Keywords

PyOpenCAP uses Python dictionaries which contain key/value pairs to specify the parameters of the calculation. Here, we outline the valid key/value combinations. Importantly, all key value pairs should be specified as strings.

System keywords

The System object contains the basis set and geometry information, which can be obtained in a few different ways.

Keyword	Required	Valid values	Description
molecule	yes	molden,qchem_fchk rassi_h5,inline	Specifies which format to read the molecular geometry. If “inline” is chosen, the “geometry” keyword is also required.
geometry	no	See below	Specifies the geometry in an inline format described below. Required when the “molecule” field is set to “inline”.
basis_file	yes	path to basis file	Specifies the path to the basis file. When “molecule” is set to “molden”,”rassi_h5”, or “qchem_fchk”, this field should be set to a path to a file of the specified type. When “molecule” is set to “inline”, this field should be set to a path to a basis set file formatted in “Psi4” style.
cart_bf	no	‘d’, ‘df’, ‘dfg’ ‘dg’, ‘f’, ‘g’, ‘fg’	Controls the use of pure or Cartesian angular forms of GTOs. The letters corresponding to the angular momenta listed in this field will be expanded in cartesians, those not listed will be expanded in pure GTOs. For example, “df” means d and f-type functions will be cartesian, and all others will be pure harmonic. This keyword is only active when “molecule” is set to “inline”.
bohr_coordinates	no	“True” or “False”	Set this keyword to true when the coordinates specified in “geometry” keyword are in bohr units. This keyword is only active when “molecule” is set to “inline”.

When specifying the geometry inline, use the following format:

atom1 x-coordinate y-coordinate z-coordinate

atom2 x-coordinate y-coordinate z-coordinate ...

Ghost centers with zero nuclear charge can be specified using the symbol “X”.

Units are assumed to be Angstroms unless the bohr_coordinates keyword is set to True.

Example:

sys_dict = {"geometry":    '''N  0  0   1.039
                          N  0  0   -1.039
                          X   0  0   0.0''',
                    "molecule" : "read",
                    "basis_file":"path/to/basis.bas",
                    "cart_bf":"d",
                    "bohr_coordinates:": "true"}

CAP keywords

PyOpenCAP supports Voronoi and Box-type absorbing potentials. We also allow some customization of the numerical grid used for integration. Please see https://github.com/dftlibs/numgrid for more details on the radial_precision and angular_points keywords.

General Keywords

Keyword	Required	Default/valid values	Description
cap_type	yes	“box” or “voronoi”	Type of absorbing potential.
radial_precision	no	“16”	Radial precision for numerical integration grid. A precision of 1x10^(-N), where N is the value specified is used.
angular_points	no	“590”	Number of angular points used for the grid. See https://github.com/dftlibs/numgrid for allowed numbers of points.
thresh	no	“7”	Threshold for exponents of GTO which contribute to CAP integrals. All GTOs with exponents smaller than \(1.0 x 10^{-thresh}\) will be discarded for CAP integrals. If you’re getting errors about allocating the grid, try reducing thresh.
do_numerical	no	True for box CAPs, false for other CAPs	Analytical [Santra1999] integrals are available for Box CAPs only, and are used by default. All other CAPs must be integrated numerically.

Box CAP

A quadratic potential which encloses the system in a 3D rectangular box. Analytical integrals are available for these types of CAPs.

\[W= W_x + W_y +W_z\]

\[\begin{split}W_{\alpha} = \begin{Bmatrix} 0 &\left|r_{\alpha}\right| < R_{\alpha}^0 \\ \left(r_{\alpha} - R_{\alpha}^0 \right)^2 & \left|r_{\alpha}\right| > R_{\alpha}^0 \end{Bmatrix}\end{split}\]

Keyword	Description
cap_x	Onset of CAP in x-direction. Specify in bohr units.
cap_y	Onset of CAP in y-direction. Specify in bohr units.
cap_y	Onset of CAP in z-direction. Specify in bohr units.

Smooth Voronoi CAP

A quadratic potential which uniformly wraps around the system at a specified cutoff radius. The edges between between Voronoi cells are smoothed out to make the potential more amenable to numerical integration [Sommerfeld2015].

\[\begin{split}W(\vec{r}) = \begin{Bmatrix} 0 &r_{WA} \leq r_{cut} \\ (r_{WA} - r_{cut} )^2 & r_{WA} > r_{cut} \end{Bmatrix}\end{split}\]

\[ \begin{align}\begin{aligned}r_{WA}(\vec{r}) = \sqrt{\frac{\sum_{i} w_{i}|\vec{r}-\vec{R}_i|^2}{\sum_{i} w_{i}}}\\ w_{i} = \frac{1}{(|\vec{r}-\vec{R}_i|^2-r_{min}^2+1 a.u.)^2}\end{aligned}\end{align} \]

\[r_{min} = \min\limits_{i}{|\vec{r}-\vec{R}_i|}\]

Keyword	Description
r_cut	Cutoff radius for Voronoi CAP. Specify in bohr units.

Example

cap_dict = {"cap_type": "box",
            "cap_x":"2.76",
            "cap_y":"2.76",
            "cap_z":"4.88",
            "Radial_precision": "14",
            "angular_points": "110"}

Electronic structure keywords

The read_data() function is able to parse the zeroth order Hamiltonian and load the densities when supplied with an appropriate formatted dictionary. All keywords must be specified to use this function. Currently, this is only supported for calculations using the OpenMolcas and Q-Chem interfaces.

Keyword	Description
method	Electronic structure method used in the calculation. Valid options are “MS-CASPT2”, “EOM”, and “TDDFT”.
molcas_output	Path to OpenMolcas output file.
h0_file	Path to Zeroth order Hamiltonian file. Can be full matrix or diagonal. See https://github.com/gayverjr/opencap/tree/main/examples/opencap
package	“OpenMolcas” or “QChem”
rassi_h5	Path to OpenMolcas rassi.h5 file.
qchem_output	Path to Q-Chem output file.
qchem_fchk	Path to Q-Chem .fchk file.

Example:

es_dict = { "package": "openmolcas",
"method" : "ms-caspt2",
       "molcas_output":"path/to/output.out",
       "rassi_h5":"path/to/rassi.h5"}
pc.read_data(es_dict)

References

Sommerfeld2015: Sommerfeld, T.; Ehara, M. Complex Absorbing Potentials with Voronoi Isosurfaces Wrapping Perfectly around Molecules. J. Chem. Theory Comput. 2015, 11 (10), 4627–4633.
Santra1999: Santra, R.; Cederbaum, L. ~S.; Meyer, H.-D. Electronic Decay of Molecular Clusters: Non-Stationary States Computed by Standard Quantum Chemistry Methods. Chem. Phys. Lett. 1999, 303 (3), 413–419.