def file_print(self):
if len(self.outfile) == 0:
print('Warning: no file is going to output')
print(' : please try to change the input chargefile')
exit()
else:
print('\nOne sample of generated GROMACS_top files is:\n')
print(' [ atoms ]')
for i in self.atomndx:
print(self.outfile[0][i], end='')
print('\nDo you want to continue? y/yes, else quit')
print(' this will generate \'top\' files >', end=' ')
get_input = input()
if get_input.upper() != 'Y' and get_input.upper != 'YES':
print('\nWarning: you have decided to quit ...')
print(' : nothing is generated\n')
exit()
else:
print('\nGreat! Going to generate files ...\n')
topnamelist = []
for top in self.outfile:
fname = file_gen_new(self.fname, fextend='top', foriginal=False)
topnamelist.append(fname)
with open(fname, mode='wt') as f:
for line in top:
f.write(line)
fnamelist = self.fname + '_NameList'
fnamelist = file_gen_new(fnamelist, fextend='txt', foriginal=False)
with open(fnamelist, mode='wt') as f:
f.write(
'# This is a collection of all the generated GROMACS topfile names \n'
)
f.write('# The topfile used is:\n')
f.write('# {:s}\n'.format(self.toppath))
f.write('# The charge_file used is:\n')
f.write('# {:s}\n\n'.format(self.file_line_chargepath))
if len(self.file_line_symmetry) != 0:
f.write('# The symmetry_list used is:\n')
f.write('# {:s}\n\n'.format(self.file_line_symmetry))
for i in topnamelist:
f.write(i)
f.write('\n')
def file_print(self):
"""write files"""
bo = False
if len(self.outfile) == 0:
print('Warning: no file is going to output')
print(' : please try to change the input chargefile')
else:
print('\nOne sample of generated GROMACS_top files is:\n')
print(' [ atoms ]')
for i in self.atomndx:
print(self.outfile[0][i], end='')
line = "This will generate 'top' files, "
line += '({:} topfiles will be generated)\n'.format(self.gennm)
line += 'Do you want to continue? y/yes, else quit'
print(line, end=' ')
get_input = input()
if get_input.upper() != 'Y' and get_input.upper != 'YES':
print('\nWarning: you have decided to quit ...')
print(' : nothing is generated\n')
else:
print('\nGreat! Going to generate files ...\n')
bo = True
if bo:
topnamelist = []
for top in self.outfile:
fname = file_gen_new(self.fname,
fextend='top',
foriginal=False)
topnamelist.append(fname)
with open(fname, mode='wt') as f:
for line in top:
f.write(line)
fnamelist = self.fname + '_NameList'
fnamelist = file_gen_new(fnamelist, fextend='txt', foriginal=False)
print('Note: please check file: < {:} >'.format(fnamelist))
with open(fnamelist, mode='wt') as f:
f.write('# The collection of all GROMACS topfile names \n')
f.write('# The topfile used is:\n')
f.write('# {:s}\n'.format(self.toppath))
f.write('# The charge_file used is:\n')
f.write('# {:s}\n\n'.format(self.file_line_chargepath))
f.write('# The symmetry_list used is:\n')
f.write('# {:s}\n\n'.format(str(self.symmetry_list)))
for i in topnamelist:
f.write(i)
f.write('\n')
def file_print(self):
pf = file_gen_new('bash_GAML_AutoTraining', fextend='sh')
with open(pf, mode='wt') as f:
f.write('#!/bin/bash\n')
f.write('# -*- coding: utf-8 -*-\n\n')
for key in sorted(self.parameters):
if 'RAW' in key:
pass
elif self.parameters[key] is None:
f.write("{:}= \n".format(key))
else:
if key == 'symmetry_list' or key == 'counter_list' or \
key == 'offset_list':
f.write("{:}='{:}'\n".format(
key, self.parameters[key + 'RAW']))
elif key == 'pn_limit' or key == 'gromacs_energy_kw' or \
key == 'literature_value':
f.write("{:}='{:}'\n".format(key,
self.parameters[key]))
else:
f.write('{:}={:}\n'.format(key, self.parameters[key]))
f.write('\n\n\n')
f.write(self._shfile)
print('Note: the file < {:} > has been generated, '.format(pf))
print(' : which can be directly executed for auto-training')
def file_print(self):
"""writing to file"""
print('One sample of generated Gaussian_com files is:\n')
print(self.outfile[0], end='')
print('Do you want to continue? y/yes, else quit')
line = 'This will generate < {:} > files'.format(len(self.outfile))
print(line)
tmp = input()
if tmp.lower() != 'y' and tmp.lower != 'yes':
print('Note: exiting...')
