[pull] develop from lammps:develop

src/ADIOS/adios_common.h

@@ -16,24 +16,9 @@
 #ifndef LMP_ADIOS_COMMON_H
 #define LMP_ADIOS_COMMON_H
 
-// common definitions for all ADIOS package classes
-
-static const char default_config[] = "<?xml version=\"1.0\"?>\n"
-                                     "<adios-config>\n"
-                                     "    <io name=\"atom\">\n"
-                                     "        <engine type=\"BP4\">\n"
-                                     "            <parameter key=\"substreams\" value=\"1\"/>\n"
-                                     "        </engine>\n"
-                                     "    </io>\n"
-                                     "    <io name=\"custom\">\n"
-                                     "        <engine type=\"BP4\">\n"
-                                     "            <parameter key=\"substreams\" value=\"1\"/>\n"
-                                     "        </engine>\n"
-                                     "    </io>\n"
-                                     "    <io name=\"read_dump\">\n"
-                                     "        <engine type=\"BP4\">\n"
-                                     "        </engine>\n"
-                                     "    </io>\n"
-                                     "</adios-config>\n";
+// common definition for all ADIOS package classes
+namespace LAMMPS_ADIOS {
+extern const char *default_config;
+}
 
 #endif

src/ADIOS/dump_atom_adios.cpp

@@ -32,6 +32,28 @@
 #include "adios_common.h"
 
 using namespace LAMMPS_NS;
+using namespace LAMMPS_ADIOS;
+
+// common definition for all ADIOS package classes
+
+const char *LAMMPS_ADIOS::default_config =
+    (const char *) "<?xml version=\"1.0\"?>\n"
+                   "<adios-config>\n"
+                   "    <io name=\"atom\">\n"
+                   "        <engine type=\"BP4\">\n"
+                   "            <parameter key=\"substreams\" value=\"1\"/>\n"
+                   "        </engine>\n"
+                   "    </io>\n"
+                   "    <io name=\"custom\">\n"
+                   "        <engine type=\"BP4\">\n"
+                   "            <parameter key=\"substreams\" value=\"1\"/>\n"
+                   "        </engine>\n"
+                   "    </io>\n"
+                   "    <io name=\"read_dump\">\n"
+                   "        <engine type=\"BP4\">\n"
+                   "        </engine>\n"
+                   "    </io>\n"
+                   "</adios-config>\n";
 
 namespace LAMMPS_NS {
 class DumpAtomADIOSInternal {
@@ -235,24 +257,29 @@ void DumpAtomADIOS::init_style()
 
   // setup column string
 
-  std::vector<std::string> columnNames;
-
-  if (scale_flag == 0 && image_flag == 0) {
-    columns = (char *) "id type x y z";
-    columnNames = {"id", "type", "x", "y", "z"};
-  } else if (scale_flag == 0 && image_flag == 1) {
-    columns = (char *) "id type x y z ix iy iz";
-    columnNames = {"id", "type", "x", "y", "z", "ix", "iy", "iz"};
-  } else if (scale_flag == 1 && image_flag == 0) {
-    columns = (char *) "id type xs ys zs";
-    columnNames = {"id", "type", "xs", "ys", "zs"};
-  } else if (scale_flag == 1 && image_flag == 1) {
-    columns = (char *) "id type xs ys zs ix iy iz";
-    columnNames = {"id", "type", "xs", "ys", "zs", "ix", "iy", "iz"};
-  }
+  std::string default_columns;
 
-  for (int icol = 0; icol < (int) columnNames.size(); ++icol)
-    if (keyword_user[icol].size()) columnNames[icol] = keyword_user[icol];
+  if (scale_flag == 0 && image_flag == 0)
+    default_columns = "id type x y z";
+  else if (scale_flag == 0 && image_flag == 1)
+    default_columns = "id type x y z ix iy iz";
+  else if (scale_flag == 1 && image_flag == 0)
+    default_columns = "id type xs ys zs";
+  else if (scale_flag == 1 && image_flag == 1)
+    default_columns = "id type xs ys zs ix iy iz";
+
+  std::vector<std::string> columnNames = utils::split_words(default_columns);
+
+  int icol = 0;
+  columns.clear();
+  for (const auto &item : columnNames) {
+    if (columns.size()) columns += " ";
+    if (keyword_user[icol].size())
+      columns += keyword_user[icol];
+    else
+      columns += item;
+    ++icol;
+  }
 
