add python interface with optional numpy support for lammps_gather_bonds()

unit tests are included

doc/src/Library_scatter.rst

@@ -56,6 +56,7 @@ It documents the following functions:
    :project: progguide
 
 -----------------------
+
 .. doxygenfunction:: lammps_gather
    :project: progguide
 

python/lammps/core.py

@@ -201,6 +201,9 @@ class lammps(object):
       [c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
     self.lib.lammps_scatter_atoms_subset.restype = None
 
+    self.lib.lammps_gather_bonds.argtypes = [c_void_p,c_void_p]
+    self.lib.lammps_gather_bonds.restype = None
+
     self.lib.lammps_gather.argtypes = \
       [c_void_p,c_char_p,c_int,c_int,c_void_p]
     self.lib.lammps_gather.restype = None
@@ -1206,6 +1209,32 @@ class lammps(object):
     with ExceptionCheck(self):
       self.lib.lammps_scatter_atoms_subset(self.lmp,name,dtype,count,ndata,ids,data)
 
+
+  # -------------------------------------------------------------------------
+
+  def gather_bonds(self):
+    """Retrieve global list of bonds
+
+    This is a wrapper around the :cpp:func:`lammps_gather_bonds`
+    function of the C-library interface.
+
+    This function returns a tuple with the number of bonds and a
+    flat list of ctypes integer values with the bond type, bond atom1,
+    bond atom2 for each bond.
+
+    .. versionadded:: 28Jul2021
+
+    :return: a tuple with the number of bonds and a list of c_int or c_long
+    :rtype: (int, 3*nbonds*c_tagint)
+    """
+    nbonds = self.extract_global("nbonds")
+    with ExceptionCheck(self):
+        data = ((3*nbonds)*self.c_tagint)()
+        self.lib.lammps_gather_bonds(self.lmp,data)
+        return nbonds,data
+
+  # -------------------------------------------------------------------------
+
   # return vector of atom/compute/fix properties gathered across procs
   # 3 variants to match src/library.cpp
   # name = atom property recognized by LAMMPS in atom->extract()

python/lammps/numpy_wrapper.py

@@ -248,6 +248,24 @@ class numpy_wrapper:
 
     # -------------------------------------------------------------------------
 
+  def gather_bonds(self):
+    """Retrieve global list of bonds as NumPy array
+
+    This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
+    It behaves the same as the original method, but returns a NumPy array instead
+    of a ``ctypes`` list.
+
+    .. versionadded:: 28Jul2021
+
+    :return: the requested data as a 2d-integer numpy array
+    :rtype: numpy.array(nbonds,3)
+    """
+    import numpy as np
+    nbonds, value = self.lmp.gather_bonds()
+    return np.ctypeslib.as_array(value).reshape(nbonds,3)
+
+    # -------------------------------------------------------------------------
+
   def fix_external_get_force(self, fix_id):
     """Get access to the array with per-atom forces of a fix external instance with a given fix ID.
 

src/library.cpp

@@ -2695,15 +2695,17 @@ the calling code. The buffer will be filled with bond type, bond atom 1,
 bond atom 2 for each bond. Thus the buffer has to be allocated to the
 dimension of 3 times the **total** number of bonds times the size of
 the LAMMPS "tagint" type, which is either 4 or 8 bytes depending on
- whether they are stored in 32-bit or 64-bit integers, respectively.
+whether they are stored in 32-bit or 64-bit integers, respectively.
 This size depends on the compile time settings used when compiling
 the LAMMPS library and can be queried by calling
- :cpp:func:`lammps_extract_setting()` with the keyword "tagint".
+:cpp:func:`lammps_extract_setting()` with the keyword "tagint".
 
 When running in parallel, the data buffer must be allocated on **all**
 MPI ranks and will be filled with the information for **all** bonds
 in the system.
 
+.. versionadded:: 28Jul2021
+
 Below is a brief C code demonstrating accessing this collected bond information.
 
