Functions
std::string	moduleName ()
	Helper function to make a std::string containing the module name.

std::vector< LinkFrontierAtom >	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	c_activeTag_ = "active"
	Following Tags denote names of parameters from .mdp file. More...

const std::string	c_modelFileNameTag_ = "modelfile"

const std::string	c_inputGroupTag_ = "input-group"

const std::string	c_linkTypeTag_ = "link-type"

const std::string	c_linkDistanceTag_ = "link-distance"

const std::string	c_pairCutoffTag_ = "pair-cutoff"

const std::string	c_nnpChargeTag_ = "nnp-charge"

const std::string	c_embeddingTag_ = "embedding"

const EnumerationArray < NNPotEmbedding, const char * >	c_embeddingSchemeNames
	The names of the supported embedding schemes. More...

const std::string	c_modelInput1Tag_ = "model-input1"
	User defined input to NN model. More...

const std::string	c_modelInput2Tag_ = "model-input2"

const std::string	c_modelInput3Tag_ = "model-input3"

const std::string	c_modelInput4Tag_ = "model-input4"

const std::string	c_modelInput5Tag_ = "model-input5"

const std::string	c_modelInput6Tag_ = "model-input6"

const std::string	c_modelInput7Tag_ = "model-input7"

const std::string	c_modelInput8Tag_ = "model-input8"

const std::string	c_modelInput9Tag_ = "model-input9"


const std::string	c_mmGroupTag_ = "mm-group"
	Following tags are needed to write parameters generated during preprocessing (grompp) to the .tpr file via KVT.

const std::string	c_nnpLinkTag_ = "nnp-link"

const std::string	c_mmLinkTag_ = "mm-link"

Function Documentation

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.

This function performs the following modifications:

Variable Documentation

const std::string gmx::anonymous_namespace{nnpotoptions.cpp}::c_activeTag_ = "active"

Following Tags denote names of parameters from .mdp file.

const EnumerationArray<NNPotEmbedding, const char*> gmx::anonymous_namespace{nnpotoptions.cpp}::c_embeddingSchemeNames

Initial value:

= {
    { "mechanical", "electrostatic-model" }
}

The names of the supported embedding schemes.

const std::string gmx::anonymous_namespace{nnpotoptions.cpp}::c_modelInput1Tag_ = "model-input1"

User defined input to NN model.

Possible values: