts the Hessian matrix.
MNDO Main sequence: MAIN program. MNDO first reads in data using
READ, then calls either FLEPO to do geometry optimization,
FORCE to do a FORCE calculation, PATHS for a reaction with a
supplied coordinate, NLLSQ for a gradient minimization or
REACT1 for locating the transition state. Starts the timer.
MOLDAT Main Sequence: Sets up all the invariant parameters used during
the calculation, e.g. number of electrons, initial atomic
orbital populations, number of open shells, etc. Called once by
MNDO only.
MOLVAL Utility: Calculates the contribution from each M.O. to the
total valency in the molecule. Empty M.O.'s normally
have a negative molecular valency.
MTXM Utility: Part of the matrix package. Multiplies together two
rectangular packed arrays, i.e., C = A.B.
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DESCRIPTION OF SUBROUTINES IN MOPAC Page C-10
MTXMC Utility: Part of the matrix package. Similar to MTXM.
MULLIK Utility: Constructs and prints the Mulliken Population
Analysis. Available only for RHF calculations. Called by
WRITE.
MULT Utility: Used by MULLIK only, MULT multiplies two square
matrices together.
MXM Utility: Part of the matrix package. Similar to MTXM.
MXMT Utility: Part of the matrix package. Similar to MTXM.
MYWORD Utility: Called in WRTKEY, MYWORD checks for the existance of
a specific string. If it is found, MYWORD is set true, and
the all occurances of string are deleted. Any words
not recognised will be flagged and the job stopped.
NAICAP Utility: Called by ESP.
NAICAP Utility: Called by ESP.
NLLSQ Main sequence: Used in the gradient norm minimization.
NUCHAR Takes a character string and reads all the numbers in it
and stores these in an array.
OSINV Utility: Inverts a square matrix. Called by PULAY only.
OVERLP Utility: Part of EF. OVERLP decides which normal mode to
follow.
OVLP Utility: Called by ESP only. OVLP calculates the overlap
over Gaussian STO's.
PARSAV Utility: Stores and restores data used in the gradient-norm
minimization calculation.
PARTXY Utility: Called by IJKL only, PARTXY calculates the partial
product <i,j (1/r) in <i,j (1/r) k,l>.
PATHK Main sequence: Calculates a reaction coordinate which uses
a constant step-size. Invoked by keywords STEP and POINTS.
PATHS Main sequence: Given a reaction coordinate as a row-vector,
PATHS performs a FLEPO geometry optimization for each point,
the later geometries being initially guessed from a knowledge
of the already optimized geometries, and the current step.
Called by MNDO only.
PDGRID Utility: Part of ESP. Calculates the Williams surface.
PERM Utility: Permutes n1 electrons of alpha or beta spin among
n2 M.O.'s.
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DESCRIPTION OF SUBROUTINES IN MOPAC Page C-11
POLAR Utility: Calculates the polarizability volumes for a molecule
or ion. Uses 19 SCF calculations, so appears after WRITE has
finished. Cannot be used with FORCE, but can be used anywhere
else. Called by WRITE.
POWSAV Utility: Calculation store and restart for SIGMA
calculation. Called by POWSQ.
POWSQ Main sequence: The McIver - Komornicki gradient
minimization routine. Constructs a full Hessian matrix
and proceeds by line-searches Called from MAIN when
SIGMA is specified.
PRTDRC Utility: Prints DRC and IRC results according to instructions.
Output can be (a) every point calculated (default), (b) in
constant steps in time, space or energy.
PULAY Utility: A new converger. Uses a powerful
mathematical non-iterative method for obtaining the SCF Fock
matrix. Principle is that at SCF the eigenvectors of the Fock
and density matrices are identical, so [F.P] is a measure of
the non-self consistency. While very powerful, PULAY is not
universally applicable. Used by ITER.
QUADR: Utility: Used in printing the IRC - DRC results. Sets up
a quadratic in time of calculated quantities so that PRTDRC
can select specific reaction times for printing.
REACT1 Main sequence: Uses reactants and products to find the
transition state. A hypersphere of N dimensions is centered on
each moiety, and the radius steadily reduced. The entity of
lower energy is moved, and when the radius vanishes, the
transition state is reached. Called by MNDO only.
READ Main sequence: Almost all the data are read in through READ.
There is a lot of data-checking in READ, but very little
calculation. Called by MNDO.
READA Utility: General purpose character number reader. Used to enter
numerical data in the control line as " <variable>=n.nnn " where
<variable> is a mnemonic such as SCFCRT or CHARGE.
Called by READ, FLEPO, ITER, FORCE, and many other subroutines.
REFER Utility: Prints the original references for atomic data.
