# Copyright (c) 2026, PyRETIS Development Team.
# Distributed under the LGPLv2.1+ License. See LICENSE for more info.
"""This module handles parsing of input settings.
This module defines the file format for PyRETIS input files.
Important methods defined here
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
parse_settings_file (:py:func:`.parse_settings_file`)
Method for parsing settings from a given input file.
write_settings_file (:py:func:`.write_settings_file`)
Method for writing settings from a simulation to a given file.
"""
import ast
import copy
import logging
import os
import pprint
import re
from pyretis.inout.restart import read_restart_file
from pyretis.inout.common import create_backup, create_empty_ensembles
from pyretis.inout.formats.cp2k import cp2k_settings
from pyretis.inout.formats.gromacs import gromacs_settings
from pyretis.info import PROGRAM_NAME, URL
from pyretis.inout.checker import check_interfaces, check_for_bullshitt
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
logger.addHandler(logging.NullHandler())
__all__ = ['parse_settings_file', 'write_settings_file', 'SECTIONS',
'RESTART_OVERRIDE_KEYWORDS', 'RESTART_FORBIDDEN_KEYWORDS',
'fill_up_tis_and_retis_settings', 'add_default_settings',
'add_specific_default_settings']
SECTIONS = {}
TITLE = f'{PROGRAM_NAME} input settings'
SECTIONS['heading'] = {
'text': (f"{TITLE}\n{'=' * len(TITLE)}\n"
f"For more info, please see: {URL}\n"
f"Have Fun!")
}
HERE = os.path.abspath('.')
