def gmxmmpbsa():
# Adapted to run with MPI ?
if len(sys.argv) > 1 and sys.argv[1] in ['MPI', 'mpi']:
args = sys.argv
args.pop(1) # remove mpi arg before passed it to app
try:
from mpi4py import MPI
except ImportError:
raise MMPBSA_Error(
'Could not import mpi4py package! Use serial version '
'or install mpi4py.')
else:
# If we're not running "gmx_MMPBSA MPI", bring MPI into the top-level namespace
# (which will overwrite the MPI from mpi4py, which we *want* to do in serial)
from GMXMMPBSA.fake_mpi import MPI
args = sys.argv
# Set up error/signal handlers
main.setup_run()
# Instantiate the main MMPBSA_App
app = main.MMPBSA_App(MPI)
# Read the command-line arguments
try:
app.get_cl_args(args[1:])
except CommandlineError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.exit(1)
# Perform our MMPBSA --clean now
if app.FILES.clean:
sys.stdout.write('Cleaning temporary files and quitting.\n')
app.remove(0)
sys.exit(0)
# See if we wanted to print out our input file options
if app.FILES.infilehelp:
app.input_file.print_contents(sys.stdout)
sys.exit(0)
# If we're not rewriting output do whole shebang, otherwise load info and parms
# Throw up a barrier before and after running the actual calcs
if not app.FILES.rewrite_output:
try:
app.read_input_file()
except InputError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.stderr.write(' Enter `%s --help` for help\n' %
(split(sys.argv[0])[1]))
sys.exit(1)
app.process_input()
app.check_for_bad_input()
app.loadcheck_prmtops()
app.file_setup()
app.run_mmpbsa()
# If we are rewriting output, load the info and check prmtops
else:
info = InfoFile(app)
info.read_info()
app.loadcheck_prmtops()
# Now we parse the output, print, and finish
app.parse_output_files()
app.write_final_outputs()
app.finalize()
def gmxmmpbsa():
stream_handler = logging.StreamHandler()
stream_handler.setLevel(logging.INFO)
formatter = logging.Formatter("[%(levelname)-7s] %(message)s")
stream_handler.setFormatter(formatter)
logging.basicConfig(
level=logging.DEBUG,
format="[%(levelname)-7s] %(message)s",
handlers=[logging.FileHandler("gmx_MMPBSA.log", 'w'), stream_handler])
# Just for compatibility as mpi4py works as serial when run without mpirun
# (since v1.4.2)
if len(sys.argv) > 1 and sys.argv[1] in ['MPI', 'mpi']:
from mpi4py import MPI
else:
# If we're not running "gmx_MMPBSA MPI", bring MPI into the top-level namespace
# (which will overwrite the MPI from mpi4py, which we *want* to do in serial)
from GMXMMPBSA.fake_mpi import MPI
# Set up error/signal handlers
main.setup_run()
# Instantiate the main MMPBSA_App
app = main.MMPBSA_App(MPI)
# Read the command-line arguments
try:
app.get_cl_args(sys.argv[1:])
except CommandlineError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.exit(1)
if app.FILES.createinput is not None:
args_list = create_input_args(app.FILES.createinput)
app.input_file.print_contents('mmpbsa.in', args_list)
logging.info(
f'Input file creation successful. Path: {Path("mmpbsa.in").absolute()}'
)
sys.exit(0)
# Perform our MMPBSA --clean now
if app.FILES.clean:
logging.info('Cleaning temporary files and quitting.\n')
app.remove(-1)
sys.exit(0)
# See if we wanted to print out our input file options
if app.FILES.infilehelp:
app.input_file.print_contents(sys.stdout)
sys.exit(0)
# If we're not rewriting output do whole shebang, otherwise load info and parms
# Throw up a barrier before and after running the actual calcs
if not app.FILES.rewrite_output:
try:
app.read_input_file()
except InputError as e:
sys.stderr.write('%s: %s' % (type(e).__name__, e) + '\n')
sys.stderr.write(' Enter `%s --help` for help\n' %
(split(sys.argv[0])[1]))
sys.exit(1)
app.process_input()
app.check_for_bad_input()
app.make_prmtops()
app.loadcheck_prmtops()
app.file_setup()
app.run_mmpbsa()
# If we are rewriting output, load the info and check prmtops
else:
info = InfoFile(app)
info.read_info()
app.loadcheck_prmtops()
# Now we parse the output, print, and finish
app.parse_output_files()
app.write_final_outputs()
app.finalize()