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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11341 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-01-27 16:59:18 +00:00
parent 806a382bd0
commit 9b1cc599f6
16 changed files with 122 additions and 109 deletions
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2
src/MOLECULE/atom_vec_angle.h
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@ -62,7 +62,7 @@ class AtomVecAngle : public AtomVec {
int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
tagint *molecule;
int **nspecial;
tagint **special;
int *num_bond;

2
src/MOLECULE/atom_vec_bond.h
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@ -61,7 +61,7 @@ class AtomVecBond : public AtomVec {
int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
tagint *molecule;
int **nspecial;
tagint **special;
int *num_bond;

2
src/MOLECULE/atom_vec_full.h
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@ -63,7 +63,7 @@ class AtomVecFull : public AtomVec {
imageint *image;
double **x,**v,**f;
double *q;
int *molecule;
tagint *molecule;
int **nspecial;
tagint **special;
int *num_bond;

2
src/MOLECULE/atom_vec_template.cpp
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@ -63,7 +63,7 @@ void AtomVecTemplate::process_args(int narg, char **arg)
// error check on molecule template fields
for (int i = 0; i < nset; i++) {
for (int i = 0; i < nset; i++)
if (onemols[i]->typeflag == 0)
error->all(FLERR,"Atom style template molecule must have atom types");

6
src/MOLECULE/atom_vec_template.h
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@ -59,10 +59,12 @@ class AtomVecTemplate : public AtomVec {
bigint memory_usage();
protected:
int *tag,*type,*mask;
tagint *tag;
int *type,*mask;
tagint *image;
double **x,**v,**f;
int *molecule,*molindex,*molatom;
tagint *molecule;
int *molindex,*molatom;
};
}

10
src/MOLECULE/pair_hbond_dreiding_lj.cpp
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@ -88,7 +88,6 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
double r2inv,r10inv;
double switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
int *tlist;
tagint *klist;
evdwl = ehbond = 0.0;
@ -129,7 +128,7 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
tlist = onemols[imol]->special[iatom];
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = tag[i] - iatom - 1;
}
@ -151,7 +150,7 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(tlist[kk]+tagprev);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];
m = type2param[itype][jtype][ktype];
@ -478,7 +477,6 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
double rsq1,rsq2,r1,r2,c,s,ac,r2inv,r10inv,factor_hb;
double switch1,switch2;
double delr1[3],delr2[3];
int *tlist;
tagint *klist;
double **x = atom->x;
@ -502,7 +500,7 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
Molecule **onemols = atom->avec->onemols;
tlist = onemols[imol]->special[iatom];
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = atom->tag[i] - iatom - 1;
}
@ -511,7 +509,7 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(tlist[kk]+tagprev);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];

10
src/MOLECULE/pair_hbond_dreiding_morse.cpp
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@ -58,7 +58,6 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
double fi[3],fj[3],delr1[3],delr2[3];
double r,dr,dexp,eng_morse,switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
int *tlist;
tagint *klist;
evdwl = ehbond = 0.0;
@ -99,7 +98,7 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
tlist = onemols[imol]->special[iatom];
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = tag[i] - iatom - 1;
}
@ -121,7 +120,7 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(tlist[kk]+tagprev);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];
m = type2param[itype][jtype][ktype];
@ -381,7 +380,6 @@ double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
double rsq1,rsq2,r1,r2,c,s,ac,r,dr,dexp,factor_hb;
double switch1,switch2;
double delr1[3],delr2[3];
int *tlist;
tagint *klist;
double **x = atom->x;
@ -405,7 +403,7 @@ double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
int imol = atom->molindex[i];
int iatom = atom->molatom[i];
Molecule **onemols = atom->avec->onemols;
tlist = onemols[imol]->special[iatom];
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = atom->tag[i] - iatom - 1;
}
@ -414,7 +412,7 @@ double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(tlist[kk]+tagprev);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];

