diff --git a/python/lammps/.pylintrc.toml b/python/lammps/.pylintrc.toml new file mode 100644 index 0000000000..5a2c0cc7df --- /dev/null +++ b/python/lammps/.pylintrc.toml @@ -0,0 +1,556 @@ +[tool.pylint.main] +# Analyse import fallback blocks. This can be used to support both Python 2 and 3 +# compatible code, which means that the block might have code that exists only in +# one or another interpreter, leading to false positives when analysed. +# analyse-fallback-blocks = + +# Clear in-memory caches upon conclusion of linting. Useful if running pylint in +# a server-like mode. +# clear-cache-post-run = + +# Always return a 0 (non-error) status code, even if lint errors are found. This +# is primarily useful in continuous integration scripts. +# exit-zero = + +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code. +# extension-pkg-allow-list = + +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code. (This is an alternative name to extension-pkg-allow-list +# for backward compatibility.) +# extension-pkg-whitelist = + +# Return non-zero exit code if any of these messages/categories are detected, +# even if score is above --fail-under value. Syntax same as enable. Messages +# specified are enabled, while categories only check already-enabled messages. +# fail-on = + +# Specify a score threshold under which the program will exit with error. +fail-under = 10 + +# Interpret the stdin as a python script, whose filename needs to be passed as +# the module_or_package argument. +# from-stdin = + +# Files or directories to be skipped. They should be base names, not paths. +ignore = ["CVS"] + +# Add files or directories matching the regular expressions patterns to the +# ignore-list. The regex matches against paths and can be in Posix or Windows +# format. Because '\\' represents the directory delimiter on Windows systems, it +# can't be used as an escape character. +# ignore-paths = + +# Files or directories matching the regular expression patterns are skipped. The +# regex matches against base names, not paths. The default value ignores Emacs +# file locks +ignore-patterns = ["^\\.#"] + +# List of module names for which member attributes should not be checked and will +# not be imported (useful for modules/projects where namespaces are manipulated +# during runtime and thus existing member attributes cannot be deduced by static +# analysis). It supports qualified module names, as well as Unix pattern +# matching. +# ignored-modules = + +# Python code to execute, usually for sys.path manipulation such as +# pygtk.require(). +# init-hook = + +# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the +# number of processors available to use, and will cap the count on Windows to +# avoid hangs. +jobs = 1 + +# Control the amount of potential inferred values when inferring a single object. +# This can help the performance when dealing with large functions or complex, +# nested conditions. +limit-inference-results = 100 + +# List of plugins (as comma separated values of python module names) to load, +# usually to register additional checkers. +# load-plugins = + +# Pickle collected data for later comparisons. +persistent = true + +# Resolve imports to .pyi stubs if available. May reduce no-member messages and +# increase not-an-iterable messages. +# prefer-stubs = + +# Minimum Python version to use for version dependent checks. Will default to the +# version used to run pylint. +py-version = "3.13" + +# Discover python modules and packages in the file system subtree. +# recursive = + +# Add paths to the list of the source roots. Supports globbing patterns. The +# source root is an absolute path or a path relative to the current working +# directory used to determine a package namespace for modules located under the +# source root. +# source-roots = + +# When enabled, pylint would attempt to guess common misconfiguration and emit +# user-friendly hints instead of false-positive error messages. +suggestion-mode = true + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +# unsafe-load-any-extension = + +[tool.pylint.basic] +# Naming style matching correct argument names. +argument-naming-style = "snake_case" + +# Regular expression matching correct argument names. Overrides argument-naming- +# style. If left empty, argument names will be checked with the set naming style. +# argument-rgx = + +# Naming style matching correct attribute names. +attr-naming-style = "snake_case" + +# Regular expression matching correct attribute names. Overrides attr-naming- +# style. If left empty, attribute names will be checked with the set naming +# style. +# attr-rgx = + +# Bad variable names which should always be refused, separated by a comma. +bad-names = ["foo", "bar", "baz", "toto", "tutu", "tata"] + +# Bad variable names regexes, separated by a comma. If names match any regex, +# they will always be refused +# bad-names-rgxs = + +# Naming style matching correct class attribute names. +class-attribute-naming-style = "any" + +# Regular expression matching correct class attribute names. Overrides class- +# attribute-naming-style. If left empty, class attribute names will be checked +# with the set naming style. +# class-attribute-rgx = + +# Naming style matching correct class constant names. +class-const-naming-style = "UPPER_CASE" + +# Regular expression matching correct class constant names. Overrides class- +# const-naming-style. If left empty, class constant names will be checked with +# the set naming style. +# class-const-rgx = + +# Naming style matching correct class names. +class-naming-style = "PascalCase" + +# Regular expression matching correct class names. Overrides class-naming-style. +# If left empty, class names will be checked with the set naming style. +# class-rgx = + +# Naming style matching correct constant names. +const-naming-style = "UPPER_CASE" + +# Regular expression matching correct constant names. Overrides const-naming- +# style. If left empty, constant names will be checked with the set naming style. +# const-rgx = + +# Minimum line length for functions/classes that require docstrings, shorter ones +# are exempt. +docstring-min-length = -1 + +# Naming style matching correct function names. +function-naming-style = "snake_case" + +# Regular expression matching correct function names. Overrides function-naming- +# style. If left empty, function names will be checked with the set naming style. +# function-rgx = + +# Good variable names which should always be accepted, separated by a comma. +good-names = ["i", "j", "k", "ex", "Run", "_"] + +# Good variable names regexes, separated by a comma. If names match any regex, +# they will always be accepted +# good-names-rgxs = + +# Include a hint for the correct naming format with invalid-name. +# include-naming-hint = + +# Naming style matching correct inline iteration names. +inlinevar-naming-style = "any" + +# Regular expression matching correct inline iteration names. Overrides +# inlinevar-naming-style. If left empty, inline iteration names will be checked +# with the set naming style. +# inlinevar-rgx = + +# Naming style matching correct method names. +method-naming-style = "snake_case" + +# Regular expression matching correct method names. Overrides method-naming- +# style. If left empty, method names will be checked with the set naming style. +# method-rgx = + +# Naming style matching correct module names. +module-naming-style = "snake_case" + +# Regular expression matching correct module names. Overrides module-naming- +# style. If left empty, module names will be