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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5472 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-01-04 21:08:27 +00:00
parent a7f69eac0c
commit c9495408a1
16 changed files with 69 additions and 61 deletions
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2
src/MANYBODY/fix_qeq_comb.cpp
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@ -119,7 +119,7 @@ void FixQEQComb::init()
nlevels_respa = ((Respa *) update->integrate)->nlevels;
ngroup = group->count(igroup);
if (ngroup == 0.0) error->all("Fix qeq/comb group has no atoms");
if (ngroup == 0) error->all("Fix qeq/comb group has no atoms");
}
/* ---------------------------------------------------------------------- */

3
src/MANYBODY/fix_qeq_comb.h
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@ -22,6 +22,7 @@ FixStyle(qeq/comb,FixQEQComb)
#include "stdio.h"
#include "fix.h"
#include "lmptype.h"
namespace LAMMPS_NS {
@ -40,7 +41,7 @@ class FixQEQComb : public Fix {
int me,firstflag;
double precision;
int nlevels_respa;
double ngroup;
bigint ngroup;
FILE *fp;
class PairComb *comb;

28
src/SRD/fix_srd.cpp
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@ -1075,7 +1075,7 @@ void FixSRD::vbin_unpack(double *buf, BinAve *vbin, int n, int *list)
void FixSRD::collisions_single()
{
int i,j,k,m,type,nbig,ibin,ibounce,inside,collide_flag;
int i,j,k,m,type,mbig,ibin,ibounce,inside,collide_flag;
double dt,t_remain;
double norm[3],xscoll[3],xbcoll[3],vsnew[3];
Big *big;
@ -1107,11 +1107,11 @@ void FixSRD::collisions_single()
dt = dt_big;
while (collide_flag) {
nbig = nbinbig[ibin];
if (ibounce == 0) ncheck += nbig;
mbig = nbinbig[ibin];
if (ibounce == 0) ncheck += mbig;
collide_flag = 0;
for (m = 0; m < nbig; m++) {
for (m = 0; m < mbig; m++) {
k = binbig[ibin][m];
big = &biglist[k];
j = big->index;
@ -1236,7 +1236,7 @@ void FixSRD::collisions_single()
void FixSRD::collisions_multi()
{
int i,j,k,m,type,nbig,ibin,ibounce,inside,jfirst,typefirst;
int i,j,k,m,type,mbig,ibin,ibounce,inside,jfirst,typefirst;
double dt,t_remain,t_first;
double norm[3],xscoll[3],xbcoll[3],vsnew[3];
double normfirst[3],xscollfirst[3],xbcollfirst[3];
@ -1268,11 +1268,11 @@ void FixSRD::collisions_multi()
dt = dt_big;
while (1) {
nbig = nbinbig[ibin];
if (ibounce == 0) ncheck += nbig;
mbig = nbinbig[ibin];
if (ibounce == 0) ncheck += mbig;
t_first = 0.0;
for (m = 0; m < nbig; m++) {
for (m = 0; m < mbig; m++) {
k = binbig[ibin][m];
big = &biglist[k];
j = big->index;
@ -2236,9 +2236,9 @@ void FixSRD::parameterize()
// particle counts
double nbig = 0.0;
if (bigexist) nbig = group->count(biggroup);
double nsrd = group->count(igroup);
bigint mbig = 0;
if (bigexist) mbig = group->count(biggroup);
bigint nsrd = group->count(igroup);
// mass_big = total mass of all big particles
@ -2293,7 +2293,7 @@ void FixSRD::parameterize()
else
ncell = volsrd / (binsize3x*binsize3y);
srd_per_cell = nsrd / ncell;
srd_per_cell = (double) nsrd / ncell;
// kinematic viscosity of SRD fluid
// output in cm^2/sec units, converted by xxt2kmu
@ -2317,7 +2317,7 @@ void FixSRD::parameterize()
if (me == 0) {
if (screen) {
fprintf(screen,"SRD info:\n");
fprintf(screen," SRD/big particles = %g %g\n",nsrd,nbig);
fprintf(screen," SRD/big particles = %lu %lu\n",nsrd,mbig);
fprintf(screen," big particle diameter max/min = %g %g\n",
maxbigdiam,minbigdiam);
fprintf(screen," SRD temperature & lamda = %g %g\n",
@ -2332,7 +2332,7 @@ void FixSRD::parameterize()
}
if (logfile) {
fprintf(logfile,"SRD info:\n");
fprintf(logfile," SRD/big particles = %g %g\n",nsrd,nbig);
fprintf(logfile," SRD/big particles = %lu %lu\n",nsrd,mbig);
fprintf(logfile," big particle diameter max/min = %g %g\n",
maxbigdiam,minbigdiam);
fprintf(logfile," SRD temperature & lamda = %g %g\n",