return
print('\nGreat! Going to generate files ...\n')
fnamelist = []
for line in self.outfile:
filename = file_gen_new(self.fname, fextend='com', foriginal=False)
fnamelist.append(filename)
new = filename[:filename.rfind('.')]
line = '%chk={:}.chk\n'.format(new) + line
with open(filename, 'wt') as f:
f.write(line)
pf = self.fname + '_namelist'
pf = file_gen_new(pf, fextend='txt', foriginal=False)
print('Note: please check file: < {:} >'.format(pf))
with open(pf, mode='wt') as f:
f.write('# Collection of generated file names\n\n')
f.write('# The topfile is:\n')
f.write('# {:}\n\n'.format(self.toppath))
f.write('# The pdbfile is:\n')
f.write('# {:}\n\n'.format(self.file_path))
f.write('# The select_range is < {:} > Angstrom\n'.format(
self.select_range))
f.write('# Reference format: [residue-index, molecule-index]\n\n')
for i, j in enumerate(fnamelist):
line = ''
for t in self.chooselist[i]:
line += '[' + str(t[0] + 1) + ',' + str(t[1] + 1) + '] '
line = line.strip()
f.write('{:<6d}: {:} \n'.format(i + 1, line))
def file_print(self):
pfname = file_gen_new(self.fname, fextend='txt', foriginal=False)
with open(pfname, mode='wt') as f:
f.write('# Simulation process result\n\n')
f.write('# The input file used is:\n')
f.write('# {:}\n\n'.format(self.file))
f.write('# The charge file used is:\n')
f.write('# {:}\n\n'.format(self.chargefile))
f.write('# Note the used MAE value is < {:} >\n\n'.format(
self.MAE))
if self.bool_gas:
f.write('# The total number of atoms are < {:} >\n'.format(
self.atomnm))
f.write('# The temperature is < {:} K >\n'.format(
self.temperature))
self.kwlist = [
'HVAP' if i == 'Potential' else i for i in self.kwlist
]
f.write('\n\n')
cnt = 0
endlist = []
for pair in self.prochargefile:
bool_end = False
line = 'PAIR '
for ch in pair:
line += '{:>7.4f} '.format(ch)
err = self.errlist[cnt]
if 'NaN' in err:
line += 'MAE NaN'
else:
maerr = sum([abs(tmp) for tmp in err]) / len(err)
if maerr <= self.MAE:
bool_end = True
line += 'MAE {:>6.4f}'.format(maerr)
ndx = 0
for kw in self.kwlist:
line += ' {:} '.format(kw)
line += '{:>7.4f}'.format(err[ndx])
ndx += 1
f.write(line)
f.write('\n')
if bool_end:
endlist.append(line.replace('PAIR', 'HEAD'))
cnt += 1
if len(endlist) != 0:
f.write('\n\n')
f.write('# The training MAE requirement has been fulfilled\n')
for t in endlist:
f.write(t)
f.write('\n')
def file_print(self):
fname = file_gen_new(self.fname,fextend='txt',foriginal=True)
print('Note: new file: < {:} >'.format(fname))
with open(fname,mode='wt') as f:
f.write('# File charge ranges based on the input charge_file \n')
f.write('# The charge file used is:\n')
f.write('# {:s}\n'.format(self.charge_path))
f.write('# Line is corresponded to each atom \n\n')
j = 1
for i in self.charge_range:
f.write('ATOM {:>6d} {:>11.4f} {:>11.4f}\n'.format(j,i[0],i[1]))
j += 1
def file_print(self):
"""the module used, file_gen_new"""
fnamelist = []
for sys in self.outfile:
filename = file_gen_new(pfname, fextend='com', foriginal=False)
fnamelist.append(filename)
with open(filename, mode='wt') as f:
