def test_total_possible_bonds(self, tmpdir, datadir):
import epoxpy.abc_type_epoxy_dpd_simulation as es
import epoxpy.temperature_profile_builder as tpb
import os
mix_time = 3e4
mix_kt = 2.0
cure_kt = 2.0
time_scale = 100
temp_scale = 1
type_A_md_temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=mix_kt, initial_time=mix_time)
type_A_md_temp_profile.add_state_point(500 * time_scale, cure_kt)
out_dir = str(tmpdir)
sim_name = 'shrunk_freud_bonding'
out_dir = os.path.join(out_dir, sim_name)
initial_structure_path = os.path.join(datadir, 'shrunk_init.hoomdxml')
myEpoxySim = es.ABCTypeEpoxyDPDSimulation(
sim_name,
mix_time=mix_time,
mix_kt=mix_kt,
temp_prof=type_A_md_temp_profile,
bond=True,
n_mul=1000.0,
shrink=True,
output_dir=out_dir,
ext_init_struct_path=initial_structure_path,
reset_random_after_initialize=True)
possible_bonds = myEpoxySim.total_possible_bonds()
expected_possible_bonds = 40000 #becuase n_mul is 1000.0 and 10,000 A particles and 20,000 B particles can make a maximum of 40,000 bonds
assert (possible_bonds == expected_possible_bonds)
curing_percent = myEpoxySim.get_curing_percentage()
expected_curing_percent = 0
assert (curing_percent == expected_curing_percent)
def test_epoxy_sim_legacy_bonding(self, datadir, tmpdir):
import epoxpy.abc_type_epoxy_dpd_simulation as es
import epoxpy.temperature_profile_builder as tpb
import random
import os
import numpy as np
import gsd.hoomd
random.seed(1020)
shrink = False
legacy_bonding = True
bonding = True
exclude_mixing_in_output = False
mix_time = 3e4
mix_kt = 2.0
time_scale = 100
cure_kt = 2.0
nmul = 2.0
log_period = 1e5
dump_period = 1e2
curing_log_period = 1e1
type_A_md_temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=mix_kt, initial_time=mix_time)
type_A_md_temp_profile.add_state_point(500 * time_scale, cure_kt)
sim_name = 'legacy_bonding'
out_dir = str(tmpdir)
out_dir = os.path.join(out_dir, sim_name)
myEpoxySim = es.ABCTypeEpoxyDPDSimulation(
sim_name,
mix_time=mix_time,
mix_kt=mix_kt,
temp_prof=type_A_md_temp_profile,
bond=bonding,
n_mul=nmul,
shrink=shrink,
legacy_bonding=legacy_bonding,
exclude_mixing_in_output=exclude_mixing_in_output,
log_curing=False,
curing_log_period=curing_log_period,
log_write=log_period,
dcd_write=dump_period,
output_dir=out_dir)
myEpoxySim.execute()
current_gsd = tmpdir.join(sim_name, 'data.gsd')
gsd_path = str(current_gsd)
print('reading gsd: ', gsd_path)
f = gsd.fl.GSDFile(gsd_path, 'rb')
t = gsd.hoomd.HOOMDTrajectory(f)
snapshot = t[-1]
assert snapshot.particles.N == 100
current_bonds = snapshot.bonds.N
print('test_epoxy_sim_legacy_bonding_count. legacy bonds:{}'.format(
current_bonds))
assert current_bonds > 30 #Just checking if some bonds are being made
def test_epoxy_sim_wo_bonding(self, datadir, tmpdir):
import epoxpy.abc_type_epoxy_dpd_simulation as es
import epoxpy.temperature_profile_builder as tpb
import random
import os
import numpy as np
import gsd.hoomd
random.seed(1020)
print('\n# Test: test_epoxy_sim_wo_bonding')
mix_time = 3e4
mix_kt = 2.0
cure_kt = 2.0
time_scale = 100
temp_scale = 1
type_A_md_temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=mix_kt, initial_time=mix_time)
type_A_md_temp_profile.add_state_point(500 * time_scale, cure_kt)
sim_name = 'wo_bonding'
out_dir = str(tmpdir)
exclude_mixing_in_output = False
out_dir = os.path.join(out_dir, sim_name)
myEpoxySim = es.ABCTypeEpoxyDPDSimulation(
sim_name,
mix_time=mix_time,
mix_kt=mix_kt,
temp_prof=type_A_md_temp_profile,
output_dir=out_dir,
n_mul=2.0,
exclude_mixing_in_output=exclude_mixing_in_output,
shrink=False)
myEpoxySim.execute()
total_time = type_A_md_temp_profile.get_total_sim_time()
md_time = total_time - mix_time
gsd_write_period = myEpoxySim.dcd_write
total_frames = int(round(total_time / gsd_write_period))
total_md_frames = int(round(md_time / gsd_write_period))
print('total_frames:{}, md frames:{}'.format(total_frames,
total_md_frames))
print('current directory: {}'.format(os.getcwd()))
print('tmp dir: {}'.format(tmpdir))
print('datadir: {}'.format(datadir))
current_gsd = tmpdir.join(sim_name, 'data.gsd')
gsd_path = str(current_gsd)
f = gsd.fl.GSDFile(gsd_path, 'rb')
t = gsd.hoomd.HOOMDTrajectory(f)
snapshot = t[-1]
assert snapshot.particles.N == 100
import epoxpy.temperature_profile_builder as tpb
import epoxpy.bonding as bondClass
import random
import os
import gsd.hoomd
import numpy as np
import epoxpy.common as cmn
random.seed(1020)
mix_time = 1e3
mix_kt = 2.0
cure_kt = 2.0
time_scale = 100
temp_scale = 1
type_A_md_temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=mix_kt, initial_time=mix_time)
type_A_md_temp_profile.add_state_point(500 * time_scale, cure_kt)
out_dir = str('.')
