def test_custom_system(self, peek_from_file):
simulation = simulate.Simulation(peek_from_file, mode="cpu")
simulation.quench(kT=2,
n_steps=1e3,
shrink_kT=2,
shrink_steps=1e3,
shrink_period=20,
walls=False)
def test_quench(self, peek_system):
simulation = simulate.Simulation(peek_system, dt=0.0001, mode="cpu")
simulation.quench(
kT=2,
n_steps=1e3,
shrink_kT=8,
shrink_steps=1e3,
shrink_period=1,
walls=False,
)
def test_walls_quench(self, peek_system_noH):
simulation = simulate.Simulation(peek_system_noH, dt=0.001, mode="cpu")
simulation.quench(
kT=2,
n_steps=1e3,
shrink_kT=8,
shrink_steps=1e3,
shrink_period=20,
walls=True,
)
def test_anneal_no_shrink(self, peek_system):
simulation = simulate.Simulation(peek_system, dt=0.0001, mode="cpu")
simulation.anneal(
kT_init=4,
kT_final=2,
step_sequence=[1e3, 1e3],
shrink_kT=None,
shrink_steps=None,
shrink_period=None,
walls=False,
)
def test_walls_anneal(self, peek_system_noH):
simulation = simulate.Simulation(peek_system_noH, dt=0.001, mode="cpu")
simulation.anneal(
kT_init=4,
kT_final=2,
step_sequence=[1e3, 1e3],
shrink_kT=8,
shrink_steps=1e3,
shrink_period=20,
walls=True,
)
def test_quench_no_shrink(self, peek_system):
simulation = simulate.Simulation(peek_system,
tau_p=0.1,
dt=0.0001,
mode="cpu")
simulation.quench(
kT=2,
pressure=0.1,
n_steps=1e3,
shrink_kT=None,
shrink_steps=None,
shrink_period=None,
walls=False,
)
def test_anneal_npt(self, pekk_system):
simulation = simulate.Simulation(pekk_system,
dt=0.0001,
tau_p=0.1,
mode="cpu")
simulation.anneal(
kT_init=4,
kT_final=2,
pressure=0.1,
step_sequence=[1e3, 1e3],
shrink_kT=8,
shrink_steps=1e3,
shrink_period=1,
walls=False,
)
def test_bad_inputs(self, peek_system):
simulation = simulate.Simulation(peek_system,
tau_p=0.1,
dt=0.0001,
mode="cpu")
# Only 1 of shrink params given
with pytest.raises(ValueError):
simulation.quench(
kT=2,
n_steps=1e3,
shrink_kT=5,
shrink_steps=None,
shrink_period=None,
walls=True,
)
# Pressure and walls quench
with pytest.raises(ValueError):
simulation.quench(
kT=2,
pressure=0.1,
n_steps=1e3,
shrink_kT=None,
shrink_steps=None,
shrink_period=None,
walls=True,
)
# Pressure and walls anneal
with pytest.raises(ValueError):
simulation.anneal(
kT_init=2,
kT_final=1,
step_sequence=[1e3, 1e3],
pressure=0.1,
shrink_kT=None,
shrink_steps=None,
shrink_period=None,
walls=True,
)
def sample(job):
from uli_init import simulate, system
from uli_init.utils import base_units, unit_conversions
import numpy as np
import logging
with job:
print(job.id)
logging.info("Creating system...")
