Interfacing a QM program and PCMSolver¶
For the impatients: tl;dr¶
In these examples, we want to show how every function in the API works. If your program is written in Fortran, head over to Interfacing with a Fortran host If your program is written in C/C++, head over to Interfacing with a C host
How PCMSolver handles potentials and charges: surface functions¶
Electrostatic potential vectors and the corresponding apparent surface charge vectors are handled internally as surface functions. The actual values are stored into Eigen vectors and saved into a map. The mapping is between the name of the surface function, given by the programmer writing the interface to the library, and the vector holding the values.
What you should care about: API functions¶
These are the contents of the pcmsolver.h
file defining
the public API of the PCMSolver library. The Fortran bindings
for the API are in the pcmsolver.f90
file.
The indexing of symmetry operations and their mapping to a bitstring
is explained in the following Table. This is important when passing
symmetry information to the pcmsolver_new()
function.
Index | zyx | Generator | Parity |
---|---|---|---|
0 | 000 | E | 1.0 |
1 | 001 | Oyz | -1.0 |
2 | 010 | Oxz | -1.0 |
3 | 011 | C2z | 1.0 |
4 | 100 | Oxy | -1.0 |
5 | 101 | C2y | 1.0 |
6 | 110 | C2x | 1.0 |
7 | 111 | i | -1.0 |
Typedefs
-
typedef bool
pcmsolver_bool_t
¶
-
typedef
pcmsolver_context_t
¶ Workaround to have pcmsolver_context_t available to C
-
typedef
HostWriter
¶ Flushes module output to host program
- Parameters
message
: contents of the module output
Enums
Functions
-
pcmsolver_context_t *
pcmsolver_new
(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], struct PCMInput *host_input, HostWriter writer)¶ Creates a new PCM context object.
The molecular point group information is passed as an array of 4 integers: number of generators, first, second and third generator respectively. Generators map to integers as in table :ref:
symmetry-ops
- Parameters
input_reading
: input processing strategynr_nuclei
: number of atoms in the moleculecharges
: atomic chargescoordinates
: atomic coordinatessymmetry_info
: molecular point group informationhost_input
: input to the module, as read by the hostwriter
: flush-to-host function
-
pcmsolver_context_t *
pcmsolver_new_v1112
(pcmsolver_reader_t input_reading, int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], const char *parsed_fname, struct PCMInput *host_input, HostWriter writer)¶ Creates a new PCM context object, updated in v1.1.12.
The molecular point group information is passed as an array of 4 integers: number of generators, first, second and third generator respectively. Generators map to integers as in table :ref:
symmetry-ops
- Parameters
input_reading
: input processing strategynr_nuclei
: number of atoms in the moleculecharges
: atomic chargescoordinates
: atomic coordinatessymmetry_info
: molecular point group informationparsed_fname
: name of the input file parsed by pcmsolver.pyhost_input
: input to the module, as read by the hostwriter
: flush-to-host function
-
void
pcmsolver_delete
(pcmsolver_context_t *context)¶ Deletes a PCM context object.
- Parameters
context
: the PCM context object to be deleted
-
pcmsolver_bool_t
pcmsolver_is_compatible_library
(void)¶ Whether the library is compatible with the header file Checks that the compiled library and header file version match. Host should abort when that is not the case.
- Warning
- This function should be called before instantiating any PCM context objects.
-
void
pcmsolver_print
(pcmsolver_context_t *context)¶ Prints citation and set up information.
- Parameters
context
: the PCM context object
-
int
pcmsolver_get_cavity_size
(pcmsolver_context_t *context)¶ Getter for the number of finite elements composing the molecular cavity.
- Return
- the size of the cavity
- Parameters
context
: the PCM context object
-
int
pcmsolver_get_irreducible_cavity_size
(pcmsolver_context_t *context)¶ Getter for the number of irreducible finite elements composing the molecular cavity.
- Return
- the number of irreducible finite elements
- Parameters
context
: the PCM context object
-
void
pcmsolver_get_centers
(pcmsolver_context_t *context, double centers[])¶ Getter for the centers of the finite elements composing the molecular cavity.
- Parameters
context
: the PCM context objectcenters
: array holding the coordinates of the finite elements centers
-
void
pcmsolver_get_center
(pcmsolver_context_t *context, int its, double center[])¶ Getter for the center of the i-th finite element.
