Merge pull request #688 from lammps/history (7dfc6b7e) · Commits · 郑智淋 / lammps

src/CORESHELL/pair_lj_cut_coul_long_cs.cpp

+12 −12

Original line number	Diff line number	Diff line
		@@ -225,10 +225,10 @@ void PairLJCutCoulLongCS::compute_inner()
		int newton_pair = force->newton_pair;
		double qqrd2e = force->qqrd2e;

		inum = listinner->inum;
		ilist = listinner->ilist;
		numneigh = listinner->numneigh;
		firstneigh = listinner->firstneigh;
		inum = list->inum_inner;
		ilist = list->ilist_inner;
		numneigh = list->numneigh_inner;
		firstneigh = list->firstneigh_inner;

		double cut_out_on = cut_respa[0];
		double cut_out_off = cut_respa[1];
		@@ -311,10 +311,10 @@ void PairLJCutCoulLongCS::compute_middle()
		int newton_pair = force->newton_pair;
		double qqrd2e = force->qqrd2e;

		inum = listmiddle->inum;
		ilist = listmiddle->ilist;
		numneigh = listmiddle->numneigh;
		firstneigh = listmiddle->firstneigh;
		inum = list->inum_middle;
		ilist = list->ilist_middle;
		numneigh = list->numneigh_middle;
		firstneigh = list->firstneigh_middle;

		double cut_in_off = cut_respa[0];
		double cut_in_on = cut_respa[1];
		@@ -412,10 +412,10 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag)
		int newton_pair = force->newton_pair;
		double qqrd2e = force->qqrd2e;

		inum = listouter->inum;
		ilist = listouter->ilist;
		numneigh = listouter->numneigh;
		firstneigh = listouter->firstneigh;
		inum = list->inum;
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;

		double cut_in_off = cut_respa[2];
		double cut_in_on = cut_respa[3];

src/DIPOLE/pair_lj_long_dipole_long.cpp

+0 −16

Original line number	Diff line number	Diff line
		@@ -263,22 +263,6 @@ void PairLJLongDipoleLong::init_style()
		if (force->kspace) g_ewald = force->kspace->g_ewald;
		}

		/* ----------------------------------------------------------------------
		neighbor callback to inform pair style of neighbor list to use
		regular or rRESPA
		------------------------------------------------------------------------- */

		void PairLJLongDipoleLong::init_list(int id, NeighList *ptr)
		{
		if (id == 0) list = ptr;
		else if (id == 1) listinner = ptr;
		else if (id == 2) listmiddle = ptr;
		else if (id == 3) listouter = ptr;

		if (id)
		error->all(FLERR,"Pair style lj/long/dipole/long does not currently support respa");
		}

		/* ----------------------------------------------------------------------
		init for one type pair i,j and corresponding j,i
		------------------------------------------------------------------------- */

src/DIPOLE/pair_lj_long_dipole_long.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -34,7 +34,6 @@ class PairLJLongDipoleLong : public Pair {
		virtual void settings(int, char **);
		void coeff(int, char **);
		void init_style();
		void init_list(int, class NeighList *);
		double init_one(int, int);
		void write_restart(FILE *);
		void read_restart(FILE *);

src/GRANULAR/pair_gran_hertz_history.cpp

+4 −3

Original line number	Diff line number	Diff line
		@@ -24,6 +24,7 @@
		#include "update.h"
		#include "force.h"
		#include "fix.h"
		#include "fix_neigh_history.h"
		#include "neighbor.h"
		#include "neigh_list.h"
		#include "comm.h"
		@@ -95,8 +96,8 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;
		firsttouch = list->listhistory->firstneigh;
		firstshear = list->listhistory->firstdouble;
		firsttouch = fix_history->firstflag;
		firstshear = fix_history->firstvalue;

