def test_restart_run_name_single_file(self):
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
Path("equil.inp").touch()
restart_from, run_name = get_restart_name(None, None)
assert run_name == "equil.rst.001"
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
Path("equil.rst.001.inp").touch()
restart_from, run_name = get_restart_name(None, None)
assert run_name == "equil.rst.002"
def test_restart_run_name_multiple_invalid_files(self):
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
Path("prod.inp").touch()
Path("equil.rst.001.inp").touch()
Path("equil.rst.002.inp").touch()
with pytest.raises(ValueError, match=r"Multiple"):
get_restart_name(None, None)
def main():
# Create a water molecule with the spce geometry
water = spce_water
ff = foyer.Forcefield(get_ff("pore-spce-jc.xml"))
water_typed = ff.apply(water)
# Define conditions
temperature = 298.0 * u.K
# Define a range of (shifted) chemical potentials
mus_adsorbate = np.arange(-58, -42, 2) * u.Unit("kJ/mol")
# Define custom_args that are the same for all pure phase simulations
custom_args = {
"cutoff_style": "cut",
"charge_style": "ewald",
"rcut_min": 0.5 * u.angstrom,
"vdw_cutoff": 9.0 * u.angstrom,
"prop_freq": 10,
"angle_style": ["fixed"],
}
for mu_adsorbate in mus_adsorbate:
print(f"\nRun simulation: T = {temperature}, mu = {mu_adsorbate}\n")
dirname = f"T_{temperature:0.1f}_mu_{mu_adsorbate:.1f}".replace(
" ", "_"
).replace(
"/", "-"
)
if not os.path.isdir(dirname):
os.mkdir(dirname)
else:
pass
with temporary_cd(dirname):
# Box size depends on chemical potential
# Test simulations show mu' = -48 kJ/mol; p ~ 0.01 bar
# Employ IG law to estimate remaining box sizes; target 40 waters
mu_0 = -48 * u.kJ/u.mol
p_0 = 0.01 * u.bar
n_water_target = 40
p_ig = p_0 * np.exp((mu_adsorbate-mu_0)/(u.kb * temperature))
vol = n_water_target * u.kb * temperature / p_ig
boxl = (vol**(1./3.)).to_value("nm")
custom_args["charge_cutoff"] = 0.25 * boxl * u.nm
species_list = [water_typed]
box_list = [mbuild.Box([boxl, boxl, boxl])]
system = mc.System(
box_list, species_list,
)
moveset = mc.MoveSet("gcmc", species_list)
moveset.prob_regrow = 0.0
moveset.prob_translate = 0.3
moveset.prob_rotate = 0.3
moveset.prob_insert = 0.2
mc.run(
system=system,
moveset=moveset,
run_type="equil",
run_length=500000,
temperature=temperature,
run_name="equil",
chemical_potentials=[mu_adsorbate],
**custom_args,
)
mc.restart(
system=system,
moveset=moveset,
run_type="prod",
run_length=1000000,
temperature=temperature,
run_name="prod",
restart_name="equil",
chemical_potentials=[mu_adsorbate],
**custom_args,
)
def main():
# Load TON from a CIF file, replicate the cell
# Use mbuild to create a zeolite supercell from CIF
cif_path = resource_filename(
"mc_examples",
"realistic_workflows/zeolite_adsorption/resources/structures/TON.cif")
lattice = mbuild.lattice.load_cif(cif_path)
compound_dict = {
"Si": mbuild.Compound(name="Si"),
"O": mbuild.Compound(name="O"),
}
zeolite = lattice.populate(compound_dict, 2, 2, 6)
# Create a CG methane, load and apply ff
methane = mbuild.Compound(name="_CH4")
ff_path = resource_filename(
"mc_examples",
"realistic_workflows/zeolite_adsorption/resources/ffxml/adsorbates.xml",
)
ff_ads = foyer.Forcefield(ff_path)
methane_ff = ff_ads.apply(methane)
# Define pure fluid temperatures and chemical potentials
temperatures = [298 * u.K, 309 * u.K, 350 * u.K]
mus_fluid = np.arange(-49, -30, 3) * u.Unit("kJ/mol")
# Define the pressures at which we wish to study adsorption
pressures = [
0.01,
0.1,
0.25,
0.5,
0.75,
1.0,
2.0,
3.0,
5.0,
] * u.bar
# Select the zeolite ff
zeo_ff_names = ["june", "trappe"]
# Define a few custom_args that will be
# the same for all zeolite simulations
custom_args = {
"charge_style": "none",
"vdw_cutoff": 14.0 * u.angstrom,
"prop_freq": 10,
"max_molecules": [1, 10000],
}
# Loop over different zeolite ff's
for zeo_ff_name in zeo_ff_names:
# Load and apply ff to the zeolite structure
ff_path = resource_filename(
"mc_examples",
f"realistic_workflows/zeolite_adsorption/resources/ffxml/zeo_{zeo_ff_name}.xml",
)
ff_zeo = foyer.Forcefield(ff_path)
zeolite_ff = ff_zeo.apply(zeolite)
