recover non-labelmap functionality with Kokkos. Error out when maps are used with Kokkos

doc/src/labelmap.rst

@@ -86,6 +86,8 @@ This command must come after the simulation box is defined by a
 :doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
 :doc:`create_box <create_box>` command.
 
+Labelmaps are currently not supported when using the KOKKOS package.
+
 Related commands
 """"""""""""""""
 

doc/src/read_data.rst

@@ -1519,11 +1519,14 @@ To read gzipped data files, you must compile LAMMPS with the
 -DLAMMPS_GZIP option.  See the :doc:`Build settings <Build_settings>`
 doc page for details.
 
+Labelmaps are currently not supported when using the KOKKOS package.
+
 Related commands
 """"""""""""""""
 
 :doc:`read_dump <read_dump>`, :doc:`read_restart <read_restart>`,
-:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`
+:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`,
+:doc:`labelmap <labelmap>`
 
 Default
 """""""

src/KOKKOS/atom_vec_angle_kokkos.cpp

@@ -1633,7 +1633,7 @@ void AtomVecAngleKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp,
-                                  const std::vector<std::string> &values)
+                                  const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
@@ -1642,6 +1642,7 @@ void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp,
   h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
   h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp);
   h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp);
+  extract = values[2];
   if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_angle_kokkos.h

@@ -51,7 +51,7 @@ class AtomVecAngleKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/KOKKOS/atom_vec_atomic_kokkos.cpp

@@ -824,13 +824,14 @@ void AtomVecAtomicKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecAtomicKokkos::data_atom(double *coord, imageint imagetmp,
-                                    const std::vector<std::string> &values)
+                                    const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
 
   h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp);
   h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
+  extract = values[1];
   if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_atomic_kokkos.h

@@ -44,7 +44,7 @@ class AtomVecAtomicKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   void pack_data(double **) override;
   void write_data(FILE *, int, double **) override;
   double memory_usage() override;

src/KOKKOS/atom_vec_bond_kokkos.cpp

@@ -1059,7 +1059,7 @@ void AtomVecBondKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
-                                  const std::vector<std::string> &values)
+                                  const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atomKK->nlocal;
   if (nlocal == nmax) grow(0);
@@ -1068,6 +1068,7 @@ void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
   h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
   h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp);
   h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp);
+  extract = values[2];
   if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_bond_kokkos.h

@@ -45,7 +45,7 @@ class AtomVecBondKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/KOKKOS/atom_vec_charge_kokkos.cpp

@@ -957,13 +957,14 @@ void AtomVecChargeKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp,
-                                    const std::vector<std::string> &values)
+                                    const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
 
   h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp);
   h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
+  extract = values[1];
   if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_charge_kokkos.h

@@ -46,7 +46,7 @@ class AtomVecChargeKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int , const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/KOKKOS/atom_vec_dpd_kokkos.cpp

@@ -1719,13 +1719,14 @@ void AtomVecDPDKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecDPDKokkos::data_atom(double *coord, imageint imagetmp,
-                                 const std::vector<std::string> &values)
+                                 const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
 
   h_tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp);
   h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
+  extract = values[1];
   if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_dpd_kokkos.h

@@ -54,7 +54,7 @@ class AtomVecDPDKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/KOKKOS/atom_vec_full_kokkos.cpp

@@ -1491,7 +1491,7 @@ void AtomVecFullKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp,
-                                  const std::vector<std::string> &values)
+                                  const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
@@ -1500,6 +1500,7 @@ void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp,
   h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
   h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp);
   h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp);
+  extract = values[2];
   if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_full_kokkos.h

@@ -45,7 +45,7 @@ class AtomVecFullKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/KOKKOS/atom_vec_hybrid_kokkos.cpp

@@ -971,7 +971,7 @@ void AtomVecHybridKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp,
-                                    const std::vector<std::string> &values)
+                                    const std::vector<std::string> &values, std::string &extract)
 {
   atomKK->sync(Host,X_MASK|TAG_MASK|TYPE_MASK|IMAGE_MASK|MASK_MASK|V_MASK|OMEGA_MASK/*|ANGMOM_MASK*/);
 
@@ -980,6 +980,7 @@ void AtomVecHybridKokkos::data_atom(double *coord, imageint imagetmp,
 
   h_tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp);
   h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
+  extract = values[1];
   if (h_type[nlocal] <= 0 || h_type[nlocal] > atom->ntypes)
     error->one(FLERR,"Invalid atom h_type in Atoms section of data file");
 

src/KOKKOS/atom_vec_hybrid_kokkos.h

@@ -57,7 +57,7 @@ class AtomVecHybridKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override {return 0;}
   void data_vel(int, const std::vector<std::string> &) override;
   void pack_data(double **) override;

src/KOKKOS/atom_vec_molecular_kokkos.cpp

@@ -1892,7 +1892,7 @@ void AtomVecMolecularKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp,
-                                       const std::vector<std::string> &values)
+                                       const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
@@ -1901,6 +1901,7 @@ void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp,
   h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
   h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp);
   h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp);
+  extract = values[2];
   if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_molecular_kokkos.h

