def test_icvm_log(self):
"""
icvm log
"""
path = os.path.join(TEST_PATH, 'montecarlo/i-s/fcci/Ti1C1/str_energy.txt')
path = os.path.join(TEST_PATH, 'montecarlo/i-s/fcci/Ti1C1/R5N4/log.txt')
log = CVMLogEnth.from_file_ternary(path)
log.stable.data += log.meta.data
print(log.stable['c_a'] )
conc_A = log.stable['c_a']
print(conc_A)
conc_C = log.stable['c_c'] / (0.5 + log.stable['c_a'])
print(conc_C)
data_xyz = np.c_[conc_A, conc_C,
log.stable['enth']]
fig = pylab.figure()
ax = Axes3D(fig)
pt3d = convex_hull.PlotTriangularCoord(ax)
pt3d.plt_dot(data_xyz)
path = os.path.join(TEST_PATH, 'montecarlo/i-s/fcci/Ti0C1/str_energy.txt')
log = CVMLogEnth.from_file_ternary(path)
log.stable.data += log.meta.data
print(log.stable['c_a'] )
conc_A = log.stable['c_a']
print(conc_A)
conc_C = (0.5 - log.stable['c_c']) / (0.5 + log.stable['c_a'])
print(conc_C)
data_xyz = np.c_[conc_A, conc_C,
log.stable['enth']]
pt3d.plt_dot(data_xyz, color='r')
pylab.show()
def plot(save, log_file, with_cem, vac_corr, end, wo_zero_zero,
set_yrange, set_xrange):
def get_correction(x, vac_corr):
if Fraction(vac_corr):
return 1/(x+Fraction(vac_corr))
else:
return 1
def get_slope(x, end):
return end[0]*(1-x) + end[1]*(x)
data = CVMCv1Parser.from_file('cv1.txt')
seaborn.set_style('whitegrid')
fig = pylab.figure()
plot1 = fig.add_subplot(111)
plot1.set_ylabel("Free energy (kJ/mol)", fontsize=16)
plot1.set_xlabel("Fraction of atom A", fontsize=16)
pylab.xticks(fontsize=14)
pylab.ylabel("Free energy (kJ/mol)", fontsize=16)
pylab.xlabel("Fraction of atom A", fontsize=16)
pylab.yticks(fontsize=14)
fig.subplots_adjust(bottom=0.15)
# seaborn.set_palette("winter", len(data.data))
dict_data = {}
for data_tmp in data.data:
dict_data.update({data_tmp['temp']: data_tmp['data']})
for i, temp in enumerate(sorted(dict_data.keys())):
color = pylab.cm.cool(i/len(dict_data)) #pylint: disable=E1101
if wo_zero_zero:
dict_data[temp].set_free_energy_00(0, 0)
else:
dict_data[temp].set_free_energy_00_from_logtxt(log_file)
dict_data[temp].set_end_energy(end[0], end[1])
label = str(temp) + "K"
x = dict_data[temp]['comp1']
corr = get_correction(x, vac_corr)
pylab.plot(x*corr, dict_data[temp]['corrected_g']*corr,
'o', label=label, color=color)
pylab.legend(loc='lower left')
if with_cem:
cem = CVMLogEnth.from_file(log_file)
x = cem.stable['c_a']
corr = get_correction(x, vac_corr)
pylab.plot(x * corr,
(cem.stable['enth']*96.485/1000+get_slope(x, end))*corr, '*',
color='orange')
x = cem.meta['c_a']
corr = get_correction(x, vac_corr)
pylab.plot(x * corr,
(cem.meta['enth']*96.485/1000+get_slope(x, end))*corr, '*',
color='orange')
x = cem.unstable['c_a']
corr = get_correction(x, vac_corr)
pylab.plot(x * corr,
(cem.unstable['enth']*96.485/1000+get_slope(x, end))*corr,
'*', color='orange')
x = cem.exact['c_a']
corr = get_correction(x, vac_corr)
pylab.plot(x * corr,
(cem.exact['exact']*96.485/1000+get_slope(x, end))*corr,
'.', color='magenta')
if set_yrange != (0, 0):
pylab.ylim(*set_yrange)
if set_xrange != (0, 0):
pylab.xlim(*set_xrange)
if save:
pylab.savefig("plot.eps")
else:
pylab.show()
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
cvm 関連の perser
"""
from parse_cvm import CVMLogEnth
from pyhull import qconvex
# 二元系のみ対応
# もしかしたら使えるかもしれないが、三元系以上は未検証
log = CVMLogEnth.from_file('log.txt')
lines = log.print_all_phase_energy()
# print(lines)
# # print gs
# data = [(float(x.split()[0]), float(x.split()[1]))
# for x in lines.split('\n')[1:-1]]
# # print(qconvex('s i', data))
# gs = qconvex('s p', data)
# print('\nGS_calc')
# for g in gs[2:]:
# print(g)
# # print gs
# data = [(float(x.split()[0]), float(x.split()[2])) for x in lines.split('\n')[1:-1]]
# # print(qconvex('s i', data))
# gs = qconvex('s p', data)
# print('\nGS_exact')
# for g in gs[2:]:
# print(g)
#!/opt/anaconda/bin/python
# -*- coding: utf-8 -*-
"""
cvm 関連の perser
"""
from parse_cvm import CVMLogEnth
log = CVMLogEnth.from_file("log.txt")
log.print_all_phase_energy()