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GabrielgerezGabrielgerez
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Update input for PCM
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‎doc/users/user_ref.rst

+60-58
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@@ -860,114 +860,116 @@ User input reference
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**Default** ``user['SCF']['kain']``
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:Cavity: Define the interlocking spheres cavity.
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:red:`Keywords`
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:mode: Determines how to set up the interlocking spheres cavity. ``atoms``: centers are taken from the molecular geometry, radii taken from tabulated data (van der Waals radius), and rescaled using the parameters ``alpha``, ``beta`` and ``sigma`` (R_i <- alpha*R_i + beta*sigma). Default spheres can be modified and/or extra spheres added, using the ``$spheres`` section, see documentation. ``explicit``: centers and radii given explicitly in the ``spheres`` block.
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**Type** ``str``
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**Default** ``atoms``
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:Solvent: Parameters for the Self-Consistent Reaction Field optimization.
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**Predicates**
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- ``value.lower() in ['atoms', 'explicit']``
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:red:`Sections`
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:Permittivity: Parameters for the permittivity function.
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:spheres: This input parameter affects the list of spheres used to generate the cavity. In all cases, values for the radius, the radius scaling factor (``alpha``), the width (``sigma``), and the width scaling factor (``beta``) can be modified. If they are not specified their global default values are used. In ``atoms`` mode, we *modify* the default list of spheres, built with centers from the molecular geometry and radii from internal tabulated van der Waals values. To *substitute* a sphere, include a line like: `` $spheres i R [alpha] [beta] [sigma] $end `` to specify that the ``i`` atom in the molecule (0-based indexing) should use radius ``R`` instead of the pre-tabulated vdW radius. To *add* a sphere, include a line like: `` $spheres x y z R [alpha] [beta] [sigma] $end ``` to specify that a sphere of radius ``R`` should be added at position ``(x, y, z)``. Spheres added in this way are not aware of their parent atom, if any. They will **not** contribute to the molecular gradient. In ``explicit`` mode, we *build* the complete sphere list from scratch. You can add a line like: `` $spheres x y z R [alpha] [beta] [sigma] $end `` to specify that a sphere of radius ``R`` should be added at position ``(x, y, z)``. Spheres added in this way are not aware of their parent atom, if any. They will **not** contribute to the molecular gradient. Alternatively, you can specify a line like: `` $spheres i R [alpha] [beta] [sigma] $end `` to specify that the ``i`` atom in the molecule (0-based indexing) should use radius ``R``. Spheres added in this way are aware of their parent atom. They will contribute to the molecular gradient.
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:red:`Keywords`
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:epsilon_in: Permittivity inside the cavity. 1.0 is the permittivity of free space, anything other than this is undefined behaviour.
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**Type** ``str``
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**Type** ``float``
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**Default** ````
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**Default** ``1.0``
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:alpha: Scaling factor on the radius term for the cavity rescaling (R_i <- alpha*R_i + beta*sigma). Only used for the default vdW radii in `atoms` mode, not if explicit ``$spheres`` are given.
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:formulation: Formulation of the Permittivity function. Currently only the exponential is available.
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**Type** ``float``
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**Type** ``str``
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**Default** ``1.1``
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**Default** ``exponential``
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:beta: Scaling factor on the boundary width term for the cavity rescaling (R_i <- alpha*R_i + beta*sigma). Only used for the default vdW radii in `atoms` mode, not if explicit ``$spheres`` are given.
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**Predicates**
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- ``value.lower() in ['exponential']``
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**Type** ``float``
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:red:`Sections`
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:epsilon_out: Parameters for the continuum solvent outside the cavity.
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**Default** ``0.5``
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:red:`Keywords`
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:nonequilibrium: Whether to use the nonequilibrium formulation of response, *i.e.* use the dynamic permittivity for the calculation of the response reaction field. Defaults to false.
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:sigma: Width of cavity boundary, smaller value means sharper transition. **This quantity has dimensions of length. The default value is in atomic units**.
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**Type** ``bool``
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**Type** ``float``
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**Default** ``False``
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**Default** ``0.2``
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:static: Static permittivity outside the cavity. This is characteristic of the solvent used.
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:Permittivity: Parameters for the permittivity function.
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**Type** ``float``
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:red:`Keywords`
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:epsilon_in: Permittivity inside the cavity. 1.0 is the permittivity of free space, anything other than this is undefined behaviour.
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**Default** ``1.0``
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**Type** ``float``
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:dynamic: Dynamic permittivity outside the cavity. This is characteristic of the solvent used and relevant only in response calculations. Defaults to the same value as `epsilon_static`.
