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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11293 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-01-22 17:44:32 +00:00
parent 25613401a4
commit 127eb167c1
60 changed files with 421 additions and 375 deletions
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4
src/GRANULAR/fix_pour.cpp
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@ -666,7 +666,7 @@ void FixPour::pre_exchange()
void FixPour::find_maxid()
{
tagint *tag = atom->tag;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint max = 0;
@ -676,7 +676,7 @@ void FixPour::find_maxid()
if (mode == MOLECULE && molecule) {
max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
MPI_Allreduce(&max,&maxmol_all,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
}
}

3
src/GRANULAR/fix_pour.h
View File

@ -62,8 +62,7 @@ class FixPour : public Fix {
int *recvcounts,*displs;
int nfreq,nfirst,ninserted,nper;
double lo_current,hi_current;
tagint maxtag_all;
int maxmol_all;
tagint maxtag_all,maxmol_all;
class RanPark *random,*random2;
void find_maxid();

5
src/MC/fix_bond_swap.cpp
View File

@ -126,7 +126,8 @@ void FixBondSwap::init()
// require an atom style with molecule IDs
if (atom->molecule == NULL)
error->all(FLERR,"Must use atom style with molecule IDs with fix bond/swap");
error->all(FLERR,
"Must use atom style with molecule IDs with fix bond/swap");
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
@ -193,7 +194,7 @@ void FixBondSwap::pre_neighbor()
tagint *tag = atom->tag;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;

65
src/MC/fix_gcmc.cpp
View File

@ -252,7 +252,7 @@ void FixGCMC::init()
// if molflag not set, warn if any deletable atom has a mol ID
if (molflag == 0 && atom->molecule_flag) {
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
@ -268,7 +268,7 @@ void FixGCMC::init()
// if molflag set, check for unset mol IDs
if (molflag == 1) {
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
@ -578,7 +578,7 @@ void FixGCMC::attempt_molecule_translation()
if (ngas == 0) return;
int translation_molecule = pick_random_gas_molecule();
tagint translation_molecule = pick_random_gas_molecule();
if (translation_molecule == -1) return;
double energy_before_sum = molecule_energy(translation_molecule);
@ -637,7 +637,7 @@ void FixGCMC::attempt_molecule_rotation()
if (ngas == 0) return;
int rotation_molecule = pick_random_gas_molecule();
tagint rotation_molecule = pick_random_gas_molecule();
if (rotation_molecule == -1) return;
double energy_before_sum = molecule_energy(rotation_molecule);
@ -719,7 +719,7 @@ void FixGCMC::attempt_molecule_deletion()
if (ngas == 0) return;
int deletion_molecule = pick_random_gas_molecule();
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
double deletion_energy_sum = molecule_energy(deletion_molecule);
@ -756,13 +756,20 @@ void FixGCMC::attempt_molecule_insertion()
double com_coord[3];
if (regionflag) {
int region_attempt = 0;
com_coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
com_coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
com_coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
while (domain->regions[iregion]->match(com_coord[0],com_coord[1],com_coord[2]) == 0) {
com_coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
com_coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
com_coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
com_coord[0] = region_xlo + random_equal->uniform() *
(region_xhi-region_xlo);
com_coord[1] = region_ylo + random_equal->uniform() *
(region_yhi-region_ylo);
com_coord[2] = region_zlo + random_equal->uniform() *
(region_zhi-region_zlo);
while (domain->regions[iregion]->match(com_coord[0],com_coord[1],
com_coord[2]) == 0) {
com_coord[0] = region_xlo + random_equal->uniform() *
(region_xhi-region_xlo);
com_coord[1] = region_ylo + random_equal->uniform() *
(region_yhi-region_ylo);
com_coord[2] = region_zlo + random_equal->uniform() *
(region_zhi-region_zlo);
region_attempt++;
if (region_attempt >= max_region_attempts) return;
}
@ -779,9 +786,12 @@ void FixGCMC::attempt_molecule_insertion()
double insertion_energy = 0.0;
bool procflag[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
atom_coord[i][0] = rot[0]*model_x[i][0] + rot[1]*model_x[i][1] + rot[2]*model_x[i][2] + com_coord[0];
atom_coord[i][1] = rot[3]*model_x[i][0] + rot[4]*model_x[i][1] + rot[5]*model_x[i][2] + com_coord[1];
atom_coord[i][2] = rot[6]*model_x[i][0] + rot[7]*model_x[i][1] + rot[8]*model_x[i][2] + com_coord[2];
atom_coord[i][0] = rot[0]*model_x[i][0] +
rot[1]*model_x[i][1] + rot[2]*model_x[i][2] + com_coord[0];
atom_coord[i][1] = rot[3]*model_x[i][0] +
rot[4]*model_x[i][1] + rot[5]*model_x[i][2] + com_coord[1];
atom_coord[i][2] = rot[6]*model_x[i][0] +
rot[7]*model_x[i][1] + rot[8]*model_x[i][2] + com_coord[2];
double xtmp[3];
xtmp[0] = atom_coord[i][0];
@ -799,11 +809,13 @@ void FixGCMC::attempt_molecule_insertion()
}
double insertion_energy_sum = 0.0;
MPI_Allreduce(&insertion_energy,&insertion_energy_sum,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&insertion_energy,&insertion_energy_sum,1,
MPI_DOUBLE,MPI_SUM,world);
if (random_equal->uniform() < zz*volume*natoms_per_molecule*exp(-beta*insertion_energy_sum)/(ngas+1)) {
if (random_equal->uniform() < zz*volume*natoms_per_molecule*
exp(-beta*insertion_energy_sum)/(ngas+1)) {
maxmol++;
if (maxmol >= MAXSMALLINT)
if (maxmol >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
tagint maxtag = 0;
@ -883,13 +895,13 @@ void FixGCMC::attempt_molecule_insertion()
compute particle's interaction energy with the rest of the system
------------------------------------------------------------------------- */
double FixGCMC::energy(int i, int itype, int imolecule, double *coord)
double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
{
double delx,dely,delz,rsq;
double **x = atom->x;
int *type = atom->type;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
pair = force->pair;
cutsq = force->pair->cutsq;
@ -941,7 +953,7 @@ int FixGCMC::pick_random_gas_atom()
int FixGCMC::pick_random_gas_molecule()
{
int iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
int gas_molecule_id = 0;
tagint gas_molecule_id = 0;
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
int iwhichlocal = iwhichglobal - ngas_before;
@ -949,8 +961,9 @@ int FixGCMC::pick_random_gas_molecule()
gas_molecule_id = atom->molecule[i];
}
int gas_molecule_id_all = 0;
MPI_Allreduce(&gas_molecule_id,&gas_molecule_id_all,1,MPI_INT,MPI_MAX,world);
tagint gas_molecule_id_all = 0;
MPI_Allreduce(&gas_molecule_id,&gas_molecule_id_all,1,
MPI_LMP_TAGINT,MPI_MAX,world);
return gas_molecule_id_all;
}
@ -960,7 +973,7 @@ int FixGCMC::pick_random_gas_molecule()
sum across all procs that own atoms of the given molecule
------------------------------------------------------------------------- */
double FixGCMC::molecule_energy(int gas_molecule_id)
double FixGCMC::molecule_energy(tagint gas_molecule_id)
{
double mol_energy = 0.0;
for (int i = 0; i < atom->nlocal; i++)
@ -1040,8 +1053,8 @@ void FixGCMC::get_model_molecule()
if (atom->molecular) {
for (int i = 0; i < atom->nlocal; i++)
maxmol = MAX(atom->molecule[i],maxmol);
int maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_INT,MPI_MAX,world);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol = maxmol_all;
}

