changes to start to make atom style hybrid work (6c18e366) · Commits · 郑智淋 / lammps

src/DIPOLE/atom_vec_dipole.cpp

+4 −8

Changes for src/DIPOLE/atom_vec_dipole.cpp: 4 added lines, 8 removed lines.
Original line number	Diff line number	Diff line
		@@ -55,16 +55,12 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)
		}

		/* ----------------------------------------------------------------------
		unpack one line from Atoms section of data file
		modify what the default AtomVec::data_atom() just initialized
		modify what AtomVec::data_atom() just unpacked
		or initialize other atom quantities
		------------------------------------------------------------------------- */

		void AtomVecDipole::data_atom(double coord, imageint imagetmp, char *values)
		void AtomVecDipole::data_atom_post(int ilocal)
		{
		AtomVec::data_atom(coord,imagetmp,values);

		int ilocal = atom->nlocal-1;
		double mu = atom->mu[ilocal];
		double *mu = atom->mu[ilocal];
		mu[3] = sqrt(mu[0]mu[0] + mu[1]mu[1] + mu[2]*mu[2]);
		}

src/DIPOLE/atom_vec_dipole.h

+1 −1

Changes for src/DIPOLE/atom_vec_dipole.h: 1 added line, 1 removed line.
Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ namespace LAMMPS_NS {
		class AtomVecDipole : public AtomVec {
		public:
		AtomVecDipole(class LAMMPS *);
		void data_atom(double , imageint, char *);
		void data_atom_post(int);
		};

		}

src/MOLECULE/atom_vec_angle.cpp

+17 −20

Changes for src/MOLECULE/atom_vec_angle.cpp: 17 added lines, 20 removed lines.
Original line number	Diff line number	Diff line
		@@ -67,11 +67,10 @@ AtomVecAngle::~AtomVecAngle()
		}

		/* ----------------------------------------------------------------------
		pack atom I's data for restart file
		modify/unmodify values for default AtomVec::pack_restart() to pack
		modify values for AtomVec::pack_restart() to pack
		------------------------------------------------------------------------- */

		int AtomVecAngle::pack_restart(int i, double *buf)
		void AtomVecAngle::pack_restart_pre(int i)
		{
		// insure negative vectors are needed length

		@@ -110,51 +109,49 @@ int AtomVecAngle::pack_restart(int i, double *buf)
		any_angle_negative = 1;
		} else angle_negative[m] = 0;
		}
		}

		// perform the pack with adjusted values

		int n = AtomVec::pack_restart(i,buf);
		/* ----------------------------------------------------------------------
		unmodify values packed by AtomVec::pack_restart()
		------------------------------------------------------------------------- */

		void AtomVecAngle::pack_restart_post(int i)
		{
		// restore the flagged types to their negative values

		if (any_bond_negative) {
		int *num_bond = atom->num_bond;
		int **bond_type = atom->bond_type;
		for (int m = 0; m < num_bond[i]; m++)
		if (bond_negative[m]) bond_type[i][m] = -bond_type[i][m];
		}

		if (any_angle_negative) {
		int *num_angle = atom->num_angle;
		int **angle_type = atom->angle_type;
		for (int m = 0; m < num_angle[i]; m++)
		if (angle_negative[m]) angle_type[i][m] = -angle_type[i][m];
		}

		return n;
		}

		/* ----------------------------------------------------------------------
		unpack data for one atom from restart file including extra quantities
		initialize other atom quantities
		initialize other atom quantities after AtomVec::unpack_restart()
		------------------------------------------------------------------------- */

		int AtomVecAngle::unpack_restart(double *buf)
		void AtomVecAngle::unpack_restart_init(int ilocal)
		{
		AtomVec::unpack_restart(buf);
		int ilocal = atom->nlocal-1;

		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;
		atom->nspecial[ilocal][2] = 0;
		}