if job.sp["system_type"] != "interface":
system_parms = system.System(
density=job.sp['density'],
molecule=job.sp['molecule'],
n_compounds=job.sp['n_compounds'],
polymer_lengths=job.sp["polymer_lengths"],
para_weight=job.sp['para_weight'],
monomer_sequence=job.sp['monomer_sequence'],
sample_pdi=job.doc.sample_pdi,
pdi=job.sp['pdi'],
Mn=job.sp['Mn'],
Mw=job.sp['Mw'],
seed=job.sp['system_seed'])
system = system.Initializer(
system=system_parms,
system_type=job.sp["system_type"],
forcefield=job.sp["forcefield"],
remove_hydrogens=job.sp["remove_hydrogens"],
**job.sp["kwargs"])
if any(list(job.sp["box_constraints"].values())):
system.target_box = system.set_target_box(
job.sp["box_constraints"]["x"],
job.sp["box_constraints"]["y"],
job.sp["box_constraints"]["z"])
job.doc["target_volume"] = system.target_box
shrink_kT = job.sp['shrink_kT']
shrink_steps = job.sp['shrink_steps']
shrink_period = job.sp['shrink_period']
job.doc['num_para'] = system_parms.para
job.doc['num_meta'] = system_parms.meta
job.doc['num_compounds'] = system_parms.n_compounds
job.doc['polymer_lengths'] = system_parms.polymer_lengths
job.doc["chain_sequences"] = system_parms.molecule_sequences
elif job.sp["system_type"] == "interface":
slab_files = []
ref_distances = []
if job.doc['use_signac'] is True:
signac_args = []
if isinstance(job.sp['signac_args'], list):
slab_1_arg = job.sp['signac_args'][0]
signac_args.append(slab_1_arg)
if len(job.sp['signac_args']) == 2:
slab_2_arg = job.sp['signac_args'][1]
signac_args.append(slab_2_args)
elif not isinstance(job.sp['signac_args'], list):
signac_args.append(job.sp['signac_args'])
project = signac.get_project(root=job.sp['signac_project'],
search=True)
for arg in signac_args:
if isinstance(arg, dict):
_job = list(project.find_jobs(filter=arg))[0]
slab_files.append(_job.fn('restart.gsd'))
ref_distances.append(_job.doc['ref_distance'] / 10)
elif isinstance(arg, str): # Find job using job ID
_job = project.open_job(id=arg)
slab_files.append(_job.fn('restart.gsd'))
ref_distances.append(_job.doc['ref_distance'] / 10)
elif job.doc['use_signac'] is False:
slab_files.append(job.sp.slab_file)
ref_distances.append(job.sp['reference_distance'])
system = system.Interface(
slabs=slab_files,
ref_distance=ref_distances[0],
gap=job.sp['interface_gap'],
weld_axis=job.sp["weld_axis"],
)
job.doc['slab_ref_distances'] = system.ref_distance
shrink_kT = None
shrink_steps = None
shrink_period = None
system.system.save('init.mol2', overwrite=True)
logging.info("System generated...")
logging.info("Starting simulation...")
simulation = simulate.Simulation(
system,
r_cut=job.sp["r_cut"],
tau_kt=job.sp['tau_kt'],
tau_p=job.sp['tau_p'],
nlist=job.sp['neighbor_list'],
dt=job.sp['dt'],
seed=job.sp['sim_seed'],
auto_scale=True,
ref_values=None,
mode="gpu",
gsd_write=max([int(job.doc['steps'] / 100), 1]),
log_write=max([int(job.doc['steps'] / 10000), 1]))
logging.info("Simulation object generated...")
job.doc['ref_energy'] = simulation.ref_energy
job.doc['ref_distance'] = simulation.ref_distance
job.doc['ref_mass'] = simulation.ref_mass
job.doc['real_timestep'] = unit_conversions.convert_to_real_time(
simulation.dt, simulation.ref_energy, simulation.ref_distance,
simulation.ref_mass)
job.doc['time_unit'] = 'fs'
job.doc['steps_per_frame'] = simulation.gsd_write
job.doc['steps_per_log'] = simulation.log_write
if job.sp['procedure'] == "quench":
job.doc['T_SI'] = unit_conversions.kelvin_from_reduced(
job.sp['kT_quench'], simulation.ref_energy)
job.doc['T_unit'] = 'K'
logging.info("Beginning quench simulation...")
simulation.quench(kT=job.sp['kT_quench'],
pressure=job.sp['pressure'],
n_steps=job.sp['n_steps'],
shrink_kT=shrink_kT,
shrink_steps=shrink_steps,
wall_axis=job.sp['walls'],
shrink_period=shrink_period)
elif job.sp['procedure'] == "anneal":
logging.info("Beginning anneal simulation...")
if not job.sp['schedule']:
kT_list = np.linspace(
job.sp['kT_anneal'][0],
job.sp['kT_anneal'][1],
len(job.sp['anneal_sequence']),
)
kT_SI = [
unit_conversions.kelvin_from_reduced(
kT, simulation.ref_energy) for kT in kT_list
]
job.doc['T_SI'] = kT_SI
job.doc['T_unit'] = 'K'
simulation.anneal(kT_init=job.sp['kT_anneal'][0],
kT_final=job.sp['kT_anneal'][1],
pressure=job.sp['pressure'],
step_sequence=job.sp['anneal_sequence'],
schedule=job.sp['schedule'],
shrink_kT=shrink_kT,
shrink_steps=shrink_steps,
wall_axis=job.sp['walls'],
shrink_period=shrink_period)
def test_slabs_anneal(self, test_slab):
simulation = simulate.Simulation(test_slab, dt=0.0001, mode="cpu")
simulation.anneal(kT_init=4,
kT_final=2,
step_sequence=[1e3, 1e3, 1e3],
walls=True)
def test_slabs_quench(self, test_slab):
simulation = simulate.Simulation(test_slab, dt=0.0001, mode="cpu")
simulation.quench(kT=2, n_steps=1e3, walls=True)