diff --git a/CMakeLists.txt b/CMakeLists.txt index 2cd856a96..0e52554fb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -58,6 +58,7 @@ include(${PROJECT_SOURCE_DIR}/cmake/downloaded/autocmake_code_coverage.cmake) include(${PROJECT_SOURCE_DIR}/cmake/custom/mpi.cmake) include(${PROJECT_SOURCE_DIR}/cmake/custom/omp.cmake) include(${PROJECT_SOURCE_DIR}/cmake/custom/sad_basis.cmake) +include(${PROJECT_SOURCE_DIR}/cmake/custom/hirshfeld.cmake) include(${PROJECT_SOURCE_DIR}/cmake/custom/main.cmake) include(${PROJECT_SOURCE_DIR}/cmake/custom/feature_summary.cmake) include(${PROJECT_SOURCE_DIR}/cmake/custom/tests.cmake) diff --git a/cmake/custom/hirshfeld.cmake b/cmake/custom/hirshfeld.cmake new file mode 100644 index 000000000..1152a3952 --- /dev/null +++ b/cmake/custom/hirshfeld.cmake @@ -0,0 +1,7 @@ + +set(HIRSHFELD_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/hirshfeld CACHE STRING "Path to azora potentials") +set(HIRSHFELD_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/hirshfeld) +install( + DIRECTORY share/hirshfeld + DESTINATION share/${PROJECT_NAME} + ) \ No newline at end of file diff --git a/doc/users/user_ref.rst b/doc/users/user_ref.rst index 1d9aee2d7..5095d996f 100644 --- a/doc/users/user_ref.rst +++ b/doc/users/user_ref.rst @@ -440,6 +440,12 @@ User input reference **Default** ``[]`` + :hirshfeld_charges: Compute Hirshfeld charges. + + **Type** ``bool`` + + **Default** ``False`` + :geometric_derivative: Compute geometric derivative. **Type** ``bool`` diff --git a/python/mrchem/helpers.py b/python/mrchem/helpers.py index 43fdef69b..360ce75a5 100644 --- a/python/mrchem/helpers.py +++ b/python/mrchem/helpers.py @@ -295,6 +295,12 @@ def write_scf_properties(user_dict, origin): "precision": user_dict["world_prec"], "smoothing": user_dict["Precisions"]["nuclear_prec"], } + if user_dict["Properties"]["hirshfeld_charges"]: + prop_dict["hirshfeld_charges"] = {} + prop_dict["hirshfeld_charges"]["hirshfeld-1"] = { + 'precision': user_dict["world_prec"] + } + return prop_dict diff --git a/python/mrchem/input_parser/README.md b/python/mrchem/input_parser/README.md index 4a63faa3b..95c597320 100644 --- a/python/mrchem/input_parser/README.md +++ b/python/mrchem/input_parser/README.md @@ -1,2 +1,2 @@ -This file was automatically generated by parselglossy on 2024-05-14 +This file was automatically generated by parselglossy on 2024-08-15 Editing is *STRONGLY DISCOURAGED* diff --git a/python/mrchem/input_parser/__init__.py b/python/mrchem/input_parser/__init__.py index 913954567..4fd0863d9 100644 --- a/python/mrchem/input_parser/__init__.py +++ b/python/mrchem/input_parser/__init__.py @@ -1,4 +1,4 @@ # -*- coding: utf-8 -*- -# This file was automatically generated by parselglossy on 2024-05-14 +# This file was automatically generated by parselglossy on 2024-08-15 # Editing is *STRONGLY DISCOURAGED* diff --git a/python/mrchem/input_parser/api.py b/python/mrchem/input_parser/api.py index 0d511dbc5..062022f1a 100644 --- a/python/mrchem/input_parser/api.py +++ b/python/mrchem/input_parser/api.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -# This file was automatically generated by parselglossy on 2024-05-14 +# This file was automatically generated by parselglossy on 2024-08-15 # Editing is *STRONGLY DISCOURAGED* from copy import deepcopy @@ -359,6 +359,9 @@ def stencil() -> JSONDict: { 'default': [], 'name': 'plot_orbitals', 'type': 'List[int]'}, + { 'default': False, + 'name': 'hirshfeld_charges', + 'type': 'bool'}, { 'default': "user['GeometryOptimizer']['run']", 'name': 'geometric_derivative', 'type': 'bool'}], diff --git a/python/mrchem/input_parser/cli.py b/python/mrchem/input_parser/cli.py index a2b743d2e..3659c3588 100644 --- a/python/mrchem/input_parser/cli.py +++ b/python/mrchem/input_parser/cli.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -# This file was automatically generated by parselglossy on 2024-05-14 +# This file was automatically generated by parselglossy on 2024-08-15 # Editing is *STRONGLY DISCOURAGED* import argparse diff --git a/python/mrchem/input_parser/docs/user_ref.rst b/python/mrchem/input_parser/docs/user_ref.rst index 1d9aee2d7..5095d996f 100644 --- a/python/mrchem/input_parser/docs/user_ref.rst +++ b/python/mrchem/input_parser/docs/user_ref.rst @@ -440,6 +440,12 @@ User input reference **Default** ``[]`` + :hirshfeld_charges: Compute Hirshfeld charges. + + **Type** ``bool`` + + **Default** ``False`` + :geometric_derivative: Compute geometric derivative. **Type** ``bool`` diff --git a/python/mrchem/input_parser/plumbing/lexer.py b/python/mrchem/input_parser/plumbing/lexer.py index ffe9b5b24..19701f0de 100644 --- a/python/mrchem/input_parser/plumbing/lexer.py +++ b/python/mrchem/input_parser/plumbing/lexer.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -# This file was automatically generated by parselglossy on 2024-05-14 +# This file was automatically generated by parselglossy on 2024-08-15 # Editing is *STRONGLY DISCOURAGED* import json diff --git a/python/mrchem/input_parser/plumbing/pyparsing/__init__.py b/python/mrchem/input_parser/plumbing/pyparsing/__init__.py index 3dbc3cf83..79d8153ce 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/__init__.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/__init__.py @@ -120,8 +120,8 @@ def __repr__(self): return f"{__name__}.{type(self).__name__}({', '.join('{}={!r}'.format(*nv) for nv in zip(self._fields, self))})" -__version_info__ = version_info(3, 1, 1, "final", 1) -__version_time__ = "29 Jul 2023 22:27 UTC" +__version_info__ = version_info(3, 1, 2, "final", 1) +__version_time__ = "06 Mar 2024 07:08 UTC" __version__ = __version_info__.__version__ __versionTime__ = __version_time__ __author__ = "Paul McGuire " diff --git a/python/mrchem/input_parser/plumbing/pyparsing/actions.py b/python/mrchem/input_parser/plumbing/pyparsing/actions.py index ca6e4c6af..ce51b3957 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/actions.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/actions.py @@ -111,7 +111,6 @@ def with_attribute(*args, **attr_dict):
1,3 2,3 1,1
this has no type
- ''' div,div_end = make_html_tags("div") @@ -199,19 +198,9 @@ def with_class(classname, namespace=""): # pre-PEP8 compatibility symbols # fmt: off -@replaced_by_pep8(replace_with) -def replaceWith(): ... - -@replaced_by_pep8(remove_quotes) -def removeQuotes(): ... - -@replaced_by_pep8(with_attribute) -def withAttribute(): ... - -@replaced_by_pep8(with_class) -def withClass(): ... - -@replaced_by_pep8(match_only_at_col) -def matchOnlyAtCol(): ... - +replaceWith = replaced_by_pep8("replaceWith", replace_with) +removeQuotes = replaced_by_pep8("removeQuotes", remove_quotes) +withAttribute = replaced_by_pep8("withAttribute", with_attribute) +withClass = replaced_by_pep8("withClass", with_class) +matchOnlyAtCol = replaced_by_pep8("matchOnlyAtCol", match_only_at_col) # fmt: on diff --git a/python/mrchem/input_parser/plumbing/pyparsing/common.py b/python/mrchem/input_parser/plumbing/pyparsing/common.py index 7a666b276..74faa4608 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/common.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/common.py @@ -206,7 +206,7 @@ class pyparsing_common: scientific notation and returns a float""" # streamlining this expression makes the docs nicer-looking - number = (sci_real | real | signed_integer).setName("number").streamline() + number = (sci_real | real | signed_integer).set_name("number").streamline() """any numeric expression, returns the corresponding Python type""" fnumber = ( @@ -216,6 +216,13 @@ class pyparsing_common: ) """any int or real number, returned as float""" + ieee_float = ( + Regex(r"(?i)[+-]?((\d+\.?\d*(e[+-]?\d+)?)|nan|inf(inity)?)") + .set_name("ieee_float") + .set_parse_action(convert_to_float) + ) + """any floating-point literal (int, real number, infinity, or NaN), returned as float""" + identifier = Word(identchars, identbodychars).set_name("identifier") """typical code identifier (leading alpha or '_', followed by 0 or more alphas, nums, or '_')""" diff --git a/python/mrchem/input_parser/plumbing/pyparsing/core.py b/python/mrchem/input_parser/plumbing/pyparsing/core.py index 73514ed09..b19d12216 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/core.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/core.py @@ -571,6 +571,7 @@ def set_results_name( Example:: + integer = Word(nums) date_str = (integer.set_results_name("year") + '/' + integer.set_results_name("month") + '/' + integer.set_results_name("day")) @@ -610,9 +611,8 @@ def breaker(instring, loc, doActions=True, callPreParse=True): breaker._originalParseMethod = _parseMethod # type: ignore [attr-defined] self._parse = breaker # type: ignore [assignment] - else: - if hasattr(self._parse, "_originalParseMethod"): - self._parse = self._parse._originalParseMethod # type: ignore [attr-defined, assignment] + elif hasattr(self._parse, "_originalParseMethod"): + self._parse = self._parse._originalParseMethod # type: ignore [attr-defined, assignment] return self def set_parse_action(self, *fns: ParseAction, **kwargs) -> "ParserElement": @@ -692,13 +692,15 @@ def is_valid_date(instring, loc, toks): """ if list(fns) == [None]: self.parseAction = [] - else: - if not all(callable(fn) for fn in fns): - raise TypeError("parse actions must be callable") - self.parseAction = [_trim_arity(fn) for fn in fns] - self.callDuringTry = kwargs.get( - "call_during_try", kwargs.get("callDuringTry", False) - ) + return self + + if not all(callable(fn) for fn in fns): + raise TypeError("parse actions must be callable") + self.parseAction = [_trim_arity(fn) for fn in fns] + self.callDuringTry = kwargs.get( + "call_during_try", kwargs.get("callDuringTry", False) + ) + return self def add_parse_action(self, *fns: ParseAction, **kwargs) -> "ParserElement": @@ -944,11 +946,9 @@ class to help type checking not_in_cache: bool - def get(self, *args): - ... + def get(self, *args): ... - def set(self, *args): - ... + def set(self, *args): ... # argument cache for optimizing repeated calls when backtracking through recursive expressions packrat_cache = ( @@ -1080,7 +1080,7 @@ def enable_left_recursion( elif cache_size_limit > 0: ParserElement.recursion_memos = _LRUMemo(capacity=cache_size_limit) # type: ignore[assignment] else: - raise NotImplementedError("Memo size of %s" % cache_size_limit) + raise NotImplementedError(f"Memo size of {cache_size_limit}") ParserElement._left_recursion_enabled = True @staticmethod @@ -1121,13 +1121,16 @@ def enable_packrat( ParserElement.disable_memoization() elif ParserElement._left_recursion_enabled: raise RuntimeError("Packrat and Bounded Recursion are not compatible") - if not ParserElement._packratEnabled: - ParserElement._packratEnabled = True - if cache_size_limit is None: - ParserElement.packrat_cache = _UnboundedCache() - else: - ParserElement.packrat_cache = _FifoCache(cache_size_limit) # type: ignore[assignment] - ParserElement._parse = ParserElement._parseCache + + if ParserElement._packratEnabled: + return + + ParserElement._packratEnabled = True + if cache_size_limit is None: + ParserElement.packrat_cache = _UnboundedCache() + else: + ParserElement.packrat_cache = _FifoCache(cache_size_limit) # type: ignore[assignment] + ParserElement._parse = ParserElement._parseCache def parse_string( self, instring: str, parse_all: bool = False, *, parseAll: bool = False @@ -1285,9 +1288,9 @@ def scan_string( except ParseBaseException as exc: if ParserElement.verbose_stacktrace: raise - else: - # catch and re-raise exception from here, clears out pyparsing internal stack trace - raise exc.with_traceback(None) + + # catch and re-raise exception from here, clears out pyparsing internal stack trace + raise exc.with_traceback(None) def transform_string(self, instring: str, *, debug: bool = False) -> str: """ @@ -1317,23 +1320,27 @@ def transform_string(self, instring: str, *, debug: bool = False) -> str: try: for t, s, e in self.scan_string(instring, debug=debug): out.append(instring[lastE:s]) - if t: - if isinstance(t, ParseResults): - out += t.as_list() - elif isinstance(t, Iterable) and not isinstance(t, str_type): - out.extend(t) - else: - out.append(t) lastE = e + + if not t: + continue + + if isinstance(t, ParseResults): + out += t.as_list() + elif isinstance(t, Iterable) and not isinstance(t, str_type): + out.extend(t) + else: + out.append(t) + out.append(instring[lastE:]) out = [o for o in out if o] return "".join([str(s) for s in _flatten(out)]) except ParseBaseException as exc: if ParserElement.verbose_stacktrace: raise - else: - # catch and re-raise exception from here, clears out pyparsing internal stack trace - raise exc.with_traceback(None) + + # catch and re-raise exception from here, clears out pyparsing internal stack trace + raise exc.with_traceback(None) def search_string( self, @@ -1371,9 +1378,9 @@ def search_string( except ParseBaseException as exc: if ParserElement.verbose_stacktrace: raise - else: - # catch and re-raise exception from here, clears out pyparsing internal stack trace - raise exc.with_traceback(None) + + # catch and re-raise exception from here, clears out pyparsing internal stack trace + raise exc.with_traceback(None) def split( self, @@ -1502,9 +1509,12 @@ def __mul__(self, other) -> "ParserElement": elif isinstance(other, tuple) and other[:1] == (Ellipsis,): other = ((0,) + other[1:] + (None,))[:2] + if not isinstance(other, (int, tuple)): + return NotImplemented + if isinstance(other, int): minElements, optElements = other, 0 - elif isinstance(other, tuple): + else: other = tuple(o if o is not Ellipsis else None for o in other) other = (other + (None, None))[:2] if other[0] is None: @@ -1521,8 +1531,6 @@ def __mul__(self, other) -> "ParserElement": optElements -= minElements else: return NotImplemented - else: - return NotImplemented if minElements < 0: raise ValueError("cannot multiply ParserElement by negative value") @@ -1711,8 +1719,8 @@ def __call__(self, name: typing.Optional[str] = None) -> "ParserElement": """ if name is not None: return self._setResultsName(name) - else: - return self.copy() + + return self.copy() def suppress(self) -> "ParserElement": """ @@ -1770,7 +1778,7 @@ def ignore(self, other: "ParserElement") -> "ParserElement": Example:: - patt = Word(alphas)[1, ...] + patt = Word(alphas)[...] patt.parse_string('ablaj /* comment */ lskjd') # -> ['ablaj'] @@ -1778,8 +1786,6 @@ def ignore(self, other: "ParserElement") -> "ParserElement": patt.parse_string('ablaj /* comment */ lskjd') # -> ['ablaj', 'lskjd'] """ - import typing - if isinstance(other, str_type): other = Suppress(other) @@ -1887,11 +1893,14 @@ def set_name(self, name: str) -> "ParserElement": Example:: - Word(nums).parse_string("ABC") # -> Exception: Expected W:(0-9) (at char 0), (line:1, col:1) - Word(nums).set_name("integer").parse_string("ABC") # -> Exception: Expected integer (at char 0), (line:1, col:1) + integer = Word(nums) + integer.parse_string("ABC") # -> Exception: Expected W:(0-9) (at char 0), (line:1, col:1) + + integer.set_name("integer") + integer.parse_string("ABC") # -> Exception: Expected integer (at char 0), (line:1, col:1) """ self.customName = name - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" if __diag__.enable_debug_on_named_expressions: self.set_debug() return self @@ -1957,9 +1966,9 @@ def parse_file( except ParseBaseException as exc: if ParserElement.verbose_stacktrace: raise - else: - # catch and re-raise exception from here, clears out pyparsing internal stack trace - raise exc.with_traceback(None) + + # catch and re-raise exception from here, clears out pyparsing internal stack trace + raise exc.with_traceback(None) def __eq__(self, other): if self is other: @@ -2137,6 +2146,7 @@ def run_tests( success = True NL = Literal(r"\n").add_parse_action(replace_with("\n")).ignore(quoted_string) BOM = "\ufeff" + nlstr = "\n" for t in tests: if comment_specified and comment.matches(t, False) or comments and not t: comments.append( @@ -2146,7 +2156,7 @@ def run_tests( if not t: continue out = [ - "\n" + "\n".join(comments) if comments else "", + f"{nlstr}{nlstr.join(comments) if comments else ''}", pyparsing_test.with_line_numbers(t) if with_line_numbers else t, ] comments = [] @@ -2155,9 +2165,9 @@ def run_tests( t = NL.transform_string(t.lstrip(BOM)) result = self.parse_string(t, parse_all=parseAll) except ParseBaseException as pe: - fatal = "(FATAL)" if isinstance(pe, ParseFatalException) else "" + fatal = "(FATAL) " if isinstance(pe, ParseFatalException) else "" out.append(pe.explain()) - out.append("FAIL: " + str(pe)) + out.append(f"FAIL: {fatal}{pe}") if ParserElement.verbose_stacktrace: out.extend(traceback.format_tb(pe.