- Parameters
context
: the PCM context objectits
: index of the finite elementcenter
: array holding the coordinates of the finite element center
-
void
pcmsolver_get_areas
(pcmsolver_context_t *context, double areas[])¶ Getter for the areas/weights of the finite elements.
- Parameters
context
: the PCM context objectareas
: array holding the weights/areas of the finite elements
-
void
pcmsolver_compute_asc
(pcmsolver_context_t *context, const char *mep_name, const char *asc_name, int irrep)¶ Computes ASC given a MEP and the desired irreducible representation.
- Parameters
context
: the PCM context objectmep_name
: label of the MEP surface functionasc_name
: label of the ASC surface functionirrep
: index of the desired irreducible representation The module uses the surface function concept to handle potentials and charges. Given labels for each, this function retrieves the MEP and computes the corresponding ASC.
-
void
pcmsolver_compute_response_asc
(pcmsolver_context_t *context, const char *mep_name, const char *asc_name, int irrep)¶ Computes response ASC given a MEP and the desired irreducible representation.
- Parameters
context
: the PCM context objectmep_name
: label of the MEP surface functionasc_name
: label of the ASC surface functionirrep
: index of the desired irreducible representation IfNonequilibrium = True
in the input, calculates a response ASC using the dynamic permittivity. Falls back to the solver with static permittivity otherwise.
-
double
pcmsolver_compute_polarization_energy
(pcmsolver_context_t *context, const char *mep_name, const char *asc_name)¶ Computes the polarization energy.
- Return
- the polarization energy This function calculates the dot product of the given MEP and ASC vectors.
- Parameters
context
: the PCM context objectmep_name
: label of the MEP surface functionasc_name
: label of the ASC surface function
-
double
pcmsolver_get_asc_dipole
(pcmsolver_context_t *context, const char *asc_name, double dipole[])¶ Getter for the ASC dipole.
- Return
- the ASC dipole, i.e. { ^2}
- Parameters
context
: the PCM context objectasc_name
: label of the ASC surface functiondipole
: the Cartesian components of the ASC dipole moment
-
void
pcmsolver_get_surface_function
(pcmsolver_context_t *context, int size, double values[], const char *name)¶ Retrieves data wrapped in a given surface function.
- Parameters
context
: the PCM context objectsize
: the size of the surface functionvalues
: the values wrapped in the surface functionname
: label of the surface function
-
void
pcmsolver_set_surface_function
(pcmsolver_context_t *context, int size, double values[], const char *name)¶ Sets a surface function given data and label.
- Parameters
context
: the PCM context objectsize
: the size of the surface functionvalues
: the values to be wrapped in the surface functionname
: label of the surface function
-
void
pcmsolver_print_surface_function
(pcmsolver_context_t *context, const char *name)¶ Prints surface function contents to host output.
- Parameters
context
: the PCM context objectname
: label of the surface function
-
void
pcmsolver_save_surface_functions
(pcmsolver_context_t *context)¶ Dumps all currently saved surface functions to NumPy arrays in .npy files.
- Parameters
context
: the PCM context object
-
void
pcmsolver_save_surface_function
(pcmsolver_context_t *context, const char *name)¶ Dumps a surface function to NumPy array in .npy file.
- Note
- The name parameter is the name of the NumPy array file without .npy extension
- Parameters
context
: the PCM context objectname
: label of the surface function
-
void
pcmsolver_load_surface_function
(pcmsolver_context_t *context, const char *name)¶ Loads a surface function from a .npy file.
- Note
- The name parameter is the name of the NumPy array file without .npy extension
- Parameters
context
: the PCM context objectname
: label of the surface function
-
void
pcmsolver_write_timings
(pcmsolver_context_t *context)¶ Writes timing results for the API.
- Parameters
context
: the PCM context object
Host input forwarding¶
-
struct
PCMInput
¶ Data structure for host-API input communication.
Forward-declare PCMInput input wrapping struct
Public Members
-
char
cavity_type
[8]¶ Type of cavity requested.
-
int
patch_level
¶ Wavelet cavity mesh patch level.
-
double
coarsity
¶ Wavelet cavity mesh coarsity.
-
double
area
¶ Average tesserae area.
