Try to support latest lammps version

.ci_support/environment.yml

@@ -4,7 +4,7 @@ dependencies:
   - coveralls
   - coverage
   - codacy-coverage
-  - lammps >=2020.12.24
+  - lammps >=2021.05.27
   - mpi4py =3.0.3
   - openmpi
   - numpy

README.md

@@ -87,7 +87,7 @@ lmp.mass(1, 20)
 
 
 ```python
-lmp.extract_global("boxxhi", 1)
+lmp.extract_global("boxxhi")
 ```
 
 

binder/environment.yml

@@ -4,7 +4,7 @@ dependencies:
 - openmpi
 - mpi4py
 - numpy
-- lammps >=2020.12.24
+- lammps >=2021.05.27
 - pytest
 - distributed
 - dask-jobqueue

notebooks/lammps_local.ipynb

@@ -185,7 +185,7 @@
     }
    ],
    "source": [
-    "lmp.extract_global(\"boxxhi\", 1)"
+    "lmp.extract_global(\"boxxhi\")"
    ]
   },
   {
@@ -542,6 +542,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "lmp.delete_atoms(\"group\", \"all\")\n",
     "lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)"
    ]
   }

notebooks/lammps_local_cluster.ipynb

@@ -292,7 +292,7 @@
     }
    ],
    "source": [
-    "lmp.extract_global(\"boxxhi\", 1)"
+    "lmp.extract_global(\"boxxhi\")"
    ]
   },
   {
@@ -649,6 +649,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "lmp.delete_atoms(\"group\", \"all\")\n",
     "lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)"
    ]
   }

notebooks/lammps_slurm_cluster.ipynb

@@ -297,7 +297,7 @@
     }
    ],
    "source": [
-    "lmp.extract_global(\"boxxhi\", 1)"
+    "lmp.extract_global(\"boxxhi\")"
    ]
   },
   {
@@ -654,6 +654,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "lmp.delete_atoms(\"group\", \"all\")\n",
     "lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)"
    ]
   },

pylammpsmpi/utils/lammps.py

@@ -112,7 +112,7 @@ def extract_setting(self, *args):
         self._send(command="extract_setting", data=list(args))
         return self._receive()
 
-    def extract_global(self, name, type):
+    def extract_global(self, name):
         """
         Extract value of global simulation parameters
 
@@ -121,10 +121,6 @@ def extract_global(self, name, type):
         name : string
             see notes for a set of possible options
 
-        type : {0, 1}
-            0 if output value is integer
-            1 if output value is float
-
         Notes
         -----
         The possible options for `name` are-
@@ -142,7 +138,7 @@ def extract_global(self, name, type):
         "mvh2r", "angstrom", "femtosecond", "qelectron"
 
         """
-        self._send(command="extract_global", data=[name, type])
+        self._send(command="extract_global", data=[name])
         return self._receive()
 
     def extract_box(self):

tests/test_pylammpsmpi_cluster.py

@@ -12,11 +12,11 @@
 class TestLocalLammpsLibrary(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        execution_path = os.path.dirname(os.path.abspath(__file__))
+        cls.execution_path = os.path.dirname(os.path.abspath(__file__))
         cluster = LocalCluster(n_workers=1, threads_per_worker=2)
         client = Client(cluster)
         cls.lmp = LammpsLibrary(cores=2, mode='dask', client=client)
-        cls.lmp.file(os.path.join(execution_path, "in.simple"))
+        cls.lmp.file(os.path.join(cls.execution_path, "in.simple"))
 
     @classmethod
     def tearDownClass(cls):
@@ -40,18 +40,6 @@ def test_gather_atoms(self):
         ids = self.lmp.extract_atom("id")
         self.assertEqual(len(ids), 256)
 
-    def test_extract_box(self):
-        box = self.lmp.extract_box()
-        self.assertEqual(len(box), 7)
-
-        self.assertEqual(box[0][0], 0.0)
-        self.assertEqual(np.round(box[1][0], 2), 6.72)
-
-        self.lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)
-        box = self.lmp.extract_box()
-        self.assertEqual(box[0][0], 0.0)
-        self.assertEqual(np.round(box[1][0], 2), 8.0)
-
     def test_extract_fix(self):
         x = self.lmp.extract_fix("2", 0, 1, 1)
         self.assertEqual(np.round(x, 2), -2.61)
@@ -79,6 +67,21 @@ def test_scatter_atoms(self):
         f1 = self.lmp.gather_atoms("f", ids=[1,2])
         self.assertEqual(f1[1][1], val)
 
+    def test_extract_box(self):
+        box = self.lmp.extract_box()
+        self.assertEqual(len(box), 7)
+
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 6.72)
+
+        self.lmp.delete_atoms("group", "all")
+        self.lmp.reset_box([0.0,0.0,0.0], [8.0,8.0,8.0], 0.0,0.0,0.0)
+        box = self.lmp.extract_box()
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 8.0)
+        self.lmp.clear()
+        self.lmp.file(os.path.join(self.execution_path, "in.simple"))
+
 
 if __name__ == "__main__":
     unittest.main()

tests/test_pylammpsmpi_local.py

@@ -11,9 +11,9 @@
 class TestLocalLammpsLibrary(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
-        execution_path = os.path.dirname(os.path.abspath(__file__))
+        cls.execution_path = os.path.dirname(os.path.abspath(__file__))
         cls.lmp = LammpsLibrary(cores=2, mode='local')
-        cls.lmp.file(os.path.join(execution_path, "in.simple"))
+        cls.lmp.file(os.path.join(cls.execution_path, "in.simple"))
 
     @classmethod
     def tearDownClass(cls):
@@ -37,19 +37,6 @@ def test_gather_atoms(self):
         ids = self.lmp.extract_atom("id")
         self.assertEqual(len(ids), 256)
 
-    def test_extract_box(self):
-
-        box = self.lmp.extract_box()
-        self.assertEqual(len(box), 7)
-
-        self.assertEqual(box[0][0], 0.0)
-        self.assertEqual(np.round(box[1][0], 2), 6.72)
-
-        self.lmp.reset_box([0.0, 0.0, 0.0], [8.0, 8.0, 8.0], 0.0, 0.0, 0.0)
-        box = self.lmp.extract_box()
-        self.assertEqual(box[0][0], 0.0)
-        self.assertEqual(np.round(box[1][0], 2), 8.0)
-
     def test_extract_fix(self):
         x = self.lmp.extract_fix("2", 0, 1, 1)
         self.assertEqual(np.round(x, 2), -2.61)
@@ -77,6 +64,22 @@ def test_scatter_atoms(self):
         f1 = self.lmp.gather_atoms("f", ids=[1, 2])
         self.assertEqual(f1[1][1], val)
 
+    def test_extract_box(self):
+
+        box = self.lmp.extract_box()
+        self.assertEqual(len(box), 7)
+
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 6.72)
+
+        self.lmp.delete_atoms("group", "all")
+        self.lmp.reset_box([0.0, 0.0, 0.0], [8.0, 8.0, 8.0], 0.0, 0.0, 0.0)
+        box = self.lmp.extract_box()
+        self.assertEqual(box[0][0], 0.0)
+        self.assertEqual(np.round(box[1][0], 2), 8.0)
+        self.lmp.clear()
+        self.lmp.file(os.path.join(self.execution_path, "in.simple"))
+
 
 if __name__ == "__main__":
     unittest.main()