Simplify extract_atom and extract_global in Python interface

Both extract methods now can auto-detect the datatype of both global
and per-atom properties. Callers can still enforce different types
if needed by specifying the now optional dtype argument.

The numpy wrapper now has a new extract_atom function method, which
replace the extract_atom_darray and extract_atom_iarray method and
autodetects both type and size. All parameters can still be forced
to use different values if needed.

unittest/python/python-numpy.py

@@ -73,7 +73,7 @@ class PythonNumpy(unittest.TestCase):
         # TODO
         pass
 
-    def testExtractAtom(self):
+    def testExtractAtomDeprecated(self):
         self.lmp.command("units lj")
         self.lmp.command("atom_style atomic")
         self.lmp.command("atom_modify map array")
@@ -100,6 +100,39 @@ class PythonNumpy(unittest.TestCase):
         x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3)
         v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3)
         self.assertEqual(len(x), 2)
+        self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all())
+        self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all())
+        self.assertEqual(len(v), 2)
+
+    def testExtractAtom(self):
+        self.lmp.command("units lj")
+        self.lmp.command("atom_style atomic")
+        self.lmp.command("atom_modify map array")
+        self.lmp.command("region box block 0 2 0 2 0 2")
+        self.lmp.command("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)
+        nlocal = self.lmp.extract_global("nlocal")
+        self.assertEqual(nlocal, 2)
+
+        ident = self.lmp.numpy.extract_atom("id")
+        self.assertEqual(len(ident), 2)
+
+        ntypes = self.lmp.extract_global("ntypes")
+        self.assertEqual(ntypes, 1)
+
+        x = self.lmp.numpy.extract_atom("x", dim=3)
+        v = self.lmp.numpy.extract_atom("v", dim=3)
+        self.assertEqual(len(x), 2)
+        self.assertTrue((x[0] == (1.0, 1.0, 1.0)).all())
+        self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all())
         self.assertEqual(len(v), 2)
 
 if __name__ == "__main__":