Merge pull request #785 from jrgissing/imp_dihed_print (dc4dd159) · Commits · 郑智淋 / lammps

src/atom_vec.cpp

+14 −2

Changes for src/atom_vec.cpp: 14 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -274,7 +274,7 @@ void AtomVec::write_angle(FILE fp, int n, tagint *buf, int index)
		pack dihedral info for data file
		------------------------------------------------------------------------- */

		void AtomVec::pack_dihedral(tagint **buf)
		int AtomVec::pack_dihedral(tagint **buf)
		{
		tagint *tag = atom->tag;
		int *num_dihedral = atom->num_dihedral;
		@@ -291,25 +291,31 @@ void AtomVec::pack_dihedral(tagint **buf)
		if (newton_bond) {
		for (i = 0; i < nlocal; i++)
		for (j = 0; j < num_dihedral[i]; j++) {
		if (buf) {
		buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
		buf[m][1] = dihedral_atom1[i][j];
		buf[m][2] = dihedral_atom2[i][j];
		buf[m][3] = dihedral_atom3[i][j];
		buf[m][4] = dihedral_atom4[i][j];
		}
		m++;
		}
		} else {
		for (i = 0; i < nlocal; i++)
		for (j = 0; j < num_dihedral[i]; j++)
		if (tag[i] == dihedral_atom2[i][j]) {
		if (buf) {
		buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
		buf[m][1] = dihedral_atom1[i][j];
		buf[m][2] = dihedral_atom2[i][j];
		buf[m][3] = dihedral_atom3[i][j];
		buf[m][4] = dihedral_atom4[i][j];
		}
		m++;
		}
		}

		return m;
		}

		/* ----------------------------------------------------------------------
		@@ -330,7 +336,7 @@ void AtomVec::write_dihedral(FILE fp, int n, tagint *buf, int index)
		pack improper info for data file
		------------------------------------------------------------------------- */

		void AtomVec::pack_improper(tagint **buf)
		int AtomVec::pack_improper(tagint **buf)
		{
		tagint *tag = atom->tag;
		int *num_improper = atom->num_improper;
		@@ -347,25 +353,31 @@ void AtomVec::pack_improper(tagint **buf)
		if (newton_bond) {
		for (i = 0; i < nlocal; i++)
		for (j = 0; j < num_improper[i]; j++) {
		if (buf) {
		buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
		buf[m][1] = improper_atom1[i][j];
		buf[m][2] = improper_atom2[i][j];
		buf[m][3] = improper_atom3[i][j];
		buf[m][4] = improper_atom4[i][j];
		}
		m++;
		}
		} else {
		for (i = 0; i < nlocal; i++)
		for (j = 0; j < num_improper[i]; j++)
		if (tag[i] == improper_atom2[i][j]) {
		if (buf) {
		buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
		buf[m][1] = improper_atom1[i][j];
		buf[m][2] = improper_atom2[i][j];
		buf[m][3] = improper_atom3[i][j];
		buf[m][4] = improper_atom4[i][j];
		}
		m++;
		}
		}

		return m;
		}

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

src/atom_vec.h

+2 −2

Changes for src/atom_vec.h: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -107,9 +107,9 @@ class AtomVec : protected Pointers {
		void write_bond(FILE , int, tagint *, int);
		int pack_angle(tagint **);
		void write_angle(FILE , int, tagint *, int);
		void pack_dihedral(tagint **);
		int pack_dihedral(tagint **);
		void write_dihedral(FILE , int, tagint *, int);
		void pack_improper(tagint **);
		int pack_improper(tagint **);
		void write_improper(FILE , int, tagint *, int);

		virtual int property_atom(char *) {return -1;}

src/write_data.cpp

+12 −2

Changes for src/write_data.cpp: 12 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -152,8 +152,8 @@ void WriteData::write(char *file)
		if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
		error->all(FLERR,"Atom count is inconsistent, cannot write data file");

		// sum up bond,angle counts
		// may be different than atom->nbonds,nangles if broken/turned-off
		// sum up bond,angle,dihedral,improper counts
		// may be different than atom->nbonds,nangles, etc. if broken/turned-off

		if (atom->molecular == 1 && (atom->nbonds \|\| atom->nbondtypes)) {
		nbonds_local = atom->avec->pack_bond(NULL);
		@@ -164,6 +164,16 @@ void WriteData::write(char *file)
		MPI_Allreduce(&nangles_local,&nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
		}

		if (atom->molecular == 1 && (atom->ndihedrals \|\| atom->ndihedraltypes)) {
		ndihedrals_local = atom->avec->pack_dihedral(NULL);
		MPI_Allreduce(&ndihedrals_local,&ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
		}

		if (atom->molecular == 1 && (atom->nimpropers \|\| atom->nimpropertypes)) {
		nimpropers_local = atom->avec->pack_improper(NULL);
		MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
		}

		// open data file

		if (me == 0) {

src/write_data.h

+2 −0

Changes for src/write_data.h: 2 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		@@ -38,6 +38,8 @@ class WriteData : protected Pointers {
		FILE *fp;
		bigint nbonds_local,nbonds;
		bigint nangles_local,nangles;
		bigint ndihedrals_local,ndihedrals;
		bigint nimpropers_local,nimpropers;

		void header();
		void type_arrays();

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