(906520c0) · Commits · 郑智淋 / lammps

src/MOLECULE/Install.csh

+4 −0

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@ if ($1 == 1) then
		cp angle_hybrid.cpp ..
		cp atom_vec_angle.cpp ..
		cp atom_vec_bond.cpp ..
		cp atom_vec_full.cpp ..
		cp atom_vec_molecular.cpp ..
		cp bond.cpp ..
		cp bond_fene.cpp ..
		@@ -47,6 +48,7 @@ if ($1 == 1) then
		cp angle_hybrid.h ..
		cp atom_vec_angle.h ..
		cp atom_vec_bond.h ..
		cp atom_vec_full.h ..
		cp atom_vec_molecular.h ..
		# cp bond.h ..
		cp bond_fene.h ..
		@@ -84,6 +86,7 @@ else if ($1 == 0) then
		rm ../angle_hybrid.cpp
		rm ../atom_vec_angle.cpp
		rm ../atom_vec_bond.cpp
		rm ../atom_vec_full.cpp
		rm ../atom_vec_molecular.cpp
		rm ../bond.cpp
		rm ../bond_fene.cpp
		@@ -116,6 +119,7 @@ else if ($1 == 0) then
		rm ../angle_hybrid.h
		rm ../atom_vec_angle.h
		rm ../atom_vec_bond.h
		rm ../atom_vec_full.h
		rm ../atom_vec_molecular.h
		# rm ../bond.h
		rm ../bond_fene.h

src/MOLECULE/atom_vec_molecular.cpp

+3 −21

Original line number	Diff line number	Diff line
		@@ -40,10 +40,10 @@ AtomVecMolecular::AtomVecMolecular(LAMMPS lmp, int narg, char *arg) :
		mass_type = 1;
		size_comm = 3;
		size_reverse = 3;
		size_border = 8;
		size_data_atom = 7;
		size_border = 7;
		size_data_atom = 6;
		size_data_vel = 4;
		xcol_data = 5;
		xcol_data = 4;
		}

		/* ----------------------------------------------------------------------
		@@ -70,8 +70,6 @@ void AtomVecMolecular::grow(int n)
		v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
		f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");

		q = atom->q = (double *)
		memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
		molecule = atom->molecule = (int *)
		memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");

		@@ -158,7 +156,6 @@ void AtomVecMolecular::reset_ptrs()
		v = atom->v;
		f = atom->f;

		q = atom->q;
		molecule = atom->molecule;
		nspecial = atom->nspecial;
		special = atom->special;
		@@ -195,7 +192,6 @@ void AtomVecMolecular::reset_ptrs()

		void AtomVecMolecular::zero_owned(int i)
		{
		q[i] = 0.0;
		molecule[i] = 0;
		num_bond[i] = 0;
		num_angle[i] = 0;
		@@ -217,7 +213,6 @@ void AtomVecMolecular::zero_ghost(int n, int first)
		int last = first + n;
		for (int i = first; i < last; i++) {
		if (i == nmax) atom->avec->grow(0);
		q[i] = 0.0;
		molecule[i] = 0;
		}
		}
		@@ -239,7 +234,6 @@ void AtomVecMolecular::copy(int i, int j)
		v[j][1] = v[i][1];
		v[j][2] = v[i][2];

		q[j] = q[i];
		molecule[j] = molecule[i];

		num_bond[j] = num_bond[i];
		@@ -375,7 +369,6 @@ int AtomVecMolecular::pack_border(int n, int list, double buf,
		buf[m++] = tag[j];
		buf[m++] = type[j];
		buf[m++] = mask[j];
		buf[m++] = q[j];
		buf[m++] = molecule[j];
		}
		} else {
		@@ -390,7 +383,6 @@ int AtomVecMolecular::pack_border(int n, int list, double buf,
		buf[m++] = tag[j];
		buf[m++] = type[j];
		buf[m++] = mask[j];
		buf[m++] = q[j];
		buf[m++] = molecule[j];
		}
		}
		@@ -401,7 +393,6 @@ int AtomVecMolecular::pack_border(int n, int list, double buf,

		int AtomVecMolecular::pack_border_one(int i, double *buf)
		{
		buf[0] = q[i];
		buf[1] = molecule[i];
		return 2;
		}
		@@ -422,7 +413,6 @@ void AtomVecMolecular::unpack_border(int n, int first, double *buf)
		tag[i] = static_cast<int> (buf[m++]);
		type[i] = static_cast<int> (buf[m++]);
		mask[i] = static_cast<int> (buf[m++]);
		q[i] = buf[m++];
		molecule[i] = static_cast<int> (buf[m++]);
		}
		}
		@@ -431,7 +421,6 @@ void AtomVecMolecular::unpack_border(int n, int first, double *buf)

		int AtomVecMolecular::unpack_border_one(int i, double *buf)
		{
		q[i] = buf[0];
		molecule[i] = static_cast<int> (buf[1]);
		return 2;
		}
		@@ -457,7 +446,6 @@ int AtomVecMolecular::pack_exchange(int i, double *buf)
		buf[m++] = mask[i];
		buf[m++] = image[i];

