From 0592e581e22dfc777e5186e419c16b0c6ec3ad47 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:05:08 +0200 Subject: [PATCH 01/50] add azora optionss --- python/template.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/python/template.yml b/python/template.yml index 296115289..e12858b87 100644 --- a/python/template.yml +++ b/python/template.yml @@ -290,12 +290,14 @@ sections: type: str default: none predicates: - - value.lower() in ['none', 'zora', 'nzora'] + - value.lower() in ['none', 'zora', 'nzora', 'azora'] docstring: | Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). + ``azora`` uses atomic ZORA potentials, which are precomputed and read from the directory + specified in the ``azora_potential_path`` keyword. - name: environment type: str default: none @@ -335,6 +337,11 @@ sections: default: true docstring: | Include the XC potential ``V_xc`` in the ZORA potential. + - name: azora_potential_path + type: str + default: /home/moritz/Documents/mrchem/share/azora_potentials/ + docstring: | + Path to the directory containing the AZORA potentials. - name: DFT docstring: | Define the exchange-correlation functional in case of DFT. From 092820398492d9f260766b286945dc054298d3be Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:05:21 +0200 Subject: [PATCH 02/50] add azora logic --- python/mrchem/helpers.py | 37 ++++++++++++++++++++++++++++--------- 1 file changed, 28 insertions(+), 9 deletions(-) diff --git a/python/mrchem/helpers.py b/python/mrchem/helpers.py index cff57844e..14965dd5a 100644 --- a/python/mrchem/helpers.py +++ b/python/mrchem/helpers.py @@ -59,6 +59,17 @@ def write_scf_fock(user_dict, wf_dict, origin): "include_nuclear": user_dict["ZORA"]["include_nuclear"], "include_coulomb": user_dict["ZORA"]["include_coulomb"], "include_xc": user_dict["ZORA"]["include_xc"], + "isAZORA": False, + "azora_potential_path": user_dict["ZORA"]["azora_potential_path"] + } + # AZORA + if user_dict["WaveFunction"]["relativity"].lower() == "azora": + fock_dict["zora_operator"] = { + "include_nuclear": False, + "include_coulomb": False, + "include_xc": False, + "isAZORA": True, + "azora_potential_path": user_dict["ZORA"]["azora_potential_path"] } # Kinetic @@ -333,7 +344,7 @@ def write_rsp_calc(omega, user_dict, origin): rsp_calc["unperturbed"] = { "precision": user_dict["world_prec"], "localize": rsp_dict["localize"], - "fock_operator": write_scf_fock(user_dict, wf_dict, origin), + "fock_operator": (user_dict, wf_dict, origin), } guess_str = rsp_dict["guess_type"].lower() @@ -506,12 +517,22 @@ def parse_wf_method(user_dict): # Determine relativity name label for print outs to the output file relativity_name = "None" + wf_dict = dict() if user_dict["WaveFunction"]["relativity"].lower() in ["none"]: user_dict["WaveFunction"]["relativity"] = "off" user_dict["ZORA"]["include_nuclear"] = False user_dict["ZORA"]["include_coulomb"] = False user_dict["ZORA"]["include_xc"] = False + if user_dict["WaveFunction"]["relativity"].lower() in ["azora"]: + relativity_name = "AZORA" + user_dict["WaveFunction"]["relativity"] = "azora" + user_dict["ZORA"]["include_nuclear"] = False + user_dict["ZORA"]["include_coulomb"] = False + user_dict["ZORA"]["include_xc"] = False + user_dict["ZORA"]["isAZORA"] = True + wf_dict['azora_potential_path'] = user_dict["ZORA"]["azora_potential_path"] + if user_dict["WaveFunction"]["relativity"].lower() in ["nzora"]: user_dict["WaveFunction"]["relativity"] = "zora" user_dict["ZORA"]["include_nuclear"] = True @@ -560,14 +581,12 @@ def parse_wf_method(user_dict): # Labels to aggregate external_name = f"Electric field ({x}, {y}, {z})" - wf_dict = { - "relativity_name": relativity_name, - "environment_name": environment_name, - "external_name": external_name, - "method_name": method_name, - "method_type": method_type, - "dft_funcs": dft_funcs, - } + wf_dict["relativity_name"] = relativity_name + wf_dict["environment_name"] = environment_name + wf_dict["external_name"] = external_name + wf_dict["method_name"] = method_name + wf_dict["method_type"] = method_type + wf_dict["dft_funcs"] = dft_funcs return wf_dict From 73b46360a9e0b4a02f399b0b6f7aaca2da0f933b Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:06:28 +0200 Subject: [PATCH 03/50] changes made by update_parser script --- doc/users/user_ref.rst | 22 +- python/mrchem/input_parser/README.md | 2 +- python/mrchem/input_parser/__init__.py | 2 +- python/mrchem/input_parser/api.py | 10 +- python/mrchem/input_parser/cli.py | 2 +- python/mrchem/input_parser/docs/user_ref.rst | 16 +- python/mrchem/input_parser/plumbing/lexer.py | 2 +- .../plumbing/pyparsing/__init__.py | 4 +- .../plumbing/pyparsing/actions.py | 21 +- .../input_parser/plumbing/pyparsing/common.py | 9 +- .../input_parser/plumbing/pyparsing/core.py | 760 ++++++++---------- .../plumbing/pyparsing/diagram/__init__.py | 2 +- .../plumbing/pyparsing/exceptions.py | 81 +- .../plumbing/pyparsing/helpers.py | 86 +- .../plumbing/pyparsing/results.py | 211 ++--- .../plumbing/pyparsing/testing.py | 118 +-- .../plumbing/pyparsing/unicode.py | 13 +- .../input_parser/plumbing/pyparsing/util.py | 13 +- 18 files changed, 650 insertions(+), 724 deletions(-) diff --git a/doc/users/user_ref.rst b/doc/users/user_ref.rst index 828e3f0b1..d6ac88086 100644 --- a/doc/users/user_ref.rst +++ b/doc/users/user_ref.rst @@ -231,13 +231,13 @@ User input reference **Default** ``-1`` - :omp_threads: Force the number of OpenMP threads. - + :omp_threads: Force the number of omp threads (leave default is better). + **Type** ``int`` - + **Default** ``-1`` - - :Basis: Define polynomial basis. + + :Basis: Define polynomial basis. :red:`Keywords` :order: Polynomial order of multiwavelet basis. Negative value means it will be set automatically based on the world precision. @@ -326,14 +326,14 @@ User input reference **Default** ``True`` - :relativity: Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). + :relativity: Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). ``azora`` uses atomic ZORA potentials, which are precomputed and read from the directory specified in the ``azora_potential_path`` keyword. **Type** ``str`` **Default** ``none`` **Predicates** - - ``value.lower() in ['none', 'zora', 'nzora']`` + - ``value.lower() in ['none', 'zora', 'nzora', 'azora']`` :environment: Set method for treatment of environment. ``none`` for vacuum calculation. ``PCM`` for Polarizable Continuum Model, which will activate the ``PCM`` input section for further parametrization options. The ``PB`` and ``LPB`` variants add the Poisson-Boltzmann and Linearized Poisson-Boltzmann solvers, respectively. @@ -374,6 +374,12 @@ User input reference **Default** ``True`` + :azora_potential_path: Path to the directory containing the AZORA potentials. + + **Type** ``str`` + + **Default** ``/home/moritz/Documents/mrchem/share/azora_potentials/`` + :DFT: Define the exchange-correlation functional in case of DFT. :red:`Keywords` @@ -12209,4 +12215,4 @@ User input reference **Type** ``float`` **Default** ``0.00011186082063`` - + \ No newline at end of file diff --git a/python/mrchem/input_parser/README.md b/python/mrchem/input_parser/README.md index adc3dafc4..06b56f741 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 2024-01-29 +This file was automatically generated by parselglossy on 2024-05-28 Editing is *STRONGLY DISCOURAGED* diff --git a/python/mrchem/input_parser/__init__.py b/python/mrchem/input_parser/__init__.py index d5fc0a13b..1448968cd 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 2024-01-29 +# This file was automatically generated by parselglossy on 2024-05-28 # Editing is *STRONGLY DISCOURAGED* diff --git a/python/mrchem/input_parser/api.py b/python/mrchem/input_parser/api.py index 47095a3d2..a6edf3dc9 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 2024-02-08 +# This file was automatically generated by parselglossy on 2024-05-28 # Editing is *STRONGLY DISCOURAGED* from copy import deepcopy @@ -297,7 +297,8 @@ def stencil() -> JSONDict: 'predicates': [ 'value.lower() ' "in ['none', " "'zora', " - "'nzora']"], + "'nzora', " + "'azora']"], 'type': 'str'}, { 'default': 'none', 'name': 'environment', @@ -326,7 +327,10 @@ def stencil() -> JSONDict: 'type': 'bool'}, { 'default': True, 'name': 'include_xc', - 'type': 'bool'}], + 'type': 'bool'}, + { 'default': '/home/moritz/Documents/mrchem/share/azora_potentials/', + 'name': 'azora_potential_path', + 'type': 'str'}], 'name': 'ZORA'}, { 'keywords': [ { 'default': 0.0, 'name': 'density_cutoff', diff --git a/python/mrchem/input_parser/cli.py b/python/mrchem/input_parser/cli.py index caf1fcbe5..93dac8a76 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 2024-01-29 +# This file was automatically generated by parselglossy on 2024-05-28 # 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 75ac097cd..d6ac88086 100644 --- a/python/mrchem/input_parser/docs/user_ref.rst +++ b/python/mrchem/input_parser/docs/user_ref.rst @@ -231,6 +231,12 @@ User input reference **Default** ``-1`` + :omp_threads: Force the number of omp threads (leave default is better). + + **Type** ``int`` + + **Default** ``-1`` + :Basis: Define polynomial basis. :red:`Keywords` @@ -320,14 +326,14 @@ User input reference **Default** ``True`` - :relativity: Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). + :relativity: Set method for relativistic treatment. ``ZORA`` for fully self-consistent ZORA potential, by default including all potentials (``V_nuc``, ``J``, ``V_xc``) but this can be overwritten in the ``ZORA`` section. ``nZORA`` is shortcut for nuclear-ZORA, i.e. only ``V_nuc`` is included (this keyword takes precedence over keywords in the ``ZORA`` section). ``azora`` uses atomic ZORA potentials, which are precomputed and read from the directory specified in the ``azora_potential_path`` keyword. **Type** ``str`` **Default** ``none`` **Predicates** - - ``value.lower() in ['none', 'zora', 'nzora']`` + - ``value.lower() in ['none', 'zora', 'nzora', 'azora']`` :environment: Set method for treatment of environment. ``none`` for vacuum calculation. ``PCM`` for Polarizable Continuum Model, which will activate the ``PCM`` input section for further parametrization options. The ``PB`` and ``LPB`` variants add the Poisson-Boltzmann and Linearized Poisson-Boltzmann solvers, respectively. @@ -368,6 +374,12 @@ User input reference **Default** ``True`` + :azora_potential_path: Path to the directory containing the AZORA potentials. + + **Type** ``str`` + + **Default** ``/home/moritz/Documents/mrchem/share/azora_potentials/`` + :DFT: Define the exchange-correlation functional in case of DFT. :red:`Keywords` diff --git a/python/mrchem/input_parser/plumbing/lexer.py b/python/mrchem/input_parser/plumbing/lexer.py index f7b824b46..6da8d1898 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 2024-01-29 +# This file was automatically generated by parselglossy on 2024-05-28 # 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) From a10a42b31c973ec65c28fbaf20ceb70b0d910dd9 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:11:45 +0200 Subject: [PATCH 04/50] prepare fockbuilder for azora action --- src/driver.cpp | 9 +++++---- src/qmoperators/two_electron/FockBuilder.cpp | 3 ++- src/qmoperators/two_electron/FockBuilder.h | 4 +++- 3 files changed, 10 insertions(+), 6 deletions(-) diff --git a/src/driver.cpp b/src/driver.cpp index 3acffc882..3779064b8 100644 --- a/src/driver.cpp +++ b/src/driver.cpp @@ -1018,10 +1018,11 @@ void driver::build_fock_operator(const json &json_fock, Molecule &mol, FockBuild auto c = PhysicalConstants::get("light_speed"); F.setLightSpeed(c); - auto include_nuclear = json_fock["zora_operator"]["include_nuclear"]; - auto include_coulomb = json_fock["zora_operator"]["include_coulomb"]; - auto include_xc = json_fock["zora_operator"]["include_xc"]; - F.setZoraType(include_nuclear, include_coulomb, include_xc); + bool include_nuclear = json_fock["zora_operator"]["include_nuclear"]; + bool include_coulomb = json_fock["zora_operator"]["include_coulomb"]; + bool include_xc = json_fock["zora_operator"]["include_xc"]; + bool is_azora = json_fock["zora_operator"]["isAZORA"]; + F.setZoraType(include_nuclear, include_coulomb, include_xc, is_azora); } /////////////////////////////////////////////////////////// ////////////////// Coulomb Operator /////////////////// diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index ad9aaa5d9..a4ae36ea3 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -323,10 +323,11 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentNREL(OrbitalVector &Phi, Orbita return out; } -void FockBuilder::setZoraType(bool has_nuc, bool has_coul, bool has_xc) { +void FockBuilder::setZoraType(bool has_nuc, bool has_coul, bool has_xc, bool is_azora) { this->zora_has_nuc = has_nuc; this->zora_has_coul = has_coul; this->zora_has_xc = has_xc; + this->zora_is_azora = is_azora; } std::shared_ptr FockBuilder::collectZoraBasePotential() { diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index 53db4958e..78023b698 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -76,8 +76,9 @@ class FockBuilder final { void setLightSpeed(double c) { this->light_speed = c; } double getLightSpeed() const { return this->light_speed; } + bool isAzora() const { return zora_is_azora; } bool isZora() const { return (zora_has_nuc || zora_has_coul || zora_has_xc); } - void setZoraType(bool has_nuc, bool has_coul, bool has_xc); + void setZoraType(bool has_nuc, bool has_coul, bool has_xc, bool is_azora); SCFEnergy trace(OrbitalVector &Phi, const Nuclei &nucs); ComplexMatrix operator()(OrbitalVector &bra, OrbitalVector &ket); @@ -88,6 +89,7 @@ class FockBuilder final { bool zora_has_nuc{false}; bool zora_has_coul{false}; bool zora_has_xc{false}; + bool zora_is_azora{false}; double light_speed{-1.0}; double exact_exchange{1.0}; From 902ce68756fd181881f4fa6e9048b0287faa873d Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:17:30 +0200 Subject: [PATCH 05/50] set azora directory in fockbuilder --- src/driver.cpp | 3 +++ src/qmoperators/two_electron/FockBuilder.h | 3 +++ 2 files changed, 6 insertions(+) diff --git a/src/driver.cpp b/src/driver.cpp index 3779064b8..c07a2d111 100644 --- a/src/driver.cpp +++ b/src/driver.cpp @@ -1023,6 +1023,9 @@ void driver::build_fock_operator(const json &json_fock, Molecule &mol, FockBuild bool include_xc = json_fock["zora_operator"]["include_xc"]; bool is_azora = json_fock["zora_operator"]["isAZORA"]; F.setZoraType(include_nuclear, include_coulomb, include_xc, is_azora); + if (is_azora) { + F.setAZORADirectory(json_fock["zora_operator"]["azora_potential_path"]); + } } /////////////////////////////////////////////////////////// ////////////////// Coulomb Operator /////////////////// diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index 78023b698..7846c66c0 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -28,6 +28,7 @@ #include "qmoperators/QMPotential.h" #include "tensor/RankOneOperator.h" #include "tensor/RankZeroOperator.h" +#include /** @class FockOperator * @@ -79,6 +80,7 @@ class FockBuilder final { bool isAzora() const { return zora_is_azora; } bool isZora() const { return (zora_has_nuc || zora_has_coul || zora_has_xc); } void setZoraType(bool has_nuc, bool has_coul, bool has_xc, bool is_azora); + void setAZORADirectory(const std::string &dir) {azora_dir = dir;} SCFEnergy trace(OrbitalVector &Phi, const Nuclei &nucs); ComplexMatrix operator()(OrbitalVector &bra, OrbitalVector &ket); @@ -90,6 +92,7 @@ class FockBuilder final { bool zora_has_coul{false}; bool zora_has_xc{false}; bool zora_is_azora{false}; + std::string azora_dir = ""; double light_speed{-1.0}; double exact_exchange{1.0}; From 0e9da9261b58ffaa159c53a05753c76b7b9d8b43 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:27:51 +0200 Subject: [PATCH 06/50] add readme --- share/azora_potentials/README.