		/* ----------------------------------------------------------------------
		unpack one line from Atoms section of data file
		modify what default AtomVec::data_atom() just unpacked
		modify what AtomVec::data_atom() just unpacked
		or initialize other atom quantities
		------------------------------------------------------------------------- */

		void AtomVecAngle::data_atom(double coord, imageint imagetmp, char *values)
		void AtomVecAngle::data_atom_post(int ilocal)
		{
		AtomVec::data_atom(coord,imagetmp,values);
		int ilocal = atom->nlocal-1;

		atom->num_bond[ilocal] = 0;
		atom->num_angle[ilocal] = 0;
		atom->nspecial[ilocal][0] = 0;

src/MOLECULE/atom_vec_angle.h

+5 −3

Changes for src/MOLECULE/atom_vec_angle.h: 5 added lines, 3 removed lines.
Original line number	Diff line number	Diff line
		@@ -28,11 +28,13 @@ class AtomVecAngle : public AtomVec {
		public:
		AtomVecAngle(class LAMMPS *);
		~AtomVecAngle();
		int pack_restart(int, double *);
		int unpack_restart(double *);
		void data_atom(double , imageint, char *);
		void pack_restart_pre(int);
		void pack_restart_post(int);
		void unpack_restart_init(int);
		void data_atom_post(int);

		private:
		int any_bond_negative,any_angle_negative;
		int bond_per_atom,angle_per_atom;
		int bond_negative,angle_negative;
		};

src/MOLECULE/atom_vec_bond.cpp

+15 −21

Changes for src/MOLECULE/atom_vec_bond.cpp: 15 added lines, 21 removed lines.
Original line number	Diff line number	Diff line
		@@ -61,11 +61,10 @@ AtomVecBond::~AtomVecBond()
		}

		/* ----------------------------------------------------------------------
		pack atom I's data for restart file
		modify/unmodify values for default AtomVec::pack_restart() to pack
		modify values for AtomVec::pack_restart() to pack
		------------------------------------------------------------------------- */

		int AtomVecBond::pack_restart(int i, double *buf)
		void AtomVecBond::pack_restart_pre(int i)
		{
		// insure bond_negative vector is needed length

		@@ -80,7 +79,7 @@ int AtomVecBond::pack_restart(int i, double *buf)
		int *num_bond = atom->num_bond;
		int **bond_type = atom->bond_type;

		int any_bond_negative = 0;
		any_bond_negative = 0;
		for (int m = 0; m < num_bond[i]; m++) {
		if (bond_type[i][m] < 0) {
		bond_negative[m] = 1;
		@@ -88,47 +87,42 @@ int AtomVecBond::pack_restart(int i, double *buf)
		any_bond_negative = 1;
		} else bond_negative[m] = 0;
		}
		}

		// perform the pack with adjusted values

		int n = AtomVec::pack_restart(i,buf);
		/* ----------------------------------------------------------------------
		unmodify values packed by AtomVec::pack_restart()
		------------------------------------------------------------------------- */

		void AtomVecBond::pack_restart_post(int i)
		{
		// restore the flagged types to their negative values

		if (any_bond_negative) {
		int *num_bond = atom->num_bond;
		int **bond_type = atom->bond_type;
		for (int m = 0; m < num_bond[i]; m++)
		if (bond_negative[m]) bond_type[i][m] = -bond_type[i][m];
		}

		return n;
		}

		/* ----------------------------------------------------------------------
		unpack data for one atom from restart file including extra quantities
		initialize other atom quantities
		initialize other atom quantities after AtomVec::unpack_restart()
		------------------------------------------------------------------------- */

		int AtomVecBond::unpack_restart(double *buf)
		void AtomVecBond::unpack_restart_init(int ilocal)
		{
		AtomVec::unpack_restart(buf);
		int ilocal = atom->nlocal-1;

		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;
		atom->nspecial[ilocal][2] = 0;
		}

		/* ----------------------------------------------------------------------
		unpack one line from Atoms section of data file
		modify what default AtomVec::data_atom() just unpacked
		modify what AtomVec::data_atom() just unpacked
		or initialize other atom quantities
		------------------------------------------------------------------------- */

		void AtomVecBond::data_atom(double coord, imageint imagetmp, char *values)
		void AtomVecBond::data_atom_post(int ilocal)
		{
		AtomVec::data_atom(coord,imagetmp,values);
		int ilocal = atom->nlocal-1;

		atom->num_bond[ilocal] = 0;
		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;

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