The Absolute Beginners Guide to Gaussian
David Young
Cytoclonal Pharmaceutics Inc.
Introduction:
This is to teach the beginner how to use the Gaussian XX series of programs.
This guide is intended for use by someone who has never used the program
before.
This guide is in no way intended to be a comprehensive or advanced guide to
the Gaussian program. Also, this is not an explanation of the theory behind
the types of calculations or their strengths, weaknesses, accuracy, etc.
The term 'ab initio' in this guide refers to methods which calculate purely
from the principle of quantum mechanics with no experimental data involved.
The term 'semiempirical' refers to methods which use the general process
dictated by quantum mechanics, but simplify it to gain speed then correct for
the simplification by the use of some experimental data.
The Gaussian programs are given version numbers according to which year they
were released (i.e. Gaussian 90 is the 1990 version). Gaussian is a program
for doing ab initio and semiempirical calculations on atoms and molecules. The
program is operated by making an ASCII input file using any convenient text
editor then running the program. The results of the calculation are put in one
or more output file. Gaussian itself currently has no provisions for graphical
or interactive inputs or outputs. However, such things do exist for use with
Gaussian and can be obtained from other sources.
This guide gives the input description by showing three sample input files and
describing what they mean. A section is provided on the calculation of
vibrational frequencies followed by a brief description of outputs and lists of
the input options.
Input file for an atom:
Input files can have any name but often use the extension '.inp' or '.input'
or '.com' depending on the system. Here is a sample input file for a single
atom calculation.
$ RunGauss
#n test rohf/sto-3g pop=full GFINPUT
O sto-3g triplet
0 3
O
Line 1: '$ RunGauss' This line is always the same. Although optional on some
machines it is a good practice to use it always.
Line 2: (blank) Line 2 is blank for many calculations. It can be used to
specify a checkpoint file name or memory allocation.
Line 3: '#n test rohf/sto-3g pop=full GFINPUT' Line 3 is called the route
card. It specifies what type of calculation to do and what to calculate and
output. The line always starts with '#'. The 'n' suppresses printing of
debugging messages. The 'test' suppresses keeping a summary of the job in a
central data bank called an archive. 'rohf' is the ab initio keyword. It
stands for 'restricted open-shell Hartree Fock'. Ab initio keywords must
always be followed by a '/' and a basis set designation such as 'sto-3g'. The
'pop=full' specifies the printing of a full Mulliken population analysis. The
'GFINPUT' puts a copy of the basis set in the output file.
Line 4 is blank.
Line 5: 'O sto-3g triplet' Line 5 is a comment for the users reference only.
Line 6 is blank.
Line 7: '0 3' Line 7 consists of two numbers. The first is the charge and
the second is the spin multiplicity.
Line 8: 'O' Line 8 specifies that oxygen is the atom to be calculated.
Line 9: Leave at least one extra blank line at the end of the input file.
Input example for a diatomic molecule:
Here is a sample input for a diatomic molecule
$ RunGauss
# test rhf/STO-3G opt
CO sto-3g
0 1
C
O 1 R
R 0.955
Only significant differences from the atom input file will be mentioned.
Line 3: '# test rhf/STO-3G opt' The 'rhf' stands for 'restricted Hartree
Fock'. The 'opt' specifies that the program is to find the correct geometry
for the molecule, as predicted by the specified ab initio method and basis set
(in this case the bond distance).
Lines 8-11 are called the Z-matrix. These lines specify the geometry of the
molecule and which parameters are to be optimized if an 'opt' keyword is on the
route card.
Line 8: 'C' This specifies that the first atom is a carbon atom.
Line 9: 'O 1 R' specifies that an oxygen atom is at a distance R from the
first atom (the carbon). R is defined (in Angstroms) on line 11. If an
optimization is being done, a new value for R representing the most stable
geometry will be given in the output file.
Input file for a polyatomic molecule:
Here is an input file for a formaldehyde molecule.
