CP-DRIVER MANUAL
13-Feb-16
Pedro Salvador
Dept. of Chemistry, Oakland University, Rochester, Michigan, US
Institute of Computational Chemistry, University of Girona, Spain
The CP program automatically calls Gaussian94/98 in order to perform either
energy, gradient optimizations or frequency corrected for Basis Set Superposition
Error. Three methods can be used automatically to correct for BSSE. Moreover,
the user can define which fragment calculations are necesary in each case in
terms of the fragment symmetry of the supermolecule or any further
approximation.
In order to carry on geometry optimizations with high accuracy, link l103 of
Gaussian must be slightly modified to output (to the file fort.99) the gradient
vector with full precision.
The modification consists in adding the following lines in subroutine GrdOpt,
open(unit=99,status='unknown',form='unformatted')
rewind 99
write(99) Nvar
write(99) (aprint(2,iii),iii=1,Nvar)
close (99)
after line:
515
Continue
A bug in link l301 (Massge subroutine) must be fixed too. The massage of an
atom located in the z-matrix just before a dummy atom induces to an error that
stops the gradient calculation. To fix the bug substitute the following lines
Do 210 J = 1, NZ
If(IAnZ(J).ge.0) I = I + 1
If(I.eq.ICntr) IAnZ(J) = IAn(ICntr)
210 Continue
by
1
Do 210 J = 1, NZ
If(IAnZ(J).ge.0) I = I + 1
If(I.eq.ICntr) then
IAnZ(J) = IAn(ICntr)
goto 213
endif
210 Continue
213 continue
(Note that in Gaussian98 label 210 is changed to 20)
To create the new l103.exe and l301.exe files, first rename the original l103.exe
and l301.exe , use the update utility of Gaussian from the $g9*root/g9* directory,
mg l103.exe
mg l301.exe
then move the new l103.exe and l301.exe files to the desired directory and finally
restore the original l103.exe and l301.exe files.
The new links must be used for the CP-corrected geometry optimizations, hence,
before the route card of the Gaussian calculation the following lines must be
included:
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% subst l301 /home/usr/CP
% subst l103 /home/usr/CP
(full path of the directory where the
l301.exe and l103.exe files are placed)
Counterpoise-correction methods
Site-Site CP method:
The BSSE is defined as the difference between the energy (gradient) of each
fragment with its own basis set and the basis set of the whole molecule, and
summed up to the uncorrected supermolecule respective values.
Pairwise Aditive CP method:
In this case, the BSSE is defined as the difference, for all pairwise interactions,
between the energy (gradient) of each fragment with its own basis set and the
basis set of each dimer in the supermolecule geometry. Again, the resulting
energy(gradient) is summed up to the uncorrected supermolecule respective
values.
Hierarchical CP method:
The BSSE is split in one ,two-body, three-body etc… contributions to the
supermolecule energy. The number of calculations increases dramatically with
the number of fragments. Note that 17 calculations are needed for a three-body
calculation.
Files:
cp.f -> Source code of the driver program.
Input file: cp.met
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Output files: cp.out, cp.res (info to restart calculation), cpfreq.out
(only for frequency calculations)
Scratch files: *.in, cp.geo, cp.com, cp.fchk, cpfreq.fchk (only for
frequency calculations)
Use Fortran77 compiler to create the executable, e.g. cp.x
hess.f -> Program to yield inverse hessian from a Gaussian output file.
matrix is created in file HESS and can be read by the driver program.
Usage : hess.x < gaussian_file
Use Fortran77 compiler to create the executable, e.g. hess.x
glocal.com -> Unix script to invoke Gaussian and formchk Gaussian utility.
For instance:
#!/bin/csh
setenv g98root /usr/soft
source $g98root/g98/bsd/g98.login
setenv GAUSS_SCRDIR /scratch
g98 < $1.in > cp.qfi
formchk $1.chk cp.fchk
rm cp.qfi
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The
freqlocal.com -> Unix script to invoke Freqchk Gaussian utility.
For instance:
#!/bin/csh
setenv g98root /usr/soft
source $g98root/g98/bsd/g98.login
freqchk cpfreq.chk <fc.inp> cpfreq.out
Note that formchk output MUST be cp.fchk whereas Gaussian output for $1.in
calculation can be overwritten. Also, input file for freqchk MUST be named
cpfreq.chk. File fc.inp is used to include the desired options for the freqchk utility
(temperature, pressure, etc..)
The cpfreq.fchk Gaussian formatted checkpoint file is obtained from the
respective supermolecule calculation checkpoint file (cp.fchk), where ONLY the
second derivative matrix has been substituted by the CP-corrected one. Hence,
one can further use the freqchk utility to extract the uncorrected frequencies from
the cp.fchk file (at the given geometry).
