(cc44a572) · Commits · 郑智淋 / lammps

src/GRANULAR/atom_vec_granular.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -460,7 +460,7 @@ int AtomVecGranular::size_restart()
		int i;

		int nlocal = atom->nlocal;
		int n = 19 * nlocal;
		int n = 16 * nlocal;

		if (atom->nextra_restart)
		for (int iextra = 0; iextra < atom->nextra_restart; iextra++)

src/PERI/atom_vec_peri.cpp

+46 −49

Original line number	Diff line number	Diff line
		@@ -37,13 +37,12 @@ AtomVec(lmp, narg, arg)
		comm_x_only = 0;
		size_comm = 4;
		size_reverse = 3;
		size_border = 13;
		size_border = 11;
		size_data_atom = 7;
		size_data_vel = 4;
		xcol_data = 3;
		xcol_data = 5;

		atom->rmass_flag = atom->vfrac_flag = atom->s0_flag = 1;
		atom->vinter_flag = 1;
		atom->vfrac_flag = atom->density_flag = atom->rmass_flag = 1;
		}

		/* ----------------------------------------------------------------------
		@@ -72,13 +71,13 @@ void AtomVecPeri::grow(int n)

		vfrac = atom->vfrac = (double *)
		memory->srealloc(atom->vfrac,nmax*sizeof(double),"atom:vfrac");
		density = atom->density = (double *)
		memory->srealloc(atom->density,nmax*sizeof(double),"atom:density");
		rmass = atom->rmass = (double *)
		memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");
		s0 = atom->s0 = (double *)
		memory->srealloc(atom->s0,nmax*sizeof(double),"atom:s0");
		x0 = atom->x0 = memory->grow_2d_double_array(atom->x0,nmax,3,"atom:x0");
		vinter = atom->vinter = (double *)
		memory->srealloc(atom->vinter,nmax*sizeof(double),"atom:vinter");

		if (atom->nextra_grow)
		for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
		@@ -101,12 +100,12 @@ void AtomVecPeri::copy(int i, int j)
		v[j][2] = v[i][2];

		vfrac[j] = vfrac[i];
		density[j] = density[i];
		rmass[j] = rmass[i];
		s0[j] = s0[i];
		x0[j][0] = x0[i][0];
		x0[j][1] = x0[i][1];
		x0[j][2] = x0[i][2];
		vinter[j] = vinter[i];

		if (atom->nextra_grow)
		for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
		@@ -234,12 +233,10 @@ int AtomVecPeri::pack_border(int n, int list, double buf,
		buf[m++] = type[j];
		buf[m++] = mask[j];
		buf[m++] = vfrac[j];
		buf[m++] = rmass[j];
		buf[m++] = s0[j];
		buf[m++] = x0[j][0];
		buf[m++] = x0[j][1];
		buf[m++] = x0[j][2];
		buf[m++] = vinter[j];
		}
		} else {
		if (domain->triclinic == 0) {
		@@ -260,12 +257,10 @@ int AtomVecPeri::pack_border(int n, int list, double buf,
		buf[m++] = type[j];
		buf[m++] = mask[j];
		buf[m++] = vfrac[j];
		buf[m++] = rmass[j];
		buf[m++] = s0[j];
		buf[m++] = x0[j][0];
		buf[m++] = x0[j][1];
		buf[m++] = x0[j][2];
		buf[m++] = vinter[j];
		}
		}
		return m;
		@@ -276,13 +271,11 @@ int AtomVecPeri::pack_border(int n, int list, double buf,
		int AtomVecPeri::pack_border_one(int i, double *buf)
		{
		buf[0] = vfrac[i];
		buf[1] = rmass[i];
		buf[2] = s0[i];
		buf[3] = x0[i][0];
		buf[4] = x0[i][1];
		buf[5] = x0[i][2];
		buf[6] = vinter[i];
		return 7;
		buf[1] = s0[i];
		buf[2] = x0[i][0];
		buf[3] = x0[i][1];
		buf[4] = x0[i][2];
		return 5;
		}

