diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h
index ddb0b5ceaa51cf1bae036d014f6aa24220bdc98d..56a4f15f1bff5a18ee050badf8acfb420c97b28b 100644
--- a/src/GPU/gpu_extra.h
+++ b/src/GPU/gpu_extra.h
@@ -61,13 +61,13 @@ namespace GPU_EXTRA {
else
error->all(FLERR,"Unknown error in GPU library");
}
- };
+ }
inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) {
int ifix = modify->find_fix("package_gpu");
if (ifix < 0)
error->all(FLERR,"The package gpu command is required for gpu styles");
- };
+ }
}
#endif
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index 46e843158abe6649ba751b7480bba01e4ba94ebe..fe638214baabe8205172d78d898bd21ee75096e5 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -1264,15 +1264,15 @@ void *PairKIM::extract(const char *str, int &dim)
int ier;
int dummyint;
int isIndexed = 0;
- int maxLine = 1024;
+ const int MAXLINE = 1024;
int rank;
int validParam = 0;
int numParams;
- int *speciesIndex = new int[maxLine];
- char *paramStr = new char[maxLine];
+ int *speciesIndex = new int[MAXLINE];
+ char *paramStr = new char[MAXLINE];
char *paramName;
char *indexStr;
- char message[maxLine];
+ char message[MAXLINE];
int offset;
double* paramPtr;
@@ -1354,7 +1354,7 @@ void *PairKIM::extract(const char *str, int &dim)
}
kim_error(__LINE__,"get_rank",kimerror);
- int *shape = new int[maxLine];
+ int *shape = new int[MAXLINE];
dummyint = (*pkim).get_shape(paramName, shape, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index cc1ea027eec3a115ebc58400663863194ca3b93e..9f3221449bb2329923cfa9ed987beb6f26e58e3f 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -2261,7 +2261,7 @@ void MSM::restriction(int n)
double ***qgrid2 = qgrid[n+1];
int k = 0;
- int index[p+2];
+ int *index = new int[p+2];
for (int nu=-p; nu<=p; nu++) {
if (nu%2 == 0 && nu != 0) continue;
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
@@ -2317,7 +2317,7 @@ void MSM::restriction(int n)
}
qgrid2[kp][jp][ip] += q2sum;
}
-
+ delete[] index;
}
/* ----------------------------------------------------------------------
@@ -2348,7 +2348,7 @@ void MSM::prolongation(int n)
double ***v5grid2 = v5grid[n+1];
int k = 0;
- int index[p+2];
+ int *index = new int[p+2];
for (int nu=-p; nu<=p; nu++) {
if (nu%2 == 0 && nu != 0) continue;
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
@@ -2420,7 +2420,7 @@ void MSM::prolongation(int n)
}
}
-
+ delete[] index;
}
/* ----------------------------------------------------------------------
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index e38a05c6edffb4eab8a6e34089c86762d94971de..b4f9c02206f926d39307b19317bd7e00b9cd16eb 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -310,10 +310,10 @@ double PairComb3::init_one(int i, int j)
void PairComb3::read_lib()
{
- unsigned int maxlib = 1024;
+ const unsigned int MAXLIB = 1024;
int i,j,k,l,nwords,m;
int ii,jj,kk,ll,mm,iii;
- char s[maxlib];
+ char s[MAXLIB];
char **words = new char*[80];
// open libraray file on proc 0
@@ -327,8 +327,8 @@ void PairComb3::read_lib()
}
// read and store at the same time
- fgets(s,maxlib,fp);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -339,7 +339,7 @@ void PairComb3::read_lib()
ccutoff[4] = atof(words[4]);
ccutoff[5] = atof(words[5]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -351,7 +351,7 @@ void PairComb3::read_lib()
ch_a[5] = atof(words[5]);
ch_a[6] = atof(words[6]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -359,7 +359,7 @@ void PairComb3::read_lib()
nsplrad = atoi(words[1]);
nspltor = atoi(words[2]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -367,7 +367,7 @@ void PairComb3::read_lib()
maxy = atoi(words[1]);
maxz = atoi(words[2]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -376,7 +376,7 @@ void PairComb3::read_lib()
maxconj = atoi(words[2]);
for (l=0; l<nsplpcn; l++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -385,14 +385,14 @@ void PairComb3::read_lib()
dvmaxxcn[l] = atof(words[3]);
}
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ntab = atoi(words[0]);
for (i=0; i<ntab+1; i++){
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -405,7 +405,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx+1; i++)
for (j=0; j<maxy+1; j++)
