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Merge pull request #2935 from akohlmey/python-module-fixes-and-tests

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Python module fixes and tests
This commit is contained in:
Axel Kohlmeyer
2021-09-09 23:31:16 -04:00
committed by GitHub
parent b535e58e16 3fd4bd1fcd
commit 0dd35bdb66
2 changed files with 43 additions and 9 deletions
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17
python/lammps/pylammps.py
View File

@ -508,11 +508,6 @@ class PyLammps(object):
:py:attr:`PyLammps.last_run`.
"""
output = self.__getattr__('run')(*args, **kwargs)
comm = self.lmp.get_mpi_comm()
if comm:
output = self.lmp.comm.bcast(output, root=0)
self.runs += get_thermo_data(output)
return output
@ -643,7 +638,7 @@ class PyLammps(object):
return [x.strip() for x in value.split('=')]
def _parse_info_system(self, output):
lines = output[6:-2]
lines = output[5:-2]
system = {}
for line in lines:
@ -704,7 +699,7 @@ class PyLammps(object):
return system
def _parse_info_communication(self, output):
lines = output[6:-3]
lines = output[5:-3]
comm = {}
for line in lines:
@ -725,7 +720,7 @@ class PyLammps(object):
return comm
def _parse_element_list(self, output):
lines = output[6:-3]
lines = output[5:-3]
elements = []
for line in lines:
@ -737,7 +732,7 @@ class PyLammps(object):
return elements
def _parse_groups(self, output):
lines = output[6:-3]
lines = output[5:-3]
groups = []
group_pattern = re.compile(r"(?P<name>.+) \((?P<type>.+)\)")
@ -784,6 +779,10 @@ class PyLammps(object):
self.command(cmd)
output = capture.output
comm = self.lmp.get_mpi_comm()
if comm:
output = self.lmp.comm.bcast(output, root=0)
if 'verbose' in kwargs and kwargs['verbose']:
print(output)

35
unittest/python/python-pylammps.py
View File

@ -84,5 +84,40 @@ class PythonPyLammps(unittest.TestCase):
self.assertEqual(len(self.pylmp.last_run.thermo.TotEng), 2)
self.assertEqual(len(self.pylmp.last_run.thermo.Press), 2)
def test_info_queries(self):
self.pylmp.lattice("fcc", 0.8442),
self.pylmp.region("box block", 0, 4, 0, 4, 0, 4)
self.pylmp.create_box(1, "box")
self.pylmp.variable("a equal 10.0")
self.pylmp.variable("b string value")
self.assertEqual(self.pylmp.variables['a'].value, 10.0)
self.assertEqual(self.pylmp.variables['b'].value, 'value')
self.assertEqual(len(self.pylmp.variables),2)
self.assertEqual(self.pylmp.system.units,'lj')
self.assertEqual(self.pylmp.system.atom_style,'atomic')
self.assertEqual(self.pylmp.system.ntypes,1)
self.assertEqual(self.pylmp.system.natoms,0)
self.assertEqual(self.pylmp.communication.comm_style,'brick')
self.assertEqual(self.pylmp.communication.comm_layout,'uniform')
self.assertEqual(self.pylmp.communication.nprocs,1)
self.assertEqual(len(self.pylmp.computes),3)
self.assertEqual(self.pylmp.computes[0]['name'], 'thermo_temp')
self.assertEqual(self.pylmp.computes[0]['style'], 'temp')
self.assertEqual(self.pylmp.computes[0]['group'], 'all')
self.assertEqual(self.pylmp.computes[1]['name'], 'thermo_press')
self.assertEqual(self.pylmp.computes[1]['style'], 'pressure')
self.assertEqual(self.pylmp.computes[1]['group'], 'all')
self.assertEqual(self.pylmp.computes[2]['name'], 'thermo_pe')
self.assertEqual(self.pylmp.computes[2]['style'], 'pe')
self.assertEqual(self.pylmp.computes[2]['group'], 'all')
self.assertEqual(len(self.pylmp.dumps),0)
self.pylmp.fix('one','all','nve')
self.assertEqual(len(self.pylmp.fixes),1)
self.assertEqual(self.pylmp.fixes[0]['name'], 'one')
self.assertEqual(self.pylmp.fixes[0]['style'], 'nve')
self.assertEqual(self.pylmp.fixes[0]['group'], 'all')
self.pylmp.group('none','empty')
self.assertEqual(len(self.pylmp.groups),2)
if __name__ == "__main__":
unittest.main()