apply more pylint recommendations
This commit is contained in:
Axel Kohlmeyer
@ -11,14 +11,15 @@
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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 output formats
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# Written by Richard Berger <richard.berger@temple.edu>
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# and Axel Kohlmeyer <akohlmey@gmail.com>
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################################################################################
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"""
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Output formats for LAMMPS python module
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Written by Richard Berger <richard.berger@temple.edu>
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and Axel Kohlmeyer <akohlmey@gmail.com>
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"""
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import re
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# pylint: disable=C0103
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has_yaml = False
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try:
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import yaml
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@ -32,6 +33,7 @@ except ImportError:
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pass
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class LogFile:
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# pylint: disable=R0903
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"""Reads LAMMPS log files and extracts the thermo information
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It supports the line, multi, and yaml thermo output styles.
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@ -55,73 +57,73 @@ class LogFile:
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yamllog = ""
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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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with open(filename, 'rt', encoding='utf-8') 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 re.match(r'^ *Step ', line):
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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 re.match(r'^ *Step ', line):
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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 re.match(r'^(keywords:.*$|data:$|---$| - \[.*\]$)', line):
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if not has_yaml:
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raise Exception('Cannot process YAML format logs without the PyYAML Python module')
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style = LogFile.STYLE_YAML
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yamllog += line;
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current_run = {}
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elif re.match(r'^(keywords:.*$|data:$|---$| - \[.*\]$)', line):
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if not has_yaml:
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raise RuntimeError('Cannot process YAML format logs without the PyYAML Python module')
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style = LogFile.STYLE_YAML
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yamllog += line
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current_run = {}
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elif re.match(r'^\.\.\.$', line):
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thermo = yaml.load(yamllog, Loader=Loader)
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for k in thermo['keywords']:
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current_run[k] = []
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for step in thermo['data']:
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icol = 0
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for k in thermo['keywords']:
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current_run[k].append(step[icol])
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icol += 1
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self.runs.append(current_run)
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yamllog = ""
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elif re.match(r'^\.\.\.$', line):
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thermo = yaml.load(yamllog, Loader=Loader)
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for k in thermo['keywords']:
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current_run[k] = []
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for step in thermo['data']:
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icol = 0
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for k in thermo['keywords']:
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current_run[k].append(step[icol])
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icol += 1
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self.runs.append(current_run)
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yamllog = ""
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elif re.match(r'^------* Step ', line):
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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 re.match(r'^------* Step ', line):
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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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if style != LogFile.STYLE_YAML:
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self.runs.append(current_run)
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elif line.startswith('Loop time of'):
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in_thermo = False
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if style != LogFile.STYLE_YAML:
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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 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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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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"""Reads files generated by fix ave/chunk
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@ -134,9 +136,13 @@ class AvgChunkFile:
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:ivar chunks: List of chunks. Each chunk is a dictionary containing its ID, the coordinates, and the averaged quantities
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"""
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def __init__(self, filename):
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with open(filename, 'rt') as f:
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with open(filename, 'rt', encoding='utf-8') as f:
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timestep = None
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chunks_read = 0
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compress = False
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coord_start = None
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coord_end = None
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data_start = None
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self.timesteps = []
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self.total_count = []
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@ -145,24 +151,24 @@ class AvgChunkFile:
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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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raise RuntimeError("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 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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raise RuntimeError("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 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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raise RuntimeError("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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coord_end = columns.index(f"Coord{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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@ -216,8 +222,8 @@ class AvgChunkFile:
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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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if not num_chunks == int(parts[1]):
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raise RuntimeError("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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