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Merge branch 'master' of github.com:lammps/lammps

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This commit is contained in:
Steve Plimpton
2016-10-19 08:58:22 -06:00
parent 58141e0559 b0cf1ded38
commit 3d254780de
10 changed files with 23 additions and 23 deletions
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1
doc/src/fixes.txt
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@ -48,6 +48,7 @@ Fixes :h1
fix_gld
fix_gle
fix_gravity
fix_halt
fix_heat
fix_imd
fix_indent

1
doc/src/lammps.book
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@ -170,6 +170,7 @@ fix_gcmc.html
fix_gld.html
fix_gle.html
fix_gravity.html
fix_halt.html
fix_heat.html
fix_imd.html
fix_indent.html

18
src/REPLICA/prd.cpp
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@ -795,7 +795,7 @@ void PRD::replicate(int ireplica)
if (cmode == SINGLE_PROC_DIRECT) {
MPI_Bcast(atom->x[0],3*atom->nlocal,MPI_DOUBLE,ireplica,comm_replica);
MPI_Bcast(atom->image,atom->nlocal,MPI_INT,ireplica,comm_replica);
MPI_Bcast(atom->image,atom->nlocal,MPI_LMP_IMAGEINT,ireplica,comm_replica);
return;
}
@ -815,9 +815,9 @@ void PRD::replicate(int ireplica)
memcpy(imageall,image,nlocal*sizeof(imageint));
}
MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,ireplica,comm_replica);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,ireplica,comm_replica);
for (i = 0; i < nlocal; i++) {
m = atom->map(tagall[i]);
@ -844,8 +844,8 @@ void PRD::replicate(int ireplica)
displacements[i+1] = displacements[i] + counts[i];
MPI_Gatherv(atom->tag,atom->nlocal,MPI_LMP_TAGINT,
tagall,counts,displacements,MPI_LMP_TAGINT,0,world);
MPI_Gatherv(atom->image,atom->nlocal,MPI_LMP_TAGINT,
imageall,counts,displacements,MPI_LMP_TAGINT,0,world);
MPI_Gatherv(atom->image,atom->nlocal,MPI_LMP_IMAGEINT,
imageall,counts,displacements,MPI_LMP_IMAGEINT,0,world);
for (i = 0; i < nprocs; i++) counts[i] *= 3;
for (i = 0; i < nprocs-1; i++)
displacements[i+1] = displacements[i] + counts[i];
@ -854,13 +854,13 @@ void PRD::replicate(int ireplica)
}
if (me == 0) {
MPI_Bcast(tagall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_INT,ireplica,comm_replica);
MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,ireplica,comm_replica);
MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,ireplica,comm_replica);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,ireplica,comm_replica);
}
MPI_Bcast(tagall,natoms,MPI_INT,0,world);
MPI_Bcast(imageall,natoms,MPI_INT,0,world);
MPI_Bcast(tagall,natoms,MPI_LMP_TAGINT,0,world);
MPI_Bcast(imageall,natoms,MPI_LMP_IMAGEINT,0,world);
MPI_Bcast(xall[0],3*natoms,MPI_DOUBLE,0,world);
double **x = atom->x;

2
src/compute_bond_local.cpp
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@ -148,7 +148,7 @@ int ComputeBondLocal::compute_bonds(int flag)
double vvib,vrotsq;
double inertia,omegasq;
double mvv2e;
double engpot,engtrans,engvib,engrot,engtot,fbond;
double engpot,engtrans,engvib,engrot,fbond;
double *ptr;
double **x = atom->x;

2
src/dump.cpp
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@ -874,7 +874,7 @@ void Dump::modify_params(int narg, char **arg)
format_float_user = NULL;
// pass format none to child classes which may use it
// not an error if they don't
int n = modify_param(narg-iarg,&arg[iarg]);
modify_param(narg-iarg,&arg[iarg]);
iarg += 2;
continue;
}

2
src/finish.cpp
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@ -1,5 +1,5 @@
/* ----------------------------------------------------------------------
LAMMRDS - Large-scale Atomic/Molecular Massively Parallel Simulator
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov

2
src/fix_halt.cpp
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@ -194,10 +194,8 @@ void FixHalt::post_run()
double FixHalt::bondmax()
{
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int i1,i2;
double delx,dely,delz,rsq;

3
src/lmptype.h
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@ -89,6 +89,7 @@ typedef int64_t bigint;
#define MAXBIGINT INT64_MAX
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_IMAGEINT MPI_INT
#define MPI_LMP_BIGINT MPI_LL
#define TAGINT_FORMAT "%d"
@ -120,6 +121,7 @@ typedef int64_t bigint;
#define MAXBIGINT INT64_MAX
#define MPI_LMP_TAGINT MPI_LL
#define MPI_LMP_IMAGEINT MPI_LL
#define MPI_LMP_BIGINT MPI_LL
#define TAGINT_FORMAT "%" PRId64
@ -150,6 +152,7 @@ typedef int bigint;
#define MAXBIGINT INT_MAX
#define MPI_LMP_TAGINT MPI_INT
#define MPI_LMP_IMAGEINT MPI_INT
#define MPI_LMP_BIGINT MPI_INT
#define TAGINT_FORMAT "%d"

14
src/neigh_derive.cpp
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@ -232,8 +232,8 @@ void Neighbor::skip_from_granular(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
tagint jtag;
int *neighptr,*jlist,*touchptr,*touchptr_skip;
double *shearptr,*shearptr_skip;
int *neighptr,*jlist,*touchptr;
double *shearptr;
NeighList *listgranhistory;
int *npartner;
@ -364,8 +364,8 @@ void Neighbor::skip_from_granular_off2on(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,dnum,dnumbytes;
tagint itag,jtag;
int *neighptr,*jlist,*touchptr,*touchptr_skip;
double *shearptr,*shearptr_skip;
int *neighptr,*jlist,*touchptr;
double *shearptr;
NeighList *listgranhistory;
int *npartner;
@ -502,8 +502,8 @@ void Neighbor::skip_from_granular_off2on(NeighList *list)
void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
{
int i,j,ii,jj,m,n,nn,itype,jnum,joriginal,flip,dnum,dnumbytes,tmp;
tagint itag,jtag;
int *surf,*neighptr,*jlist;
tagint jtag;
int *surf,*jlist;
NeighList *listgranhistory;
int *npartner;
@ -571,7 +571,6 @@ void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
itag = tag[i];
n = 0;
@ -625,7 +624,6 @@ void Neighbor::skip_from_granular_off2on_onesided(NeighList *list)
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
itag = tag[i];
// loop over parent non-skip granular list and optionally its history info

1
src/region.cpp
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@ -517,7 +517,6 @@ void Region::set_velocity()
void Region::velocity_contact(double *vwall, double *x, int ic)
{
Contact c = contact[ic];
double xc[3];
vwall[0] = vwall[1] = vwall[2] = 0.0;