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PyLammps: alternative OutputCapture using tempfiles

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This commit is contained in:
Richard Berger
2022-02-03 19:49:52 -05:00
parent f550460ecd
commit 050ce421e9
1 changed files with 56 additions and 43 deletions
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99
python/lammps/pylammps.py
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@ -20,47 +20,47 @@
from __future__ import print_function
import io
import os
import re
import select
import sys
import tempfile
from collections import namedtuple
from .core import lammps
# -------------------------------------------------------------------------
class OutputCapture(object):
""" Utility class to capture LAMMPS library output """
def __init__(self):
self.stdout_pipe_read, self.stdout_pipe_write = os.pipe()
self.stdout_fd = 1
self.stdout_fd = sys.stdout.fileno()
self.captured_output = ""
def __enter__(self):
self.stdout = os.dup(self.stdout_fd)
os.dup2(self.stdout_pipe_write, self.stdout_fd)
self.tmpfile = tempfile.TemporaryFile(mode='w+b')
sys.stdout.flush()
# make copy of original stdout
self.stdout_orig = os.dup(self.stdout_fd)
# replace stdout and redirect to temp file
os.dup2(self.tmpfile.fileno(), self.stdout_fd)
return self
def __exit__(self, exc_type, exc_value, traceback):
os.dup2(self.stdout, self.stdout_fd)
os.close(self.stdout)
os.close(self.stdout_pipe_read)
os.close(self.stdout_pipe_write)
# check if we have more to read from the pipe
def more_data(self, pipe):
r, _, _ = select.select([pipe], [], [], 0)
return bool(r)
# read the whole pipe
def read_pipe(self, pipe):
out = ""
while self.more_data(pipe):
out += os.read(pipe, 1024).decode()
return out
os.dup2(self.stdout_orig, self.stdout_fd)
os.close(self.stdout_orig)
self.tmpfile.close()
@property
def output(self):
return self.read_pipe(self.stdout_pipe_read)
sys.stdout.flush()
self.tmpfile.flush()
self.tmpfile.seek(0, io.SEEK_SET)
self.captured_output = self.tmpfile.read().decode('utf-8')
return self.captured_output
# -------------------------------------------------------------------------
@ -109,9 +109,9 @@ class AtomList(object):
"""
if index not in self._loaded:
if self.dimensions == 2:
atom = Atom2D(self._pylmp, index + 1)
atom = Atom2D(self._pylmp, index)
else:
atom = Atom(self._pylmp, index + 1)
atom = Atom(self._pylmp, index)
self._loaded[index] = atom
return self._loaded[index]
@ -612,7 +612,8 @@ class PyLammps(object):
:getter: Returns an object with properties storing the current system state
:type: namedtuple
"""
output = self.info("system")
output = self.lmp_info("system")
output = output[output.index("System information:")+1:]
d = self._parse_info_system(output)
return namedtuple('System', d.keys())(*d.values())
@ -624,7 +625,8 @@ class PyLammps(object):
:getter: Returns an object with properties storing the current communication state
:type: namedtuple
"""
output = self.info("communication")
output = self.lmp_info("communication")
output = output[output.index("Communication information:")+1:]
d = self._parse_info_communication(output)
return namedtuple('Communication', d.keys())(*d.values())
@ -636,7 +638,8 @@ class PyLammps(object):
:getter: Returns a list of computes that are currently active in this LAMMPS instance
:type: list
"""
output = self.info("computes")
output = self.lmp_info("computes")
output = output[output.index("Compute information:")+1:]
return self._parse_element_list(output)
@property
@ -647,7 +650,8 @@ class PyLammps(object):
:getter: Returns a list of dumps that are currently active in this LAMMPS instance
:type: list
"""
output = self.info("dumps")
output = self.lmp_info("dumps")
output = output[output.index("Dump information:")+1:]
return self._parse_element_list(output)
@property
@ -658,7 +662,8 @@ class PyLammps(object):
:getter: Returns a list of fixes that are currently active in this LAMMPS instance
:type: list
"""
output = self.info("fixes")
output = self.lmp_info("fixes")
output = output[output.index("Fix information:")+1:]
return self._parse_element_list(output)
@property
@ -669,7 +674,8 @@ class PyLammps(object):
:getter: Returns a list of atom groups that are currently active in this LAMMPS instance
:type: list
"""
output = self.info("groups")
output = self.lmp_info("groups")
output = output[output.index("Group information:")+1:]
return self._parse_groups(output)
@property
@ -680,11 +686,12 @@ class PyLammps(object):
:getter: Returns a dictionary of all variables that are defined in this LAMMPS instance
:type: dict
"""
output = self.info("variables")
vars = {}
output = self.lmp_info("variables")
output = output[output.index("Variable information:")+1:]
variables = {}
for v in self._parse_element_list(output):
vars[v['name']] = Variable(self, v['name'], v['style'], v['def'])
return vars
variables[v['name']] = Variable(self, v['name'], v['style'], v['def'])
return variables
def eval(self, expr):
"""
@ -709,10 +716,9 @@ class PyLammps(object):
return [x.strip() for x in value.split('=')]
def _parse_info_system(self, output):
lines = output[5:-2]
system = {}
for line in lines:
for line in output:
if line.startswith("Units"):
system['units'] = self._get_pair(line)[1]
elif line.startswith("Atom style"):
@ -770,10 +776,9 @@ class PyLammps(object):
return system
def _parse_info_communication(self, output):
lines = output[5:-3]
comm = {}
for line in lines:
for line in output:
if line.startswith("MPI library"):
comm['mpi_version'] = line.split(':')[1].strip()
elif line.startswith("Comm style"):
@ -791,10 +796,10 @@ class PyLammps(object):
return comm
def _parse_element_list(self, output):
lines = output[5:-3]
elements = []
for line in lines:
for line in output:
if not line or (":" not in line): continue
element_info = self._split_values(line.split(':')[1].strip())
element = {'name': element_info[0]}
for key, value in [self._get_pair(x) for x in element_info[1:]]:
@ -803,11 +808,10 @@ class PyLammps(object):
return elements
def _parse_groups(self, output):
lines = output[5:-3]
groups = []
group_pattern = re.compile(r"(?P<name>.+) \((?P<type>.+)\)")
for line in lines:
for line in output:
m = group_pattern.match(line.split(':')[1].strip())
group = {'name': m.group('name'), 'type': m.group('type')}
groups.append(group)
@ -830,6 +834,15 @@ class PyLammps(object):
'thermo_modify', 'thermo_style', 'timestep', 'undump', 'unfix', 'units',
'variable', 'velocity', 'write_restart'] + self.lmp.available_styles("command")))
def lmp_info(self, s):
# skip anything before and after Info-Info-Info
# also skip timestamp line
output = self.__getattr__("info")(s)
indices = [index for index, line in enumerate(output) if line.startswith("Info-Info-Info-Info")]
start = indices[0]
end = indices[1]
return [line for line in output[start+2:end] if line]
def __getattr__(self, name):
"""
This method is where the Python 'magic' happens. If a method is not