$RunGauss
# test MNDO pop=reg
Formaldehyde single point w/ populations
0 1
C
O 1 OC
H 1 HC 2 A
H 1 HC 2 A 3 180.0
OC 1.2
HC 1.08
A 120.0
Line 3: '# test MNDO pop=reg' The ab initio method and basis have been
replaced by a semiempirical method keyword 'MNDO'. The 'pop=reg' specifies a
Mulliken population analysis, but not as much information printed as with
'pop=full'.
Line 5: 'Formaldehyde single point w/ populations' Note that a calculation,
which is not a geometry optimization is referred to as a single point
calculation.
Line 8: 'C' The first atom is a carbon.
Line 9: 'O 1 OC' The second atom is an oxygen with a distance to the first
atom of OC.
Line 10: 'H 1 HC 2 A' The third atom is a hydrogen with a distance to the
first atom of HC and an angle between the third, first and second atoms of A
(in degrees).
Line 11: 'H 1 HC 2 A 3 180.0' The fourth atom is a hydrogen with a distance
to the first atom of HC and an angle between the third, first and second atoms
of A. The dihedral angle between the first, second, third and fourth atoms is
180 degrees (a planar molecule).
If an optimization were being done, the parameters OC, HC and A would be
optimized, but the molecule would be kept planar. Note that parameters can be
used more than once.
Additional atoms are added by adding lines like line 11 consisting of
distance, angle and dihedral angle specifications.
Gaussian does have provisions for entering geometries as x, y, z Cartesian
coordinates.
Geometry specifications sometimes uses points not on atomic centers out of
convenience or necessity. These are called dummy atoms. These will not be
covered in this guide.
Calculating frequencies:
Gaussian can calculate vibrational modes along with their frequencies and
force constants, using the 'FREQ' keyword. These calculations are only
meaningful if the molecule is at its equilibrium geometry for the given level
of theory. Also, geometry optimizations and frequency calculations cannot be
done in the same job. Therefore, to get a frequency calculation, first a
geometry optimization should be done then the optimized geometry must be used
to run a frequency calculation.
The output file:
At least one output file is always produced. It can have any filename, but
many systems are set up to use extensions '.lis' or '.out'. This is an ASCII
file which contains most of the results of the calculation, such as energies,
geometries, frequencies and population analysis. Many things are put in this
file that the user often ignores on any given calculation.
Checkpoint files:
When a subsequent calculation is to use results from a previous
calculation as
its inputs, these results can be kept in a special file to avoid having to type
them into the new input file. Many such result are put in a file called a
checkpoint file. It is a binary file. The use of a checkpoint file can be
specified using the correct options on line 2 and the route card.
Cube files:
Properties, such as electron density or spin density can be calculated for a
regular grid of points in space and saved as a cube file. This is a file with
both binary and ASCII formats, which is often used as an input for other
graphical visualization programs.
Cube file generation is prompted by usage of the 'CubeDensity' keyword and
specification of a grid of points.
Other files:
Gaussian has many other optional input and output files. Often these are
accessed as standard FORTRAN units according to the conventions of the specific
operating system being used.
List of ab initio keywords:
Note that an ab initio keyword must be accompanied by a basis set keyword in
the format 'ab_initio/basis'. All of these can be prefaced by R for
closed-shell restricted wave functions, U for unrestricted open-shell
wavefunctions or RO for restricted open-shell wavefunctions. This list is
provided for the sake of seeing what is available. Many of these have
additional options describing how to control the calculation which are listed
in the Gaussian User's Guide and Programmer's Reference.
HF - Hartree Fock (uses RHF for singlets and UHF for others)
RHF - restricted Hartree Fock
UHF - unrestricted Hartree Fock
ROHF - spin-restricted open-shell Hartree Fock
OSS - two open shell singlet wave function
GVB - generalized valence bond
CASSCF - complete active space MCSCF
MP2 - Moller-Plesset second order correlation energy correction
MP3 - Moller-Plesset third order correlation energy correction
MP4 - same as MP4SDTQ
MP4DQ - Moller-Plesset fourth order correlation energy correction with double
and quadruple substitutions.
MP4SDQ - Moller-Plesset fourth order correlation energy correction with single,
double and quadruple substitutions.