__traceback__)) success = success and failureTests @@ -2244,91 +2254,42 @@ def create_diagram( show_groups=show_groups, diagram_kwargs=kwargs, ) - if isinstance(output_html, (str, Path)): - with open(output_html, "w", encoding="utf-8") as diag_file: - diag_file.write(railroad_to_html(railroad, embed=embed, **kwargs)) - else: + if not isinstance(output_html, (str, Path)): # we were passed a file-like object, just write to it output_html.write(railroad_to_html(railroad, embed=embed, **kwargs)) + return + + with open(output_html, "w", encoding="utf-8") as diag_file: + diag_file.write(railroad_to_html(railroad, embed=embed, **kwargs)) # Compatibility synonyms # fmt: off - @staticmethod - @replaced_by_pep8(inline_literals_using) - def inlineLiteralsUsing(): ... - - @staticmethod - @replaced_by_pep8(set_default_whitespace_chars) - def setDefaultWhitespaceChars(): ... - - @replaced_by_pep8(set_results_name) - def setResultsName(self): ... - - @replaced_by_pep8(set_break) - def setBreak(self): ... - - @replaced_by_pep8(set_parse_action) - def setParseAction(self): ... - - @replaced_by_pep8(add_parse_action) - def addParseAction(self): ... - - @replaced_by_pep8(add_condition) - def addCondition(self): ... - - @replaced_by_pep8(set_fail_action) - def setFailAction(self): ... - - @replaced_by_pep8(try_parse) - def tryParse(self): ... - - @staticmethod - @replaced_by_pep8(enable_left_recursion) - def enableLeftRecursion(): ... - - @staticmethod - @replaced_by_pep8(enable_packrat) - def enablePackrat(): ... - - @replaced_by_pep8(parse_string) - def parseString(self): ... - - @replaced_by_pep8(scan_string) - def scanString(self): ... - - @replaced_by_pep8(transform_string) - def transformString(self): ... - - @replaced_by_pep8(search_string) - def searchString(self): ... - - @replaced_by_pep8(ignore_whitespace) - def ignoreWhitespace(self): ... - - @replaced_by_pep8(leave_whitespace) - def leaveWhitespace(self): ... - - @replaced_by_pep8(set_whitespace_chars) - def setWhitespaceChars(self): ... - - @replaced_by_pep8(parse_with_tabs) - def parseWithTabs(self): ... - - @replaced_by_pep8(set_debug_actions) - def setDebugActions(self): ... - - @replaced_by_pep8(set_debug) - def setDebug(self): ... - - @replaced_by_pep8(set_name) - def setName(self): ... - - @replaced_by_pep8(parse_file) - def parseFile(self): ... - - @replaced_by_pep8(run_tests) - def runTests(self): ... - + inlineLiteralsUsing = replaced_by_pep8("inlineLiteralsUsing", inline_literals_using) + setDefaultWhitespaceChars = replaced_by_pep8( + "setDefaultWhitespaceChars", set_default_whitespace_chars + ) + setResultsName = replaced_by_pep8("setResultsName", set_results_name) + setBreak = replaced_by_pep8("setBreak", set_break) + setParseAction = replaced_by_pep8("setParseAction", set_parse_action) + addParseAction = replaced_by_pep8("addParseAction", add_parse_action) + addCondition = replaced_by_pep8("addCondition", add_condition) + setFailAction = replaced_by_pep8("setFailAction", set_fail_action) + tryParse = replaced_by_pep8("tryParse", try_parse) + enableLeftRecursion = replaced_by_pep8("enableLeftRecursion", enable_left_recursion) + enablePackrat = replaced_by_pep8("enablePackrat", enable_packrat) + parseString = replaced_by_pep8("parseString", parse_string) + scanString = replaced_by_pep8("scanString", scan_string) + transformString = replaced_by_pep8("transformString", transform_string) + searchString = replaced_by_pep8("searchString", search_string) + ignoreWhitespace = replaced_by_pep8("ignoreWhitespace", ignore_whitespace) + leaveWhitespace = replaced_by_pep8("leaveWhitespace", leave_whitespace) + setWhitespaceChars = replaced_by_pep8("setWhitespaceChars", set_whitespace_chars) + parseWithTabs = replaced_by_pep8("parseWithTabs", parse_with_tabs) + setDebugActions = replaced_by_pep8("setDebugActions", set_debug_actions) + setDebug = replaced_by_pep8("setDebug", set_debug) + setName = replaced_by_pep8("setName", set_name) + parseFile = replaced_by_pep8("parseFile", parse_file) + runTests = replaced_by_pep8("runTests", run_tests) canParseNext = can_parse_next resetCache = reset_cache defaultName = default_name @@ -2358,7 +2319,7 @@ def must_skip(t): def show_skip(t): if t._skipped.as_list()[-1:] == [""]: t.pop("_skipped") - t["_skipped"] = "missing <" + repr(self.anchor) + ">" + t["_skipped"] = f"missing <{self.anchor!r}>" return ( self.anchor + skipper().add_parse_action(must_skip) @@ -2409,9 +2370,9 @@ class Literal(Token): Example:: - Literal('blah').parse_string('blah') # -> ['blah'] - Literal('blah').parse_string('blahfooblah') # -> ['blah'] - Literal('blah').parse_string('bla') # -> Exception: Expected "blah" + Literal('abc').parse_string('abc') # -> ['abc'] + Literal('abc').parse_string('abcdef') # -> ['abc'] + Literal('abc').parse_string('ab') # -> Exception: Expected "abc" For case-insensitive matching, use :class:`CaselessLiteral`. @@ -2441,7 +2402,7 @@ def __init__(self, match_string: str = "", *, matchString: str = ""): self.match = match_string self.matchLen = len(match_string) self.firstMatchChar = match_string[:1] - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" self.mayReturnEmpty = False self.mayIndexError = False @@ -2555,40 +2516,37 @@ def parseImpl(self, instring, loc, doActions=True): or instring[loc + self.matchLen].upper() not in self.identChars ): return loc + self.matchLen, self.match - else: - # followed by keyword char - errmsg += ", was immediately followed by keyword character" - errloc = loc + self.matchLen - else: - # preceded by keyword char - errmsg += ", keyword was immediately preceded by keyword character" - errloc = loc - 1 - # else no match just raise plain exception - else: - if ( - instring[loc] == self.firstMatchChar - and self.matchLen == 1 - or instring.startswith(self.match, loc) - ): - if loc == 0 or instring[loc - 1] not in self.identChars: - if ( - loc >= len(instring) - self.matchLen - or instring[loc + self.matchLen] not in self.identChars - ): - return loc + self.matchLen, self.match - else: - # followed by keyword char - errmsg += ( - ", keyword was immediately followed by keyword character" - ) - errloc = loc + self.matchLen + # followed by keyword char + errmsg += ", was immediately followed by keyword character" + errloc = loc + self.matchLen else: # preceded by keyword char errmsg += ", keyword was immediately preceded by keyword character" errloc = loc - 1 # else no match just raise plain exception + elif ( + instring[loc] == self.firstMatchChar + and self.matchLen == 1 + or instring.startswith(self.match, loc) + ): + if loc == 0 or instring[loc - 1] not in self.identChars: + if ( + loc >= len(instring) - self.matchLen + or instring[loc + self.matchLen] not in self.identChars + ): + return loc + self.matchLen, self.match + + # followed by keyword char + errmsg += ", keyword was immediately followed by keyword character" + errloc = loc + self.matchLen + else: + # preceded by keyword char + errmsg += ", keyword was immediately preceded by keyword character" + errloc = loc - 1 + # else no match just raise plain exception + raise ParseException(instring, errloc, errmsg, self) @staticmethod @@ -2620,7 +2578,7 @@ def __init__(self, match_string: str = "", *, matchString: str = ""): super().__init__(match_string.upper()) # Preserve the defining literal. self.returnString = match_string - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" def parseImpl(self, instring, loc, doActions=True): if instring[loc : loc + self.matchLen].upper() == self.match: @@ -2795,7 +2753,7 @@ class Word(Token): integer = Word(nums) # equivalent to Word("0123456789") or Word(srange("0-9")) # a word with a leading capital, and zero or more lowercase - capital_word = Word(alphas.upper(), alphas.lower()) + capitalized_word = Word(alphas.upper(), alphas.lower()) # hostnames are alphanumeric, with leading alpha, and '-' hostname = Word(alphas, alphanums + '-') @@ -2872,7 +2830,7 @@ def __init__( self.maxLen = exact self.minLen = exact - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" self.mayIndexError = False self.asKeyword = asKeyword if self.asKeyword: @@ -2929,10 +2887,11 @@ def _generateDefaultName(self) -> str: def charsAsStr(s): max_repr_len = 16 s = _collapse_string_to_ranges(s, re_escape=False) + if len(s) > max_repr_len: return s[: max_repr_len - 3] + "..." - else: - return s + + return s if self.initChars != self.bodyChars: base = f"W:({charsAsStr(self.initChars)}, {charsAsStr(self.bodyChars)})" @@ -2970,14 +2929,11 @@ def parseImpl(self, instring, loc, doActions=True): throwException = True elif self.maxSpecified and loc < instrlen and instring[loc] in bodychars: throwException = True - elif self.asKeyword: - if ( - start > 0 - and instring[start - 1] in bodychars - or loc < instrlen - and instring[loc] in bodychars - ): - throwException = True + elif self.asKeyword and ( + (start > 0 and instring[start - 1] in bodychars) + or (loc < instrlen and instring[loc] in bodychars) + ): + throwException = True if throwException: raise ParseException(instring, loc, self.errmsg, self) @@ -3077,7 +3033,7 @@ def __init__( "Regex may only be constructed with a string or a compiled RE object" ) - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" self.mayIndexError = False self.asGroupList = asGroupList self.asMatch = asMatch @@ -3090,11 +3046,11 @@ def __init__( def re(self): if self._re: return self._re - else: - try: - return re.compile(self.pattern, self.flags) - except re.error: - raise ValueError(f"invalid pattern ({self.pattern!r}) passed to Regex") + + try: + return re.compile(self.pattern, self.flags) + except re.error: + raise ValueError(f"invalid pattern ({self.pattern!r}) passed to Regex") @cached_property def re_match(self): @@ -3115,9 +3071,10 @@ def parseImpl(self, instring, loc, doActions=True): loc = result.end() ret = ParseResults(result.group()) d = result.groupdict() - if d: - for k, v in d.items(): - ret[k] = v + + for k, v in d.items(): + ret[k] = v + return loc, ret def parseImplAsGroupList(self, instring, loc, doActions=True): @@ -3209,6 +3166,7 @@ class QuotedString(Token): [['This is the "quote"']] [['This is the quote with "embedded" quotes']] """ + ws_map = dict(((r"\t", "\t"), (r"\n", "\n"), (r"\f", "\f"), (r"\r", "\r"))) def __init__( @@ -3328,7 +3286,7 @@ def __init__( except re.error: raise ValueError(f"invalid pattern {self.pattern!r} passed to Regex") - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" self.mayIndexError = False self.mayReturnEmpty = True @@ -3428,8 +3386,8 @@ def __init__( if min < 1: raise ValueError( - "cannot specify a minimum length < 1; use " - "Opt(CharsNotIn()) if zero-length char group is permitted" + "cannot specify a minimum length < 1; use" + " Opt(CharsNotIn()) if zero-length char group is permitted" ) self.minLen = min @@ -3443,7 +3401,7 @@ def __init__( self.maxLen = exact self.minLen = exact - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" self.mayReturnEmpty = self.minLen == 0 self.mayIndexError = False @@ -3516,7 +3474,7 @@ def __init__(self, ws: str = " \t\r\n", min: int = 1, max: int = 0, exact: int = ) # self.leave_whitespace() self.mayReturnEmpty = True - self.errmsg = "Expected " + self.name + self.errmsg = f"Expected {self.name}" self.minLen = min @@ -3565,16 +3523,19 @@ def __init__(self, colno: int): self.col = colno def preParse(self, instring: str, loc: int) -> int: - if col(loc, instring) != self.col: - instrlen = len(instring) - if self.ignoreExprs: - loc = self._skipIgnorables(instring, loc) - while ( - loc < instrlen - and instring[loc].isspace() - and col(loc, instring) != self.col - ): - loc += 1 + if col(loc, instring) == self.col: + return loc + + instrlen = len(instring) + if self.ignoreExprs: + loc = self._skipIgnorables(instring, loc) + while ( + loc < instrlen + and instring[loc].isspace() + and col(loc, instring) != self.col + ): + loc += 1 + return loc def parseImpl(self, instring, loc, doActions=True): @@ -3620,12 +3581,14 @@ def __init__(self): def preParse(self, instring: str, loc: int) -> int: if loc == 0: return loc - else: - ret = self.skipper.preParse(instring, loc) - if "\n" in self.orig_whiteChars: - while instring[ret : ret + 1] == "\n": - ret = self.skipper.preParse(instring, ret + 1) - return ret + + ret = self.skipper.preParse(instring, loc) + + if "\n" in self.orig_whiteChars: + while instring[ret : ret + 1] == "\n": + ret = self.skipper.preParse(instring, ret + 1) + + return ret def parseImpl(self, instring, loc, doActions=True): if col(loc, instring) == 1: @@ -3666,10 +3629,10 @@ def __init__(self): self.errmsg = "Expected start of text" def parseImpl(self, instring, loc, doActions=True): - if loc != 0: - # see if entire string up to here is just whitespace and ignoreables - if loc != self.preParse(instring, 0): - raise ParseException(instring, loc, self.errmsg, self) + # see if entire string up to here is just whitespace and ignoreables + if loc != 0 and loc != self.preParse(instring, 0): + raise ParseException(instring, loc, self.errmsg, self) + return loc, [] @@ -3685,12 +3648,12 @@ def __init__(self): def parseImpl(self, instring, loc, doActions=True): if loc < len(instring): raise ParseException(instring, loc, self.errmsg, self) - elif loc == len(instring): + if loc == len(instring): return loc + 1, [] - elif loc > len(instring): + if loc > len(instring): return loc, [] - else: - raise ParseException(instring, loc, self.errmsg, self) + + raise ParseException(instring, loc, self.errmsg, self) class WordStart(PositionToken): @@ -3823,7 +3786,7 @@ def ignore(self, other) -> ParserElement: return self def _generateDefaultName(self) -> str: - return f"{self.