SECTIONS['simulation'] = {
'endcycle': None,
'exe_path': HERE,
'flux': None,
'interfaces': None,
'restart': None,
'rgen': 'rgen',
'seed': None,
'startcycle': None,
'steps': None,
'task': 'md',
'zero_ensemble': None,
'zero_left': None,
'permeability': None,
'swap_attributes': None,
'priority_shooting': False,
'umbrella': None,
'overlap': None,
'maxdx': None,
'mincycle': None
}
SECTIONS['system'] = {
'dimensions': 3,
'input_file': None,
'temperature': 1.0,
'units': 'lj',
# The random generator used for path-ensemble sampling is taken from
# this section by pyretis.setup.createsimulation.create_ensemble. The
# key is intentionally accepted here so that "rgen" in a [System]
# block is honoured rather than silently dropped.
'rgen': 'rgen',
}
SECTIONS['unit-system'] = {
'charge': None,
'energy': None,
'length': None,
'mass': None,
'name': None,
}
SECTIONS['engine'] = {
'class': None,
'exe_path': HERE,
'module': None,
'rgen': 'rgen',
}
SECTIONS['box'] = {
'cell': None,
'high': None,
'low': None,
'periodic': None,
}
SECTIONS['particles'] = {
'mass': None,
'name': None,
'npart': None,
'position': None,
'ptype': None,
'type': 'internal',
'velocity': None,
}
SECTIONS['forcefield'] = {
'description': None
}
SECTIONS['potential'] = {
'class': None,
'parameter': None
}
SECTIONS['orderparameter'] = {
'class': None,
'module': None,
'name': None,
}
SECTIONS['collective-variable'] = {
'class': None,
'module': None,
'name': None
}
SECTIONS['output'] = {
'backup': 'append',
'cross-file': 1,
'energy-file': 1,
'pathensemble-file': 1,
'prefix': None,
'order-file': 1,
'restart-file': 1,
'screen': 10,
'trajectory-file': 100,
}
SECTIONS['tis'] = {
'allowmaxlength': False,
'aimless': True,
'ensemble_number': None,
'detect': None,
'freq': None,
'maxlength': None,
'nullmoves': None,
'n_jumps': None,
'high_accept': False,
'interface_sour': None,
'interface_cap': None,
'relative_shoots': None,
'rescale_energy': False,
'rgen': 'rgen',
'seed': None,
'shooting_move': 'sh',
'shooting_moves': [],
'sigma_v': -1,
'zero_momentum': False,
'mirror_freq': 0,
'target_freq': 0,
'target_indices': [],
}
SECTIONS['initial-path'] = {
'method': None
}
SECTIONS['retis'] = {
'nullmoves': None,
'relative_shoots': None,
'rgen': None,
'seed': None,
'swapfreq': None,
'swapsimul': None,
}
SECTIONS['repptis'] = {
'memory': None
}
SECTIONS['ensemble'] = {
'interface': None
}
SECTIONS['analysis'] = {
'blockskip': 1,
'bins': 100,
'maxblock': 1000,
'maxordermsd': -1,
'ngrid': 1001,
'plot': {'plotter': 'mpl', 'output': 'png',
'style': 'pyretis'},
'report': ['latex', 'rst', 'html'],
'report-dir': None,
'skipcross': 1000,
'txt-output': 'txt.gz',
'tau_ref_bin': [],
'skip': 0
}
SPECIAL_KEY = {'parameter'}
# Section aliases: alternate section-header names that are silently mapped
# to a canonical section. Listed here so they are not flagged as unknown.
# Keys are the alias (first word of a section header, lower-cased);
# values are the canonical SECTIONS key they merge into.
SECTION_ALIASES = {
'md': 'simulation',
}
# This dictionary contains sections where the keywords
# can not be defined before we parse the input. The reason
# for this is that we support user-defined external modules
# and that the user should have the freedom to define keywords
# for these modules:
ALLOW_MULTIPLE = {
'collective-variable',
'engine',
'ensemble',
'initial-path',
'orderparameter',
'potential',
}
# This dictionary contains sections that can be defined
# multiple times. When parsing, these sections will be
# prefixed with a number to distinguish them.
SPECIAL_MULTIPLE = {
'collective-variable',
'ensemble',
'potential',
}
# Keywords that the new input file is allowed to change on a restart.
# When a value in the new input differs from the value stored in the
# restart, a WARNING is emitted and the new value replaces the restarted
# one. A restart is meant to *extend* an existing simulation, so the keys
# here are limited to those that do not invalidate previously saved state
# (cycle counts, RNG seeds, log verbosity, … but not the interface set or
# any other topology-defining quantity — for those see
# RESTART_FORBIDDEN_KEYWORDS).
RESTART_OVERRIDE_KEYWORDS = {
'simulation': [
'steps',
'seed',
'priority_shooting',
],
'output': [
'screen',
'backup',
'trajectory-file',
'energy-file',
'order-file',
'cross-file',
'restart-file',
'pathensemble-file',
],
'tis': [
# General shooting
'freq',
'sigma_v',
'aimless',
'allowmaxlength',
'maxlength',
'shooting_move',
'shooting_moves',
# wt / ss / wf specific
'high_accept',
'n_jumps',
'mirror_freq',
'target_freq',
'target_indices',
'nullmoves',
],
'retis': [
'swapfreq',
'swapsimul',
'nullmoves',
],
}
# Keywords that define the topology of the simulation (state space,
# ensemble layout, …). Changing any of these in a restart would
# invalidate the previously saved path data, so the restart must abort
# with a clear error if the new input disagrees with the stored value.
# Keys are section names; values are lists of keyword names.
RESTART_FORBIDDEN_KEYWORDS = {
'simulation': [
'interfaces',
'task',
'zero_left',
'zero_ensemble',
'flux',
'permeability',
],
}
[docs]def parse_settings_file(filename, add_default=True):
"""Parse settings from a file name.
Here, we read the file line-by-line and check if the current line
contains a keyword, if so, we parse that keyword.
Parameters
----------
filename : string
The file to parse.
add_default : boolean
If True, we will add default settings as well for keywords
not found in the input.
Returns
-------
settings : dict
A dictionary with settings for PyRETIS.
"""
with open(filename, 'r', encoding='utf-8') as fileh:
raw_sections = _parse_sections(fileh)
settings = _parse_all_raw_sections(raw_sections)
if add_default:
logger.debug('Adding default settings')
add_default_settings(settings)
add_specific_default_settings(settings)
if settings['simulation']['task'] in {'retis', 'tis',
'repptis', 'pptis',
'explore', 'make-tis-files'}:
fill_up_tis_and_retis_settings(settings)
# Set up checks before to continue. This section shall GROW.
check_interfaces(settings)
check_for_bullshitt(settings)
return _clean_settings(settings)
def parse_primitive(text):
"""Parse text to Python using the ast module.
