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import os
import unittest
from lammps.formats import LogFile, AvgChunkFile
has_yaml = False
try:
import yaml
has_yaml = True
try:
from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
except ImportError:
from yaml import SafeLoader, SafeDumper
except:
pass
EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
DEFAULT_STYLE_EXAMPLE_LOG="melt/log.8Apr21.melt.g++.1"
MULTI_STYLE_EXAMPLE_LOG="peptide/log.27Nov18.peptide.g++.1"
AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1"
YAML_STYLE_EXAMPLE_LOG="yaml/log.7Apr22.yaml.g++.1"
class Logfiles(unittest.TestCase):
def testLogFileNotFound(self):
with self.assertRaises(FileNotFoundError):
LogFile('test.log')
def testDefaultLogFile(self):
log = LogFile(os.path.join(EXAMPLES_DIR, DEFAULT_STYLE_EXAMPLE_LOG))
self.assertEqual(len(log.runs), 1)
run = log.runs[0]
self.assertEqual(len(run.keys()), 6)
self.assertIn("Step", run)
self.assertIn("Temp", run)
self.assertIn("E_pair", run)
self.assertIn("E_mol", run)
self.assertIn("TotEng", run)
self.assertIn("Press", run)
self.assertEqual(len(run["Step"]), 6)
self.assertEqual(len(run["Temp"]), 6)
self.assertEqual(len(run["E_pair"]), 6)
self.assertEqual(len(run["E_mol"]), 6)
self.assertEqual(len(run["TotEng"]), 6)
self.assertEqual(len(run["Press"]), 6)
self.assertEqual(log.runs[0]["Step"], [0, 50, 100, 150, 200, 250])
def testMultiLogFile(self):
log = LogFile(os.path.join(EXAMPLES_DIR, MULTI_STYLE_EXAMPLE_LOG))
self.assertEqual(len(log.runs), 1)
run0 = log.runs[0]
self.assertEqual(len(run0.keys()), 14)
self.assertIn("Step", run0)
self.assertIn("CPU", run0)
self.assertIn("TotEng", run0)
self.assertIn("KinEng", run0)
self.assertIn("Temp", run0)
self.assertIn("PotEng", run0)
self.assertIn("E_bond", run0)
self.assertIn("E_angle", run0)
self.assertIn("E_dihed", run0)
self.assertIn("E_impro", run0)
self.assertIn("E_vdwl", run0)
self.assertIn("E_coul", run0)
self.assertIn("E_long", run0)
self.assertIn("Press", run0)
for k in run0:
self.assertEqual(len(run0[k]), 7)
self.assertEqual(run0["Step"], list(range(0,350, 50)))
@unittest.skipIf(not has_yaml,"Missing the PyYAML python module")
def testYamlLogFile(self):
log = LogFile(os.path.join(EXAMPLES_DIR, YAML_STYLE_EXAMPLE_LOG))
self.assertEqual(len(log.runs), 2)
run = log.runs[0]
self.assertEqual(len(run.keys()), 12)
self.assertIn("Step", run)
self.assertIn("Temp", run)
self.assertIn("E_vdwl", run)
self.assertIn("E_coul", run)
self.assertIn("E_bond", run)
self.assertIn("E_angle", run)
self.assertIn("Press", run)
self.assertEqual(len(run["Step"]), 11)
self.assertEqual(len(run["Temp"]), 11)
self.assertEqual(len(run["E_vdwl"]), 11)
self.assertEqual(len(run["E_coul"]), 11)
self.assertEqual(len(run["E_bond"]), 11)
self.assertEqual(len(run["E_angle"]), 11)
self.assertEqual(len(run["Press"]), 11)
self.assertEqual(log.runs[0]["Step"], [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100])
class AvgChunkFiles(unittest.TestCase):
def testAvgChunkFileNotFound(self):
with self.assertRaises(FileNotFoundError):
AvgChunkFile('test.log')
def testRead(self):
cfile = AvgChunkFile(os.path.join(EXAMPLES_DIR, AVG_CHUNK_FILE))
self.assertEqual(cfile.fix_name, "4")
self.assertEqual(cfile.group_name, "all")
self.assertEqual(cfile.timesteps, list(range(10000, 110000, 5000)))
ntimesteps = len(cfile.timesteps)
ntotal_count = len(cfile.total_count)
nchunks = len(cfile.chunks)
self.assertEqual(ntimesteps, ntotal_count)
self.assertEqual(nchunks, 20)
for i in range(1, nchunks+1):
chunk = cfile.chunks[i-1];
self.assertEqual(chunk['id'], i)
self.assertEqual(len(chunk['coord']), ntimesteps)
self.assertEqual(len(chunk['ncount']), ntimesteps)
self.assertIn("vx", chunk)
self.assertEqual(len(chunk['vx']), ntimesteps)
self.assertEqual(len(chunk['coord'][0]), 1)
from lammps import lammps
has_dump_yaml = False
try:
machine=None
if 'LAMMPS_MACHINE_NAME' in os.environ:
machine=os.environ['LAMMPS_MACHINE_NAME']
lmp=lammps(name=machine)
has_dump_yaml = lmp.has_style("atom","full") and lmp.has_style("dump", "yaml")
lmp.close()
except:
pass
@unittest.skipIf(not (has_dump_yaml and has_yaml), "Either atom_style full, dump_style yaml, or the python PyYAML module are not available")
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'])
def tearDown(self):
del self.lmp
def testDumpYaml(self):
dumpfile = os.path.join(os.path.abspath('.'), 'dump.yaml')
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 yaml 2 " + dumpfile + " id type mol q x y z vx vy vz")
self.lmp.command("dump_modify 1 time yes sort id units yes")
self.lmp.command("run 4 post no")
with open(dumpfile) as d:
traj = tuple(yaml.load_all(d, Loader=Loader))
self.assertEqual(len(traj), 3)
self.assertEqual(traj[0]['timestep'], 0)
self.assertEqual(traj[0]['time'], 0)
self.assertEqual(traj[0]['natoms'], 29)
self.assertEqual(traj[0]['units'], 'real')
self.assertEqual(len(traj[0]['boundary']), 6)
self.assertEqual(traj[0]['boundary'][0], 'p')
self.assertEqual(traj[1]['timestep'], 2)
self.assertEqual(traj[1]['time'], 0.2)
self.assertEqual(traj[2]['timestep'], 4)
self.assertEqual(traj[2]['time'], 0.4)
self.assertEqual(traj[0]['keywords'],['id', 'type', 'mol', 'q', 'x', 'y', 'z',
'vx', 'vy', 'vz'])
self.assertEqual(traj[0]['data'][0],[1, 3, 1, -0.47, -0.279937, 2.47266, -0.172009,
0.000778678, 0.000589703, -0.000221795])
if __name__ == "__main__":
unittest.main()
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