for res in sys:
for line in res:
f.write(line)
f.write('\n')
pfname = pfname + '_namelist'
pfname = file_gen_new(pfname, fextend='txt', foriginal=False)
with open(pfname, mode='wt') as f:
f.write('# This file is a name_list of chosen_residue \n\n')
f.write('# The topfile used is:\n')
f.write('# {:s}\n\n'.format(self.toppath))
f.write('# The pdbfile used is:\n')
f.write('# {:s}\n\n'.format(self.file_path))
f.write(
'# The value corresponds to the input pdb file residue number \n'
)
f.write('# The select_range used is < {:} > Angstrom\n'.format(
self.select_range))
f.write('\n [namelist] \n\n')
f.write('# nm res_1 res_2 ... filename\n\n')
j = 1
count = 0
for i in fnamelist:
f.write('{:>6d} {:s} {:>20s} \n'.format(
j, resnmprint[count], i))
count += 1
j += 1
def file_print(self):
self.figure_plot()
pfname = file_gen_new(self.fname, fextend='txt', foriginal=False)
with open(pfname, mode='wt') as f:
f.write(
'# This is the final calculation result, which is not normalized \n\n'
)
f.write('# The corresponded parameters are: \n\n')
f.write('# The input file used is: \n')
f.write('# {:s} \n\n'.format(self.filepath))
f.write('# The error_tolerance is: < {} > \n'.format(
self.error_tolerance))
f.write('# The percent_range is: < {} > \n'.format(self.percent))
f.write('# The stepsize is: < {} > \n'.format(self.stepsize))
f.write('# The plot pallette_number is: < {} > \n\n\n'.format(
self.pallette_nm))
f.write(
'# Note: each column is corresponded to its own data_range \n')
f.write(
'# and those data_ranges are the final optimal charge_range \n\n'
)
f.write('# For each different atomtype, the charge_range is: \n')
i = 0
for j in self.valuerangelist:
f.write('# {}'.format(self.atomtype_list[i]))
f.write(' {:>8.3f} {:>8.3f} \n'.format(j[0], j[1]))
i += 1
f.write('\n\n')
f.write(
'# From the Feature Statistical Standard Error Selection,\n')
f.write('# the most influenced atomtype sequence is: \n')
f.write('# ')
for i in self.ndxlist:
f.write(' {} '.format(self.atomtype_list[i]))
f.write('\n\n\n')
f.write(
'# In total, the selected_charge_pair_number is: < {} > \n'.
format(self.select_pairnm))
f.write('# the dataset is:\n\n')
for line in self.profile:
f.write(line)
f.write('\n')
def run(self):
"""get built-in script file"""
details = {
'bash_analysesDES.sh': 'For DES result analyses',
'bash_DES.sh': 'For DES training',
'bash_GAML.sh': 'For conventional solvents training',
'bash_genTopfiles.sh': 'For GROMACS topology file generations',
'bash_rmfilesIndividual.sh': 'For folder cleanup',
'bash_visAdd.sh': 'For viscosity property training',
'bash_visAnalysisByFolder.sh': 'For viscosity property analyzing',
'GAML-BASH-Interface.sh': 'For command GAML_autotrain',
'py_bool_repeatsChk.py': 'For charge pair repeats check out',
}
if self.available:
print('Available scripts:')
for cnt, f in enumerate(self.files):
if f in details:
print(' {:2d} --> {:<30} {:}'.format(
cnt + 1, f, details[f]))
else:
print(' {:2d} --> {:}'.format(cnt + 1, f))
print('\nWhich scripts do you want to get?')