7
src/MC/fix_gcmc.h
View File

@ -41,7 +41,7 @@ class FixGCMC : public Fix {
void attempt_molecule_insertion();
double energy(int, int, int, double *);
int pick_random_gas_atom();
int pick_random_gas_molecule();
tagint pick_random_gas_molecule();
double molecule_energy(int);
void get_rotation_matrix(double, double *);
void get_model_molecule();
@ -63,9 +63,10 @@ class FixGCMC : public Fix {
int regionflag; // 0 = anywhere in box, 1 = specific region
int iregion; // GCMC region
char *idregion; // GCMC region id
bool pressure_flag; // true if user specified reservoir pressure, false otherwise
bool pressure_flag; // true if user specified reservoir pressure
// else false
int maxmol; // largest molecule tag across all existing atoms
tagint maxmol; // largest molecule tag across all existing atoms
int natoms_per_molecule; // number of atoms in each gas molecule
double ntranslation_attempts;

4
src/MISC/fix_deposit.cpp
View File

@ -523,7 +523,7 @@ void FixDeposit::pre_exchange()
void FixDeposit::find_maxid()
{
tagint *tag = atom->tag;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint max = 0;
@ -533,7 +533,7 @@ void FixDeposit::find_maxid()
if (mode == MOLECULE && molecule) {
max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
MPI_Allreduce(&max,&maxmol_all,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
}
}

3
src/MISC/fix_deposit.h
View File

@ -55,8 +55,7 @@ class FixDeposit : public Fix {
class Fix *fixrigid,*fixshake;
int nfirst,ninserted;
tagint maxtag_all;
int maxmol_all;
tagint maxtag_all,maxmol_all;
class RanPark *random;
void find_maxid();

13
src/MISC/fix_evaporate.cpp
View File

@ -137,7 +137,7 @@ void FixEvaporate::init()
// if molflag not set, warn if any deletable atom has a mol ID
if (molflag == 0 && atom->molecule_flag) {
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
@ -234,8 +234,9 @@ void FixEvaporate::pre_exchange()
// keep ndel,ndeltopo,ncount,nall,nbefore current after each mol deletion
} else {
int me,proc,iatom,imolecule,ndelone,ndelall;
int *molecule = atom->molecule;
int me,proc,iatom,ndelone,ndelall;
tagint imol;
tagint *molecule = atom->molecule;
ndeltopo[0] = ndeltopo[1] = ndeltopo[2] = ndeltopo[3] = 0;
@ -247,7 +248,7 @@ void FixEvaporate::pre_exchange()
if (iwhichglobal >= nbefore && iwhichglobal < nbefore + ncount) {
iwhichlocal = iwhichglobal - nbefore;
iatom = list[iwhichlocal];
imolecule = molecule[iatom];
imol = molecule[iatom];
me = comm->me;
} else me = -1;
@ -257,10 +258,10 @@ void FixEvaporate::pre_exchange()
// be careful to delete correct # of bond,angle,etc for newton on or off
MPI_Allreduce(&me,&proc,1,MPI_INT,MPI_MAX,world);
MPI_Bcast(&imolecule,1,MPI_INT,proc,world);
MPI_Bcast(&imol,1,MPI_LMP_TAGINT,proc,world);
ndelone = 0;
for (i = 0; i < nlocal; i++) {
if (imolecule && molecule[i] == imolecule) {
if (imol && molecule[i] == imol) {
mark[i] = 1;
ndelone++;

21
src/MOLECULE/atom_vec_angle.cpp
View File

@ -478,7 +478,7 @@ void AtomVecAngle::unpack_border(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
}
if (atom->nextra_border)
@ -503,7 +503,7 @@ void AtomVecAngle::unpack_border_vel(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
@ -524,7 +524,7 @@ int AtomVecAngle::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
return m;
}
@ -599,7 +599,7 @@ int AtomVecAngle::unpack_exchange(double *buf)
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -725,7 +725,7 @@ int AtomVecAngle::unpack_restart(double *buf)
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -794,7 +794,7 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values)
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(values[1]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@ -822,7 +822,7 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values)
int AtomVecAngle::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
molecule[nlocal] = ATOTAGINT(values[0]);
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
@ -867,8 +867,9 @@ int AtomVecAngle::pack_data_hybrid(int i, double *buf)
void AtomVecAngle::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
buf[i][3],buf[i][4],buf[i][5],
(int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i,
@ -881,7 +882,7 @@ void AtomVecAngle::write_data(FILE *fp, int n, double **buf)
int AtomVecAngle::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d",(int) ubuf(buf[0]).i);
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[0]).i);
return 1;
}

23
src/MOLECULE/atom_vec_bond.cpp
View File

@ -436,7 +436,7 @@ int AtomVecBond::pack_border_hybrid(int n, int *list, double *buf)
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = molecule[j];
buf[m++] = ubuf(molecule[j]).d;
}
return m;
}
@ -457,7 +457,7 @@ void AtomVecBond::unpack_border(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
}
if (atom->nextra_border)
@ -482,7 +482,7 @@ void AtomVecBond::unpack_border_vel(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
@ -503,7 +503,7 @@ int AtomVecBond::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
return m;
}
@ -570,7 +570,7 @@ int AtomVecBond::unpack_exchange(double *buf)
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -680,7 +680,7 @@ int AtomVecBond::unpack_restart(double *buf)
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -740,7 +740,7 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values)
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(values[1]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@ -767,7 +767,7 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values)
int AtomVecBond::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
molecule[nlocal] = ATOTAGINT(values[0]);
num_bond[nlocal] = 0;
@ -811,8 +811,9 @@ int AtomVecBond::pack_data_hybrid(int i, double *buf)
void AtomVecBond::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
buf[i][3],buf[i][4],buf[i][5],
(int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i,
@ -825,7 +826,7 @@ void AtomVecBond::write_data(FILE *fp, int n, double **buf)
int AtomVecBond::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d",(int) ubuf(buf[0]).i);
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[0]).i);
return 1;
}

24
src/MOLECULE/atom_vec_full.cpp
View File

@ -473,7 +473,7 @@ int AtomVecFull::pack_border_vel(int n, int *list, double *buf,
buf[m++] = ubuf(type[j]).d;
buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = molecule[j];
buf[m++] = ubuf(molecule[j]).d;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
@ -544,7 +544,7 @@ void AtomVecFull::unpack_border(int n, int first, double *buf)
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
}
if (atom->nextra_border)
@ -570,7 +570,7 @@ void AtomVecFull::unpack_border_vel(int n, int first, double *buf)
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
@ -592,7 +592,7 @@ int AtomVecFull::unpack_border_hybrid(int n, int first, double *buf)
last = first + n;
for (i = first; i < last; i++) {
q[i] = buf[m++];
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
}
return m;
}
@ -688,7 +688,7 @@ int AtomVecFull::unpack_exchange(double *buf)
image[nlocal] = (imageint) ubuf(buf[m++]).i;
q[nlocal] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -853,7 +853,7 @@ int AtomVecFull::unpack_restart(double *buf)
v[nlocal][2] = buf[m++];
q[nlocal] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -943,7 +943,7 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values)
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(values[1]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@ -975,7 +975,7 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values)
int AtomVecFull::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
molecule[nlocal] = ATOTAGINT(values[0]);
q[nlocal] = atof(values[1]);
num_bond[nlocal] = 0;
@ -1025,9 +1025,9 @@ int AtomVecFull::pack_data_hybrid(int i, double *buf)
void AtomVecFull::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
buf[i][3],buf[i][4],buf[i][5],buf[i][6],
(int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i,
@ -1040,7 +1040,7 @@ void AtomVecFull::write_data(FILE *fp, int n, double **buf)
int AtomVecFull::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d %-1.16e",(int) ubuf(buf[0]).i,buf[1]);
fprintf(fp," " TAGINT_FORMAT " %-1.16e",(tagint) ubuf(buf[0]).i,buf[1]);
return 2;
}