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**Default** ``1.0``
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**Type** ``float``
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:formulation: Formulation of the Permittivity function. Currently only the exponential is available.
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**Default** ``user['PCM']['Solvent']['Permittivity']['epsilon_out']['static']``
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**Type** ``str``
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:DebyeHuckelScreening: Parameters for the Debye-Huckel screening factor
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**Default** ``exponential``
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:red:`Keywords`
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:ion_strength: Ionic strength of the electrolyte in mol/L. This represents the concentration of the ions in the bulk solvent.
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**Predicates**
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- ``value.lower() in ['exponential']``
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**Type** ``float``
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:red:`Sections`
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:epsilon_out: Parameters for the continuum solvent outside the cavity.
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**Default** ``1.0``
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:red:`Keywords`
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:nonequilibrium: Whether to use the nonequilibrium formulation of response, *i.e.* use the dynamic permittivity for the calculation of the response reaction field. Defaults to false.
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:ion_radius: Amount with which the vdw-radius of the atoms will be increased. The screening factor will have an area of effect that is often going to be larger than the vdw-cavity, but centered in the same atoms.
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**Type** ``bool``
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**Type** ``float``
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**Default** ``False``
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**Default** ``0.0``
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:static: Static permittivity outside the cavity. This is characteristic of the solvent used.
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:ion_width: Width of the transition between the solute and the ion accessible part.
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**Type** ``float``
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**Default** ``1.0``
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**Default** ``0.2``
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:dynamic: Dynamic permittivity outside the cavity. This is characteristic of the solvent used and relevant only in response calculations. Defaults to the same value as `epsilon_static`.
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:formulation: formulation of the debye-huckel screening factor. Currently only the variable factor is implemented. ``variable``: implement the screening functions as k = (1-C_ion)k_out
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**Type** ``float``
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**Type** ``str``
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**Default** ``user['PCM']['Permittivity']['epsilon_out']['static']``
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**Default** ``variable``
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:D_H_screening: Parameters for the Debye-Huckel screening factor
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**Predicates**
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- ``value.lower() in ['variable']``
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:Cavity: Define the interlocking spheres cavity.
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:red:`Keywords`
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:ion_strength: Ionic strength of the electrolyte in mol/L. This represents the concentration of the ions in the bulk solvent.
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:mode: Determines how to set up the interlocking spheres cavity. ``atoms``: centers are taken from the molecular geometry, radii taken from tabulated data (van der Waals radius), and rescaled using the parameters ``alpha``, ``beta`` and ``sigma`` (R_i <- alpha*R_i + beta*sigma). Default spheres can be modified and/or extra spheres added, using the ``$spheres`` section, see documentation. ``explicit``: centers and radii given explicitly in the ``spheres`` block.
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**Type** ``float``
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**Type** ``str``
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**Default** ``1.0``
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**Default** ``atoms``
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:ion_radius: Amount with which the vdw-radius of the atoms will be increased. The screening factor will have an area of effect that is often going to be larger than the vdw-cavity, but centered in the same atoms.
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**Predicates**
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- ``value.lower() in ['atoms', 'explicit']``
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**Type** ``float``
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:spheres: This input parameter affects the list of spheres used to generate the cavity. In all cases, values for the radius, the radius scaling factor (``alpha``), the width (``sigma``), and the width scaling factor (``beta``) can be modified. If they are not specified their global default values are used. In ``atoms`` mode, we *modify* the default list of spheres, built with centers from the molecular geometry and radii from internal tabulated van der Waals values. To *substitute* a sphere, include a line like: `` $spheres i R [alpha] [beta] [sigma] $end `` to specify that the ``i`` atom in the molecule (0-based indexing) should use radius ``R`` instead of the pre-tabulated vdW radius. To *add* a sphere, include a line like: `` $spheres x y z R [alpha] [beta] [sigma] $end ``` to specify that a sphere of radius ``R`` should be added at position ``(x, y, z)``. Spheres added in this way are not aware of their parent atom, if any. They will **not** contribute to the molecular gradient. In ``explicit`` mode, we *build* the complete sphere list from scratch. You can add a line like: `` $spheres x y z R [alpha] [beta] [sigma] $end `` to specify that a sphere of radius ``R`` should be added at position ``(x, y, z)``. Spheres added in this way are not aware of their parent atom, if any. They will **not** contribute to the molecular gradient. Alternatively, you can specify a line like: `` $spheres i R [alpha] [beta] [sigma] $end `` to specify that the ``i`` atom in the molecule (0-based indexing) should use radius ``R``. Spheres added in this way are aware of their parent atom. They will contribute to the molecular gradient.