If an atom does not have a reference, i.e., it has not been
parameterized, then a warning message will be printed and
the calculation stopped.
REPP Utility: Calculates the 22 two-electron reduced repulsion
integrals, and the 8 electron-nuclear attraction integrals.
These are in a local coordinate system. Arguments: atomic
numbers of the two atoms, interatomic distance, and arrays to
hold the calculated integrals. Called by ROTATE only.
ROTAT Utility: Rotates analytical two-electron derivatives from
- 178 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-12
atomic to molecular frame.
ROTATE Utility: All the two-electron repulsion integrals, the electron-
nuclear attraction integrals, and the nuclear-nuclear repulsion
term between two atoms are calculated here. Typically 100 two-
electron integrals are evaluated.
RSP Utility: Rapid diagonalization routine. Accepts a secular
determinant, and produces a set of eigenvectors and
eigenvalues. The secular determinant is destroyed.
SAXPY Utility: Called by the utility SUPDOT only!
SCHMIB Utility: Part of Camp-King converger.
SCHMIT Utility: Part of Camp-King converger.
SCOPY Utility: Copies an array into another array.
SDOT Utility: Forms the scalar of the product of two vectors.
SEARCH Utility: Part of the SIGMA and NLLSQ gradient minimizations.
The line-search subroutine, SEARCH locates the gradient
minimum and calculates the second derivative of the energy
in the search direction. Called by POWSQ and NLLSQ.
SECOND Utility: Contains VAX specific code. Function SECOND
returns the number of CPU seconds elapsed since an arbitrary
starting time. If the SHUTDOWN command has been issued,
the CPU time is in error by exactly 1,000,000 seconds, and
the job usually terminates with the message "time exceeded".
SET Utility: Called by DIAT2, evaluates some terms used in overlap
calculation.
SETUP3 Utility: Sets up the Gaussian expansion of Slater orbitals
using a STO-3G basis set.
SETUPG Utility: Sets up the Gaussian expansion of Slater orbitals
using a STO-6G basis set.
SOLROT Utility: For Cluster systems, adds all the two-electron
integrals of the same type, between different unit cells, and
stores them in a single array. Has no effect on molecules.
SORT Utility: Part of CDIAG, the complex diagonalizer.
SPACE Utility: Called by DIIS only.
SPCG Written out of Version 6.00.
SPLINE Utility: Part of Camp-King converger.
SS Utility: An almost general Slater orbital overlap calculation.
Called by DIAT.
- 179 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-13
SUPDOT Utility: Matrix mutiplication A=B.C
SURFAC Utility: Part of the ESP.
SWAP Utility: Used with FILL=, SWAP ensures that a specified
M.O. is filled. Called by ITER only.
SYMTRY Utility: Calculates values for geometric parameters from known
geometric parameters and symmetry data. Called whenever GMETRY
is called.
THERMO Main sequence: After the vibrational frequencies have been
calculated, THERMO calculates thermodynamic quantities such as
internal energy, heat capacity, entropy, etc, for translational,
vibrational, and rotational, degrees of freedom.
TIMCLK Utility: Vax-specific code for determining CPU time.
TIMER Utility: Prints times of various steps.
TIMOUT Utility: Prints total CPU time in elegant format.
TQL2 Utility: Part of the RSP.
TQLRAT Utility: Part of the RSP.
TRBAK3 Utility: Part of the RSP.
TRED3 Utility: Part of the RSP.
UPDATE Utility: Given a set of new parameters, stores these
in their appropriate arrays. Invoked by EXTERNAL.
UPDHES Utility: Called by EF, UPDHES updates the Hessian matrix.
VECPRT Utility: Prints out a packed, lower-half triangular matrix.
The labeling of the sides of the matrix depend on the matrix's
size: if it is equal to the number of orbitals, atoms, or other.
Arguments: The matrix to be printed, size of matrix. No data
are changed by a call of VECPRT.
WRITE Main sequence: Most of the results are printed here. All
relevant arrays are assumed to be filled. A call of WRITE only
changes the number of SCF calls made, this is reset to zero.
No other data are changed. Called by MAIN, FLEPO, FORCE.
WRTKEY Main Sequence: Prints all keywords and checks for
compatability and to see if any are not recognised.
WRTKEY can stop the job if any errors are found.
WRTTXT Main Sequence: Writes out KEYWRD, KOMENT and TITLE. The
inverse of GETTXT.
XXX Utility: Forms a unique logical name for a Gaussian Z-matrix
logical. Called by GEOUTG only.
- 180 -
DESCRIPTION OF SUBROUTINES IN MOPAC Page C-14
XYZINT Utility: Converts from cartesian coordinates into internal.
