169 lines
6.4 KiB
Python
169 lines
6.4 KiB
Python
import os
|
|
import unittest
|
|
from lammps.formats import LogFile, AvgChunkFile
|
|
|
|
import yaml
|
|
try:
|
|
from yaml import CSafeLoader as Loader, CSafeDumper as Dumper
|
|
except ImportError:
|
|
from yaml import SafeLoader, SafeDumper
|
|
|
|
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)))
|
|
|
|
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, "Either atom_style full or dump_style yaml 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()
|