print('Please input its number. (Input q/quit to quit)')
while True:
tmp = input()
if tmp.lower() in ['q', 'quit']: break
try:
self.n = int(float(tmp))
if self.n <= 0:
self.n = None
raise ValueError
except ValueError:
pass
if isinstance(self.n, int) and self.n <= len(self.files):
self.available = False
break
else:
print('Wrong choose. (Input q/quit to quit)')
if self.available:
print('You decided to quit..')
else:
cwd = os.getcwd()
fname = self.files[self.n - 1]
fp = resource_filename(__name__, 'scripts/' + fname)
if os.path.isfile(fp):
fname = file_gen_new(fname)
print('Note: script file: < {:} >'.format(fname))
shutil.copy(fp, cwd + '/' + fname)
def file_print(self):
fname = file_gen_new(self.fname,fextend='txt',foriginal=True)
charge_range = self.charge_range()
with open(fname,mode='wt') as f:
f.write('# This is the generated charge_range based on the input charge_file \n')
f.write('# The charge file used is:\n')
f.write('# {:s}\n'.format(self.charge_path))
f.write('# Each line\'s charge_range is corresponded to each atom \n\n')
j = 1
for i in charge_range:
f.write('ATOM {:>6d} {:>8.4f} {:>8.4f}\n'.format(j,i[0],i[1]))
j += 1
def file_print(self):
fname = file_gen_new(self.fname, fextend='txt')
print('Note: new file < {:} >'.format(fname))
with open(fname, mode='wt') as f:
f.write('# GAML charge scheme \n\n')
if len(self.symmetry_list) != 0:
f.write('# symmetry_list: < {:} >\n'.format(
self.file_line_symmetry))
if len(self.offset_list) != 0:
f.write('# offset_list: < {:} >\n'.format(
self.file_line_offset))
if len(self.counter_list) != 0:
f.write('# counter_list: < {:} >\n'.format(
self.file_line_counter))
if len(self.pn_limit) != 0:
tmp = [str(i[0] + 1) + i[1] for i in self.pn_limit]
f.write('# pn_limit: < {:} >\n'.format(tmp))
f.write('# total_charge: < {:} >\n'.format(self.total_charge))
f.write('# bool_neutral: < {:} >\n'.format(self.bool_neutral))
f.write('# bool_nozero: < {:} >\n\n'.format(self.bool_nozero))
if self.charge_path is None:
f.write('# charge_range file: < NotDefined >\n')
else:
f.write('# charge_range file: < {:} >\n'.format(
self.charge_path))
f.write('# For each entry, the charge_range:\n')
j = 1
for i in self.charge_list:
f.write('#ATOM {:>4} {:>6} {:>6}\n'.format(
j, i[0], i[1]))
j += 1
f.write('\n\n# generated charge pairs: \n\n')
for i in self.chargepair:
f.write('PAIR ')
for j in i:
f.write('{:>7.3}'.format(j))
f.write('\n')
f.write('\n\n')
def file_print(self):
fname = file_gen_new(self.fname,fextend='txt')
with open(fname,mode='wt') as f:
f.write('# This is the randomly generated charge pairs based on charge_range_list \n\n')
if self.symmetry_list is not None:
f.write('# The symmetry_list used is:\n')
f.write('# {:s}\n\n'.format(self.prolist.file_line_symmetry))
if len(self.prolist.file_line_offset) != 0:
f.write('# The offset_list used is:\n')
f.write('# {:s}\n\n'.format(self.prolist.file_line_offset))
if (self.counter_list is not None) and len(self.counter_list) != 0:
f.write('# The counter_list used is:\n')
f.write('# {:s}\n\n'.format(self.prolist.file_line_counter))
if len(self.pn_limit) != 0:
f.write('# The pn_limit used is:\n')
f.write('# {:s}\n\n'.format(self.file_line_pn_limit))
f.write('# The total_charge is: < {:} >\n\n'.format(self.total_charge))
f.write('# The bool_neutral is: < {:s} >\n\n'.format('ON' if self.bool_neutral else 'OFF'))
f.write('# The bool_nozero is: < {:s} >\n\n'.format('ON' if self.bool_nozero else 'OFF'))
