# Input description¶

PCMSolver needs a number of input parameters at runtime. The API provides two ways of providing them:

by means of an additional input file, parsed by the

`go_pcm.py`

script;by means of a special section in the host program input.

Method 1 is more flexible: all parameters that can be modified by the user are available. The host program needs only copy the additional input file to the scratch directory before execution. Method 2 just gives access to the core parameters.

In this page, input style and input parameters available in Method 1 will be documented.

Note that it is also possible to run the module standalone and use a classical charge
distribution.
The classical charge distribution can be specified by giving a molecular geometry
in the molecule section and an additional point multipoles distribution
in the charge distribution section.
The `run_pcm`

executable has to be compiled for a standalone run with:

```
python <build-path/bin>/go_pcm.py --exe <build-path/bin> --inp molecule.inp
```

where the `molecule.inp`

input file looks like:

```
units = angstrom
codata = 2002
medium
{
solvertype = cpcm
correction = 0.5
solvent = cyclohexane
}
cavity
{
type = gepol
area = 0.6
radiiset = uff
mode = implicit
}
molecule
{
# x, y, z, q
geometry = [0.000000000, 0.00000000, 0.08729478, 9.0,
0.000000000, 0.00000000, -1.64558444, 1.0]
}
```

The script and the executable do not need to be in the same directory.

## Input style¶

The input for PCMSolver is parsed through the Getkw library written by Jonas Juselius
and is organized in **sections** and **keywords**. Input reading is
case-insensitive. An example input structure is shown below, there are also
some working examples in the directory `examples`

. A general input
parameter has the following form (Keyword = [Data type]):

```
Units = [String]
CODATA = [Integer]
Cavity {
Type = [String]
NpzFile = [String]
Area = [Double]
Scaling = [Bool]
RadiiSet = [String]
MinRadius = [Double]
Mode = [String]
Atoms = [Array of Integers]
Radii = [Array of Doubles]
Spheres = [Array of Doubles]
}
Medium {
Nonequilibrium = [Bool]
Solvent = [String]
SolverType = [String]
MatrixSymm = [Bool]
Correction = [Double]
DiagonalIntegrator = [String]
DiagonalScaling = [Double]
ProbeRadius = [Double]
Green<GreenTag> {
Type = [String]
Der = [String]
Eps = [Double]
EpsDyn = [Double]
Eps1 = [Double]
EpsDyn1 = [Double]
Eps2 = [Double]
EpsDyn2 = [Double]
Center = [Double]
Width = [Double]
InterfaceOrigin = [Array of Doubles]
MaxL = [Integer]
}
}
Molecule {
MEP = [Bool]
Geometry = [Double]
}
ChargeDistribution {
Monopoles = [Double]
Dipoles = [Double]
}
MMFQ {
SitesPerFragment = [Integer]
Sites = [Array of Doubles]
NonPolarizable = [Bool]
}
```

Array-valued keywords will expect the array to be given in comma-separated format and enclosed in square brackets. The purpose of tags is to distinguish between cases in which multiple instances of the same kind of object can be managed by the program. There exist only certain legal tagnames and these are determined in the C++ code. Be aware that the input parsing script does not check the correctness of tags.

# Input parameters¶

Available sections:

top section: sets up parameters affecting the module globally;

Cavity: sets up all information needed to form the cavity and discretize its surface;

Medium: sets up the solver to be used and the properties of the medium, i.e. the Green’s functions inside and outside the cavity;

Green, subsection of medium. Sets up the Green’s function inside and outside the cavity.

Molecule: molecular geometry to be used in a standalone run.

ChargeDistribution: sets up a classical multipolar (currently up to dipoles) charge distribution to use as additional source of electrostatic potential.

Note

The Molecule and ChargeDistribution sections only make sense in a standalone run,
i.e. when using the `run_pcm`

executable.

Warning

Exactly matching results obtained from implementations of IEFPCM and/or CPCM (COSMO) given in other program packages requires careful selection of all the parameters involved. A partial checklist of parameters you should always keep in mind:

solvent permittivities (static and optical)

atomic radii set

scaling of the atomic radii

cavity surface

cavity partition (tesselation)

PCM matrix formation algorithm

strategy used to solve the PCM linear equations system.

## Top section keywords¶

- Units
Units of measure used in the input file. If Angstrom is given, all relevant input parameters are first converted in au and subsequently parsed.

**Type**: string**Valid values**: AU | Angstrom**Default**: No Default

- CODATA
Set of fundamental physical constants to be used in the module.

