Defines MOPAC optimizers.

class MOPAC(mopac_path, hamiltonian='PM7', method='OPT', minimum_gradient=0.01, eps=80.1, charge=0, fileout='PDBOUT', timeout=172800, use_cache=False)

Bases: stk.calculators.optimization.optimizers.Optimizer

Uses MOPAC to optimize molcules.

mopac_path

The full path to the MOPAC suite on the user’s machine. For example, in a default MacOS installation the folder will probably be something like /opt/mopac/MOPAC2016.exe.

Type

str

hamiltonian

A series of different methods can be selected: 'PM7', 'PM6', 'AM1', 'CIS' '(CISD, CISDT)', 'MNDO', 'RM1', etc.

'PM7' is the latest version of the reparametrization of NDDO theory, where all the atomic and diatomic parameters were re-optimized / updated from PM6 1.

Type

str, optional

method

The default calculation consists of a geometry optimization. You can run single point calculations (SCF) or transition search algorithms (TS). Refer to the MOPAC website for specific keywords.

Type

str, optional

minimum_gradient

The gradient at which the geometry optimization reaches the convergence criteria (kcal / mol / Angstrom). For small system and high precision work, 0.01 is recommended.

Type

float, optional

eps

Sets the dielectric constant for the solvent. Presence of this keyword will cause the COSMO (Conductor-like Screening Model) method to be used to approximate the effect of a solvent model surrounding the molecule. Solvents with a low dielectric constant are not likely to work well with this model. 0 means that the dielectric constant is not included in the calculation. 80.1 can be used to model a water environment at room temperature.

Type

float, optional

charge

The charge of the system.

Type

float, optional

fileout

Determines the output file type.

Type

str, optional

timeout

The amount in seconds the optimization is allowed to run before being terminated. The default value is 2 days or 172,800 seconds. None means there is no timeout.

Type

float, optional

References

1

http://openmopac.net/PM7_accuracy/PM7_accuracy.html

Methods

add_to_cache(self, mol[, value])

Add a molecule to the cache.

generate_mop(self, mol, conformer)

Creates the .mop file for the optimization.

get_cached_value(self, mol)

Return the value stored in the cache for mol.

is_caching(self)

True if the calculator has caching turned on.

is_in_cache(self, mol)

Return True if mol is cached.

kill_mopac(self, mol)

Kills an in-progress MOPAC run.

mop_header(self)

Returns the header of the .mop file.

optimize(self, mol[, conformer])

Optimizes a molecule.

set_cache_use(self, use_cache)

Set cache use on or off.

run_mopac
__init__(self, mopac_path, hamiltonian='PM7', method='OPT', minimum_gradient=0.01, eps=80.1, charge=0, fileout='PDBOUT', timeout=172800, use_cache=False)

Initializes a MOPAC instance.

Parameters

  • mopac_path (str) – The full path to the MOPAC suite on the user’s machine. For example, in a default MacOS installation the folder will probably be something like /opt/mopac/MOPAC2016.exe.

  • hamiltonian (str, optional) –

    A series of different methods can be selected: 'PM7', 'PM6', 'AM1', 'CIS' '(CISD, CISDT)', 'MNDO', 'RM1', etc.

    'PM7' is the latest version of the reparametrization of NDDO theory, where all the atomic and diatomic parameters were re-optimized / updated from PM6 2.

  • method (str, optional) – The default calculation consists of a geometry optimization. You can run single point calculations (SCF) or transition search algorithms (TS). Refer to the MOPAC website for specific keywords.

  • minimum_gradient (float, optional) – The gradient at which the geometry optimization reaches the convergence criteria (kcal / mol / Angstrom). For small system and high precision work, 0.01 is recommended.

  • eps (float, optional) – Sets the dielectric constant for the solvent. Presence of this keyword will cause the COSMO (Conductor-like Screening Model) method to be used to approximate the effect of a solvent model surrounding the molecule. Solvents with a low dielectric constant are not likely to work well with this model. 0 means that the dielectric constant is not included in the calculation. 80.1 can be used to model a water environment at room temperature.

  • charge (float, optional) – The charge of the system.

  • fileout (str, optional) – Determines the output file type.

  • timeout (float, optional) – The amount in seconds the optimization is allowed to run before being terminated. The default value is 2 days or 172,800 seconds. None means there is no timeout.

  • use_cache (bool, optional) – If True optimize() will not run twice on the same molecule and conformer.

References

2

http://openmopac.net/PM7_accuracy/PM7_accuracy.html

add_to_cache(self, mol, value=None)

Add a molecule to the cache.

Parameters

  • mol (Molecule) – The molecule to be added to the cache.

  • value (class:object, optional) – The cached value associated with the molecule.

Returns

The calculator.

Return type

MoleculeCalculator

Raises

NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

generate_mop(self, mol, conformer)

Creates the .mop file for the optimization.

Parameters

  • mol (Molecule) – The molecule which is to be optimized. Its molecular structure file is converted to a .mop file.

  • conformer (int) – The conformer of the molecule to be used.

Returns

The full path of the newly created .mop file.

Return type

str

get_cached_value(self, mol)

Return the value stored in the cache for mol.

Parameters

mol (Molecule) – The molecule whose cached value is to be returned.

Returns

The cached value.

Return type

object

Raises

NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

is_caching(self)

True if the calculator has caching turned on.

Returns

True if the calculator has caching turned on.

Return type

bool

Raises

NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

is_in_cache(self, mol)

Return True if mol is cached.

Parameters

mol (Molecule) – The molecule being checked.

Returns

True if mol is cached.

Return type

bool

Raises

NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

kill_mopac(self, mol)

Kills an in-progress MOPAC run.

To kill a MOPAC run, a file with the molecule’s name and a .end extension is written.

Parameters

mol (Molecule) – The molecule being optimized.

Returns

None

Return type

NoneType

mop_header(self)

Returns the header of the .mop file.

Returns

String containing all the MOPAC keywords correctly formatted for the input file.

Return type

str

optimize(self, mol, conformer=-1)

Optimizes a molecule.

Parameters

  • mol (Molecule) – The molecule to be optimized.

  • conformer (int, optional) – The conformer to use.

Returns

None

Return type

NoneType

run_mopac(self, mol, mopac_path, settings, timeout=7200)
set_cache_use(self, use_cache)

Set cache use on or off.

Parameters

use_cache (bool) – True if the cache is to be used.

Returns

The calculator.

Return type

MoleculeCalculator

Raises

NotImplementedError – This is a virtual method and needs to be implemented in a subclass.