(5b579876) · Commits · 郑智淋 / lammps

src/GRANULAR/fix_pour.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -30,6 +30,7 @@ class FixPour : public Fix {
		friend class PairGranHooke;
		friend class PairGranHookeOMP;
		friend class PairGranHookeHistory;
		friend class PairGranHookeHistory2;
		friend class PairGranHookeHistoryOMP;
		friend class PairGranHookeCuda;

		@@ -61,7 +62,6 @@ class FixPour : public Fix {
		int recvcounts,displs;
		int nfreq,nfirst,ninserted,nper;
		double lo_current,hi_current;
		class FixShearHistory *fix_history;
		class RanPark *random;

		int overlap(int);

src/comm.cpp

+2 −6

Original line number	Diff line number	Diff line
		@@ -1024,8 +1024,7 @@ void Comm::borders()

		// pack up list of border atoms

		if (nsend*size_border > maxsend)
		grow_send(nsend*size_border,0);
		if (nsendsize_border > maxsend) grow_send(nsendsize_border,0);
		if (ghost_velocity)
		n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send,
		pbc_flag[iswap],pbc[iswap]);
		@@ -1466,10 +1465,7 @@ void Comm::forward_comm_array(int n, double **array)
		MPI_Request request;
		MPI_Status status;

		// check that buf_send and buf_recv are big enough



		// NOTE: check that buf_send and buf_recv are big enough

		for (iswap = 0; iswap < nswap; iswap++) {

src/fix_shear_history.cpp

+114 −39

Original line number	Diff line number	Diff line
		@@ -11,6 +11,7 @@
		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#include "mpi.h"
		#include "string.h"
		#include "stdio.h"
		#include "fix_shear_history.h"
		@@ -27,8 +28,6 @@
		using namespace LAMMPS_NS;
		using namespace FixConst;

		#define MAXTOUCH 15

		/* ---------------------------------------------------------------------- */

		FixShearHistory::FixShearHistory(LAMMPS lmp, int narg, char *arg) :
		@@ -47,10 +46,15 @@ FixShearHistory::FixShearHistory(LAMMPS lmp, int narg, char *arg) :
		atom->add_callback(0);
		atom->add_callback(1);

		ipage = NULL;
		dpage = NULL;
		pgsize = oneatom = 0;

		// initialize npartner to 0 so neighbor list creation is OK the 1st time

		int nlocal = atom->nlocal;
		for (int i = 0; i < nlocal; i++) npartner[i] = 0;
		maxtouch = 0;
		}

		/* ---------------------------------------------------------------------- */
		@@ -65,8 +69,10 @@ FixShearHistory::~FixShearHistory()
		// delete locally stored arrays

		memory->destroy(npartner);
		memory->destroy(partner);
		memory->destroy(shearpartner);
		memory->sfree(partner);
		memory->sfree(shearpartner);
		delete ipage;
		delete dpage;
		}

		/* ---------------------------------------------------------------------- */
		@@ -89,6 +95,21 @@ void FixShearHistory::init()

		int dim;
		computeflag = (int *) pair->extract("computeflag",dim);

		// create pages if first time or if neighbor pgsize/oneatom has changed
		// note that latter could cause shear history info to be discarded

		int create = 0;
		if (ipage == NULL) create = 1;
		if (pgsize != neighbor->pgsize) create = 1;
		if (oneatom != neighbor->oneatom) create = 1;

		if (create) {
		pgsize = neighbor->pgsize;
		oneatom = neighbor->oneatom;
		ipage = new MyPage<int>(oneatom,pgsize);
		dpage = new MyPage<double[3]>(oneatom,pgsize);
		}
		}

		/* ----------------------------------------------------------------------
		@@ -119,17 +140,22 @@ void FixShearHistory::setup_pre_exchange()

		void FixShearHistory::pre_exchange()
		{
		int i,j,ii,jj,m,inum,jnum;
		int i,j,ii,jj,m,n,inum,jnum;
		int ilist,jlist,numneigh,*firstneigh;
		int touch,*firsttouch;
		double shear,allshear,**firstshear;

		// zero npartner for all current atoms
		// clear 2 page data structures

		int nlocal = atom->nlocal;
		for (i = 0; i < nlocal; i++) npartner[i] = 0;

		// copy shear info from neighbor list atoms to atom arrays
		ipage->reset();
		dpage->reset();