**Type**: integer**Valid values**: 2010 | 2006 | 2002 | 1998**Default**: 2010

## Cavity section keywords¶

- Type
The type of the cavity. Completely specifies type of molecular surface and its discretization. Only one type is allowed. Restart cavity will read the file specified by NpzFile keyword and create a GePol cavity from that.

**Type**: string**Valid values**: GePol | Restart**Default**: none

- NpzFile
The name of the

`.npz`

file to be used for the GePol cavity restart.**Type**: string**Default**: empty string

- Area
Average area (weight) of the surface partition for the GePol cavity.

**Type**: double**Valid values**: \(d \geq 0.01\,\text{a.u.}^2\)**Valid for**: GePol cavity**Default value**: \(0.3\,\text{a.u.}^2\)

- Scaling
If true, the radii for the spheres will be scaled by 1.2. For finer control on the scaling factor for each sphere, select explicit creation mode.

**Type**: bool**Valid for**: all cavities except Restart**Default value**: True

- RadiiSet
Select set of atomic radii to be used. Currently Bondi-Mantina [Bondi64][MantinaChamberlinValero+09], UFF [RCC+92] and Allinger’s MM3 [AZB94] sets available, see Available radii.

**Type**: string**Valid values**: Bondi | UFF | Allinger**Valid for**: all cavities except Restart**Default value**: Bondi

Note

Radii in Allinger’s MM3 set are obtained by

**dividing**the value in the original paper by 1.2, as done in the ADF COSMO implementation We advise to turn off scaling of the radii by 1.2 when using this set.- MinRadius
Minimal radius for additional spheres not centered on atoms. An arbitrarily big value is equivalent to switching off the use of added spheres, which is the default.

**Type**: double**Valid values**: \(d \geq 0.4\,\text{a.u.}\)**Valid for**: GePol cavity**Default value**: \(100.0\,\text{a.u.}\)

- Mode
How to create the list of spheres for the generation of the molecular surface:

in Implicit mode, the atomic coordinates and charges will be obtained from the QM host program. Spheres will be centered on the atoms and the atomic radii, as specified in one the built-in sets, will be used. Scaling by 1.2 will be applied according to the keyword Scaling;

in Atoms mode, the atomic coordinates and charges will be obtained from the QM host program. For the atoms specified by the array given in keyword Atoms, the built-in radii will be substituted by the radii provided in the keyword Radii. Scaling by 1.2 will be applied according to the keyword Scaling;

in Explicit mode, both centers and radii of the spheres are to be specified in the keyword Spheres. The user has full control over the generation of the list of spheres. Scaling by 1.2 is

**not**applied, regardless of the value of the Scaling keyword.

**Type**: string**Valid values**: Implicit | Atoms | Explicit**Valid for**: all cavities except Restart**Default value**: Implicit

- Atoms
Array of atoms whose radius has to be substituted by a custom value.

**Type**: array of integers**Valid for**: all cavities except Restart

- Radii
Array of radii replacing the built-in values for the selected atoms.

**Type**: array of doubles**Valid for**: all cavities except Restart

- Spheres
Array of coordinates and centers for construction of the list of spheres in explicit mode. Format is \([\ldots, x_i, y_i, z_i, R_i, \ldots]\)

**Type**: array of doubles**Valid for**: all cavities except Restart

## Medium section keywords¶

- SolverType
Type of solver to be used. All solvers are based on the Integral Equation Formulation of the Polarizable Continuum Model [CancesMennucci98]

IEFPCM. Collocation solver for a general dielectric medium

CPCM. Collocation solver for a conductor-like approximation to the dielectric medium

**Type**: string**Valid values**: IEFPCM | CPCM**Default value**: IEFPCM

- Nonequilibrium
Initializes an additional solver using the dynamic permittivity. To be used in response calculations.

**Type**: bool**Valid for**: all solvers**Default value**: False

- Solvent
Specification of the dielectric medium outside the cavity. This keyword

**must always**be given a value. If the solvent name given is different from Explicit any other settings in the Green’s function section will be overridden by the built-in values for the solvent specified. See Table Available solvents for details.`Solvent = Explicit`

, triggers parsing of the Green’s function sections.**Type**: string**Valid values**:Water , H2O;

Propylene Carbonate , C4H6O3;

Dimethylsulfoxide , DMSO;

Nitromethane , CH3NO2;

Acetonitrile , CH3CN;

Methanol , CH3OH;

Ethanol , CH3CH2OH;

Acetone , C2H6CO;

1,2-Dichloroethane , C2H4CL2;

Methylenechloride , CH2CL2;

Tetrahydrofurane , THF;

Aniline , C6H5NH2;

Chlorobenzene , C6H5CL;

Chloroform , CHCL3;

Toluene , C6H5CH3;

1,4-Dioxane , C4H8O2;

Benzene , C6H6;

Carbon Tetrachloride , CCL4;

Cyclohexane , C6H12;

N-heptane , C7H16;

Explicit.

