nnpotoptions.cpp File Reference

#include "gmxpre.h"
#include "nnpotoptions.h"
#include "gromacs/domdec/localatomset.h"
#include "gromacs/domdec/localatomsetmanager.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/imdpoptionprovider_helpers.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/optionsection.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/embedded_system_preprocessing.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/mpicomm.h"
#include "gromacs/utility/stringutil.h"
#include "nnpot.h"

Include dependency graph for nnpotoptions.cpp:

Description

Implements the options for NNPot MDModule class.

Author

Lukas Müllender lukas.nosp@m..mue.nosp@m.llend.nosp@m.er@g.nosp@m.mail..nosp@m.com

Functions
std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::moduleName ()
	Helper function to make a std::string containing the module name.
std::vector< LinkFrontierAtom >	gmx::anonymous_namespace{nnpotoptions.cpp}::preprocessNNPotTopology (gmx_mtop_t *mtop, ArrayRef< const Index > nnpIndices, const NNPotEmbedding &embedding, const real &nnpCharge, const MDLogger &logger, WarningHandler *wi)
	Helper function to preprocess topology for NNP. More...

Variables
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_activeTag_ = "active"
	Following Tags denote names of parameters from .mdp file. More...
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelFileNameTag_ = "modelfile"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_inputGroupTag_ = "input-group"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_linkTypeTag_ = "link-type"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_linkDistanceTag_ = "link-distance"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_pairCutoffTag_ = "pair-cutoff"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_nnpChargeTag_ = "nnp-charge"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_embeddingTag_ = "embedding"
const EnumerationArray < NNPotEmbedding, const char * >	gmx::anonymous_namespace{nnpotoptions.cpp}::c_embeddingSchemeNames
	The names of the supported embedding schemes. More...
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput1Tag_ = "model-input1"
	User defined input to NN model. More...
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput2Tag_ = "model-input2"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput3Tag_ = "model-input3"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput4Tag_ = "model-input4"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput5Tag_ = "model-input5"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput6Tag_ = "model-input6"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput7Tag_ = "model-input7"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput8Tag_ = "model-input8"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput9Tag_ = "model-input9"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_mmGroupTag_ = "mm-group"
	Following tags are needed to write parameters generated during preprocessing (grompp) to the .tpr file via KVT.
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_nnpLinkTag_ = "nnp-link"
const std::string	gmx::anonymous_namespace{nnpotoptions.cpp}::c_mmLinkTag_ = "mm-link"