From bad19033d01593c66f38c16d25fb695d491a4608 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 17 Jan 2014 18:43:09 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11250
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/CLASS2/dihedral_class2.cpp | 4 +-
src/CLASS2/improper_class2.cpp | 5 +-
src/DIPOLE/atom_vec_dipole.cpp | 18 +-
src/DIPOLE/atom_vec_dipole.h | 3 +-
src/FLD/pair_lubricateU.cpp | 1 -
src/GRANULAR/fix_pour.cpp | 10 +-
src/GRANULAR/fix_pour.h | 3 +-
src/KSPACE/pair_lj_cut_tip4p_long.cpp | 9 +-
src/KSPACE/pair_lj_long_tip4p_long.cpp | 36 +-
src/KSPACE/pair_tip4p_long.cpp | 9 +-
src/MANYBODY/fix_qeq_comb.cpp | 1 -
src/MANYBODY/pair_airebo.cpp | 15 +-
src/MANYBODY/pair_bop.cpp | 29 +-
src/MANYBODY/pair_comb.cpp | 10 +-
src/MANYBODY/pair_comb3.cpp | 24 +-
src/MANYBODY/pair_lcbop.cpp | 12 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 5 +-
src/MANYBODY/pair_sw.cpp | 5 +-
src/MANYBODY/pair_tersoff.cpp | 5 +-
src/MC/fix_bond_break.cpp | 12 +-
src/MC/fix_bond_break.h | 2 +-
src/MC/fix_bond_create.cpp | 15 +-
src/MC/fix_bond_create.h | 2 +-
src/MC/fix_bond_swap.cpp | 17 +-
src/MC/fix_gcmc.cpp | 19 +-
src/MISC/fix_deposit.cpp | 16 +-
src/MISC/fix_deposit.h | 3 +-
src/MISC/fix_evaporate.cpp | 2 +-
src/MISC/fix_orient_fcc.cpp | 13 +-
src/MISC/fix_orient_fcc.h | 4 +-
src/MOLECULE/atom_vec_angle.cpp | 62 +-
src/MOLECULE/atom_vec_angle.h | 11 +-
src/MOLECULE/atom_vec_bond.cpp | 24 +-
src/MOLECULE/atom_vec_bond.h | 9 +-
src/MOLECULE/atom_vec_full.cpp | 75 +-
src/MOLECULE/atom_vec_full.h | 15 +-
src/MOLECULE/atom_vec_molecular.cpp | 21 +-
src/MOLECULE/atom_vec_molecular.h | 15 +-
src/MOLECULE/bond_fene.cpp | 3 +-
src/MOLECULE/bond_fene_expand.cpp | 3 +-
src/MOLECULE/dihedral_charmm.cpp | 4 +-
src/MOLECULE/dihedral_harmonic.cpp | 4 +-
src/MOLECULE/dihedral_helix.cpp | 4 +-
src/MOLECULE/dihedral_multi_harmonic.cpp | 4 +-
src/MOLECULE/dihedral_opls.cpp | 4 +-
src/MOLECULE/improper_cvff.cpp | 5 +-
src/MOLECULE/improper_harmonic.cpp | 5 +-
src/MOLECULE/improper_umbrella.cpp | 5 +-
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 9 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 9 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 9 +-
src/MOLECULE/pair_tip4p_cut.cpp | 9 +-
src/OPT/pair_lj_cut_tip4p_long_opt.cpp | 9 +-
src/PERI/atom_vec_peri.cpp | 18 +-
src/PERI/atom_vec_peri.h | 3 +-
src/PERI/compute_damage_atom.cpp | 2 +-
src/PERI/fix_peri_neigh.cpp | 6 +-
src/PERI/fix_peri_neigh.h | 2 +-
src/PERI/pair_peri_lps.cpp | 4 +-
src/PERI/pair_peri_pmb.cpp | 4 +-
src/PERI/pair_peri_ves.cpp | 4 +-
src/REPLICA/neb.cpp | 6 +-
src/REPLICA/prd.cpp | 4 +-
src/REPLICA/prd.h | 3 +-
src/REPLICA/verlet_split.cpp | 3 +-
src/RIGID/fix_rigid_small.cpp | 35 +-
src/RIGID/fix_rigid_small.h | 6 +-
src/RIGID/fix_shake.cpp | 90 +-
src/RIGID/fix_shake.h | 8 +-
src/SHOCK/fix_append_atoms.cpp | 16 +-
src/SRD/fix_srd.cpp | 40 +-
src/USER-AWPMD/atom_vec_wavepacket.cpp | 29 +-
src/USER-AWPMD/atom_vec_wavepacket.h | 3 +-
src/USER-EFF/atom_vec_electron.cpp | 22 +-
src/USER-EFF/atom_vec_electron.h | 3 +-
src/USER-EFF/pair_eff_cut.cpp | 2 -
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 4 +-
src/USER-MISC/dihedral_fourier.cpp | 4 +-
src/USER-MISC/dihedral_nharmonic.cpp | 4 +-
src/USER-MISC/dihedral_quadratic.cpp | 6 +-
src/USER-MISC/improper_cossq.cpp | 8 +-
src/USER-MISC/improper_fourier.cpp | 5 +-
src/USER-MISC/pair_edip.cpp | 2 -
src/USER-MISC/pair_list.cpp | 8 +-
src/USER-MISC/pair_list.h | 2 +-
src/USER-MISC/pair_tersoff_table.cpp | 2 -
src/USER-SPH/atom_vec_meso.cpp | 21 +-
src/USER-SPH/atom_vec_meso.h | 3 +-
src/XTC/dump_xtc.cpp | 4 +-
src/XTC/dump_xtc.h | 2 +-
src/atom.cpp | 525 ++++---
src/atom.h | 62 +-
src/atom_map.cpp | 156 ++-
src/atom_vec.cpp | 72 +-
src/atom_vec.h | 20 +-
src/atom_vec_atomic.cpp | 17 +-
src/atom_vec_atomic.h | 3 +-
src/atom_vec_body.cpp | 21 +-
src/atom_vec_body.h | 3 +-
src/atom_vec_charge.cpp | 17 +-
src/atom_vec_charge.h | 3 +-
src/atom_vec_ellipsoid.cpp | 23 +-
src/atom_vec_ellipsoid.h | 3 +-
src/atom_vec_hybrid.cpp | 17 +-
src/atom_vec_hybrid.h | 3 +-
src/atom_vec_line.cpp | 24 +-
src/atom_vec_line.h | 3 +-
src/atom_vec_sphere.cpp | 23 +-
src/atom_vec_sphere.h | 3 +-
src/atom_vec_tri.cpp | 24 +-
src/atom_vec_tri.h | 3 +-
src/compute_angle_local.cpp | 8 +-
src/compute_bond_local.cpp | 4 +-
src/compute_cluster_atom.cpp | 2 +-
src/compute_dihedral_local.cpp | 10 +-
src/compute_improper_local.cpp | 10 +-
src/compute_property_atom.cpp | 2 +-
src/compute_property_local.cpp | 63 +-
src/create_atoms.cpp | 127 +-
src/delete_atoms.cpp | 4 +-
src/domain.cpp | 4 +-
src/dump.cpp | 54 +-
src/dump.h | 9 +-
src/dump_atom.cpp | 38 +-
src/dump_atom.h | 16 +-
src/dump_cfg.cpp | 12 +-
src/dump_custom.cpp | 19 +-
src/dump_custom.h | 2 +-
src/dump_dcd.cpp | 4 +-
src/dump_dcd.h | 2 +-
src/dump_image.cpp | 4 +-
src/dump_local.cpp | 2 +-
src/dump_local.h | 2 +-
src/dump_xyz.cpp | 4 +-
src/dump_xyz.h | 2 +-
src/fix.h | 13 +-
src/fix_external.h | 2 +-
src/fix_property_atom.cpp | 29 +-
src/fix_property_atom.h | 12 -
src/fix_restrain.cpp | 4 +-
src/fix_shear_history.cpp | 12 +-
src/fix_shear_history.h | 4 +-
src/fix_store_state.cpp | 2 +-
src/fix_tmd.cpp | 10 +-
src/force.cpp | 52 +
src/force.h | 2 +
src/group.cpp | 129 +-
src/lammps.cpp | 8 +-
src/library.cpp | 6 +-
src/lmptype.h | 11 +-
src/molecule.cpp | 13 +-
src/molecule.h | 4 +
src/neigh_bond.cpp | 100 +-
src/neigh_full.cpp | 20 +-
src/neigh_gran.cpp | 12 +-
src/neigh_half_bin.cpp | 16 +-
src/neigh_half_multi.cpp | 12 +-
src/neigh_half_nsq.cpp | 12 +-
src/neigh_respa.cpp | 20 +-
src/neighbor.h | 4 +-
src/read_data.cpp | 1366 +++++++++----------
src/read_data.h | 22 +-
src/read_dump.cpp | 22 +-
src/read_restart.cpp | 17 +-
src/replicate.cpp | 60 +-
src/set.cpp | 9 +-
src/special.cpp | 85 +-
src/special.h | 2 +-
src/variable.cpp | 27 +-
src/variable.h | 1 +
src/velocity.cpp | 1 -
src/write_data.cpp | 40 +-
172 files changed, 2472 insertions(+), 2133 deletions(-)
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index aab7f3cd86..e4f58e0560 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -205,7 +205,9 @@ void DihedralClass2::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index 628a106300..b4ccd77e77 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -156,8 +156,9 @@ void ImproperClass2::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 59d8b5e8eb..08067d567d 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -512,7 +512,7 @@ void AtomVecDipole::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -541,7 +541,7 @@ void AtomVecDipole::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -625,7 +625,7 @@ int AtomVecDipole::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -716,7 +716,7 @@ int AtomVecDipole::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -781,10 +781,7 @@ void AtomVecDipole::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -872,9 +869,10 @@ int AtomVecDipole::pack_data_hybrid(int i, double *buf)
void AtomVecDipole::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
+ fprintf(fp,TAGINT_FORMAT \
+ " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],
buf[i][5],buf[i][6],buf[i][7],buf[i][8],
(int) ubuf(buf[i][9]).i,(int) ubuf(buf[i][10]).i,
diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h
index aaa8801aca..436973f3ac 100644
--- a/src/DIPOLE/atom_vec_dipole.h
+++ b/src/DIPOLE/atom_vec_dipole.h
@@ -59,7 +59,8 @@ class AtomVecDipole : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *q,**mu,**omega,**torque;
diff --git a/src/FLD/pair_lubricateU.cpp b/src/FLD/pair_lubricateU.cpp
index 4fda281140..4a48800697 100644
--- a/src/FLD/pair_lubricateU.cpp
+++ b/src/FLD/pair_lubricateU.cpp
@@ -40,7 +40,6 @@
#include "memory.h"
#include "error.h"
-
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index 562edd42c2..9a439d87d6 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -630,12 +630,16 @@ void FixPour::pre_exchange()
if (ninserted_atoms) {
atom->natoms += ninserted_atoms;
+ if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemol->nbonds * ninserted_mols;
atom->nangles += onemol->nangles * ninserted_mols;
atom->ndihedrals += onemol->ndihedrals * ninserted_mols;
atom->nimpropers += onemol->nimpropers * ninserted_mols;
}
+ if (maxtag_all >= MAXTAGINT)
+ error->all(FLERR,"New atom IDs exceed maximum allowed ID");
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
@@ -661,13 +665,13 @@ void FixPour::pre_exchange()
void FixPour::find_maxid()
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int max = 0;
+ tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
- MPI_Allreduce(&max,&maxtag_all,1,MPI_INT,MPI_MAX,world);
+ MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (mode == MOLECULE && molecule) {
max = 0;
diff --git a/src/GRANULAR/fix_pour.h b/src/GRANULAR/fix_pour.h
index 6b955fd801..34d13da985 100644
--- a/src/GRANULAR/fix_pour.h
+++ b/src/GRANULAR/fix_pour.h
@@ -62,7 +62,8 @@ class FixPour : public Fix {
int *recvcounts,*displs;
int nfreq,nfirst,ninserted,nper;
double lo_current,hi_current;
- int maxtag_all,maxmol_all;
+ tagint maxtag_all;
+ int maxmol_all;
class RanPark *random,*random2;
void find_maxid();
diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
index a6881c86f5..05aa14e2c6 100644
--- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
@@ -117,6 +117,7 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -144,8 +145,8 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -214,8 +215,8 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag)
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp
index 31623fc732..04723a27a1 100755
--- a/src/KSPACE/pair_lj_long_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp
@@ -116,6 +116,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -144,8 +145,8 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
itype = type[i];
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -253,8 +254,8 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag)
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -499,6 +500,7 @@ void PairLJLongTIP4PLong::compute_inner()
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -526,8 +528,8 @@ void PairLJLongTIP4PLong::compute_inner()
itype = type[i];
if (itype == typeO && order1) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -594,8 +596,8 @@ void PairLJLongTIP4PLong::compute_inner()
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -749,6 +751,7 @@ void PairLJLongTIP4PLong::compute_middle()
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -777,8 +780,8 @@ void PairLJLongTIP4PLong::compute_middle()
itype = type[i];
if (itype == typeO && order1) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -849,8 +852,8 @@ void PairLJLongTIP4PLong::compute_middle()
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -1017,6 +1020,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -1053,8 +1057,8 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
itype = type[i];
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -1174,8 +1178,8 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp
index b6b6ef0034..c08b422229 100644
--- a/src/KSPACE/pair_tip4p_long.cpp
+++ b/src/KSPACE/pair_tip4p_long.cpp
@@ -115,6 +115,7 @@ void PairTIP4PLong::compute(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
@@ -141,8 +142,8 @@ void PairTIP4PLong::compute(int eflag, int vflag)
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -185,8 +186,8 @@ void PairTIP4PLong::compute(int eflag, int vflag)
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index 54d6b49e01..05264d3502 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -212,7 +212,6 @@ void FixQEQComb::post_force(int vflag)
double *q = atom->q;
int *mask = atom->mask;
- int *tag = atom->tag;
int nlocal = atom->nlocal;
if (comb) {
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index f6555063dc..be96881bc5 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -391,7 +391,8 @@ void PairAIREBO::REBO_neigh()
void PairAIREBO::FREBO(int eflag, int vflag)
{
- int i,j,k,m,ii,inum,itype,jtype,itag,jtag;
+ int i,j,k,m,ii,inum,itype,jtype;
+ tagint itag,jtag;
double delx,dely,delz,evdwl,fpair,xtmp,ytmp,ztmp;
double rsq,rij,wij;
double Qij,Aij,alphaij,VR,pre,dVRdi,VA,term,bij,dVAdi,dVA;
@@ -403,7 +404,7 @@ void PairAIREBO::FREBO(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@@ -489,9 +490,10 @@ void PairAIREBO::FREBO(int eflag, int vflag)
void PairAIREBO::FLJ(int eflag, int vflag)
{
- int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype,itag,jtag;
+ int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype;
int atomi,atomj,atomk,atomm;
int testpath,npath,done;
+ tagint itag,jtag;
double evdwl,fpair,xtmp,ytmp,ztmp;
double rsq,best,wik,wkm,cij,rij,dwij,dwik,dwkj,dwkm,dwmj;
double delij[3],rijsq,delik[3],rik,deljk[3];
@@ -520,7 +522,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@@ -855,7 +857,8 @@ void PairAIREBO::FLJ(int eflag, int vflag)
void PairAIREBO::TORSION(int eflag, int vflag)
{
- int i,j,k,l,ii,inum,itag,jtag;
+ int i,j,k,l,ii,inum;
+ tagint itag,jtag;
double evdwl,fpair,xtmp,ytmp,ztmp;
double cos321;
double w21,dw21,cos234,w34,dw34;
@@ -880,7 +883,7 @@ void PairAIREBO::TORSION(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
inum = list->inum;
ilist = list->ilist;
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 2f72fc8be0..e9b41c2375 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -274,7 +274,8 @@ void PairBOP::compute(int eflag, int vflag)
int ago,delay,every;
int i,j,ii,jj,iij;
int n,inum,temp_ij,ks;
- int itype,jtype,i_tag,j_tag;
+ int itype,jtype;
+ tagint i_tag,j_tag;
int *ilist,*iilist,*numneigh;
int **firstneigh;
double dpr1,ps;
@@ -288,7 +289,7 @@ void PairBOP::compute(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@@ -846,7 +847,7 @@ void PairBOP::sigmaBo()
int n,i,j,k,kp,m,pp,kkp;
int iij,ji,ki;
int itmp,jtmp,ktmp,ltmp,mtmp;
- int i_tag,j_tag;
+ tagint i_tag,j_tag;
int ngi,ngj,ngk,nglkp,ngli,nglj,ngl;
int ngji,ngjk,nikj,ngki,ngkj,ngjkp;
int ngkpk,ngkpj,ngkkp,nglk;
@@ -890,7 +891,7 @@ void PairBOP::sigmaBo()
double ftmp[3];
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int *type = atom->type;
@@ -2401,7 +2402,7 @@ void PairBOP::sigmaBo_noa()
int n,i,j,k,kp,m,pp;
int iij,ji,ki;
int itmp,jtmp,ktmp,ltmp,mtmp;
- int i_tag,j_tag;
+ tagint i_tag,j_tag;
int ngi,ngj,ngk,ngli,nglj,ngl;
int ngji,ngjk,nikj,ngki,ngkj;
int njik,nijk,nikkp,nkp,nijkp;
@@ -2437,7 +2438,7 @@ void PairBOP::sigmaBo_noa()
double ftmp[3];
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int *type = atom->type;
@@ -3379,7 +3380,7 @@ void PairBOP::sigmaBo_otf()
int nb_t,new_n_tot;
int n,i,j,k,kp,m,pp,kpj,kpk,kkp;
int itmp,jtmp,ktmp,ltmp,mtmp;
- int i_tag,j_tag;
+ tagint i_tag,j_tag;
int kp1,kp2,kp1type;
int iij,iik,ijk,ikkp,ji,iikp,ijkp;
int nkp;
@@ -3448,7 +3449,7 @@ void PairBOP::sigmaBo_otf()
double ftmp[3],xtmp[3];
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int *type = atom->type;
@@ -5303,7 +5304,7 @@ void PairBOP::sigmaBo_noa_otf()
int nb_t,new_n_tot;
int n,i,j,k,kp,m,pp;
int itmp,jtmp,ktmp,ltmp,mtmp;
- int i_tag,j_tag;
+ tagint i_tag,j_tag;
int kp1,kp2,kp1type;
int iij,iik,ijk,ikkp,ji,iikp,ijkp;
int nkp;
@@ -5368,7 +5369,7 @@ void PairBOP::sigmaBo_noa_otf()
double ftmp[3],xtmp[3];
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
int *type = atom->type;
@@ -6541,7 +6542,7 @@ void PairBOP::PiBo()
int i,j,k,kp,m,n,pp,nb_t;
int iij,ji,ki;
int nsearch,ncmp;
- int i_tag,j_tag;
+ tagint i_tag,j_tag;
int njik,ngj,ngk,nglj,ngl,ngi;
int nkjkp,nijkp,ngli,nkikp,njikp;
int itmp,ltmp,jtmp,ktmp;
@@ -6570,7 +6571,7 @@ void PairBOP::PiBo()
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_pair = force->newton_pair;
nlocal = atom->nlocal;
@@ -7265,7 +7266,7 @@ void PairBOP::PiBo_otf()
int i,j,k,kp,m,n,pp,nb_t;
int iij,iik,iikp,ji,ki,ijkp,ijk;
int nsearch,ncmp;
- int i_tag,j_tag;
+ tagint i_tag,j_tag;
int itmp,ltmp,jtmp,ktmp;
int pi_flag,ks;
int nlocal;
@@ -7317,7 +7318,7 @@ void PairBOP::PiBo_otf()
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
nlocal = atom->nlocal;
numneigh = list->numneigh;
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index 02096c0002..7c18ccd3fc 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -125,7 +125,8 @@ PairComb::~PairComb()
void PairComb::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum,iparam_i;
- int itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk;
+ int itype,jtype,ktype,iparam_ij,iparam_ijk;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
@@ -151,7 +152,7 @@ void PairComb::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@@ -1630,8 +1631,9 @@ void PairComb::field(Param *param, double rsq, double iq,double jq,
double PairComb::yasu_char(double *qf_fix, int &igroup)
{
- int i,j,ii,jj,jnum,itag,jtag;
+ int i,j,ii,jj,jnum;
int itype,jtype,iparam_i,iparam_ij;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp;
double rsq1,delr1[3];
int *ilist,*jlist,*numneigh,**firstneigh;
@@ -1643,7 +1645,7 @@ double PairComb::yasu_char(double *qf_fix, int &igroup)
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int inum = list->inum;
ilist = list->ilist;
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index afc0adf021..2d6bf9f9ef 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -860,12 +860,11 @@ void PairComb3::Short_neigh()
int n,nj,*neighptrj,icontrol;
int iparam_ij,iparam_ji,iparam_jk,*ilist,*jlist,*numneigh,**firstneigh;
int inum,jnum,i,j,k,l,ii,jj,kk,ll,itype,jtype,ktype,ltype;
- int itag, jtag;
+ tagint itag,jtag;
double rr1,rr2,rsq1,rsq2,delrj[3],delrk[3];
int sht_knum,*sht_klist;
double **x = atom->x;
- int *tag = atom->tag;
int *type = atom->type;
int ntype = atom->ntypes;
int nlocal = atom->nlocal;
@@ -896,7 +895,6 @@ void PairComb3::Short_neigh()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
- itag = tag[i];
dpl[i][0] = dpl[i][1] = dpl[i][2] = 0.0;
nj = 0;
@@ -913,7 +911,6 @@ void PairComb3::Short_neigh()
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
- jtag = tag[j];
delrj[0] = x[i][0] - x[j][0];
delrj[1] = x[i][1] - x[j][1];
@@ -957,12 +954,13 @@ void PairComb3::Short_neigh()
void PairComb3::compute(int eflag, int vflag)
{
- int i,ii,k,kk,j,jj,im,inum,jnum,itag,jtag,itype,jtype,ktype;
+ int i,ii,k,kk,j,jj,im,inum,jnum,itype,jtype,ktype;
int iparam_i,iparam_ij,iparam_ji;
int iparam_ijk,iparam_jik,iparam_ikj,iparam_jli,iparam_jki,iparam_ikl;
int sht_jnum,*sht_jlist,sht_lnum,*sht_llist;
int sht_mnum,*sht_mlist,sht_pnum,*sht_plist;
int *ilist,*jlist,*numneigh,**firstneigh,mr1,mr2,mr3,inty,nj;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rr,rsq,rsq1,rsq2,rsq3,iq,jq,yaself;
double fqi,fqij,eng_tmp,vionij,fvionij,sr1,sr2,sr3;
@@ -975,7 +973,7 @@ void PairComb3::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
int ntype = atom->ntypes;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
double **x = atom->x;
double **f = atom->f;
@@ -1833,11 +1831,12 @@ void PairComb3::force_zeta(Param *parami, Param *paramj, double rsq,
double boij, dbij1, dbij2, dbij3, dbij4, dbij5;
double boji, dbji1, dbji2, dbji3, dbji4, dbji5;
double pradx, prady;
+
int inti=parami->ielement;
int intj=paramj->ielement;
- int *tag=atom->tag;
- int itag=tag[i];
- int jtag=tag[j];
+ tagint *tag=atom->tag;
+ tagint itag=tag[i];
+ tagint jtag=tag[j];
r = sqrt(rsq);
if (r > parami->bigr + parami->bigd) return;
@@ -3348,10 +3347,11 @@ void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
double PairComb3::combqeq(double *qf_fix, int &igroup)
{
- int i,j,ii, jj,itag,jtag,itype,jtype,jnum;
+ int i,j,ii,jj,itype,jtype,jnum;
int iparam_i,iparam_ji,iparam_ij;
int *ilist,*jlist,*numneigh,**firstneigh;
int mr1,mr2,mr3,inty,nj;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp,rr,rsq,rsq1,rsq2,delrj[3],zeta_ij;
double iq,jq,fqi,fqj,fqij,fqji,yaself,yaself_d,sr1,sr2,sr3;
double rr_sw,ij_sw,ji_sw,fq_swi,fq_swj;
@@ -3360,7 +3360,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
double **x = atom->x;
double *q = atom->q;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int inum = list->inum;
int *mask = atom->mask;
@@ -3507,7 +3507,7 @@ double PairComb3::combqeq(double *qf_fix, int &igroup)
i = ilist[ii];
if (mask[i] & groupbit){
eneg += qf[i];
- itag=tag[i];
+ itag=tag[i];
}
}
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index cc511d59a4..8ccb7ee8aa 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -355,7 +355,8 @@ void PairLCBOP::SR_neigh()
void PairLCBOP::FSR(int eflag, int vflag)
{
- int i,j,jj,ii,inum,itag,jtag;
+ int i,j,jj,ii,inum;
+ tagint itag,jtag;
double delx,dely,delz,fpair,xtmp,ytmp,ztmp;
double r_sq,rijmag,f_c_ij,df_c_ij;
double VR,dVRdi,VA,Bij,dVAdi,dVA;
@@ -364,7 +365,7 @@ void PairLCBOP::FSR(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@@ -450,19 +451,18 @@ void PairLCBOP::FSR(int eflag, int vflag)
void PairLCBOP::FLR(int eflag, int vflag)
{
-
- int i,j,jj,m,ii,itag,jtag;
+ int i,j,jj,m,ii;
+ tagint itag,jtag;
double delx,dely,delz,fpair,xtmp,ytmp,ztmp;
double r_sq,rijmag,f_c_ij,df_c_ij;
double V,dVdi;
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
-
int inum = list->inum;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index 1130479d3f..d2121b0752 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -77,8 +77,9 @@ PairNb3bHarmonic::~PairNb3bHarmonic()
void PairNb3bHarmonic::compute(int eflag, int vflag)
{
- int i,j,k,ii,jj,kk,inum,jnum,jnumm1,itag,jtag;
+ int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fj[3],fk[3];
@@ -90,7 +91,7 @@ void PairNb3bHarmonic::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index d3cc168389..3928ff0d0b 100755
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -75,8 +75,9 @@ PairSW::~PairSW()
void PairSW::compute(int eflag, int vflag)
{
- int i,j,k,ii,jj,kk,inum,jnum,jnumm1,itag,jtag;
+ int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fj[3],fk[3];
@@ -88,7 +89,7 @@ void PairSW::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index fbbe857f09..fe02371fec 100755
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -77,7 +77,8 @@ PairTersoff::~PairTersoff()
void PairTersoff::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum;
- int itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk;
+ int itype,jtype,ktype,iparam_ij,iparam_ijk;
+ tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
@@ -90,7 +91,7 @@ void PairTersoff::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 0ae5ae94be..50f718492c 100755
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -155,7 +155,7 @@ void FixBondBreak::post_integrate()
{
int i,j,k,m,n,i1,i2,n1,n3,type;
double delx,dely,delz,rsq;
- int *slist;
+ tagint *slist;
if (update->ntimestep % nevery) return;
@@ -188,7 +188,7 @@ void FixBondBreak::post_integrate()
// setup possible partner list of bonds to break
double **x = atom->x;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
@@ -237,10 +237,10 @@ void FixBondBreak::post_integrate()
// and probability constraint is satisfied
int **bond_type = atom->bond_type;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
- int **special = atom->special;
+ tagint **special = atom->special;
int nbreak = 0;
for (i = 0; i < nlocal; i++) {
@@ -333,7 +333,7 @@ void FixBondBreak::unpack_comm(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++) {
- partner[i] = static_cast<int> (buf[m++]);
+ partner[i] = static_cast<tagint> (buf[m++]);
probability[i] = buf[m++];
}
}
@@ -363,7 +363,7 @@ void FixBondBreak::unpack_reverse_comm(int n, int *list, double *buf)
for (i = 0; i < n; i++) {
j = list[i];
if (buf[m+1] > distsq[j]) {
- partner[j] = static_cast<int> (buf[m++]);
+ partner[j] = static_cast<tagint> (buf[m++]);
distsq[j] = buf[m++];
} else m += 2;
}
diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h
index a625e0ff80..6c8f749861 100755
--- a/src/MC/fix_bond_break.h
+++ b/src/MC/fix_bond_break.h
@@ -47,7 +47,7 @@ class FixBondBreak : public Fix {
int breakcount,breakcounttotal;
int nmax;
- int *partner;
+ tagint *partner;
double *distsq,*probability;
class RanMars *random;
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 7d0850c57e..015a527015 100755
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -235,7 +235,7 @@ void FixBondCreate::setup(int vflag)
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int nall = nlocal + nghost;
@@ -269,7 +269,8 @@ void FixBondCreate::post_integrate()
{
int i,j,m,ii,jj,inum,jnum,itype,jtype,n1,n3,possible;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *ilist,*jlist,*numneigh,**firstneigh,*slist;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ tagint *slist;
if (update->ntimestep % nevery) return;
@@ -307,7 +308,7 @@ void FixBondCreate::post_integrate()
// each atom sets one closest eligible partner atom ID to bond with
double **x = atom->x;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int *type = atom->type;
@@ -385,10 +386,10 @@ void FixBondCreate::post_integrate()
// and probability constraint is satisfied
int **bond_type = atom->bond_type;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int **nspecial = atom->nspecial;
- int **special = atom->special;
+ tagint **special = atom->special;
int newton_bond = force->newton_bond;
int ncreate = 0;
@@ -506,7 +507,7 @@ void FixBondCreate::unpack_comm(int n, int first, double *buf)
} else {
for (i = first; i < last; i++) {
- partner[i] = static_cast<int> (buf[m++]);
+ partner[i] = static_cast<tagint> (buf[m++]);
probability[i] = buf[m++];
}
}
@@ -554,7 +555,7 @@ void FixBondCreate::unpack_reverse_comm(int n, int *list, double *buf)
j = list[i];
if (buf[m] < distsq[j]) {
distsq[j] = buf[m++];
- partner[j] = static_cast<int> (buf[m++]);
+ partner[j] = static_cast<tagint> (buf[m++]);
} else m += 2;
}
}
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
index 36519d7741..52f9b09de2 100755
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -58,7 +58,7 @@ class FixBondCreate : public Fix {
int nmax;
int *bondcount; // count of created bonds this atom is part of
- int *partner; // ID of preferred atom for this atom to bond to
+ tagint *partner; // ID of preferred atom for this atom to bond to
double *distsq; // distance to preferred bond partner
double *probability; // random # to use in decision to form bond
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index 24474052f5..31bdb75682 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -179,9 +179,9 @@ void FixBondSwap::pre_neighbor()
{
int i,j,ii,jj,m,inum,jnum;
int inext,iprev,ilast,jnext,jprev,jlast,ibond,iangle,jbond,jangle;
- int itag,inexttag,iprevtag,ilasttag,jtag,jnexttag,jprevtag,jlasttag;
int ibondtype,jbondtype,iangletype,inextangletype,jangletype,jnextangletype;
- int i1,i2,i3,j1,j2,j3,tmp;
+ tagint itag,inexttag,iprevtag,ilasttag,jtag,jnexttag,jprevtag,jlasttag;
+ tagint i1,i2,i3,j1,j2,j3;
int *ilist,*jlist,*numneigh,**firstneigh;
double delta,factor;
@@ -191,19 +191,19 @@ void FixBondSwap::pre_neighbor()
// local ptrs to atom arrays
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int *molecule = atom->molecule;
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_angle = atom->num_angle;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int **nspecial = atom->nspecial;
- int **special = atom->special;
+ tagint **special = atom->special;
int newton_bond = force->newton_bond;
int nlocal = atom->nlocal;
@@ -231,6 +231,7 @@ void FixBondSwap::pre_neighbor()
alist[neligible++] = i;
}
+ int tmp;
for (i = 0; i < neligible; i++) {
j = static_cast<int> (random->uniform() * neligible);
tmp = alist[i];
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index eb8fba2daf..ab85e6e21b 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -282,9 +282,10 @@ void FixGCMC::init()
}
if ((molflag && (atom->molecule_flag == 0)) ||
- (molflag && ((!atom->tag_enable) || (!atom->map_style))))
+ (molflag && (!atom->tag_enable || !atom->map_style)))
error->all(FLERR,
- "Fix gcmc molecule command requires that atoms have molecule attributes");
+ "Fix gcmc molecule command requires that "
+ "atoms have molecule attributes");
if (force->pair->single_enable == 0)
error->all(FLERR,"Fix gcmc incompatible with given pair_style");
@@ -805,18 +806,18 @@ void FixGCMC::attempt_molecule_insertion()
if (maxmol >= MAXSMALLINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
- int maxtag = 0;
+ tagint maxtag = 0;
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
- int maxtag_all;
- MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
- int atom_offset = maxtag_all;
+ tagint maxtag_all;
+ MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
+ tagint atom_offset = maxtag_all;
int k = 0;
double **x = atom->x;
double **v = atom->v;
imageint *image = atom->image;
int *molecule = atom->molecule;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int i = 0; i < natoms_per_molecule; i++) {
k += atom->avec->unpack_exchange(&model_atom_buf[k]);
if (procflag[i]) {
@@ -1165,9 +1166,9 @@ void FixGCMC::get_model_molecule()
x[i][2] -= com[2];
}
- int mintag = atom->tag[0];
+ tagint mintag = atom->tag[0];
for (int i = 0; i < atom->nlocal; i++) mintag = MIN(mintag,atom->tag[i]);
- int atom_offset = mintag - 1;
+ tagint atom_offset = mintag - 1;
for (int i = 0; i < nlocal; i++) {
atom->mask[i] = 1 | groupbit;
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index fa8dbf6c69..ea8fb37be9 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -488,16 +488,18 @@ void FixDeposit::pre_exchange()
if (success) {
atom->natoms += natom;
+ if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemol->nbonds;
atom->nangles += onemol->nangles;
atom->ndihedrals += onemol->ndihedrals;
atom->nimpropers += onemol->nimpropers;
}
- if (idnext) {
- maxtag_all += natom;
- if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
- }
+ maxtag_all += natom;
+ if (maxtag_all >= MAXTAGINT)
+ error->all(FLERR,"New atom IDs exceed maximum allowed ID");
+ if (mode == MOLECULE && atom->molecule_flag) maxmol_all++;
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
@@ -520,13 +522,13 @@ void FixDeposit::pre_exchange()
void FixDeposit::find_maxid()
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int max = 0;
+ tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
- MPI_Allreduce(&max,&maxtag_all,1,MPI_INT,MPI_MAX,world);
+ MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (mode == MOLECULE && molecule) {
max = 0;
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index 7e9bea0f37..56bf34c6dd 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -55,7 +55,8 @@ class FixDeposit : public Fix {
class Fix *fixrigid,*fixshake;
int nfirst,ninserted;
- int maxtag_all,maxmol_all;
+ tagint maxtag_all;
+ int maxmol_all;
class RanPark *random;
void find_maxid();
diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp
index 5fe5c1412f..ab153f805e 100644
--- a/src/MISC/fix_evaporate.cpp
+++ b/src/MISC/fix_evaporate.cpp
@@ -186,7 +186,7 @@ void FixEvaporate::pre_exchange()
double **x = atom->x;
int *mask = atom->mask;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int ncount = 0;
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index a7fc2eceaa..722dc04854 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -243,7 +243,8 @@ void FixOrientFCC::setup(int vflag)
void FixOrientFCC::post_force(int vflag)
{
- int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort,id_self;
+ int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort;
+ tagint id_self;
int *ilist,*jlist,*numneigh,**firstneigh;
double edelta,omega;
double dx,dy,dz,rsq,xismooth,xi_sq,duxi,duxi_other;
@@ -256,7 +257,7 @@ void FixOrientFCC::post_force(int vflag)
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
@@ -480,8 +481,10 @@ double FixOrientFCC::compute_scalar()
int FixOrientFCC::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
- int i,j,k,id,num;
- int *tag = atom->tag;
+ int i,j,k,num;
+ tagint id;
+
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int m = 0;
@@ -531,7 +534,7 @@ void FixOrientFCC::unpack_comm(int n, int first, double *buf)
nbr[i].dxi[j][0] = buf[m++];
nbr[i].dxi[j][1] = buf[m++];
nbr[i].dxi[j][2] = buf[m++];
- nbr[i].id[j] = static_cast<int> (buf[m++]);
+ nbr[i].id[j] = static_cast<tagint> (buf[m++]);
}
m += (12-num) * 3;
diff --git a/src/MISC/fix_orient_fcc.h b/src/MISC/fix_orient_fcc.h
index 727be00539..399c34970e 100644
--- a/src/MISC/fix_orient_fcc.h
+++ b/src/MISC/fix_orient_fcc.h
@@ -28,7 +28,7 @@ class FixOrientFCC : public Fix {
public:
struct Nbr { // neighbor info for each owned and ghost atom
int n; // # of closest neighbors (up to 12)
- int id[12]; // IDs of each neighbor
+ tagint id[12]; // IDs of each neighbor
// if center atom is owned, these are local IDs
// if center atom is ghost, these are global IDs
double xismooth[12]; // distance weighting factor for each neighbors
@@ -37,7 +37,7 @@ class FixOrientFCC : public Fix {
};
struct Sort { // data structure for sorting to find 12 closest
- int id; // ID of neighbor atom
+ int id; // local ID of neighbor atom
double rsq; // distance between center and neighbor atom
double delta[3]; // displacement between center and neighbor atom
double xismooth; // distance weighting factor
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 224c25605a..9b303451c3 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -475,7 +475,7 @@ void AtomVecAngle::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -500,7 +500,7 @@ void AtomVecAngle::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -594,7 +594,7 @@ int AtomVecAngle::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -604,22 +604,22 @@ int AtomVecAngle::unpack_exchange(double *buf)
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+ bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_angle[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
+ angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
nspecial[nlocal][0] = (int) ubuf(buf[m++]).i;
nspecial[nlocal][1] = (int) ubuf(buf[m++]).i;
nspecial[nlocal][2] = (int) ubuf(buf[m++]).i;
for (k = 0; k < nspecial[nlocal][2]; k++)
- special[nlocal][k] = (int) ubuf(buf[m++]).i;
+ special[nlocal][k] = (tagint) ubuf(buf[m++]).i;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -666,28 +666,28 @@ int AtomVecAngle::pack_restart(int i, double *buf)
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
- buf[m++] = tag[i];
- buf[m++] = type[i];
- buf[m++] = mask[i];
- *((imageint *) &buf[m++]) = image[i];
+ buf[m++] = ubuf(tag[i]).d;
+ buf[m++] = ubuf(type[i]).d;
+ buf[m++] = ubuf(mask[i]).d;
+ buf[m++] = ubuf(image[i]).d;
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
- buf[m++] = molecule[i];
+ buf[m++] = ubuf(molecule[i]).d;
- buf[m++] = num_bond[i];
+ buf[m++] = ubuf(num_bond[i]).d;
for (k = 0; k < num_bond[i]; k++) {
- buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
- buf[m++] = bond_atom[i][k];
+ buf[m++] = ubuf(MAX(bond_type[i][k],-bond_type[i][k])).d;
+ buf[m++] = ubuf(bond_atom[i][k]).d;
}
- buf[m++] = num_angle[i];
+ buf[m++] = ubuf(num_angle[i]).d;
for (k = 0; k < num_angle[i]; k++) {
- buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
- buf[m++] = angle_atom1[i][k];
- buf[m++] = angle_atom2[i][k];