- MatrixSymm
If True, the PCM matrix obtained by the IEFPCM collocation solver is symmetrized \(\mathbf{K} := \frac{\mathbf{K} + \mathbf{K}^\dagger}{2}\)

**Type**: bool**Valid for**: IEFPCM solver**Default**: True

- Correction
Correction, \(k\) for the apparent surface charge scaling factor in the CPCM solver \(f(\varepsilon) = \frac{\varepsilon - 1}{\varepsilon + k}\)

**Type**: double**Valid values**: \(k > 0.0\)**Valid for**: CPCM solver**Default**: 0.0

- DiagonalIntegrator
Type of integrator for the diagonal of the boundary integral operators

**Type**: string**Valid values**: COLLOCATION**Valid for**: IEFPCM, CPCM**Default**: COLLOCATION**Notes**: in future releases we will add PURISIMA and NUMERICAL as options

- DiagonalScaling
Scaling factor for diagonal of collocation matrices

**Type**: double**Valid values**: \(f > 0.0\)**Valid for**: IEFPCM, CPCM**Default**: 1.07**Notes**: values commonly used in the literature are 1.07 and 1.0694

- ProbeRadius
Radius of the spherical probe approximating a solvent molecule. Used for generating the solvent-excluded surface (SES) or an approximation of it. Overridden by the built-in value for the chosen solvent.

**Type**: double**Valid values**: \(d \in [0.1, 100.0]\,\text{a.u.}\)**Valid for**: all solvers**Default**: 1.0

## Green section keywords¶

If `Solvent = Explicit`

, **two** Green’s functions sections must be specified
with tags `inside`

and `outside`

, i.e. `Green<inside>`

and
`Green<outside>`

. The Green’s function inside will always be the vacuum,
while the Green’s function outside might vary.

- Type
Which Green’s function characterizes the medium.

**Type**: string**Valid values**: Vacuum | UniformDielectric | SphericalDiffuse | SphericalSharp**Default**: Vacuum

- Der
How to calculate the directional derivatives of the Green’s function:

Numerical, perform numerical differentiation

**debug option**;Derivative, use automatic differentiation to get the directional derivative;

Gradient, use automatic differentiation to get the full gradient

**debug option**;Hessian, use automatic differentiation to get the full hessian

**debug option**;

**Type**: string**Valid values**: Numerical | Derivative | Gradient | Hessian**Default**: Derivative

Note

The spherical diffuse Green’s function

**always**uses numerical differentiation.- Eps
Static dielectric permittivity of the medium

**Type**: double**Valid values**: \(\varepsilon \geq 1.0\)**Default**: 1.0

- EpsDyn
Dynamic dielectric permittivity of the medium

**Type**: double**Valid values**: \(\varepsilon \geq 1.0\)**Default**: 1.0

- Profile
Functional form of the dielectric profile

**Type**: string**Valid values**: Tanh | Erf | Log**Valid for**: SphericalDiffuse**Default**: Log

- Eps1
Static dielectric permittivity inside the interface

**Type**: double**Valid values**: \(\varepsilon \geq 1.0\)**Valid for**: SphericalDiffuse, SphericalSharp**Default**: 1.0

- EpsDyn1
Dynamic dielectric permittivity inside the interface

**Type**: double**Valid values**: \(\varepsilon \geq 1.0\)**Valid for**: SphericalDiffuse, SphericalSharp**Default**: 1.0

- Eps2
Static dielectric permittivity outside the interface

**Type**: double**Valid values**: \(\varepsilon \geq 1.0\)**Valid for**: SphericalDiffuse, SphericalSharp**Default**: 1.0

- EpsDyn2
Dynamic dielectric permittivity outside the interface

**Type**: double**Valid values**: \(\varepsilon \geq 1.0\)**Valid for**: SphericalDiffuse, SphericalSharp**Default**: 1.0

- Center
Center of the interface layer. This corresponds to the radius of the spherical droplet.

