enable replicate to work with local ptrs (b6374bac) · Commits · 郑智淋 / lammps

src/DIPOLE/atom_vec_dipole.cpp

+13 −2

Original line number	Diff line number	Diff line
		@@ -54,6 +54,16 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)
		setup_fields();
		}

		/* ----------------------------------------------------------------------
		set local copies of all grow ptrs used by this class, except defaults
		needed in replicate when 2 atom classes exist and it calls pack_restart()
		------------------------------------------------------------------------- */

		void AtomVecDipole::grow_pointers()
		{
		mu = atom->mu;
		}

		/* ----------------------------------------------------------------------
		modify what AtomVec::data_atom() just unpacked
		or initialize other atom quantities
		@@ -61,6 +71,7 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)

		void AtomVecDipole::data_atom_post(int ilocal)
		{
		double *mu = atom->mu[ilocal];
		mu[3] = sqrt(mu[0]mu[0] + mu[1]mu[1] + mu[2]*mu[2]);
		double *mu_one = mu[ilocal];
		mu_one[3] =
		sqrt(mu_one[0]mu_one[0] + mu_one[1]mu_one[1] + mu_one[2]*mu_one[2]);
		}

src/DIPOLE/atom_vec_dipole.h

+5 −0

Original line number	Diff line number	Diff line
		@@ -27,7 +27,12 @@ namespace LAMMPS_NS {
		class AtomVecDipole : public AtomVec {
		public:
		AtomVecDipole(class LAMMPS *);

		void grow_pointers();
		void data_atom_post(int);

		private:
		double **mu;
		};

		}

src/MOLECULE/atom_vec_angle.cpp

+22 −17

Original line number	Diff line number	Diff line
		@@ -66,6 +66,20 @@ AtomVecAngle::~AtomVecAngle()
		delete [] angle_negative;
		}

		/* ----------------------------------------------------------------------
		set local copies of all grow ptrs used by this class, except defaults
		needed in replicate when 2 atom classes exist and it calls pack_restart()
		------------------------------------------------------------------------- */

		void AtomVecAngle::grow_pointers()
		{
		num_bond = atom->num_bond;
		bond_type = atom->bond_type;
		num_angle = atom->num_angle;
		angle_type = atom->angle_type;
		nspecial = atom->nspecial;
		}

		/* ----------------------------------------------------------------------
		modify values for AtomVec::pack_restart() to pack
		------------------------------------------------------------------------- */
		@@ -87,11 +101,6 @@ void AtomVecAngle::pack_restart_pre(int ilocal)

		// flip any negative types to positive and flag which ones

		int *num_bond = atom->num_bond;
		int **bond_type = atom->bond_type;
		int *num_angle = atom->num_angle;
		int **angle_type = atom->angle_type;

		int any_bond_negative = 0;
		for (int m = 0; m < num_bond[ilocal]; m++) {
		if (bond_type[ilocal][m] < 0) {
		@@ -120,15 +129,11 @@ void AtomVecAngle::pack_restart_post(int ilocal)
		// 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[ilocal]; m++)
		if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
		}

		if (any_angle_negative) {
		int *num_angle = atom->num_angle;
		int **angle_type = atom->angle_type;
		for (int m = 0; m < num_angle[ilocal]; m++)
		if (angle_negative[m]) angle_type[ilocal][m] = -angle_type[ilocal][m];
		}
		@@ -140,9 +145,9 @@ void AtomVecAngle::pack_restart_post(int ilocal)

		void AtomVecAngle::unpack_restart_init(int ilocal)
		{
		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;
		atom->nspecial[ilocal][2] = 0;
		nspecial[ilocal][0] = 0;
		nspecial[ilocal][1] = 0;
		nspecial[ilocal][2] = 0;
		}

		/* ----------------------------------------------------------------------
		@@ -152,9 +157,9 @@ void AtomVecAngle::unpack_restart_init(int ilocal)

		void AtomVecAngle::data_atom_post(int ilocal)
		{
		atom->num_bond[ilocal] = 0;
		atom->num_angle[ilocal] = 0;
		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;
		atom->nspecial[ilocal][2] = 0;
		num_bond[ilocal] = 0;
		num_angle[ilocal] = 0;
		nspecial[ilocal][0] = 0;
		nspecial[ilocal][1] = 0;
		nspecial[ilocal][2] = 0;
		}

src/MOLECULE/atom_vec_angle.h

+6 −0

Original line number	Diff line number	Diff line
		@@ -28,12 +28,18 @@ class AtomVecAngle : public AtomVec {
		public:
		AtomVecAngle(class LAMMPS *);
		~AtomVecAngle();

		void grow_pointers();
		void pack_restart_pre(int);
		void pack_restart_post(int);
		void unpack_restart_init(int);
		void data_atom_post(int);

		private:
		int num_bond,num_angle;
		int bond_type,angle_type;
		int **nspecial;

		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

+11 −18

Original line number	Diff line number	Diff line
		@@ -61,19 +61,17 @@ AtomVecBond::~AtomVecBond()
		}

		/* ----------------------------------------------------------------------
		grow atom arrays
		must set local copy of body ptr
		needed in replicate when 2 atom classes exist and pack_restart() is called
		set local copies of all grow ptrs used by this class, except defaults
		needed in replicate when 2 atom classes exist and it calls pack_restart()
		------------------------------------------------------------------------- */

		void AtomVecBond::grow(int n)
		void AtomVecBond::grow_pointers()
		{
		AtomVec::grow(n);
		num_bond = atom->num_bond;
		bond_type = atom->bond_type;
		nspecial = atom->nspecial;
		}


		/* ----------------------------------------------------------------------
		modify values for AtomVec::pack_restart() to pack
		------------------------------------------------------------------------- */
		@@ -90,9 +88,6 @@ void AtomVecBond::pack_restart_pre(int ilocal)

		// flip any negative types to positive and flag which ones

		//int *num_bond = atom->num_bond;
		//int **bond_type = atom->bond_type;

		any_bond_negative = 0;
		for (int m = 0; m < num_bond[ilocal]; m++) {
		if (bond_type[ilocal][m] < 0) {
		@@ -112,8 +107,6 @@ void AtomVecBond::pack_restart_post(int ilocal)
		// 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[ilocal]; m++)
		if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
		}
		@@ -125,9 +118,9 @@ void AtomVecBond::pack_restart_post(int ilocal)

		void AtomVecBond::unpack_restart_init(int ilocal)
		{
		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;
		atom->nspecial[ilocal][2] = 0;
		nspecial[ilocal][0] = 0;
		nspecial[ilocal][1] = 0;
		nspecial[ilocal][2] = 0;
		}

		/* ----------------------------------------------------------------------
		@@ -137,8 +130,8 @@ void AtomVecBond::unpack_restart_init(int ilocal)

		void AtomVecBond::data_atom_post(int ilocal)
		{
		atom->num_bond[ilocal] = 0;
		atom->nspecial[ilocal][0] = 0;
		atom->nspecial[ilocal][1] = 0;
		atom->nspecial[ilocal][2] = 0;
		num_bond[ilocal] = 0;
		nspecial[ilocal][0] = 0;
		nspecial[ilocal][1] = 0;
		nspecial[ilocal][2] = 0;
		}

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