This is the github repository for the Python LAMMPS Analysis Tools.
Some of the properties utilize Fortran for speedup. Before using this code, run either the shell script compile.sh or the python script compile.py
numpy>=1.14.1
scipy>=1.0.0
The following information can be accessed by running the command "python PyLAT.py -h"
usage:
PyLAT.py [-h] [-p PATH] [-i INPUT] [-f OUTPUT] [-g] [-c] [-m] [-d]
[--NEC] [--GKC] [--IPL] [--DEC] [--DS] [--Visc] --mol MOL
--nummol NUMMOL [-T TEMP] [-v VERBOSE] [--MSD_skip MSD_SKIP]
[--MSD_num_init MSD_NUM_INIT] [--D_Tolerance D_TOLERANCE]
[--RDF_Timesteps RDF_TIMESTEPS] [--RDF_maxr RDF_MAXR]
[--RDF_binsize RDF_BINSIZE] [--GKC_skip GKC_SKIP]
[--GKC_Tolerance GKC_TOLERANCE] [--GKC_J_Output]
[--IPL_skip IPL_SKIP] [--DEC_start DEC_START]
[--DS_MOL1 DS_MOL1] [--DS_MOL2 DS_MOL2] [--DS_Dist DS_DIST]
[--DS_Dist_Tol DS_DIST_TOL] [--DS_First_Frame DS_FIRST_FRAME]
[--DS_Num_Samples DS_NUM_SAMPLES] [--Visc_Dir VISC_DIR]
[--Visc_Num VISC_NUM] [--Visc_Skip VISC_SKIP]
[--Visc_Num_Boots VISC_NUM_BOOTS]
[--Visc_Samples VISC_SAMPLES] [--Visc_Plot]
[--Visc_Guess VISC_GUESS VISC_GUESS VISC_GUESS VISC_GUESS]
LOG DAT TRJ [TRJ ...]
Analyze output from LAMMPS simulation
Required files are the log file, the data file and at least one trajectory
file in that order
Also required is the name and number of each molecule type in the system.
To do this, use the --mol and --nummol flags. Use the same order as they
were entered into the data file.
If you want to calculate an ionic conductivity or dielectric constant, a
temperature must be included using a --temp flag.
The output of this program is a json file with all of the requested
information. Default file name is output.json. To use data in this file,
use the following python code:
import json
openfile = open("filename")
dict = json.load(openfile)
This yields a dictionary with all of the information that you can query.
plot.py is an interactive program written to parse and display the
information in the json output files. Proper usage is
plots.py {output file}
optional arguments:
-h, --help show this help message and exit
-v VERBOSE, --verbose VERBOSE
Verbosity of program:
0: No print statements
1: Print after each major step
2: Print after each major step and progress of the major step at each minor step.
Not recommended for cluster calculations
File arguments:
LOG LAMMPS log file.
DAT LAMMPS data dile.
TRJ LAMMPS trajectory file. Can include multiple trajectory files.
-p PATH, --path PATH Path to directory containing files. Will also save output in same directory.
Default is current directory. Example: path/to/directory/
-i INPUT, --input INPUT
json file if properties have already been calculated for this system
-f OUTPUT, --output OUTPUT
File name for output file. Defult file name is output.json
Possible Properties:
-g, --RDF Radial Distribution Function.
-c, --coord Coordination Number. Will determine the first three minima of the RDF
and calculates the coordination numbers integrating to those points.
-m, --MSD Mean Square Displacement.
-d, --D Diffusivity using MSD. Automatically includes MSD calculations.
--NEC Nernst Einstein ionic conductivity.
Automatically includes MSD and diffusivity calculations.
--GKC Green-Kubo ionic conductivity.
--IPL Ion Pair Lifetime.
--DEC Dielectric Constant
--DS Search for molecules of given types at a given distance
--Visc Calculate the viscosity of the system.
Requires multiple log files in different directories.
