def get_density(molecule_name,
temperature=273.15,
pressure=101325,
cycles=5000,
init_cycles="auto",
forcefield="CrystalGenerator"):
"""Calculates the density of a gas through an NPT ensemble.
Args:
molecule_name: The molecule to test for adsorption. A file of the same
name must exist in `$RASPA_DIR/share/raspa/molecules/TraPPE`.
temperature: (Optional) The temperature of the simulation, in Kelvin.
pressure: (Optional) The pressure of the simulation, in Pascals.
cycles: (Optional) The number of simulation cycles to run.
init_cycles: (Optional) The number of initialization cycles to run.
Defaults to the minimum of cycles / 2 and 10,000.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
Returns:
The density, as a float, in kg/m^3.
"""
print_every = cycles // 10
if init_cycles == "auto":
init_cycles = min(cycles // 2, 10000)
script = dedent("""
SimulationType {simulation_type}
NumberOfCycles {cycles}
NumberOfInitializationCycles {init_cycles}
PrintEvery {print_every}
Forcefield {forcefield}
Box 0
BoxLengths 30 30 30
ExternalTemperature {temperature}
ExternalPressure {pressure}
VolumeChangeProbability 0.25
Component 0 MoleculeName {molecule_name}
MoleculeDefinition TraPPE
TranslationProbability 0.5
ReinsertionProbability 0.5
CreateNumberOfMolecules 256
""".format(**locals())).strip()
output = parse(run_script(script))
return output["Average Density"]["[kg/m^3]"][0]
def get_geometric_surface_area(structure,
unit_cells=(1, 1, 1),
cycles=500,
input_file_type="cif",
units="m^2/g",
forcefield="CrystalGenerator"):
"""Calculates the geometric surface area of an inputted structure.
Args:
structure: The structure to use, as a string of type
`input_file_type` (default is "cif").
input_file_type: (Optional) The type of input structure. Assumes cif.
unit_cells: (Optional) The number of unit cells to use, by dimension.
cycles: (Optional) The number of simulation cycles to run.
units: (Optional) The units in which to return the surface area. Can be
"m^2/g", "A^2", or "m^2/cm^3".
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
Returns:
The geometric surface area, as a float.
"""
print_every = cycles // 10
a, b, c = unit_cells
script = dedent("""
SimulationType MonteCarlo
NumberOfCycles {cycles}
PrintEvery {print_every}
PrintPropertiesEvery {print_every}
Forcefield {forcefield}
CutOff 12.8
Framework 0
FrameworkName streamed
InputFileType {input_file_type}
UnitCells {a} {b} {c}
SurfaceAreaProbeDistance Sigma
Component 0 MoleculeName N2
StartingBead 0
MoleculeDefinition TraPPE
SurfaceAreaProbability 1.0
CreateNumberOfMolecules 0
""".format(**locals())).strip()
output = parse(run_script(script, structure))
return output["Average Surface Area"]["[{}]".format(units)][0]
def get_density(molecule_name, temperature=273.15, pressure=101325,
cycles=5000, init_cycles="auto",
forcefield="CrystalGenerator"):
"""Calculates the density of a gas through an NPT ensemble.
Args:
molecule_name: The molecule to test for adsorption. A file of the same
name must exist in `$RASPA_DIR/share/raspa/molecules/TraPPE`.
temperature: (Optional) The temperature of the simulation, in Kelvin.
pressure: (Optional) The pressure of the simulation, in Pascals.
cycles: (Optional) The number of simulation cycles to run.
init_cycles: (Optional) The number of initialization cycles to run.
Defaults to the minimum of cycles / 2 and 10,000.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
Returns:
The density, as a float, in kg/m^3.
"""
print_every = cycles // 10
if init_cycles == "auto":
init_cycles = min(cycles // 2, 10000)
script = dedent("""
SimulationType {simulation_type}
NumberOfCycles {cycles}
NumberOfInitializationCycles {init_cycles}
PrintEvery {print_every}
Forcefield {forcefield}
Box 0
BoxLengths 30 30 30
ExternalTemperature {temperature}
ExternalPressure {pressure}
VolumeChangeProbability 0.25
Component 0 MoleculeName {molecule_name}
MoleculeDefinition TraPPE
TranslationProbability 0.5
ReinsertionProbability 0.5
CreateNumberOfMolecules 256
""".format(**locals())).strip()
output = parse(run_script(script))
return output["Average Density"]["[kg/m^3]"][0]
def get_geometric_surface_area(structure, unit_cells=(1, 1, 1), cycles=500,
input_file_type="cif", units="m^2/g",
forcefield="CrystalGenerator"):
"""Calculates the geometric surface area of an inputted structure.
Args:
structure: The structure to use, as a string of type
`input_file_type` (default is "cif").
input_file_type: (Optional) The type of input structure. Assumes cif.
unit_cells: (Optional) The number of unit cells to use, by dimension.
cycles: (Optional) The number of simulation cycles to run.
units: (Optional) The units in which to return the surface area. Can be
"m^2/g", "A^2", or "m^2/cm^3".
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
Returns:
The geometric surface area, as a float.
