(6888a80d) · Commits · 郑智淋 / lammps

src/dump_custom.cpp

+147 −25

Original line number	Diff line number	Diff line
		@@ -26,6 +26,7 @@
		#include "modify.h"
		#include "compute.h"
		#include "fix.h"
		#include "fix_store.h"
		#include "memory.h"
		#include "error.h"

		@@ -82,10 +83,17 @@ DumpCustom::DumpCustom(LAMMPS lmp, int narg, char *arg) :
		buffer_flag = 1;
		iregion = -1;
		idregion = NULL;

		nthresh = 0;
		thresh_array = NULL;
		thresh_op = NULL;
		thresh_value = NULL;
		thresh_last = NULL;

		nthreshlast = 0;
		thresh_fix = NULL;
		thresh_fixID = NULL;
		thresh_first = NULL;

		// computes, fixes, variables which the dump accesses

		@@ -193,6 +201,17 @@ DumpCustom::~DumpCustom()
		memory->destroy(thresh_array);
		memory->destroy(thresh_op);
		memory->destroy(thresh_value);
		memory->destroy(thresh_last);

		// check nfix in case all fixes have already been deleted

		for (int i = 0; i < nthreshlast; i++) {
		if (modify->nfix) modify->delete_fix(thresh_fixID[i]);
		delete [] thresh_fixID[i];
		}
		memory->sfree(thresh_fix);
		memory->sfree(thresh_fixID);
		memory->destroy(thresh_first);

		for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
		memory->sfree(id_compute);
		@@ -498,9 +517,10 @@ int DumpCustom::count()
		// un-choose if any threshold criterion isn't met

		if (nthresh) {
		double *ptr;
		double ptr,ptrhold;
		double *values;
		double value;
		int nstride;
		int nstride,lastflag;
		int nlocal = atom->nlocal;

		for (int ithresh = 0; ithresh < nthresh; ithresh++) {
		@@ -926,34 +946,93 @@ int DumpCustom::count()
		}

		// unselect atoms that don't meet threshold criterion
		// compare to single value or values stored in threshfix
		// copy ptr attribute into thresh_fix if this is first comparison

		if (thresh_last[ithresh] < 0) {
		lastflag = 0;
		value = thresh_value[ithresh];
		} else {
		lastflag = 1;
		int ilast = thresh_last[ithresh];
		values = thresh_fix[ilast]->vstore;
		ptrhold = ptr;
		if (thresh_first[ilast]) {
		thresh_first[ilast] = 0;
		for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
		ptr = ptrhold;
		}
		}

		if (thresh_op[ithresh] == LT) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr >= values[i]) choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr >= value) choose[i] = 0;
		}
		} else if (thresh_op[ithresh] == LE) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr > values[i]) choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr > value) choose[i] = 0;
		}
		} else if (thresh_op[ithresh] == GT) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr <= values[i]) choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr <= value) choose[i] = 0;
		}
		} else if (thresh_op[ithresh] == GE) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr < values[i]) choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr < value) choose[i] = 0;
		}
		} else if (thresh_op[ithresh] == EQ) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr != values[i]) choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr != value) choose[i] = 0;
		}
		} else if (thresh_op[ithresh] == NEQ) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr == values[i]) choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && *ptr == value) choose[i] = 0;
		}
		} else if (thresh_op[ithresh] == XOR) {
		if (lastflag) {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) \|\|
		(*ptr != 0.0 && values[i] != 0.0))
		choose[i] = 0;
		} else {
		for (i = 0; i < nlocal; i++, ptr += nstride)
		if (choose[i] && (*ptr == 0.0 && value == 0.0) \|\|
		(*ptr != 0.0 && value != 0.0))
		choose[i] = 0;
		}
		}

		// update values stored in threshfix

		if (lastflag) {
		ptr = ptrhold;
		for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
		}
		}
		}

		// compress choose flags into clist
		@@ -1594,8 +1673,16 @@ int DumpCustom::modify_param(int narg, char **arg)
		thresh_array = NULL;
		thresh_op = NULL;
		thresh_value = NULL;
		thresh_last = NULL;
		for (int i = 0; i < nthreshlast; i++) {
		modify->delete_fix(thresh_fixID[i]);
		delete [] thresh_fixID[i];
		}
		nthresh = 0;
		thresh_fix = NULL;
		thresh_fixID = NULL;
		thresh_first = NULL;
		}
		nthresh = nthreshlast = 0;
		return 2;
		}

