Merge branch 'develop' into msmeam-adr

# Conflicts: # src/MEAM/pair_meam.cpp
2023-01-26 15:46:34 -05:00
parent 18171af1ea 30f459da92
commit b48d483fd6
677 changed files with 18240 additions and 94551 deletions
--- a/unittest/commands/test_groups.cpp
+++ b/unittest/commands/test_groups.cpp
@ -109,9 +109,9 @@ TEST_F(GroupTest, EmptyDelete)
    command("atom_modify first new5");
    END_HIDE_OUTPUT();
    ASSERT_EQ(group->ngroup, 7);
-    TEST_FAILURE(".*ERROR: Illegal group command.*", command("group new3 xxx"););
-    TEST_FAILURE(".*ERROR: Illegal group command.*", command("group new3 empty xxx"););
-    TEST_FAILURE(".*ERROR: Group command requires atom attribute molecule.*",
+    TEST_FAILURE(".*ERROR: Unknown group command keyword: xxx.*", command("group new3 xxx"););
+    TEST_FAILURE(".*ERROR: Illegal group empty command.*", command("group new3 empty xxx"););
+    TEST_FAILURE(".*ERROR: Group include molecule command requires atom attribute molecule.*",
                 command("group new2 include molecule"););

    BEGIN_HIDE_OUTPUT();
@ -119,7 +119,8 @@ TEST_F(GroupTest, EmptyDelete)
    END_HIDE_OUTPUT();
    ASSERT_EQ(group->ngroup, 6);

-    TEST_FAILURE(".*ERROR: Illegal group command.*", command("group new2 delete xxx"););
+    TEST_FAILURE(".*ERROR: Illegal group delete command: too many arguments.*",
+                 command("group new2 delete xxx"););
    TEST_FAILURE(".*ERROR: Cannot delete group all.*", command("group all delete"););
    TEST_FAILURE(".*ERROR: Could not find group delete.*", command("group new0 delete"););
    TEST_FAILURE(".*ERROR: Cannot delete group new2 currently used by fix.*",
@ -150,8 +151,9 @@ TEST_F(GroupTest, RegionClear)
    ASSERT_EQ(group->count(group->find("all")), lmp->atom->natoms);
    ASSERT_EQ(group->count_all(), lmp->atom->natoms);

-    TEST_FAILURE(".*ERROR: Illegal group command.*", command("group three region left xxx"););
-    TEST_FAILURE(".*ERROR: Group region dummy does not exist.*",
+    TEST_FAILURE(".*ERROR: Illegal group region command.*",
+                 command("group three region left xxx"););
+    TEST_FAILURE(".*ERROR: Region dummy for group region does not exist.*",
                 command("group four region dummy"););

    BEGIN_HIDE_OUTPUT();
@ -221,10 +223,11 @@ TEST_F(GroupTest, SelectRestart)
    command("group six clear");
    END_HIDE_OUTPUT();

-    TEST_FAILURE(".*ERROR: Group ID does not exist.*", command("group four union one two xxx"););
-    TEST_FAILURE(".*ERROR: Group ID does not exist.*",
+    TEST_FAILURE(".*ERROR: Group ID xxx does not exist.*",
+                 command("group four union one two xxx"););
+    TEST_FAILURE(".*ERROR: Group ID xxx does not exist.*",
                 command("group five subtract all half xxx"););
-    TEST_FAILURE(".*ERROR: Group ID does not exist.*",
+    TEST_FAILURE(".*ERROR: Group ID xxx does not exist.*",
                 command("group five intersect half top xxx"););
 }

@ -248,7 +251,8 @@ TEST_F(GroupTest, Molecular)
    ASSERT_NEAR(group->charge(group->find("top")), 0, 1.0e-14);
    ASSERT_NEAR(group->charge(group->find("right"), domain->get_region_by_id("top")), 0, 1.0e-14);

-    TEST_FAILURE(".*ERROR: Illegal group command.*", command("group three include xxx"););
+    TEST_FAILURE(".*ERROR: Unknown group include keyword xxx.*",
+                 command("group three include xxx"););
 }