8
src/RIGID/fix_shake.cpp
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@ -2264,7 +2264,7 @@ int FixShake::bondtype_findset(int i, tagint n1, tagint n2, int setflag)
int iatom = atom->molatom[i];
tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1;
int *batom = onemols[imol]->bond_atom[iatom];
tagint *batom = onemols[imol]->bond_atom[iatom];
btype = onemols[imol]->bond_type[iatom];
nbonds = onemols[imol]->num_bond[iatom];
@ -2320,8 +2320,8 @@ int FixShake::angletype_findset(int i, tagint n1, tagint n2, int setflag)
int iatom = atom->molatom[i];
tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1;
int *aatom1 = onemols[imol]->angle_atom1[iatom];
int *aatom3 = onemols[imol]->angle_atom3[iatom];
tagint *aatom1 = onemols[imol]->angle_atom1[iatom];
tagint *aatom3 = onemols[imol]->angle_atom3[iatom];
atype = onemols[imol]->angle_type[iatom];
nangles = onemols[imol]->num_angle[iatom];
@ -2467,7 +2467,7 @@ void FixShake::set_molecule(int nlocalprev, tagint tagprev,
if (nlocalprev == nlocal) return;
tagint *tag = atom->tag;
int **mol_shake_atom = onemol->shake_atom;
tagint **mol_shake_atom = onemol->shake_atom;
int **mol_shake_type = onemol->shake_type;
for (int i = nlocalprev; i < nlocal; i++) {

47
src/molecule.cpp
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@ -551,7 +551,8 @@ void Molecule::masses(char *line)
void Molecule::bonds(int flag, char *line)
{
int m,tmp,itype,atom1,atom2;
int tmp,itype;
tagint m,atom1,atom2;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -561,7 +562,8 @@ void Molecule::bonds(int flag, char *line)
for (int i = 0; i < nbonds; i++) {
readline(line);
sscanf(line,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms)
@ -605,7 +607,8 @@ void Molecule::bonds(int flag, char *line)
void Molecule::angles(int flag, char *line)
{
int m,tmp,itype,atom1,atom2,atom3;
int tmp,itype;
tagint m,atom1,atom2,atom3;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -615,7 +618,8 @@ void Molecule::angles(int flag, char *line)
for (int i = 0; i < nangles; i++) {
readline(line);
sscanf(line,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms ||
@ -673,7 +677,8 @@ void Molecule::angles(int flag, char *line)
void Molecule::dihedrals(int flag, char *line)
{
int m,tmp,itype,atom1,atom2,atom3,atom4;
int tmp,itype;
tagint m,atom1,atom2,atom3,atom4;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -683,7 +688,9 @@ void Molecule::dihedrals(int flag, char *line)
for (int i = 0; i < ndihedrals; i++) {
readline(line);
sscanf(line,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms ||
@ -751,7 +758,8 @@ void Molecule::dihedrals(int flag, char *line)
void Molecule::impropers(int flag, char *line)
{
int m,tmp,itype,atom1,atom2,atom3,atom4;
int tmp,itype;
tagint m,atom1,atom2,atom3,atom4;
int newton_bond = force->newton_bond;
if (flag == 0)
@ -761,7 +769,9 @@ void Molecule::impropers(int flag, char *line)
for (int i = 0; i < nimpropers; i++) {
readline(line);
sscanf(line,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > natoms ||
atom2 <= 0 || atom2 > natoms ||
@ -861,7 +871,7 @@ void Molecule::special_read(char *line)
"does not match special count");
for (m = 1; m < nwords; m++) {
special[i][m-1] = atoi(words[m]);
special[i][m-1] = ATOTAGINT(words[m]);
if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
special[i][m-1] == i+1)
error->all(FLERR,"Invalid special atom index in molecule file");
@ -898,16 +908,18 @@ void Molecule::shakeatom_read(char *line)
for (int i = 0; i < natoms; i++) {
readline(line);
if (shake_flag[i] == 1)
sscanf(line,"%d %d %d %d",&tmp,
&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
else if (shake_flag[i] == 2)
sscanf(line,"%d %d %d",&tmp,&shake_atom[i][0],&shake_atom[i][1]);
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1]);
else if (shake_flag[i] == 3)
sscanf(line,"%d %d %d %d",&tmp,
&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
else if (shake_flag[i] == 4)
sscanf(line,"%d %d %d %d %d",&tmp,
&shake_atom[i][0],&shake_atom[i][1],
sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&shake_atom[i][0],&shake_atom[i][1],
&shake_atom[i][2],&shake_atom[i][3]);
}
@ -1066,7 +1078,8 @@ void Molecule::initialize()
special = NULL;
shake_flag = NULL;
shake_atom = shake_type = NULL;
shake_atom = NULL;
shake_type = NULL;
dx = NULL;
dxcom = NULL;