15
src/USER-IMD/fix_imd.cpp
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@ -230,7 +230,7 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
imd_port = atoi(arg[3]);
if (imd_port < 1024)
error->all("Illegal fix imd parameter. port < 1024.");
error->all("Illegal fix imd parameter: port < 1024");
/* default values for optional flags */
unwrap_flag = 0;
@ -259,7 +259,7 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
} else if (0 == strcmp(arg[argsdone], "trate")) {
imd_trate = atoi(arg[argsdone+1]);
} else {
error->all("Unknown fix imd parameter.");
error->all("Unknown fix imd parameter");
}
++argsdone; ++argsdone;
}
@ -268,12 +268,11 @@ FixIMD::FixIMD(LAMMPS *lmp, int narg, char **arg) :
if (imd_trate < 1)
error->all("Illegal fix imd parameter. trate < 1.");
if (igroup == group->find("all")) {
num_coords = static_cast<int> (atom->natoms);
} else {
num_coords = static_cast<int> (group->count(igroup));
if (num_coords <= 0) error->all("Invalid number of group atoms for 'fix imd'");
}
bigint n;
if (igroup == group->find("all")) n = atom->natoms;
else n = group->count(igroup);
if (n > MAXINT32) error->all("Too many atoms for fix imd");
num_coords = static_cast<int> (n);
MPI_Comm_rank(world,&me);

18
src/compute_reduce.cpp
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@ -14,6 +14,7 @@
#include "string.h"
#include "stdlib.h"
#include "compute_reduce.h"
#include "lmptype.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
@ -589,7 +590,7 @@ double ComputeReduce::compute_one(int m, int flag)
/* ---------------------------------------------------------------------- */
double ComputeReduce::count(int m)
bigint ComputeReduce::count(int m)
{
int vidx = value2index[m];
int aidx = argindex[m];
@ -601,9 +602,9 @@ double ComputeReduce::count(int m)
if (flavor[m] == PERATOM) {
return group->count(igroup);
} else if (flavor[m] == LOCAL) {
double ncount = compute->size_local_rows;
double ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_DOUBLE,MPI_SUM,world);
bigint ncount = compute->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == FIX) {
@ -611,15 +612,16 @@ double ComputeReduce::count(int m)
if (flavor[m] == PERATOM) {
return group->count(igroup);
} else if (flavor[m] == LOCAL) {
double ncount = fix->size_local_rows;
double ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_DOUBLE,MPI_SUM,world);
bigint ncount = fix->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == VARIABLE)
return group->count(igroup);
return 0.0;
bigint dummy = 0;
return dummy;
}
/* ----------------------------------------------------------------------

3
src/compute_reduce.h
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@ -21,6 +21,7 @@ ComputeStyle(reduce,ComputeReduce)
#define LMP_COMPUTE_REDUCE_H
#include "compute.h"
#include "lmptype.h"
namespace LAMMPS_NS {
@ -53,7 +54,7 @@ class ComputeReduce : public Compute {
Pair pairme,pairall;
virtual double compute_one(int, int);
virtual double count(int);
virtual bigint count(int);
void combine(double &, double, int);
};

13
src/compute_reduce_region.cpp
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@ -220,7 +220,7 @@ double ComputeReduceRegion::compute_one(int m, int flag)
/* ---------------------------------------------------------------------- */
double ComputeReduceRegion::count(int m)
bigint ComputeReduceRegion::count(int m)
{
int n = value2index[m];
int j = argindex[m];
@ -235,8 +235,8 @@ double ComputeReduceRegion::count(int m)
if (flavor[m] == PERATOM) {
return group->count(igroup,iregion);
} else if (flavor[m] == LOCAL) {
double ncount = compute->size_local_rows;
double ncountall;
bigint ncount = compute->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_DOUBLE,MPI_SUM,world);
return ncountall;
}
@ -245,13 +245,14 @@ double ComputeReduceRegion::count(int m)
if (flavor[m] == PERATOM) {
return group->count(igroup,iregion);
} else if (flavor[m] == LOCAL) {
double ncount = fix->size_local_rows;
double ncountall;
bigint ncount = fix->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_DOUBLE,MPI_SUM,world);
return ncountall;
}
} else if (which[m] == VARIABLE)
return group->count(igroup,iregion);
return 0.0;
bigint dummy = 0;
return dummy;
}

3
src/compute_reduce_region.h
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@ -21,6 +21,7 @@ ComputeStyle(reduce/region,ComputeReduceRegion)
#define LMP_COMPUTE_REDUCE_REGION_H
#include "compute_reduce.h"
#include "lmptype.h"
namespace LAMMPS_NS {
@ -31,7 +32,7 @@ class ComputeReduceRegion : public ComputeReduce {
private:
double compute_one(int, int);
double count(int);
bigint count(int);
};
}

