def test_void_fraction_one_sphere_across_pbc():
atoms = [(0, 0, 0, 2)]
assert calculate_void_fraction(atoms, (4, 4, 4)) == approx(
1 - r1volume / 4**3, 0.01)
atoms = [(4, 4, 4, 2)]
assert calculate_void_fraction(atoms, (4, 4, 4)) == approx(
1 - r1volume / 4**3, 0.01)
def test_void_fraction_one_sphere():
atoms = [(2, 2, 2, 2)]
# NOTE on approx void fraction calculations:
# the volume of one sphere of radius r = 1 is equal to r1volume. The % of the volume taken up by
# the sphere is equal to r1volume / box volume = r1volume/4**3
assert calculate_void_fraction(atoms, (4, 4, 4)) == approx(
1 - r1volume / 4**3, 0.01)
def run(material, simulation_config, config):
"""Runs void fraction simulation.
Args:
material (Material): material record.
Returns:
results (dict): void fraction simulation results.
"""
output_dir = "output_{}_{}".format(material.uuid, uuid4())
slog("Output directory : {}".format(output_dir))
os.makedirs(output_dir, exist_ok=True)
write_output_files(material, simulation_config, output_dir)
# Run simulations
slog("Probe : {}".format(simulation_config["adsorbate"]))
if "do_geo" in simulation_config:
slog("Probe radius [geo]: {}".format(simulation_config["probe_radius"]))
slog("Temperature : {}".format(simulation_config["temperature"]))
void_fraction = VoidFraction()
void_fraction.adsorbate = simulation_config["adsorbate"]
void_fraction.temperature = simulation_config["temperature"]
if "do_raspa" in simulation_config and simulation_config["do_raspa"]:
tbegin = time.perf_counter()
process = subprocess.run(["simulate", "-i", "./void_fraction.input"], check=True, cwd=output_dir, capture_output=True, text=True)
data_files = glob(os.path.join(output_dir, "Output", "System_0", "*.data"))
if len(data_files) != 1:
raise Exception("ERROR: There should only be one data file in the output directory for %s. Check code!" % output_dir)
output_file = data_files[0]
# Parse output
parse_output(output_file, material, void_fraction)
slog("RASPA void fraction simulation time: %5.2f seconds" % (time.perf_counter() - tbegin))
slog("RASPA VOID FRACTION : {}".format(void_fraction.void_fraction))
if material.parent:
slog("(parent VOID FRACTION : {})".format(material.parent.void_fraction[0].void_fraction))
# run geometric void fraction
if "do_geo" in simulation_config and simulation_config["do_geo"]:
tbegin = time.perf_counter()
atoms = [(a.x * material.structure.a, a.y * material.structure.b, a.z * material.structure.c, a.atom_types.sigma) for a in material.structure.atom_sites]
box = (material.structure.a, material.structure.b, material.structure.c)
void_fraction.void_fraction_geo = calculate_void_fraction(atoms, box, probe_r=simulation_config["probe_radius"])
slog("GEOMETRIC void fraction: %f" % void_fraction.void_fraction_geo)
slog("GEOMETRIC void fraction simulation time: %5.2f seconds" % (time.perf_counter() - tbegin))
if "do_zeo" in simulation_config:
pass
# run zeo void fraction here
material.void_fraction.append(void_fraction)
if not config['keep_configs']:
shutil.rmtree(output_dir, ignore_errors=True)
sys.stdout.flush()
def test_void_fraction_two_separate_spheres():
atoms = [(1, 1, 1, 2),
(2.9, 2.9, 2.9, 2)] #2.9 so it doesn't hit the right boundary
assert calculate_void_fraction(atoms, (4, 4, 4)) == approx(
1 - 2 * r1volume / 4**3, 0.01)
def test_void_fraction_two_identical_spheres():
atoms = [(2, 2, 2, 2), (2, 2, 2, 2)]
assert calculate_void_fraction(atoms, (4, 4, 4)) == approx(
1 - r1volume / 4**3, 0.01)
def test_void_fraction_one_sphere_w_he_probe():
atoms = [(2, 2, 2, 2)]
assert calculate_void_fraction(atoms, (4, 4, 4), probe_r=1.0) == approx(
1 - r1volume * 2**3 / 4**3, 0.01)
def test_void_fraction_huger_atom():
assert calculate_void_fraction([(2, 2, 2, 100)], (4, 4, 4),
points_per_angstrom=2) == 0.0
def test_void_fraction_empty_crystal():
assert calculate_void_fraction([], (4, 4, 4)) == 1.0