From 127eb167c1162552294dfc60b60138615bb79dea Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 22 Jan 2014 17:44:32 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11293
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/GRANULAR/fix_pour.cpp | 4 +-
src/GRANULAR/fix_pour.h | 3 +-
src/MC/fix_bond_swap.cpp | 5 +-
src/MC/fix_gcmc.cpp | 65 +++++++++++++++-----------
src/MC/fix_gcmc.h | 7 +--
src/MISC/fix_deposit.cpp | 4 +-
src/MISC/fix_deposit.h | 3 +-
src/MISC/fix_evaporate.cpp | 13 +++---
src/MOLECULE/atom_vec_angle.cpp | 21 +++++----
src/MOLECULE/atom_vec_bond.cpp | 23 ++++-----
src/MOLECULE/atom_vec_full.cpp | 24 +++++-----
src/MOLECULE/atom_vec_molecular.cpp | 21 +++++----
src/MOLECULE/atom_vec_molecular.h | 2 +-
src/POEMS/fix_poems.cpp | 38 ++++++++-------
src/RIGID/fix_rigid.cpp | 16 ++++---
src/RIGID/fix_rigid_small.cpp | 40 ++++++++--------
src/RIGID/fix_rigid_small.h | 2 +-
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 36 ++++++++------
src/USER-OMP/neigh_full_omp.cpp | 10 ++--
src/USER-OMP/neigh_gran_omp.cpp | 10 ++--
src/USER-OMP/neigh_half_bin_omp.cpp | 8 ++--
src/USER-OMP/neigh_half_multi_omp.cpp | 6 +--
src/USER-OMP/neigh_half_nsq_omp.cpp | 6 +--
src/USER-OMP/neigh_respa_omp.cpp | 10 ++--
src/USER-REAXC/fix_reaxc_bonds.cpp | 4 +-
src/atom.h | 3 +-
src/atom_vec_line.cpp | 25 +++++-----
src/atom_vec_tri.cpp | 23 ++++-----
src/compute.cpp | 20 ++++----
src/compute.h | 2 +-
src/compute_atom_molecule.h | 2 +-
src/compute_com_molecule.cpp | 20 ++++----
src/compute_com_molecule.h | 2 +-
src/compute_gyration_molecule.cpp | 42 +++++++++--------
src/compute_gyration_molecule.h | 2 +-
src/compute_inertia_molecule.cpp | 19 ++++----
src/compute_inertia_molecule.h | 2 +-
src/compute_msd_molecule.cpp | 26 +++++------
src/compute_msd_molecule.h | 2 +-
src/compute_property_molecule.cpp | 12 +++--
src/compute_property_molecule.h | 2 +-
src/create_atoms.cpp | 10 ++--
src/delete_atoms.cpp | 16 +++----
src/dump_custom.cpp | 4 +-
src/fix_property_atom.cpp | 22 +++++----
src/fix_store_state.cpp | 2 +-
src/group.cpp | 63 ++++++++++---------------
src/lammps.cpp | 6 ++-
src/lmptype.h | 4 +-
src/neigh_full.cpp | 10 ++--
src/neigh_gran.cpp | 10 ++--
src/neigh_half_bin.cpp | 8 ++--
src/neigh_half_multi.cpp | 6 +--
src/neigh_half_nsq.cpp | 6 +--
src/neigh_respa.cpp | 10 ++--
src/neighbor.cpp | 2 +-
src/neighbor.h | 2 +-
src/replicate.cpp | 10 ++--
src/set.cpp | 7 +--
src/variable.cpp | 13 +++++-
60 files changed, 421 insertions(+), 375 deletions(-)
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index 9a439d87d6..4dc0c5cbef 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -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);
}
}
diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h
index 34d13da985..e57379906e 100644
--- a/src/GRANULAR/fix_pour.h
+++ b/src/GRANULAR/fix_pour.h
@@ -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();
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index 31bdb75682..79b298391a 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -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;
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index ab85e6e21b..90202ad7eb 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -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;
}
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index 7fdd1f70c6..ee532820b8 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -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;
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index ea8fb37be9..f83af6d7d6 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -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);
}
}
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index 56bf34c6dd..0c43a423d9 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -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();
diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp
index ab153f805e..421c22e666 100644
--- a/src/MISC/fix_evaporate.cpp
+++ b/src/MISC/fix_evaporate.cpp
@@ -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++;
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 9b303451c3..bafac2391f 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -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;
}
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 7e5e639918..030a86ac86 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -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;
}
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 09175dd034..f132fdc599 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -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;
}
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 2f2265b5df..766da9e354 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -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;
}
diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h
index 58aa039e1e..293b44a826 100644
--- a/src/MOLECULE/atom_vec_molecular.h
+++ b/src/MOLECULE/atom_vec_molecular.h
@@ -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;
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index 1aea5795a1..cbada23c5a 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -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
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index eee93e95c6..c79fa2359e 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -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");