Files cp.x, glocal.com and freqlocal.com must be in the same directory and this
directory should be included in the user’s PATH, in order to allow user to run the
calculations in another directory.
When executing the driver program several gaussian input files (*.in) will be
created, as well as a the file cp.geo, containing the current geometry.
The cp.res file is either read upon request in cp.met file or created in order to
save information to resume the calculation. Unix script cp.com is also created for
each calculation and called by the previously set glocal.com script.
Note that only one calculation can be performed correctly in a given directory.
Use different directories for simultaneous calculations.
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Input file: cp.met
File consists in several sections, each starting with the following set of
characters:
# NAME_OF_SECTION #.
1-# METODE # section:
Main section of the input file. Includes several fields in the form:
NAME_OF_FIELD= integer (I) or real (R) numbers
Fields in # METODE # section:
NFRAG= I, being I the number of fragments of the calculation
NVAR= I, being I the number of variables for the calculation. (up to 100)
-Options for the geometry optimization:
TOL= R, being R the threshold of the RMS of the gradient for the
geometry
optimization.
MAXIT= I, being I the maximum number of iterations for the geometry
optimization
NDIIS= I, being I the maximum dimension of the DIIS subspace for the
geometry optimization (up to 10)
HESS= 1 if file HESS is to be used as starting hessian for the optimization,
0 if no initial hessian is given (default)
UPDATE= 1 to activate the BFGS method to update the hessian for the
optimization, 0 otherwise (default)
HESS= 1 if file HESS is to be used as starting hessian for the optimization,
0 if no initial hessian is given (default)
-Options for the CP method and fragment definition
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BSSE = 0 for the SSCP method, 1 for the hierarchical NBODY method, or 2
for the PACP method, default 0.
SYM= 1 to use symmetry, included in # SYMMETRY # section (see below),
0 otherwise, default 0
RESTART= 1 to use cp.res file data to resume the calculation, 0 otherwise
(cp.res file will be overwritten), default 0
SPIN= 0 to use supermolecule charge and multiplicity for all fragments, 1 to use
specific values for each fragment calculation, either in #
FRAG
SYMMETRY # sections (see below). If BSSE=1 then specific
multiplicity must be introduced in # SYMMETRY
#
charge
or
#
and
# section.
Problems and restrictions:
Using the hierarchical counterpoise method, the number of fragment calculations
needed increase enormously with the number of fragments. For this reason,
automatic calculations of either energy or geometry optimizations are not allowed
if NFRAG > 3 and BSSE=1. However, in this case, if symmetry between the
fragments exists, the calculation can be performed by including in the #
SYMMETRY # section the necessary fragment calculations and their respective
scale factors for both energy and gradient.
2-# GEOM # section:
Enter Z-matrix or Cartesian coordinates in Gaussian format. Dummy atoms can
be used, however BQ should be avoided.
eg.
# GEOM ####
X
F1 1 r1
F2 1 r1 2 120.
F3 1 r1 3 120. 2 180.
H1 2 rh1 1 alpha 4 180.
H2 3 rh1 1 alpha 2 180.
H3 4 rh1 1 alpha 3 180.
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3-# FRAGS # section:
Free format input. Fist line must include the number of atoms included in each
fragment. The next N lines include, for each fragment, the number of the atoms
(as specified in the z-matrix or cartesian coordinates in # GEOM # section)
belonging to it.
Finally, if SPIN=1 then two extra lines are needed. First one including the charge
and the second one the multiplicity of each fragment. Note that, in this case, if
BSSE=1 the charge and multiplicity must be included instead in the #
SYMMETRY # section.
4-# VARIABLES # section:
Free format. Enter initial values for the variables specified in the z-matrix or
cartesian coordinates. Do not use “=” between variable name and its value
5-# VARTYP # section:
Free format. Single line including, for each variable 1 if it represents a distance or
2 if is an angle.
6-# GAUSSIAN # section:
Enter route card and charge and multiplicity for Gaussian calculation. Nosymm
keyword must be included. If force keyword is present CP-geometry optimization
is performed. If freq is present CP-frequency calculation is carried out (see
below). If none of the above keywords are present then a single-point CP-energy
is performed
If a general basis is used for the calculation, the basis set specification MUST be
included in file cp.gbs but not in this section.
For instance,
# GAUSSIAN ###
%mem=100Mb
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%subst l103 /usr/users/pedros/bin
# mp2/6-31++G(d,p) 6d nosymm force
MP2 HF-trimer CP-corrected optimization
01
Restrictions and problems:
Input is CASE SENTITIVE. Please, use lower case for force, freq and gen
Gaussian keywords.
Frequency calculations:
No symmetry can be used. Note that the second derivatives for the fragment
calculations are obtained using the following Gaussian keywords:
opt=CalcFC optcyc=1
Hence, most probably, an error message will appear at the end of each Gaussian
calculation, which, however, will not affect the CP-corrected frequency
calculation.