21
src/MOLECULE/atom_vec_molecular.cpp
View File

@ -535,7 +535,7 @@ void AtomVecMolecular::unpack_border(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
}
if (atom->nextra_border)
@ -560,7 +560,7 @@ void AtomVecMolecular::unpack_border_vel(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
@ -581,7 +581,7 @@ int AtomVecMolecular::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
return m;
}
@ -674,7 +674,7 @@ int AtomVecMolecular::unpack_exchange(double *buf)
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -837,7 +837,7 @@ int AtomVecMolecular::unpack_restart(double *buf)
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
@ -927,7 +927,7 @@ void AtomVecMolecular::data_atom(double *coord, imageint imagetmp,
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(values[1]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@ -957,7 +957,7 @@ void AtomVecMolecular::data_atom(double *coord, imageint imagetmp,
int AtomVecMolecular::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
molecule[nlocal] = ATOTAGINT(values[0]);
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
@ -1004,8 +1004,9 @@ int AtomVecMolecular::pack_data_hybrid(int i, double *buf)
void AtomVecMolecular::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT " %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,
buf[i][3],buf[i][4],buf[i][5],
(int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i,
@ -1018,7 +1019,7 @@ void AtomVecMolecular::write_data(FILE *fp, int n, double **buf)
int AtomVecMolecular::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d",(int) ubuf(buf[0]).i);
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[0]).i);
return 1;
}

2
src/MOLECULE/atom_vec_molecular.h
View File

@ -61,7 +61,7 @@ class AtomVecMolecular : public AtomVec {
int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
tagint *molecule;
int **nspecial;
tagint **special;
int *num_bond;

38
src/POEMS/fix_poems.cpp
View File

@ -144,7 +144,7 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
if (!(mask[i] & groupbit)) natom2body[i] = 0;
// each molecule in fix group is a rigid body
// maxmol = largest molecule #
// maxmol = largest molecule ID
// ncount = # of atoms in each molecule (have to sum across procs)
// nbody = # of non-zero ncount values
// use nall as incremented ptr to set atom2body[] values for each atom
@ -152,31 +152,36 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[3],"molecule") == 0) {
if (narg != 4) error->all(FLERR,"Illegal fix poems command");
if (atom->molecular == 0)
error->all(FLERR,"Must use a molecular atom style with fix poems molecule");
error->all(FLERR,
"Must use a molecular atom style with fix poems molecule");
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int maxmol = -1;
tagint maxmol_tag = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
if (mask[i] & groupbit) maxmol_tag = MAX(maxmol_tag,molecule[i]);
int itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_INT,MPI_MAX,world);
maxmol = itmp + 1;
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix poems");
maxmol = (int) itmp;
int *ncount = new int[maxmol];
for (i = 0; i < maxmol; i++) ncount[i] = 0;
int *ncount;
memory->create(ncount,maxmol+1,"rigid:ncount");
for (i = 0; i <= maxmol; i++) ncount[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) ncount[molecule[i]]++;
int *nall = new int[maxmol];
MPI_Allreduce(ncount,nall,maxmol,MPI_INT,MPI_SUM,world);
int *nall;
memory->create(nall,maxmol+1,"rigid:ncount");
MPI_Allreduce(ncount,nall,maxmol+1,MPI_INT,MPI_SUM,world);
nbody = 0;
for (i = 0; i < maxmol; i++)
for (i = 0; i <= maxmol; i++)
if (nall[i]) nall[i] = nbody++;
else nall[i] = -1;
@ -188,8 +193,8 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
}
}
delete [] ncount;
delete [] nall;
memory->destroy(ncount);
memory->destroy(nall);
} else error->all(FLERR,"Illegal fix poems command");
@ -203,7 +208,8 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
if (natom2body[i] > MAXBODY) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Atom in too many rigid bodies - boost MAXBODY");
if (flagall)
error->all(FLERR,"Atom in too many rigid bodies - boost MAXBODY");
// create all nbody-length arrays

16
src/RIGID/fix_rigid.cpp
View File

@ -109,7 +109,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
}
// each molecule in fix group is a rigid body
// maxmol = largest molecule #
// maxmol = largest molecule ID
// ncount = # of atoms in each molecule (have to sum across procs)
// nbody = # of non-zero ncount values
// use nall as incremented ptr to set body[] values for each atom
@ -121,16 +121,18 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
maxmol = -1;
tagint maxmol_tag = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
if (mask[i] & groupbit) maxmol_tag = MAX(maxmol_tag,molecule[i]);
int itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_INT,MPI_MAX,world);
maxmol = itmp;
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix rigid");
maxmol = (int) itmp;
int *ncount;
memory->create(ncount,maxmol+1,"rigid:ncount");

40
src/RIGID/fix_rigid_small.cpp
View File

@ -107,15 +107,15 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// maxmol = largest molecule #
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
maxmol = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
int itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_INT,MPI_MAX,world);
tagint itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol = itmp;
// parse optional args
@ -2147,8 +2147,8 @@ void FixRigidSmall::setup_bodies_dynamic()
void FixRigidSmall::readfile(int which, double **array, int *inbody)
{
int i,j,m,nchunk,id,eofflag;
int nlines;
int i,j,m,nchunk,eofflag,nlines;
tagint id;
FILE *fp;
char *eof,*start,*next,*buf;
char line[MAXLINE];
@ -2157,10 +2157,10 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
// key = mol ID of bodies my atoms own
// value = index into local body array
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
hash = new std::map<int,int>();
hash = new std::map<tagint,int>();
for (int i = 0; i < nlocal; i++)
if (bodyown[i] >= 0) (*hash)[atom->molecule[i]] = bodyown[i];
@ -2219,28 +2219,28 @@ void FixRigidSmall::readfile(int which, double **array, int *inbody)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
id = atoi(values[0]);
id = ATOTAGINT(values[0]);
if (id <= 0 || id > maxmol)
error->all(FLERR,"Invalid rigid body ID in fix rigid/small file");
if (hash->find(id) == hash->end()) {
buf = next + 1;
continue;
}
id = (*hash)[id];
inbody[id] = 1;
m = (*hash)[id];
inbody[m] = 1;
if (which == 0) {
body[id].mass = atof(values[1]);
body[id].xcm[0] = atof(values[2]);
body[id].xcm[1] = atof(values[3]);
body[id].xcm[2] = atof(values[4]);
body[m].mass = atof(values[1]);
body[m].xcm[0] = atof(values[2]);
body[m].xcm[1] = atof(values[3]);
body[m].xcm[2] = atof(values[4]);
} else {
array[id][0] = atof(values[5]);
array[id][1] = atof(values[6]);
array[id][2] = atof(values[7]);
array[id][3] = atof(values[10]);
array[id][4] = atof(values[9]);
array[id][5] = atof(values[8]);
array[m][0] = atof(values[5]);
array[m][1] = atof(values[6]);
array[m][2] = atof(values[7]);
array[m][3] = atof(values[10]);
array[m][4] = atof(values[9]);
array[m][5] = atof(values[8]);
}
buf = next + 1;

2
src/RIGID/fix_rigid_small.h
View File

@ -81,7 +81,7 @@ class FixRigidSmall : public Fix {
int firstflag; // 1 for first-time setup of rigid bodies
int commflag; // various modes of forward/reverse comm
int nbody; // total # of rigid bodies
int maxmol; // max mol-ID
tagint maxmol; // max mol-ID
double maxextent; // furthest distance from body owner to body atom
struct Body {