-
char
radii_set
[8]¶ The built-in radii set to be used.
-
double
min_distance
¶ Minimal distance between sampling points.
-
int
der_order
¶ Derivative order for the switching function.
-
pcmsolver_bool_t
scaling
¶ Whether to scale or not the atomic radii.
-
char
restart_name
[20]¶ Name of the .npz file for GePol cavity restart.
-
double
min_radius
¶ Minimal radius for the added spheres.
-
char
solver_type
[7]¶ Type of solver requested.
-
double
correction
¶ Correction in the CPCM apparent surface charge scaling factor.
-
char
solvent
[16]¶ Name of the solvent.
-
double
probe_radius
¶ Radius of the spherical probe mimicking the solvent.
-
char
equation_type
[11]¶ Type of the integral equation to be used.
-
char
inside_type
[7]¶ Type of Green’s function requested inside the cavity.
-
double
outside_epsilon
¶ Value of the static permittivity outside the cavity.
-
char
outside_type
[22]¶ Type of Green’s function requested outside the cavity.
-
char
Internal details of the API¶
-
class
pcm::
Meddle
¶ Contains functions exposing an interface to the module internals.
- Author
- Roberto Di Remigio
- Date
- 2015-2017
Public Functions
-
Meddle
(const Input &input, const HostWriter &writer)¶ CTOR from Input object.
- Warning
- This CTOR is meant to be used with the standalone executable only
- Parameters
input
: an Input objectwriter
: the global HostWriter object
-
Meddle
(const std::string &inputFileName, const HostWriter &writer)¶ CTOR from own input reader.
- Warning
- This CTOR is meant to be used with the standalone executable only
- Parameters
inputFileName
: name of the parsed, machine-readable input filewriter
: the global HostWriter object
-
Meddle
(int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], const HostWriter &writer, const std::string &inputFileName = "@pcmsolver.inp")¶ CTOR from parsed input file name.
- Parameters
inputFileName
: name of the parsed, machine-readable input filenr_nuclei
: number of atoms in the moleculecharges
: atomic chargescoordinates
: atomic coordinatessymmetry_info
: molecular point group informationwriter
: the global HostWriter object
-
Meddle
(int nr_nuclei, double charges[], double coordinates[], int symmetry_info[], const PCMInput &host_input, const HostWriter &writer)¶ Constructor.
The molecular point group information is passed as an array of 4 integers: number of generators, first, second and third generator respectively. Generators map to integers as in table :ref:
symmetry-ops
- Parameters
nr_nuclei
: number of atoms in the moleculecharges
: atomic chargescoordinates
: atomic coordinatessymmetry_info
: molecular point group informationhost_input
: input to the module, as read by the hostwriter
: the global HostWriter object
-
PCMSolverIndex
getCavitySize
() const¶ Getter for the number of finite elements composing the molecular cavity.
- Return
- the size of the cavity
-
PCMSolverIndex
getIrreducibleCavitySize
() const¶ Getter for the number of irreducible finite elements composing the molecular cavity.
- Return
- the number of irreducible finite elements
-
void
getCenters
(double centers[]) const¶ Getter for the centers of the finite elements composing the molecular cavity.
- Parameters
centers
: array holding the coordinates of the finite elements centers
-
void
getCenter
(int its, double center[]) const¶ Getter for the center of the i-th finite element.
- Parameters
its
: index of the finite elementcenter
: array holding the coordinates of the finite element center
-
Eigen::Matrix3Xd
getCenters
() const¶ Getter for the centers of the finite elements composing the molecular cavity.
- Return
- a matrix with the finite elements centers (dimensions 3 x number of finite elements)
-
void
getAreas
(double areas[]) const¶ Getter for the areas/weights of the finite elements.
- Parameters
areas
: array holding the weights/areas of the finite elements
-
void
computeASC
(const char *mep_name, const char *asc_name, int irrep) const¶ Computes ASC given a MEP and the desired irreducible representation.
- Parameters
mep_name
: label of the MEP surface functionasc_name
: label of the ASC surface functionirrep
: index of the desired irreducible representation The module uses the surface function concept to handle potentials and charges. Given labels for each, this function retrieves the MEP and computes the corresponding ASC.
