git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14655 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/CLASS2/improper_class2.cpp

@@ -657,6 +657,9 @@ void ImproperClass2::angleangle(int eflag, int vflag)
     i4 = improperlist[n][3];
     type = improperlist[n][4];
 
+    if ((aa_k1[type] == 0.0) && (aa_k2[type] == 0.0)
+        && (aa_k3[type] == 0.0)) continue;
+
     // difference vectors
 
     delxAB = x[i1][0] - x[i2][0];

src/KOKKOS/atom_vec_full_kokkos.cpp

@@ -764,8 +764,11 @@ struct AtomVecFullKokkos_PackBorder {
   union ubuf {
     double d;
     int64_t i;
+    KOKKOS_INLINE_FUNCTION
     ubuf(double arg) : d(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int64_t arg) : i(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int arg) : i(arg) {}
   };
 
@@ -1030,8 +1033,11 @@ struct AtomVecFullKokkos_UnpackBorder {
   union ubuf {
     double d;
     int64_t i;
+    KOKKOS_INLINE_FUNCTION
     ubuf(double arg) : d(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int64_t arg) : i(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int arg) : i(arg) {}
   };
 
@@ -1177,8 +1183,11 @@ struct AtomVecFullKokkos_PackExchangeFunctor {
   union ubuf {
     double d;
     int64_t i;
+    KOKKOS_INLINE_FUNCTION
     ubuf(double arg) : d(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int64_t arg) : i(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int arg) : i(arg) {}
   };
 
@@ -1527,8 +1536,11 @@ struct AtomVecFullKokkos_UnpackExchangeFunctor {
   union ubuf {
     double d;
     int64_t i;
+    KOKKOS_INLINE_FUNCTION
     ubuf(double arg) : d(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int64_t arg) : i(arg) {}
+    KOKKOS_INLINE_FUNCTION
     ubuf(int arg) : i(arg) {}
   };
 

src/KOKKOS/dihedral_opls_kokkos.h

@@ -13,9 +13,9 @@
 
 #ifdef DIHEDRAL_CLASS
 
-DihedralStyle(charmm/kk,DihedralOPLSKokkos<LMPDeviceType>)
+DihedralStyle(opls/kk,DihedralOPLSKokkos<LMPDeviceType>)
-DihedralStyle(charmm/kk/device,DihedralOPLSKokkos<LMPDeviceType>)
+DihedralStyle(opls/kk/device,DihedralOPLSKokkos<LMPDeviceType>)
-DihedralStyle(charmm/kk/host,DihedralOPLSKokkos<LMPHostType>)
+DihedralStyle(opls/kk/host,DihedralOPLSKokkos<LMPHostType>)
 
 #else
 

src/USER-COLVARS/ndx_group.cpp

@@ -120,7 +120,8 @@ void Ndx2Group::command(int narg, char **arg)
         // if we had processed a section, before we need to step back
         if (name != NULL) {
           rewind(fp);
-          find_section(fp,name);
+          char *tmp = find_section(fp,name);
+          delete[] tmp;
           delete[] name;
           name = NULL;
         }
@@ -171,6 +172,7 @@ void Ndx2Group::command(int narg, char **arg)
         len = 0;
 
         // find named section, search from beginning of file
+        if (name != NULL) delete[] name;
         rewind(fp);
         name = find_section(fp,arg[idx]);
         if (name != NULL) len=strlen(name);

src/USER-DPD/fix_eos_table.cpp

@@ -395,7 +395,7 @@ double FixEOStable::splint(double *xa, double *ya, double *y2a, int n, double x)
 void FixEOStable::energy_lookup(double t, double &u)
 {
   int itable;
-  double fraction,a,b;
+  double fraction;
 
   Table *tb = &tables[0];
   if(t < tb->lo || t > tb->hi){
@@ -417,7 +417,7 @@ void FixEOStable::energy_lookup(double t, double &u)
 void FixEOStable::temperature_lookup(double u, double &t)
 {
   int itable;
-  double fraction,a,b;
+  double fraction;
 