XYZGEO XYZINT sets up its own numbering system, so no connectivity
is needed.
- 181 -
APPENDIX D
HEATS OF FORMATION OF SOME MNDO, PM3 AND AM1 COMPOUNDS
In order to verify that MOPAC is working correctly, a large number
of tests need to be done. These take about 45 minutes on a VAX 11-780,
and even then many potential bugs remain undetected. It is obviously
impractical to ask users to test MOPAC. However, users must be able to
verify the basic working of MOPAC, and to do this the following tests
for the elements have been provided.
Each element can be tested by making up a data-file using estimated
geometries and running that file using MOPAC. The optimized geometries
should give rise to heats of formation as shown. Any difference greater
than 0.1 Kcal/mole indicates a serious error in the program.
Caveats
1. Geometry definitions must be correct.
2. Heats of formation may be too high for certain
compounds. This is due to a poor starting geometry
trapping the system in an excited state. (Affects
ICl at times)
- 182 -
HEATS OF FORMATION OF SOME MNDO, PM3 AND AM1 COMPOUNDS Page D-2
Element Test Compound Heat of Formation
MINDO/3 MNDO AM1 PM3
Hydrogen CH4 -6.3 -11.9 -8.8 -13.0
Lithium LiH +23.2
Beryllium BeO +38.6 +53.0
Boron BF3 -270.2 -261.0 -272.1*
Carbon CH4 -6.3 -11.9 -8.8 -13.0
Nitrogen NH3 -9.1 -6.4 -7.3 -3.1
Oxygen CO2 -95.7 -75.1 -79.8 -85.0
Fluorine CF4 -223.9 -214.2 -225.7 -225.1
Magnesium MgF2 -160.7
Aluminium AlF -83.6 -77.9 -50.1
Silicon SiH +82.9 +90.2 +89.8 +94.6
Phosphorus PH3 +2.5 +3.9 +10.2 +0.2
Sulfur H2S -2.6 +3.8 +1.2 -0.9
Chlorine HCl -21.1 -15.3 -24.6 -20.5
Zinc ZnMe2 +19.9 +19.8 8.2
Gallium GaCl3 -79.7
Germanium GeF -16.4 -19.7 -3.3
Arsenic AsH3 +12.7
Selenium SeCl2 -38.0
Bromine HBr +3.6 -10.5 +5.3
Cadmium CdCl2 -48.6
Indium InCl3 -72.8
Tin SnF -20.4 -17.5
Antimony SbCl3 -72.4
Tellurium TeH2 +23.8
Iodine ICl -6.7 -4.6 +10.8
- 183 -
HEATS OF FORMATION OF SOME MNDO, PM3 AND AM1 COMPOUNDS Page D-3
Mercury HgCl2 -36.9 -44.8 -32.7
Thallium TlCl -13.4
Lead PbF -22.6 -21.0
Bismuth BiCl3 -42.6
* Not an exhaustive test of AM1 boron.
- 184 -
APPENDIX E
REFERENCES
On G-DIIS
"Computational Strategies for the Optimization of
Equilibrium Geometry and Transition-State Structures at
the Semiempirical Level", Peter L. Cummings, Jill E. Gready,
J. Comp. Chem., 10, 939-950 (1989).
On Analytical C.I. Derivatives
" An Efficient Procedure for Calculating the Molecular
Gradient, using SCF-CI Semiempirical Wavefunctions with
a Limited Number of Configurations", M. J. S. Dewar,
D. A. Liotard, J. Mol. Struct. (Theochem), 206, 123-133
(1990).
On Eigenvector Following
J. Baker, J. Comp. Chem., 7, 385 (1986).
On ElectroStatic Potentials (ESP)
"Atomic Charges Derived from Semiempirical Methods",
B. H. Besler, K. M. Merz, Jr., P. A. Kollman,
J. Comp. Chem., 11 431-439 (1990).
On MNDO
"Ground States of Molecules. 38. The MNDO Method.
Approximations and Parameters.", M.J.S. Dewar, W.Thiel,
J. Am. Chem. Soc., 99, 4899, (1977).
Original References for Elements Parameterized in MNDO
H M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc., 99, 4907, (1977).
Li Parameters taken from the MNDOC program, written by Walter Thiel,
Quant. Chem. Prog. Exch. No. 438; 2, 63, (1982)
Be M.J.S. Dewar, H.S. Rzepa, J. Am. Chem. Soc, 100, 777, (1978)
B M.J.S. Dewar, M.L. McKee, J. Am. Chem. Soc., 99, 5231, (1977).
C M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc., 99, 4907, (1977).
N M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc., 99, 4907, (1977).