# Create the box_list, species_list, System, and MoveSet.
# These are not dependent upon (T,P) condition
box_list = [zeolite]
species_list = [zeolite_ff, methane_ff]
mols_in_boxes = [[1, 0]]
system = mc.System(box_list, species_list, mols_in_boxes=mols_in_boxes)
moveset = mc.MoveSet("gcmc", species_list)
# Loop over each temperature to compute an isotherm
for temperature in temperatures:
# Before we begin we must determine the
# chemical potentials required to achieve
# the desired pressures
fluid_pressures = []
for mu_fluid in mus_fluid:
dirname = f"fluid_T_{temperature:0.1f}_mu_{mu_fluid:.1f}".replace(
" ", "_").replace("/", "-")
thermo = ThermoProps(dirname + "/prod.out.prp")
fluid_pressures.append(np.mean(thermo.prop("Pressure")))
fluid_pressures = u.unyt_array(fluid_pressures)
# Fit a line to mu vs. P
slope, intercept, r_value, p_value, stderr = linregress(
np.log(fluid_pressures.to_value(u.bar)).flatten(),
y=mus_fluid.to_value("kJ/mol").flatten(),
)
# Determine chemical potentials
mus = (slope * np.log(pressures.in_units(u.bar)) +
intercept) * u.Unit("kJ/mol")
# Loop over each pressure and run the MC simulation!
for (pressure, mu) in zip(pressures, mus):
print(f"\nRun simulation: T = {temperature}, P = {pressure}\n")
dirname = f"zeo_ff_{zeo_ff_name}_T_{temperature:0.1f}_P_{pressure:0.2f}".replace(
" ", "_").replace("/", "-")
if not os.path.isdir(dirname):
os.mkdir(dirname)
else:
pass
with temporary_cd(dirname):
mc.run(
system=system,
moveset=moveset,
run_type="equil",
run_length=50000,
temperature=temperature,
run_name="equil",
chemical_potentials=["none", mu],
**custom_args,
)
mc.restart(
restart_from="equil",
run_name="prod",
run_type="prod",
total_run_length=200000,
)
def main():
# Create a CG methane, load and apply ff
methane = mbuild.Compound(name="_CH4")
ff_path = resource_filename(
"mc_examples",
"realistic_workflows/zeolite_adsorption/resources/ffxml/adsorbates.xml",
)
ff_ads = foyer.Forcefield(ff_path)
methane_ff = ff_ads.apply(methane)
# Define a few keyword args that will be the
# same for all fluid phase simulations
custom_args = {
"charge_style": "none",
"vdw_cutoff": 14.0 * u.angstrom,
"prop_freq": 10,
}
# Define temperatures and chemical potential values
# for the single phase GCMC simulations
temperatures = [298 * u.K, 309 * u.K, 350 * u.K]
mus = np.arange(-49, -30, 3) * u.Unit("kJ/mol")
# Loop over temperatures and mus and run simulations
for temperature in temperatures:
for mu in mus:
# For each simulation -- first estimate
# the box volume to target ~40 molecules
n_methane_target = 40
beta = 1.0 / (u.kb * temperature)
mass = 16.04 * u.amu
debroglie = np.sqrt(2 * np.pi * u.hbar**2 * beta / mass)
vol = n_methane_target * debroglie**3 * np.exp(
-beta.to("mol/kJ") * mu)
boxl = (vol**(1.0 / 3.0)).to_value("nm")
if boxl < 2.0 * custom_args["vdw_cutoff"].to_value("nm"):
boxl = 2.0 * custom_args["vdw_cutoff"].to_value("nm")
# Define the species list, box list, system, moveset
# We start with an empty box
species_list = [methane_ff]
box_list = [mbuild.Box([boxl, boxl, boxl])]
system = mc.System(box_list, species_list)
moveset = mc.MoveSet("gcmc", species_list)
# Create a new directory, temporary cd, and run
# the equilibration and production simulations!
print(f"\nRun simulation: T = {temperature}, mu = {mu}\n")
dirname = f"fluid_T_{temperature:0.1f}_mu_{mu:.1f}".replace(
" ", "_").replace("/", "-")
if not os.path.isdir(dirname):
os.mkdir(dirname)
else:
pass
with temporary_cd(dirname):
mc.run(
system=system,
moveset=moveset,
run_type="equil",
run_length=50000,
temperature=temperature,
run_name="equil",
chemical_potentials=[mu],
**custom_args,
)
mc.restart(
restart_from="equil",
run_name="prod",
run_type="prod",
total_run_length=400000,
)