fix issues with reading and writing data files for systems without atom IDs

src/atom_vec.cpp

@@ -1714,7 +1714,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std:
 
   // error checks applicable to all styles
 
-  if (tag[nlocal] <= 0)
+  if ((atom->tag_enable && (tag[nlocal] <= 0)) || (!atom->tag_enable && (tag[nlocal] != 0)))
     error->one(FLERR, "Invalid atom ID {} in line {} of Atoms section of data file", tag[nlocal],
                nlocal + 1);
 

src/read_data.cpp

@@ -1465,8 +1465,23 @@ void ReadData::atoms()
 
 void ReadData::velocities()
 {
+  bigint nread = 0;
   int nchunk, eof;
 
+  // cannot map velocities to atoms without atom IDs
+
+  if (!atom->tag_enable) {
+    if (me == 0) utils::logmesg(lmp, "  skipping velocities without atom IDs ...\n");
+
+    while (nread < natoms) {
+      nchunk = MIN(natoms - nread, CHUNK);
+      eof = utils::read_lines_from_file(fp, nchunk, MAXLINE, buffer, me, world);
+      if (eof) error->all(FLERR, "Unexpected end of data file");
+      nread += nchunk;
+    }
+    return;
+  }
+
   if (me == 0) utils::logmesg(lmp, "  reading velocities ...\n");
 
   int mapflag = 0;
@@ -1476,8 +1491,6 @@ void ReadData::velocities()
     atom->map_set();
   }
 
-  bigint nread = 0;
-
   while (nread < natoms) {
     nchunk = MIN(natoms - nread, CHUNK);
     eof = utils::read_lines_from_file(fp, nchunk, MAXLINE, buffer, me, world);

src/write_data.cpp

@@ -191,8 +191,7 @@ void WriteData::write(const std::string &file)
   if (me == 0) {
     fp = fopen(file.c_str(),"w");
     if (fp == nullptr)
-      error->one(FLERR,"Cannot open data file {}: {}",
+      error->one(FLERR,"Cannot open data file {}: {}", file, utils::getsyserror());
-                                   file, utils::getsyserror());
   }
 
   // proc 0 writes header, ntype-length arrays, force fields
@@ -206,9 +205,15 @@ void WriteData::write(const std::string &file)
   }
 
   // per atom info in Atoms and Velocities sections
+  // must not write velocities without tags since we cannot read them back
 
   if (natoms) atoms();
-  if (natoms) velocities();
+  if (atom->tag_enable) {
+    if (natoms) velocities();
+  } else {
+    if (me == 0)
+      error->warning(FLERR, "Not writing Velocities section of data file without atom IDs");
+  }
 
   // molecular topology info if defined
   // do not write molecular topology for atom_style template

unittest/formats/test_atom_styles.cpp

@@ -693,6 +693,112 @@ TEST_F(AtomStyleTest, atomic)
     EXPECT_NEAR(x[GETIDX(16)][2], 7.9, EPSILON);
 }
 