O M.J.S. Dewar, W. Thiel, J. Am. Chem. Soc., 99, 4907, (1977).
F M.J.S. Dewar, H.S. Rzepa, J. Am. Chem. Soc., 100, 58, (1978).
- 185 -
REFERENCES Page E-2
Al L.P. Davis, R.M. Guidry, J.R. Williams, M.J.S. Dewar, H.S. Rzepa
J. Comp. Chem., 2 433, (1981).
Si (a) M.J.S. Dewar, M.L. McKee, H.S. Rzepa, J. Am. Chem. Soc., 100,
3607 (1978). *
(c) M.J.S. Dewar, J. Friedheim, G. Grady, E.F. Healy,
J.J.P. Stewart, Organometallics, 5, 375 (1986).
P M.J.S. Dewar, M.L. McKee, H.S. Rzepa, J. Am. Chem. Soc., 100,
3607 (1978).
S (a) M.J.S. Dewar, M.L. McKee, H.S. Rzepa, J. Am. Chem. Soc., 100,
3607 (1978). *
(b) M.J.S. Dewar, C. H. Reynolds, J. Comp. Chem., 7, 140 (1986).
Cl (a) M.J.S. Dewar, M.L. McKee, H.S. Rzepa, J. Am. Chem. Soc.,
100, 3607 (1978). *
(b) M.J.S. Dewar, H.S. Rzepa, J. Comp. Chem., 4, 158, (1983)
Zn M.J.S. Dewar, K. M. Merz, Organometallics, 5, 1494 (1986).
Ge M.J.S. Dewar, G.L. Grady, E.F. Healy, Organometallics, 6,
186 (1987).
Br M.J.S. Dewar, E.F. Healy, J. Comp. Chem., 4, 542, (1983)
I M.J.S. Dewar, E.F. Healy, J.J.P. Stewart, J. Comp. Chem.,
5, 358, (1984)
Sn M.J.S. Dewar, G.L. Grady, J.J.P. Stewart, J. Am. Chem. Soc.,
106, 6771 (1984).
Hg M.J.S. Dewar, G.L. Grady, K. Merz, J.J.P. Stewart,
Organometallics, 4, 1964, (1985).
Pb M.J.S. Dewar, M. Holloway, G.L. Grady, J.J.P. Stewart,
Organometallics, 4, 1973, (1985).
* - Parameters defined here are obsolete.
On MINDO/3
Part XXVI, Bingham, R.C., Dewar, M.J.S., Lo, D.H,
J. Am. Chem. Soc., 97, (1975).
On AM1
"AM1: A New General Purpose Quantum Mechanical Molecular
Model", M.J.S. Dewar, E.G. Zoebisch, E.F. Healy,
J.J.P. Stewart, J. Am. Chem. Soc., 107, 3902-3909 (1985).
On PM3
"Optimization of Parameters for Semi-Empirical Methods
I-Method", J.J.P. Stewart, J. Comp. Chem. 10, 221 (1989).
"Optimization of Parameters for Semi-Empirical Methods
II-Applications, J.J.P. Stewart, J. Comp. Chem. 10, 221
(1989).
(These two references refer to H, C, N, O, F, Al, Si, P,
S, Cl, Br, and I).
"Optimization of Parameters for Semi-Empirical Methods
III-Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd,
In, Sn, Sb, Te, Hg, Tl, Pb, and Bi", J.J.P. Stewart,
J. Comp. Chem. (In press, expected date of publication,
Feb. 1991).
Original References for Elements Parameterized in AM1
H M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am.
Chem. Soc., 107, 3902-3909 (1985).
- 186 -
REFERENCES Page E-3
B M.J.S. Dewar, C Jie, E. G. Zoebisch, Organometallics,
7 513-521 (1988).
C M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am.
Chem. Soc., 107, 3902-3909 (1985).
N M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am.
Chem. Soc., 107, 3902-3909 (1985).
O M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, J.J.P. Stewart, J. Am.
Chem. Soc., 107, 3902-3909 (1985).
F M.J.S. Dewar, E.G. Zoebisch, Theochem, 180, 1 (1988).
Al M.J.S. Dewar, A.J. Holder, Organometallics, 9, 508 (1990).
Si M.J.S. Dewar, C. Jie, Organometallics, 6, 1486-1490 (1987).
P M.J.S. Dewar, C.Jie, Theochem, 187, 1 (1989)
S (No reference)
Cl M.J.S. Dewar, E.G. Zoebisch, Theochem, 180, 1 (1988).
Zn M.J.S. Dewar, K.M. Merz, Jr., Organometallics, 7, 522 (1988).
Ga M.J.S. Dewar, C. Jie, Organometallics, 8, 1544 (1989).