		@@ -1606,6 +1693,7 @@ int DumpCustom::modify_param(int narg, char **arg)
		memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
		memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
		memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
		memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");

		// set attribute type of threshold
		// customize by adding to if statement
		@@ -1830,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
		field2index[nfield+nthresh] = add_custom(suffix,0);
		delete [] suffix;

		} else error->all(FLERR,"Invalid dump_modify threshhold operator");
		} else error->all(FLERR,"Invalid dump_modify threshold operator");

		// set operation type of threshold

		@@ -1843,9 +1931,43 @@ int DumpCustom::modify_param(int narg, char **arg)
		else if (strcmp(arg[2],"\|^") == 0) thresh_op[nthresh] = XOR;
		else error->all(FLERR,"Invalid dump_modify threshold operator");

		// set threshold value
		// set threshold value as number or special LAST keyword
		// create FixStore to hold LAST values, should work with restart
		// id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group

		if (strcmp(arg[3],"LAST") != 0) {
		thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
		thresh_last[nthresh] = -1;
		} else {
		thresh_fix = (FixStore **)
		memory->srealloc(thresh_fix,(nthreshlast+1)sizeof(FixStore ),
		"dump:thresh_fix");
		thresh_fixID = (char **)
		memory->srealloc(thresh_fixID,(nthreshlast+1)sizeof(char ),
		"dump:thresh_fixID");
		memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");

		int n = strlen(id) + strlen("_DUMP_STORE") + 8;
		thresh_fixID[nthreshlast] = new char[n];
		strcpy(thresh_fixID[nthreshlast],id);
		sprintf(&thresh_fixID[nthreshlast][strlen(id)],"%d",nthreshlast);
		strcat(thresh_fixID[nthreshlast],"_DUMP_STORE");

		char *newarg = new char[6];
		newarg[0] = thresh_fixID[nthreshlast];
		newarg[1] = group->names[igroup];
		newarg[2] = (char *) "STORE";
		newarg[3] = (char *) "peratom";
		newarg[4] = (char *) "1";
		newarg[5] = (char *) "1";
		modify->add_fix(6,newarg);
		thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1];
		delete [] newarg;

		thresh_last[nthreshlast] = nthreshlast;
		thresh_first[nthreshlast] = 1;
		nthreshlast++;
		}

		nthresh++;
		return 4;

src/dump_custom.h

+18 −8

Original line number	Diff line number	Diff line
		@@ -33,10 +33,20 @@ class DumpCustom : public Dump {
		int nevery; // dump frequency for output
		int iregion; // -1 if no region, else which region
		char *idregion; // region ID
		int nthresh; // # of defined threshholds
		int *thresh_array; // array to threshhhold on for each nthresh
		int *thresh_op; // threshhold operation for each nthresh
		double *thresh_value; // threshhold value for each nthresh

		int nthresh; // # of defined thresholds
		int nthreshlast; // # of defined thresholds with value = LAST

		int *thresh_array; // array to threshold on for each nthresh
		int *thresh_op; // threshold operation for each nthresh
		double *thresh_value; // threshold value for each nthresh
		int *thresh_last; // for threshold value = LAST,
		// index into thresh_fix
		// -1 if not LAST, value is numeric

		class FixStore **thresh_fix; // stores values for each threshold LAST
		char **thresh_fixID; // IDs of thresh_fixes
		int *thresh_first; // 1 the first time a FixStore values accessed

		int expand; // flag for whether field args were expanded
		char **earg; // field names with wildcard expansion
		@@ -50,7 +60,7 @@ class DumpCustom : public Dump {
		int nchoose; // # of selected atoms
		int maxlocal; // size of atom selection and variable arrays
		int *choose; // local indices of selected atoms
		double *dchoose; // value for each atom to threshhold against
		double *dchoose; // value for each atom to threshold against
		int *clist; // compressed list of indices of selected atoms

		int nfield; // # of keywords listed by user
		@@ -233,9 +243,9 @@ E: Compute used in dump between runs is not current
		The compute was not invoked on the current timestep, therefore it
		cannot be used in a dump between runs.

