def peek_from_file(self):
peek = os.path.join(SYSTEM_DIR, "test_peek.mol2")
peek_system = system.System(system_type="custom",
density=0.8,
forcefield="gaff",
remove_hydrogens=True,
file_path=peek)
return peek_system
def test_stack(self):
stacked_system = system.System(molecule="PEEK",
para_weight=0.50,
density=0.7,
n_compounds=[10],
polymer_lengths=[5],
system_type="stack",
forcefield="gaff",
remove_hydrogens=False,
expand_factor=4)
def test_weighted_sequence(self):
para_system = system.System(molecule="PEEK",
para_weight=1.0,
n_compounds=[1],
polymer_lengths=[10],
density=0.1,
system_type="pack")
assert para_system.molecule_sequences[0] == "P" * 10
random_system = system.System(molecule="PEEK",
para_weight=0.40,
n_compounds=[1],
polymer_lengths=[20],
density=0.1,
system_type="pack")
random.seed(24)
sequence = system.random_sequence(para_weight=0.40, length=20)
sequence = "".join(sequence)
assert random_system.molecule_sequences[0] == sequence
def bad_system_type(self):
with pytest.raises(ValueError):
stacked_system = system.System(molecule="PEEK",
para_weight=0.50,
density=0.7,
n_compounds=[10],
polymer_lengths=[5],
system_type="wrong",
forcefield="gaff",
remove_hydrogens=False,
expand_factor=4)
def test_multiple_compounds(self):
simple_system = system.System(molecule="PEEK",
para_weight=0.60,
density=.1,
n_compounds=[5, 4, 3, 2, 1],
polymer_lengths=[2, 4, 5, 11, 22],
forcefield=None,
system_type="pack",
assert_dihedrals=False,
remove_hydrogens=False,
expand_factor=7)
def pekk_system_noH(self):
pekk_sys = system.System(molecule="PEKK",
para_weight=0.50,
density=1.2,
n_compounds=[3],
polymer_lengths=[3],
system_type="pack",
forcefield="gaff",
remove_hydrogens=True,
expand_factor=5)
return pekk_sys
def test_monomer_sequence(self):
with pytest.warns(UserWarning):
system_even = system.System(molecule="PEEK",
monomer_sequence="PM",
para_weight=0.5,
n_compounds=[1],
polymer_lengths=[4],
density=.1,
system_type="pack",
remove_hydrogens=True)
system_even = system.System(molecule="PEEK",
monomer_sequence="PM",
n_compounds=[1],
polymer_lengths=[4],
density=.1,
system_type="pack",
remove_hydrogens=True)
assert system_even.para == system_even.meta == 2
assert system_even.molecule_sequences[0] == "PMPM"
system_odd = system.System(molecule="PEEK",
monomer_sequence="PM",
n_compounds=[1],
polymer_lengths=[5],
density=.1,
system_type="pack",
remove_hydrogens=True)
assert system_odd.para == 3
assert system_odd.meta == 2
assert system_odd.molecule_sequences[0] == "PMPMP"
system_large_seq = system.System(molecule="PEEK",
monomer_sequence="PMPMPMPMPM",
n_compounds=[1],
polymer_lengths=[4],
density=.1,
system_type="pack",
remove_hydrogens=True)
assert system_large_seq.para == system_large_seq.meta == 2
assert system_large_seq.molecule_sequences[0] == "PMPM"
def test_dihedrals(self):
simple_system = system.System(
molecule="PEEK",
para_weight=0.60,
density=.1,
n_compounds=[1],
polymer_lengths=[2],
forcefield="gaff",
system_type="pack",
assert_dihedrals=True,
remove_hydrogens=False,
)
def test_mw_mn(self):
simple_system = system.System(molecule="PEEK",
para_weight=0.60,
density=0.1,
n_compounds=3,
sample_pdi=True,
Mn=5.0,
Mw=6.0,
system_type="pack",
forcefield=None,
assert_dihedrals=False,
remove_hydrogens=False,
expand_factor=7)
def test_too_few_pdi_vals(self):
with pytest.raises(AssertionError):
simple_system = system.System(
molecule="PEEK",
para_weight=0.60,
density=0.1,
n_compounds=3,
sample_pdi=True,
pdi=1.2,
forcefield=None,
system_type="pack",
assert_dihedrals=False,
remove_hydrogens=False,
)
def test_remove_hydrogens(self):
simple_system = system.System(
molecule="PEEK",
para_weight=0.60,
density=.1,
n_compounds=[1],
polymer_lengths=[2],
system_type="pack",
forcefield="gaff",
assert_dihedrals=False,
remove_hydrogens=True,
)
post_remove_h = simple_system.system
assert sum([int(item.type == "H")
for item in post_remove_h.atoms]) == 0
def test_custom_bad_params(self):
file_path = os.path.join(SYSTEM_DIR, "test_peek.mol2")
with pytest.warns(UserWarning):
custom_sys = system.System(system_type="custom",
density=0.7,
molecule="PEEK",
para_weight=0.50,
n_compounds=10,
polymer_lengths=5,
file_path=file_path)
ignore_args = [
custom_sys.molecule, custom_sys.para_weight,
custom_sys.polymer_lengths, custom_sys.n_compounds
]
assert not any(ignore_args)
def test_gauss_dist(self):
random.seed(42)
simple_system = system.System(
molecule="PEEK",
para_weight=0.60,
density=0.1,
n_compounds=3,
sample_pdi=True,
pdi=1.001,
Mn=5.0,
system_type="pack",
forcefield=None,
assert_dihedrals=False,
remove_hydrogens=False,
mass_dist_type="gaussian",
)
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)