Parameters
----------
text : string
The text to parse.
Returns
-------
out[0] : string, dict, list, boolean, or other type
The parsed text.
out[1] : boolean
True if we managed to parse the text, False otherwise.
"""
parsed = None
success = False
try:
parsed = ast.literal_eval(text.strip())
success = True
except SyntaxError:
parsed = text.strip()
success = True
except ValueError:
parsed = text.strip()
success = True
return parsed, success
def look_for_keyword(line):
"""Search for a keyword in the given string.
A string is assumed to define a keyword if the keyword appears as
the first word in the string, ending with a `=`.
Parameters
----------
line : string
A string to check for a keyword.
Returns
-------
out[0] : string
The matched keyword. It may contain spaces and it will also
contain the matched `=` separator.
out[1] : string
A lower-case, stripped version of `out[0]`.
out[2] : boolean
`True` if we found a possible keyword.
"""
# Match a word followed by a '=':
key = re.match(r'(.*?)=', line)
if key:
keyword = ''.join([key.group(1), '='])
keyword_low = key.group(1).strip().lower()
for i in SPECIAL_KEY:
if keyword_low.startswith(i):
return keyword, i, True
# Here we assume that keys with len One or Two are Atoms names
if len(keyword_low) <= 2:
keyword_low = key.group(1).strip()
return keyword, keyword_low, True
return None, None, False
[docs]def _parse_sections(inputtxt):
"""Find sections in the input file with raw data.
This method will find sections in the input file and
collect the corresponding raw data.
Parameters
----------
inputtxt : list of strings or iterable file object
The raw data to parse.
Returns
-------
raw_data : dict
A dictionary with keys corresponding to the sections found
in the input file. `raw_data[key]` contains the raw data
for the section corresponding to `key`.
"""
multiple = {key: 0 for key in SPECIAL_MULTIPLE}
raw_data = {'heading': []}
previous_line = None
add_section = 'heading'
data = []
for lines in inputtxt:
current_line, _, _ = lines.strip().partition('#')
if not current_line:
continue
if current_line.startswith('---'):
if previous_line is None:
continue
section_title = previous_line.split()[0].lower()
if section_title in SPECIAL_MULTIPLE:
new_section_title = f'{section_title}{multiple[section_title]}'
multiple[section_title] += 1
section_title = new_section_title
if section_title not in raw_data:
raw_data[section_title] = []
raw_data[add_section].extend(data[:-1])
data = []
add_section = section_title
else:
data += [current_line]
previous_line = current_line
if add_section is not None:
raw_data[add_section].extend(data)
return raw_data
[docs]def _parse_section_heading(raw_section):
"""Parse the heading section.
Parameters
----------
raw_section : list of strings
The text data for a given section which will be parsed.
Returns
-------
setting : dict
A dict with keys corresponding to the settings.
"""
if not raw_section:
return None
return {'text': '\n'.join(raw_section)}
[docs]def _merge_section_text(raw_section):
"""Merge text for settings that are split across lines.
This method supports keyword settings that are split across several
lines. Here we merge these lines by assuming that keywords separate
different settings.
Parameters
----------
raw_section : string
The text we will merge.
"""
merged = []
for line in raw_section:
_, _, found_keyword = look_for_keyword(line)
if found_keyword or not merged:
merged.append(line)
else:
merged[-1] = ''.join((merged[-1], line))
return merged
[docs]def _parse_section_default(raw_section):
"""Parse a raw section.
This is the default parser for sections.
Parameters
----------
raw_section : list of strings
The text data for a given section which will be parsed.
Returns
-------
setting : dict
A dict with keys corresponding to the settings.