		buf[m++] = q[i];
		buf[m++] = molecule[i];

		buf[m++] = num_bond[i];
		@@ -526,7 +514,6 @@ int AtomVecMolecular::unpack_exchange(double *buf)
		mask[nlocal] = static_cast<int> (buf[m++]);
		image[nlocal] = static_cast<int> (buf[m++]);

		q[nlocal] = buf[m++];
		molecule[nlocal] = static_cast<int> (buf[m++]);

		num_bond[nlocal] = static_cast<int> (buf[m++]);
		@@ -633,7 +620,6 @@ int AtomVecMolecular::pack_restart(int i, double *buf)
		buf[m++] = v[i][1];
		buf[m++] = v[i][2];

		buf[m++] = q[i];
		buf[m++] = molecule[i];

		buf[m++] = num_bond[i];
		@@ -705,7 +691,6 @@ int AtomVecMolecular::unpack_restart(double *buf)
		v[nlocal][1] = buf[m++];
		v[nlocal][2] = buf[m++];

		q[nlocal] = buf[m++];
		molecule[nlocal] = static_cast<int> (buf[m++]);

		num_bond[nlocal] = static_cast<int> (buf[m++]);
		@@ -772,7 +757,6 @@ void AtomVecMolecular::create_atom(int itype, double x0, double y0, double z0,
		v[nlocal][1] = 0.0;
		v[nlocal][2] = 0.0;

		q[nlocal] = 0.0;
		molecule[nlocal] = 0;
		num_bond[nlocal] = 0;
		num_angle[nlocal] = 0;
		@@ -803,8 +787,6 @@ void AtomVecMolecular::data_atom(double xtmp, double ytmp, double ztmp,
		if (type[nlocal] <= 0 \|\| type[nlocal] > atom->ntypes)
		error->one("Invalid atom type in Atoms section of data file");

		q[nlocal] = atof(values[3]);

		x[nlocal][0] = xtmp;
		x[nlocal][1] = ytmp;
		x[nlocal][2] = ztmp;

src/MOLECULE/atom_vec_molecular.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -47,7 +47,6 @@ class AtomVecMolecular : public AtomVec {
		private:
		int tag,type,mask,image;
		double x,v,**f;
		double *q;
		int *molecule;
		int nspecial,special;
		int *num_bond;

src/MOLECULE/style_molecule.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -30,12 +30,14 @@ AngleStyle(hybrid,AngleHybrid)
		#ifdef AtomInclude
		#include "atom_vec_angle.h"
		#include "atom_vec_bond.h"
		#include "atom_vec_full.h"
		#include "atom_vec_molecular.h"
		#endif

		#ifdef AtomClass
		AtomStyle(angle,AtomVecAngle)
		AtomStyle(bond,AtomVecBond)
		AtomStyle(full,AtomVecFull)
		AtomStyle(molecular,AtomVecMolecular)
		#endif

src/dump_custom.cpp

+5 −0

Original line number	Diff line number	Diff line
		@@ -561,6 +561,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		} else if (strcmp(arg[iarg],"type") == 0) {
		pack_choice[i] = &DumpCustom::pack_type;
		vtype[i] = INT;

		} else if (strcmp(arg[iarg],"x") == 0) {
		pack_choice[i] = &DumpCustom::pack_x;
		vtype[i] = DOUBLE;
		@@ -597,6 +598,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		} else if (strcmp(arg[iarg],"iz") == 0) {
		pack_choice[i] = &DumpCustom::pack_iz;
		vtype[i] = INT;

		} else if (strcmp(arg[iarg],"vx") == 0) {
		pack_choice[i] = &DumpCustom::pack_vx;
		vtype[i] = DOUBLE;
		@@ -615,6 +617,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		} else if (strcmp(arg[iarg],"fz") == 0) {
		pack_choice[i] = &DumpCustom::pack_fz;
		vtype[i] = DOUBLE;

		} else if (strcmp(arg[iarg],"q") == 0) {
		if (atom->q == NULL)
		error->all("Dumping an atom quantity that isn't allocated");
		@@ -650,6 +653,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		error->all("Dumping an atom quantity that isn't allocated");
		pack_choice[i] = &DumpCustom::pack_tqz;
		vtype[i] = DOUBLE;

		} else if (strcmp(arg[iarg],"epair") == 0) {
		pack_choice[i] = &DumpCustom::pack_epair;
		vtype[i] = DOUBLE;
		@@ -667,6 +671,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
		pack_choice[i] = &DumpCustom::pack_centro;
		vtype[i] = DOUBLE;
		index_centro = add_compute(style_centro,1);

		} else if (strcmp(arg[iarg],"sxx") == 0) {
		pack_choice[i] = &DumpCustom::pack_sxx;
		vtype[i] = DOUBLE;

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