import ast
import re
import subprocess
from pathlib import Path
import ase
import ase.io
import matplotlib.pyplot as plt
import numpy as np
from pypotlib.systems import cu_slab_h2 as cuh2slab
from pyprotochemgp.systems.cuh2slab import prepare_scatter_points
from rgpycrumbs._aux import get_gitroot, getstrform
from rgpycrumbs.xts.cuh2.datgen import get_from_gitroot_con
[docs]
TRUE_E_DAT = get_from_gitroot_con(
fname="cuh2.con",
hh_range=cuh2slab.PltRange(low=-0.05, high=5),
h2slab_range=cuh2slab.PltRange(low=-0.05, high=5),
n_points=cuh2slab.PlotPoints(x_npt=40, y_npt=40),
)
[docs]
CUH2_MIN = ase.io.read(getstrform(get_gitroot() / "cuh2.con"))
[docs]
def plot_band(_index, _band, _k, _method="xts", _opt="SD", _ci="False"):
plot_last = _band
cuh2slab.contour_plot(
TRUE_E_DAT.pltpts,
scatter_points=prepare_scatter_points(plot_last, CUH2_MIN),
title=f"({_opt}, CI: {_ci}, {_k})\n Band {_index} ({_method})",
)
oname = f"{_method}_{_opt}_{_ci}"
plt.savefig(f"neb_path_{oname}_{_index:04d}.png")
plt.close()
if __name__ == "__main__":
import argparse
[docs]
parser = argparse.ArgumentParser(description="Script to plot output.txt for CuH2")
parser.add_argument(
"--nimgs",
help="Number of images",
required=True,
)
parser.add_argument(
"--ifile",
help="Input file",
default="output.txt",
)
parser.add_argument(
"--spring_const",
help="Spring constant",
default="8.2",
)
args = parser.parse_args()
otext = Path(args.ifile).open().readlines()
ilines = [x for x in otext if "Iteration" in x]
iparser = re.compile(r"Iteration\s(?P<iter>\d*): (?P<coords>\[\d?.*\])")
path_arr = np.vstack(
[
np.array(ast.literal_eval(iparser.match(x).group("coords")))
for x in ilines
if iparser.match(x)
]
)
# Ham handed approach
n_bands = int(path_arr.shape[0] / path_arr.shape[1])
n_imgs = int(args.nimgs)
for idx in range(n_bands):
_start = idx * n_imgs
_end = _start + n_imgs
band = path_arr[_start:_end]
plot_band(idx, band, args.spring_const, "xts", "SD", "False")