The name of the log files will be taken from the LOG option
System Properties:
--mol MOL Add molecule name to list of molecules. Required
--nummol NUMMOL Add number of molecule type to list. Must have same number as --mol. Required
-T TEMP, --temp TEMP Temperature of system. Required for conductivity calculations
MSD Options:
--MSD_skip MSD_SKIP Number of timesteps to skip at the beginning of the
trajectory file before calculating MSD.
Default is 0
--MSD_num_init MSD_NUM_INIT
Number of initial timesteps to consider in MSD calculation.
Default is half of frames being used in MSD calculation
Diffusivity Options:
--D_Tolerance D_TOLERANCE
Tolerance for determining linear region in Log-Log plot. Default is 0.075
RDF Options:
--RDF_Timesteps RDF_TIMESTEPS
Number of timesteps to use in the RDF calculation.
Will use the last n timesteps.
Default is to use all timesteps
--RDF_maxr RDF_MAXR Maximum r for RDF calculation. Default is half the shortest box length.
--RDF_binsize RDF_BINSIZE
Bin size for RDF calculation. Default is 0.1
GK Conductivity options:
--GKC_skip GKC_SKIP Number of timesteps to skip at the beginning of the trajectory file
before calculating GK Conductivity. Default is 0
--GKC_Tolerance GKC_TOLERANCE
Tolerance for finding the converged region for GK conductivity calculation.
Default is 0.001
--GKC_J_Output Option to output the charge flux correlation function.
If included, a file J.dat will be created with the values
of the correlation function.
Ion Pair Lifetime options:
--IPL_skip IPL_SKIP Number of timesteps to skip at the beginning of the trajectory file
before calculating Ion Pair Lifetime. Default is 0
Dielectric Constant options:
--DEC_start DEC_START
Starting frame for dielectric constant calculations. Default is 1
Distance Search Options:
--DS_MOL1 DS_MOL1 Molecule name for the first molecule type. Required for Distance Search
--DS_MOL2 DS_MOL2 Molecule name for the second molecule type. Required for Distance Search
--DS_Dist DS_DIST Distance between molecules. Required for Distance Search
--DS_Dist_Tol DS_DIST_TOL
Tolerance for distance. Required for Distance Search
--DS_First_Frame DS_FIRST_FRAME
First frame for distance search calculation. Default is 1
--DS_Num_Samples DS_NUM_SAMPLES
Number of samples to find. Default is 1
Viscosity options:
--Visc_Dir VISC_DIR Basename for the viscosity directories.
For example, if basename is "visc" the directories should be visc1, visc2, ...
If no base name is given, directories should be 1, 2, 3, ...
--Visc_Num VISC_NUM Number of Trajectories to use in the viscosity calculation.
Each trajectory should have a seperate trajectory
--Visc_Skip VISC_SKIP
Number of timesteps to skip in the viscosity calculation.
Default of 0 should only be used if the simulations were equilibrated
before the start of the production run
--Visc_Num_Boots VISC_NUM_BOOTS
Number of times to sample trajectories for bootstrapping. Default is 10
--Visc_Samples VISC_SAMPLES
Number of samples for each bootstrapping iteration. Default is 30
--Visc_Plot Include plotting for viscosity fitting.
Matplotlib required for fitting. Will output to x11
--Visc_Guess VISC_GUESS VISC_GUESS VISC_GUESS VISC_GUESS
Initial guess for viscosity fitting parameters.
Must add all four parameters with one call.
Order of parameters is A, alpha, tau1, tau2.
Default is the equivalent of calling "--Visc_Guess 1e-3 1.5e-1 1e2 1e3".
Example: For diffusivity and RDF of a system with 500 water and 500
methanol in the directory methanol/inwater
python PyLAT.py -d -g --mol H2O --mol CH3OH --nummol 500
--nummol 500 -p methanol/inwater/ -f methanolwater.json -v 2 mol.log
restart.dat mol1.lammpstrj mol2.lammpstrj