36
src/USER-LB/fix_lb_rigid_pc_sphere.cpp
View File

@ -95,31 +95,36 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[3],"molecule") == 0) {
iarg = 4;
if (atom->molecular == 0)
error->all(FLERR,"Must use a molecular atom style with fix lb/rigid/pc/sphere molecule");
error->all(FLERR,"Must use a molecular atom style with "
"fix lb/rigid/pc/sphere molecule");
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int maxmol = -1;
tagint maxmol_tag = -1;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
if (mask[i] & groupbit) maxmol_tag = MAX(maxmol_tag,molecule[i]);
int itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_INT,MPI_MAX,world);
maxmol = itmp + 1;
tagint itmp;
MPI_Allreduce(&maxmol_tag,&itmp,1,MPI__LMP_TAGINT,MPI_MAX,world);
if (itmp+1 > MAXSMALLINT)
error->all(FLERR,"Too many molecules for fix lb/rigid/pc/sphere");
maxmol = (int) itmp;
int *ncount = new int[maxmol];
for (i = 0; i < maxmol; i++) ncount[i] = 0;
int *ncount;
memory->create(ncount,maxmol+1,"rigid:ncount");
for (i = 0; i <= maxmol; i++) ncount[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) ncount[molecule[i]]++;
int *nall = new int[maxmol];
MPI_Allreduce(ncount,nall,maxmol,MPI_INT,MPI_SUM,world);
int *nall;
memory->create(nall,maxmol+1,"rigid:ncount");
MPI_Allreduce(ncount,nall,maxmol+1,MPI_LMP_TAGINT,MPI_SUM,world);
nbody = 0;
for (i = 0; i < maxmol; i++)
for (i = 0; i <= maxmol; i++)
if (nall[i]) nall[i] = nbody++;
else nall[i] = -1;
@ -128,8 +133,8 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
if (mask[i] & groupbit) body[i] = nall[molecule[i]];
}
delete [] ncount;
delete [] nall;
memory->destroy(ncount);
memory->destroy(nall);
// each listed group is a rigid body
// check if all listed groups exist
@ -140,7 +145,8 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) :
if (narg < 5) error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
nbody = atoi(arg[4]);
if (nbody <= 0) error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
if (narg < 5+nbody) error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
if (narg < 5+nbody)
error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command");
iarg = 5 + nbody;
int *igroups = new int[nbody];

10
src/USER-OMP/neigh_full_omp.cpp
View File

@ -50,7 +50,7 @@ void Neighbor::full_nsq_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
@ -138,7 +138,7 @@ void Neighbor::full_nsq_ghost_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -242,7 +242,7 @@ void Neighbor::full_bin_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -341,7 +341,7 @@ void Neighbor::full_bin_ghost_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -469,7 +469,7 @@ void Neighbor::full_multi_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;

10
src/USER-OMP/neigh_gran_omp.cpp
View File

@ -63,7 +63,7 @@ void Neighbor::granular_nsq_no_newton_omp(NeighList *list)
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
@ -192,7 +192,7 @@ void Neighbor::granular_nsq_newton_omp(NeighList *list)
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
@ -304,7 +304,7 @@ void Neighbor::granular_bin_no_newton_omp(NeighList *list)
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -443,7 +443,7 @@ void Neighbor::granular_bin_newton_omp(NeighList *list)
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@ -552,7 +552,7 @@ void Neighbor::granular_bin_newton_tri_omp(NeighList *list)
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *ilist = list->ilist;
int *numneigh = list->numneigh;

8
src/USER-OMP/neigh_half_bin_omp.cpp
View File

@ -56,7 +56,7 @@ void Neighbor::half_bin_no_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -159,7 +159,7 @@ void Neighbor::half_bin_no_newton_ghost_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -288,7 +288,7 @@ void Neighbor::half_bin_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -414,7 +414,7 @@ void Neighbor::half_bin_newton_tri_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;

6
src/USER-OMP/neigh_half_multi_omp.cpp
View File

@ -58,7 +58,7 @@ void Neighbor::half_multi_no_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -164,7 +164,7 @@ void Neighbor::half_multi_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -298,7 +298,7 @@ void Neighbor::half_multi_newton_tri_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;

6
src/USER-OMP/neigh_half_nsq_omp.cpp
View File

@ -52,7 +52,7 @@ void Neighbor::half_nsq_no_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -141,7 +141,7 @@ void Neighbor::half_nsq_no_newton_ghost_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -250,7 +250,7 @@ void Neighbor::half_nsq_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;

10
src/USER-OMP/neigh_respa_omp.cpp
View File

@ -59,7 +59,7 @@ void Neighbor::respa_nsq_no_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
@ -210,7 +210,7 @@ void Neighbor::respa_nsq_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
@ -382,7 +382,7 @@ void Neighbor::respa_bin_no_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -545,7 +545,7 @@ void Neighbor::respa_bin_newton_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;
@ -749,7 +749,7 @@ void Neighbor::respa_bin_newton_tri_omp(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int molecular = atom->molecular;
int *ilist = list->ilist;

4
src/USER-REAXC/fix_reaxc_bonds.cpp
View File

@ -290,7 +290,7 @@ void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
avqtmp = buf[j+3];
numbonds = nint(buf[j+4]);
fprintf(fp," %d %d %d",itag,itype,numbonds);
fprintf(fp," " TAGINT_FORMAT " %d %d",itag,itype,numbonds);
for (k = 5; k < 5+numbonds; k++) {
jtag = static_cast<tagint> (buf[j+k]);
@ -298,7 +298,7 @@ void FixReaxCBonds::RecvBuffer(double *buf, int nbuf, int nbuf_local,
}
j += (5+numbonds);
fprintf(fp," %d",nint(buf[j]));
fprintf(fp," " TAGINT_FORMAT,static_cast<tagint> (buf[j]));
j ++;
for (k = 0; k < numbonds; k++) {

3
src/atom.h
View File

@ -50,7 +50,8 @@ class Atom : protected Pointers {
imageint *image;
double **x,**v,**f;
int *molecule,*molindex,*molatom;
tagint *molecule;
int *molindex,*molatom;
double *q,**mu;
double **omega,**angmom,**torque;
double *radius,*rmass,*vfrac,*s0;

25
src/atom_vec_line.cpp
View File

@ -642,7 +642,7 @@ int AtomVecLine::pack_border_hybrid(int n, int *list, double *buf)
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = molecule[j];
buf[m++] = ubuf(molecule[j]).d;
if (line[j] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -669,7 +669,7 @@ void AtomVecLine::unpack_border(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
@ -705,7 +705,7 @@ void AtomVecLine::unpack_border_vel(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
@ -740,7 +740,7 @@ int AtomVecLine::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++) {
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
line[i] = (int) ubuf(buf[m++]).i;
if (line[i] == 0) line[i] = -1;
else {
@ -816,7 +816,7 @@ int AtomVecLine::unpack_exchange(double *buf)
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
@ -931,7 +931,7 @@ int AtomVecLine::unpack_restart(double *buf)
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
omega[nlocal][0] = buf[m++];
omega[nlocal][1] = buf[m++];
@ -1000,7 +1000,7 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values)
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(values[1]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@ -1038,7 +1038,7 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values)
int AtomVecLine::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
molecule[nlocal] = ATOTAGINT(values[0]);
line[nlocal] = atoi(values[1]);
if (line[nlocal] == 0) line[nlocal] = -1;
@ -1166,9 +1166,9 @@ int AtomVecLine::pack_data_hybrid(int i, double *buf)
void AtomVecLine::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,(int) ubuf(buf[i][3]).i,
buf[i][4],buf[i][5],buf[i][6],buf[i][7],
(int) ubuf(buf[i][8]).i,(int) ubuf(buf[i][9]).i,
@ -1181,7 +1181,8 @@ void AtomVecLine::write_data(FILE *fp, int n, double **buf)
int AtomVecLine::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d %d %-1.16e",(int) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,buf[2]);
fprintf(fp," " TAGINT_FORMAT " %d %-1.16e",
(tagint) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,buf[2]);
return 3;
}