   // setup function ptrs
 

src/ADIOS/dump_custom_adios.cpp

@@ -36,6 +36,7 @@
 #include "adios_common.h"
 
 using namespace LAMMPS_NS;
+using namespace LAMMPS_ADIOS;
 
 namespace LAMMPS_NS {
 class DumpCustomADIOSInternal {
@@ -80,15 +81,15 @@ DumpCustomADIOS::DumpCustomADIOS(LAMMPS *lmp, int narg, char **arg) : DumpCustom
   }
 
   internal->columnNames.reserve(nfield);
-  for (int i = 0; i < nfield; ++i) { internal->columnNames.emplace_back(earg[i]); }
+  for (int i = 0; i < nfield; ++i) internal->columnNames.emplace_back(earg[i]);
 }
 
 /* ---------------------------------------------------------------------- */
 
 DumpCustomADIOS::~DumpCustomADIOS()
 {
   internal->columnNames.clear();
-  if (internal->fh) { internal->fh.Close(); }
+  if (internal->fh) internal->fh.Close();
   delete internal->ad;
   delete internal;
 }
@@ -216,10 +217,10 @@ void DumpCustomADIOS::write()
   internal->fh.Put<uint64_t>("nme", bnme);
   internal->fh.Put<uint64_t>("offset", atomOffset);
   // now write the atoms
-  internal->fh.Put<double>("atoms", buf);
+  internal->fh.Put<double>(internal->varAtoms, buf);
   internal->fh.EndStep();    // I/O will happen now...
 
-  if (multifile) { internal->fh.Close(); }
+  if (multifile) internal->fh.Close();
 }
 
 /* ---------------------------------------------------------------------- */

src/ADIOS/reader_adios.cpp

@@ -30,6 +30,7 @@
 #include "adios_common.h"
 
 using namespace LAMMPS_NS;
+using namespace LAMMPS_ADIOS;
 
 static constexpr double SMALL = 1.0e-6;
 

src/EXTRA-COMMAND/group2ndx.cpp

@@ -61,7 +61,9 @@ void Group2Ndx::command(int narg, char **arg)
   }
 
   if (narg == 1) {    // write out all groups
-    for (int i = 0; i < group->ngroup; ++i) { write_group(fp, i); }
+    for (int i = 0; i < Group::MAX_GROUP; ++i) {
+      if (group->names[i]) write_group(fp, i);
+    }
   } else {    // write only selected groups
     for (int i = 1; i < narg; ++i) {
       int gid = group->find(arg[i]);

src/GRAPHICS/image.cpp

@@ -52,6 +52,7 @@ namespace {
 constexpr int NCOLORS = 140;
 constexpr int NELEMENTS = 109;
 constexpr double EPSILON = 1.0e-6;
+constexpr double TRANS_DELTA = 0.01;
 
 enum { NUMERIC, MINVALUE, MAXVALUE };
 enum { CONTINUOUS, DISCRETE, SEQUENTIAL };
@@ -888,9 +889,9 @@ void Image::draw_pixmap(int xc, int yc, int pixwidth, int pixheight, const unsig
       // we allow a few steps difference for each channel to account
       // for rounding errors and reduce "bleeding" from interpolation
 
-      if ((fabs(pixelcolor[0] - transcolor[0]) < 0.01) &&
-          (fabs(pixelcolor[1] - transcolor[1]) < 0.01) &&
-          (fabs(pixelcolor[2] - transcolor[2]) < 0.01)) continue;
+      if ((fabs(pixelcolor[0] - transcolor[0]) < TRANS_DELTA) &&
+          (fabs(pixelcolor[1] - transcolor[1]) < TRANS_DELTA) &&
+          (fabs(pixelcolor[2] - transcolor[2]) < TRANS_DELTA)) continue;
 
       draw_pixel(ix, iy, dist, normal, pixelcolor);
     }
@@ -1359,6 +1360,7 @@ void Image::draw_pixel(int ix, int iy, double depth,
                        const double *surface, const double *surfaceColor)
 {
   if (!std::isfinite(depth)) return; // reject pixels with invalid depth buffer values
+  if (!surfaceColor) return;         // reject pixels with an invalid color
 
   double diffuseKey,diffuseFill,diffuseBack,specularKey;
   if (depth < 0 || (depthBuffer[ix + iy*width] >= 0 && depth >= depthBuffer[ix + iy*width])) return;
@@ -2552,5 +2554,6 @@ double *ColorMap::value2color(double value)
     return mentry[ibin%nentry].color;
   }
 