for (k=0; k<maxz+1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -423,7 +423,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx; i++)
for (j=0; j<maxy; j++)
for (k=0; k<maxz; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -432,7 +432,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3]);
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -447,7 +447,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -465,7 +465,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -474,7 +474,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3])-1;
for (iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -489,7 +489,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -507,7 +507,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -516,7 +516,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3])-1;
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 08fe7de5cb4a12402698e60410e9936609d8bf49..6221e6d52c26b359d9efd7d87460a1ed3ceacaf3 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -1349,7 +1349,7 @@ void FixGCMC::attempt_molecule_insertion()
MathExtra::quat_to_mat(quat,rotmat);
double insertion_energy = 0.0;
- bool procflag[natoms_per_molecule];
+ bool *procflag = new bool[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
MathExtra::matvec(rotmat,onemols[imol]->x[i],molcoords[i]);
@@ -1472,6 +1472,7 @@ void FixGCMC::attempt_molecule_insertion()
update_gas_atoms_list();
ninsertion_successes += 1.0;
}
+ delete[] procflag;
}
/* ----------------------------------------------------------------------
@@ -1934,7 +1935,7 @@ void FixGCMC::attempt_molecule_deletion_full()
grow_molecule_arrays(nmolq);
int m = 0;
- int tmpmask[atom->nlocal];
+ int *tmpmask = new int[atom->nlocal];
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
tmpmask[i] = atom->mask[i];
@@ -1982,6 +1983,7 @@ void FixGCMC::attempt_molecule_deletion_full()
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
+ delete[] tmpmask;
}
/* ----------------------------------------------------------------------
@@ -2426,9 +2428,9 @@ void FixGCMC::update_gas_atoms_list()
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
- double comx[maxmol_all];
- double comy[maxmol_all];
- double comz[maxmol_all];
+ double *comx = new double[maxmol_all];
+ double *comy = new double[maxmol_all];
+ double *comz = new double[maxmol_all];
for (int imolecule = 0; imolecule < maxmol_all; imolecule++) {
for (int i = 0; i < nlocal; i++) {
if (molecule[i] == imolecule) {
@@ -2458,7 +2460,9 @@ void FixGCMC::update_gas_atoms_list()
}
}
}
-
+ delete[] comx;
+ delete[] comy;
+ delete[] comz;
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp
index 7331a75db68448ed1b3dbd6a892981637e851daa..b330ab79450b805e595e6b5d52710722d962ee32 100644
--- a/src/PYTHON/fix_python_move.cpp
+++ b/src/PYTHON/fix_python_move.cpp
@@ -47,7 +47,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
PyGILState_STATE gstate = PyGILState_Ensure();
// add current directory to PYTHONPATH
- PyObject * py_path = PySys_GetObject("path");
+ PyObject * py_path = PySys_GetObject((char *)"path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
@@ -136,7 +136,7 @@ void FixPythonMove::init()
{
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init");
+ PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init");
if (!py_init) {
PyErr_Print();
PyErr_Clear();
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 35225b3c1e2bd6f192896a96294bc42b4477c76c..c9aedf74018409a5913ed1055d554775e4704746 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -303,7 +303,7 @@ void NEB::run()
update->minimize->setup();
if (me_universe == 0) {
- if (uscreen)
+ if (uscreen) {
if (verbose) {
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT "
@@ -317,7 +317,8 @@ void NEB::run()
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
- if (ulogfile)
+ }
+ if (ulogfile) {
if (verbose) {
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT "
@@ -331,6 +332,7 @@ void NEB::run()
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
+ }
}
print_status();
@@ -588,7 +590,7 @@ void NEB::print_status()
MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);
}
- double one[numall];
+ double one[7];
one[0] = fneb->veng;
one[1] = fneb->plen;