23
src/atom_vec_tri.cpp
View File

@ -885,7 +885,7 @@ void AtomVecTri::unpack_border(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
else {
@ -941,7 +941,7 @@ void AtomVecTri::unpack_border_vel(int n, int first, double *buf)
tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
else {
@ -996,7 +996,7 @@ int AtomVecTri::unpack_border_hybrid(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++) {
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
tri[i] = (int) ubuf(buf[m++]).i;
if (tri[i] == 0) tri[i] = -1;
else {
@ -1110,7 +1110,7 @@ int AtomVecTri::unpack_exchange(double *buf)
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
@ -1263,7 +1263,7 @@ int AtomVecTri::unpack_restart(double *buf)
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = (int) ubuf(buf[m++]).i;
molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
rmass[nlocal] = buf[m++];
angmom[nlocal][0] = buf[m++];
angmom[nlocal][1] = buf[m++];
@ -1351,7 +1351,7 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values)
if (nlocal == nmax) grow(0);
tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(values[1]);
molecule[nlocal] = ATOTAGINT(values[1]);
type[nlocal] = atoi(values[2]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@ -1389,7 +1389,7 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values)
int AtomVecTri::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
molecule[nlocal] = ATOTAGINT(values[0]);
tri[nlocal] = atoi(values[1]);
if (tri[nlocal] == 0) tri[nlocal] = -1;
@ -1614,9 +1614,9 @@ int AtomVecTri::pack_data_hybrid(int i, double *buf)
void AtomVecTri::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
fprintf(fp,TAGINT_FORMAT
" %d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
fprintf(fp,TAGINT_FORMAT " " TAGINT_FORMAT
" %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
(tagint) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
(int) ubuf(buf[i][2]).i,(int) ubuf(buf[i][3]).i,
buf[i][4],buf[i][5],buf[i][6],buf[i][7],
(int) ubuf(buf[i][8]).i,(int) ubuf(buf[i][9]).i,
@ -1629,7 +1629,8 @@ void AtomVecTri::write_data(FILE *fp, int n, double **buf)
int AtomVecTri::write_data_hybrid(FILE *fp, double *buf)
{
fprintf(fp," %d %d %-1.16e",(int) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,buf[2]);
fprintf(fp," " TAGINT_FORMAT " %d %-1.16e",
(tagint) ubuf(buf[0]).i,(int) ubuf(buf[1]).i,buf[2]);
return 3;
}

20
src/compute.cpp
View File

@ -29,7 +29,7 @@
using namespace LAMMPS_NS;
#define DELTA 4
#define BIG 2000000000
#define BIG MAXTAGINT
/* ---------------------------------------------------------------------- */
@ -215,7 +215,7 @@ void Compute::clearstep()
return idlo and idhi
------------------------------------------------------------------------- */
int Compute::molecules_in_group(int &idlo, int &idhi)
int Compute::molecules_in_group(tagint &idlo, tagint &idhi)
{
int i;
@ -225,12 +225,12 @@ int Compute::molecules_in_group(int &idlo, int &idhi)
// find lo/hi molecule ID for any atom in group
// warn if atom in group has ID = 0
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int lo = BIG;
int hi = -BIG;
tagint lo = BIG;
tagint hi = -BIG;
int flag = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -245,14 +245,18 @@ int Compute::molecules_in_group(int &idlo, int &idhi)
error->warning(FLERR,"Atom with molecule ID = 0 included in "
"compute molecule group");
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&lo,&idlo,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (idlo == BIG) return 0;
// molmap = vector of length nlen
// set to 1 for IDs that appear in group across all procs, else 0
int nlen = idhi-idlo+1;
tagint nlen_tag = idhi-idlo+1;
if (nlen_tag > MAXSMALLINT)
error->all(FLERR,"Too many molecules for compute");
int nlen = (int) nlen_tag;
memory->create(molmap,nlen,"compute:molmap");
for (i = 0; i < nlen; i++) molmap[i] = 0;

2
src/compute.h
View File

@ -130,7 +130,7 @@ class Compute : protected Pointers {
int *molmap; // convert molecule ID to local index
int molecules_in_group(int &, int &);
int molecules_in_group(tagint &, tagint &);
inline int sbmask(int j) {
return j >> SBBITS & 3;

2
src/compute_atom_molecule.h
View File

@ -35,7 +35,7 @@ class ComputeAtomMolecule : public Compute {
private:
int nvalues,nmolecules;
int idlo,idhi;
tagint idlo,idhi;
int *which,*argindex,*flavor,*value2index;
char **ids;

20
src/compute_com_molecule.cpp
View File

@ -48,18 +48,18 @@ ComputeCOMMolecule::ComputeCOMMolecule(LAMMPS *lmp, int narg, char **arg) :
// compute masstotal for each molecule
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int i,imol;
tagint imol;
double massone;
for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (int i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
@ -95,18 +95,18 @@ void ComputeCOMMolecule::init()
void ComputeCOMMolecule::compute_array()
{
int i,imol;
tagint imol;
double massone;
double unwrap[3];
invoked_array = update->ntimestep;
for (i = 0; i < nmolecules; i++)
for (int i = 0; i < nmolecules; i++)
com[i][0] = com[i][1] = com[i][2] = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
@ -128,7 +128,7 @@ void ComputeCOMMolecule::compute_array()
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
for (int i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
@ -141,8 +141,8 @@ void ComputeCOMMolecule::compute_array()
double ComputeCOMMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
double bytes = (bigint) nmolecules * 2 * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
bytes += (bigint) nmolecules * 2*3 * sizeof(double);
return bytes;
}

2
src/compute_com_molecule.h
View File

@ -34,7 +34,7 @@ class ComputeCOMMolecule : public Compute {
private:
int nmolecules;
int idlo,idhi;
tagint idlo,idhi;
double *massproc,*masstotal;
double **com,**comall;

42
src/compute_gyration_molecule.cpp
View File

@ -73,18 +73,18 @@ ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp,
// compute masstotal for each molecule
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int i,imol;
tagint imol;
double massone;
for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (int i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
@ -122,7 +122,7 @@ void ComputeGyrationMolecule::init()
void ComputeGyrationMolecule::compute_vector()
{
int i,imol;
tagint imol;
double dx,dy,dz,massone;
double unwrap[3];
@ -130,18 +130,18 @@ void ComputeGyrationMolecule::compute_vector()
molcom();
for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
for (int i = 0; i < nmolecules; i++) rg[i] = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
@ -157,14 +157,16 @@ void ComputeGyrationMolecule::compute_vector()
MPI_Allreduce(rg,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) vector[i] = sqrt(vector[i]/masstotal[i]);
for (int i = 0; i < nmolecules; i++)
vector[i] = sqrt(vector[i]/masstotal[i]);
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationMolecule::compute_array()
{
int i,j,imol;
int i,j;
tagint imol;
double dx,dy,dz,massone;
double unwrap[3];
@ -178,7 +180,7 @@ void ComputeGyrationMolecule::compute_array()
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
@ -220,23 +222,23 @@ void ComputeGyrationMolecule::compute_array()
void ComputeGyrationMolecule::molcom()
{
int i,imol;
tagint imol;
double dx,dy,dz,massone;
double unwrap[3];
for (i = 0; i < nmolecules; i++)
for (int i = 0; i < nmolecules; i++)
com[i][0] = com[i][1] = com[i][2] = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
@ -251,7 +253,7 @@ void ComputeGyrationMolecule::molcom()
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
for (int i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
@ -264,10 +266,10 @@ void ComputeGyrationMolecule::molcom()
double ComputeGyrationMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
double bytes = (bigint) nmolecules * 2 * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
if (tensor) bytes += 2*6*nmolecules * sizeof(double);
else bytes += 2*nmolecules * sizeof(double);
bytes += (bigint) nmolecules * 2*3 * sizeof(double);
if (tensor) bytes += (bigint) nmolecules * 2*6 * sizeof(double);
else bytes += (bigint) nmolecules * 2 * sizeof(double);
return bytes;
}

