Merge pull request #1553 from athomps/read_dump_xyz (64faa6c6) · Commits · 郑智淋 / lammps

src/USER-MOLFILE/reader_molfile.cpp

+14 −4

Original line number	Diff line number	Diff line
		@@ -195,7 +195,7 @@ void ReaderMolfile::skip()
		only called by proc 0
		------------------------------------------------------------------------- */

		bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
		bigint ReaderMolfile::read_header(double box[3][3], int &boxinfo, int &triclinic,
		int fieldinfo, int nfield,
		int fieldtype, char * /* fieldlabel */,
		int scaleflag, int wrapflag, int &fieldflag,
		@@ -204,17 +204,24 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
		nid = 0;

		// signal that we have no box info at all so far.
		triclinic = -1;

		boxinfo = 0;
		triclinic = 0;

		// heuristics to determine if we have boxinfo (first if)
		// and whether we have an orthogonal box (second if)

		if (!is_smalldiff(cell[0]cell[1]cell[2], 0.0f)) {
		boxinfo = 1;
		if (is_smalldiff(cell[3],90.0f) && is_smalldiff(cell[4],90.0f) &&
		is_smalldiff(cell[5],90.0f)) {

		triclinic = 0;

		// we have no information about the absolute location
		// of the box, so we assume that the origin is in the middle.
		// also we cannot tell periodicity. we assume, yes.

		box[0][0] = -0.5*static_cast<double>(cell[0]);
		box[0][1] = 0.5*static_cast<double>(cell[0]);
		box[0][2] = 0.0;
		@@ -224,6 +231,7 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
		box[2][0] = -0.5*static_cast<double>(cell[2]);
		box[2][1] = 0.5*static_cast<double>(cell[2]);
		box[2][2] = 0.0;

		} else {

		triclinic = 1;
		@@ -243,7 +251,8 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
		(lblccos(alpha/90.0MY_PI2) - xyxz) / ly : 0.0;
		const double lz = sqrt(lclc - xzxz - yz*yz);

		/* go from box length to boundary */
		// go from box length to boundary

		double xbnd;

		xbnd = 0.0;
		@@ -275,6 +284,7 @@ bigint ReaderMolfile::read_header(double box[3][3], int &triclinic,
		}

		// if no field info requested, just return

		if (!fieldinfo) return natoms;

		memory->create(fieldindex,nfield,"read_dump:fieldindex");

src/USER-MOLFILE/reader_molfile.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ class ReaderMolfile : public Reader {

		virtual int read_time(bigint &);
		virtual void skip();
		virtual bigint read_header(double [3][3], int &, int, int, int , char *,
		virtual bigint read_header(double [3][3], int &, int &, int, int, int , char *,
		int, int, int &, int &, int &, int &);
		virtual void read_atoms(int, int, double **);

src/read_dump.cpp

+36 −32

Original line number	Diff line number	Diff line
		@@ -483,30 +483,33 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)

		void ReadDump::header(int fieldinfo)
		{
		int triclinic_snap;
		int boxinfo, triclinic_snap;
		int fieldflag,xflag,yflag,zflag;

		if (filereader) {
		for (int i = 0; i < nreader; i++)
		nsnapatoms[i] = readers[i]->read_header(box,triclinic_snap,fieldinfo,
		nsnapatoms[i] = readers[i]->read_header(box,boxinfo,triclinic_snap,fieldinfo,
		nfield,fieldtype,fieldlabel,
		scaleflag,wrapflag,fieldflag,
		xflag,yflag,zflag);
		}

		MPI_Bcast(nsnapatoms,nreader,MPI_LMP_BIGINT,0,clustercomm);
		MPI_Bcast(&boxinfo,1,MPI_INT,0,clustercomm);
		MPI_Bcast(&triclinic_snap,1,MPI_INT,0,clustercomm);
		MPI_Bcast(&box[0][0],9,MPI_DOUBLE,0,clustercomm);

		// local copy of snapshot box parameters
		// used in xfield,yfield,zfield when converting dump atom to absolute coords

		if (boxinfo) {
		xlo = box[0][0];
		xhi = box[0][1];
		ylo = box[1][0];
		yhi = box[1][1];
		zlo = box[2][0];
		zhi = box[2][1];

		if (triclinic_snap) {
		xy = box[0][2];
		xz = box[1][2];
		@@ -525,6 +528,7 @@ void ReadDump::header(int fieldinfo)
		xprd = xhi - xlo;
		yprd = yhi - ylo;
		zprd = zhi - zlo;
		}

		// done if not checking fields

		@@ -536,17 +540,17 @@ void ReadDump::header(int fieldinfo)
		MPI_Bcast(&zflag,1,MPI_INT,0,clustercomm);

		// error check on current vs new box and fields
		// triclinic_snap < 0 means no box info in file
		// boxinfo == 0 means no box info in file

		if (triclinic_snap < 0 && boxflag > 0)
		if (boxflag) {
		if (!boxinfo)
		error->all(FLERR,"No box information in dump, must use 'box no'");
		if (triclinic_snap >= 0) {
		if ((triclinic_snap && !triclinic) \|\|
		else if ((triclinic_snap && !triclinic) \|\|
		(!triclinic_snap && triclinic))
		error->one(FLERR,"Read_dump triclinic status does not match simulation");
		}

		// error check on requested fields exisiting in dump file
		// error check on requested fields existing in dump file

		if (fieldflag < 0)
		error->one(FLERR,"Read_dump field not found in dump file");

src/reader.cpp

+10 −0

Original line number	Diff line number	Diff line
		@@ -75,3 +75,13 @@ void Reader::close_file()
		else fclose(fp);
		fp = NULL;
		}

		/* ----------------------------------------------------------------------
		detect unused arguments
		------------------------------------------------------------------------- */

		void Reader::settings(int narg, char** /args/)
		{
		if (narg > 0)
		error->all(FLERR,"Illegal read_dump command");
		}

src/reader.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -25,11 +25,11 @@ class Reader : protected Pointers {
		Reader(class LAMMPS *);
		virtual ~Reader() {}

		virtual void settings(int, char**) {};
		virtual void settings(int, char**);

		virtual int read_time(bigint &) = 0;
		virtual void skip() = 0;
		virtual bigint read_header(double [3][3], int &, int, int, int , char *,
		virtual bigint read_header(double [3][3], int &, int &, int, int, int , char *,
		int, int, int &, int &, int &, int &) = 0;
		virtual void read_atoms(int, int, double **) = 0;

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