Implemented lists instead of multidim arrays (0559e155) · Commits · 郑智淋 / lammps

src/SNAP/compute_sna_atom.cpp

+3 −4

Original line number	Diff line number	Diff line
		@@ -247,13 +247,12 @@ void ComputeSNAAtom::compute_peratom()
		snaptr->compute_ui(ninside);
		snaptr->compute_zi();
		snaptr->compute_bi();
		snaptr->copy_bi2bvec();
		for (int icoeff = 0; icoeff < ncoeff; icoeff++)
		sna[i][icoeff] = snaptr->bvec[icoeff];
		sna[i][icoeff] = snaptr->blist[icoeff];
		if (quadraticflag) {
		int ncount = ncoeff;
		for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
		double bi = snaptr->bvec[icoeff];
		double bi = snaptr->blist[icoeff];

		// diagonal element of quadratic matrix

		@@ -262,7 +261,7 @@ void ComputeSNAAtom::compute_peratom()
		// upper-triangular elements of quadratic matrix

		for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
		sna[i][ncount++] = bi*snaptr->bvec[jcoeff];
		sna[i][ncount++] = bi*snaptr->blist[jcoeff];
		}
		}
		} else {

src/SNAP/compute_snad_atom.cpp

+16 −18

Original line number	Diff line number	Diff line
		@@ -266,7 +266,6 @@ void ComputeSNADAtom::compute_peratom()
		snaptr->compute_zi();
		if (quadraticflag) {
		snaptr->compute_bi();
		snaptr->copy_bi2bvec();
		}

		for (int jj = 0; jj < ninside; jj++) {
		@@ -275,7 +274,6 @@ void ComputeSNADAtom::compute_peratom()
		snaptr->wj[jj],
		snaptr->rcutij[jj]);
		snaptr->compute_dbidrj();
		snaptr->copy_dbi2dbvec();

		// Accumulate -dBi/dRi, -dBi/dRj

		@@ -283,12 +281,12 @@ void ComputeSNADAtom::compute_peratom()
		double *snadj = snad[j]+typeoffset;

		for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
		snadi[icoeff] += snaptr->dbvec[icoeff][0];
		snadi[icoeff+yoffset] += snaptr->dbvec[icoeff][1];
		snadi[icoeff+zoffset] += snaptr->dbvec[icoeff][2];
		snadj[icoeff] -= snaptr->dbvec[icoeff][0];
		snadj[icoeff+yoffset] -= snaptr->dbvec[icoeff][1];
		snadj[icoeff+zoffset] -= snaptr->dbvec[icoeff][2];
		snadi[icoeff] += snaptr->dblist[icoeff][0];
		snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
		snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
		snadj[icoeff] -= snaptr->dblist[icoeff][0];
		snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
		snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
		}

		if (quadraticflag) {
		@@ -297,10 +295,10 @@ void ComputeSNADAtom::compute_peratom()
		snadj += quadraticoffset;
		int ncount = 0;
		for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
		double bi = snaptr->bvec[icoeff];
		double bix = snaptr->dbvec[icoeff][0];
		double biy = snaptr->dbvec[icoeff][1];
		double biz = snaptr->dbvec[icoeff][2];
		double bi = snaptr->blist[icoeff];
		double bix = snaptr->dblist[icoeff][0];
		double biy = snaptr->dblist[icoeff][1];
		double biz = snaptr->dblist[icoeff][2];

		// diagonal elements of quadratic matrix

		@@ -319,12 +317,12 @@ void ComputeSNADAtom::compute_peratom()
		// upper-triangular elements of quadratic matrix

		for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
		double dbxtmp = bi*snaptr->dbvec[jcoeff][0]
		+ bix*snaptr->bvec[jcoeff];
		double dbytmp = bi*snaptr->dbvec[jcoeff][1]
		+ biy*snaptr->bvec[jcoeff];
		double dbztmp = bi*snaptr->dbvec[jcoeff][2]
		+ biz*snaptr->bvec[jcoeff];
		double dbxtmp = bi*snaptr->dblist[jcoeff][0]
		+ bix*snaptr->blist[jcoeff];
		double dbytmp = bi*snaptr->dblist[jcoeff][1]
		+ biy*snaptr->blist[jcoeff];
		double dbztmp = bi*snaptr->dblist[jcoeff][2]
		+ biz*snaptr->blist[jcoeff];

		snadi[ncount] += dbxtmp;
		snadi[ncount+yoffset] += dbytmp;

src/SNAP/compute_snav_atom.cpp

+22 −24

Original line number	Diff line number	Diff line
		@@ -260,7 +260,6 @@ void ComputeSNAVAtom::compute_peratom()
		snaptr->compute_zi();
		if (quadraticflag) {
		snaptr->compute_bi();
		snaptr->copy_bi2bvec();
		}

		for (int jj = 0; jj < ninside; jj++) {
		@@ -270,7 +269,6 @@ void ComputeSNAVAtom::compute_peratom()
		snaptr->wj[jj],
		snaptr->rcutij[jj]);
		snaptr->compute_dbidrj();
		snaptr->copy_dbi2dbvec();

