Merge pull request #4535 from Bibobu/plot_forces_tool
Adding python tool to plot tabulated forces
This commit is contained in:
Axel Kohlmeyer
@ -1250,10 +1250,10 @@ tabulate tool
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.. versionadded:: 22Dec2022
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The ``tabulate`` folder contains Python scripts scripts to generate tabulated
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potential files for LAMMPS. The bulk of the code is in the ``tabulate`` module
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in the ``tabulate.py`` file. Some example files demonstrating its use are
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included. See the README file for more information.
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The ``tabulate`` folder contains Python scripts scripts to generate and
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visualize tabulated potential files for LAMMPS. The bulk of the code is in the
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``tabulate`` module in the ``tabulate.py`` file. Some example files
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demonstrating its use are included. See the README file for more information.
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----------
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@ -1276,7 +1276,7 @@ Those scripts were written by Steve Plimpton sjplimp at gmail.com
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valgrind tool
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-------------
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The ``valgrind`` folder contains additional suppressions fur LAMMPS when
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The ``valgrind`` folder contains additional suppressions for LAMMPS when
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using `valgrind's <https://valgrind.org/>`_ ` `memcheck tool
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<https://valgrind.org/info/tools.html#memcheck>`_ to search for memory
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access violation and memory leaks. These suppressions are automatically
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@ -27,6 +27,7 @@ Please see the individual tabulation scripts in this folder for examples:
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| wall_harmonic_tabulate.py | creates a table for fix wall/table with a simple repulsive harmonic potential |
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| wall_multi_tabulate.py | creates a table for fix wall/table with multiple tables |
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| pair_bi_tabulate.py | creates a table from radial distribution file using Boltzmann Inversion |
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| plot_forces.py | plots and extracts tabulated forces from table files |
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Common command line flags:
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278
tools/tabulate/plot_forces.py
Executable file
278
tools/tabulate/plot_forces.py
Executable file
@ -0,0 +1,278 @@
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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# Author: Germain Clavier (Unicaen), germain.clavier at unicaen.fr
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"""
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Plot LAMMPS tabulated forces.
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"""
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import argparse
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import numpy as np
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import os
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import logging
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import sys
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from matplotlib import pyplot as plt
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logger = logging.getLogger(__name__)
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units = {
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"lj": {
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"Distance": "Reduced units",
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"Energy": "Reduced units",
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"Force": "Reduced units",
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"kb": 1,
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},
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"real": {
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"Distance": "[A]",
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"Energy": "[kcal/mol]",
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"Force": "[kcal/mol/A]",
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"kb": 0.001985875,
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},
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"metal": {
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"Distance": "[A]",
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"Energy": "[eV]",
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"Force": "[eV/A]",
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"kb": 8.6173332e-5,
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},
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"si": {"Distance": "[m]", "Energy": "[J]", "Force": "[N]", "kb": 1.380649e-23},
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"cgs": {
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"Distance": "[cm]",
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"Energy": "[ergs]",
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"Force": "[dynes]",
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"kb": 1.3806504e-16,
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},
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"electron": {
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"Distance": "[Bohr]",
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"Energy": "[Hartrees]",
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"Force": "[Hartree/Bohr]",
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"kb": 3.16681534e-6,
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},
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"micro": {
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"Distance": "[um]",
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"Energy": "[pg·um^2/us^2]",
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"Force": "[pg·um/us^2]",
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"kb": 1.3806504e-8,
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},
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"nano": {
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"Distance": "[nm]",
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"Energy": "[ag·nm^2/ns^2]",
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"Force": "[ag·nm/ns^2]",
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"kb": 0.013806504,
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},
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}
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def compute_energy(tp):
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r = tp[0]
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fo = tp[2]
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e = np.zeros(r.shape)
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for i, (ri, fi) in enumerate(zip(r, fo)):
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if i == 0:
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continue
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dr = ri - r[i - 1]
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e[i] = e[i - 1] - dr * fo[i - 1]
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e -= e[-1]
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return e
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def main():
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parser = argparse.ArgumentParser(
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description="""
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Plots LAMMPS tabulated forces. This script takes a table
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file as an input and plots all the tabulated forces inside with their
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corresponding energy. The forces label is the token used to name the
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force in the file. It can be used to output all the forces in separate
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files and/or recompute the energy from forces through finite difference
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(assuming e(rc)=0). This script requires the matplotlib and numpy
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Python libraries. Bitmap format is not supported.