2
src/dump.cpp
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@ -173,7 +173,7 @@ void Dump::init()
if (nprocs > 1 && irregular == NULL)
irregular = new Irregular(lmp);
double size = group->count(igroup);
bigint size = group->count(igroup);
if (size > MAXINT32) error->all("Too many atoms to dump sort");
// set reorderflag = 1 if can simply reorder local atoms rather than sort

9
src/dump_dcd.cpp
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@ -22,6 +22,7 @@
#include "time.h"
#include "string.h"
#include "dump_dcd.h"
#include "lmptype.h"
#include "domain.h"
#include "atom.h"
#include "update.h"
@ -67,9 +68,11 @@ DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
// allocate global array for atom coords
if (igroup == 0) natoms = static_cast<int> (atom->natoms);
else natoms = static_cast<int> (group->count(igroup));
if (natoms <= 0) error->all("Invalid natoms for dump dcd");
bigint n;
if (igroup == 0) n = static_cast<int> (atom->natoms);
else n = static_cast<int> (group->count(igroup));
if (n > MAXINT32) error->all("Too many atoms for dump dcd");
natoms = n;
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
xf = &coords[0*natoms];

2
src/fix_heat.cpp
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@ -94,7 +94,7 @@ void FixHeat::init()
// cannot have 0 atoms in group
if (group->count(igroup) == 0.0) error->all("Fix heat group has no atoms");
if (group->count(igroup) == 0) error->all("Fix heat group has no atoms");
masstotal = group->mass(igroup);
}

2
src/fix_momentum.cpp
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@ -60,7 +60,7 @@ FixMomentum::FixMomentum(LAMMPS *lmp, int narg, char **arg) :
// cannot have 0 atoms in group
if (group->count(igroup) == 0.0)
if (group->count(igroup) == 0)
error->all("Fix momentum group has no atoms");
}

2
src/fix_recenter.cpp
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@ -91,7 +91,7 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
// cannot have 0 atoms in group
if (group->count(igroup) == 0.0)
if (group->count(igroup) == 0)
error->all("Fix recenter group has no atoms");
}

19
src/group.cpp
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@ -17,6 +17,7 @@
#include "string.h"
#include "stdlib.h"
#include "group.h"
#include "lmptype.h"
#include "domain.h"
#include "atom.h"
#include "force.h"
@ -481,10 +482,9 @@ void Group::read_restart(FILE *fp)
/* ----------------------------------------------------------------------
count atoms in group
compute in double precision in case system is huge
------------------------------------------------------------------------- */
double Group::count(int igroup)
bigint Group::count(int igroup)
{
int groupbit = bitmask[igroup];
@ -495,18 +495,17 @@ double Group::count(int igroup)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) n++;
double nsingle = n;
double nall;
MPI_Allreduce(&nsingle,&nall,1,MPI_DOUBLE,MPI_SUM,world);
bigint nsingle = n;
bigint nall;
MPI_Allreduce(&nsingle,&nall,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
return nall;
}
/* ----------------------------------------------------------------------
count atoms in group and region
compute in double precision in case system is huge
------------------------------------------------------------------------- */
double Group::count(int igroup, int iregion)
bigint Group::count(int igroup, int iregion)
{
int groupbit = bitmask[igroup];
Region *region = domain->regions[iregion];
@ -519,9 +518,9 @@ double Group::count(int igroup, int iregion)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) n++;
double nsingle = n;
double nall;
MPI_Allreduce(&nsingle,&nall,1,MPI_DOUBLE,MPI_SUM,world);
bigint nsingle = n;
bigint nall;
MPI_Allreduce(&nsingle,&nall,1,MPI_UNSIGNED_LONG,MPI_SUM,world);
return nall;
}

5
src/group.h
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@ -16,6 +16,7 @@
#include "stdio.h"
#include "pointers.h"
#include "lmptype.h"
namespace LAMMPS_NS {
@ -34,8 +35,8 @@ class Group : protected Pointers {
void write_restart(FILE *);
void read_restart(FILE *);
double count(int); // count atoms in group
double count(int,int); // count atoms in group & region
bigint count(int); // count atoms in group
bigint count(int,int); // count atoms in group & region
double mass(int); // total mass of atoms in group
double mass(int,int);
double charge(int); // total charge of atoms in group

4
src/velocity.cpp
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@ -536,7 +536,7 @@ void Velocity::zero_momentum()
{
// cannot have 0 atoms in group
if (group->count(igroup) == 0.0)
if (group->count(igroup) == 0)
error->all("Cannot zero momentum of 0 atoms");
// compute velocity of center-of-mass of group
@ -569,7 +569,7 @@ void Velocity::zero_rotation()
// cannot have 0 atoms in group
if (group->count(igroup) == 0.0)
if (group->count(igroup) == 0)
error->all("Cannot zero momentum of 0 atoms");
// compute omega (angular velocity) of group around center-of-mass