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 share/azora_potentials/README.md diff --git a/share/azora_potentials/README.md b/share/azora_potentials/README.md new file mode 100644 index 000000000..955c491b5 --- /dev/null +++ b/share/azora_potentials/README.md @@ -0,0 +1,2 @@ +Data directory that contains the radial potentials and relativistic dampening functions for the azora method. +Format of the potential files: Data is stored columnwise. First column is the dampening function (not read), second column is radius, third is atomic zora potential. \ No newline at end of file From 623375671ad1d751309f123f557aae59e94cb58f Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:28:37 +0200 Subject: [PATCH 07/50] add radial interpolater --- .../one_electron/AZORA/RadialInterpolater.h | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 src/qmoperators/one_electron/AZORA/RadialInterpolater.h diff --git a/src/qmoperators/one_electron/AZORA/RadialInterpolater.h b/src/qmoperators/one_electron/AZORA/RadialInterpolater.h new file mode 100644 index 000000000..df7b6e7f9 --- /dev/null +++ b/src/qmoperators/one_electron/AZORA/RadialInterpolater.h @@ -0,0 +1,91 @@ +#include +#include +#include +#include +#include +#include + +typedef Eigen::Spline Spline1D; +typedef Eigen::SplineFitting SplineFitting1D; + +void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ + std::vector r, v, k; + std::ifstream file(path); + std::string line; + double r_, v_, k_; + while (std::getline(file, line)) { + std::istringstream iss(line); + iss >> k_ >> r_ >> v_; + r.push_back(r_); + v.push_back(v_); + k.push_back(k_); + } + file.close(); + rGrid = Eigen::Map(r.data(), r.size()); + vZora = Eigen::Map(v.data(), v.size()); + kappa = Eigen::Map(k.data(), k.size()); + // Add factor of 2 to kappa to be consistent with Lucas paper. + // kappa = kappa * 2.0; +} + +class RadInterpolater { + + 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 + * @param mode The mode of interpolation. Either "potential" or "kappa" + */ + RadInterpolater(const std::string element, std::string data_dir, const std::string mode){ + Eigen::VectorXd rGrid; + Eigen::VectorXd vZora; + Eigen::VectorXd kappa; + + this->mode = mode; + std::string filename = data_dir + '/' + element + ".dat"; + + readZoraPotential(filename, rGrid, vZora, kappa); + if (mode == "kappa") { + const auto fitV = SplineFitting1D::Interpolate(kappa.transpose(), 3, rGrid.transpose()); + Spline1D temp (fitV); + splineAZora = temp; + } else if (mode == "potential") { + const auto fitV = SplineFitting1D::Interpolate(vZora.transpose(), 3, rGrid.transpose()); + Spline1D temp (fitV); + splineAZora = temp; + } + + } + + double evalf(const double &r) const { + return splineAZora(r).coeff(0); + } + + protected: + Spline1D splineAZora; + std::string mode; + +}; + +// int main() { + +// RadInterpolater spline_V("Ar"); + +// Eigen::VectorXd xgrid = Eigen::VectorXd::LinSpaced(100000, 00, 1); +// Eigen::VectorXd ygrid(xgrid.size()); +// for (int i = 0; i < xgrid.size(); i++) { +// ygrid(i) = spline_V.evalf(xgrid(i)); +// } + +// // open interpol.txt for writing spline +// std::ofstream file("interpol.txt"); +// for (int i = 0; i < xgrid.size(); i++) { +// // write xgrid and ygrid to file using ten digits precision +// file << std::setprecision(10) << xgrid(i) << " " << ygrid(i) << std::endl; + +// } +// file.close(); + +// return 0; +// } \ No newline at end of file From 0bd430ff341f77fc7626f8f7e49d25e28e07b3d3 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:30:06 +0200 Subject: [PATCH 08/50] add some potentials --- share/azora_potentials/Ar.txt | 192 ++++++++++++++++++++++++++++++++++ share/azora_potentials/Xe.txt | 192 ++++++++++++++++++++++++++++++++++ 2 files changed, 384 insertions(+) create mode 100644 share/azora_potentials/Ar.txt create mode 100644 share/azora_potentials/Xe.txt diff --git a/share/azora_potentials/Ar.txt b/share/azora_potentials/Ar.txt new file mode 100644 index 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0.40874217626704E+02 -0.88075080307704E+00 From f7f66ebaf01d815ce33200be51cd606b2b3aed8f Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:30:14 +0200 Subject: [PATCH 09/50] change ending --- src/qmoperators/one_electron/AZORA/RadialInterpolater.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/qmoperators/one_electron/AZORA/RadialInterpolater.h b/src/qmoperators/one_electron/AZORA/RadialInterpolater.h index df7b6e7f9..34838ca8b 100644 --- a/src/qmoperators/one_electron/AZORA/RadialInterpolater.h +++ b/src/qmoperators/one_electron/AZORA/RadialInterpolater.h @@ -43,7 +43,7 @@ class RadInterpolater { Eigen::VectorXd kappa; this->mode = mode; - std::string filename = data_dir + '/' + element + ".dat"; + std::string filename = data_dir + '/' + element + ".txt"; readZoraPotential(filename, rGrid, vZora, kappa); if (mode == "kappa") { From 8dab986c1fbdd87f87db3cb40013ce9144123627 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:42:55 +0200 Subject: [PATCH 10/50] move file --- .../one_electron/{AZORA => AZora}/RadialInterpolater.h | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/qmoperators/one_electron/{AZORA => AZora}/RadialInterpolater.h (100%) diff --git a/src/qmoperators/one_electron/AZORA/RadialInterpolater.h b/src/qmoperators/one_electron/AZora/RadialInterpolater.h similarity index 100% rename from src/qmoperators/one_electron/AZORA/RadialInterpolater.h rename to src/qmoperators/one_electron/AZora/RadialInterpolater.h From 9287e2abfa819caa93450ccbbfa6512e37a89078 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:43:03 +0200 Subject: [PATCH 11/50] add azorapotential --- src/qmoperators/one_electron/AZoraPotential.h | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 src/qmoperators/one_electron/AZoraPotential.h diff --git a/src/qmoperators/one_electron/AZoraPotential.h b/src/qmoperators/one_electron/AZoraPotential.h new file mode 100644 index 000000000..d6f0c2519 --- /dev/null +++ b/src/qmoperators/one_electron/AZoraPotential.h @@ -0,0 +1,107 @@ +#pragma once + +#include "mrchem.h" +#include "chemistry/Molecule.h" +#include "chemistry/Nucleus.h" +#include +#include +#include +#include +#include "qmoperators/one_electron/AZora/RadialInterpolater.h" + + +namespace mrchem { + +/** @class AZora + * + * @brief Operator defining the AZora potential based on molecular data. + * + * Inherits from QMPotential and adds functionality to utilize an mrchem::Molecule + * for constructing the potential. + * + */ +class AZoraPotential : public QMPotential { +public: + /** + * Constructor that takes a molecule and initializes the azora potential. + * @param molecule The molecule used to construct the potential. + * @param adap Adaptive parameter from QMPotential. + * @param prec Precision parameter from base class. + * @param shared Determines if the base potential is shared. + */ + AZoraPotential(Nuclei nucs, int adap, double prec, bool shared = false, double c = 137.035999084) + : QMPotential(adap, shared) { + this->nucs = nucs; + this->prec = prec; + this->c = c; + initAzoraPotential(); + } + + /** + * Copy constructor. + * @param other The other instance to copy from. + */ + AZoraPotential(const AZoraPotential& other) + : QMPotential(other) { + this->nucs = other.nucs; + this->prec = other.prec; + this->c = other.c; + initAzoraPotential(); + } + + /** + * Destructor. + */ + virtual ~AZoraPotential() override = default; + + // Delete copy assignment to prevent copying + AZoraPotential& operator=(const AZoraPotential&) = delete; + +protected: + Nuclei nucs; // The nuclei of the molecule + double prec; // The precision parameter + double c; // The speed of light + + /** + * Initialize the azora potential based on the molecule. + * This method would typically setup the real and imaginary function trees + * representing the potential. + */ + void initAzoraPotential() { + + int n = nucs.size(); + Eigen::VectorXd rGrid, vZora, kappa; + + std::vector atomicPotentials; + + std::string mode = "potential"; + for (int i = 0; i < n; i++) { + RadInterpolater potentialSpline(nucs[i].getElement().getSymbol(), mode); + atomicPotentials.push_back(potentialSpline); + } + + + mrcpp::ComplexFunction vtot; + auto kappa_analytic = [atomicPotentials, this](const mrcpp::Coord<3>& r) { + double V = 0.0; + // Loop over all atoms: + for (int i = 0; i < atomicPotentials.size(); i++) { + mrcpp::Coord<3> r_i = nucs[i].getCoord(); + double rr = std::sqrt((r[0] - r_i[0]) * (r[0] - r_i[0]) + (r[1] - r_i[1]) * (r[1] - r_i[1]) + (r[2] - r_i[2]) * (r[2] - r_i[2])); + V += atomicPotentials[i].evalf(rr); + } + return 1 / (1 - V / (2.0 * c * c)) - 1; + }; + mrcpp::cplxfunc::project(vtot, kappa_analytic, mrcpp::NUMBER::Real, prec); + auto ttt = [](const mrcpp::Coord<3>& r) { + return 1.0; + }; + mrcpp::ComplexFunction const_func; + mrcpp::cplxfunc::project(const_func, ttt, mrcpp::NUMBER::Real, prec); + mrcpp::ComplexDouble one = 1.0; + vtot.add(one, const_func); + this->add(one, vtot); + } +}; + +} // namespace mrchem \ No newline at end of file From d454b7e6e06cb2e0fb5f9bcff2c7663386e17edb Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:50:54 +0200 Subject: [PATCH 12/50] add nuclei to fockbuilder --- src/driver.cpp | 1 + src/qmoperators/two_electron/FockBuilder.h | 9 ++++++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/src/driver.cpp b/src/driver.cpp index c07a2d111..06f0f8b42 100644 --- a/src/driver.cpp +++ b/src/driver.cpp @@ -1025,6 +1025,7 @@ void driver::build_fock_operator(const json &json_fock, Molecule &mol, FockBuild F.setZoraType(include_nuclear, include_coulomb, include_xc, is_azora); if (is_azora) { F.setAZORADirectory(json_fock["zora_operator"]["azora_potential_path"]); + F.setNucs(mol.getNuclei()); } } /////////////////////////////////////////////////////////// diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index 7846c66c0..eccda125a 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -1,3 +1,4 @@ + /* * MRChem, a numerical real-space code for molecular electronic structure * calculations within the self-consistent field (SCF) approximations of quantum @@ -29,6 +30,7 @@ #include "tensor/RankOneOperator.h" #include "tensor/RankZeroOperator.h" #include +#include "chemistry/Nucleus.h" /** @class FockOperator * @@ -47,6 +49,7 @@ class MomentumOperator; class KineticOperator; class ZoraKineticOperator; class ZoraOperator; +class AZoraPotential; class NuclearOperator; class CoulombOperator; class ExchangeOperator; @@ -77,10 +80,11 @@ class FockBuilder final { void setLightSpeed(double c) { this->light_speed = c; } double getLightSpeed() const { return this->light_speed; } - bool isAzora() const { return zora_is_azora; } + bool isAZora() const { return zora_is_azora; } bool isZora() const { return (zora_has_nuc || zora_has_coul || zora_has_xc); } void setZoraType(bool has_nuc, bool has_coul, bool has_xc, bool is_azora); void setAZORADirectory(const std::string &dir) {azora_dir = dir;} + void setNucs(const Nuclei &nucs) { this->nucs = nucs;} SCFEnergy trace(OrbitalVector &Phi, const Nuclei &nucs); ComplexMatrix operator()(OrbitalVector &bra, OrbitalVector &ket); @@ -99,6 +103,7 @@ class FockBuilder final { RankZeroOperator zora_base; double prec; + Nuclei nucs; RankZeroOperator V; ///< Total potential energy operator RankZeroOperator H_1; ///< Perturbation operators @@ -116,6 +121,8 @@ class FockBuilder final { std::shared_ptr collectZoraBasePotential(); OrbitalVector buildHelmholtzArgumentZORA(OrbitalVector &Phi, OrbitalVector &Psi, DoubleVector eps, double prec); OrbitalVector buildHelmholtzArgumentNREL(OrbitalVector &Phi, OrbitalVector &Psi); + std::shared_ptr kappaPot{nullptr}; + std::shared_ptr kappaInvPot{nullptr}; }; } // namespace mrchem From 5b9be731cb77772121384c69d6dabd6f8fa00438 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 16:56:26 +0200 Subject: [PATCH 13/50] azora potential fix --- src/qmoperators/one_electron/AZoraPotential.h | 7 +++++-- src/qmoperators/two_electron/FockBuilder.cpp | 2 ++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/src/qmoperators/one_electron/AZoraPotential.h b/src/qmoperators/one_electron/AZoraPotential.h index d6f0c2519..41cf75f6e 100644 --- a/src/qmoperators/one_electron/AZoraPotential.h +++ b/src/qmoperators/one_electron/AZoraPotential.h @@ -29,11 +29,12 @@ class AZoraPotential : public QMPotential { * @param prec Precision parameter from base class. * @param shared Determines if the base potential is shared. */ - AZoraPotential(Nuclei nucs, int adap, double prec, bool shared = false, double c = 137.035999084) + AZoraPotential(Nuclei nucs, int adap, double prec, std::string azora_dir, bool shared = false, double c = 137.035999084) : QMPotential(adap, shared) { this->nucs = nucs; this->prec = prec; this->c = c; + this->azora_dir = azora_dir; initAzoraPotential(); } @@ -46,6 +47,7 @@ class AZoraPotential : public QMPotential { this->nucs = other.nucs; this->prec = other.prec; this->c = other.c; + this->azora_dir = other.azora_dir; initAzoraPotential(); } @@ -61,6 +63,7 @@ class AZoraPotential : public QMPotential { Nuclei nucs; // The nuclei of the molecule double prec; // The precision parameter double c; // The speed of light + std::string azora_dir; // The directory containing the azora potential data /** * Initialize the azora potential based on the molecule. @@ -76,7 +79,7 @@ class AZoraPotential : public QMPotential { std::string mode = "potential"; for (int i = 0; i < n; i++) { - RadInterpolater potentialSpline(nucs[i].getElement().getSymbol(), mode); + RadInterpolater potentialSpline(nucs[i].getElement().getSymbol(), this->azora_dir, mode); atomicPotentials.push_back(potentialSpline); } diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index a4ae36ea3..306957c16 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -47,6 +47,8 @@ #include "qmoperators/qmoperator_utils.h" #include "utils/math_utils.h" +#include "qmoperators/one_electron/AZoraPotential.h" + using mrcpp::Printer; using mrcpp::Timer; From 49533d03a0f235a3ec75152ae6cd8da58e07c485 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 17:09:10 +0200 Subject: [PATCH 14/50] add wrong file for heliym --- share/azora_potentials/He.txt | 192 ++++++++++++++++++++++++++++++++++ 1 file changed, 192 insertions(+) create mode 100644 share/azora_potentials/He.txt diff --git a/share/azora_potentials/He.txt b/share/azora_potentials/He.txt new file mode 100644 index 000000000..3a1bdc20f --- /dev/null +++ b/share/azora_potentials/He.txt @@ -0,0 +1,192 @@ + 0.78046262509927869E-01 0.97578195523695E-18 -0.20305425173135E+06 + 0.79951828178479734E-01 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0.24840437840854E+02 0.51181281435220E-13 + 0.50000000000000000E+00 0.25666712333901E+02 0.49515946898282E-13 + 0.50000000000000000E+00 0.26502712219579E+02 0.47961634663807E-13 + 0.50000000000000000E+00 0.27347995024993E+02 0.46518344731794E-13 + 0.50000000000000000E+00 0.28202127010389E+02 0.45075054799781E-13 + 0.50000000000000000E+00 0.29064684357170E+02 0.43742787170231E-13 + 0.50000000000000000E+00 