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plug some memory leaks

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This commit is contained in:
Axel Kohlmeyer
2017-05-19 16:14:59 -04:00
parent 6ef79d3715
commit 546aed7ccd
1 changed files with 29 additions and 32 deletions
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61
src/REPLICA/fix_neb.cpp
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@ -115,13 +115,14 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
int *iroots = new int[nreplica]; int *iroots = new int[nreplica];
MPI_Group uworldgroup,rootgroup; MPI_Group uworldgroup,rootgroup;
if (NEBLongRange) { if (NEBLongRange) {
for (int iIm =0; iIm < nreplica;iIm++) for (int i=0; i<nreplica; i++)
iroots[iIm]=universe->root_proc[iIm]; iroots[i]=universe->root_proc[i];
MPI_Comm_group(uworld, &uworldgroup); MPI_Comm_group(uworld, &uworldgroup);
MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup); MPI_Group_incl(uworldgroup, nreplica, iroots, &rootgroup);
// MPI_Comm_create_group(uworld, rootgroup, 0, &rootworld);
MPI_Comm_create(uworld, rootgroup, &rootworld); MPI_Comm_create(uworld, rootgroup, &rootworld);
} }
delete[] iroots;
// create a new compute pe style // create a new compute pe style
// id = fix-ID + pe, compute group = all // id = fix-ID + pe, compute group = all
@ -139,8 +140,8 @@ FixNEB::FixNEB(LAMMPS *lmp, int narg, char **arg) :
// initialize local storage // initialize local storage
maxlocal = 0; maxlocal = -1;
ntotal = 0; ntotal = -1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -153,6 +154,7 @@ FixNEB::~FixNEB()
memory->destroy(xprev); memory->destroy(xprev);
memory->destroy(xnext); memory->destroy(xnext);
memory->destroy(tangent); memory->destroy(tangent);
memory->destroy(fnext);
memory->destroy(springF); memory->destroy(springF);
memory->destroy(xsend); memory->destroy(xsend);
memory->destroy(xrecv); memory->destroy(xrecv);
@ -171,9 +173,10 @@ FixNEB::~FixNEB()
memory->destroy(counts); memory->destroy(counts);
memory->destroy(displacements); memory->destroy(displacements);
if (NEBLongRange) if (NEBLongRange) {
MPI_Comm_free(&rootworld);
memory->destroy(nlenall); memory->destroy(nlenall);
}
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -246,11 +249,11 @@ void FixNEB::min_setup(int vflag)
void FixNEB::min_post_force(int vflag) void FixNEB::min_post_force(int vflag)
{ {
double vprev,vnext,vmax,vmin; double vprev,vnext;
double delxp,delyp,delzp,delxn,delyn,delzn; double delxp,delyp,delzp,delxn,delyn,delzn;
double vIni =0.0; double vIni=0.0;
vprev=vnext=veng = pe->compute_scalar(); vprev=vnext=veng=pe->compute_scalar();
if (ireplica < nreplica-1 && me ==0) if (ireplica < nreplica-1 && me ==0)
MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld); MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
@ -302,7 +305,7 @@ void FixNEB::min_post_force(int vflag)
double **x = atom->x; double **x = atom->x;
int *mask = atom->mask; int *mask = atom->mask;
double dot = 0.0; double dot = 0.0;
double prefactor; double prefactor = 0.0;
double **f = atom->f; double **f = atom->f;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
@ -364,9 +367,9 @@ void FixNEB::min_post_force(int vflag)
} }
} }
} else { } else {
//not the first or last replica // not the first or last replica
vmax = MAX(fabs(vnext-veng),fabs(vprev-veng)); double vmax = MAX(fabs(vnext-veng),fabs(vprev-veng));
vmin = MIN(fabs(vnext-veng),fabs(vprev-veng)); double vmin = MIN(fabs(vnext-veng),fabs(vprev-veng));
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
@ -658,7 +661,6 @@ void FixNEB::inter_replica_comm()
MPI_Send(f[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld); MPI_Send(f[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE); if (ireplica < nreplica-1) MPI_Wait(&request,MPI_STATUS_IGNORE);
return; return;
} }
@ -832,17 +834,19 @@ void FixNEB::inter_replica_comm()
void FixNEB::reallocate() void FixNEB::reallocate()
{ {
maxlocal = atom->nmax;
memory->destroy(xprev); memory->destroy(xprev);
memory->destroy(xnext); memory->destroy(xnext);
memory->destroy(tangent); memory->destroy(tangent);
memory->destroy(fnext); memory->destroy(fnext);
memory->destroy(springF); memory->destroy(springF);
if (NEBLongRange) { memory->create(xprev,maxlocal,3,"neb:xprev");
memory->destroy(nlenall); memory->create(xnext,maxlocal,3,"neb:xnext");
memory->create(nlenall,nreplica,"neb:nlenall"); memory->create(tangent,maxlocal,3,"neb:tangent");
} memory->create(fnext,maxlocal,3,"neb:fnext");
memory->create(springF,maxlocal,3,"neb:springF");
if (cmode != SINGLE_PROC_DIRECT) { if (cmode != SINGLE_PROC_DIRECT) {
memory->destroy(xsend); memory->destroy(xsend);
@ -851,18 +855,6 @@ void FixNEB::reallocate()
memory->destroy(frecv); memory->destroy(frecv);
memory->destroy(tagsend); memory->destroy(tagsend);
memory->destroy(tagrecv); memory->destroy(tagrecv);
}
maxlocal = atom->nmax;
memory->create(xprev,maxlocal,3,"neb:xprev");
memory->create(xnext,maxlocal,3,"neb:xnext");
memory->create(tangent,maxlocal,3,"neb:tangent");
memory->create(fnext,maxlocal,3,"neb:fnext");
memory->create(springF,maxlocal,3,"neb:springF");
if (cmode != SINGLE_PROC_DIRECT) {
memory->create(xsend,maxlocal,3,"neb:xsend"); memory->create(xsend,maxlocal,3,"neb:xsend");
memory->create(fsend,maxlocal,3,"neb:fsend"); memory->create(fsend,maxlocal,3,"neb:fsend");
memory->create(xrecv,maxlocal,3,"neb:xrecv"); memory->create(xrecv,maxlocal,3,"neb:xrecv");
@ -870,4 +862,9 @@ void FixNEB::reallocate()
memory->create(tagsend,maxlocal,"neb:tagsend"); memory->create(tagsend,maxlocal,"neb:tagsend");
memory->create(tagrecv,maxlocal,"neb:tagrecv"); memory->create(tagrecv,maxlocal,"neb:tagrecv");
} }
if (NEBLongRange) {
memory->destroy(nlenall);
memory->create(nlenall,nreplica,"neb:nlenall");
}
} }