代码：
def main(args):
parser = argparse.ArgumentParser(
description='Physical validation suite for GROMACS.',
prog='gmx_physicalvalidation.py',
formatter_class=argparse.RawTextHelpFormatter,
epilog='Use --tests for details about the available tests and their arguments.'
)
parser.add_argument('json', type=open,
metavar='systems.json',
help='Json file containing systems and tests to be ran.')
parser.add_argument('--tests', default=False, action='store_true',
help='Print details about the available tests and their arguments and exit.')
parser.add_argument('-v', '--verbosity', type=int,
metavar='v', default=0,
help='Verbosity level. Default: 0 (quiet).')
parser.add_argument('--gmx', type=str, metavar='exe', default=None,
help=('GROMACS executable. Default: Trying to use \'gmx\'.\n' +
'Note: If -p is used, the GROMACS executable is not needed.'))
parser.add_argument('--bindir', type=str, metavar='dir', default=None,
help=('GROMACS binary directory.\n' +
'If set, trying to use \'bindir/gmx\' instead of plain \'gmx\'\n' +
'Note: If --gmx is set, --bindir and --suffix are ignored.'))
parser.add_argument('--suffix', type=str, metavar='_s', default=None,
help=('Suffix of the GROMACS executable.\n' +
'If set, trying to use \'gmx_s\' instead of plain \'gmx\'\n' +
'Note: If --gmx is set, --bindir and --suffix are ignored.'))
group = parser.add_mutually_exclusive_group()
group.add_argument('-p', '--prepare', action='store_true',
default=False,
help=('Only prepare simulations and output a \'run.sh\' file\n' +
'containing the necessary commands to run the systems.\n' +
'This allows to separate running simulations from analyzing them,\n' +
'useful e.g. to analyze the results on a different machine.\n' +
'Default: If none of \'-p\', \'-r\' or \'-a\' is given,\n' +
' the systems are prepared, ran and analyzed in one call.'))
group.add_argument('-r', '--run', action='store_true',
default=False,
help=('Only prepare and run simulations.\n' +
'Default: If none of \'-p\', \'-r\' or \'-a\' is given,\n' +
' the systems are prepared, ran and analyzed in one call.'))
group.add_argument('-a', '--analyze', action='store_true',
default=False,
help=('Only analyze previously ran simulations.\n' +
'This requires that the systems have been prepared using this program.\n' +
'Default: If none of \'-p\', \'-r\' or \'-a\' is given,\n' +
' the systems are prepared, ran and analyzed in one call.'))
parser.add_argument('-s', '--system', action='append', dest='systems',
metavar='system',
help=('Specify which system to run.\n' +
'\'system\' needs to match a system defined in the json file.\n' +
'Several systems can be specified by chaining several \'-s\' arguments.\n' +
'Defaults: If no \'-s\' argument is given, all systems and tests\n' +
' defined in the json file are ran.\n' +
'Note: \'system\' can be a regular expression matching more than one system.'))
parser.add_argument('--mpicmd', type=str, metavar='cmd', default=None,
help='MPI command used to invoke run command')
parser.add_argument('--wd', '--working_dir', type=str,
metavar='dir', default=None,
help='Working directory (default: current directory)')
parser.add_argument('--nobackup', default=False, action='store_true',
help='Do not create backups of files or folders.')
if '--tests' in args:
message = ('Physical validation suite for GROMACS\n'
'Available tests and their arguments\n'
'=====================================\n\n'
'The following tests can be specified in the json file:\n\n')
for test in all_tests:
message += ' * ' + test + '\n'
message += '\nAll tests accept additional arguments:\n'
for test, test_cls in all_tests.items():
message += '\n'
test_help = test_cls.parser().format_help()
test_help = test_help.replace(test_cls.__name__, test).replace('usage: ', '')
test_help = test_help.replace(' -h, --help show this help message and exit\n', '')
test_help = test_help.replace(' [-h]', '')
test_help = test_help.replace(' ' * (len(test_cls.__name__) + 7), ' ' * len(test))
first_line = test_help.split('\n')[0]
separator = '-' * 70
message += test_help.replace(first_line, separator + '\n' + first_line)
sys.stderr.write(message)
return
args = parser.parse_args(args)
# the input files are expected to be located where this script is
source_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'systems')
# target directory can be current or user chosen
if args.wd is None:
target_path = os.getcwd()
else:
if not os.path.exists(args.wd):
os.makedirs(args.wd)
target_path = args.wd
# parse simulation stage to perform
do_all = not (args.prepare or args.run or args.analyze)
do_prepare = do_all or args.prepare or args.run
write_script = args.prepare
do_run = do_all or args.run
do_analysis = do_all or args.analyze
# get ordered dict of systems from combination of json file and user choices
systems = parse_systems(args.json, args.systems, source_path, args.analyze)
# prepare GROMACS interface
if args.gmx:
gmx = args.gmx
else:
gmx = 'gmx'
if args.suffix:
gmx += args.suffix
if args.bindir:
gmx = os.path.join(args.bindir, gmx)
gmx_interface = None
gmx_parser = None
if do_run or do_analysis:
gmx_interface = GromacsInterface(exe=gmx)
gmx_parser = GromacsParser(exe=gmx)
if do_prepare:
nsystems = len(systems)
n = 0
runs = [] # this will contain all information needed to run the system
for system_name, system in systems.items():
n += 1
print('\rPreparing run files for systems... [{:d}/{:d}] '.format(n, nsystems), end='')
sys.stdout.flush() # py2 compatibility
system_dir = system['dir']
system_dirs = [] # list of directories with subsystems
# prepare the base system
input_dir = os.path.join(source_path, system_dir, 'input')
target_dir = os.path.join(target_path, system_dir)
mkdir_bk(target_dir, nobackup=args.nobackup)
basedir = os.path.join(target_dir, 'base')
mkdir_bk(basedir, nobackup=args.nobackup)
for suffix in ['mdp', 'gro', 'top']:
shutil.copy2(os.path.join(input_dir, 'system.' + suffix),
basedir)
system_dirs.append(basedir)
# call prepare method of chosen tests
for test_name, test in system['tests'].items():
for test_args in test['args']:
system_dirs.extend(
all_tests[test_name].prepare_parser(input_dir, target_dir, system_name,
args.nobackup, test_args)
)
# save run information
for d in system_dirs:
runs.append({
'dir': d,
'grompp_args': system['grompp_args'],
'mdrun_args': system['mdrun_args']
})
# end of loop over systems
print('-- done.')