@@ -51,7 +51,7 @@ class AtomVecMolecularKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/KOKKOS/atom_vec_sphere_kokkos.cpp

@@ -2546,13 +2546,14 @@ void AtomVecSphereKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecSphereKokkos::data_atom(double *coord, imageint imagetmp,
-                                    const std::vector<std::string> &values)
+                                    const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
 
   tag[nlocal] = utils::tnumeric(FLERR,values[0],true,lmp);
   type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
+  extract = values[1];
   if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_sphere_kokkos.h

@@ -58,7 +58,7 @@ class AtomVecSphereKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void data_vel(int, const std::vector<std::string> &) override;
   int data_vel_hybrid(int, const std::vector<std::string> &, int) override;

src/KOKKOS/atom_vec_spin_kokkos.cpp

@@ -1058,13 +1058,14 @@ void AtomVecSpinKokkos::create_atom(int itype, double *coord)
 ------------------------------------------------------------------------- */
 
 void AtomVecSpinKokkos::data_atom(double *coord, imageint imagetmp,
-                                  const std::vector<std::string> &values)
+                                  const std::vector<std::string> &values, std::string &extract)
 {
   int nlocal = atom->nlocal;
   if (nlocal == nmax) grow(0);
 
   h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp);
   h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
+  extract = values[1];
   if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
     error->one(FLERR,"Invalid atom type in Atoms section of data file");
 

src/KOKKOS/atom_vec_spin_kokkos.h

@@ -45,7 +45,7 @@ class AtomVecSpinKokkos : public AtomVecKokkos {
   int pack_restart(int, double *) override;
   int unpack_restart(double *) override;
   void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &) override;
+  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
   int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
   void pack_data(double **) override;
   int pack_data_hybrid(int, double *) override;

src/atom.cpp

@@ -1200,7 +1200,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
             break;
           }
           case 1: {    // type label
-            if (!atom->labelmapflag)
+            if (!labelmapflag)
               error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
             type[nlocal - 1] = lmap->find(typestr, Atom::ATOM);
             if (type[nlocal - 1] == -1)
@@ -2195,6 +2195,8 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
 
 void Atom::add_label_map()
 {
+  if (lmp->kokkos)
+    error->all(FLERR, "Label maps are currently not supported with Kokkos");
   labelmapflag = 1;
   lmap = new LabelMap(lmp,ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes);
 }

src/atom_vec.cpp

@@ -1650,17 +1650,6 @@ void AtomVec::create_atom(int itype, double *coord)
   atom->nlocal++;
 }
 
-/* ----------------------------------------------------------------------
-   version of data_atom without extract option
-   temporary fix for Kokkos compilation
-------------------------------------------------------------------------- */
-
-void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std::string> &values)
-{
-  std::string strtmp;
-  data_atom(coord, imagetmp, values, strtmp);
-}
-
 /* ----------------------------------------------------------------------
    unpack one line from Atoms section of data file
    initialize other peratom quantities

src/atom_vec.h

@@ -123,7 +123,6 @@ class AtomVec : protected Pointers {
   virtual void create_atom(int, double *);
   virtual void create_atom_post(int) {}
 
-  virtual void data_atom(double *, imageint, const std::vector<std::string> &);
   virtual void data_atom(double *, imageint, const std::vector<std::string> &, std::string &);
   virtual void data_atom_post(int) {}
   virtual void data_atom_bonus(int, const std::vector<std::string> &) {}

src/special.cpp

@@ -857,10 +857,10 @@ void Special::combine()
     utils::logmesg(lmp,"{:>6} = max # of special neighbors\n",atom->maxspecial);
 
   if (lmp->kokkos) {
-    auto  atomKK = dynamic_cast<AtomKokkos*>( atom);
+    auto  atomKK = dynamic_cast<AtomKokkos*>(atom);
     atomKK->modified(Host,SPECIAL_MASK);
     atomKK->sync(Device,SPECIAL_MASK);
-    auto  memoryKK = dynamic_cast<MemoryKokkos*>( memory);
+    auto  memoryKK = dynamic_cast<MemoryKokkos*>(memory);
     memoryKK->grow_kokkos(atomKK->k_special,atom->special,
                         atom->nmax,atom->maxspecial,"atom:special");
     atomKK->modified(Device,SPECIAL_MASK);