forked from lijiext/lammps
Add LogFile and AvgChunkFile readers
Implements changes proposed in #144
This commit is contained in:
Richard Berger
parent
f245467f32
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# ----------------------------------------------------------------------
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# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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# http://lammps.sandia.gov, Sandia National Laboratories
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# Steve Plimpton, sjplimp@sandia.gov
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#
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# Copyright (2003) Sandia Corporation. Under the terms of Contract
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# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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# certain rights in this software. This software is distributed under
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# the GNU General Public License.
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#
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# See the README file in the top-level LAMMPS directory.
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# -------------------------------------------------------------------------
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################################################################################
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# LAMMPS data formats
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# Written by Richard Berger <richard.berger@temple.edu>
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################################################################################
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import re
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class LogFile:
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STYLE_DEFAULT = 0
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STYLE_MULTI = 1
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def __init__(self, filename):
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alpha = re.compile(r'[a-df-zA-DF-Z]') # except e or E for floating-point numbers
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kvpairs = re.compile(r'([a-zA-Z_0-9]+)\s+=\s*([0-9\.eE\-]+)')
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style = LogFile.STYLE_DEFAULT
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self.runs = []
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self.errors = []
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with open(filename, 'rt') as f:
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in_thermo = False
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in_data_section = False
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for line in f:
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if "ERROR" in line or "exited on signal" in line:
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self.errors.append(line)
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elif line.startswith('Step '):
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in_thermo = True
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in_data_section = True
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keys = line.split()
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current_run = {}
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for k in keys:
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current_run[k] = []
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elif line.startswith('---------------- Step'):
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if not in_thermo:
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current_run = {'Step': [], 'CPU': []}
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in_thermo = True
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in_data_section = True
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style = LogFile.STYLE_MULTI
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str_step, str_cpu = line.strip('-\n').split('-----')
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step = float(str_step.split()[1])
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cpu = float(str_cpu.split('=')[1].split()[0])
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current_run["Step"].append(step)
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current_run["CPU"].append(cpu)
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elif line.startswith('Loop time of'):
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in_thermo = False
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self.runs.append(current_run)
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elif in_thermo and in_data_section:
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if style == LogFile.STYLE_DEFAULT:
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if alpha.search(line):
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continue
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for k, v in zip(keys, map(float, line.split())):
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current_run[k].append(v)
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elif style == LogFile.STYLE_MULTI:
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if '=' not in line:
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in_data_section = False
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continue
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for k,v in kvpairs.findall(line):
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if k not in current_run:
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current_run[k] = [float(v)]
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else:
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current_run[k].append(float(v))
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class AvgChunkFile:
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def __init__(self, filename):
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with open(filename, 'rt') as f:
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timestep = None
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chunks_read = 0
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self.timesteps = []
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self.total_count = []
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self.chunks = []
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for lineno, line in enumerate(f):
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if lineno == 0:
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if not line.startswith("# Chunk-averaged data for fix"):
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raise Exception("Chunk data reader only supports default avg/chunk headers!")
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parts = line.split()
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self.fix_name = parts[5]
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self.group_name = parts[8]
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continue
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elif lineno == 1:
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if not line.startswith("# Timestep Number-of-chunks Total-count"):
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raise Exception("Chunk data reader only supports default avg/chunk headers!")
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continue
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elif lineno == 2:
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if not line.startswith("#"):
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raise Exception("Chunk data reader only supports default avg/chunk headers!")
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columns = line.split()[1:]
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ndim = line.count("Coord")
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compress = 'OrigID' in line
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if ndim > 0:
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coord_start = columns.index("Coord1")
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coord_end = columns.index("Coord%d" % ndim)
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ncount_start = coord_end + 1
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data_start = ncount_start + 1
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else:
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coord_start = None
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coord_end = None
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ncount_start = 2
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data_start = 3
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continue
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parts = line.split()
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if timestep is None:
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timestep = int(parts[0])
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num_chunks = int(parts[1])
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total_count = float(parts[2])
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self.timesteps.append(timestep)
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for i in range(num_chunks):
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self.chunks.append({
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'coord' : [],
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'ncount' : []
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})
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elif chunks_read < num_chunks:
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chunk = int(parts[0])
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ncount = float(parts[ncount_start])
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if compress:
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chunk_id = int(parts[1])
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else:
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chunk_id = chunk
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current = self.chunks[chunk_id - 1]
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current['id'] = chunk_id
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current['ncount'].append(ncount)
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if ndim > 0:
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coord = tuple(map(float, parts[coord_start:coord_end+1]))
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current['coord'].append(coord)
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for i, data_column in list(enumerate(columns))[data_start:]:
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value = float(parts[i])
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if data_column in current:
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current[data_column].append(value)
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else:
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current[data_column] = [value]
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chunks_read += 1
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assert (chunk == chunks_read)
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else:
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# do not support changing number of chunks
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if not (num_chunks == int(parts[1])):
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raise Exception("Currently, changing numbers of chunks are not supported.")