checked with the set naming style. +# module-rgx = + +# Colon-delimited sets of names that determine each other's naming style when the +# name regexes allow several styles. +# name-group = + +# Regular expression which should only match function or class names that do not +# require a docstring. +no-docstring-rgx = "^_" + +# List of decorators that produce properties, such as abc.abstractproperty. Add +# to this list to register other decorators that produce valid properties. These +# decorators are taken in consideration only for invalid-name. +property-classes = ["abc.abstractproperty"] + +# Regular expression matching correct type alias names. If left empty, type alias +# names will be checked with the set naming style. +# typealias-rgx = + +# Regular expression matching correct type variable names. If left empty, type +# variable names will be checked with the set naming style. +# typevar-rgx = + +# Naming style matching correct variable names. +variable-naming-style = "snake_case" + +# Regular expression matching correct variable names. Overrides variable-naming- +# style. If left empty, variable names will be checked with the set naming style. +# variable-rgx = + +[tool.pylint.classes] +# Warn about protected attribute access inside special methods +# check-protected-access-in-special-methods = + +# List of method names used to declare (i.e. assign) instance attributes. +defining-attr-methods = ["__init__", "__new__", "setUp", "asyncSetUp", "__post_init__"] + +# List of member names, which should be excluded from the protected access +# warning. +exclude-protected = ["_asdict", "_fields", "_replace", "_source", "_make", "os._exit"] + +# List of valid names for the first argument in a class method. +valid-classmethod-first-arg = ["cls"] + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg = ["mcs"] + +[tool.pylint.design] +# List of regular expressions of class ancestor names to ignore when counting +# public methods (see R0903) +# exclude-too-few-public-methods = + +# List of qualified class names to ignore when counting class parents (see R0901) +# ignored-parents = + +# Maximum number of arguments for function / method. +max-args = 10 + +# Maximum number of attributes for a class (see R0902). +max-attributes = 20 + +# Maximum number of boolean expressions in an if statement (see R0916). +max-bool-expr = 5 + +# Maximum number of branch for function / method body. +max-branches = 50 + +# Maximum number of locals for function / method body. +max-locals = 20 + +# Maximum number of parents for a class (see R0901). +max-parents = 7 + +# Maximum number of positional arguments for function / method. +max-positional-arguments = 10 + +# Maximum number of public methods for a class (see R0904). +max-public-methods = 100 + +# Maximum number of return / yield for function / method body. +max-returns = 15 + +# Maximum number of statements in function / method body. +max-statements = 500 + +# Minimum number of public methods for a class (see R0903). +min-public-methods = 2 + +[tool.pylint.exceptions] +# Exceptions that will emit a warning when caught. +overgeneral-exceptions = ["builtins.BaseException", "builtins.Exception"] + +[tool.pylint.format] +# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. +# expected-line-ending-format = + +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines = "^\\s*(# )??$" + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren = 2 + +# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 +# tab). +indent-string = " " + +# Maximum number of characters on a single line. +max-line-length = 160 + +# Maximum number of lines in a module. +max-module-lines = 5000 + +# Allow the body of a class to be on the same line as the declaration if body +# contains single statement. +# single-line-class-stmt = + +# Allow the body of an if to be on the same line as the test if there is no else. +# single-line-if-stmt = + +[tool.pylint.imports] +# List of modules that can be imported at any level, not just the top level one. +# allow-any-import-level = + +# Allow explicit reexports by alias from a package __init__. +# allow-reexport-from-package = + +# Allow wildcard imports from modules that define __all__. +# allow-wildcard-with-all = + +# Deprecated modules which should not be used, separated by a comma. +# deprecated-modules = + +# Output a graph (.gv or any supported image format) of external dependencies to +# the given file (report RP0402 must not be disabled). +# ext-import-graph = + +# Output a graph (.gv or any supported image format) of all (i.e. internal and +# external) dependencies to the given file (report RP0402 must not be disabled). +# import-graph = + +# Output a graph (.gv or any supported image format) of internal dependencies to +# the given file (report RP0402 must not be disabled). +# int-import-graph = + +# Force import order to recognize a module as part of the standard compatibility +# libraries. +# known-standard-library = + +# Force import order to recognize a module as part of a third party library. +known-third-party = ["enchant"] + +# Couples of modules and preferred modules, separated by a comma. +# preferred-modules = + +[tool.pylint.logging] +# The type of string formatting that logging methods do. `old` means using % +# formatting, `new` is for `{}` formatting. +logging-format-style = "old" + +# Logging modules to check that the string format arguments are in logging +# function parameter format. +logging-modules = ["logging"] + +[tool.pylint."messages control"] +# Only show warnings with the listed confidence levels. Leave empty to show all. +# Valid levels: HIGH, CONTROL_FLOW, INFERENCE, INFERENCE_FAILURE, UNDEFINED. +confidence = ["HIGH", "CONTROL_FLOW", "INFERENCE", "INFERENCE_FAILURE", "UNDEFINED"] + +# Disable the message, report, category or checker with the given id(s). You can +# either give multiple identifiers separated by comma (,) or put this option +# multiple times (only on the command line, not in the configuration file where +# it should appear only once). You can also use "--disable=all" to disable +# everything first and then re-enable specific checks. For example, if you want +# to run only the similarities checker, you can use "--disable=all +# --enable=similarities". If you want to run only the classes checker, but have +# no Warning level messages displayed, use "--disable=all --enable=classes +# --disable=W". +disable = ["raw-checker-failed", "bad-inline-option", "locally-disabled", "file-ignored", "suppressed-message", "useless-suppression", "deprecated-pragma", "use-implicit-booleaness-not-comparison-to-string", "use-implicit-booleaness-not-comparison-to-zero", "use-symbolic-message-instead"] + +# Enable the message, report, category or checker with the given id(s). You can +# either give multiple identifier separated by comma (,) or put this option +# multiple time (only on the command line, not in the configuration file where it +# should appear only once). See also the "--disable" option for examples. +# enable = + +[tool.pylint.method_args] +# List of qualified names (i.e., library.method) which require a timeout +# parameter e.g. 