if write_script:
print('Writing run script... ', end='')
sys.stdout.flush() # py2 compatibility
script_file = os.path.join(target_path, 'run_simulations.sh')
if not args.nobackup:
file_bk(script_file)
with open(script_file, 'w') as f:
f.write('# This file was created by the physical validation suite for GROMACS.\n')
f.write('\n# Define run variables\n')
f.write('WORKDIR=' + os.path.abspath(target_path) + '\n')
f.write('GROMPPCMD="' + os.path.abspath(gmx) + ' grompp"\n')
f.write('MDRUNCMD="' + os.path.abspath(gmx) + ' mdrun"\n')
f.write('\n# Run systems\n')
f.write('startpath=$PWD\n')
f.write('cd $WORKDIR\n')
for run in runs:
for cmd in basic_run_cmds(directory=os.path.relpath(os.path.abspath(run['dir']),
os.path.abspath(target_path)),
grompp_args=run['grompp_args'],
mdrun_args=run['mdrun_args']):
f.write(cmd + '\n')
f.write('\n')
f.write('cd $startpath\n')
print('-- done.')
print('Run script written to ' + script_file)
print('Adapt script as necessary and run simulations. Make sure to preserve the folder structure!')
print('Once all simulations have ran, analyze the results using `make check-phys-analyze` or '
'using the `-a` flag of `gmx_physicalvalidation.py`.')
# end if write_script
if do_run:
nruns = len(runs)
# send messages from GROMACS to log
gmx_log = open(os.path.join(target_path, 'physicalvalidation_gmx.log'), 'w')
for n, run in enumerate(runs):
print('\rRunning (sub)systems... [{:d}/{:d}] '.format(n+1, nruns), end='')
sys.stdout.flush() # py2 compatibility
gmx_interface.grompp(mdp='system.mdp',
top='system.top',
gro='system.gro',
tpr='system.tpr',
cwd=run['dir'],
args=run['grompp_args'],
stdout=gmx_log,
stderr=gmx_log)
gmx_interface.mdrun(tpr='system.tpr',
deffnm='system',
cwd=run['dir'],
args=run['mdrun_args'],
stdout=gmx_log,
stderr=gmx_log,
mpicmd=args.mpicmd)
gmx_log.close()
print('-- done.')
# end if do_run
# end if do_prepare
if do_analysis:
title = 'GROMACS PHYSICAL VALIDATION RESULTS'
width = 70
indent = int((width - len(title))/2)
print()
print(' ' * indent + '=' * len(title))
print(' ' * indent + title)
print(' ' * indent + '=' * len(title))
print()
passed = True
for system_name, system in systems.items():
system_dir = system['dir']
# save system data if re-used for different test
# massively reduces run time of multiple tests
system_data = {
'reduced': None,
'full': None
}
# system directory
target_dir = os.path.join(target_path, system_dir)
print('Analyzing system ' + system_name)
# call analyze method of chosen tests
for test_name, test in system['tests'].items():
for test_args in test['args']:
try:
result = all_tests[test_name].analyze_parser(gmx_parser, target_dir,
system_name, system_data,
args.verbosity, test_args)
except Exception as err:
print(' ' + all_tests[test_name].__name__ + ' FAILED (Exception in evaluation)')
print(' '*2 + type(err).__name__ + ': ' + str(err))
passed = False
else:
for line in result['message'].split('\n'):
print(' ' + line)
passed = passed and result['test']
# end loop over tests
print()
# end loop over systems
return int(not passed)
# end if do_analysis
# assuming everything is ok if we ended up here
return 0
if __name__ == "__main__":
return_value = main(sys.argv[1:])
sys.exit(return_value)
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