(bfba361f) · Commits · 郑智淋 / lammps

src/dump.cpp

+79 −2

Original line number	Diff line number	Diff line
		@@ -81,6 +81,7 @@ Dump::Dump(LAMMPS lmp, int narg, char *arg) : Pointers(lmp)
		buffer_allow = 0;
		buffer_flag = 0;
		padflag = 0;
		pbcflag = 0;

		maxbuf = maxids = maxsort = maxproc = 0;
		buf = bufsort = NULL;
		@@ -91,6 +92,10 @@ Dump::Dump(LAMMPS lmp, int narg, char *arg) : Pointers(lmp)
		maxsbuf = 0;
		sbuf = NULL;

		maxpbc = 0;
		xpbc = vpbc = NULL;
		imagepbc = NULL;

		// parse filename for special syntax
		// if contains '%', write one file per proc and replace % with proc-ID
		// if contains '', write one file per timestep and replace with timestep
		@@ -164,6 +169,12 @@ Dump::~Dump()

		memory->destroy(sbuf);

		if (pbcflag) {
		memory->destroy(xpbc);
		memory->destroy(vpbc);
		memory->destroy(imagepbc);
		}

		if (multiproc) MPI_Comm_free(&clustercomm);

		// XTC style sets fp to NULL since it closes file in its destructor
		@@ -262,6 +273,10 @@ void Dump::init()
		}
		}
		}

		// preallocation for PBC copies if requested

		if (pbcflag && atom->nlocal > maxpbc) pbc_allocate();
		}

		/* ---------------------------------------------------------------------- */
		@@ -352,6 +367,28 @@ void Dump::write()
		memory->create(ids,maxids,"dump:ids");
		}

		// apply PBC on copy of x,v,image if requested

		if (pbcflag) {
		int nlocal = atom->nlocal;
		if (nlocal > maxpbc) pbc_allocate();
		if (nlocal) {
		memcpy(&xpbc[0][0],&atom->x[0][0],3nlocalsizeof(double));
		memcpy(&vpbc[0][0],&atom->v[0][0],3nlocalsizeof(double));
		memcpy(imagepbc,atom->image,nlocal*sizeof(imageint));
		}
		double **dtmp = atom->x;
		atom->x = xpbc;
		xpbc = dtmp;
		dtmp = atom->v;
		atom->v = vpbc;
		vpbc = dtmp;
		imageint *itmp = atom->image;
		atom->image = imagepbc;
		imagepbc = itmp;
		domain->pbc();
		}

		// pack my data into buf
		// if sorting on IDs also request ID list from pack()
		// sort buf as needed
		@@ -430,6 +467,20 @@ void Dump::write()
		}
		}

		// restore original x,v,image unaltered by PBC

		if (pbcflag) {
		double **dtmp = atom->x;
		atom->x = xpbc;
		xpbc = dtmp;
		dtmp = atom->v;
		atom->v = vpbc;
		vpbc = dtmp;
		imageint *itmp = atom->image;
		atom->image = imagepbc;
		imagepbc = itmp;
		}

		// if file per timestep, close file if I am filewriter

		if (multifile) {
		@@ -887,6 +938,13 @@ void Dump::modify_params(int narg, char **arg)
		if (padflag < 0) error->all(FLERR,"Illegal dump_modify command");
		iarg += 2;

		} else if (strcmp(arg[iarg],"pbc") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
		if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1;
		else if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0;
		else error->all(FLERR,"Illegal dump_modify command");
		iarg += 2;

		} else if (strcmp(arg[iarg],"sort") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
		if (strcmp(arg[iarg+1],"off") == 0) sort_flag = 0;
		@@ -919,6 +977,21 @@ void Dump::modify_params(int narg, char **arg)
		return # of bytes of allocated memory
		------------------------------------------------------------------------- */

		void Dump::pbc_allocate()
		{
		memory->destroy(xpbc);
		memory->destroy(vpbc);
		memory->destroy(imagepbc);
		maxpbc = atom->nmax;
		memory->create(xpbc,maxpbc,3,"dump:xbpc");
		memory->create(vpbc,maxpbc,3,"dump:vbpc");
		memory->create(imagepbc,maxpbc,"dump:imagebpc");
		}

		/* ----------------------------------------------------------------------
		return # of bytes of allocated memory
		------------------------------------------------------------------------- */

		bigint Dump::memory_usage()
		{
		bigint bytes = memory->usage(buf,size_one*maxbuf);
		@@ -931,5 +1004,9 @@ bigint Dump::memory_usage()
		bytes += memory->usage(proclist,maxproc);
		if (irregular) bytes += irregular->memory_usage();
		}
		if (pbcflag) {
		bytes += 6maxpbc sizeof(double);
		bytes += maxpbc * sizeof(imageint);
		}
		return bytes;
		}

src/dump.h

+7 −1

Original line number	Diff line number	Diff line
		@@ -71,6 +71,7 @@ class Dump : protected Pointers {
		int buffer_allow; // 1 if style allows for buffer_flag, 0 if not
		int buffer_flag; // 1 if buffer output as one big string, 0 if not
		int padflag; // timestep padding in filename
		int pbcflag; // 1 if remap dumped atoms via PBC, 0 if not
		int singlefile_opened; // 1 = one big file, already opened, else 0
		int sortcol; // 0 to sort on ID, 1-N on columns
		int sortcolm1; // sortcol - 1
		@@ -116,6 +117,10 @@ class Dump : protected Pointers {
		tagint *idsort;
		int index,proclist;

		double xpbc,vpbc;
		int *imagepbc;
		int maxpbc;

		class Irregular *irregular;

		virtual void init_style() = 0;
		@@ -126,6 +131,7 @@ class Dump : protected Pointers {
		virtual void pack(tagint *) = 0;
		virtual int convert_string(int, double *) {return 0;}
		virtual void write_data(int, double *) = 0;
		void pbc_allocate();

		void sort();
		static int idcompare(const void , const void );

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