qm

class isicle.qm.NWChemWrapper[source]

Wrapper for NWChem functionality.

temp_dir

Path to temporary directory used for simulation.

Type:: str

geom

Internal molecule representation.

Type:: Geometry

result

Dictionary containing simulation results.

Type:: dict

_abc_impl = <_abc._abc_data object>

_configure_basis(basis_set='6-31G*', ao_basis='cartesian')[source]

Generate basis set block of NWChem configuration.

Parameters:

basis_set (str) – Basis set selection.
ao_basis (str) – Angular function selection (“spherical”, “cartesian”).

Returns:

Basis set block of NWChem configuration.

Return type:

str

_configure_cosmo(solvent='H2O', gas=False)[source]

Generate COSMO block of NWChem configuration.

Parameters:

solvent (str) – Solvent selection.
gas (bool) – Indicate whether to use gas phase calculations.

Returns:

COSMO block of NWChem configuration.

Return type:

str

_configure_dft(functional='b3lyp', odft=False)[source]

Generate DFT block of NWChem configuration.

Parameters:

functional (str) – Functional selection.
odft (bool) – Indicate whether to use open DFT functional (required for spin-spin couplings).

Returns:

DFT block of NWChem configuration.

Return type:

str

_configure_driver(max_iter=150)[source]

Generate driver block of NWChem configuration.

Parameters:: max_iter (int) – Maximum number of optimization iterations.
Returns:: Driver block of NWChem configuration.
Return type:: str

_configure_energy(basis_set='6-31G*', ao_basis='cartesian', functional='b3lyp', cosmo=False, solvent='H2O', gas=False, **kwargs)[source]

Configure energy block of NWChem configuration.

Parameters:

basis_set (str) – Basis set selection.
ao_basis (str) – Angular function selection (“spherical”, “cartesian”).
functional (str) – Functional selection.
cosmo (bool) – Indicate whether to include COSMO block.
solvent (str) – Solvent selection. Only used if cosmo is True.
gas (bool) – Indicate whether to use gas phase calculations. Only used if cosmo is True.

Returns:

Energy block of NWChem configuration.

Return type:

str

_configure_frequency(temp=298.15, basis_set='6-31G*', ao_basis='cartesian', functional='b3lyp', cosmo=False, solvent='H2O', gas=False, **kwargs)[source]

Configure frequency block of NWChem configuration.

Parameters:

temp (float) – Temperature for frequency calculation.
basis_set (str) – Basis set selection.
ao_basis (str) – Angular function selection (“spherical”, “cartesian”).
functional (str) – Functional selection.
cosmo (bool) – Indicate whether to include COSMO block.
solvent (str) – Solvent selection. Only used if cosmo is True.
gas (bool) – Indicate whether to use gas phase calculations. Only used if cosmo is True.

Returns:

Frequency block of NWChem configuration.

Return type:

str

_configure_header(scratch_dir=None, mem_global=1600, mem_heap=100, mem_stack=600)[source]

Generate header block of NWChem configuration.

Parameters:

scratch_dir (str) – Path to simulation scratch directory.
mem_global (int) – Global memory allocation in MB.
mem_heap (int) – Heap memory allocation in MB.
mem_stack (int) – Stack memory allocation in MB.

Returns:

Header block of NWChem configuration.

Return type:

str

_configure_load()[source]

Generate geometry load block of NWChem configuration.

Returns:: Load block of NWChem configuration.
Return type:: str

_configure_optimize(basis_set='6-31G*', ao_basis='cartesian', functional='b3lyp', max_iter=150, cosmo=False, solvent='H2O', gas=False, **kwargs)[source]

Generate meta optimization block of NWChem configuration.

Includes basis, DFT, and driver blocks; can include COSMO block.

Parameters:

basis_set (str) – Basis set selection.
ao_basis (str) – Angular function selection (“spherical”, “cartesian”).
functional (str) – Functional selection.
max_iter (int) – Maximum number of optimization iterations.
cosmo (bool) – Indicate whether to include COSMO block.
solvent (str) – Solvent selection. Only used if cosmo is True.
gas (bool) – Indicate whether to u se gas phase calculations. Only used if cosmo is True.

Returns:

Optimization meta block of NWChem configuration.

Return type:

str

_configure_shielding(basis_set='6-31G*', ao_basis='cartesian', functional='b3lyp', cosmo=True, solvent='H2O', gas=False, **kwargs)[source]

Generate meta shielding block of NWChem configuration.

