Skip to content
No description, website, or topics provided.
Jupyter Notebook Python Shell CSS JavaScript HTML
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
bin frequency for ts Apr 22, 2019
jupyterNotebooks standalone pyfrag for gaussian orca turbomole and excel figure Mar 11, 2019
process code with old remains Jan 30, 2019
qmworks add function to support the HOMO-1 or LUMO+3 Jun 13, 2019
server frequency for ts Apr 22, 2019
.pyfragrc check out Apr 21, 2019
.travis.yml add plams as part of qmworks Apr 13, 2019
README.rst PyFrag 2019 Apr 20, 2019 installation update Apr 17, 2019
jobresult.png doc update Apr 17, 2019
requirements.txt doc Feb 6, 2019



PyFrag 2019

See documentation for tutorials and documentation.


The PyFrag 2019 program was specially designed to facilitate the analysis of reaction mechanism in a more efficient and user-friendly way. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. This approach is routinely applied in the Bickelhaupt Group to understand numerous organic, inorganic, and biomolecular reactions/processes. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring of the entire computational process along with the extraction and plotting of relevant information from large amounts of data; and 3) the analysis and presentation of these data in a clear and informative way. The activation strain and canonical energy decomposition results that are generated, relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species.



In order to see all the commands that can be used in this program, the user can type pyfrag -h, 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 is job input
pyfrag -x restart
pyfrag -s -x summary

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 parameters, and geometry parameters. Additional information about the input file can be found in input explanation and main specifications in the following webpages.

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



type TZ2P
core Small

gga OPBE

relativistic SCALAR ZORA

iterations 299
converge 0.00001
mixing 0.20

numericalquality verygood

charge 0 0
symmetry auto



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

PyFrag END


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

Result example

After the job has been submitted, a website as provided in the figure below will be launched that summarizes all relevant information, including: a) the convergence information, b) the latest structure from the optimization in the form of movie, c) the latest energy and coordinates, and d) the activation strain analysis (if a job is finished). The user can decide if the trend of optimization is right or wrong, and if necessary, the job can be stopped. If the input file has been modified, the job will be resubmitted and the overall workflow will resume from where it stopped before.



For installation, please read installation.

You can’t perform that action at this time.