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timestep = int(parts[0])
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total_count = float(parts[2])
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chunks_read = 0
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self.timesteps.append(timestep)
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self.total_count.append(total_count)
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@ -79,6 +79,11 @@ if(Python_EXECUTABLE)
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COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-pylammps.py -v
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WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
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set_tests_properties(PythonPyLammps PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
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add_test(NAME PythonFormats
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COMMAND ${PYTHON_TEST_RUNNER} ${CMAKE_CURRENT_SOURCE_DIR}/python-formats.py -v
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WORKING_DIRECTORY ${EXECUTABLE_OUTPUT_PATH})
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set_tests_properties(PythonFormats PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
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else()
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message(STATUS "Skipping Tests for the LAMMPS Python Module: no suitable Python interpreter")
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endif()
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@ -0,0 +1,91 @@
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import os
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import unittest
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from lammps.formats import LogFile, AvgChunkFile
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EXAMPLES_DIR=os.path.abspath(os.path.join(__file__, '..', '..', '..', 'examples'))
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DEFAULT_STYLE_EXAMPLE_LOG="melt/log.27Nov18.melt.g++.1"
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MULTI_STYLE_EXAMPLE_LOG="USER/fep/CC-CO/fep10/log.lammps"
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AVG_CHUNK_FILE="VISCOSITY/profile.13Oct16.nemd.2d.g++.1"
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class Logfiles(unittest.TestCase):
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def testLogFileNotFound(self):
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with self.assertRaises(FileNotFoundError):
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LogFile('test.log')
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def testDefaultLogFile(self):
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log = LogFile(os.path.join(EXAMPLES_DIR, DEFAULT_STYLE_EXAMPLE_LOG))
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self.assertEqual(len(log.runs), 1)
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run = log.runs[0]
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self.assertEqual(len(run.keys()), 6)
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self.assertIn("Step", run)
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self.assertIn("Temp", run)
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self.assertIn("E_pair", run)
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self.assertIn("E_mol", run)
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self.assertIn("TotEng", run)
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self.assertIn("Press", run)
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self.assertEqual(len(run["Step"]), 6)
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self.assertEqual(len(run["Temp"]), 6)
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self.assertEqual(len(run["E_pair"]), 6)
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self.assertEqual(len(run["E_mol"]), 6)
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self.assertEqual(len(run["TotEng"]), 6)
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self.assertEqual(len(run["Press"]), 6)
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self.assertEqual(log.runs[0]["Step"], [0, 50, 100, 150, 200, 250])
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def testMultiLogFile(self):
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log = LogFile(os.path.join(EXAMPLES_DIR, MULTI_STYLE_EXAMPLE_LOG))
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self.assertEqual(len(log.runs), 2)
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run0 = log.runs[0]
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run1 = log.runs[1]
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self.assertEqual(len(run0.keys()), 15)
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self.assertIn("Step", run0)
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self.assertIn("CPU", run0)
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self.assertIn("TotEng", run0)
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self.assertIn("KinEng", run0)
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self.assertIn("Temp", run0)
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self.assertIn("PotEng", run0)
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self.assertIn("E_bond", run0)
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self.assertIn("E_angle", run0)
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self.assertIn("E_dihed", run0)
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self.assertIn("E_impro", run0)
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self.assertIn("E_vdwl", run0)
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self.assertIn("E_coul", run0)
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self.assertIn("E_long", run0)
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self.assertIn("Press", run0)
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self.assertIn("Volume", run0)
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for k in run0:
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self.assertEqual(len(run0[k]), 51)
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self.assertEqual(run0["Step"], list(range(0,255000, 5000)))
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class AvgChunkFiles(unittest.TestCase):
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def testAvgChunkFileNotFound(self):
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with self.assertRaises(FileNotFoundError):
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AvgChunkFile('test.log')
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def testRead(self):
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cfile = AvgChunkFile(os.path.join(EXAMPLES_DIR, AVG_CHUNK_FILE))
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self.assertEqual(cfile.fix_name, "4")
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self.assertEqual(cfile.group_name, "all")
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self.assertEqual(cfile.timesteps, list(range(10000, 110000, 5000)))
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ntimesteps = len(cfile.timesteps)
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nchunks = len(cfile.chunks)
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self.assertEqual(nchunks, 20)
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for i in range(1, nchunks+1):
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chunk = cfile.chunks[i-1];
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self.assertEqual(chunk['id'], i)
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self.assertEqual(len(chunk['coord']), ntimesteps)
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self.assertEqual(len(chunk['ncount']), ntimesteps)
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self.assertIn("vx", chunk)
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self.assertEqual(len(chunk['vx']), ntimesteps)
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self.assertEqual(len(chunk['coord'][0]), 1)
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if __name__ == "__main__":
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unittest.main()
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