- buf[m++] = angle_atom3[i][k];
+ buf[m++] = ubuf(MAX(angle_type[i][k],-angle_type[i][k])).d;
+ buf[m++] = ubuf(angle_atom1[i][k]).d;
+ buf[m++] = ubuf(angle_atom2[i][k]).d;
+ buf[m++] = ubuf(angle_atom3[i][k]).d;
}
if (atom->nextra_restart)
@@ -717,7 +717,7 @@ int AtomVecAngle::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -730,15 +730,15 @@ int AtomVecAngle::unpack_restart(double *buf)
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+ bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_angle[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
+ angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
@@ -793,12 +793,8 @@ void AtomVecAngle::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(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");
@@ -871,8 +867,8 @@ 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,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
diff --git a/src/MOLECULE/atom_vec_angle.h b/src/MOLECULE/atom_vec_angle.h
index b269fda174..d33dbcd013 100644
--- a/src/MOLECULE/atom_vec_angle.h
+++ b/src/MOLECULE/atom_vec_angle.h
@@ -58,16 +58,19 @@ class AtomVecAngle : public AtomVec {
bigint memory_usage();
protected:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
- int **nspecial,**special;
+ int **nspecial;
+ tagint **special;
int *num_bond;
- int **bond_type,**bond_atom;
+ int **bond_type;
+ tagint **bond_atom;
int *num_angle;
int **angle_type;
- int **angle_atom1,**angle_atom2,**angle_atom3;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
};
}
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index c06d3eed29..7e5e639918 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -454,7 +454,7 @@ void AtomVecBond::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -479,7 +479,7 @@ void AtomVecBond::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -565,7 +565,7 @@ int AtomVecBond::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -575,14 +575,14 @@ int AtomVecBond::unpack_exchange(double *buf)
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+ bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
nspecial[nlocal][0] = (int) ubuf(buf[m++]).i;
nspecial[nlocal][1] = (int) ubuf(buf[m++]).i;
nspecial[nlocal][2] = (int) ubuf(buf[m++]).i;
for (k = 0; k < nspecial[nlocal][2]; k++)
- special[nlocal][k] = (int) ubuf(buf[m++]).i;
+ special[nlocal][k] = (tagint) ubuf(buf[m++]).i;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -672,7 +672,7 @@ int AtomVecBond::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -685,7 +685,7 @@ int AtomVecBond::unpack_restart(double *buf)
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+ bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
@@ -739,12 +739,8 @@ void AtomVecBond::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(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");
@@ -815,8 +811,8 @@ 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,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
diff --git a/src/MOLECULE/atom_vec_bond.h b/src/MOLECULE/atom_vec_bond.h
index 4e98d21e81..7e8b538d5e 100644
--- a/src/MOLECULE/atom_vec_bond.h
+++ b/src/MOLECULE/atom_vec_bond.h
@@ -57,13 +57,16 @@ class AtomVecBond : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
- int **nspecial,**special;
+ int **nspecial;
+ tagint **special;
int *num_bond;
- int **bond_type,**bond_atom;
+ int **bond_type;
+ tagint **bond_atom;
};
}
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 6d44289d4e..09175dd034 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -469,9 +469,9 @@ int AtomVecFull::pack_border_vel(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
- buf[m++] = tag[j];
- buf[m++] = type[j];
- buf[m++] = mask[j];
+ buf[m++] = ubuf(tag[j]).d;
+ buf[m++] = ubuf(type[j]).d;
+ buf[m++] = ubuf(mask[j]).d;
buf[m++] = q[j];
buf[m++] = molecule[j];
buf[m++] = v[j][0];
@@ -540,7 +540,7 @@ void AtomVecFull::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -566,7 +566,7 @@ void AtomVecFull::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -682,7 +682,7 @@ int AtomVecFull::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -693,40 +693,40 @@ int AtomVecFull::unpack_exchange(double *buf)
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+ bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_angle[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
+ angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_dihedral[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+ dihedral_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ dihedral_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ dihedral_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ dihedral_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_improper[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+ improper_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ improper_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ improper_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ improper_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
nspecial[nlocal][0] = (int) ubuf(buf[m++]).i;
nspecial[nlocal][1] = (int) ubuf(buf[m++]).i;
nspecial[nlocal][2] = (int) ubuf(buf[m++]).i;
for (k = 0; k < nspecial[nlocal][2]; k++)
- special[nlocal][k] = (int) ubuf(buf[m++]).i;
+ special[nlocal][k] = (tagint) ubuf(buf[m++]).i;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -844,7 +844,7 @@ int AtomVecFull::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -858,33 +858,33 @@ int AtomVecFull::unpack_restart(double *buf)
num_bond[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+ bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_angle[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
+ angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_dihedral[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
- dihedral_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+ dihedral_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ dihedral_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ dihedral_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ dihedral_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
num_improper[nlocal] = (int) ubuf(buf[m++]).i;
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
- improper_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+ improper_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ improper_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ improper_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+ improper_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
}
nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;
@@ -942,12 +942,8 @@ void AtomVecFull::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(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");
@@ -1029,8 +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,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h
index c8987e2894..f42072322d 100644
--- a/src/MOLECULE/atom_vec_full.h
+++ b/src/MOLECULE/atom_vec_full.h
@@ -58,23 +58,26 @@ class AtomVecFull : public AtomVec {
bigint memory_usage();
protected:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *q;
int *molecule;
- int **nspecial,**special;
+ int **nspecial;
+ tagint **special;
int *num_bond;
- int **bond_type,**bond_atom;
+ int **bond_type;
+ tagint **bond_atom;
int *num_angle;
int **angle_type;
- int **angle_atom1,**angle_atom2,**angle_atom3;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
- int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+ tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
- int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+ tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
};
}
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 9feb31e1c2..2f2265b5df 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -532,7 +532,7 @@ void AtomVecMolecular::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -557,7 +557,7 @@ void AtomVecMolecular::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -669,7 +669,7 @@ int AtomVecMolecular::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -829,7 +829,7 @@ int AtomVecMolecular::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -920,17 +920,14 @@ void AtomVecMolecular::create_atom(int itype, double *coord)
initialize other atom quantities
------------------------------------------------------------------------- */
-void AtomVecMolecular::data_atom(double *coord, imageint imagetmp, char **values)
+void AtomVecMolecular::data_atom(double *coord, imageint imagetmp,
+ char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(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");
@@ -1007,8 +1004,8 @@ 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,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h
index dcd87721d5..58aa039e1e 100644
--- a/src/MOLECULE/atom_vec_molecular.h
+++ b/src/MOLECULE/atom_vec_molecular.h
@@ -57,22 +57,25 @@ class AtomVecMolecular : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
- int **nspecial,**special;
+ int **nspecial;
+ tagint **special;
int *num_bond;
- int **bond_type,**bond_atom;
+ int **bond_type;
+ tagint **bond_atom;
int *num_angle;
int **angle_type;
- int **angle_atom1,**angle_atom2,**angle_atom3;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
- int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+ tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
- int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+ tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
};
}
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index 8eca809d1b..fb69de6e56 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -85,7 +85,8 @@ void BondFENE::compute(int eflag, int vflag)
if (rlogarg < 0.1) {
char str[128];
- sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
+ sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index 214e632795..439b09a5a7 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -90,7 +90,8 @@ void BondFENEExpand::compute(int eflag, int vflag)
if (rlogarg < 0.1) {
char str[128];
- sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %d %d %g",
+ sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 8029e7b4fa..671514fc5d 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -150,7 +150,9 @@ void DihedralCharmm::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index a7f353269b..0c0ff327ba 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -137,7 +137,9 @@ void DihedralHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index fd5d72e845..744f3b4915 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -165,7 +165,9 @@ void DihedralHelix::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index 2e3b4e79dc..48f4f2b45f 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -155,7 +155,9 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index 074c8bf15c..f73b85f9b4 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -164,7 +164,9 @@ void DihedralOPLS::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index 06485e9189..3d33b3b9f7 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -151,8 +151,9 @@ void ImproperCvff::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index 4db32456b3..19f845452a 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -125,8 +125,9 @@ void ImproperHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index ef8c1a1352..a3b7295b3d 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -128,8 +128,9 @@ void ImproperUmbrella::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index 381629e161..a25e116e96 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -84,7 +84,8 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
double fi[3],fj[3],delr1[3],delr2[3];
double r2inv,r10inv;
double switch1,switch2;
- int *ilist,*jlist,*klist,*numneigh,**firstneigh;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ tagint *klist;
evdwl = ehbond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@@ -92,7 +93,7 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int **special = atom->special;
+ tagint **special = atom->special;
int *type = atom->type;
int **nspecial = atom->nspecial;
double *special_lj = force->special_lj;
@@ -457,10 +458,10 @@ double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
double rsq1,rsq2,r1,r2,c,s,ac,r2inv,r10inv,factor_hb;
double switch1,switch2;
double delr1[3],delr2[3];
- int *klist;
+ tagint *klist;
double **x = atom->x;
- int **special = atom->special;
+ tagint **special = atom->special;
int *type = atom->type;
int **nspecial = atom->nspecial;
double *special_lj = force->special_lj;
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index e3c26a5dc2..975bc94331 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -54,7 +54,8 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
double c,s,a,b,d,ac,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;
double fi[3],fj[3],delr1[3],delr2[3];
double r,dr,dexp,eng_morse,switch1,switch2;
- int *ilist,*jlist,*klist,*numneigh,**firstneigh;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ tagint *klist;
evdwl = ehbond = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
@@ -62,7 +63,7 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
- int **special = atom->special;
+ tagint **special = atom->special;
int *type = atom->type;
int **nspecial = atom->nspecial;
double *special_lj = force->special_lj;
@@ -360,10 +361,10 @@ double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
double rsq1,rsq2,r1,r2,c,s,ac,r,dr,dexp,factor_hb;
double switch1,switch2;
double delr1[3],delr2[3];
- int *klist;
+ tagint *klist;
double **x = atom->x;
- int **special = atom->special;
+ tagint **special = atom->special;
int *type = atom->type;
int **nspecial = atom->nspecial;
double *special_lj = force->special_lj;
diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
index 04b37635b6..39f8a3c1f9 100644
--- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
@@ -114,6 +114,7 @@ void PairLJCutTIP4PCut::compute(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_lj = force->special_lj;
double *special_coul = force->special_coul;
@@ -137,8 +138,8 @@ void PairLJCutTIP4PCut::compute(int eflag, int vflag)
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -207,8 +208,8 @@ void PairLJCutTIP4PCut::compute(int eflag, int vflag)
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index d1ce9b2569..57bb72da8b 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -103,6 +103,7 @@ void PairTIP4PCut::compute(int eflag, int vflag)
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
+ tagint *tag = atom->tag;
int *type = atom->type;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
@@ -125,8 +126,8 @@ void PairTIP4PCut::compute(int eflag, int vflag)
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -169,8 +170,8 @@ void PairTIP4PCut::compute(int eflag, int vflag)
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
index 30ef318799..e045eeec75 100644
--- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
@@ -125,6 +125,7 @@ void PairLJCutTIP4PLongOpt::eval()
const double * const * const x = atom->x;
double * const * const f = atom->f;
const double * const q = atom->q;
+ const tagint * const tag = atom->tag;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
const double * const special_coul = force->special_coul;
@@ -154,8 +155,8 @@ void PairLJCutTIP4PLongOpt::eval()
if (itype == typeO) {
if (hneigh[i][0] < 0) {
- hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1);
- hneigh[i][1] = iH2 = atom->map(atom->tag[i] + 2);
+ hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
+ hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
if (iH1 == -1 || iH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
@@ -225,8 +226,8 @@ void PairLJCutTIP4PLongOpt::eval()
if (jtype == typeO) {
if (hneigh[j][0] < 0) {
- hneigh[j][0] = jH1 = atom->map(atom->tag[j] + 1);
- hneigh[j][1] = jH2 = atom->map(atom->tag[j] + 2);
+ hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
+ hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
if (jH1 == -1 || jH2 == -1)
error->one(FLERR,"TIP4P hydrogen is missing");
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index 28e7ff1db9..c2791ce01f 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -517,7 +517,7 @@ void AtomVecPeri::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
vfrac[i] = buf[m++];
@@ -546,7 +546,7 @@ void AtomVecPeri::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
vfrac[i] = buf[m++];
@@ -631,7 +631,7 @@ int AtomVecPeri::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -725,7 +725,7 @@ int AtomVecPeri::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -792,10 +792,7 @@ void AtomVecPeri::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -881,8 +878,9 @@ int AtomVecPeri::pack_data_hybrid(int i, double *buf)
void AtomVecPeri::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ fprintf(fp,TAGINT_FORMAT
+ " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],buf[i][5],buf[i][6],
(int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i,
(int) ubuf(buf[i][9]).i);
diff --git a/src/PERI/atom_vec_peri.h b/src/PERI/atom_vec_peri.h
index 253c054e73..57dfe41807 100755
--- a/src/PERI/atom_vec_peri.h
+++ b/src/PERI/atom_vec_peri.h
@@ -59,7 +59,8 @@ class AtomVecPeri : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *vfrac,*density,*rmass,*s0,**x0;
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index bd8228faf5..9b51cd34b3 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -90,7 +90,7 @@ void ComputeDamageAtom::compute_peratom()
int *mask = atom->mask;
double *vfrac = atom->vfrac;
double *vinter = ((FixPeriNeigh *) modify->fix[ifix_peri])->vinter;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
int i,j,jj,jnum;
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index a7ef294140..cd6e3d5c81 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -152,7 +152,7 @@ void FixPeriNeigh::setup(int vflag)
double **x = atom->x;
double *vfrac = atom->vfrac;
int *type = atom->type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// only build list of bonds on very first run
@@ -450,7 +450,7 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
int m = 0;
npartner[nlocal] = static_cast<int> (buf[m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
- partner[nlocal][n] = static_cast<int> (buf[m++]);
+ partner[nlocal][n] = static_cast<tagint> (buf[m++]);
if (isVES) {
deviatorextention[nlocal][n] = buf[m++];
deviatorBackextention[nlocal][n] = buf[m++];
@@ -565,7 +565,7 @@ void FixPeriNeigh::unpack_restart(int nlocal, int nth)
npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
- partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
+ partner[nlocal][n] = static_cast<tagint> (extra[nlocal][m++]);
if (isVES) {
deviatorextention[nlocal][n] = extra[nlocal][m++];
deviatorBackextention[nlocal][n] = extra[nlocal][m++];
diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h
index 0640bbccde..bfa815be6b 100644
--- a/src/PERI/fix_peri_neigh.h
+++ b/src/PERI/fix_peri_neigh.h
@@ -60,7 +60,7 @@ class FixPeriNeigh : public Fix {
int first; // flag for first time initialization
int maxpartner; // max # of peridynamic neighs for any atom
int *npartner; // # of neighbors for each atom
- int **partner; // neighs for each atom, stored as global IDs
+ tagint **partner; // neighs for each atom, stored as global IDs
double **deviatorextention; // Deviatoric extention
double **deviatorBackextention; // Deviatoric back extention
double **r0; // initial distance to partners
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index a140c77e5c..639ac6fb43 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -104,7 +104,7 @@ void PairPeriLPS::compute(int eflag, int vflag)
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
@@ -550,7 +550,7 @@ void PairPeriLPS::compute_dilatation()
double half_lc = 0.5*lc;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index 439f4b5d09..77ca26d1e3 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -96,7 +96,7 @@ void PairPeriPMB::compute(int eflag, int vflag)
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
// lc = lattice constant
@@ -450,7 +450,7 @@ double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
double *vfrac = atom->vfrac;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double lc = domain->lattice->xlattice;
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index 5586abc965..ec7852feb5 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -115,7 +115,7 @@ void PairPeriVES::compute(int eflag, int vflag)
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorextention;
double **deviatorBackextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorBackextention;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
@@ -621,7 +621,7 @@ void PairPeriVES::compute_dilatation()
double half_lc = 0.5*lc;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- int **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index d374c89e97..7754bd7a10 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -335,8 +335,8 @@ void NEB::run()
void NEB::readfile(char *file, int flag)
{
- int i,j,m,nchunk,tag,eofflag;
- int nlines;
+ int i,j,m,nchunk,eofflag,nlines;
+ tagint tag;
char *eof,*start,*next,*buf;
char line[MAXLINE];
double xx,yy,zz,delx,dely,delz;
@@ -430,7 +430,7 @@ void NEB::readfile(char *file, int flag)
// will be remapped back into box when simulation starts
// its image flags will then be adjusted
- tag = atoi(values[0]);
+ tag = ATOTAGINT(values[0]);
m = atom->map(tag);
if (m >= 0 && m < nlocal) {
ncount++;
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 3e70e7a3b8..145435e1a1 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -737,8 +737,8 @@ void PRD::replicate(int ireplica)
displacements[0] = 0;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
- MPI_Gatherv(atom->tag,atom->nlocal,MPI_INT,
- tagall,counts,displacements,MPI_INT,0,world);
+ MPI_Gatherv(atom->tag,atom->nlocal,MPI_LMP_TAGINT,
+ tagall,counts,displacements,MPI_LMP_TAGINT,0,world);
MPI_Gatherv(atom->image,atom->nlocal,MPI_INT,
imageall,counts,displacements,MPI_INT,0,world);
for (i = 0; i < nprocs; i++) counts[i] *= 3;
diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h
index dabaffafa8..07af513d91 100644
--- a/src/REPLICA/prd.h
+++ b/src/REPLICA/prd.h
@@ -46,7 +46,8 @@ class PRD : protected Pointers {
double time_start;
MPI_Comm comm_replica;
- int *tagall,*displacements,*imageall;
+ tagint *tagall;
+ int *displacements,*imageall;
double **xall;
int ncoincident;
diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp
index b9eadde447..1ede274a76 100644
--- a/src/REPLICA/verlet_split.cpp
+++ b/src/REPLICA/verlet_split.cpp
@@ -471,7 +471,8 @@ void VerletSplit::rk_setup()
if (tip4p_flag) {
//r2k_comm();
MPI_Gatherv(atom->type,n,MPI_INT,atom->type,qsize,qdisp,MPI_INT,0,block);
- MPI_Gatherv(atom->tag,n,MPI_INT,atom->tag,qsize,qdisp,MPI_INT,0,block);
+ MPI_Gatherv(atom->tag,n,MPI_LMP_TAGINT,
+ atom->tag,qsize,qdisp,MPI_LMP_TAGINT,0,block);
if (!master) {
if (triclinic) domain->x2lamda(atom->nlocal);
if (domain->box_change) comm->setup();
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 33fff6a7be..46809d1b34 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -182,7 +182,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// set nlocal_body and allocate bodies I own
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
nlocal_body = nghost_body = 0;
for (i = 0; i < nlocal; i++)
@@ -1350,14 +1350,14 @@ void FixRigidSmall::create_bodies()
// pack my atoms into buffer as molecule ID, atom ID, unwrapped coords
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
m = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
buf[m++] = molecule[i];
- buf[m++] = tag[i];
+ buf[m++] = ubuf(tag[i]).d;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
@@ -1388,7 +1388,7 @@ void FixRigidSmall::create_bodies()
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
- buf[m++] = bodytag[i];
+ buf[m++] = ubuf(bodytag[i]).i;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
@@ -1460,13 +1460,14 @@ void FixRigidSmall::ring_nearest(int n, char *cbuf)
{
std::map<int,int> *hash = frsptr->hash;
double **ctr = frsptr->ctr;
- int *idclose = frsptr->idclose;
+ tagint *idclose = frsptr->idclose;
double *rsqclose = frsptr->rsqclose;
double *buf = (double *) cbuf;
int ndatums = n/5;
- int j,imol,tag;
+ int j,imol;
+ tagint tag;
double delx,dely,delz,rsq;
double *x;
@@ -1475,7 +1476,7 @@ void FixRigidSmall::ring_nearest(int n, char *cbuf)
imol = static_cast<int> (buf[m]);
if (hash->find(imol) != hash->end()) {
j = hash->find(imol)->second;
- tag = static_cast<int> (buf[m+1]);
+ tag = (tagint) ubuf(buf[m+1]).i;
x = &buf[m+2];
delx = x[0] - ctr[j][0];
dely = x[1] - ctr[j][1];
@@ -1504,15 +1505,16 @@ void FixRigidSmall::ring_farthest(int n, char *cbuf)
double *buf = (double *) cbuf;
int ndatums = n/4;
- int itag,iowner;
+ int iowner;
+ tagint tag;
double delx,dely,delz,rsq;
double *xx;
double unwrap[3];
int m = 0;
for (int i = 0; i < ndatums; i++, m += 4) {
- itag = static_cast<int> (buf[m]);
- iowner = frsptr->atom->map(itag);
+ tag = (tagint) ubuf(buf[m]).i;
+ iowner = frsptr->atom->map(tag);
if (iowner < 0 || iowner >= nlocal) continue;
frsptr->domain->unmap(x[iowner],image[iowner],unwrap);
xx = &buf[m+1];
@@ -2439,7 +2441,7 @@ void FixRigidSmall::set_arrays(int i)
relative to template in Molecule class
------------------------------------------------------------------------- */
-void FixRigidSmall::set_molecule(int nlocalprev, int tagprev,
+void FixRigidSmall::set_molecule(int nlocalprev, tagint tagprev,
double *xgeom, double *vcm, double *quat)
{
int m;
@@ -2450,7 +2452,7 @@ void FixRigidSmall::set_molecule(int nlocalprev, int tagprev,
if (nlocalprev == nlocal) return;
double **x = atom->x;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int i = nlocalprev; i < nlocal; i++) {
bodytag[i] = tagprev + onemol->comatom;
@@ -2510,7 +2512,7 @@ void FixRigidSmall::set_molecule(int nlocalprev, int tagprev,
int FixRigidSmall::pack_exchange(int i, double *buf)
{
- buf[0] = bodytag[i];
+ buf[0] = ubuf(bodytag[i]).d;
buf[1] = displace[i][0];
buf[2] = displace[i][1];
buf[3] = displace[i][2];
@@ -2554,7 +2556,7 @@ int FixRigidSmall::pack_exchange(int i, double *buf)
int FixRigidSmall::unpack_exchange(int nlocal, double *buf)
{
- bodytag[nlocal] = static_cast<int> (buf[0]);
+ bodytag[nlocal] = (tagint) ubuf(buf[0]).i;
displace[nlocal][0] = buf[1];
displace[nlocal][1] = buf[2];
displace[nlocal][2] = buf[3];
@@ -2839,7 +2841,6 @@ void FixRigidSmall::unpack_reverse_comm(int n, int *list, double *buf)
int i,j,k;
double *fcm,*torque,*vcm,*angmom,*xcm;
- int *tag = atom->tag;
int nlocal = atom->nlocal;
int m = 0;
@@ -2940,8 +2941,8 @@ void FixRigidSmall::reset_atom2body()
if (iowner == -1) {
char str[128];
sprintf(str,
- "Rigid body atoms %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ "Rigid body atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
atom->tag[i],bodytag[i],comm->me,update->ntimestep);
error->one(FLERR,str);
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 5cc63c3dd6..6f73a9c03a 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -48,7 +48,7 @@ class FixRigidSmall : public Fix {
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
- void set_molecule(int, int, double *, double *, double *);
+ void set_molecule(int, tagint, double *, double *, double *);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
@@ -112,7 +112,7 @@ class FixRigidSmall : public Fix {
// only defined for owned atoms, except bodyown for own+ghost
int *bodyown; // index of body if atom owns a body, -1 if not
- int *bodytag; // ID of body this atom is in, 0 if none
+ tagint *bodytag; // ID of body this atom is in, 0 if none
// ID = tag of atom that owns body
int *atom2body; // index of owned/ghost body this atom is in, -1 if not
// can point to original or any image of the body
@@ -160,7 +160,7 @@ class FixRigidSmall : public Fix {
std::map<int,int> *hash;
double **bbox;
double **ctr;
- int *idclose;
+ tagint *idclose;
double *rsqclose;
double rsqfar;
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 301cfd815a..7024f0281b 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -66,7 +66,8 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
// register with Atom class
shake_flag = NULL;
- shake_atom = shake_type = NULL;
+ shake_atom = NULL;
+ shake_type = NULL;
xshake = NULL;
grow_arrays(atom->nmax);
@@ -493,8 +494,8 @@ void FixShake::pre_neighbor()
atom2 = atom->map(shake_atom[i][1]);
if (atom1 == -1 || atom2 == -1) {
char str[128];
- sprintf(str,
- "Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ sprintf(str,"Shake atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(FLERR,str);
}
@@ -505,9 +506,9 @@ void FixShake::pre_neighbor()
atom3 = atom->map(shake_atom[i][2]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
- sprintf(str,
- "Shake atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Shake atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep);
error->one(FLERR,str);
@@ -520,9 +521,10 @@ void FixShake::pre_neighbor()
atom4 = atom->map(shake_atom[i][3]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
- sprintf(str,
- "Shake atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Shake atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],
shake_atom[i][2],shake_atom[i][3],
me,update->ntimestep);
@@ -618,7 +620,7 @@ int FixShake::dof(int igroup)
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// count dof in a cluster if and only if
@@ -653,7 +655,7 @@ void FixShake::find_clusters()
int i,j,m,n;
int flag,flag_all,messtag,loop,nbuf,nbufmax,size;
double massone;
- int *buf,*bufcopy;
+ tagint *buf;
MPI_Request request;
MPI_Status status;
@@ -661,7 +663,7 @@ void FixShake::find_clusters()
// local copies of atom ptrs
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
@@ -669,7 +671,7 @@ void FixShake::find_clusters()
int **bond_type = atom->bond_type;
int **angle_type = atom->angle_type;
int **nspecial = atom->nspecial;
- int **special = atom->special;
+ tagint **special = atom->special;
int nlocal = atom->nlocal;
int angles_allow = atom->avec->angles_allow;
@@ -702,8 +704,9 @@ void FixShake::find_clusters()
memory->create(npartner,nlocal,"shake:npartner");
memory->create(nshake,nlocal,"shake:nshake");
- int **partner_tag,**partner_mask,**partner_type,**partner_massflag;
- int ** partner_bondtype,**partner_shake,**partner_nshake;
+ tagint **partner_tag;
+ int **partner_mask,**partner_type,**partner_massflag;
+ int **partner_bondtype,**partner_shake,**partner_nshake;
memory->create(partner_tag,nlocal,max,"shake:partner_tag");
memory->create(partner_mask,nlocal,max,"shake:partner_mask");
memory->create(partner_type,nlocal,max,"shake:partner_type");
@@ -718,7 +721,8 @@ void FixShake::find_clusters()
for (i = 0; i < nlocal; i++) {
npartner[i] = nspecial[i][0];
- for (j = 0; j < npartner[i]; j++) partner_tag[i][j] = special[i][j];
+ for (j = 0; j < npartner[i]; j++)
+ partner_tag[i][j] = special[i][j];
}
// -----------------------------------------------------
@@ -786,7 +790,7 @@ void FixShake::find_clusters()
// cycle buffer around ring of procs back to self
fsptr = this;
- comm->ring(size,sizeof(int),buf,1,ring_bonds,buf);
+ comm->ring(size,sizeof(tagint),buf,1,ring_bonds,buf);
// store partner info returned to me
@@ -912,7 +916,7 @@ void FixShake::find_clusters()
// cycle buffer around ring of procs back to self
fsptr = this;
- comm->ring(size,sizeof(int),buf,2,ring_nshake,buf);
+ comm->ring(size,sizeof(tagint),buf,2,ring_nshake,buf);
// store partner info returned to me
@@ -1066,7 +1070,7 @@ void FixShake::find_clusters()
// cycle buffer around ring of procs back to self
fsptr = this;
- comm->ring(size,sizeof(int),buf,3,ring_shake,NULL);
+ comm->ring(size,sizeof(tagint),buf,3,ring_shake,NULL);
memory->destroy(buf);
@@ -1173,7 +1177,7 @@ void FixShake::ring_bonds(int ndatum, char *cbuf)
int nlocal = atom->nlocal;
int nmass = fsptr->nmass;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int m,n;
double massone;
@@ -1207,7 +1211,7 @@ void FixShake::ring_nshake(int ndatum, char *cbuf)
int *nshake = fsptr->nshake;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i += 3) {
@@ -1227,10 +1231,10 @@ void FixShake::ring_shake(int ndatum, char *cbuf)
int nlocal = atom->nlocal;
int *shake_flag = fsptr->shake_flag;
- int **shake_atom = fsptr->shake_atom;
+ tagint **shake_atom = fsptr->shake_atom;
int **shake_type = fsptr->shake_type;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i += 9) {
@@ -2234,10 +2238,10 @@ void FixShake::stats()
return bond index if do find it
------------------------------------------------------------------------- */
-int FixShake::bondfind(int i, int n1, int n2)
+int FixShake::bondfind(int i, tagint n1, tagint n2)
{
- int *tag = atom->tag;
- int **bond_atom = atom->bond_atom;
+ tagint *tag = atom->tag;
+ tagint **bond_atom = atom->bond_atom;
int nbonds = atom->num_bond[i];
int m;
@@ -2255,10 +2259,10 @@ int FixShake::bondfind(int i, int n1, int n2)
return angle index if do find it
------------------------------------------------------------------------- */
-int FixShake::anglefind(int i, int n1, int n2)
+int FixShake::anglefind(int i, tagint n1, tagint n2)
{
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom3 = atom->angle_atom3;
int nangles = atom->num_angle[i];
int m;
@@ -2379,7 +2383,7 @@ void FixShake::update_arrays(int i, int atom_offset)
xgeom,vcm,quat ignored
------------------------------------------------------------------------- */
-void FixShake::set_molecule(int nlocalprev, int tagprev,
+void FixShake::set_molecule(int nlocalprev, tagint tagprev,
double *xgeom, double *vcm, double *quat)
{
int m,flag;
@@ -2387,7 +2391,7 @@ void FixShake::set_molecule(int nlocalprev, int tagprev,
int nlocal = atom->nlocal;
if (nlocalprev == nlocal) return;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int **mol_shake_atom = onemol->shake_atom;
int **mol_shake_type = onemol->shake_type;
@@ -2472,27 +2476,27 @@ int FixShake::unpack_exchange(int nlocal, double *buf)
int m = 0;
int flag = shake_flag[nlocal] = static_cast<int> (buf[m++]);
if (flag == 1) {
- shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][2] = static_cast<int> (buf[m++]);
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
} else if (flag == 2) {
- shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
} else if (flag == 3) {
- shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][2] = static_cast<int> (buf[m++]);
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
} else if (flag == 4) {
- shake_atom[nlocal][0] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][1] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][2] = static_cast<int> (buf[m++]);
- shake_atom[nlocal][3] = static_cast<int> (buf[m++]);
+ shake_atom[nlocal][0] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][1] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][2] = static_cast<tagint> (buf[m++]);