-  return nullptr;
+  // always return a non-NULL pointer
+  return mentry[0].color;
 }

src/KOKKOS/atom_vec_ellipsoid_kokkos.cpp

@@ -944,7 +944,7 @@ void AtomVecEllipsoidKokkos::sync_pinned(ExecutionSpace space, uint64_t mask, in
     if ((mask & V_MASK) && atomKK->k_v.need_sync_device())
       perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_v,space,async_flag);
     if ((mask & F_MASK) && atomKK->k_f.need_sync_device())
-      perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_f,space,async_flag);
+      perform_pinned_copy_transform<DAT::ttransform_kkacc_1d_3>(atomKK->k_f,space,async_flag);
     if ((mask & TAG_MASK) && atomKK->k_tag.need_sync_device())
       perform_pinned_copy<DAT::tdual_tagint_1d>(atomKK->k_tag,space,async_flag);
     if ((mask & TYPE_MASK) && atomKK->k_type.need_sync_device())
@@ -958,7 +958,7 @@ void AtomVecEllipsoidKokkos::sync_pinned(ExecutionSpace space, uint64_t mask, in
     if ((mask & ANGMOM_MASK) && atomKK->k_angmom.need_sync_device())
       perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_angmom,space,async_flag);
     if ((mask & TORQUE_MASK) && atomKK->k_torque.need_sync_device())
-      perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_torque,space,async_flag);
+      perform_pinned_copy_transform<DAT::ttransform_kkacc_1d_3>(atomKK->k_torque,space,async_flag);
     if ((mask & ELLIPSOID_MASK) && atomKK->k_ellipsoid.need_sync_device())
       perform_pinned_copy<DAT::tdual_int_1d>(atomKK->k_ellipsoid,space,async_flag);
     if ((mask & BONUS_MASK) && k_bonus.need_sync_device())
@@ -969,7 +969,7 @@ void AtomVecEllipsoidKokkos::sync_pinned(ExecutionSpace space, uint64_t mask, in
     if ((mask & V_MASK) && atomKK->k_v.need_sync_host())
       perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_v,space,async_flag);
     if ((mask & F_MASK) && atomKK->k_f.need_sync_host())
-      perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_f,space,async_flag);
+      perform_pinned_copy_transform<DAT::ttransform_kkacc_1d_3>(atomKK->k_f,space,async_flag);
     if ((mask & TAG_MASK) && atomKK->k_tag.need_sync_host())
       perform_pinned_copy<DAT::tdual_tagint_1d>(atomKK->k_tag,space,async_flag);
     if ((mask & TYPE_MASK) && atomKK->k_type.need_sync_host())
@@ -983,7 +983,7 @@ void AtomVecEllipsoidKokkos::sync_pinned(ExecutionSpace space, uint64_t mask, in
     if ((mask & ANGMOM_MASK) && atomKK->k_angmom.need_sync_host())
       perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_angmom,space,async_flag);
     if ((mask & TORQUE_MASK) && atomKK->k_torque.need_sync_host())
-      perform_pinned_copy_transform<DAT::ttransform_kkfloat_1d_3>(atomKK->k_torque,space,async_flag);
+      perform_pinned_copy_transform<DAT::ttransform_kkacc_1d_3>(atomKK->k_torque,space,async_flag);
     if ((mask & ELLIPSOID_MASK) && atomKK->k_ellipsoid.need_sync_host())
       perform_pinned_copy<DAT::tdual_int_1d>(atomKK->k_ellipsoid,space,async_flag);
     if ((mask & BONUS_MASK) && k_bonus.need_sync_host())

src/KOKKOS/atom_vec_ellipsoid_kokkos.h

@@ -132,14 +132,14 @@ class AtomVecEllipsoidKokkos : public AtomVecKokkos, public AtomVecEllipsoid {
 
   DAT::t_kkfloat_1d_3_lr d_x;
   DAT::t_kkfloat_1d_3 d_v;
-  DAT::t_kkfloat_1d_3 d_f;
+  DAT::t_kkacc_1d_3 d_f;
 
   DAT::t_kkfloat_1d d_rmass;
   HAT::t_kkfloat_1d h_rmass;
   DAT::t_kkfloat_1d_3 d_angmom;
   HAT::t_kkfloat_1d_3 h_angmom;
-  DAT::t_kkfloat_1d_3 d_torque;
-  HAT::t_kkfloat_1d_3 h_torque;
+  DAT::t_kkacc_1d_3 d_torque;
+  HAT::t_kkacc_1d_3 h_torque;
   DAT::t_int_1d d_ellipsoid;
   HAT::t_int_1d h_ellipsoid;
 

src/KOKKOS/bond_hybrid_kokkos.h

@@ -46,7 +46,7 @@ class BondHybridKokkos : public BondHybrid {
 
   DAT::tdual_int_1d k_map;       // which style each bond type points to
   DAT::tdual_int_1d k_nbondlist; // # of bonds in sub-style bondlists
-  DAT::tdual_int_3d k_bondlist;  // bondlist for each sub-style
+  DAT::tdual_int_3d_lr k_bondlist;  // bondlist for each sub-style
 
   void allocate() override;
   void deallocate() override;

src/KOKKOS/dihedral_hybrid_kokkos.h

@@ -46,7 +46,7 @@ class DihedralHybridKokkos : public DihedralHybrid {
 
   DAT::tdual_int_1d k_map;       // which style each dihedral type points to
   DAT::tdual_int_1d k_ndihedrallist; // # of dihedrals in sub-style dihedrallists
-  DAT::tdual_int_3d k_dihedrallist;  // dihedrallist for each sub-style
+  DAT::tdual_int_3d_lr k_dihedrallist;  // dihedrallist for each sub-style
 
   void allocate() override;
   void deallocate() override;

src/KOKKOS/fix_langevin_kokkos.h

@@ -144,7 +144,7 @@ namespace LAMMPS_NS {
     // For angmom thermostat
     class AtomVecEllipsoidKokkos *avecEllipKK;
     typename AtomVecEllipsoidKokkosBonusArray<DeviceType>::t_bonus_1d bonus;
-    typename ArrayTypes<DeviceType>::t_kkfloat_1d_3 torque;
+    typename ArrayTypes<DeviceType>::t_kkacc_1d_3 torque;
     typename ArrayTypes<DeviceType>::t_kkfloat_1d_3 angmom;
     typename ArrayTypes<DeviceType>::t_int_1d ellipsoid;
     void angmom_thermostat();

src/KOKKOS/fix_nve_asphere_kokkos.h

@@ -54,9 +54,9 @@ class FixNVEAsphereKokkos : public FixNVEAsphere {
     typename ArrayTypes<DeviceType>::t_int_1d ellipsoid;
     typename ArrayTypes<DeviceType>::t_kkfloat_1d_3_lr x;
     typename ArrayTypes<DeviceType>::t_kkfloat_1d_3 v;
-    typename ArrayTypes<DeviceType>::t_kkfloat_1d_3 f;
+    typename ArrayTypes<DeviceType>::t_kkacc_1d_3 f;
     typename ArrayTypes<DeviceType>::t_kkfloat_1d_3 angmom;
-    typename ArrayTypes<DeviceType>::t_kkfloat_1d_3 torque;
+    typename ArrayTypes<DeviceType>::t_kkacc_1d_3 torque;
     typename ArrayTypes<DeviceType>::t_kkfloat_1d rmass;
     typename ArrayTypes<DeviceType>::t_int_1d mask;
 };

src/KOKKOS/fix_shake_kokkos.cpp

@@ -447,7 +447,7 @@ void FixShakeKokkos<DeviceType>::operator()(TagFixShakeMinPostForce<NEIGHFLAG,VF
   const int i0 = d_closest_list(i, 0);
 
   auto apply_restraint = [&](int idx0, int idx1, int type_idx, bool is_angle) {
-    if (idx0 < 0 || idx1 < 0) return 0.0;
+    if (idx0 < 0 || idx1 < 0) return (KK_FLOAT)0.0;
     const KK_FLOAT d0 = is_angle ? d_angle_distance[type_idx] : d_bond_distance[type_idx];
     const KK_FLOAT delx = d_x(idx0, 0) - d_x(idx1, 0);
     const KK_FLOAT dely = d_x(idx0, 1) - d_x(idx1, 1);