2
src/compute_gyration_molecule.h
View File

@ -36,7 +36,7 @@ class ComputeGyrationMolecule : public Compute {
private:
int tensor;
int nmolecules;
int idlo,idhi;
tagint idlo,idhi;
double *massproc,*masstotal;
double **com,**comall;

19
src/compute_inertia_molecule.cpp
View File

@ -51,18 +51,18 @@ ComputeInertiaMolecule(LAMMPS *lmp, int narg, char **arg) :
// compute masstotal for each molecule
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int i,imol;
tagint imol;
double massone;
for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (int i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
@ -100,7 +100,8 @@ void ComputeInertiaMolecule::init()
void ComputeInertiaMolecule::compute_array()
{
int i,j,imol;
int i,j;
tagint imol;
double dx,dy,dz,massone;
double unwrap[3];
@ -108,7 +109,7 @@ void ComputeInertiaMolecule::compute_array()
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
@ -176,9 +177,9 @@ void ComputeInertiaMolecule::compute_array()
double ComputeInertiaMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
double bytes = (bigint) nmolecules * 2 * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
bytes += 2*nmolecules*6 * sizeof(double);
bytes += (bigint) nmolecules * 2*3 * sizeof(double);
bytes += (bigint) nmolecules * 2*6 * sizeof(double);
return bytes;
}

2
src/compute_inertia_molecule.h
View File

@ -34,7 +34,7 @@ class ComputeInertiaMolecule : public Compute {
private:
int nmolecules;
int idlo,idhi;
tagint idlo,idhi;
double *massproc,*masstotal;
double **com,**comall;

26
src/compute_msd_molecule.cpp
View File

@ -50,18 +50,18 @@ ComputeMSDMolecule::ComputeMSDMolecule(LAMMPS *lmp, int narg, char **arg) :
// compute masstotal for each molecule
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int i,imol;
tagint imol;
double massone;
for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (int i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (i = 0; i < nlocal; i++)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
@ -77,7 +77,7 @@ ComputeMSDMolecule::ComputeMSDMolecule(LAMMPS *lmp, int narg, char **arg) :
firstflag = 1;
compute_array();
for (i = 0; i < nmolecules; i++) {
for (int i = 0; i < nmolecules; i++) {
cominit[i][0] = comall[i][0];
cominit[i][1] = comall[i][1];
cominit[i][2] = comall[i][2];
@ -110,7 +110,7 @@ void ComputeMSDMolecule::init()
void ComputeMSDMolecule::compute_array()
{
int i,imol;
tagint imol;
double dx,dy,dz,massone;
double unwrap[3];
@ -118,12 +118,12 @@ void ComputeMSDMolecule::compute_array()
// compute current COM positions
for (i = 0; i < nmolecules; i++)
for (int i = 0; i < nmolecules; i++)
com[i][0] = com[i][1] = com[i][2] = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *type = atom->type;
imageint *image = atom->image;
double *mass = atom->mass;
@ -145,7 +145,7 @@ void ComputeMSDMolecule::compute_array()
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
for (int i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
@ -156,7 +156,7 @@ void ComputeMSDMolecule::compute_array()
if (firstflag) return;
for (i = 0; i < nmolecules; i++) {
for (int i = 0; i < nmolecules; i++) {
dx = comall[i][0] - cominit[i][0];
dy = comall[i][1] - cominit[i][1];
dz = comall[i][2] - cominit[i][2];
@ -173,9 +173,9 @@ void ComputeMSDMolecule::compute_array()
double ComputeMSDMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
double bytes = (bigint) nmolecules * 2 * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
bytes += nmolecules*4 * sizeof(double);
bytes += (bigint) nmolecules * 2*3 * sizeof(double);
bytes += (bigint) nmolecules * 4 * sizeof(double);
return bytes;
}

2
src/compute_msd_molecule.h
View File

@ -34,7 +34,7 @@ class ComputeMSDMolecule : public Compute {
private:
int nmolecules;
int idlo,idhi;
tagint idlo,idhi;
int firstflag;
double *massproc,*masstotal;

12
src/compute_property_molecule.cpp
View File

@ -43,7 +43,8 @@ ComputePropertyMolecule(LAMMPS *lmp, int narg, char **arg) :
pack_choice[i] = &ComputePropertyMolecule::pack_mol;
else if (strcmp(arg[iarg],"count") == 0)
pack_choice[i] = &ComputePropertyMolecule::pack_count;
else error->all(FLERR,"Invalid keyword in compute property/molecule command");
else error->all(FLERR,
"Invalid keyword in compute property/molecule command");
}
// setup molecule-based data
@ -116,7 +117,7 @@ void ComputePropertyMolecule::compute_array()
double ComputePropertyMolecule::memory_usage()
{
double bytes = nmolecules*nvalues * sizeof(double);
double bytes = (bigint) nmolecules * nvalues * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
return bytes;
}
@ -129,7 +130,7 @@ double ComputePropertyMolecule::memory_usage()
void ComputePropertyMolecule::pack_mol(int n)
{
for (int m = idlo; m <= idhi; m++)
for (tagint m = idlo; m <= idhi; m++)
if (molmap == NULL || molmap[m-idlo] >= 0) {
buf[n] = m;
n += nvalues;
@ -140,12 +141,13 @@ void ComputePropertyMolecule::pack_mol(int n)
void ComputePropertyMolecule::pack_count(int n)
{
int i,m,imol;
int i,m;
tagint imol;
int *count_one = new int[nmolecules];
for (m = 0; m < nmolecules; m++) count_one[m] = 0;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;

2
src/compute_property_molecule.h
View File

@ -35,7 +35,7 @@ class ComputePropertyMolecule : public Compute {
private:
int nvalues,nmolecules;
int idlo,idhi;
tagint idlo,idhi;
double *buf;

10
src/create_atoms.cpp
View File

@ -292,13 +292,13 @@ void CreateAtoms::command(int narg, char **arg)
// moloffset = max molecule ID for all molecules owned by previous procs
// including molecules existing before this creation
int moloffset;
int *molecule = atom->molecule;
tagint moloffset;
tagint *molecule = atom->molecule;
if (molecule) {
int max = 0;
tagint max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
int maxmol;
MPI_Allreduce(&max,&maxmol,1,MPI_INT,MPI_MAX,world);
tagint maxmol;
MPI_Allreduce(&max,&maxmol,1,MPI_LMP_TAGINT,MPI_MAX,world);
MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
moloffset = moloffset - molcreate + maxmol;
}

16
src/delete_atoms.cpp
View File

@ -172,15 +172,15 @@ void DeleteAtoms::delete_region(int narg, char **arg)
// store list of molecule IDs I delete atoms from in list
// pass list from proc to proc via ring communication
hash = new std::map<int,int>();
hash = new std::map<tagint,int>();
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
for (int i = 0; i < nlocal; i++)
if (dlist[i] && hash->find(molecule[i]) == hash->end())
(*hash)[molecule[i]] = 1;
int n = hash->size();
int *list;
tagint *list;
memory->create(list,n,"delete_atoms:list");
n = 0;
@ -188,7 +188,7 @@ void DeleteAtoms::delete_region(int narg, char **arg)
for (pos = hash->begin(); pos != hash->end(); ++pos) list[n++] = pos->first;
cptr = this;
comm->ring(n,sizeof(int),list,1,molring,NULL);
comm->ring(n,sizeof(tagint),list,1,molring,NULL);
delete hash;
memory->destroy(list);
@ -197,16 +197,16 @@ void DeleteAtoms::delete_region(int narg, char **arg)
/* ----------------------------------------------------------------------
callback from comm->ring()
cbuf = list of N molecule IDs, put them in hash
loop over my atoms, if matches moleculed ID in hash, delete that atom
loop over my atoms, if matches molecule ID in hash, delete that atom
------------------------------------------------------------------------- */
void DeleteAtoms::molring(int n, char *cbuf)
{
int *list = (int *) cbuf;
tagint *list = (int *) cbuf;
int *dlist = cptr->dlist;
std::map<int,int> *hash = cptr->hash;
std::map<tagint,int> *hash = cptr->hash;
int nlocal = cptr->atom->nlocal;
int *molecule = cptr->atom->molecule;
tagint *molecule = cptr->atom->molecule;
hash->clear();
for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;