**Type**: double**Valid for**: SphericalDiffuse, SphericalSharp**Default**: 100.0 a.u.

- Width
Physical width of the interface layer. This value is divided by 6.0 internally.

**Type**: double**Valid for**: SphericalDiffuse**Default**: 5.0 a.u.

Warning

Numerical instabilities may arise if a too small value is selected.

- InterfaceOrigin
Center of the spherical droplet

**Type**: array of doubles**Valid for**: SphericalDiffuse, SphericalSharp**Default**: \([0.0, 0.0, 0.0]\)

- MaxL
Maximum value of the angular momentum in the expansion of the Green’s function for the spherical diffuse Green’s function

**Type**: integer**Valid for**: SphericalDiffuse, SphericalSharp**Default**: 30

## Molecule section keywords¶

It is possible to run the module standalone and use a classical charge
distribution as specified in this section of the input.
The `run_pcm`

executable has to be compiled for a standalone run with:

```
python go_pcm.py -x molecule.inp
```

where the `molecule.inp`

input file looks like:

```
units = angstrom
codata = 2002
medium
{
solvertype = cpcm
correction = 0.5
solvent = cyclohexane
}
cavity
{
type = gepol
area = 0.6
radiiset = uff
mode = implicit
}
molecule
{
# x, y, z, q
geometry = [0.000000000, 0.00000000, 0.08729478, 9.0,
0.000000000, 0.00000000, -1.64558444, 1.0]
}
```

- Geometry
Coordinates and charges of the molecular aggregate. Format is \([\ldots, x_i, y_i, z_i, Q_i, \ldots]\) Charges are always assumed to be in atomic units

**Type**: array of doubles

## ChargeDistribution section keywords¶

Set a classical charge distribution, inside or outside the cavity No additional spheres will be generated.

- Monopoles
Array of point charges Format is \([\ldots, x_i, y_i, z_i, Q_i, \ldots]\)

**Type**: array of doubles

- Dipoles
Array of point dipoles. Format is \([\ldots, x_i, y_i, z_i, \mu_{x_i}, \mu_{y_i}, \mu_{z_i} \ldots]\) The dipole moment components are always read in atomic units.

**Type**: array of doubles

## MMFQ section keywords¶

Set a classical fluctuating charge force field. This is incompatible with any options specifying a continuum model. No additional spheres will be generated.

- SitesPerFragment
Number of sites per MM fragment. For water this is 3.

**Type**: integer**Default**: 3

- Sites
Array of MM sites for the FQ model Format is \([\ldots, x_i, y_i, z_i, chi_i, eta_i \ldots]\)

**Type**: array of doubles

- NonPolarizable
Whether to make this force field nonpolarizable.

**Type**: bool**Default**: false

## Available solvents¶

The macroscopic properties for the built-in list of solvents are:

static permittivity, \(\varepsilon_s\)

optical permittivity, \(\varepsilon_\infty\)

probe radius, \(r_\mathrm{probe}\) in Angstrom.

The following table summarizes the built-in solvents and their properties. Solvents are ordered by decreasing static permittivity.

Name

Formula

\(\varepsilon_s\)

\(\varepsilon_\infty\)

\(r_\mathrm{probe}\)

Water

H2O

78.39

1.776

1.385

Propylene Carbonate

C4H6O3

64.96

2.019

1.385

Dimethylsulfoxide

DMSO

46.7

2.179

2.455

Nitromethane

CH3NO2

38.20

1.904

2.155

Acetonitrile

CH3CN

36.64

1.806

2.155

Methanol

CH3OH

32.63

1.758

1.855

Ethanol

CH3CH2OH

24.55

1.847

2.180

Acetone

C2H6CO

20.7

1.841

2.38

1,2-Dichloroethane

C2H4Cl2

10.36

2.085

2.505

Methylenechloride

CH2Cl2

8.93

2.020

2.27

Tetrahydrofurane

THF

7.58

1.971

2.9

Aniline

C6H5NH2

6.89

2.506

2.80

Chlorobenzene

C6H5Cl

5.621

2.320

2.805

Chloroform

CHCl3

4.90

2.085

2.48

Toluene

C6H5CH3

2.379

2.232

2.82

1,4-Dioxane

C4H8O2

2.250

2.023

2.630

Benzene

C6H6

2.247

2.244

2.630

Carbon tetrachloride

CCl4

2.228

2.129

2.685

Cyclohexane

C6H12

2.023

2.028

2.815

N-heptane

C7H16

1.92

1.918

3.125