'requests.api.get,requests.api.post' +timeout-methods = ["requests.api.delete", "requests.api.get", "requests.api.head", "requests.api.options", "requests.api.patch", "requests.api.post", "requests.api.put", "requests.api.request"] + +[tool.pylint.miscellaneous] +# List of note tags to take in consideration, separated by a comma. +notes = ["FIXME", "XXX", "TODO"] + +# Regular expression of note tags to take in consideration. +# notes-rgx = + +[tool.pylint.refactoring] +# Maximum number of nested blocks for function / method body +max-nested-blocks = 5 + +# Complete name of functions that never returns. When checking for inconsistent- +# return-statements if a never returning function is called then it will be +# considered as an explicit return statement and no message will be printed. +never-returning-functions = ["sys.exit", "argparse.parse_error"] + +# Let 'consider-using-join' be raised when the separator to join on would be non- +# empty (resulting in expected fixes of the type: ``"- " + " - ".join(items)``) +suggest-join-with-non-empty-separator = true + +[tool.pylint.reports] +# Python expression which should return a score less than or equal to 10. You +# have access to the variables 'fatal', 'error', 'warning', 'refactor', +# 'convention', and 'info' which contain the number of messages in each category, +# as well as 'statement' which is the total number of statements analyzed. This +# score is used by the global evaluation report (RP0004). +evaluation = "max(0, 0 if fatal else 10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10))" + +# Template used to display messages. This is a python new-style format string +# used to format the message information. See doc for all details. +# msg-template = + +# Set the output format. Available formats are: 'text', 'parseable', 'colorized', +# 'json2' (improved json format), 'json' (old json format), msvs (visual studio) +# and 'github' (GitHub actions). You can also give a reporter class, e.g. +# mypackage.mymodule.MyReporterClass. +# output-format = + +# Tells whether to display a full report or only the messages. +# reports = + +# Activate the evaluation score. +score = true + +[tool.pylint.similarities] +# Comments are removed from the similarity computation +ignore-comments = true + +# Docstrings are removed from the similarity computation +ignore-docstrings = true + +# Imports are removed from the similarity computation +ignore-imports = true + +# Signatures are removed from the similarity computation +ignore-signatures = true + +# Minimum lines number of a similarity. +min-similarity-lines = 4 + +[tool.pylint.spelling] +# Limits count of emitted suggestions for spelling mistakes. +max-spelling-suggestions = 4 + +# Spelling dictionary name. Available dictionaries: en_AG (hunspell), en_AU +# (hunspell), en_BS (hunspell), en_BW (hunspell), en_BZ (hunspell), en_CA +# (hunspell), en_DK (hunspell), en_GB (hunspell), en_GH (hunspell), en_HK +# (hunspell), en_IE (hunspell), en_IN (hunspell), en_JM (hunspell), en_MW +# (hunspell), en_NA (hunspell), en_NG (hunspell), en_NZ (hunspell), en_PH +# (hunspell), en_SG (hunspell), en_TT (hunspell), en_US (hunspell), en_ZA +# (hunspell), en_ZM (hunspell), en_ZW (hunspell). +# spelling-dict = + +# List of comma separated words that should be considered directives if they +# appear at the beginning of a comment and should not be checked. +spelling-ignore-comment-directives = "fmt: on,fmt: off,noqa:,noqa,nosec,isort:skip,mypy:" + +# List of comma separated words that should not be checked. +# spelling-ignore-words = + +# A path to a file that contains the private dictionary; one word per line. +# spelling-private-dict-file = + +# Tells whether to store unknown words to the private dictionary (see the +# --spelling-private-dict-file option) instead of raising a message. +# spelling-store-unknown-words = + +[tool.pylint.typecheck] +# List of decorators that produce context managers, such as +# contextlib.contextmanager. Add to this list to register other decorators that +# produce valid context managers. +contextmanager-decorators = ["contextlib.contextmanager"] + +# List of members which are set dynamically and missed by pylint inference +# system, and so shouldn't trigger E1101 when accessed. Python regular +# expressions are accepted. +# generated-members = + +# Tells whether missing members accessed in mixin class should be ignored. A +# class is considered mixin if its name matches the mixin-class-rgx option. +# Tells whether to warn about missing members when the owner of the attribute is +# inferred to be None. +ignore-none = true + +# This flag controls whether pylint should warn about no-member and similar +# checks whenever an opaque object is returned when inferring. The inference can +# return multiple potential results while evaluating a Python object, but some +# branches might not be evaluated, which results in partial inference. In that +# case, it might be useful to still emit no-member and other checks for the rest +# of the inferred objects. +ignore-on-opaque-inference = true + +# List of symbolic message names to ignore for Mixin members. +ignored-checks-for-mixins = ["no-member", "not-async-context-manager", "not-context-manager", "attribute-defined-outside-init"] + +# List of class names for which member attributes should not be checked (useful +# for classes with dynamically set attributes). This supports the use of +# qualified names. +ignored-classes = ["optparse.Values", "thread._local", "_thread._local", "argparse.Namespace"] + +# Show a hint with possible names when a member name was not found. The aspect of +# finding the hint is based on edit distance. +missing-member-hint = true + +# The maximum edit distance a name should have in order to be considered a +# similar match for a missing member name. +missing-member-hint-distance = 1 + +# The total number of similar names that should be taken in consideration when +# showing a hint for a missing member. +missing-member-max-choices = 1 + +# Regex pattern to define which classes are considered mixins. +mixin-class-rgx = ".*[Mm]ixin" + +# List of decorators that change the signature of a decorated function. +# signature-mutators = + +[tool.pylint.variables] +# List of additional names supposed to be defined in builtins. Remember that you +# should avoid defining new builtins when possible. +# additional-builtins = + +# Tells whether unused global variables should be treated as a violation. +allow-global-unused-variables = true + +# List of names allowed to shadow builtins +# allowed-redefined-builtins = + +# List of strings which can identify a callback function by name. A callback name +# must start or end with one of those strings. +callbacks = ["cb_", "_cb"] + +# A regular expression matching the name of dummy variables (i.e. expected to not +# be used). +dummy-variables-rgx = "_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_" + +# Argument names that match this expression will be ignored. +ignored-argument-names = "_.