one[2] = fneb->nlen;
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 554412330c955fd187dbb61ee9857c849c1c65ca..3d9e24ced96d2a274f782177508b93fedfe99aeb 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -2342,7 +2342,7 @@ void FixRigid::write_restart_file(char *file)
sprintf(outfile,"%s.rigid",file);
FILE *fp = fopen(outfile,"w");
if (fp == NULL) {
- char str[128];
+ char str[192];
sprintf(str,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index b8b002a7fa11df5e5a2f5fe93ba3ad82be8f1c70..c370f8abe6ebe0fb35fae63730a909ae44dcf335 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -260,6 +260,7 @@ void FixRX::post_constructor()
error->all(FLERR,"fix rx cannot be combined with fix property/atom");
char **tmpspecies = new char*[maxspecies];
+ int tmpmaxstrlen = 0;
for(int jj=0; jj < maxspecies; jj++)
tmpspecies[jj] = NULL;
@@ -320,6 +321,7 @@ void FixRX::post_constructor()
error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx.");
tmpspecies[nUniqueSpecies] = new char[strlen(word)+1];
strcpy(tmpspecies[nUniqueSpecies],word);
+ tmpmaxstrlen = MAX(tmpmaxstrlen,strlen(word));
nUniqueSpecies++;
}
word = strtok(NULL, " \t\n\r\f");
@@ -354,9 +356,9 @@ void FixRX::post_constructor()
newarg2[0] = id_fix_species_old;
newarg2[1] = group->names[igroup];
newarg2[2] = (char *) "property/atom";
+ char *str1 = new char[tmpmaxstrlen+3];
+ char *str2 = new char[tmpmaxstrlen+6];
for(int ii=0; ii<nspecies; ii++){
- char str1[2+strlen(tmpspecies[ii])+1];
- char str2[2+strlen(tmpspecies[ii])+4];
strcpy(str1,"d_");
strcpy(str2,"d_");
strncat(str1,tmpspecies[ii],strlen(tmpspecies[ii]));
@@ -367,6 +369,8 @@ void FixRX::post_constructor()
strcpy(newarg[ii+3],str1);
strcpy(newarg2[ii+3],str2);
}
+ delete[] str1;
+ delete[] str2;
newarg[nspecies+3] = (char *) "ghost";
newarg[nspecies+4] = (char *) "yes";
newarg2[nspecies+3] = (char *) "ghost";
diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp
index 29c1ff88211085fb9769e3d292b6bc3352d9d02d..34742a0683311a8e1286b4e122897434d845209b 100644
--- a/src/USER-DRUDE/fix_drude_transform.cpp
+++ b/src/USER-DRUDE/fix_drude_transform.cpp
@@ -75,7 +75,7 @@ void FixDrudeTransform<inverse>::setup(int) {
if (!rmass) {
if (!mcoeff) mcoeff = new double[ntypes+1];
- double mcoeff_loc[ntypes+1];
+ double *mcoeff_loc = new double[ntypes+1];
for (int itype=0; itype<=ntypes; itype++) mcoeff_loc[itype] = 2.; // an impossible value: mcoeff is at most 1.
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
@@ -95,6 +95,7 @@ void FixDrudeTransform<inverse>::setup(int) {
// mcoeff is 2 for non polarizable
// 0 < mcoeff < 1 for drude
// mcoeff < 0 for core
+ delete[] mcoeff_loc;
}
}
@@ -313,6 +314,6 @@ void FixDrudeTransform<inverse>::unpack_forward_comm(int n, int first, double *b
}
/* ---------------------------------------------------------------------- */
-template class FixDrudeTransform<false>;
-template class FixDrudeTransform<true>;
+template class LAMMPS_NS::FixDrudeTransform<false>;
+template class LAMMPS_NS::FixDrudeTransform<true>;
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index 6cf2d3bfd09a5b8f857a44cc73ced2f3ad78c182..490b95ef719a132448c2925ba2879c9f1874f163 100644
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -102,8 +102,8 @@ void FixLbMomentum::end_of_step()
double masslb,masslbloc;
double momentumlbloc[3],momentumlb[3];
double vcmtotal[3];
- int numvel = fix_lb_fluid->numvel;
- double etacov[numvel];
+ const int numvel = fix_lb_fluid->numvel;
+ double etacov[19]; // = double etacov[numvel]; i.e. 15 or 19
double rho;
if (linear) {
diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 8a439a2118394c01bc6bb6787152e6e4ec587d68..42fd722e016ce4dce882599cb1ff37fe24dd7422 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -255,5 +255,5 @@ static inline double fdiv_zero(const double n, const double d) {
return n / d;
}
-};
+}
#endif
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index f1d9c215b4207670e657c7fb2249b590235b23b9..351637a842018c6469c09a1929e5552487c20695 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -59,7 +59,6 @@ static const char cite_pair_edpd[] =
" volume = {51},\n"
" pages = {11038--11040}\n"
"}\n\n";
-;