Br M.J.S. Dewar, E.G. Zoebisch, Theochem, 180, 1 (1988).
I M.J.S. Dewar, E.G. Zoebisch, Theochem, 180, 1 (1988).
Hg M. J. S. Dewar, C. Jie, Organometallics, 8, 1547 (1989).
(see also PARASOK for the use of MNDO parameters for other elements)
On Shift
"The Dynamic 'Level Shift' Method for Improving the
Convergence of the SCF Procedure", A. V. Mitin, J. Comp.
Chem. 9, 107-110 (1988).
On Half-Electron
"Ground States of Conjugated Molecules.
IX. Hydrocarbon Radicals and Radical Ions", M.J.S. Dewar,
J.A. Hashmall, C.G. Venier, J.A.C.S. 90, 1953 (1968).
"Triplet States of Aromatic Hydrocarbons", M.J.S. Dewar,
N. Trinajstic, Chem. Comm., 646, (1970).
"Semiempirical SCF-MO Treatment of Excited States of
Aromatic Compounds" M.J.S. Dewar, N. Trinajstic,
J. Chem. Soc., (A), 1220, (1971).
On Pulay's Converger
"Convergence Acceleration of Iterative Sequences.
The Case of SCF Iteration", Pulay, P., Chem. Phys. Lett.,
73, 393, (1980).
On Pseudodiagonalization
"Fast Semiempirical Calculations",
Stewart. J.J.P., Csaszar, P., Pulay, P., J. Comp. Chem.,
3, 227, (1982).
On Localization
"A New Rapid Method for Orbital Localization."
P.G. Perkins and J.J.P. Stewart, J.C.S. Faraday
(II) 77, 000, (1981).
On Diagonalization
Beppu, Y., Computers and Chemistry,
Vol.6 (1982).
- 187 -
REFERENCES Page E-4
On MECI
"Molecular Orbital Theory for the Excited States of
Transition Metal Complexes", D.R. Armstrong, R. Fortune,
P.G. Perkins, and J.J.P. Stewart, J. Chem. Soc., Faraday
2, 68 1839-1846 (1972)
On Broyden-Fletcher-Goldfarb-Shanno Method
Broyden, C. G., Journal of the Institute for Mathematics
and Applications, Vol. 6 pp 222-231, 1970.
Fletcher, R., Computer Journal, Vol. 13, pp 317-322, 1970.
Goldfarb, D. Mathematics of Computation, Vol. 24,
pp 23-26, 1970.
Shanno, D. F. Mathematics of Computation, Vol. 24,
pp 647-656 1970.
See also summary in
Shanno, D. F., J. of Optimization Theory and Applications
Vol.46, No 1 pp 87-94 1985.
On Polarizability
"Calculation of Nonlinear Optical Properties of
Molecules", H. A. Kurtz, J. J. P. Stewart, K. M. Dieter,
J. Comp. Chem., 11, 82 (1990).
see also
"Semiempirical Calculation of the
Hyperpolarizability of Polyenes",
H. A. Kurtz, I. J. Quant. Chem. Symp., 24, xxx (1990).
On Thermodynamics
"Ground States of Molecules. 44 MINDO/3 Calculations of
Absolute Heat Capacities and Entropies of Molecules
without Internal Rotations." Dewar, M.J.S., Ford, G.P.,
J. Am. Chem. Soc., 99, 7822 (1977).
On SIGMA Method
Komornicki, A., McIver, J. W., Chem. Phys. Lett., 10,
303, (1971).
Komornicki, A., McIver, J. W., J. Am. Chem. Soc., H
94, 2625 (1971)
On Molecular Orbital Valency
"Valency and Molecular Structure", Gopinathan, M. S.,
Siddarth, P., Ravimohan, C., Theor. Chim. Acta
70, 303 (1986).
On Bonds
"Bond Indices and Valency", Armstrong, D.R.,
Perkins, P.G., Stewart, J.J.P., J. Chem. Soc.,
Dalton, 838 (1973).
For a second, equivalent, description, see also
Gopinathan, M. S., and Jug, K., Theor. Chim. Acta,
- 188 -
REFERENCES Page E-5
63, 497 (1983).
On Locating Transition States
"Location of Transition States in Reaction Mechanisms",
M.J.S. Dewar, E.F. Healy, J.J.P. Stewart, J. Chem. Soc.,
Faraday Trans. 2, 3, 227, (1984)
On Dipole Moments for Ions
"Molecular Quadrupole Moments", A.D. Buckingham, Quarterly
Reviews, 182 (1958 or 1959)
On Polymers
"MNDO Cluster Model Calculations on Organic Polymers",
J.J.P. Stewart, New Polymeric Materials, 1, 53-61 (1987).
see also
"Calculation of Elastic Moduli using Semiempirical
Methods", H. E. Klei, J.J.P. Stewart, Int. J. Quant. Chem.
