Basic Usage Tutorial

Usage

The user can type pyfrag -h to see all the commands that can be used in this program, which will show:

Usage: pyfrag [-h] [-s] [-x command]  [...]
-h          : print this information
-s          : run job quietly
-x          : start the executable named command
            : command include restart, which restart job
            : restart, which restart a job after it is stoped
            : summary, which summarize all job result after jobs finished
            : default command is pyfrag itself
The example command is like as follow, in which job.in is job input
pyfrag job.in
or
pyfrag -x restart job.in
or
pyfrag -s -x summary job.in

To submit a job, create a directory and generate a input file and run the following command to submit a job. Note for each job, a new directory and a new job name should be given. Note: The user should avoid running more than one job in a single directory.

pyfrag job.in

To obtain the latest information about your job, the user can run:

pyfrag -x summary job.in

If a change in the input file is required, make the change and the resubmit the job using:

pyfrag -x restart job.in

Sample Input Example

A simple job input is provided below. The input script can be roughly divided into four section: the required submit information for a job scheduling system (Slurm in this example), ADF parameters, PyFrag 2019 parameters, and geometry parameters.

''''
JOBSUB section is for the information passed to the remote host machine
where the heavy computational job is done! It is written in the fashion of Slurm.
''''
JOBSUB

#!/bin/bash
#SBATCH -J frag_1
#SBATCH -N 1
#SBATCH -t 50:00
#SBATCH --ntasks-per-node=24
#SBATCH --partition=short
#SBATCH --output=%job.stdout
#SBATCH --error=%job.stdout
export NSCM=24

JOBSUB END

''''
Provide the parameters for a DFT calculation using ADF software.
''''
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 0
symmetry auto


ADF END

''''
Provide the parameters for an activation strain analysis.
Noted a bondlength calculation is needed to provilde x axis value for ASA.
''''

PyFrag

fragment  2
fragment  1 3 4 5 6
strain    0
strain   -554.09
bondlength 1 6  1.09

PyFrag END


''''
Guessed geometry coordinate for reactent1, reactent2, reactent complex,
transition state and product.
''''

Geometrycoor

R1: Fe-II(CO)4 + CH4
Pd       0.00000000       0.00000000       0.32205546

R2: CH4
C       0.00000000       0.00000000      -1.93543634
H      -0.96181082       0.00000000      -1.33610429
H       0.00000000      -0.90063254      -2.55201285
H       0.00000000       0.90063254      -2.55201285
H       0.96181082       0.00000000      -1.33610429

RC: Fe-II(CO)4 + CH4
C       0.00000000       0.00000000      -1.93543615
Pd       0.00000000       0.00000000       0.322055
H      -0.96181082       0.00000000      -1.33610429
H       0.00000000      -0.90063254      -2.55201285
H       0.00000000       0.90063254      -2.55201285
H       0.96181082       0.00000000      -1.33610429

TS: Fe-II(CO)4 + CH4
C      -1.74196777      -2.22087997       0.00000000
Pd     -2.13750904      -0.23784341       0.00000000
H      -2.80956968      -2.49954731       0.00000000
H      -1.26528821      -2.62993236       0.8956767
H      -1.26528821      -2.62993236      -0.895676
H      -0.75509932      -0.88569836       0.00000000

P: Fe-II(CO)4 + CH4
C      -2.10134690      -2.41901732       0.1862099
Pd      -2.73145901      -0.57025833       0.419766
H      -3.88639130      -1.04648079      -0.43099501
H      -2.78392696      -3.12497645       0.66994616
H      -1.97386865      -2.66955518      -0.87144525
H      -1.12556673      -2.41201402       0.698583

Geometrycoor END

The user might want to specify an additional input for the different sections of the overall workflow. To specify additional information for say, fragment1 and fragment2 see the syntax shown below. Additional complex insert statements for the fragment analysis calculation can be added. Similarly, the R1 EXTRA, R2 EXTRA, RC EXTRA, TS EXTRA, P EXTRA, IR EXTRA insert statements for R1, R2, RC, TS, P, IRC calculation.

fragment1 EXTRA
charge 1
fragment1 EXTRA END

fragment2 EXTRA
charge -1
fragment2 EXTRA END

complex EXTRA
charge 2
complex EXTRA END

R1 EXTRA
charge 0
R1 EXTRA END

R2 EXTRA
charge 0
R2 EXTRA END

RC EXTRA
charge 0
RC EXTRA END

TS EXTRA
charge 0
tsrc
Bond 1 2 -1
end
TS EXTRA END

P EXTRA
charge 0
P EXTRA END

IR EXTRA
Geometry
 IRC Backward POINTS=20 STEP=1
ITERATIONS 300
CONVERGE 0.000001
End
IR EXTRA END

Result example

After the job has been submitted, a website as shown in the figure below will be launched. The website summarizes all relevant information, including: a) the convergence criteria, b) the latest structure from the optimization in the form of movie, c) the latest energy and coordinates, and d) the activation strain analysis (once the complete workflow has finished). The user can decide if the optimization process is correct or incorrect, and if necessary, can stop the job. If the input file is then modified or updated, the job will be resubmitted and the overall workflow will resume from where it left off.

result