4
src/dump_custom.cpp
View File

@ -446,7 +446,7 @@ int DumpCustom::count()
if (!atom->molecule_flag)
error->all(FLERR,
"Threshhold for an atom property that isn't allocated");
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
ptr = dchoose;
nstride = 1;
@ -1725,7 +1725,7 @@ void DumpCustom::pack_id(int n)
void DumpCustom::pack_molecule(int n)
{
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
for (int i = 0; i < nchoose; i++) {
buf[n] = molecule[clist[i]];

22
src/fix_property_atom.cpp
View File

@ -222,7 +222,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
if ((m = atom->map(itag)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) atom->molecule[m] = atoi(values[j+1]);
if (style[j] == MOLECULE) atom->molecule[m] = ATOTAGINT(values[j+1]);
else if (style[j] == CHARGE) atom->q[m] = atof(values[j+1]);
else if (style[j] == INTEGER)
atom->ivector[index[j]][m] = atoi(values[j+1]);
@ -284,7 +284,7 @@ void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
for (int m = 0; m < nvalue; m++) {
int mp1 = m+1;
if (style[m] == MOLECULE) {
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(molecule[i]).d;
} else if (style[m] == CHARGE) {
double *q = atom->q;
@ -327,7 +327,9 @@ void FixPropertyAtom::write_data_section(int mth, FILE *fp,
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
for (m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE || style[m] == INTEGER)
if (style[m] == MOLECULE)
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][m+1]).i);
else if (style[m] == INTEGER)
fprintf(fp," %d",(int) ubuf(buf[i][m+1]).i);
else fprintf(fp," %g",buf[i][m+1]);
}
@ -343,7 +345,7 @@ double FixPropertyAtom::memory_usage()
{
double bytes = 0.0;
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(int);
if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
else if (style[m] == CHARGE) bytes = atom->nmax * sizeof(double);
else if (style[m] == INTEGER) bytes = atom->nmax * sizeof(int);
else if (style[m] == DOUBLE) bytes = atom->nmax * sizeof(double);
@ -363,7 +365,7 @@ void FixPropertyAtom::grow_arrays(int nmax)
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) {
memory->grow(atom->molecule,nmax,"atom:molecule");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
size_t nbytes = (nmax-nmax_old) * sizeof(tagint);
memset(&atom->molecule[nmax_old],0,nbytes);
} else if (style[m] == CHARGE) {
memory->grow(atom->q,nmax,"atom:q");
@ -412,7 +414,7 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
int m = 0;
for (k = 0; k < nvalue; k++) {
if (style[k] == MOLECULE) {
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(molecule[j]).d;
@ -452,10 +454,10 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
int m = 0;
for (k = 0; k < nvalue; k++) {
if (style[k] == MOLECULE) {
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = (int) ubuf(buf[m++]).i;
molecule[i] = (tagint) ubuf(buf[m++]).i;
} else if (style[k] == CHARGE) {
double *q = atom->q;
last = first + n;
@ -500,7 +502,7 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
atom->molecule[nlocal] = (int) ubuf(buf[m]).i;
atom->molecule[nlocal] = (tagint) ubuf(buf[m]).i;
else if (style[m] == CHARGE)
atom->q[nlocal] = buf[m];
else if (style[m] == INTEGER)
@ -546,7 +548,7 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
for (int i = 0; i < nvalue; i++) {
if (style[i] == MOLECULE)
atom->molecule[nlocal] = (int) ubuf(extra[nlocal][m++]).i;
atom->molecule[nlocal] = (tagint) ubuf(extra[nlocal][m++]).i;
else if (style[i] == CHARGE)
atom->q[nlocal] = extra[nlocal][m++];
else if (style[i] == INTEGER)

2
src/fix_store_state.cpp
View File

@ -603,7 +603,7 @@ void FixStoreState::pack_id(int n)
void FixStoreState::pack_molecule(int n)
{
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int *mask = atom->mask;
int nlocal = atom->nlocal;

47
src/group.cpp
View File

@ -199,11 +199,11 @@ void Group::assign(int narg, char **arg)
bound2 = force->bnumeric(FLERR,arg[4]);
} else if (narg != 4) error->all(FLERR,"Illegal group command");
tagint *tag = atom->tag;
int *attribute;
int *attribute = NULL;
tagint *tattribute = NULL;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) attribute = atom->molecule;
else if (category == ID) attribute = NULL;
else if (category == MOLECULE) tattribute = atom->molecule;
else if (category == ID) tattribute = atom->tag;
// add to group if meets condition
@ -234,25 +234,25 @@ void Group::assign(int narg, char **arg)
} else {
if (condition == LT) {
for (i = 0; i < nlocal; i++)
if (tag[i] < bound1) mask[i] |= bit;
if (tattribute[i] < bound1) mask[i] |= bit;
} else if (condition == LE) {
for (i = 0; i < nlocal; i++)
if (tag[i] <= bound1) mask[i] |= bit;
if (tattribute[i] <= bound1) mask[i] |= bit;
} else if (condition == GT) {
for (i = 0; i < nlocal; i++)
if (tag[i] > bound1) mask[i] |= bit;
if (tattribute[i] > bound1) mask[i] |= bit;
} else if (condition == GE) {
for (i = 0; i < nlocal; i++)
if (tag[i] >= bound1) mask[i] |= bit;
if (tattribute[i] >= bound1) mask[i] |= bit;
} else if (condition == EQ) {
for (i = 0; i < nlocal; i++)
if (tag[i] == bound1) mask[i] |= bit;
if (tattribute[i] == bound1) mask[i] |= bit;
} else if (condition == NEQ) {
for (i = 0; i < nlocal; i++)
if (tag[i] != bound1) mask[i] |= bit;
if (tattribute[i] != bound1) mask[i] |= bit;
} else if (condition == BETWEEN) {
for (i = 0; i < nlocal; i++)
if (tag[i] >= bound1 && tag[i] <= bound2)
if (tattribute[i] >= bound1 && tattribute[i] <= bound2)
mask[i] |= bit;
}
}
@ -260,28 +260,16 @@ void Group::assign(int narg, char **arg)
// args = list of values
} else {
tagint *tag = atom->tag;
int *attribute;
int *attribute = NULL;
tagint *tattribute = NULL;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) attribute = atom->molecule;
else if (category == ID) attribute = NULL;
else if (category == MOLECULE) tattribute = atom->molecule;
else if (category == ID) tattribute = atom->tag;
char *ptr;
tagint start,stop,delta;
for (int iarg = 2; iarg < narg; iarg++) {
if (attribute) {
if (strchr(arg[iarg],':')) {
start = atoi(strtok(arg[iarg],":"));
stop = atoi(strtok(NULL,":"));
ptr = strtok(NULL,":");
if (ptr) delta = atoi(ptr);
else delta = 1;
} else {
start = stop = atoi(arg[iarg]);
delta = 1;
}
} else {
if (strchr(arg[iarg],':')) {
start = ATOTAGINT(strtok(arg[iarg],":"));
stop = ATOTAGINT(strtok(NULL,":"));
@ -292,7 +280,6 @@ void Group::assign(int narg, char **arg)
start = stop = ATOTAGINT(arg[iarg]);
delta = 1;
}
}
// add to group if attribute matches value or sequence
@ -302,8 +289,8 @@ void Group::assign(int narg, char **arg)
(attribute[i]-start) % delta == 0) mask[i] |= bit;
} else {
for (i = 0; i < nlocal; i++)
if (tag[i] >= start && tag[i] <= stop &&
(tag[i]-start) % delta == 0) mask[i] |= bit;
if (tattribute[i] >= start && tattribute[i] <= stop &&
(tattribute[i]-start) % delta == 0) mask[i] |= bit;
}
}
}