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**Default** ``0.0``
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**Type** ``str``
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**Default** ````
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:ion_width: Width of the transition between the solute and the ion accessible part.
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:alpha: Scaling factor on the radius term for the cavity rescaling (R_i <- alpha*R_i + beta*sigma). Only used for the default vdW radii in `atoms` mode, not if explicit ``$spheres`` are given.
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**Type** ``float``
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**Default** ``0.2``
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**Default** ``1.1``
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:beta: Scaling factor on the boundary width term for the cavity rescaling (R_i <- alpha*R_i + beta*sigma). Only used for the default vdW radii in `atoms` mode, not if explicit ``$spheres`` are given.
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:formulation: formulation of the debye-huckel screening factor. Currently only the variable factor is implemented. ``variable``: implement the screening functions as k = (1-C_ion)k_out
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**Type** ``float``
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**Type** ``str``
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**Default** ``0.5``
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**Default** ``variable``
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:sigma: Width of cavity boundary, smaller value means sharper transition. **This quantity has dimensions of length. The default value is in atomic units**.
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**Predicates**
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- ``value.lower() in ['variable']``
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**Type** ``float``
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**Default** ``0.2``
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:GeometryOptimizer: Includes parameters related to the internal geometry optimization using the SQNM (Stabilized Quasi-Newton Method) for noisy PES.
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:GeometryOptimizer: Includes parameters related to the internal geometry optimization using the SQNM (Stabilized Quasi-Newton Method) for noisy PES.
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:red:`Keywords`
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:run: Run optimizer. Otherwise single point energy/properties are computed.

‎python/mrchem/helpers.py

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@@ -138,24 +138,24 @@ def _reaction_operator_handler(user_dict, rsp=False):
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"dynamic_thrs": user_dict["PCM"]["SCRF"]["dynamic_thrs"],
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# if doing a response calculation, then density_type is set to 1 (electronic only)
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"density_type": 1 if rsp else density_type,
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"epsilon_in": user_dict["PCM"]["Permittivity"]["epsilon_in"],
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"epsilon_static": user_dict["PCM"]["Permittivity"]["epsilon_out"]["static"],
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"epsilon_dynamic": user_dict["PCM"]["Permittivity"]["epsilon_out"]["dynamic"],
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"nonequilibrium": user_dict["PCM"]["Permittivity"]["epsilon_out"][
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"epsilon_in": user_dict["PCM"]["Solvent"]["Permittivity"]["epsilon_in"],
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"epsilon_static": user_dict["PCM"]["Solvent"]["Permittivity"]["epsilon_out"]["static"],
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"epsilon_dynamic": user_dict["PCM"]["Solvent"]["Permittivity"]["epsilon_out"]["dynamic"],
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"nonequilibrium": user_dict["PCM"]["Solvent"]["Permittivity"]["epsilon_out"][
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"nonequilibrium"
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],
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"formulation": user_dict["PCM"]["Permittivity"]["formulation"],
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"formulation": user_dict["PCM"]["Solvent"]["Permittivity"]["formulation"],
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"kappa_out": 0.0,
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"ion_radius": user_dict["PCM"]["D_H_screening"]["ion_radius"],
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"ion_width": user_dict["PCM"]["D_H_screening"]["ion_width"],
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"DHS-formulation": user_dict["PCM"]["D_H_screening"]["formulation"],
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"ion_radius": user_dict["PCM"]["Solvent"]["DebyeHuckelScreening"]["ion_radius"],
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"ion_width": user_dict["PCM"]["Solvent"]["DebyeHuckelScreening"]["ion_width"],
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"DHS-formulation": user_dict["PCM"]["Solvent"]["DebyeHuckelScreening"]["formulation"],
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}
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# ionic solvent continuum model
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ionic_model = user_dict["WaveFunction"]["environment"].lower().split("_")[-1]
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if ionic_model in ("pb", "lpb"):
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permittivity = user_dict["PCM"]["Permittivity"]["epsilon_out"]["static"]
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ionic_strength = user_dict["PCM"]["D_H_screening"]["ion_strength"]
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permittivity = user_dict["PCM"]["Solvent"]["Permittivity"]["epsilon_out"]["static"]
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ionic_strength = user_dict["PCM"]["Solvent"]["DebyeHuckelScreening"]["ion_strength"]
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kappa_out = compute_kappa(user_dict["Constants"], permittivity, ionic_strength)
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reo_dict |= {
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"kappa_out": kappa_out,

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