+ shake_atom[nlocal][3] = static_cast<tagint> (buf[m++]);
shake_type[nlocal][0] = static_cast<int> (buf[m++]);
shake_type[nlocal][1] = static_cast<int> (buf[m++]);
shake_type[nlocal][2] = static_cast<int> (buf[m++]);
diff --git a/src/RIGID/fix_shake.h b/src/RIGID/fix_shake.h
index a1cfe0e2f4..2077d79936 100644
--- a/src/RIGID/fix_shake.h
+++ b/src/RIGID/fix_shake.h
@@ -40,7 +40,7 @@ class FixShake : public Fix {
void copy_arrays(int, int, int);
void set_arrays(int);
void update_arrays(int, int);
- void set_molecule(int, int, double *, double *, double *);
+ void set_molecule(int, tagint, double *, double *, double *);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
@@ -79,7 +79,7 @@ class FixShake : public Fix {
int *shake_flag; // 0 if atom not in SHAKE cluster
// 1 = size 3 angle cluster
// 2,3,4 = size of bond-only cluster
- int **shake_atom; // global IDs of atoms in cluster
+ tagint **shake_atom; // global IDs of atoms in cluster
// central atom is 1st
// lowest global ID is 1st for size 2
int **shake_type; // bondtype of each bond in cluster
@@ -115,8 +115,8 @@ class FixShake : public Fix {
void shake4(int);
void shake3angle(int);
void stats();
- int bondfind(int, int, int);
- int anglefind(int, int, int);
+ int bondfind(int, tagint, tagint);
+ int anglefind(int, tagint, tagint);
// static variable for ring communication callback to access class data
// callback functions for ring communication
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index af9056bb7f..295337e6f0 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -495,14 +495,14 @@ void FixAppendAtoms::pre_exchange()
if (addtotal) {
domain->reset_box();
- if (atom->tag_enable) {
- atom->tag_extend();
- atom->natoms += addtotal;
- if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
- }
+ atom->natoms += addtotal;
+ if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ error->all(FLERR,"Too many total atoms");
+ if (atom->tag_enable) atom->tag_extend();
+ if (atom->map_style) {
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
}
}
}
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 01ff4e8f2a..c100fb69fe 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -572,10 +572,12 @@ void FixSRD::pre_neighbor()
if (jx < 0 || jx >= nbin2x || jy < 0 || jy >= nbin2y ||
jz < 0 || jz >= nbin2z) {
- printf("Big particle %d %d %g %g %g\n",
- atom->tag[i],i,x[i][0],x[i][1],x[i][2]);
- printf("Bin indices: %d %d %d, %d %d %d, %d %d %d\n",
- ix,iy,iz,jx,jy,jz,nbin2x,nbin2y,nbin2z);
+ if (screen) {
+ fprintf(screen,"Big particle " TAGINT_FORMAT " %d %g %g %g\n",
+ atom->tag[i],i,x[i][0],x[i][1],x[i][2]);
+ fprintf(screen,"Bin indices: %d %d %d, %d %d %d, %d %d %d\n",
+ ix,iy,iz,jx,jy,jz,nbin2x,nbin2y,nbin2z);
+ }
error->one(FLERR,"Fix SRD: bad stencil bin for big particle");
}
rsq = point_bin_distance(x[i],jx,jy,jz);
@@ -742,7 +744,8 @@ void FixSRD::post_force(int vflag)
if (ix < 0 || ix >= nbin2x || iy < 0 || iy >= nbin2y ||
iz < 0 || iz >= nbin2z) {
if (screen) {
- fprintf(screen,"SRD particle %d on step " BIGINT_FORMAT "\n",
+ fprintf(screen,"SRD particle " TAGINT_FORMAT
+ " on step " BIGINT_FORMAT "\n",
atom->tag[i],update->ntimestep);
fprintf(screen,"v = %g %g %g\n",v[i][0],v[i][1],v[i][2]);
fprintf(screen,"x = %g %g %g\n",x[i][0],x[i][1],x[i][2]);
@@ -1224,15 +1227,15 @@ void FixSRD::collisions_single()
char str[128];
if (type != WALL)
sprintf(str,
- "SRD particle %d started "
- "inside big particle %d on step " BIGINT_FORMAT
- " bounce %d",
+ "SRD particle " TAGINT_FORMAT " started "
+ "inside big particle " TAGINT_FORMAT
+ " on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
else
sprintf(str,
- "SRD particle %d started "
- "inside big particle %d on step " BIGINT_FORMAT
- " bounce %d",
+ "SRD particle " TAGINT_FORMAT " started "
+ "inside big particle " TAGINT_FORMAT
+ " on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
error->warning(FLERR,str);
@@ -1380,9 +1383,9 @@ void FixSRD::collisions_multi()
if (insideflag == INSIDE_ERROR || insideflag == INSIDE_WARN) {
char str[128];
sprintf(str,
- "SRD particle %d started "
- "inside big particle %d on step " BIGINT_FORMAT
- " bounce %d",
+ "SRD particle " TAGINT_FORMAT " started "
+ "inside big particle " TAGINT_FORMAT
+ " on step " BIGINT_FORMAT " bounce %d",
atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1);
if (insideflag == INSIDE_ERROR) error->one(FLERR,str);
error->warning(FLERR,str);
@@ -2381,7 +2384,8 @@ int FixSRD::update_srd(int i, double dt, double *xscoll, double *vsnew,
xs[2] < srdlo[2] || xs[2] > srdhi[2]) {
if (screen) {
error->warning(FLERR,"Fix srd particle moved outside valid domain");
- fprintf(screen," particle %d on proc %d at timestep " BIGINT_FORMAT,
+ fprintf(screen," particle " TAGINT_FORMAT
+ " on proc %d at timestep " BIGINT_FORMAT,
atom->tag[i],me,update->ntimestep);
fprintf(screen," xnew %g %g %g\n",xs[0],xs[1],xs[2]);
fprintf(screen," srdlo/hi x %g %g\n",srdlo[0],srdhi[0]);
@@ -3883,7 +3887,8 @@ void FixSRD::print_collision(int i, int j, int ibounce,
double **v = atom->v;
if (type != WALL) {
- printf("COLLISION between SRD %d and BIG %d\n",atom->tag[i],atom->tag[j]);
+ printf("COLLISION between SRD " TAGINT_FORMAT
+ " and BIG " TAGINT_FORMAT "\n",atom->tag[i],atom->tag[j]);
printf(" bounce # = %d\n",ibounce+1);
printf(" local indices: %d %d\n",i,j);
printf(" timestep = %g\n",dt);
@@ -3928,7 +3933,8 @@ void FixSRD::print_collision(int i, int j, int ibounce,
} else {
int dim = wallwhich[j] / 2;
- printf("COLLISION between SRD %d and WALL %d\n",atom->tag[i],j);
+ printf("COLLISION between SRD " TAGINT_FORMAT " and WALL %d\n",
+ atom->tag[i],j);
printf(" bounce # = %d\n",ibounce+1);
printf(" local indices: %d %d\n",i,j);
printf(" timestep = %g\n",dt);
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp
index 35c6e582d9..9903e889fa 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.cpp
+++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp
@@ -618,7 +618,7 @@ void AtomVecWavepacket::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -646,7 +646,7 @@ void AtomVecWavepacket::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -737,7 +737,7 @@ int AtomVecWavepacket::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -834,7 +834,7 @@ int AtomVecWavepacket::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -902,17 +902,14 @@ void AtomVecWavepacket::create_atom(int itype, double *coord)
AWPMD: 0-tag 1-type 2-q 3-spin 4-eradius 5-etag 6-cs_re 7-cs_im
------------------------------------------------------------------------- */
-void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, char **values)
+void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp,
+ char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of "
- "data file (ID tag must be >0)");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -923,12 +920,10 @@ void AtomVecWavepacket::data_atom(double *coord, imageint imagetmp, char **value
if (eradius[nlocal] < 0.0)
error->one(FLERR,"Invalid eradius in Atoms section of data file");
-
etag[nlocal] = atoi(values[5]);
cs[2*nlocal] = atoi(values[6]);
cs[2*nlocal+1] = atof(values[7]);
-
x[nlocal][0] = coord[0];
x[nlocal][1] = coord[1];
x[nlocal][2] = coord[2];
@@ -961,7 +956,6 @@ int AtomVecWavepacket::data_atom_hybrid(int nlocal, char **values)
cs[2*nlocal] = atoi(values[4]);
cs[2*nlocal+1] = atof(values[5]);
-
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
@@ -1039,9 +1033,10 @@ int AtomVecWavepacket::pack_data_hybrid(int i, double *buf)
void AtomVecWavepacket::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %d %-1.16e %d %-1.16e %-1.16e %-1.16e "
+ fprintf(fp,TAGINT_FORMAT
+ " %d %-1.16e %d %-1.16e %d %-1.16e %-1.16e %-1.16e "
"%-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],(int) ubuf(buf[i][3]).i,buf[i][4],
(int) ubuf(buf[i][5]).i,buf[i][6],buf[i][8],
buf[i][8],buf[i][9],buf[i][10],
@@ -1094,8 +1089,8 @@ int AtomVecWavepacket::pack_vel_hybrid(int i, double *buf)
void AtomVecWavepacket::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
+ fprintf(fp,TAGINT_FORMAT " %-1.16e %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
}
/* ----------------------------------------------------------------------
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/USER-AWPMD/atom_vec_wavepacket.h
index c4fe70f133..8265e817e7 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.h
+++ b/src/USER-AWPMD/atom_vec_wavepacket.h
@@ -73,7 +73,8 @@ public:
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index 1658d48921..c68e348035 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -534,7 +534,7 @@ void AtomVecElectron::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -561,7 +561,7 @@ void AtomVecElectron::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -639,7 +639,7 @@ int AtomVecElectron::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -727,7 +727,7 @@ int AtomVecElectron::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -791,10 +791,7 @@ void AtomVecElectron::data_atom(double *coord, imageint imagetmp, char **values)
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -904,8 +901,9 @@ int AtomVecElectron::pack_data_hybrid(int i, double *buf)
void AtomVecElectron::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,buf[i][2],
+ fprintf(fp,TAGINT_FORMAT
+ " %d %-1.16e %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,buf[i][2],
(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,
(int) ubuf(buf[i][10]).i);
@@ -954,8 +952,8 @@ int AtomVecElectron::pack_vel_hybrid(int i, double *buf)
void AtomVecElectron::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
+ fprintf(fp,TAGINT_FORMAT " %-1.16e %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
}
/* ----------------------------------------------------------------------
diff --git a/src/USER-EFF/atom_vec_electron.h b/src/USER-EFF/atom_vec_electron.h
index 64ba79865e..f604613599 100644
--- a/src/USER-EFF/atom_vec_electron.h
+++ b/src/USER-EFF/atom_vec_electron.h
@@ -68,7 +68,8 @@ class AtomVecElectron : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
int *spin;
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index 12467b57bc..121217751c 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -93,8 +93,6 @@ void PairEffCut::compute(int eflag, int vflag)
int *type = atom->type;
int nlocal = atom->nlocal;
- int *id = atom->tag;
-
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
index ea2c5e51e7..ec6cc01fb9 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
@@ -137,7 +137,9 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp
index 3ddf4cd246..c00dcfcfa5 100644
--- a/src/USER-MISC/dihedral_fourier.cpp
+++ b/src/USER-MISC/dihedral_fourier.cpp
@@ -149,7 +149,9 @@ void DihedralFourier::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp
index d06ef08a9f..6370b85739 100644
--- a/src/USER-MISC/dihedral_nharmonic.cpp
+++ b/src/USER-MISC/dihedral_nharmonic.cpp
@@ -156,7 +156,9 @@ void DihedralNHarmonic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp
index 06391b7128..bec383f214 100644
--- a/src/USER-MISC/dihedral_quadratic.cpp
+++ b/src/USER-MISC/dihedral_quadratic.cpp
@@ -161,8 +161,10 @@ void DihedralQuadratic::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
+ me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index 36aeb61138..53fd31e02c 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -110,8 +110,11 @@ void ImproperCossq::compute(int eflag, int vflag)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
- me,update->ntimestep,atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",me,x[i2][0],x[i2][1],x[i2][2]);
@@ -120,7 +123,6 @@ void ImproperCossq::compute(int eflag, int vflag)
}
}
-
/* Apply corrections to round-off errors. */
if (cosphi > 1.0) cosphi -= SMALL;
if (cosphi < -1.0) cosphi += SMALL;
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index 43944727ff..a4be0ea35c 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -157,8 +157,9 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,
- "Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Improper problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index a9938f409a..4c236649a2 100755
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -841,8 +841,6 @@ void PairEDIP::coeff(int narg, char **arg)
void PairEDIP::init_style()
{
- if (atom->tag_enable == 0)
- error->all(FLERR,"Pair style EDIP requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style EDIP requires newton pair on");
diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp
index 3b6f5c2d10..265532e56f 100644
--- a/src/USER-MISC/pair_list.cpp
+++ b/src/USER-MISC/pair_list.cpp
@@ -233,7 +233,9 @@ void PairList::settings(int narg, char **arg)
// now read and parse pair list file for real
npairs = 0;
char *ptr;
- int id1, id2, nharm=0, nmorse=0, nlj126=0;
+ tagint id1, id2;
+ int nharm=0, nmorse=0, nlj126=0;
+
while(fgets(line,1024,fp)) {
ptr = strtok(line," \t\n\r\f");
@@ -244,11 +246,11 @@ void PairList::settings(int narg, char **arg)
if (*ptr == '#') continue;
// get atom ids of pair
- id1 = atoi(ptr);
+ id1 = ATOTAGINT(ptr);
ptr = strtok(NULL," \t\n\r\f");
if (!ptr)
error->all(FLERR,"Incorrectly formatted pair list file");
- id2 = atoi(ptr);
+ id2 = ATOTAGINT(ptr);
// get potential type
ptr = strtok(NULL," \t\n\r\f");
diff --git a/src/USER-MISC/pair_list.h b/src/USER-MISC/pair_list.h
index 9d199f5ba7..4059b0ef29 100644
--- a/src/USER-MISC/pair_list.h
+++ b/src/USER-MISC/pair_list.h
@@ -53,7 +53,7 @@ class PairList : public Pair {
};
typedef struct {
- int id1,id2; // global atom ids
+ tagint id1,id2; // global atom ids
double cutsq; // cutoff**2 for this pair
double offset; // energy offset
union parm_u parm; // parameters for style
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index d5850ac81c..db58c023b1 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -815,8 +815,6 @@ void PairTersoffTable::coeff(int narg, char **arg)
void PairTersoffTable::init_style()
{
- if (atom->tag_enable == 0)
- error->all(FLERR,"Pair style Tersoff requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style Tersoff requires newton pair on");
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
index 4df4b1503c..bca14645d5 100644
--- a/src/USER-SPH/atom_vec_meso.cpp
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -578,7 +578,7 @@ void AtomVecMeso::unpack_border(int n, int first, double *buf) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
rho[i] = buf[m++];
@@ -609,7 +609,7 @@ void AtomVecMeso::unpack_border_vel(int n, int first, double *buf) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
@@ -677,7 +677,7 @@ int AtomVecMeso::unpack_exchange(double *buf) {
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -765,7 +765,7 @@ int AtomVecMeso::unpack_restart(double *buf) {
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -830,13 +830,9 @@ void AtomVecMeso::create_atom(int itype, double *coord) {
void AtomVecMeso::data_atom(double *coord, imageint imagetmp, char **values) {
int nlocal = atom->nlocal;
- if (nlocal == nmax)
- grow(0);
-
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+ if (nlocal == nmax) grow(0);
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -923,9 +919,10 @@ int AtomVecMeso::pack_data_hybrid(int i, double *buf)
void AtomVecMeso::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
+ fprintf(fp,TAGINT_FORMAT
+ " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
"%d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],
buf[i][5],buf[i][6],buf[i][7],
(int) ubuf(buf[i][8]).i,(int) ubuf(buf[i][9]).i,
diff --git a/src/USER-SPH/atom_vec_meso.h b/src/USER-SPH/atom_vec_meso.h
index 945e4a42cc..7da470fdb6 100644
--- a/src/USER-SPH/atom_vec_meso.h
+++ b/src/USER-SPH/atom_vec_meso.h
@@ -62,7 +62,8 @@ class AtomVecMeso : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ int *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *rho, *drho, *e, *de, *cv;
diff --git a/src/XTC/dump_xtc.cpp b/src/XTC/dump_xtc.cpp
index 80f1013afe..f7c2f8ec0a 100644
--- a/src/XTC/dump_xtc.cpp
+++ b/src/XTC/dump_xtc.cpp
@@ -190,11 +190,11 @@ void DumpXTC::write_header(bigint nbig)
/* ---------------------------------------------------------------------- */
-void DumpXTC::pack(int *ids)
+void DumpXTC::pack(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
imageint *image = atom->image;
int *mask = atom->mask;
diff --git a/src/XTC/dump_xtc.h b/src/XTC/dump_xtc.h
index 081891b224..f1e960af6c 100644
--- a/src/XTC/dump_xtc.h
+++ b/src/XTC/dump_xtc.h
@@ -49,7 +49,7 @@ class DumpXTC : public Dump {
int modify_param(int, char **);
void openfile();
void write_header(bigint);
- void pack(int *);
+ void pack(tagint *);
void write_data(int, double *);
bigint memory_usage();
diff --git a/src/atom.cpp b/src/atom.cpp
index 75c2bf4a83..aba59b819a 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -57,8 +57,6 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
ntypes = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
- bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
- extra_bond_per_atom = 0;
firstgroupname = NULL;
sortfreq = 1000;
@@ -71,7 +69,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// initialize atom arrays
// customize by adding new array
- tag = type = mask = NULL;
+ tag = NULL;
+ type = mask = NULL;
image = NULL;
x = v = f = NULL;
@@ -92,23 +91,29 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
cv = NULL;
vest = NULL;
- maxspecial = 1;
- nspecial = NULL;
- special = NULL;
-
+ bond_per_atom = extra_bond_per_atom = 0;
num_bond = NULL;
- bond_type = bond_atom = NULL;
+ bond_type = NULL;
+ bond_atom = NULL;
+ angle_per_atom = extra_angle_per_atom = 0;
num_angle = NULL;
- angle_type = angle_atom1 = angle_atom2 = angle_atom3 = NULL;
+ angle_type = NULL;
+ angle_atom1 = angle_atom2 = angle_atom3 = NULL;
+ dihedral_per_atom = extra_dihedral_per_atom = 0;
num_dihedral = NULL;
- dihedral_type = dihedral_atom1 = dihedral_atom2 = NULL;
- dihedral_atom3 = dihedral_atom4 = NULL;
+ dihedral_type = NULL;
+ dihedral_atom1 = dihedral_atom2 = dihedral_atom3 = dihedral_atom4 = NULL;
+ improper_per_atom = extra_improper_per_atom = 0;
num_improper = NULL;
- improper_type = improper_atom1 = improper_atom2 = NULL;
- improper_atom3 = improper_atom4 = NULL;
+ improper_type = NULL;
+ improper_atom1 = improper_atom2 = improper_atom3 = improper_atom4 = NULL;
+
+ maxspecial = 1;
+ nspecial = NULL;
+ special = NULL;
// user-defined molecules
@@ -148,14 +153,14 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nextra_store = 0;
extra = NULL;
- // default mapping values
+ // default atom ID and mapping values
tag_enable = 1;
- map_style = 0;
+ map_style = map_user = 0;
map_tag_max = 0;
map_nhash = 0;
- smax = 0;
+ max_same = 0;
sametag = NULL;
map_array = NULL;
map_bucket = NULL;
@@ -283,7 +288,8 @@ Atom::~Atom()
void Atom::settings(Atom *old)
{
- map_style = old->map_style;
+ tag_enable = old->tag_enable;
+ map_user = old->map_user;
}
/* ----------------------------------------------------------------------
@@ -333,10 +339,11 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
strcpy(atom_style,style);
}
- // if molecular system, default is to have array map
+ // if molecular system, atom IDs must be defined
molecular = avec->molecular;
- if (map_style == 0 && molecular) map_style = 1;
+ if (molecular && tag_enable == 0)
+ error->all(FLERR,"Atom IDs must be used for molecular systems");
}
/* ----------------------------------------------------------------------
@@ -444,14 +451,23 @@ void Atom::modify_params(int narg, char **arg)
int iarg = 0;
while (iarg < narg) {
- if (strcmp(arg[iarg],"map") == 0) {
+ if (strcmp(arg[iarg],"id") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
- if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
- else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
+ if (domain->box_exist)
+ error->all(FLERR,
+ "Atom_modify id command after simulation box is defined");
+ if (strcmp(arg[iarg+1],"yes") == 0) tag_enable = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 2;
else error->all(FLERR,"Illegal atom_modify command");
+ iarg += 2;
+ } if (strcmp(arg[iarg],"map") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
if (domain->box_exist)
error->all(FLERR,
"Atom_modify map command after simulation box is defined");
+ if (strcmp(arg[iarg+1],"array") == 0) map_user = 1;
+ else if (strcmp(arg[iarg+1],"hash") == 0) map_user = 2;
+ else error->all(FLERR,"Illegal atom_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
@@ -479,37 +495,82 @@ void Atom::modify_params(int narg, char **arg)
}
}
+/* ----------------------------------------------------------------------
+ check that atom IDs are valid
+ error if any atom ID < 0 or atom ID = MAXTAGINT
+ if any atom ID > 0, error if any atom ID == 0
+ if all atom IDs = 0, tag_enable must be 0
+ OK if atom IDs > natoms
+ NOTE: not checking that atom IDs are unique
+------------------------------------------------------------------------- */
+
+void Atom::tag_check()
+{
+ int nlocal = atom->nlocal;
+ tagint *tag = atom->tag;
+
+ tagint min = MAXTAGINT;
+ tagint max = 0;
+
+ for (int i = 0; i < nlocal; i++) {
+ min = MIN(min,tag[i]);
+ max = MAX(max,tag[i]);
+ }
+
+ tagint minall,maxall;
+ MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
+ MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
+
+ if (minall < 0) error->all(FLERR,"Atom ID is negative");
+ if (maxall >= MAXTAGINT) error->all(FLERR,"Atom ID is too big");
+ if (maxall > 0 && minall == 0) error->all(FLERR,"Atom ID is zero");
+ if (maxall == 0 && tag_enable && natoms)
+ error->all(FLERR,"Not all atom IDs are 0");
+}
+
/* ----------------------------------------------------------------------
add unique tags to any atoms with tag = 0
new tags are grouped by proc and start after max current tag
called after creating new atoms
+ error if new tags will exceed MAXTAGINT
------------------------------------------------------------------------- */
void Atom::tag_extend()
{
// maxtag_all = max tag for all atoms
- int maxtag = 0;
+ tagint maxtag = 0;
for (int i = 0; i < nlocal; i++) maxtag = MAX(maxtag,tag[i]);
- int maxtag_all;
- MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
+ tagint maxtag_all;
+ MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
+
+ // DEBUG: useful for generating 64-bit IDs even for small systems
+ // use only when LAMMPS is compiled with BIGBIG
+
+ //maxtag_all += 1000000000000;
// notag = # of atoms I own with no tag (tag = 0)
// notag_sum = # of total atoms on procs <= me with no tag
- int notag = 0;
+ bigint notag = 0;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) notag++;
- int notag_sum;
- MPI_Scan(¬ag,¬ag_sum,1,MPI_INT,MPI_SUM,world);
+
+ bigint notag_total;
+ MPI_Allreduce(¬ag,¬ag_total,1,MPI_LMP_BIGINT,MPI_SUM,world);
+ if (notag_total >= MAXTAGINT)
+ error->all(FLERR,"New atom IDs exceed maximum allowed ID");
+
+ bigint notag_sum;
+ MPI_Scan(¬ag,¬ag_sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
// itag = 1st new tag that my untagged atoms should use
- int itag = maxtag_all + notag_sum - notag + 1;
+ tagint itag = maxtag_all + notag_sum - notag + 1;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) tag[i] = itag++;
}
/* ----------------------------------------------------------------------
- check that atom IDs span range from 1 to Natoms
+ check that atom IDs span range from 1 to Natoms inclusive
return 0 if mintag != 1 or maxtag != Natoms
return 1 if OK
doesn't actually check if all tag values are used
@@ -517,20 +578,18 @@ void Atom::tag_extend()
int Atom::tag_consecutive()
{
- // change this when allow tagint = bigint
- //int idmin = MAXTAGINT;
- int idmin = MAXSMALLINT;
- int idmax = 0;
+ tagint idmin = MAXTAGINT;
+ tagint idmax = 0;
for (int i = 0; i < nlocal; i++) {
idmin = MIN(idmin,tag[i]);
idmax = MAX(idmax,tag[i]);
}
- int idminall,idmaxall;
- MPI_Allreduce(&idmin,&idminall,1,MPI_INT,MPI_MIN,world);
- MPI_Allreduce(&idmax,&idmaxall,1,MPI_INT,MPI_MAX,world);
+ tagint idminall,idmaxall;
+ MPI_Allreduce(&idmin,&idminall,1,MPI_LMP_TAGINT,MPI_MIN,world);
+ MPI_Allreduce(&idmax,&idmaxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
- if (idminall != 1 || idmaxall != static_cast<int> (natoms)) return 0;
+ if (idminall != 1 || idmaxall != natoms) return 0;
return 1;
}
@@ -683,7 +742,8 @@ void Atom::data_atoms(int n, char *buf)
void Atom::data_vels(int n, char *buf)
{
- int j,m,tagdata;
+ int j,m;
+ tagint tagdata;
char *next;
next = strchr(buf,'\n');
@@ -707,7 +767,7 @@ void Atom::data_vels(int n, char *buf)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
- tagdata = atoi(values[0]);
+ tagdata = ATOTAGINT(values[0]);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
@@ -719,120 +779,45 @@ void Atom::data_vels(int n, char *buf)
}
/* ----------------------------------------------------------------------
- unpack n lines from atom-style specific section of data file
- check that atom IDs are > 0 and <= map_tag_max
- call style-specific routine to parse line
-------------------------------------------------------------------------- */
-
-void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
-{
- int j,m,tagdata;
- char *next;
-
- next = strchr(buf,'\n');
- *next = '\0';
- int nwords = count_words(buf);
- *next = '\n';
-
- if (nwords != avec_bonus->size_data_bonus)
- error->all(FLERR,"Incorrect bonus data format in data file");
-
- char **values = new char*[nwords];
-
- // loop over lines of bonus atom data
- // tokenize the line into values
- // if I own atom tag, unpack its values
-
- for (int i = 0; i < n; i++) {
- next = strchr(buf,'\n');
-
- values[0] = strtok(buf," \t\n\r\f");
- for (j = 1; j < nwords; j++)
- values[j] = strtok(NULL," \t\n\r\f");
-
- tagdata = atoi(values[0]);
- if (tagdata <= 0 || tagdata > map_tag_max)
- error->one(FLERR,"Invalid atom ID in Bonus section of data file");
-
- // ok to call child's data_atom_bonus() method thru parent avec_bonus,
- // since data_bonus() was called with child ptr, and method is virtual
-
- if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
-
- buf = next + 1;
- }
-
- delete [] values;
-}
-
-/* ----------------------------------------------------------------------
- unpack n lines from atom-style specific section of data file
+ process N bonds read into buf from data files
+ if count is non-NULL, just count bonds per atom
+ else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
- call style-specific routine to parse line
------------------------------------------------------------------------- */
-void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
+void Atom::data_bonds(int n, char *buf, int *count)
{
- int j,m,tagdata,ninteger,ndouble;
-
- char **ivalues = new char*[10*MAXBODY];
- char **dvalues = new char*[10*MAXBODY];
-
- // loop over lines of body data
- // tokenize the lines into ivalues and dvalues
- // if I own atom tag, unpack its values
-
- for (int i = 0; i < n; i++) {
- if (i == 0) tagdata = atoi(strtok(buf," \t\n\r\f"));
- else tagdata = atoi(strtok(NULL," \t\n\r\f"));
- ninteger = atoi(strtok(NULL," \t\n\r\f"));
- ndouble = atoi(strtok(NULL," \t\n\r\f"));
-
- for (j = 0; j < ninteger; j++)
- ivalues[j] = strtok(NULL," \t\n\r\f");
- for (j = 0; j < ndouble; j++)
- dvalues[j] = strtok(NULL," \t\n\r\f");
-
- if (tagdata <= 0 || tagdata > map_tag_max)
- error->one(FLERR,"Invalid atom ID in Bodies section of data file");
-
- if ((m = map(tagdata)) >= 0)
- avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
- }
-
- delete [] ivalues;
- delete [] dvalues;
-}
-
-/* ----------------------------------------------------------------------
- check that atom IDs are > 0 and <= map_tag_max
-------------------------------------------------------------------------- */
-
-void Atom::data_bonds(int n, char *buf)
-{
- int m,tmp,itype,atom1,atom2;
+ int m,tmp,itype;
+ tagint atom1,atom2;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
+ sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file");
if ((m = map(atom1)) >= 0) {
- bond_type[m][num_bond[m]] = itype;
- bond_atom[m][num_bond[m]] = atom2;
- num_bond[m]++;
+ if (count) count[m]++;
+ else {
+ bond_type[m][num_bond[m]] = itype;
+ bond_atom[m][num_bond[m]] = atom2;
+ num_bond[m]++;
+ }
}
if (newton_bond == 0) {
if ((m = map(atom2)) >= 0) {
- bond_type[m][num_bond[m]] = itype;
- bond_atom[m][num_bond[m]] = atom1;
- num_bond[m]++;
+ if (count) count[m]++;
+ else {
+ bond_type[m][num_bond[m]] = itype;
+ bond_atom[m][num_bond[m]] = atom1;
+ num_bond[m]++;
+ }
}
}
buf = next + 1;
@@ -840,19 +825,24 @@ void Atom::data_bonds(int n, char *buf)
}
/* ----------------------------------------------------------------------
+ process N angles read into buf from data files
+ if count is non-NULL, just count angles per atom
+ else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
-void Atom::data_angles(int n, char *buf)
+void Atom::data_angles(int n, char *buf, int *count)
{
- int m,tmp,itype,atom1,atom2,atom3;
+ int m,tmp,itype;
+ tagint atom1,atom2,atom3;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
+ sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2,&atom3);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
@@ -860,26 +850,35 @@ void Atom::data_angles(int n, char *buf)
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file");
if ((m = map(atom2)) >= 0) {
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
- }
- if (newton_bond == 0) {
- if ((m = map(atom1)) >= 0) {
+ if (count) count[m]++;
+ else {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
+ }
+ if (newton_bond == 0) {
+ if ((m = map(atom1)) >= 0) {
+ if (count) count[m]++;
+ else {
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
+ }
+ }
if ((m = map(atom3)) >= 0) {
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
+ if (count) count[m]++;
+ else {
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
+ }
}
}
buf = next + 1;
@@ -887,19 +886,25 @@ void Atom::data_angles(int n, char *buf)
}
/* ----------------------------------------------------------------------
+ process N dihedrals read into buf from data files
+ if count is non-NULL, just count diihedrals per atom
+ else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
-void Atom::data_dihedrals(int n, char *buf)
+void Atom::data_dihedrals(int n, char *buf, int *count)
{
- int m,tmp,itype,atom1,atom2,atom3,atom4;
+ int m,tmp,itype;
+ tagint atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+ sscanf(buf,"%d %d "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
@@ -909,15 +914,8 @@ void Atom::data_dihedrals(int n, char *buf)
error->one(FLERR,
"Invalid dihedral type in Dihedrals section of data file");
if ((m = map(atom2)) >= 0) {
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
- }
- if (newton_bond == 0) {
- if ((m = map(atom1)) >= 0) {
+ if (count) count[m]++;
+ else {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
@@ -925,21 +923,40 @@ void Atom::data_dihedrals(int n, char *buf)
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
+ }
+ if (newton_bond == 0) {
+ if ((m = map(atom1)) >= 0) {
+ if (count) count[m]++;
+ else {
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ }
+ }
if ((m = map(atom3)) >= 0) {
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ if (count) count[m]++;
+ else {
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ }
}
if ((m = map(atom4)) >= 0) {
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ if (count) count[m]++;
+ else {
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ }
}
}
buf = next + 1;
@@ -947,19 +964,25 @@ void Atom::data_dihedrals(int n, char *buf)
}
/* ----------------------------------------------------------------------
+ process N impropers read into buf from data files
+ if count is non-NULL, just count impropers per atom
+ else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
-void Atom::data_impropers(int n, char *buf)
+void Atom::data_impropers(int n, char *buf, int *count)
{
- int m,tmp,itype,atom1,atom2,atom3,atom4;
+ int m,tmp,itype;
+ tagint atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+ sscanf(buf,"%d %d "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
@@ -969,15 +992,8 @@ void Atom::data_impropers(int n, char *buf)
error->one(FLERR,
"Invalid improper type in Impropers section of data file");
if ((m = map(atom2)) >= 0) {
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
- }
- if (newton_bond == 0) {
- if ((m = map(atom1)) >= 0) {
+ if (count) count[m]++;
+ else {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
@@ -985,27 +1001,132 @@ void Atom::data_impropers(int n, char *buf)
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
+ }
+ if (newton_bond == 0) {
+ if ((m = map(atom1)) >= 0) {
+ if (count) count[m]++;
+ else {
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ }
+ }
if ((m = map(atom3)) >= 0) {
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ if (count) count[m]++;
+ else {
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ }
}
if ((m = map(atom4)) >= 0) {
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ if (count) count[m]++;
+ else {
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ }
}
}
buf = next + 1;
}
}
+/* ----------------------------------------------------------------------
+ unpack n lines from atom-style specific section of data file
+ check that atom IDs are > 0 and <= map_tag_max
+ call style-specific routine to parse line
+------------------------------------------------------------------------- */
+
+void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
+{
+ int j,m,tagdata;
+ char *next;
+
+ next = strchr(buf,'\n');
+ *next = '\0';
+ int nwords = count_words(buf);
+ *next = '\n';
+
+ if (nwords != avec_bonus->size_data_bonus)
+ error->all(FLERR,"Incorrect bonus data format in data file");
+
+ char **values = new char*[nwords];
+
+ // loop over lines of bonus atom data
+ // tokenize the line into values
+ // if I own atom tag, unpack its values
+
+ for (int i = 0; i < n; i++) {
+ next = strchr(buf,'\n');
+
+ values[0] = strtok(buf," \t\n\r\f");
+ for (j = 1; j < nwords; j++)
+ values[j] = strtok(NULL," \t\n\r\f");
+
+ tagdata = ATOTAGINT(values[0]);
+ if (tagdata <= 0 || tagdata > map_tag_max)
+ error->one(FLERR,"Invalid atom ID in Bonus section of data file");
+
+ // ok to call child's data_atom_bonus() method thru parent avec_bonus,
+ // since data_bonus() was called with child ptr, and method is virtual
+
+ if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
+
+ buf = next + 1;
+ }
+
+ delete [] values;
+}
+
+/* ----------------------------------------------------------------------
+ unpack n lines from atom-style specific section of data file
+ check that atom IDs are > 0 and <= map_tag_max
+ call style-specific routine to parse line
+------------------------------------------------------------------------- */
+
+void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
+{
+ int j,m,tagdata,ninteger,ndouble;
+
+ char **ivalues = new char*[10*MAXBODY];
+ char **dvalues = new char*[10*MAXBODY];
+
+ // loop over lines of body data
