diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index 6ef6759f7fe1ca2db57e2018b87dc7522fd417fa..d20b359fb25cb2c067882736c26b3eea2e8dd0dd 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -671,7 +671,7 @@ void FixPour::pre_exchange()
if (ninserted_atoms) {
atom->natoms += ninserted_atoms;
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemols[imol]->nbonds * ninserted_mols;
diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp
index c107fc85c75603f722e1dde093e835d6057b89aa..2f0874cf117f527a97e425bf7feac3c1a60b2264 100644
--- a/src/KSPACE/ewald_disp.cpp
+++ b/src/KSPACE/ewald_disp.cpp
@@ -52,7 +52,7 @@ EwaldDisp::EwaldDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
ewaldflag = dispersionflag = dipoleflag = 1;
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
- memset(function, 0, EWALD_NORDER*sizeof(int));
+ memset(function, 0, EWALD_NFUNCS*sizeof(int));
kenergy = kvirial = NULL;
cek_local = cek_global = NULL;
ekr_local = NULL;
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 7134ed4326b68f858da964969d70c5ee93b7b1b7..fcb483b6803f0de0353aada6a52b65e8fa30be30 100755
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -245,7 +245,7 @@ void PPPMDisp::init()
int *ptr = pair ? (int *) pair->extract("ewald_order",tmp) : NULL;
double *p_cutoff = pair ? (double *) pair->extract("cut_coul",tmp) : NULL;
double *p_cutoff_lj = pair ? (double *) pair->extract("cut_LJ",tmp) : NULL;
- if (!(ptr||*p_cutoff||*p_cutoff_lj))
+ if (!(ptr||p_cutoff||p_cutoff_lj))
error->all(FLERR,"KSpace style is incompatible with Pair style");
cutoff = *p_cutoff;
cutoff_lj = *p_cutoff_lj;
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 2afd694dfddf09be75edd07457b3b90c5fc3d7f7..58bbeffbfc22697b8a13e1a8a1ac924b9a713cc0 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -620,19 +620,19 @@ void PairAIREBO::FLJ(int eflag, int vflag)
if (wik*wkj > best) {
best = wik*wkj;
npath = 3;
- atomk = k;
- delikS[0] = delik[0];
- delikS[1] = delik[1];
- delikS[2] = delik[2];
- rikS = rik;
- wikS = wik;
- dwikS = dwik;
- deljkS[0] = deljk[0];
- deljkS[1] = deljk[1];
- deljkS[2] = deljk[2];
- rkjS = rkj;
- wkjS = wkj;
- dwkjS = dwkj;
+ atomk = k;
+ delikS[0] = delik[0];
+ delikS[1] = delik[1];
+ delikS[2] = delik[2];
+ rikS = rik;
+ wikS = wik;
+ dwikS = dwik;
+ deljkS[0] = deljk[0];
+ deljkS[1] = deljk[1];
+ deljkS[2] = deljk[2];
+ rkjS = rkj;
+ wkjS = wkj;
+ dwkjS = dwkj;
if (best == 1.0) {
done = 1;
break;
@@ -803,7 +803,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
if (vflag_atom)
v_tally3(atomi,atomj,atomk,fi,fj,delikS,deljkS);
- } else {
+ } else if (npath == 4) {
fpair1 = dC*dwikS*wkmS*wmjS / rikS;
fi[0] = delikS[0]*fpair1;
fi[1] = delikS[1]*fpair1;
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 94fbe62a99154323062721e6417e83e415484e7e..20febf3a3791064250c9d72000f4538c96883700 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -5108,11 +5108,7 @@ void PairBOP::read_table(char *filename)
fgets(s,MAXLINE,fp);
sscanf(s,"%lf%lf",&sigma_delta[i],&pi_delta[i]);
fgets(s,MAXLINE,fp);
- if(nws==3) {
- sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
- } else {
- sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
- }
+ sscanf(s,"%lf%lf%lf",&sigma_f[i],&sigma_k[i],&small3[i]);
}
if(nws==3) {
for(i=0;i<bop_types;i++)
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 60616e4f1fabb6e30dbe70397f7764d2a5535d2e..82f69c76b6365f4b98c286038bdeaab218426bd5 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -79,6 +79,8 @@ PairEAM::~PairEAM()
memory->destroy(cutsq);
delete [] map;
delete [] type2frho;
+ map = NULL;
+ type2frho = NULL;
memory->destroy(type2rhor);
memory->destroy(type2z2r);
}
@@ -91,6 +93,7 @@ PairEAM::~PairEAM()
memory->destroy(funcfl[i].zr);
}
memory->sfree(funcfl);
+ funcfl = NULL;
}
if (setfl) {
@@ -101,6 +104,7 @@ PairEAM::~PairEAM()
memory->destroy(setfl->rhor);
memory->destroy(setfl->z2r);
delete setfl;
+ setfl = NULL;
}
if (fs) {
@@ -111,6 +115,7 @@ PairEAM::~PairEAM()
memory->destroy(fs->rhor);
memory->destroy(fs->z2r);
delete fs;
+ fs = NULL;
}
memory->destroy(frho);
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index d65ea8bda02befbdfc606373b83db37476c3c13c..d41e3ef325131b5ab453830e83b17889262fcd2c 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -1308,7 +1308,7 @@ void FixGCMC::attempt_molecule_insertion()
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
@@ -1957,7 +1957,7 @@ void FixGCMC::attempt_molecule_insertion_full()
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index 0b35627ebe8915973b8b8ccf551f3f36435ebd74..7aa3f72ce04e885349f777bbb04428b0454e75c9 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -563,7 +563,7 @@ void FixDeposit::pre_exchange()
if (success) {
atom->natoms += natom;
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (mode == MOLECULE) {
atom->nbonds += onemols[imol]->nbonds;
diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp
index 2ed15f81ed060d0bf19fbf76ba3d5b883a84f5cb..2f25b714b053935a0620629606a91826376272b0 100644
--- a/src/MISC/fix_oneway.cpp
+++ b/src/MISC/fix_oneway.cpp
@@ -43,7 +43,7 @@ FixOneWay::FixOneWay(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (nevery < 1) error->all(FLERR,"Illegal fix oneway command");
int len = strlen(arg[4]);
- regionstr = new char[len];
+ regionstr = new char[len+1];
