def run_namd(self):
"""Runs namd executable with # cores"""
log('info', 'Running namd with ' + str(self.cores) + ' cores.')
conf_file = self.restart + self.file_name + '.conf'
log_file = self.restart + self.file_name + '.log'
err_file = self.restart + self.file_name + '.err'
cmd = [self.namd_exe, conf_file]
if self.cores != 1:
cmd.insert(1, '+p' + str(self.cores))
try:
with open(log_file, 'w') as out, open(err_file, "w") as err:
process = subprocess.Popen(cmd, stdout=out, stderr=err)
while process.poll() is None:
if self.backup:
self.backup_restart()
sleep(300)
else:
finish_dynamic(err_file)
except (PermissionError, FileNotFoundError):
log('error', 'Namd exe not found! Please specify path with -e.')
def resolve_restart(files, silent):
"""Check for size on restart files"""
files = files.stdout.readlines()
if len(files) == 0:
if not silent:
log('critical', 'Restart files not found. Aborting!')
return False
files_size = dict()
new_restart = list()
old_restart = list()
backup_restart = list()
for file in files:
file = file.decode('utf-8').strip().split('\t')
file_name = file[1]
files_size[file_name] = file[0]
if file_name.endswith(".xsc") or file_name.endswith(
".coor") or file_name.endswith(".vel"):
new_restart.append(file_name)
if file_name.endswith(".old"):
old_restart.append(file_name)
if file_name.endswith(".bak"):
backup_restart.append(file_name)
return choose_restart(files_size, new_restart, old_restart, backup_restart,
silent)
def save_conf(self):
"""Save conf file"""
log('info', 'Saving .conf file at ' + self.restart)
conf = self.restart + self.file_name + '.conf'
with open(conf, 'w') as file:
for line in self.conf_file:
file.write(line)
def prepare_restart(self):
"""Check if output folder exists and is empty"""
if not os.path.exists(self.restart):
os.makedirs(self.restart)
else:
if len(os.listdir(self.restart)) != 0:
log('warning', 'Output folder not empty. Subscribing.')
sleep(1)
def search_previous(path, silent=False):
"""Search restart files on previous folder"""
if not silent:
log('info', 'Searching restart files.')
cmd = 'find ' + path + ' -name "*restart*" -exec du -sh {} \\;'
output = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
return resolve_restart(output, silent)
def read_conf(self):
"""Read conf file to list"""
with open(self.conf) as conf:
conf_file = conf.readlines()
if len(conf_file) == 0:
log('error', 'Could not open .conf file.')
return False
return conf_file
def edit_run_steps(self, restart_step):
"""Edit the number of run steps"""
if self.run:
log('info', 'Setting run steps to ' + self.run + '.')
self.update_conf('run ' + self.run)
else:
steps = self.get_remaining_steps(restart_step)
log('info', 'Setting run steps to ' + steps + '.')
self.update_conf('run ' + steps)
def finish_dynamic(err):
"""Check for errors on dynamic end"""
with open(err, 'r') as err_file:
err_message = err_file.read()
if len(err_message) > 1:
log('error', 'Dynamic ended with error status:')
print(err_message)
else:
log('info', 'Dynamic finished.')
def get_restart_step(restart_files):
"""Get last step on xsc file"""
with open(restart_files['xsc']) as xsc:
step = xsc.readlines()
if len(step) == 0:
log('error', 'Could not open .xsc file.')
return False
step = step[2].split(' ')[0]
log('info', 'Using restart step ' + step + '.')
return step
def comment_conf(self, option):
"""Edit conf file to comment option"""
option = format_option(option)
option_index = self.search_option(option[0])
if option_index:
if not self.conf_file[option_index].startswith('#'):
self.conf_file[
option_index] = '#' + self.conf_file[option_index]
else:
log('warning',
'Option "' + ' '.join(option) + '" not found. Ignoring.')