   Table *tb = &tables[1];
   if(u < tb->lo || u > tb->hi){ 

src/USER-DPD/fix_shardlow.cpp

@@ -156,7 +156,7 @@ void FixShardlow::initial_integrate(int vflag)
   int i,j,ii,jj,inum,jnum,itype,jtype;
   int *ilist,*jlist,*numneigh,**firstneigh;
   double xtmp,ytmp,ztmp,delx,dely,delz;
-  double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
+  double delvx,delvy,delvz;
   double rsq,r,rinv;
   double dot,wd,wr,randnum,factor_dpd,factor_dpd1;
   double dpx,dpy,dpz;
@@ -170,7 +170,6 @@ void FixShardlow::initial_integrate(int vflag)
   int nlocal = atom->nlocal;
   int nghost = atom->nghost;
   int nall = nlocal + nghost;
-  double *special_lj = force->special_lj;
   int newton_pair = force->newton_pair;
   double randPair;
 
@@ -179,7 +178,7 @@ void FixShardlow::initial_integrate(int vflag)
   double *duCond = atom->duCond;
   double *duMech = atom->duMech;
   double *dpdTheta = atom->dpdTheta;
-  double kappa_ij, alpha_ij, theta_ij, gamma_ij, sigma_ij, u_ij;
+  double kappa_ij, alpha_ij, theta_ij, gamma_ij, sigma_ij;
   double vxi, vyi, vzi, vxj, vyj, vzj;
   double vx0i, vy0i, vz0i, vx0j, vy0j, vz0j;
   double dot1, dot2, dot3, dot4;

src/USER-DPD/pair_dpd_fdt.cpp

@@ -212,8 +212,7 @@ void PairDPDfdt::coeff(int narg, char **arg)
   double a0_one = force->numeric(FLERR,arg[2]);
   double sigma_one = force->numeric(FLERR,arg[3]);
   double cut_one = cut_global;
-  double kappa_one;
+ 
-  
   if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
 
   int count = 0;

src/comm.h

@@ -147,7 +147,7 @@ class Comm : protected Pointers {
 W: OMP_NUM_THREADS environment is not set.
 
 This environment variable must be set appropriately to use the
-USER-OMP pacakge.
+USER-OMP package.
 
 E: Illegal ... command
 

src/dump_custom.cpp

@@ -451,7 +451,7 @@ int DumpCustom::count()
         choose[i] = 0;
   }
 
-  // un-choose if any threshhold criterion isn't met
+  // un-choose if any threshold criterion isn't met
 
   if (nthresh) {
     double *ptr;
@@ -471,7 +471,7 @@ int DumpCustom::count()
       } else if (thresh_array[ithresh] == MOL) {
         if (!atom->molecule_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         tagint *molecule = atom->molecule;
         for (i = 0; i < nlocal; i++) dchoose[i] = molecule[i];
         ptr = dchoose;
@@ -740,44 +740,44 @@ int DumpCustom::count()
       } else if (thresh_array[ithresh] == Q) {
         if (!atom->q_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = atom->q;
         nstride = 1;
       } else if (thresh_array[ithresh] == MUX) {
         if (!atom->mu_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][0];
         nstride = 4;
       } else if (thresh_array[ithresh] == MUY) {
         if (!atom->mu_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][1];
         nstride = 4;
       } else if (thresh_array[ithresh] == MUZ) {
         if (!atom->mu_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][2];
         nstride = 4;
       } else if (thresh_array[ithresh] == MU) {
         if (!atom->mu_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->mu[0][3];
         nstride = 4;
 