"""
print_every = cycles // 10
a, b, c = unit_cells
script = dedent("""
SimulationType MonteCarlo
NumberOfCycles {cycles}
PrintEvery {print_every}
PrintPropertiesEvery {print_every}
Forcefield {forcefield}
CutOff 12.8
Framework 0
FrameworkName streamed
InputFileType {input_file_type}
UnitCells {a} {b} {c}
SurfaceAreaProbeDistance Sigma
Component 0 MoleculeName N2
StartingBead 0
MoleculeDefinition TraPPE
SurfaceAreaProbability 1.0
CreateNumberOfMolecules 0
""".format(**locals())).strip()
output = parse(run_script(script, structure))
return output["Average Surface Area"]["[{}]".format(units)][0]
def run(structure,
molecule_name,
temperature=273.15,
pressure=101325,
helium_void_fraction=1.0,
unit_cells=(1, 1, 1),
framework_name="streamed",
simulation_type="MonteCarlo",
cycles=2000,
init_cycles="auto",
forcefield="CrystalGenerator",
input_file_type="cif"):
"""Runs a simulation with the specified parameters.
Args:
structure: The structure to test for adsorption, as a string of type
`input_file_type` (default is "cif").
molecule_name: The molecule to test for adsorption. A file of the same
name must exist in `$RASPA_DIR/share/raspa/molecules/TraPPE`.
temperature: (Optional) The temperature of the simulation, in Kelvin.
pressure: (Optional) The pressure of the simulation, in Pascals.
helium_void_fraction: (Optional) The helium void fraction of the input
structure. Required for excess adsorption back-calculation.
unit_cells: (Optional) The number of unit cells to use, by dimension.
framework_name: (Optional) If not streaming, this will load the
structure at `$RASPA_DIR/share/raspa/structures`. Ignored if
streaming.
simulation_type: (Optional) The type of simulation to run, defaults
to "MonteCarlo".
cycles: (Optional) The number of simulation cycles to run.
init_cycles: (Optional) The number of initialization cycles to run.
Defaults to the minimum of cycles / 2 and 10,000.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
input_file_type: (Optional) The type of input structure. Assumes cif.
Returns:
A string representing the contents of a simulation input file.
The goal of this function is to mask the complexity of RASPA by limiting
parameters and assuming sensible defaults. This should streamline common-
case usage, but it means that this function won't work in all use cases.
In these cases, look into loading your own simulation input file and
passing it to `RASPA.run_script`.
"""
return parse(run_script(create_script(**locals()), structure))
def get_helium_void_fraction(structure,
unit_cells=(1, 1, 1),
cycles=2000,
input_file_type="cif",
forcefield="CrystalGenerator"):
"""Calculates the helium void fraction of the inputted structure.
Args:
structure: The structure to test for helium void fraction,
as a string of type 'input_file_type` (default is "cif").
unit_cells: (Optional) The number of unit cells to use, by dimension.
cycles: (Optional) The number of simulation cycles to run.
input_file_type: (Optional) The type of input structure. Assumes cif.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
Returns:
The helium void fraction of the structure, as a float.
"""
print_every = cycles // 10
a, b, c = unit_cells
script = dedent("""
SimulationType MonteCarlo
NumberOfCycles {cycles}
PrintEvery {print_every}
PrintPropertiesEvery {print_every}
Forcefield {forcefield}
CutOff 12.8
Framework 0
FrameworkName streamed
InputFileType {input_file_type}
UnitCells {a} {b} {c}
ExternalTemperature 298.0
Component 0 MoleculeName helium
MoleculeDefinition TraPPE
WidomProbability 1.0
CreateNumberOfMolecules 0
""".format(**locals())).strip()
output = parse(run_script(script, structure))
return output["Average Widom Rosenbluth factor"]["Widom"][0]
def get_helium_void_fraction(structure, unit_cells=(1, 1, 1), cycles=2000,
input_file_type="cif",
forcefield="CrystalGenerator"):
"""Calculates the helium void fraction of the inputted structure.
Args:
structure: The structure to test for helium void fraction,
as a string of type 'input_file_type` (default is "cif").
unit_cells: (Optional) The number of unit cells to use, by dimension.
cycles: (Optional) The number of simulation cycles to run.
input_file_type: (Optional) The type of input structure. Assumes cif.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
Returns:
The helium void fraction of the structure, as a float.
"""
print_every = cycles // 10
a, b, c = unit_cells
script = dedent("""
SimulationType MonteCarlo
NumberOfCycles {cycles}
PrintEvery {print_every}
PrintPropertiesEvery {print_every}
Forcefield {forcefield}
CutOff 12.8
Framework 0
FrameworkName streamed
InputFileType {input_file_type}
UnitCells {a} {b} {c}
ExternalTemperature 298.0
Component 0 MoleculeName helium
MoleculeDefinition TraPPE
WidomProbability 1.0
CreateNumberOfMolecules 0
""".format(**locals())).strip()
output = parse(run_script(script, structure))
return output["Average Widom Rosenbluth factor"]["Widom"][0]
def run(structure, molecule_name, temperature=273.15, pressure=101325,
helium_void_fraction=1.0, unit_cells=(1, 1, 1),
framework_name="streamed", simulation_type="MonteCarlo", cycles=2000,
init_cycles="auto", forcefield="CrystalGenerator",
input_file_type="cif"):
"""Runs a simulation with the specified parameters.