		// loop over neighbors of my atoms

		@@ -407,7 +408,7 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,

		int jnum = list->numneigh[i];
		int *jlist = list->firstneigh[i];
		double *allshear = list->listhistory->firstdouble[i];
		double *allshear = fix_history->firstvalue[i];

		for (int jj = 0; jj < jnum; jj++) {
		neighprev++;

src/GRANULAR/pair_gran_hooke_history.cpp

+14 −43

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@
		#include "update.h"
		#include "modify.h"
		#include "fix.h"
		#include "fix_shear_history.h"
		#include "fix_neigh_history.h"
		#include "comm.h"
		#include "neighbor.h"
		#include "neigh_list.h"
		@@ -64,7 +64,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
		PairGranHookeHistory::~PairGranHookeHistory()
		{
		delete [] svector;
		if (fix_history) modify->delete_fix("SHEAR_HISTORY");
		if (fix_history) modify->delete_fix("NEIGH_HISTORY");

		if (allocated) {
		memory->destroy(setflag);
		@@ -137,8 +137,8 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;
		firsttouch = listhistory->firstneigh;
		firstshear = listhistory->firstdouble;
		firsttouch = fix_history->firstflag;
		firstshear = fix_history->firstvalue;

		// loop over neighbors of my atoms

		@@ -400,35 +400,28 @@ void PairGranHookeHistory::init_style()
		if (comm->ghost_velocity == 0)
		error->all(FLERR,"Pair granular requires ghost atoms store velocity");

		// need a granular neigh list and optionally a granular history neigh list
		// need a granular neigh list

		int irequest = neighbor->request(this,instance_me);
		neighbor->requests[irequest]->size = 1;
		if (history) {
		irequest = neighbor->request(this,instance_me);
		neighbor->requests[irequest]->id = 1;
		neighbor->requests[irequest]->history = 1;
		neighbor->requests[irequest]->dnum = 3;
		}
		if (history) neighbor->requests[irequest]->history = 1;

		dt = update->dt;

		// if shear history is stored:
		// if first init, create Fix needed for storing shear history

		if (history && fix_history == NULL) {
		char dnumstr[16];
		sprintf(dnumstr,"%d",3);
		char *fixarg = new char[4];
		fixarg[0] = (char *) "SHEAR_HISTORY";
		fixarg[0] = (char *) "NEIGH_HISTORY";
		fixarg[1] = (char *) "all";
		fixarg[2] = (char *) "SHEAR_HISTORY";
		fixarg[2] = (char *) "NEIGH_HISTORY";
		fixarg[3] = dnumstr;
		modify->add_fix(4,fixarg);
		modify->add_fix(4,fixarg,1);
		delete [] fixarg;
		fix_history = (FixShearHistory *) modify->fix[modify->nfix-1];
		fix_history = (FixNeighHistory *) modify->fix[modify->nfix-1];
		fix_history->pair = this;
		neighbor->requests[irequest]->fix_history = fix_history;
		}

		// check for FixFreeze and set freeze_group_bit
		@@ -494,23 +487,12 @@ void PairGranHookeHistory::init_style()
		// set fix which stores history info

		if (history) {
		int ifix = modify->find_fix("SHEAR_HISTORY");
		if (ifix < 0) error->all(FLERR,"Could not find pair fix ID");
		fix_history = (FixShearHistory *) modify->fix[ifix];
		int ifix = modify->find_fix("NEIGH_HISTORY");
		if (ifix < 0) error->all(FLERR,"Could not find pair fix neigh history ID");
		fix_history = (FixNeighHistory *) modify->fix[ifix];
		}
		}

		/* ----------------------------------------------------------------------
		neighbor callback to inform pair style of neighbor list to use
		optional granular history list
		------------------------------------------------------------------------- */

		void PairGranHookeHistory::init_list(int id, NeighList *ptr)
		{
		if (id == 0) list = ptr;
		else if (id == 1) listhistory = ptr;
		}

		/* ----------------------------------------------------------------------
		init for one type pair i,j and corresponding j,i
		------------------------------------------------------------------------- */
		@@ -704,7 +686,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,

		int jnum = list->numneigh[i];
		int *jlist = list->firstneigh[i];
		double *allshear = list->listhistory->firstdouble[i];
		double *allshear = fix_history->firstvalue[i];

		for (int jj = 0; jj < jnum; jj++) {
		neighprev++;
		@@ -797,14 +779,3 @@ double PairGranHookeHistory::memory_usage()
		double bytes = nmax * sizeof(double);
		return bytes;
		}

		/* ----------------------------------------------------------------------
		return ptr to FixShearHistory class
		called by Neighbor when setting up neighbor lists
		------------------------------------------------------------------------- */

		void PairGranHookeHistory::extract(const char str, int &dim)
		{
		if (strcmp(str,"history") == 0) return (void *) fix_history;
		return NULL;
		}

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