20, 529-540 (1986).
- 189 -
Page Index-1
INDEX
&, 1-7, 2-5 Gaussian, 2-7, 3-2
+, 1-7, 2-5 example, 6-1
Internal to Cartesian, 3-2
Ab initio total energies, 6-10 reaction, 6-17
Abbreviations, 2-1 unoptimizable, 3-8
AIDER, 2-7 Copyright status, 1-3
AIGIN, 2-7 Coulson, 4-8
AIGOUT, 2-7 CRAY-XMP, 1-1
AM1, 2-7
Elements in, 3-6 Damping kinetic energy, 2-13,
AMPAC, 1-3 6-20
ANALYT, 2-7 Data
Analytical Derivatives, 6-5 commas in, 3-1
Avogadro's number, 6-10 example of
for Ethylene, 1-6
Band structure, 2-20 free format input, 3-1
BAR=, 2-8 layout, 1-6
Bartel, 4-7 MNRSD1, 4-1
BIRADICAL, 2-8 output, 4-2
use in EXCITED states, 2-15 Polyethylene, 3-10
use to achieve a SCF, 6-8 Polytetrahydrofuran, 1-8
Boltzmann constant tabs in, 3-1
definition, 6-9 TESTDATA, 5-1
Bond Indices, 1-1 output, 5-2
BONDS, 2-9 Data General, 1-1
Born-von Karman, 6-46 DCART, 2-11
Brillouin Zones, 2-20 DEBUG, 2-11
Debugging, 10-1
C.I., 2-9 keywords, 10-1
incompatible keywords, 2-1 Definition
keyword Boltzmann constant, 6-9
examples of, 2-10 speed of light, 6-9
selection of states, 2-30 DENOUT, 2-11
subroutine to calculate, C-9 DENSITY, 2-11
use in EXCITED states, 2-15 DEP, 2-12
Capped Bonds, 3-7 DEPVAR=n.nn, 2-12
Cartesian Coordinate Dewar Research Group, 1-4
definition, 3-4 Dihedral Angle Coherency, 6-8
CDC 205, 1-1 DIPOLE, 2-12
CHARGE=, 2-11 Dipoles, for ions, E-5
Cluster model, 6-47 DIPX, 2-12
Command Files DIPY, 2-12
COMPILE, 11-3 DIPZ, 2-12
MOPAC, 11-4 DMAX=n.n, 2-13
MOPACCOM, 11-4 DOUBLET, 2-13
RMOPAC, 11-5 DRAW
CONH Linkage, 6-2 Program, 1-5
Constants, Physical, 6-9 DRC, 2-13
Coordinates background, 6-17
dummy atoms in, 2-41 conservation of momentum, 6-19
examples, 3-8 definition of, 6-17
Page Index-2
dummy atoms in, 6-21 definition of, 6-21
general description, 6-19 Heat Capacity, 6-10
introduction, 6-17 Heat of Formation
print limited to extrema, 6-21 COMPFG, C-2
RESTART, 6-20 Criteria, 9-2
use of keywords, 6-21 definition, 4-7, 6-14
DRC=, 2-13 from gaussians, 2-7
description, 6-20 Molecular Standards, D-2
DUMP, 2-13 Precision, 2-31
SYMMETRY effect, 2-34
ECHO, 2-14 HELP
EF, 2-14 description, 1-5
EIGINV, 2-14 HESS=n, 2-18
1ELECTRON, 2-6 Hirano, Tsuneo, 6-9
Elements Hyperpolarizability, 2-27
specification of, 3-5
ENPART, 2-14 Installing MOPAC, 11-1
Entropy, 6-10 Internal Coordinate
ESP, 2-14 definition, 3-1
installing, 11-6 Internal Rotations, 2-38
ESPRST, 2-14 Ions, 1-1
ESR, 2-15 dipoles for, E-5
EXCITED, 2-15 IRC, 2-19
EXTERNAL=, 2-15 definition of, 6-19
example of, 6-22
FILL=, 2-16 example of restart, 6-23
FLEPO, 2-16 general description, 6-19
FMAT (O), 2-17 Hessian matrix in, 6-19
FORCE, 2-17 introduction, 6-17
example of, 5-8 normal operation, 6-19
Force RESTART, 6-20
constants, 1-1, 5-8 transition states, 6-19
reduced masses, 6-40 use of keywords, 6-21
Frame ISOTOPE, 2-19
description of, 6-32 Isotopes, 1-1
