def load_sample_simulation(mof='single',
setup='run',
tests_dir=tests_dir,
parameters=k_parameters.copy()):
""" Load a sample simulation object from the tests directory """
from thermof import Simulation
if mof == 'single':
trial = os.path.join(tests_dir, 'ideal-mof-trial')
if setup == 'run':
sample_simulation = Simulation(read=os.path.join(trial, 'Run1'),
setup='run',
parameters=parameters)
elif setup == 'trial':
sample_simulation = Simulation(read=trial,
setup='trial',
parameters=parameters)
else:
trial = os.path.join(tests_dir, 'ip-mof-trial')
if setup == 'run':
sample_simulation = Simulation(read=os.path.join(trial, 'Run1'),
setup='run',
parameters=parameters)
elif setup == 'trial':
sample_simulation = Simulation(read=trial,
setup='trial',
parameters=parameters)
return sample_simulation
def test_simulation_read_run():
"""Test Simulation class read method for reading a single run with read_run"""
par = Parameters()
par.k['read_thermo'] = True
par.k['read_info'] = True
par.thermof['kpar'] = par.k
run_dir = os.path.join(trial_dir, 'Run1')
run_data = read_run(run_dir, k_par=par.k)
sim = Simulation(read=run_dir, parameters=par)
sim.read(run_dir, setup='run')
with open(thermo_ref_file, 'r') as tref:
thermo_ref = yaml.load(tref)
assert sim.run == run_data
assert sim.run['thermo'] == thermo_ref
assert len(sim) == 1
assert str(sim) == 'Run1'
def test_simulation_get_plot_data_for_trial():
"""Test Simulation class get_plot_data method for pulling correct data for different plots of a trial"""
par = Parameters()
sim = Simulation(read=trial_dir, parameters=par, setup='trial')
with open(time_ref_file, 'r') as tiref:
time_ref = yaml.load(tiref)
assert get_plot_data(sim, 'k')['x'] == time_ref
assert get_plot_data(sim, 'k_sub')['x'] == time_ref
assert get_plot_data(sim, 'k')['legend'] == sim.trial['runs']
def test_simulation_read_trial_set():
"""Test Simulation class read method for reading a trial set"""
par = Parameters()
par.k['isotropic'] = True
par.k['average'] = True
par.thermof['kpar'] = par.k
trial_set = read_trial_set(trial_set_dir, k_par=par.k)
sim = Simulation(read=trial_set_dir, setup='trial_set', parameters=par)
assert trial_set == sim.trial_set
assert len(sim) == 4
assert str(sim) == 'ideal-mof-trial-set'
def test_simulation_get_plot_data_for_run():
"""Test Simulation class get_plot_data method for pulling correct data for different plots of a run"""
par = Parameters()
par.k['read_thermo'] = True
par.thermof['kpar']['read_thermo'] = True
par.thermof['kpar']['kb'] = 0.001987
run_dir = os.path.join(trial_dir, 'Run1')
sim = Simulation(read=run_dir, parameters=par, setup='run')
with open(k_ref_file, 'r') as kref:
k_ref = yaml.load(kref)
with open(time_ref_file, 'r') as tiref:
time_ref = yaml.load(tiref)
with open(thermo_ref_file, 'r') as tref:
thermo_ref = yaml.load(tref)
assert get_plot_data(sim, 'thermo') == thermo_ref
k_plot_data = get_plot_data(sim, 'k')
assert k_plot_data['x'] == time_ref
assert k_plot_data['y'][sim.run['directions'].index('x')] == k_ref
assert k_plot_data['legend'] == sim.run['directions']
def main():
parser = argparse.ArgumentParser(
description="""
----------------------------------------------------------------------------
████████╗██╗ ██╗███████╗██████╗ ███╗ ███╗ ██████╗ ███████╗
╚══██╔══╝██║ ██║██╔════╝██╔══██╗████╗ ████║██╔═══██╗██╔════╝
██║ ███████║█████╗ ██████╔╝██╔████╔██║██║ ██║█████╗
██║ ██╔══██║██╔══╝ ██╔══██╗██║╚██╔╝██║██║ ██║██╔══╝
██║ ██║ ██║███████╗██║ ██║██║ ╚═╝ ██║╚██████╔╝██║
╚═╝ ╚═╝ ╚═╝╚══════╝╚═╝ ╚═╝╚═╝ ╚═╝ ╚═════╝ ╚═╝
TherMOF: Thermal transport in Metal-Organic Frameworks
-----------------------------------------------------------------------------
""",
epilog="""
Example:
python thermof_read.py IRMOF-1
would read simulation results from IRMOF-1 directory.
You would need a Lammps log file and simpar.yaml (produced by thermof) to be able to
read simulation results.