-
void
computeResponseASC
(const char *mep_name, const char *asc_name, int irrep) const¶ Computes response ASC given a MEP and the desired irreducible representation.
- Parameters
mep_name
: label of the MEP surface functionasc_name
: label of the ASC surface functionirrep
: index of the desired irreducible representation IfNonequilibrium = True
in the input, calculates a response ASC using the dynamic permittivity. Falls back to the solver with static permittivity otherwise.
-
double
computePolarizationEnergy
(const char *mep_name, const char *asc_name) const¶ Computes the polarization energy.
- Return
- the polarization energy This function calculates the dot product of the given MEP and ASC vectors.
- Parameters
mep_name
: label of the MEP surface functionasc_name
: label of the ASC surface function
-
double
getASCDipole
(const char *asc_name, double dipole[]) const¶ Getter for the ASC dipole.
- Return
- the ASC dipole, i.e. { ^2}
- Parameters
asc_name
: label of the ASC surface functiondipole
: the Cartesian components of the ASC dipole moment
-
void
getSurfaceFunction
(PCMSolverIndex size, double values[], const char *name) const¶ Retrieves data wrapped in a given surface function.
- Parameters
size
: the size of the surface functionvalues
: the values wrapped in the surface functionname
: label of the surface function
-
void
setSurfaceFunction
(PCMSolverIndex size, double values[], const char *name) const¶ Sets a surface function given data and label.
- Parameters
size
: the size of the surface functionvalues
: the values to be wrapped in the surface functionname
: label of the surface function
-
void
printSurfaceFunction
(const char *name) const¶ Prints surface function contents to host output.
- Parameters
name
: label of the surface function
-
void
saveSurfaceFunctions
() const¶ Dumps all currently saved surface functions to NumPy arrays in .npy files.
-
void
saveSurfaceFunction
(const char *name) const¶ Dumps a surface function to NumPy array in .npy file.
- Note
- The name parameter is the name of the NumPy array file without .npy extension
- Parameters
name
: label of the surface function
-
void
loadSurfaceFunction
(const char *name) const¶ Loads a surface function from a .npy file.
- Note
- The name parameter is the name of the NumPy array file without .npy extension
- Parameters
name
: label of the surface function
-
void
printInfo
() const¶ Prints citation and set up information.
-
void
writeTimings
() const¶ Writes timing results for the API.
Private Functions
-
void
CTORBody
()¶ Common implemenation for the CTOR-s
-
void
initInput
(int nr_nuclei, double charges[], double coordinates[], int symmetry_info[])¶ Initialize input_.
- Parameters
nr_nuclei
: number of atoms in the moleculecharges
: atomic chargescoordinates
: atomic coordinatessymmetry_info
: molecular point group information
-
void
initCavity
()¶ Initialize cavity_
-
void
initStaticSolver
()¶ Initialize static solver K_0_
-
void
initDynamicSolver
()¶ Initialize dynamic solver K_d_
-
void
mediumInfo
(IGreensFunction *gf_i, IGreensFunction *gf_o) const¶ Collect info on medium
-
class
pcm::
Input
¶ A wrapper class for the Getkw Library C++ bindings.
An Input object is to be used as the unique point of access to user-provided input: input > parsed input (Python script) > Input object (contains all the input data) Definition of input parameters is to be done in the Python script and in this class. They must be specified as private data members with public accessor methods (get-ters). Most of the data members are anyway accessed through the input wrapping struct-s In general, no mutator methods (set-ters) should be needed, exceptions to this rule should be carefully considered.
- Author
- Roberto Di Remigio
- Date
- 2013
Public Functions
-
Input
()¶ Default constructor.
-
Input
(const std::string &filename)¶ Constructor from human-readable input file name.
-
std::string
units
() const¶ Accessor methods.
Top-level section input
-
bool
scaling
() const¶ Cavity section input.
-
Solvent
solvent
() const¶ Medium section input.
-
std::string
providedBy
() const¶ Keeps track of who did the parsing: the API or the host program.
-
CavityData
cavityParams
() const¶ Get-ters for input wrapping structs.
Private Functions
-
void
reader
(const PCMInput &host_input)¶ Read host data structures (host-side syntactic input parsing) into Input object. It provides access to a limited number of options only, basically the ones that can be filled into the cavityInput, solverInput and greenInput data structures. Lengths and areas are expected to be in Angstrom/Angstrom^2 and will hence be converted to au/au^2.