Args:
structure: The structure to test for adsorption, as a string of type
`input_file_type` (default is "cif").
molecule_name: The molecule to test for adsorption. A file of the same
name must exist in `$RASPA_DIR/share/raspa/molecules/TraPPE`.
temperature: (Optional) The temperature of the simulation, in Kelvin.
pressure: (Optional) The pressure of the simulation, in Pascals.
helium_void_fraction: (Optional) The helium void fraction of the input
structure. Required for excess adsorption back-calculation.
unit_cells: (Optional) The number of unit cells to use, by dimension.
framework_name: (Optional) If not streaming, this will load the
structure at `$RASPA_DIR/share/raspa/structures`. Ignored if
streaming.
simulation_type: (Optional) The type of simulation to run, defaults
to "MonteCarlo".
cycles: (Optional) The number of simulation cycles to run.
init_cycles: (Optional) The number of initialization cycles to run.
Defaults to the minimum of cycles / 2 and 10,000.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
input_file_type: (Optional) The type of input structure. Assumes cif.
Returns:
A string representing the contents of a simulation input file.
The goal of this function is to mask the complexity of RASPA by limiting
parameters and assuming sensible defaults. This should streamline common-
case usage, but it means that this function won't work in all use cases.
In these cases, look into loading your own simulation input file and
passing it to `RASPA.run_script`.
"""
return parse(run_script(create_script(**locals()), structure))
def run_mixture(structure, molecules, mol_fractions, temperature=273.15,
pressure=101325, helium_void_fraction=1.0,
unit_cells=(1, 1, 1), simulation_type="MonteCarlo",
cycles=2000, init_cycles="auto", forcefield="CrystalGenerator",
input_file_type="cif"):
"""Runs a simulation with mixture of gases.
Args:
structure: The structure to test for adsorption, as a string of type
`input_file_type` (default is "cif").
molecules: The molecules to test for adsorption. Files of the same
names must exist in `$RASPA_DIR/share/raspa/molecules/TraPPE`.
mol_fractions: The mol fractions of each gas that you want to separate.
Corresponds to the `molecules` list.
temperature: (Optional) The temperature of the simulation, in Kelvin.
pressure: (Optional) The pressure of the simulation, in Pascals.
helium_void_fraction: (Optional) The helium void fraction of the input
structure. Required for excess adsorption back-calculation.
unit_cells: (Optional) The number of unit cells to use, by dimension.
simulation_type: (Optional) The type of simulation to run, defaults
to "MonteCarlo".
cycles: (Optional) The number of simulation cycles to run.
init_cycles: (Optional) The number of initialization cycles to run.
Defaults to the minimum of cycles / 2 and 10,000.
forcefield: (Optional) The forcefield to use. Name must match a folder
in `$RASPA_DIR/share/raspa/forcefield`, which contains the properly
named `.def` files.
input_file_type: (Optional) The type of input structure. Assumes cif.
Returns:
A string representing the contents of a simulation input file.
The goal of this function is to mask the complexity of RASPA by limiting
parameters and assuming sensible defaults. This should streamline common-
case usage, but it means that this function won't work in all use cases.
In these cases, look into loading your own simulation input file and
passing it to `RASPA.run_script`.
"""
is_mol = "yes" if input_file_type.lower() == "mol" else "no"
print_every = cycles // 10
a, b, c = unit_cells
molecule_list = " ".join(str(n) for n in range(len(molecules)))
molecule_count = len(molecules)
if init_cycles == "auto":
init_cycles = min(cycles // 2, 10000)
script = dedent("""
SimulationType {simulation_type}
NumberOfCycles {cycles}
NumberOfInitializationCycles {init_cycles}
PrintEvery {print_every}
RestartFile no
Forcefield {forcefield}
CutOff 12.8
ChargeMethod Ewald
EwaldPrecision 1e-6
UseChargesFromMOLFile {is_mol}
Framework 0
FrameworkName streamed
InputFileType {input_file_type}
UnitCells {a} {b} {c}
HeliumVoidFraction {helium_void_fraction}
ExternalTemperature {temperature}
ExternalPressure {pressure}
Movies no
WriteMoviesEvery 100
""".format(**locals())).strip()
for i, (molecule, fraction) in enumerate(zip(molecules, mol_fractions)):
script += dedent("""
Component {i} MoleculeName {molecule}
StartingBead 0
MoleculeDefinition TraPPE
MolFraction {fraction}
IdentityChangeProbability 1.0
NumberOfIdentityChanges {molecule_count}
IdentityChangesList {molecule_list}
IdealGasRosenbluthWeight 1.0
TranslationProbability 1.0
RotationProbability 1.0
ReinsertionProbability 1.0
SwapProbability 1.0
CreateNumberOfMolecules 0
""".format(**locals()))
return parse(run_script(script, structure))