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 0d0d2a3a0ad5ab7f7fd6545aaa07f91e2c5f2abe..b8bbf6d622f51e16f15813cbeb1af08a692adceb 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -280,7 +280,9 @@ void PairTDPD::coeff(int narg, char **arg)
double power_one = force->numeric(FLERR,arg[4]);
double cut_one = force->numeric(FLERR,arg[5]);
double cutcc_one = force->numeric(FLERR,arg[6]);
- double kappa_one[cc_species],epsilon_one[cc_species],powercc_one[cc_species];
+ double *kappa_one = new double[cc_species];
+ double *epsilon_one = new double[cc_species];
+ double *powercc_one = new double[cc_species];
for(int k=0; k<cc_species; k++) {
kappa_one[k] = force->numeric(FLERR,arg[7+3*k]);
epsilon_one[k] = force->numeric(FLERR,arg[8+3*k]);
@@ -304,6 +306,9 @@ void PairTDPD::coeff(int narg, char **arg)
setflag[i][j] = 1;
count++;
}
+ delete[] kappa_one;
+ delete[] epsilon_one;
+ delete[] powercc_one;
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index 1da43a6bafb18693cfbb70450d2a68a53f14820c..4d8627a11fb66534b0e982413790156d4efaf524 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -204,8 +204,11 @@ void ComputeBasalAtom::compute_peratom()
double bond_angle;
double norm_j, norm_k;
chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
- double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0],
- xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
+ double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik, xmean5, ymean5, zmean5,
+ xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
+ double *x3 = new double[n0];
+ double *y3 = new double[n0];
+ double *z3 = new double[n0];
for (j = 0; j < n0; j++) {
x_ij = x[i][0]-x[nearest_n0[j]][0];
y_ij = x[i][1]-x[nearest_n0[j]][1];
@@ -411,9 +414,12 @@ void ComputeBasalAtom::compute_peratom()
}
}
}
- }
- //if there are less than two ~180 degree bond angles, the algorithm returns null
- else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
+ //if there are less than two ~180 degree bond angles, the algorithm returns null
+ } else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
+
+ delete[] x3;
+ delete[] y3;
+ delete[] z3;
//normalize BPV:
double Mag = sqrt(BPV[i][0]*BPV[i][0] +
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index a5f0e5704116c78b88793c35722b5f208ef74269..91c70335133e4fdf6a37c0ec212d5d38dc9501fb 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -1527,7 +1527,10 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
//derivative:
//dn1dx:
- double sum1[3][3*N];
+
+ double **sum1;
+ memory->create(sum1,3,3*N,"filter_corotate:sum1");
+
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
sum1[i][j] = 0;
@@ -1564,10 +1567,12 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn1dx[i][j] = norm1*sum;
}
}
+ memory->destroy(sum1);
//dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
- double sum2[3][3*N];
+ double **sum2;
+ memory->create(sum2,3,3*N,"filter_corotate:sum2");
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
sum2[i][j] = 0;
@@ -1618,7 +1623,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
//dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
//sum3 = (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
- double sum3[3][3*N];
+ double **sum3;
+ memory->create(sum3,3,3*N,"filter_corotate:sum3");
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++) {
double sum = 0;
@@ -1627,6 +1633,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
sum3[i][j] = sum;
}
+ memory->destroy(sum2);
//dn2dx = norm2 * I3mn2n2T * sum3
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++) {
@@ -1636,6 +1643,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn2dx[i][j] = norm2*sum;
}
+ memory->destroy(sum3);
//dn3dx = norm3 * I3mn3n3T * cross
double I3mn3n3T[3][3]; //(I_3 - n3n3T)
for (int i=0; i<3; i++) {
@@ -1644,7 +1652,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
I3mn3n3T[i][i] += 1.0;
}
- double cross[3][3*N];
+ double **cross;
+ memory->create(cross,3,3*N,"filter_corotate:cross");
for (int j=0; j<3*N; j++) {
cross[0][j] = dn1dx[1][j]*n2[2] -dn1dx[2][j]*n2[1] +
@@ -1663,6 +1672,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn3dx[i][j] = norm3*sum;
}
+ memory->destroy(cross);
for (int l=0; l<N; l++)