       } else if (thresh_array[ithresh] == RADIUS) {
         if (!atom->radius_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = atom->radius;
         nstride = 1;
       } else if (thresh_array[ithresh] == DIAMETER) {
         if (!atom->radius_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         double *radius = atom->radius;
         for (i = 0; i < nlocal; i++) dchoose[i] = 2.0*radius[i];
         ptr = dchoose;
@@ -785,55 +785,55 @@ int DumpCustom::count()
       } else if (thresh_array[ithresh] == OMEGAX) {
         if (!atom->omega_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->omega[0][0];
         nstride = 3;
       } else if (thresh_array[ithresh] == OMEGAY) {
         if (!atom->omega_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->omega[0][1];
         nstride = 3;
       } else if (thresh_array[ithresh] == OMEGAZ) {
         if (!atom->omega_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->omega[0][2];
         nstride = 3;
       } else if (thresh_array[ithresh] == ANGMOMX) {
         if (!atom->angmom_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->angmom[0][0];
         nstride = 3;
       } else if (thresh_array[ithresh] == ANGMOMY) {
         if (!atom->angmom_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->angmom[0][1];
         nstride = 3;
       } else if (thresh_array[ithresh] == ANGMOMZ) {
         if (!atom->angmom_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->angmom[0][2];
         nstride = 3;
       } else if (thresh_array[ithresh] == TQX) {
         if (!atom->torque_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->torque[0][0];
         nstride = 3;
       } else if (thresh_array[ithresh] == TQY) {
         if (!atom->torque_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->torque[0][1];
         nstride = 3;
       } else if (thresh_array[ithresh] == TQZ) {
         if (!atom->torque_flag)
           error->all(FLERR,
-                     "Threshhold for an atom property that isn't allocated");
+                     "Threshold for an atom property that isn't allocated");
         ptr = &atom->torque[0][2];
         nstride = 3;
 
@@ -881,7 +881,7 @@ int DumpCustom::count()
         nstride = 1;
       }
 
-      // unselect atoms that don't meet threshhold criterion
+      // unselect atoms that don't meet threshold criterion
 
       value = thresh_value[ithresh];
 
@@ -1459,6 +1459,7 @@ int DumpCustom::modify_param(int narg, char **arg)
       iregion = domain->find_region(arg[1]);
       if (iregion == -1)
         error->all(FLERR,"Dump_modify region ID does not exist");
+      delete [] idregion;
       int n = strlen(arg[1]) + 1;
       idregion = new char[n];
       strcpy(idregion,arg[1]);
@@ -1502,13 +1503,13 @@ int DumpCustom::modify_param(int narg, char **arg)
 
     if (narg < 4) error->all(FLERR,"Illegal dump_modify command");
 
-    // grow threshhold arrays
+    // grow threshold arrays
 
     memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
     memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
     memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
 
-    // set attribute type of threshhold
+    // set attribute type of threshold
     // customize by adding to if statement
 
     if (strcmp(arg[1],"id") == 0) thresh_array[nthresh] = ID;
@@ -1733,7 +1734,7 @@ int DumpCustom::modify_param(int narg, char **arg)
 
     } else error->all(FLERR,"Invalid dump_modify threshhold operator");
 
-    // set operation type of threshhold
+    // set operation type of threshold
 
     if (strcmp(arg[2],"<") == 0) thresh_op[nthresh] = LT;
     else if (strcmp(arg[2],"<=") == 0) thresh_op[nthresh] = LE;
@@ -1741,9 +1742,9 @@ int DumpCustom::modify_param(int narg, char **arg)
     else if (strcmp(arg[2],">=") == 0) thresh_op[nthresh] = GE;
     else if (strcmp(arg[2],"==") == 0) thresh_op[nthresh] = EQ;
     else if (strcmp(arg[2],"!=") == 0) thresh_op[nthresh] = NEQ;
-    else error->all(FLERR,"Invalid dump_modify threshhold operator");
+    else error->all(FLERR,"Invalid dump_modify threshold operator");
 