"""
merged = _merge_section_text(raw_section)
setting = {}
for line in merged:
match, keyword, found_keyword = look_for_keyword(line)
if found_keyword:
raw = line[len(match):].strip()
parsed, success = parse_primitive(raw)
if success:
special = None
for skey in SPECIAL_MULTIPLE:
# To avoid a false True for ensemble_number
if keyword.startswith(skey) and keyword[len(skey)] != '_':
special = skey
if special is not None:
var = [''.join(line.split(keyword.split()[0])[1])]
new_setting = _parse_section_default(var)
var = line.split(special)[1].split()[0]
num = 0 if not var.isdigit() else int(var)
if special not in setting:
setting[special] = [{}]
while num >= len(setting[special]):
setting[special].append({})
setting[special][num].update(new_setting)
elif keyword in SPECIAL_KEY:
if keyword not in setting:
setting[keyword] = {}
var = line.split(keyword)[1].split()[0]
# Yes, in some cases we really want an integer.
# Note: This will only work for positive numbers
# (which we are assuming here).
if var.isdigit():
setting[keyword][int(var)] = parsed
else:
setting[keyword][var] = parsed
elif len(keyword.split()) > 1:
key_0 = match.split()[0]
var = [' '.join(line.split()[1:])]
new_setting = _parse_section_default(var)
if key_0 not in setting:
setting[key_0] = {}
for key, val in new_setting.items():
if key in setting[key_0]:
setting[key_0][key].update(val)
else:
setting[key_0][key] = val
else:
setting[keyword] = parsed
else: # pragma: no cover
msg = [f'Could read keyword {keyword}']
msg += ['Keyword was skipped, please check your input!']
msg += [f'Input setting: {raw}']
msgtxt = '\n'.join(msg)
logger.critical(msgtxt)
return setting
[docs]def _parse_raw_section(raw_section, section):
"""Parse the raw data from a section.
Parameters
----------
raw_section : list of strings
The text data for a given section which will be parsed.
section : string
A text identifying the section we are parsing for. This is
used to get a list over valid keywords for the section.
Returns
-------
out : dict
A dict with keys corresponding to the settings.
"""
if section in SECTION_ALIASES:
# Parse against the canonical section's keyword list.
canonical = SECTION_ALIASES[section]
return _parse_raw_section(raw_section, canonical)
if section not in SECTIONS:
# Unknown section, just ignore it and give a warning.
msgtxt = f'Ignoring unknown input section "{section}"'
logger.warning(msgtxt)
return None
if section == 'heading':
return _parse_section_heading(raw_section)
return _parse_section_default(raw_section)
[docs]def _parse_all_raw_sections(raw_sections):
"""Parse all raw sections.
This method is helpful for running tests etc.
Parameters
----------
raw_sections : dict
The dictionary with the raw data in sections.
Returns
-------
settings : dict
The parsed settings, with one key for each section parsed.
"""
settings = {}
for key, val in raw_sections.items():
special = None
for i in SPECIAL_MULTIPLE:
if key.startswith(i):
special = i
if special is not None:
new_setting = _parse_raw_section(val, special)
if special not in settings:
settings[special] = []
settings[special].append(new_setting)
else:
new_setting = _parse_raw_section(val, key)
if new_setting is None:
continue
# Aliases (e.g. 'md') are merged into their canonical section.
dest_key = SECTION_ALIASES.get(key, key)
if dest_key not in settings:
settings[dest_key] = {}
for sub_key in new_setting:
settings[dest_key][sub_key] = new_setting[sub_key]
return settings
[docs]def fill_up_tis_and_retis_settings(settings):
"""Make the life of sloppy users easier.
The full input set-up will be here completed.
Parameters
----------
settings : dict
The current input settings.
Returns
-------
None, but this method might add data to the input settings.
"""
create_empty_ensembles(settings)
ensemble_save = copy.deepcopy(settings['ensemble'])