+ // tokenize the lines into ivalues and dvalues
+ // if I own atom tag, unpack its values
+
+ for (int i = 0; i < n; i++) {
+ if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f"));
+ else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f"));
+ ninteger = atoi(strtok(NULL," \t\n\r\f"));
+ ndouble = atoi(strtok(NULL," \t\n\r\f"));
+
+ for (j = 0; j < ninteger; j++)
+ ivalues[j] = strtok(NULL," \t\n\r\f");
+ for (j = 0; j < ndouble; j++)
+ dvalues[j] = strtok(NULL," \t\n\r\f");
+
+ if (tagdata <= 0 || tagdata > map_tag_max)
+ error->one(FLERR,"Invalid atom ID in Bodies section of data file");
+
+ if ((m = map(tagdata)) >= 0)
+ avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
+ }
+
+ delete [] ivalues;
+ delete [] dvalues;
+}
+
/* ----------------------------------------------------------------------
allocate arrays of length ntypes
only done after ntypes is set
@@ -1210,7 +1331,7 @@ int Atom::find_molecule(char *id)
------------------------------------------------------------------------- */
void Atom::add_molecule_atom(Molecule *onemol, int iatom,
- int ilocal, int offset)
+ int ilocal, tagint offset)
{
if (onemol->qflag) q[ilocal] = onemol->q[iatom];
if (onemol->radiusflag) radius[ilocal] = onemol->radius[iatom];
@@ -1709,9 +1830,9 @@ bigint Atom::memory_usage()
bigint bytes = avec->memory_usage();
memory->destroy(memstr);
- bytes += smax*sizeof(int);
+ bytes += max_same*sizeof(int);
if (map_style == 1)
- bytes += memory->usage(map_array,map_tag_max+1);
+ bytes += memory->usage(map_array,max_array);
else if (map_style == 2) {
bytes += map_nbucket*sizeof(int);
bytes += map_nhash*sizeof(HashElem);
diff --git a/src/atom.h b/src/atom.h
index 3dfc010d5b..8a5a0b643f 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -45,7 +45,8 @@ class Atom : protected Pointers {
// per-atom arrays
// customize by adding new array
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
@@ -65,24 +66,24 @@ class Atom : protected Pointers {
double *cv;
int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
- int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
+ tagint **special; // IDs of 1-2,1-3,1-4 neighs of each atom
int maxspecial; // special[nlocal][maxspecial]
int *num_bond;
int **bond_type;
- int **bond_atom;
+ tagint **bond_atom;
int *num_angle;
int **angle_type;
- int **angle_atom1,**angle_atom2,**angle_atom3;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
int *num_dihedral;
int **dihedral_type;
- int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+ tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int *num_improper;
int **improper_type;
- int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+ tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
// custom arrays used by fix property/atom
@@ -133,9 +134,9 @@ class Atom : protected Pointers {
int nextra_border_max;
int nextra_store;
- int map_style; // default or user-specified style of map
- // 0 = none, 1 = array, 2 = hash
- int map_tag_max; // max atom ID that map() is setup for
+ int map_style; // style of atom map: 0=none, 1=array, 2=hash
+ int map_user; // user selected style = same 0,1,2
+ tagint map_tag_max; // max atom ID that map() is setup for
// spatial sorting of atoms
@@ -159,6 +160,7 @@ class Atom : protected Pointers {
class AtomVec *style_match(const char *);
void modify_params(int, char **);
+ void tag_check();
void tag_extend();
int tag_consecutive();
@@ -167,14 +169,15 @@ class Atom : protected Pointers {
void data_atoms(int, char *);
void data_vels(int, char *);
+
+ void data_bonds(int, char *, int *);
+ void data_angles(int, char *, int *);
+ void data_dihedrals(int, char *, int *);
+ void data_impropers(int, char *, int *);
+
void data_bonus(int, char *, class AtomVec *);
void data_bodies(int, char *, class AtomVecBody *);
- void data_bonds(int, char *);
- void data_angles(int, char *);
- void data_dihedrals(int, char *);
- void data_impropers(int, char *);
-
void allocate_type_arrays();
void set_mass(const char *);
void set_mass(int, double);
@@ -187,7 +190,7 @@ class Atom : protected Pointers {
void add_molecule(int, char **);
int find_molecule(char *);
- void add_molecule_atom(class Molecule *, int, int, int);
+ void add_molecule_atom(class Molecule *, int, int, tagint);
void first_reorder();
void sort();
@@ -212,7 +215,7 @@ class Atom : protected Pointers {
// map lookup function inlined for efficiency
// return -1 if no map defined
- inline int map(int global) {
+ inline int map(tagint global) {
if (map_style == 1) return map_array[global];
else if (map_style == 2) return map_find_hash(global);
else return -1;
@@ -221,28 +224,31 @@ class Atom : protected Pointers {
void map_init();
void map_clear();
void map_set();
- void map_one(int, int);
+ void map_one(tagint, int);
void map_delete();
- int map_find_hash(int);
+ int map_find_hash(tagint);
private:
// global to local ID mapping
int *map_array; // direct map of length map_tag_max + 1
- int smax; // max size of sametag
struct HashElem {
- int global; // key to search on = global ID
- int local; // value associated with key = local index
- int next; // next entry in this bucket, -1 if last
+ tagint global; // key to search on = global ID
+ int local; // value associated with key = local index
+ int next; // next entry in this bucket, -1 if last
};
- int map_nhash; // # of entries hash table can hold
- int map_nused; // # of actual entries in hash table
- int map_free; // ptr to 1st unused entry in hash table
- int map_nbucket; // # of hash buckets
- int *map_bucket; // ptr to 1st entry in each bucket
- HashElem *map_hash; // hash table
+ int map_nhash; // # of entries hash table can hold
+ int map_nused; // # of actual entries in hash table
+ int map_free; // ptr to 1st unused entry in hash table
+ int map_nbucket; // # of hash buckets
+ int *map_bucket; // ptr to 1st entry in each bucket
+ HashElem *map_hash; // hash table
+
+ int max_array; // allocated size of map_array (+1)
+ int max_nhash; // allocated size of hash table
+ int max_same; // allocated size of sametag
// spatial sorting of atoms
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index 93c377b81e..eab9b226f3 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -25,61 +25,100 @@ using namespace LAMMPS_NS;
allocate and initialize array or hash table for global -> local map
set map_tag_max = largest atom ID (may be larger than natoms)
for array option:
- array length = 1 to largest tag of any atom
+ array length = 1 to map_tag_max
set entire array to -1 as initial values
for hash option:
map_nhash = length of hash table
- map_nbucket = # of hash buckets, prime larger than map_nhash
+ map_nbucket = # of hash buckets, prime larger than map_nhash * 2
so buckets will only be filled with 0 or 1 atoms on average
------------------------------------------------------------------------- */
void Atom::map_init()
{
- map_delete();
-
if (tag_enable == 0)
error->all(FLERR,"Cannot create an atom map unless atoms have IDs");
- int max = 0;
- for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
- MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
-
- memory->destroy(sametag);
- smax = nlocal + nghost + EXTRA;
- memory->create(sametag,smax,"atom:sametag");
-
- if (map_style == 1) {
- memory->create(map_array,map_tag_max+1,"atom:map_array");
- for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
-
- } else {
-
- // map_nhash = max # of atoms that can be hashed on this proc
- // set to max of ave atoms/proc or atoms I can store
- // multiply by 2, require at least 1000
- // doubling means hash table will be re-init only rarely
+ int map_style_old = map_style;
- int nper = static_cast<int> (natoms/comm->nprocs);
- map_nhash = MAX(nper,nmax);
- map_nhash *= 2;
- map_nhash = MAX(map_nhash,1000);
+ // map_tag_max = max ID of any atom that will be in new map
- // map_nbucket = prime just larger than map_nhash
-
- map_nbucket = next_prime(map_nhash);
-
- // set all buckets to empty
- // set hash to map_nhash in length
- // put all hash entries in free list and point them to each other
+ tagint max = 0;
+ for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
+ MPI_Allreduce(&max,&map_tag_max,1,MPI_LMP_TAGINT,MPI_MAX,world);
+
+ // set map_style for new map
+ // if user-selected, use that setting
+ // else if map_tag_max > 1M, use hash
+ // else use array
+
+ if (map_user) map_style = map_user;
+ else if (map_tag_max > 1000000) map_style = 2;
+ else map_style = 1;
+
+ // recreate = 1 if must delete old map and create new map
+ // recreate = 0 if can re-use old map w/out realloc and just adjust settings
+
+ int recreate = 0;
+ if (map_style != map_style_old) recreate = 1;
+ else if (map_style == 1 && map_tag_max > max_array) recreate = 1;
+ else if (map_style == 2 && nlocal+nghost > map_nhash) recreate = 1;
+
+ // if not recreating:
+ // for array, just initialize current map_tag_max values
+ // for hash, set all buckets to empty, put all entries in free list
+
+ if (!recreate) {
+ if (map_style == 1) {
+ for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
+ } else {
+ for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
+ map_nused = 0;
+ map_free = 0;
+ for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
+ map_hash[map_nhash-1].next = -1;
+ }
- map_bucket = new int[map_nbucket];
- for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
+ // delete old map and create new one for array or hash
- map_hash = new HashElem[map_nhash];
- map_nused = 0;
- map_free = 0;
- for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
- map_hash[map_nhash-1].next = -1;
+ } else {
+ map_delete();
+
+ if (map_style == 1) {
+ max_array = map_tag_max;
+ memory->create(map_array,max_array+1,"atom:map_array");
+ for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
+
+ } else {
+
+ // map_nhash = max # of atoms that can be hashed on this proc
+ // set to max of ave atoms/proc or atoms I can store
+ // multiply by 2, require at least 1000
+ // doubling means hash table will need to be re-init only rarely
+
+ int nper = static_cast<int> (natoms/comm->nprocs);
+ map_nhash = MAX(nper,nmax);
+ map_nhash *= 2;
+ map_nhash = MAX(map_nhash,1000);
+
+ // map_nbucket = prime just larger than map_nhash
+ // next_prime() should be fast enough,
+ // about 10% of odd integers are prime above 1M
+
+ map_nbucket = next_prime(map_nhash);
+
+ // set all buckets to empty
+ // set hash to map_nhash in length
+ // put all hash entries in free list and point them to each other
+
+ map_bucket = new int[map_nbucket];
+ for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
+
+ map_hash = new HashElem[map_nhash];
+ map_nused = 0;
+ map_free = 0;
+ for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
+ map_hash[map_nhash-1].next = -1;
+ }
}
}
@@ -99,7 +138,8 @@ void Atom::map_clear()
}
} else {
- int previous,global,ibucket,index;
+ int previous,ibucket,index;
+ tagint global;
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) {
sametag[i] = -1;
@@ -144,21 +184,37 @@ void Atom::map_clear()
void Atom::map_set()
{
int nall = nlocal + nghost;
- if (nall > smax) {
- smax = nall + EXTRA;
- memory->destroy(sametag);
- memory->create(sametag,smax,"atom:sametag");
- }
if (map_style == 1) {
+
+ // possible reallocation of sametag must come before loop over atoms
+ // since loop sets sametag
+
+ if (nall > max_same) {
+ max_same = nall + EXTRA;
+ memory->destroy(sametag);
+ memory->create(sametag,max_same,"atom:sametag");
+ }
+
for (int i = nall-1; i >= 0 ; i--) {
sametag[i] = map_array[tag[i]];
map_array[tag[i]] = i;
}
} else {
- int previous,global,ibucket,index;
+
+ // possible reallocation of sametag must come after map_init()
+ // since map_init() will invoke map_delete(), whacking sametag
+
if (nall > map_nhash) map_init();
+ if (nall > max_same) {
+ max_same = nall + EXTRA;
+ memory->destroy(sametag);
+ memory->create(sametag,max_same,"atom:sametag");
+ }
+
+ int previous,ibucket,index;
+ tagint global;
for (int i = nall-1; i >= 0 ; i--) {
sametag[i] = map_find_hash(tag[i]);
@@ -203,7 +259,7 @@ void Atom::map_set()
called by Special class
------------------------------------------------------------------------- */
-void Atom::map_one(int global, int local)
+void Atom::map_one(tagint global, int local)
{
if (map_style == 1) map_array[global] = local;
else {
@@ -246,6 +302,7 @@ void Atom::map_delete()
{
memory->destroy(sametag);
sametag = NULL;
+ max_same = 0;
if (map_style == 1) {
memory->destroy(map_array);
@@ -259,7 +316,6 @@ void Atom::map_delete()
}
map_nhash = 0;
}
- map_tag_max = 0;
}
/* ----------------------------------------------------------------------
@@ -267,7 +323,7 @@ void Atom::map_delete()
called by map() in atom.h
------------------------------------------------------------------------- */
-int Atom::map_find_hash(int global)
+int Atom::map_find_hash(tagint global)
{
int local = -1;
int index = map_bucket[global % map_nbucket];
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index 04964d5d1c..fba68e808e 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -82,7 +82,7 @@ void AtomVec::data_vel(int m, char **values)
void AtomVec::pack_vel(double **buf)
{
double **v = atom->v;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
@@ -100,8 +100,8 @@ void AtomVec::pack_vel(double **buf)
void AtomVec::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
+ fprintf(fp,TAGINT_FORMAT " %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
}
/* ----------------------------------------------------------------------
@@ -111,12 +111,12 @@ void AtomVec::write_vel(FILE *fp, int n, double **buf)
if bondtype is negative, flip back to positive
------------------------------------------------------------------------- */
-int AtomVec::pack_bond(int **buf)
+int AtomVec::pack_bond(tagint **buf)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -154,10 +154,11 @@ int AtomVec::pack_bond(int **buf)
write bond info to data file
------------------------------------------------------------------------- */
-void AtomVec::write_bond(FILE *fp, int n, int **buf, int index)
+void AtomVec::write_bond(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d %d %d %d\n",index,buf[i][0],buf[i][1],buf[i][2]);
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
+ index,buf[i][0],buf[i][1],buf[i][2]);
index++;
}
}
@@ -169,14 +170,14 @@ void AtomVec::write_bond(FILE *fp, int n, int **buf, int index)
if angletype is negative, flip back to positive
------------------------------------------------------------------------- */
-int AtomVec::pack_angle(int **buf)
+int AtomVec::pack_angle(tagint **buf)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_angle = atom->num_angle;
int **angle_type = atom->angle_type;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -216,11 +217,12 @@ int AtomVec::pack_angle(int **buf)
write angle info to data file
------------------------------------------------------------------------- */
-void AtomVec::write_angle(FILE *fp, int n, int **buf, int index)
+void AtomVec::write_angle(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d %d %d %d %d\n",index,
- buf[i][0],buf[i][1],buf[i][2],buf[i][3]);
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT "\n",
+ index,buf[i][0],buf[i][1],buf[i][2],buf[i][3]);
index++;
}
}
@@ -229,15 +231,15 @@ void AtomVec::write_angle(FILE *fp, int n, int **buf, int index)
pack dihedral info for data file
------------------------------------------------------------------------- */
-void AtomVec::pack_dihedral(int **buf)
+void AtomVec::pack_dihedral(tagint **buf)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_dihedral = atom->num_dihedral;
int **dihedral_type = atom->dihedral_type;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -271,11 +273,12 @@ void AtomVec::pack_dihedral(int **buf)
write dihedral info to data file
------------------------------------------------------------------------- */
-void AtomVec::write_dihedral(FILE *fp, int n, int **buf, int index)
+void AtomVec::write_dihedral(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d %d %d %d %d %d\n",index,
- buf[i][0],buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
+ index,buf[i][0],buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
index++;
}
}
@@ -284,15 +287,15 @@ void AtomVec::write_dihedral(FILE *fp, int n, int **buf, int index)
pack improper info for data file
------------------------------------------------------------------------- */
-void AtomVec::pack_improper(int **buf)
+void AtomVec::pack_improper(tagint **buf)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_improper = atom->num_improper;
int **improper_type = atom->improper_type;
- int **improper_atom1 = atom->improper_atom1;
- int **improper_atom2 = atom->improper_atom2;
- int **improper_atom3 = atom->improper_atom3;
- int **improper_atom4 = atom->improper_atom4;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -326,11 +329,12 @@ void AtomVec::pack_improper(int **buf)
write improper info to data file
------------------------------------------------------------------------- */
-void AtomVec::write_improper(FILE *fp, int n, int **buf, int index)
+void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index)
{
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d %d %d %d %d %d\n",index,
- buf[i][0],buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
+ fprintf(fp,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
+ index,buf[i][0],buf[i][1],buf[i][2],buf[i][3],buf[i][4]);
index++;
}
}
diff --git a/src/atom_vec.h b/src/atom_vec.h
index 0d0ba775f5..b9683d38fb 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -99,14 +99,14 @@ class AtomVec : protected Pointers {
virtual int write_vel_hybrid(FILE *, double *) {return 0;}
void reset();
- int pack_bond(int **);
- void write_bond(FILE *, int, int **, int);
- int pack_angle(int **);
- void write_angle(FILE *, int, int **, int);
- void pack_dihedral(int **);
- void write_dihedral(FILE *, int, int **, int);
- void pack_improper(int **);
- void write_improper(FILE *, int, int **, int);
+ int pack_bond(tagint **);
+ void write_bond(FILE *, int, tagint **, int);
+ int pack_angle(tagint **);
+ void write_angle(FILE *, int, tagint **, int);
+ void pack_dihedral(tagint **);
+ void write_dihedral(FILE *, int, tagint **, int);
+ void pack_improper(tagint **);
+ void write_improper(FILE *, int, tagint **, int);
virtual bigint memory_usage() = 0;
@@ -128,8 +128,8 @@ class AtomVec : protected Pointers {
// the cast prevents compiler warnings about possible truncation
union ubuf {
- double d;
- int64_t i;
+ double d;
+ int64_t i;
ubuf(double arg) : d(arg) {}
ubuf(int64_t arg) : i(arg) {}
ubuf(int arg) : i(arg) {}
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index f27178b8fd..5d96dc139e 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -402,7 +402,7 @@ void AtomVecAtomic::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
}
@@ -426,7 +426,7 @@ void AtomVecAtomic::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
@@ -481,7 +481,7 @@ int AtomVecAtomic::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -560,7 +560,7 @@ int AtomVecAtomic::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -613,10 +613,7 @@ void AtomVecAtomic::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -661,8 +658,8 @@ void AtomVecAtomic::pack_data(double **buf)
void AtomVecAtomic::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4],
(int) ubuf(buf[i][5]).i,(int) ubuf(buf[i][6]).i,
(int) ubuf(buf[i][7]).i);
diff --git a/src/atom_vec_atomic.h b/src/atom_vec_atomic.h
index b19ecdd85c..86914f760b 100644
--- a/src/atom_vec_atomic.h
+++ b/src/atom_vec_atomic.h
@@ -53,7 +53,8 @@ class AtomVecAtomic : public AtomVec {
bigint memory_usage();
protected:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
};
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index b91ecdde9c..429ac39137 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -834,7 +834,7 @@ void AtomVecBody::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
body[i] = (int) ubuf(buf[m++]).i;
@@ -882,7 +882,7 @@ void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
body[i] = (int) ubuf(buf[m++]).i;
@@ -1027,7 +1027,7 @@ int AtomVecBody::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -1176,7 +1176,7 @@ int AtomVecBody::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -1305,10 +1305,7 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -1442,8 +1439,8 @@ int AtomVecBody::pack_data_hybrid(int i, double *buf)
void AtomVecBody::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %d %g %g %g %g %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ fprintf(fp,TAGINT_FORMAT " %d %d %g %g %g %g %d %d %d\n",
+ (tagint) ubuf(buf[i][0]).i,(int) 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,
@@ -1497,8 +1494,8 @@ int AtomVecBody::pack_vel_hybrid(int i, double *buf)
void AtomVecBody::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %g %g %g %g %g %g\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
+ fprintf(fp,TAGINT_FORMAT " %g %g %g %g %g %g\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h
index aad592fe4d..c16be4e2c8 100644
--- a/src/atom_vec_body.h
+++ b/src/atom_vec_body.h
@@ -90,7 +90,8 @@ class AtomVecBody : public AtomVec {
void data_body(int, int, int, char **, char **);
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *rmass;
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index 38b4385c9b..d8b4b7430c 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -428,7 +428,7 @@ void AtomVecCharge::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -453,7 +453,7 @@ void AtomVecCharge::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
q[i] = buf[m++];
@@ -524,7 +524,7 @@ int AtomVecCharge::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -607,7 +607,7 @@ int AtomVecCharge::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -664,10 +664,7 @@ void AtomVecCharge::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -737,8 +734,8 @@ int AtomVecCharge::pack_data_hybrid(int i, double *buf)
void AtomVecCharge::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ fprintf(fp,TAGINT_FORMAT " %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,
buf[i][2],buf[i][3],buf[i][4],buf[i][5],
(int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i,
(int) ubuf(buf[i][8]).i);
diff --git a/src/atom_vec_charge.h b/src/atom_vec_charge.h
index ac36ab9439..3e019d21e3 100644
--- a/src/atom_vec_charge.h
+++ b/src/atom_vec_charge.h
@@ -58,7 +58,8 @@ class AtomVecCharge : public AtomVec {
bigint memory_usage();
protected:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *q;
diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
index 2eda8b0e6a..512f3ba74b 100755
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@ -768,7 +768,7 @@ void AtomVecEllipsoid::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
ellipsoid[i] = (int) ubuf(buf[m++]).i;
@@ -811,7 +811,7 @@ void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
ellipsoid[i] = (int) ubuf(buf[m++]).i;
@@ -939,7 +939,7 @@ int AtomVecEllipsoid::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -1061,7 +1061,7 @@ int AtomVecEllipsoid::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -1143,10 +1143,7 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp,
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -1307,8 +1304,9 @@ int AtomVecEllipsoid::pack_data_hybrid(int i, double *buf)
void AtomVecEllipsoid::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
@@ -1362,8 +1360,9 @@ int AtomVecEllipsoid::pack_vel_hybrid(int i, double *buf)
void AtomVecEllipsoid::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
+ fprintf(fp,TAGINT_FORMAT
+ " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h
index b23597e35a..cc8ba2e85d 100755
--- a/src/atom_vec_ellipsoid.h
+++ b/src/atom_vec_ellipsoid.h
@@ -84,7 +84,8 @@ class AtomVecEllipsoid : public AtomVec {
void set_shape(int, double, double, double);
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *rmass;
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 710d15e2bd..d88f67a854 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -616,7 +616,7 @@ void AtomVecHybrid::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
}
@@ -647,7 +647,7 @@ void AtomVecHybrid::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
v[i][0] = buf[m++];
@@ -864,10 +864,7 @@ void AtomVecHybrid::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -954,8 +951,8 @@ void AtomVecHybrid::write_data(FILE *fp, int n, double **buf)
int k,m;
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e",
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],buf[i][4]);
m = 5;
@@ -998,8 +995,8 @@ void AtomVecHybrid::write_vel(FILE *fp, int n, double **buf)
int k,m;
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d %g %g %g",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
+ fprintf(fp,TAGINT_FORMAT " %g %g %g",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3]);
m = 4;
for (k = 0; k < nstyles; k++)
diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h
index 016a131680..2a5113d4d8 100644
--- a/src/atom_vec_hybrid.h
+++ b/src/atom_vec_hybrid.h
@@ -67,7 +67,8 @@ class AtomVecHybrid : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double **omega,**angmom;
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index f8785eed9f..5c89d237fc 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -666,7 +666,7 @@ void AtomVecLine::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -702,7 +702,7 @@ void AtomVecLine::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -811,7 +811,7 @@ int AtomVecLine::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -923,7 +923,7 @@ int AtomVecLine::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -999,12 +999,8 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(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");
@@ -1170,8 +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,"%d %d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
@@ -1225,8 +1222,9 @@ int AtomVecLine::pack_vel_hybrid(int i, double *buf)
void AtomVecLine::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
+ fprintf(fp,TAGINT_FORMAT
+ " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h
index b266c91f36..8aec9ea8d1 100644
--- a/src/atom_vec_line.h
+++ b/src/atom_vec_line.h
@@ -84,7 +84,8 @@ class AtomVecLine : public AtomVec {
void set_length(int, double);
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index c1d7e3a1d8..acb1251981 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -702,7 +702,7 @@ void AtomVecSphere::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
radius[i] = buf[m++];
@@ -729,7 +729,7 @@ void AtomVecSphere::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ tag[i] = (tagint) ubuf(buf[m++]).i;
type[i] = (int) ubuf(buf[m++]).i;
mask[i] = (int) ubuf(buf[m++]).i;
radius[i] = buf[m++];
@@ -810,7 +810,7 @@ int AtomVecSphere::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -901,7 +901,7 @@ int AtomVecSphere::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -966,10 +966,7 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
type[nlocal] = atoi(values[1]);
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
@@ -1095,8 +1092,9 @@ int AtomVecSphere::pack_data_hybrid(int i, double *buf)
void AtomVecSphere::write_data(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
+ fprintf(fp,TAGINT_FORMAT
+ " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6],
(int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i,
@@ -1150,8 +1148,9 @@ int AtomVecSphere::pack_vel_hybrid(int i, double *buf)
void AtomVecSphere::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
+ fprintf(fp,TAGINT_FORMAT
+ " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
diff --git a/src/atom_vec_sphere.h b/src/atom_vec_sphere.h
index b1600625fa..e7ba894e59 100644
--- a/src/atom_vec_sphere.h
+++ b/src/atom_vec_sphere.h
@@ -69,7 +69,8 @@ class AtomVecSphere : public AtomVec {
bigint memory_usage();
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
double *radius,*density,*rmass;
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index 591ad31976..d170c8b5d0 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -882,7 +882,7 @@ void AtomVecTri::unpack_border(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -938,7 +938,7 @@ void AtomVecTri::unpack_border_vel(int n, int first, double *buf)
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- tag[i] = (int) ubuf(buf[m++]).i;
+ 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;
@@ -1105,7 +1105,7 @@ int AtomVecTri::unpack_exchange(double *buf)
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -1255,7 +1255,7 @@ int AtomVecTri::unpack_restart(double *buf)
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
- tag[nlocal] = (int) ubuf(buf[m++]).i;
+ tag[nlocal] = (tagint) ubuf(buf[m++]).i;
type[nlocal] = (int) ubuf(buf[m++]).i;
mask[nlocal] = (int) ubuf(buf[m++]).i;
image[nlocal] = (imageint) ubuf(buf[m++]).i;
@@ -1350,12 +1350,8 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values)
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
- tag[nlocal] = atoi(values[0]);
- if (tag[nlocal] <= 0)
- error->one(FLERR,"Invalid atom ID in Atoms section of data file");
-
+ tag[nlocal] = ATOTAGINT(values[0]);
molecule[nlocal] = atoi(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");
@@ -1618,8 +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,"%d %d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
- (int) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).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,
(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,
@@ -1673,8 +1670,9 @@ int AtomVecTri::pack_vel_hybrid(int i, double *buf)
void AtomVecTri::write_vel(FILE *fp, int n, double **buf)
{
for (int i = 0; i < n; i++)
- fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
- (int) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
+ fprintf(fp,TAGINT_FORMAT
+ " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n",
+ (tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
buf[i][4],buf[i][5],buf[i][6]);
}
diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h
index c0c5b35ae0..cf4af31cc2 100644
--- a/src/atom_vec_tri.h
+++ b/src/atom_vec_tri.h
@@ -86,7 +86,8 @@ class AtomVecTri : public AtomVec {
void set_equilateral(int, double);
private:
- int *tag,*type,*mask;
+ tagint *tag;
+ int *type,*mask;
imageint *image;
double **x,**v,**f;
int *molecule;
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index 626fc7df84..6e2cd57322 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -116,11 +116,11 @@ int ComputeAngleLocal::compute_angles(int flag)
double **x = atom->x;
int *num_angle = atom->num_angle;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 344157eec4..ad6697e048 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -122,9 +122,9 @@ int ComputeBondLocal::compute_bonds(int flag)
double **x = atom->x;
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 030090dcb2..b1713873b2 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -120,7 +120,7 @@ void ComputeClusterAtom::compute_peratom()
// every atom starts in its own cluster, with clusterID = atomID
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
for (ii = 0; ii < inum; ii++) {
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index e0f600521c..438f665da6 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -115,11 +115,11 @@ int ComputeDihedralLocal::compute_dihedrals(int flag)
double **x = atom->x;
int *num_dihedral = atom->num_dihedral;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
- int *tag = atom->tag;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp
index 862169fbbc..4e66856df3 100644
--- a/src/compute_improper_local.cpp
+++ b/src/compute_improper_local.cpp
@@ -116,11 +116,11 @@ int ComputeImproperLocal::compute_impropers(int flag)
double **x = atom->x;
int *num_improper = atom->num_improper;
- int **improper_atom1 = atom->improper_atom1;
- int **improper_atom2 = atom->improper_atom2;
- int **improper_atom3 = atom->improper_atom3;
- int **improper_atom4 = atom->improper_atom4;
- int *tag = atom->tag;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index 9b3dc754bc..250451950e 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -434,7 +434,7 @@ double ComputePropertyAtom::memory_usage()
void ComputePropertyAtom::pack_id(int n)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index fa1fbbabde..b9fc3ab4d0 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -334,7 +334,6 @@ int ComputePropertyLocal::count_pairs(int allflag, int forceflag)
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
- int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -407,9 +406,9 @@ int ComputePropertyLocal::count_bonds(int flag)
int i,atom1,atom2;
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -448,11 +447,11 @@ int ComputePropertyLocal::count_angles(int flag)
int i,atom1,atom2,atom3;
int *num_angle = atom->num_angle;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -490,11 +489,11 @@ int ComputePropertyLocal::count_dihedrals(int flag)
int i,atom1,atom2,atom3,atom4;
int *num_dihedral = atom->num_dihedral;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
- int *tag = atom->tag;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -533,11 +532,11 @@ int ComputePropertyLocal::count_impropers(int flag)
int i,atom1,atom2,atom3,atom4;
int *num_improper = atom->num_improper;
- int **improper_atom1 = atom->improper_atom1;
- int **improper_atom2 = atom->improper_atom2;
- int **improper_atom3 = atom->improper_atom3;
- int **improper_atom4 = atom->improper_atom4;
- int *tag = atom->tag;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -607,7 +606,7 @@ double ComputePropertyLocal::memory_usage()
void ComputePropertyLocal::pack_patom1(int n)
{
int i;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -621,7 +620,7 @@ void ComputePropertyLocal::pack_patom1(int n)
void ComputePropertyLocal::pack_patom2(int n)
{
int i;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int m = 0; m < ncount; m++) {
i = indices[m][1];
@@ -663,7 +662,7 @@ void ComputePropertyLocal::pack_ptype2(int n)
void ComputePropertyLocal::pack_batom1(int n)
{
int i;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -677,7 +676,7 @@ void ComputePropertyLocal::pack_batom1(int n)
void ComputePropertyLocal::pack_batom2(int n)
{
int i,j;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -707,7 +706,7 @@ void ComputePropertyLocal::pack_btype(int n)
void ComputePropertyLocal::pack_aatom1(int n)
{
int i,j;
- int **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom1 = atom->angle_atom1;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -722,7 +721,7 @@ void ComputePropertyLocal::pack_aatom1(int n)
void ComputePropertyLocal::pack_aatom2(int n)
{
int i,j;
- int **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom2 = atom->angle_atom2;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -737,7 +736,7 @@ void ComputePropertyLocal::pack_aatom2(int n)
void ComputePropertyLocal::pack_aatom3(int n)
