1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
|
import os,unittest
from lammps import lammps
try:
import numpy
NUMPY_INSTALLED = True
except ImportError:
NUMPY_INSTALLED = False
@unittest.skipIf(not NUMPY_INSTALLED, "numpy is not available")
class PythonCmdWrapper(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.cmd.units("lj")
self.lmp.cmd.atom_style("atomic")
self.lmp.cmd.atom_modify("map array")
if 'LAMMPS_CMAKE_CACHE' in os.environ:
self.cmake_cache = {}
with open(os.environ['LAMMPS_CMAKE_CACHE'], 'r') as f:
for line in f:
line = line.strip()
if not line or line.startswith('#') or line.startswith('//'): continue
parts = line.split('=')
key, value_type = parts[0].split(':')
if len(parts) > 1:
value = parts[1]
if value_type == "BOOL":
value = (value.upper() == "ON")
else:
value = None
self.cmake_cache[key] = value
def tearDown(self):
self.lmp.close()
del self.lmp
def test_version(self):
self.assertGreaterEqual(self.lmp.version(), 20200824)
def test_create_atoms(self):
self.lmp.cmd.region("box block", 0, 2, 0, 2, 0, 2)
self.lmp.cmd.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)
self.assertEqual(self.lmp.extract_global("natoms"), 2)
pos = self.lmp.numpy.extract_atom("x")
self.assertEqual(pos.shape[0], 2)
numpy.testing.assert_array_equal(pos[0], tuple(x[0:3]))
numpy.testing.assert_array_equal(pos[1], tuple(x[3:6]))
def test_thermo_capture(self):
self.lmp.cmd.lattice("fcc", 0.8442),
self.lmp.cmd.region("box block", 0, 4, 0, 4, 0, 4)
self.lmp.cmd.create_box(1, "box")
self.lmp.cmd.create_atoms(1, "box")
self.lmp.cmd.mass(1, 1.0)
self.lmp.cmd.velocity("all create", 1.44, 87287, "loop geom")
self.lmp.cmd.pair_style("lj/cut", 2.5)
self.lmp.cmd.pair_coeff(1, 1, 1.0, 1.0, 2.5)
self.lmp.cmd.neighbor(0.3, "bin")
self.lmp.cmd.neigh_modify("delay 0 every 20 check no")
self.lmp.cmd.fix("1 all nve")
current_run = {}
def append_thermo_data(lmp):
for k, v in lmp.last_thermo().items():
current_run.setdefault(k, []).append(v)
# thermo data is only captured during a run if PYTHON package is enabled
# without it, it will only capture the final thermo at completion
nvalues = 1
if self.lmp.has_package("PYTHON"):
self.lmp.cmd.fix("myfix", "all", "python/invoke", 10, "end_of_step", append_thermo_data)
nvalues = 2
self.lmp.cmd.run(10)
append_thermo_data(self.lmp)
for k in ('Step', 'Temp', 'E_pair', 'E_mol', 'TotEng', 'Press'):
self.assertIn(k, current_run)
self.assertEqual(len(current_run[k]), nvalues)
if __name__ == "__main__":
unittest.main()
|
