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add python interface with optional numpy support for lammps_gather_bonds()

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unit tests are included
This commit is contained in:
Axel Kohlmeyer
2021-07-26 22:36:00 -04:00
parent cc87e7eee3
commit 458253b452
9 changed files with 447 additions and 2 deletions
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63
unittest/python/python-numpy.py
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@ -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