sleep(1)
def main(self):
"""Main routine"""
# Gets conf file
self.conf = self.search_conf()
if not self.conf:
return False
sleep(1)
# Prepares restart files
restart_files = search_previous(self.previous)
if not restart_files:
return False
sleep(1)
self.file_name = self.get_file_name(restart_files)
# Loads conf file in memory for editing
self.conf_file = self.read_conf()
if not self.conf_file:
return False
sleep(1)
# Gets last step
restart_step = get_restart_step(restart_files)
if not restart_step:
return False
sleep(1)
# Analyze restart folder
self.prepare_restart()
sleep(1)
# Make basic edits on conf file
self.configure_restart(restart_step, restart_files)
sleep(1)
# Edit optional arguments on conf file
self.configure_optional()
self.save_conf()
sleep(1)
# Run namd when enabled
if self.namd:
self.run_namd()
else:
log('info', 'Done.')
def __init__(self, **kwargs):
self.conf = kwargs['conf']
self.backup = kwargs['backup']
self.namd = kwargs['namd']
self.namd_exe = kwargs['namd_exe']
self.options = kwargs['options']
self.previous = os.path.abspath(kwargs['previous']) + '/'
self.restart = os.path.abspath(kwargs['restart']) + '/'
self.run = kwargs['run']
self.cores = kwargs['threads']
self.file_name = kwargs['file_name']
self.conf_file = None
try:
self.main()
except KeyboardInterrupt:
log('error', 'Interrupted by user.')
def annotate_restart(file_list, silent):
"""Create dict with restart files"""
annotated_files = dict()
for file in file_list:
if '.restart.xsc' in file:
annotated_files['xsc'] = file
elif '.restart.coor' in file:
annotated_files['coor'] = file
elif '.restart.vel' in file:
annotated_files['vel'] = file
else:
if not silent:
log('error', 'Missing restart file.')
return False
if not silent:
log('info', 'Restart files ready.')
return annotated_files
def configure_restart(self, restart_step, restart_files):
"""Make basic edits on conf file"""
log('info', 'Preparing .conf file.')
restart_insert = [
'set outputname ' + self.restart + self.file_name,
'bincoordinates ' + restart_files['coor'],
'binvelocities ' + restart_files['vel'],
'extendedSystem ' + restart_files['xsc'],
'firsttimestep ' + restart_step
]
restart_comment = ['temperature', 'minimize', 'reinitvels']
coord_index = self.search_option('coordinates') + 1
self.conf_file.insert(coord_index, '\n')
self.edit_run_steps(restart_step)
for option in restart_insert:
self.update_conf(option, coord_index)
for option in restart_comment:
self.comment_conf(option)
def search_conf(self):
"""Search conf files archive"""
if self.conf is not None:
if self.conf.endswith('.conf'):
return self.conf
else:
log('error', 'Please provide a valid .conf file.')
return False
log('info', 'Searching conf file.')
cmd = 'find ' + self.previous + ' -name "*conf"'
output = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
output = output.stdout.readlines()
if len(output) != 1:
log('error', 'Conf file not found! Please specify path with -c.')
return False
else:
return output[0].decode('utf-8').strip()
def choose_restart(files_dic, new, old, back, silent):
"""Choose restart files not empty"""
if len(new) >= 3:
for file in new:
if files_dic[file] == '0':
break
else:
return annotate_restart(new, silent)
if len(old) >= 3:
for file in old:
if files_dic[file] == '0':
break
else:
if not silent:
log(
'warning',
'Restart files empty or missing, using old restart files.'
)
sleep(1)
return annotate_restart(old, silent)
if len(back) >= 3:
for file in back:
if files_dic[file] == '0':
break
else:
if not silent:
log(
'warning',
'Restart files empty or missing, using backup restart files.'
)
sleep(1)
return annotate_restart(back, silent)
if not silent:
log('critical', 'Restart files empty or missing. Aborting!')
return False
def configure_optional(self):
"""Make additional edits on conf file"""
for item in self.options:
log('info', 'Setting parameter "' + ' '.join(item) + '".')
self.update_conf(' '.join(item))