0.29935254177814E+02 0.42410519540681E-13 + 0.50000000000000000E+00 0.30813435356248E+02 0.41189274213593E-13 + 0.50000000000000000E+00 0.31698839228624E+02 0.40079051188968E-13 + 0.50000000000000000E+00 0.32591090115412E+02 0.38968828164343E-13 + 0.50000000000000000E+00 0.33489825716383E+02 0.37969627442180E-13 + 0.50000000000000000E+00 0.34394697380382E+02 0.36970426720018E-13 + 0.50000000000000000E+00 0.35305370261891E+02 0.35971225997855E-13 + 0.50000000000000000E+00 0.36221523376224E+02 0.35138558729386E-13 + 0.50000000000000000E+00 0.37142849564891E+02 0.34250380309686E-13 + 0.50000000000000000E+00 0.38069055382202E+02 0.33473224192448E-13 + 0.50000000000000000E+00 0.38999860913611E+02 0.32585045772748E-13 + 0.50000000000000000E+00 0.39934999535663E+02 0.31918911957973E-13 + 0.50000000000000000E+00 0.40874217626704E+02 0.31141755840736E-13 From df1f3eb0e7c27c4f23e732680b39d9be3d8455d7 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 17:09:26 +0200 Subject: [PATCH 15/50] check if file exists before opening --- src/qmoperators/one_electron/AZora/RadialInterpolater.h | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/qmoperators/one_electron/AZora/RadialInterpolater.h b/src/qmoperators/one_electron/AZora/RadialInterpolater.h index 34838ca8b..54a962e07 100644 --- a/src/qmoperators/one_electron/AZora/RadialInterpolater.h +++ b/src/qmoperators/one_electron/AZora/RadialInterpolater.h @@ -4,12 +4,19 @@ #include #include #include +#include typedef Eigen::Spline Spline1D; typedef Eigen::SplineFitting SplineFitting1D; void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ std::vector r, v, k; + bool file_exists = std::filesystem::exists(path); + if (!file_exists) { + std::cerr << "File " << path << " does not exist." << std::endl; + std::cout << "File " << path << " does not exist." << std::endl; + exit(1); + } std::ifstream file(path); std::string line; double r_, v_, k_; From 196b79523f478ad6a61f49ade581118f4eee4170 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 28 May 2024 17:09:53 +0200 Subject: [PATCH 16/50] update zora operator --- src/qmoperators/one_electron/ZoraOperator.cpp | 14 +++++++++++++- src/qmoperators/one_electron/ZoraOperator.h | 4 ++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index e2b38f505..8bc283360 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -30,6 +30,7 @@ #include "qmoperators/QMPotential.h" #include "utils/print_utils.h" +#include using mrcpp::Printer; using mrcpp::Timer; @@ -40,7 +41,7 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv Timer timer; double two_cc = 2.0 * c * c; - auto k = std::make_shared(1); + std::shared_ptr k = std::make_shared(1); mrcpp::cplxfunc::deep_copy(*k, vz); if (k->hasImag()) MSG_ERROR("Inverse of complex function"); @@ -65,4 +66,15 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv print_utils::qmfunction(2, "ZORA operator (" + kappa.name() + ")", *k, timer); } +/** + * @brief Constructor for ZoraOperator used to construct an atomic zora operator + * @param relativisticDampening shared pointer to QMPotential that contains the precompouted kappa function + * @param name name of the operator should be either "kappa" or "kappa_inv" +*/ +ZoraOperator::ZoraOperator(std::shared_ptr &relativisticDampening, std::string name) { + RankZeroOperator &kappa = (*this); + kappa = relativisticDampening; + kappa.name() = name; +} + } // namespace mrchem diff --git a/src/qmoperators/one_electron/ZoraOperator.h b/src/qmoperators/one_electron/ZoraOperator.h index 8dd2ee7ce..189a7c050 100644 --- a/src/qmoperators/one_electron/ZoraOperator.h +++ b/src/qmoperators/one_electron/ZoraOperator.h @@ -26,6 +26,7 @@ #pragma once #include "tensor/RankZeroOperator.h" +#include namespace mrchem { @@ -34,6 +35,9 @@ class QMPotential; class ZoraOperator final : public RankZeroOperator { public: ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inverse = false); + + ZoraOperator(std::shared_ptr &relativisticDampening, std::string name); + }; } // namespace mrchem From 0a2fc7edb976d42bb0cf352d874f51296bdea252 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Wed, 29 May 2024 09:11:47 +0200 Subject: [PATCH 17/50] simulations working --- src/qmoperators/two_electron/FockBuilder.cpp | 58 +++++++++++++++++--- 1 file changed, 50 insertions(+), 8 deletions(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index 306957c16..6b29cd395 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -92,7 +92,7 @@ void FockBuilder::setup(double prec) { if (isZora()) { Timer t_zora; - auto c = getLightSpeed(); + double c = getLightSpeed(); mrcpp::print::header(3, "Building ZORA operators"); mrcpp::print::value(3, "Precision", prec, "(rel)", 5); mrcpp::print::value(3, "Light speed", c, "(au)", 5); @@ -105,7 +105,31 @@ void FockBuilder::setup(double prec) { this->kappa_inv->setup(prec); this->zora_base.setup(prec); mrcpp::print::footer(3, t_zora, 2); - }; + } + if (isAZora()) { + Timer t_zora; + double c = getLightSpeed(); + mrcpp::print::header(3, "Building AZORA operators"); + mrcpp::print::value(3, "Precision", prec, "(rel)", 5); + mrcpp::print::value(3, "Light speed", c, "(au)", 5); + mrcpp::print::separator(3, '-'); + int adap = 0; + bool share = false; + kappaPot = std::make_shared(nucs, adap, prec, this->azora_dir); + + kappaInvPot = std::make_shared(adap); + + mrcpp::cplxfunc::deep_copy(*kappaInvPot, *kappaPot); + + kappaInvPot->real().map([](double val) { return 1.0 / val; }); + + this->kappa = std::make_shared(kappaPot, "kappa"); + this->kappa_inv = std::make_shared(kappaInvPot, "kappa_inv"); + this->kappa->setup(prec); + this->kappa_inv->setup(prec); + + mrcpp::print::footer(3, t_zora, 2); + } t_tot.stop(); if (plevel == 2) mrcpp::print::footer(2, t_tot, 2); @@ -126,6 +150,10 @@ void FockBuilder::clear() { this->kappa_inv->clear(); this->zora_base.clear(); } + if (isAZora()) { + kappa->clear(); + kappa_inv->clear(); + } } /** @brief rotate orbitals of two-electron operators @@ -181,7 +209,7 @@ SCFEnergy FockBuilder::trace(OrbitalVector &Phi, const Nuclei &nucs) { } // Kinetic part - if (isZora()) { + if (isZora() || isAZora()) { E_kin = qmoperator::calc_kinetic_trace(momentum(), *this->kappa, Phi).real(); } else { E_kin = qmoperator::calc_kinetic_trace(momentum(), Phi); @@ -206,7 +234,7 @@ ComplexMatrix FockBuilder::operator()(OrbitalVector &bra, OrbitalVector &ket) { mrcpp::print::header(2, "Computing Fock matrix"); ComplexMatrix T_mat = ComplexMatrix::Zero(bra.size(), ket.size()); - if (isZora()) { + if (isZora() || isAZora()) { T_mat = qmoperator::calc_kinetic_matrix(momentum(), *this->kappa, bra, ket); } else { T_mat = qmoperator::calc_kinetic_matrix(momentum(), bra, ket); @@ -230,7 +258,7 @@ OrbitalVector FockBuilder::buildHelmholtzArgument(double prec, OrbitalVector Phi mrcpp::print::time(2, "Rotating orbitals", t_rot); OrbitalVector out; - if (isZora()) { + if (isZora() || isAZora()) { out = buildHelmholtzArgumentZORA(Phi, Psi, F_mat.real().diagonal(), prec); } else { out = buildHelmholtzArgumentNREL(Phi, Psi); @@ -251,10 +279,24 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &V = potential(); RankZeroOperator &kappa = *this->kappa; RankZeroOperator &kappa_m1 = *this->kappa_inv; - RankZeroOperator &V_zora = this->zora_base; - RankZeroOperator operOne = 0.5 * tensor::dot(p(kappa), p); - RankZeroOperator operThree = kappa * V_zora; + + std::shared_ptr operThreePtr = nullptr; + + if (isZora()) { + RankZeroOperator &V_zora = this->zora_base; + operThreePtr = std::make_shared(V_zora * kappa); + } else if (isAZora()) { + std::shared_ptr vTimesKappa = std::make_shared(0); + mrcpp::cplxfunc::deep_copy(*vTimesKappa, *kappaPot); + vTimesKappa->real().map([two_cc](double val) { return two_cc * (val - 1); }); + operThreePtr = std::make_shared(vTimesKappa); + } else { + MSG_ABORT("At this point, the ZORA or AZORA operator should be set. Exiting."); + } + + RankZeroOperator operThree = *operThreePtr; + operOne.setup(prec); operThree.setup(prec); From a3319d5fa7bb1248e4453acf6a8595ce7b2de34f Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Wed, 29 May 2024 16:58:16 +0200 Subject: [PATCH 18/50] install azora files --- CMakeLists.txt | 1 + cmake/custom/azora_potentials.cmake | 7 +++++++ 2 files changed, 8 insertions(+) create mode 100644 cmake/custom/azora_potentials.cmake diff --git a/CMakeLists.txt b/CMakeLists.txt index 2cd856a96..70e2f4d75 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/azora_potentials.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/azora_potentials.cmake b/cmake/custom/azora_potentials.cmake new file mode 100644 index 000000000..8b983d825 --- /dev/null +++ b/cmake/custom/azora_potentials.cmake @@ -0,0 +1,7 @@ +set(SAD_BASIS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/azora_potentials CACHE STRING "Path to azora potentials") +set(SAD_BASIS_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/azora_potentials) +install( + DIRECTORY share/azora_potentials + DESTINATION share/${PROJECT_NAME} + ) + From 7b00b37e220063a4d4787b7dee11d5715248a8d8 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 08:58:04 +0200 Subject: [PATCH 19/50] correct name of variable --- cmake/custom/azora_potentials.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/custom/azora_potentials.cmake b/cmake/custom/azora_potentials.cmake index 8b983d825..1478838ff 100644 --- a/cmake/custom/azora_potentials.cmake +++ b/cmake/custom/azora_potentials.cmake @@ -1,5 +1,5 @@ -set(SAD_BASIS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/azora_potentials CACHE STRING "Path to azora potentials") -set(SAD_BASIS_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/azora_potentials) +set(AZORA_POTENTIALS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/azora_potentials CACHE STRING "Path to azora potentials") +set(AZORA_POTENTIALS_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/azora_potentials) install( DIRECTORY share/azora_potentials DESTINATION share/${PROJECT_NAME} From a8bb6ecb367ad7e82b894ed97e1d27913fff061d Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 09:22:21 +0200 Subject: [PATCH 20/50] add preprocessor logic for azora dirs --- src/CMakeLists.txt | 5 ++++ src/qmoperators/two_electron/FockBuilder.cpp | 25 ++++++++++++++++++++ src/qmoperators/two_electron/FockBuilder.h | 2 ++ 3 files changed, 32 insertions(+) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 260f6f688..a2f1f9918 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -38,6 +38,11 @@ add_subdirectory(scf_solver) add_subdirectory(tensor) add_subdirectory(utils) +target_compile_definitions(mrchem PRIVATE + AZORA_POTENTIALS_SOURCE_DIR="${AZORA_POTENTIALS_SOURCE_DIR}" + AZORA_POTENTIALS_INSTALL_DIR="${AZORA_POTENTIALS_INSTALL_DIR}" +) + target_link_libraries(mrchem PRIVATE Eigen3::Eigen diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index 6b29cd395..65748f478 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -49,6 +49,8 @@ #include "qmoperators/one_electron/AZoraPotential.h" +#include + using mrcpp::Printer; using mrcpp::Timer; @@ -115,6 +117,29 @@ void FockBuilder::setup(double prec) { mrcpp::print::separator(3, '-'); int adap = 0; bool share = false; + + azora_dir_src = AZORA_POTENTIALS_SOURCE_DIR; + azora_dir_install = AZORA_POTENTIALS_INSTALL_DIR; + + std::string azora_dir_final; + if (azora_dir != "") { + azora_dir_final = azora_dir; + } else { + // check if azora_dir_install directory exists using cpp standard library + if (std::filesystem::exists(azora_dir_install)) { + azora_dir_final = azora_dir_install; + } else { + // check if azora_dir_src directory exists using cpp standard library + if (std::filesystem::exists(azora_dir_src)) { + azora_dir_final = azora_dir_src; + } else { + MSG_ABORT("AZORA: No directory provided and no default directories found."); + } + } + + } + + kappaPot = std::make_shared(nucs, adap, prec, this->azora_dir); kappaInvPot = std::make_shared(adap); diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index eccda125a..c89773500 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -97,6 +97,8 @@ class FockBuilder final { bool zora_has_xc{false}; bool zora_is_azora{false}; std::string azora_dir = ""; + std::string azora_dir_src = ""; + std::string azora_dir_install = ""; double light_speed{-1.0}; double exact_exchange{1.0}; From 89f33c96deb3caeff9a7b5e4d146955afe64112d Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 09:48:47 +0200 Subject: [PATCH 21/50] more parsing logic --- python/mrchem/helpers.py | 6 +++--- src/driver.cpp | 4 +++- src/qmoperators/two_electron/FockBuilder.cpp | 3 +-- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/python/mrchem/helpers.py b/python/mrchem/helpers.py index 14965dd5a..291c6c76e 100644 --- a/python/mrchem/helpers.py +++ b/python/mrchem/helpers.py @@ -68,9 +68,10 @@ def write_scf_fock(user_dict, wf_dict, origin): "include_nuclear": False, "include_coulomb": False, "include_xc": False, - "isAZORA": True, - "azora_potential_path": user_dict["ZORA"]["azora_potential_path"] + "isAZORA": True } + if user_dict["ZORA"]["azora_potential_path"].lower() != "none": + fock_dict["zora_operator"]["azora_potential_path"] = user_dict["ZORA"]["azora_potential_path"] # Kinetic fock_dict["kinetic_operator"] = {"derivative": user_dict["Derivatives"]["kinetic"]} @@ -531,7 +532,6 @@ def parse_wf_method(user_dict): user_dict["ZORA"]["include_coulomb"] = False user_dict["ZORA"]["include_xc"] = False user_dict["ZORA"]["isAZORA"] = True - wf_dict['azora_potential_path'] = user_dict["ZORA"]["azora_potential_path"] if user_dict["WaveFunction"]["relativity"].lower() in ["nzora"]: user_dict["WaveFunction"]["relativity"] = "zora" diff --git a/src/driver.cpp b/src/driver.cpp index 06f0f8b42..30292ba8a 100644 --- a/src/driver.cpp +++ b/src/driver.cpp @@ -1024,7 +1024,9 @@ void driver::build_fock_operator(const json &json_fock, Molecule &mol, FockBuild bool is_azora = json_fock["zora_operator"]["isAZORA"]; F.setZoraType(include_nuclear, include_coulomb, include_xc, is_azora); if (is_azora) { - F.setAZORADirectory(json_fock["zora_operator"]["azora_potential_path"]); + if (json_fock["zora_operator"].contains("azora_potential_path")) { + F.setAZORADirectory(json_fock["zora_operator"]["azora_potential_path"]); + } F.setNucs(mol.getNuclei()); } } diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index 65748f478..758b969d6 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -136,11 +136,10 @@ void FockBuilder::setup(double prec) { MSG_ABORT("AZORA: No directory provided and no default directories found."); } } - } - kappaPot = std::make_shared(nucs, adap, prec, this->azora_dir); + kappaPot = std::make_shared(nucs, adap, prec, azora_dir_final, share, c); kappaInvPot = std::make_shared(adap); From 6edc1b11dbb229f5cd8d333190dfe7639cc87949 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 09:49:01 +0200 Subject: [PATCH 22/50] changes made by update parse script --- doc/users/user_ref.