__class__.__name__}:({str(self.exprs)})" + return f"{type(self).__name__}:({self.exprs})" def streamline(self) -> ParserElement: if self.streamlined: @@ -3862,7 +3825,7 @@ def streamline(self) -> ParserElement: self.mayReturnEmpty |= other.mayReturnEmpty self.mayIndexError |= other.mayIndexError - self.errmsg = "Expected " + str(self) + self.errmsg = f"Expected {self}" return self @@ -3884,38 +3847,36 @@ def copy(self) -> ParserElement: return ret def _setResultsName(self, name, listAllMatches=False): - if ( + if not ( __diag__.warn_ungrouped_named_tokens_in_collection and Diagnostics.warn_ungrouped_named_tokens_in_collection not in self.suppress_warnings_ ): - for e in self.exprs: - if ( - isinstance(e, ParserElement) - and e.resultsName - and Diagnostics.warn_ungrouped_named_tokens_in_collection + return super()._setResultsName(name, listAllMatches) + + for e in self.exprs: + if ( + isinstance(e, ParserElement) + and e.resultsName + and ( + Diagnostics.warn_ungrouped_named_tokens_in_collection not in e.suppress_warnings_ - ): - warnings.warn( - "{}: setting results name {!r} on {} expression " - "collides with {!r} on contained expression".format( - "warn_ungrouped_named_tokens_in_collection", - name, - type(self).__name__, - e.resultsName, - ), - stacklevel=3, - ) + ) + ): + warning = ( + "warn_ungrouped_named_tokens_in_collection:" + f" setting results name {name!r} on {type(self).__name__} expression" + f" collides with {e.resultsName!r} on contained expression" + ) + warnings.warn(warning, stacklevel=3) + break return super()._setResultsName(name, listAllMatches) # Compatibility synonyms # fmt: off - @replaced_by_pep8(leave_whitespace) - def leaveWhitespace(self): ... - - @replaced_by_pep8(ignore_whitespace) - def ignoreWhitespace(self): ... + leaveWhitespace = replaced_by_pep8("leaveWhitespace", leave_whitespace) + ignoreWhitespace = replaced_by_pep8("ignoreWhitespace", ignore_whitespace) # fmt: on @@ -3952,18 +3913,18 @@ def __init__( if exprs and Ellipsis in exprs: tmp = [] for i, expr in enumerate(exprs): - if expr is Ellipsis: - if i < len(exprs) - 1: - skipto_arg: ParserElement = typing.cast( - ParseExpression, (Empty() + exprs[i + 1]) - ).exprs[-1] - tmp.append(SkipTo(skipto_arg)("_skipped*")) - else: - raise Exception( - "cannot construct And with sequence ending in ..." - ) - else: + if expr is not Ellipsis: tmp.append(expr) + continue + + if i < len(exprs) - 1: + skipto_arg: ParserElement = typing.cast( + ParseExpression, (Empty() + exprs[i + 1]) + ).exprs[-1] + tmp.append(SkipTo(skipto_arg)("_skipped*")) + continue + + raise Exception("cannot construct And with sequence ending in ...") exprs[:] = tmp super().__init__(exprs, savelist) if self.exprs: @@ -3982,25 +3943,24 @@ def __init__( def streamline(self) -> ParserElement: # collapse any _PendingSkip's - if self.exprs: - if any( - isinstance(e, ParseExpression) - and e.exprs - and isinstance(e.exprs[-1], _PendingSkip) - for e in self.exprs[:-1] - ): - deleted_expr_marker = NoMatch() - for i, e in enumerate(self.exprs[:-1]): - if e is deleted_expr_marker: - continue - if ( - isinstance(e, ParseExpression) - and e.exprs - and isinstance(e.exprs[-1], _PendingSkip) - ): - e.exprs[-1] = e.exprs[-1] + self.exprs[i + 1] - self.exprs[i + 1] = deleted_expr_marker - self.exprs = [e for e in self.exprs if e is not deleted_expr_marker] + if self.exprs and any( + isinstance(e, ParseExpression) + and e.exprs + and isinstance(e.exprs[-1], _PendingSkip) + for e in self.exprs[:-1] + ): + deleted_expr_marker = NoMatch() + for i, e in enumerate(self.exprs[:-1]): + if e is deleted_expr_marker: + continue + if ( + isinstance(e, ParseExpression) + and e.exprs + and isinstance(e.exprs[-1], _PendingSkip) + ): + e.exprs[-1] = e.exprs[-1] + self.exprs[i + 1] + self.exprs[i + 1] = deleted_expr_marker + self.exprs = [e for e in self.exprs if e is not deleted_expr_marker] super().streamline() @@ -4079,7 +4039,7 @@ def _generateDefaultName(self) -> str: # strip off redundant inner {}'s while len(inner) > 1 and inner[0 :: len(inner) - 1] == "{}": inner = inner[1:-1] - return "{" + inner + "}" + return f"{{{inner}}}" class Or(ParseExpression): @@ -4200,10 +4160,8 @@ def parseImpl(self, instring, loc, doActions=True): if maxExcLoc == loc: maxException.msg = self.errmsg raise maxException - else: - raise ParseException( - instring, loc, "no defined alternatives to match", self - ) + + raise ParseException(instring, loc, "no defined alternatives to match", self) def __ixor__(self, other): if isinstance(other, str_type): @@ -4213,7 +4171,7 @@ def __ixor__(self, other): return self.append(other) # Or([self, other]) def _generateDefaultName(self) -> str: - return "{" + " ^ ".join(str(e) for e in self.exprs) + "}" + return f"{{{' ^ '.join(str(e) for e in self.exprs)}}}" def _setResultsName(self, name, listAllMatches=False): if ( @@ -4227,17 +4185,14 @@ def _setResultsName(self, name, listAllMatches=False): not in e.suppress_warnings_ for e in self.exprs ): - warnings.warn( - "{}: setting results name {!r} on {} expression " - "will return a list of all parsed tokens in an And alternative, " - "in prior versions only the first token was returned; enclose " - "contained argument in Group".format( - "warn_multiple_tokens_in_named_alternation", - name, - type(self).__name__, - ), - stacklevel=3, + warning = ( + "warn_multiple_tokens_in_named_alternation:" + f" setting results name {name!r} on {type(self).__name__} expression" + " will return a list of all parsed tokens in an And alternative," + " in prior versions only the first token was returned; enclose" + " contained argument in Group" ) + warnings.warn(warning, stacklevel=3) return super()._setResultsName(name, listAllMatches) @@ -4290,11 +4245,7 @@ def parseImpl(self, instring, loc, doActions=True): for e in self.exprs: try: - return e._parse( - instring, - loc, - doActions, - ) + return e._parse(instring, loc, doActions) except ParseFatalException as pfe: pfe.__traceback__ = None pfe.parser_element = e @@ -4316,10 +4267,8 @@ def parseImpl(self, instring, loc, doActions=True): if maxExcLoc == loc: maxException.msg = self.errmsg raise maxException - else: - raise ParseException( - instring, loc, "no defined alternatives to match", self - ) + + raise ParseException(instring, loc, "no defined alternatives to match", self) def __ior__(self, other): if isinstance(other, str_type): @@ -4329,7 +4278,7 @@ def __ior__(self, other): return self.append(other) # MatchFirst([self, other]) def _generateDefaultName(self) -> str: - return "{" + " | ".join(str(e) for e in self.exprs) + "}" + return f"{{{' | '.join(str(e) for e in self.exprs)}}}" def _setResultsName(self, name, listAllMatches=False): if ( @@ -4343,17 +4292,14 @@ def _setResultsName(self, name, listAllMatches=False): not in e.suppress_warnings_ for e in self.exprs ): - warnings.warn( - "{}: setting results name {!r} on {} expression " - "will return a list of all parsed tokens in an And alternative, " - "in prior versions only the first token was returned; enclose " - "contained argument in Group".format( - "warn_multiple_tokens_in_named_alternation", - name, - type(self).__name__, - ), - stacklevel=3, + warning = ( + "warn_multiple_tokens_in_named_alternation:" + f" setting results name {name!r} on {type(self).__name__} expression" + " will return a list of all parsed tokens in an And alternative," + " in prior versions only the first token was returned; enclose" + " contained argument in Group" ) + warnings.warn(warning, stacklevel=3) return super()._setResultsName(name, listAllMatches) @@ -4529,7 +4475,7 @@ def parseImpl(self, instring, loc, doActions=True): return loc, total_results def _generateDefaultName(self) -> str: - return "{" + " & ".join(str(e) for e in self.exprs) + "}" + return f"{{{' & '.join(str(e) for e in self.exprs)}}}" class ParseElementEnhance(ParserElement): @@ -4564,16 +4510,17 @@ def recurse(self) -> List[ParserElement]: return [self.expr] if self.expr is not None else [] def parseImpl(self, instring, loc, doActions=True): - if self.expr is not None: - try: - return self.expr._parse(instring, loc, doActions, callPreParse=False) - except ParseBaseException as pbe: - if not isinstance(self, Forward) or self.customName is not None: - pbe.msg = self.errmsg - raise - else: + if self.expr is None: raise ParseException(instring, loc, "No expression defined", self) + try: + return self.expr._parse(instring, loc, doActions, callPreParse=False) + except ParseBaseException as pbe: + if not isinstance(self, Forward) or self.customName is not None: + if self.errmsg: + pbe.msg = self.errmsg + raise + def leave_whitespace(self, recursive: bool = True) -> ParserElement: super().leave_whitespace(recursive) @@ -4593,15 +4540,11 @@ def ignore_whitespace(self, recursive: bool = True) -> ParserElement: return self def ignore(self, other) -> ParserElement: - if isinstance(other, Suppress): - if other not in self.ignoreExprs: - super().ignore(other) - if self.expr is not None: - self.expr.ignore(self.ignoreExprs[-1]) - else: + if not isinstance(other, Suppress) or other not in self.ignoreExprs: super().ignore(other) if self.expr is not None: self.expr.ignore(self.ignoreExprs[-1]) + return self def streamline(self) -> ParserElement: @@ -4631,15 +4574,12 @@ def validate(self, validateTrace=None) -> None: self._checkRecursion([]) def _generateDefaultName(self) -> str: - return f"{self.__class__.__name__}:({str(self.expr)})" + return f"{type(self).__name__}:({self.expr})" # Compatibility synonyms # fmt: off - @replaced_by_pep8(leave_whitespace) - def leaveWhitespace(self): ... - - @replaced_by_pep8(ignore_whitespace) - def ignoreWhitespace(self): ... + leaveWhitespace = replaced_by_pep8("leaveWhitespace", leave_whitespace) + ignoreWhitespace = replaced_by_pep8("ignoreWhitespace", ignore_whitespace) # fmt: on @@ -4849,7 +4789,7 @@ def __init__( retreat = 0 self.exact = True self.retreat = retreat - self.errmsg = "not preceded by " + str(expr) + self.errmsg = f"not preceded by {expr}" self.skipWhitespace = False self.parseAction.append(lambda s, l, t: t.__delitem__(slice(None, None))) @@ -4859,23 +4799,24 @@ def parseImpl(self, instring, loc=0, doActions=True): raise ParseException(instring, loc, self.errmsg) start = loc - self.retreat _, ret = self.expr._parse(instring, start) - else: - # retreat specified a maximum lookbehind window, iterate - test_expr = self.expr + StringEnd() - instring_slice = instring[max(0, loc - self.retreat) : loc] - last_expr = ParseException(instring, loc, self.errmsg) - for offset in range(1, min(loc, self.retreat + 1) + 1): - try: - # print('trying', offset, instring_slice, repr(instring_slice[loc - offset:])) - _, ret = test_expr._parse( - instring_slice, len(instring_slice) - offset - ) - except ParseBaseException as pbe: - last_expr = pbe - else: - break + return loc, ret + + # retreat specified a maximum lookbehind window, iterate + test_expr = self.expr + StringEnd() + instring_slice = instring[max(0, loc - self.retreat) : loc] + last_expr = ParseException(instring, loc, self.errmsg) + + for offset in range(1, min(loc, self.retreat + 1) + 1): + try: + # print('trying', offset, instring_slice, repr(instring_slice[loc - offset:])) + _, ret = test_expr._parse(instring_slice, len(instring_slice) - offset) + except ParseBaseException as pbe: + last_expr = pbe else: - raise last_expr + break + else: + raise last_expr + return loc, ret @@ -4953,7 +4894,7 @@ def __init__(self, expr: Union[ParserElement, str]): self.skipWhitespace = False self.mayReturnEmpty = True - self.errmsg = "Found unwanted token, " + str(self.expr) + self.errmsg = f"Found unwanted token, {self.expr}" def parseImpl(self, instring, loc, doActions=True): if self.expr.can_parse_next(instring, loc, do_actions=doActions): @@ -4961,7 +4902,7 @@ def parseImpl(self, instring, loc, doActions=True): return loc, [] def _generateDefaultName(self) -> str: - return "~{" + str(self.expr) + "}" + return f"~{{{self.expr}}}" class _MultipleMatch(ParseElementEnhance): @@ -5024,19 +4965,18 @@ def _setResultsName(self, name, listAllMatches=False): if ( isinstance(e, ParserElement) and e.resultsName - and Diagnostics.warn_ungrouped_named_tokens_in_collection - not in e.suppress_warnings_ + and ( + Diagnostics.warn_ungrouped_named_tokens_in_collection + not in e.suppress_warnings_ + ) ): - warnings.warn( - "{}: setting results name {!r} on {} expression " - "collides with {!r} on contained expression".format( - "warn_ungrouped_named_tokens_in_collection", - name, - type(self).__name__, - e.resultsName, - ), - stacklevel=3, + warning = ( + "warn_ungrouped_named_tokens_in_collection:" + f" setting results name {name!r} on {type(self).__name__} expression" + f" collides with {e.resultsName!r} on contained expression" ) + warnings.warn(warning, stacklevel=3) + break return super()._setResultsName(name, listAllMatches) @@ -5070,7 +5010,7 @@ class OneOrMore(_MultipleMatch): """ def _generateDefaultName(self) -> str: - return "{" + str(self.expr) + "}..." + return f"{{{self.expr}}}..." class ZeroOrMore(_MultipleMatch): @@ -5104,7 +5044,7 @@ def parseImpl(self, instring, loc, doActions=True): return loc, ParseResults([], name=self.resultsName) def _generateDefaultName(self) -> str: - return "[" + str(self.expr) + "]..." + return f"[{self.expr}]..." class DelimitedList(ParseElementEnhance): @@ -5139,12 +5079,11 @@ def __init__( expr = ParserElement._literalStringClass(expr) expr = typing.cast(ParserElement, expr) - if min is not None: - if min < 1: - raise ValueError("min must be greater than 0") - if max is not None: - if min is not None and max < min: - raise ValueError("max must be greater than, or equal to min") + if min is not None and min < 1: + raise ValueError("min must be greater than 0") + + if max is not None and min is not None and max < min: + raise ValueError("max must be greater than, or equal to min") self.content = expr self.raw_delim = str(delim) @@ -5169,7 +5108,8 @@ def __init__( super().