		// 1st loop over neighbor list
		// calculate npartner for each owned atom

		int *tag = atom->tag;
		NeighList *list = pair->list;
		@@ -140,6 +166,39 @@ void FixShearHistory::pre_exchange()
		firsttouch = list->listgranhistory->firstneigh;
		firstshear = list->listgranhistory->firstdouble;

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		jlist = firstneigh[i];
		jnum = numneigh[i];
		touch = firsttouch[i];

		for (jj = 0; jj < jnum; jj++) {
		if (touch[jj]) {
		npartner[i]++;
		j = jlist[jj];
		j &= NEIGHMASK;
		if (j < nlocal) npartner[j]++;
		}
		}
		}

		// get page chunks to store atom IDs and shear history for my atoms

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		n = npartner[i];
		partner[i] = ipage->get(n);
		shearpartner[i] = dpage->get(n);
		if (partner[i] == NULL \|\| shearpartner[i] == NULL)
		error->one(FLERR,"Shear history overflow, boost neigh_modify one");
		}

		// 2nd loop over neighbor list
		// store atom IDs and shear history for my atoms
		// re-zero npartner to use as counter for all my atoms

		for (i = 0; i < nlocal; i++) npartner[i] = 0;

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		jlist = firstneigh[i];
		@@ -152,37 +211,28 @@ void FixShearHistory::pre_exchange()
		shear = &allshear[3*jj];
		j = jlist[jj];
		j &= NEIGHMASK;
		if (npartner[i] < MAXTOUCH) {
		m = npartner[i];
		partner[i][m] = tag[j];
		shearpartner[i][m][0] = shear[0];
		shearpartner[i][m][1] = shear[1];
		shearpartner[i][m][2] = shear[2];
		}
		npartner[i]++;
		if (j < nlocal) {
		if (npartner[j] < MAXTOUCH) {
		m = npartner[j];
		partner[j][m] = tag[i];
		shearpartner[j][m][0] = -shear[0];
		shearpartner[j][m][1] = -shear[1];
		shearpartner[j][m][2] = -shear[2];
		}
		npartner[j]++;
		}
		}
		}
		}

		// test for too many touching neighbors
		// set maxtouch = max # of partners of any owned atom

		int flag = 0;
		for (i = 0; i < nlocal; i++)
		if (npartner[i] >= MAXTOUCH) flag = 1;
		int flag_all;
		MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
		if (flag_all)
		error->all(FLERR,"Too many touching neighbors - boost MAXTOUCH");
		maxtouch = 0;
		for (i = 0; i < nlocal; i++) maxtouch = MAX(maxtouch,npartner[i]);
		}

		/* ---------------------------------------------------------------------- */
		@@ -208,8 +258,10 @@ double FixShearHistory::memory_usage()
		{
		int nmax = atom->nmax;
		double bytes = nmax * sizeof(int);
		bytes += nmaxMAXTOUCH sizeof(int);
		bytes += nmaxMAXTOUCH3 * sizeof(double);
		bytes = nmax * sizeof(int *);
		bytes = nmax * sizeof(double *);
		bytes += ipage->ndatum * sizeof(int);
		bytes += dpage->ndatum * sizeof(double[3]);
		return bytes;
		}

		@@ -220,8 +272,12 @@ double FixShearHistory::memory_usage()
		void FixShearHistory::grow_arrays(int nmax)
		{
		memory->grow(npartner,nmax,"shear_history:npartner");
		memory->grow(partner,nmax,MAXTOUCH,"shear_history:partner");
		memory->grow(shearpartner,nmax,MAXTOUCH,3,"shear_history:shearpartner");
		partner = (int *) memory->srealloc(partner,nmaxsizeof(int *),
		"shear_history:partner");
		typedef double (*sptype)[3];
		shearpartner = (sptype *)
		memory->srealloc(shearpartner,nmax*sizeof(sptype),
		"shear_history:shearpartner");
		}

		/* ----------------------------------------------------------------------
		@@ -230,13 +286,15 @@ void FixShearHistory::grow_arrays(int nmax)

		void FixShearHistory::copy_arrays(int i, int j, int delflag)
		{
		// just copy pointers for partner and shearpartner
		// b/c can't overwrite chunk allocation inside ipage,dpage
		// incoming atoms in unpack_exchange just grab new chunks
		// so are orphaning chunks for migrating atoms
		// OK, b/c will reset ipage,dpage on next reneighboring

		npartner[j] = npartner[i];
		for (int m = 0; m < npartner[j]; m++) {
		partner[j][m] = partner[i][m];
		shearpartner[j][m][0] = shearpartner[i][m][0];
		shearpartner[j][m][1] = shearpartner[i][m][1];
		shearpartner[j][m][2] = shearpartner[i][m][2];
		}
		partner[j] = partner[i];
		shearpartner[j] = shearpartner[i];
		}