		/* ---------------------------------------------------------------------- */
		@@ -302,12 +295,10 @@ void AtomVecPeri::unpack_border(int n, int first, double *buf)
		type[i] = static_cast<int> (buf[m++]);
		mask[i] = static_cast<int> (buf[m++]);
		vfrac[i] = buf[m++];
		rmass[i] = buf[m++];
		s0[i] = buf[m++];
		x0[i][0] = buf[m++];
		x0[i][1] = buf[m++];
		x0[i][2] = buf[m++];
		vinter[i] = buf[m++];
		}
		}

		@@ -316,13 +307,11 @@ void AtomVecPeri::unpack_border(int n, int first, double *buf)
		int AtomVecPeri::unpack_border_one(int i, double *buf)
		{
		vfrac[i] = buf[0];
		rmass[i] = buf[1];
		s0[i] = buf[2];
		x0[i][0] = buf[3];
		x0[i][1] = buf[4];
		x0[i][2] = buf[5];
		vinter[i]= buf[6];
		return 7;
		s0[i] = buf[1];
		x0[i][0] = buf[2];
		x0[i][1] = buf[3];
		x0[i][2] = buf[4];
		return 5;
		}

		/* ----------------------------------------------------------------------
		@@ -345,12 +334,12 @@ int AtomVecPeri::pack_exchange(int i, double *buf)
		buf[m++] = image[i];

		buf[m++] = vfrac[i];
		buf[m++] = density[i];
		buf[m++] = rmass[i];
		buf[m++] = s0[i];
		buf[m++] = x0[i][0];
		buf[m++] = x0[i][1];
		buf[m++] = x0[i][2];
		buf[m++] = vinter[i];

		if (atom->nextra_grow)
		for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
		@@ -380,12 +369,12 @@ int AtomVecPeri::unpack_exchange(double *buf)
		image[nlocal] = static_cast<int> (buf[m++]);

		vfrac[nlocal] = buf[m++];
		density[nlocal] = buf[m++];
		rmass[nlocal] = buf[m++];
		s0[nlocal] = buf[m++];
		x0[nlocal][0] = buf[m++];
		x0[nlocal][1] = buf[m++];
		x0[nlocal][2] = buf[m++];
		vinter[nlocal] = buf[m++];

		if (atom->nextra_grow)
		for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
		@@ -437,13 +426,13 @@ int AtomVecPeri::pack_restart(int i, double *buf)
		buf[m++] = v[i][1];
		buf[m++] = v[i][2];

		buf[m++] = rmass[i];
		buf[m++] = vfrac[i];
		buf[m++] = density[i];
		buf[m++] = rmass[i];
		buf[m++] = s0[i];
		buf[m++] = x0[i][0];
		buf[m++] = x0[i][1];
		buf[m++] = x0[i][2];
		buf[m++] = vinter[i];

		if (atom->nextra_restart)
		for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
		@@ -480,13 +469,13 @@ int AtomVecPeri::unpack_restart(double *buf)
		v[nlocal][1] = buf[m++];
		v[nlocal][2] = buf[m++];

		rmass[nlocal] = buf[m++];
		vfrac[nlocal] = buf[m++];
		density[nlocal] = buf[m++];
		rmass[nlocal] = buf[m++];
		s0[nlocal] = buf[m++];
		x0[nlocal][0] = buf[m++];
		x0[nlocal][1] = buf[m++];
		x0[nlocal][2] = buf[m++];
		vinter[nlocal] = buf[m++];

		double **extra = atom->extra;
		if (atom->nextra_store) {
		@@ -520,12 +509,12 @@ void AtomVecPeri::create_atom(int itype, double *coord)
		v[nlocal][2] = 0.0;

		vfrac[nlocal] = 1.0;
		rmass[nlocal] = 1.0;
		density[nlocal] = 1.0;
		rmass[nlocal] = density[nlocal];
		s0[nlocal] = MAXDOUBLE;
		x0[nlocal][0] = x[nlocal][0];
		x0[nlocal][1] = x[nlocal][1];
		x0[nlocal][2] = x[nlocal][2];
		vinter[nlocal] = 0.0;
		x0[nlocal][0] = coord[0];
		x0[nlocal][1] = coord[1];
		x0[nlocal][2] = coord[2];