		E: Threshhold for an atom property that isn't allocated
		E: Threshold for an atom property that isn't allocated

		A dump threshhold has been requested on a quantity that is
		A dump threshold has been requested on a quantity that is
		not defined by the atom style used in this simulation.

		E: Dumping an atom property that isn't allocated
		@@ -362,7 +372,7 @@ E: Could not find dump modify custom atom integer property ID

		Self-explanatory.

		E: Invalid dump_modify threshhold operator
		E: Invalid dump_modify threshold operator

		Operator keyword used for threshold specification in not recognized.

src/fix_store.cpp

+3 −0

Original line number	Diff line number	Diff line
		@@ -154,6 +154,9 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
		if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
		else memory->create(astore,nrow,ncol,"fix/store:astore");
		memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");


		printf("AAA HOW GET HERE\n");
		}

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

src/modify.cpp

+81 −13

Original line number	Diff line number	Diff line
		@@ -68,10 +68,12 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
		list_timeflag = NULL;

		nfix_restart_global = 0;
		id_restart_global = style_restart_global = state_restart_global = NULL;
		id_restart_global = style_restart_global = NULL;
		state_restart_global = NULL;
		used_restart_global = NULL;
		nfix_restart_peratom = 0;
		id_restart_peratom = style_restart_peratom = NULL;
		index_restart_peratom = NULL;
		index_restart_peratom = used_restart_peratom = NULL;

		ncompute = maxcompute = 0;
		compute = NULL;
		@@ -140,7 +142,7 @@ Modify::~Modify()
		delete [] end_of_step_every;
		delete [] list_timeflag;

		restart_deallocate();
		restart_deallocate(0);

		delete compute_map;
		delete fix_map;
		@@ -156,7 +158,7 @@ void Modify::init()

		// delete storage of restart info since it is not valid after 1st run

		restart_deallocate();
		restart_deallocate(1);

		// create lists of fixes to call at each stage of run

		@@ -819,11 +821,16 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
		if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
		strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
		fix[ifix]->restart(state_restart_global[i]);
		used_restart_global[i] = 1;
		if (comm->me == 0) {
		const char str = (const char ) ("Resetting global state of Fix %s "
		"Style %s from restart file info\n");
		if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
		if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
		if (screen)
		fprintf(screen,"Resetting global fix info from restart file:\n");
		if (logfile)
		fprintf(logfile,"Resetting global fix info from restart file:\n");
		if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
		fix[ifix]->style,fix[ifix]->id);
		if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
		fix[ifix]->style,fix[ifix]->id);
		}
		}

		@@ -833,14 +840,19 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
		for (int i = 0; i < nfix_restart_peratom; i++)
		if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
		strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
		used_restart_peratom[i] = 1;
		for (int j = 0; j < atom->nlocal; j++)
		fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
		fix[ifix]->restart_reset = 1;
		if (comm->me == 0) {
		char str = (char ) ("Resetting per-atom state of Fix %s Style %s "
		"from restart file info\n");
		if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
		if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
		if (screen)
		fprintf(screen,"Resetting peratom fix info from restart file:\n");
		if (logfile)
		fprintf(logfile,"Resetting peratom fix info from restart file:\n");
		if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
		fix[ifix]->style,fix[ifix]->id);
		if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
		fix[ifix]->style,fix[ifix]->id);
		}
		}

		@@ -1158,6 +1170,7 @@ int Modify::read_restart(FILE *fp)
		id_restart_global = new char*[nfix_restart_global];
		style_restart_global = new char*[nfix_restart_global];
		state_restart_global = new char*[nfix_restart_global];
		used_restart_global = new int[nfix_restart_global];
		}

		// read each entry and Bcast to all procs
		@@ -1182,6 +1195,8 @@ int Modify::read_restart(FILE *fp)
		state_restart_global[i] = new char[n];
		if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
		MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);

		used_restart_global[i] = 0;
		}

		// nfix_restart_peratom = # of restart entries with peratom info
		@@ -1197,6 +1212,7 @@ int Modify::read_restart(FILE *fp)
		id_restart_peratom = new char*[nfix_restart_peratom];
		style_restart_peratom = new char*[nfix_restart_peratom];
		index_restart_peratom = new int[nfix_restart_peratom];
		used_restart_peratom = new int[nfix_restart_peratom];
		}