		/* ----------------------------------------------------------------------
		@@ -254,6 +312,9 @@ void FixShearHistory::set_arrays(int i)

		int FixShearHistory::pack_exchange(int i, double *buf)
		{
		// NOTE: how do I know comm buf is big enough if extreme # of touching neighs
		// Comm::BUFEXTRA may need to be increased

		int m = 0;
		buf[m++] = npartner[i];
		for (int n = 0; n < npartner[i]; n++) {
		@@ -271,8 +332,13 @@ int FixShearHistory::pack_exchange(int i, double *buf)

		int FixShearHistory::unpack_exchange(int nlocal, double *buf)
		{
		// allocate new chunks from ipage,dpage for incoming values

		int m = 0;
		npartner[nlocal] = static_cast<int> (buf[m++]);
		maxtouch = MAX(maxtouch,npartner[nlocal]);
		partner[nlocal] = ipage->get(npartner[nlocal]);
		shearpartner[nlocal] = dpage->get(npartner[nlocal]);
		for (int n = 0; n < npartner[nlocal]; n++) {
		partner[nlocal][n] = static_cast<int> (buf[m++]);
		shearpartner[nlocal][n][0] = buf[m++];
		@@ -314,7 +380,12 @@ void FixShearHistory::unpack_restart(int nlocal, int nth)
		for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
		m++;

		// allocate new chunks from ipage,dpage for incoming values

		npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
		maxtouch = MAX(maxtouch,npartner[nlocal]);
		partner[nlocal] = ipage->get(npartner[nlocal]);
		shearpartner[nlocal] = dpage->get(npartner[nlocal]);
		for (int n = 0; n < npartner[nlocal]; n++) {
		partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
		shearpartner[nlocal][n][0] = extra[nlocal][m++];
		@@ -329,7 +400,11 @@ void FixShearHistory::unpack_restart(int nlocal, int nth)

		int FixShearHistory::maxsize_restart()
		{
		return 4*MAXTOUCH + 2;
		// maxtouch_all = max touching partners across all procs

		int maxtouch_all;
		MPI_Allreduce(&maxtouch,&maxtouch_all,1,MPI_INT,MPI_MAX,world);
		return 4*maxtouch_all + 2;
		}

		/* ----------------------------------------------------------------------

src/fix_shear_history.h

+7 −2

Original line number	Diff line number	Diff line
		@@ -21,13 +21,13 @@ FixStyle(SHEAR_HISTORY,FixShearHistory)
		#define LMP_FIX_SHEAR_HISTORY_H

		#include "fix.h"
		#include "my_page.h"

		namespace LAMMPS_NS {

		class FixShearHistory : public Fix {
		friend class Neighbor;
		friend class PairGranHookeHistory;
		friend class FixPour;

		public:
		FixShearHistory(class LAMMPS , int, char *);
		@@ -53,10 +53,15 @@ class FixShearHistory : public Fix {
		protected:
		int *npartner; // # of touching partners of each atom
		int **partner; // tags for the partners
		double ***shearpartner; // 3 shear values with the partner
		double (**shearpartner)[3]; // 3 shear values with the partner
		int maxtouch; // max # of touching partners for my atoms

		class Pair *pair;
		int *computeflag; // computeflag in PairGranHookeHistory

		int pgsize,oneatom; // copy of settings in Neighbor
		MyPage<int> *ipage; // pages of partner atom IDs
		MyPage<double[3]> *dpage; // pages of shear history with partners
		};

		}

src/modify.cpp

+2 −1

Original line number	Diff line number	Diff line
		@@ -863,7 +863,8 @@ void Modify::modify_compute(int narg, char **arg)
		int icompute;
		for (icompute = 0; icompute < ncompute; icompute++)
		if (strcmp(arg[0],compute[icompute]->id) == 0) break;
		if (icompute == ncompute) error->all(FLERR,"Could not find compute_modify ID");
		if (icompute == ncompute)
		error->all(FLERR,"Could not find compute_modify ID");

		compute[icompute]->modify_params(narg-1,&arg[1]);
		}

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