Parameters:

basis_set (str) – Basis set selection.
ao_basis (str) – Angular function selection (“spherical”, “cartesian”).
functional (str) – Functional selection.
max_iter (int) – Maximum number of optimization iterations.
cosmo (bool) – Indicate whether to include COSMO block.
solvent (str) – Solvent selection. Only used if cosmo is True.
gas (bool) – Indicate whether to use gas phase calculations. Only used if cosmo is True.

Returns:

Shielding meta block of NWChem configuration.

Return type:

str

_configure_spin(bonds=1, basis_set='6-31G*', ao_basis='spherical', functional='b3lyp', cosmo=True, solvent='H2O', gas=False, **kwargs)[source]

Generate meta spin-spin coupling block of NWChem configuration.

Parameters:

max_pairs (int) – Maximum number of spin-spin pairs per spin-spin coupling block. Note: do not modify.
basis_set (str) – Basis set selection.
ao_basis (str) – Angular function selection (“spherical”, “cartesian”).
functional (str) – Functional selection.
cosmo (bool) – Indicate whether to include COSMO block.
solvent (str) – Solvent selection. Only used if cosmo is True.
gas (bool) – Indicate whether to use gas phase calculations. Only used if cosmo is True.

Returns:

Spin-spin coupling meta block of NWChem configuration.

Return type:

str

_default_value = None

_defaults = ['geom', 'result', 'temp_dir']

_save_geometry()[source]: Save internal Geometry representation to file.

configure(tasks='energy', functional='b3lyp', basis_set='6-31g*', ao_basis='cartesian', atoms=['C', 'H'], bonds=1, temp=298.15, cosmo=False, solvent='H2O', gas=False, max_iter=150, mem_global=1600, mem_heap=100, mem_stack=600, scratch_dir=None, processes=12)[source]

Configure NWChem simulation.

Parameters:

tasks (str or list of str) – Tasks text. Tasks text.
functional (str or list of str) – Functional selection. Supply globally or per task.
basis_set (str or list of str) – Basis set selection. Supply globally or per task.
ao_basis (str or list of str) – Angular function selection (“spherical”, “cartesian”). Supply globally or per task.
atoms (list of str) – Atom types of interest. Only used for spin and shielding tasks.
temp (float) – Temperature for frequency calculation. Only used if frequency is a selected task.
cosmo (bool) – Indicate whether to include COSMO block. Supply globally or per task.
solvent (str) – Solvent selection. Only used if cosmo is True. Supply globally or per task.
gas (bool) – Indicate whether to use gas phase calculations. Only used if cosmo is True. Supply globally or per task.
max_iter (int) – Maximum number of optimization iterations.
scratch_dir (str) – Path to simulation scratch directory.
mem_global (int) – Global memory allocation in MB.
mem_heap (int) – Heap memory allocation in MB.
mem_stack (int) – Stack memory allocation in MB.

Returns:

NWChem configuration.

Return type:

str

configure_from_template(path, basename_override=None, dirname_override=None, **kwargs)[source]

Configure NWChem simulation from template file.

Use for NWChem functionality not exposed by the wrapper. Template contains ${keyword} entries that will be replaced by entries in **kwargs, if present. By default, ${basename} and ${dirname} must be included in the template and will be populated automatically. Override this behavior through use of appropriate keyword arguments.

Parameters:

path (str) – Path to template file.
basename_override (str) – Override managed basename with user-supplied alternative.
dirname_override (str) – Override managed directory name with user-supplied alternative.
**kwargs – Keyword arguments that will be subsituted in the template.

Returns:

NWChem configuration.

Return type:

str

finish()[source]

Parse NWChem simulation results.

Returns:: Dictionary containing simulation results.
Return type:: dict

parse()[source]

Parse NWChem simulation results.

Returns:: Dictionary containing parsed outputs from the simulation.
Return type:: dict

run(geom, template=None, tasks='energy', functional='b3lyp', basis_set='6-31g*', ao_basis='cartesian', atoms=['C', 'H'], bonds=1, temp=298.15, cosmo=False, solvent='H2O', gas=False, max_iter=150, mem_global=1600, mem_heap=100, mem_stack=600, scratch_dir=None, processes=12)[source]

Perform density functional theory calculations according to supplied task list and configuration parameters.