{
int i,j;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom3 = atom->angle_atom3;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -767,7 +766,7 @@ void ComputePropertyLocal::pack_atype(int n)
void ComputePropertyLocal::pack_datom1(int n)
{
int i,j;
- int **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -782,7 +781,7 @@ void ComputePropertyLocal::pack_datom1(int n)
void ComputePropertyLocal::pack_datom2(int n)
{
int i,j;
- int **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -797,7 +796,7 @@ void ComputePropertyLocal::pack_datom2(int n)
void ComputePropertyLocal::pack_datom3(int n)
{
int i,j;
- int **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -812,7 +811,7 @@ void ComputePropertyLocal::pack_datom3(int n)
void ComputePropertyLocal::pack_datom4(int n)
{
int i,j;
- int **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -842,7 +841,7 @@ void ComputePropertyLocal::pack_dtype(int n)
void ComputePropertyLocal::pack_iatom1(int n)
{
int i,j;
- int **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom1 = atom->improper_atom1;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -857,7 +856,7 @@ void ComputePropertyLocal::pack_iatom1(int n)
void ComputePropertyLocal::pack_iatom2(int n)
{
int i,j;
- int **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom2 = atom->improper_atom2;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -872,7 +871,7 @@ void ComputePropertyLocal::pack_iatom2(int n)
void ComputePropertyLocal::pack_iatom3(int n)
{
int i,j;
- int **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom3 = atom->improper_atom3;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
@@ -887,7 +886,7 @@ void ComputePropertyLocal::pack_iatom3(int n)
void ComputePropertyLocal::pack_iatom4(int n)
{
int i,j;
- int **improper_atom4 = atom->improper_atom4;
+ tagint **improper_atom4 = atom->improper_atom4;
for (int m = 0; m < ncount; m++) {
i = indices[m][0];
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index f83edfa638..1e1f5716da 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -22,6 +22,7 @@
#include "irregular.h"
#include "modify.h"
#include "force.h"
+#include "special.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
@@ -121,7 +122,7 @@ void CreateAtoms::command(int narg, char **arg)
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
- if (iarg+3 > narg) error->all(FLERR,"Illegal fix create_atoms command");
+ if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule ID for create_atoms does not exist");
@@ -152,20 +153,21 @@ void CreateAtoms::command(int narg, char **arg)
ranmol = NULL;
if (mode == MOLECULE) {
- if (atom->molecule_flag == 0)
- error->all(FLERR,"Create_atoms mol requires atom attribute molecule");
if (onemol->xflag == 0)
error->all(FLERR,"Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Create_atoms molecule must have atom types");
if (ntype+onemol->maxtype <= 0 || ntype+onemol->maxtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms mol command");
+ if (onemol->tag_require && !atom->tag_enable)
+ error->all(FLERR,
+ "Create_atoms molecule has atom IDs, but system does not");
// create_atoms uses geoemetric center of molecule for insertion
onemol->compute_center();
- // molecule random number generator, same for all procs
+ // molecule random number generator, different for each proc
ranmol = new RanMars(lmp,molseed+comm->me);
}
@@ -251,99 +253,88 @@ void CreateAtoms::command(int narg, char **arg)
fix->set_arrays(i);
}
- // new total # of atoms and error check
- // for MOLECULE mode, require atom IDs
+ // set new total # of atoms and error check
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
error->all(FLERR,"Too many total atoms");
- if (atom->natoms > MAXSMALLINT) {
- if (mode == ATOM) {
- if (comm->me == 0)
- error->warning(FLERR,"Total atom count exceeds ID limit, "
- "atoms will not have individual IDs");
- atom->tag_enable = 0;
- } else error->all(FLERR,"Total atom count exceeds ID limit");
- }
- // for ATOM mode:
- // add IDs for newly created atoms if IDs are still enabled
- // if global map exists, reset it
+ // add IDs for newly created atoms
+ // check that atom IDs are valid
- if (mode == ATOM) {
- if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
- if (atom->map_style) {
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
- }
+ if (atom->tag_enable) atom->tag_extend();
+ atom->tag_check();
+
+ // if molecular system or user-requested, create global mapping of atoms
+ // zero nghost in case are adding new atoms to existing atoms
+
+ if (atom->molecular || atom->map_user) {
+ atom->nghost = 0;
+ atom->map_init();
+ atom->map_set();
}
// for MOLECULE mode:
- // set atom and molecule IDs for created atoms
+ // set molecule IDs for created atoms if used
+ // reset new molecule bond,angle,etc and special values
// send atoms to new owning procs via irregular comm
- // since not all created atoms will be within my sub-domain
+ // since not all atoms I created will be within my sub-domain
+ // perform special list build if needed
if (mode == MOLECULE) {
- // add atom IDs for newly created atoms and reset global map
- // global map must exist since atom->molecular is required to be set
-
- atom->tag_extend();
- atom->nghost = 0;
- atom->map_init();
- atom->map_set();
-
- // maxmol = max molecule ID across all procs, for previous atoms
+ // molcreate = # of molecules I created
- int *molecule = atom->molecule;
+ int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
- int 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);
-
- // molcreate = # of molecules I created
+ // maxmol = max molecule ID across all procs, for previous atoms
// moloffset = max molecule ID for all molecules owned by previous procs
// including molecules existing before this creation
- int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
int moloffset;
- MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
- moloffset = moloffset - molcreate + maxmol;
+ int *molecule = atom->molecule;
+ if (molecule) {
+ int 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);
+ MPI_Scan(&molcreate,&moloffset,1,MPI_INT,MPI_SUM,world);
+ moloffset = moloffset - molcreate + maxmol;
+ }
// loop over molecules I created
// set their molecule ID
// reset their bond,angle,etc and special values
int natoms = onemol->natoms;
+ tagint offset = 0;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int *num_improper = atom->num_improper;
- int **bond_atom = atom->bond_atom;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
- int **improper_atom1 = atom->improper_atom1;
- int **improper_atom2 = atom->improper_atom2;
- int **improper_atom3 = atom->improper_atom3;
- int **improper_atom4 = atom->improper_atom4;
+ tagint **bond_atom = atom->bond_atom;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial;
- int **special = atom->special;
+ tagint **special = atom->special;
int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) {
- int offset = tag[ilocal]-1;
+ if (tag) offset = tag[ilocal]-1;
for (int m = 0; m < natoms; m++) {
- molecule[ilocal] = moloffset + i+1;
+ if (molecule) molecule[ilocal] = moloffset + i+1;
if (onemol->bondflag)
for (int j = 0; j < num_bond[ilocal]; j++)
bond_atom[ilocal][j] += offset;
@@ -404,6 +395,17 @@ void CreateAtoms::command(int narg, char **arg)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
}
+
+ // for MOLECULE mode:
+ // create special bond lists for molecular systems
+ // only if onemol added bonds but not special info
+
+ if (mode == MOLECULE) {
+ if (atom->molecular && onemol->bondflag && !onemol->specialflag) {
+ Special special(lmp);
+ special.build();
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -439,7 +441,6 @@ void CreateAtoms::add_single()
}
}
-
/* ----------------------------------------------------------------------
add Nrandom atoms at random locations
------------------------------------------------------------------------- */
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index db752d0b2c..ac1c354d29 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -85,7 +85,7 @@ void DeleteAtoms::command(int narg, char **arg)
// set all atom IDs to 0, call tag_extend()
if (atom->molecular == 0 && compress_flag) {
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (i = 0; i < nlocal; i++) tag[i] = 0;
atom->tag_extend();
}
@@ -292,7 +292,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
// at end of loop, there are no more overlaps
// only ever delete owned atom I, never J even if owned
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
double **x = atom->x;
double *special_coul = force->special_coul;
diff --git a/src/domain.cpp b/src/domain.cpp
index a2d88c94cf..c3f78ff873 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -582,7 +582,7 @@ void Domain::image_check()
// which means image flags in that dimension were different
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
double delx,dely,delz;
@@ -654,7 +654,7 @@ void Domain::box_too_small_check()
// assuming 2 atoms have consistent image flags
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
double **x = atom->x;
int nlocal = atom->nlocal;
diff --git a/src/dump.cpp b/src/dump.cpp
index c37a324564..965aa29a75 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -34,7 +34,6 @@ using namespace LAMMPS_NS;
Dump *Dump::dumpptr;
#define BIG 1.0e20
-#define IBIG 2147483647
#define EPSILON 1.0e-6
enum{ASCEND,DESCEND};
@@ -77,7 +76,8 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
maxbuf = maxids = maxsort = maxproc = 0;
buf = bufsort = NULL;
- ids = idsort = index = proclist = NULL;
+ ids = idsort = NULL;
+ index = proclist = NULL;
irregular = NULL;
maxsbuf = 0;
@@ -177,7 +177,8 @@ void Dump::init()
maxids = maxsort = maxproc = 0;
bufsort = NULL;
- ids = idsort = index = proclist = NULL;
+ ids = idsort = NULL;
+ index = proclist = NULL;
irregular = NULL;
}
@@ -194,6 +195,7 @@ void Dump::init()
bigint size = group->count(igroup);
if (size > MAXSMALLINT) error->all(FLERR,"Too many atoms to dump sort");
+ int isize = static_cast<int> (size);
// set reorderflag = 1 if can simply reorder local atoms rather than sort
// criteria: sorting by ID, atom IDs are consecutive from 1 to Natoms
@@ -202,32 +204,31 @@ void Dump::init()
reorderflag = 0;
if (sortcol == 0 && atom->tag_consecutive()) {
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
- int min = IBIG;
- int max = 0;
+ tagint min = MAXTAGINT;
+ tagint max = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
min = MIN(min,tag[i]);
max = MAX(max,tag[i]);
}
- int minall,maxall;
- MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
- MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
- int isize = static_cast<int> (size);
+ tagint minall,maxall;
+ MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
+ MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (maxall-minall+1 == isize) {
reorderflag = 1;
double range = maxall-minall + EPSILON;
idlo = static_cast<int> (range*me/nprocs + minall);
- int idhi = static_cast<int> (range*(me+1)/nprocs + minall);
+ tagint idhi = static_cast<tagint> (range*(me+1)/nprocs + minall);
- int lom1 = static_cast<int> ((idlo-1-minall)/range * nprocs);
- int lo = static_cast<int> ((idlo-minall)/range * nprocs);
- int him1 = static_cast<int> ((idhi-1-minall)/range * nprocs);
- int hi = static_cast<int> ((idhi-minall)/range * nprocs);
+ tagint lom1 = static_cast<tagint> ((idlo-1-minall)/range * nprocs);
+ tagint lo = static_cast<tagint> ((idlo-minall)/range * nprocs);
+ tagint him1 = static_cast<tagint> ((idhi-1-minall)/range * nprocs);
+ tagint hi = static_cast<tagint> ((idhi-minall)/range * nprocs);
if (me && me == lom1) idlo--;
else if (me && me != lo) idlo++;
if (me+1 == him1) idhi--;
@@ -513,7 +514,7 @@ void Dump::sort()
bufsort = dptr;
if (sortcol == 0) {
- int *iptr = ids;
+ tagint *iptr = ids;
ids = idsort;
idsort = iptr;
}
@@ -533,16 +534,21 @@ void Dump::sort()
// proclist[i] = which proc Ith datum will be sent to
if (sortcol == 0) {
- int min = IBIG;
- int max = 0;
+ tagint min = MAXTAGINT;
+ tagint max = 0;
for (i = 0; i < nme; i++) {
min = MIN(min,ids[i]);
max = MAX(max,ids[i]);
}
- int minall,maxall;
- MPI_Allreduce(&min,&minall,1,MPI_INT,MPI_MIN,world);
- MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
- double range = maxall-minall + EPSILON;
+ tagint minall,maxall;
+ MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
+ MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
+
+ // use 0.5 instead of EPSILON since atom IDs are integers
+ // if use EPSILON, it can be lost if 64-bit maxall-minall is too big
+ // then iproc == nprocs for largest ID, causing irregular to crash
+
+ double range = maxall-minall + 0.5;
for (i = 0; i < nme; i++) {
iproc = static_cast<int> ((ids[i]-minall)/range * nprocs);
proclist[i] = iproc;
@@ -589,7 +595,7 @@ void Dump::sort()
irregular->exchange_data((char *) buf,size_one*sizeof(double),
(char *) bufsort);
if (sortcol == 0)
- irregular->exchange_data((char *) ids,sizeof(int),(char *) idsort);
+ irregular->exchange_data((char *) ids,sizeof(tagint),(char *) idsort);
irregular->destroy_data();
}
@@ -645,7 +651,7 @@ void Dump::sort()
int Dump::idcompare(const void *pi, const void *pj)
{
- int *idsort = dumpptr->idsort;
+ tagint *idsort = dumpptr->idsort;
int i = *((int *) pi);
int j = *((int *) pj);
diff --git a/src/dump.h b/src/dump.h
index ce2f0dc4e7..1c8017ee9a 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -95,7 +95,7 @@ class Dump : protected Pointers {
int reorderflag; // 1 if OK to reorder instead of sort
int ntotal_reorder; // # of atoms that must be in snapshot
int nme_reorder; // # of atoms I must own in snapshot
- int idlo; // lowest ID I own when reordering
+ tagint idlo; // lowest ID I own when reordering
int maxbuf; // size of buf
double *buf; // memory for atom quantities
@@ -106,9 +106,10 @@ class Dump : protected Pointers {
int maxids; // size of ids
int maxsort; // size of bufsort, idsort, index
int maxproc; // size of proclist
- int *ids; // list of atom IDs, if sorting on IDs
+ tagint *ids; // list of atom IDs, if sorting on IDs
double *bufsort;
- int *idsort,*index,*proclist;
+ tagint *idsort;
+ int *index,*proclist;
class Irregular *irregular;
@@ -117,7 +118,7 @@ class Dump : protected Pointers {
virtual int modify_param(int, char **) {return 0;}
virtual void write_header(bigint) = 0;
virtual int count();
- virtual void pack(int *) = 0;
+ virtual void pack(tagint *) = 0;
virtual int convert_string(int, double *) {return 0;}
virtual void write_data(int, double *) = 0;
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 1a1313e3a3..068c4e3dff 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -55,8 +55,8 @@ void DumpAtom::init_style()
strcat(format,"\n");
} else {
char *str;
- if (image_flag == 0) str = (char *) "%d %d %g %g %g";
- else str = (char *) "%d %d %g %g %g %d %d %d";
+ if (image_flag == 0) str = (char *) TAGINT_FORMAT " %d %g %g %g";
+ else str = (char *) TAGINT_FORMAT " %d %g %g %g %d %d %d";
int n = strlen(str) + 2;
format = new char[n];
strcpy(format,str);
@@ -145,7 +145,7 @@ void DumpAtom::write_header(bigint ndump)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack(int *ids)
+void DumpAtom::pack(tagint *ids)
{
(this->*pack_choice)(ids);
}
@@ -237,11 +237,11 @@ void DumpAtom::header_item_triclinic(bigint ndump)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack_scale_image(int *ids)
+void DumpAtom::pack_scale_image(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
@@ -269,11 +269,11 @@ void DumpAtom::pack_scale_image(int *ids)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack_scale_noimage(int *ids)
+void DumpAtom::pack_scale_noimage(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
@@ -297,11 +297,11 @@ void DumpAtom::pack_scale_noimage(int *ids)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack_scale_image_triclinic(int *ids)
+void DumpAtom::pack_scale_image_triclinic(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
@@ -328,11 +328,11 @@ void DumpAtom::pack_scale_image_triclinic(int *ids)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack_scale_noimage_triclinic(int *ids)
+void DumpAtom::pack_scale_noimage_triclinic(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
@@ -355,11 +355,11 @@ void DumpAtom::pack_scale_noimage_triclinic(int *ids)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack_noscale_image(int *ids)
+void DumpAtom::pack_noscale_image(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
@@ -383,11 +383,11 @@ void DumpAtom::pack_noscale_image(int *ids)
/* ---------------------------------------------------------------------- */
-void DumpAtom::pack_noscale_noimage(int *ids)
+void DumpAtom::pack_noscale_noimage(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
@@ -422,7 +422,7 @@ int DumpAtom::convert_image(int n, double *mybuf)
}
offset += sprintf(&sbuf[offset],format,
- static_cast<int> (mybuf[m]),
+ static_cast<tagint> (mybuf[m]),
static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4],
static_cast<int> (mybuf[m+5]),
@@ -448,7 +448,7 @@ int DumpAtom::convert_noimage(int n, double *mybuf)
}
offset += sprintf(&sbuf[offset],format,
- static_cast<int> (mybuf[m]),
+ static_cast<tagint> (mybuf[m]),
static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
@@ -480,7 +480,7 @@ void DumpAtom::write_lines_image(int n, double *mybuf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
- static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+ static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
m += size_one;
@@ -494,7 +494,7 @@ void DumpAtom::write_lines_noimage(int n, double *mybuf)
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
- static_cast<int> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+ static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
diff --git a/src/dump_atom.h b/src/dump_atom.h
index 8b2548a964..4f8762effd 100644
--- a/src/dump_atom.h
+++ b/src/dump_atom.h
@@ -37,7 +37,7 @@ class DumpAtom : public Dump {
void init_style();
int modify_param(int, char **);
void write_header(bigint);
- void pack(int *);
+ void pack(tagint *);
int convert_string(int, double *);
void write_data(int, double *);
@@ -48,14 +48,14 @@ class DumpAtom : public Dump {
void header_item(bigint);
void header_item_triclinic(bigint);
- typedef void (DumpAtom::*FnPtrPack)(int *);
+ typedef void (DumpAtom::*FnPtrPack)(tagint *);
FnPtrPack pack_choice; // ptr to pack functions
- void pack_scale_image(int *);
- void pack_scale_noimage(int *);
- void pack_noscale_image(int *);
- void pack_noscale_noimage(int *);
- void pack_scale_image_triclinic(int *);
- void pack_scale_noimage_triclinic(int *);
+ void pack_scale_image(tagint *);
+ void pack_scale_noimage(tagint *);
+ void pack_noscale_image(tagint *);
+ void pack_noscale_noimage(tagint *);
+ void pack_scale_image_triclinic(tagint *);
+ void pack_scale_noimage_triclinic(tagint *);
typedef int (DumpAtom::*FnPtrConvert)(int, double *);
FnPtrConvert convert_choice; // ptr to convert data functions
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index e5aa145e1c..a6f05dcfcf 100755
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -33,7 +33,7 @@
using namespace LAMMPS_NS;
-enum{INT,DOUBLE,STRING}; // same as in DumpCustom
+enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
#define UNWRAPEXPAND 10.0
#define ONEFIELD 32
@@ -200,6 +200,9 @@ int DumpCFG::convert_string(int n, double *mybuf)
else if (vtype[j] == STRING)
offset +=
sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == BIGINT)
+ offset +=
+ sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
}
@@ -232,6 +235,9 @@ int DumpCFG::convert_string(int n, double *mybuf)
else if (vtype[j] == STRING)
offset +=
sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == BIGINT)
+ offset +=
+ sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
}
@@ -277,6 +283,8 @@ void DumpCFG::write_lines(int n, double *mybuf)
fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == BIGINT)
+ fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
}
@@ -301,6 +309,8 @@ void DumpCFG::write_lines(int n, double *mybuf)
fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == BIGINT)
+ fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
}
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 32b3e4eb33..f0c0371044 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -44,7 +44,7 @@ enum{ID,MOL,TYPE,ELEMENT,MASS,
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
-enum{INT,DOUBLE,STRING}; // same as in DumpCFG
+enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCFG
#define INVOKED_PERATOM 8
#define ONEFIELD 32
@@ -128,6 +128,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
if (vtype[i] == INT) strcat(format_default,"%d ");
else if (vtype[i] == DOUBLE) strcat(format_default,"%g ");
else if (vtype[i] == STRING) strcat(format_default,"%s ");
+ else if (vtype[i] == BIGINT) strcat(format_default,BIGINT_FORMAT " ");
vformat[i] = NULL;
}
@@ -437,7 +438,7 @@ int DumpCustom::count()
// customize by adding to if statement
if (thresh_array[ithresh] == ID) {
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (i = 0; i < nlocal; i++) dchoose[i] = tag[i];
ptr = dchoose;
nstride = 1;
@@ -894,11 +895,11 @@ int DumpCustom::count()
/* ---------------------------------------------------------------------- */
-void DumpCustom::pack(int *ids)
+void DumpCustom::pack(tagint *ids)
{
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
if (ids) {
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int i = 0; i < nchoose; i++)
ids[i] = tag[clist[i]];
}
@@ -929,6 +930,9 @@ int DumpCustom::convert_string(int n, double *mybuf)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
offset += sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == BIGINT)
+ offset += sprintf(&sbuf[offset],vformat[j],
+ static_cast<bigint> (mybuf[m]));
m++;
}
offset += sprintf(&sbuf[offset],"\n");
@@ -973,6 +977,8 @@ void DumpCustom::write_lines(int n, double *mybuf)
else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
+ else if (vtype[j] == BIGINT)
+ fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
m++;
}
fprintf(fp,"\n");
@@ -991,7 +997,8 @@ int DumpCustom::parse_fields(int narg, char **arg)
if (strcmp(arg[iarg],"id") == 0) {
pack_choice[i] = &DumpCustom::pack_id;
- vtype[i] = INT;
+ if (sizeof(tagint) == sizeof(smallint)) vtype[i] = INT;
+ else vtype[i] = BIGINT;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
@@ -1706,7 +1713,7 @@ void DumpCustom::pack_variable(int n)
void DumpCustom::pack_id(int n)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int i = 0; i < nchoose; i++) {
buf[n] = tag[clist[i]];
diff --git a/src/dump_custom.h b/src/dump_custom.h
index 9cfe9188ee..a873a97f21 100644
--- a/src/dump_custom.h
+++ b/src/dump_custom.h
@@ -77,7 +77,7 @@ class DumpCustom : public Dump {
virtual void init_style();
virtual void write_header(bigint);
int count();
- void pack(int *);
+ void pack(tagint *);
virtual int convert_string(int, double *);
virtual void write_data(int, double *);
bigint memory_usage();
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index 877d8a3f10..a4a6e4f704 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -175,11 +175,11 @@ void DumpDCD::write_header(bigint n)
/* ---------------------------------------------------------------------- */
-void DumpDCD::pack(int *ids)
+void DumpDCD::pack(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
imageint *image = atom->image;
int *mask = atom->mask;
diff --git a/src/dump_dcd.h b/src/dump_dcd.h
index a5b88f3caf..47b6afe0be 100644
--- a/src/dump_dcd.h
+++ b/src/dump_dcd.h
@@ -39,7 +39,7 @@ class DumpDCD : public Dump {
void init_style();
void openfile();
void write_header(bigint);
- void pack(int *);
+ void pack(tagint *);
void write_data(int, double *);
int modify_param(int, char **);
bigint memory_usage();
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 05a7486c50..53f09b02a8 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -696,8 +696,8 @@ void DumpImage::create_image()
if (bondflag) {
double **x = atom->x;
- int *tag = atom->tag;
- int **bond_atom = atom->bond_atom;
+ tagint *tag = atom->tag;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
int *type = atom->type;
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index fd914563d5..f4d7fb260e 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -265,7 +265,7 @@ int DumpLocal::count()
/* ---------------------------------------------------------------------- */
-void DumpLocal::pack(int *dummy)
+void DumpLocal::pack(tagint *dummy)
{
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
}
diff --git a/src/dump_local.h b/src/dump_local.h
index 4861141f2d..dec5e27834 100644
--- a/src/dump_local.h
+++ b/src/dump_local.h
@@ -57,7 +57,7 @@ class DumpLocal : public Dump {
int modify_param(int, char **);
void write_header(bigint);
int count();
- void pack(int *);
+ void pack(tagint *);
int convert_string(int, double *);
void write_data(int, double *);
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index f3ef0178ce..273ec06e44 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -140,11 +140,11 @@ void DumpXYZ::write_header(bigint n)
/* ---------------------------------------------------------------------- */
-void DumpXYZ::pack(int *ids)
+void DumpXYZ::pack(tagint *ids)
{
int m,n;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
diff --git a/src/dump_xyz.h b/src/dump_xyz.h
index eb28e4fee8..879b46e051 100644
--- a/src/dump_xyz.h
+++ b/src/dump_xyz.h
@@ -35,7 +35,7 @@ class DumpXYZ : public Dump {
void init_style();
void write_header(bigint);
- void pack(int *);
+ void pack(tagint *);
int convert_string(int, double *);
void write_data(int, double *);
int modify_param(int, char **);
diff --git a/src/fix.h b/src/fix.h
index 459479d999..6f11272be6 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -116,7 +116,7 @@ class Fix : protected Pointers {
virtual void copy_arrays(int, int, int) {}
virtual void set_arrays(int) {}
virtual void update_arrays(int, int) {}
- virtual void set_molecule(int, int, double *, double *, double *) {}
+ virtual void set_molecule(int, tagint, double *, double *, double *) {}
virtual int pack_border(int, int *, double *) {return 0;}
virtual int unpack_border(int, int, double *) {return 0;}
@@ -195,6 +195,17 @@ class Fix : protected Pointers {
void v_setup(int);
void v_tally(int, int *, double, double *);
+
+ // union data struct for packing 32-bit and 64-bit ints into double bufs
+ // see atom_vec.h for documentation
+
+ union ubuf {
+ double d;
+ int64_t i;
+ ubuf(double arg) : d(arg) {}
+ ubuf(int64_t arg) : i(arg) {}
+ ubuf(int arg) : i(arg) {}
+ };
};
namespace FixConst {
diff --git a/src/fix_external.h b/src/fix_external.h
index 3e38f09c42..118a678449 100644
--- a/src/fix_external.h
+++ b/src/fix_external.h
@@ -46,7 +46,7 @@ class FixExternal : public Fix {
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
- typedef void (*FnPtr)(void *, bigint, int, int *, double **, double **);
+ typedef void (*FnPtr)(void *, bigint, int, tagint *, double **, double **);
void set_callback(FnPtr, void *);
private:
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index 91f8bce591..a1be2b556b 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -174,12 +174,16 @@ void FixPropertyAtom::init()
void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
{
- int j,m,tagdata;
+ int j,m;
+ tagint itag;
char *next;
- if (atom->map_style == 0)
- error->all(FLERR,"Fix property/atom cannot read from data file "
- "unless an atom map is defined");
+ int mapflag = 0;
+ if (atom->map_style == 0) {
+ mapflag = 1;
+ atom->map_init();
+ atom->map_set();
+ }
next = strchr(buf,'\n');
*next = '\0';
@@ -198,7 +202,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
// tokenize the line into values
// if I own atom tag, unpack its values
- int map_tag_max = atom->map_tag_max;
+ tagint map_tag_max = atom->map_tag_max;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
@@ -207,8 +211,8 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
- tagdata = atoi(values[0]);
- if (tagdata <= 0 || tagdata > map_tag_max) {
+ itag = ATOTAGINT(values[0]);
+ if (itag <= 0 || itag > map_tag_max) {
char str[128];
sprintf(str,"Invalid atom ID in %s section of data file",keyword);
error->one(FLERR,str);
@@ -216,7 +220,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
// assign words in line to per-atom vectors
- if ((m = atom->map(tagdata)) >= 0) {
+ if ((m = atom->map(itag)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) atom->molecule[m] = atoi(values[j+1]);
else if (style[j] == CHARGE) atom->q[m] = atof(values[j+1]);
@@ -231,6 +235,11 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
}
delete [] values;
+
+ if (mapflag) {
+ atom->map_delete();
+ atom->map_style = 0;
+ }
}
/* ----------------------------------------------------------------------
@@ -267,7 +276,7 @@ void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
// 1st column = atom tag
// rest of columns = per-atom values
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) buf[i][0] = ubuf(tag[i]).d;
@@ -316,7 +325,7 @@ void FixPropertyAtom::write_data_section(int mth, FILE *fp,
int m;
for (int i = 0; i < n; i++) {
- fprintf(fp,"%d",(int) ubuf(buf[i][0]).i);
+ fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
for (m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE || style[m] == INTEGER)
fprintf(fp," %d",(int) ubuf(buf[i][m+1]).i);
diff --git a/src/fix_property_atom.h b/src/fix_property_atom.h
index 12ecb9694b..e8b0d67d71 100644
--- a/src/fix_property_atom.h
+++ b/src/fix_property_atom.h
@@ -57,18 +57,6 @@ class FixPropertyAtom : public Fix {
char *astyle;
int nmax_old; // length of peratom arrays the last time they grew
-
- // union data struct for packing 32-bit and 64-bit ints into double bufs
- // see atom_vec.h for documentation
-
- union ubuf {
- double d;
- int64_t i;
- ubuf(double arg) : d(arg) {}
- ubuf(int64_t arg) : i(arg) {}
- ubuf(int arg) : i(arg) {}
- };
-
};
}
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index 33f717c896..70b0d72d02 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -512,7 +512,9 @@ void FixRestrain::restrain_dihedral(int m)
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
- sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " %d %d %d %d",
+ sprintf(str,"Restrain problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str);
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index bebd23386d..96461d2930 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -119,7 +119,7 @@ void FixShearHistory::allocate_pages()
pgsize = neighbor->pgsize;
oneatom = neighbor->oneatom;
int nmypage = comm->nthreads;
- ipage = new MyPage<int>[nmypage];
+ ipage = new MyPage<tagint>[nmypage];
dpage = new MyPage<double[3]>[nmypage];
for (int i = 0; i < nmypage; i++) {
ipage[i].init(oneatom,pgsize);
@@ -177,7 +177,7 @@ void FixShearHistory::pre_exchange()
// calculate npartner for each owned atom
// nlocal_neigh = nlocal when neigh list was built, may be smaller than nlocal
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
NeighList *list = pair->list;
inum = list->inum;
ilist = list->ilist;
@@ -302,8 +302,8 @@ double FixShearHistory::memory_usage()
void FixShearHistory::grow_arrays(int nmax)
{
memory->grow(npartner,nmax,"shear_history:npartner");
- partner = (int **) memory->srealloc(partner,nmax*sizeof(int *),
- "shear_history:partner");
+ partner = (tagint **) memory->srealloc(partner,nmax*sizeof(tagint *),
+ "shear_history:partner");
typedef double (*sptype)[3];
shearpartner = (sptype *)
memory->srealloc(shearpartner,nmax*sizeof(sptype),
@@ -370,7 +370,7 @@ int FixShearHistory::unpack_exchange(int nlocal, double *buf)
partner[nlocal] = ipage->get(npartner[nlocal]);
shearpartner[nlocal] = dpage->get(npartner[nlocal]);
for (int n = 0; n < npartner[nlocal]; n++) {
- partner[nlocal][n] = static_cast<int> (buf[m++]);
+ partner[nlocal][n] = static_cast<tagint> (buf[m++]);
shearpartner[nlocal][n][0] = buf[m++];
shearpartner[nlocal][n][1] = buf[m++];
shearpartner[nlocal][n][2] = buf[m++];
@@ -421,7 +421,7 @@ void FixShearHistory::unpack_restart(int nlocal, int nth)
partner[nlocal] = ipage->get(npartner[nlocal]);
shearpartner[nlocal] = dpage->get(npartner[nlocal]);
for (int n = 0; n < npartner[nlocal]; n++) {
- partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
+ partner[nlocal][n] = static_cast<tagint> (extra[nlocal][m++]);
shearpartner[nlocal][n][0] = extra[nlocal][m++];
shearpartner[nlocal][n][1] = extra[nlocal][m++];
shearpartner[nlocal][n][2] = extra[nlocal][m++];
diff --git a/src/fix_shear_history.h b/src/fix_shear_history.h
index 0dc150c090..06b58ac607 100644
--- a/src/fix_shear_history.h
+++ b/src/fix_shear_history.h
@@ -52,7 +52,7 @@ class FixShearHistory : public Fix {
protected:
int *npartner; // # of touching partners of each atom
- int **partner; // tags for the partners
+ tagint **partner; // global atom IDs for the partners
double (**shearpartner)[3]; // 3 shear values with the partner
int maxtouch; // max # of touching partners for my atoms
@@ -60,7 +60,7 @@ class FixShearHistory : public Fix {
int *computeflag; // computeflag in PairGranHookeHistory
int pgsize,oneatom; // copy of settings in Neighbor
- MyPage<int> *ipage; // pages of partner atom IDs
+ MyPage<tagint> *ipage; // pages of partner atom IDs
MyPage<double[3]> *dpage; // pages of shear history with partners
void allocate_pages();
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index bd95daf7a2..addcffcab4 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -588,7 +588,7 @@ int FixStoreState::size_restart(int nlocal)
void FixStoreState::pack_id(int n)
{
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 1a10594478..8ac0533fff 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -394,7 +394,8 @@ void FixTMD::readfile(char *file)
char *buffer = new char[CHUNK*MAXLINE];
char *next,*bufptr;
- int i,m,nlines,tag,imageflag,ix,iy,iz;
+ int i,m,nlines,imageflag,ix,iy,iz;
+ tagint itag;
double x,y,z,xprd,yprd,zprd;
int firstline = 1;
@@ -457,11 +458,12 @@ void FixTMD::readfile(char *file)
}
if (imageflag)
- sscanf(bufptr,"%d %lg %lg %lg %d %d %d",&tag,&x,&y,&z,&ix,&iy,&iz);
+ sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d",
+ &itag,&x,&y,&z,&ix,&iy,&iz);
else
- sscanf(bufptr,"%d %lg %lg %lg",&tag,&x,&y,&z);
+ sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z);
- m = atom->map(tag);
+ m = atom->map(itag);
if (m >= 0 && m < nlocal && mask[m] & groupbit) {
if (imageflag) {
xf[m][0] = x + ix*xprd;
diff --git a/src/force.cpp b/src/force.cpp
index 23699fdb2a..d486493c92 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -690,6 +690,40 @@ void Force::bounds(char *str, int nmax, int &nlo, int &nhi, int nmin)
error->all(FLERR,"Numeric index is out of bounds");
}
+/* ----------------------------------------------------------------------
+ compute bounds implied by numeric str with a possible wildcard asterik
+ 1 = lower bound, nmax = upper bound
+ 5 possibilities:
