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import os
import sys
import unittest
from lammps import lammps
EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
PIZZA_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'tools', 'python', 'pizza'))
DEFAULT_STYLE_EXAMPLE_LOG=os.path.join('melt', 'log.*.melt.g++.1')
MULTI_STYLE_EXAMPLE_LOG=os.path.join('peptide', 'log.27Nov18.peptide.g++.1')
sys.path.insert(1,PIZZA_DIR)
# dump class uses NumPy, so only load and test dump if NumPy is available
has_numpy = False
has_molecule = False
machine = None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
tmplmp = lammps(name=machine, cmdargs=['-nocite', '-log', 'none', '-echo', 'screen'])
has_molecule = tmplmp.has_package('MOLECULE')
tmplmp.close()
try:
import numpy
has_numpy = True
import dump
except:
pass
do_dump_test = has_numpy and has_molecule
import log
class Logfiles(unittest.TestCase):
def testLogFileNotFound(self):
with self.assertRaises(ValueError):
l = log.log('test.log')
def testDefaultLogFile(self):
l = log.log(os.path.join(EXAMPLES_DIR, DEFAULT_STYLE_EXAMPLE_LOG))
self.assertEqual(l.nvec, 6)
self.assertEqual(l.nlen, 6)
self.assertEqual(l.style, 2)
self.assertEqual(l.increment, 0)
n = l.names
self.assertEqual(len(n), 6)
self.assertIn("Step", n)
self.assertIn("Temp", n)
self.assertIn("E_pair", n)
self.assertIn("E_mol", n)
self.assertIn("TotEng", n)
self.assertIn("Press", n)
s = l.get("Step")
self.assertEqual(0.0, s[0])
self.assertEqual(50.0, s[1])
self.assertEqual(100.0, s[2])
self.assertEqual(150.0, s[3])
self.assertEqual(200.0, s[4])
self.assertEqual(250.0, s[5])
t,m = l.get("Temp", "E_mol")
self.assertEqual(t[0],3.0)
self.assertEqual(m[2],0.0)
l.write("all.txt",0)
l.write("some.txt",1,"Step","Temp","Press")
with self.assertRaises(Exception):
t = l.next()
os.remove('all.txt')
os.remove('some.txt')
def testIncrementalLogFile(self):
l = log.log(os.path.join(EXAMPLES_DIR, DEFAULT_STYLE_EXAMPLE_LOG), 0)
self.assertEqual(l.style, -1)
self.assertEqual(l.nvec, 0)
self.assertEqual(l.increment, 1)
t = l.next()
self.assertEqual(l.style, 2)
self.assertEqual(l.nvec, 6)
def testMultiLogFile(self):
l = log.log(os.path.join(EXAMPLES_DIR, MULTI_STYLE_EXAMPLE_LOG))
self.assertEqual(l.nvec, 14)
self.assertEqual(l.nlen, 7)
self.assertEqual(l.style, 1)
n = l.names
self.assertEqual(len(n), 14)
self.assertIn("Step", n)
self.assertIn("CPU", n)
self.assertIn("TotEng", n)
self.assertIn("KinEng", n)
self.assertIn("Temp", n)
self.assertIn("PotEng", n)
self.assertIn("E_bond", n)
self.assertIn("E_angle", n)
self.assertIn("E_dihed", n)
self.assertIn("E_impro", n)
self.assertIn("E_vdwl", n)
self.assertIn("E_coul", n)
self.assertIn("E_long", n)
self.assertIn("Press", n)
s = l.get("Step")
self.assertEqual(0.0, s[0])
self.assertEqual(50.0, s[1])
self.assertEqual(100.0, s[2])
self.assertEqual(150.0, s[3])
self.assertEqual(200.0, s[4])
self.assertEqual(250.0, s[5])
self.assertEqual(300.0, s[6])
v,c = l.get("E_vdwl", "E_coul")
self.assertEqual(v[0],692.8945)
self.assertEqual(c[0],26772.2646)
l.write("all.txt",0)
l.write("some.txt",1,"Step","Temp","Press")
with self.assertRaises(ValueError):
v = l.get("Volume")
with self.assertRaises(Exception):
t = l.next()
os.remove('all.txt')
os.remove('some.txt')
class PythonDump(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.do_dump_test = self.lmp.has_package('MOLECULE') and has_numpy
def tearDown(self):
del self.lmp
@unittest.skipIf(not do_dump_test,"Missing the NumPy python module or MOLECULE package")
def testDumpCustom(self):
dumpfile = os.path.join(os.path.abspath('.'), 'dump.custom')
self.lmp.command('shell cd ' + os.environ['TEST_INPUT_DIR'])
self.lmp.command("newton on on")
self.lmp.file("in.fourmol")
self.lmp.command("dump 1 all custom 2 " + dumpfile + " id type mol q x y z vx vy vz")
self.lmp.command("dump_modify 1 time yes units yes")
self.lmp.command("run 4 post no")
self.lmp.command("undump 1")
d = dump.dump(dumpfile)
id1, id2 = d.minmax("id")
self.assertEqual(id1,1)
self.assertEqual(id2,29)
t = d.time()
self.assertEqual(len(t),3)
d.tselect.one(2,4)
index, time, flag = d.iterator(0)
self.assertEqual(index,1)
self.assertEqual(time,2)
self.assertEqual(flag,1)
index, time, flag = d.iterator(1)
self.assertEqual(index,2)
self.assertEqual(time,4)
self.assertEqual(flag,1)
index, time, flag = d.iterator(1)
self.assertEqual(index,0)
self.assertEqual(time,0)
self.assertEqual(flag,-1)
with self.assertRaises(Exception):
t = d.next()
os.remove(dumpfile)
if __name__ == "__main__":
unittest.main()
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