 TEST_F(GroupTest, Dynamic)
@ -286,9 +290,9 @@ TEST_F(GroupTest, Dynamic)
    command("run 10 post no");
    END_HIDE_OUTPUT();
    ASSERT_EQ(group->count(group->find("grow")), 20);
-    TEST_FAILURE(".*ERROR: Cannot subtract groups using a dynamic group.*",
+    TEST_FAILURE(".*ERROR: Cannot subtract dynamic groups.*",
                 command("group chunk subtract half grow"););
-    TEST_FAILURE(".*ERROR: Cannot union groups using a dynamic group.*",
+    TEST_FAILURE(".*ERROR: Cannot union groups from a dynamic group.*",
                 command("group chunk union half grow"););
    TEST_FAILURE(".*ERROR: Cannot intersect groups using a dynamic group.*",
                 command("group chunk intersect half grow"););
@ -301,14 +305,163 @@ TEST_F(GroupTest, Dynamic)

    TEST_FAILURE(".*ERROR: Group dynamic cannot reference itself.*",
                 command("group half dynamic half region top"););
-    TEST_FAILURE(".*ERROR: Group dynamic parent group does not exist.*",
+    TEST_FAILURE(".*ERROR: Group dynamic parent group dummy does not exist.*",
                 command("group half dynamic dummy region top"););