src/KOKKOS/improper_hybrid_kokkos.h

@@ -46,7 +46,7 @@ class ImproperHybridKokkos : public ImproperHybrid {
 
   DAT::tdual_int_1d k_map;       // which style each improper type points to
   DAT::tdual_int_1d k_nimproperlist; // # of impropers in sub-style improperlists
-  DAT::tdual_int_3d k_improperlist;  // improperlist for each sub-style
+  DAT::tdual_int_3d_lr k_improperlist;  // improperlist for each sub-style
 
   void allocate() override;
   void deallocate() override;

src/fix.cpp

@@ -186,7 +186,7 @@ void Fix::modify_params(int narg, char **arg)
   }
 }
 
-void::Fix::set_molecule(int, tagint, int, double *, double *, double *)
+void Fix::set_molecule(int, tagint, int, double *, double *, double *)
 {
   error->all(FLERR,"Molecule update not implemented for fix {}", style);
 }

src/group.cpp

@@ -39,7 +39,6 @@
 
 using namespace LAMMPS_NS;
 
-static constexpr int MAX_GROUP = 32;
 static constexpr double EPSILON = 1.0e-6;
 
 enum { NONE, TYPE, MOLECULE, ID };
@@ -152,7 +151,7 @@ void Group::assign(int narg, char **arg)
   bool created = false;
 
   if (igroup == -1) {
-    if (ngroup == MAX_GROUP) error->all(FLERR, "Too many groups (max {})", MAX_GROUP);
+    if (ngroup == MAX_GROUP) error->all(FLERR, "Too many groups (max {})", int(MAX_GROUP));
     igroup = find_unused();
     names[igroup] = utils::strdup(arg[0]);
     ngroup++;
@@ -592,7 +591,7 @@ void Group::create(const std::string &name, int *flag)
   int igroup = find(name);
 
   if (igroup == -1) {
-    if (ngroup == MAX_GROUP) error->all(FLERR, "Too many groups (max {})", MAX_GROUP);
+    if (ngroup == MAX_GROUP) error->all(FLERR, "Too many groups (max {})", int(MAX_GROUP));
     igroup = find_unused();
     names[igroup] = utils::strdup(name);
     ngroup++;
@@ -629,7 +628,7 @@ int Group::find_or_create(const char *name)
   int igroup = find(name);
   if (igroup >= 0) return igroup;
 
-  if (ngroup == MAX_GROUP) error->all(FLERR, "Too many groups (max {})", MAX_GROUP);
+  if (ngroup == MAX_GROUP) error->all(FLERR, "Too many groups (max {})", int(MAX_GROUP));
   igroup = find_unused();
   names[igroup] = utils::strdup(name);
   ngroup++;

src/group.h

@@ -23,11 +23,12 @@ class Group : protected Pointers {
   friend class FixGroup;
 
  public:
-  int ngroup;          // # of defined groups
-  char **names;        // name of each group
-  int *bitmask;        // one-bit mask for each group
-  int *inversemask;    // inverse mask for each group
-  int *dynamic;        // 1 if dynamic, 0 if not
+  enum { MAX_GROUP = 32 };    // max # of groups. limited to 32 because bitmasks are 32-bit int.
+  int ngroup;                 // # of defined groups
+  char **names;               // name of each group
+  int *bitmask;               // one-bit mask for each group
+  int *inversemask;           // inverse mask for each group
+  int *dynamic;               // 1 if dynamic, 0 if not
 
   Group(class LAMMPS *);
   ~Group() override;

src/info.cpp

@@ -494,10 +494,12 @@ void Info::command(int narg, char **arg)
     char **names = group->names;
     int *dynamic = group->dynamic;
     fputs("\nGroup information:\n",out);
-    for (int i=0; i < ngroup; ++i) {
-      if (names[i])
+    for (int i=0; i < Group::MAX_GROUP; ++i) {
+      // skip over deleted groups
+      if (names[i]) {
         utils::print(out,"Group[{:2d}]:     {:16} ({})\n",
-                   i, names[i], dynamic[i] ? "dynamic" : "static");
+                     i, names[i], dynamic[i] ? "dynamic" : "static");
+      }
     }
   }