specification of, 3-8
Gas constant 'R' ITRY=, 2-19
definition, 6-9 IUPD=n, 2-20
Gaussian
coordinates, 3-2 K=(n.nn,n), 2-20
From MOPAC Z-Matrix, 2-6 Keywords
GEO-OK, 2-17 abbreviations, 2-1
Geometry compatability, 2-1
flags for, 3-8 debugging, 10-1
Internal to Cartesian, 3-2 full list of, 2-2
Gibbs Free Energy, 6-16 priority, 1-7
GMETRY specification, 1-7
description, 7-5 KINETIC, 6-20
GNORM=, 2-18 Kinetic energy
Gould, 1-1 damping, 2-13
GRADIENTS, 2-18 description, 6-20
GRAPH, 2-18 Klyne and Prelog, 6-8
Grid map, 3-8 Komornicki, 4-7
H-PRIORITY, 2-18 LARGE, 2-20
Page Index-3
with DRC, 2-20 UNDEFINED SYMMETRY FUNCT.., 8-9
Layout of Data, 1-6 UNRECOGNIZED ELEMENT NAME, 8-9
Learning, 2-6 WARNING ****, 8-9
LET, 2-21 WARNING: INTERNAL COORD.., 8-9
Lilly Research, 6-6 Microstates
LINK, failure to, 11-4 description of, 6-35
LINMIN, 2-21 MINDO/3, 2-23
Liquids, 2-13, 6-20 allowed atom-pairs, 3-6
LOCALIZE, 2-21 MMOK, 2-23, 6-3
Localized Orbitals, 1-1 MNDO
Elements in, 3-5
Mass-weighted coordinates, 5-9 MODE=n, 2-23
MAX, 2-21 Molecular Orbitals, 1-1
McIver, 4-7 MOPAC
MECI, 2-22 copyright, 1-3
description of, 6-33 cost, 1-3
Message criteria, 9-1
AN UNOPTIMIZABLE.., 8-1 criterion
ATOM NUMBER nn IS ILL..., 8-1 SCFCRT, 9-1
ATOMIC NUMBER nn IS..., 8-2 TOL2, 9-2
*ATOMIC NUMBER OF nn, 8-2 TOLERF, 9-2
ATOMS nn AND nn ARE.., 8-2 TOLERG, 9-2
ATTEMPT TO GO DOWNHILL IS, 8-2 TOLERX, 9-2
BOTH SYSTEMS ARE ON THE..., 8-2 TOLS1, 9-3
C.I. NOT ALLOWED WITH UHF, 8-3 development, 1-4
CALCULATION ABANDONED AT.., 8-3 electronic structure, 7-3
CARTESIAN COORDINATES..., 8-3 geometric structure, 7-1
ELEMENT NOT FOUND, 8-3 installing, 11-1
ERROR IN READ AT ATOM, 8-4 precision, 6-4
FAILED IN SEARCH..., 8-4 programming policy, 7-4
FAILED TO ACHIEVE SCF., 8-4 size of, 11-10
GEOMETRY TOO UNSTABLE..., 8-4 updates, iii
GRADIENT IS TOO LARGE, 8-5 MS=n, 2-24
GRADIENT IS VERY LARGE, 8-5 MULLIK, 2-24
ILLEGAL ATOMIC NUMBER, 8-5
IMPOSSIBLE NUMBER OF OPEN, 8-5 NLLSQ, 2-24
IMPOSSIBLE OPTION REQ.., 8-5 NOANCI, 2-24
INTERNAL COORDINATES READ., 8-5 NODIIS, 2-25
to 8-6 NOINTER, 2-25
JOB STOPPED BY OPERATOR, 8-6 NOLOG, 2-25
MAX. NUMBER OF ATOMS, 8-6 NOMM, 2-25, 6-3
MAX. NUMBER OF ORBITALS, 8-6 NONR, 2-25
MAX. NUMBER OF TWO-ELEC, 8-6 Normal Coordinate Analysis, 5-8,
NAME NOT FOUND, 8-6 6-9
NUMBER OF PARTICLES..., 8-7 NOTHIEL, 2-25
NUMBER OF PERMUTATIONS..., 8-7 NSURF, 2-26
SYMMETRY SPECIFIED, BUT.., 8-7
SYSTEM DOES NOT APPEAR TO, 8-7 OLDENS, 2-26
TEMPERATURE RANGE STARTS, 8-8 OLDGEO, 2-26
THERE IS A RISK OF INF..., 8-8 One electron (keyword), 2-6
THIS MESSAGE SHOULD NEVER, 8-8 One SCF (keyword), 2-6
THREE ATOMS BEING USED.., 8-8 OPEN(n1,n2), 2-26
TIME UP - - -, 8-8 ORIDE, 2-26
TRIPLET SPECIFIED WITH..., 8-9 Original references
UNABLE TO ACHIEVE SELF..., 8-9 AM1, E-2
Page Index-4
elements, E-2 MOSOL, 1-6