+ (1) i = i to i, (2) * = nmin to nmax,
+ (3) i* = i to nmax, (4) *j = nmin to j, (5) i*j = i to j
+ return nlo,nhi
+------------------------------------------------------------------------- */
+
+void Force::boundsbig(char *str, bigint nmax, bigint &nlo, bigint &nhi,
+ bigint nmin)
+{
+ char *ptr = strchr(str,'*');
+
+ if (ptr == NULL) {
+ nlo = nhi = ATOBIGINT(str);
+ } else if (strlen(str) == 1) {
+ nlo = nmin;
+ nhi = nmax;
+ } else if (ptr == str) {
+ nlo = nmin;
+ nhi = ATOBIGINT(ptr+1);
+ } else if (strlen(ptr+1) == 0) {
+ nlo = ATOBIGINT(str);
+ nhi = nmax;
+ } else {
+ nlo = ATOBIGINT(str);
+ nhi = ATOBIGINT(ptr+1);
+ }
+
+ if (nlo < nmin || nhi > nmax)
+ error->all(FLERR,"Numeric index is out of bounds");
+}
+
/* ----------------------------------------------------------------------
read a floating point value from a string
generate an error if not a legitimate floating point value
@@ -728,6 +762,24 @@ int Force::inumeric(const char *file, int line, char *str)
return atoi(str);
}
+/* ----------------------------------------------------------------------
+ read a big integer value from a string
+ generate an error if not a legitimate integer value
+ called by various commands to check validity of their arguments
+------------------------------------------------------------------------- */
+
+bigint Force::bnumeric(const char *file, int line, char *str)
+{
+ int n = strlen(str);
+ for (int i = 0; i < n; i++) {
+ if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue;
+ error->all(file,line,
+ "Expected integer parameter in input script or data file");
+ }
+
+ return ATOLL(str);
+}
+
/* ----------------------------------------------------------------------
memory usage of force classes
------------------------------------------------------------------------- */
diff --git a/src/force.h b/src/force.h
index c866656def..c2109d0899 100644
--- a/src/force.h
+++ b/src/force.h
@@ -100,8 +100,10 @@ class Force : protected Pointers {
void set_special(int, char **);
void bounds(char *, int, int &, int &, int nmin=1);
+ void boundsbig(char *, bigint, bigint &, bigint &, bigint nmin=1);
double numeric(const char *, int, char *);
int inumeric(const char *, int, char *);
+ bigint bnumeric(const char *, int, char *);
bigint memory_usage();
private:
diff --git a/src/group.cpp b/src/group.cpp
index d525c79281..22b9035cc4 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -174,7 +174,7 @@ void Group::assign(int narg, char **arg)
strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 ||
strcmp(arg[2],"<>") == 0)) {
- int condition,bound1,bound2;
+ int condition;
if (strcmp(arg[2],"<") == 0) condition = LT;
else if (strcmp(arg[2],"<=") == 0) condition = LE;
else if (strcmp(arg[2],">") == 0) condition = GT;
@@ -184,66 +184,127 @@ void Group::assign(int narg, char **arg)
else if (strcmp(arg[2],"<>") == 0) condition = BETWEEN;
else error->all(FLERR,"Illegal group command");
- bound1 = force->inumeric(FLERR,arg[3]);
+ tagint bound1,bound2;
+ if (sizeof(tagint) == sizeof(smallint))
+ bound1 = force->inumeric(FLERR,arg[3]);
+ else
+ bound1 = force->bnumeric(FLERR,arg[3]);
bound2 = -1;
if (condition == BETWEEN) {
if (narg != 5) error->all(FLERR,"Illegal group command");
- bound2 = force->inumeric(FLERR,arg[4]);
+ if (sizeof(tagint) == sizeof(smallint))
+ bound2 = force->inumeric(FLERR,arg[4]);
+ else
+ bound2 = force->bnumeric(FLERR,arg[4]);
} else if (narg != 4) error->all(FLERR,"Illegal group command");
+ tagint *tag = atom->tag;
int *attribute;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) attribute = atom->molecule;
- else if (category == ID) attribute = atom->tag;
+ else if (category == ID) attribute = NULL;
// add to group if meets condition
- if (condition == LT) {
- for (i = 0; i < nlocal; i++) if (attribute[i] < bound1) mask[i] |= bit;
- } else if (condition == LE) {
- for (i = 0; i < nlocal; i++) if (attribute[i] <= bound1) mask[i] |= bit;
- } else if (condition == GT) {
- for (i = 0; i < nlocal; i++) if (attribute[i] > bound1) mask[i] |= bit;
- } else if (condition == GE) {
- for (i = 0; i < nlocal; i++) if (attribute[i] >= bound1) mask[i] |= bit;
- } else if (condition == EQ) {
- for (i = 0; i < nlocal; i++) if (attribute[i] == bound1) mask[i] |= bit;
- } else if (condition == NEQ) {
- for (i = 0; i < nlocal; i++) if (attribute[i] != bound1) mask[i] |= bit;
- } else if (condition == BETWEEN) {
- for (i = 0; i < nlocal; i++)
- if (attribute[i] >= bound1 && attribute[i] <= bound2) mask[i] |= bit;
+ if (attribute) {
+ if (condition == LT) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] < bound1) mask[i] |= bit;
+ } else if (condition == LE) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] <= bound1) mask[i] |= bit;
+ } else if (condition == GT) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] > bound1) mask[i] |= bit;
+ } else if (condition == GE) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] >= bound1) mask[i] |= bit;
+ } else if (condition == EQ) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] == bound1) mask[i] |= bit;
+ } else if (condition == NEQ) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] != bound1) mask[i] |= bit;
+ } else if (condition == BETWEEN) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] >= bound1 && attribute[i] <= bound2)
+ mask[i] |= bit;
+ }
+ } else {
+ if (condition == LT) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] < bound1) mask[i] |= bit;
+ } else if (condition == LE) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] <= bound1) mask[i] |= bit;
+ } else if (condition == GT) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] > bound1) mask[i] |= bit;
+ } else if (condition == GE) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] >= bound1) mask[i] |= bit;
+ } else if (condition == EQ) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] == bound1) mask[i] |= bit;
+ } else if (condition == NEQ) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] != bound1) mask[i] |= bit;
+ } else if (condition == BETWEEN) {
+ for (i = 0; i < nlocal; i++)
+ if (tag[i] >= bound1 && tag[i] <= bound2)
+ mask[i] |= bit;
+ }
}
-
+
// args = list of values
} else {
+ tagint *tag = atom->tag;
int *attribute;
if (category == TYPE) attribute = atom->type;
else if (category == MOLECULE) attribute = atom->molecule;
- else if (category == ID) attribute = atom->tag;
-
+ else if (category == ID) attribute = NULL;
+
char *ptr;
- int start,stop,delta;
+ tagint start,stop,delta;
for (int iarg = 2; iarg < narg; iarg++) {
- if (strchr(arg[iarg],':')) {
- start = atoi(strtok(arg[iarg],":"));
- stop = atoi(strtok(NULL,":"));
- ptr = strtok(NULL,":");
- if (ptr) delta = atoi(ptr);
- else delta = 1;
+ if (attribute) {
+ if (strchr(arg[iarg],':')) {
+ start = atoi(strtok(arg[iarg],":"));
+ stop = atoi(strtok(NULL,":"));
+ ptr = strtok(NULL,":");
+ if (ptr) delta = atoi(ptr);
+ else delta = 1;
+ } else {
+ start = stop = atoi(arg[iarg]);
+ delta = 1;
+ }
} else {
- 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 {
+ start = stop = ATOTAGINT(arg[iarg]);
+ delta = 1;
+ }
}
// add to group if attribute matches value or sequence
- for (i = 0; i < nlocal; i++)
- if (attribute[i] >= start && attribute[i] <= stop &&
- (attribute[i]-start) % delta == 0) mask[i] |= bit;
+ if (attribute) {
+ for (i = 0; i < nlocal; i++)
+ if (attribute[i] >= start && attribute[i] <= stop &&
+ (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;
+ }
}
}
diff --git a/src/lammps.cpp b/src/lammps.cpp
index 618ac92c3b..a896c752d2 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -374,7 +374,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->all(FLERR,"Imageint setting in lmptype.h is invalid");
if (sizeof(tagint) < sizeof(smallint))
error->all(FLERR,"Tagint setting in lmptype.h is invalid");
- if (sizeof(bigint) < sizeof(tagint))
+ if (sizeof(bigint) < sizeof(imageint) || sizeof(bigint) < sizeof(tagint))
error->all(FLERR,"Bigint setting in lmptype.h is invalid");
int mpisize;
@@ -386,17 +386,17 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
#ifdef LAMMPS_SMALLBIG
if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
sizeof(tagint) != 4 || sizeof(bigint) != 8)
- error->all(FLERR,"Small, tag, big integers are not sized correctly");
+ error->all(FLERR,"Small to big integers are not sized correctly");
#endif
#ifdef LAMMPS_BIGBIG
if (sizeof(smallint) != 4 || sizeof(imageint) != 8 ||
sizeof(tagint) != 8 || sizeof(bigint) != 8)
- error->all(FLERR,"Small, tag, big integers are not sized correctly");
+ error->all(FLERR,"Small to big integers are not sized correctly");
#endif
#ifdef LAMMPS_SMALLSMALL
if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
sizeof(tagint) != 4 || sizeof(bigint) != 4)
- error->all(FLERR,"Small, tag, big integers are not sized correctly");
+ error->all(FLERR,"Small to big integers are not sized correctly");
#endif
// create CUDA class if USER-CUDA installed, unless explicitly switched off
diff --git a/src/library.cpp b/src/library.cpp
index f31f43b929..60b07548dd 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -315,7 +315,7 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
which the caller can cast to a (double *) which points to the values
returns a NULL if name is not recognized or not equal-style or atom-style
IMPORTANT: for both equal-style and atom-style variables,
- this function allocates memory to store the variable data,
+ this function allocates memory to store the variable data in
so the caller must free this memory to avoid a leak
e.g. for equal-style variables
double *dptr = (double *) lammps_extract_variable();
@@ -412,7 +412,7 @@ void lammps_gather_atoms(void *ptr, char *name,
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
- int *tag = lmp->atom->tag;
+ tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1)
@@ -438,7 +438,7 @@ void lammps_gather_atoms(void *ptr, char *name,
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
- int *tag = lmp->atom->tag;
+ tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
diff --git a/src/lmptype.h b/src/lmptype.h
index 1c3b783e26..a23aa9113b 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -54,7 +54,7 @@ namespace LAMMPS_NS {
#define SBBITS 30
#define NEIGHMASK 0x3FFFFFFF
-// default to 32-bit smallint and tagint, 64-bit bigint
+// default to 32-bit smallint and other ints, 64-bit bigint
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
#define LAMMPS_SMALLBIG
@@ -71,7 +71,7 @@ namespace LAMMPS_NS {
#endif
// for atomic problems that exceed 2 billion (2^31) atoms
-// 32-bit smallint and imageint and tagint, 64-bit bigint
+// 32-bit smallint/imageint/tagint, 64-bit bigint
#ifdef LAMMPS_SMALLBIG
@@ -84,6 +84,7 @@ typedef int64_t bigint;
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT64_MAX
+#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_BIGINT MPI_LL
#define TAGINT_FORMAT "%d"
@@ -101,7 +102,7 @@ typedef int64_t bigint;
// for molecular problems that exceed 2 billion (2^31) atoms
// or problems where atoms wrap around the periodic box more than 512 times
-// 32-bit smallint, 64-bit imageint and tagint and bigint
+// 32-bit smallint, 64-bit imageint/tagint/bigint
#ifdef LAMMPS_BIGBIG
@@ -114,6 +115,7 @@ typedef int64_t bigint;
#define MAXTAGINT INT64_MAX
#define MAXBIGINT INT64_MAX
+#define MPI_LMP_TAGINT MPI_LL
#define MPI_LMP_BIGINT MPI_LL
#define TAGINT_FORMAT "%" PRId64
@@ -130,7 +132,7 @@ typedef int64_t bigint;
#endif
// for machines that do not support 64-bit ints
-// 32-bit smallint and imageint and tagint and bigint
+// 32-bit smallint/imageint/tagint/bigint
#ifdef LAMMPS_SMALLSMALL
@@ -143,6 +145,7 @@ typedef int bigint;
#define MAXTAGINT INT_MAX
#define MAXBIGINT INT_MAX
+#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_BIGINT MPI_INT
#define TAGINT_FORMAT "%d"
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 669a34ce13..389a9cf797 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -402,29 +402,29 @@ void Molecule::read(int flag)
} else if (strcmp(keyword,"Bonds") == 0) {
if (nbonds == 0)
error->all(FLERR,"Molecule file has bonds but no nbonds setting");
- bondflag = 1;
+ bondflag = tag_require = 1;
bonds(flag,line);
} else if (strcmp(keyword,"Angles") == 0) {
if (nangles == 0)
error->all(FLERR,"Molecule file has angles but no nangles setting");
- angleflag = 1;
+ angleflag = tag_require = 1;
angles(flag,line);
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (ndihedrals == 0) error->all(FLERR,"Molecule file has dihedrals "
"but no ndihedrals setting");
- dihedralflag = 1;
+ dihedralflag = tag_require = 1;
dihedrals(flag,line);
} else if (strcmp(keyword,"Impropers") == 0) {
if (nimpropers == 0) error->all(FLERR,"Molecule file has impropers "
"but no nimpropers setting");
- improperflag = 1;
+ improperflag = tag_require = 1;
impropers(flag,line);
} else if (strcmp(keyword,"Special Bond Counts") == 0) {
nspecialflag = 1;
nspecial_read(flag,line);
} else if (strcmp(keyword,"Special Bonds") == 0) {
- specialflag = 1;
+ specialflag = tag_require = 1;
if (flag) special_read(line);
else skip_lines(natoms,line);
@@ -433,7 +433,7 @@ void Molecule::read(int flag)
if (flag) shakeflag_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Atoms") == 0) {
- shakeatomflag = 1;
+ shakeatomflag = tag_require = 1;
if (shaketypeflag) shakeflag = 1;
if (!shakeflagflag)
error->all(FLERR,"Molecule file shake flags not before shake atoms");
@@ -1007,6 +1007,7 @@ void Molecule::initialize()
shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
centerflag = massflag = comflag = inertiaflag = 0;
+ tag_require = 0;
x = NULL;
type = NULL;
diff --git a/src/molecule.h b/src/molecule.h
index 11a9c9a22d..7b35f77d1f 100644
--- a/src/molecule.h
+++ b/src/molecule.h
@@ -44,6 +44,10 @@ class Molecule : protected Pointers {
int centerflag,massflag,comflag,inertiaflag;
+ // 1 if molecule fields require atom IDs
+
+ int tag_require;
+
// attributes
double **x; // displacement of each atom from origin
diff --git a/src/neigh_bond.cpp b/src/neigh_bond.cpp
index a73ed41b44..17a6e55fd8 100644
--- a/src/neigh_bond.cpp
+++ b/src/neigh_bond.cpp
@@ -41,9 +41,9 @@ void Neighbor::bond_all()
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_bond = force->newton_bond;
int lostbond = output->thermo->lostbond;
@@ -57,8 +57,8 @@ void Neighbor::bond_all()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(FLERR,str);
}
@@ -98,9 +98,9 @@ void Neighbor::bond_partial()
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int newton_bond = force->newton_bond;
int lostbond = output->thermo->lostbond;
@@ -115,8 +115,8 @@ void Neighbor::bond_partial()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
+ sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(FLERR,str);
}
@@ -181,9 +181,9 @@ void Neighbor::angle_all()
int nlocal = atom->nlocal;
int *num_angle = atom->num_angle;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int newton_bond = force->newton_bond;
@@ -200,9 +200,9 @@ void Neighbor::angle_all()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Angle atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Angle atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
error->one(FLERR,str);
@@ -246,9 +246,9 @@ void Neighbor::angle_partial()
int nlocal = atom->nlocal;
int *num_angle = atom->num_angle;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom2 = atom->angle_atom2;
- int **angle_atom3 = atom->angle_atom3;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int newton_bond = force->newton_bond;
@@ -266,9 +266,9 @@ void Neighbor::angle_partial()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Angle atoms %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Angle atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
error->one(FLERR,str);
@@ -351,10 +351,10 @@ void Neighbor::dihedral_all()
int nlocal = atom->nlocal;
int *num_dihedral = atom->num_dihedral;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int newton_bond = force->newton_bond;
@@ -372,9 +372,10 @@ void Neighbor::dihedral_all()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Dihedral atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Dihedral atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
me,update->ntimestep);
@@ -422,10 +423,10 @@ void Neighbor::dihedral_partial()
int nlocal = atom->nlocal;
int *num_dihedral = atom->num_dihedral;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int newton_bond = force->newton_bond;
@@ -444,9 +445,10 @@ void Neighbor::dihedral_partial()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Dihedral atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Dihedral atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
me,update->ntimestep);
@@ -550,10 +552,10 @@ void Neighbor::improper_all()
int nlocal = atom->nlocal;
int *num_improper = atom->num_improper;
- int **improper_atom1 = atom->improper_atom1;
- int **improper_atom2 = atom->improper_atom2;
- int **improper_atom3 = atom->improper_atom3;
- int **improper_atom4 = atom->improper_atom4;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int newton_bond = force->newton_bond;
@@ -571,9 +573,10 @@ void Neighbor::improper_all()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Improper atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Improper atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
me,update->ntimestep);
@@ -621,10 +624,10 @@ void Neighbor::improper_partial()
int nlocal = atom->nlocal;
int *num_improper = atom->num_improper;
- int **improper_atom1 = atom->improper_atom1;
- int **improper_atom2 = atom->improper_atom2;
- int **improper_atom3 = atom->improper_atom3;
- int **improper_atom4 = atom->improper_atom4;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int newton_bond = force->newton_bond;
@@ -643,9 +646,10 @@ void Neighbor::improper_partial()
nmissing++;
if (lostbond == ERROR) {
char str[128];
- sprintf(str,
- "Improper atoms %d %d %d %d missing on proc %d at step "
- BIGINT_FORMAT,
+ sprintf(str,"Improper atoms "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT
+ " missing on proc %d at step " BIGINT_FORMAT,
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
me,update->ntimestep);
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index 0c830b3720..7b536f4699 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -32,9 +32,9 @@ void Neighbor::full_nsq(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -115,9 +115,9 @@ void Neighbor::full_nsq_ghost(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -212,9 +212,9 @@ void Neighbor::full_bin(NeighList *list)
bin_atoms();
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -303,9 +303,9 @@ void Neighbor::full_bin_ghost(NeighList *list)
bin_atoms();
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -424,9 +424,9 @@ void Neighbor::full_multi(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index 204988e230..465e6af863 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -37,7 +37,8 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
double *shearptr;
NeighList *listgranhistory;
- int *npartner,**partner;
+ int *npartner;
+ tagint **partner;
double (**shearpartner)[3];
int **firsttouch;
double **firstshear;
@@ -46,7 +47,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
double **x = atom->x;
double *radius = atom->radius;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
@@ -174,7 +175,7 @@ void Neighbor::granular_nsq_newton(NeighList *list)
double **x = atom->x;
double *radius = atom->radius;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
@@ -264,7 +265,8 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
double *shearptr;
NeighList *listgranhistory;
- int *npartner,**partner;
+ int *npartner;
+ tagint **partner;
double (**shearpartner)[3];
int **firsttouch;
double **firstshear;
@@ -279,7 +281,7 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
double **x = atom->x;
double *radius = atom->radius;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
index ef55cb5ba1..75736e97d2 100644
--- a/src/neigh_half_bin.cpp
+++ b/src/neigh_half_bin.cpp
@@ -39,9 +39,9 @@ void Neighbor::half_bin_no_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -134,9 +134,9 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -256,9 +256,9 @@ void Neighbor::half_bin_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -375,9 +375,9 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
index 46a76be6db..fddc683fb7 100644
--- a/src/neigh_half_multi.cpp
+++ b/src/neigh_half_multi.cpp
@@ -41,9 +41,9 @@ void Neighbor::half_multi_no_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -140,9 +140,9 @@ void Neighbor::half_multi_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -267,9 +267,9 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
index 8446c9d982..f8fad972bb 100644
--- a/src/neigh_half_nsq.cpp
+++ b/src/neigh_half_nsq.cpp
@@ -32,9 +32,9 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -116,9 +116,9 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -221,9 +221,9 @@ void Neighbor::half_nsq_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index 8d1ea14ae5..738426abdb 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -36,9 +36,9 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -179,9 +179,9 @@ void Neighbor::respa_nsq_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -344,9 +344,9 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -497,9 +497,9 @@ void Neighbor::respa_bin_newton(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
@@ -691,9 +691,9 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
// loop over each atom, storing neighbors
- int **special = atom->special;
+ tagint **special = atom->special;
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
diff --git a/src/neighbor.h b/src/neighbor.h
index 13590dd473..751e155231 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -284,8 +284,8 @@ class Neighbor : protected Pointers {
// if it is and special flag is 2 (otherwise), return 1,2,3
// for which level of neighbor it is (and which coeff it maps to)
- inline int find_special(const int *list, const int *nspecial,
- const int tag) const {
+ inline int find_special(const tagint *list, const int *nspecial,
+ const tagint tag) const {
const int n1 = nspecial[0];
const int n2 = nspecial[1];
const int n3 = nspecial[2];
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 52f7f50820..c32976d28a 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -138,243 +138,338 @@ void ReadData::command(int narg, char **arg)
} else error->all(FLERR,"Illegal read_data command");
}
- // scan data file to determine max topology needed per atom
- // allocate initial topology arrays
- if (atom->molecular) {
- if (me == 0) {
- if (screen) fprintf(screen,"Scanning data file ...\n");
- open(arg[0]);
- header(0);
- scan(atom->bond_per_atom,atom->angle_per_atom,
- atom->dihedral_per_atom,atom->improper_per_atom);
- if (compressed) pclose(fp);
- else fclose(fp);
- atom->bond_per_atom += atom->extra_bond_per_atom;
- atom->angle_per_atom += atom->extra_angle_per_atom;
- atom->dihedral_per_atom += atom->extra_dihedral_per_atom;
- atom->improper_per_atom += atom->extra_improper_per_atom;
- }
+ // perform 1-pass read if no molecular topoogy in file
+ // perform 2-pass read if molecular topology
+ // 1st pass calculates max topology/atom
- MPI_Bcast(&atom->bond_per_atom,1,MPI_INT,0,world);
- MPI_Bcast(&atom->angle_per_atom,1,MPI_INT,0,world);
- MPI_Bcast(&atom->dihedral_per_atom,1,MPI_INT,0,world);
- MPI_Bcast(&atom->improper_per_atom,1,MPI_INT,0,world);
+ int atomflag,topoflag;
+ int bondflag,angleflag,dihedralflag,improperflag;
+ int ellipsoidflag,lineflag,triflag,bodyflag;
- } else
- atom->bond_per_atom = atom->angle_per_atom =
- atom->dihedral_per_atom = atom->improper_per_atom = 0;
+ atomflag = topoflag = 0;
+ bondflag = angleflag = dihedralflag = improperflag = 0;
+ ellipsoidflag = lineflag = triflag = bodyflag = 0;
- // read header info
+ int firstpass = 1;
- if (me == 0) {
- if (screen) fprintf(screen,"Reading data file ...\n");
- open(arg[0]);
- } else fp = NULL;
- header(1);
- domain->box_exist = 1;
-
- // problem setup using info from header
+ while (1) {
- update->ntimestep = 0;
+ // open file on proc 0
- int n;
- if (comm->nprocs == 1) n = static_cast<int> (atom->natoms);
- else n = static_cast<int> (LB_FACTOR * atom->natoms / comm->nprocs);
+ if (me == 0) {
+ if (firstpass && screen) fprintf(screen,"Reading data file ...\n");
+ open(arg[0]);
+ } else fp = NULL;
+
+ // read header info
+
+ header();
+
+ // problem setup using info from header
+ // 1st pass only
+
+ if (firstpass) {
+ domain->box_exist = 1;
+ update->ntimestep = 0;
+
+ int n;
+ if (comm->nprocs == 1) n = static_cast<int> (atom->natoms);
+ else n = static_cast<int> (LB_FACTOR * atom->natoms / comm->nprocs);
+
+ atom->allocate_type_arrays();
+ atom->avec->grow(n);
+ n = atom->nmax;
+
+ domain->print_box(" ");
+ domain->set_initial_box();
+ domain->set_global_box();
+ comm->set_proc_grid();
+ domain->set_local_box();
+ }
- atom->allocate_type_arrays();
- atom->avec->grow(n);
- n = atom->nmax;
+ // customize for new sections
+ // read rest of file in free format
- domain->print_box(" ");
- domain->set_initial_box();
- domain->set_global_box();
- comm->set_proc_grid();
- domain->set_local_box();
+ while (strlen(keyword)) {
- // customize for new sections
- // read rest of file in free format
+ // if special fix matches, it processes section
- int atomflag = 0;
+ if (nfix) {
+ int i;
+ for (i = 0; i < nfix; i++)
+ if (strcmp(keyword,fix_section[i]) == 0) {
+ if (firstpass) fix(i,keyword);
+ else skip_lines(modify->fix[fix_index[i]]->
+ read_data_skip_lines(keyword));
+ parse_keyword(0);
+ break;
+ }
+ if (i < nfix) continue;
+ }
- while (strlen(keyword)) {
+ if (strcmp(keyword,"Atoms") == 0) {
+ atomflag = 1;
+ if (firstpass) atoms();
+ else skip_lines(atom->natoms);
+ } else if (strcmp(keyword,"Velocities") == 0) {
+ if (atomflag == 0)
+ error->all(FLERR,"Must read Atoms before Velocities");
+ if (firstpass) velocities();
+ else skip_lines(atom->natoms);
+
+ } else if (strcmp(keyword,"Bonds") == 0) {
+ topoflag = bondflag = 1;
+ if (atom->avec->bonds_allow == 0)
+ error->all(FLERR,"Invalid data file section: Bonds");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
+ bonds(firstpass);
+ } else if (strcmp(keyword,"Angles") == 0) {
+ topoflag = angleflag = 1;
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: Angles");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
+ angles(firstpass);
+ } else if (strcmp(keyword,"Dihedrals") == 0) {
+ topoflag = dihedralflag = 1;
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: Dihedrals");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
+ dihedrals(firstpass);
+ } else if (strcmp(keyword,"Impropers") == 0) {
+ topoflag = improperflag = 1;
+ if (atom->avec->impropers_allow == 0)
+ error->all(FLERR,"Invalid data file section: Impropers");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
+ impropers(firstpass);
+
+ } else if (strcmp(keyword,"Ellipsoids") == 0) {
+ ellipsoidflag = 1;
+ if (!avec_ellipsoid)
+ error->all(FLERR,"Invalid data file section: Ellipsoids");
+ if (atomflag == 0)
+ error->all(FLERR,"Must read Atoms before Ellipsoids");
+ if (firstpass)
+ bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
+ else skip_lines(nellipsoids);
+ } else if (strcmp(keyword,"Lines") == 0) {
+ lineflag = 1;
+ if (!avec_line)
+ error->all(FLERR,"Invalid data file section: Lines");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines");
+ if (firstpass) bonus(nlines,(AtomVec *) avec_line,"lines");
+ else skip_lines(nlines);
+ } else if (strcmp(keyword,"Triangles") == 0) {
+ triflag = 1;
+ if (!avec_tri)
+ error->all(FLERR,"Invalid data file section: Triangles");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
+ if (firstpass) bonus(ntris,(AtomVec *) avec_tri,"triangles");
+ else skip_lines(ntris);
+ } else if (strcmp(keyword,"Bodies") == 0) {
+ bodyflag = 1;
+ if (!avec_body)
+ error->all(FLERR,"Invalid data file section: Bodies");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bodies");
+ bodies(firstpass);
+
+ } else if (strcmp(keyword,"Masses") == 0) {
+ if (firstpass) mass();
+ else skip_lines(atom->ntypes);
+ } else if (strcmp(keyword,"Pair Coeffs") == 0) {
+ if (force->pair == NULL)
+ error->all(FLERR,"Must define pair_style before Pair Coeffs");
+ if (firstpass) paircoeffs();
+ else skip_lines(atom->ntypes);
+ } else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
+ if (force->pair == NULL)
+ error->all(FLERR,"Must define pair_style before PairIJ Coeffs");
+ if (firstpass) pairIJcoeffs();
+ else skip_lines(atom->ntypes*(atom->ntypes+1)/2);
+ } else if (strcmp(keyword,"Bond Coeffs") == 0) {
+ if (atom->avec->bonds_allow == 0)
+ error->all(FLERR,"Invalid data file section: Bond Coeffs");
+ if (force->bond == NULL)
+ error->all(FLERR,"Must define bond_style before Bond Coeffs");
+ if (firstpass) bondcoeffs();
+ else skip_lines(atom->nbondtypes);
+ } else if (strcmp(keyword,"Angle Coeffs") == 0) {
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: Angle Coeffs");
+ if (force->angle == NULL)
+ error->all(FLERR,"Must define angle_style before Angle Coeffs");
+ if (firstpass) anglecoeffs(0);
+ else skip_lines(atom->nangletypes);
+ } else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
+ if (firstpass) dihedralcoeffs(0);
+ else skip_lines(atom->ndihedraltypes);
+ } else if (strcmp(keyword,"Improper Coeffs") == 0) {
+ if (atom->avec->impropers_allow == 0)
+ error->all(FLERR,"Invalid data file section: Improper Coeffs");
+ if (force->improper == NULL)
+ error->all(FLERR,"Must define improper_style before Improper Coeffs");
+ if (firstpass) impropercoeffs(0);
+ else skip_lines(atom->nimpropertypes);
+
+ } else if (strcmp(keyword,"BondBond Coeffs") == 0) {
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: BondBond Coeffs");
+ if (force->angle == NULL)
+ error->all(FLERR,"Must define angle_style before BondBond Coeffs");
+ if (firstpass) anglecoeffs(1);
+ else skip_lines(atom->nangletypes);
+ } else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
+ if (atom->avec->angles_allow == 0)
+ error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
+ if (force->angle == NULL)
+ error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
+ if (firstpass) anglecoeffs(2);
+ else skip_lines(atom->nangletypes);
+
+ } else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,
+ "Invalid data file section: MiddleBondTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before "
+ "MiddleBondTorsion Coeffs");
+ if (firstpass) dihedralcoeffs(1);
+ else skip_lines(atom->ndihedraltypes);
+ } else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before EndBondTorsion Coeffs");
+ if (firstpass) dihedralcoeffs(2);
+ else skip_lines(atom->ndihedraltypes);
+ } else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before AngleTorsion Coeffs");
+ if (firstpass) dihedralcoeffs(3);
+ else skip_lines(atom->ndihedraltypes);
+ } else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,
+ "Invalid data file section: AngleAngleTorsion Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before "
+ "AngleAngleTorsion Coeffs");
+ if (firstpass) dihedralcoeffs(4);
+ else skip_lines(atom->ndihedraltypes);
+ } else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
+ if (atom->avec->dihedrals_allow == 0)
+ error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
+ if (force->dihedral == NULL)
+ error->all(FLERR,
+ "Must define dihedral_style before BondBond13 Coeffs");
+ if (firstpass) dihedralcoeffs(5);
+ else skip_lines(atom->ndihedraltypes);
+
+ } else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
+ if (atom->avec->impropers_allow == 0)
+ error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
+ if (force->improper == NULL)
+ error->all(FLERR,
+ "Must define improper_style before AngleAngle Coeffs");
+ if (firstpass) impropercoeffs(1);
+ else skip_lines(atom->nimpropertypes);
+
+ } else {
+ char str[128];
+ sprintf(str,"Unknown identifier in data file: %s",keyword);
+ error->all(FLERR,str);
+ }
+
+ parse_keyword(0);
+ }
- // allow special fixes first chance to match and process the section
- // if fix matches, continue to next section
+ // error if natoms > 0 yet no atoms were read
- if (nfix) {
- for (n = 0; n < nfix; n++)
- if (strcmp(keyword,fix_section[n]) == 0) {
- fix(n,keyword);
- parse_keyword(0,1);
- break;
- }
- if (n < nfix) continue;
+ if (atom->natoms > 0 && atomflag == 0)
+ error->all(FLERR,"No atoms in data file");
+
+ // close file
+
+ if (me == 0) {
+ if (compressed) pclose(fp);
+ else fclose(fp);
}
- if (strcmp(keyword,"Atoms") == 0) {
- atoms();
- atomflag = 1;
- } else if (strcmp(keyword,"Velocities") == 0) {
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Velocities");
- velocities();
-
- } else if (strcmp(keyword,"Ellipsoids") == 0) {
- if (!avec_ellipsoid)
- error->all(FLERR,"Invalid data file section: Ellipsoids");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Ellipsoids");
- bonus(nellipsoids,(AtomVec *) avec_ellipsoid,"ellipsoids");
- } else if (strcmp(keyword,"Lines") == 0) {
- if (!avec_line)
- error->all(FLERR,"Invalid data file section: Lines");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Lines");
- bonus(nlines,(AtomVec *) avec_line,"lines");
- } else if (strcmp(keyword,"Triangles") == 0) {
- if (!avec_tri)
- error->all(FLERR,"Invalid data file section: Triangles");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
- bonus(ntris,(AtomVec *) avec_tri,"triangles");
- } else if (strcmp(keyword,"Bodies") == 0) {
- if (!avec_body)
- error->all(FLERR,"Invalid data file section: Bodies");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bodies");
- bodies();
-
- } else if (strcmp(keyword,"Bonds") == 0) {
- if (atom->avec->bonds_allow == 0)
- error->all(FLERR,"Invalid data file section: Bonds");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bonds");
- bonds();
- } else if (strcmp(keyword,"Angles") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: Angles");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Angles");
- angles();
- } else if (strcmp(keyword,"Dihedrals") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: Dihedrals");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Dihedrals");
- dihedrals();
- } else if (strcmp(keyword,"Impropers") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Invalid data file section: Impropers");
- if (atomflag == 0) error->all(FLERR,"Must read Atoms before Impropers");
- impropers();
-
- } else if (strcmp(keyword,"Masses") == 0) {
- mass();
- } else if (strcmp(keyword,"Pair Coeffs") == 0) {
- if (force->pair == NULL)
- error->all(FLERR,"Must define pair_style before Pair Coeffs");
- paircoeffs();
- } else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
- if (force->pair == NULL)
- error->all(FLERR,"Must define pair_style before PairIJ Coeffs");
- pairIJcoeffs();
- } else if (strcmp(keyword,"Bond Coeffs") == 0) {
- if (atom->avec->bonds_allow == 0)
