rename reset_ids command to reset_atom_ids

doc/src/Commands_all.rst

@@ -101,7 +101,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_atom_ids <reset_atom_ids>`
    * :doc:`reset_mol_ids <reset_mol_ids>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`

doc/src/commands_list.rst

@@ -88,7 +88,7 @@ Commands
    region
    replicate
    rerun
-   reset_ids
+   reset_atom_ids
    reset_mol_ids
    reset_timestep
    restart

doc/src/delete_atoms.rst

@@ -89,7 +89,7 @@ number of atoms in the system.  Note that this is not done for
 molecular systems (see the :doc:`atom_style <atom_style>` command),
 regardless of the *compress* setting, since it would foul up the bond
 connectivity that has already been assigned.  However, the
-:doc:`reset_ids <reset_ids>` command can be used after this command to
+:doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to
 accomplish the same thing.
 
 Note that the re-assignment of IDs is not really a compression, where
@@ -157,7 +157,7 @@ using molecule template files via the :doc:`molecule <molecule>` and
 Related commands
 """"""""""""""""
 
-:doc:`create_atoms <create_atoms>`, :doc:`reset_ids <reset_ids>`
+:doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>`
 
 Default
 """""""

doc/src/reset_atom_ids.rst

@@ -1,14 +1,14 @@
-.. index:: reset_ids
+.. index:: reset_atom_ids
 
-reset_ids command
+reset_atom_ids command
-=================
+======================
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   reset_ids keyword values ...
+   reset_atom_ids keyword values ...
 
    * zero or more keyword/value pairs may be appended
    * keyword = *sort*
@@ -22,8 +22,8 @@ Examples
 
 .. code-block:: LAMMPS
 
-   reset_ids
+   reset_atom_ids
-   reset_ids sort yes
+   reset_atom_ids sort yes
 
 Description
 """""""""""
@@ -77,7 +77,7 @@ processor have consecutive IDs, as the :doc:`create_atoms
    that are owned by other processors.  The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue.
    Or you can define a pair style before using this command.  If you do
    the former, you should unset the comm_modify cutoff after using
-   reset_ids so that subsequent communication is not inefficient.
+   reset_atom_ids so that subsequent communication is not inefficient.
 
 Restrictions
 """"""""""""

doc/src/reset_mol_ids.rst

@@ -46,7 +46,7 @@ none
 Related commands
 """"""""""""""""
 
-:doc:`reset_ids <reset_ids>`, :doc:`fix bond/react <fix_bond_react>`,
+:doc:`reset_atom_ids <reset_atom_ids>`, :doc:`fix bond/react <fix_bond_react>`,
 :doc:`fix bond/create <fix_bond_create>`,
 :doc:`fix bond/break <fix_bond_break>`,
 :doc:`fix evaporate <fix_evaporate>`,

src/deprecated.cpp

@@ -16,19 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "deprecated.h"
-#include <cstring>
+#include <string>
 #include "comm.h"
 #include "error.h"
 #include "input.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
-static void writemsg(LAMMPS *lmp, const char *msg, int abend=1)
+static void writemsg(LAMMPS *lmp, const std::string &msg, int abend=1)
 {
-  if (lmp->comm->me == 0) {
+  if (lmp->comm->me == 0) utils::logmesg(lmp,msg);
-    if (lmp->screen) fputs(msg,lmp->screen);
-    if (lmp->logfile) fputs(msg,lmp->logfile);
-  }
   if (abend)
     lmp->error->all(FLERR,"This command is no longer available");
 }
@@ -37,8 +35,11 @@ static void writemsg(LAMMPS *lmp, const char *msg, int abend=1)
 
 void Deprecated::command(int /* narg */, char ** /* arg */)
 {
-  if (strcmp(input->command,"DEPRECATED") == 0) {
+  const std::string cmd = input->command;
-    writemsg(lmp,"\nCommand 'DEPRECATED' is a dummy command\n\n",0);
 
+  if (cmd == "DEPRECATED") {
+    writemsg(lmp,"\nCommand 'DEPRECATED' is a dummy command\n\n",0);
+  } else if (cmd == "reset_ids") {
+    writemsg(lmp,"\n'reset_ids' has been renamed to 'reset_atom_ids'\n\n");
   }
 }

src/deprecated.h

@@ -14,6 +14,7 @@
 #ifdef COMMAND_CLASS
 
 CommandStyle(DEPRECATED,Deprecated)
+CommandStyle(reset_ids,Deprecated)
 