+TEST_F(AtomStyleTest, no_tags)
+{
+    BEGIN_HIDE_OUTPUT();
+    command("atom_modify id no");
+    command("create_box 2 box");
+    command("create_atoms 1 single -2.0  2.0  0.1");
+    command("create_atoms 1 single -2.0 -2.0 -0.1");
+    command("create_atoms 2 single  2.0  2.0 -0.1");
+    command("create_atoms 2 single  2.0 -2.0  0.1");
+    command("mass 1 4.0");
+    command("mass 2 2.4");
+    command("pair_coeff * *");
+    END_HIDE_OUTPUT();
+
+    ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
+    ASSERT_NE(lmp->atom->avec, nullptr);
+    ASSERT_EQ(lmp->atom->natoms, 4);
+    ASSERT_EQ(lmp->atom->nlocal, 4);
+    ASSERT_EQ(lmp->atom->nghost, 0);
+    ASSERT_NE(lmp->atom->nmax, -1);
+    ASSERT_EQ(lmp->atom->tag_enable, 0);
+    ASSERT_EQ(lmp->atom->molecular, Atom::ATOMIC);
+    ASSERT_EQ(lmp->atom->ntypes, 2);
+
+    ASSERT_NE(lmp->atom->mass, nullptr);
+    ASSERT_NE(lmp->atom->mass_setflag, nullptr);
+    ASSERT_EQ(lmp->atom->sametag, nullptr);
+    ASSERT_EQ(lmp->atom->map_style, Atom::MAP_NONE);
+    ASSERT_EQ(lmp->atom->map_user, Atom::MAP_NONE);
+    ASSERT_EQ(lmp->atom->map_tag_max, -1);
+    ASSERT_EQ(lmp->atom->tag_consecutive(), 0);
+
+    BEGIN_HIDE_OUTPUT();
+    command("pair_coeff * *");
+    command("write_data test_atom_styles.data nocoeff");
+    command("clear");
+    command("atom_style atomic");
+    command("pair_style zero 4.0");
+    command("atom_modify id no");
+    command("units real");
+    command("read_data test_atom_styles.data");
+    END_HIDE_OUTPUT();
+    ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
+    ASSERT_NE(lmp->atom->avec, nullptr);
+    ASSERT_EQ(lmp->atom->natoms, 4);
+    ASSERT_EQ(lmp->atom->nlocal, 4);
+    ASSERT_EQ(lmp->atom->nghost, 0);
+    ASSERT_NE(lmp->atom->nmax, -1);
+    ASSERT_EQ(lmp->atom->tag_enable, 0);
+    ASSERT_EQ(lmp->atom->molecular, Atom::ATOMIC);
+    ASSERT_EQ(lmp->atom->ntypes, 2);
+
+    ASSERT_NEAR(lmp->atom->mass[1], 4.0, EPSILON);
+    ASSERT_NEAR(lmp->atom->mass[2], 2.4, EPSILON);
+    ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
+    ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
+    ASSERT_EQ(lmp->atom->map_style, Atom::MAP_NONE);
+    ASSERT_EQ(lmp->atom->map_user, Atom::MAP_NONE);
+    ASSERT_EQ(lmp->atom->map_tag_max, -1);
+    ASSERT_EQ(lmp->atom->tag_consecutive(), 0);
+
+    BEGIN_HIDE_OUTPUT();
+    command("pair_coeff * *");
+    command("write_restart test_atom_styles.restart");
+    command("clear");
+    command("read_restart test_atom_styles.restart");
+    END_HIDE_OUTPUT();
+    ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
+    ASSERT_NE(lmp->atom->avec, nullptr);
+    ASSERT_EQ(lmp->atom->natoms, 4);
+    ASSERT_EQ(lmp->atom->nlocal, 4);
+    ASSERT_EQ(lmp->atom->nghost, 0);
+    ASSERT_NE(lmp->atom->nmax, -1);
+    ASSERT_EQ(lmp->atom->tag_enable, 0);
+    ASSERT_EQ(lmp->atom->molecular, Atom::ATOMIC);
+    ASSERT_EQ(lmp->atom->ntypes, 2);
+    ASSERT_EQ(lmp->atom->tag_consecutive(), 0);
+
+    ASSERT_NEAR(lmp->atom->mass[1], 4.0, EPSILON);
+    ASSERT_NEAR(lmp->atom->mass[2], 2.4, EPSILON);
+    ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
+    ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
+    ASSERT_EQ(lmp->atom->map_style, Atom::MAP_NONE);
+    ASSERT_EQ(lmp->atom->map_user, Atom::MAP_NONE);
+    ASSERT_EQ(lmp->atom->map_tag_max, -1);
+
+    BEGIN_HIDE_OUTPUT();
+    command("comm_style tiled");
+    command("change_box all triclinic");
+    command("replicate 2 2 2");
+    END_HIDE_OUTPUT();
+
+    ASSERT_EQ(lmp->atom->natoms, 32);
+    ASSERT_EQ(lmp->atom->nlocal, 32);
+    ASSERT_EQ(lmp->atom->nghost, 0);
+    ASSERT_NE(lmp->atom->nmax, -1);
+    ASSERT_EQ(lmp->atom->tag_enable, 0);
+    ASSERT_EQ(lmp->atom->molecular, Atom::ATOMIC);
+    ASSERT_EQ(lmp->atom->ntypes, 2);
+    ASSERT_EQ(lmp->atom->tag_consecutive(), 0);
+    ASSERT_EQ(lmp->atom->map_tag_max, -1);
+
+    TEST_FAILURE(".*ERROR: Cannot use reset_atoms id unless atoms have IDs.*",
+                 command("reset_atoms id"););
+}
+
 TEST_F(AtomStyleTest, charge)
 {
     BEGIN_HIDE_OUTPUT();