# The previously constructed dictionary is inserted in the settings.
# This is done such that the specific input given per ensemble
# OVERWRITES the general input.
for i_ens, val in enumerate(ensemble_save):
for key in settings:
if key in val:
if key not in SPECIAL_MULTIPLE:
val[key] = {**copy.deepcopy(settings[key]),
**copy.deepcopy(val[key])}
else:
for i_sub, sub in enumerate(settings[key]):
while len(val[key]) < len(settings[key]):
val[key].append({})
val[key][i_sub] = {
**copy.deepcopy(sub),
**copy.deepcopy(val[key][i_sub])
}
ensemble_save[i_ens] = {**copy.deepcopy(settings),
**copy.deepcopy(val)}
del ensemble_save[i_ens]['ensemble']
for i_ens, ens in enumerate(ensemble_save):
add_default_settings(settings)
add_specific_default_settings(settings)
settings['ensemble'][i_ens] = copy.deepcopy(ens)
if 'make-tis-files' in settings['simulation']['task']:
settings['ensemble'][i_ens]['simulation']['task'] = 'tis'
if settings['tis'].get('shooting_moves', False):
for i_ens, ens_set in enumerate(settings['ensemble']):
ens_set['tis']['shooting_move'] = \
settings['tis']['shooting_moves'][i_ens]
[docs]def add_default_settings(settings):
"""Add default settings.
Parameters
----------
settings : dict
The current input settings.
Returns
-------
None, but this method might add data to the input settings.
"""
if settings.get('initial-path', {}).get('method') == 'restart':
if settings['simulation'].get('restart') is None:
settings['simulation']['restart'] = 'pyretis.restart'
for sec, sec_val in SECTIONS.items():
if sec not in settings:
settings[sec] = {}
for key, val in sec_val.items():
if val is not None and key not in settings[sec]:
settings[sec][key] = val
to_remove = [key for key in settings if len(settings[key]) == 0]
for key in to_remove:
settings.pop(key, None)
[docs]def add_specific_default_settings(settings):
"""Add specific default settings for each simulation task.
Parameters
----------
settings : dict
The current input settings.
Returns
-------
None, but this method might add data to the input settings.
"""
task = settings['simulation'].get('task')
if task not in settings and task in SECTIONS:
settings[task] = {}
if 'exp' in task:
settings['tis']['shooting_move'] = 'exp'
if task in {'pptis', 'tis', 'make-tis-files'}:
if 'flux' not in settings['simulation']:
settings['simulation']['flux'] = False
if 'zero_ensemble' not in settings['simulation']:
settings['simulation']['zero_ensemble'] = False
if task in {'repptis', 'retis'}:
if 'flux' not in settings['simulation']:
settings['simulation']['flux'] = True
if 'zero_ensemble' not in settings['simulation']:
settings['simulation']['zero_ensemble'] = True
eng_name = settings['engine'].get('class', 'NoneEngine')
if eng_name[:7].lower() in {'gromacs', 'cp2k', 'lammps'}:
settings['particles']['type'] = 'external'
settings['engine']['type'] = 'external'
input_path = os.path.join(settings['engine'].get('exe_path', '.'),
settings['engine'].get('input_path', '.'))
engine_checker = {'gromacs': gromacs_settings,
'cp2k': cp2k_settings}
# Checks engine specific settings
if engine_checker.get(eng_name[:7].lower()):
engine_checker[eng_name[:7].lower()](settings, input_path)
else:
settings['particles']['type'] = 'internal'
settings['engine']['type'] = settings['engine'].get('type', 'internal')
[docs]def _check_restart_forbidden(new_set, settings):
"""Raise if topology-defining keywords disagree between input and restart.
Keywords listed in :data:`RESTART_FORBIDDEN_KEYWORDS` describe the
state space of the simulation (interfaces, task, …). They must match
the value stored in the restart, otherwise the already-saved paths
would be reinterpreted against a different topology and the
continuation would be silently wrong.
Parameters
----------
new_set : dict
Settings loaded from the restart file.
settings : dict
Settings parsed from the new input file.
Raises
------
ValueError
When the new input changes a forbidden keyword.
"""
for section, keys in RESTART_FORBIDDEN_KEYWORDS.items():
if section not in settings or section not in new_set:
continue
for key in keys:
if key not in settings[section]:
continue
new_val = settings[section][key]
old_val = new_set[section].get(key)
if new_val != old_val:
raise ValueError(
f'Restart refused: "{section}.{key}" differs between '
f'the new input ({new_val!r}) and the restart file '
f'({old_val!r}). This keyword is part of the '
f'simulation topology and cannot be changed by a '
f'restart — use "load" instead to start a new '
f'simulation with different settings.'
)
[docs]def _apply_restart_overrides(new_set, settings):
"""Apply allowed keyword overrides from a new input onto restart settings.