6
src/lammps.cpp
View File

@ -366,7 +366,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
}
}
// check datatype settings in lmptype.h
// check consistency of datatype settings in lmptype.h
if (sizeof(smallint) != sizeof(int))
error->all(FLERR,"Smallint setting in lmptype.h is invalid");
@ -378,6 +378,10 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->all(FLERR,"Bigint setting in lmptype.h is invalid");
int mpisize;
MPI_Type_size(MPI_LMP_TAGINT,&mpisize);
if (mpisize != sizeof(tagint))
error->all(FLERR,"MPI_LMP_TAGINT and tagint in "
"lmptype.h are not compatible");
MPI_Type_size(MPI_LMP_BIGINT,&mpisize);
if (mpisize != sizeof(bigint))
error->all(FLERR,"MPI_LMP_BIGINT and bigint in "

4
src/lmptype.h
View File

@ -15,13 +15,13 @@
// smallint = variables for on-procesor system (nlocal, nmax, etc)
// imageint = variables for atom image flags (image)
// tagint = variables for atom IDs (tag)
// tagint = variables for atom IDs and molecule IDs (tag,molecule)
// bigint = variables for total system (natoms, ntimestep, etc)
// smallint must be an int, as defined by C compiler
// imageint can be 32-bit or 64-bit int, must be >= smallint
// tagint can be 32-bit or 64-bit int, must be >= smallint
// bigint can be 32-bit or 64-bit int, must be >= tagint
// bigint can be 32-bit or 64-bit int, must be >= imageint,tagint
// MPI_LMP_BIGINT = MPI data type corresponding to a bigint

10
src/neigh_full.cpp
View File

@ -39,7 +39,7 @@ void Neighbor::full_nsq(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -122,7 +122,7 @@ void Neighbor::full_nsq_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -219,7 +219,7 @@ void Neighbor::full_bin(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -310,7 +310,7 @@ void Neighbor::full_bin_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -431,7 +431,7 @@ void Neighbor::full_multi(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;

10
src/neigh_gran.cpp
View File

@ -50,7 +50,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) {
@ -178,7 +178,7 @@ void Neighbor::granular_nsq_newton(NeighList *list)
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) {
@ -284,7 +284,7 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -420,7 +420,7 @@ void Neighbor::granular_bin_newton(NeighList *list)
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
@ -522,7 +522,7 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
double *radius = atom->radius;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;

8
src/neigh_half_bin.cpp
View File

@ -46,7 +46,7 @@ void Neighbor::half_bin_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int molecular = atom->molecular;
@ -141,7 +141,7 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -263,7 +263,7 @@ void Neighbor::half_bin_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int molecular = atom->molecular;
@ -382,7 +382,7 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int molecular = atom->molecular;

6
src/neigh_half_multi.cpp
View File

@ -48,7 +48,7 @@ void Neighbor::half_multi_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -147,7 +147,7 @@ void Neighbor::half_multi_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -274,7 +274,7 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;

6
src/neigh_half_nsq.cpp
View File

@ -39,7 +39,7 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -123,7 +123,7 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -228,7 +228,7 @@ void Neighbor::half_nsq_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;

10
src/neigh_respa.cpp
View File

@ -43,7 +43,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -186,7 +186,7 @@ void Neighbor::respa_nsq_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
@ -351,7 +351,7 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -504,7 +504,7 @@ void Neighbor::respa_bin_newton(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;
@ -698,7 +698,7 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
if (includegroup) nlocal = atom->nfirst;

2
src/neighbor.cpp
View File

@ -1929,7 +1929,7 @@ int Neighbor::coord2bin(double *x, int &ix, int &iy, int &iz)
------------------------------------------------------------------------- */
int Neighbor::exclusion(int i, int j, int itype, int jtype,
int *mask, int *molecule) const {
int *mask, tagint *molecule) const {
int m;
if (nex_type && ex_type[itype][jtype]) return 1;

2
src/neighbor.h
View File

@ -171,7 +171,7 @@ class Neighbor : protected Pointers {
int coord2bin(double *, int &, int &, int&); // ditto
int exclusion(int, int, int,
int, int *, int *) const; // test for pair exclusion
int, int *, tagint *) const; // test for pair exclusion
virtual void choose_build(int, class NeighRequest *);
void choose_stencil(int, class NeighRequest *);

10
src/replicate.cpp
View File

@ -83,11 +83,11 @@ void Replicate::command(int narg, char **arg)
// maxmol = largest molecule tag across all existing atoms
int maxmol = 0;
tagint maxmol = 0;
if (atom->molecule_flag) {
for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
int maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_INT,MPI_MAX,world);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol = maxmol_all;
}
@ -254,8 +254,8 @@ void Replicate::command(int narg, char **arg)
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
int ix,iy,iz,mol_offset;
tagint atom_offset;
int ix,iy,iz;
tagint atom_offset,mol_offset;
imageint image;
double x[3],lamda[3];
double *coord;

7
src/set.cpp
View File

@ -451,11 +451,12 @@ void Set::selection(int n)
} else if (style == MOL_SELECT) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Cannot use set mol with no molecule IDs defined");
else force->bounds(id,BIG,nlo,nhi,0);
bigint nlobig,nhibig;
force->boundsbig(id,MAXTAGINT,nlobig,nhibig);
int *molecule = atom->molecule;
tagint *molecule = atom->molecule;
for (int i = 0; i < n; i++)
if (molecule[i] >= nlo && molecule[i] <= nhi) select[i] = 1;
if (molecule[i] >= nlobig && molecule[i] <= nhibig) select[i] = 1;
else select[i] = 0;
} else if (style == TYPE_SELECT) {

11
src/variable.cpp
View File

@ -3521,6 +3521,7 @@ void Variable::atom_vector(char *word, Tree **tree,
newtree->barray = (bigint *) atom->tag;
}
newtree->nstride = 1;
} else if (strcmp(word,"mass") == 0) {
if (atom->rmass) {
newtree->nstride = 1;
@ -3529,17 +3530,25 @@ void Variable::atom_vector(char *word, Tree **tree,
newtree->type = TYPEARRAY;
newtree->array = atom->mass;
}
} else if (strcmp(word,"type") == 0) {
newtree->type = INTARRAY;
newtree->nstride = 1;
newtree->iarray = atom->type;
} else if (strcmp(word,"mol") == 0) {
if (!atom->molecule_flag)
error->one(FLERR,"Variable uses atom property that isn't allocated");
if (sizeof(tagint) == sizeof(smallint)) {
newtree->type = INTARRAY;
newtree->nstride = 1;
newtree->iarray = atom->molecule;
} else {
newtree->type = BIGINTARRAY;
newtree->barray = (bigint *) atom->molecule;
}
newtree->nstride = 1;
}
else if (strcmp(word,"x") == 0) newtree->array = &atom->x[0][0];
else if (strcmp(word,"y") == 0) newtree->array = &atom->x[0][1];
else if (strcmp(word,"z") == 0) newtree->array = &atom->x[0][2];