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 46809d1b34..78ef0ed0f2 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -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;
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 6f73a9c03a..392a928bee 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -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 {
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index a0e3016698..6a1e4e531e 100755
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -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];
diff --git a/src/USER-OMP/neigh_full_omp.cpp b/src/USER-OMP/neigh_full_omp.cpp
index e609627897..d1230555ce 100644
--- a/src/USER-OMP/neigh_full_omp.cpp
+++ b/src/USER-OMP/neigh_full_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/neigh_gran_omp.cpp b/src/USER-OMP/neigh_gran_omp.cpp
index 5f0402f363..e293102e9a 100644
--- a/src/USER-OMP/neigh_gran_omp.cpp
+++ b/src/USER-OMP/neigh_gran_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/neigh_half_bin_omp.cpp b/src/USER-OMP/neigh_half_bin_omp.cpp
index f501684a19..76f36ea965 100644
--- a/src/USER-OMP/neigh_half_bin_omp.cpp
+++ b/src/USER-OMP/neigh_half_bin_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/neigh_half_multi_omp.cpp b/src/USER-OMP/neigh_half_multi_omp.cpp
index b46594870f..a804e8008f 100644
--- a/src/USER-OMP/neigh_half_multi_omp.cpp
+++ b/src/USER-OMP/neigh_half_multi_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/neigh_half_nsq_omp.cpp b/src/USER-OMP/neigh_half_nsq_omp.cpp
index a98c4721f3..fa90945d55 100644
--- a/src/USER-OMP/neigh_half_nsq_omp.cpp
+++ b/src/USER-OMP/neigh_half_nsq_omp.cpp
@@ -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;
diff --git a/src/USER-OMP/neigh_respa_omp.cpp b/src/USER-OMP/neigh_respa_omp.cpp
index 11c7fd9ae3..458b2bbac4 100644
--- a/src/USER-OMP/neigh_respa_omp.cpp
+++ b/src/USER-OMP/neigh_respa_omp.cpp
@@ -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;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index 3ced20a289..8d8818a49b 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -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++) {
diff --git a/src/atom.h b/src/atom.h
index 8a5a0b643f..c552cad6c2 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -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;
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index 5c89d237fc..bd5a5ea2b3 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -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;
}
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index d170c8b5d0..20528ff0d6 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -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;
}
diff --git a/src/compute.cpp b/src/compute.cpp
index 9be14029dc..f9a95e8d10 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -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;
diff --git a/src/compute.h b/src/compute.h
index e7cb31bae1..3ae91e5b1a 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -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;
diff --git a/src/compute_atom_molecule.h b/src/compute_atom_molecule.h
index 769f58d5ec..cd135e47d8 100644
--- a/src/compute_atom_molecule.h
+++ b/src/compute_atom_molecule.h
@@ -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;
diff --git a/src/compute_com_molecule.cpp b/src/compute_com_molecule.cpp
index 130072cc63..74b2cb5ac3 100644
--- a/src/compute_com_molecule.cpp
+++ b/src/compute_com_molecule.cpp
@@ -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;
}
diff --git a/src/compute_com_molecule.h b/src/compute_com_molecule.h
index a4f941c52a..3e6fdedd99 100644
--- a/src/compute_com_molecule.h
+++ b/src/compute_com_molecule.h
@@ -34,7 +34,7 @@ class ComputeCOMMolecule : public Compute {
private:
int nmolecules;
- int idlo,idhi;
+ tagint idlo,idhi;
double *massproc,*masstotal;
double **com,**comall;
diff --git a/src/compute_gyration_molecule.cpp b/src/compute_gyration_molecule.cpp
index bf4a70a296..f81a373830 100644
--- a/src/compute_gyration_molecule.cpp
+++ b/src/compute_gyration_molecule.cpp
@@ -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;
}
diff --git a/src/compute_gyration_molecule.h b/src/compute_gyration_molecule.h
index 99910782fa..78b49231a2 100644
--- a/src/compute_gyration_molecule.h
+++ b/src/compute_gyration_molecule.h
@@ -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;
diff --git a/src/compute_inertia_molecule.cpp b/src/compute_inertia_molecule.cpp
index 8cdb3cb64c..df9958a04a 100644
--- a/src/compute_inertia_molecule.cpp
+++ b/src/compute_inertia_molecule.cpp
@@ -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;
}
diff --git a/src/compute_inertia_molecule.h b/src/compute_inertia_molecule.h
index 80657108e7..a081dd1ad5 100644
--- a/src/compute_inertia_molecule.h
+++ b/src/compute_inertia_molecule.h
@@ -34,7 +34,7 @@ class ComputeInertiaMolecule : public Compute {
private:
int nmolecules;
- int idlo,idhi;
+ tagint idlo,idhi;
double *massproc,*masstotal;
double **com,**comall;
diff --git a/src/compute_msd_molecule.cpp b/src/compute_msd_molecule.cpp
index 736ac9cfc6..515436ba3a 100644
--- a/src/compute_msd_molecule.cpp
+++ b/src/compute_msd_molecule.cpp
@@ -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;
}
diff --git a/src/compute_msd_molecule.h b/src/compute_msd_molecule.h
index b4c5bd53a1..839698cabd 100644
--- a/src/compute_msd_molecule.h
