Simple Pyfrag Calculation¶
The user may choose to only install the part of the program needed to perform the Activation Strain Analysis (ASA) based on Activation Strain Model (ASM). The ASA can be performed using a variety of quantum chemical software packages, including: ADF, Gaussian, Orca, and Turbomole. The user must only provide a series of coordinate from the reaction path. An input sample is provided in the standalone example folder for either ADF, Gaussian, Orca and Turbomole.
ADF¶
The basic PyFrag 2019 input for the Activation Strain Analysis (ASA) using ADF is similar to the previous input example, except the coordinate section:
JOBSUB
#!/bin/bash
#SBATCH -J NNC
#SBATCH -N 1
#SBATCH -t 24:00:00
#SBATCH --ntasks-per-node=24
#SBATCH --partition=normal
#SBATCH --output=%job.stdout
#SBATCH --error=%job.stdout
export NSCM=24
JOBSUB END
PyFrag
ircpath /home/x2sun/pyfragnew/test/molecule.xyz
fragment 2
fragment 1 3 4 5 6
strain 0
strain -554.09
bondlength 1 6 1.09
PyFrag END
ADF
basis
type TZ2P
core Small
end
xc
gga OPBE
end
relativistic SCALAR ZORA
scf
iterations 299
converge 0.00001
mixing 0.20
end
numericalquality verygood
charge 0
symmetry auto
ADF END
The only difference compared with the previous job input is that the user must provide the path to a series of coordinates. For additional specifications, the user can read the previous page. The user can specify the filename of a linear transit (LT), scan, IRC, or a simple text output file you wish to analyze. Note: When using a TAPE21, the file should have the .t21 extension. The user can specify two output files for an IRC TAPE21 (backward and forward). A text file containing coordinates of an IRC calculation is also acceptable, for example, a text file generated by ADFmovie or Gaussian.
ircpath path/filename.xyz
irct21 path/filename.t21
lt path/filename.t21
To submit a job, create a directory and generate a input file and run the following command to submit a job:
pyfrag job.in
If more terms needed to be printed, user can simply re-run the job as long as the plams directory exists. During the process, PyFrag just extracts the new information from the previous result without actually doing new calculation. In order to do that, the path to the plams directory should be specified in the job file in the PyFrag section, such as:
PyFrag
restartjob /path/to/plams/directory
ircpath /home/x2sun/pyfragnew/test/molecule.xyz
fragment 2
fragment 1 3 4 5 6
strain 0
strain -554.09
bondlength 1 6 1.09
PyFrag END
To submit a job, create a directory and generate a input file and run the following command to submit a job:
pyfrag job.in
Gaussian¶
The basic PyFrag 2019 input for the Activation Strain Analysis (ASA) using Gaussian is as follows:
INPUT_SPECS
type = IRC
output file = Ethylene-forward.amv
frag1 = C4H6
1
2
3
4
5
6
7
8
13
14
end frag1
frag2 = C2H4
9
10
11
12
15
16
end frag2
print bond 1 9 1.384
print strain frag1 1000
print strain frag2 2000
END INPUT_SPECS
"g09" <<eor
%nprocs=16
%mem=14000mb
#OPBE/6-31G*
Comments
0 1
END INPUT
The first section between INPUT_SPECS and END INPUT_SPECS is used to define fragment and provide coordinate path. The second section between END INPUT_SPECS and END INPUT is used to do Gaussian parameter set up.
User can also specify different parameters for fragment 1, fragment 2 and tatol complex in the extra section such as between EXTRA frag1 and END EXTRA frag1 using input example as below:
INPUT_SPECS
type = IRC
output file = Ethylene-forward.amv
fa1_name = complex
frag1 = C4H6
1.C
2.H
3.C
4.H
5.C
6.H
7.C
8.H
13.H
14.H
end frag1
frag2 = C2H4
9.C
10.C
11.H
12.H
15.H
16.H
end frag2
print bond 1 9 1.384
print strain frag1 1000
print strain frag2 2000
END INPUT_SPECS
END INPUT
EXTRA frag1
"g09" <<eor
%nprocs=16
%mem=14000mb
#OPBE/6-31G* -1
Comments
0 1
END EXTRA frag1
EXTRA frag2
"g09" <<eor
%nprocs=16
%mem=14000mb
#OPBE/6-31G* 0
Comments
0 1
END EXTRA frag2
EXTRA fa
"g09" <<eor
%nprocs=16
%mem=14000mb
#OPBE/6-31G* -1
Comments
0 1
END EXTRA fa
To submit a job, create a directory and generate a input file and run the following command to submit a job:
pyfrag -x gaussian job.in
Orca¶
The basic PyFrag 2019 input for the Activation Strain Analysis (ASA) using Orca is as follows:
INPUT_SPECS
type = IRC
output file = irc.amv
frag1 = H2
1
2
end frag1
frag2 = H2
3
4
end frag2
print bond 1 3 1.00
print strain frag1 100
print strain frag2 200
END INPUT_SPECS
! SP B3LYP 6-31G(d)
* xyz 0 1
END INPUT
The first section between INPUT_SPECS and END INPUT_SPECS is used to define fragment and provide coordinate path. The second section between END INPUT_SPECS and END INPUT is used to do Orca parameter set up. To submit a job, create a directory and generate a input file and run the following command to submit a job:
pyfrag -x orca job.in
Turbomole¶
The basic PyFrag 2019 input for the Activation Strain Analysis (ASA) using Turbomole is as follows:
INPUT_SPECS
type = IRC
output file = irc.amv
frag1 = pd
1
2
end frag1
frag2 = cc
3
4
end frag2
print bond 1 3 1.00
print strain frag1 100
print strain frag2 200
END INPUT_SPECS
%method
ENRGY :: b-p/SVP [gen_stat=1,scf_msil=99,&
scf_grid=m4]
%charge
0
%coord
%end
END INPUT
The first section between INPUT_SPECS and END INPUT_SPECS is used to define fragment and provide coordinate path. The second section between END INPUT_SPECS and END INPUT is used to do Turbomole parameter set up. To submit a job, create a directory and generate a input file and run the following command to submit a job:
pyfrag -x turbomole job.in