 .. code-block:: c

unittest/python/CMakeLists.txt

@@ -29,6 +29,7 @@ if(Python_EXECUTABLE)
   # prepare to augment the environment so that the LAMMPS python module and the shared library is found.
   set(PYTHON_TEST_ENVIRONMENT PYTHONPATH=${LAMMPS_PYTHON_DIR}:$ENV{PYTHONPATH})
   list(APPEND PYTHON_TEST_ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
+  list(APPEND PYTHON_TEST_ENVIRONMENT "TEST_INPUT_DIR=${CMAKE_CURRENT_SOURCE_DIR}")
   if(APPLE)
     list(APPEND PYTHON_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:$ENV{DYLD_LIBRARY_PATH};LAMMPS_CMAKE_CACHE=${CMAKE_BINARY_DIR}/CMakeCache.txt")
   else()
@@ -90,6 +91,12 @@ if(Python_EXECUTABLE)
            COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-fix-external.py -v
            WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
   set_tests_properties(PythonFixExternal PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
+
+  add_test(NAME PythonScatterGather
+           COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-scatter-gather.py -v
+           WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
+  set_tests_properties(PythonScatterGather PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
+
 else()
   message(STATUS "Skipping Tests for the LAMMPS Python Module: no suitable Python interpreter")
 endif()