BFGS optimization, E-4 Publication Quality, 6-4
bonds, E-4 PULAY, 2-28
C.I. Derivatives, E-1 converger, description of, 6-7
diagonalization, E-3
EF, E-1 QCPE
ESP, E-1 Address, 1-3
G-DIIS, E-1 QUARTET, 2-29
half-electron, E-3 QUINTET, 2-29
localization, E-3
M.O. Valency, E-4 Radicals, 1-1
MECI, E-4 Reaction Coordinate
MINDO/3, E-2 specification of, 3-8
MNDO, E-1 Reaction Coordinates, 6-17
elements, E-1 Reaction Path
PM3, E-2 example of, 5-11
polarizability, E-4 RECALC=n, 2-29
Polymers, E-5 RESTART, 2-29
pseudodiagonalization, E-3 example of in IRC, 6-23
Pulay's converger, E-3 in IRC or DRC, 6-20
SADDLE, E-5 ROOT=, 2-30
SHIFT, E-3 ROT
SIGMA method, E-4 example of, 5-8
thermodynamics, E-4 ROT=, 2-30
Rotational constants, definition,
Partition function, 6-10 6-10
PATH calculation, 5-11
Peptides, 6-2 SADDLE, 2-31
Phonon band structure, 2-20 example of data for, 6-40
Physical Constants, 6-9 limitations, 6-42
PI, 2-27 three atoms in a line, 4-2
Planck's constant, definition, SCALE, 2-31
6-9 0SCF, 2-6
PM3 1SCF, 2-6
Elements in, 3-6 use in debugging, 10-3
Keyword, 2-27 use with FILL=, 2-16
POINT, 2-27 use with GRADIENTS, 2-18
POINT1=n, 2-27 use with PULAY, 2-28
POINT2=n, 2-27 use with RESTART., 2-29
POLAR, 2-27 SCF
Polarizability convergence, 6-6
background, 6-44 damping, 6-7
calculation of, 6-46 failure to achieve., 6-8
MNDO monatomic terms, 6-46 1SCF on an optimized geometry,
Polymers, 1-1 6-5
data for, 1-8, 3-10 SCF Test
POTWRT, 2-27 description of, 6-6
PRECISE, 2-28 SCFCRT=, 2-31
Precision SCINCR, 2-31
changing default, 6-4 Second order hyperpolarizability,
criticisms, 6-4 2-27
low default, 6-4 SELCON, 6-6
Program SETUP, 2-31
DENSITY, 1-5 SETUP=name, 2-32
MOHELP, 1-5 SEXTET, 2-32
Page Index-5
SHIFT THERMO(nnn,mmm), 2-37
description of, 6-7 THERMO(nnn,mmm,lll), 2-37
SHIFT=, 2-32 Thermochemistry
Short version, 11-9 Note on, 6-9
Shutdown, command, 8-6 Third order hyperpolarizability,
Shutdown, working, 11-6 2-27
SIGMA, 2-32 Torsion Angle Coherency, 6-8
SINGLET, 2-33 TRANS, 2-38
SLOPE, 2-33 TRANS=n, 2-38
Sparkles, 3-7 Transition States, 1-1
full description of, 6-31 Translation
Speed of light symmetry, 6-47
definition, 6-9 vectors, 6-47
SPIN, 2-33 TRIPLET, 2-38
STEP, 2-33 TS, 2-39
STEP1, 2-34
STEP2, 2-34 UHF, 2-39
STO3G, 2-34 UNIX systems, 11-7
STO6G, 6-5 Unoptimizable coordinates, 3-8
Subroutines UNOPTIMIZABLE.., 8-1
brief description of, C-1 Updates, iii
calls made by, B-1
calls to, B-5 VAX 11-780, 1-1
full list of, A-1 VECTORS, 2-39
Supercomputers, 1-1 VELOCITY, 2-39
SYMAVG, 2-34 Version Number, 4-5
SYMMETRY, 2-34 Vibrational Analysis, 5-9, 6-9
example of, 2-35
functions, 2-36 WILLIAMS, 2-40
T-PRIORITY, 2-37 X-PRIORITY, 2-40
definition of, 6-21 definition of, 6-21
T=, 2-36 XYZ, 2-40
THERMO, 2-37
example of, 5-8 Zero Point Energy, 5-8
THERMO(nnn), 2-37 Zero SCF (keyword), 2-6