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/users/user_ref.rst b/doc/users/user_ref.rst index d6ac88086..09c08445a 100644 --- a/doc/users/user_ref.rst +++ b/doc/users/user_ref.rst @@ -374,11 +374,11 @@ User input reference **Default** ``True`` - :azora_potential_path: Path to the directory containing the AZORA potentials. + :azora_potential_path: Path to the directory containing the AZORA potentials. If not specified, the default potentials will be used. Look into the readme file in the share/azora_potentials directory for information about the potential file format. **Type** ``str`` - **Default** ``/home/moritz/Documents/mrchem/share/azora_potentials/`` + **Default** ``none`` :DFT: Define the exchange-correlation functional in case of DFT. From 903644a455218e07ae6df2c05a1225ef8d744af7 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 09:49:22 +0200 Subject: [PATCH 23/50] changes made by parser --- python/mrchem/input_parser/README.md | 2 +- python/mrchem/input_parser/__init__.py | 2 +- python/mrchem/input_parser/api.py | 4 ++-- python/mrchem/input_parser/cli.py | 2 +- python/mrchem/input_parser/docs/user_ref.rst | 4 ++-- python/mrchem/input_parser/plumbing/lexer.py | 2 +- python/template.yml | 5 +++-- 7 files changed, 11 insertions(+), 10 deletions(-) diff --git a/python/mrchem/input_parser/README.md b/python/mrchem/input_parser/README.md index 06b56f741..fe043318b 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 2024-05-28 +This file was automatically generated by parselglossy on 2024-05-30 Editing is *STRONGLY DISCOURAGED* diff --git a/python/mrchem/input_parser/__init__.py b/python/mrchem/input_parser/__init__.py index 1448968cd..9b89ec905 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 2024-05-28 +# This file was automatically generated by parselglossy on 2024-05-30 # Editing is *STRONGLY DISCOURAGED* diff --git a/python/mrchem/input_parser/api.py b/python/mrchem/input_parser/api.py index a6edf3dc9..6b9caa6c9 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 2024-05-28 +# This file was automatically generated by parselglossy on 2024-05-30 # Editing is *STRONGLY DISCOURAGED* from copy import deepcopy @@ -328,7 +328,7 @@ def stencil() -> JSONDict: { 'default': True, 'name': 'include_xc', 'type': 'bool'}, - { 'default': '/home/moritz/Documents/mrchem/share/azora_potentials/', + { 'default': 'none', 'name': 'azora_potential_path', 'type': 'str'}], 'name': 'ZORA'}, diff --git a/python/mrchem/input_parser/cli.py b/python/mrchem/input_parser/cli.py index 93dac8a76..56c2a3ac7 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 2024-05-28 +# This file was automatically generated by parselglossy on 2024-05-30 # 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 d6ac88086..09c08445a 100644 --- a/python/mrchem/input_parser/docs/user_ref.rst +++ b/python/mrchem/input_parser/docs/user_ref.rst @@ -374,11 +374,11 @@ User input reference **Default** ``True`` - :azora_potential_path: Path to the directory containing the AZORA potentials. + :azora_potential_path: Path to the directory containing the AZORA potentials. If not specified, the default potentials will be used. Look into the readme file in the share/azora_potentials directory for information about the potential file format. **Type** ``str`` - **Default** ``/home/moritz/Documents/mrchem/share/azora_potentials/`` + **Default** ``none`` :DFT: Define the exchange-correlation functional in case of DFT. diff --git a/python/mrchem/input_parser/plumbing/lexer.py b/python/mrchem/input_parser/plumbing/lexer.py index 6da8d1898..9016316a9 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 2024-05-28 +# This file was automatically generated by parselglossy on 2024-05-30 # Editing is *STRONGLY DISCOURAGED* import json diff --git a/python/template.yml b/python/template.yml index e12858b87..8132305f3 100644 --- a/python/template.yml +++ b/python/template.yml @@ -339,9 +339,10 @@ sections: Include the XC potential ``V_xc`` in the ZORA potential. - name: azora_potential_path type: str - default: /home/moritz/Documents/mrchem/share/azora_potentials/ + default: none docstring: | - Path to the directory containing the AZORA potentials. + Path to the directory containing the AZORA potentials. If not specified, the default potentials will be used. + Look into the readme file in the share/azora_potentials directory for information about the potential file format. - name: DFT docstring: | Define the exchange-correlation functional in case of DFT. From 23ae8e8b6602f04da6be5d9521b44e0396c5c5db Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 09:56:23 +0200 Subject: [PATCH 24/50] add documentation --- .../one_electron/AZora/RadialInterpolater.h | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/src/qmoperators/one_electron/AZora/RadialInterpolater.h b/src/qmoperators/one_electron/AZora/RadialInterpolater.h index 54a962e07..dd6bffcfa 100644 --- a/src/qmoperators/one_electron/AZora/RadialInterpolater.h +++ b/src/qmoperators/one_electron/AZora/RadialInterpolater.h @@ -3,12 +3,18 @@ #include #include #include -#include #include typedef Eigen::Spline Spline1D; typedef Eigen::SplineFitting SplineFitting1D; +/** + * @brief Read ZORA potential from file. Check if file exists and abort if it does not. + * @param path Path to the file containing the ZORA potential + * @param rGrid Vector containing the radial grid + * @param vZora Vector containing the ZORA potential + * @param kappa Vector containing the kappa parameter +*/ void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ std::vector r, v, k; bool file_exists = std::filesystem::exists(path); @@ -31,8 +37,9 @@ void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::Ve rGrid = Eigen::Map(r.data(), r.size()); vZora = Eigen::Map(v.data(), v.size()); kappa = Eigen::Map(k.data(), k.size()); - // Add factor of 2 to kappa to be consistent with Lucas paper. - // kappa = kappa * 2.0; + // The kappa function is half of what is defined in the paper Scalar + // Relativistic Effects with Multiwavelets: Implementation and Benchmark + // it is not used in the code, only the potential is used } class RadInterpolater { From 2e739f618ea94df15837fc0df7df47028e415539 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 30 May 2024 10:01:42 +0200 Subject: [PATCH 25/50] more docs --- src/qmoperators/two_electron/FockBuilder.cpp | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index 758b969d6..da56944e9 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -294,7 +294,9 @@ OrbitalVector FockBuilder::buildHelmholtzArgument(double prec, OrbitalVector Phi return out; } -// Take 1 in notes on Overleaf +/** + * @brief Build the Helmholtz argument for the ZORA operator. Eq. 17 in J. Chem. Theory and Comput. 2024, 20, 728-737 +*/ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, OrbitalVector &Psi, DoubleVector eps, double prec) { // Get necessary operators double c = getLightSpeed(); @@ -311,6 +313,10 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &V_zora = this->zora_base; operThreePtr = std::make_shared(V_zora * kappa); } else if (isAZora()) { + /* + Note that V_z * kappa = 2 c^2 * (kappa - 1) + With this trick, the expensive projection of the potential is avoided + */ std::shared_ptr vTimesKappa = std::make_shared(0); mrcpp::cplxfunc::deep_copy(*vTimesKappa, *kappaPot); vTimesKappa->real().map([two_cc](double val) { return two_cc * (val - 1); }); From cd7906764c5ed5c7e90af78c26c11598df73bf6d Mon Sep 17 00:00:00 2001 From: Moritz Gubler Date: Sat, 1 Jun 2024 10:07:24 +0200 Subject: [PATCH 26/50] more potentials --- share/azora_potentials/C.txt | 192 +++++++++++++++++ share/azora_potentials/H.txt | 192 +++++++++++++++++ share/azora_potentials/He.txt | 384 +++++++++++++++++----------------- share/azora_potentials/N.txt | 192 +++++++++++++++++ share/azora_potentials/Ne.txt | 192 +++++++++++++++++ share/azora_potentials/O.txt | 192 +++++++++++++++++ 6 files changed, 1152 insertions(+), 192 deletions(-) create mode 100644 share/azora_potentials/C.txt create mode 100644 share/azora_potentials/H.txt create mode 100644 share/azora_potentials/N.txt create mode 100644 share/azora_potentials/Ne.txt create mode 100644 share/azora_potentials/O.txt diff --git a/share/azora_potentials/C.txt b/share/azora_potentials/C.txt new file mode 100644 index 000000000..2f17f2f11 --- /dev/null +++ b/share/azora_potentials/C.txt @@ -0,0 +1,192 @@ + 0.17841993112380777E+00 0.97578195523695E-18 -0.67693210975527E+05 + 0.18172034946062149E+00 0.29483069282768E-04 -0.65781635572751E+05 + 0.19221859355362231E+00 0.61082173640461E-04 -0.60137634605896E+05 + 0.21003804511133289E+00 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+ 0.50000000000000000E+00 0.24840437840854E+02 0.39968028886506E-14 + 0.50000000000000000E+00 0.25666712333901E+02 0.38857805861880E-14 + 0.50000000000000000E+00 0.26502712219579E+02 0.37747582837255E-14 + 0.50000000000000000E+00 0.27347995024993E+02 0.36082248300318E-14 + 0.50000000000000000E+00 0.28202127010389E+02 0.34972025275692E-14 + 0.50000000000000000E+00 0.29064684357170E+02 0.34416913763380E-14 + 0.50000000000000000E+00 0.29935254177814E+02 0.33306690738755E-14 + 0.50000000000000000E+00 0.30813435356248E+02 0.32196467714130E-14 + 0.50000000000000000E+00 0.31698839228624E+02 0.31086244689504E-14 + 0.50000000000000000E+00 0.32591090115412E+02 0.30253577421036E-14 + 0.50000000000000000E+00 0.33489825716383E+02 0.29698465908723E-14 + 0.50000000000000000E+00 0.34394697380382E+02 0.28865798640254E-14 + 0.50000000000000000E+00 0.35305370261891E+02 0.28033131371785E-14 + 0.50000000000000000E+00 0.36221523376224E+02 0.27200464103316E-14 + 0.50000000000000000E+00 0.37142849564891E+02 0.26645352591004E-14 + 0.50000000000000000E+00 0.38069055382202E+02 0.25812685322535E-14 + 0.50000000000000000E+00 0.38999860913611E+02 0.25535129566379E-14 + 0.50000000000000000E+00 0.39934999535663E+02 0.24980018054066E-14 + 0.50000000000000000E+00 0.40874217626704E+02 0.24424906541753E-14 From 33036cc9179f78209f9b68704460c5b9699fce9a Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 6 Jun 2024 08:12:45 +0200 Subject: [PATCH 27/50] improve things --- src/qmoperators/one_electron/ZoraOperator.cpp | 12 +++++++++--- src/qmoperators/two_electron/FockBuilder.cpp | 9 ++++++++- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index e2b38f505..51151b910 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -45,13 +45,19 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv if (k->hasImag()) MSG_ERROR("Inverse of complex function"); if (k->hasReal()) { - mrcpp::refine_grid(k->real(), 1); + // mrcpp::refine_grid(k->real(), 1); if (inverse) { - k->real().map([two_cc](double val) { return (two_cc - val) / two_cc; }); + k->real().map([two_cc](double val) { return (two_cc - val) / two_cc - 1.0; }); } else { - k->real().map([two_cc](double val) { return two_cc / (two_cc - val); }); + k->real().map([two_cc](double val) { return two_cc / (two_cc - val) - 1.0; }); } k->real().crop(proj_prec); + auto const_analytic = [](const mrcpp::Coord<3>& r) { + return 1.0; + }; + mrcpp::ComplexFunction const_func; + mrcpp::cplxfunc::project(const_func, const_analytic, mrcpp::NUMBER::Real, proj_prec); + k->add(1.0, const_func); } RankZeroOperator &kappa = (*this); diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index ad9aaa5d9..d5353dbae 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -47,6 +47,8 @@ #include "qmoperators/qmoperator_utils.h" #include "utils/math_utils.h" +#include "qmoperators/one_electron/NablaOperator.h" + using mrcpp::Printer; using mrcpp::Timer; @@ -251,7 +253,11 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &kappa_m1 = *this->kappa_inv; RankZeroOperator &V_zora = this->zora_base; - RankZeroOperator operOne = 0.5 * tensor::dot(p(kappa), p); + std::shared_ptr> dd = std::make_shared>(*MRA, true); + NablaOperator nabla(dd, true); + nabla.setup(prec); + + RankZeroOperator operOne = 0.5 * tensor::dot(nabla(kappa), p); RankZeroOperator operThree = kappa * V_zora; operOne.setup(prec); operThree.setup(prec); @@ -298,6 +304,7 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita Timer t_kappa; auto out = kappa_m1(arg); mrcpp::print::time(2, "Applying kappa inverse", t_kappa); + nabla.clear(); return out; } From 1f3200fe03d72167ce10eec51fdeb2bec647bf66 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Fri, 9 Aug 2024 11:31:38 +0200 Subject: [PATCH 28/50] refine potential before kappa transform --- src/qmoperators/one_electron/ZoraOperator.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index 51151b910..7e2800838 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -45,7 +45,7 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv if (k->hasImag()) MSG_ERROR("Inverse of complex function"); if (k->hasReal()) { - // mrcpp::refine_grid(k->real(), 1); + mrcpp::refine_grid(k->real(), 1); if (inverse) { k->real().map([two_cc](double val) { return (two_cc - val) / two_cc - 1.0; }); } else { From 6c4c3d5ae9fc13f01b0f694ea49b4566f7771ea3 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Fri, 9 Aug 2024 13:23:45 +0200 Subject: [PATCH 29/50] project and store kappa minus one --- .../one_electron/ZoraKineticOperator.h | 2 +- src/qmoperators/one_electron/ZoraOperator.cpp | 15 ++++++++------- src/qmoperators/two_electron/FockBuilder.cpp | 12 ++++++++---- 3 files changed, 17 insertions(+), 12 deletions(-) diff --git a/src/qmoperators/one_electron/ZoraKineticOperator.h b/src/qmoperators/one_electron/ZoraKineticOperator.h index 1f763761a..6cef1bd1e 100644 --- a/src/qmoperators/one_electron/ZoraKineticOperator.h +++ b/src/qmoperators/one_electron/ZoraKineticOperator.h @@ -40,7 +40,7 @@ class ZoraKineticOperator final : public RankZeroOperator { ZoraKineticOperator(MomentumOperator p, ZoraOperator kappa) { // Invoke operator= to assign *this operator RankZeroOperator &t = (*this); - t = 0.5 * (p[0] * kappa * p[0] + p[1] * kappa * p[1] + p[2] * kappa * p[2]); + t = 0.5 * (p[0] * kappa * p[0] + p[1] * kappa * p[1] + p[2] * kappa * p[2]) + 0.5 * (p[0] * p[0] + p[1] * p[1] + p[2] * p[2]); t.name() = "T_zora"; } }; diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index 7e2800838..15f8228f5 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -49,15 +49,16 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv if (inverse) { k->real().map([two_cc](double val) { return (two_cc - val) / two_cc - 1.0; }); } else { - k->real().map([two_cc](double val) { return two_cc / (two_cc - val) - 1.0; }); + // k->real().map([two_cc](double val) { return two_cc / (two_cc - val) - 1.0; }); + k->real().map([two_cc](double val) { return (val) / (two_cc - val); }); } k->real().crop(proj_prec); - auto const_analytic = [](const mrcpp::Coord<3>& r) { - return 1.0; - }; - mrcpp::ComplexFunction const_func; - mrcpp::cplxfunc::project(const_func, const_analytic, mrcpp::NUMBER::Real, proj_prec); - k->add(1.0, const_func); + // auto const_analytic = [](const mrcpp::Coord<3>& r) { + // return 1.0; + // }; + // mrcpp::ComplexFunction const_func; + // mrcpp::cplxfunc::project(const_func, const_analytic, mrcpp::NUMBER::Real, proj_prec); + // k->add(1.0, const_func); } RankZeroOperator &kappa = (*this); diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index d5353dbae..affe20b09 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -182,7 +182,7 @@ SCFEnergy FockBuilder::trace(OrbitalVector &Phi, const Nuclei &nucs) { // Kinetic part if (isZora()) { - E_kin = qmoperator::calc_kinetic_trace(momentum(), *this->kappa, Phi).real(); + E_kin = qmoperator::calc_kinetic_trace(momentum(), *this->kappa, Phi).real() + qmoperator::calc_kinetic_trace(momentum(), Phi); } else { E_kin = qmoperator::calc_kinetic_trace(momentum(), Phi); } @@ -207,7 +207,7 @@ ComplexMatrix FockBuilder::operator()(OrbitalVector &bra, OrbitalVector &ket) { ComplexMatrix T_mat = ComplexMatrix::Zero(bra.size(), ket.size()); if (isZora()) { - T_mat = qmoperator::calc_kinetic_matrix(momentum(), *this->kappa, bra, ket); + T_mat = qmoperator::calc_kinetic_matrix(momentum(), *this->kappa, bra, ket) + qmoperator::calc_kinetic_matrix(momentum(), bra, ket); } else { T_mat = qmoperator::calc_kinetic_matrix(momentum(), bra, ket); } @@ -258,7 +258,7 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita nabla.setup(prec); RankZeroOperator operOne = 0.5 * tensor::dot(nabla(kappa), p); - RankZeroOperator operThree = kappa * V_zora; + RankZeroOperator operThree = kappa * V_zora + V_zora; operOne.setup(prec); operThree.setup(prec); @@ -302,7 +302,11 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita operOne.clear(); Timer t_kappa; - auto out = kappa_m1(arg); + mrchem::OrbitalVector out = kappa_m1(arg); + for (int i = 0; i < arg.size(); i++) { + if (not mrcpp::mpi::my_orb(out[i])) continue; + out[i].add(1.0, arg[i]); + } mrcpp::print::time(2, "Applying kappa inverse", t_kappa); nabla.clear(); return out; From 6493589af43aae8a918a080c68ee41551c3f704f Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 15 Aug 2024 13:53:33 +0200 Subject: [PATCH 30/50] apply product rule --- src/qmoperators/two_electron/FockBuilder.cpp | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index affe20b09..a3600b79a 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -253,11 +253,21 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &kappa_m1 = *this->kappa_inv; RankZeroOperator &V_zora = this->zora_base; - std::shared_ptr> dd = std::make_shared>(*MRA, true); - NablaOperator nabla(dd, true); + std::shared_ptr> dd = std::make_shared>(*MRA, 1); + std::shared_ptr> dd2 = std::make_shared>(*MRA, 2); + + NablaOperator nabla(dd, false); // gradient operator + NablaOperator nabla2(dd2, false); // containts second derivatives nabla.setup(prec); + nabla2.setup(prec); + + RankOneOperator nabla_kappa = nabla(kappa); + RankZeroOperator operOne = 0.5 * (nabla_kappa[0] * nabla[0] + nabla_kappa[1] * nabla[1] + nabla_kappa[2] * nabla[2] + + kappa * nabla2[0] + kappa * nabla2[1] + kappa * nabla2[2]); + // + nabla2[0] + nabla2[1] + nabla2[2]); - RankZeroOperator operOne = 0.5 * tensor::dot(nabla(kappa), p); + // this works much better than the above. Also, removing the laplacian terms on line 266 appears to be equivalent to the line below but why? + // RankZeroOperator operOne = 0.5 * (nabla_kappa[0](nabla[0]) + nabla_kappa[1](nabla[1]) + nabla_kappa[2](nabla[2])); RankZeroOperator operThree = kappa * V_zora + V_zora; operOne.setup(prec); operThree.setup(prec); @@ -309,6 +319,7 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita } mrcpp::print::time(2, "Applying kappa inverse", t_kappa); nabla.clear(); + nabla2.clear(); return out; } From be09264716ff560a3ebf9dd1d8957ee69f430a18 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Fri, 16 Aug 2024 13:09:53 +0200 Subject: [PATCH 31/50] rever product rule change --- src/qmoperators/two_electron/FockBuilder.cpp | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index a3600b79a..81c14ba1d 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -254,20 +254,13 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &V_zora = this->zora_base; std::shared_ptr> dd = std::make_shared>(*MRA, 1); - std::shared_ptr> dd2 = std::make_shared>(*MRA, 2); NablaOperator nabla(dd, false); // gradient operator - NablaOperator nabla2(dd2, false); // containts second derivatives nabla.setup(prec); - nabla2.setup(prec); RankOneOperator nabla_kappa = nabla(kappa); - RankZeroOperator operOne = 0.5 * (nabla_kappa[0] * nabla[0] + nabla_kappa[1] * nabla[1] + nabla_kappa[2] * nabla[2] - + kappa * nabla2[0] + kappa * nabla2[1] + kappa * nabla2[2]); - // + nabla2[0] + nabla2[1] + nabla2[2]); - // this works much better than the above. Also, removing the laplacian terms on line 266 appears to be equivalent to the line below but why? - // RankZeroOperator operOne = 0.5 * (nabla_kappa[0](nabla[0]) + nabla_kappa[1](nabla[1]) + nabla_kappa[2](nabla[2])); + RankZeroOperator operOne = 0.5 * (nabla_kappa[0](nabla[0]) + nabla_kappa[1](nabla[1]) + nabla_kappa[2](nabla[2])); RankZeroOperator operThree = kappa * V_zora + V_zora; operOne.setup(prec); operThree.setup(prec); @@ -319,7 +312,6 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita } mrcpp::print::time(2, "Applying kappa inverse", t_kappa); nabla.clear(); - nabla2.clear(); return out; } From baebb5776f89d05f3ce4dbb214801c691874fccc Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Fri, 16 Aug 2024 14:41:23 +0200 Subject: [PATCH 32/50] use other derivative operator --- src/qmoperators/two_electron/FockBuilder.cpp | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index 81c14ba1d..a25e71865 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -253,14 +253,11 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &kappa_m1 = *this->kappa_inv; RankZeroOperator &V_zora = this->zora_base; - std::shared_ptr> dd = std::make_shared>(*MRA, 1); - - NablaOperator nabla(dd, false); // gradient operator + std::shared_ptr> dd = std::make_shared>(*MRA, true); + NablaOperator nabla(dd, true); nabla.setup(prec); - RankOneOperator nabla_kappa = nabla(kappa); - - RankZeroOperator operOne = 0.5 * (nabla_kappa[0](nabla[0]) + nabla_kappa[1](nabla[1]) + nabla_kappa[2](nabla[2])); + RankZeroOperator operOne = 0.5 * tensor::dot(p(kappa), p); RankZeroOperator operThree = kappa * V_zora + V_zora; operOne.setup(prec); operThree.setup(prec); From 87bc1c4884916391bfc8dcf9520b22fcf367e680 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Fri, 16 Aug 2024 14:42:38 +0200 Subject: [PATCH 33/50] remove unused operator --- src/qmoperators/two_electron/FockBuilder.cpp | 7 ------- 1 file changed, 7 deletions(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index a25e71865..bce8e5468 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -47,8 +47,6 @@ #include "qmoperators/qmoperator_utils.h" #include "utils/math_utils.h" -#include "qmoperators/one_electron/NablaOperator.h" - using mrcpp::Printer; using mrcpp::Timer; @@ -253,10 +251,6 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita RankZeroOperator &kappa_m1 = *this->kappa_inv; RankZeroOperator &V_zora = this->zora_base; - std::shared_ptr> dd = std::make_shared>(*MRA, true); - NablaOperator nabla(dd, true); - nabla.setup(prec); - RankZeroOperator operOne = 0.5 * tensor::dot(p(kappa), p); RankZeroOperator operThree = kappa * V_zora + V_zora; operOne.setup(prec); @@ -308,7 +302,6 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita out[i].add(1.0, arg[i]); } mrcpp::print::time(2, "Applying kappa inverse", t_kappa); - nabla.clear(); return out; } From 2f4f90d936445cf480d3b9cc8d67f9a60e04e40d Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Mon, 19 Aug 2024 11:25:53 +0200 Subject: [PATCH 34/50] delete unused zora_kinetic operator --- .../one_electron/ZoraKineticOperator.h | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 src/qmoperators/one_electron/ZoraKineticOperator.h diff --git a/src/qmoperators/one_electron/ZoraKineticOperator.h b/src/qmoperators/one_electron/ZoraKineticOperator.h deleted file mode 100644 index 6cef1bd1e..000000000 --- a/src/qmoperators/one_electron/ZoraKineticOperator.h +++ /dev/null @@ -1,48 +0,0 @@ -/* - * MRChem, a numerical real-space code for molecular electronic structure - * calculations within the self-consistent field (SCF) approximations of quantum - * chemistry (Hartree-Fock and Density Functional Theory). - * Copyright (C) 2023 Stig Rune Jensen, Luca Frediani, Peter Wind and contributors. - * - * This file is part of MRChem. - * - * MRChem is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * MRChem is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with MRChem. If not, see . - * - * For information on the complete list of contributors to MRChem, see: - * - */ - -#pragma once - -#include "tensor/RankZeroOperator.h" - -#include "MomentumOperator.h" -#include "ZoraOperator.h" - -namespace mrchem { - -class ZoraKineticOperator final : public RankZeroOperator { -public: - ZoraKineticOperator(std::shared_ptr> D, ZoraOperator kappa) - : ZoraKineticOperator(MomentumOperator(D), kappa) {} - - ZoraKineticOperator(MomentumOperator p, ZoraOperator kappa) { - // Invoke operator= to assign *this operator - RankZeroOperator &t = (*this); - t = 0.5 * (p[0] * kappa * p[0] + p[1] * kappa * p[1] + p[2] * kappa * p[2]) + 0.5 * (p[0] * p[0] + p[1] * p[1] + p[2] * p[2]); - t.name() = "T_zora"; - } -}; - -} // namespace mrchem From 451b192471a2ceaf302856ce06e4490ef08b45fb Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Mon, 19 Aug 2024 11:32:50 +0200 Subject: [PATCH 35/50] remove old comments --- src/qmoperators/one_electron/ZoraOperator.cpp | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index 15f8228f5..d4ed96a81 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -49,27 +49,20 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv if (inverse) { k->real().map([two_cc](double val) { return (two_cc - val) / two_cc - 1.0; }); } else { - // k->real().map([two_cc](double val) { return two_cc / (two_cc - val) - 1.0; }); k->real().map([two_cc](double val) { return (val) / (two_cc - val); }); } k->real().crop(proj_prec); - // auto const_analytic = [](const mrcpp::Coord<3>& r) { - // return 1.0; - // }; - // mrcpp::ComplexFunction const_func; - // mrcpp::cplxfunc::project(const_func, const_analytic, mrcpp::NUMBER::Real, proj_prec); - // k->add(1.0, const_func); } - RankZeroOperator &kappa = (*this); - kappa = k; + RankZeroOperator &chi = (*this); + chi = k; if (inverse) { - kappa.name() = "kappa_m1"; + chi.name() = "chi_inv"; } else { - kappa.name() = "kappa"; + chi.name() = "chi"; } auto plevel = Printer::getPrintLevel(); - print_utils::qmfunction(2, "ZORA operator (" + kappa.name() + ")", *k, timer); + print_utils::qmfunction(2, "ZORA operator (" + chi.name() + ")", *k, timer); } } // namespace mrchem From 06f8591e7111efa8acdce2cb645ae668a9339b03 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Mon, 19 Aug 2024 11:32:59 +0200 Subject: [PATCH 36/50] add some documentation --- src/qmoperators/one_electron/ZoraOperator.h | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/qmoperators/one_electron/ZoraOperator.h b/src/qmoperators/one_electron/ZoraOperator.h index 8dd2ee7ce..2cadfb83c 100644 --- a/src/qmoperators/one_electron/ZoraOperator.h +++ b/src/qmoperators/one_electron/ZoraOperator.h @@ -31,8 +31,22 @@ namespace mrchem { class QMPotential; +/** + * @class ZoraOperator + * @brief Implements chi = kappa - 1 relativistic dampening function. This has to be done in order to + * avoid numerical instabilities in the ZORA operator. Whenever this operator is applied, the + 1 has to be added to chi i + * in order to get the kappa operator. kappa * phi = chi * phi + phi + * This has to be done manually. + */ class ZoraOperator final : public RankZeroOperator { public: + /** + * @brief Constructor for the ZoraOperator that contains the chi = kappa - 1 function. + * @param vz The potential used to calculate the kappa function. + * @param c Speed of light. + * @param proj_prec The precision of the MW projection. + * @param inverse If true, the inverse of the chi function is calculated. + */ ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inverse = false); }; From 1bcf590d51eb091f57f3e458b00ce358b8366399 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Mon, 19 Aug 2024 11:41:08 +0200 Subject: [PATCH 37/50] rename kappa to chi --- src/qmoperators/two_electron/FockBuilder.cpp | 27 ++++++++++---------- src/qmoperators/two_electron/FockBuilder.h | 4 +-- 2 files changed, 16 insertions(+), 15 deletions(-) diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index bce8e5468..e36df3d1f 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -96,11 +96,12 @@ void FockBuilder::setup(double prec) { mrcpp::print::value(3, "Light speed", c, "(au)", 5); mrcpp::print::separator(3, '-'); auto vz = collectZoraBasePotential(); - this->kappa = std::make_shared(*vz, c, prec, false); - this->kappa_inv = std::make_shared(*vz, c, prec, true); + // chi = kappa - 1. See ZoraOperator.h for more information. + this->chi = std::make_shared(*vz, c, prec, false); + this->chi_inv = std::make_shared(*vz, c, prec, true); this->zora_base = RankZeroOperator(vz); - this->kappa->setup(prec); - this->kappa_inv->setup(prec); + this->chi->setup(prec); + this->chi_inv->setup(prec); this->zora_base.setup(prec); mrcpp::print::footer(3, t_zora, 2); }; @@ -120,8 +121,8 @@ void FockBuilder::clear() { this->potential().clear(); this->perturbation().clear(); if (isZora()) { - this->kappa->clear(); - this->kappa_inv->clear(); + this->chi->clear(); + this->chi_inv->clear(); this->zora_base.clear(); } } @@ -180,7 +181,7 @@ SCFEnergy FockBuilder::trace(OrbitalVector &Phi, const Nuclei &nucs) { // Kinetic part if (isZora()) { - E_kin = qmoperator::calc_kinetic_trace(momentum(), *this->kappa, Phi).real() + qmoperator::calc_kinetic_trace(momentum(), Phi); + E_kin = qmoperator::calc_kinetic_trace(momentum(), *this->chi, Phi).real() + qmoperator::calc_kinetic_trace(momentum(), Phi); } else { E_kin = qmoperator::calc_kinetic_trace(momentum(), Phi); } @@ -205,7 +206,7 @@ ComplexMatrix FockBuilder::operator()(OrbitalVector &bra, OrbitalVector &ket) { ComplexMatrix T_mat = ComplexMatrix::Zero(bra.size(), ket.size()); if (isZora()) { - T_mat = qmoperator::calc_kinetic_matrix(momentum(), *this->kappa, bra, ket) + qmoperator::calc_kinetic_matrix(momentum(), bra, ket); + T_mat = qmoperator::calc_kinetic_matrix(momentum(), *this->chi, bra, ket) + qmoperator::calc_kinetic_matrix(momentum(), bra, ket); } else { T_mat = qmoperator::calc_kinetic_matrix(momentum(), bra, ket); } @@ -247,12 +248,12 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita double two_cc = 2.0 * c * c; MomentumOperator &p = momentum(); RankZeroOperator &V = potential(); - RankZeroOperator &kappa = *this->kappa; - RankZeroOperator &kappa_m1 = *this->kappa_inv; + RankZeroOperator &chi = *this->chi; + RankZeroOperator &chi_inv = *this->chi_inv; RankZeroOperator &V_zora = this->zora_base; - RankZeroOperator operOne = 0.5 * tensor::dot(p(kappa), p); - RankZeroOperator operThree = kappa * V_zora + V_zora; + RankZeroOperator operOne = 0.5 * tensor::dot(p(chi), p); + RankZeroOperator operThree = chi * V_zora + V_zora; operOne.setup(prec); operThree.setup(prec); @@ -296,7 +297,7 @@ OrbitalVector FockBuilder::buildHelmholtzArgumentZORA(OrbitalVector &Phi, Orbita operOne.clear(); Timer t_kappa; - mrchem::OrbitalVector out = kappa_m1(arg); + mrchem::OrbitalVector out = chi_inv(arg); for (int i = 0; i < arg.size(); i++) { if (not mrcpp::mpi::my_orb(out[i])) continue; out[i].add(1.0, arg[i]); diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index 53db4958e..34cb0ca41 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -105,8 +105,8 @@ class FockBuilder final { std::shared_ptr xc{nullptr}; std::shared_ptr Ro{nullptr}; // Reaction field operator std::shared_ptr ext{nullptr}; // Total external potential - std::shared_ptr kappa{nullptr}; - std::shared_ptr kappa_inv{nullptr}; + std::shared_ptr chi{nullptr}; + std::shared_ptr chi_inv{nullptr}; std::shared_ptr collectZoraBasePotential(); OrbitalVector buildHelmholtzArgumentZORA(OrbitalVector &Phi, OrbitalVector &Psi, DoubleVector eps, double prec); From af58f3640daf7b1c74ded0fe1a52e3143538a8bd Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 5 Sep 2024 16:24:45 +0200 Subject: [PATCH 38/50] implement unrestricted zora --- python/mrchem/helpers.py | 8 ++++---- src/qmoperators/two_electron/FockBuilder.cpp | 2 +- src/qmoperators/two_electron/XCPotential.cpp | 4 ++++ src/qmoperators/two_electron/XCPotential.h | 1 + 4 files changed, 10 insertions(+), 5 deletions(-) diff --git a/python/mrchem/helpers.py b/python/mrchem/helpers.py index 43fdef69b..7bd01ff07 100644 --- a/python/mrchem/helpers.py +++ b/python/mrchem/helpers.py @@ -535,10 +535,10 @@ def parse_wf_method(user_dict): else: raise RuntimeError("ZORA selected, but no ZORA potential included") - if user_dict["ZORA"]["include_xc"] and not restricted: - raise RuntimeError( - "ZORA (V_xc) not available for unrestricted wavefunctions" - ) + # if user_dict["ZORA"]["include_xc"] and not restricted: + # raise RuntimeError( + # "ZORA (V_xc) not available for unrestricted wavefunctions" + # ) # Determine environment name label for print outs to the output file environment_name = "None" diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index e36df3d1f..f49fd4cc6 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -357,7 +357,7 @@ std::shared_ptr FockBuilder::collectZoraBasePotential() { } if (zora_has_xc) { if (getXCOperator() != nullptr) { - getXCOperator()->setSpin(SPIN::Alpha); + getXCOperator()->setSpin(SPIN::Paired); auto &xc = static_cast(getXCOperator()->getRaw(0, 0)); if (not xc.hasReal()) MSG_ERROR("ZORA: Adding empty XC potential"); vz->add(1.0, xc); diff --git a/src/qmoperators/two_electron/XCPotential.cpp b/src/qmoperators/two_electron/XCPotential.cpp index 8d06a336d..763a87db2 100644 --- a/src/qmoperators/two_electron/XCPotential.cpp +++ b/src/qmoperators/two_electron/XCPotential.cpp @@ -144,6 +144,10 @@ FunctionTree<3> &XCPotential::getPotential(int spin) { pot_idx = 1; } else if (not spinFunctional) { pot_idx = 0; + } else if (spinFunctional and spin == SPIN::Paired) { + this->v_tot = std::make_shared>(*MRA); + mrcpp::add(prec(), *this->v_tot, this->potentials); + return *this->v_tot; } else { NOT_IMPLEMENTED_ABORT; } diff --git a/src/qmoperators/two_electron/XCPotential.h b/src/qmoperators/two_electron/XCPotential.h index ef0c257fd..307477690 100644 --- a/src/qmoperators/two_electron/XCPotential.h +++ b/src/qmoperators/two_electron/XCPotential.h @@ -69,6 +69,7 @@ class XCPotential : public QMPotential { double energy; ///< XC energy std::vector densities; ///< XC densities (total or alpha/beta) mrcpp::FunctionTreeVector<3> potentials; ///< XC Potential functions collected in a vector + std::shared_ptr> v_tot{nullptr}; ///< Total XC potential std::shared_ptr orbitals; ///< External set of orbitals used to build the density std::unique_ptr mrdft; ///< External XC functional to be used From b9065bf4ca5c825da9ac08cb337e0733f36f7b93 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Wed, 25 Sep 2024 17:20:30 +0200 Subject: [PATCH 39/50] add all densities --- share/azora_potentials/Ag.txt | 192 +++++++++++++++++ share/azora_potentials/Al.txt | 192 +++++++++++++++++ share/azora_potentials/Ar.txt | 384 +++++++++++++++++----------------- share/azora_potentials/As.txt | 192 +++++++++++++++++ share/azora_potentials/At.txt | 192 +++++++++++++++++ share/azora_potentials/Au.txt | 192 +++++++++++++++++ share/azora_potentials/B.txt | 192 +++++++++++++++++ share/azora_potentials/Ba.txt | 192 +++++++++++++++++ share/azora_potentials/Be.txt | 192 +++++++++++++++++ share/azora_potentials/Bi.txt | 192 +++++++++++++++++ share/azora_potentials/Br.txt | 192 +++++++++++++++++ share/azora_potentials/C.txt | 384 +++++++++++++++++----------------- share/azora_potentials/Ca.txt | 192 +++++++++++++++++ share/azora_potentials/Cd.txt | 192 +++++++++++++++++ share/azora_potentials/Ce.txt | 192 +++++++++++++++++ share/azora_potentials/Cl.txt | 192 +++++++++++++++++ share/azora_potentials/Co.txt | 192 +++++++++++++++++ share/azora_potentials/Cr.txt | 192 +++++++++++++++++ share/azora_potentials/Cs.txt | 192 +++++++++++++++++ share/azora_potentials/Cu.txt | 192 +++++++++++++++++ share/azora_potentials/Dy.txt | 192 +++++++++++++++++ share/azora_potentials/Er.txt | 192 +++++++++++++++++ share/azora_potentials/Eu.txt | 192 +++++++++++++++++ share/azora_potentials/F.txt | 192 +++++++++++++++++ share/azora_potentials/Fe.txt | 192 +++++++++++++++++ share/azora_potentials/Ga.txt | 192 +++++++++++++++++ share/azora_potentials/Gd.txt | 192 +++++++++++++++++ share/azora_potentials/Ge.txt | 192 +++++++++++++++++ share/azora_potentials/H.txt | 336 ++++++++++++++--------------- share/azora_potentials/He.txt | 384 +++++++++++++++++----------------- share/azora_potentials/Hf.txt | 192 +++++++++++++++++ share/azora_potentials/Hg.txt | 192 +++++++++++++++++ share/azora_potentials/Ho.txt | 192 +++++++++++++++++ share/azora_potentials/I.txt | 192 +++++++++++++++++ share/azora_potentials/In.txt | 192 +++++++++++++++++ share/azora_potentials/Ir.txt | 192 +++++++++++++++++ share/azora_potentials/K.txt | 192 +++++++++++++++++ share/azora_potentials/Kr.txt | 192 +++++++++++++++++ share/azora_potentials/La.txt | 192 +++++++++++++++++ share/azora_potentials/Li.txt | 192 +++++++++++++++++ share/azora_potentials/Lu.txt | 192 +++++++++++++++++ share/azora_potentials/Mg.txt | 192 +++++++++++++++++ share/azora_potentials/Mn.txt | 192 +++++++++++++++++ share/azora_potentials/Mo.txt | 192 +++++++++++++++++ share/azora_potentials/N.txt | 384 +++++++++++++++++----------------- share/azora_potentials/Na.txt | 192 +++++++++++++++++ share/azora_potentials/Nb.txt | 192 +++++++++++++++++ share/azora_potentials/Nd.txt | 192 +++++++++++++++++ share/azora_potentials/Ne.txt | 384 +++++++++++++++++----------------- share/azora_potentials/Ni.txt | 192 +++++++++++++++++ share/azora_potentials/O.txt | 334 ++++++++++++++--------------- share/azora_potentials/Os.txt | 192 +++++++++++++++++ share/azora_potentials/P.txt | 192 +++++++++++++++++ share/azora_potentials/Pb.txt | 192 +++++++++++++++++ share/azora_potentials/Pd.txt | 192 +++++++++++++++++ share/azora_potentials/Pm.txt | 192 +++++++++++++++++ share/azora_potentials/Po.txt | 192 +++++++++++++++++ share/azora_potentials/Pr.txt | 192 +++++++++++++++++ share/azora_potentials/Pt.txt | 192 +++++++++++++++++ share/azora_potentials/Rb.txt | 192 +++++++++++++++++ share/azora_potentials/Re.txt | 192 +++++++++++++++++ share/azora_potentials/Rh.txt | 192 +++++++++++++++++ share/azora_potentials/Rn.txt | 192 +++++++++++++++++ share/azora_potentials/Ru.txt | 192 +++++++++++++++++ share/azora_potentials/S.txt | 192 +++++++++++++++++ share/azora_potentials/Sb.txt | 192 +++++++++++++++++ share/azora_potentials/Sc.txt | 192 +++++++++++++++++ share/azora_potentials/Se.txt | 192 +++++++++++++++++ share/azora_potentials/Si.txt | 192 +++++++++++++++++ share/azora_potentials/Sm.txt | 192 +++++++++++++++++ share/azora_potentials/Sn.txt | 192 +++++++++++++++++ share/azora_potentials/Sr.txt | 192 +++++++++++++++++ share/azora_potentials/Ta.txt | 192 +++++++++++++++++ share/azora_potentials/Tb.txt | 192 +++++++++++++++++ share/azora_potentials/Tc.txt | 192 +++++++++++++++++ share/azora_potentials/Te.txt | 192 +++++++++++++++++ share/azora_potentials/Ti.txt | 192 +++++++++++++++++ share/azora_potentials/Tl.txt | 192 +++++++++++++++++ share/azora_potentials/Tm.txt | 192 +++++++++++++++++ share/azora_potentials/V.txt | 192 +++++++++++++++++ share/azora_potentials/W.txt | 192 +++++++++++++++++ share/azora_potentials/Xe.txt | 384 +++++++++++++++++----------------- share/azora_potentials/Y.txt | 192 +++++++++++++++++ share/azora_potentials/Yb.txt | 192 +++++++++++++++++ share/azora_potentials/Zn.txt | 192 +++++++++++++++++ share/azora_potentials/Zr.txt | 192 +++++++++++++++++ 86 files changed, 16463 insertions(+), 1487 deletions(-) create mode 100644 share/azora_potentials/Ag.txt create mode 100644 share/azora_potentials/Al.txt create mode 100644 share/azora_potentials/As.txt create mode 100644 share/azora_potentials/At.txt create mode 100644 share/azora_potentials/Au.txt create mode 100644 share/azora_potentials/B.txt create mode 100644 share/azora_potentials/Ba.txt create mode 100644 share/azora_potentials/Be.txt create mode 100644 share/azora_potentials/Bi.txt create mode 100644 share/azora_potentials/Br.txt create mode 100644 share/azora_potentials/Ca.txt create mode 100644 share/azora_potentials/Cd.txt create mode 100644 share/azora_potentials/Ce.txt 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0.49649173661237E-12 + 0.50000000000000000E+00 0.32591090115412E+02 0.48294701571194E-12 + 0.50000000000000000E+00 0.33489825716383E+02 0.47006842862629E-12 + 0.50000000000000000E+00 0.34394697380382E+02 0.45785597535541E-12 + 0.50000000000000000E+00 0.35305370261891E+02 0.44586556668946E-12 + 0.50000000000000000E+00 0.36221523376224E+02 0.43454129183829E-12 + 0.50000000000000000E+00 0.37142849564891E+02 0.42388315080188E-12 + 0.50000000000000000E+00 0.38069055382202E+02 0.41366909897533E-12 + 0.50000000000000000E+00 0.38999860913611E+02 0.40367709175371E-12 + 0.50000000000000000E+00 0.39934999535663E+02 0.39435121834686E-12 + 0.50000000000000000E+00 0.40874217626704E+02 0.38535841184739E-12 From 7669ebc23dc9c15a8f5dc3ebb30fd0aad294b644 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 13:25:13 +0200 Subject: [PATCH 40/50] update potentials --- share/azora_potentials/Ag.txt | 384 +++++++++++++++---------------- share/azora_potentials/Al.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ar.txt | 384 +++++++++++++++---------------- share/azora_potentials/As.txt | 384 +++++++++++++++---------------- share/azora_potentials/At.txt | 384 +++++++++++++++---------------- share/azora_potentials/Au.txt | 384 +++++++++++++++---------------- share/azora_potentials/B.txt | 376 +++++++++++++++--------------- share/azora_potentials/Ba.txt | 384 +++++++++++++++---------------- share/azora_potentials/Be.txt | 384 +++++++++++++++---------------- share/azora_potentials/Bi.txt | 384 +++++++++++++++---------------- share/azora_potentials/Br.txt | 384 +++++++++++++++---------------- share/azora_potentials/C.txt | 382 +++++++++++++++--------------- share/azora_potentials/Ca.txt | 384 +++++++++++++++---------------- share/azora_potentials/Cd.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ce.txt | 384 +++++++++++++++---------------- share/azora_potentials/Cl.txt | 384 +++++++++++++++---------------- share/azora_potentials/Co.txt | 384 +++++++++++++++---------------- share/azora_potentials/Cr.txt | 384 +++++++++++++++---------------- share/azora_potentials/Cs.txt | 384 +++++++++++++++---------------- share/azora_potentials/Cu.txt | 384 +++++++++++++++---------------- share/azora_potentials/Dy.txt | 384 +++++++++++++++---------------- share/azora_potentials/Er.txt | 384 +++++++++++++++---------------- share/azora_potentials/Eu.txt | 384 +++++++++++++++---------------- share/azora_potentials/F.txt | 384 +++++++++++++++---------------- share/azora_potentials/Fe.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ga.txt | 384 +++++++++++++++---------------- share/azora_potentials/Gd.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ge.txt | 384 +++++++++++++++---------------- share/azora_potentials/H.txt | 384 +++++++++++++++---------------- share/azora_potentials/He.txt | 384 +++++++++++++++---------------- share/azora_potentials/Hf.txt | 384 +++++++++++++++---------------- share/azora_potentials/Hg.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ho.txt | 384 +++++++++++++++---------------- share/azora_potentials/I.txt | 384 +++++++++++++++---------------- share/azora_potentials/In.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ir.txt | 384 +++++++++++++++---------------- share/azora_potentials/K.txt | 384 +++++++++++++++---------------- share/azora_potentials/Kr.txt | 384 +++++++++++++++---------------- share/azora_potentials/La.txt | 384 +++++++++++++++---------------- share/azora_potentials/Li.txt | 368 ++++++++++++++--------------- share/azora_potentials/Lu.txt | 384 +++++++++++++++---------------- share/azora_potentials/Mg.txt | 384 +++++++++++++++---------------- share/azora_potentials/Mn.txt | 384 +++++++++++++++---------------- share/azora_potentials/Mo.txt | 384 +++++++++++++++---------------- share/azora_potentials/N.txt | 384 +++++++++++++++---------------- share/azora_potentials/Na.txt | 384 +++++++++++++++---------------- share/azora_potentials/Nb.txt | 384 +++++++++++++++---------------- share/azora_potentials/Nd.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ne.txt | 368 ++++++++++++++--------------- share/azora_potentials/Ni.txt | 384 +++++++++++++++---------------- share/azora_potentials/O.txt | 376 +++++++++++++++--------------- share/azora_potentials/Os.txt | 384 +++++++++++++++---------------- share/azora_potentials/P.txt | 384 +++++++++++++++---------------- share/azora_potentials/Pb.txt | 384 +++++++++++++++---------------- share/azora_potentials/Pd.txt | 384 +++++++++++++++---------------- share/azora_potentials/Pm.txt | 384 +++++++++++++++---------------- share/azora_potentials/Po.txt | 384 +++++++++++++++---------------- share/azora_potentials/Pr.txt | 384 +++++++++++++++---------------- share/azora_potentials/Pt.txt | 384 +++++++++++++++---------------- share/azora_potentials/README.md | 3 +- share/azora_potentials/Rb.txt | 384 +++++++++++++++---------------- share/azora_potentials/Re.txt | 384 +++++++++++++++---------------- share/azora_potentials/Rh.txt | 384 +++++++++++++++---------------- share/azora_potentials/Rn.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ru.txt | 384 +++++++++++++++---------------- share/azora_potentials/S.txt | 384 +++++++++++++++---------------- share/azora_potentials/Sb.txt | 384 +++++++++++++++---------------- share/azora_potentials/Sc.txt | 384 +++++++++++++++---------------- share/azora_potentials/Se.txt | 384 +++++++++++++++---------------- share/azora_potentials/Si.txt | 384 +++++++++++++++---------------- share/azora_potentials/Sm.txt | 384 +++++++++++++++---------------- share/azora_potentials/Sn.txt | 384 +++++++++++++++---------------- share/azora_potentials/Sr.