Correctly reproduced examples/in.snap.compute, not yet for quadratic case (bc365117) · Commits · 郑智淋 / lammps

src/MLIAP/compute_mliap.cpp

+4 −8

Original line number	Diff line number	Diff line
		@@ -93,8 +93,8 @@ ComputeMLIAP::ComputeMLIAP(LAMMPS lmp, int narg, char *arg) :
		nperdim = nparams;
		ndims_force = 3;
		ndims_virial = 6;
		yoffset = nperdim;
		zoffset = 2*nperdim;
		yoffset = nperdim*atom->ntypes;
		zoffset = 2*yoffset;
		natoms = atom->natoms;
		size_array_rows = 1+ndims_force*natoms+ndims_virial;
		size_array_cols = nperdim*atom->ntypes+1;
		@@ -169,14 +169,12 @@ void ComputeMLIAP::init()

		// allocate memory for global array

		printf("size_array_rows = %d size_array_cols = %d\n",size_array_rows,size_array_cols);
		memory->create(mliap,size_array_rows,size_array_cols,
		"mliap:mliap");
		memory->create(mliapall,size_array_rows,size_array_cols,
		"mliap:mliapall");
		array = mliapall;

		printf("nelements = %d nparams = %d\n",nelements,nparams);
		memory->create(egradient,nelements*nparams,"ComputeMLIAP:egradient");

		// find compute for reference energy
		@@ -227,7 +225,6 @@ void ComputeMLIAP::compute_array()
		if (atom->nmax > nmax) {
		memory->destroy(mliap_peratom);
		nmax = atom->nmax;
		printf("nmax = %d size_peratom = %d\n",nmax,size_peratom);
		memory->create(mliap_peratom,nmax,size_peratom,
		"mliap:mliap_peratom");
		}
		@@ -256,7 +253,6 @@ void ComputeMLIAP::compute_array()
		memory->grow(gamma,list->inum,gamma_nnz,"ComputeMLIAP:gamma");
		gamma_max = list->inum;
		}
		printf("gamma_max %d %d %d %d %d %d %p\n",gamma_max, ndescriptors, gamma_nnz, nelements, nparams, list->inum, list);

		// compute descriptors, if needed

		@@ -283,7 +279,7 @@ void ComputeMLIAP::compute_array()
		// accumulate descriptor gradient contributions to global array

		for (int itype = 0; itype < atom->ntypes; itype++) {
		const int typeoffset_local = ndims_peratomnperdimitype;
		const int typeoffset_local = nperdim*itype;
		const int typeoffset_global = nperdim*itype;
		for (int icoeff = 0; icoeff < nperdim; icoeff++) {
		int irow = 1;
		@@ -360,7 +356,7 @@ void ComputeMLIAP::dbdotr_compute()
		int nall = atom->nlocal + atom->nghost;
		for (int i = 0; i < nall; i++)
		for (int itype = 0; itype < atom->ntypes; itype++) {
		const int typeoffset_local = ndims_peratomnperdimitype;
		const int typeoffset_local = nperdim*itype;
		const int typeoffset_global = nperdim*itype;
		double *snadi = mliap_peratom[i]+typeoffset_local;
		for (int icoeff = 0; icoeff < nperdim; icoeff++) {

src/MLIAP/mliap_descriptor_snap.cpp

+16 −19

Original line number	Diff line number	Diff line
		@@ -228,9 +228,6 @@ void MLIAPDescriptorSNAP::backward(PairMLIAP* pairmliap, NeighList* list, double
		// add to Fi, subtract from Fj

		snaptr->compute_yi(beta[ii]);
		//for (int q=0; q<snaptr->idxu_max*2; q++){
		// fprintf(screen, "%i %f\n",q, snaptr->ylist_r[q]);
		//}

		for (int jj = 0; jj < ninside; jj++) {
		int j = snaptr->inside[jj];
		@@ -294,11 +291,11 @@ void MLIAPDescriptorSNAP::param_backward(int map, NeighList list,
		const double ytmp = x[i][1];
		const double ztmp = x[i][2];
		const int itype = type[i];
		int ielem = 0;
		if (chemflag)
		int ielem = itype-1;
		// element map not yet implemented
		// if (chemflag)
		// element map not yet implemented
		// ielem = map[itype];
		const int ielem = itype-1;

		jlist = firstneigh[i];
		jnum = numneigh[i];
		@@ -322,14 +319,17 @@ void MLIAPDescriptorSNAP::param_backward(int map, NeighList list,
		delz = x[j][2] - ztmp;
		rsq = delxdelx + delydely + delz*delz;
		int jtype = type[j];
		int jelem = jtype-1;
		// element map not yet implemented
		// int jelem = map[jtype];
		const int jelem = jtype-1;
		// if (chemflag)
		// jelem = map[jtype];

		if (rsq < cutsq[ielem][jelem]) {
		snaptr->rij[ninside][0] = delx;
		snaptr->rij[ninside][1] = dely;
		snaptr->rij[ninside][2] = delz;
		snaptr->inside[ninside] = j;
		// element map not yet implemented
		snaptr->wj[ninside] = wjelem[jelem];
		snaptr->rcutij[ninside] = sqrt(cutsq[ielem][jelem]);
		snaptr->element[ninside] = jelem; // element index for chem snap
		@@ -342,7 +342,6 @@ void MLIAPDescriptorSNAP::param_backward(int map, NeighList list,
		else
		snaptr->compute_ui(ninside, 0);


		snaptr->compute_zi();
		if (chemflag)
		snaptr->compute_bi(ielem);
		@@ -541,11 +540,9 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
		cut = 2.0radelem[ielem]rcutfac;
		if (cut > cutmax) cutmax = cut;
		cutsq[ielem][ielem] = cut*cut;
		printf("ielem = %d ielem = %d cutsq[i][i] = %g\n",ielem, ielem, cutsq[ielem][ielem]);
		for(int jelem = ielem+1; jelem < nelements; jelem++) {
		cut = (radelem[ielem]+radelem[jelem])*rcutfac;
		cutsq[ielem][jelem] = cutsq[jelem][ielem] = cut*cut;
		printf("ielem = %d jelem = %d cutsq[i][j] = %g\n",ielem, jelem, cutsq[ielem][jelem]);
		}
		}
		}

src/thermo.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -315,6 +315,7 @@ void Thermo::header()

		std::string hdr;
		for (int i = 0; i < nfield; i++) hdr += keyword[i] + std::string(" ");
		hdr += "\n";
		if (me == 0) utils::logmesg(lmp,hdr);
		}

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