- Note
- Specification of the solvent by name overrides any input given through the greenInput data structure!
- Warning
- The cavity can only be built in the “Implicit” mode, i.e. by grabbing the coordinates for the sphere centers from the host program. Atomic coordinates are expected to be in au! The “Atoms” and “Explicit” methods are only available using the explicit parsing by our Python script of a separate input file.
-
void
semanticCheck
() const¶ Perform semantic input parsing aka sanity check
Private Members
-
std::string
units_
¶ Units of measure.
-
int
CODATAyear_
¶ Year of the CODATA set to be used.
-
std::string
cavityType_
¶ The type of cavity.
-
std::string
cavFilename_
¶ Filename for the .npz cavity restart file.
-
double
area_
¶ GePol cavity average element area.
-
bool
scaling_
¶ Whether the radii should be scaled by 1.2.
-
std::string
radiiSet_
¶ The set of radii to be used.
-
std::string
radiiSetName_
¶ Collects info on atomic radii set.
-
double
minimalRadius_
¶ Minimal radius of an added sphere.
-
std::string
mode_
¶ How the API should get the coordinates of the sphere centers.
-
std::vector<int>
atoms_
¶ List of selected atoms with custom radii.
-
std::vector<double>
radii_
¶ List of radii attached to the selected atoms.
-
std::vector<Sphere>
spheres_
¶ List of spheres for fully custom cavity generation.
-
Solvent
solvent_
¶ The solvent for a vacuum/uniform dielectric run.
-
bool
hasSolvent_
¶ Whether the medium was initialized from a solvent object.
-
std::string
solverType_
¶ The solver type.
-
double
correction_
¶ Correction factor (C-PCM)
-
bool
hermitivitize_
¶ Whether the PCM matrix should be hermitivitized (collocation solvers)
-
bool
isDynamic_
¶ Whether the dynamic PCM matrix should be used.
-
double
probeRadius_
¶ Solvent probe radius.
-
std::string
integratorType_
¶ Type of integrator for the diagonal of the boundary integral operators.
-
double
integratorScaling_
¶ Scaling factor for the diagonal of the approximate collocation boundary integral operators
-
std::string
greenInsideType_
¶ The Green’s function type inside the cavity. It encodes the Green’s function type, derivative calculation strategy and dielectric profile: TYPE_DERIVATIVE_PROFILE
-
std::string
greenOutsideType_
¶ The Green’s function type outside the cavity It encodes the Green’s function type, derivative calculation strategy and dielectric profile: TYPE_DERIVATIVE_PROFILE
-
double
epsilonInside_
¶ Permittivity inside the cavity.
-
double
epsilonStaticOutside_
¶ Static permittivity outside the cavity.
-
double
epsilonDynamicOutside_
¶ Dynamic permittivity outside the cavity.
-
double
epsilonReal_
¶ Real part of the metal NP permittivity.
-
double
epsilonImaginary_
¶ Imaginary part of the metal NP permittivity.
-
std::vector<double>
spherePosition_
¶ Center of the spherical metal NP.
-
double
sphereRadius_
¶ Radius of the spherical metal NP.
-
double
epsilonStatic1_
¶ Diffuse interface: static permittivity inside the interface.
-
double
epsilonDynamic1_
¶ Diffuse interface: dynamic permittivity inside the interface.
-
double
epsilonStatic2_
¶ Diffuse interface: static permittivity outside the interface.
-
double
epsilonDynamic2_
¶ Diffuse interface: dynamic permittivity outside the interface.
-
double
center_
¶ Center of the diffuse interface.
-
double
width_
¶ Width of the diffuse interface.
-
int
maxL_
¶ Maximum angular momentum.
-
std::vector<double>
origin_
¶ Center of the dielectric sphere.
-
std::vector<double>
geometry_
¶ Molecular geometry.
-
bool
MEPfromMolecule_
¶ Whether to calculate the MEP from the molecular geometry.
-
ChargeDistribution
multipoles_
¶ Classical charge distribution of point multipoles.
-
std::string
providedBy_
¶ Who performed the syntactic input parsing.
Friends
-
std::ostream &
operator<<
(std::ostream &os, const Input &input)¶ Operators operator<<