*|^ignored_|^unused_" + +# Tells whether we should check for unused import in __init__ files. +# init-import = + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules = ["six.moves", "past.builtins", "future.builtins", "builtins", "io"] + + diff --git a/python/lammps/__init__.py b/python/lammps/__init__.py index 0cc658371f..e6b6994063 100644 --- a/python/lammps/__init__.py +++ b/python/lammps/__init__.py @@ -15,38 +15,39 @@ from .pylammps import * # lgtm [py/polluting-import] # convert installed module string version to numeric version def get_version_number(): - import time - from os.path import join - from sys import version_info + # pylint: disable=C0415 + import time + from os import path + from sys import version_info - # must report 0 when inside LAMMPS source tree - if __file__.find(join('python', 'lammps', '__init__.py')) > 0: - return 0 + # must report 0 when inside LAMMPS source tree + if __file__.find(path.join('python', 'lammps', '__init__.py')) > 0: + return 0 - if version_info.major < 3 or (version_info.major == 3 and version_info.minor < 6): - raise SystemError('LAMMPS only supports Python version 3.6 or later') + if version_info.major < 3 or (version_info.major == 3 and version_info.minor < 6): + raise SystemError('LAMMPS only supports Python version 3.6 or later') - vstring = None - if version_info.major == 3 and version_info.minor >= 8: - from importlib.metadata import version, PackageNotFoundError - try: - vstring = version('lammps') - except PackageNotFoundError: - # nothing to do, ignore - pass + vstring = None + if version_info.major == 3 and version_info.minor >= 8: + from importlib.metadata import version, PackageNotFoundError + try: + vstring = version('lammps') + except PackageNotFoundError: + # nothing to do, ignore + pass - else: - from pkg_resources import get_distribution, DistributionNotFound - try: - vstring = get_distribution('lammps').version - except DistributionNotFound: - # nothing to do, ignore - pass + else: + from pkg_resources import get_distribution, DistributionNotFound + try: + vstring = get_distribution('lammps').version + except DistributionNotFound: + # nothing to do, ignore + pass - if not vstring: - return 0 + if not vstring: + return 0 - t = time.strptime(vstring, "%Y.%m.%d") - return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday + t = time.strptime(vstring, "%Y.%m.%d") + return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday __version__ = get_version_number() diff --git a/python/lammps/core.py b/python/lammps/core.py index 473bf7f084..349ccf2e1e 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -12,11 +12,10 @@ # ------------------------------------------------------------------------- # Python wrapper for the LAMMPS library via ctypes -# for python2/3 compatibility - -from __future__ import print_function - +# avoid pylint warnings about naming conventions +# pylint: disable=C0103 import os +import platform from ctypes import CDLL, POINTER, RTLD_GLOBAL, CFUNCTYPE, py_object, byref, cast, sizeof, \ create_string_buffer, c_int, c_int32, c_int64, c_double, c_void_p, c_char_p, c_char, \ pythonapi @@ -58,15 +57,11 @@ class ExceptionCheck: # ------------------------------------------------------------------------- -class command_wrapper(object): +class command_wrapper: def __init__(self, lmp): self.lmp = lmp self.auto_flush = False - def lmp_print(self, s): - """ needed for Python2 compatibility, since print is a reserved keyword """ - return self.__getattr__("print")(s) - def __dir__(self): return sorted(set(['angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'atom_style', 'bond_coeff', 'bond_style', 'boundary', 'change_box', 'communicate', 'compute', @@ -81,19 +76,21 @@ class command_wrapper(object): 'variable', 'velocity', 'write_restart'] + self.lmp.available_styles("command"))) def _wrap_args(self, x): - if callable(x): - import hashlib - import __main__ - sha = hashlib.sha256() - sha.update(str(x).encode()) - func_name = f"_lmp_cb_{sha.hexdigest()}" - def handler(*args, **kwargs): - args = list(args) - args[0] = lammps(ptr=args[0]) - x(*args) - setattr(__main__, func_name, handler) - return func_name + if callable(x): + # pylint: disable=C0415 + import hashlib + import __main__ + sha = hashlib.sha256() + sha.update(str(x).encode()) + func_name = f"_lmp_cb_{sha.hexdigest()}" + def handler(*args, **kwargs): + args = list(args) + args[0] = lammps(ptr=args[0]) + x(*args) + setattr(__main__, func_name, handler) + return func_name return x + return None def __getattr__(self, name): """ @@ -114,22 +111,22 @@ class command_wrapper(object): cmd_args = [name] + [str(self._wrap_args(x)) for x in args] # Python 3.6+ maintains ordering of kwarg keys - for k in kwargs.keys(): - cmd_args.append(k) - if type(kwargs[k]) == bool: - cmd_args.append("true" if kwargs[k] else "false") - else: - cmd_args.append(str(self._wrap_args(kwargs[k]))) + for kw, arg in kwargs.items(): + cmd_args.append(kw) + if isinstance(arg,bool): + cmd_args.append("true" if arg else "false") + else: + cmd_args.append(str(self._wrap_args(arg))) cmd = ' '.join(cmd_args) self.lmp.command(cmd) if self.auto_flush: - self.lmp.flush_buffers() + self.lmp.flush_buffers() return handler # ------------------------------------------------------------------------- -class lammps(object): +class lammps: """Create an instance of the LAMMPS Python class. .. _mpi4py_docs: https://mpi4py.readthedocs.io/ @@ -169,7 +166,7 @@ class lammps(object): # for windows installers the shared library is in a different folder winpath = abspath(os.path.join(modpath,'..','..','bin')) # allow override for running tests on Windows - if (os.environ.get("LAMMPSDLLPATH")): + if os.environ.get("LAMMPSDLLPATH"): winpath = os.environ.get("LAMMPSDLLPATH") self.lib = None self.lmp = None @@ -183,7 +180,8 @@ class lammps(object): # load a shared object. try: - if ptr is not None: self.lib = CDLL("",RTLD_GLOBAL) + if ptr is not None: + self.lib = CDLL("",RTLD_GLOBAL) except OSError: self.lib = None @@ -196,21 +194,17 @@ class lammps(object): # typically requires LD_LIBRARY_PATH to be set appropriately # guess shared library extension based on OS, if not inferred from actual file - if any([f.startswith('liblammps') and f.endswith('.dylib') - for f in os.listdir(modpath)]): + if any(f.startswith('liblammps') and f.endswith('.dylib') for f in os.listdir(modpath)): lib_ext = ".dylib" - elif any([f.startswith('liblammps') and f.endswith('.dll') - for f in os.listdir(modpath)]): + elif any(f.startswith('liblammps') and f.endswith('.dll') for f in os.listdir(modpath)): lib_ext = ".dll" - elif os.path.exists(winpath) and any([f.startswith('liblammps') and f.endswith('.dll') - for f in os.listdir(winpath)]): + elif os.path.exists(winpath) and \ + any(f.startswith('liblammps') and f.endswith('.dll') for f in os.listdir(winpath)): lib_ext = ".dll" modpath = winpath - elif any([f.startswith('liblammps') and f.endswith('.so') - for f in os.listdir(modpath)]): + elif any(f.startswith('liblammps') and f.endswith('.so') for f in os.listdir(modpath)): lib_ext = ".so" else: - import platform if platform.system() == "Darwin": lib_ext = ".dylib" elif platform.system() == "Windows": @@ -220,14 +214,14 @@ class lammps(object): if not self.lib: if name: - libpath = join(modpath,"liblammps_%s" % name + lib_ext) + libpath = join(modpath,f'liblammps_{name + lib_ext}') else: - libpath = join(modpath,"liblammps" + lib_ext) + libpath = join(modpath,'liblammps' + lib_ext) if not os.path.isfile(libpath): if name: - libpath = "liblammps_%s" % name + lib_ext + libpath = f'liblammps_{name + lib_ext}' else: - libpath = "liblammps" + lib_ext + libpath = 'liblammps' + lib_ext self.lib = CDLL(libpath,RTLD_GLOBAL) # declare all argument and return types for all library methods here. @@ -442,10 +436,11 @@ class lammps(object): # only needed if LAMMPS has been compiled with MPI support. self.has_mpi4py = False if self.has_mpi_support: + # pylint: disable=C0415 try: from mpi4py import __version__ as mpi4py_version # tested to work with mpi4py versions 2, 3, and 4 - self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3','4'] + self.has_mpi4py = mpi4py_version.split('.',maxsplit=1)[0] in ['2','3','4'] except ImportError: # ignore failing import pass @@ -464,14 +459,16 @@ class lammps(object): # need to adjust for type of MPI communicator object # allow for int (like MPICH) or void* (like OpenMPI) if self.has_mpi_support and self.has_mpi4py: + # pylint: disable=C0415 from mpi4py import MPI self.MPI = MPI if comm is not None: + # pylint: disable=I1101 if not self.has_mpi_support: - raise Exception('LAMMPS not compiled with real MPI library') + raise RuntimeError('LAMMPS not compiled with real MPI library') if not self.has_mpi4py: - raise Exception('Python mpi4py version is not 2, 3, or 4') + raise RuntimeError('Python mpi4py version is not 2, 3, or 4') if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int): MPI_Comm = c_int else: @@ -479,7 +476,7 @@ class lammps(object): # Detect whether LAMMPS and mpi4py definitely use different MPI libs if sizeof(MPI_Comm) != self.lib.lammps_config_has_mpi_support(): - raise Exception('Inconsistent MPI library in LAMMPS and mpi4py') + raise RuntimeError('Inconsistent MPI library in LAMMPS and mpi4py') narg = 0 cargs = None @@ -487,9 +484,9 @@ class lammps(object): myargs = ["lammps".encode()] narg = len(cmdargs) + 1 for arg in cmdargs: - if type(arg) is str: + if isinstance(arg,str): myargs.append(arg.encode()) - elif type(arg) is bytes: + elif isinstance(arg,bytes): myargs.append(arg) else: raise TypeError('Unsupported cmdargs type ', type(arg)) @@ -506,15 +503,16 @@ class lammps(object): else: if self.has_mpi4py and self.has_mpi_support: + # pylint: disable=I1101 self.comm = self.MPI.COMM_WORLD self.opened = 1 if cmdargs is not None: myargs = ["lammps".encode()] narg = len(cmdargs) + 1 for arg in cmdargs: - if type(arg) is str: + if isinstance(arg,str): myargs.append(arg.encode()) - elif type(arg) is bytes: + elif isinstance(arg,bytes): myargs.append(arg) else: raise TypeError('Unsupported cmdargs type ', type(arg)) @@ -535,7 +533,7 @@ class lammps(object): # check if library initilialization failed if not self.lmp: - raise(RuntimeError("Failed to initialize LAMMPS object")) + raise RuntimeError("Failed to initialize LAMMPS object") # optional numpy support (lazy loading) self._numpy = None @@ -545,14 +543,16 @@ class lammps(object): # check if liblammps version matches the installed python module version # but not for in-place usage, i.e. when the version is 0 - import lammps - if lammps.__version__ > 0 and lammps.__version__ != self.lib.lammps_version(self.lmp): - raise(AttributeError("LAMMPS Python module installed for LAMMPS version %d, but shared library is version %d" \ - % (lammps.__version__, self.lib.lammps_version(self.lmp)))) + # pylint: disable=C0415 disable=C0209 + import lammps as mylammps + if mylammps.__version__ > 0 and mylammps.__version__ != self.lib.lammps_version(self.lmp): + raise AttributeError("LAMMPS Python module installed for LAMMPS version %d, but shared library is version %d" \ + % (mylammps.__version__, self.lib.lammps_version(self.lmp))) # add way to insert Python callback for fix external self.callback = {} - self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double))) + self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, \ + POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double))) self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object] self.lib.lammps_set_fix_external_callback.restype = None @@ -585,6 +585,7 @@ class lammps(object): :rtype: numpy_wrapper """ if not self._numpy: + # pylint: disable=C0415 from .numpy_wrapper import numpy_wrapper self._numpy = numpy_wrapper(self) return self._numpy @@ -640,6 +641,7 @@ class lammps(object): :rtype: ipython.wrapper """ if not self._ipython: + # pylint: disable=C0415 from .ipython import wrapper self._ipython = wrapper(self) return self._ipython @@ -687,8 +689,10 @@ class lammps(object): :param error_text: :type error_text: string """ - if error_text: new_error_text = error_text.encode() - else: new_error_text = "(unknown error)".encode() + if error_text: + new_error_text = error_text.encode() + else: + new_error_text = "(unknown error)".encode() with ExceptionCheck(self): self.lib.lammps_error(self.lmp, error_type, new_error_text) @@ -735,12 +739,12 @@ class lammps(object): """ if self.has_mpi4py and self.has_mpi_support: - from mpi4py import MPI - f_comm = self.lib.lammps_get_mpi_comm(self.lmp) - c_comm = MPI.Comm.f2py(f_comm) - return c_comm - else: - return None + # pylint: disable=I1101 disable=C0415 + from mpi4py import MPI + f_comm = self.lib.lammps_get_mpi_comm(self.lmp) + c_comm = MPI.Comm.f2py(f_comm) + return c_comm + return None # ------------------------------------------------------------------------- @@ -767,8 +771,10 @@ class lammps(object): :return: expanded string :rtype: string """ - if line: newline = line.encode() - else: return None + if line: + newline = line.encode() + else: + return None with ExceptionCheck(self): strptr = self.lib.lammps_expand(self.lmp, newline) @@ -797,8 +803,10 @@ class lammps(object): :param path: Name of the file/path with LAMMPS commands :type path: string """ - if path: newpath = path.encode() - else: return + if path: + newpath = path.encode() + else: + return with ExceptionCheck(self): self.lib.lammps_file(self.lmp, newpath) @@ -814,8 +822,10 @@ class lammps(object): :param cmd: a single lammps command :type cmd: string """ - if cmd: newcmd = cmd.encode() - else: return + if cmd: + newcmd = cmd.encode() + else: + return with ExceptionCheck(self): self.lib.lammps_command(self.lmp, newcmd) @@ -832,7 +842,7 @@ class lammps(object): :param cmdlist: a single lammps command :type cmdlist: list of strings """ - cmds = [x.encode() for x in cmdlist if type(x) is str] + cmds = [x.encode() for x in cmdlist if isinstance(x,str)] narg = len(cmdlist) args = (c_char_p * narg)(*cmds) self.lib.lammps_commands_list.argtypes = [c_void_p, c_int, c_char_p * narg] @@ -852,8 +862,10 @@ class lammps(object): :param multicmd: text block of lammps commands :type multicmd: string """ - if type(multicmd) is str: newmulticmd = multicmd.encode() - else: newmulticmd = multicmd + if isinstance(multicmd,str): + newmulticmd = multicmd.encode() + else: + newmulticmd = multicmd with ExceptionCheck(self): self.lib.lammps_commands_string(self.lmp,c_char_p(newmulticmd)) @@ -942,8 +954,10 @@ class lammps(object): :return: value of thermo keyword :rtype: double or None """ - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None with ExceptionCheck(self): return self.lib.lammps_get_thermo(self.lmp, newname) @@ -972,7 +986,7 @@ class lammps(object): :rtype: dict or None """ - rv = dict() + rv = {} mystep = self.last_thermo_step if mystep < 0: return None @@ -1020,8 +1034,10 @@ class lammps(object): :return: value of the setting :rtype: int """ - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None return int(self.lib.lammps_extract_setting(self.lmp, newname)) # ------------------------------------------------------------------------- @@ -1043,8 +1059,10 @@ class lammps(object): :return: data type of global property, see :ref:`py_datatype_constants` :rtype: int """ - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None return self.lib.lammps_extract_global_datatype(self.lmp, newname) # ------------------------------------------------------------------------- @@ -1089,8 +1107,10 @@ class lammps(object): else: veclen = 1 - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None if dtype == LAMMPS_INT: self.lib.lammps_extract_global.restype = POINTER(c_int32) @@ -1116,7 +1136,7 @@ class lammps(object): for i in range(0,veclen): result.append(target_type(ptr[i])) return result - else: return target_type(ptr[0]) + return target_type(ptr[0]) return None # ------------------------------------------------------------------------- @@ -1145,8 +1165,7 @@ class lammps(object): if dim < 0: return None - else: - return dim; + return dim # ------------------------------------------------------------------------- # get access to pair style extractable data @@ -1178,7 +1197,7 @@ class lammps(object): dim = self.extract_pair_dimension(name) if dim is None: return None - elif dim == 0: + if dim == 0: self.lib.lammps_extract_pair.restype = POINTER(c_double) elif dim == 1: self.lib.lammps_extract_pair.restype = POINTER(c_double) @@ -1192,12 +1211,12 @@ class lammps(object): if ptr: if dim == 0: return float(ptr[0]) - elif dim == 1: + if dim == 1: result = [0.0] for i in range(1,ntypes+1): result.append(float(ptr[i])) return result - elif dim == 2: + if dim == 2: result = [] inner = [] for i in range(0,ntypes+1): @@ -1209,26 +1228,25 @@ class lammps(object): inner.append(float(ptr[i][j])) result.append(inner) return result - else: - return None + return None return None # ------------------------------------------------------------------------- # map global atom ID to local atom index - def map_atom(self, id): + def map_atom(self, atomid): """Map a global atom ID (aka tag) to the local atom index This is a wrapper around the :cpp:func:`lammps_map_atom` function of the C-library interface. - :param id: atom ID - :type id: int + :param atomid: atom ID + :type atomid: int :return: local index :rtype: int """ - tag = self.c_tagint(id) + tag = self.c_tagint(atomid) return self.lib.lammps_map_atom(self.lmp, byref(tag)) # ------------------------------------------------------------------------- @@ -1250,8 +1268,10 @@ class lammps(object): :return: data type of per-atom property (see :ref:`py_datatype_constants`) :rtype: int """ - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None return self.lib.lammps_extract_atom_datatype(self.lmp, newname) # ------------------------------------------------------------------------- @@ -1278,8 +1298,10 @@ class lammps(object): :return: data type of per-atom property (see :ref:`py_datatype_constants`) :rtype: int """ - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None return self.lib.lammps_extract_atom_size(self.lmp, newname, dtype) # ------------------------------------------------------------------------- @@ -1322,8 +1344,10 @@ class lammps(object): if dtype == LAMMPS_AUTODETECT: dtype = self.extract_atom_datatype(name) - if name: newname = name.encode() - else: return None + if name: + newname = name.encode() + else: + return None if dtype == LAMMPS_INT: self.lib.lammps_extract_atom.restype = POINTER(c_int32) @@ -1340,9 +1364,9 @@ class lammps(object): else: return None ptr = self.lib.lammps_extract_atom(self.lmp, newname) - if ptr: return ptr - else: return None - + if ptr: + return ptr + return None # ------------------------------------------------------------------------- @@ -1367,8 +1391,10 @@ class lammps(object): :return: requested data as scalar, pointer to 1d or 2d double array, or None :rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType """ - if cid: newcid = cid.encode() - else: return None + if cid: + newcid = cid.encode() + else: + return None if ctype == LMP_TYPE_SCALAR: if cstyle == LMP_STYLE_GLOBAL: @@ -1376,9 +1402,9 @@ class lammps(object): with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype) return ptr[0] - elif cstyle == LMP_STYLE_ATOM: + if cstyle == LMP_STYLE_ATOM: return None - elif cstyle == LMP_STYLE_LOCAL: + if cstyle == LMP_STYLE_LOCAL: self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype) @@ -1397,14 +1423,14 @@ class lammps(object): return ptr elif ctype == LMP_SIZE_COLS: - if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL: + if cstyle in (LMP_STYLE_GLOBAL,LMP_STYLE_ATOM,LMP_STYLE_LOCAL): self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype) return ptr[0] - elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS: - if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL: + elif ctype in (LMP_SIZE_VECTOR,LMP_SIZE_ROWS): + if cstyle in (LMP_STYLE_GLOBAL,LMP_STYLE_LOCAL): self.lib.lammps_extract_compute.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype) @@ -1452,8 +1478,10 @@ class lammps(object): :rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType """ - if fid: newfid = fid.encode() - else: return None + if fid: + newfid = fid.encode() + else: + return None if fstyle == LMP_STYLE_GLOBAL: if ftype in (LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY): @@ -1463,15 +1491,14 @@ class lammps(object): result = ptr[0] self.lib.lammps_free(ptr) return result - elif ftype in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS): + if ftype in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS): self.lib.lammps_extract_fix.restype = POINTER(c_int) with ExceptionCheck(self): ptr = self.lib.lammps_extract_fix(self.lmp,newfid,fstyle,ftype,nrow,ncol) return ptr[0] - else: - return None + return None - elif fstyle == LMP_STYLE_ATOM: + if fstyle == LMP_STYLE_ATOM: if ftype == LMP_TYPE_VECTOR: self.lib.lammps_extract_fix.restype = POINTER(c_double) elif ftype == LMP_TYPE_ARRAY: @@ -1484,10 +1511,9 @@ class lammps(object): ptr = self.lib.lammps_extract_fix(self.lmp,newfid,fstyle,ftype,nrow,ncol) if ftype == LMP_SIZE_COLS: return ptr[0] - else: - return ptr + return ptr - elif fstyle == LMP_STYLE_LOCAL: + if fstyle == LMP_STYLE_LOCAL: if ftype == LMP_TYPE_VECTOR: self.lib.lammps_extract_fix.restype = POINTER(c_double) elif ftype == LMP_TYPE_ARRAY: @@ -1500,10 +1526,8 @@ class lammps(object): ptr = self.lib.lammps_extract_fix(self.lmp,newfid,fstyle,ftype,nrow,ncol) if ftype in (LMP_TYPE_VECTOR, LMP_TYPE_ARRAY): return ptr - else: - return ptr[0] - else: - return None + return ptr[0] + return None # ------------------------------------------------------------------------- # extract variable info @@ -1538,32 +1562,40 @@ class lammps(object): :return: the requested data :rtype: c_double, (c_double), or NoneType """ - if name: newname = name.encode() - else: return None - if group: newgroup = group.encode() - else: newgroup = None + if name: + newname = name.encode() + else: + return None + if group: + newgroup = group.encode() + else: + newgroup = None if vartype is None : vartype = self.lib.lammps_extract_variable_datatype(self.lmp, newname) if vartype == LMP_VAR_EQUAL: self.lib.lammps_extract_variable.restype = POINTER(c_double) with ExceptionCheck(self): ptr = self.lib.lammps_extract_variable(self.lmp, newname, newgroup) - if ptr: result = ptr[0] - else: return None + if ptr: + result = ptr[0] + else: + return None self.lib.lammps_free(ptr) return result - elif vartype == LMP_VAR_ATOM: + if vartype == LMP_VAR_ATOM: nlocal = self.extract_global("nlocal") result = (c_double*nlocal)() self.lib.lammps_extract_variable.restype = POINTER(c_double) with ExceptionCheck(self): ptr = self.lib.lammps_extract_variable(self.lmp, newname, newgroup) if ptr: - for i in range(nlocal): result[i] = ptr[i] + for i in range(nlocal): + result[i] = ptr[i] self.lib.lammps_free(ptr) - else: return None + else: + return None return result - elif vartype == LMP_VAR_VECTOR : + if vartype == LMP_VAR_VECTOR : nvector = 0 self.lib.lammps_extract_variable.restype = POINTER(c_int) ptr = self.lib.lammps_extract_variable(self.lmp, newname, @@ -1581,9 +1613,8 @@ class lammps(object): result[i] = values[i] # do NOT free the values pointer (points to internal vector data) return result - else: - return None - elif vartype == LMP_VAR_STRING : + return None + if vartype == LMP_VAR_STRING : self.lib.lammps_extract_variable.restype = c_char_p with ExceptionCheck(self) : ptr = self.lib.lammps_extract_variable(self.lmp, newname, newgroup) @@ -1592,7 +1623,7 @@ class