add python interface with optional numpy support for lammps_gather_bonds()

unit tests are included

unittest/python/python-scatter-gather.py

@@ -0,0 +1,90 @@
+
+import sys,os,unittest
+from lammps import lammps
+
+has_full=False
+try:
+    machine=None
+    if 'LAMMPS_MACHINE_NAME' in os.environ:
+        machine=os.environ['LAMMPS_MACHINE_NAME']
+    lmp=lammps(name=machine)
+    has_full = lmp.has_style("atom","full")
+    lmp.close()
+except:
+    pass
+
+class PythonGather(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.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
+
+    # clean up temporary files
+    def tearDown(self):
+        self.lmp.close()
+
+    # bond data comparison
+    def checkBond(self, vals, btype, batom1, batom2):
+        if ((vals[1] == batom1 and vals[2] == batom2)
+            or (vals[1] == batom2 and vals[2] == batom1)):
+            self.assertEqual(vals[0], btype)
+            return 1
+        else:
+            return 0
+
+    ##############################
+    @unittest.skipIf(not has_full, "Gather_bonds test")
+    def testGatherBond_newton_on(self):
+        """Test gather_bonds() with newton on"""
+        self.lmp.command("newton on on")
+        self.lmp.file("in.fourmol")
+        self.lmp.command("run 0 post no")
+        nbonds, bonds = self.lmp.gather_bonds()
+        self.assertEqual(nbonds, 24)
+        self.assertEqual(len(bonds), 3*24)
+        count = 0;
+        for i in range(0,nbonds):
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2)
+            count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3)
+            count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4)
+            count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5)
+            count += self.checkBond(bonds[3*i:3*i+3], 1, 6, 3)
+            count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8)
+            count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7)
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9)
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28)
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 29, 27)
+        self.assertEqual(count,10)
+
+    @unittest.skipIf(not has_full, "Gather_bonds test")
+    def testGatherBond_newton_off(self):
+        """Test gather_bonds() with newton off"""
+        self.lmp.command("newton off off")
+        self.lmp.file("in.fourmol")
+        self.lmp.command("run 0 post no")
+        nbonds, bonds = self.lmp.gather_bonds()
+        self.assertEqual(nbonds, 24)
+        self.assertEqual(len(bonds), 3*24)
+        count = 0;
+        for i in range(0,nbonds):
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 1, 2)
+            count += self.checkBond(bonds[3*i:3*i+3], 3, 1, 3)
+            count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 4)
+            count += self.checkBond(bonds[3*i:3*i+3], 2, 3, 5)
+            count += self.checkBond(bonds[3*i:3*i+3], 1, 3, 6)
+            count += self.checkBond(bonds[3*i:3*i+3], 3, 6, 8)
+            count += self.checkBond(bonds[3*i:3*i+3], 4, 6, 7)
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 8, 9)
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 28)
+            count += self.checkBond(bonds[3*i:3*i+3], 5, 27, 29)
+        self.assertEqual(count,10)
+
+##############################
+if __name__ == "__main__":
+    unittest.main()