__init__(delim_list_expr, savelist=True) def _generateDefaultName(self) -> str: - return "{0} [{1} {0}]...".format(self.content.streamline(), self.raw_delim) + content_expr = self.content.streamline() + return f"{content_expr} [{self.raw_delim} {content_expr}]..." class _NullToken: @@ -5251,7 +5191,7 @@ def _generateDefaultName(self) -> str: # strip off redundant inner {}'s while len(inner) > 1 and inner[0 :: len(inner) - 1] == "{}": inner = inner[1:-1] - return "[" + inner + "]" + return f"[{inner}]" Optional = Opt @@ -5586,14 +5526,13 @@ def parseImpl(self, instring, loc, doActions=True): del memo[peek_key] return prev_loc, prev_peek.copy() # the match did get better: see if we can improve further - else: - if doActions: - try: - memo[act_key] = super().parseImpl(instring, loc, True) - except ParseException as e: - memo[peek_key] = memo[act_key] = (new_loc, e) - raise - prev_loc, prev_peek = memo[peek_key] = new_loc, new_peek + if doActions: + try: + memo[act_key] = super().parseImpl(instring, loc, True) + except ParseException as e: + memo[peek_key] = memo[act_key] = (new_loc, e) + raise + prev_loc, prev_peek = memo[peek_key] = new_loc, new_peek def leave_whitespace(self, recursive: bool = True) -> ParserElement: self.skipWhitespace = False @@ -5637,7 +5576,7 @@ def _generateDefaultName(self) -> str: else: retString = "None" finally: - return self.__class__.__name__ + ": " + retString + return f"{type(self).__name__}: {retString}" def copy(self) -> ParserElement: if self.expr is not None: @@ -5648,29 +5587,26 @@ def copy(self) -> ParserElement: return ret def _setResultsName(self, name, list_all_matches=False): + # fmt: off if ( __diag__.warn_name_set_on_empty_Forward - and Diagnostics.warn_name_set_on_empty_Forward - not in self.suppress_warnings_ + and Diagnostics.warn_name_set_on_empty_Forward not in self.suppress_warnings_ + and self.expr is None ): - if self.expr is None: - warnings.warn( - "{}: setting results name {!r} on {} expression " - "that has no contained expression".format( - "warn_name_set_on_empty_Forward", name, type(self).__name__ - ), - stacklevel=3, - ) + warning = ( + "warn_name_set_on_empty_Forward:" + f" setting results name {name!r} on {type(self).__name__} expression" + " that has no contained expression" + ) + warnings.warn(warning, stacklevel=3) + # fmt: on return super()._setResultsName(name, list_all_matches) # Compatibility synonyms # fmt: off - @replaced_by_pep8(leave_whitespace) - def leaveWhitespace(self): ... - - @replaced_by_pep8(ignore_whitespace) - def ignoreWhitespace(self): ... + leaveWhitespace = replaced_by_pep8("leaveWhitespace", leave_whitespace) + ignoreWhitespace = replaced_by_pep8("ignoreWhitespace", ignore_whitespace) # fmt: on @@ -5774,8 +5710,8 @@ def postParse(self, instring, loc, tokenlist): if isinstance(tokenlist, ParseResults) else list(tokenlist) ) - else: - return [tokenlist] + + return [tokenlist] class Dict(TokenConverter): @@ -5861,8 +5797,8 @@ def postParse(self, instring, loc, tokenlist): if self._asPythonDict: return [tokenlist.as_dict()] if self.resultsName else tokenlist.as_dict() - else: - return [tokenlist] if self.resultsName else tokenlist + + return [tokenlist] if self.resultsName else tokenlist class Suppress(TokenConverter): @@ -5904,14 +5840,14 @@ def __init__(self, expr: Union[ParserElement, str], savelist: bool = False): def __add__(self, other) -> "ParserElement": if isinstance(self.expr, _PendingSkip): return Suppress(SkipTo(other)) + other - else: - return super().__add__(other) + + return super().__add__(other) def __sub__(self, other) -> "ParserElement": if isinstance(self.expr, _PendingSkip): return Suppress(SkipTo(other)) - other - else: - return super().__sub__(other) + + return super().__sub__(other) def postParse(self, instring, loc, tokenlist): return [] @@ -5951,7 +5887,7 @@ def z(*paArgs): thisFunc = f.__name__ s, l, t = paArgs[-3:] if len(paArgs) > 3: - thisFunc = paArgs[0].__class__.__name__ + "." + thisFunc + thisFunc = f"{type(paArgs[0]).__name__}.{thisFunc}" sys.stderr.write(f">>entering {thisFunc}(line: {line(l, s)!r}, {l}, {t!r})\n") try: ret = f(*paArgs) @@ -6019,8 +5955,8 @@ def srange(s: str) -> str: - any combination of the above (``'aeiouy'``, ``'a-zA-Z0-9_$'``, etc.) """ - _expanded = ( - lambda p: p + _expanded = lambda p: ( + p if not isinstance(p, ParseResults) else "".join(chr(c) for c in range(ord(p[0]), ord(p[1]) + 1)) ) @@ -6144,16 +6080,8 @@ def autoname_elements() -> None: lineEnd = line_end stringStart = string_start stringEnd = string_end - -@replaced_by_pep8(null_debug_action) -def nullDebugAction(): ... - -@replaced_by_pep8(trace_parse_action) -def traceParseAction(): ... - -@replaced_by_pep8(condition_as_parse_action) -def conditionAsParseAction(): ... - -@replaced_by_pep8(token_map) -def tokenMap(): ... +nullDebugAction = replaced_by_pep8("nullDebugAction", null_debug_action) +traceParseAction = replaced_by_pep8("traceParseAction", trace_parse_action) +conditionAsParseAction = replaced_by_pep8("conditionAsParseAction", condition_as_parse_action) +tokenMap = replaced_by_pep8("tokenMap", token_map) # fmt: on diff --git a/python/mrchem/input_parser/plumbing/pyparsing/diagram/__init__.py b/python/mrchem/input_parser/plumbing/pyparsing/diagram/__init__.py index 267f34474..700d0b561 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/diagram/__init__.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/diagram/__init__.py @@ -473,7 +473,7 @@ def _to_diagram_element( :param show_groups: bool flag indicating whether to show groups using bounding box """ exprs = element.recurse() - name = name_hint or element.customName or element.__class__.__name__ + name = name_hint or element.customName or type(element).__name__ # Python's id() is used to provide a unique identifier for elements el_id = id(element) diff --git a/python/mrchem/input_parser/plumbing/pyparsing/exceptions.py b/python/mrchem/input_parser/plumbing/pyparsing/exceptions.py index 12219f124..1aaea56f5 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/exceptions.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/exceptions.py @@ -14,11 +14,13 @@ from .unicode import pyparsing_unicode as ppu -class ExceptionWordUnicode(ppu.Latin1, ppu.LatinA, ppu.LatinB, ppu.Greek, ppu.Cyrillic): +class _ExceptionWordUnicodeSet( + ppu.Latin1, ppu.LatinA, ppu.LatinB, ppu.Greek, ppu.Cyrillic +): pass -_extract_alphanums = _collapse_string_to_ranges(ExceptionWordUnicode.alphanums) +_extract_alphanums = _collapse_string_to_ranges(_ExceptionWordUnicodeSet.alphanums) _exception_word_extractor = re.compile("([" + _extract_alphanums + "]{1,16})|.") @@ -86,41 +88,39 @@ def explain_exception(exc, depth=16): ret.append(" " * (exc.column - 1) + "^") ret.append(f"{type(exc).__name__}: {exc}") - if depth > 0: - callers = inspect.getinnerframes(exc.__traceback__, context=depth) - seen = set() - for i, ff in enumerate(callers[-depth:]): - frm = ff[0] - - f_self = frm.f_locals.get("self", None) - if isinstance(f_self, ParserElement): - if not frm.f_code.co_name.startswith( - ("parseImpl", "_parseNoCache") - ): - continue - if id(f_self) in seen: - continue - seen.add(id(f_self)) - - self_type = type(f_self) - ret.append( - f"{self_type.__module__}.{self_type.__name__} - {f_self}" - ) - - elif f_self is not None: - self_type = type(f_self) - ret.append(f"{self_type.__module__}.{self_type.__name__}") + if depth <= 0: + return "\n".join(ret) - else: - code = frm.f_code - if code.co_name in ("wrapper", ""): - continue + callers = inspect.getinnerframes(exc.__traceback__, context=depth) + seen = set() + for ff in callers[-depth:]: + frm = ff[0] + + f_self = frm.f_locals.get("self", None) + if isinstance(f_self, ParserElement): + if not frm.f_code.co_name.startswith(("parseImpl", "_parseNoCache")): + continue + if id(f_self) in seen: + continue + seen.add(id(f_self)) + + self_type = type(f_self) + ret.append(f"{self_type.__module__}.{self_type.__name__} - {f_self}") + + elif f_self is not None: + self_type = type(f_self) + ret.append(f"{self_type.__module__}.{self_type.__name__}") + + else: + code = frm.f_code + if code.co_name in ("wrapper", ""): + continue - ret.append(code.co_name) + ret.append(code.co_name) - depth -= 1 - if not depth: - break + depth -= 1 + if not depth: + break return "\n".join(ret) @@ -220,8 +220,10 @@ def explain(self, depth=16) -> str: Example:: + # an expression to parse 3 integers expr = pp.Word(pp.nums) * 3 try: + # a failing parse - the third integer is prefixed with "A" expr.parse_string("123 456 A789") except pp.ParseException as pe: print(pe.explain(depth=0)) @@ -244,8 +246,7 @@ def explain(self, depth=16) -> str: return self.explain_exception(self, depth) # fmt: off - @replaced_by_pep8(mark_input_line) - def markInputline(self): ... + markInputline = replaced_by_pep8("markInputline", mark_input_line) # fmt: on @@ -255,16 +256,16 @@ class ParseException(ParseBaseException): Example:: + integer = Word(nums).set_name("integer") try: - Word(nums).set_name("integer").parse_string("ABC") + integer.parse_string("ABC") except ParseException as pe: print(pe) - print("column: {}".format(pe.column)) + print(f"column: {pe.column}") prints:: - Expected integer (at char 0), (line:1, col:1) - column: 1 + Expected integer (at char 0), (line:1, col:1) column: 1 """ diff --git a/python/mrchem/input_parser/plumbing/pyparsing/helpers.py b/python/mrchem/input_parser/plumbing/pyparsing/helpers.py index 018f0d6ac..dcfdb8fe4 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/helpers.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/helpers.py @@ -74,7 +74,7 @@ def count_field_parse_action(s, l, t): intExpr = intExpr.copy() intExpr.set_name("arrayLen") intExpr.add_parse_action(count_field_parse_action, call_during_try=True) - return (intExpr + array_expr).set_name("(len) " + str(expr) + "...") + return (intExpr + array_expr).set_name(f"(len) {expr}...") def match_previous_literal(expr: ParserElement) -> ParserElement: @@ -95,15 +95,17 @@ def match_previous_literal(expr: ParserElement) -> ParserElement: rep = Forward() def copy_token_to_repeater(s, l, t): - if t: - if len(t) == 1: - rep << t[0] - else: - # flatten t tokens - tflat = _flatten(t.as_list()) - rep << And(Literal(tt) for tt in tflat) - else: + if not t: rep << Empty() + return + + if len(t) == 1: + rep << t[0] + return + + # flatten t tokens + tflat = _flatten(t.as_list()) + rep << And(Literal(tt) for tt in tflat) expr.add_parse_action(copy_token_to_repeater, callDuringTry=True) rep.set_name("(prev) " + str(expr)) @@ -230,7 +232,7 @@ def one_of( if isequal(other, cur): del symbols[i + j + 1] break - elif masks(cur, other): + if masks(cur, other): del symbols[i + j + 1] symbols.insert(i, other) break @@ -534,7 +536,9 @@ def nested_expr( ) else: ret <<= Group(Suppress(opener) + ZeroOrMore(ret | content) + Suppress(closer)) - ret.set_name("nested %s%s expression" % (opener, closer)) + ret.set_name(f"nested {opener}{closer} expression") + # don't override error message from content expressions + ret.errmsg = None return ret @@ -580,7 +584,7 @@ def _makeTags(tagStr, xml, suppress_LT=Suppress("<"), suppress_GT=Suppress(">")) ) closeTag = Combine(Literal("", adjacent=False) - openTag.set_name("<%s>" % resname) + openTag.set_name(f"<{resname}>") # add start results name in parse action now that ungrouped names are not reported at two levels openTag.add_parse_action( lambda t: t.__setitem__( @@ -589,7 +593,7 @@ def _makeTags(tagStr, xml, suppress_LT=Suppress("<"), suppress_GT=Suppress(">")) ) closeTag = closeTag( "end" + "".join(resname.replace(":", " ").title().split()) - ).set_name("" % resname) + ).set_name(f"") openTag.tag = resname closeTag.tag = resname openTag.tag_body = SkipTo(closeTag()) @@ -777,7 +781,7 @@ def parseImpl(self, instring, loc, doActions=True): rpar = Suppress(rpar) # if lpar and rpar are not suppressed, wrap in group - if not (isinstance(rpar, Suppress) and isinstance(rpar, Suppress)): + if not (isinstance(lpar, Suppress) and isinstance(rpar, Suppress)): lastExpr = base_expr | Group(lpar + ret + rpar) else: lastExpr = base_expr | (lpar + ret + rpar) @@ -787,7 +791,7 @@ def parseImpl(self, instring, loc, doActions=True): pa: typing.Optional[ParseAction] opExpr1: ParserElement opExpr2: ParserElement - for i, operDef in enumerate(op_list): + for operDef in op_list: opExpr, arity, rightLeftAssoc, pa = (operDef + (None,))[:4] # type: ignore[assignment] if isinstance(opExpr, str_type): opExpr = ParserElement._literalStringClass(opExpr) @@ -1058,43 +1062,17 @@ def delimited_list( cppStyleComment = cpp_style_comment javaStyleComment = java_style_comment pythonStyleComment = python_style_comment - -@replaced_by_pep8(DelimitedList) -def delimitedList(): ... - -@replaced_by_pep8(DelimitedList) -def delimited_list(): ... - -@replaced_by_pep8(counted_array) -def countedArray(): ... - -@replaced_by_pep8(match_previous_literal) -def matchPreviousLiteral(): ... - -@replaced_by_pep8(match_previous_expr) -def matchPreviousExpr(): ... - -@replaced_by_pep8(one_of) -def oneOf(): ... - -@replaced_by_pep8(dict_of) -def dictOf(): ... - -@replaced_by_pep8(original_text_for) -def originalTextFor(): ... - -@replaced_by_pep8(nested_expr) -def nestedExpr(): ... - -@replaced_by_pep8(make_html_tags) -def makeHTMLTags(): ... - -@replaced_by_pep8(make_xml_tags) -def makeXMLTags(): ... - -@replaced_by_pep8(replace_html_entity) -def replaceHTMLEntity(): ... - -@replaced_by_pep8(infix_notation) -def infixNotation(): ... +delimitedList = replaced_by_pep8("delimitedList", DelimitedList) +delimited_list = replaced_by_pep8("delimited_list", DelimitedList) +countedArray = replaced_by_pep8("countedArray", counted_array) +matchPreviousLiteral = replaced_by_pep8("matchPreviousLiteral", match_previous_literal) +matchPreviousExpr = replaced_by_pep8("matchPreviousExpr", match_previous_expr) +oneOf = replaced_by_pep8("oneOf", one_of) +dictOf = replaced_by_pep8("dictOf", dict_of) +originalTextFor = replaced_by_pep8("originalTextFor", original_text_for) +nestedExpr = replaced_by_pep8("nestedExpr", nested_expr) +makeHTMLTags = replaced_by_pep8("makeHTMLTags", make_html_tags) +makeXMLTags = replaced_by_pep8("makeXMLTags", make_xml_tags) +replaceHTMLEntity = replaced_by_pep8("replaceHTMLEntity", replace_html_entity) +infixNotation = replaced_by_pep8("infixNotation", infix_notation) # fmt: on diff --git a/python/mrchem/input_parser/plumbing/pyparsing/results.py b/python/mrchem/input_parser/plumbing/pyparsing/results.py index 031304976..3e5fe2089 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/results.