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"""
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)
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parser.add_argument(
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"-u",
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"--units",
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dest="units",
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default="real",
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help="Units of the file (LAMMPS units system)",
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)
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parser.add_argument(
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"-f",
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"--file",
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dest="infile",
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default="",
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help="File to read",
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)
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parser.add_argument(
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"-x",
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dest="xrange",
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default="",
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help="xrange separated by : (for negative values use the '=' sign: -x=-3:10)",
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)
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parser.add_argument(
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"-y",
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dest="yrange",
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default="",
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help="yrange separated by :",
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)
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parser.add_argument(
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"-t",
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dest="temp",
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default=None,
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type=float,
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help="temperature for KbT plot [default none]",
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)
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parser.add_argument(
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"-d",
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"--diff-num",
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dest="recompute",
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action="store_true",
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help="Recompute the energies from forces and distances through finite differences",
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)
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parser.add_argument(
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"-e",
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dest="extract",
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action="store_true",
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help="Extract the forces in separate files",
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)
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args = parser.parse_args()
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logging.basicConfig(level=logging.INFO)
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##########
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# Manage arguments
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udistance = units[args.units]["Distance"]
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uenergy = units[args.units]["Energy"]
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uforce = units[args.units]["Force"]
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kb = units[args.units]["kb"]
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rlabel = " ".join(["Rij", udistance])
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elabel = " ".join(["E", uenergy])
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flabel = " ".join(["F", uforce])
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etitle = "Energy"
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ftitle = "Force"
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font = "DejaVu Sans"
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fontsize = 30
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infile = args.infile
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if not os.path.isfile(infile):
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logger.error("Input file not found")
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sys.exit(1)
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toplot = []
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with open(infile, "r") as f:
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lines = iter(f.readlines())
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while True:
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try:
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r = []
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force = []
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ener = []
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tok = []
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while not tok:
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tok = next(lines).partition("#")[0].rstrip()
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logger.info("Found {} token".format(tok))
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infos = next(lines).split()
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npoints = int(infos[1])
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next(lines)
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if "bitmap" in infos:
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logger.info("Unsupported bitmap format for token {:s}".format(tok))
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for _ in range(npoints):
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continue
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else:
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for i in range(npoints):
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line = next(lines).split()
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r.append(float(line[1]))
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ener.append(float(line[2]))
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force.append(float(line[3]))
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r = np.array(r)
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ener = np.array(ener)
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force = np.array(force)
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toplot.append([r, ener, force, tok])
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tok = []
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next(lines)
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except StopIteration:
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break
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if args.recompute:
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etitle = "Estimated energy"
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for tp in toplot:
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tp[1] = compute_energy(tp)
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fig, axes = plt.subplots(1, 2)
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for tp in toplot:
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axes[0].plot(tp[0], tp[1], label=tp[3], linewidth=3)
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axes[1].plot(tp[0], tp[2], label=tp[3], linewidth=3)
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hmin, hmax = axes[1].get_xlim()
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axes[1].hlines(0, hmin, hmax, color="black", linewidth=3, linestyles="dashdot")
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if args.temp:
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if args.temp > 0:
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hmin, hmax = axes[0].get_xlim()
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axes[0].hlines(
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kb * args.temp,
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hmin,
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hmax,
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color="orange",
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label=r"$k_BT$",
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linewidth=3,
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linestyles="dashdot",
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)
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axes[0].text(hmax / 2.0, kb * args.temp, "KbT", fontsize=0.7 * fontsize)
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logger.info("KbT value= {:e} {:s}".format(kb * args.temp, uenergy))
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else:
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logger.info("Invalid temperature value: {:e}".format(args.temp))
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if args.xrange:
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xmin, xmax = list(map(float, args.xrange.split(":")))
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axes[0].set_xlim(xmin, xmax)
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axes[1].set_xlim(xmin, xmax)
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if args.yrange:
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ymin, ymax = list(map(float, args.yrange.split(":")))
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axes[0].set_ylim(ymin, ymax)
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axes[1].set_ylim(ymin, ymax)
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# Setting axes 0
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axes[0].set_title(etitle, fontsize=fontsize)
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axes[0].set_xlabel(
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rlabel, fontname=font, fontsize=fontsize
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) # xlabel name, size 30pts
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axes[0].set_ylabel(
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elabel, fontname=font, fontsize=fontsize
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) # ylabel name, size 30pts
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axes[0].tick_params(
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axis="both", which="major", labelsize=fontsize
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) # Biggers ticks, bigger tick labels!
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# Setting axes 1
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axes[1].set_title(ftitle, fontsize=fontsize)
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axes[1].legend(frameon=False, fontsize=fontsize) # Fat font, no frame
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axes[1].set_xlabel(
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rlabel, fontname=font, fontsize=fontsize
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)
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axes[1].set_ylabel(
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flabel, fontname=font, fontsize=fontsize
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)
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axes[1].tick_params(
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axis="both", which="major", labelsize=fontsize
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)
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figManager = plt.get_current_fig_manager()
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figManager.window.showMaximized()
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plt.show()
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if args.extract:
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for tp in toplot:
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outfile = "".join([tp[3], ".plot"])
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logger.info("Writing file {}".format(outfile))
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with open(outfile, "w") as f:
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f.write("# {} force extracted from {}\n".format(tp[3], infile))
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f.write("# {:^20} {:^20} {:^20}\n".format("r", "energy", "force"))
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for a, b, c in zip(tp[0], tp[1], tp[2]):
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f.write("{:>18.16e} {:>18.16e} {:>18.16e}\n".format(a, b, c))
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return
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if __name__ == "__main__":
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try:
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main()
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except KeyboardInterrupt:
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raise SystemExit("User interruption.")
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