		atom->nlocal++;
		}
		@@ -548,10 +537,9 @@ void AtomVecPeri::data_atom(double coord, int imagetmp, char *values)
		if (type[nlocal] <= 0 \|\| type[nlocal] > atom->ntypes)
		error->one("Invalid atom type in Atoms section of data file");

		vfrac[nlocal] = atof(values[5]);
		rmass[nlocal] = atof(values[6]);
		s0[nlocal] = MAXDOUBLE;
		vinter[nlocal] = 0.0;
		vfrac[nlocal] = atof(values[3]);
		density[nlocal] = atof(values[4]);
		rmass[nlocal] = density[nlocal];

		x[nlocal][0] = coord[0];
		x[nlocal][1] = coord[1];
		@@ -564,6 +552,11 @@ void AtomVecPeri::data_atom(double coord, int imagetmp, char *values)
		v[nlocal][1] = 0.0;
		v[nlocal][2] = 0.0;

		s0[nlocal] = MAXDOUBLE;
		x0[nlocal][0] = coord[0];
		x0[nlocal][1] = coord[1];
		x0[nlocal][2] = coord[2];

		atom->nlocal++;
		}

		@@ -576,14 +569,18 @@ void AtomVecPeri::data_atom(double coord, int imagetmp, char *values)
		int AtomVecPeri::data_atom_hybrid(int nlocal, char **values)
		{
		vfrac[nlocal] = atof(values[0]);
		rmass[nlocal] = atof(values[1]);
		density[nlocal] = atof(values[1]);
		rmass[nlocal] = density[nlocal];

		s0[nlocal] = MAXDOUBLE;
		vinter[nlocal] = 0.0;
		v[nlocal][0] = 0.0;
		v[nlocal][1] = 0.0;
		v[nlocal][2] = 0.0;

		s0[nlocal] = MAXDOUBLE;
		x0[nlocal][0] = x[nlocal][0];
		x0[nlocal][1] = x[nlocal][1];
		x0[nlocal][2] = x[nlocal][2];

		return 2;
		}

		@@ -604,10 +601,10 @@ double AtomVecPeri::memory_usage()
		if (atom->memcheck("f")) bytes += nmax3 sizeof(double);

		if (atom->memcheck("vfrac")) bytes += nmax * sizeof(double);
		if (atom->memcheck("density")) bytes += nmax * sizeof(double);
		if (atom->memcheck("rmass")) bytes += nmax * sizeof(double);
		if (atom->memcheck("s0")) bytes += nmax * sizeof(double);
		if (atom->memcheck("x0")) bytes += nmax3 sizeof(double);
		if (atom->memcheck("vinter")) bytes += nmax * sizeof(double);

		return bytes;
		}

src/PERI/atom_vec_peri.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -46,7 +46,7 @@ class AtomVecPeri : public AtomVec {
		private:
		int tag,type,mask,image;
		double x,v,**f;
		double rmass,vfrac,s0,x0,vinter;
		double vfrac,density,rmass,s0,**x0;
		};

		}

src/PERI/compute_damage_atom.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -87,8 +87,8 @@ void ComputeDamageAtom::compute_peratom()
		int nlocal = atom->nlocal;
		int *mask = atom->mask;
		double **x = atom->x;
		double *vinter = atom->vinter;
		double *vfrac = atom->vfrac;
		double vinter = ((FixPeriNeigh ) modify->fix[ifix_peri])->vinter;
		int *partner = ((FixPeriNeigh ) modify->fix[ifix_peri])->partner;
		int npartner = ((FixPeriNeigh ) modify->fix[ifix_peri])->npartner;
		int i,j,jj,jnum;

src/PERI/fix_peri_neigh.cpp

+20 −9

Original line number	Diff line number	Diff line
		@@ -50,6 +50,8 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS lmp,int narg, char *arg) :
		npartner = NULL;
		partner = NULL;
		r0 = NULL;
		vinter = NULL;

		grow_arrays(atom->nmax);
		atom->add_callback(0);
		atom->add_callback(1);
		@@ -75,6 +77,7 @@ FixPeriNeigh::~FixPeriNeigh()
		memory->sfree(npartner);
		memory->destroy_2d_int_array(partner);
		memory->destroy_2d_double_array(r0);
		memory->sfree(vinter);
		}