lammps(object): # ------------------------------------------------------------------------- - def clearstep_compute(self, nextstep): + def clearstep_compute(self): with ExceptionCheck(self): return self.lib.lammps_clearstep_compute(self.lmp) @@ -1637,10 +1668,14 @@ class lammps(object): :return: either 0 on success or -1 on failure :rtype: int """ - if name: newname = name.encode() - else: return -1 - if value: newvalue = str(value).encode() - else: return -1 + if name: + newname = name.encode() + else: + return -1 + if value: + newvalue = str(value).encode() + else: + return -1 with ExceptionCheck(self): return self.lib.lammps_set_variable(self.lmp, newname, newvalue) @@ -1661,10 +1696,14 @@ class lammps(object): :return: either 0 on success or -1 on failure :rtype: int """ - if name: newname = name.encode() - else: return -1 - if value: newvalue = str(value).encode() - else: return -1 + if name: + newname = name.encode() + else: + return -1 + if value: + newvalue = str(value).encode() + else: + return -1 with ExceptionCheck(self): return self.lib.lammps_set_string_variable(self.lmp,newname,newvalue) @@ -1685,8 +1724,10 @@ class lammps(object): :return: either 0 on success or -1 on failure :rtype: int """ - if name: newname = name.encode() - else: return -1 + if name: + newname = name.encode() + else: + return -1 with ExceptionCheck(self): return self.lib.lammps_set_internal_variable(self.lmp,newname,value) @@ -1707,8 +1748,10 @@ class lammps(object): :rtype: c_double """ - if expr: newexpr = expr.encode() - else: return None + if expr: + newexpr = expr.encode() + else: + return None with ExceptionCheck(self): return self.lib.lammps_eval(self.lmp, newexpr) @@ -1725,8 +1768,10 @@ class lammps(object): # e.g. for Python list or NumPy or ctypes def gather_atoms(self,name,dtype,count): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None natoms = self.get_natoms() with ExceptionCheck(self): if dtype == 0: @@ -1742,8 +1787,10 @@ class lammps(object): # ------------------------------------------------------------------------- def gather_atoms_concat(self,name,dtype,count): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None natoms = self.get_natoms() with ExceptionCheck(self): if dtype == 0: @@ -1753,12 +1800,14 @@ class lammps(object): data = ((count*natoms)*c_double)() self.lib.lammps_gather_atoms_concat(self.lmp,newname,dtype,count,data) else: - return None + return None return data def gather_atoms_subset(self,name,dtype,count,ndata,ids): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None with ExceptionCheck(self): if dtype == 0: data = ((count*ndata)*c_int)() @@ -1782,16 +1831,20 @@ class lammps(object): # e.g. for Python list or NumPy or ctypes def scatter_atoms(self,name,dtype,count,data): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None with ExceptionCheck(self): self.lib.lammps_scatter_atoms(self.lmp,newname,dtype,count,data) # ------------------------------------------------------------------------- def scatter_atoms_subset(self,name,dtype,count,ndata,ids,data): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None with ExceptionCheck(self): self.lib.lammps_scatter_atoms_subset(self.lmp,newname,dtype,count,ndata,ids,data) @@ -1815,9 +1868,9 @@ class lammps(object): """ nbonds = self.extract_global("nbonds") with ExceptionCheck(self): - data = ((3*nbonds)*self.c_tagint)() - self.lib.lammps_gather_bonds(self.lmp,data) - return nbonds,data + data = ((3*nbonds)*self.c_tagint)() + self.lib.lammps_gather_bonds(self.lmp,data) + return nbonds,data # ------------------------------------------------------------------------- @@ -1838,9 +1891,9 @@ class lammps(object): """ nangles = self.extract_global("nangles") with ExceptionCheck(self): - data = ((4*nangles)*self.c_tagint)() - self.lib.lammps_gather_angles(self.lmp,data) - return nangles,data + data = ((4*nangles)*self.c_tagint)() + self.lib.lammps_gather_angles(self.lmp,data) + return nangles,data # ------------------------------------------------------------------------- @@ -1861,9 +1914,9 @@ class lammps(object): """ ndihedrals = self.extract_global("ndihedrals") with ExceptionCheck(self): - data = ((5*ndihedrals)*self.c_tagint)() - self.lib.lammps_gather_dihedrals(self.lmp,data) - return ndihedrals,data + data = ((5*ndihedrals)*self.c_tagint)() + self.lib.lammps_gather_dihedrals(self.lmp,data) + return ndihedrals,data # ------------------------------------------------------------------------- @@ -1884,9 +1937,9 @@ class lammps(object): """ nimpropers = self.extract_global("nimpropers") with ExceptionCheck(self): - data = ((5*nimpropers)*self.c_tagint)() - self.lib.lammps_gather_impropers(self.lmp,data) - return nimpropers,data + data = ((5*nimpropers)*self.c_tagint)() + self.lib.lammps_gather_impropers(self.lmp,data) + return nimpropers,data # ------------------------------------------------------------------------- @@ -1899,8 +1952,10 @@ class lammps(object): # NOTE: need to ensure are converting to/from correct Python type # e.g. for Python list or NumPy or ctypes def gather(self,name,dtype,count): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None natoms = self.get_natoms() with ExceptionCheck(self): if dtype == 0: @@ -1914,8 +1969,10 @@ class lammps(object): return data def gather_concat(self,name,dtype,count): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None natoms = self.get_natoms() with ExceptionCheck(self): if dtype == 0: @@ -1929,8 +1986,10 @@ class lammps(object): return data def gather_subset(self,name,dtype,count,ndata,ids): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None with ExceptionCheck(self): if dtype == 0: data = ((count*ndata)*c_int)() @@ -1952,14 +2011,18 @@ class lammps(object): # e.g. for Python list or NumPy or ctypes def scatter(self,name,dtype,count,data): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None with ExceptionCheck(self): self.lib.lammps_scatter(self.lmp,newname,dtype,count,data) def scatter_subset(self,name,dtype,count,ndata,ids,data): - if name: newname = name.encode() - else: newname = None + if name: + newname = name.encode() + else: + newname = None with ExceptionCheck(self): self.lib.lammps_scatter_subset(self.lmp,newname,dtype,count,ndata,ids,data) @@ -2006,15 +2069,15 @@ class lammps(object): # create N atoms on all procs # N = global number of atoms - # id = ID of each atom (optional, can be None) - # type = type of each atom (1 to Ntypes) (required) + # atomid = ID of each atom (optional, can be None) + # atype = type of each atom (1 to Ntypes) (required) # x = coords of each atom as (N,3) array (required) # v = velocity of each atom as (N,3) array (optional, can be None) # NOTE: how could we ensure are passing correct type to LAMMPS # e.g. for Python list or NumPy, etc # ditto for gather_atoms() above - def create_atoms(self,n,id,type,x,v=None,image=None,shrinkexceed=False): + def create_atoms(self,n,atomid,atype,x,v=None,image=None,shrinkexceed=False): """ Create N atoms from list of coordinates and properties @@ -2034,10 +2097,10 @@ class lammps(object): :param n: number of atoms for which data is provided :type n: int - :param id: list of atom IDs with at least n elements or None - :type id: list of lammps.tagint - :param type: list of atom types - :type type: list of int + :param atomid: list of atom IDs with at least n elements or None + :type atomid: list of lammps.tagint + :param atype: list of atom types + :type atype: list of int :param x: list of coordinates for x-, y-, and z (flat list of 3n entries) :type x: list of float :param v: list of velocities for x-, y-, and z (flat list of 3n entries) or None (optional) @@ -2049,10 +2112,10 @@ class lammps(object): :return: number of atoms created. 