""",
formatter_class=argparse.RawDescriptionHelpFormatter)
default_params = {}
# Positional arguments
parser.add_argument('simdir',
type=str,
help='Lammps simulation directory.')
# Optional arguments
parser.add_argument('--setup',
'-s',
default='run',
type=str,
metavar='',
help='Simulation setup (run | trial | trial_set).')
parser.add_argument('--no_parameters',
'-np',
action='store_true',
default=False,
help='Dont read simulation parameters, use default.')
parser.add_argument('--plot',
'-p',
nargs='+',
default=[],
help='Plot HCACF, k, and thermodynamic properties.')
parser.add_argument(
'--kavg',
'-k',
nargs=2,
default=[10, 20],
help='Average thermal conductivity btw. given time interval (ps).')
parser.add_argument('--write',
'-w',
action='store_true',
default=False,
help='Write results to a file.')
# Parse arguments
args = parser.parse_args()
# Initialize simulation and read
simdir = os.path.abspath(args.simdir)
if args.no_parameters:
sim = Simulation(setup=args.setup)
else:
sim = Simulation(setup=args.setup)
sim.simdir = simdir
sim.read_parameters()
sim.parameters.thermof['kpar']['t0'] = int(args.kavg[0])
sim.parameters.thermof['kpar']['t1'] = int(args.kavg[1])
sim.read(simdir, setup=args.setup)
# Plotting
if len(args.plot) > 0:
sim.parameters.plot = plot_parameters.copy()
sim.parameters.plot['k_sub']['k_est_t0'] = int(args.kavg[0])
sim.parameters.plot['k_sub']['k_est_t1'] = int(args.kavg[1])
for plt in args.plot:
sim.parameters.plot[plt]['save'] = os.path.join(
simdir, '%s-%s.png' % (os.path.basename(simdir), plt))
sim.plot(plt)
def main():
parser = argparse.ArgumentParser(
description="""
----------------------------------------------------------------------------
████████╗██╗ ██╗███████╗██████╗ ███╗ ███╗ ██████╗ ███████╗
╚══██╔══╝██║ ██║██╔════╝██╔══██╗████╗ ████║██╔═══██╗██╔════╝
██║ ███████║█████╗ ██████╔╝██╔████╔██║██║ ██║█████╗
██║ ██╔══██║██╔══╝ ██╔══██╗██║╚██╔╝██║██║ ██║██╔══╝
██║ ██║ ██║███████╗██║ ██║██║ ╚═╝ ██║╚██████╔╝██║
╚═╝ ╚═╝ ╚═╝╚══════╝╚═╝ ╚═╝╚═╝ ╚═╝ ╚═════╝ ╚═╝
TherMOF: Thermal transport in Metal-Organic Frameworks
-----------------------------------------------------------------------------
""",
epilog="""
Example:
>>> python thermof_write.py IRMOF-1.cif
would read IRMOF-1 cif file, analyze topology, assign force field (default: UFF) and
create input files for a Lammps simulation.
>>> python thermof_write.py IRMOF-1.cif --forcefield UFF4MOF --fix MIN NPT NVT NVE --scheduler pbs
would initialize Lammps simulation files with UFF4MOF force field for following procedure:
Minimization, NPT, NVT, and NVE emsembles. It would also create a job submission script for pbs scheduler.
""",
formatter_class=argparse.RawDescriptionHelpFormatter)
default_params = {}
# Positional arguments
parser.add_argument('molecule', type=str, help='Molecule file to read (must be in .cif format).')
# Optional arguments
parser.add_argument('--runs', '-r', default=1, type=int, metavar='',
help='Number of runs (different seed number is used for each run).')
parser.add_argument('--forcefield', '-ff', default='UFF', type=str, metavar='',
help='Force field for molecule file ([UFF] / BTW_FF / Dreiding / UFF4MOF / Dubbeldam).')
parser.add_argument('--fix', nargs='+', default=['NVT'], type=str,
help='Lammps fix types (MIN / NPT / NVT / NVE).')
parser.add_argument('--scheduler', default='slurm', type=str, metavar='',
help='Job scheduler (pbs / [slurm] / slurm-scratch).')
# Parse arguments
args = parser.parse_args()
# Initialize simulation
simpar = Parameters()
sim = Simulation(mof=args.molecule, parameters=simpar)
mof_name = os.path.splitext(os.path.basename(args.molecule))[0]
sim.simdir = os.path.join(os.path.dirname(args.molecule), mof_name)
sim.parameters.lammps['force_field'] = args.forcefield
sim.parameters.lammps['mol_ff'] = args.forcefield
sim.parameters.thermof['fix'] = args.fix
sim.parameters.job['scheduler'] = args.scheduler
try:
if args.runs == 1:
sim.initialize()
elif args.runs > 1:
sim.initialize_runs(args.runs)
except Exception as e:
print(e)