Merge remote-tracking branch 'github/develop' into collected-small-changes

unittest/python/CMakeLists.txt

@@ -105,6 +105,11 @@ if(Python_EXECUTABLE)
     set_tests_properties(PythonPyLammps PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
   endif()
 
+  add_test(NAME PythonCmdWrapper
+           COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-cmdwrapper.py -v
+           WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
+  set_tests_properties(PythonCmdWrapper PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
+
   add_test(NAME PythonFormats
            COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-formats.py -v
            WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})

unittest/python/python-cmdwrapper.py

@@ -0,0 +1,97 @@
+import os,unittest
+from lammps import lammps
+
+try:
+    import numpy
+    NUMPY_INSTALLED = True
+except ImportError:
+    NUMPY_INSTALLED = False
+
+@unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available")
+class PythonCmdWrapper(unittest.TestCase):
+    def setUp(self):
+        machine = None
+        if 'LAMMPS_MACHINE_NAME' in os.environ:
+            machine=os.environ['LAMMPS_MACHINE_NAME']
+        self.lmp = lammps(name=machine,  cmdargs=['-nocite', '-log','none', '-echo', 'screen'])
+        self.lmp.cmd.units("lj")
+        self.lmp.cmd.atom_style("atomic")
+        self.lmp.cmd.atom_modify("map array")
+
+        if 'LAMMPS_CMAKE_CACHE' in os.environ:
+            self.cmake_cache = {}
+
+            with open(os.environ['LAMMPS_CMAKE_CACHE'], 'r') as f:
+                for line in f:
+                    line = line.strip()
+                    if not line or line.startswith('#') or line.startswith('//'): continue
+                    parts = line.split('=')
+                    key, value_type = parts[0].split(':')
+                    if len(parts) > 1:
+                        value = parts[1]
+                        if value_type == "BOOL":
+                            value = (value.upper() == "ON")
+                    else:
+                        value = None
+                    self.cmake_cache[key] = value
+
+    def tearDown(self):
+        self.lmp.close()
+        del self.lmp
+
+    def test_version(self):
+        self.assertGreaterEqual(self.lmp.version(), 20200824)
+
+    def test_create_atoms(self):
+        self.lmp.cmd.region("box block", 0, 2, 0, 2, 0, 2)
+        self.lmp.cmd.create_box(1, "box")
+
+        x = [
+          1.0, 1.0, 1.0,
+          1.0, 1.0, 1.5
+        ]
+
+        types = [1, 1]
+
+        self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2)
+        self.assertEqual(self.lmp.extract_global("natoms"), 2)
+        pos = self.lmp.numpy.extract_atom("x")
+        self.assertEqual(pos.shape[0], 2)
+        numpy.testing.assert_array_equal(pos[0], tuple(x[0:3]))
+        numpy.testing.assert_array_equal(pos[1], tuple(x[3:6]))
+
+    def test_thermo_capture(self):
+        self.lmp.cmd.lattice("fcc", 0.8442),
+        self.lmp.cmd.region("box block", 0, 4, 0, 4, 0, 4)
+        self.lmp.cmd.create_box(1, "box")
+        self.lmp.cmd.create_atoms(1, "box")
+        self.lmp.cmd.mass(1, 1.0)
+        self.lmp.cmd.velocity("all create", 1.44, 87287, "loop geom")
+        self.lmp.cmd.pair_style("lj/cut", 2.5)
+        self.lmp.cmd.pair_coeff(1, 1, 1.0, 1.0, 2.5)
+        self.lmp.cmd.neighbor(0.3, "bin")
+        self.lmp.cmd.neigh_modify("delay 0 every 20 check no")
+        self.lmp.cmd.fix("1 all nve")
+
+        current_run = {}
+
+        def append_thermo_data(lmp):
+          for k, v in lmp.last_thermo().items():
+            current_run.setdefault(k, []).append(v)
+
+        # thermo data is only captured during a run if PYTHON package is enabled
+        # without it, it will only capture the final thermo at completion
+        nvalues = 1
+        if self.lmp.has_package("PYTHON"):
+            self.lmp.cmd.fix("myfix", "all", "python/invoke", 10, "end_of_step", append_thermo_data)
+            nvalues = 2
+
+        self.lmp.cmd.run(10)
+        append_thermo_data(self.lmp)
+
+        for k in ('Step', 'Temp', 'E_pair', 'E_mol', 'TotEng', 'Press'):
+            self.assertIn(k, current_run)
+            self.assertEqual(len(current_run[k]), nvalues)
+
+if __name__ == "__main__":
+    unittest.main()