7.1.1. Frog.Molecules package

7.1.1.1. Submodules

7.1.1.2. Frog.Molecules.Chlore module

Frog.Molecules.Chlore.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Chlore.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Chlore.electrostatic_description(pe_order, electro_neigh, L_pos=False)

TODO

Frog.Molecules.Chlore.info_molecule(smparameter)

Frog.Molecules.Chlore.info_molecule_typical_size()

Frog.Molecules.Chlore.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Chlore.typical_geometry()

7.1.1.3. Frog.Molecules.Ethanol_OPLSAA module

Frog.Molecules.Ethanol_OPLSAA.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Ethanol_OPLSAA.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Ethanol_OPLSAA.electrostatic_description(pe_order, electro_neigh, L_pos=False)

TODO

Frog.Molecules.Ethanol_OPLSAA.info_molecule(smparameter)

Frog.Molecules.Ethanol_OPLSAA.info_molecule_typical_size()

Frog.Molecules.Ethanol_OPLSAA.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Ethanol_OPLSAA.typical_geometry()

7.1.1.4. Frog.Molecules.Methanol_OPLSAA module

Frog.Molecules.Methanol_OPLSAA.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Methanol_OPLSAA.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Methanol_OPLSAA.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. The first 3 angles are the projection of the C-O bond in the laboratory axis. The last 3 angles are the projection of the O-H bond in the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Methanol_OPLSAA.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Methanol_OPLSAA.electrostatic_description(pe_order, electro_neigh, L_pos=False)

Electrostatic description of the Methanol_OPLSAA molecule type. These charges are the same as the usual OPLS/AA force field. The charge are given in e units.

Frog.Molecules.Methanol_OPLSAA.info_molecule(smparameter)

Frog.Molecules.Methanol_OPLSAA.info_molecule_for_layer()

Defines the radii of every atoms for the layer analysis.

Frog.Molecules.Methanol_OPLSAA.info_molecule_typical_size()

Frog.Molecules.Methanol_OPLSAA.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Methanol_OPLSAA.typical_geometry()

7.1.1.5. Frog.Molecules.Sodium module

Frog.Molecules.Sodium.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Sodium.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Sodium.electrostatic_description(pe_order, electro_neigh, L_pos=False)

TODO

Frog.Molecules.Sodium.info_molecule(smparameter)

Frog.Molecules.Sodium.info_molecule_typical_size()

Frog.Molecules.Sodium.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Sodium.typical_geometry()

7.1.1.6. Frog.Molecules.Water_Osted2006_ESdescription module

This is a custom Water description mixing MD trajectories obtained using TIP4P/2005 force field and the electrostatic description of the SPCP force field. This is done in order to compare with the article of Osted et. al. JCP 2006: https://doi.org/10.1063/1.2176615

Frog.Molecules.Water_Osted2006_ESdescription.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Water_Osted2006_ESdescription.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Water_Osted2006_ESdescription.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. Here its the projection of the dipole moment on the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Water_Osted2006_ESdescription.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Water_Osted2006_ESdescription.electrostatic_description(pe_level, electro_description, L_pos=False)

Frog.Molecules.Water_Osted2006_ESdescription.info_molecule(smparameter)

Frog.Molecules.Water_Osted2006_ESdescription.info_molecule_typical_size()

Frog.Molecules.Water_Osted2006_ESdescription.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Water_Osted2006_ESdescription.ref_polarizability(frequency=False)

Frog.Molecules.Water_Osted2006_ESdescription.test_electrostatic(electro_neigh, L_pos=False)

Frog.Molecules.Water_Osted2006_ESdescription.typical_geometry()

7.1.1.7. Frog.Molecules.Water_PSPC module

This description holds for SPCP water description using Drud’model for the polarizability: a fourth atom (the Drud particle) is expected. This is done in order to compare with the article of Osted et. al. JCP 2006: https://doi.org/10.1063/1.2176615

Frog.Molecules.Water_PSPC.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Water_PSPC.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Water_PSPC.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. Here its the projection of the dipole moment on the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Water_PSPC.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Water_PSPC.electrostatic_description(pe_level, electro_description, L_pos=False)

Frog.Molecules.Water_PSPC.info_molecule(smparameter)

Frog.Molecules.Water_PSPC.info_molecule_typical_size()

Frog.Molecules.Water_PSPC.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Water_PSPC.ref_polarizability(frequency=False)

Frog.Molecules.Water_PSPC.test_electrostatic(electro_neigh, L_pos=False)

Frog.Molecules.Water_PSPC.typical_geometry()