		// Accumulate -dBi/dRiRi, -dBi/dRjRj

		@@ -278,18 +276,18 @@ void ComputeSNAVAtom::compute_peratom()
		double *snavj = snav[j]+typeoffset;

		for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
		snavi[icoeff] += snaptr->dbvec[icoeff][0]*xtmp;
		snavi[icoeff+nperdim] += snaptr->dbvec[icoeff][1]*ytmp;
		snavi[icoeff+2nperdim] += snaptr->dbvec[icoeff][2]ztmp;
		snavi[icoeff+3nperdim] += snaptr->dbvec[icoeff][1]ztmp;
		snavi[icoeff+4nperdim] += snaptr->dbvec[icoeff][0]ztmp;
		snavi[icoeff+5nperdim] += snaptr->dbvec[icoeff][0]ytmp;
		snavj[icoeff] -= snaptr->dbvec[icoeff][0]*x[j][0];
		snavj[icoeff+nperdim] -= snaptr->dbvec[icoeff][1]*x[j][1];
		snavj[icoeff+2nperdim] -= snaptr->dbvec[icoeff][2]x[j][2];
		snavj[icoeff+3nperdim] -= snaptr->dbvec[icoeff][1]x[j][2];
		snavj[icoeff+4nperdim] -= snaptr->dbvec[icoeff][0]x[j][2];
		snavj[icoeff+5nperdim] -= snaptr->dbvec[icoeff][0]x[j][1];
		snavi[icoeff] += snaptr->dblist[icoeff][0]*xtmp;
		snavi[icoeff+nperdim] += snaptr->dblist[icoeff][1]*ytmp;
		snavi[icoeff+2nperdim] += snaptr->dblist[icoeff][2]ztmp;
		snavi[icoeff+3nperdim] += snaptr->dblist[icoeff][1]ztmp;
		snavi[icoeff+4nperdim] += snaptr->dblist[icoeff][0]ztmp;
		snavi[icoeff+5nperdim] += snaptr->dblist[icoeff][0]ytmp;
		snavj[icoeff] -= snaptr->dblist[icoeff][0]*x[j][0];
		snavj[icoeff+nperdim] -= snaptr->dblist[icoeff][1]*x[j][1];
		snavj[icoeff+2nperdim] -= snaptr->dblist[icoeff][2]x[j][2];
		snavj[icoeff+3nperdim] -= snaptr->dblist[icoeff][1]x[j][2];
		snavj[icoeff+4nperdim] -= snaptr->dblist[icoeff][0]x[j][2];
		snavj[icoeff+5nperdim] -= snaptr->dblist[icoeff][0]x[j][1];
		}

		if (quadraticflag) {
		@@ -298,10 +296,10 @@ void ComputeSNAVAtom::compute_peratom()
		snavj += quadraticoffset;
		int ncount = 0;
		for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
		double bi = snaptr->bvec[icoeff];
		double bix = snaptr->dbvec[icoeff][0];
		double biy = snaptr->dbvec[icoeff][1];
		double biz = snaptr->dbvec[icoeff][2];
		double bi = snaptr->blist[icoeff];
		double bix = snaptr->dblist[icoeff][0];
		double biy = snaptr->dblist[icoeff][1];
		double biz = snaptr->dblist[icoeff][2];

		// diagonal element of quadratic matrix

		@@ -325,12 +323,12 @@ void ComputeSNAVAtom::compute_peratom()
		// upper-triangular elements of quadratic matrix

		for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
		double dbxtmp = bi*snaptr->dbvec[jcoeff][0]
		+ bix*snaptr->bvec[jcoeff];
		double dbytmp = bi*snaptr->dbvec[jcoeff][1]
		+ biy*snaptr->bvec[jcoeff];
		double dbztmp = bi*snaptr->dbvec[jcoeff][2]
		+ biz*snaptr->bvec[jcoeff];
		double dbxtmp = bi*snaptr->dblist[jcoeff][0]
		+ bix*snaptr->blist[jcoeff];
		double dbytmp = bi*snaptr->dblist[jcoeff][1]
		+ biy*snaptr->blist[jcoeff];
		double dbztmp = bi*snaptr->dblist[jcoeff][2]
		+ biz*snaptr->blist[jcoeff];
		snavi[ncount] += dbxtmp*xtmp;
		snavi[ncount+nperdim] += dbytmp*ytmp;
		snavi[ncount+2nperdim] += dbztmpztmp;

src/SNAP/pair_snap.cpp

+2 −6

Original line number	Diff line number	Diff line
		@@ -166,17 +166,14 @@ void PairSNAP::compute(int eflag, int vflag)
		}
		}

		// compute Ui, Zi, and Bi for atom I
		// compute Ui, Yi for atom I

		snaptr->compute_ui(ninside);
		snaptr->compute_zi();

		// for neighbors of I within cutoff:
		// compute Fij = dEi/dRj = -dEi/dRi
		// add to Fi, subtract from Fj

		// compute beta_i*Z_i = Y_i

		snaptr->compute_yi(beta[ii]);

		for (int jj = 0; jj < ninside; jj++) {
		@@ -310,10 +307,9 @@ void PairSNAP::compute_bispectrum()
		snaptr->compute_ui(ninside);
		snaptr->compute_zi();
		snaptr->compute_bi();
		snaptr->copy_bi2bvec();

		for (int k = 0; k < ncoeff; k++)
		bispectrum[ii][k] = snaptr->bvec[k];
		bispectrum[ii][k] = snaptr->blist[k];
		}
		}

src/SNAP/sna.cpp

+525 −647

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