 #else
 

src/reset_atom_ids.cpp

@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "reset_ids.h"
+#include "reset_atom_ids.h"
 #include <mpi.h>
 #include <cstring>
 #include "atom.h"
@@ -53,11 +53,11 @@ void ResetIDs::command(int narg, char **arg)
   if (domain->box_exist == 0)
     error->all(FLERR,"Reset_ids command before simulation box is defined");
   if (atom->tag_enable == 0)
-    error->all(FLERR,"Cannot use reset_ids unless atoms have IDs");
+    error->all(FLERR,"Cannot use reset_atom_ids unless atoms have IDs");
 
   for (int i = 0; i < modify->nfix; i++)
     if (modify->fix[i]->stores_ids)
-      error->all(FLERR,"Cannot use reset_ids when a fix exists that stores atom IDs");
+      error->all(FLERR,"Cannot use reset_atom_ids when a fix exists that stores atom IDs");
 
   if (comm->me == 0) utils::logmesg(lmp,"Resetting atom IDs ...\n");
 
@@ -68,12 +68,12 @@ void ResetIDs::command(int narg, char **arg)
   int iarg = 0;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"sort") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal reset_ids command");
+      if (iarg+2 > narg) error->all(FLERR,"Illegal reset_atom_ids command");
       if (strcmp(arg[iarg+1],"yes") == 0) sortflag = 1;
       else if (strcmp(arg[iarg+1],"no") == 0) sortflag = 0;
-      else error->all(FLERR,"Illegal reset_ids command");
+      else error->all(FLERR,"Illegal reset_atom_ids command");
       iarg += 2;
-    } else error->all(FLERR,"Illegal reset_ids command");
+    } else error->all(FLERR,"Illegal reset_atom_ids command");
   }
 
   // create an atom map if one doesn't exist already
@@ -110,7 +110,7 @@ void ResetIDs::command(int narg, char **arg)
   int nall = nlocal + atom->nghost;
 
   tagint *oldIDs;
-  memory->create(oldIDs,nlocal,"reset_ids:oldIDs");
+  memory->create(oldIDs,nlocal,"reset_atom_ids:oldIDs");
 
   for (int i = 0; i < nlocal; i++) {
     oldIDs[i] = tag[i];
@@ -129,7 +129,7 @@ void ResetIDs::command(int narg, char **arg)
   // forward_comm_array acquires new IDs for ghost atoms
 
   double **newIDs;
-  memory->create(newIDs,nall,1,"reset_ids:newIDs");
+  memory->create(newIDs,nall,1,"reset_atom_ids:newIDs");
 
   for (int i = 0; i < nlocal; i++) {
     newIDs[i][0] = ubuf(tag[i]).d;
@@ -468,7 +468,7 @@ int ResetIDs::sort_bins(int n, char *inbuf,
     if (in[i].ibin < binlo || in[i].ibin >= binhi) {
       //printf("BAD me %d i %d %d ibin %d binlohi %d %d\n",
       //	     rptr->comm->me,i,n,in[i].ibin,binlo,binhi);
-      error->one(FLERR,"Bad spatial bin assignment in reset_ids sort");
+      error->one(FLERR,"Bad spatial bin assignment in reset_atom_ids sort");
     }
     ibin = in[i].ibin - binlo;
     if (head[ibin] < 0) head[ibin] = i;

src/reset_atom_ids.h

@@ -13,7 +13,7 @@
 
 #ifdef COMMAND_CLASS
 
-CommandStyle(reset_ids,ResetIDs)
+CommandStyle(reset_atom_ids,ResetIDs)
 
 #else
 
@@ -70,7 +70,7 @@ E: Illegal ... command
 
 UNDOCUMENTED
 
-E: Cannot use reset_ids unless atoms have IDs
+E: Cannot use reset_atom_ids unless atoms have IDs
 