7.1.1.8. Frog.Molecules.Water_RESD_Beerepoot2016 module

This is a custom Water description mixing MD trajectories obtained using TIP4P/2005 force field and the electrostatic description ‘RESD averaged’ obtained in the paper of Beerepoot et. al. PCTC 2016: https://doi.org/10.1021/acs.jctc.5b01000

Frog.Molecules.Water_RESD_Beerepoot2016.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Water_RESD_Beerepoot2016.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Water_RESD_Beerepoot2016.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. Here its the projection of the dipole moment on the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Water_RESD_Beerepoot2016.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Water_RESD_Beerepoot2016.electrostatic_description(pe_level, electro_description, L_pos=False)

Frog.Molecules.Water_RESD_Beerepoot2016.info_molecule(smparameter)

Frog.Molecules.Water_RESD_Beerepoot2016.info_molecule_typical_size()

Frog.Molecules.Water_RESD_Beerepoot2016.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Water_RESD_Beerepoot2016.ref_polarizability(frequency=False)

Frog.Molecules.Water_RESD_Beerepoot2016.test_electrostatic(electro_neigh, L_pos=False)

Frog.Molecules.Water_RESD_Beerepoot2016.typical_geometry()

7.1.1.9. Frog.Molecules.Water_TIP4P2005 module

Frog.Molecules.Water_TIP4P2005.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Water_TIP4P2005.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position. Here at the ‘negative charge’ position.

Frog.Molecules.Water_TIP4P2005.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. Here its the projection of the dipole moment on the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Water_TIP4P2005.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Water_TIP4P2005.electrostatic_description(pe_level, electro_description, L_pos=False)

How to represent this molecule in an explicite electrostatic environement. The same electrostatic parameters are used as in the MD. The negative charge IS NOT at the oxygen position but at localisation X. The positive charge are at the Hydrogen positions.

Frog.Molecules.Water_TIP4P2005.info_molecule(smparameter)

Basic information for a water MT.

Frog.Molecules.Water_TIP4P2005.info_molecule_for_layer()

Defines the radii of every atoms for the layer analysis. These value are used by the pytim module.

Frog.Molecules.Water_TIP4P2005.info_molecule_typical_size()

This function is not ‘mandatory’. It is used within info_molecule.

Frog.Molecules.Water_TIP4P2005.qm_target_description(qmparameter, qmdescription, L_pos=False)

How to define the molecule in an QM box.

Frog.Molecules.Water_TIP4P2005.test_electrostatic(electro_neigh, L_pos=False)

An example of a very complex electrostatic description

Frog.Molecules.Water_TIP4P2005.typical_geometry()

Defines a typical geometry of this molecule. Should return a 3D numpy array.

7.1.1.10. Frog.Molecules.Water_TIP4P2005_O module

Frog.Molecules.Water_TIP4P2005_O.check_molecule_position(L_pos_molecule, L_box)

Frog.Molecules.Water_TIP4P2005_O.compute_hbonds(L_target, name_partner, L_partner, parameter, info=False)

Define how to compute the ‘’hbonds’’ of this molecule type with a partner molecule type. The definition should depend on the partner molecule.

Frog.Molecules.Water_TIP4P2005_O.compute_mean_position(L_pos)

Define how to compute the ‘’mean position’’ of the molecule given its position.

Frog.Molecules.Water_TIP4P2005_O.compute_molecular_orientation(L_pos)

Define how to compute the ‘’molecular orientation’’ of the molecule given its position. Here its the projection of the dipole moment on the laboratory axis. WARNING: THIS SHOULD RETURN VALUE BETWEEN -1 AND 1.

Frog.Molecules.Water_TIP4P2005_O.compute_rotational_matrix(L_pos)

Define the matrix to go from the Molecular to the Laboratory frame: X_{lab} = Rot_matrix * X_{mol}

Frog.Molecules.Water_TIP4P2005_O.dalton_input_parameters(L_pos_molecule=[])

Frog.Molecules.Water_TIP4P2005_O.electrostatic_description(pe_order, electro_description, L_pos=False)

Frog.Molecules.Water_TIP4P2005_O.info_molecule(smparameter)

Frog.Molecules.Water_TIP4P2005_O.info_molecule_typical_size()

Frog.Molecules.Water_TIP4P2005_O.md_parameters(coord, LL_molecular_prop_t)

Frog.Molecules.Water_TIP4P2005_O.qm_target_description(qmparameter, qmdescription, L_pos=False)

TODO

Frog.Molecules.Water_TIP4P2005_O.test_electrostatic(electro_neigh, L_pos=False)

Frog.Molecules.Water_TIP4P2005_O.typical_geometry()

7.1.1.11. Module contents