- error->all(FLERR,"Invalid data file section: Bond Coeffs");
- if (force->bond == NULL)
- error->all(FLERR,"Must define bond_style before Bond Coeffs");
- bondcoeffs();
- } else if (strcmp(keyword,"Angle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: Angle Coeffs");
- if (force->angle == NULL)
- error->all(FLERR,"Must define angle_style before Angle Coeffs");
- anglecoeffs(0);
- } else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: Dihedral Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,"Must define dihedral_style before Dihedral Coeffs");
- dihedralcoeffs(0);
- } else if (strcmp(keyword,"Improper Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Invalid data file section: Improper Coeffs");
- if (force->improper == NULL)
- error->all(FLERR,"Must define improper_style before Improper Coeffs");
- impropercoeffs(0);
-
- } else if (strcmp(keyword,"BondBond Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: BondBond Coeffs");
- if (force->angle == NULL)
- error->all(FLERR,"Must define angle_style before BondBond Coeffs");
- anglecoeffs(1);
- } else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->all(FLERR,"Invalid data file section: BondAngle Coeffs");
- if (force->angle == NULL)
- error->all(FLERR,"Must define angle_style before BondAngle Coeffs");
- anglecoeffs(2);
-
- } else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before "
- "MiddleBondTorsion Coeffs");
- dihedralcoeffs(1);
- } else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before EndBondTorsion Coeffs");
- dihedralcoeffs(2);
- } else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: AngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before AngleTorsion Coeffs");
- dihedralcoeffs(3);
- } else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,
- "Must define dihedral_style before "
- "AngleAngleTorsion Coeffs");
- dihedralcoeffs(4);
- } else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->all(FLERR,"Invalid data file section: BondBond13 Coeffs");
- if (force->dihedral == NULL)
- error->all(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
- dihedralcoeffs(5);
-
- } else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->all(FLERR,"Invalid data file section: AngleAngle Coeffs");
- if (force->improper == NULL)
- error->all(FLERR,"Must define improper_style before AngleAngle Coeffs");
- impropercoeffs(1);
+ // done if this was 2nd pass
- } else {
- char str[128];
- sprintf(str,"Unknown identifier in data file: %s",keyword);
- error->all(FLERR,str);
- }
+ if (!firstpass) break;
- parse_keyword(0,1);
- }
+ // at end of 1st pass, error check for required sections
+ // customize for new sections
- // close file
+ if ((atom->nbonds && !bondflag) || (atom->nangles && !angleflag) ||
+ (atom->ndihedrals && !dihedralflag) ||
+ (atom->nimpropers && !improperflag))
+ error->one(FLERR,"Needed molecular topology not in data file");
- if (me == 0) {
- if (compressed) pclose(fp);
- else fclose(fp);
- }
+ if ((nellipsoids && !ellipsoidflag) || (nlines && !lineflag) ||
+ (ntris && !triflag) || (nbodies && !bodyflag))
+ error->one(FLERR,"Needed bonus data not in data file");
- // error if natoms > 0 yet no atoms were read
+ // break out of loop if no molecular topology in file
+ // else make 2nd pass
+
+ if (!topoflag) break;
+ firstpass = 0;
- if (atom->natoms > 0 && atomflag == 0)
- error->all(FLERR,"No atoms in data file");
+ // reallocate bond,angle,diehdral,improper arrays via grow(),
+ // using new bond,angle,dihedral,improper per-atom values from 1st pass
+ // should leave other atom arrays unchanged, since already nmax in length
- // create bond topology now that system is defined
+ if (bondflag) {
+ memory->destroy(atom->bond_type);
+ memory->destroy(atom->bond_atom);
+ atom->bond_type = NULL;
+ atom->bond_atom = NULL;
+ }
+ if (angleflag) {
+ memory->destroy(atom->angle_type);
+ memory->destroy(atom->angle_atom1);
+ memory->destroy(atom->angle_atom2);
+ memory->destroy(atom->angle_atom3);
+ atom->angle_type = NULL;
+ atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
+ }
+ if (dihedralflag) {
+ memory->destroy(atom->dihedral_type);
+ memory->destroy(atom->dihedral_atom1);
+ memory->destroy(atom->dihedral_atom2);
+ memory->destroy(atom->dihedral_atom3);
+ memory->destroy(atom->dihedral_atom4);
+ atom->dihedral_type = NULL;
+ atom->dihedral_atom1 = atom->dihedral_atom2 =
+ atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
+ }
+ if (improperflag) {
+ memory->destroy(atom->improper_type);
+ memory->destroy(atom->improper_atom1);
+ memory->destroy(atom->improper_atom2);
+ memory->destroy(atom->improper_atom3);
+ memory->destroy(atom->improper_atom4);
+ atom->improper_type = NULL;
+ atom->improper_atom1 = atom->improper_atom2 =
+ atom->improper_atom3 = atom->improper_atom4 = NULL;
+ }
+
+ atom->avec->grow(atom->nmax);
+ }
+
+ // create special bond lists for molecular systems
if (atom->molecular) {
Special special(lmp);
@@ -384,8 +479,6 @@ void ReadData::command(int narg, char **arg)
/* ----------------------------------------------------------------------
read free-format header of data file
- if flag = 0, only called by proc 0
- if flag = 1, called by all procs so bcast lines as read them
1st line and blank lines are skipped
non-blank lines are checked for header keywords and leading value is read
header ends with EOF or non-blank line containing no header keyword
@@ -393,7 +486,7 @@ void ReadData::command(int narg, char **arg)
else line has first keyword line for rest of file
------------------------------------------------------------------------- */
-void ReadData::header(int flag)
+void ReadData::header()
{
int n;
char *ptr;
@@ -426,7 +519,7 @@ void ReadData::header(int flag)
if (fgets(line,MAXLINE,fp) == NULL) n = 0;
else n = strlen(line) + 1;
}
- if (flag) MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(&n,1,MPI_INT,0,world);
// if n = 0 then end-of-file so return with blank line
@@ -435,9 +528,7 @@ void ReadData::header(int flag)
return;
}
- // bcast line if flag is set
-
- if (flag) MPI_Bcast(line,n,MPI_CHAR,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
// trim anything from '#' onward
// if line is blank, continue
@@ -525,17 +616,17 @@ void ReadData::header(int flag)
// error check on total system size
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT ||
- atom->nbonds < 0 || atom->nbonds > MAXBIGINT ||
- atom->nangles < 0 || atom->nangles > MAXBIGINT ||
- atom->ndihedrals < 0 || atom->ndihedrals > MAXBIGINT ||
- atom->nimpropers < 0 || atom->nimpropers > MAXBIGINT) {
+ if (atom->natoms < 0 || atom->natoms >= MAXBIGINT ||
+ atom->nbonds < 0 || atom->nbonds >= MAXBIGINT ||
+ atom->nangles < 0 || atom->nangles >= MAXBIGINT ||
+ atom->ndihedrals < 0 || atom->ndihedrals >= MAXBIGINT ||
+ atom->nimpropers < 0 || atom->nimpropers >= MAXBIGINT) {
if (me == 0) error->one(FLERR,"System in data file is too big");
}
// check that exiting string is a valid section keyword
- parse_keyword(1,flag);
+ parse_keyword(1);
for (n = 0; n < NSECTIONS; n++)
if (strcmp(keyword,section_keywords[n]) == 0) break;
if (n == NSECTIONS && me == 0) {
@@ -577,6 +668,11 @@ void ReadData::atoms()
{
int i,m,nchunk,eof;
+ if (me == 0) {
+ if (screen) fprintf(screen," reading atoms ...\n");
+ if (logfile) fprintf(logfile," reading atoms ...\n");
+ }
+
bigint nread = 0;
bigint natoms = atom->natoms;
@@ -600,41 +696,14 @@ void ReadData::atoms()
if (natoms != atom->natoms)
error->all(FLERR,"Did not assign all atoms correctly");
+
+ // check that atom IDs are valid
- // if any atom ID < 0, error
- // if all atom IDs = 0, tag_enable = 0
- // if any atom ID > 0, error if any atom ID == 0
- // not checking if atom IDs > natoms or are unique
-
- int nlocal = atom->nlocal;
- int *tag = atom->tag;
-
- int flag = 0;
- for (int i = 0; i < nlocal; i++)
- if (tag[i] < 0) flag = 1;
- int flag_all;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all)
- error->all(FLERR,"Invalid atom ID in Atoms section of data file");
-
- flag = 0;
- for (int i = 0; i < nlocal; i++)
- if (tag[i] > 0) flag = 1;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
- if (flag_all == 0) atom->tag_enable = 0;
-
- if (atom->tag_enable) {
- flag = 0;
- for (int i = 0; i < nlocal; i++)
- if (tag[i] == 0) flag = 1;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
- if (flag_all)
- error->all(FLERR,"Invalid atom ID in Atoms section of data file");
- }
+ atom->tag_check();
- // create global mapping
+ // if molecular system or user-requested, create global mapping of atoms
- if (atom->map_style) {
+ if (atom->molecular || atom->map_user) {
atom->map_init();
atom->map_set();
}
@@ -649,10 +718,14 @@ void ReadData::velocities()
{
int i,m,nchunk,eof;
+ if (me == 0) {
+ if (screen) fprintf(screen," reading velocities ...\n");
+ if (logfile) fprintf(logfile," reading velocities ...\n");
+ }
+
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
- atom->map_style = 1;
atom->map_init();
atom->map_set();
}
@@ -680,149 +753,66 @@ void ReadData::velocities()
}
/* ----------------------------------------------------------------------
- read all bonus data
- to find atoms, must build atom map if not a molecular system
+ scan or read all bonds
------------------------------------------------------------------------- */
-void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
+void ReadData::bonds(int firstpass)
{
- int i,m,nchunk,eof;
-
- int mapflag = 0;
- if (atom->map_style == 0) {
- mapflag = 1;
- atom->map_style = 1;
- atom->map_init();
- atom->map_set();
- }
-
- bigint nread = 0;
- bigint natoms = nbonus;
-
- while (nread < natoms) {
- nchunk = MIN(natoms-nread,CHUNK);
- eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
- if (eof) error->all(FLERR,"Unexpected end of data file");
- atom->data_bonus(nchunk,buffer,ptr);
- nread += nchunk;
- }
-
- if (mapflag) {
- atom->map_delete();
- atom->map_style = 0;
- }
-
if (me == 0) {
- if (screen) fprintf(screen," " BIGINT_FORMAT " %s\n",natoms,type);
- if (logfile) fprintf(logfile," " BIGINT_FORMAT " %s\n",natoms,type);
- }
-}
-
-/* ----------------------------------------------------------------------
- read all body data
- variable amount of info per body, described by ninteger and ndouble
- to find atoms, must build atom map if not a molecular system
-------------------------------------------------------------------------- */
-
-void ReadData::bodies()
-{
- int i,m,nchunk,nmax,ninteger,ndouble,tmp,onebody;
- char *eof;
-
- int mapflag = 0;
- if (atom->map_style == 0) {
- mapflag = 1;
- atom->map_style = 1;
- atom->map_init();
- atom->map_set();
- }
-
- // nmax = max # of bodies to read in this chunk
- // nchunk = actual # read
-
- bigint nread = 0;
- bigint natoms = nbodies;
-
- while (nread < natoms) {
- if (natoms-nread > CHUNK) nmax = CHUNK;
- else nmax = natoms-nread;
-
- if (me == 0) {
- nchunk = 0;
- nlines = 0;
- m = 0;
-
- while (nchunk < nmax && nlines <= CHUNK-MAXBODY) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
- m += strlen(&buffer[m]);
-
- onebody = 0;
- if (ninteger) onebody += (ninteger-1)/10 + 1;
- if (ndouble) onebody += (ndouble-1)/10 + 1;
- if (onebody+1 > MAXBODY)
- error->one(FLERR,
- "Too many lines in one body in data file - boost MAXBODY");
-
- for (i = 0; i < onebody; i++) {
- eof = fgets(&buffer[m],MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- m += strlen(&buffer[m]);
- }
-
- nchunk++;
- nlines += onebody+1;
- }
-
- if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
- m++;
+ if (firstpass) {
+ if (screen) fprintf(screen," scanning bonds ...\n");
+ if (logfile) fprintf(logfile," scanning bonds ...\n");
+ } else {
+ if (screen) fprintf(screen," reading bonds ...\n");
+ if (logfile) fprintf(logfile," reading bonds ...\n");
}
-
- MPI_Bcast(&nchunk,1,MPI_INT,0,world);
- MPI_Bcast(&m,1,MPI_INT,0,world);
- MPI_Bcast(buffer,m,MPI_CHAR,0,world);
-
- atom->data_bodies(nchunk,buffer,avec_body);
- nread += nchunk;
}
- if (mapflag) {
- atom->map_delete();
- atom->map_style = 0;
- }
+ // allocate count if firstpass
- if (me == 0) {
- if (screen) fprintf(screen," " BIGINT_FORMAT " bodies\n",natoms);
- if (logfile) fprintf(logfile," " BIGINT_FORMAT " bodies\n",natoms);
+ int nlocal = atom->nlocal;
+ int *count = NULL;
+ if (firstpass) {
+ memory->create(count,nlocal,"read_data:count");
+ for (int i = 0; i < nlocal; i++) count[i] = 0;
}
-}
-/* ---------------------------------------------------------------------- */
-
-void ReadData::bonds()
-{
- int i,m,nchunk,eof;
+ // read and process bonds
+ int nchunk,eof;
bigint nread = 0;
bigint nbonds = atom->nbonds;
- bigint natoms = atom->natoms;
-
while (nread < nbonds) {
nchunk = MIN(nbonds-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
- atom->data_bonds(nchunk,buffer);
+ atom->data_bonds(nchunk,buffer,count);
nread += nchunk;
}
- // check that bonds were assigned correctly
+ // if firstpass: tally max bond/atom and return
+
+ if (firstpass) {
+ int max = 0;
+ for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
+ int maxall;
+ MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
+
+ if (me == 0) {
+ if (screen) fprintf(screen," %d = max bonds/atom\n",maxall);
+ if (logfile) fprintf(logfile," %d = max bonds/atom\n",maxall);
+ }
+ atom->bond_per_atom = maxall;
+ memory->destroy(count);
+ return;
+ }
+
+ // if 2nd pass: check that bonds were assigned correctly
- int nlocal = atom->nlocal;
- bigint sum;
bigint n = 0;
- for (i = 0; i < nlocal; i++) n += atom->num_bond[i];
+ for (int i = 0; i < nlocal; i++) n += atom->num_bond[i];
+ bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 2;
@@ -831,16 +821,39 @@ void ReadData::bonds()
if (screen) fprintf(screen," " BIGINT_FORMAT " bonds\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " bonds\n",sum/factor);
}
+
if (sum != factor*atom->nbonds)
error->all(FLERR,"Bonds assigned incorrectly");
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ scan or read all angles
+------------------------------------------------------------------------- */
-void ReadData::angles()
+void ReadData::angles(int firstpass)
{
- int i,m,nchunk,eof;
+ if (me == 0) {
+ if (firstpass) {
+ if (screen) fprintf(screen," scanning angles ...\n");
+ if (logfile) fprintf(logfile," scanning angles ...\n");
+ } else {
+ if (screen) fprintf(screen," reading angles ...\n");
+ if (logfile) fprintf(logfile," reading angles ...\n");
+ }
+ }
+
+ // allocate count if firstpass
+ int nlocal = atom->nlocal;
+ int *count = NULL;
+ if (firstpass) {
+ memory->create(count,nlocal,"read_data:count");
+ for (int i = 0; i < nlocal; i++) count[i] = 0;
+ }
+
+ // read and process angles
+
+ int nchunk,eof;
bigint nread = 0;
bigint nangles = atom->nangles;
@@ -848,16 +861,32 @@ void ReadData::angles()
nchunk = MIN(nangles-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
- atom->data_angles(nchunk,buffer);
+ atom->data_angles(nchunk,buffer,count);
nread += nchunk;
}
- // check that ang
+ // if firstpass: tally max angle/atom and return
+
+ if (firstpass) {
+ int max = 0;
+ for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
+ int maxall;
+ MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
+
+ if (me == 0) {
+ if (screen) fprintf(screen," %d = max angles/atom\n",maxall);
+ if (logfile) fprintf(logfile," %d = max angles/atom\n",maxall);
+ }
+ atom->angle_per_atom = maxall;
+ memory->destroy(count);
+ return;
+ }
+
+ // if 2nd pass: check that angles were assigned correctly
- int nlocal = atom->nlocal;
- bigint sum;
bigint n = 0;
- for (i = 0; i < nlocal; i++) n += atom->num_angle[i];
+ for (int i = 0; i < nlocal; i++) n += atom->num_angle[i];
+ bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 3;
@@ -866,16 +895,39 @@ void ReadData::angles()
if (screen) fprintf(screen," " BIGINT_FORMAT " angles\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " angles\n",sum/factor);
}
+
if (sum != factor*atom->nangles)
error->all(FLERR,"Angles assigned incorrectly");
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ scan or read all dihedrals
+------------------------------------------------------------------------- */
-void ReadData::dihedrals()
+void ReadData::dihedrals(int firstpass)
{
- int i,m,nchunk,eof;
+ if (me == 0) {
+ if (firstpass) {
+ if (screen) fprintf(screen," scanning dihedrals ...\n");
+ if (logfile) fprintf(logfile," scanning dihedrals ...\n");
+ } else {
+ if (screen) fprintf(screen," reading dihedrals ...\n");
+ if (logfile) fprintf(logfile," reading dihedrals ...\n");
+ }
+ }
+
+ // allocate count if firstpass
+ int nlocal = atom->nlocal;
+ int *count = NULL;
+ if (firstpass) {
+ memory->create(count,nlocal,"read_data:count");
+ for (int i = 0; i < nlocal; i++) count[i] = 0;
+ }
+
+ // read and process dihedrals
+
+ int nchunk,eof;
bigint nread = 0;
bigint ndihedrals = atom->ndihedrals;
@@ -883,16 +935,32 @@ void ReadData::dihedrals()
nchunk = MIN(ndihedrals-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
- atom->data_dihedrals(nchunk,buffer);
+ atom->data_dihedrals(nchunk,buffer,count);
nread += nchunk;
}
- // check that dihedrals were assigned correctly
+ // if firstpass: tally max dihedral/atom and return
+
+ if (firstpass) {
+ int max = 0;
+ for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
+ int maxall;
+ MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
+
+ if (me == 0) {
+ if (screen) fprintf(screen," %d = max dihedrals/atom\n",maxall);
+ if (logfile) fprintf(logfile," %d = max dihedrals/atom\n",maxall);
+ }
+ atom->dihedral_per_atom = maxall;
+ memory->destroy(count);
+ return;
+ }
+
+ // if 2nd pass: check that dihedrals were assigned correctly
- int nlocal = atom->nlocal;
- bigint sum;
bigint n = 0;
- for (i = 0; i < nlocal; i++) n += atom->num_dihedral[i];
+ for (int i = 0; i < nlocal; i++) n += atom->num_dihedral[i];
+ bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 4;
@@ -901,16 +969,39 @@ void ReadData::dihedrals()
if (screen) fprintf(screen," " BIGINT_FORMAT " dihedrals\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " dihedrals\n",sum/factor);
}
+
if (sum != factor*atom->ndihedrals)
error->all(FLERR,"Dihedrals assigned incorrectly");
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ scan or read all impropers
+------------------------------------------------------------------------- */
-void ReadData::impropers()
+void ReadData::impropers(int firstpass)
{
- int i,m,nchunk,eof;
+ if (me == 0) {
+ if (firstpass) {
+ if (screen) fprintf(screen," scanning impropers ...\n");
+ if (logfile) fprintf(logfile," scanning impropers ...\n");
+ } else {
+ if (screen) fprintf(screen," reading impropers ...\n");
+ if (logfile) fprintf(logfile," reading impropers ...\n");
+ }
+ }
+
+ // allocate count if firstpass
+
+ int nlocal = atom->nlocal;
+ int *count = NULL;
+ if (firstpass) {
+ memory->create(count,nlocal,"read_data:count");
+ for (int i = 0; i < nlocal; i++) count[i] = 0;
+ }
+ // read and process impropers
+
+ int nchunk,eof;
bigint nread = 0;
bigint nimpropers = atom->nimpropers;
@@ -918,16 +1009,32 @@ void ReadData::impropers()
nchunk = MIN(nimpropers-nread,CHUNK);
eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
if (eof) error->all(FLERR,"Unexpected end of data file");
- atom->data_impropers(nchunk,buffer);
+ atom->data_impropers(nchunk,buffer,count);
nread += nchunk;
}
- // check that impropers were assigned correctly
+ // if firstpass: tally max improper/atom and return
+
+ if (firstpass) {
+ int max = 0;
+ for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
+ int maxall;
+ MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
+
+ if (me == 0) {
+ if (screen) fprintf(screen," %d = max impropers/atom\n",maxall);
+ if (logfile) fprintf(logfile," %d = max impropers/atom\n",maxall);
+ }
+ atom->improper_per_atom = maxall;
+ memory->destroy(count);
+ return;
+ }
+
+ // if 2nd pass: check that impropers were assigned correctly
- int nlocal = atom->nlocal;
- bigint sum;
bigint n = 0;
- for (i = 0; i < nlocal; i++) n += atom->num_improper[i];
+ for (int i = 0; i < nlocal; i++) n += atom->num_improper[i];
+ bigint sum;
MPI_Allreduce(&n,&sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
int factor = 1;
if (!force->newton_bond) factor = 4;
@@ -936,10 +1043,129 @@ void ReadData::impropers()
if (screen) fprintf(screen," " BIGINT_FORMAT " impropers\n",sum/factor);
if (logfile) fprintf(logfile," " BIGINT_FORMAT " impropers\n",sum/factor);
}
+
if (sum != factor*atom->nimpropers)
error->all(FLERR,"Impropers assigned incorrectly");
}
+/* ----------------------------------------------------------------------
+ read all bonus data
+ to find atoms, must build atom map if not a molecular system
+------------------------------------------------------------------------- */
+
+void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
+{
+ int i,m,nchunk,eof;
+
+ int mapflag = 0;
+ if (atom->map_style == 0) {
+ mapflag = 1;
+ atom->map_init();
+ atom->map_set();
+ }
+
+ bigint nread = 0;
+ bigint natoms = nbonus;
+
+ while (nread < natoms) {
+ nchunk = MIN(natoms-nread,CHUNK);
+ eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
+ if (eof) error->all(FLERR,"Unexpected end of data file");
+ atom->data_bonus(nchunk,buffer,ptr);
+ nread += nchunk;
+ }
+
+ if (mapflag) {
+ atom->map_delete();
+ atom->map_style = 0;
+ }
+
+ if (me == 0) {
+ if (screen) fprintf(screen," " BIGINT_FORMAT " %s\n",natoms,type);
+ if (logfile) fprintf(logfile," " BIGINT_FORMAT " %s\n",natoms,type);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ read all body data
+ variable amount of info per body, described by ninteger and ndouble
+ to find atoms, must build atom map if not a molecular system
+ if not firstpass, just read but no processing of data
+------------------------------------------------------------------------- */
+
+void ReadData::bodies(int firstpass)
+{
+ int i,m,nchunk,nmax,ninteger,ndouble,tmp,onebody;
+ char *eof;
+
+ int mapflag = 0;
+ if (atom->map_style == 0 && firstpass) {
+ mapflag = 1;
+ atom->map_init();
+ atom->map_set();
+ }
+
+ // nmax = max # of bodies to read in this chunk
+ // nchunk = actual # read
+
+ bigint nread = 0;
+ bigint natoms = nbodies;
+
+ while (nread < natoms) {
+ if (natoms-nread > CHUNK) nmax = CHUNK;
+ else nmax = natoms-nread;
+
+ if (me == 0) {
+ nchunk = 0;
+ nlines = 0;
+ m = 0;
+
+ while (nchunk < nmax && nlines <= CHUNK-MAXBODY) {
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
+ m += strlen(&buffer[m]);
+
+ onebody = 0;
+ if (ninteger) onebody += (ninteger-1)/10 + 1;
+ if (ndouble) onebody += (ndouble-1)/10 + 1;
+ if (onebody+1 > MAXBODY)
+ error->one(FLERR,
+ "Too many lines in one body in data file - boost MAXBODY");
+
+ for (i = 0; i < onebody; i++) {
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
+ }
+
+ nchunk++;
+ nlines += onebody+1;
+ }
+
+ if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
+ m++;
+ }
+
+ MPI_Bcast(&nchunk,1,MPI_INT,0,world);
+ MPI_Bcast(&m,1,MPI_INT,0,world);
+ MPI_Bcast(buffer,m,MPI_CHAR,0,world);
+
+ if (firstpass) atom->data_bodies(nchunk,buffer,avec_body);
+ nread += nchunk;
+ }
+
+ if (mapflag && firstpass) {
+ atom->map_delete();
+ atom->map_style = 0;
+ }
+
+ if (me == 0 && firstpass) {
+ if (screen) fprintf(screen," " BIGINT_FORMAT " bodies\n",natoms);
+ if (logfile) fprintf(logfile," " BIGINT_FORMAT " bodies\n",natoms);
+ }
+}
+
/* ---------------------------------------------------------------------- */
void ReadData::mass()
@@ -1120,314 +1346,6 @@ void ReadData::fix(int ifix, char *keyword)
}
}
-/* ----------------------------------------------------------------------
- proc 0 scans the data file for topology maximums
-------------------------------------------------------------------------- */
-
-void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
- int &dihedral_per_atom, int &improper_per_atom)
-{
- int i,tmp1,tmp2,atom1,atom2,atom3,atom4;
- char *eof;
-
- if (atom->natoms > MAXSMALLINT)
- error->one(FLERR,"Molecular data file has too many atoms");
-
- // customize for new sections
-
- int natoms = static_cast<int> (atom->natoms);
- bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
- int ellipsoid_flag = 0;
- int line_flag = 0;
- int tri_flag = 0;
- int body_flag = 0;
-
- // customize for new sections
- // allocate topology counting vector
- // initially, array length = 1 to natoms
- // will grow via reallocate() if atom IDs > natoms
-
- int cmax = natoms + 1;
- int *count;
- memory->create(count,cmax,"read_data:count");
-
- while (strlen(keyword)) {
-
- // allow special fixes first chance to match and process the section
- // if fix matches, continue to next section
-
- if (nfix) {
- for (i = 0; i < nfix; i++) {
- if (strcmp(keyword,fix_section[i]) == 0) {
- int n = modify->fix[fix_index[i]]->read_data_skip_lines(keyword);
- skip_lines(n);
- parse_keyword(0,0);
- break;
- }
- }
- if (i < nfix) continue;
- }
-
- if (strcmp(keyword,"Masses") == 0) skip_lines(atom->ntypes);
- else if (strcmp(keyword,"Atoms") == 0) skip_lines(natoms);
- else if (strcmp(keyword,"Velocities") == 0) skip_lines(natoms);
-
- else if (strcmp(keyword,"Ellipsoids") == 0) {
- if (!avec_ellipsoid)
- error->one(FLERR,"Invalid data file section: Ellipsoids");
- ellipsoid_flag = 1;
- skip_lines(nellipsoids);
- } else if (strcmp(keyword,"Lines") == 0) {
- if (!avec_line) error->one(FLERR,"Invalid data file section: Lines");
- line_flag = 1;
- skip_lines(nlines);
- } else if (strcmp(keyword,"Triangles") == 0) {
- if (!avec_tri) error->one(FLERR,"Invalid data file section: Triangles");
- tri_flag = 1;
- skip_lines(ntris);
- } else if (strcmp(keyword,"Bodies") == 0) {
- if (!avec_body) error->one(FLERR,"Invalid data file section: Bodies");
- body_flag = 1;
- skip_lines(nbodies);
-
- } else if (strcmp(keyword,"Pair Coeffs") == 0) {
- if (force->pair == NULL)
- error->one(FLERR,"Must define pair_style before Pair Coeffs");
- skip_lines(atom->ntypes);
- } else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
- if (force->pair == NULL)
- error->one(FLERR,"Must define pair_style before Pair Coeffs");
- skip_lines(atom->ntypes*(atom->ntypes+1)/2);
- } else if (strcmp(keyword,"Bond Coeffs") == 0) {
- if (atom->avec->bonds_allow == 0)
- error->one(FLERR,"Invalid data file section: Bond Coeffs");
- if (force->bond == NULL)
- error->one(FLERR,"Must define bond_style before Bond Coeffs");
- skip_lines(atom->nbondtypes);
- } else if (strcmp(keyword,"Angle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->one(FLERR,"Invalid data file section: Angle Coeffs");
- if (force->angle == NULL)
- error->one(FLERR,"Must define angle_style before Angle Coeffs");
- skip_lines(atom->nangletypes);
- } else if (strcmp(keyword,"Dihedral Coeffs") == 0) {
- skip_lines(atom->ndihedraltypes);
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: Dihedral Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,"Must define dihedral_style before Dihedral Coeffs");
- } else if (strcmp(keyword,"Improper Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->one(FLERR,"Invalid data file section: Improper Coeffs");
- if (force->improper == NULL)
- error->one(FLERR,"Must define improper_style before Improper Coeffs");
- skip_lines(atom->nimpropertypes);
-
- } else if (strcmp(keyword,"BondBond Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->one(FLERR,"Invalid data file section: BondBond Coeffs");
- if (force->angle == NULL)
- error->one(FLERR,"Must define angle_style before BondBond Coeffs");
- skip_lines(atom->nangletypes);
- } else if (strcmp(keyword,"BondAngle Coeffs") == 0) {
- if (atom->avec->angles_allow == 0)
- error->one(FLERR,"Invalid data file section: BondAngle Coeffs");
- if (force->angle == NULL)
- error->one(FLERR,"Must define angle_style before BondAngle Coeffs");
- skip_lines(atom->nangletypes);
- } else if (strcmp(keyword,"MiddleBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: MiddleBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before "
- "MiddleBondTorsion Coeffs");
- skip_lines(atom->ndihedraltypes);
- } else if (strcmp(keyword,"EndBondTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: EndBondTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before EndBondTorsion Coeffs");
- skip_lines(atom->ndihedraltypes);
- } else if (strcmp(keyword,"AngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: AngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before AngleTorsion Coeffs");
- skip_lines(atom->ndihedraltypes);
- } else if (strcmp(keyword,"AngleAngleTorsion Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: AngleAngleTorsion Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,
- "Must define dihedral_style before "
- "AngleAngleTorsion Coeffs");
- skip_lines(atom->ndihedraltypes);
- } else if (strcmp(keyword,"BondBond13 Coeffs") == 0) {
- if (atom->avec->dihedrals_allow == 0)
- error->one(FLERR,"Invalid data file section: BondBond13 Coeffs");
- if (force->dihedral == NULL)
- error->one(FLERR,"Must define dihedral_style before BondBond13 Coeffs");
- skip_lines(atom->ndihedraltypes);
- } else if (strcmp(keyword,"AngleAngle Coeffs") == 0) {
- if (atom->avec->impropers_allow == 0)
- error->one(FLERR,"Invalid data file section: AngleAngle Coeffs");
- if (force->improper == NULL)
- error->one(FLERR,"Must define improper_style before AngleAngle Coeffs");
- skip_lines(atom->nimpropertypes);
-
- } else if (strcmp(keyword,"Bonds") == 0) {
- for (i = 1; i < cmax; i++) count[i] = 0;
- if (force->newton_bond)
- for (i = 0; i < atom->nbonds; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
- if (atom1 >= cmax) cmax = reallocate(&count,cmax,atom1);
- count[atom1]++;
- }
- else
- for (i = 0; i < atom->nbonds; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d",&tmp1,&tmp2,&atom1,&atom2);
- int amax = MAX(atom1,atom2);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- }
- for (i = 1; i < cmax; i++) bond_per_atom = MAX(bond_per_atom,count[i]);
- if (screen) fprintf(screen," %d = max bonds/atom\n",bond_per_atom);
- if (logfile) fprintf(logfile," %d = max bonds/atom\n",bond_per_atom);
-
- } else if (strcmp(keyword,"Angles") == 0) {
- for (i = 1; i < cmax; i++) count[i] = 0;
- if (force->newton_bond)
- for (i = 0; i < atom->nangles; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
- if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
- count[atom2]++;
- }
- else
- for (i = 0; i < atom->nangles; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d",&tmp1,&tmp2,&atom1,&atom2,&atom3);
- int amax = MAX(atom1,atom2);
- amax = MAX(amax,atom3);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- count[atom3]++;
- }
- for (i = 1; i < cmax; i++) angle_per_atom = MAX(angle_per_atom,count[i]);
- if (screen) fprintf(screen," %d = max angles/atom\n",angle_per_atom);
- if (logfile) fprintf(logfile," %d = max angles/atom\n",angle_per_atom);
-
- } else if (strcmp(keyword,"Dihedrals") == 0) {
- for (i = 1; i < cmax; i++) count[i] = 0;
- if (force->newton_bond)
- for (i = 0; i < atom->ndihedrals; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
- count[atom2]++;
- }
- else
- for (i = 0; i < atom->ndihedrals; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- int amax = MAX(atom1,atom2);
- amax = MAX(amax,atom3);
- amax = MAX(amax,atom4);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- count[atom3]++;
- count[atom4]++;
- }
- for (i = 1; i < cmax; i++)
- dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
- if (screen)
- fprintf(screen," %d = max dihedrals/atom\n",dihedral_per_atom);
- if (logfile)
- fprintf(logfile," %d = max dihedrals/atom\n",dihedral_per_atom);
-
- } else if (strcmp(keyword,"Impropers") == 0) {
- for (i = 1; i < cmax; i++) count[i] = 0;
- if (force->newton_bond)
- for (i = 0; i < atom->nimpropers; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- if (atom2 >= cmax) cmax = reallocate(&count,cmax,atom2);
- count[atom2]++;
- }
- else
- for (i = 0; i < atom->nimpropers; i++) {
- eof = fgets(line,MAXLINE,fp);
- if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
- sscanf(line,"%d %d %d %d %d %d",
- &tmp1,&tmp2,&atom1,&atom2,&atom3,&atom4);
- int amax = MAX(atom1,atom2);
- amax = MAX(amax,atom3);
- amax = MAX(amax,atom4);
- if (amax >= cmax) cmax = reallocate(&count,cmax,amax);
- count[atom1]++;
- count[atom2]++;
- count[atom3]++;
- count[atom4]++;
- }
- for (i = 1; i < cmax; i++)
- improper_per_atom = MAX(improper_per_atom,count[i]);
- if (screen)
- fprintf(screen," %d = max impropers/atom\n",improper_per_atom);
- if (logfile)
- fprintf(logfile," %d = max impropers/atom\n",improper_per_atom);
-
- } else {
- char str[128];
- sprintf(str,"Unknown identifier in data file: %s",keyword);
- error->one(FLERR,str);
- }
-
- parse_keyword(0,0);
- }
-
- // free topology counting vector
-
- memory->destroy(count);
-
- // error check that topology was specified in file
-
- if ((atom->nbonds && !bond_per_atom) ||
- (atom->nangles && !angle_per_atom) ||
- (atom->ndihedrals && !dihedral_per_atom) ||
- (atom->nimpropers && !improper_per_atom))
- error->one(FLERR,"Needed topology not in data file");
-
- // customize for new sections
- // error check that Bonus sections were speficied in file
-
- if (nellipsoids && !ellipsoid_flag)
- error->one(FLERR,"Needed bonus data not in data file");
- if (nlines && !line_flag)
- error->one(FLERR,"Needed bonus data not in data file");
- if (ntris && !tri_flag)
- error->one(FLERR,"Needed bonus data not in data file");
- if (nbodies && !body_flag)
- error->one(FLERR,"Needed bonus data not in data file");
-}
-
/* ----------------------------------------------------------------------
reallocate the count vector from cmax to amax+1 and return new length
zero new locations
@@ -1477,11 +1395,9 @@ void ReadData::open(char *file)
read one additional line (assumed blank)
if any read hits EOF, set keyword to empty
if first = 1, line variable holds non-blank line that ended header
- if flag = 0, only proc 0 is calling so no bcast
- else flag = 1, bcast keyword line to all procs
------------------------------------------------------------------------- */
-void ReadData::parse_keyword(int first, int flag)
+void ReadData::parse_keyword(int first)
{
int eof = 0;
@@ -1500,7 +1416,7 @@ void ReadData::parse_keyword(int first, int flag)
// if eof, set keyword empty and return
- if (flag) MPI_Bcast(&eof,1,MPI_INT,0,world);
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) {
keyword[0] = '\0';
return;
@@ -1508,12 +1424,10 @@ void ReadData::parse_keyword(int first, int flag)
// bcast keyword line to all procs
- if (flag) {
- int n;
- if (me == 0) n = strlen(line) + 1;
- MPI_Bcast(&n,1,MPI_INT,0,world);
- MPI_Bcast(line,n,MPI_CHAR,0,world);
- }
+ int n;
+ if (me == 0) n = strlen(line) + 1;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
// copy non-whitespace portion of line into keyword
@@ -1527,14 +1441,14 @@ void ReadData::parse_keyword(int first, int flag)
/* ----------------------------------------------------------------------
proc 0 reads N lines from file
- NOTE: needs to be called with bigint in some cases
- if called with int, will it be promoted to bigint?