if isinstance(self.charge_path,str):
f.write('# The used charge_range file is:\n# {:s}\n\n'.format(self.charge_path))
f.write('# For each entry, the charge_range is:\n\n')
j = 1
for i in self.charge_list:
f.write('# ATOM {:>3} {:>8} {:>8}\n'.format(j,i[0],i[1]))
j += 1
f.write('\n\n# The randomly generated charges are: \n\n')
for i in self.chargepair:
f.write('PAIR ')
for j in i:
f.write('{:>7.3}'.format(j))
f.write('\n')
f.write('\n\n')
def figure_plot(self):
cmap = plt.get_cmap(self.color_map)
fig = plt.figure(facecolor='w', figsize=(10, 6))
ax = fig.add_subplot(111)
ax.set_yticks(range(len(self.yticklist)))
ax.set_yticklabels(self.yticklist)
ax.get_xaxis().set_visible(False)
ax.set_title('Error Tolerance: {}, Percent: {}'.format(
self.error_tolerance, self.percent))
getcmap = ax.imshow(self.prolist, cmap=cmap, aspect='auto')
cb = plt.colorbar(mappable=getcmap, shrink=1.0, pad=0.02)
cb.set_ticks([])
pfname = file_gen_new(self.fname, fextend='png', foriginal=False)
pfname = pfname[:pfname.rfind('.png')]
plt.tight_layout()
fig.savefig(pfname)
def file_print(self):
"""write to file"""
self.figure_plot()
pfname = file_gen_new(self.fname, fextend='txt', foriginal=False)
print('Note: new file < {:} >'.format(pfname))
with open(pfname, mode='wt') as f:
f.write('# Final calculation result (not normalized)\n\n')
f.write('# input file: < {:} >\n'.format(self.filepath))
f.write('# error_tolerance: < {:} >\n'.format(
self.error_tolerance))
f.write('# percent_range: < {:} >\n'.format(self.percent))
f.write('# stepsize: < {:} >\n'.format(self.stepsize))
f.write('# pallette_number: < {:} >\n\n\n'.format(
self.pallette_nm))
f.write('# Column corresponds to its own data range (optimized)\n')
f.write('# For each different atomtype, charge range is:\n')
for i, j in enumerate(self.valuerangelist):
f.write('# {:}'.format(self.atomtype_list[i]))
f.write(' {:>8.3f} {:>8.3f}\n'.format(j[0], j[1]))
f.write('\n\n')
f.write('# Feature Statistical Standard Error Selection\n')
f.write('# the most influenced atomtype sequence is:\n')
f.write('#')
for i in self.ndxlist:
f.write(' {:} '.format(self.atomtype_list[i]))
f.write('\n\n\n')
f.write('# Number of selection is: < {:} >\n'.format(self.pnm))
f.write('# Dataset is:\n')
for line in self.profile:
f.write(line)
f.write('\n')
def file_print(self):
"""overwrite parent method"""
self.fname = file_gen_new(self.fname, fextend='txt', foriginal=False)
print('Note: new file < {:} >'.format(self.fname))
with open(self.fname, mode='wt') as f:
f.write('# Genetic Algorithm Machine Learning\n')
f.write('# Total number of charge_pairs are: < {:} >\n\n'.format(
self.gennm))
if len(self.symmetry_list) != 0:
f.write('# symmetry_list: < {:} >\n'.format(
self.file_line_symmetry))
if len(self.offset_list) != 0:
f.write('# offset_list: < {:} >\n'.format(
self.file_line_offset))
f.write('# offset_nm: < {:} >\n'.format(self.offset_nm))
if len(self.counter_list) != 0:
f.write('# counter_list: < {:} >\n'.format(
self.file_line_counter))
if len(self.pn_limit) != 0:
tmp = [str(i[0] + 1) + i[1] for i in self.pn_limit]
line = ','.join(tmp).strip(',')
f.write('# pn_limit: < {:} >\n\n'.format(line))
f.write('# ratio: (ML:Average:Mutation) < {:} >\n'.format(
self.ratio))
f.write('# using ratio: (ML:Average:Mutation) < {:} >\n'.format(
self.ratio_new))
f.write('# threshold: < {:} >\n'.format(self.threshold))
f.write('# total_charge: < {:} >\n\n'.format(self.total_charge))