Topology-defining keywords (see :data:`RESTART_FORBIDDEN_KEYWORDS`)
are first checked for equality; any disagreement aborts the restart.
For every section and key listed in :data:`RESTART_OVERRIDE_KEYWORDS`,
if the value supplied in the new input file differs from the one stored
in the restart, a WARNING is logged and the new value replaces the old
one. Sections or keys absent from *settings* are silently skipped.
Parameters
----------
new_set : dict
Settings loaded from the restart file (modified in-place).
settings : dict
Settings parsed from the new input file.
"""
_check_restart_forbidden(new_set, settings)
for section, keys in RESTART_OVERRIDE_KEYWORDS.items():
if section not in settings or section not in new_set:
continue
for key in keys:
if key not in settings[section]:
continue
new_val = settings[section][key]
old_val = new_set[section].get(key)
if new_val != old_val:
logger.warning(
'Restart override: "%s.%s" changed from %r to %r.',
section, key, old_val, new_val,
)
new_set[section][key] = new_val
for i, ens_new in enumerate(settings.get('ensemble', [])):
if i >= len(new_set.get('ensemble', [])):
break
ens_restart = new_set['ensemble'][i]
for section, keys in RESTART_OVERRIDE_KEYWORDS.items():
if section not in ens_new or section not in ens_restart:
continue
for key in keys:
if key not in ens_new[section]:
continue
new_val = ens_new[section][key]
old_val = ens_restart[section].get(key)
if new_val != old_val:
logger.warning(
'Restart override (ensemble %i): "%s.%s" '
'changed from %r to %r.',
i, section, key, old_val, new_val,
)
ens_restart[section][key] = new_val
def settings_from_restart(settings):
"""Overwrite the settings with restart info.
Here, we attempt to remove unwanted stuff from the input settings.
NOTE: This structure doesn't allow modifications to a simulation
with a restart. That is, restart ONLY extends one simulation.
Load should be used for any other purpose.
Keywords listed in :data:`RESTART_OVERRIDE_KEYWORDS` are an exception:
when their value in the new input differs from the restarted value, a
WARNING is emitted and the new value is applied.
Parameters
----------
settings : dict
The current input settings that is going to be mostly overwritten.
Returns
-------
new_set : dict
The current input settings with the restart info.
restart_info : dict
The info to restart the various simulation objects.
"""
cycle = settings['simulation']['steps']
exe_path = settings['simulation']['exe_path']
filename = os.path.join(settings['simulation']['exe_path'],
settings['simulation']['restart'])
restart = read_restart_file(filename)
if settings.get('initial-path', {}).get('flexible_restart', False):
new_set = copy_settings(settings)
else:
new_set = restart.pop('settings')
_apply_restart_overrides(new_set, settings)
new_set['restart'] = restart
new_set['simulation']['startcycle'] = new_set['simulation']['steps']
new_set['simulation']['steps'] = cycle
new_set['simulation']['restart'] = filename
new_set['simulation']['exe_path'] = exe_path
# This won't loop if it is an empty list
for i in range(len(new_set.get('ensemble', []))):
new_set['ensemble'][i]['simulation']['exe_path'] = exe_path
new_set['ensemble'][i]['initial-path'] = {'method': 'restart'}
new_set['ensemble'][i]['engine']['input_path'] = \
settings['ensemble'][i]['engine'].get('input_path', '.')
# Priority shooting aims is to recover a failed job, so it must be
# allowed here to interfere to the initial settings.
new_set['simulation']['priority_shooting'] = settings['simulation'].get(
'priority_shooting', False)
new_set['engine']['input_path'] = settings['engine'].get('input_path', '.')
return new_set, restart
def look_for_input_files(input_path, required_files,
extra_files=None):
"""Check that required files for external engines are present.
It will first search for the default files.
If not present, it will search for the files with the
same extension. In this search,
if there are no files or multiple files for a required
extension, the function will raise an Error.
There might also be optional files which are not required, but
might be passed in here. If these are not present we will
not fail, but delete the reference to this file.
Parameters
----------
input_path : string
The path to the folder where the input files are stored.
required_files : dict of strings
These are the file names types of the required files.
extra_files : list of strings, optional
These are the file names of the extra files.
