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plotmsd.py
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plotmsd.py
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import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
color = ['k', 'b', 'g', 'r', 'm', 'c', 'y', 'r',
'darkred', 'darkblue', 'darkgreen', 'darkmagenta']
lsty = ['-', '-', '-', '-', '--', '--', '--', '--', '-', '-', '-', '-']
def get_msd(file_path):
msd_data = []
with open(file_path, 'r') as f:
_ = f.readline().strip().split()
notation = f.readline().strip().split()
for x in f.readlines():
line = x.strip().split()
if line[0] != '#':
data = [float(i) for i in line]
msd_data.append(data)
return np.array(msd_data)
def plot_msd(ha_msd, ah_msd, fig_name):
# 在msd文件中，1-9列为Br原子的数据。10-12列的数据为Ca，Cd的数据，13-15列为Cs的数据。
# plt.figure(figsize=(6,6))
plt.plot(ha_msd[:, 0], ha_msd[:, 2], linestyle='-',
color='orange', label="HA-$U_{11}$($U_{22}$)Br")
plt.plot(ah_msd[:, 0], ah_msd[:, 2], linestyle='--', color='orange', marker='o', markerfacecolor='w',
label="SCP-$U_{11}$($U_{22}$)Br")
plt.plot(ha_msd[:, 0], ha_msd[:, 1], linestyle='-',
color='gray', label="HA-$U_{33}$Br")
plt.plot(ah_msd[:, 0], ah_msd[:, 1], linestyle='--', color='gray', marker='o', markerfacecolor='w',
label="SCP-$U_{33}$Br")
if fig_name.split('.')[0]=='Br3CsSn_msd':
#### for the BrCsSn system, the atom positions are Br Cs Sn, so it's a little different from other two materials.
plt.plot(ha_msd[:, 0], ha_msd[:, 11], linestyle='-',
color='cornflowerblue', label="HA-$U_{ii}$Cs")
plt.plot(ah_msd[:, 0], ah_msd[:, 11], linestyle='--', color='cornflowerblue', marker='s', markerfacecolor='w',
label="SCP-$U_{ii}$Cs")
plt.plot(ha_msd[:, 0], ha_msd[:, 13], linestyle='-',
color='gold', label="HA-$U_{ii}$Sn")
plt.plot(ah_msd[:, 0], ah_msd[:, 13], linestyle='--', color='gold', marker='s', markerfacecolor='w',
label="SCP-$U_{ii}$Sn")
plt.plot(300, 0.147, marker='s', color='orange')
plt.plot(300, 0.025, marker='s', color='gray')
else:
plt.plot(ha_msd[:, 0], ha_msd[:, 13], linestyle='-',
color='cornflowerblue', label="HA-$U_{ii}$Cs")
plt.plot(ah_msd[:, 0], ah_msd[:, 13], linestyle='--', color='cornflowerblue', marker='s', markerfacecolor='w',
label="SCP-$U_{ii}$Cs")
plt.xlabel("Temperature (K)", fontsize=14)
plt.ylabel("Mean Square Displacement ($\AA^{2}$)", fontsize=14, labelpad=20)
# xmin=0
# plt.axis([xmin, xmax, ymin, ymax])
plt.xlim(left=0, right=1000)
plt.minorticks_on()
plt.tick_params(axis='both', which='both', direction='in', top=True, right=True)
plt.xticks(fontsize=14)
plt.yticks(fontsize=14)
plt.legend(loc='upper left', prop={'size': 12})
plt.tight_layout()
plt.gca().set_aspect(1.0 / plt.gca().get_data_ratio(), adjustable='box')
# plt.savefig(fig_name, dpi=600)
plt.show()
# ############------Br3Ca1Cs1-------#####################
# file_path_1 = './Br3Ca1Cs1/msd/pc_dos.msd'
# file_path_2 = './Br3Ca1Cs1/msd/pc_scfph.scph_msd'
# ha_msd = get_msd(file_path_1)
# ah_msd = get_msd(file_path_2)
# fig_name = 'Br3Ca1Cs1_msd.png'
# plot_msd(ha_msd,ah_msd, fig_name)
# #############------Br3Cs1Sn-------#####################
file_path_1 = './BrCsSn/msd/pc_dos.msd'
file_path_2 = './BrCsSn/msd/pc_scfph.scph_msd'
ha_msd = get_msd(file_path_1)
ah_msd = get_msd(file_path_2)
fig_name = 'Br3CsSn_msd.eps'
plot_msd(ha_msd,ah_msd, fig_name)
############------Br3CdCs-------#####################
# file_path_1 = './Br3Cd1Cs1/msd/pc_dos.msd'
# file_path_2 = './Br3Cd1Cs1/msd/pc_scfph.scph_msd'
# ha_msd = get_msd(file_path_1)
# ah_msd = get_msd(file_path_2)
# fig_name = 'Br3Cd1Cs1_msd.png'
# plot_msd(ha_msd,ah_msd, fig_name)