From 3b6a06fcf53da95d2f2f246aec27b7e97aa3684e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2022 18:18:44 -0400
Subject: [PATCH] small behavior tweaks for inputs without labelmap, add
 warnings about type offsets

---
 src/molecule.cpp                    |  8 ++++++++
 src/read_data.cpp                   | 13 +++++++++++--
 src/utils.cpp                       |  4 +++-
 unittest/commands/test_labelmap.cpp | 11 ++++++++---
 4 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/molecule.cpp b/src/molecule.cpp
index 00c4d962af..3ec2a22757 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -115,6 +115,14 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
 
   index = iarg;
 
+  if (atom->labelmapflag &&
+      ((toffset > 0) || (boffset > 0) || (aoffset > 0) || (doffset > 0) || (ioffset > 0))) {
+    if (comm->me == 0)
+      error->warning(FLERR,
+                     "Using molecule command with type offsets and a labelmap. "
+                     "Offsets will be only applied to numeric types and not to type labels");
+  }
+
   // last molecule if have scanned all args
 
   if (iarg == narg)
diff --git a/src/read_data.cpp b/src/read_data.cpp
index a880ae83f6..2e3dd82c72 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -337,8 +337,17 @@ void ReadData::command(int narg, char **arg)
     error->all(FLERR, "Cannot use read_data without add keyword after simulation box is defined");
   if (!domain->box_exist && addflag)
     error->all(FLERR, "Cannot use read_data add before simulation box is defined");
-  if (offsetflag && addflag == NONE)
-    error->all(FLERR, "Cannot use read_data offset without add keyword");
+  if (offsetflag) {
+    if (addflag == NONE) {
+      error->all(FLERR, "Cannot use read_data offset without add keyword");
+    } else {
+      if (atom->labelmapflag) {
+        if (comm->me == 0)
+          error->warning(FLERR, "Using read_data offset with a labelmap. Offsets will be only "
+                         "applied to numeric types and not to type labels");
+      }
+    }
+  }
   if (shiftflag && addflag == NONE)
     error->all(FLERR, "Cannot use read_data shift without add keyword");
   if (addflag != NONE &&
diff --git a/src/utils.cpp b/src/utils.cpp
index cd4c0892d1..f0e37424a2 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -777,7 +777,9 @@ static const char *labeltypes[] = {"Atom", "Bond", "Angle", "Dihedral", "Imprope
 char *utils::expand_type(const char *file, int line, const std::string &str, int mode, LAMMPS *lmp)
 {
   if (!lmp) return nullptr;
-  const std::string typestr = utils::utf8_subst(str);
+  if (!lmp->atom->labelmapflag) return nullptr;
+
+  const std::string typestr = utils::utf8_subst(utils::trim(str));
   if (is_type(typestr) == 1) {
     if (!lmp->atom->labelmapflag)
       lmp->error->all(file, line, "{} type string {} cannot be used without a labelmap",
diff --git a/unittest/commands/test_labelmap.cpp b/unittest/commands/test_labelmap.cpp
index 1f2b599550..f847beba13 100644
--- a/unittest/commands/test_labelmap.cpp
+++ b/unittest/commands/test_labelmap.cpp
@@ -56,6 +56,7 @@ TEST_F(LabelMapTest, Atoms)
 {
     EXPECT_EQ(atom->natoms, 0);
     EXPECT_EQ(domain->box_exist, 0);
+    EXPECT_EQ(atom->labelmapflag, 0);
     ASSERT_EQ(atom->lmap, nullptr);
     TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*",
                  command("labelmap atom 3 C1"););
@@ -66,8 +67,8 @@ TEST_F(LabelMapTest, Atoms)
     END_HIDE_OUTPUT();
     EXPECT_EQ(domain->box_exist, 1);
     EXPECT_EQ(atom->lmap, nullptr);
-    TEST_FAILURE(".*ERROR: Atom type string C1 cannot be used without a labelmap.*",
-                 utils::expand_type(FLERR, "C1", Atom::ATOM, lmp););
+    EXPECT_EQ(atom->labelmapflag, 0);
+    EXPECT_EQ(utils::expand_type(FLERR, "C1", Atom::ATOM, lmp), nullptr);
 
     BEGIN_HIDE_OUTPUT();
     command("labelmap atom 2 N1");
@@ -77,6 +78,7 @@ TEST_F(LabelMapTest, Atoms)
     command("mass N1 2.0");
     command("mass H1 4.0");
     END_HIDE_OUTPUT();
+    EXPECT_EQ(atom->labelmapflag, 1);
     ASSERT_NE(atom->lmap, nullptr);
     EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
     EXPECT_DOUBLE_EQ(atom->mass[1], 1.0);
@@ -182,6 +184,7 @@ TEST_F(LabelMapTest, Topology)
     EXPECT_EQ(atom->ndihedrals, 0);
     EXPECT_EQ(atom->nimpropers, 0);
     EXPECT_EQ(domain->box_exist, 0);
+    EXPECT_EQ(atom->labelmapflag, 0);
     ASSERT_EQ(atom->lmap, nullptr);
     TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*",
                  command("labelmap atom 3 C1"););
@@ -192,6 +195,7 @@ TEST_F(LabelMapTest, Topology)
     command("create_box 2 box bond/types 3 angle/types 2 dihedral/types 1 improper/types 1");
     command("labelmap atom 1 C1");
     END_HIDE_OUTPUT();
+    EXPECT_EQ(atom->labelmapflag, 1);
     ASSERT_NE(atom->lmap, nullptr);
     EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
     EXPECT_FALSE(atom->lmap->is_complete(Atom::BOND));
@@ -233,7 +237,8 @@ TEST_F(LabelMapTest, Topology)
     command("labelmap clear");
     command("labelmap atom 1 C1");
     END_HIDE_OUTPUT();
-    EXPECT_NE(atom->lmap, nullptr);
+    EXPECT_EQ(atom->labelmapflag, 1);
+    ASSERT_NE(atom->lmap, nullptr);
     EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
     EXPECT_FALSE(atom->lmap->is_complete(Atom::BOND));
     EXPECT_FALSE(atom->lmap->is_complete(Atom::ANGLE));