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ta.txt | 384 +++++++++++++++---------------- share/azora_potentials/Tb.txt | 384 +++++++++++++++---------------- share/azora_potentials/Tc.txt | 384 +++++++++++++++---------------- share/azora_potentials/Te.txt | 384 +++++++++++++++---------------- share/azora_potentials/Ti.txt | 384 +++++++++++++++---------------- share/azora_potentials/Tl.txt | 384 +++++++++++++++---------------- share/azora_potentials/Tm.txt | 384 +++++++++++++++---------------- share/azora_potentials/V.txt | 384 +++++++++++++++---------------- share/azora_potentials/W.txt | 384 +++++++++++++++---------------- share/azora_potentials/Xe.txt | 384 +++++++++++++++---------------- share/azora_potentials/Y.txt | 384 +++++++++++++++---------------- share/azora_potentials/Yb.txt | 384 +++++++++++++++---------------- share/azora_potentials/Zn.txt | 384 +++++++++++++++---------------- share/azora_potentials/Zr.txt | 384 +++++++++++++++---------------- 87 files changed, 16489 insertions(+), 16488 deletions(-) diff --git a/share/azora_potentials/Ag.txt b/share/azora_potentials/Ag.txt index 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b/share/azora_potentials/README.md @@ -1,2 +1,3 @@ Data directory that contains the radial potentials and relativistic dampening functions for the azora method. -Format of the potential files: Data is stored columnwise. First column is the dampening function (not read), second column is radius, third is atomic zora potential. \ No newline at end of file +Format of the potential files: Data is stored columnwise. First column is the dampening function (not read), second column is radius, third is atomic zora potential. +The potentials were generated with a sperically symmetric LDA calculation and a gaussian nuclear potential of width 1e-4. \ No newline at end of file diff --git a/share/azora_potentials/Rb.txt b/share/azora_potentials/Rb.txt index 2d4b85dd0..8de0eb374 100644 --- a/share/azora_potentials/Rb.txt +++ b/share/azora_potentials/Rb.txt @@ -1,192 +1,192 @@ - 0.23726393453446865E+00 0.97578195523695E-18 -0.41589845527547E+05 - 0.23730019532569901E+00 0.29483069282768E-04 -0.41577751337162E+05 - 0.23741952224435525E+00 0.61082173640461E-04 -0.41537977888257E+05 - 0.23763963639081273E+00 0.94949178290611E-04 -0.41464715343904E+05 - 0.23798105960125676E+00 0.13124684686428E-03 -0.41351344568529E+05 - 0.23846743002337031E+00 0.17014962340302E-03 -0.41190404182332E+05 - 0.23912581807845157E+00 0.21184447044981E-03 -0.40973585974110E+05 - 0.23998702053948057E+00 0.25653176725507E-03 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0.50000000000000000E+00 0.29064684357170E+02 0.95945473788106E-12 + 0.50000000000000000E+00 0.29935254177814E+02 0.93214325147528E-12 + 0.50000000000000000E+00 0.30813435356248E+02 0.90594198809413E-12 + 0.50000000000000000E+00 0.31698839228624E+02 0.88040685852775E-12 + 0.50000000000000000E+00 0.32591090115412E+02 0.85642604119585E-12 + 0.50000000000000000E+00 0.33489825716383E+02 0.83333340228364E-12 + 0.50000000000000000E+00 0.34394697380382E+02 0.81157303100099E-12 + 0.50000000000000000E+00 0.35305370261891E+02 0.79047879353311E-12 + 0.50000000000000000E+00 0.36221523376224E+02 0.77049477908986E-12 + 0.50000000000000000E+00 0.37142849564891E+02 0.75139894306631E-12 + 0.50000000000000000E+00 0.38069055382202E+02 0.73319128546245E-12 + 0.50000000000000000E+00 0.38999860913611E+02 0.71564976167338E-12 + 0.50000000000000000E+00 0.39934999535663E+02 0.69899641630400E-12 + 0.50000000000000000E+00 0.40874217626704E+02 0.68300920474940E-12 From cfa34c381e0687b111828b26ff5dfcd619ff71e9 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 13:33:14 +0200 Subject: [PATCH 41/50] fix merge fail --- src/qmoperators/one_electron/ZoraOperator.cpp | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index c5c782fad..6dd1dbbfc 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -44,29 +44,23 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv std::shared_ptr k = std::make_shared(1); mrcpp::cplxfunc::deep_copy(*k, vz); - if (k->hasImag()) MSG_ERROR("Inverse of complex function"); + if (k->hasImag()) MSG_ERROR("Inverse of complex function in zora potential"); if (k->hasReal()) { mrcpp::refine_grid(k->real(), 1); if (inverse) { k->real().map([two_cc](double val) { return (two_cc - val) / two_cc - 1.0; }); - k->real().map([two_cc](double val) { return (two_cc - val) / two_cc - 1.0; }); } else { k->real().map([two_cc](double val) { return (val) / (two_cc - val); }); - k->real().map([two_cc](double val) { return (val) / (two_cc - val); }); } k->real().crop(proj_prec); } - RankZeroOperator &chi = (*this); - chi = k; RankZeroOperator &chi = (*this); chi = k; if (inverse) { chi.name() = "chi_inv"; - chi.name() = "chi_inv"; } else { chi.name() = "chi"; - chi.name() = "chi"; } auto plevel = Printer::getPrintLevel(); print_utils::qmfunction(2, "ZORA operator (" + chi.name() + ")", *k, timer); From 86cd1db5b61fd9f67c42c12806f434ed0fdf6b83 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 13:42:23 +0200 Subject: [PATCH 42/50] remove eigen interpolator --- .../one_electron/AZora/RadialInterpolater.h | 41 +++---------------- src/utils/PolyInterpolator.h | 22 ++++++++++ 2 files changed, 28 insertions(+), 35 deletions(-) diff --git a/src/qmoperators/one_electron/AZora/RadialInterpolater.h b/src/qmoperators/one_electron/AZora/RadialInterpolater.h index dd6bffcfa..abfb51196 100644 --- a/src/qmoperators/one_electron/AZora/RadialInterpolater.h +++ b/src/qmoperators/one_electron/AZora/RadialInterpolater.h @@ -1,13 +1,10 @@ #include #include #include -#include +#include "utils/PolyInterpolator.h" #include #include -typedef Eigen::Spline Spline1D; -typedef Eigen::SplineFitting SplineFitting1D; - /** * @brief Read ZORA potential from file. Check if file exists and abort if it does not. * @param path Path to the file containing the ZORA potential @@ -61,45 +58,19 @@ class RadInterpolater { readZoraPotential(filename, rGrid, vZora, kappa); if (mode == "kappa") { - const auto fitV = SplineFitting1D::Interpolate(kappa.transpose(), 3, rGrid.transpose()); - Spline1D temp (fitV); - splineAZora = temp; + interpolator = std::make_shared(rGrid, kappa); } else if (mode == "potential") { - const auto fitV = SplineFitting1D::Interpolate(vZora.transpose(), 3, rGrid.transpose()); - Spline1D temp (fitV); - splineAZora = temp; + interpolator = std::make_shared(rGrid, vZora); } } double evalf(const double &r) const { - return splineAZora(r).coeff(0); + return interpolator->evalfLeftNoRightConstant(r); } protected: - Spline1D splineAZora; + std::shared_ptr interpolator; std::string mode; -}; - -// int main() { - -// RadInterpolater spline_V("Ar"); - -// Eigen::VectorXd xgrid = Eigen::VectorXd::LinSpaced(100000, 00, 1); -// Eigen::VectorXd ygrid(xgrid.size()); -// for (int i = 0; i < xgrid.size(); i++) { -// ygrid(i) = spline_V.evalf(xgrid(i)); -// } - -// // open interpol.txt for writing spline -// std::ofstream file("interpol.txt"); -// for (int i = 0; i < xgrid.size(); i++) { -// // write xgrid and ygrid to file using ten digits precision -// file << std::setprecision(10) << xgrid(i) << " " << ygrid(i) << std::endl; - -// } -// file.close(); - -// return 0; -// } \ No newline at end of file +}; \ No newline at end of file diff --git a/src/utils/PolyInterpolator.h b/src/utils/PolyInterpolator.h index 26bf2cd98..ab048d27a 100644 --- a/src/utils/PolyInterpolator.h +++ b/src/utils/PolyInterpolator.h @@ -124,6 +124,28 @@ class PolyInterpolator { 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), the last value is returned for x > xmax. + */ + double evalfLeftNoRightConstant(const double &xval){ + double y; + if (xval > xmax) { // constant + y = this->y(n - 1); + 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; + } + private: int adjustIndexToBoundaries(int i) const { int j = i; From 7078c83b77ecdba670fedb2b8e52d01ef55c60e0 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 13:58:38 +0200 Subject: [PATCH 43/50] make new function const --- src/utils/PolyInterpolator.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/PolyInterpolator.h b/src/utils/PolyInterpolator.h index ab048d27a..aa00162d3 100644 --- a/src/utils/PolyInterpolator.h +++ b/src/utils/PolyInterpolator.h @@ -129,7 +129,7 @@ class PolyInterpolator { * @brief Evaluate the interpolated function at x. * No extrapolation for x < xmin (meaning that the polynomial is evaluated at x < xmin), the last value is returned for x > xmax. */ - double evalfLeftNoRightConstant(const double &xval){ + double evalfLeftNoRightConstant(const double &xval) const { double y; if (xval > xmax) { // constant y = this->y(n - 1); From 04f7f45c0c7144e19d4ed986e05e6e884396a8c1 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 16:27:11 +0200 Subject: [PATCH 44/50] change signature --- src/qmoperators/one_electron/ZoraOperator.cpp | 2 +- src/qmoperators/one_electron/ZoraOperator.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/qmoperators/one_electron/ZoraOperator.cpp b/src/qmoperators/one_electron/ZoraOperator.cpp index 6dd1dbbfc..1a28d8ea0 100644 --- a/src/qmoperators/one_electron/ZoraOperator.cpp +++ b/src/qmoperators/one_electron/ZoraOperator.cpp @@ -71,7 +71,7 @@ ZoraOperator::ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inv * @param relativisticDampening shared pointer to QMPotential that contains the precompouted kappa function * @param name name of the operator should be either "kappa" or "kappa_inv" */ -ZoraOperator::ZoraOperator(std::shared_ptr &relativisticDampening, std::string name) { +ZoraOperator::ZoraOperator(std::shared_ptr relativisticDampening, std::string name) { RankZeroOperator &kappa = (*this); kappa = relativisticDampening; kappa.name() = name; diff --git a/src/qmoperators/one_electron/ZoraOperator.h b/src/qmoperators/one_electron/ZoraOperator.h index 44802bf8a..239ad87ff 100644 --- a/src/qmoperators/one_electron/ZoraOperator.h +++ b/src/qmoperators/one_electron/ZoraOperator.h @@ -50,7 +50,7 @@ class ZoraOperator final : public RankZeroOperator { */ ZoraOperator(QMPotential &vz, double c, double proj_prec, bool inverse = false); - ZoraOperator(std::shared_ptr &relativisticDampening, std::string name); + ZoraOperator(std::shared_ptr relativisticDampening, std::string name); }; From 6fd1a7e95721edb27cd7e179ac1c4d0ec151e100 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 16:46:20 +0200 Subject: [PATCH 45/50] clean up code --- src/driver.cpp | 28 ++++- .../one_electron/AZora/RadialInterpolater.h | 76 ------------ src/qmoperators/one_electron/AZoraPotential.h | 109 +++++++++++++----- src/qmoperators/two_electron/FockBuilder.cpp | 27 +---- src/qmoperators/two_electron/FockBuilder.h | 6 +- 5 files changed, 111 insertions(+), 135 deletions(-) delete mode 100644 src/qmoperators/one_electron/AZora/RadialInterpolater.h diff --git a/src/driver.cpp b/src/driver.cpp index 9aada163a..a87e04e7b 100644 --- a/src/driver.cpp +++ b/src/driver.cpp @@ -56,6 +56,7 @@ #include "qmoperators/one_electron/NuclearGradientOperator.h" #include "qmoperators/one_electron/NuclearOperator.h" #include "qmoperators/one_electron/ZoraOperator.h" +#include "qmoperators/one_electron/AZoraPotential.h" #include "qmoperators/one_electron/H_BB_dia.h" #include "qmoperators/one_electron/H_BM_dia.h" @@ -1070,10 +1071,33 @@ void driver::build_fock_operator(const json &json_fock, Molecule &mol, FockBuild bool is_azora = json_fock["zora_operator"]["isAZORA"]; F.setZoraType(include_nuclear, include_coulomb, include_xc, is_azora); if (is_azora) { + std::string azora_dir_src = AZORA_POTENTIALS_SOURCE_DIR; + std::string azora_dir_install = AZORA_POTENTIALS_INSTALL_DIR; + std::string azora_dir = ""; if (json_fock["zora_operator"].contains("azora_potential_path")) { - F.setAZORADirectory(json_fock["zora_operator"]["azora_potential_path"]); + azora_dir = json_fock["zora_operator"]["azora_potential_path"]; } - F.setNucs(mol.getNuclei()); + + std::string azora_dir_final; + if (azora_dir != "") { + azora_dir_final = azora_dir; + } else { + if (std::filesystem::exists(azora_dir_install)) { + azora_dir_final = azora_dir_install; + } else { + if (std::filesystem::exists(azora_dir_src)) { + azora_dir_final = azora_dir_src; + } else { + MSG_ABORT("AZORA: No directory provided and no default directories found."); + } + } + } + int adap = 0; + bool share = false; + + mrchem::Nuclei nuclei = mol.getNuclei(); + F.getAZoraChiPotential() = std::make_shared(nuclei, adap, azora_dir_final, share, c); + F.setNucs(nuclei); } } /////////////////////////////////////////////////////////// diff --git a/src/qmoperators/one_electron/AZora/RadialInterpolater.h b/src/qmoperators/one_electron/AZora/RadialInterpolater.h deleted file mode 100644 index abfb51196..000000000 --- a/src/qmoperators/one_electron/AZora/RadialInterpolater.h +++ /dev/null @@ -1,76 +0,0 @@ -#include -#include -#include -#include "utils/PolyInterpolator.h" -#include -#include - -/** - * @brief Read ZORA potential from file. Check if file exists and abort if it does not. - * @param path Path to the file containing the ZORA potential - * @param rGrid Vector containing the radial grid - * @param vZora Vector containing the ZORA potential - * @param kappa Vector containing the kappa parameter -*/ -void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ - std::vector r, v, k; - bool file_exists = std::filesystem::exists(path); - if (!file_exists) { - std::cerr << "File " << path << " does not exist." << std::endl; - std::cout << "File " << path << " does not exist." << std::endl; - exit(1); - } - std::ifstream file(path); - std::string line; - double r_, v_, k_; - while (std::getline(file, line)) { - std::istringstream iss(line); - iss >> k_ >> r_ >> v_; - r.push_back(r_); - v.push_back(v_); - k.push_back(k_); - } - file.close(); - rGrid = Eigen::Map(r.data(), r.size()); - vZora = Eigen::Map(v.data(), v.size()); - kappa = Eigen::Map(k.data(), k.size()); - // The kappa function is half of what is defined in the paper Scalar - // Relativistic Effects with Multiwavelets: Implementation and Benchmark - // it is not used in the code, only the potential is used -} - -class RadInterpolater { - - 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 - * @param mode The mode of interpolation. Either "potential" or "kappa" - */ - RadInterpolater(const std::string element, std::string data_dir, const std::string mode){ - Eigen::VectorXd rGrid; - Eigen::VectorXd vZora; - Eigen::VectorXd kappa; - - this->mode = mode; - std::string filename = data_dir + '/' + element + ".txt"; - - readZoraPotential(filename, rGrid, vZora, kappa); - if (mode == "kappa") { - interpolator = std::make_shared(rGrid, kappa); - } else if (mode == "potential") { - interpolator = std::make_shared(rGrid, vZora); - } - - } - - double evalf(const double &r) const { - return interpolator->evalfLeftNoRightConstant(r); - } - - protected: - std::shared_ptr interpolator; - std::string mode; - -}; \ No newline at end of file diff --git a/src/qmoperators/one_electron/AZoraPotential.h b/src/qmoperators/one_electron/AZoraPotential.h index 046033985..5b69a914b 100644 --- a/src/qmoperators/one_electron/AZoraPotential.h +++ b/src/qmoperators/one_electron/AZoraPotential.h @@ -7,11 +7,47 @@ #include #include #include -#include "qmoperators/one_electron/AZora/RadialInterpolater.h" +// #include "qmoperators/one_electron/AZora/RadialInterpolater.h" +#include "utils/PolyInterpolator.h" +#include "qmoperators/QMOperator.h" namespace mrchem { +/** + * @brief Read ZORA potential from file. Check if file exists and abort if it does not. + * @param path Path to the file containing the ZORA potential + * @param rGrid Vector containing the radial grid + * @param vZora Vector containing the ZORA potential + * @param kappa Vector containing the kappa parameter +*/ +inline void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ + std::vector r, v, k; + bool file_exists = std::filesystem::exists(path); + if (!file_exists) { + std::cerr << "File " << path << " does not exist." << std::endl; + std::cout << "File " << path << " does not exist." << std::endl; + exit(1); + } + std::ifstream file(path); + std::string line; + double r_, v_, k_; + while (std::getline(file, line)) { + std::istringstream iss(line); + iss >> k_ >> r_ >> v_; + r.push_back(r_); + v.push_back(v_); + k.push_back(k_); + } + file.close(); + rGrid = Eigen::Map(r.data(), r.size()); + vZora = Eigen::Map(v.data(), v.size()); + kappa = Eigen::Map(k.data(), k.size()); + // The kappa function is half of what is defined in the paper Scalar + // Relativistic Effects with Multiwavelets: Implementation and Benchmark + // it is not used in the code, only the potential is used +} + /** @class AZora * * @brief Operator defining the AZora potential based on molecular data. @@ -26,13 +62,11 @@ class AZoraPotential : public QMPotential { * Constructor that takes a molecule and initializes the azora potential. * @param molecule The molecule used to construct the potential. * @param