strcpy(regionstr,arg[4]);
if (strcmp(arg[5], "x") == 0) direction = X|PLUS;
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index b288c470295ff61709e87a031d0a77d718c53dd0..8198f3d4b4dab6953e147b670622dfd34bc282d8 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -57,7 +57,7 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
int i,i1,i2,i3,n,m,type,b_factor;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
- double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
+ double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
double tn,tn_1,tn_2,un,un_1,un_2;
eangle = 0.0;
@@ -120,10 +120,6 @@ void AngleCosinePeriodic::compute(int eflag, int vflag)
un_1 = 2.0;
un_2 = 0.0;
- s = sqrt(1.0 - c*c);
- if (s < SMALL) s = SMALL;
- s = 1.0/s;
-
// force & energy
tn_2 = c;
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index 0eadf1686ac541d24d69dbb032ddb5ca2216d8d6..28b3fe8924fbf6b9d40e3ddc67d908d619d230d4 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -145,8 +145,8 @@ void ImproperUmbrella::compute(int eflag, int vflag)
}
}
- if (c > 1.0) s = 1.0;
- if (c < -1.0) s = -1.0;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
diff --git a/src/OPT/pair_eam_alloy_opt.h b/src/OPT/pair_eam_alloy_opt.h
index c6056e3cff46821a4208d529f84b76930a4749b3..3fdfc449e9e48820a8f9815d8306f2d65325553f 100644
--- a/src/OPT/pair_eam_alloy_opt.h
+++ b/src/OPT/pair_eam_alloy_opt.h
@@ -28,6 +28,7 @@ namespace LAMMPS_NS {
class PairEAMAlloyOpt : public PairEAMAlloy, public PairEAMOpt {
public:
PairEAMAlloyOpt(class LAMMPS *);
+ virtual ~PairEAMAlloyOpt() {}
};
}
diff --git a/src/OPT/pair_eam_fs_opt.h b/src/OPT/pair_eam_fs_opt.h
index f8fba9871755867c84372af6a06de0f1c6276b2c..f0288d5c57011fdfb684cf0264d4c1b368086e98 100644
--- a/src/OPT/pair_eam_fs_opt.h
+++ b/src/OPT/pair_eam_fs_opt.h
@@ -28,6 +28,7 @@ namespace LAMMPS_NS {
class PairEAMFSOpt : public PairEAMFS, public PairEAMOpt {
public:
PairEAMFSOpt(class LAMMPS *);
+ virtual ~PairEAMFSOpt() {}
};
}
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 8cb0be74625f0b817ac55286ee56c20bd8770cb9..6e5399ba8263bbea09a013d5127272c3268de4b9 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -207,7 +207,7 @@ void NEB::run()
update->endstep = update->laststep = update->firststep + n1steps;
update->nsteps = n1steps;
update->max_eval = n1steps;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many timesteps for NEB");
update->minimize->setup();
@@ -275,7 +275,7 @@ void NEB::run()
update->endstep = update->laststep = update->firststep + n2steps;
update->nsteps = n2steps;
update->max_eval = n2steps;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
update->minimize->init();
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index de3447db98ae57bd3c8185e83f81a09fc1996e69..57aaf485f49a7e46de181f729d2e58700cafaacf 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -220,7 +220,7 @@ void PRD::command(int narg, char **arg)
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
update->restrict_output = 1;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
@@ -568,7 +568,7 @@ void PRD::quench()
update->whichflag = 2;
update->nsteps = maxiter;
update->endstep = update->laststep = update->firststep + maxiter;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many iterations");
// full init works
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index 80381a7a3bac5321507151084a195845fbc0eb82..0f46867f99bc587ac44b42f3a84908995c7e67bc 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -199,7 +199,7 @@ void TAD::command(int narg, char **arg)
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
update->restrict_output = 1;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
@@ -406,7 +406,7 @@ void TAD::command(int narg, char **arg)
timer->get_wall(Timer::TOTAL),nprocs_universe,nsteps,atom->natoms);
}
- if (me_universe == 0) fclose(ulogfile_neb);
+ if ((me_universe == 0) && ulogfile_neb) fclose(ulogfile_neb);
if (me == 0) {
if (screen) fprintf(screen,"\nTAD done\n");
@@ -478,7 +478,7 @@ void TAD::quench()
update->whichflag = 2;
update->nsteps = maxiter;
update->endstep = update->laststep = update->firststep + maxiter;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many iterations");
// full init works
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index 45e100ad521787acac40639f28a5f2b28e759482..8771ab53758642a83d3f8a3694e6435777c6bfc4 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -107,7 +107,7 @@ void Temper::command(int narg, char **arg)
update->nsteps = nsteps;
update->beginstep = update->firststep = update->ntimestep;
update->endstep = update->laststep = update->firststep + nsteps;
- if (update->laststep < 0 || update->laststep > MAXBIGINT)
+ if (update->laststep < 0)
error->all(FLERR,"Too many timesteps");
lmp->init();
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index 571e77b12998c43e7e9d6f97a86989a66748f0c1..f01fbdfbbb38e51a5ccd973815d61f899cb3e8e9 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -506,7 +506,7 @@ void FixAppendAtoms::pre_exchange()
if (addtotal) {
domain->reset_box();
atom->natoms += addtotal;
- if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
+ if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
if (atom->tag_enable) atom->tag_extend();
if (atom->map_style) {