unittest/python/data.fourmol

@@ -0,0 +1,210 @@
+LAMMPS data file via write_data, version 5 May 2020, timestep = 0
+
+29 atoms
+5 atom types
+24 bonds
+5 bond types
+30 angles
+4 angle types
+31 dihedrals
+5 dihedral types
+2 impropers
+2 improper types
+
+ -6.024572 8.975428  xlo xhi
+ -7.692866 7.307134  ylo yhi
+ -8.086924 6.913076  zlo zhi
+
+Masses
+
+1 12.0107
+2 4.00794
+3 14.0067
+4 15.9994
+5 15.9994
+
+Pair Coeffs # zero
+
+1
+2
+3
+4
+5
+
+Bond Coeffs # zero
+
+1 1.5
+2 1.1
+3 1.3
+4 1.2
+5 1
+
+Angle Coeffs # zero
+
+1 110.1
+2 111
+3 120
+4 108.5
+
+Atoms # full
+
+10 2 1 7.0000000000000007e-02 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01 0 0 0
+11 2 2 8.9999999999999997e-02 1.7929780509347666e+00 -1.9871047540768743e+00 -1.8840626643185674e+00 0 0 0
+12 2 1 -2.7000000000000002e-01 3.0030247876861225e+00 -4.8923319967572748e-01 -1.6188658531537248e+00 0 0 0
+13 2 2 8.9999999999999997e-02 4.0447273787895934e+00 -9.0131998547446246e-01 -1.6384447268320836e+00 0 0 0
+14 2 2 8.9999999999999997e-02 2.6033152817257075e+00 -4.0789761505963579e-01 -2.6554413538823063e+00 0 0 0
+2 1 2 3.1000000000000000e-01 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 0 0 0
+3 1 1 -2.0000000000000000e-02 -6.9435377880558602e-01 1.2440473127136711e+00 -6.2233801468892025e-01 0 0 0
+4 1 2 8.9999999999999997e-02 -1.5771614164685133e+00 1.4915333140468066e+00 -1.2487126845040522e+00 0 0 0
+6 1 1 5.1000000000000001e-01 2.9412607937706009e-01 2.2719282656652909e-01 -1.2843094067857870e+00 0 0 0
+7 1 4 -5.1000000000000001e-01 3.4019871062879609e-01 -9.1277350075786561e-03 -2.4633113224304561e+00 0 0 0
+19 3 2 4.2359999999999998e-01 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 0 0 0
+15 2 2 8.9999999999999997e-02 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 0 0 0
+18 3 4 -8.4719999999999995e-01 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 0 0 0
+20 3 2 4.2359999999999998e-01 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 0 0 0
+8 2 3 -4.6999999999999997e-01 1.1641187171852805e+00 -4.8375305955385234e-01 -6.7659823767368688e-01 0 0 0
+9 2 2 3.1000000000000000e-01 1.3777459838125838e+00 -2.5366338669522998e-01 2.6877644730326306e-01 0 0 0
+16 2 1 5.1000000000000001e-01 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 0 0 0
+17 2 4 -5.1000000000000001e-01 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 0 0 0
+1 1 3 -4.6999999999999997e-01 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 0 0 0
+5 1 2 8.9999999999999997e-02 -8.9501761359359255e-01 9.3568128743071344e-01 4.0227731871484346e-01 0 0 0
+21 4 5 -8.4719999999999995e-01 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00 0 0 0
+22 4 2 4.2359999999999998e-01 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00 0 0 0
+23 4 2 4.2359999999999998e-01 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00 0 0 0
+24 5 5 -8.4719999999999995e-01 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00 0 0 0
+25 5 2 4.2359999999999998e-01 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00 0 0 0
+26 5 2 4.2359999999999998e-01 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00 0 0 0
+27 6 5 -8.4719999999999995e-01 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 0 0 0
+28 6 2 4.2359999999999998e-01 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 0 0 0
+29 6 2 4.2359999999999998e-01 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 0 0 0
+
+Velocities
+
+1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04
+2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03
+3 -1.2736791029204805e-03 1.6108674226414498e-03 -3.3618185901550799e-04
+4 -9.2828595122009308e-04 -1.2537885319521818e-03 -4.1204974953432108e-03
+5 -1.1800848061603740e-03 7.5424401975844038e-04 6.9023177964912290e-05
+6 -3.0914004879905335e-04 1.2755385764678133e-03 7.9574303350202582e-04
+7 -1.1037894966874103e-04 -7.6764845099077425e-04 -7.7217630460203659e-04
+8 3.9060281273221989e-04 -8.1444231918053418e-04 1.5134641148324972e-04
+9 1.2475530960659720e-03 -2.6608454451432528e-03 1.1117602907112732e-03
+10 4.5008983776042893e-04 4.9530197647538077e-04 -2.3336234361093645e-04
+11 -3.6977669078869707e-04 -1.5289071951960539e-03 -2.9176389881837113e-03
+12 1.0850834530183159e-03 -6.4965897903201833e-04 -1.2971152622619948e-03
+13 4.0754559196230639e-03 3.5043502394946119e-03 -7.8324487687854666e-04
+14 -1.3837220448746613e-04 -4.0656048637594394e-03 -3.9333461173944500e-03
+15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
+16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
+17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04
+18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
+19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
+20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03
+21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04
+22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03
+23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03
+24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04
+25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03
+26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03
+27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
+28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
+29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
+
+Bonds
+
+1 5 1 2
+2 3 1 3
+3 2 3 4
+4 2 3 5
+5 1 3 6
+6 3 6 8
+7 4 6 7
+8 5 8 9
+9 3 8 10
+10 2 10 11
+11 1 10 12
+12 1 10 16
+13 2 12 13
+14 2 12 14
+15 2 12 15
+16 4 16 17
+17 5 18 19
+18 5 18 20
+19 5 21 22
+20 5 21 23
+21 5 24 25
+22 5 24 26
+23 5 27 28
+24 5 27 29
+
+Angles
+
+1 4 2 1 3
+2 4 1 3 5
+3 4 1 3 4
+4 4 1 3 6
+5 4 4 3 5
+6 2 5 3 6
+7 2 4 3 6
+8 3 3 6 7
+9 3 3 6 8
+10 3 7 6 8
+11 2 6 8 9
+12 2 9 8 10
+13 3 6 8 10
+14 2 8 10 11
+15 3 8 10 16
+16 2 11 10 12
+17 1 12 10 16
+18 1 8 10 12
+19 2 11 10 16
+20 2 10 12 15
+21 2 10 12 14
+22 2 10 12 13
+23 4 13 12 15
+24 4 13 12 14
+25 4 14 12 15
+26 4 10 16 17
+27 1 19 18 20
+28 1 22 21 23
+29 1 25 24 26
+30 1 28 27 29
+
+Dihedrals
+
+1 2 2 1 3 6
+2 2 2 1 3 4
+3 3 2 1 3 5
+4 1 1 3 6 8
+5 1 1 3 6 7
+6 5 4 3 6 8
+7 5 4 3 6 7
+8 5 5 3 6 8
+9 5 5 3 6 7
+10 4 3 6 8 9
+11 3 3 6 8 10
+12 3 7 6 8 9
+13 4 7 6 8 10
+14 2 6 8 10 12
+15 2 6 8 10 16
+16 2 6 8 10 11
+17 2 9 8 10 12
+18 4 9 8 10 16
+19 5 9 8 10 11
+20 5 8 10 12 13
+21 1 8 10 12 14
+22 5 8 10 12 15
+23 4 8 10 16 17
+24 5 11 10 12 13
+25 5 11 10 12 14
+26 5 11 10 12 15
+27 2 11 10 16 17
+28 2 12 10 16 17
+29 5 16 10 12 13
+30 5 16 10 12 14
+31 5 16 10 12 15
+
+Impropers
+
+1 1 6 3 8 7
+2 2 8 6 10 9

