ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11921 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-05-06 21:16:26 +00:00
parent aa6458d35c
commit 650f5ef4f8
3 changed files with 23 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
src/MISC/fix_deposit.cpp
View File

@ -367,7 +367,7 @@ void FixDeposit::pre_exchange()
natom = onemols[imol]->natoms; natom = onemols[imol]->natoms;
if (dimension == 3) { if (dimension == 3) {
r[0] = random->uniform() - 0.5; r[0] = random->uniform() - 0.5;
r[1] = random->uniform() - 0.5 r[1] = random->uniform() - 0.5;
r[2] = random->uniform() - 0.5; r[2] = random->uniform() - 0.5;
} else { } else {
r[0] = r[1] = 0.0; r[0] = r[1] = 0.0;

40
src/RIGID/fix_shake.cpp
View File

@ -148,7 +148,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
// parse optional args // parse optional args
onemol = NULL; onemols = NULL;
int iarg = next; int iarg = next;
while (iarg < narg) { while (iarg < narg) {
@ -160,17 +160,17 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
if (atom->molecules[imol]->nset > 1 && comm->me == 0) if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for " error->warning(FLERR,"Molecule template for "
"fix shake has multiple molecules"); "fix shake has multiple molecules");
onemol = atom->molecules[imol]; onemols = &atom->molecules[imol];
nmol = onemol->nset; nmol = onemols[0]->nset;
iarg += 2; iarg += 2;
} else error->all(FLERR,"Illegal fix shake command"); } else error->all(FLERR,"Illegal fix shake command");
} }
// error check for Molecule template // error check for Molecule template
if (onemol) { if (onemols) {
for (int i = 0; i < nmol; i++) for (int i = 0; i < nmol; i++)
if (onemol[i].shakeflag == 0) if (onemols[i]->shakeflag == 0)
error->all(FLERR,"Fix shake molecule template must have shake info"); error->all(FLERR,"Fix shake molecule template must have shake info");
} }
@ -656,7 +656,7 @@ void FixShake::find_clusters()
if (me == 0 && screen) fprintf(screen,"Finding SHAKE clusters ...\n"); if (me == 0 && screen) fprintf(screen,"Finding SHAKE clusters ...\n");
onemols = atom->avec->onemols; atommols = atom->avec->onemols;
tagint *tag = atom->tag; tagint *tag = atom->tag;
int *type = atom->type; int *type = atom->type;
@ -701,7 +701,7 @@ void FixShake::find_clusters()
imol = molindex[i]; imol = molindex[i];
if (imol < 0) continue; if (imol < 0) continue;
iatom = molatom[i]; iatom = molatom[i];
max = MAX(max,onemols[imol]->nspecial[iatom][0]); max = MAX(max,atommols[imol]->nspecial[iatom][0]);
} }
} }
@ -736,9 +736,9 @@ void FixShake::find_clusters()
if (imol < 0) continue; if (imol < 0) continue;
iatom = molatom[i]; iatom = molatom[i];
tagprev = tag[i] - iatom - 1; tagprev = tag[i] - iatom - 1;
npartner[i] = onemols[imol]->nspecial[iatom][0]; npartner[i] = atommols[imol]->nspecial[iatom][0];
for (j = 0; j < npartner[i]; j++) for (j = 0; j < npartner[i]; j++)
partner_tag[i][j] = onemols[imol]->special[iatom][j] + tagprev;; partner_tag[i][j] = atommols[imol]->special[iatom][j] + tagprev;;
} }
} }
@ -2266,9 +2266,9 @@ int FixShake::bondtype_findset(int i, tagint n1, tagint n2, int setflag)
int iatom = atom->molatom[i]; int iatom = atom->molatom[i];
tagint *tag = atom->tag; tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1; tagint tagprev = tag[i] - iatom - 1;
tagint *batom = onemols[imol]->bond_atom[iatom]; tagint *batom = atommols[imol]->bond_atom[iatom];
btype = onemols[imol]->bond_type[iatom]; btype = atommols[imol]->bond_type[iatom];
nbonds = onemols[imol]->num_bond[iatom]; nbonds = atommols[imol]->num_bond[iatom];
for (m = 0; m < nbonds; m++) { for (m = 0; m < nbonds; m++) {
if (n1 == tag[i] && n2 == batom[m]+tagprev) break; if (n1 == tag[i] && n2 == batom[m]+tagprev) break;
@ -2322,10 +2322,10 @@ int FixShake::angletype_findset(int i, tagint n1, tagint n2, int setflag)
int iatom = atom->molatom[i]; int iatom = atom->molatom[i];
tagint *tag = atom->tag; tagint *tag = atom->tag;
tagint tagprev = tag[i] - iatom - 1; tagint tagprev = tag[i] - iatom - 1;
tagint *aatom1 = onemols[imol]->angle_atom1[iatom]; tagint *aatom1 = atommols[imol]->angle_atom1[iatom];
tagint *aatom3 = onemols[imol]->angle_atom3[iatom]; tagint *aatom3 = atommols[imol]->angle_atom3[iatom];
atype = onemols[imol]->angle_type[iatom]; atype = atommols[imol]->angle_type[iatom];
nangles = onemols[imol]->num_angle[iatom]; nangles = atommols[imol]->num_angle[iatom];
for (m = 0; m < nangles; m++) { for (m = 0; m < nangles; m++) {
if (n1 == aatom1[m]+tagprev && n2 == aatom3[m]+tagprev) break; if (n1 == aatom1[m]+tagprev && n2 == aatom3[m]+tagprev) break;
@ -2469,13 +2469,13 @@ void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol,
if (nlocalprev == nlocal) return; if (nlocalprev == nlocal) return;
tagint *tag = atom->tag; tagint *tag = atom->tag;
tagint **mol_shake_atom = onemol[imol].shake_atom; tagint **mol_shake_atom = onemols[imol]->shake_atom;
int **mol_shake_type = onemol[imol].shake_type; int **mol_shake_type = onemols[imol]->shake_type;
for (int i = nlocalprev; i < nlocal; i++) { for (int i = nlocalprev; i < nlocal; i++) {
m = tag[i] - tagprev-1; m = tag[i] - tagprev-1;
flag = shake_flag[i] = onemol[imol].shake_flag[m]; flag = shake_flag[i] = onemols[imol]->shake_flag[m];
if (flag == 1) { if (flag == 1) {
shake_atom[i][0] = mol_shake_atom[m][0] + tagprev; shake_atom[i][0] = mol_shake_atom[m][0] + tagprev;
@ -2653,7 +2653,7 @@ void *FixShake::extract(const char *str, int &dim)
{ {
dim = 0; dim = 0;
if (strcmp(str,"onemol") == 0) { if (strcmp(str,"onemol") == 0) {
return onemol; return onemols;
} }
return NULL; return NULL;
} }

4
src/RIGID/fix_shake.h
View File

@ -103,8 +103,8 @@ class FixShake : public Fix {
double *a_ave,*a_max,*a_min; double *a_ave,*a_max,*a_min;
double *a_ave_all,*a_max_all,*a_min_all; double *a_ave_all,*a_max_all,*a_min_all;
class Molecule **onemols; // atom style template pointer class Molecule **atommols; // atom style template pointer
class Molecule *onemol; // molecule added on-the-fly class Molecule **onemols; // molecule added on-the-fly
int nmol; int nmol;
void find_clusters(); void find_clusters();