+++ b/src/compute_msd_molecule.h
@@ -34,7 +34,7 @@ class ComputeMSDMolecule : public Compute {
private:
int nmolecules;
- int idlo,idhi;
+ tagint idlo,idhi;
int firstflag;
double *massproc,*masstotal;
diff --git a/src/compute_property_molecule.cpp b/src/compute_property_molecule.cpp
index c0bcafc9ea..dafe2db680 100644
--- a/src/compute_property_molecule.cpp
+++ b/src/compute_property_molecule.cpp
@@ -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;
diff --git a/src/compute_property_molecule.h b/src/compute_property_molecule.h
index 0c5ae68df0..27cebe8fe1 100644
--- a/src/compute_property_molecule.h
+++ b/src/compute_property_molecule.h
@@ -35,7 +35,7 @@ class ComputePropertyMolecule : public Compute {
private:
int nvalues,nmolecules;
- int idlo,idhi;
+ tagint idlo,idhi;
double *buf;
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 1e1f5716da..40c7fe4ec4 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -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;
}
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index ac1c354d29..5c353c7fe5 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -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;
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index f0c0371044..9619214b94 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -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]];
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index a1be2b556b..115750e271 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -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)
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index addcffcab4..6863576884 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -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;
diff --git a/src/group.cpp b/src/group.cpp
index 22b9035cc4..ce99834a6e 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -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;
}
}
@@ -260,38 +260,25 @@ 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;
- }
+ if (strchr(arg[iarg],':')) {
+ start = ATOTAGINT(strtok(arg[iarg],":"));
+ stop = ATOTAGINT(strtok(NULL,":"));
+ ptr = strtok(NULL,":");
+ if (ptr) delta = ATOTAGINT(ptr);
+ else delta = 1;
} else {
- if (strchr(arg[iarg],':')) {
- start = ATOTAGINT(strtok(arg[iarg],":"));
- stop = ATOTAGINT(strtok(NULL,":"));
- ptr = strtok(NULL,":");
- if (ptr) delta = ATOTAGINT(ptr);
- else delta = 1;
- } else {
- start = stop = ATOTAGINT(arg[iarg]);
- delta = 1;
- }
+ 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;
}
}
}
diff --git a/src/lammps.cpp b/src/lammps.cpp
index a896c752d2..5bd15ace42 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -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 "
diff --git a/src/lmptype.h b/src/lmptype.h
index a23aa9113b..29301058b8 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -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
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index 7b536f4699..6df4bfb512 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -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;
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index 465e6af863..e6ef93c5eb 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -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;
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
index 75736e97d2..68f7832fa2 100644
--- a/src/neigh_half_bin.cpp
+++ b/src/neigh_half_bin.cpp
@@ -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;
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
index fddc683fb7..6dc03a43ef 100644
--- a/src/neigh_half_multi.cpp
+++ b/src/neigh_half_multi.cpp
@@ -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;
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
index f8fad972bb..efdd26a311 100644
--- a/src/neigh_half_nsq.cpp
+++ b/src/neigh_half_nsq.cpp
@@ -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;
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index 738426abdb..b2d19b11e0 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -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;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 10f7ce0a10..15ac28378b 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -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;
diff --git a/src/neighbor.h b/src/neighbor.h
index 751e155231..2bf33d22e1 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -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 *);
diff --git a/src/replicate.cpp b/src/replicate.cpp
index 9b4e9bcf48..b31506d6c1 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -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;
diff --git a/src/set.cpp b/src/set.cpp
index 562b8f94ce..108aecc239 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -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) {
diff --git a/src/variable.cpp b/src/variable.cpp
index 87fed075c1..c866a02ad7 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -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");
- newtree->type = INTARRAY;
+ if (sizeof(tagint) == sizeof(smallint)) {
+ newtree->type = INTARRAY;
+ newtree->iarray = atom->molecule;
+ } else {
+ newtree->type = BIGINTARRAY;
+ newtree->barray = (bigint *) atom->molecule;
+ }
newtree->nstride = 1;
- newtree->iarray = atom->molecule;
}
+
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];
--
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