Basic Usage Tutorial¶
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.
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
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.