+ could be skipping Natoms lines, so use bigints
------------------------------------------------------------------------- */
-void ReadData::skip_lines(int n)
+void ReadData::skip_lines(bigint n)
{
+ if (me) return;
char *eof;
- for (int i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
+ for (bigint i = 0; i < n; i++) eof = fgets(line,MAXLINE,fp);
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
}
diff --git a/src/read_data.h b/src/read_data.h
index 48602c30ff..95c5b54705 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -38,7 +38,7 @@ class ReadData : protected Pointers {
int narg,maxarg,compressed;
char **arg;
- int nfix; // # of extra fixes that process/store info in data file
+ int nfix; // # of extra fixes that process/store info in data file
int *fix_index;
char **fix_header;
char **fix_section;
@@ -55,20 +55,22 @@ class ReadData : protected Pointers {
void open(char *);
void scan(int &, int &, int &, int &);
int reallocate(int **, int, int);
- void header(int);
- void parse_keyword(int, int);
- void skip_lines(int);
+ void header();
+ void parse_keyword(int);
+ void skip_lines(bigint);
void parse_coeffs(char *, const char *, int);
void atoms();
void velocities();
- void bonus(bigint, class AtomVec *, const char *);
- void bodies();
- void bonds();
- void angles();
- void dihedrals();
- void impropers();
+ void bonds(int);
+ void bond_scan(int, char *, int *);
+ void angles(int);
+ void dihedrals(int);
+ void impropers(int);
+
+ void bonus(bigint, class AtomVec *, const char *);
+ void bodies(int);
void mass();
void paircoeffs();
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 6196f876c1..3256d28a46 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -444,7 +444,6 @@ void ReadDump::atoms()
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
- atom->map_style = 1;
atom->map_init();
atom->map_set();
}
@@ -477,11 +476,9 @@ void ReadDump::atoms()
if (addflag) {
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0 || atom->natoms >= MAXBIGINT)
error->all(FLERR,"Too many total atoms");
- // change these to MAXTAGINT when allow tagint = bigint
- if (atom->natoms > MAXSMALLINT) atom->tag_enable = 0;
- if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
+ if (atom->tag_enable) atom->tag_extend();
}
// if trimflag set, delete atoms not replaced by snapshot atoms
@@ -553,6 +550,10 @@ void ReadDump::atoms()
irregular->migrate_atoms();
delete irregular;
if (triclinic) domain->lamda2x(atom->nlocal);
+
+ // check that atom IDs are valid
+
+ atom->tag_check();
}
/* ----------------------------------------------------------------------
@@ -710,24 +711,27 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
void ReadDump::process_atoms(int n)
{
- int i,m,ifield,itype,itag;;
+ int i,m,ifield,itype;
int xbox,ybox,zbox;
+ tagint tag;
double **x = atom->x;
double **v = atom->v;
double *q = atom->q;
imageint *image = atom->image;
int nlocal = atom->nlocal;
- int map_tag_max = atom->map_tag_max;
+ tagint map_tag_max = atom->map_tag_max;
for (i = 0; i < n; i++) {
ucflag[i] = 0;
// check if new atom matches one I own
// setting m = -1 forces new atom not to match
+ // NOTE: atom ID in fields is stored as double, not as ubuf
+ // so can only cast it to tagint, thus cannot be full 64-bit ID
- itag = static_cast<int> (fields[i][0]);
- if (itag <= map_tag_max) m = atom->map(static_cast<int> (fields[i][0]));
+ tag = static_cast<tagint> (fields[i][0]);
+ if (tag <= map_tag_max) m = atom->map(tag);
else m = -1;
if (m < 0 || m >= nlocal) continue;
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 937b10548b..31549b69dc 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -503,20 +503,19 @@ void ReadRestart::command(int narg, char **arg)
}
}
- // check if tags are being used
- // create global mapping and bond topology now that system is defined
+ // check that atom IDs are valid
- flag = 0;
- for (int i = 0; i < atom->nlocal; i++)
- if (atom->tag[i] > 0) flag = 1;
- int flag_all;
- MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
- if (flag_all == 0) atom->tag_enable = 0;
+ atom->tag_check();
- if (atom->map_style) {
+ // if molecular system or user-requested, create global mapping of atoms
+
+ if (atom->molecular || atom->map_user) {
atom->map_init();
atom->map_set();
}
+
+ // create special bond lists for molecular systems
+
if (atom->molecular) {
Special special(lmp);
special.build();
diff --git a/src/replicate.cpp b/src/replicate.cpp
index d0b3b71ab2..9b4e9bcf48 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -73,11 +73,13 @@ void Replicate::command(int narg, char **arg)
// maxtag = largest atom tag across all existing atoms
- int maxtag = 0;
- for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
- int maxtag_all;
- MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
- maxtag = maxtag_all;
+ tagint maxtag = 0;
+ if (atom->tag_enable) {
+ for (i = 0; i < atom->nlocal; i++) maxtag = MAX(atom->tag[i],maxtag);
+ tagint maxtag_all;
+ MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
+ maxtag = maxtag_all;
+ }
// maxmol = largest molecule tag across all existing atoms
@@ -124,25 +126,20 @@ void Replicate::command(int narg, char **arg)
atom->create_avec(old->atom_style,nstyles,keywords);
// check that new system will not be too large
- // if molecular and N > MAXTAGINT, error
- // if atomic and new N > MAXTAGINT, turn off tags for existing and new atoms
- // new system cannot exceed MAXBIGINT
- // NOTE: change these 2 to MAXTAGINT when allow tagint = bigint
-
- if (atom->molecular &&
- (nrep*old->natoms < 0 || nrep*old->natoms > MAXSMALLINT))
- error->all(FLERR,"Replicated molecular system atom IDs are too big");
- if (nrep*old->natoms < 0 || nrep*old->natoms > MAXSMALLINT)
- atom->tag_enable = 0;
- if (atom->tag_enable == 0)
- for (int i = 0; i < atom->nlocal; i++)
- atom->tag[i] = 0;
-
- if (nrep*old->natoms < 0 || nrep*old->natoms > MAXBIGINT ||
- nrep*old->nbonds < 0 || nrep*old->nbonds > MAXBIGINT ||
- nrep*old->nangles < 0 || nrep*old->nangles > MAXBIGINT ||
- nrep*old->ndihedrals < 0 || nrep*old->ndihedrals > MAXBIGINT ||
- nrep*old->nimpropers < 0 || nrep*old->nimpropers > MAXBIGINT)
+ // new tags cannot exceed MAXTAGINT
+ // new system sizes cannot exceed MAXBIGINT
+
+ if (atom->tag_enable) {
+ bigint maxnewtag = maxtag + (nrep-1)*old->natoms;
+ if (maxnewtag < 0 || maxnewtag >= MAXTAGINT)
+ error->all(FLERR,"Replicated system atom IDs are too big");
+ }
+
+ if (nrep*old->natoms < 0 || nrep*old->natoms >= MAXBIGINT ||
+ nrep*old->nbonds < 0 || nrep*old->nbonds >= MAXBIGINT ||
+ nrep*old->nangles < 0 || nrep*old->nangles >= MAXBIGINT ||
+ nrep*old->ndihedrals < 0 || nrep*old->ndihedrals >= MAXBIGINT ||
+ nrep*old->nimpropers < 0 || nrep*old->nimpropers >= MAXBIGINT)
error->all(FLERR,"Replicated system is too big");
// assign atom and topology counts in new class from old one
@@ -257,7 +254,8 @@ void Replicate::command(int narg, char **arg)
AtomVec *old_avec = old->avec;
AtomVec *avec = atom->avec;
- int ix,iy,iz,atom_offset,mol_offset;
+ int ix,iy,iz,mol_offset;
+ tagint atom_offset;
imageint image;
double x[3],lamda[3];
double *coord;
@@ -393,13 +391,19 @@ void Replicate::command(int narg, char **arg)
}
}
- // create global mapping and bond topology now that system is defined
+ // check that atom IDs are valid
- if (atom->map_style) {
- atom->nghost = 0;
+ atom->tag_check();
+
+ // if molecular system or user-requested, create global mapping of atoms
+
+ if (atom->molecular || atom->map_user) {
atom->map_init();
atom->map_set();
}
+
+ // create special bond lists for molecular systems
+
if (atom->molecular) {
Special special(lmp);
special.build();
diff --git a/src/set.cpp b/src/set.cpp
index 046dc67f48..562b8f94ce 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -440,11 +440,12 @@ void Set::selection(int n)
if (style == ATOM_SELECT) {
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use set atom with no atom IDs defined");
- force->bounds(id,BIG,nlo,nhi);
+ bigint nlobig,nhibig;
+ force->boundsbig(id,MAXTAGINT,nlobig,nhibig);
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
for (int i = 0; i < n; i++)
- if (tag[i] >= nlo && tag[i] <= nhi) select[i] = 1;
+ if (tag[i] >= nlobig && tag[i] <= nhibig) select[i] = 1;
else select[i] = 0;
} else if (style == MOL_SELECT) {
@@ -711,7 +712,7 @@ void Set::set(int keyword)
/* ----------------------------------------------------------------------
set an owned atom property randomly
- set seed based on atom tag
+ set seed based on atom coordinates
make atom result independent of what proc owns it
------------------------------------------------------------------------- */
diff --git a/src/special.cpp b/src/special.cpp
index 170115521f..d081a82abe 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -56,15 +56,15 @@ void Special::build()
{
int i,j,k,size;
int max,maxall,nbuf;
- int *buf;
+ tagint *buf;
MPI_Barrier(world);
int nlocal = atom->nlocal;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
- int **bond_atom = atom->bond_atom;
+ tagint **bond_atom = atom->bond_atom;
int **nspecial = atom->nspecial;
if (me == 0 && screen) fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n");
@@ -109,7 +109,7 @@ void Special::build()
// when find one, increment nspecial count for that atom
sptr = this;
- comm->ring(size,sizeof(int),buf,1,ring_one,NULL);
+ comm->ring(size,sizeof(tagint),buf,1,ring_one,NULL);
memory->destroy(buf);
}
@@ -167,7 +167,7 @@ void Special::build()
// when find one, add 1st-atom tag to onetwo list for 2nd atom
sptr = this;
- comm->ring(size,sizeof(int),buf,2,ring_two,NULL);
+ comm->ring(size,sizeof(tagint),buf,2,ring_two,NULL);
memory->destroy(buf);
}
@@ -214,7 +214,7 @@ void Special::build()
// subtracting one since my list will contain original atom
sptr = this;
- comm->ring(size,sizeof(int),buf,3,ring_three,buf);
+ comm->ring(size,sizeof(tagint),buf,3,ring_three,buf);
// extract count from buffer that has cycled back to me
// nspecial[i][1] = # of 1-3 neighbors of atom i
@@ -275,7 +275,7 @@ void Special::build()
// this process may include duplicates but they will be culled later
sptr = this;
- comm->ring(size,sizeof(int),buf,4,ring_four,buf);
+ comm->ring(size,sizeof(tagint),buf,4,ring_four,buf);
// fill onethree with buffer values that have been returned to me
// sanity check: accumulated buf[i+3] count should equal
@@ -330,7 +330,7 @@ void Special::build()
// may include duplicates and original atom but they will be culled later
sptr = this;
- comm->ring(size,sizeof(int),buf,5,ring_five,buf);
+ comm->ring(size,sizeof(tagint),buf,5,ring_five,buf);
// extract count from buffer that has cycled back to me
// nspecial[i][2] = # of 1-4 neighbors of atom i
@@ -389,7 +389,7 @@ void Special::build()
// this process may include duplicates but they will be culled later
sptr = this;
- comm->ring(size,sizeof(int),buf,6,ring_six,buf);
+ comm->ring(size,sizeof(tagint),buf,6,ring_six,buf);
// fill onefour with buffer values that have been returned to me
// sanity check: accumulated buf[i+2] count should equal
@@ -418,7 +418,8 @@ void Special::build()
void Special::dedup()
{
- int i,j,m;
+ int i,j;
+ tagint m;
// clear map so it can be used as scratch space
@@ -430,7 +431,7 @@ void Special::dedup()
// must unset map for each atom
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
int unique;
@@ -494,13 +495,14 @@ void Special::dedup()
void Special::combine()
{
- int i,j,m;
+ int i,j;
+ tagint m;
int me;
MPI_Comm_rank(world,&me);
int **nspecial = atom->nspecial;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// ----------------------------------------------------
@@ -574,7 +576,7 @@ void Special::combine()
memory->create(atom->special,atom->nmax,atom->maxspecial,"atom:special");
atom->avec->grow_reset();
- int **special = atom->special;
+ tagint **special = atom->special;
// ----------------------------------------------------
// fill special array with 1-2, 1-3, 1-4 neighs for each atom
@@ -638,12 +640,12 @@ void Special::angle_trim()
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
- int **angle_atom1 = atom->angle_atom1;
- int **angle_atom3 = atom->angle_atom3;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom2 = atom->dihedral_atom2;
- int **dihedral_atom3 = atom->dihedral_atom3;
- int **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom3 = atom->angle_atom3;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
@@ -716,7 +718,7 @@ void Special::angle_trim()
// when find one, scan its 1-3 neigh list and mark I,J as in an angle
sptr = this;
- comm->ring(size,sizeof(int),buf,7,ring_seven,NULL);
+ comm->ring(size,sizeof(tagint),buf,7,ring_seven,NULL);
// delete 1-3 neighbors if they are not flagged in dflag
@@ -764,8 +766,8 @@ void Special::dihedral_trim()
int i,j,m,n;
int *num_dihedral = atom->num_dihedral;
- int **dihedral_atom1 = atom->dihedral_atom1;
- int **dihedral_atom4 = atom->dihedral_atom4;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
@@ -822,7 +824,7 @@ void Special::dihedral_trim()
// when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
sptr = this;
- comm->ring(size,sizeof(int),buf,8,ring_eight,NULL);
+ comm->ring(size,sizeof(tagint),buf,8,ring_eight,NULL);
// delete 1-4 neighbors if they are not flagged in dflag
@@ -871,7 +873,7 @@ void Special::ring_one(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int m;
for (int i = 0; i < ndatum; i++) {
@@ -890,10 +892,10 @@ void Special::ring_two(int ndatum, char *cbuf)
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
- int **onetwo = sptr->onetwo;
+ tagint **onetwo = sptr->onetwo;
int *count = sptr->count;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int m;
for (int i = 1; i < ndatum; i += 2) {
@@ -914,7 +916,7 @@ void Special::ring_three(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int i,j,m,n,num12;
i = 0;
@@ -945,10 +947,11 @@ void Special::ring_four(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int **onetwo = sptr->onetwo;
+ tagint **onetwo = sptr->onetwo;
- int *buf = (int *) cbuf;
- int i,j,k,m,n,original,num12,num13;
+ tagint *buf = (tagint *) cbuf;
+ tagint original;
+ int i,j,k,m,n,num12,num13;
i = 0;
while (i < ndatum) {
@@ -980,7 +983,7 @@ void Special::ring_five(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int i,j,m,n,num13;
i = 0;
@@ -1009,9 +1012,9 @@ void Special::ring_six(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int **onetwo = sptr->onetwo;
+ tagint **onetwo = sptr->onetwo;
- int *buf = (int *) cbuf;
+ tagint *buf = (tagint *) cbuf;
int i,j,k,m,n,num13,num14;
i = 0;
@@ -1041,11 +1044,12 @@ void Special::ring_seven(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int **onethree = sptr->onethree;
+ tagint **onethree = sptr->onethree;
int **dflag = sptr->dflag;
- int *buf = (int *) cbuf;
- int i,m,iglobal,jglobal,ilocal,jlocal;
+ tagint *buf = (tagint *) cbuf;
+ tagint iglobal,jglobal;
+ int i,m,ilocal,jlocal;
i = 0;
while (i < ndatum) {
@@ -1080,11 +1084,12 @@ void Special::ring_eight(int ndatum, char *cbuf)
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
- int **onefour = sptr->onefour;
+ tagint **onefour = sptr->onefour;
int **dflag = sptr->dflag;
- int *buf = (int *) cbuf;
- int i,m,iglobal,jglobal,ilocal,jlocal;
+ tagint *buf = (tagint *) cbuf;
+ tagint iglobal,jglobal;
+ int i,m,ilocal,jlocal;
i = 0;
while (i < ndatum) {
diff --git a/src/special.h b/src/special.h
index 3ebf620690..90a23a3408 100644
--- a/src/special.h
+++ b/src/special.h
@@ -26,7 +26,7 @@ class Special : protected Pointers {
private:
int me,nprocs;
- int **onetwo,**onethree,**onefour;
+ tagint **onetwo,**onethree,**onefour;
int dihedral_flag;
// data used by ring callback methods
diff --git a/src/variable.cpp b/src/variable.cpp
index 33163ba733..87fed075c1 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -60,7 +60,7 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY,
SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2,
RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,STRIDE,
VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,GRMASK,
- VALUE,ATOMARRAY,TYPEARRAY,INTARRAY};
+ VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY};
// customize by adding a special function
@@ -1685,7 +1685,8 @@ double Variable::evaluate(char *str, Tree **tree)
/* ----------------------------------------------------------------------
one-time collapse of an atom-style variable parse tree
tree was created by one-time parsing of formula string via evaulate()
- only keep tree nodes that depend on ATOMARRAY, TYPEARRAY, INTARRAY
+ only keep tree nodes that depend on
+ ATOMARRAY, TYPEARRAY, INTARRAY, BIGINTARRAY
remainder is converted to single VALUE
this enables optimal eval_tree loop over atoms
customize by adding a function:
@@ -1704,6 +1705,7 @@ double Variable::collapse_tree(Tree *tree)
if (tree->type == ATOMARRAY) return 0.0;
if (tree->type == TYPEARRAY) return 0.0;
if (tree->type == INTARRAY) return 0.0;
+ if (tree->type == BIGINTARRAY) return 0.0;
if (tree->type == ADD) {
arg1 = collapse_tree(tree->left);
@@ -2149,6 +2151,7 @@ double Variable::eval_tree(Tree *tree, int i)
if (tree->type == ATOMARRAY) return tree->array[i*tree->nstride];
if (tree->type == TYPEARRAY) return tree->array[atom->type[i]];
if (tree->type == INTARRAY) return (double) tree->iarray[i*tree->nstride];
+ if (tree->type == BIGINTARRAY) return (double) tree->barray[i*tree->nstride];
if (tree->type == ADD)
return eval_tree(tree->left,i) + eval_tree(tree->right,i);
@@ -3510,9 +3513,14 @@ void Variable::atom_vector(char *word, Tree **tree,
treestack[ntreestack++] = newtree;
if (strcmp(word,"id") == 0) {
- newtree->type = INTARRAY;
+ if (sizeof(tagint) == sizeof(smallint)) {
+ newtree->type = INTARRAY;
+ newtree->iarray = (int *) atom->tag;
+ } else {
+ newtree->type = BIGINTARRAY;
+ newtree->barray = (bigint *) atom->tag;
+ }
newtree->nstride = 1;
- newtree->iarray = atom->tag;
} else if (strcmp(word,"mass") == 0) {
if (atom->rmass) {
newtree->nstride = 1;
@@ -3998,7 +4006,8 @@ int VarReader::read_scalar(char *str)
int VarReader::read_peratom()
{
- int i,m,n,tagdata,nchunk,eof;
+ int i,m,n,nchunk,eof;
+ tagint tag;
char *ptr,*next;
double value;
@@ -4031,7 +4040,7 @@ int VarReader::read_peratom()
MPI_Bcast(str,n,MPI_CHAR,0,world);
bigint nlines = ATOBIGINT(str);
- int map_tag_max = atom->map_tag_max;
+ tagint map_tag_max = atom->map_tag_max;
bigint nread = 0;
while (nread < nlines) {
@@ -4043,10 +4052,10 @@ int VarReader::read_peratom()
for (i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
*next = '\0';
- sscanf(buf,"%d %lg",&tagdata,&value);
- if (tagdata <= 0 || tagdata > map_tag_max)
+ sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value);
+ if (tag <= 0 || tag > map_tag_max)
error->one(FLERR,"Invalid atom ID in variable file");
- if ((m = atom->map(tagdata)) >= 0) vstore[m] = value;
+ if ((m = atom->map(tag)) >= 0) vstore[m] = value;
buf = next + 1;
}
diff --git a/src/variable.h b/src/variable.h
index 0d70232233..b3a57436f8 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -63,6 +63,7 @@ class Variable : protected Pointers {
double value; // single scalar
double *array; // per-atom or per-type list of doubles
int *iarray; // per-atom list of ints
+ bigint *barray; // per-atom list of bigints
int type; // operation, see enum{} in variable.cpp
int nstride; // stride between atoms if array is a 2d array
int selfalloc; // 1 if array is allocated here, else 0
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 1d44bcaf58..f27aa57058 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -205,7 +205,6 @@ void Velocity::create(double t_desired, int seed)
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
- atom->map_style = 1;
atom->nghost = 0;
atom->map_init();
atom->map_set();
diff --git a/src/write_data.cpp b/src/write_data.cpp
index a0868d700b..6c9cd49894 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -415,7 +415,7 @@ void WriteData::bonds()
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
- int **buf;
+ tagint **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
@@ -436,10 +436,10 @@ void WriteData::bonds()
fprintf(fp,"\nBonds\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
- MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
+ MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&recvrow);
+ MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
@@ -449,7 +449,7 @@ void WriteData::bonds()
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
- MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
+ MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
@@ -468,7 +468,7 @@ void WriteData::angles()
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
- int **buf;
+ tagint **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
@@ -489,10 +489,10 @@ void WriteData::angles()
fprintf(fp,"\nAngles\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
- MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
+ MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&recvrow);
+ MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
@@ -502,7 +502,7 @@ void WriteData::angles()
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
- MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
+ MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
@@ -519,9 +519,9 @@ void WriteData::dihedrals()
int ncol = 5;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_dihedral = atom->num_dihedral;
- int **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -539,7 +539,7 @@ void WriteData::dihedrals()
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
- int **buf;
+ tagint **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
@@ -560,10 +560,10 @@ void WriteData::dihedrals()
fprintf(fp,"\nDihedrals\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
- MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
+ MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&recvrow);
+ MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
@@ -573,7 +573,7 @@ void WriteData::dihedrals()
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
- MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
+ MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
@@ -590,9 +590,9 @@ void WriteData::impropers()
int ncol = 5;
- int *tag = atom->tag;
+ tagint *tag = atom->tag;
int *num_improper = atom->num_improper;
- int **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom2 = atom->improper_atom2;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -610,7 +610,7 @@ void WriteData::impropers()
int maxrow;
MPI_Allreduce(&sendrow,&maxrow,1,MPI_INT,MPI_MAX,world);
- int **buf;
+ tagint **buf;
if (me == 0) memory->create(buf,MAX(1,maxrow),ncol,"write_data:buf");
else memory->create(buf,MAX(1,sendrow),ncol,"write_data:buf");
@@ -631,10 +631,10 @@ void WriteData::impropers()
fprintf(fp,"\nImpropers\n\n");
for (int iproc = 0; iproc < nprocs; iproc++) {
if (iproc) {
- MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_INT,iproc,0,world,&request);
+ MPI_Irecv(&buf[0][0],maxrow*ncol,MPI_LMP_TAGINT,iproc,0,world,&request);
MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
MPI_Wait(&request,&status);
- MPI_Get_count(&status,MPI_INT,&recvrow);
+ MPI_Get_count(&status,MPI_LMP_TAGINT,&recvrow);
recvrow /= ncol;
} else recvrow = sendrow;
@@ -644,7 +644,7 @@ void WriteData::impropers()
} else {
MPI_Recv(&tmp,0,MPI_INT,0,0,world,&status);
- MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_INT,0,0,world);
+ MPI_Rsend(&buf[0][0],sendrow*ncol,MPI_LMP_TAGINT,0,0,world);
}
memory->destroy(buf);
--
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