def _writeCubeFile(self, step, molID, numCube=-1):
"""
Converts each molecular wavefunction to a cube file to be loaded in vmd
"""
self.__createCubeFileTxt(step, molID)
start_data_write_time = time.time()
if all_settings['keep_cube_files']:
RDataFName = "%s-%i-%i.cube" % ('Real', step, molID)
IDataFName = "%s-%i-%i.cube" % ('Imag', step, molID)
else:
RDataFName = "tmp%s-%i.cube" % ('Real', molID)
IDataFName = "tmp%s-%i.cube" % ('Imag', molID)
RDataFPath = self.all_settings['data_fold'] / RDataFName
IDataFPath = self.all_settings['data_fold'] / IDataFName
if not all_settings['keep_cube_files']:
self.all_settings['delete_these'].append(RDataFPath)
self.all_settings['delete_these'].append(IDataFPath)
if self.writeRealCube:
self.data_files_to_visualise.append(RDataFPath)
if self.writeImagCube:
self.data_files_to_visualise.append(IDataFPath)
self.all_settings['tcl']['cube_files'] = \
' '.join(map(str, self.data_files_to_visualise))
self.tga_folderpath, _, self.tga_filepath = io.file_handler(
self.all_settings['img_prefix'],
'tga',
self.all_settings)
# if all_settings['draw_time']:
# replace = str(self.all_settings['Mtime-steps'][self.step])
# tLabelTxt = self.all_settings['time_lab_txt'].replace("*", replace)
# self.all_settings['tcl']['time_step'] = '"%s"' % (tLabelTxt)
self.all_settings['tcl']['cube_files'] = ' '.join(
map(str, self.data_files_to_visualise)
)
if self.writeRealCube:
io.open_write(RDataFPath, self.RCubeTxt)
if self.writeImagCube:
io.open_write(IDataFPath, self.ICubeTxt)
end_time = time.time() - start_data_write_time
self.all_settings['times']['Write Cube File'][step] += end_time
msg = "Trajectory %i/%i %s Timestep %s" % (step + 1,
num_steps,
timeTaken,
timeStep)
traj_print = "\n"+txt_lib.align(msg, 69, "l") + "*"
if self.all_settings['verbose_output']:
print("*"*70)
print(traj_print)
io.times_print(self.all_settings['times'], step, 70, tmpTime)
else:
io.print_same_line(traj_print, sys, print)
if self.all_settings['verbose_output']:
print("*"*70, "\n")
self.all_settings['times_taken'].append(time.time() - start_step_time)
if __name__ == '__main__':
all_settings['img_prefix'] = consts.Orig_img_prefix.replace("$fs_", "")
tgaFiles = [io.file_handler(all_settings['img_prefix'],
'tga',
all_settings)[2]
for step in INIT.all_steps]
all_settings['to_stitch'] = '\n'.join(map(str, tgaFiles))
errors = {}
step_data = MainLoop(INIT.all_settings, INIT.all_steps, errors)