Created MLIAP class for data, passes all tests (6c08503d) · Commits · 郑智淋 / lammps

src/MLIAP/compute_mliap.cpp

+10 −10

Original line number	Diff line number	Diff line
		@@ -312,9 +312,9 @@ void ComputeMLIAP::compute_array()
		for (int i = 0; i < atom->nlocal; i++) {
		int iglobal = atom->tag[i];
		int irow = 3*(iglobal-1)+1;
		mliaparray[irow][mliap->lastcol] = atom->f[i][0];
		mliaparray[irow+1][mliap->lastcol] = atom->f[i][1];
		mliaparray[irow+2][mliap->lastcol] = atom->f[i][2];
		mliaparray[irow][lastcol] = atom->f[i][0];
		mliaparray[irow+1][lastcol] = atom->f[i][1];
		mliaparray[irow+2][lastcol] = atom->f[i][2];
		}

		// accumulate bispectrum virial contributions to global array
		@@ -337,19 +337,19 @@ void ComputeMLIAP::compute_array()

		int irow = 0;
		double reference_energy = c_pe->compute_scalar();
		mliaparrayall[irow++][mliap->lastcol] = reference_energy;
		mliaparrayall[irow++][lastcol] = reference_energy;

		// copy virial stress to last column
		// switch to Voigt notation

		c_virial->compute_vector();
		irow += 3*mliap->natoms;
		mliaparrayall[irow++][mliap->lastcol] = c_virial->vector[0];
		mliaparrayall[irow++][mliap->lastcol] = c_virial->vector[1];
		mliaparrayall[irow++][mliap->lastcol] = c_virial->vector[2];
		mliaparrayall[irow++][mliap->lastcol] = c_virial->vector[5];
		mliaparrayall[irow++][mliap->lastcol] = c_virial->vector[4];
		mliaparrayall[irow++][mliap->lastcol] = c_virial->vector[3];
		mliaparrayall[irow++][lastcol] = c_virial->vector[0];
		mliaparrayall[irow++][lastcol] = c_virial->vector[1];
		mliaparrayall[irow++][lastcol] = c_virial->vector[2];
		mliaparrayall[irow++][lastcol] = c_virial->vector[5];
		mliaparrayall[irow++][lastcol] = c_virial->vector[4];
		mliaparrayall[irow++][lastcol] = c_virial->vector[3];

		}

src/MLIAP/mliap.cpp

+5 −2

Original line number	Diff line number	Diff line
		@@ -33,7 +33,7 @@
		using namespace LAMMPS_NS;

		MLIAP::MLIAP(LAMMPS *lmp, int ndescriptors_in, int nparams_in, int nelements_in,
		int gradgradflag_in, int map_in, class MLIAPModel, class MLIAPDescriptor*) :
		int gradgradflag_in, int map_in, class MLIAPModel model_in, class MLIAPDescriptor* descriptor_in) :
		Pointers(lmp),
		list(NULL),
		gradforce(NULL),
		@@ -47,6 +47,8 @@ MLIAP::MLIAP(LAMMPS *lmp, int ndescriptors_in, int nparams_in, int nelements_in,
		nelements = nelements_in;
		gradgradflag = gradgradflag_in;
		map = map_in;
		model = model_in;
		descriptor = descriptor_in;

		gamma_nnz = model->get_gamma_nnz();
		ndims_force = 3;
		@@ -54,7 +56,8 @@ MLIAP::MLIAP(LAMMPS *lmp, int ndescriptors_in, int nparams_in, int nelements_in,
		yoffset = nparams*nelements;
		zoffset = 2*yoffset;
		natoms = atom->natoms;

		size_array_rows = 1+ndims_force*natoms+ndims_virial;
		size_array_cols = nparams*nelements+1;
		size_gradforce = ndims_forcenparamsnelements;

		natomdesc_max = 0;

src/MLIAP/mliap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -31,7 +31,7 @@ class MLIAP : protected Pointers {

		// private:
		int size_array_rows, size_array_cols;
		int natoms, size_gradforce, lastcol;
		int natoms, size_gradforce;
		int yoffset, zoffset;
		int ndims_force, ndims_virial;
		class NeighList *list;

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