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 5857bafc2ef9fb07062812b3992d1460d969fd3c..584b33bfe7da1bc93d041ee15388d7e72ebe36d5 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -44,6 +44,7 @@ using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
+
//#define GLE_DEBUG 1
#define MAXLINE 1024
@@ -62,35 +63,37 @@ namespace GLE {
//"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t
void StabCholesky(int n, const double* MMt, double* M)
{
- double L[n*n], D[n];
-
- int i,j,k;
- for(i=0; i<n; ++i) D[i]=0.;
- for(i=0; i<n*n; ++i) L[i]=0.;
-
- for(i=0; i<n; ++i)
- {
- L[midx(n,i,i)]=1.;
- for (j=0; j<i; j++)
- {
- L[midx(n,i,j)]=MMt[midx(n,i,j)];
- for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
- if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
- else L[midx(n,i,j)]=0.0;
- }
- D[i]=MMt[midx(n,i,i)];
- for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
+ double *L = new double[n*n];
+ double *D = new double[n];
+
+ int i,j,k;
+ for (i=0; i<n; ++i) D[i]=0.0;
+ for (i=0; i<n*n; ++i) L[i]=0.0;
+
+ for (i=0; i<n; ++i) {
+ L[midx(n,i,i)]=1.0;
+ for (j=0; j<i; j++) {
+ L[midx(n,i,j)]=MMt[midx(n,i,j)];
+ for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
+ if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
+ else L[midx(n,i,j)]=0.0;
}
+ D[i]=MMt[midx(n,i,i)];
+ for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
+ }
- for(i=0; i<n; ++i)
- {
+ for (i=0; i<n; ++i) {
#ifdef GLE_DEBUG
- if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
+ if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
#endif
- D[i]=(D[i]>0.?sqrt(D[i]):0.);
- }
+ D[i]=(D[i]>0.0) ? sqrt(D[i]):0.0;
+ }
+
+ for (i=0; i<n; ++i)
+ for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
- for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
+ delete[] D;
+ delete[] L;
}
void MyMult(int n, int m, int r, const double* A, const double* B, double* C, double cf=0.0)
@@ -162,26 +165,32 @@ void MyPrint(int n, const double* A)
//matrix exponential by scaling and squaring.
void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
{
- double tc[j+1], SM[n*n], TMP[n*n];
- double onetotwok=pow(0.5,1.0*k);
+ double *tc = new double[j+1];
+ double *SM = new double[n*n];
+ double *TMP = new double[n*n];
+ double onetotwok=pow(0.5,1.0*k);
- tc[0]=1;
- for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
+ tc[0]=1;
+ for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
- for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
+ for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
- for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
+ for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
- //taylor exp of scaled matrix
- for (int p=j-1; p>=0; p--)
- {
- MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
- for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
- }
+ //taylor exp of scaled matrix
+ for (int p=j-1; p>=0; p--) {
+ MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
+ for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
+ }
- for (int p=0; p<k; p++)
- { MyMult(n, n, n, EM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i]; }
+ for (int p=0; p<k; p++) {
+ MyMult(n, n, n, EM, EM, TMP);
+ for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
+ }
+ delete[] tc;
+ delete[] SM;
+ delete[] TMP;
}
}
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 090a330af66ff0fed4e87bd58e1ac7363067ec97..c4750ce49e211b22c6f3b1ddc8e8d812f1843402 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -428,7 +428,7 @@ void FixIPI::final_integrate()
int nat=bsize/3;
double **f= atom->f;
- double lbuf[bsize];
+ double *lbuf = new double[bsize];
// reassembles the force vector from the local arrays
int nlocal = atom->nlocal;
@@ -440,6 +440,7 @@ void FixIPI::final_integrate()
lbuf[3*(atom->tag[i]-1)+2]=f[i][2]*forceconv;
}
MPI_Allreduce(lbuf,buffer,bsize,MPI_DOUBLE,MPI_SUM,world);
+ delete[] lbuf;
for (int i = 0; i < 9; ++i) vir[i]=0.0;
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index cc92bfc30f9f906b7202c266df8d015163122366..523b2ca71a7b466f35939a67c7b5e9ac77501cac 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -539,7 +539,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
double &fforce)
{
double r2inv,r6inv;
