update angle.h and angle.cpp to compute per-atom centroid virial according to vflag=8 (239edc34) · Commits · 郑智淋 / lammps

src/angle.cpp

+100 −3

Original line number	Diff line number	Diff line
		@@ -34,9 +34,10 @@ Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
		allocated = 0;
		suffix_flag = Suffix::NONE;

		maxeatom = maxvatom = 0;
		maxeatom = maxvatom = maxcvatom = 0;
		eatom = NULL;
		vatom = NULL;
		cvatom = NULL;
		setflag = NULL;

		execution_space = Host;
		@@ -54,6 +55,7 @@ Angle::~Angle()

		memory->destroy(eatom);
		memory->destroy(vatom);
		memory->destroy(cvatom);
		}

		/* ----------------------------------------------------------------------
		@@ -85,9 +87,10 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
		eflag_global = eflag % 2;
		eflag_atom = eflag / 2;

		vflag_either = vflag;
		vflag_global = vflag % 4;
		vflag_atom = vflag / 4;
		vflag_atom = vflag & 4;
		cvflag_atom = vflag & 8;
		vflag_either = vflag_global \|\| vflag_atom;

		// reallocate per-atom arrays if necessary

		@@ -105,6 +108,13 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
		memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom");
		}
		}
		if (cvflag_atom && atom->nmax > maxcvatom) {
		maxcvatom = atom->nmax;
		if (alloc) {
		memory->destroy(cvatom);
		memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom");
		}
		}

		// zero accumulators

		@@ -127,6 +137,22 @@ void Angle::ev_setup(int eflag, int vflag, int alloc)
		vatom[i][5] = 0.0;
		}
		}
		if (cvflag_atom && alloc) {
		n = atom->nlocal;
		if (force->newton_bond) n += atom->nghost;
		for (i = 0; i < n; i++) {
		cvatom[i][0] = 0.0;
		cvatom[i][1] = 0.0;
		cvatom[i][2] = 0.0;
		cvatom[i][3] = 0.0;
		cvatom[i][4] = 0.0;
		cvatom[i][5] = 0.0;
		cvatom[i][6] = 0.0;
		cvatom[i][7] = 0.0;
		cvatom[i][8] = 0.0;
		cvatom[i][9] = 0.0;
		}
		}
		}

		/* ----------------------------------------------------------------------
		@@ -230,6 +256,76 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
		}
		}
		}

		// per-atom centroid virial
		if (cvflag_atom) {

		// r0 = (r1+r2+r3)/3
		// rij = ri-rj
		// total virial = r10f1 + r20f2 + r30*f3
		// del1: r12
		// del2: r32

		if (newton_bond \|\| i < nlocal) {
		double a1[3];

		// a1 = r10 = (2*r12 - r32)/3
		a1[0] = THIRD(2delx1-delx2);
		a1[1] = THIRD(2dely1-dely2);
		a1[2] = THIRD(2delz1-delz2);

		cvatom[i][0] += a1[0]*f1[0];
		cvatom[i][1] += a1[1]*f1[1];
		cvatom[i][2] += a1[2]*f1[2];
		cvatom[i][3] += a1[0]*f1[1];
		cvatom[i][4] += a1[0]*f1[2];
		cvatom[i][5] += a1[1]*f1[2];
		cvatom[i][6] += a1[1]*f1[0];
		cvatom[i][7] += a1[2]*f1[0];
		cvatom[i][8] += a1[2]*f1[1];
		}
		if (newton_bond \|\| j < nlocal) {
		double a2[3];
		double f2[3];

		// a2 = r20 = ( -r12 - r32)/3
		a2[0] = THIRD*(-delx1-delx2);
		a2[1] = THIRD*(-dely1-dely2);
		a2[2] = THIRD*(-delz1-delz2);

		f2[0] = - f1[0] - f3[0];
		f2[1] = - f1[1] - f3[1];
		f2[2] = - f1[2] - f3[2];

		cvatom[j][0] += a2[0]*f2[0];
		cvatom[j][1] += a2[1]*f2[1];
		cvatom[j][2] += a2[2]*f2[2];
		cvatom[j][3] += a2[0]*f2[1];
		cvatom[j][4] += a2[0]*f2[2];
		cvatom[j][5] += a2[1]*f2[2];
		cvatom[j][6] += a2[1]*f2[0];
		cvatom[j][7] += a2[2]*f2[0];
		cvatom[j][8] += a2[2]*f2[1];
		}
		if (newton_bond \|\| k < nlocal) {
		double a3[3];

		// a3 = r30 = ( -r12 + 2*r32)/3
		a3[0] = THIRD(-delx1+2delx2);
		a3[1] = THIRD(-dely1+2dely2);
		a3[2] = THIRD(-delz1+2delz2);

		cvatom[k][0] += a3[0]*f3[0];
		cvatom[k][1] += a3[1]*f3[1];
		cvatom[k][2] += a3[2]*f3[2];
		cvatom[k][3] += a3[0]*f3[1];
		cvatom[k][4] += a3[0]*f3[2];
		cvatom[k][5] += a3[1]*f3[2];
		cvatom[k][6] += a3[1]*f3[0];
		cvatom[k][7] += a3[2]*f3[0];
		cvatom[k][8] += a3[2]*f3[1];
		}
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -238,5 +334,6 @@ double Angle::memory_usage()
		{
		double bytes = comm->nthreadsmaxeatom sizeof(double);
		bytes += comm->nthreadsmaxvatom6 * sizeof(double);
		bytes += comm->nthreadsmaxcvatom9 * sizeof(double);
		return bytes;
		}

src/angle.h

+4 −3

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@ class Angle : protected Pointers {
		double energy; // accumulated energies
		double virial[6]; // accumulated virial
		double eatom,*vatom; // accumulated per-atom energy/virial
		double **cvatom; // accumulated per-atom centroid virial

		// KOKKOS host/device flag and data masks

		@@ -56,12 +57,12 @@ class Angle : protected Pointers {

		int evflag;
		int eflag_either,eflag_global,eflag_atom;
		int vflag_either,vflag_global,vflag_atom;
		int maxeatom,maxvatom;
		int vflag_either,vflag_global,vflag_atom,cvflag_atom;
		int maxeatom,maxvatom,maxcvatom;

		void ev_init(int eflag, int vflag, int alloc = 1) {
		if (eflag\|\|vflag) ev_setup(eflag, vflag, alloc);
		else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0;
		else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = cvflag_atom = 0;
		}
		void ev_setup(int, int, int alloc = 1);
		void ev_tally(int, int, int, int, int, double, double , double ,

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