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 2f908bccb44264d1aba900121961ce11aae88a96..9217a24f6f57f7895c4c98469ad6cad8f3d2fcb6 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -41,6 +41,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal fix wall/piston command");
randomt = NULL;
+ gfactor1 = gfactor2 = NULL;
tempflag = 0;
scaleflag = 1;
roughflag = 0;
@@ -150,6 +151,15 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
+FixWallPiston::~FixWallPiston()
+{
+ delete[] gfactor2;
+ delete[] gfactor1;
+ delete randomt;
+}
+
+/* ---------------------------------------------------------------------- */
+
int FixWallPiston::setmask()
{
int mask = 0;
diff --git a/src/SHOCK/fix_wall_piston.h b/src/SHOCK/fix_wall_piston.h
index 8ad3c25b579f6b1d0459e66e4c90f9dcde098cb9..28135b235903057841928c0844f97038794f08bf 100644
--- a/src/SHOCK/fix_wall_piston.h
+++ b/src/SHOCK/fix_wall_piston.h
@@ -26,6 +26,7 @@ namespace LAMMPS_NS {
class FixWallPiston : public Fix {
public:
FixWallPiston(class LAMMPS *, int, char **);
+ virtual ~FixWallPiston();
int setmask();
void post_integrate();
void initial_integrate(int);
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index 85a08d1838997e6d03bd2fed90bd9d8d015679dc..cf90b50d8a39140796768d4bd8be4c4734b8485a 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -243,7 +243,7 @@ void ComputeBasalAtom::compute_peratom()
j1[1]=2;
j1[2]=2;
}
- xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0;
+ xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0.0;
for (j = 0; j < chi[0]; j++) {
for (k = j+1; k < chi[0]; k++) {
//get cross products
@@ -261,27 +261,29 @@ void ComputeBasalAtom::compute_peratom()
y7[count] = y4[count]*copysign(1.0,z4[count]);
z7[count] = z4[count]*copysign(1.0,z4[count]);
//get average cross products
- xmean5 = xmean5 + x5[count];
- ymean5 = ymean5 + y5[count];
- zmean5 = zmean5 + z5[count];
- xmean6 = xmean6 + x6[count];
- ymean6 = ymean6 + y6[count];
- zmean6 = zmean6 + z6[count];
- xmean7 = xmean7 + x7[count];
- ymean7 = ymean7 + y7[count];
- zmean6 = zmean6 + z7[count];
+ xmean5 += x5[count];
+ ymean5 += y5[count];
+ zmean5 += z5[count];
+ xmean6 += x6[count];
+ ymean6 += y6[count];
+ zmean6 += z6[count];
+ xmean7 += x7[count];
+ ymean7 += y7[count];
+ zmean6 += z7[count];
count++;
}
}
- xmean5 = xmean5/count;
- xmean6 = xmean6/count;
- xmean7 = xmean7/count;
- ymean5 = ymean5/count;
- ymean6 = ymean6/count;
- ymean7 = ymean7/count;
- zmean5 = zmean5/count;
- zmean6 = zmean6/count;
- zmean7 = zmean7/count;
+ if (count > 0) {
+ xmean5 /= count;
+ xmean6 /= count;
+ xmean7 /= count;
+ ymean5 /= count;
+ ymean6 /= count;
+ ymean7 /= count;
+ zmean5 /= count;
+ zmean6 /= count;
+ zmean7 /= count;
+ }
var5 = var6 = var7 = 0.0;
//find standard deviations
for (j=0;j<count;j++){
diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp
index 7ce69f6834946a71f04050db06345b5d93497a3c..befaffc3634f9c5ac56936dfcbdc75a6e9b5e743 100644
--- a/src/USER-MISC/dihedral_table.cpp
+++ b/src/USER-MISC/dihedral_table.cpp
@@ -81,7 +81,7 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
const double offdiag[], size_t o_stride,
const double b[], size_t b_stride,
double x[], size_t x_stride,
- size_t N)
+ size_t N, bool warn)
{
int status = GSL_SUCCESS;
double * delta = (double *) malloc (N * sizeof (double));
@@ -91,8 +91,15 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
double * z = (double *) malloc (N * sizeof (double));
if (delta == 0 || gamma == 0 || alpha == 0 || c == 0 || z == 0) {
- cerr << "Internal Cyclic Spline Error: failed to allocate working space\n";
- exit(GSL_ENOMEM);
+ if (warn)
+ fprintf(stderr,"Internal Cyclic Spline Error: failed to allocate working space\n");
+
+ if (delta) free(delta);
+ if (gamma) free(gamma);
+ if (alpha) free(alpha);
+ if (c) free(c);
+ if (z) free(z);
+ return GSL_ENOMEM;
}
else
{
@@ -104,6 +111,11 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
if (N == 1)
{
x[0] = b[0] / diag[0];
+ free(delta);
+ free(gamma);
+ free(alpha);
+ free(c);
+ free(z);
return GSL_SUCCESS;
}
@@ -165,21 +177,14 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
}
}
- if (z != 0)
- free (z);
- if (c != 0)
- free (c);
- if (alpha != 0)
- free (alpha);
- if (gamma != 0)
- free (gamma);
- if (delta != 0)
- free (delta);
-
- if (status == GSL_EZERODIV) {
- cerr <<"Internal Cyclic Spline Error: Matrix must be positive definite.\n";
- exit(GSL_EZERODIV);
- }
+ free (z);
+ free (c);
+ free (alpha);
+ free (gamma);
+ free (delta);
+
+ if ((status == GSL_EZERODIV) && warn)
+ fprintf(stderr, "Internal Cyclic Spline Error: Matrix must be positive definite.\n");
return status;
} //solve_cyc_tridiag()
@@ -188,11 +193,11 @@ static int solve_cyc_tridiag( const double diag[], size_t d_stride,
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
-static void cyc_spline(double const *xa,
- double const *ya,
- int n,
- double period,
- double *y2a)
+static int cyc_spline(double const *xa,
+ double const *ya,
+ int n,
+ double period,
+ double *y2a, bool warn)
{
double *diag = new double[n];
@@ -234,18 +239,25 @@ static void cyc_spline(double const *xa,
((ya[i] - ya[im1]) / (xa[i] - xa_im1));
}
- // Because this matix is tridiagonal (and cyclic), we can use the following
+ // Because this matrix is tridiagonal (and cyclic), we can use the following
// cheap method to invert it.