f.write('# bool_neutral: < {:} >\n'.format(self.bool_neutral))
f.write('# bool_nozero: < {:} >\n\n'.format(self.bool_nozero))
if self.file_path is not None:
f.write('# file_path: < {:} >\n'.format(self.file_path))
if self.charge_path is not None:
f.write('# charge_path: < {:} >\n\n'.format(self.charge_path))
nm_nor = len(self.chargepair_nor)
if nm_nor > 0:
f.write('# normal charge_range:\n')
j = 1
for i in self.charge_list_nor:
f.write('#ATOM {:>4} {:>7} {:>7}\n'.format(
j, i[0], i[1]))
j += 1
f.write('\n\n')
print(
'Number of charge pairs generated by the normal charge range are: ',
nm_nor)
f.write(
'# The charge_pair generated by normal charge_range: ({:})\n\n'
.format(nm_nor))
for i in self.chargepair_nor:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
nm_new = len(self.chargepair_new)
if nm_new > 0:
f.write('\n\n# charge_extend_by: < {:} >\n'.format(
self.charge_extend_by))
f.write(
'# With the addition or subtraction, or keeping constant, in both low and high bound\n'
)
f.write('# New charge_range:\n\n')
j = 1
for i in self.charge_list_new:
f.write('#ATOM {:>4} {:>7} {:>7}\n'.format(
j, round(i[0], 3), round(i[1], 3)))
j += 1
f.write('\n\n')
print(
'Number of charge pairs generated by the new charge range are: ',
nm_new)
f.write(
'# The charge_pair generated by modified charge_range: ({:})\n\n'
.format(nm_new))
for i in self.chargepair_new:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
if self.file_path is not None: f.write('\n\n')
nm_ml = len(self.chargepair_ml)
if nm_ml > 0:
print(
'Number of charge pairs generated by the Genetic Algorithm are: ',
nm_ml)
f.write(
'# The charge_pair generated by Genetic Algorithm: ({:})\n\n'
.format(nm_ml))
for i in self.chargepair_ml:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
nm_av = len(self.chargepair_av)
if nm_av > 0:
print('Number of charge_pairs generated by the Average are: ',
nm_av)
f.write(
'\n\n# The charge_pair generated by Average: ({:})\n\n'.
format(nm_av))
for i in self.chargepair_av:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
def file_print(self):
self.fname = file_gen_new(self.fname, fextend='txt', foriginal=False)
print('The combined generated charge file name is:', end=' ')
print(self.fname)
with open(self.fname, mode='wt') as f:
f.write(
'# This is the genetic algorithm machine learning generated charge file\n'
)
f.write(
'# The total number of generated charge_pairs are: < {:} >\n\n'
.format(self.gennm))
if len(self.symmetry_list) != 0:
f.write('# The symmetry_list used is:\n')
f.write('# {:}\n\n'.format(self.file_line_symmetry))
if len(self.file_line_offset) != 0:
f.write('# The offset_list used is:\n')
f.write('# {:}\n'.format(self.file_line_offset))
f.write('# The offset_nm used is: < {:} >\n\n'.format(
self.offset_nm))
if len(self.reflist) != 0:
f.write('# The counter_list used is:\n')
f.write('# {:}\n\n'.format(self.file_line_counter))
if len(self.pn_limit) != 0:
f.write('# The pn_limit used is:\n')
f.write('# {:}\n\n'.format(self.file_line_limit))
if self.ratio is not None:
f.write('# The ratio used is:\n')
f.write('# {:}\n'.format(self.ratio))
f.write(
'# For each entry, the threshold used is: < {:} >\n'.format(
self.threshold))
f.write('# The bool_neutral is: < {:} >\n'.format(
'ON' if self.bool_neutral else 'OFF'))
f.write('# The total_charge is: < {:} >\n\n'.format(
self.total_charge))
if self.file_path is not None:
f.write('# The file_path used is:\n')
f.write('# {:}\n'.format(self.file_path))