0 if insufficient or invalid data :rtype: int """ - if id is not None: + if atomid is not None: id_lmp = (self.c_tagint*n)() try: - id_lmp[:] = id[0:n] + id_lmp[:] = atomid[0:n] except ValueError: return 0 else: @@ -2060,7 +2123,7 @@ class lammps(object): type_lmp = (c_int*n)() try: - type_lmp[:] = type[0:n] + type_lmp[:] = atype[0:n] except ValueError: return 0 @@ -2103,7 +2166,7 @@ class lammps(object): # ------------------------------------------------------------------------- - def create_molecule(self, id, jsonstr): + def create_molecule(self, molid, jsonstr): """ Create new molecule template from string with JSON data .. versionadded:: TBD @@ -2111,15 +2174,19 @@ class lammps(object): This is a wrapper around the :cpp:func:`lammps_create_molecule` function of the library interface. - :param id: molecule-id of the new molecule template + :param molid: molecule-id of the new molecule template :type name: string :param jsonstr: JSON data defining a new molecule template :type jsonstr: string """ - if id: newid = id.encode() - else: newid = None - if id: newjsonstr = jsonstr.encode() - else: newjsonstr = None + if molid: + newid = molid.encode() + else: + newid = None + if jsonstr: + newjsonstr = jsonstr.encode() + else: + newjsonstr = None with ExceptionCheck(self): self.lib.lammps_create_molecule(self.lmp, newid, newjsonstr) @@ -2476,7 +2543,7 @@ class lammps(object): # ------------------------------------------------------------------------- - def available_plugins(self, category): + def available_plugins(self, category=None): """Returns a list of plugins available for a given category .. versionadded:: 10Mar2021 @@ -2494,7 +2561,8 @@ class lammps(object): nam = create_string_buffer(LMP_BUFSIZE) for idx in range(num): self.lib.lammps_plugin_name(idx, sty, nam, LMP_BUFSIZE) - available_plugins.append([sty.value.decode(), nam.value.decode()]) + if not category or (category == sty.value): + available_plugins.append([sty.value.decode(), nam.value.decode()]) return available_plugins # ------------------------------------------------------------------------- @@ -2618,7 +2686,7 @@ class lammps(object): nlocal = self.extract_setting('nlocal') if len(eatom) < nlocal: - raise Exception('per-atom energy list length must be at least nlocal') + raise ValueError('per-atom energy list length must be at least nlocal') ceatom = (nlocal*c_double)(*eatom) with ExceptionCheck(self): return self.lib.lammps_fix_external_set_energy_peratom(self.lmp, fix_id.encode(), ceatom) @@ -2642,16 +2710,16 @@ class lammps(object): # copy virial data to C compatible buffer nlocal = self.extract_setting('nlocal') if len(vatom) < nlocal: - raise Exception('per-atom virial first dimension must be at least nlocal') + raise ValueError('per-atom virial first dimension must be at least nlocal') if len(vatom[0]) != 6: - raise Exception('per-atom virial second dimension must be 6') - vbuf = (c_double * 6) + raise ValueError('per-atom virial second dimension must be 6') + vbuf = c_double * 6 vptr = POINTER(c_double) c_virial = (vptr * nlocal)() for i in range(nlocal): - c_virial[i] = vbuf() - for j in range(6): - c_virial[i][j] = vatom[i][j] + c_virial[i] = vbuf() + for j in range(6): + c_virial[i][j] = vatom[i][j] with ExceptionCheck(self): return self.lib.lammps_fix_external_set_virial_peratom(self.lmp, fix_id.encode(), c_virial) @@ -2708,7 +2776,7 @@ class lammps(object): :rtype: NeighList """ if idx < 0: - return None + return None return NeighList(self, idx) # ------------------------------------------------------------------------- diff --git a/python/lammps/pylammps.py b/python/lammps/pylammps.py index bd058943c8..22e47d21fb 100644 --- a/python/lammps/pylammps.py +++ b/python/lammps/pylammps.py @@ -16,10 +16,6 @@ # Written by Richard Berger ################################################################################ -# for python2/3 compatibility - -from __future__ import print_function - import io import os import re @@ -130,10 +126,10 @@ class AtomList(object): :rtype: Atom or Atom2D """ if index not in self._loaded: - if self.dimensions == 2: - atom = Atom2D(self._pylmp, index) - else: - atom = Atom(self._pylmp, index) + if self.dimensions == 2: + atom = Atom2D(self._pylmp, index) + else: + atom = Atom(self._pylmp, index) self._loaded[index] = atom return self._loaded[index] @@ -762,7 +758,7 @@ class PyLammps(object): if self.comm_me > 0: raise Exception("PyLammps.eval() may only be used on MPI rank 0") - value = self.lmp_print('"$(%s)"' % expr).strip() + value = print('"$(%s)"' % expr).strip() try: return float(value) except ValueError: @@ -847,10 +843,6 @@ class PyLammps(object): elements.append(element) return elements - def lmp_print(self, s): - """ needed for Python2 compatibility, since print is a reserved keyword """ - return self.__getattr__("print")(s) - def __dir__(self): return sorted(set(['angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'atom_style', 'bond_coeff', 'bond_style', 'boundary', 'change_box', 'communicate', 'compute', diff --git a/unittest/python/python-commands.py b/unittest/python/python-commands.py index 06dcacd412..d58998109e 100644 --- a/unittest/python/python-commands.py +++ b/unittest/python/python-commands.py @@ -122,7 +122,7 @@ create_atoms 1 single & x = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.5 ] types = [1, 1] - self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) + self.assertEqual(self.lmp.create_atoms(2, atomid=None, atype=types, x=x), 2) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 2) @@ -167,7 +167,7 @@ create_atoms 1 single & tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] - self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) @@ -207,7 +207,7 @@ create_atoms 1 single & tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] - self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) @@ -237,7 +237,7 @@ create_atoms 1 single & tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] - self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) @@ -276,7 +276,7 @@ create_atoms 1 single & tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] - self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) @@ -310,7 +310,7 @@ create_atoms 1 single & tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 2, 2, 2] - self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) @@ -378,7 +378,7 @@ create_atoms 1 single & tags = [1, 2, 3, 4, 5, 6, 7] types = [1, 1, 1, 1, 1, 1, 1] - self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7) + self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7) nlocal = self.lmp.extract_global("nlocal") self.assertEqual(nlocal, 7) @@ -522,7 +522,7 @@ create_atoms 1 single & types = [1, 1] - self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2) + self.assertEqual(self.lmp.create_atoms(2, atomid=None, atype=types, x=x), 2) self.lmp.command("variable a atom x*x+y*y+z*z") a = self.lmp.extract_variable("a", "all", LMP_VAR_ATOM) self.assertEqual(a[0], x[0]*x[0]+x[1]*x[1]+x[2]*x[2]) @@ -573,7 +573,7 @@ create_atoms 1 single & ] types = [1, 1] - self.lmp.create_atoms(2, id=None, type=types, x=x) + self.lmp.create_atoms(2, atomid=None, atype=types, x=x) state = { "step": 0, @@ -611,7 +611,7 @@ create_atoms 1 single & 1.5, 1.5, 1.5 ] types = [1, 1] - self.lmp.create_atoms(2, id=None, type=types, x=x) + self.lmp.create_atoms(2, atomid=None, atype=types, x=x) self.assertEqual(self.lmp.last_thermo(), None) self.lmp.command("run 2 post no")