sim_name = 'shrunk_freud_bonding'
out_dir = os.path.join(out_dir, sim_name)
myEpoxySim = es.ABCTypeEpoxyLJHarmonicSimulation(
sim_name,
mix_time=mix_time,
mix_kt=mix_kt,
temp_prof=type_A_md_temp_profile,
bond=True,
n_mul=4.0,
shrink=True,
shrink_time=1e4,
mix_dt=1e-4,
av_calibrationT = 439.3636 #K
av_aij_DDS_DEGBA = 30.729
av_aij_DDS_PES = 25.003
av_aij_DEGBA_PES = 30.532
temperature_profile = 'iso' #'lin_ramp''step'
bonding_period = 10
percent_bonds_per_step = 0.005
kT = 500 / av_calibrationT
AB_bond_const = 4.0
AB_bond_dist = 0.0
CC_bond_const = 4.0
CC_bond_dist = 0.0
if temperature_profile is 'iso':
temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=kT, initial_time=mixing_time)
temp_profile.add_state_point(t_Final, kT)
elif temperature_profile is 'lin_ramp':
temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=300 / calibrationT, initial_time=mixing_time)
temp_profile.add_state_point(t_Final, kT)
elif temperature_profile is 'step':
temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=300 / calibrationT, initial_time=mixing_time)
temp_profile.add_state_point(t_SetT, kT)
temp_profile.add_state_point(t_Final * time_scale, kT)
output_dir = os.path.join('.', temperature_profile)
myEpoxySim = es.ABCTypeEpoxySimulation(
temperature_profile,
output_dir=output_dir,
mix_time=mixing_time,
def test_epoxy_sim_dybond_lj_harmonic_langevin(self, datadir, tmpdir):
"""
Here we are doing regression testing for the new bonding routine that operates and the mbuild initial structure
whose volume is shrunk to a density of 1.0
:param datadir:
:param tmpdir:
:return:
"""
import epoxpy.abc_type_epoxy_lj_harmonic_simulation as es
import epoxpy.temperature_profile_builder as tpb
import epoxpy.bonding as bondClass
import random
import os
import gsd.hoomd
import numpy as np
import epoxpy.common as cmn
random.seed(1020)
mix_time = 1e3
mix_kt = 2.0
cure_kt = 2.0
time_scale = 100
temp_scale = 1
type_A_md_temp_profile = tpb.LinearTemperatureProfileBuilder(
initial_temperature=mix_kt, initial_time=mix_time)
type_A_md_temp_profile.add_state_point(500 * time_scale, cure_kt)
out_dir = str(tmpdir)
sim_name = 'shrunk_freud_bonding'
out_dir = os.path.join(out_dir, sim_name)
myEpoxySim = es.ABCTypeEpoxyLJHarmonicSimulation(
sim_name,
mix_time=mix_time,
mix_kt=mix_kt,
temp_prof=type_A_md_temp_profile,
bond=True,
n_mul=6.0,
shrink=True,
shrink_time=1e5,
mix_dt=1e-4,
md_dt=1e-2,
integrator=cmn.Integrators.LANGEVIN.name,
output_dir=out_dir,
use_dybond_plugin=True)
myEpoxySim.execute()
current_gsd = tmpdir.join(sim_name, 'data.gsd')
gsd_path = str(current_gsd)
print('reading gsd: ', gsd_path)
f = gsd.fl.GSDFile(gsd_path, 'rb')
t = gsd.hoomd.HOOMDTrajectory(f)
snapshot = t[-1]
current_bonds = snapshot.bonds.N
assert snapshot.particles.N == 300
print('test_epoxy_sim_freud_shrunk_regression. current:{}'.format(
current_bonds))
assert current_bonds > 30 #Just checking if some bonds are being made
idxs, counts = np.unique(snapshot.bonds.group, return_counts=True)
print('########################idxs', idxs, counts)
print(snapshot.bonds.group)
for index, idx in enumerate(idxs):
p_typeid = snapshot.particles.typeid[idx]
p_type = snapshot.particles.types[p_typeid]
if p_type == 'A':
assert (counts[index] <= bondClass.FreudBonding.MAX_A_BONDS)
elif p_type == 'B':
assert (counts[index] <= bondClass.FreudBonding.MAX_B_BONDS)