unittest/python/in.fourmol

@@ -0,0 +1,25 @@
+variable  units           index  real
+variable  input_dir       index  .
+variable  data_file       index ${input_dir}/data.fourmol
+variable  pair_style      index 'zero 8.0'
+variable  bond_style      index zero
+variable  angle_style     index zero
+variable  dihedral_style  index zero
+variable  improper_style  index zero
+
+atom_style       full
+atom_modify      map array
+neigh_modify     delay 2 every 2 check no
+units            ${units}
+timestep         0.1
+
+pair_style       ${pair_style}
+bond_style       ${bond_style}
+angle_style      ${angle_style}
+dihedral_style   ${dihedral_style}
+improper_style   ${improper_style}
+
+read_data        ${data_file}
+dihedral_coeff   *
+improper_coeff   *
+

unittest/python/python-numpy.py

@@ -15,6 +15,17 @@ try:
 except:
     pass
 
+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
+
 try:
     import numpy
     NUMPY_INSTALLED = True
@@ -32,6 +43,14 @@ class PythonNumpy(unittest.TestCase):
     def tearDown(self):
         del self.lmp
 
+    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
+
     def testLammpsPointer(self):
         self.assertEqual(type(self.lmp.lmp), c_void_p)
 
@@ -148,6 +167,50 @@ class PythonNumpy(unittest.TestCase):
         self.assertTrue((x[1] == (1.0, 1.0, 1.5)).all())
         self.assertEqual(len(v), 2)
 
+    @unittest.skipIf(not has_full,"Gather bonds test")
+    def testGatherBond_newton_on(self):
+        self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
+        self.lmp.command("newton on on")
+        self.lmp.file("in.fourmol")
+        self.lmp.command("run 0 post no")
+        bonds = self.lmp.numpy.gather_bonds()
+        self.assertEqual(len(bonds),24)
+        count = 0
+        for bond in bonds:
+            count += self.checkBond(bond, 5, 1, 2)
+            count += self.checkBond(bond, 3, 1, 3)
+            count += self.checkBond(bond, 2, 3, 4)
+            count += self.checkBond(bond, 2, 3, 5)
+            count += self.checkBond(bond, 1, 6, 3)
+            count += self.checkBond(bond, 3, 6, 8)
+            count += self.checkBond(bond, 4, 6, 7)
+            count += self.checkBond(bond, 5, 8, 9)
+            count += self.checkBond(bond, 5, 27, 28)
+            count += self.checkBond(bond, 5, 29, 27)
+        self.assertEqual(count,10)
+
+    @unittest.skipIf(not has_full,"Gather bonds test")
+    def testGatherBond_newton_off(self):
+        self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
+        self.lmp.command("newton off off")
+        self.lmp.file("in.fourmol")
+        self.lmp.command("run 0 post no")
+        bonds = self.lmp.numpy.gather_bonds()
+        self.assertEqual(len(bonds),24)
+        count = 0
+        for bond in bonds:
+            count += self.checkBond(bond, 5, 1, 2)
+            count += self.checkBond(bond, 3, 1, 3)
+            count += self.checkBond(bond, 2, 3, 4)
+            count += self.checkBond(bond, 2, 3, 5)
+            count += self.checkBond(bond, 1, 6, 3)
+            count += self.checkBond(bond, 3, 6, 8)
+            count += self.checkBond(bond, 4, 6, 7)
+            count += self.checkBond(bond, 5, 8, 9)
+            count += self.checkBond(bond, 5, 27, 28)
+            count += self.checkBond(bond, 5, 29, 27)
+        self.assertEqual(count,10)
+
     def testNeighborListSimple(self):
         self.lmp.commands_string("""
         units lj

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()