- solve_cyc_tridiag(diag, 1,
+ if (solve_cyc_tridiag(diag, 1,
offdiag, 1,
rhs, 1,
y2a, 1,
- n);
-
+ n, warn) != GSL_SUCCESS) {
+ if (warn)
+ fprintf(stderr,"Error in inverting matrix for splines.\n");
+
+ delete [] diag;
+ delete [] offdiag;
+ delete [] rhs;
+ return 1;
+ }
delete [] diag;
delete [] offdiag;
delete [] rhs;
-
+ return 0;
} // cyc_spline()
/* ---------------------------------------------------------------------- */
@@ -913,6 +925,11 @@ void DihedralTable::coeff(int narg, char **arg)
tb->ffile[I] = ffile_tmp[i];
I++;
}
+
+ // clean up temporary storage
+ delete[] phifile_tmp;
+ delete[] ffile_tmp;
+ delete[] efile_tmp;
}
// spline read-in and compute r,e,f vectors within table
@@ -1147,10 +1164,14 @@ void DihedralTable::spline_table(Table *tb)
memory->create(tb->e2file,tb->ninput,"dihedral:e2file");
memory->create(tb->f2file,tb->ninput,"dihedral:f2file");
- cyc_spline(tb->phifile, tb->efile, tb->ninput, MY_2PI, tb->e2file);
+ if (cyc_spline(tb->phifile, tb->efile, tb->ninput,
+ MY_2PI,tb->e2file,comm->me == 0))
+ error->one(FLERR,"Error computing dihedral spline tables");
if (! tb->f_unspecified) {
- cyc_spline(tb->phifile, tb->ffile, tb->ninput, MY_2PI, tb->f2file);
+ if (cyc_spline(tb->phifile, tb->ffile, tb->ninput,
+ MY_2PI, tb->f2file, comm->me == 0))
+ error->one(FLERR,"Error computing dihedral spline tables");
}
// CHECK to help make sure the user calculated forces in a way
@@ -1302,9 +1323,9 @@ void DihedralTable::compute_table(Table *tb)
- cyc_spline(tb->phi, tb->e, tablength, MY_2PI, tb->e2);
+ cyc_spline(tb->phi, tb->e, tablength, MY_2PI, tb->e2, comm->me == 0);
if (! tb->f_unspecified)
- cyc_spline(tb->phi, tb->f, tablength, MY_2PI, tb->f2);
+ cyc_spline(tb->phi, tb->f, tablength, MY_2PI, tb->f2, comm->me == 0);
}
@@ -1339,13 +1360,13 @@ void DihedralTable::param_extract(Table *tb, char *line)
else if (strcmp(word,"CHECKU") == 0) {
word = strtok(NULL," \t\n\r\f");
memory->sfree(checkU_fname);
- memory->create(checkU_fname,strlen(word),"dihedral_table:checkU");
+ memory->create(checkU_fname,strlen(word)+1,"dihedral_table:checkU");
strcpy(checkU_fname, word);
}
else if (strcmp(word,"CHECKF") == 0) {
word = strtok(NULL," \t\n\r\f");
memory->sfree(checkF_fname);
- memory->create(checkF_fname,strlen(word),"dihedral_table:checkF");
+ memory->create(checkF_fname,strlen(word)+1,"dihedral_table:checkF");
strcpy(checkF_fname, word);
}
// COMMENTING OUT: equilibrium angles are not supported
diff --git a/src/USER-MISC/fix_ave_spatial_sphere.cpp b/src/USER-MISC/fix_ave_spatial_sphere.cpp
index c654db7ef80a8fd7453c6952a9db2fa14deb0ad2..bf82173be2813a0b215cae822e704c3f3ea753f9 100644
--- a/src/USER-MISC/fix_ave_spatial_sphere.cpp
+++ b/src/USER-MISC/fix_ave_spatial_sphere.cpp
@@ -827,7 +827,7 @@ void FixAveSpatialSphere::end_of_step()
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
- ftruncate(fileno(fp),fileend);
+ if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 58251a814e8fe26bfb5f5a8517d68d70ba8bf61f..07dbeb2500cff75e4c92f8382111ebbbb0a1a322 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -18,6 +18,7 @@
#include "mpi.h"
#include "stdio.h"
#include "string.h"
+#include "stdlib.h"
#include "fix_ipi.h"
#include "atom.h"
#include "force.h"
@@ -187,8 +188,8 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[1],"all"))
error->warning(FLERR,"Fix ipi always uses group all");
- strcpy(host, arg[3]);
- port=force->inumeric(FLERR,arg[4]);
+ host = strdup(arg[3]);
+ port = force->inumeric(FLERR,arg[4]);
inet = ((narg > 5) && (strcmp(arg[5],"unix") ==0) ) ? 0 : 1;
master = (comm->me==0) ? 1 : 0;
@@ -218,6 +219,7 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) :
FixIPI::~FixIPI()
{
if (bsize) delete[] buffer;
+ free(host);
modify->delete_compute("IPI_TEMP");
modify->delete_compute("IPI_PRESS");
}
diff --git a/src/USER-MISC/fix_ipi.h b/src/USER-MISC/fix_ipi.h
index 010f0ba17dd20adfaafa0d40631c39c028a0fc0a..0859a513c5b13f4f8ccf9646285e893a133e15fb 100644
--- a/src/USER-MISC/fix_ipi.h
+++ b/src/USER-MISC/fix_ipi.h
@@ -34,7 +34,7 @@ class FixIPI : public Fix {
virtual void final_integrate();
protected:
- char host[1024]; int port; int inet, master, hasdata;
+ char *host; int port; int inet, master, hasdata;
int ipisock, me; double *buffer; long bsize;
int kspace_flag;
};
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index 833dc41d2892c72a1e0b7fe751cd57e4620dfff3..613204a55e55272e23e0634485e825e1ab054e32 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -178,7 +178,9 @@ void FixSRP::setup_pre_force(int zz)
for (int n = 0; n < nbondlist; n++) {
// consider only the user defined bond type
- if(bondlist[n][2] != btype) continue;
+ // btype of zero considers all bonds
+ if(btype > 0 && bondlist[n][2] != btype)
+ continue;
i = bondlist[n][0];
j = bondlist[n][1];
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index 139795557ca3e18fa5c1b1b20bf31697675238d5..529e6509788d87c5913127a10e71561caf88798e 100755
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -76,8 +76,8 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
t_switch = atoi(arg[4]); // Switching time.
t_equil = atoi(arg[5]); // Equilibration time.
t0 = update->ntimestep; // Initial time.
