Command line interface#

ReacNetGenerator is an automatic reaction network generator for reactive molecular dynamics simulation.

usage: reacnetgenerator [-h] -i [INPUTFILENAME ...] -a [ATOMNAME ...]
                        [--nohmm] [--miso MISO]
                        [--dump | --type {bond,lammpsbondfile,dump,lammpsdumpfile,xyz}]
                        [--nopbc] [--cell CELL [CELL ...]] [-n NPROC]
                        [-s [SELECTATOMS ...]] [--stepinterval STEPINTERVAL]
                        [--split SPLIT] [--maxspecies MAXSPECIES]
                        [--matrixa MATRIXA MATRIXA MATRIXA MATRIXA]
                        [--matrixb MATRIXB MATRIXB MATRIXB MATRIXB]
                        [--urls URLS URLS] [--version]

Named Arguments#

-i, --inputfilename

Input trajectory file(s), e.g. bonds.reaxc; If multiple file are given, they are concatenated.

-a, --atomname

Atomic names in the trajectory, e.g. C H O


Process trajectory without Hidden Markov Model (HMM). If one wants to enable HMM, firstly read the related section in the paper

Default: False


Merge the isomers

Default: 0


(deprecated) Process the LAMMPS dump file. Please use –type dump instead.

Default: False

--type, -t

Possible choices: bond, lammpsbondfile, dump, lammpsdumpfile, xyz

Input file type

Default: “lammpsbondfile”


Disable PBC.

Default: False

--cell, -c

Cell information if PBC is enabled and the input file does not contain cell information. The cell information should be in 3x3 matrix format.

-n, -np, --nproc

Number of processes, by default using all processes

-s, --selectatoms

Select element(s) in the reaction network, e.g. C


Step interval, i.e. read every N step from the trajectory

Default: 1


Split number for the time axis; the whole trajectroy will be splited into N parts for analysis

Default: 1


Max number of nodes (species) in the network

Default: 20


Transition matrix A of HMM parameters

Default: [0.999, 0.001, 0.001, 0.999]


Emission matrix B of HMM parameters

Default: [0.6, 0.4, 0.4, 0.6]


Download files before analysis, in the format of –urls filename url


show program’s version number and exit

Examples: reacnetgenerator –type bond -i bonds.reaxc -a C H O –nohmm reacnetgenerator –type dump -i dump.reaxc -a C H O –nohmm reacnetgenerator –type xyz -i -a C H O –nohmm -c 10 0 0 0 10 0 0 0 10