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/results.py @@ -173,42 +173,48 @@ def __init__( ): self._tokdict: Dict[str, _ParseResultsWithOffset] self._modal = modal - if name is not None and name != "": - if isinstance(name, int): - name = str(name) - if not modal: - self._all_names = {name} - self._name = name - if toklist not in self._null_values: - if isinstance(toklist, (str_type, type)): - toklist = [toklist] - if asList: - if isinstance(toklist, ParseResults): - self[name] = _ParseResultsWithOffset( - ParseResults(toklist._toklist), 0 - ) - else: - self[name] = _ParseResultsWithOffset( - ParseResults(toklist[0]), 0 - ) - self[name]._name = name - else: - try: - self[name] = toklist[0] - except (KeyError, TypeError, IndexError): - if toklist is not self: - self[name] = toklist - else: - self._name = name + + if name is None or name == "": + return + + if isinstance(name, int): + name = str(name) + + if not modal: + self._all_names = {name} + + self._name = name + + if toklist in self._null_values: + return + + if isinstance(toklist, (str_type, type)): + toklist = [toklist] + + if asList: + if isinstance(toklist, ParseResults): + self[name] = _ParseResultsWithOffset(ParseResults(toklist._toklist), 0) + else: + self[name] = _ParseResultsWithOffset(ParseResults(toklist[0]), 0) + self[name]._name = name + return + + try: + self[name] = toklist[0] + except (KeyError, TypeError, IndexError): + if toklist is not self: + self[name] = toklist + else: + self._name = name def __getitem__(self, i): if isinstance(i, (int, slice)): return self._toklist[i] - else: - if i not in self._all_names: - return self._tokdict[i][-1][0] - else: - return ParseResults([v[0] for v in self._tokdict[i]]) + + if i not in self._all_names: + return self._tokdict[i][-1][0] + + return ParseResults([v[0] for v in self._tokdict[i]]) def __setitem__(self, k, v, isinstance=isinstance): if isinstance(v, _ParseResultsWithOffset): @@ -226,27 +232,28 @@ def __setitem__(self, k, v, isinstance=isinstance): sub._parent = self def __delitem__(self, i): - if isinstance(i, (int, slice)): - mylen = len(self._toklist) - del self._toklist[i] - - # convert int to slice - if isinstance(i, int): - if i < 0: - i += mylen - i = slice(i, i + 1) - # get removed indices - removed = list(range(*i.indices(mylen))) - removed.reverse() - # fixup indices in token dictionary - for name, occurrences in self._tokdict.items(): - for j in removed: - for k, (value, position) in enumerate(occurrences): - occurrences[k] = _ParseResultsWithOffset( - value, position - (position > j) - ) - else: + if not isinstance(i, (int, slice)): del self._tokdict[i] + return + + mylen = len(self._toklist) + del self._toklist[i] + + # convert int to slice + if isinstance(i, int): + if i < 0: + i += mylen + i = slice(i, i + 1) + # get removed indices + removed = list(range(*i.indices(mylen))) + removed.reverse() + # fixup indices in token dictionary + for occurrences in self._tokdict.values(): + for j in removed: + for k, (value, position) in enumerate(occurrences): + occurrences[k] = _ParseResultsWithOffset( + value, position - (position > j) + ) def __contains__(self, k) -> bool: return k in self._tokdict @@ -376,7 +383,7 @@ def insert_locn(locn, tokens): """ self._toklist.insert(index, ins_string) # fixup indices in token dictionary - for name, occurrences in self._tokdict.items(): + for occurrences in self._tokdict.values(): for k, (value, position) in enumerate(occurrences): occurrences[k] = _ParseResultsWithOffset( value, position + (position > index) @@ -652,58 +659,52 @@ def dump(self, indent="", full=True, include_list=True, _depth=0) -> str: NL = "\n" out.append(indent + str(self.as_list()) if include_list else "") - if full: - if self.haskeys(): - items = sorted((str(k), v) for k, v in self.items()) - for k, v in items: - if out: - out.append(NL) - out.append(f"{indent}{(' ' * _depth)}- {k}: ") - if isinstance(v, ParseResults): - if v: - out.append( - v.dump( - indent=indent, - full=full, - include_list=include_list, - _depth=_depth + 1, - ) - ) - else: - out.append(str(v)) - else: - out.append(repr(v)) - if any(isinstance(vv, ParseResults) for vv in self): - v = self - for i, vv in enumerate(v): - if isinstance(vv, ParseResults): - out.append( - "\n{}{}[{}]:\n{}{}{}".format( - indent, - (" " * (_depth)), - i, - indent, - (" " * (_depth + 1)), - vv.dump( - indent=indent, - full=full, - include_list=include_list, - _depth=_depth + 1, - ), - ) - ) - else: - out.append( - "\n%s%s[%d]:\n%s%s%s" - % ( - indent, - (" " * (_depth)), - i, - indent, - (" " * (_depth + 1)), - str(vv), - ) - ) + if not full: + return "".join(out) + + if self.haskeys(): + items = sorted((str(k), v) for k, v in self.items()) + for k, v in items: + if out: + out.append(NL) + out.append(f"{indent}{(' ' * _depth)}- {k}: ") + if not isinstance(v, ParseResults): + out.append(repr(v)) + continue + + if not v: + out.append(str(v)) + continue + + out.append( + v.dump( + indent=indent, + full=full, + include_list=include_list, + _depth=_depth + 1, + ) + ) + if not any(isinstance(vv, ParseResults) for vv in self): + return "".join(out) + + v = self + incr = " " + nl = "\n" + for i, vv in enumerate(v): + if isinstance(vv, ParseResults): + vv_dump = vv.dump( + indent=indent, + full=full, + include_list=include_list, + _depth=_depth + 1, + ) + out.append( + f"{nl}{indent}{incr * _depth}[{i}]:{nl}{indent}{incr * (_depth + 1)}{vv_dump}" + ) + else: + out.append( + f"{nl}{indent}{incr * _depth}[{i}]:{nl}{indent}{incr * (_depth + 1)}{vv}" + ) return "".join(out) diff --git a/python/mrchem/input_parser/plumbing/pyparsing/testing.py b/python/mrchem/input_parser/plumbing/pyparsing/testing.py index 6a254c1c5..5654d47d6 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/testing.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/testing.py @@ -1,8 +1,10 @@ # testing.py from contextlib import contextmanager +import re import typing + from .core import ( ParserElement, ParseException, @@ -49,23 +51,23 @@ def save(self): self._save_context["default_whitespace"] = ParserElement.DEFAULT_WHITE_CHARS self._save_context["default_keyword_chars"] = Keyword.DEFAULT_KEYWORD_CHARS - self._save_context[ - "literal_string_class" - ] = ParserElement._literalStringClass + self._save_context["literal_string_class"] = ( + ParserElement._literalStringClass + ) self._save_context["verbose_stacktrace"] = ParserElement.verbose_stacktrace self._save_context["packrat_enabled"] = ParserElement._packratEnabled if ParserElement._packratEnabled: - self._save_context[ - "packrat_cache_size" - ] = ParserElement.packrat_cache.size + self._save_context["packrat_cache_size"] = ( + ParserElement.packrat_cache.size + ) else: self._save_context["packrat_cache_size"] = None self._save_context["packrat_parse"] = ParserElement._parse - self._save_context[ - "recursion_enabled" - ] = ParserElement._left_recursion_enabled + self._save_context["recursion_enabled"] = ( + ParserElement._left_recursion_enabled + ) self._save_context["__diag__"] = { name: getattr(__diag__, name) for name in __diag__._all_names @@ -180,49 +182,52 @@ def assertRunTestResults( """ run_test_success, run_test_results = run_tests_report - if expected_parse_results is not None: - merged = [ - (*rpt, expected) - for rpt, expected in zip(run_test_results, expected_parse_results) - ] - for test_string, result, expected in merged: - # expected should be a tuple containing a list and/or a dict or an exception, - # and optional failure message string - # an empty tuple will skip any result validation - fail_msg = next( - (exp for exp in expected if isinstance(exp, str)), None + if expected_parse_results is None: + self.assertTrue( + run_test_success, msg=msg if msg is not None else "failed runTests" + ) + return + + merged = [ + (*rpt, expected) + for rpt, expected in zip(run_test_results, expected_parse_results) + ] + for test_string, result, expected in merged: + # expected should be a tuple containing a list and/or a dict or an exception, + # and optional failure message string + # an empty tuple will skip any result validation + fail_msg = next((exp for exp in expected if isinstance(exp, str)), None) + expected_exception = next( + ( + exp + for exp in expected + if isinstance(exp, type) and issubclass(exp, Exception) + ), + None, + ) + if expected_exception is not None: + with self.assertRaises( + expected_exception=expected_exception, msg=fail_msg or msg + ): + if isinstance(result, Exception): + raise result + else: + expected_list = next( + (exp for exp in expected if isinstance(exp, list)), None ) - expected_exception = next( - ( - exp - for exp in expected - if isinstance(exp, type) and issubclass(exp, Exception) - ), - None, + expected_dict = next( + (exp for exp in expected if isinstance(exp, dict)), None ) - if expected_exception is not None: - with self.assertRaises( - expected_exception=expected_exception, msg=fail_msg or msg - ): - if isinstance(result, Exception): - raise result - else: - expected_list = next( - (exp for exp in expected if isinstance(exp, list)), None + if (expected_list, expected_dict) != (None, None): + self.assertParseResultsEquals( + result, + expected_list=expected_list, + expected_dict=expected_dict, + msg=fail_msg or msg, ) - expected_dict = next( - (exp for exp in expected if isinstance(exp, dict)), None - ) - if (expected_list, expected_dict) != (None, None): - self.assertParseResultsEquals( - result, - expected_list=expected_list, - expected_dict=expected_dict, - msg=fail_msg or msg, - ) - else: - # warning here maybe? - print(f"no validation for {test_string!r}") + else: + # warning here maybe? + print(f"no validation for {test_string!r}") # do this last, in case some specific test results can be reported instead self.assertTrue( @@ -230,9 +235,18 @@ def assertRunTestResults( ) @contextmanager - def assertRaisesParseException(self, exc_type=ParseException, msg=None): - with self.assertRaises(exc_type, msg=msg): - yield + def assertRaisesParseException( + self, exc_type=ParseException, expected_msg=None, msg=None + ): + if expected_msg is not None: + if isinstance(expected_msg, str): + expected_msg = re.escape(expected_msg) + with self.assertRaisesRegex(exc_type, expected_msg, msg=msg) as ctx: + yield ctx + + else: + with self.assertRaises(exc_type, msg=msg) as ctx: + yield ctx @staticmethod def with_line_numbers( diff --git a/python/mrchem/input_parser/plumbing/pyparsing/unicode.py b/python/mrchem/input_parser/plumbing/pyparsing/unicode.py index b0a87b235..426b8b238 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/unicode.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/unicode.py @@ -102,17 +102,10 @@ def identbodychars(cls): all characters in this range that are valid identifier body characters, plus the digits 0-9, and · (Unicode MIDDLE DOT) """ - return "".join( - sorted( - set( - cls.identchars - + "0123456789·" - + "".join( - [c for c in cls._chars_for_ranges if ("_" + c).isidentifier()] - ) - ) - ) + identifier_chars = set( + c for c in cls._chars_for_ranges if ("_" + c).isidentifier() ) + return "".join(sorted(identifier_chars | set(cls.identchars + "0123456789·"))) @_lazyclassproperty def identifier(cls): diff --git a/python/mrchem/input_parser/plumbing/pyparsing/util.py b/python/mrchem/input_parser/plumbing/pyparsing/util.py index d8d3f414c..4ae018a96 100644 --- a/python/mrchem/input_parser/plumbing/pyparsing/util.py +++ b/python/mrchem/input_parser/plumbing/pyparsing/util.py @@ -237,7 +237,7 @@ def _flatten(ll: list) -> list: return ret -def _make_synonym_function(compat_name: str, fn: C) -> C: +def replaced_by_pep8(compat_name: str, fn: C) -> C: # In a future version, uncomment the code in the internal _inner() functions # to begin emitting DeprecationWarnings. @@ -251,7 +251,7 @@ def _make_synonym_function(compat_name: str, fn: C) -> C: @wraps(fn) def _inner(self, *args, **kwargs): # warnings.warn( - # f"Deprecated - use {fn.__name__}", DeprecationWarning, stacklevel=3 + # f"Deprecated - use {fn.__name__}", DeprecationWarning, stacklevel=2 # ) return fn(self, *args, **kwargs) @@ -260,7 +260,7 @@ def _inner(self, *args, **kwargs): @wraps(fn) def _inner(*args, **kwargs): # warnings.warn( - # f"Deprecated - use {fn.__name__}", DeprecationWarning, stacklevel=3 + # f"Deprecated - use {fn.__name__}", DeprecationWarning, stacklevel=2 # ) return fn(*args, **kwargs) @@ -275,10 +275,3 @@ def _inner(*args, **kwargs): _inner.__kwdefaults__ = None _inner.__qualname__ = fn.__qualname__ return cast(C, _inner) - - -def replaced_by_pep8(fn: C) -> Callable[[Callable], C]: - """ - Decorator for pre-PEP8 compatibility synonyms, to link them to the new function. - """ - return lambda other: _make_synonym_function(other.__name__, fn) diff --git a/python/template.yml b/python/template.yml index 1e247b1c7..224cc003c 100644 --- a/python/template.yml +++ b/python/template.yml @@ -403,6 +403,11 @@ sections: docstring: | Plot converged molecular orbitals from list of indices, negative index plots all orbitals. + - name: hirshfeld_charges + type: bool + default: false + docstring: | + Compute Hirshfeld charges. - name: ExternalFields docstring: | Define external electromagnetic fields. diff --git a/share/hirshfeld/lda/Ag.density b/share/hirshfeld/lda/Ag.density new file mode 100644 index 000000000..93dbe8d17 --- /dev/null +++ b/share/hirshfeld/lda/Ag.density @@ -0,0 +1,192 @@ +9.757819552000000172e-19 1.523042765000000072e+05 +2.948306927999999936e-05 1.520417942000000039e+05 +6.108217363999999779e-05 1.496829188000000140e+05 +9.494917828999999360e-05 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6.532461317999999774e-23 diff --git a/share/hirshfeld/lda/readme b/share/hirshfeld/lda/readme new file mode 100644 index 000000000..db1fd1dc7 --- /dev/null +++ b/share/hirshfeld/lda/readme @@ -0,0 +1,2 @@ +This directory contains the tabulated hirshfeld charge densities. +The data is stored column wise. The first column contains a radial grid and the second column the charge density at this radius. \ No newline at end of file diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 260f6f688..de5a8ac0e 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -32,12 +32,18 @@ add_subdirectory(analyticfunctions) add_subdirectory(chemistry) add_subdirectory(environment) add_subdirectory(mrdft) +add_subdirectory(properties) add_subdirectory(qmfunctions) add_subdirectory(qmoperators) add_subdirectory(scf_solver) add_subdirectory(tensor) add_subdirectory(utils) +target_compile_definitions(mrchem PRIVATE + HIRSHFELD_SOURCE_DIR="${HIRSHFELD_SOURCE_DIR}" + HIRSHFELD_INSTALL_DIR="${HIRSHFELD_INSTALL_DIR}" +) + target_link_libraries(mrchem PRIVATE Eigen3::Eigen diff --git a/src/chemistry/Molecule.cpp b/src/chemistry/Molecule.cpp index 68238ddb8..f5e856e45 100644 --- a/src/chemistry/Molecule.cpp +++ b/src/chemistry/Molecule.cpp @@ -226,6 +226,7 @@ void Molecule::printProperties() const { for (const auto &mag : magnetizability) mag.second.print(mag.first); for (const auto &nmr : nmr_shielding) nmr.second.print(nmr.first); for (const auto &geo : geometric_derivative) geo.second.print(geo.first); + for (const auto &hir : hirshfeld_charges) hir.second.print(hir.first); } nlohmann::json Molecule::json() const { @@ -256,6 +257,7 @@ nlohmann::json Molecule::json() const { for (const auto &mag : magnetizability) json_out["magnetizability"][mag.first] = mag.second.json(); for (const auto &nmr : nmr_shielding) json_out["nmr_shielding"][nmr.first] = nmr.second.json(); for (const auto &geo : geometric_derivative) json_out["geometric_derivative"][geo.first] = geo.second.json(); + for (const auto &hir : hirshfeld_charges) json_out["hirshfeld_charges"][hir.first] = hir.second.json(); return json_out; } diff --git a/src/chemistry/Molecule.h b/src/chemistry/Molecule.h index 6eb9656ed..2dae81136 100644 --- a/src/chemistry/Molecule.h +++ b/src/chemistry/Molecule.h @@ -51,6 +51,7 @@ #include "properties/QuadrupoleMoment.h" #include "properties/SCFEnergy.h" #include "qmfunctions/Orbital.h" +#include "properties/HirshfeldCharges.h" /** @class Molecule * @@ -118,6 +119,7 @@ class Molecule final { Magnetizability &getMagnetizability(const std::string &id) { return this->magnetizability.at(id); } NMRShielding &getNMRShielding(const std::string &id) { return this->nmr_shielding.at(id); } GeometricDerivative &getGeometricDerivative(const std::string &id) { return this->geometric_derivative.at(id); } + HirshfeldCharges &getHirshfeldCharges(const std::string &id) { return this->hirshfeld_charges.at(id); } PropertyMap &getDipoleMoments() { return this->dipole; } PropertyMap &getQuadrupoleMoments() { return this->quadrupole; } @@ -125,6 +127,7 @@ class Molecule final { PropertyMap &getMagnetizabilities() { return this->magnetizability; } PropertyMap &getNMRShieldings() { return this->nmr_shielding; } PropertyMap &getGeometricDerivatives() { return this->geometric_derivative; } + PropertyMap &getHirshfeldCharges() { return this->hirshfeld_charges; } protected: int charge{0}; @@ -146,6 +149,7 @@ class Molecule final { PropertyMap magnetizability{}; PropertyMap nmr_shielding{}; PropertyMap geometric_derivative{}; + PropertyMap hirshfeld_charges{}; void readCoordinateFile(const std::string &file); void readCoordinateString(const std::vector &coord_str); diff --git a/src/driver.cpp b/src/driver.cpp index 29d75c2da..1d076c08b 100644 --- a/src/driver.cpp +++ b/src/driver.cpp @@ -27,6 +27,7 @@ #include #include +#include #include "driver.h" #include "chemistry/Molecule.h" @@ -82,6 +83,8 @@ #include "environment/PBESolver.h" #include "environment/Permittivity.h" +#include "properties/hirshfeld/HirshfeldPartition.h" + #include "mrdft/Factory.h" using mrcpp::ABGVOperator; @@ -217,6 +220,13 @@ void driver::init_properties(const json &json_prop, Molecule &mol) { if (not geom_map.count(id)) geom_map.insert({id, GeometricDerivative(mol.getNNuclei())}); } } + if (json_prop.contains("hirshfeld_charges")) { + for (const auto &item : json_prop["hirshfeld_charges"].items()) { + const auto &id = item.key(); + auto &hir_map = mol.getHirshfeldCharges(); + if (not hir_map.count(id)) hir_map.insert({id, HirshfeldCharges()}); + } + } } /** @brief Run ground-state SCF calculation @@ -575,6 +585,41 @@ void driver::scf::calc_properties(const json &json_prop, Molecule &mol) { if (plevel == 1) mrcpp::print::time(1, "NMR shielding (dia)", t_lap); } + if (json_prop.contains("hirshfeld_charges")) { + t_lap.start(); + std::string source_dir = HIRSHFELD_SOURCE_DIR; + std::string install_dir = HIRSHFELD_INSTALL_DIR; + std::string data_dir = ""; + // check if data_dir exists + if (std::filesystem::exists(install_dir)) { + data_dir = install_dir + "/lda/"; + } else if (std::filesystem::exists(source_dir)) { + data_dir = source_dir + "/lda/"; + } else { + MSG_ABORT("Hirshfeld data directory not found"); + } + for (const auto &item : json_prop["hirshfeld_charges"].items()) { + const auto &id = item.key(); + double prec = item.value()["precision"]; + + HirshfeldPartition partitioner(mol, data_dir); + mrchem::Density rho(false); + mrchem::density::compute(prec, rho, Phi, DensityType::Total); + Eigen::VectorXd charges = Eigen::VectorXd::Zero(mol.getNNuclei()); + for (int i = 0; i < mol.getNNuclei(); i++) { + if ( ! mrcpp::mpi::my_orb(i) ) continue; // my_orb also works for atoms. + double charge = partitioner.getHirshfeldPartitionIntegral(i, rho, prec); + charge = - charge + mol.getNuclei()[i].getCharge(); + charges(i) = charge; + } + mrcpp::mpi::allreduce_vector(charges, mrcpp::mpi::comm_wrk); + HirshfeldCharges &hir = mol.getHirshfeldCharges(id); + hir.setVector(charges); + } + mrcpp::print::footer(2, t_lap, 2); + if (plevel == 1) mrcpp::print::time(1, "Computing Hirshfeld charges", t_lap); + } + if (json_prop.contains("hyperpolarizability")) MSG_ERROR("Hyperpolarizability not implemented"); if (json_prop.contains("hyperfine_coupling")) MSG_ERROR("Hyperfine coupling not implemented"); if (json_prop.contains("spin_spin_coupling")) MSG_ERROR("Spin-spin coupling not implemented"); diff --git a/src/properties/CMakeLists.txt b/src/properties/CMakeLists.txt new file mode 100644 index 000000000..0c0448ed0 --- /dev/null +++ b/src/properties/CMakeLists.txt @@ -0,0 +1 @@ +add_subdirectory("hirshfeld") \ No newline at end of file diff --git a/src/properties/HirshfeldCharges.h b/src/properties/HirshfeldCharges.h new file mode 100644 index 000000000..f5dca8f77 --- /dev/null +++ b/src/properties/HirshfeldCharges.h @@ -0,0 +1,40 @@ +#pragma once + +#include + +#include "mrchem.h" + +#include "utils/math_utils.h" +#include "utils/print_utils.h" +#include + +namespace mrchem { + +class HirshfeldCharges final { +public: + + DoubleVector getVector() const { return this->hirshfeld_charges; } + + void setVector(const DoubleVector &v) { this->hirshfeld_charges = v; } + + void print(const std::string &id) const { + mrcpp::print::header(0, "Hirshfeld Charges (" + id + ")"); + mrcpp::print::separator(0, '-'); + for (int i = 0; i < hirshfeld_charges.size(); i++) { + std::string text = "Charge of atom " + std::to_string(i); + print_utils::scalar(0, text, hirshfeld_charges(i)); + } + mrcpp::print::separator(0, '-'); + print_utils::scalar(0, "Sum of Hirshfeld charges", getVector().sum(), "(au)", -1, true); + mrcpp::print::separator(0, '='); + } + + nlohmann::json json() const { + return {{"total", print_utils::eigen_to_vector(getVector(), 1.0e-12)}}; + } + +protected: + DoubleVector hirshfeld_charges; +}; + +} // namespace mrchem \ No newline at end of file diff --git a/src/properties/hirshfeld/CMakeLists.txt b/src/properties/hirshfeld/CMakeLists.txt new file mode 100644 index 000000000..11141cb12 --- /dev/null +++ b/src/properties/hirshfeld/CMakeLists.txt @@ -0,0 +1,4 @@ +target_sources(mrchem PRIVATE + ${CMAKE_CURRENT_SOURCE_DIR}/HirshfeldInterpolator.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/HirshfeldPartition.cpp + ) \ No newline at end of file diff --git a/src/properties/hirshfeld/HirshfeldInterpolator.cpp b/src/properties/hirshfeld/HirshfeldInterpolator.cpp new file mode 100644 index 000000000..ef67aa1bf --- /dev/null +++ b/src/properties/hirshfeld/HirshfeldInterpolator.cpp @@ -0,0 +1,49 @@ +#include "HirshfeldInterpolator.h" +#include "qmfunctions/density_utils.h" + +double HirshfeldRadInterpolater::getNorm() const { + double norm = 0.0; + double xmax = 20; + int n = 1000; + double dx = xmax / n; + for (int i = 0; i < n; i++) { + double x = i * dx; + double y = std::exp(evalf(x)); + norm += y * x * x; + } + norm *= dx * 4 * M_PI; + return norm; +} + +// Constructor +HirshfeldRadInterpolater::HirshfeldRadInterpolater(const std::string element, std::string data_dir, bool writeToFile) { + Eigen::VectorXd rGrid; + Eigen::VectorXd rhoGrid; + + std::string filename = data_dir + '/' + element + ".density"; + + mrchem::density::readAtomicDensity(filename, rGrid, rhoGrid); + + rhoGrid = rhoGrid.array().log(); + + lnRho = std::make_shared(rGrid, rhoGrid); + if (writeToFile) { + writeInterpolatedDensity(element + ".interpolated"); + } +} + +// Function to evaluate the interpolated function +double HirshfeldRadInterpolater::evalf(const double &r) const { + double y; + return lnRho->evalfLeftNoRightLinear(r); +} + +void HirshfeldRadInterpolater::writeInterpolatedDensity(const std::string path) { + std::ofstream file; + file.open(path); + for (double r = 0.0; r < 50.0; r += 0.01) { + double rho = this->evalf(r); + file << r << " " << rho << std::endl; + } + file.close(); +} \ No newline at end of file diff --git a/src/properties/hirshfeld/HirshfeldInterpolator.h b/src/properties/hirshfeld/HirshfeldInterpolator.h new file mode 100644 index 000000000..990c51ded --- /dev/null +++ b/src/properties/hirshfeld/HirshfeldInterpolator.h @@ -0,0 +1,40 @@ +#pragma once + +#include +#include +#include "utils/PolyInterpolator.h" + +class HirshfeldRadInterpolater { + +public: + /** + * @brief Construct a new Rad Interpolater object + * @param element The element for which the ZORA potential is to be interpolated + * @param data_dir The directory containing the ZORA potential data + */ + HirshfeldRadInterpolater(const std::string element, std::string data_dir, bool writeToFile = false); + + /** + * @brief Evaluate the interpolated function at a given point + * @param r The point at which to evaluate + * @return The interpolated value at the given point + */ + double evalf(const double &r) const; + + /** + * @brief Integrates the atomic charge density to get the charge of the tabulated + * atomic density. The numeric is performed from 0 to 20 bohr. Only useful for debugging. + */ + double getNorm() const; + +protected: + /** + * @brief The interpolator for the atomic density + */ + std::shared_ptr lnRho = nullptr; + /** + * @brief Write the interpolated density to a file for debugging. + * @param path The path to the file to write the interpolated density to. + */ + void writeInterpolatedDensity(const std::string path); +}; diff --git a/src/properties/hirshfeld/HirshfeldPartition.cpp b/src/properties/hirshfeld/HirshfeldPartition.cpp new file mode 100644 index 000000000..eb5a7fb32 --- /dev/null +++ b/src/properties/hirshfeld/HirshfeldPartition.cpp @@ -0,0 +1,51 @@ +#include "HirshfeldPartition.h" +#include "utils/math_utils.h" + +HirshfeldPartition::HirshfeldPartition(const mrchem::Molecule &mol, std::string data_dir) { + + this->nucs = std::make_shared(mol.getNuclei()); + this->nNucs = this->nucs->size(); + + for (int i = 0; i < this->nNucs; i++) { + std::string element = this->nucs->at(i).getElement().getSymbol(); + this->logDensities.push_back(HirshfeldRadInterpolater(element, data_dir)); + // Uncomment the following line to print the charge of the atomic density + // std::cout << "Norm of " << element << " = " << this->logDensities[i].getNorm() << std::endl; + } + +} + +double HirshfeldPartition::getHirshfeldPartitionIntegral(int index, mrcpp::ComplexFunction &rho, double prec) const { + auto w_i_analytic = [index, this](const mrcpp::Coord<3> &r) { + return this->evalf(r, index); + }; + mrcpp::ComplexFunction w_i_MW; + mrcpp::AnalyticFunction<3> w_i_analytic_func(w_i_analytic); + mrcpp::cplxfunc::multiply(w_i_MW, rho.real(), w_i_analytic_func, prec); + mrcpp::ComplexDouble c_complex = w_i_MW.integrate(); + double charge = c_complex.real(); + + return charge; +} + +double HirshfeldPartition::lseLogDens(const mrcpp::Coord<3> &r) const { + Eigen::VectorXd lseLogDens_r(this->nNucs); + double rr; + mrcpp::Coord<3> nucPos; + for (int i = 0; i < this->nNucs; i++) { + nucPos = this->nucs->at(i).getCoord(); + rr = std::sqrt((r[0] - nucPos[0]) * (r[0] - nucPos[0]) + + (r[1] - nucPos[1]) * (r[1] - nucPos[1]) + + (r[2] - nucPos[2]) * (r[2] - nucPos[2])); + lseLogDens_r(i) = this->logDensities[i].evalf(rr); + } + return mrchem::math_utils::logsumexp(lseLogDens_r); +} + +double HirshfeldPartition::evalf(const mrcpp::Coord<3> &r, int iAt) const { + mrcpp::Coord<3> nucPos = this->nucs->at(iAt).getCoord(); + double rr = std::sqrt((r[0] - nucPos[0]) * (r[0] - nucPos[0]) + + (r[1] - nucPos[1]) * (r[1] - nucPos[1]) + + (r[2] - nucPos[2]) * (r[2] - nucPos[2])); + return std::exp(this->logDensities[iAt].evalf(rr) - this->lseLogDens(r)); +} \ No newline at end of file diff --git a/src/properties/hirshfeld/HirshfeldPartition.h b/src/properties/hirshfeld/HirshfeldPartition.h new file mode 100644 index 000000000..2f28f4854 --- /dev/null +++ b/src/properties/hirshfeld/HirshfeldPartition.h @@ -0,0 +1,57 @@ +#pragma once + +#include +#include +#include "chemistry/Molecule.h" +#include +#include "chemistry/Nucleus.h" +#include "properties/hirshfeld/HirshfeldInterpolator.h" + +/** + * @brief Class for computing the Hirshfeld partitioning of a molecule. Reads and interpolates the Hirshfeld partitioning data. + * can create MW representation of the Hirshfeld partitioning functions. + */ +class HirshfeldPartition{ + + public: + /** + * @brief Construct a new Hirshfeld Partition object + * @param mol The molecule for which the Hirshfeld partitioning is to be computed + * @param data_dir The directory containing the Hirshfeld partitioning data + */ + HirshfeldPartition(const mrchem::Molecule &mol, std::string data_dir); + + /** + * @brief Get the integral rho * w_i for a given atom i + */ + double getHirshfeldPartitionIntegral(int index, mrcpp::ComplexFunction &rho, double prec) const; + + protected: + + /** + * @brief Evaluate the analytic, interpolated Hirshfeld partitioning function at a given point + */ + double evalf(const mrcpp::Coord<3> &r, int iAt) const; + + /** + * @brief Evaluate the log sum of the exponential of the log atomic densities at a given point. + */ + double lseLogDens(const mrcpp::Coord<3> &r) const; + + /** + * @brief The nuclei of the molecule + */ + std::shared_ptr nucs{nullptr}; + + /** + * @brief The number of nuclei in the molecule + */ + int nNucs; + + /** + * @brief The atomic density interpolators for the nuclei + */ + std::vector logDensities; + + +}; \ No newline at end of file diff --git a/src/qmfunctions/density_utils.cpp b/src/qmfunctions/density_utils.cpp index 423017543..543ee96e2 100644 --- a/src/qmfunctions/density_utils.cpp +++ b/src/qmfunctions/density_utils.cpp @@ -33,6 +33,7 @@ #include "Orbital.h" #include "density_utils.h" #include "orbital_utils.h" +#include using mrcpp::FunctionTree; using mrcpp::FunctionTreeVector; @@ -274,4 +275,24 @@ void density::allreduce_density(double prec, Density &rho_tot, Density &rho_loc) } } + +// Function to read atomic density data from a file +void density::readAtomicDensity(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &rhoGrid) { + std::vector r, rho; + std::ifstream file(path); + std::string line; + double r_, rho_; + while (std::getline(file, line)) { + std::istringstream iss(line); + iss >> r_ >> rho_; + if (rho_ > 0) { + r.push_back(r_); + rho.push_back(rho_); + } + } + file.close(); + rGrid = Eigen::Map(r.data(), r.size()); + rhoGrid = Eigen::Map(rho.data(), rho.size()); +} + } // namespace mrchem diff --git a/src/qmfunctions/density_utils.h b/src/qmfunctions/density_utils.h index 2c2f02bac..b177ccfac 