		/* ---------------------------------------------------------------------- */
		@@ -120,7 +123,6 @@ void FixPeriNeigh::setup(int vflag)

		double **x = atom->x;
		double *vfrac = atom->vfrac;
		double *vinter = atom->vinter;
		int *type = atom->type;
		int *tag = atom->tag;
		int nlocal = atom->nlocal;
		@@ -144,8 +146,6 @@ void FixPeriNeigh::setup(int vflag)
		Pair *anypair = force->pair_match("peri");
		double **cutsq = anypair->cutsq;

		double *s0 = atom->s0;

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		xtmp = x[i][0];
		@@ -173,9 +173,8 @@ void FixPeriNeigh::setup(int vflag)
		int maxall;
		MPI_Allreduce(&maxpartner,&maxall,1,MPI_INT,MPI_MAX,world);

		// realloc arrays stored by fix with correct value for maxpartner
		// realloc arrays with correct value for maxpartner

		memory->sfree(npartner);
		memory->destroy_2d_int_array(partner);
		memory->destroy_2d_double_array(r0);
		npartner = NULL;
		@@ -184,8 +183,12 @@ void FixPeriNeigh::setup(int vflag)
		grow_arrays(atom->nmax);

		// create partner list and r0 values from neighbor list
		// compute vinter for each atom

		for (i = 0; i < nlocal; i++) npartner[i] = 0;
		for (i = 0; i < nlocal; i++) {
		npartner[i] = 0;
		vinter[i] = 0.0;
		}

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		@@ -195,7 +198,6 @@ void FixPeriNeigh::setup(int vflag)
		itype = type[i];
		jlist = firstneigh[i];
		jnum = numneigh[i];
		vinter[i] = 0.0;

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		@@ -246,6 +248,7 @@ double FixPeriNeigh::memory_usage()
		int bytes = nmax * sizeof(int);
		bytes += nmaxmaxpartner sizeof(int);
		bytes += nmaxmaxpartner sizeof(double);
		bytes += nmax * sizeof(double);
		return bytes;
		}

		@@ -260,6 +263,8 @@ void FixPeriNeigh::grow_arrays(int nmax)
		partner = memory->grow_2d_int_array(partner,nmax,maxpartner,
		"peri_neigh:partner");
		r0 = memory->grow_2d_double_array(r0,nmax,maxpartner,"peri_neigh:r0");
		vinter = (double ) memory->srealloc(vinter,nmaxsizeof(double),
		"peri_neigh:vinter");
		}

		/* ----------------------------------------------------------------------
		@@ -273,6 +278,7 @@ void FixPeriNeigh::copy_arrays(int i, int j)
		partner[j][m] = partner[i][m];
		r0[j][m] = r0[i][m];
		}
		vinter[j] = vinter[i];
		}

		/* ----------------------------------------------------------------------
		@@ -290,7 +296,9 @@ int FixPeriNeigh::pack_exchange(int i, double *buf)
		buf[m++] = partner[i][n];
		buf[m++] = r0[i][n];
		}

		buf[0] = m/2;
		buf[m++] = vinter[i];
		return m;
		}

		@@ -306,6 +314,7 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
		partner[nlocal][n] = static_cast<int> (buf[m++]);
		r0[nlocal][n] = buf[m++];
		}
		vinter[nlocal] = buf[m++];
		return m;
		}

		@@ -322,6 +331,7 @@ int FixPeriNeigh::pack_restart(int i, double *buf)
		buf[m++] = partner[i][n];
		buf[m++] = r0[i][n];
		}
		buf[m++] = vinter[i];
		return m;
		}

		@@ -344,6 +354,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
		partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
		r0[nlocal][n] = extra[nlocal][m++];
		}
		vinter[nlocal] = extra[nlocal][m++];
		}

		/* ----------------------------------------------------------------------
		@@ -352,7 +363,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)

		int FixPeriNeigh::maxsize_restart()
		{
		return 2*maxpartner + 2;
		return 2*maxpartner + 3;
		}

		/* ----------------------------------------------------------------------
		@@ -361,5 +372,5 @@ int FixPeriNeigh::maxsize_restart()

		int FixPeriNeigh::size_restart(int nlocal)
		{
		return 2*npartner[nlocal] + 2;
		return 2*npartner[nlocal] + 3;
		}

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