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gmx::DensityFittingOptions Class Referencefinal

#include <gromacs/applied_forces/densityfittingoptions.h>

+ Inheritance diagram for gmx::DensityFittingOptions:
+ Collaboration diagram for gmx::DensityFittingOptions:


Input data storage for density fitting.

Public Member Functions

void initMdpTransform (IKeyValueTreeTransformRules *rules) override
 From IMdpOptionProvider.
void buildMdpOutput (KeyValueTreeObjectBuilder *builder) const override
 Build mdp parameters for density fitting to be output after pre-processing. More...
void initMdpOptions (IOptionsContainerWithSections *options) override
 Connect option name and data.
bool active () const
 Report if this set of options is active.
const DensityFittingParametersbuildParameters ()
 Process input options to parameters, including input file reading.
void setFitGroupIndices (const IndexGroupsAndNames &indexGroupsAndNames)
 Evaluate and store atom indices. More...
void writeInternalParametersToKvt (KeyValueTreeObjectBuilder treeBuilder)
 Store the paramers that are not mdp options in the tpr file.
void readInternalParametersFromKvt (const KeyValueTreeObject &tree)
 Set the internal parameters that are stored in the tpr file.
const std::string & referenceDensityFileName () const
 Return the file name of the reference density.
void checkEnergyCaluclationFrequency (EnergyCalculationFrequencyErrors *energyCalculationFrequencyErrors) const
 Check if input parameters are consistent with other simulation parameters.

Member Function Documentation

void gmx::DensityFittingOptions::buildMdpOutput ( KeyValueTreeObjectBuilder builder) const

Build mdp parameters for density fitting to be output after pre-processing.

[in,out]builderthe builder for the mdp options output KV-tree.
This should be symmetrical to option initialization without employing manual prefixing with the section name string once the legacy code blocking this design is removed.

Implements gmx::IMdpOptionProvider.

void gmx::DensityFittingOptions::setFitGroupIndices ( const IndexGroupsAndNames indexGroupsAndNames)

Evaluate and store atom indices.

During pre-processing, use the group string from the options to evaluate the indices of the atoms to be subject to forces from this module.

The documentation for this class was generated from the following files: