Command line interface#

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

usage: reacnetgenerator [-h] -i [INPUTFILENAME [INPUTFILENAME ...]] -a
                        [ATOMNAME [ATOMNAME ...]] [--nohmm] [--miso MISO]
                        [--dump]
                        [--type {lammpsbondfile,bond,lammpsdumpfile,dump,xyz}]
                        [--nopbc] [--cell CELL [CELL ...]] [-n NPROC]
                        [-s [SELECTATOMS [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

--nohmm

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

Default: False

--miso

Merge the isomers

Default: 0

--dump

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

Default: False

--type, -t

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

Input file type

Default: “lammpsbondfile”

--nopbc

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

--stepinterval

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

Default: 1

--split

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

Default: 1

--maxspecies

Max number of nodes (species) in the network

Default: 20

--matrixa

Transition matrix A of HMM parameters

Default: [0.999, 0.001, 0.001, 0.999]

--matrixb

Emission matrix B of HMM parameters

Default: [0.6, 0.4, 0.4, 0.6]

--urls

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

--version

show program’s version number and exit

Examples: reacnetgenerator –type bond -i bonds.reaxc -a C H O –nohmm