if self.charge_path is not None:
if isinstance(self.charge_path, str):
f.write('# The charge_path used is:\n')
f.write('# {:}\n\n'.format(self.charge_path))
f.write('# The normal charge_range used is:\n\n')
j = 1
for i in self.charge_nor_list:
f.write('# ATOM {:>4} {:>7} {:>7}\n'.format(
j, i[0], i[1]))
j += 1
f.write('\n\n')
print(
'The number of charge_pairs generated by the normal charge range are: ',
len(self.schemelist_nor))
f.write(
'# The charge_pair generated by normal charge_range;\n\n')
for i in self.schemelist_nor:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
f.write(
'\n\n# The value of charge_extention is: < {:} >\n'.format(
self.charge_extend_by))
f.write(
'# With the addition or subtraction, or keeping constant, in both low and high bound\n'
)
f.write('# The new charge_range used is:\n\n')
j = 1
for i in self.charge_new_list:
f.write('# ATOM {:>4} {:>7} {:>7}\n'.format(
j, round(i[0], 3), round(i[1], 3)))
j += 1
f.write('\n\n')
print(
'The number of charge_pairs generated by the new charge range are: ',
len(self.schemelist_new))
f.write(
'# The charge_pair generated by modified charge_range;\n\n'
)
for i in self.schemelist_new:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
if self.file_path is not None:
f.write('\n\n')
if len(self.galist_ml) != 0:
print(
'The number of charge_pairs generated by the Genetic Algorithm are: ',
len(self.galist_ml))
f.write(
'# The charge_pair generated by Genetic Algorithm\n\n')
for i in self.galist_ml:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
if len(self.galist_average) != 0:
print(
'The number of charge_pairs generated by the Average are: ',
len(self.galist_average))
f.write('\n\n# The charge_pair generated by Average\n\n')
for i in self.galist_average:
f.write('PAIR ')
for j in i:
f.write('{:>7}'.format(j))
f.write('\n')
def file_print(self):
pfname = file_gen_new(self.fname, fextend='txt', foriginal=False)
print('Note: new file < {:} >'.format(pfname))
with open(pfname, mode='wt') as f:
f.write('# Simulation process result\n\n')
f.write('# input file: < {:} >\n\n'.format(self.file))
f.write('# charge file: < {:} >\n\n'.format(self.chargefile))
f.write('# MAE: < {:} >\n'.format(self.MAE))
if self.bool_gas:
f.write('# total number of atoms: < {:} >\n'.format(
self.atomnm))
f.write('# temperature: < {:} K >\n'.format(self.temperature))
self.kwlist = [
'HVAP' if i == 'potential' else i.capitalize()
for i in self.kwlist
]
f.write('\n')
f.write('# corresponding Keywords and literature values are:\n')
f.write('#Keywords: ')
for kw in self.kwlist:
f.write(' {:>8}'.format(kw))
f.write('\n#LiValues: ')
for v in self.literature_value:
f.write(' {:8}'.format(v))
f.write('\n\n\n')
endlist = []
lenkw = len(self.kwlist)
for cnt, pair in enumerate(self.prochargefile):
bool_end = False
line = 'PAIR '
for ch in pair:
line += '{:>7.4f} '.format(ch)
err = self.errlist[cnt]
if 'NaN' in err:
line += 'MAE NaN'
else:
maerr = sum([abs(tmp) for tmp in err]) / lenkw
if maerr <= self.MAE: bool_end = True
line += 'MAE {:>6.4f}'.format(maerr)
for ndx, kw in enumerate(self.kwlist):
line += ' {:} '.format(kw)
if err[ndx] == 'NaN':
line += ' NaN'
else:
line += '{:>7.4f}'.format(err[ndx])
f.write(line)
f.write('\n')
if bool_end:
endlist.append(line.replace('PAIR', 'HEAD'))
if len(endlist) != 0:
f.write('\n\n')
f.write('# The training MAE requirement is fulfilled\n')
for t in endlist:
f.write(t)
f.write('\n')