7-# SYMETRY # section
Must be included if SYM=1 on # METODE # section.
First, enter number of fragment calculations will be performed. Then enter,
separated by commas, name of calculation to be performed, scale factor for the
gradient and energies. Charge and multiplicity for each calculation must also be
included if BSSE=1 and SPIN=0 in # METODE # section.
The name of each calculation is set in this way:
(fragments included) _ (basis set used)
For instance, the following line
12_123 , -2.0 , 0 ,1
specifies that fragments 1 and 2 (as defined in # FRAGS # section) using basis
set of fragments 1, 2 and 3 are included in the calculation. Also, both energy and
gradient will be scaled by -2.0 and summed up to the corresponding uncorrected
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supermolecule energy and gradient respectively. Charge=0 and multiplicity=1
will be used.
Restrictions and problems:
The uncorrected supermolecule calculation must be included in the last line.
eg. for N fragments:
12...N_12...N, 1.0, 0 , 1
8-Ending card:
Line including “---“ set of characters indicates the end of the input file.
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EXAMPLE 1:
HF trimer SCF/SSCP geometry optimization using symmetry:
# METODE ##
NVAR=3 NFRAG=3 NDIIS=5 MAXIT=9 UPDATE=1 HESS=1 SPIN=0
BSSE=0 RESTART=0 SYM=1 TOL=0.0001
# VARIABLES #####
rh1
0.941
r1
1.550
alpha
52.3
# VARTYP ####
112
(Type of variable, in the same order as in previous section)
# FRAGS #####
222
14
25
36
000
(charge optional as SPIN=0)
111
(multiplicity optional as SPIN=0)
# GEOM ####
X
(dummy atom not considered in previous section)
F1 1 r1
F2 1 r1 2 120.
F3 1 r1 3 120. 2 180.
H1 2 rh1 1 alpha 4 180.
H2 3 rh1 1 alpha 2 180.
H3 4 rh1 1 alpha 3 180.
# GAUSSIAN ###
%subst l103 /usr/users/pedros/bin
%subst l301 /usr/users/pedros/bin
# MP2/6-31G(d,p) nosymm force
(CP-geometry optimization)
MP2 calculation of HF trimer using symmetry
01
# SYMETRY ##
3
1_1 , 3.0
1_123 ,-3.0
123_123 ,1.0
---
(three calculations are needed)
(HF basis calculation, equiv. to the other HF’s in molecule)
(HF full basis calc., equiv. to the other HF’s in molecule)
(Trimer calculation introduced last)
(end of file line)
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EXAMPLE 2:
HF trimer SCF/PACP energy calculation:
# METODE ##
NVAR=3 NFRAG=3 NDIIS=5 MAXIT=9 UPDATE=1 HESS=1 SPIN=0 TOL=0.0001
BSSE=2 SYM=0
(any field not present set to default value)
# VARIABLES #####
rh1
0.941
r1
1.550
alpha
52.3
# VARTYP ####
112
(Type of variable, in the same order as in previous section)
# FRAGS #####
222
14
25
36
# GEOM ####
X
(dummy atom not considered in previous section)
F1 1 r1
F2 1 r1 2 120.
F3 1 r1 3 120. 2 180.
H1 2 rh1 1 alpha 4 180.
H2 3 rh1 1 alpha 2 180.
H3 4 rh1 1 alpha 3 180.
# GAUSSIAN ###
%subst l301 /usr/users/pedros/bin
%subst l103 /usr/users/pedros/bin
# SCF/6-31G(d,p) nosymm 6d
(CP-corrected energy calculation)
gfinput
HF calculation of HF trimer
01
---
(end of file line)
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EXAMPLE 3:
HF trimer MP2/ Hierachical CP-corrected frequencies:
# METODE ##
NVAR=3 NFRAG=3 NDIIS=5 MAXIT=9 UPDATE=1 HESS=1 SPIN=0
BSSE=1 RESTART=0 SYM=0
# VARIABLES #####
rh1
0.941
r1
1.550
alpha
52.3
# VARTYP ####
112
(Type of variable, in the same order as in previous section)
# FRAGS #####
222
14
25
36
# GEOM ####
X
(dummy atom not considered in previous section)
F1 1 r1
F2 1 r1 2 120.
F3 1 r1 3 120. 2 180.
H1 2 rh1 1 alpha 4 180.
H2 3 rh1 1 alpha 2 180.
H3 4 rh1 1 alpha 3 180.
# GAUSSIAN ###
%subst l103 /usr/users/pedros/bin
%subst l301 /usr/users/pedros/bin
# MP2/6-31G(d,p) nosymm freq
(CP-frequency calculation)
MP2 calculation of HF trimer
01
# SYMETRY ##
(No symmetry can be used for frequencies)
---
(end of file line)
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