Parameters:

geom (Geometry) – Molecule representation.
template (str) – Path to optional template to bypass default configuration process.
tasks (str or list of str) – List of calculations to perform. One or more of “optimize”, “energy”, “frequency”, “shielding”, “spin”.
functional (str or list of str) – Functional selection. Supply globally or per task.
basis_set (str or list of str) – Basis set selection. Supply globally or per task.
ao_basis (str or list of str) – Angular function selection (“spherical”, “cartesian”). Supply globally or per task.
atoms (list of str) – Atom types of interest. Only used for spin and shielding tasks.
temp (float) – Temperature for frequency calculation. Only used if frequency is a selected task.
cosmo (bool) – Indicate whether to include COSMO block. Supply globally or per task.
solvent (str) – Solvent selection. Only used if cosmo is True. Supply globally or per task.
gas (bool) – Indicate whether to use gas phase calculations. Only used if cosmo is True. Supply globally or per task.
max_iter (int) – Maximum number of optimization iterations.
scratch_dir (str) – Path to simulation scratch directory.
mem_global (int) – Global memory allocation in MB.
mem_heap (int) – Heap memory allocation in MB.
mem_stack (int) – Stack memory allocation in MB.

Returns:

Dictionary containing simulation results.

Return type:

dict

save(path)[source]

Save result as pickle file.

Parameters:: path (str) – Path to output file.

save_config()[source]: Write generated NWChem configuration to file.

set_geometry(geom)[source]

Set Geometry instance for simulation.

Parameters:: geom (Geometry) – Molecule representation.

submit()[source]: Submit the NWChem simulation according to configured inputs.

class isicle.qm.ORCAWrapper[source]

Wrapper for ORCA functionality.

Implements WrapperInterface to ensure required methods are exposed.

temp_dir

Path to temporary directory used for simulation.

Type:: str

geom

Internal molecule representation.

Type:: Geometry

config

Configuration information for simulation.

Type:: str

result

Dictionary containing simulation results.

Type:: dict

_abc_impl = <_abc._abc_data object>

_default_value = None

_defaults = ['geom', 'result', 'temp_dir']

_save_config()[source]: Write generated ORCA configuration to file.

_save_geometry()[source]: Save internal Geometry representation to file in XYZ format.

configure(simple_input=[], block_input={}, spin_multiplicity=1, processes=1, **kwargs)[source]

Configure ORCA simulation.

Parameters:

simple_input (list) – List of simple input keywords. See this section of the ORCA docs.
block_input (dict) – Dictionary defining configuration “blocks”. Use names of blocks as keys, lists of each block’s content as values. To configure a line of block content directly, include as a complete string. Include key:value pairs as tuples. See this section of the ORCA docs.
spin_multiplicity (int) – Spin multiplicity of the molecule.
processes (int) – Number of parallel processes.
kwargs – Additional keyword arguments fed as key:value pairs.

Returns:

ORCA configuration text.

Return type:

str

finish()[source]

Collect ORCA simulation results.

Returns:: Dictionary containing relevant outputs from the simulation.
Return type:: dict

parse()[source]

Parse ORCA simulation results.

Returns:: Dictionary containing parsed outputs from the simulation.
Return type:: dict

run(geom, **kwargs)[source]

Optimize geometry via density functional theory using supplied functional and basis set.

Parameters:

geom (Geometry) – Molecule representation.
template (str) – Path to optional template to bypass default configuration process.
**kwargs – Keyword arguments to configure the simulation. See configure().

Returns:

Dictionary containing relevant outputs from the simulation.

Return type:

dict

save(path)[source]

Save result as pickle file.

Parameters:: path (str) – Path to output file.

set_geometry(geom)[source]

Set Geometry instance for simulation.

Parameters:: geom (Geometry) – Molecule representation.

submit()[source]: Submit the ORCA simulation according to configured inputs.

isicle.qm._backend_selector(backend)[source]

Selects a supported quantum mechanical backend for associated simulation. Currently only NWChem and ORCA have been implemented.

Parameters:: backend (str) – Alias for backend selection (e.g. NWChem, ORCA).
Returns:: Wrapped functionality of the selected backend. Must implement WrapperInterface.
Return type:: backend

isicle.qm.dft(geom, backend='NWChem', **kwargs)[source]

Perform density functional theory calculations according to supplied task list and configuration parameters.

Parameters:

geom (Geometry) – Molecule representation.
backend (str) – Alias for backend selection (NWChem, ORCA).
kwargs – Keyword arguments passed to selected backend.

Returns:

Wrapper object containing relevant outputs from the simulation.

Return type:

QMWrapper