- if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
- if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
+ if (t_switch <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
+ if (t_equil <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
// Coupling parameter initialization.
sf = 1;
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index d66e49d6a25cf31775ad1d3df81ecae4083e725c..3a6aafe700bffa9478c85a525525a586c7444613 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -225,6 +225,10 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
t_surface_l = surface_l;
mult_factor = intensity;
duration = 0.0;
+ v_0_sq = v_0*v_0;
+ // error checks
+ if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
+ error->all(FLERR,"Fix ttm number of nodes must be > 0");
surface_double = double(t_surface_l)*(domain->xprd/nxnodes);
if ((C_limit+esheat_0) < 0.0)
error->all(FLERR,"Fix ttm electronic_specific_heat must be >= 0.0");
@@ -234,10 +238,6 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
if (gamma_s < 0.0) error->all(FLERR,"Fix ttm gamma_s must be >= 0.0");
if (v_0 < 0.0) error->all(FLERR,"Fix ttm v_0 must be >= 0.0");
if (ionic_density <= 0.0) error->all(FLERR,"Fix ttm ionic_density must be > 0.0");
- v_0_sq = v_0*v_0;
- // error check
- if (nxnodes <= 0 || nynodes <= 0 || nznodes <= 0)
- error->all(FLERR,"Fix ttm number of nodes must be > 0");
if (seed <= 0) error->all(FLERR,"Invalid random number seed in fix ttm command");
if (surface_l < 0) error->all(FLERR,"Surface coordinates must be >= 0");
if (surface_l >= surface_r) error->all(FLERR, "Left surface coordinate must be less than right surface coordinate");
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index edfd95f20f02a1da94f6c12e86b2c3ce9f525831..f3fe065d6ed6d81f3e2d91b003de1b2865046016 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -173,8 +173,8 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
}
}
- if (c > 1.0) s = 1.0;
- if (c < -1.0) s = -1.0;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp
index ec7730a1f210043df899a7965772e20b3d57bf4a..fedbe0a302539c8634cbdfeb689bbed29443bb4b 100644
--- a/src/USER-MISC/pair_srp.cpp
+++ b/src/USER-MISC/pair_srp.cpp
@@ -59,6 +59,8 @@ static const char cite_srp[] =
" pages = {134903}\n"
"}\n\n";
+static int srp_instance = 0;
+
/* ----------------------------------------------------------------------
set size of pair comms in constructor
---------------------------------------------------------------------- */
@@ -71,6 +73,10 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
nextra = 1;
segment = NULL;
+ fix_id = strdup("XX_FIX_SRP");
+ fix_id[0] = '0' + srp_instance / 10;
+ fix_id[1] = '0' + srp_instance % 10;
+ ++srp_instance;
}
/* ----------------------------------------------------------------------
@@ -112,9 +118,10 @@ PairSRP::~PairSRP()
}
// check nfix in case all fixes have already been deleted
- if (modify->nfix) modify->delete_fix("mysrp");
-}
-
+ if (modify->nfix) modify->delete_fix(fix_id);
+ free(fix_id);
+}
+
/* ----------------------------------------------------------------------
compute bond-bond repulsions
------------------------------------------------------------------------- */
@@ -336,8 +343,14 @@ void PairSRP::settings(int narg, char **arg)
error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
- btype = force->inumeric(FLERR,arg[1]);
- if (btype > atom->nbondtypes) error->all(FLERR,"Illegal pair_style command");
+ // wildcard
+ if (strcmp(arg[1],"*") == 0)
+ btype = 0;
+ else {
+ btype = force->inumeric(FLERR,arg[1]);
+ if ((btype > atom->nbondtypes) || (btype <= 0))
+ error->all(FLERR,"Illegal pair_style command");
+ }
// settings
midpoint = 0;
@@ -426,7 +439,7 @@ void PairSRP::init_style()
// invoke here instead of constructor
// to make restart possible
char **fixarg = new char*[3];
- fixarg[0] = (char *) "mysrp";
+ fixarg[0] = fix_id;
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "SRP";
modify->add_fix(3,fixarg);
diff --git a/src/USER-MISC/pair_srp.h b/src/USER-MISC/pair_srp.h
index 998f8a17e21d541f4e4b859669186cef45a3fa2f..ecd352cdeb89f0d4416f7874c61f5d69334ff933 100644
--- a/src/USER-MISC/pair_srp.h
+++ b/src/USER-MISC/pair_srp.h
@@ -54,6 +54,7 @@ class PairSRP : public Pair {
int bptype;
int btype;
class Fix *f_srp;
+ char *fix_id;
int exclude,maxcount;
int **segment;
};
diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp
index d0aff40f322fc227a651f99e804e8436a0780339..b9ee2238a981d8a0c9b83a4b07f982dd9bc5d942 100644
--- a/src/USER-MOLFILE/molfile_interface.cpp
+++ b/src/USER-MOLFILE/molfile_interface.cpp
@@ -756,10 +756,13 @@ int MolfileInterface::timestep(float *coords, float *vels,
*simtime = t->physical_time;
}
- if (rv == MOLFILE_EOF)
+ if (rv == MOLFILE_EOF) {
+ delete t;
return 1;
+ }
}
+ delete t;
return 0;
}
diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp
index 311152f06c0ce85b2ede936a4651ec8658789a3d..3bd4ef1212cc0edbf06ee7528490007ab7cb8033 100644
--- a/src/USER-OMP/angle_cosine_periodic_omp.cpp
+++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp
@@ -91,7 +91,7 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
int i,i1,i2,i3,n,m,type,b_factor;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
- double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
+ double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
double tn,tn_1,tn_2,un,un_1,un_2;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
@@ -149,10 +149,6 @@ void AngleCosinePeriodicOMP::eval(int nfrom, int nto, ThrData * const thr)
un_1 = 2.0;
un_2 = 0.0;
- s = sqrt(1.0 - c*c);
- if (s < SMALL) s = SMALL;
- s = 1.0/s;
-
// force & energy
tn_2 = c;
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index 49fcef23d45578267a807770daed838ea040766d..6c32c8e538b3edd7b62847bf2175f1e279f7bb3c 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -206,8 +206,8 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