 UNDOCUMENTED
 

unittest/commands/CMakeLists.txt

@@ -3,7 +3,7 @@ add_executable(test_simple_commands test_simple_commands.cpp)
 target_link_libraries(test_simple_commands PRIVATE lammps GTest::GMock GTest::GTest)
 add_test(NAME SimpleCommands COMMAND test_simple_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 
-add_executable(test_reset_mol_ids test_reset_mol_ids.cpp)
+add_executable(test_reset_ids test_reset_ids.cpp)
-target_compile_definitions(test_reset_mol_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
+target_compile_definitions(test_reset_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
-target_link_libraries(test_reset_mol_ids PRIVATE lammps GTest::GMock GTest::GTest)
+target_link_libraries(test_reset_ids PRIVATE lammps GTest::GMock GTest::GTest)
-add_test(NAME ResetMolIDs COMMAND test_reset_mol_ids WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+add_test(NAME ResetIDs COMMAND test_reset_ids WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

unittest/commands/test_reset_ids.cpp

@@ -45,13 +45,13 @@ using ::testing::MatchesRegex;
 #define STRINGIFY(val) XSTR(val)
 #define XSTR(val) #val
 
-class ResetMolIDsTest : public ::testing::Test {
+class ResetIDsTest : public ::testing::Test {
 protected:
     LAMMPS *lmp;
 
     void SetUp() override
     {
-        const char *args[] = {"ResetMolIDsTest", "-log", "none", "-nocite", "-echo", "screen"};
+        const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"};
         char **argv        = (char **)args;
         int argc           = sizeof(args) / sizeof(char *);
         if (!verbose) ::testing::internal::CaptureStdout();
@@ -72,7 +72,7 @@ protected:
     }
 };
 
-TEST_F(ResetMolIDsTest, Plain)
+TEST_F(ResetIDsTest, MolIDAll)
 {
     if (lmp->atom->natoms == 0) GTEST_SKIP();
 
@@ -144,7 +144,7 @@ TEST_F(ResetMolIDsTest, Plain)
     ASSERT_EQ(molid[GETIDX(29)], 5);
 }
 
-TEST_F(ResetMolIDsTest, DeletePlusAtomID)
+TEST_F(ResetIDsTest, DeletePlusAtomID)
 {
     if (lmp->atom->natoms == 0) GTEST_SKIP();
 
@@ -214,7 +214,7 @@ TEST_F(ResetMolIDsTest, DeletePlusAtomID)
     EXPECT_GE(GETIDX(26), 0);
 
     if (!verbose) ::testing::internal::CaptureStdout();
-    lmp->input->one("reset_ids");
+    lmp->input->one("reset_atom_ids");
     if (!verbose) ::testing::internal::GetCapturedStdout();
 
     ASSERT_EQ(lmp->atom->map_tag_max, 23);

unittest/formats/test_atom_styles.cpp

@@ -415,7 +415,7 @@ TEST_F(AtomStyleTest, atomic)
     ASSERT_EQ(lmp->atom->map_user, 1);
     ASSERT_EQ(lmp->atom->map_tag_max, 3);
     if (!verbose) ::testing::internal::CaptureStdout();
-    lmp->input->one("reset_ids");
+    lmp->input->one("reset_atom_ids");
     if (!verbose) ::testing::internal::GetCapturedStdout();
     ASSERT_EQ(lmp->atom->map_tag_max, 2);
     ASSERT_EQ(lmp->atom->tag_consecutive(), 1);
@@ -802,7 +802,7 @@ TEST_F(AtomStyleTest, charge)
     ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
 
     if (!verbose) ::testing::internal::CaptureStdout();
-    lmp->input->one("reset_ids");
+    lmp->input->one("reset_atom_ids");
     lmp->input->one("replicate 2 2 2");
     if (!verbose) ::testing::internal::GetCapturedStdout();
     ASSERT_EQ(lmp->atom->map_tag_max, 16);
@@ -1129,7 +1129,7 @@ TEST_F(AtomStyleTest, sphere)
     EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
     lmp->input->one("read_restart test_atom_styles.restart");
     lmp->input->one("replicate 1 1 2");
-    lmp->input->one("reset_ids");
+    lmp->input->one("reset_atom_ids");
     if (!verbose) ::testing::internal::GetCapturedStdout();
     ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("sphere"));
     ASSERT_NE(lmp->atom->avec, nullptr);