Merge branch 'lammps:develop' into develop

src/DRUDE/compute_temp_drude.cpp

@@ -89,9 +89,7 @@ void ComputeTempDrude::dof_compute()
   int dim = domain->dimension;
   int *drudetype = fix_drude->drudetype;
 
-  fix_dof = 0;
-  for (int i = 0; i < modify->nfix; i++)
-    fix_dof += modify->fix[i]->dof(igroup);
+  adjust_dof_fix();
 
   bigint dof_core_loc = 0, dof_drude_loc = 0;
   for (int i = 0; i < nlocal; i++) {

src/DRUDE/compute_temp_drude.h

@@ -35,7 +35,6 @@ class ComputeTempDrude : public Compute {
   int modify_param(int, char **);
 
  private:
-  int fix_dof;
   class FixDrude *fix_drude;
   char *id_temp;
   class Compute *temperature;

src/EXTRA-COMPUTE/compute_temp_rotate.h

@@ -43,7 +43,6 @@ class ComputeTempRotate : public Compute {
   double memory_usage();
 
  private:
-  int fix_dof;
   double tfactor, masstotal;
   double **vbiasall;    // stored velocity bias for all atoms
   int maxbias;          // size of vbiasall array

src/MACHDYN/atom_vec_smd.cpp

@@ -115,6 +115,7 @@ void AtomVecSMD::grow_pointers()
   vfrac = atom->vfrac;
   rmass = atom->rmass;
   x0 = atom->x0;
+  x = atom->x;
   radius = atom->radius;
   contact_radius = atom->contact_radius;
   molecule = atom->molecule;
@@ -129,13 +130,11 @@ void AtomVecSMD::grow_pointers()
 /* ----------------------------------------------------------------------
    clear extra forces starting at atom N
    nbytes = # of bytes to clear for a per-atom vector
-   NOTE: does f need to be re-cleared?
 ------------------------------------------------------------------------- */
 
 void AtomVecSMD::force_clear(int n, size_t nbytes)
 {
   memset(&desph[n],0,nbytes);
-  memset(&f[n][0],0,3*nbytes);
 }
 
 /* ----------------------------------------------------------------------

src/MACHDYN/compute_smd_triangle_vertices.cpp

@@ -53,7 +53,7 @@ ComputeSMDTriangleVertices::ComputeSMDTriangleVertices(LAMMPS *lmp, int narg, ch
 /* ---------------------------------------------------------------------- */
 
 ComputeSMDTriangleVertices::~ComputeSMDTriangleVertices() {
-    memory->sfree(outputVector);
+    memory->destroy(outputVector);
 }
 
 /* ---------------------------------------------------------------------- */

src/MACHDYN/pair_smd_ulsph.cpp

@@ -85,7 +85,8 @@ PairULSPH::PairULSPH(LAMMPS *lmp) :
 
 PairULSPH::~PairULSPH() {
         if (allocated) {
-                //printf("... deallocating\n");
+                memory->destroy(setflag);
+                memory->destroy(cutsq);
                 memory->destroy(Q1);
                 memory->destroy(rho0);
                 memory->destroy(eos);

src/fix_deposit.cpp

@@ -569,10 +569,12 @@ void FixDeposit::pre_exchange()
     //   coord is new position of geometric center of mol, not COM
     // FixShake::set_molecule stores shake info for molecule
 
-    if (rigidflag)
-      fixrigid->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
-    else if (shakeflag)
-      fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
+    if (mode == MOLECULE) {
+      if (rigidflag)
+        fixrigid->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
+      else if (shakeflag)
+        fixshake->set_molecule(nlocalprev,maxtag_all,imol,coord,vnew,quat);
+    }
 
     success = 1;
     break;

src/verlet.cpp

@@ -54,7 +54,7 @@ void Verlet::init()
 
   bool do_time_integrate = false;
   for (const auto &fix : modify->get_fix_list())
-    if (fix->time_integrate) do_time_integrate;
+    if (fix->time_integrate) do_time_integrate = true;
 
   if (!do_time_integrate && (comm->me == 0))
     error->warning(FLERR,"No fixes with time integration, atoms won't move");