MP4SDTQ - Moller-Plesset fourth order correlation energy correction with single,
double, triple and quaduple substitutions.
CI - same as CISD
CIS - configuration interaction with single excitations
CID - configuration interaction with double excitations
CISD - configuration interaction with single and double excitations
QCISD - quadratic configuration interaction with single and double excitations
QCISD(T) - quadratic configuration interaction with single and double excitations
and triples contribution to the energy
List of basis sets available:
Note that a basis set must accompany an ab initio keyword. The '*' and '**'
indicate polarization functions (i.e. 6-31G**). The '+' and '++' indicate
diffuse functions. For other options and how to use these options, see the
Gaussian User's Guide and Programmer's Reference.
| basis | options | atoms |
|---|---|---|
| STO-3G | * | H - Xe |
| 3-21G | * ** | H - Cl |
| 4-21G | * ** | |
| 4-31G | * ** | H - Ne |
| 6-21G | * ** | |
| 6-31G | + ++ * ** | H - Cl |
| LP-31G | * ** | |
| LP-41G | * ** | |
| 6-311G | + ++ * ** | H - Ar |
| MC-311G | none | H - Ar |
| D95 | + ++ * ** | H - Cl |
| D95V | + ++ * ** | H - Ne |
| SEC | + ++ * ** | H - Cl (same as SHC) |
| CEP-4G | + ++ * ** | H - Cl |
| CEP-31G | + ++ * ** | H - Cl |
| CEP-121G | + ++ * ** | H - Cl |
| LANLIMB | none | H - Bi (except lanthanides) |
| LANLIDZ | none | H - Bi (except lanthanides) |
The GEN keyword allows the basis set to be read from the input file.
List of semiempirical keywords:
Note that semiempirical methods do not require a separate basis set. All of
these can be prefaced by R for closed-shell restricted wavefunctions, U for
unrestricted open-shell wavefunctions or RO for restricted open-shell
wavefunctions. This list is provided for the sake of seeing what is available.
Many of these have additional options describing how to control the calculation
which are listed in the Gaussian User's Guide and Programmer's Reference.
AM1 - Austin method one
CNDO - complete neglect of differential overlap
INDO - intermediate neglect of differential overlap
MINDO3 - modified intermediate neglect of differential overlap third
modification.
MNDO - modified neglect of differential overlap
List of keywords:
This is the list of what to calculate and what to print and how to manage the
calculation. This is not a comprehensive list. This list is provided for the
sake of seeing what is available. For other options and how to use these
options, see the Gaussian User's Guide and Programmer's Reference.
ANG - distances in Angstroms
AU - distances in bohrs
DEG - angles in degrees
RAD - angles in radians
CubeDensity - generate a cube file
Density - for cube file generation
direct - do integrals as needed (vice in a file on the disk)
InCore - do integrals in core memory
field - add a finite field to the calculation
freq - frequency determination
freq=noraman - frequency determination without Raman intensities
GFPRINT - put basis in output file
GFINPUT - put basis in output file in format for generalized input
IRC - follow a reaction path
LST - linear synchronous transit
NoFreeze - optimize all variables
opt - geometry optimization
Polar - calculate polarizability and hyperpolarizability, if possible
pop=none - no population analysis
pop=min - minimal printing of Mulliken population analysis
pop=reg - some printing of Mulliken population analysis
pop=full - full printing of Mulliken population analysis
pop=bonding - bonding population analysis
pop=no - natural orbital analysis
pop=noab - natural orbital analysis for separate alpha and beta spins
prop=grid - computes electrostatic potential
prop=field - computes electrostatic potential and field
prop=EFG - computes electrostatic potential, field and field gradients
punch - puts various information in a separate output file
ReadIsotopes - read in masses for each atom
Restart - restart optimization from a checkpoint file
TS - optimization of a transition state
An expanded version of this article will be published in
"Computational Chemistry: A Practical Guide for Applying Techniques
to Real World Problems" by David Young, which will be available from
John Wiley & Sons in the spring of 2001.
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