}
}
- if (c > 1.0) s = 1.0;
- if (c < -1.0) s = -1.0;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index 689dbdfe65689a38548e3b22d7cccdd0e39c853e..f100d3a0a9fcad9290ac82af43deda5d4985e5cf 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -171,8 +171,8 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
}
}
- if (c > 1.0) s = 1.0;
- if (c < -1.0) s = -1.0;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
diff --git a/src/USER-OMP/neigh_full_omp.cpp b/src/USER-OMP/neigh_full_omp.cpp
index ee36e5610e3c3c334cd59e41c213eb3332fbac0c..e61611d41cad4c3179913f7efbade7ed6b6a53aa 100644
--- a/src/USER-OMP/neigh_full_omp.cpp
+++ b/src/USER-OMP/neigh_full_omp.cpp
@@ -599,7 +599,6 @@ void Neighbor::full_multi_omp(NeighList *list)
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
- which = find_special(special[i],nspecial[i],tag[j]);
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index c63ac3cd35c31343b3e88347b95f77aba7926492..f2149088c171a6b98c5f87a7ed3a3f85203229f8 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -2067,19 +2067,19 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
if (wik*wkj > best) {
best = wik*wkj;
npath = 3;
- atomk = k;
- delikS[0] = delik[0];
- delikS[1] = delik[1];
- delikS[2] = delik[2];
- rikS = rik;
- wikS = wik;
- dwikS = dwik;
- deljkS[0] = deljk[0];
- deljkS[1] = deljk[1];
- deljkS[2] = deljk[2];
- rkjS = rkj;
- wkjS = wkj;
- dwkjS = dwkj;
+ atomk = k;
+ delikS[0] = delik[0];
+ delikS[1] = delik[1];
+ delikS[2] = delik[2];
+ rikS = rik;
+ wikS = wik;
+ dwikS = dwik;
+ deljkS[0] = deljk[0];
+ deljkS[1] = deljk[1];
+ deljkS[2] = deljk[2];
+ rkjS = rkj;
+ wkjS = wkj;
+ dwkjS = dwkj;
if (best == 1.0) {
done = 1;
break;
@@ -2128,13 +2128,13 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
atomm = m;
delkmS[0] = delkm[0];
delkmS[1] = delkm[1];
- delkmS[2] = delkm[2];
+ delkmS[2] = delkm[2];
rkmS = rkm;
wkmS = wkm;
dwkmS = dwkm;
deljmS[0] = deljm[0];
deljmS[1] = deljm[1];
- deljmS[2] = deljm[2];
+ deljmS[2] = deljm[2];
rmjS = rmj;
wmjS = wmj;
dwmjS = dwmj;
@@ -2250,7 +2250,7 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
if (vflag_atom)
v_tally3_thr(atomi,atomj,atomk,fi,fj,delikS,deljkS,thr);
- } else {
+ } else if (npath == 4) {
fpair1 = dC*dwikS*wkmS*wmjS / rikS;
fi[0] = delikS[0]*fpair1;
fi[1] = delikS[1]*fpair1;
diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index 56d9dee308d63986c9a94cfd9b4d8e72312830f2..8412644ff3ccda8939b8c64aa637ef2a7239f1a6 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -48,6 +48,7 @@ PairBrownianOMP::PairBrownianOMP(LAMMPS *lmp) :
suffix_flag |= Suffix::OMP;
respa_enable = 0;
random_thr = NULL;
+ nthreads = 0;
}
/* ---------------------------------------------------------------------- */
@@ -55,7 +56,7 @@ PairBrownianOMP::PairBrownianOMP(LAMMPS *lmp) :
PairBrownianOMP::~PairBrownianOMP()
{
if (random_thr) {
- for (int i=1; i < comm->nthreads; ++i)
+ for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
@@ -72,7 +73,6 @@ void PairBrownianOMP::compute(int eflag, int vflag)
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
- const int nthreads = comm->nthreads;
const int inum = list->inum;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
@@ -116,13 +116,24 @@ void PairBrownianOMP::compute(int eflag, int vflag)
}
}
+ // number of threads has changed. reallocate pool of pRNGs
+ if (nthreads != comm->nthreads) {
+ if (random_thr) {
+ for (int i=1; i < nthreads; ++i)
+ delete random_thr[i];
- if (!random_thr)
+ delete[] random_thr;
+ }
+
+ nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
+ for (int i=1; i < nthreads; ++i)
+ random_thr[i] = NULL;
- // to ensure full compatibility with the serial Brownian style
- // we use is random number generator instance for thread 0
- random_thr[0] = random;
+ // to ensure full compatibility with the serial Brownian style
+ // we use is random number generator instance for thread 0
+ random_thr[0] = random;
+ }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@@ -137,9 +148,10 @@ void PairBrownianOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
- if (random_thr && tid > 0)
+ if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
+
if (flaglog) {
if (evflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
@@ -395,8 +407,8 @@ double PairBrownianOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairBrownian::memory_usage();
- bytes += comm->nthreads * sizeof(RanMars*);
- bytes += comm->nthreads * sizeof(RanMars);
+ bytes += nthreads * sizeof(RanMars*);
+ bytes += nthreads * sizeof(RanMars);
return bytes;
}
diff --git a/src/USER-OMP/pair_brownian_omp.h b/src/USER-OMP/pair_brownian_omp.h
index cdabe08ba1eb688daa6e8e5e8fd0ef6cdcde4519..c49560cbcac27e065cf4013be60d3e624b118e62 100644
--- a/src/USER-OMP/pair_brownian_omp.h
+++ b/src/USER-OMP/pair_brownian_omp.h
@@ -40,6 +40,7 @@ class PairBrownianOMP : public PairBrownian, public ThrOMP {
protected:
class RanMars **random_thr;
+ int nthreads;
private:
template <int LOGFLAG, int EVFLAG, int NEWTON_PAIR>
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index 0ac97a935b1f96d97119fc358272428cb2108d2c..e0124204de7bbed26dcb9ab30cfe46ae37686cab 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -48,6 +48,7 @@ PairBrownianPolyOMP::PairBrownianPolyOMP(LAMMPS *lmp) :
suffix_flag |= Suffix::OMP;
respa_enable = 0;
random_thr = NULL;
+ nthreads = 0;
}
/* ---------------------------------------------------------------------- */
@@ -55,7 +56,7 @@ PairBrownianPolyOMP::PairBrownianPolyOMP(LAMMPS *lmp) :
PairBrownianPolyOMP::~PairBrownianPolyOMP()
{
if (random_thr) {
- for (int i=1; i < comm->nthreads; ++i)
+ for (int i=1; i < nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
@@ -72,7 +73,6 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
- const int nthreads = comm->nthreads;
const int inum = list->inum;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