12
src/molecule.h
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@ -61,25 +61,25 @@ class Molecule : protected Pointers {
int *num_bond; // bonds, angles, dihedrals, impropers for each atom
int **bond_type;
int **bond_atom;
tagint **bond_atom;
int *num_angle;
int **angle_type;
int **angle_atom1,**angle_atom2,**angle_atom3;
tagint **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
int **nspecial;
int **special;
tagint **special;
int *shake_flag;
int **shake_atom;
tagint **shake_atom;
int **shake_type;
double center[3]; // geometric center of molecule

10
src/neigh_bond.cpp
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@ -100,7 +100,8 @@ void Neighbor::bond_template()
int imol,iatom;
tagint tagprev;
int *num_bond;
int **bond_atom,**bond_type;
tagint **bond_atom;
int **bond_type;
Molecule **onemols = atom->avec->onemols;
@ -320,7 +321,8 @@ void Neighbor::angle_template()
int imol,iatom;
tagint tagprev;
int *num_angle;
int **angle_atom1,**angle_atom2,**angle_atom3,**angle_type;
tagint **angle_atom1,**angle_atom2,**angle_atom3;
int **angle_type;
Molecule **onemols = atom->avec->onemols;
@ -579,7 +581,7 @@ void Neighbor::dihedral_template()
int imol,iatom;
tagint tagprev;
int *num_dihedral;
int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int **dihedral_type;
Molecule **onemols = atom->avec->onemols;
@ -870,7 +872,7 @@ void Neighbor::improper_template()
int imol,iatom;
tagint tagprev;
int *num_improper;
int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
int **improper_type;
Molecule **onemols = atom->avec->onemols;

30
src/neigh_full.cpp
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@ -38,9 +38,9 @@ void Neighbor::full_nsq(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -138,9 +138,9 @@ void Neighbor::full_nsq_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -252,9 +252,9 @@ void Neighbor::full_bin(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -360,9 +360,9 @@ void Neighbor::full_bin_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -496,9 +496,9 @@ void Neighbor::full_multi(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;

24
src/neigh_half_bin.cpp
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@ -43,9 +43,9 @@ void Neighbor::half_bin_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -156,9 +156,9 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -296,9 +296,9 @@ void Neighbor::half_bin_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -438,9 +438,9 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;

18
src/neigh_half_multi.cpp
View File

@ -45,9 +45,9 @@ void Neighbor::half_multi_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -161,9 +161,9 @@ void Neighbor::half_multi_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -311,9 +311,9 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;

18
src/neigh_half_nsq.cpp
View File

@ -38,9 +38,9 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -139,9 +139,9 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -259,9 +259,9 @@ void Neighbor::half_nsq_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;

30
src/neigh_respa.cpp
View File

@ -40,9 +40,9 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -201,9 +201,9 @@ void Neighbor::respa_nsq_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -383,9 +383,9 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -553,9 +553,9 @@ void Neighbor::respa_bin_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -770,9 +770,9 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *tag = atom->tag;
int *molecule = atom->molecule;
int **special = atom->special;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;