-    TEST_FAILURE(".*ERROR: Variable for group is invalid style.*",
+    TEST_FAILURE(".*ERROR: Variable ramp for group is invalid style.*",
                 command("group ramp variable ramp"););
-    TEST_FAILURE(".*ERROR: Variable name for group does not exist.*",
+    TEST_FAILURE(".*ERROR: Variable name grow for group does not exist.*",
                 command("group ramp variable grow"););
 }
+
+constexpr double EPSILON = 1.0e-14;
+
+TEST_F(GroupTest, VariableFunctions)
+{
+    molecular_system();
+
+    BEGIN_HIDE_OUTPUT();
+    command("group one region left");
+    command("group two region right");
+    command("group three empty");
+    command("group four region top");
+    command("set atom 5 charge $(1.0+2.0*sin(PI/32*5))");
+    command("set atom 12 charge $(-1.0+2.0*sin(PI/32*12))");
+    command("set atom 25 charge $(2.0+2.0*sin(PI/32*25))");
+    command("set atom 32 charge $(-2.0+2.0*sin(PI/32*32))");
+    command("pair_style lj/cut 5.0");
+    command("pair_coeff * * 0.4 3.0");
+    command("pair_coeff 2 2 0.5 3.3");
+    command("pair_coeff 3 3 0.2 3.5");
+    command("run 0 post no");
+    END_HIDE_OUTPUT();
+
+    int one   = group->find("one");
+    int two   = group->find("two");
+    int three = group->find("three");
+    int four  = group->find("four");
+
+    auto right = domain->get_region_by_id("right");
+    auto left  = domain->get_region_by_id("left");
+    auto top   = domain->get_region_by_id("top");
+
+    EXPECT_EQ(group->count_all(), 64);
+    EXPECT_EQ(group->count(one), 16);
+    EXPECT_EQ(group->count(two), 16);
+    EXPECT_EQ(group->count(three), 0);
+    EXPECT_EQ(group->count(four), 16);
+
+    EXPECT_EQ(group->count(0, right), 16);
+    EXPECT_EQ(group->count(one, top), 4);
+    EXPECT_EQ(group->count(two, right), 16);
+    EXPECT_EQ(group->count(two, left), 0);
+
+    EXPECT_DOUBLE_EQ(group->mass(0), 80.0);
+    EXPECT_DOUBLE_EQ(group->mass(two), 32.0);
+    EXPECT_DOUBLE_EQ(group->mass(three), 0.0);
+
+    EXPECT_DOUBLE_EQ(group->mass(0, right), 32.0);
+    EXPECT_DOUBLE_EQ(group->mass(one, top), 8.0);
+    EXPECT_DOUBLE_EQ(group->mass(two, right), 32.0);
+    EXPECT_DOUBLE_EQ(group->mass(two, left), 0.0);
+
+    EXPECT_NEAR(group->charge(0), 0.0, EPSILON);
+    EXPECT_NEAR(group->charge(two), -3.0, EPSILON);
+    EXPECT_NEAR(group->charge(four), 0.0, EPSILON);
+
+    EXPECT_NEAR(group->charge(0, right), -3.0, EPSILON);
+    EXPECT_NEAR(group->charge(one, top), 0.0, EPSILON);
+    EXPECT_NEAR(group->charge(two, right), -3.0, EPSILON);
+    EXPECT_NEAR(group->charge(two, left), 0.0, EPSILON);
+
+    double bounds[6];
+    group->bounds(0, bounds);
+    EXPECT_DOUBLE_EQ(bounds[0], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[1], 1.125);
+    EXPECT_DOUBLE_EQ(bounds[2], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[3], 1.125);
+    EXPECT_DOUBLE_EQ(bounds[4], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[5], 1.125);
+
+    group->bounds(one, bounds);
+    EXPECT_DOUBLE_EQ(bounds[0], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[1], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[2], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[3], 1.125);
+    EXPECT_DOUBLE_EQ(bounds[4], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[5], 1.125);
+
+    group->bounds(0, bounds, right);
+    EXPECT_DOUBLE_EQ(bounds[0], 1.125);
+    EXPECT_DOUBLE_EQ(bounds[1], 1.125);
+    EXPECT_DOUBLE_EQ(bounds[2], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[3], 1.125);
+    EXPECT_DOUBLE_EQ(bounds[4], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[5], 1.125);
+
+    group->bounds(one, bounds, top);
+    EXPECT_DOUBLE_EQ(bounds[0], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[1], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[2], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[3], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[4], -1.875);
+    EXPECT_DOUBLE_EQ(bounds[5], 1.125);
+
+    double center[3];
+    group->xcm(0, 80.0, center);
+    EXPECT_DOUBLE_EQ(center[0], -0.375);
+    EXPECT_DOUBLE_EQ(center[1], -0.375);
+    EXPECT_DOUBLE_EQ(center[2], -0.375);
+
+    group->xcm(two, 32.0, center);
+    EXPECT_DOUBLE_EQ(center[0], 1.125);
+    EXPECT_DOUBLE_EQ(center[1], -0.375);
+    EXPECT_DOUBLE_EQ(center[2], -0.375);
+
+    group->xcm(three, 0.0, center);
+    EXPECT_DOUBLE_EQ(center[0], 0);
+    EXPECT_DOUBLE_EQ(center[1], 0);
+    EXPECT_DOUBLE_EQ(center[2], 0);
+
+    group->xcm(one, 8.0, center, top);
+    EXPECT_DOUBLE_EQ(center[0], -1.875);
+    EXPECT_DOUBLE_EQ(center[1], -1.875);
+    EXPECT_DOUBLE_EQ(center[2], -0.375);
+
+    group->vcm(one, 80.0, center);
+    EXPECT_DOUBLE_EQ(center[0], 0);
+    EXPECT_DOUBLE_EQ(center[1], 0);
+    EXPECT_DOUBLE_EQ(center[2], 0);
+
+    group->vcm(one, 8.0, center, top);
+    EXPECT_DOUBLE_EQ(center[0], 0);
+    EXPECT_DOUBLE_EQ(center[1], 0);
+    EXPECT_DOUBLE_EQ(center[2], 0);
+
+    group->fcm(0, center);
+    EXPECT_NEAR(center[0], 1.9375372195540308e-08, EPSILON);
+    EXPECT_NEAR(center[1], -1.0289756668946382e-07, EPSILON);
+    EXPECT_NEAR(center[2], -1.3366961142124989e-07, EPSILON);
+
+    group->fcm(two, center);
+    EXPECT_NEAR(center[0], 2.4316524016576579e-08, EPSILON);
+    EXPECT_NEAR(center[1], -6.0179227712175987e-08, EPSILON);
+    EXPECT_NEAR(center[2], -1.4393012942592875e-07, EPSILON);
+
+    group->fcm(three, center);
+    EXPECT_NEAR(center[0], 0, EPSILON);
+    EXPECT_NEAR(center[1], 0, EPSILON);
+    EXPECT_NEAR(center[2], 0, EPSILON);
+
+    group->fcm(one, center, top);
+    EXPECT_NEAR(center[0], -5.5879354476928711e-09, EPSILON);
+    EXPECT_NEAR(center[1], -1.6743454178680395e-08, EPSILON);
+    EXPECT_NEAR(center[2], 2.6166095290491853e-08, EPSILON);
+
+    EXPECT_DOUBLE_EQ(group->ke(one), 0);
+    EXPECT_DOUBLE_EQ(group->ke(one, top), 0);
+}
+
 } // namespace LAMMPS_NS