-    // set threshhold value
+    // set threshold value
 
     thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
 

src/fix_adapt.cpp

@@ -89,6 +89,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
       strcpy(adapt[nadapt].pstyle,arg[iarg+1]);
       n = strlen(arg[iarg+2]) + 1;
       adapt[nadapt].pparam = new char[n];
+      adapt[nadapt].pair = NULL;
       strcpy(adapt[nadapt].pparam,arg[iarg+2]);
       force->bounds(arg[iarg+3],atom->ntypes,
                     adapt[nadapt].ilo,adapt[nadapt].ihi);
@@ -294,7 +295,7 @@ void FixAdapt::init()
 
     if (ad->which == PAIR) {
       anypair = 1;
-      Pair *pair = NULL;
+      ad->pair = NULL;
 
       // if ad->pstyle has trailing sub-style annotation ":N",
       //   strip it for pstyle arg to pair_match() and set nsub = N
@@ -317,23 +318,25 @@ void FixAdapt::init()
         strcpy(psuffix,pstyle);
         strcat(psuffix,"/");
         strcat(psuffix,lmp->suffix);
-        pair = force->pair_match(psuffix,1,nsub);
+        ad->pair = force->pair_match(psuffix,1,nsub);
         delete[] psuffix;
       }
-      if (pair == NULL) pair = force->pair_match(pstyle,1,nsub);
+      if (ad->pair == NULL) ad->pair = force->pair_match(pstyle,1,nsub);
-      if (pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
+      if (ad->pair == NULL) error->all(FLERR,"Fix adapt pair style does not exist");
-      void *ptr = pair->extract(ad->pparam,ad->pdim);
+
+      void *ptr = ad->pair->extract(ad->pparam,ad->pdim);
       if (ptr == NULL)
         error->all(FLERR,"Fix adapt pair style param not supported");
 
-      ad->pdim = 2;
+      // for pair styles only parameters that are 2-d arrays in atom types are supported
-      if (ad->pdim == 0) ad->scalar = (double *) ptr;
+      if (ad->pdim != 2)
-      if (ad->pdim == 2) ad->array = (double **) ptr;
+        error->all(FLERR,"Fix adapt pair style param is not compatible");
+      else ad->array = (double **) ptr;
 
       // if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
 
-      if (ad->pdim == 2 && (strcmp(force->pair_style,"hybrid") == 0 ||
+      if (strcmp(force->pair_style,"hybrid") == 0 ||
-                            strcmp(force->pair_style,"hybrid/overlay") == 0)) {
+          strcmp(force->pair_style,"hybrid/overlay") == 0) {
         PairHybrid *pair = (PairHybrid *) force->pair;
         for (i = ad->ilo; i <= ad->ihi; i++)
           for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
@@ -515,8 +518,14 @@ void FixAdapt::change_settings()
   // re-initialize pair styles if any PAIR settings were changed
   // this resets other coeffs that may depend on changed values,
   // and also offset and tail corrections
-
+  if (anypair) {
-  if (anypair) force->pair->reinit();
+    for (int m = 0; m < nadapt; m++) {
+      Adapt *ad = &adapt[m];
+      if (ad->which == PAIR) {
+        ad->pair->reinit();
+      }
+    }
+  }
 
   // reset KSpace charges if charges have changed
 

src/fix_adapt.h

@@ -57,6 +57,7 @@ class FixAdapt : public Fix {
     double *scalar,scalar_orig;
     double **array,**array_orig;
     int aparam;
+    class Pair *pair;
   };
 
   Adapt *adapt;
@@ -99,6 +100,10 @@ E: Fix adapt pair style param not supported
 
 The pair style does not know about the parameter you specified.
 
+E: Fix adapt pair style param is not compatible
+
+Self-explanatory
+
 E: Fix adapt type pair range is not valid for pair hybrid sub-style
 
 Self-explanatory.

src/mpiio.h

@@ -15,7 +15,7 @@
 #define LMP_MPIIO_H
 
 // true interface to MPIIO package
-// used when MPIIO pacakge is installed
+// used when MPIIO package is installed
 
 #ifdef LMP_MPIIO