Input

Input sections

An OpenCAP input file has four sections:

$system and $projected_cap are required, $geometry and $trajectory are optional.

Within each section, the user inserts keyword/value pairs which define the calculation.

All four sections have their own unique keywords, and all four must be specified to run a calculation. The general format is:

$section_name

keyword  value

keyword  value

$end

In each section, the parser will read lines until it sees the $end keyword.

Only the first two arguments per line are read, so all remaining text can be used as comments. Additionally, lines beginning with an exclamation mark '!' are ignored. All input sections (except for those referring to file paths) are case-insensitive.

System

The system section specifies information about the molecular system and the ab initio basis set. Basis sets can be downloaded from the MolSSI basis set exchange and modified to suit your purposes.

Required

Keyword	Valid options	Description
molecule	molden,qchem_fchk,rassi_h5,inline	Specifies which format to read the molecular geometry. If "inline" is chosen, the "$geometry" section is also required.
basis_file	path to basis file	Specifies the path to the basis file. When "molecule" is set to "molden","rassi_h5", or "qchem_fchk", this keyword should be set to a path to a file of the specified type. When "molecule" is set to "inline", this keyword should be set to a path to a basis set file formatted in "Psi4" style.

Optional

Keyword	default	Description
cart_bf	""(all functions pure)	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	false	Set to true when coordinates specified in "geometry" keyword are in bohr units. This keyword is only active when "molecule" is set to "inline".

Geometry

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".

By default, units are assumed to be Angstroms.

Projected_CAP

This section allows one to specify the parameters used to define the complex absorbing potential, the data read in from the electronic structure calculation, and the grid used for numerical integration.

There are two key pieces of data which must be read in from the electronic structure package: the set of one particle transition densities between each pair of states (each has a dimension of NxN where N is the number of basis functions), and the zeroth order Hamiltonian (which has a dimension of MxM, where M is the number of electronic states computed by the package). In some cases, the zeroth order Hamiltonian can be read directly from the output file of the electronic structure package, but in other cases it may be easier to just specify the zeroth order hamiltonian manually (due to its small dimensionality). For the latter option, the 'h0_file' keyword must be used, and the value must point to a properly formatted file.

A properly formatted zeroth order hamiltonian file can have one of two forms. The first is the diagonal form (where the zeroth order hamiltonian just consists of total energies on the diagonal, as is the case for EOM-CCSD), the word "Diagonal" must appear on the first line, followed by the energies, each on their own line. The second is the full form, in which the entire zeroth order hamiltonian is specified. The word "Full" must appear on the first line, followed by the matrix. The matrix is read in row-major order. We currently support two types of complex absorbing potentials; quadratic box-type potentials, and a quadratic "Voronoi isosurface" potential. Both types of CAP have their own set of parameters which must be defined. Numerical integration is performed with the aid of the numgrid package, which allocates the grid based on the molecular geometry and basis set. By default, a radial grid with precision 1e-16 is used, with an angular grid of 590 points. Both can optionally be adjusted to increase or decrease the size of the grid as needed.

Required

Keyword	Type	Description	Valid options
cap_type	string	Type of absorbing potential	'Box' or 'Voronoi'
Method	string	Name of electronic structure method	MS-CASPT2, TDDFT, EOM, SC-NEVPT2, PC-NEVPT2
Package	string	Name of electronic structure package	OpenMolcas, Q-Chem
Nstates	int	Number of electronic states	2 or greater

OpenMolcas Interface

Keyword	Type	Description
rassi_h5	string	Relative or absolute path to rassi.h5 file containing TDMs.
molcas_output	string	Relative or absolute path to OpenMolcas output file. Required when h0_file keyword is unspecified.

QChem Interface

Keyword	Type	Description
qchem_fchk	string	Relative or absolute path to qchem .fchk file containing TDMs.
qchem_output	string	Relative or absolute path to Q-Chem output file. Required when h0_file keyword is unspecified.

Box CAP

A quadratic potential which encloses the system in a 3D rectangular box. Functional form:

\( W= W_x + W_y +W_z \)

\( W_{\alpha} = 0\), \( \left|r_{\alpha}\right| < R_{\alpha}^0 \)

\( W_{\alpha} = \left(r_{\alpha} - R_{\alpha}^0 \right)^2,\) \( \left|r_{\alpha}\right| > R_{\alpha}^0 \)

Keyword	Type	Description
CAP_X	float	Onset of CAP in x-direction. Specify in bohr units.
CAP_Y	float	Onset of CAP in y-direction. Specify in bohr units.
CAP_Z	float	Onset of CAP in z-direction. Specify in bohr units.

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[1]. Functional form:

\( W(\vec{r}) = 0,\) \(r_{WA} \leq r_{cut} \)

\( W(\vec{r}) = (r_{WA} - r_{cut} )^2,\) \(r_{WA} > r_{cut} \)

\( r_{WA}(\vec{r}) = \sqrt{\frac{\sum_{i} w_{i}|\vec{r}-\vec{R}_i|^2}{\sum_{i} w_{i}}} \)

\( w_{i} = \frac{1}{(|\vec{r}-\vec{R}_i|^2-r_{min}^2+1 a.u.)^2} \)

\( r_{min} = \min\limits_{i}{|\vec{r}-\vec{R}_i|} \)

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

Optional

Keyword	Type	Description	Default
radial_precision	int	Radial precision for numerical integration grid. A precision of 1x10^(-N), where N is the value specified is used.	16
angular_points	int	Number of angular ponts used for the grid. See https://github.com/dftlibs/numgrid for allowed numbers of points.	590
thresh	int	Threshold for exponents of GTO which contribute to CAP integrals. All GTOs with exponents smaller than 1E-thresh will be discarded.	7
h0_file	string	Relative or absolute path to formatted zeroth order Hamiltonian file. Required when output from electronic structure package (e.g. molcas_output) is unspecified.	""

Trajectory

One can generate eigenvalue trajectories within OpenCAP using the $trajectory field. One can specify the range of \(\eta\) values to be explored, and for each state, the minimum of the logarithmic velocity will be printed in the output. States are tracked using eigenvector overlap. The entire trajectory can also be exported to a .data file using the save_trajectory keyword.

Keyword	Type	Description
eta_step	float	\(\eta\)-step size, in 1E-5 bohr
nsteps	int	Number of steps for eigenvalue trajectory
save_trajectory	bool	Set to true if you want to save the trajectory, it will be saved to a .data file.

References

[1] Sommerfeld, T.; Ehara, M. Complex Absorbing Potentials with Voronoi Isosurfaces Wrapping Perfectly around Molecules. J. Chem. Theory Comput. 2015, 11 (10), 4627–4633.