@@ -117,12 +117,24 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
}
- if (!random_thr)
+ // number of threads has changed. reallocate pool of pRNGs
+ if (nthreads != comm->nthreads) {
+ if (random_thr) {
+ for (int i=1; i < nthreads; ++i)
+ delete random_thr[i];
+
+ delete[] random_thr;
+ }
+
+ nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
+ for (int i=1; i < nthreads; ++i)
+ random_thr[i] = NULL;
- // to ensure full compatibility with the serial BrownianPoly style
- // we use is random number generator instance for thread 0
- random_thr[0] = random;
+ // to ensure full compatibility with the serial BrownianPoly style
+ // we use is random number generator instance for thread 0
+ random_thr[0] = random;
+ }
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
@@ -137,9 +149,10 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
- if (random_thr && tid > 0)
+ if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
+
if (flaglog) {
if (evflag)
eval<1,1>(ifrom, ito, thr);
@@ -384,8 +397,8 @@ double PairBrownianPolyOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairBrownianPoly::memory_usage();
- bytes += comm->nthreads * sizeof(RanMars*);
- bytes += comm->nthreads * sizeof(RanMars);
+ bytes += nthreads * sizeof(RanMars*);
+ bytes += nthreads * sizeof(RanMars);
return bytes;
}
diff --git a/src/USER-OMP/pair_brownian_poly_omp.h b/src/USER-OMP/pair_brownian_poly_omp.h
index 663696c6c6185b2a234f5cde9e4b143cb25ea80d..df2c0b34bd4319d77f2facb7d03d9ef135715a06 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.h
+++ b/src/USER-OMP/pair_brownian_poly_omp.h
@@ -40,6 +40,7 @@ class PairBrownianPolyOMP : public PairBrownianPoly, public ThrOMP {
protected:
class RanMars **random_thr;
+ int nthreads;
private:
template <int LOGFLAG, int EVFLAG>
diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp
index 23408469e3e94311c3395ae48b17a6d5bbf77b6b..625d5bc19fb96cb6398c960ce8761f015f372652 100644
--- a/src/USER-OMP/pair_dpd_omp.cpp
+++ b/src/USER-OMP/pair_dpd_omp.cpp
@@ -74,12 +74,13 @@ void PairDPDOMP::compute(int eflag, int vflag)
nthreads = comm->nthreads;
random_thr = new RanMars*[nthreads];
for (int i=1; i < nthreads; ++i)
- random_thr[i] = NULL;
+ random_thr[i] = NULL;
// to ensure full compatibility with the serial DPD style
// we use the serial random number generator instance for thread 0
random_thr[0] = random;
}
+
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
@@ -93,7 +94,7 @@ void PairDPDOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
- if (random_thr && (tid > 0) && (random_thr[tid] == NULL))
+ if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp
index ca5b70186bb69bac1a22f4897075be519ffa3181..37b2994e3d747d076df2e90c5f517502d3056e96 100644
--- a/src/USER-OMP/pair_dpd_tstat_omp.cpp
+++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp
@@ -93,7 +93,7 @@ void PairDPDTstatOMP::compute(int eflag, int vflag)
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
- if (random_thr && (tid > 0) && (random_thr[tid] == NULL))
+ if ((tid > 0) && (random_thr[tid] == NULL))
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h
index 3f1d866a807e60c0f09e1180ce765166e26d9996..3cea1b0018df5e76ce12f87149529128f1dfd7d4 100644
--- a/src/USER-OMP/thr_data.h
+++ b/src/USER-OMP/thr_data.h
@@ -35,7 +35,7 @@ class ThrData {
public:
ThrData(int tid, class Timer *t);
- ~ThrData() {};
+ ~ThrData() { delete _timer; _timer = NULL; };
void check_tid(int); // thread id consistency check
int get_tid() const { return _tid; }; // our thread id.
@@ -140,7 +140,7 @@ class ThrData {
// disabled default methods
private:
- ThrData() : _tid(-1) {};
+ ThrData() : _tid(-1), _timer(NULL) {};
};
////////////////////////////////////////////////////////////////////////
diff --git a/src/USER-PHONON/fix_phonon.h b/src/USER-PHONON/fix_phonon.h
index 891235cfec6f5df719144f241dad3ebabfb41424..f1a8af48126886f1c1437b6cdea584fff57b01c8 100644
--- a/src/USER-PHONON/fix_phonon.h
+++ b/src/USER-PHONON/fix_phonon.h
@@ -31,6 +31,17 @@ FixStyle(phonon,FixPhonon)
#ifndef FIX_PHONON_H
#define FIX_PHONON_H
+#include "lmptype.h"
+#include "mpi.h"
+
+#ifdef FFT_SINGLE
+typedef float FFT_SCALAR;
+#define MPI_FFT_SCALAR MPI_FLOAT
+#else
+typedef double FFT_SCALAR;
+#define MPI_FFT_SCALAR MPI_DOUBLE
+#endif
+
#include <complex>
#include "fix.h"
#include <map>
@@ -72,7 +83,7 @@ class FixPhonon : public Fix {
int mynpt,mynq,fft_nsend;
int *fft_cnts, *fft_disp;
int fft_dim, fft_dim2;
- double *fft_data;
+ FFT_SCALAR *fft_data;
tagint itag; // index variables
int idx, idq; // more index variables
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index 5c20b803e8ee73b9d353dfcf0b00bac705b8e9b1..79c22e1056d3f2387f2cd2690a3ae31e99c1204b 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -330,6 +330,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) {
int nall, countall;
MPI_Allreduce(&n, &nall, 1, MPI_INT, MPI_SUM, world);
MPI_Allreduce(&count, &countall, 1, MPI_INT, MPI_SUM, world);
+ if (countall < 1) countall = 1;
if (comm->me == 0) {
if (screen) {
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index 7c5f433bb52cff29f636fe651b0c1eeb5581d85e..65bd4eabe26ac80aa3290a2d3619d005f68b54df 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -95,6 +95,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
typecount = new int[ntypes+1];
icount = new int[npairs];
jcount = new int[npairs];
+ duplicates = new int[npairs];
}
/* ---------------------------------------------------------------------- */
@@ -113,13 +114,14 @@ ComputeRDF::~ComputeRDF()
delete [] typecount;
delete [] icount;
delete [] jcount;
+ delete [] duplicates;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::init()
{
- int i,m;
+ int i,j,m;
if (force->pair) delr = force->pair->cutforce / nbin;
else error->all(FLERR,"Compute rdf requires a pair style be defined");
@@ -143,12 +145,17 @@ void ComputeRDF::init()