100644 --- a/src/qmfunctions/density_utils.h +++ b/src/qmfunctions/density_utils.h @@ -27,6 +27,7 @@ #include "mrchem.h" #include "Orbital.h" +#include "Density.h" namespace mrchem { namespace density { @@ -38,5 +39,13 @@ void compute(double prec, Density &rho, OrbitalVector &Phi, OrbitalVector &X, Or void compute_local(double prec, Density &rho, OrbitalVector &Phi, DensityType spin); void compute_local(double prec, Density &rho, OrbitalVector &Phi, OrbitalVector &X, OrbitalVector &Y, DensityType spin); +/** + * @brief Reads atomic density data from a file + * @param path The path to the file containing the data + * @param rGrid The grid for the radial distances + * @param rhoGrid The grid for the atomic density values + */ +void readAtomicDensity(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &rhoGrid); + } // namespace density } // namespace mrchem diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt index cc1b5cce5..6652c4682 100644 --- a/src/utils/CMakeLists.txt +++ b/src/utils/CMakeLists.txt @@ -1,5 +1,6 @@ target_sources(mrchem PRIVATE + ${CMAKE_CURRENT_SOURCE_DIR}/PolyInterpolator.cpp ${CMAKE_CURRENT_SOURCE_DIR}/print_utils.cpp ${CMAKE_CURRENT_SOURCE_DIR}/math_utils.cpp ${CMAKE_CURRENT_SOURCE_DIR}/NonlinearMaximizer.cpp diff --git a/src/utils/PolyInterpolator.cpp b/src/utils/PolyInterpolator.cpp new file mode 100644 index 000000000..02dcd829a --- /dev/null +++ b/src/utils/PolyInterpolator.cpp @@ -0,0 +1,82 @@ +#include +#include "PolyInterpolator.h" + +namespace interpolation_utils{ +double polynomialInterpolate5(Eigen::VectorXd &x_in, Eigen::VectorXd &y_in, double x){ + double xm2 = x_in(0); + double xm1 = x_in(1); + double x00 = x_in(2); + double xp1 = x_in(3); + double xp2 = x_in(4); + + double ym2 = y_in(0); + double ym1 = y_in(1); + double y00 = y_in(2); + double yp1 = y_in(3); + double yp2 = y_in(4); + return ym2 + (x - xm2)*((ym1 - ym2)/(xm1 - xm2) + + (x - xm1)*(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2) + + (x - x00)*((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1) + + ((x - xp1)*(-((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/ + (-xm2 + xp1)) + (-(((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/ + (-xm1 + xp1)) + ((-y00 + yp1)/(x00 - xp1) + (yp1 - yp2)/(xp1 - xp2))/(-x00 + xp2))/ + (-xm1 + xp2)))/(-xm2 + xp2)))); +} + + +double polynomialInterpolate5_deriv(Eigen::VectorXd &x_in, Eigen::VectorXd &y_in, double x) { + double xm2 = x_in(0); + double xm1 = x_in(1); + double x00 = x_in(2); + double xp1 = x_in(3); + double xp2 = x_in(4); + + double ym2 = y_in(0); + double ym1 = y_in(1); + double y00 = y_in(2); + double yp1 = y_in(3); + double yp2 = y_in(4); + + return (ym1 - ym2)/(xm1 - xm2) + (x - xm1)*(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2) + + (x - x00)*((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1) + + ((x - xp1)*(-((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1)) + + (-(((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1)) + + ((-y00 + yp1)/(x00 - xp1) + (yp1 - yp2)/(xp1 - xp2))/(-x00 + xp2))/(-xm1 + xp2)))/(-xm2 + xp2))) + + (x - xm2)*(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2) + + (x - x00)*((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1) + + ((x - xp1)*(-((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1)) + + (-(((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1)) + + ((-y00 + yp1)/(x00 - xp1) + (yp1 - yp2)/(xp1 - xp2))/(-x00 + xp2))/(-xm1 + xp2)))/(-xm2 + xp2)) + + (x - xm1)*((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1) + + ((x - x00)*(-((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1)) + + (-(((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1)) + + ((-y00 + yp1)/(x00 - xp1) + (yp1 - yp2)/(xp1 - xp2))/(-x00 + xp2))/(-xm1 + xp2)))/(-xm2 + xp2) + + ((x - xp1)*(-((-(((y00 - ym1)/(x00 - xm1) + (-ym1 + ym2)/(xm1 - xm2))/(x00 - xm2)) + + ((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1))/(-xm2 + xp1)) + + (-(((-y00 + ym1)/(x00 - xm1) + (y00 - yp1)/(x00 - xp1))/(-xm1 + xp1)) + + ((-y00 + yp1)/(x00 - xp1) + (yp1 - yp2)/(xp1 - xp2))/(-x00 + xp2))/(-xm1 + xp2)))/(-xm2 + xp2))); +} + +int binarySearch(const Eigen::VectorXd &x, const double &x0) { + int i = 0; + int j = x.size() - 1; + int k; + while (j - i > 1) { + k = (i + j)/2; + if (x0 < x(k)) { + j = k; + } else { + i = k; + } + } + return i; +} +} // namespace interpolation_utils \ No newline at end of file diff --git a/src/utils/PolyInterpolator.h b/src/utils/PolyInterpolator.h new file mode 100644 index 000000000..26bf2cd98 --- /dev/null +++ b/src/utils/PolyInterpolator.h @@ -0,0 +1,137 @@ +#pragma once +#include +#include +#include +#include +#include +#include + +namespace interpolation_utils{ + +/** + * @brief Interpolate a 5th order polynomial through 5 points and evaluate at x. + * @param x_in x values of the 5 points + * @param y_in y values of the 5 points + * @param x x value at which to evaluate the polynomial + */ +double polynomialInterpolate5(Eigen::VectorXd &x_in, Eigen::VectorXd &y_in, double x); + +/** + * @brief Evaluate the derivative of a 5th order polynomial through 5 points at x. + * @param x_in x values of the 5 points + * @param y_in y values of the 5 points + * @param x x value at which to evaluate the derivative of the polynomial + */ +double polynomialInterpolate5_deriv(Eigen::VectorXd &x_in, Eigen::VectorXd &y_in, double x); + +/** + * @brief Binary search for the index of the largest element in x that is smaller than x0. + * @param x Vector to search in + * @param x0 Value to search for + */ +int binarySearch(const Eigen::VectorXd &x, const double &x0); + +/** + * @brief Class to interpolate a functions using a 5th order polynomials. + */ +class PolyInterpolator { + Eigen::VectorXd x; + Eigen::VectorXd y; + int n; + double xmin; + double xmax; + /** + * @brief Derivative of the interpolated function at xmax. Used for linear extrapolation. + */ + double ypxmax; + + /** + * @brief Derivative of the interpolated function at xmin. Used for linear extrapolation. + */ + double ypxmin; + + public: + /** + * @brief Constructor + * @param x_in x values of the points to interpolate + * @param y_in y values of the points to interpolate + */ + PolyInterpolator(Eigen::VectorXd &x_in, Eigen::VectorXd &y_in){ + x = x_in; + y = y_in; + n = x_in.size(); + xmin = x_in(0); + xmax = x_in(x_in.size() - 1); + Eigen::VectorXd x_in_poly(5), y_in_poly(5); + + int j = 0; + for (int i = n - 5; i < n; i++) { + x_in_poly(j) = x(i); + y_in_poly(j) = y(i); + j++; + } + ypxmax = polynomialInterpolate5_deriv(x_in_poly, y_in_poly, xmax); + for (int i = 0; i < 5; i++) { + x_in_poly(i) = x(i); + y_in_poly(i) = y(i); + } + ypxmin = polynomialInterpolate5_deriv(x_in_poly, y_in_poly, xmin); + } + + /** + * @brief Evaluate the interpolated function at x. + * No extrapolation for x < xmin (meaning that the polynomial is evaluated at x < xmin), linear extrapolation for x > xmax. + * Useful when the logarithm of the density is interpolated. + * @param x x value at which to evaluate the function + */ + double evalfLeftNoRightLinear(const double &xval) const{ + double y; + if (xval > xmax) { // linear extrapolation + y = this->y(n - 1) + ypxmax*(xval - xmax); + return y; + } + + Eigen::VectorXd x_in_poly(5), y_in_poly(5); + int i = adjustIndexToBoundaries(binarySearch(this->x, xval)); + for (int k = 0; k < 5; k++) { + x_in_poly(k) = this->x(i - 2 + k); + y_in_poly(k) = this->y(i - 2 + k); + } + y = polynomialInterpolate5(x_in_poly, y_in_poly, xval); + return y; + } + + /** + * @brief Evaluate the interpolated function at x. + * No extrapolation for x < xmin (meaning that the polynomial is evaluated at x < xmin), zero is returned for x > xmax. + * Useful when the density is interpolated. + * @param x x value at which to evaluate the function + */ + double evalfLeftNoRightZero(const double &xval) const{ + double y; + if (xval > xmax) { // constant + y = 0.0; + return y; + } + + Eigen::VectorXd x_in_poly(5), y_in_poly(5); + int j = adjustIndexToBoundaries(binarySearch(this->x, xval)); + int i = adjustIndexToBoundaries(binarySearch(this->x, xval)); + for (int k = 0; k < 5; k++) { + x_in_poly(k) = this->x(i - 2 + k); + y_in_poly(k) = this->y(i - 2 + k); + } + y = polynomialInterpolate5(x_in_poly, y_in_poly, xval); + return y; + } + private: + int adjustIndexToBoundaries(int i) const { + int j = i; + if (i == 0) j = 2; + if (i == 1) j = 2; + if (i == n - 1) j = n - 3; + if (i == n - 2) j = n - 3; + return j; + } +}; +} // namespace interpolation_utils \ No newline at end of file diff --git a/src/utils/math_utils.cpp b/src/utils/math_utils.cpp index 7fe526b56..bc9ee4fd1 100644 --- a/src/utils/math_utils.cpp +++ b/src/utils/math_utils.cpp @@ -170,5 +170,15 @@ void diagonalize_block(ComplexMatrix &A, ComplexMatrix &U, int nstart, int nsize A.block(nstart, nstart, nsize, nsize) = ei_val.asDiagonal(); } +/** + * @brief Compute the log of the sum of exponentials of the elements of a vector. + * Numerically stable for large and small x. + * @param x Vector of values where the logsumexp is to be computed. + */ +double logsumexp(const Eigen::VectorXd &x){ + double max = x.maxCoeff(); + return max + std::log((x.array() - max).exp().sum()); +} + } // namespace math_utils } // namespace mrchem diff --git a/src/utils/math_utils.h b/src/utils/math_utils.h index 43427ec98..1b8552456 100644 --- a/src/utils/math_utils.h +++ b/src/utils/math_utils.h @@ -46,6 +46,7 @@ DoubleMatrix skew_matrix_exp(const DoubleMatrix &A); ComplexMatrix hermitian_matrix_pow(const ComplexMatrix &A, double b); ComplexMatrix diagonalize_hermitian_matrix(const ComplexMatrix &A, DoubleVector &diag); void diagonalize_block(ComplexMatrix &M, ComplexMatrix &U, int nstart, int nsize); +double logsumexp(const Eigen::VectorXd &x); } // namespace math_utils } // namespace mrchem diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index e7a1417fd..42e7f36e4 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -23,6 +23,7 @@ add_subdirectory(h2_scf_hf) add_subdirectory(h2_pol_lda) add_subdirectory(h2_mag_lda) add_subdirectory(h2o_energy_blyp) +add_subdirectory(h2o_hirshfeld_lda) add_subdirectory(h2_pol_cube) add_subdirectory(li_scf_pbe0) add_subdirectory(li_pol_lda) diff --git a/tests/h2o_hirshfeld_lda/CMakeLists.txt b/tests/h2o_hirshfeld_lda/CMakeLists.txt new file mode 100644 index 000000000..110dcebbb --- /dev/null +++ b/tests/h2o_hirshfeld_lda/CMakeLists.txt @@ -0,0 +1,11 @@ +if(ENABLE_MPI) + set(_h2o_hirshfeld_lda_launcher "${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 1") +endif() + +add_integration_test( + NAME "H2O_Hirshfeld_charges_LDA" + LABELS "H2O_hirshfeld_charges_LDA;hirshfeld;mrchem;charges" + COST 100 + LAUNCH_AGENT ${_h2o_hirshfeld_lda_launcher} + INITIAL_GUESS ${CMAKE_CURRENT_LIST_DIR}/initial_guess + ) diff --git a/tests/h2o_hirshfeld_lda/h2o.inp b/tests/h2o_hirshfeld_lda/h2o.inp new file mode 100644 index 000000000..e7b0b7770 --- /dev/null +++ b/tests/h2o_hirshfeld_lda/h2o.inp @@ -0,0 +1,25 @@ +world_prec = 1.0e-4 +world_unit = angstrom + +WaveFunction { + method = lda +} + +SCF { +run = false +guess_type = GTO +guess_screen = 16.0 +} + +Molecule { +translate = true +$coords +O 0.0000 0.0000 -0.1250 +H -1.4375 0.0000 1.0250 +H 1.4375 0.0000 1.0250 +$end +} + +Properties { + hirshfeld_charges = true +} diff --git a/tests/h2o_hirshfeld_lda/initial_guess/mrchem.bas b/tests/h2o_hirshfeld_lda/initial_guess/mrchem.bas new file mode 100644 index 000000000..62a420ec7 --- /dev/null +++ b/tests/h2o_hirshfeld_lda/initial_guess/mrchem.bas @@ -0,0 +1,31 @@ +Gaussian basis cc-pVDZ + 2 + 8. 1 3 1 1 1 +O 0.0000000000 0.0000000000 -0.1250000000 + 9 3 + 11720.0000000 0.00071000 -0.00016000 0.00000000 + 1759.0000000 0.00547000 -0.00126300 0.00000000 + 400.8000000 0.02783700 -0.00626700 0.00000000 + 113.7000000 0.10480000 -0.02571600 0.00000000 + 37.0300000 0.28306200 -0.07092400 0.00000000 + 13.2700000 0.44871900 -0.16541100 0.00000000 + 5.0250000 0.27095200 -0.11695500 0.00000000 + 1.0130000 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1.8897261246257702, + "boltzmann_constant": 1.380649e-23, + "dipmom_au2debye": 2.5417464739297717, + "e0": 8.8541878128e-12, + "electron_g_factor": -2.00231930436256, + "elementary_charge": 1.602176634e-19, + "fine_structure_constant": 0.0072973525693, + "hartree2ev": 27.211386245988, + "hartree2kcalmol": 627.5094740630558, + "hartree2kjmol": 2625.4996394798254, + "hartree2simagnetizability": 78.9451185, + "hartree2wavenumbers": 219474.6313632, + "light_speed": 137.035999084, + "meter2bohr": 18897261246.2577 + }, + "geom_opt": { + "init_step_size": -0.5, + "max_force_component": 0.005, + "max_history_length": 10, + "max_iter": 100, + "minimal_step_size": 0.01, + "run": false, + "subspace_tolerance": 0.001, + "use_previous_guess": false + }, + "molecule": { + "charge": 0, + "coords": [ + { + "atom": "o", + "r_rms": 5.0580178957e-05, + "xyz": [ + 0.0, + 0.0, + -0.24317580771029856 + ] + }, + { + "atom": "h", + "r_rms": 2.6569547399e-05, + "xyz": [ + -2.7164813041495446, + 0.0, + 1.9300092356093368 + ] + }, + { + "atom": "h", + "r_rms": 2.6569547399e-05, + "xyz": [ + 2.7164813041495446, + 0.0, + 1.9300092356093368 + ] + } + ], + "multiplicity": 1 + }, + "mpi": { + "bank_size": -1, + "numerically_exact": false, + "omp_threads": -1, + "shared_memory_size": 10000 + }, + "mra": { + "basis_order": 6, + "basis_type": "interpolating", + "boxes": [ + 2, + 2, + 2 + ], + "corner": [ + -1, + -1, + -1 + ], + "max_scale": 20, + "min_scale": -5 + }, + "printer": { + "file_name": "h2o", + "print_constants": false, + "print_level": 0, + "print_mpi": false, + "print_prec": 6, + "print_width": 75 + }, + "rsp_calculations": {}, + "scf_calculation": { + "fock_operator": { + "coulomb_operator": { + "poisson_prec": 0.0001, + "shared_memory": false + }, + "exchange_operator": { + "exchange_prec": -1.0, + "poisson_prec": 0.0001 + }, + "kinetic_operator": { + "derivative": "abgv_55" + }, + "nuclear_operator": { + "nuclear_model": "point_like", + "proj_prec": 0.0001, + "shared_memory": false, + "smooth_prec": 0.0001 + }, + "xc_operator": { + "shared_memory": false, + "xc_functional": { + "cutoff": 0.0, + "functionals": [ + { + "coef": 1.0, + "name": "svwn5" + } + ], + "spin": false + } + } + }, + "initial_guess": { + "environment": "None", + "external_field": "None", + "file_CUBE_a": "cube_vectors/CUBE_a_vector.json", + "file_CUBE_b": "cube_vectors/CUBE_b_vector.json", + "file_CUBE_p": "cube_vectors/CUBE_p_vector.json", + "file_basis": "initial_guess/mrchem.bas", + "file_chk": "checkpoint/phi_scf", + "file_gto_a": "initial_guess/mrchem.moa", + "file_gto_b": "initial_guess/mrchem.mob", + "file_gto_p": "initial_guess/mrchem.mop", + "file_phi_a": "initial_guess/phi_a_scf", + "file_phi_b": "initial_guess/phi_b_scf", + "file_phi_p": "initial_guess/phi_p_scf", + "localize": false, + "method": "DFT (SVWN5)", + "prec": 0.001, + "relativity": "None", + "restricted": true, + "rotate": true, + "screen": 16.0, + "type": "gto", + "zeta": 0 + }, + "properties": { + "dipole_moment": { + "dip-1": { + "operator": "h_e_dip", + "precision": 0.0001, + "r_O": [ + 0.0, + 0.0, + 0.0 + ] + } + }, + "hirshfeld_charges": { + "hirshfeld-1": { + "precision": 0.0001 + } + } + } + }, + "schema_name": "mrchem_input", + "schema_version": 1 + }, + "output": { + "properties": { + "center_of_mass": [ + -5.341976807564934e-18, + 0.0, + -4.4424263363005454e-17 + ], + "charge": 0, + "dipole_moment": { + "dip-1": { + "magnitude": 1.6438995746893366, + "r_O": [ + 0.0, + 0.0, + 0.0 + ], + "vector": [ + 7.54141469758662e-07, + -8.797188200272936e-12, + 1.6438995746891636 + ], + "vector_el": [ + 7.541484348538293e-07, + 0.0, + -0.2707124348527402 + ], + "vector_nuc": [ + -6.965095167288382e-12, + -8.789230986014012e-12, + 1.914612009541904 + ] + } + }, + "geometry": [ + { + "symbol": "O", + "xyz": [ + 0.0, + 0.0, + -0.24317580771029856 + ] + }, + { + "symbol": "H", + "xyz": [ + -2.7164813041495446, + 0.0, + 1.9300092356093368 + ] + }, + { + "symbol": "H", + "xyz": [ + 2.7164813041495446, + 0.0, + 1.9300092356093368 + ] + } + ], + "hirshfeld_charges": { + "hirshfeld-1": { + "total": [ + -1.2256509183213495, + 0.6128254383501298, + 0.6128255933129395 + ] + } + }, + "multiplicity": 1, + "orbital_energies": { + "energy": [ + -5.831541422026438, + 0.2868881749197759, + 0.35041507983376347, + 0.4278104311862625, + 2.458354368701725 + ], + "occupation": [ + 2.0, + 2.0, + 2.0, + 2.0, + 2.0 + ], + "spin": [ + "p", + "p", + "p", + "p", + "p" + ], + "sum_occupied": -4.616146734769822 + }, + "scf_energy": { + "E_ee": 46.76254664433691, + "E_eext": 0.0, + "E_el": -48.595421761243195, + "E_en": -162.42893318609498, + "E_kin": 75.84734150946595, + "E_next": 0.0, + "E_nn": 4.783357401076065, + "E_nuc": 4.783357401076065, + "E_tot": -43.81206436016713, + "E_x": 0.0, + "E_xc": -8.77637672895107, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + } + }, + "provenance": { + "creator": "MRChem", + "mpi_processes": 1, + "nthreads": 8, + "routine": "mrchem.x", + "total_cores": 8, + "version": "1.2.0-alpha" + }, + "rsp_calculations": null, + "scf_calculation": { + "initial_energy": { + "E_ee": 46.76254664433691, + "E_eext": 0.0, + "E_el": -48.595421761243195, + "E_en": -162.42893318609498, + "E_kin": 75.84734150946595, + "E_next": 0.0, + "E_nn": 4.783357401076065, + "E_nuc": 4.783357401076065, + "E_tot": -43.81206436016713, + "E_x": 0.0, + "E_xc": -8.77637672895107, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + }, + "success": true + }, + "schema_name": "mrchem_output", + "schema_version": 1, + "success": true + } +} diff --git a/tests/h2o_hirshfeld_lda/reference/h2o.out b/tests/h2o_hirshfeld_lda/reference/h2o.out new file mode 100644 index 000000000..2ceb821ee --- /dev/null +++ b/tests/h2o_hirshfeld_lda/reference/h2o.out @@ -0,0 +1,281 @@ + + +*************************************************************************** +*** *** +*** *** +*** __ __ ____ ____ _ *** +*** | \/ | _ \ / ___| |__ ___ _ __ ___ *** +*** | |\/| | |_) | | | '_ \ / _ \ '_ ` _ \ *** +*** | | | | _ <| |___| | | | __/ | | | | | *** +*** |_| |_|_| \_\\____|_| |_|\___|_| |_| |_| *** +*** *** +*** VERSION 1.2.0-alpha *** +*** *** +*** Git branch property/hirshfeld *** +*** Git commit hash 13ea821841ed585ecac1 *** +*** Git commit author moritzgubler *** +*** Git commit date Wed Sep 25 16:32:04 2024 +0200 *** +*** *** +*** Contact: luca.frediani@uit.no *** +*** *** +*** Radovan Bast Magnar Bjorgve *** +*** Roberto Di Remigio Antoine Durdek *** +*** Luca Frediani Gabriel Gerez *** +*** Stig Rune Jensen Jonas Juselius *** +*** Rune Monstad Peter Wind *** +*** *** +*************************************************************************** + +--------------------------------------------------------------------------- + + MPI processes : (no bank) 1 + OpenMP threads : 8 + Total cores : 8 + +--------------------------------------------------------------------------- + +XCFun DFT library Copyright 2009-2020 Ulf Ekstrom and contributors. +See http://dftlibs.org/xcfun/ for more information. + +This is free software; see the source code for copying conditions. +There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or +FITNESS FOR A PARTICULAR PURPOSE. For details see the documentation. +Scientific users of this library should cite +U. Ekstrom, L. Visscher, R. Bast, A. J. Thorvaldsen and K. Ruud; +J.Chem.Theor.Comp. 2010, DOI: 10.1021/ct100117s + +--------------------------------------------------------------------------- + + MRCPP version : 1.6.0-alpha + Git branch : HEAD + Git commit hash : 720133372c9717134c5a + Git commit author : gitpeterwind + Git commit date : Thu Feb 15 13:44:31 2024 +0100 + + Linear algebra : EIGEN v3.4.0 + Parallelization : MPI/OpenMP (8 threads) + +--------------------------------------------------------------------------- + + + +=========================================================================== + MultiResolution Analysis +--------------------------------------------------------------------------- + polynomial order : 6 + polynomial type : Interpolating +--------------------------------------------------------------------------- + total boxes : 8 + boxes : [ 2 2 2 ] + unit lengths : [ 32.00000 32.00000 32.00000 ] + scaling factor : [ 1.00000 1.00000 1.00000 ] + lower bounds : [ -32.00000 -32.00000 -32.00000 ] + upper bounds : [ 32.00000 32.00000 32.00000 ] + total length : [ 64.00000 64.00000 64.00000 ] +=========================================================================== + + + +*************************************************************************** +*** *** +*** Initializing Molecule *** +*** *** +*************************************************************************** + + +=========================================================================== + Molecule +--------------------------------------------------------------------------- + Charge : 0 + Multiplicity : 1 +--------------------------------------------------------------------------- + N Atom : x y z +--------------------------------------------------------------------------- + 0 O : 0.000000 0.000000 -0.243176 + 1 H : -2.716481 0.000000 1.930009 + 2 H : 2.716481 0.000000 1.930009 +--------------------------------------------------------------------------- + Center of mass : -0.000000 0.000000 -0.000000 +=========================================================================== + + + +*************************************************************************** +*** *** +*** Computing Initial Guess Wavefunction *** +*** *** +*************************************************************************** + + +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Calculation : Compute initial orbitals + Method : Project GTO molecular orbitals + Precision : 1.00000e-03 + Screening : 1.60000e+01 StdDev + Restricted : True + MO file : initial_guess/mrchem.mop +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +=========================================================================== + Molecular Orbitals +--------------------------------------------------------------------------- + Alpha electrons : 5 + Beta electrons : 5 + Total electrons : 10 +--------------------------------------------------------------------------- + n Occ Spin : Norm +--------------------------------------------------------------------------- + 0 2 p : 1.000000203320e+00 + 1 2 p : 1.000000064900e+00 + 2 2 p : 9.999999960131e-01 + 3 2 p : 1.000000004599e+00 + 4 2 p : 9.999999947944e-01 +=========================================================================== + + +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Calculation : Compute initial energy + Method : DFT (SVWN5) + Relativity : None + Environment : None + External fields : None + Precision : 1.00000e-03 + Localization : Off +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +=========================================================================== + Molecular Energy (initial) +--------------------------------------------------------------------------- + Kinetic energy : (au) 75.847341509466 + E-N energy : (au) -162.428933186095 + Coulomb energy : (au) 46.762546644337 + Exchange energy : (au) 0.000000000000 + X-C energy : (au) -8.776376728951 + N-N energy : (au) 4.783357401076 +--------------------------------------------------------------------------- + Electronic energy : (au) -48.595421761243 + Nuclear energy : (au) 4.783357401076 +--------------------------------------------------------------------------- + Total energy : (au) -4.381206436017e+01 + : (kcal/mol) -2.749248546427e+04 + : (kJ/mol) -1.150285591825e+05 + : (eV) -1.192187005539e+03 +=========================================================================== + + +=========================================================================== + Orbital Energies (initial) +--------------------------------------------------------------------------- + n Occ Spin : Epsilon +--------------------------------------------------------------------------- + 0 2 p : (au) -5.831541422026 + 1 2 p : (au) 0.286888174920 + 2 2 p : (au) 0.350415079834 + 3 2 p : (au) 0.427810431186 + 4 2 p : (au) 2.458354368702 +--------------------------------------------------------------------------- + Sum occupied : (au) -4.616146734770 +=========================================================================== + + + +*************************************************************************** +*** *** +*** Printing Molecular Properties *** +*** *** +*************************************************************************** + + +=========================================================================== + Molecule +--------------------------------------------------------------------------- + Charge : 0 + Multiplicity : 1 +--------------------------------------------------------------------------- + N Atom : x y z +--------------------------------------------------------------------------- + 0 O : 0.000000 0.000000 -0.243176 + 1 H : -2.716481 0.000000 1.930009 + 2 H : 2.716481 0.000000 1.930009 +--------------------------------------------------------------------------- + Center of mass : -0.000000 0.000000 -0.000000 +=========================================================================== + + +=========================================================================== + Molecular Energy (final) +--------------------------------------------------------------------------- + Kinetic energy : (au) 75.847341509466 + E-N energy : (au) -162.428933186095 + Coulomb energy : (au) 46.762546644337 + Exchange energy : (au) 0.000000000000 + X-C energy : (au) -8.776376728951 + N-N energy : (au) 4.783357401076 +--------------------------------------------------------------------------- + Electronic energy : (au) -48.595421761243 + Nuclear energy : (au) 4.783357401076 +--------------------------------------------------------------------------- + Total energy : (au) -4.381206436017e+01 + : (kcal/mol) -2.749248546427e+04 + : (kJ/mol) -1.150285591825e+05 + : (eV) -1.192187005539e+03 +=========================================================================== + + +=========================================================================== + Orbital Energies (final) +--------------------------------------------------------------------------- + n Occ Spin : Epsilon +--------------------------------------------------------------------------- + 0 2 p : (au) -5.831541422026 + 1 2 p : (au) 0.286888174920 + 2 2 p : (au) 0.350415079834 + 3 2 p : (au) 0.427810431186 + 4 2 p : (au) 2.458354368702 +--------------------------------------------------------------------------- + Sum occupied : (au) -4.616146734770 +=========================================================================== + + +=========================================================================== + Dipole Moment (dip-1) +--------------------------------------------------------------------------- + r_O : 0.000000 0.000000 0.000000 +--------------------------------------------------------------------------- + Electronic vector : 0.000001 -0.000000 -0.270712 + Magnitude : (au) 0.270712 + : (Debye) 0.688082 +--------------------------------------------------------------------------- + Nuclear vector : -0.000000 -0.000000 1.914612 + Magnitude : (au) 1.914612 + : (Debye) 4.866458 +--------------------------------------------------------------------------- + Total vector : 0.000001 -0.000000 1.643900 + Magnitude : (au) 1.643900 + : (Debye) 4.178376 +=========================================================================== + + +=========================================================================== + Hirshfeld Charges (hirshfeld-1) +--------------------------------------------------------------------------- +--------------------------------------------------------------------------- + Charge of atom 0 : -1.225651 + Charge of atom 1 : 0.612825 + Charge of atom 2 : 0.612826 +--------------------------------------------------------------------------- + Sum of Hirshfeld charges: (au) 1.133417e-07 +=========================================================================== + + +*************************************************************************** +*** *** +*** Exiting MRChem *** +*** *** +*** Wall time : 0h 0m 2s *** +*** *** +*************************************************************************** + + diff --git a/tests/h2o_hirshfeld_lda/test b/tests/h2o_hirshfeld_lda/test new file mode 100755 index 000000000..014e15c90 --- /dev/null +++ b/tests/h2o_hirshfeld_lda/test @@ -0,0 +1,27 @@ +#!/usr/bin/env python3 + +import sys +from pathlib import Path + +sys.path.append(str(Path(__file__).resolve().parents[1])) + +from tester import * # isort:skip + +options = script_cli() + +filters = { + SUM_OCCUPIED: rel_tolerance(1.0e-6), + E_KIN: rel_tolerance(1.0e-6), + E_EN: rel_tolerance(1.0e-6), + E_EE: rel_tolerance(1.0e-6), + E_X: rel_tolerance(1.0e-6), + E_XC: rel_tolerance(1.0e-6), + E_EEXT: rel_tolerance(1.0e-6), + E_NEXT: rel_tolerance(1.0e-6), + E_EL: rel_tolerance(1.0e-6), + HIRSHFELD_CHARGES(1, "total"): rel_tolerance(1.0e-6) +} + +ierr = run(options, input_file="h2o", filters=filters) + +sys.exit(ierr) diff --git a/tests/tester.py b/tests/tester.py index 4cadb7013..98aa25e9c 100644 --- a/tests/tester.py +++ b/tests/tester.py @@ -71,6 +71,8 @@ def NMR_SHIELDING(atom): def GEOMETRIC_DERIVATIVE(index, comp): return ("output", "properties", "geometric_derivative", f"geom-{index}", comp) +def HIRSHFELD_CHARGES(index, comp): + return ("output", "properties", "hirshfeld_charges", f"hirshfeld-{index}", comp) def run(options, *, input_file, filters=None, extra_args=None): launcher = "mrchem"