Returns
-------
out : dict
The paths to the required and extra files we found.
"""
if not os.path.isdir(input_path):
msg = f'Input path folder {input_path} not existing'
raise ValueError(msg)
# Get the list of files in the input_path folder
files_in_input_path = \
[i.name for i in os.scandir(input_path) if i.is_file()]
input_files = {}
# Check if the required files are present
for file_type, file_to_check in required_files.items():
req_ext = os.path.splitext(file_to_check)[1][1:].lower()
if file_to_check in files_in_input_path:
input_files[file_type] = os.path.join(input_path, file_to_check)
logger.debug('%s input: %s', file_type, input_files[file_type])
else:
# If not present, let's try to explore the folder by extension
file_counter = 0
selected_file = None
for file_input in files_in_input_path:
file_ext = os.path.splitext(file_input)[1][1:].lower()
if req_ext == file_ext:
file_counter += 1
selected_file = file_input
# Since we are guessing the correct files, give an error if
# multiple entries are possible.
if file_counter == 1:
input_files[file_type] = os.path.join(input_path,
selected_file)
logger.warning('using %s as "%s" file',
input_files[file_type], file_type)
else:
msg = f'Missing input file "{file_to_check}" '
if file_counter > 1:
msg += f'and multiple files have extension ".{req_ext}"'
raise ValueError(msg)
# Check if the extra files are present. If so, add them to the input_files.
# Gromacs engine takes a dictionary as extra_files, while cp2k takes a list
# I'm not familiar with cp2k, so I'm assuming the list format is required.
# Either way, both types have their merits, so I add a check for enginetype
if extra_files:
if isinstance(extra_files, dict):
for file_type, file_to_check in extra_files.items():
logger.debug('Checking for key %s and file %s', file_type,
file_to_check)
if file_to_check in files_in_input_path:
logger.debug('Found %s', file_to_check)
input_files[file_type] = os.path.join(input_path,
file_to_check)
else:
msg = f'Extra file {file_to_check} not present '
msg += f'in {input_path}'
logger.info(msg)
elif isinstance(extra_files, list):
input_files['extra_files'] = []
for file_to_check in extra_files:
if file_to_check in files_in_input_path:
input_files['extra_files'].append(file_to_check)
else:
msg = f'Extra file {file_to_check} not present '
msg += f'in {input_path}'
logger.info(msg)
else:
msg = 'Extra files should be given in a dict or list format'
msg += f', but got {type(extra_files)}'
raise ValueError(msg)
return input_files
[docs]def _clean_settings(settings):
"""Clean up input settings.
Here, we attempt to remove unwanted stuff from the input settings.
Parameters
----------
settings : dict
The current input settings.
Returns
-------
settingsc : dict
The cleaned input settings.
"""
settingc = {}
# Add other sections:
for sec in settings:
if sec not in SECTIONS: # Well, ignore unknown ones:
msgtxt = f'Ignoring unknown section "{sec}"'
logger.warning(msgtxt)
continue
if sec in SPECIAL_MULTIPLE:
settingc[sec] = list(settings[sec])
else:
settingc[sec] = {}
if sec in ALLOW_MULTIPLE: # Here, just add multiple sections:
for key in settings[sec]:
settingc[sec][key] = settings[sec][key]
else:
for key in settings[sec]:
if key not in SECTIONS[sec]: # Ignore junk:
msgtxt = f'Ignoring unknown "{key}" in "{sec}"'
logger.warning(msgtxt)
else:
settingc[sec][key] = settings[sec][key]
to_remove = [key for key, val in settingc.items() if len(val) == 0]
for key in to_remove:
settingc.pop(key, None)
return settingc
def settings_to_text(settings):
"""Turn settings into text usable for an output file.
Parameters
----------
settings : dict
The dictionary to write
Returns
------
out : string
Text representing the settings.