		// read each entry and Bcast to all procs
		@@ -1221,6 +1237,7 @@ int Modify::read_restart(FILE *fp)
		maxsize += n;

		index_restart_peratom[i] = i;
		used_restart_peratom[i] = 0;
		}

		return maxsize;
		@@ -1228,11 +1245,36 @@ int Modify::read_restart(FILE *fp)

		/* ----------------------------------------------------------------------
		delete all lists of restart file Fix info
		if flag set, print list of restart file info not assigned to new fixes
		------------------------------------------------------------------------- */

		void Modify::restart_deallocate()
		void Modify::restart_deallocate(int flag)
		{
		if (nfix_restart_global) {
		if (flag && comm->me == 0) {
		int i;
		for (i = 0; i < nfix_restart_global; i++)
		if (used_restart_global[i] == 0) break;
		if (i == nfix_restart_global) {
		if (screen)
		fprintf(screen,"All restart file global fix info "
		"was re-assigned\n");
		if (logfile)
		fprintf(logfile,"All restart file global fix info "
		"was re-assigned\n");
		} else {
		if (screen) fprintf(screen,"Unused restart file global fix info:\n");
		if (logfile) fprintf(logfile,"Unused restart file global fix info:\n");
		for (i = 0; i < nfix_restart_global; i++) {
		if (used_restart_global[i]) continue;
		if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
		style_restart_global[i],id_restart_global[i]);
		if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
		style_restart_global[i],id_restart_global[i]);
		}
		}
		}

		for (int i = 0; i < nfix_restart_global; i++) {
		delete [] id_restart_global[i];
		delete [] style_restart_global[i];
		@@ -1241,9 +1283,34 @@ void Modify::restart_deallocate()
		delete [] id_restart_global;
		delete [] style_restart_global;
		delete [] state_restart_global;
		delete [] used_restart_global;
		}

		if (nfix_restart_peratom) {
		if (flag && comm->me == 0) {
		int i;
		for (i = 0; i < nfix_restart_peratom; i++)
		if (used_restart_peratom[i] == 0) break;
		if (i == nfix_restart_peratom) {
		if (screen)
		fprintf(screen,"All restart file peratom fix info "
		"was re-assigned\n");
		if (logfile)
		fprintf(logfile,"All restart file peratom fix info "
		"was re-assigned\n");
		} else {
		if (screen) fprintf(screen,"Unused restart file peratom fix info:\n");
		if (logfile) fprintf(logfile,"Unused restart file peratom fix info:\n");
		for (i = 0; i < nfix_restart_peratom; i++) {
		if (used_restart_peratom[i]) continue;
		if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
		style_restart_peratom[i],id_restart_peratom[i]);
		if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
		style_restart_peratom[i],id_restart_peratom[i]);
		}
		}
		}

		for (int i = 0; i < nfix_restart_peratom; i++) {
		delete [] id_restart_peratom[i];
		delete [] style_restart_peratom[i];
		@@ -1251,6 +1318,7 @@ void Modify::restart_deallocate()
		delete [] id_restart_peratom;
		delete [] style_restart_peratom;
		delete [] index_restart_peratom;
		delete [] used_restart_peratom;
		}

		nfix_restart_global = nfix_restart_peratom = 0;

src/modify.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -107,7 +107,7 @@ class Modify : protected Pointers {

		void write_restart(FILE *);
		int read_restart(FILE *);
		void restart_deallocate();
		void restart_deallocate(int);

		bigint memory_usage();

		@@ -135,10 +135,12 @@ class Modify : protected Pointers {
		char **id_restart_global; // stored fix global info
		char **style_restart_global; // from read-in restart file
		char **state_restart_global;
		int *used_restart_global;

		char **id_restart_peratom; // stored fix peratom info
		char **style_restart_peratom; // from read-in restart file
		int *index_restart_peratom;
		int *used_restart_peratom;

		int index_permanent; // fix/compute index returned to library call

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