- double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
+ double pdotp,pidotr,pjdotr,delx,dely,delz;
double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv;
double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl;
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index cf561178926cb00be0740eb5fd7348d7243286e7..3a37c67a3871f1e044ba568e256c8c57a56620c8 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -668,7 +668,8 @@ void FixPhonon::postprocess( )
}
// to get Phi = KT.G^-1; normalization of FFTW data is done here
- double boltz = force->boltz, kbtsqrt[sysdim], TempAve = 0.;
+ double boltz = force->boltz, TempAve = 0.;
+ double *kbtsqrt = new double[sysdim];
double TempFac = inv_neval * inv_nTemp;
double NormFac = TempFac * double(ntotal);
@@ -692,7 +693,7 @@ void FixPhonon::postprocess( )
MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world);
// to collect all basis info and averaged it on root
- double basis_root[fft_dim];
+ double *basis_root = new double[fft_dim];
if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world);
if (me == 0){ // output dynamic matrix by root
@@ -772,7 +773,8 @@ void FixPhonon::postprocess( )
}
fflush(flog);
}
-
+ delete[] kbtsqrt;
+ delete[] basis_root;
} // end of postprocess
/* ----------------------------------------------------------------------
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h
index ea4f46ce530ea0d40606c1c3aa157707f2a91e5a..9d954bf529aaf00ddf1df307d7f3a0b1d012538f 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.h
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.h
@@ -48,7 +48,7 @@ class FixSMDIntegrateUlsph : public Fix {
private:
class NeighList *list;
protected:
- double dtv,dtf, vlimit, vlimitsq;;
+ double dtv,dtf, vlimit, vlimitsq;
int mass_require;
bool xsphFlag;
bool adjust_radius_flag;
diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h
index 43f5bb46a9f2c97c6f3a5f784506d3c9839aed56..0629db5aa176c96e74271aef1b43e08383e0279b 100644
--- a/src/USER-UEF/fix_nh_uef.h
+++ b/src/USER-UEF/fix_nh_uef.h
@@ -23,7 +23,7 @@ namespace LAMMPS_NS {
// forward declaration
namespace UEF_utils {
class UEFBox;
- };
+ }
class FixNHUef : public FixNH {
public:
diff --git a/src/image.cpp b/src/image.cpp
index 599ac4a09132c1917f087cf2c89d6270dd696519..301a2af88f23588dfcdea129fe2c283ae6269cb0 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -1065,7 +1065,7 @@ void Image::write_PNG(FILE *fp)
png_set_text(png_ptr,info_ptr,text_ptr,1);
png_write_info(png_ptr,info_ptr);
- png_bytep row_pointers[height];
+ png_bytep *row_pointers = new png_bytep[height];
for (int i=0; i < height; ++i)
row_pointers[i] = (png_bytep) &writeBuffer[(height-i-1)*3*width];
@@ -1073,6 +1073,7 @@ void Image::write_PNG(FILE *fp)
png_write_end(png_ptr, info_ptr);
png_destroy_write_struct(&png_ptr, &info_ptr);
+ delete[] row_pointers;
#endif
}
diff --git a/src/library.cpp b/src/library.cpp
index 865bf2a0a5d41bda4e5f5c8ec349e1b2903b96af..0162c560cea7e21b66cc759a481aae6420c86d51 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -933,7 +933,7 @@ void lammps_gather_atoms_concat(void *ptr, char *name,
BEGIN_CAPTURE
{
- int i,j,offset;
+ int i,offset;
// error if tags are not defined
// NOTE: test that name = image or ids is not a 64-bit int in code?
@@ -975,7 +975,6 @@ void lammps_gather_atoms_concat(void *ptr, char *name,
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@@ -1117,7 +1116,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name,
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@@ -1163,7 +1161,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name,
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0.0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
diff --git a/src/molecule.cpp b/src/molecule.cpp
index b03142e98498eeffeeb106965098fc925ef89634..56e56dab2cd16ef45c9c6068161c29a4815d51ca 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -1111,7 +1111,7 @@ void Molecule::special_generate()
{
int newton_bond = force->newton_bond;
tagint atom1,atom2;
- int count[natoms];
+ int *count = new int[natoms];
// temporary array for special atoms
@@ -1197,6 +1197,7 @@ void Molecule::special_generate()
}
}
}
+ delete[] count;
maxspecial = 0;
for (int i = 0; i < natoms; i++)