"""
txt = []
for section in SECTIONS:
if section not in settings:
continue
if section in SPECIAL_MULTIPLE:
for sec in settings[section]:
title = section.capitalize()
line = '-' * len(title)
if section == 'ensemble':
_, raw_data = multiple_section_to_text(sec,
prefix=None,
pure=True)
else:
raw_data = section_to_text(sec)
txt.append(f'{title}\n{line}\n{raw_data}\n\n')
elif section == 'heading':
txt.append(f'{settings[section]["text"]}\n\n')
else:
if section in ('tis', 'retis'):
title = f'{section.upper()} settings'
else:
title = f'{section.capitalize()} settings'
line = '-' * len(title)
raw_data = section_to_text(settings[section])
txt.append(f'{title}\n{line}\n{raw_data}\n\n')
return ''.join(txt)
def multiple_section_to_text(settings, prefix=None, pure=False):
"""Turn settings for the ensemble into text for output.
Parameters
----------
settings : dict
A dictionary with settings to transform.
prefix : string, optional
If this string is given, it will be prepended to
the setting we are writing.
pure: boolean, optional
The flag is used to track if subroutine works on a
main section (True) or in a sub section (False).
In the first case, prefix has to be re-set.
Returns
-------
out[0] : string
Formatted text representing the prefix to use in
a recursive key-word search.
out[1] : string
Formatted text representing the settings.
"""
data = []
for key in settings:
prefix = None if pure else prefix
if key in SPECIAL_MULTIPLE:
for i, entry in enumerate(settings[key]):
temp_prefix = f'{key}{i:d}'
_, txt = multiple_section_to_text(entry,
prefix=temp_prefix)
data.append(txt)
elif key == 'interface':
pretty = pprint.pformat(settings[key], width=67)
pretty = pretty.replace('\n', '\n' + ' ' * 67)
txt = f'{key} = {pretty}'
data.append(txt)
elif key == 'heading':
txt = f'{key} = {settings[key]}'
data.append(txt)
elif isinstance(settings[key], dict):
base = prefix
if prefix is None:
prefix = key
else:
base = prefix
prefix += ' ' + key
_, txt = multiple_section_to_text(settings[key], prefix=prefix)
prefix = base
data.append(txt)
else:
txt = f'{prefix} {key} = {settings[key]}'
data.append(txt)
return prefix, '\n'.join(data)
def section_to_text(settings, prefix=None):
"""Turn settings for a section into text for output.
Parameters
----------
settings : dict
A dictionary with settings to transform.
prefix : string, optional
If this string is given, it will be prepended to
the setting we are writing.
Returns
-------
out : string
Formatted text representing the settings.
"""
data = []
for key in settings:
if key == 'parameter':
txt = section_to_text(settings[key], prefix='parameter')
else:
if prefix is not None:
leng = len(str(key)) + 3 + len(prefix) + 1
else:
leng = len(str(key)) + 3
pretty = pprint.pformat(settings[key], width=79-leng)
pretty = pretty.replace('\n', '\n' + ' ' * leng)
if prefix is not None:
txt = f'{prefix} {key} = {pretty}'
else:
txt = f'{key} = {pretty}'
if len(txt) >= 5: # Shortest text, e.g: "a = 1".
data.append(txt)
return '\n'.join(data)
[docs]def write_settings_file(settings, outfile, backup=True):
"""Write simulation settings to an output file.
This will write a dictionary to an output file in the PyRETIS input
file format.
Parameters
----------
settings : dict
The dictionary to write.
outfile : string
The file to create.
backup : boolean, optional
If True, we will backup existing files with the same file
name as the provided file name.
Note
----
This will currently fail if objects have made it into the supplied
``settings``.
"""
if backup:
msg = create_backup(outfile)
if msg:
logger.info(msg)
with open(outfile, 'w', encoding='utf-8') as fileh:
txt = settings_to_text(settings)
fileh.write(txt.strip())
def copy_settings(settings):
"""Return a copy of the given settings.
Parameters
----------
settings : dict of dicts
A dictionary which we will return a copy of.
Returns
-------
lsetting : dict of dicts
A copy of the settings.
"""
lsetting = {}
for sec in settings: # this is common for all simulations:
lsetting[sec] = {}
if sec in SPECIAL_MULTIPLE:
lsetting[sec] = [copy.deepcopy(j) for j in settings[sec]]
else:
for key in settings[sec]:
lsetting[sec][key] = settings[sec][key]
return lsetting