// icount = # of I atoms participating in I,J pairs for each histogram
// jcount = # of J atoms participating in I,J pairs for each histogram
+ // duplicates = # of atoms in both groups I and J for each histogram
for (m = 0; m < npairs; m++) {
icount[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++) icount[m] += typecount[i];
jcount[m] = 0;
for (i = jlo[m]; i <= jhi[m]; i++) jcount[m] += typecount[i];
+ duplicates[m] = 0;
+ for (i = ilo[m]; i <= ihi[m]; i++)
+ for (j = jlo[m]; j <= jhi[m]; j++)
+ if (i == j) duplicates[m] += typecount[i];
}
int *scratch = new int[npairs];
@@ -156,6 +163,8 @@ void ComputeRDF::init()
for (i = 0; i < npairs; i++) icount[i] = scratch[i];
MPI_Allreduce(jcount,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) jcount[i] = scratch[i];
+ MPI_Allreduce(duplicates,scratch,npairs,MPI_INT,MPI_SUM,world);
+ for (i = 0; i < npairs; i++) duplicates[i] = scratch[i];
delete [] scratch;
// need an occasional half neighbor list
@@ -265,25 +274,28 @@ void ComputeRDF::compute_array()
MPI_Allreduce(hist[0],histall[0],npairs*nbin,MPI_DOUBLE,MPI_SUM,world);
// convert counts to g(r) and coord(r) and copy into output array
- // nideal = # of J atoms surrounding single I atom in a single bin
- // assuming J atoms are at uniform density
+ // vfrac = fraction of volume in shell m
+ // npairs = number of pairs, corrected for duplicates
+ // duplicates = pairs in which both atoms are the same
- double constant,nideal,gr,ncoord,rlower,rupper;
+ double constant,vfrac,gr,ncoord,rlower,rupper,normfac;
if (domain->dimension == 3) {
constant = 4.0*MY_PI / (3.0*domain->xprd*domain->yprd*domain->zprd);
for (m = 0; m < npairs; m++) {
+ normfac = (icount[m] > 0) ? static_cast<double>(jcount[m])
+ - static_cast<double>(duplicates[m])/icount[m] : 0.0;
ncoord = 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
rlower = ibin*delr;
rupper = (ibin+1)*delr;
- nideal = constant *
- (rupper*rupper*rupper - rlower*rlower*rlower) * jcount[m];
- if (icount[m]*nideal != 0.0)
- gr = histall[m][ibin] / (icount[m]*nideal);
+ vfrac = constant * (rupper*rupper*rupper - rlower*rlower*rlower);
+ if (vfrac * normfac != 0.0)
+ gr = histall[m][ibin] / (vfrac * normfac * icount[m]);
else gr = 0.0;
- ncoord += gr*nideal;
+ if (icount[m] != 0)
+ ncoord += gr * vfrac * normfac;
array[ibin][1+2*m] = gr;
array[ibin][2+2*m] = ncoord;
}
@@ -294,14 +306,17 @@ void ComputeRDF::compute_array()
for (m = 0; m < npairs; m++) {
ncoord = 0.0;
+ normfac = (icount[m] > 0) ? static_cast<double>(jcount[m])
+ - static_cast<double>(duplicates[m])/icount[m] : 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
rlower = ibin*delr;
rupper = (ibin+1)*delr;
- nideal = constant * (rupper*rupper - rlower*rlower) * jcount[m];
- if (icount[m]*nideal != 0.0)
- gr = histall[m][ibin] / (icount[m]*nideal);
+ vfrac = constant * (rupper*rupper - rlower*rlower);
+ if (vfrac * normfac != 0.0)
+ gr = histall[m][ibin] / (vfrac * normfac * icount[m]);
else gr = 0.0;
- ncoord += gr*nideal;
+ if (icount[m] != 0)
+ ncoord += gr * vfrac * normfac;
array[ibin][1+2*m] = gr;
array[ibin][2+2*m] = ncoord;
}
diff --git a/src/compute_rdf.h b/src/compute_rdf.h
index 794fcc9ee65219976c8afa65fc9d5d35fbc45f45..9d0956212bd18659a6a0e3a96f4eeb0e3088a0d1 100644
--- a/src/compute_rdf.h
+++ b/src/compute_rdf.h
@@ -45,6 +45,7 @@ class ComputeRDF : public Compute {
int *typecount;
int *icount,*jcount;
+ int *duplicates;
class NeighList *list; // half neighbor list
};
diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp
index 521f0956bdfe287dc98f84f7d6639b3c7c440c0b..62b7f057afc51752e49f50763f29d77dfe8eae7d 100644
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@ -888,7 +888,7 @@ void FixAveSpatial::end_of_step()
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
- ftruncate(fileno(fp),fileend);
+ if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 9c3b9e6753f51b957b497c08c94ca1120cb700da..d502f6a9637759b403ae3d6881ff77565301ad67 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -907,7 +907,7 @@ void FixAveTime::invoke_vector(bigint ntimestep)
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
- ftruncate(fileno(fp),fileend);
+ if (fileend > 0) ftruncate(fileno(fp),fileend);
}
}
}
diff --git a/src/info.cpp b/src/info.cpp
index 7b6117acb8d8f3bef15e11c43b7b1370560d9e48..c34eb401cd37a89f38c91ae3f531a92e8fca3f27 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -104,6 +104,7 @@ void Info::command(int narg, char **arg)
++idx;
} else if ((idx+1 < narg) && (strncmp(arg[idx],"out",3) == 0)
&& (strncmp(arg[idx+1],"screen",3) == 0)) {
+ if ((out != screen) && (out != logfile)) fclose(out);
out = screen;
idx += 2;
} else if ((idx+1 < narg) && (strncmp(arg[idx],"out",3) == 0)
@@ -547,7 +548,7 @@ bool Info::is_available(const char *category, const char *name)
int match = 0;
if (strcmp(category,"command") == 0) {
- if (input->command_map->find(name) != input->command_map->end());
+ if (input->command_map->find(name) != input->command_map->end())
match = 1;
} else if (strcmp(category,"compute") == 0) {
diff --git a/src/pair.cpp b/src/pair.cpp
index a87b674608b79e854f823b188e682338da19aea3..665615edd0c5e3fd07c54a5eebdd99676d9b80fc 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -119,6 +119,7 @@ Pair::~Pair()
{
num_tally_compute = 0;
memory->sfree((void *)list_tally_compute);
+ list_tally_compute = NULL;
if (copymode) return;
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 8b83b007b55aee3a5ac02edff46afd6f6eed6932..37785af5c3c4555c6a0c0fa265ebe48d7390af61 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -364,7 +364,8 @@ void Velocity::create(double t_desired, int seed)
// no-bias compute calculates temp only for new thermal velocities
double t;
- if (bias_flag == 0) t = temperature->compute_scalar();
+ if ((bias_flag == 0) || (temperature_nobias == NULL))
+ t = temperature->compute_scalar();
else t = temperature_nobias->compute_scalar();
rescale(t,t_desired);