 int main(int argc, char **argv)
--- a/unittest/formats/test_atom_styles.cpp
+++ b/unittest/formats/test_atom_styles.cpp
@ -422,9 +422,6 @@ void ASSERT_ATOM_STATE_EQ(Atom *atom, const AtomState &expected)
    ASSERT_ARRAY_ALLOCATED(atom->edpd_temp, false);
    ASSERT_ARRAY_ALLOCATED(atom->edpd_flux, false);
    ASSERT_ARRAY_ALLOCATED(atom->edpd_cv, false);
-    ASSERT_ARRAY_ALLOCATED(atom->length, false);
-    ASSERT_ARRAY_ALLOCATED(atom->buckling, false);
-    ASSERT_ARRAY_ALLOCATED(atom->bond_nt, false);
    ASSERT_ARRAY_ALLOCATED(atom->contact_radius, false);
    ASSERT_ARRAY_ALLOCATED(atom->smd_data_9, false);
    ASSERT_ARRAY_ALLOCATED(atom->smd_stress, false);
--- a/unittest/formats/test_molecule_file.cpp
+++ b/unittest/formats/test_molecule_file.cpp
@ -399,7 +399,7 @@ TEST_F(MoleculeFileTest, bonds)
    EXPECT_DOUBLE_EQ(mol->com[0], 1.0);
    EXPECT_DOUBLE_EQ(mol->com[1], 0.5);
    EXPECT_DOUBLE_EQ(mol->com[2], 0.5);
-    EXPECT_DOUBLE_EQ(mol->maxextent, sqrt(2));
+    EXPECT_DOUBLE_EQ(mol->maxextent, sqrt(2.0));
    EXPECT_EQ(mol->comatom, 1);
    END_HIDE_OUTPUT();
 }
--- a/unittest/python/CMakeLists.txt
+++ b/unittest/python/CMakeLists.txt
@ -20,15 +20,17 @@ else()
  find_package(Python COMPONENTS Interpreter Development)
 endif()

-add_executable(test_python_package test_python_package.cpp)
-target_link_libraries(test_python_package PRIVATE lammps GTest::GMock)
-target_compile_definitions(test_python_package PRIVATE -DTEST_INPUT_FOLDER=${TEST_INPUT_FOLDER})
-# this requires CMake 3.12. don't care to add backward compatibility for this.
-if(Python_Development_FOUND)
-  target_compile_definitions(test_python_package PRIVATE -DTEST_HAVE_PYTHON_DEVELOPMENT=1)
-  target_link_libraries(test_python_package PRIVATE Python::Python)
+if(PKG_PYTHON)
+  add_executable(test_python_package test_python_package.cpp)
+  target_link_libraries(test_python_package PRIVATE lammps GTest::GMock)
+  target_compile_definitions(test_python_package PRIVATE -DTEST_INPUT_FOLDER=${TEST_INPUT_FOLDER})
+  # this requires CMake 3.12. don't care to add backward compatibility for this.
+  if(Python_Development_FOUND)
+    target_compile_definitions(test_python_package PRIVATE -DTEST_HAVE_PYTHON_DEVELOPMENT=1)
+    target_link_libraries(test_python_package PRIVATE Python::Python)
+  endif()
+  add_test(NAME PythonPackage COMMAND test_python_package)
 endif()
-add_test(NAME PythonPackage COMMAND test_python_package)

 # build list of environment variables for testing python functionality
 if(WIN32)
@ -52,7 +54,10 @@ elseif(WIN32)
 else()
  list(APPEND PYTHON_TEST_ENVIRONMENT "LD_LIBRARY_PATH=${LAMMPS_LIB_PATH}:$ENV{LD_LIBRARY_PATH}")
 endif()
-set_tests_properties(PythonPackage PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
+
+if(PKG_PYTHON)
+  set_tests_properties(PythonPackage PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
+endif()

 if(Python_EXECUTABLE)
  list(APPEND PYTHON_TEST_ENVIRONMENT "TEST_INPUT_DIR=${CMAKE_CURRENT_SOURCE_DIR}")