adap Adaptive parameter from QMPotential. - * @param prec Precision parameter from base class. * @param shared Determines if the base potential is shared. */ - AZoraPotential(Nuclei nucs, int adap, double prec, std::string azora_dir, bool shared = false, double c = 137.035999084) + AZoraPotential(Nuclei nucs, int adap, std::string azora_dir, bool shared = false, double c = 137.035999084) : QMPotential(adap, shared) { this->nucs = nucs; - this->prec = prec; this->c = c; this->azora_dir = azora_dir; initAzoraPotential(); @@ -54,16 +88,44 @@ class AZoraPotential : public QMPotential { /** * Destructor. */ - virtual ~AZoraPotential() override = default; + virtual ~AZoraPotential(){ + free(mrchem::NUMBER::Total); + isProjected = false; + } // Delete copy assignment to prevent copying AZoraPotential& operator=(const AZoraPotential&) = delete; + void project(double proj_prec){ + if (isProjected) free(mrchem::NUMBER::Total); + mrcpp::ComplexFunction vtot; + this->prec = proj_prec; + auto chi_analytic = [this](const mrcpp::Coord<3>& r) { + return this->evalf_analytic(r); + }; + mrcpp::cplxfunc::project(vtot, chi_analytic, mrcpp::NUMBER::Real, proj_prec); + this->add(1.0, vtot); + isProjected = true; + } + protected: Nuclei nucs; // The nuclei of the molecule double prec; // The precision parameter double c; // The speed of light std::string azora_dir; // The directory containing the azora potential data + std::vector atomicPotentials; + bool isProjected = false; + + double evalf_analytic(const mrcpp::Coord<3>& r){ + double V = 0.0; + // Loop over all atoms: + for (int i = 0; i < this->atomicPotentials.size(); i++) { + mrcpp::Coord<3> r_i = nucs[i].getCoord(); + double rr = std::sqrt((r[0] - r_i[0]) * (r[0] - r_i[0]) + (r[1] - r_i[1]) * (r[1] - r_i[1]) + (r[2] - r_i[2]) * (r[2] - r_i[2])); + V += this->atomicPotentials[i].evalfLeftNoRightConstant(rr); + } + return 1 / (1 - V / (2.0 * c * c)) - 1; + } /** * Initialize the azora potential based on the molecule. @@ -74,36 +136,21 @@ class AZoraPotential : public QMPotential { int n = nucs.size(); Eigen::VectorXd rGrid, vZora, kappa; + atomicPotentials.clear(); - std::vector atomicPotentials; + // std::vector atomicPotentials; - std::string mode = "potential"; + std::string element; + std::string filename; for (int i = 0; i < n; i++) { - RadInterpolater potentialSpline(nucs[i].getElement().getSymbol(), this->azora_dir, mode); - atomicPotentials.push_back(potentialSpline); - } + element = nucs[i].getElement().getSymbol(); + filename = this->azora_dir + '/' + element + ".txt"; + readZoraPotential(filename, rGrid, vZora, kappa); + interpolation_utils::PolyInterpolator potential_interpolator(rGrid, vZora); - - mrcpp::ComplexFunction vtot; - auto kappa_analytic = [atomicPotentials, this](const mrcpp::Coord<3>& r) { - double V = 0.0; - // Loop over all atoms: - for (int i = 0; i < atomicPotentials.size(); i++) { - mrcpp::Coord<3> r_i = nucs[i].getCoord(); - double rr = std::sqrt((r[0] - r_i[0]) * (r[0] - r_i[0]) + (r[1] - r_i[1]) * (r[1] - r_i[1]) + (r[2] - r_i[2]) * (r[2] - r_i[2])); - V += atomicPotentials[i].evalf(rr); - } - return 1 / (1 - V / (2.0 * c * c)) - 1; - }; - mrcpp::cplxfunc::project(vtot, kappa_analytic, mrcpp::NUMBER::Real, prec); - // auto ttt = [](const mrcpp::Coord<3>& r) { - // return 1.0; - // }; - // mrcpp::ComplexFunction const_func; - // mrcpp::cplxfunc::project(const_func, ttt, mrcpp::NUMBER::Real, prec); - mrcpp::ComplexDouble one = 1.0; - // vtot.add(one, const_func); - this->add(one, vtot); + atomicPotentials.push_back(potential_interpolator); + } + // project(this->prec); } }; diff --git a/src/qmoperators/two_electron/FockBuilder.cpp b/src/qmoperators/two_electron/FockBuilder.cpp index c7e2dc3ae..450aa1abd 100644 --- a/src/qmoperators/two_electron/FockBuilder.cpp +++ b/src/qmoperators/two_electron/FockBuilder.cpp @@ -117,31 +117,8 @@ void FockBuilder::setup(double prec) { mrcpp::print::value(3, "Light speed", c, "(au)", 5); mrcpp::print::separator(3, '-'); int adap = 0; - bool share = false; - - azora_dir_src = AZORA_POTENTIALS_SOURCE_DIR; - azora_dir_install = AZORA_POTENTIALS_INSTALL_DIR; - - std::string azora_dir_final; - if (azora_dir != "") { - azora_dir_final = azora_dir; - } else { - // check if azora_dir_install directory exists using cpp standard library - if (std::filesystem::exists(azora_dir_install)) { - azora_dir_final = azora_dir_install; - } else { - // check if azora_dir_src directory exists using cpp standard library - if (std::filesystem::exists(azora_dir_src)) { - azora_dir_final = azora_dir_src; - } else { - MSG_ABORT("AZORA: No directory provided and no default directories found."); - } - } - } - - - chiPot = std::make_shared(nucs, adap, prec, azora_dir_final, share, c); + chiPot->project(prec); chiInvPot = std::make_shared(adap); mrcpp::cplxfunc::deep_copy(*chiInvPot, *chiPot); @@ -178,6 +155,8 @@ void FockBuilder::clear() { if (isAZora()) { chi->clear(); chi_inv->clear(); + chiPot->free(mrchem::NUMBER::Total); + chiInvPot->free(mrchem::NUMBER::Total); } } diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index 0794dd9eb..800644d9d 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -56,6 +56,7 @@ class ExchangeOperator; class XCOperator; class ElectricFieldOperator; class ReactionOperator; +class AZoraPotential; class FockBuilder final { public: @@ -70,6 +71,7 @@ class FockBuilder final { std::shared_ptr &getXCOperator() { return this->xc; } std::shared_ptr &getExtOperator() { return this->ext; } std::shared_ptr &getReactionOperator() { return this->Ro; } + std::shared_ptr &getAZoraChiPotential() { return this->chiPot; } void rotate(const ComplexMatrix &U); @@ -123,8 +125,8 @@ class FockBuilder final { std::shared_ptr collectZoraBasePotential(); OrbitalVector buildHelmholtzArgumentZORA(OrbitalVector &Phi, OrbitalVector &Psi, DoubleVector eps, double prec); OrbitalVector buildHelmholtzArgumentNREL(OrbitalVector &Phi, OrbitalVector &Psi); - std::shared_ptr chiPot{nullptr}; - std::shared_ptr chiInvPot{nullptr}; + std::shared_ptr chiPot{nullptr}; // Potential for AZORA chi operator + std::shared_ptr chiInvPot{nullptr}; // Potential for AZORA chi_inv operator }; } // namespace mrchem From 761678af813baf6617607fdcdda40b79b4f711e7 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 17:11:19 +0200 Subject: [PATCH 46/50] remove duplicate defintion --- src/qmoperators/two_electron/FockBuilder.h | 1 - 1 file changed, 1 deletion(-) diff --git a/src/qmoperators/two_electron/FockBuilder.h b/src/qmoperators/two_electron/FockBuilder.h index 800644d9d..0e3aa06b7 100644 --- a/src/qmoperators/two_electron/FockBuilder.h +++ b/src/qmoperators/two_electron/FockBuilder.h @@ -56,7 +56,6 @@ class ExchangeOperator; class XCOperator; class ElectricFieldOperator; class ReactionOperator; -class AZoraPotential; class FockBuilder final { public: From b111ad753b537428dd32bbababd723f3cb96e544 Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 17:12:32 +0200 Subject: [PATCH 47/50] move implementation into seperate cpp file --- .../one_electron/AZoraPotential.cpp | 99 +++++++++++++++++++ src/qmoperators/one_electron/AZoraPotential.h | 91 ++--------------- src/qmoperators/one_electron/CMakeLists.txt | 1 + 3 files changed, 108 insertions(+), 83 deletions(-) create mode 100644 src/qmoperators/one_electron/AZoraPotential.cpp diff --git a/src/qmoperators/one_electron/AZoraPotential.cpp b/src/qmoperators/one_electron/AZoraPotential.cpp new file mode 100644 index 000000000..0b76e8e9b --- /dev/null +++ b/src/qmoperators/one_electron/AZoraPotential.cpp @@ -0,0 +1,99 @@ +#include "AZoraPotential.h" + +#include "mrchem.h" +#include "chemistry/Molecule.h" +#include "chemistry/Nucleus.h" +#include +#include +#include +#include +#include "utils/PolyInterpolator.h" +#include "qmoperators/QMOperator.h" +#include "qmoperators/QMPotential.h" + +/** + * @brief Read ZORA potential from file. Check if file exists and abort if it does not. + * @param path Path to the file containing the ZORA potential + * @param rGrid Vector containing the radial grid + * @param vZora Vector containing the ZORA potential + * @param kappa Vector containing the kappa parameter +*/ +void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ + std::vector r, v, k; + bool file_exists = std::filesystem::exists(path); + if (!file_exists) { + std::cerr << "File " << path << " does not exist." << std::endl; + std::cout << "File " << path << " does not exist." << std::endl; + exit(1); + } + std::ifstream file(path); + std::string line; + double r_, v_, k_; + while (std::getline(file, line)) { + std::istringstream iss(line); + iss >> k_ >> r_ >> v_; + r.push_back(r_); + v.push_back(v_); + k.push_back(k_); + } + file.close(); + rGrid = Eigen::Map(r.data(), r.size()); + vZora = Eigen::Map(v.data(), v.size()); + kappa = Eigen::Map(k.data(), k.size()); + // The kappa function is half of what is defined in the paper Scalar + // Relativistic Effects with Multiwavelets: Implementation and Benchmark + // it is not used in the code, only the potential is used +} + +namespace mrchem { + + /** + * Initialize the azora potential based on the molecule. + * This method would typically setup the real and imaginary function trees + * representing the potential. + */ + void AZoraPotential::initAzoraPotential() { + + int n = nucs.size(); + Eigen::VectorXd rGrid, vZora, kappa; + atomicPotentials.clear(); + + // std::vector atomicPotentials; + + std::string element; + std::string filename; + for (int i = 0; i < n; i++) { + element = nucs[i].getElement().getSymbol(); + filename = this->azora_dir + '/' + element + ".txt"; + readZoraPotential(filename, rGrid, vZora, kappa); + interpolation_utils::PolyInterpolator potential_interpolator(rGrid, vZora); + + atomicPotentials.push_back(potential_interpolator); + } + // project(this->prec); + } + + void AZoraPotential::project(double proj_prec){ + if (isProjected) free(mrchem::NUMBER::Total); + mrcpp::ComplexFunction vtot; + this->prec = proj_prec; + auto chi_analytic = [this](const mrcpp::Coord<3>& r) { + return this->evalf_analytic(r); + }; + mrcpp::cplxfunc::project(vtot, chi_analytic, mrcpp::NUMBER::Real, proj_prec); + this->add(1.0, vtot); + isProjected = true; + } + + double AZoraPotential::evalf_analytic(const mrcpp::Coord<3>& r){ + double V = 0.0; + // Loop over all atoms: + for (int i = 0; i < this->atomicPotentials.size(); i++) { + mrcpp::Coord<3> r_i = nucs[i].getCoord(); + double rr = std::sqrt((r[0] - r_i[0]) * (r[0] - r_i[0]) + (r[1] - r_i[1]) * (r[1] - r_i[1]) + (r[2] - r_i[2]) * (r[2] - r_i[2])); + V += this->atomicPotentials[i].evalfLeftNoRightConstant(rr); + } + return 1 / (1 - V / (2.0 * c * c)) - 1; + } + +} // namespace mrchem diff --git a/src/qmoperators/one_electron/AZoraPotential.h b/src/qmoperators/one_electron/AZoraPotential.h index 5b69a914b..bb9dc7e16 100644 --- a/src/qmoperators/one_electron/AZoraPotential.h +++ b/src/qmoperators/one_electron/AZoraPotential.h @@ -1,53 +1,12 @@ #pragma once - -#include "mrchem.h" -#include "chemistry/Molecule.h" #include "chemistry/Nucleus.h" #include -#include -#include -#include -// #include "qmoperators/one_electron/AZora/RadialInterpolater.h" #include "utils/PolyInterpolator.h" -#include "qmoperators/QMOperator.h" +#include "qmoperators/QMPotential.h" namespace mrchem { -/** - * @brief Read ZORA potential from file. Check if file exists and abort if it does not. - * @param path Path to the file containing the ZORA potential - * @param rGrid Vector containing the radial grid - * @param vZora Vector containing the ZORA potential - * @param kappa Vector containing the kappa parameter -*/ -inline void readZoraPotential(const std::string path, Eigen::VectorXd &rGrid, Eigen::VectorXd &vZora, Eigen::VectorXd &kappa){ - std::vector r, v, k; - bool file_exists = std::filesystem::exists(path); - if (!file_exists) { - std::cerr << "File " << path << " does not exist." << std::endl; - std::cout << "File " << path << " does not exist." << std::endl; - exit(1); - } - std::ifstream file(path); - std::string line; - double r_, v_, k_; - while (std::getline(file, line)) { - std::istringstream iss(line); - iss >> k_ >> r_ >> v_; - r.push_back(r_); - v.push_back(v_); - k.push_back(k_); - } - file.close(); - rGrid = Eigen::Map(r.data(), r.size()); - vZora = Eigen::Map(v.data(), v.size()); - kappa = Eigen::Map(k.data(), k.size()); - // The kappa function is half of what is defined in the paper Scalar - // Relativistic Effects with Multiwavelets: Implementation and Benchmark - // it is not used in the code, only the potential is used -} - /** @class AZora * * @brief Operator defining the AZora potential based on molecular data. @@ -96,17 +55,11 @@ class AZoraPotential : public QMPotential { // Delete copy assignment to prevent copying AZoraPotential& operator=(const AZoraPotential&) = delete; - void project(double proj_prec){ - if (isProjected) free(mrchem::NUMBER::Total); - mrcpp::ComplexFunction vtot; - this->prec = proj_prec; - auto chi_analytic = [this](const mrcpp::Coord<3>& r) { - return this->evalf_analytic(r); - }; - mrcpp::cplxfunc::project(vtot, chi_analytic, mrcpp::NUMBER::Real, proj_prec); - this->add(1.0, vtot); - isProjected = true; - } + /** + * Project the potential from the analytic function stored in this object. + * @param prec Projection precision. + */ + void project(double prec); protected: Nuclei nucs; // The nuclei of the molecule @@ -116,42 +69,14 @@ class AZoraPotential : public QMPotential { std::vector atomicPotentials; bool isProjected = false; - double evalf_analytic(const mrcpp::Coord<3>& r){ - double V = 0.0; - // Loop over all atoms: - for (int i = 0; i < this->atomicPotentials.size(); i++) { - mrcpp::Coord<3> r_i = nucs[i].getCoord(); - double rr = std::sqrt((r[0] - r_i[0]) * (r[0] - r_i[0]) + (r[1] - r_i[1]) * (r[1] - r_i[1]) + (r[2] - r_i[2]) * (r[2] - r_i[2])); - V += this->atomicPotentials[i].evalfLeftNoRightConstant(rr); - } - return 1 / (1 - V / (2.0 * c * c)) - 1; - } + double evalf_analytic(const mrcpp::Coord<3>& r); /** * Initialize the azora potential based on the molecule. * This method would typically setup the real and imaginary function trees * representing the potential. */ - void initAzoraPotential() { - - int n = nucs.size(); - Eigen::VectorXd rGrid, vZora, kappa; - atomicPotentials.clear(); - - // std::vector atomicPotentials; - - std::string element; - std::string filename; - for (int i = 0; i < n; i++) { - element = nucs[i].getElement().getSymbol(); - filename = this->azora_dir + '/' + element + ".txt"; - readZoraPotential(filename, rGrid, vZora, kappa); - interpolation_utils::PolyInterpolator potential_interpolator(rGrid, vZora); - - atomicPotentials.push_back(potential_interpolator); - } - // project(this->prec); - } + void initAzoraPotential(); }; } // namespace mrchem \ No newline at end of file diff --git a/src/qmoperators/one_electron/CMakeLists.txt b/src/qmoperators/one_electron/CMakeLists.txt index 264297579..e7ded7e56 100644 --- a/src/qmoperators/one_electron/CMakeLists.txt +++ b/src/qmoperators/one_electron/CMakeLists.txt @@ -1,4 +1,5 @@ target_sources(mrchem PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/NuclearOperator.cpp ${CMAKE_CURRENT_SOURCE_DIR}/ZoraOperator.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/AZoraPotential.cpp ) From dea2ca02da62714c2a770d7e36ac81a48e33da5b Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Thu, 17 Oct 2024 17:32:51 +0200 Subject: [PATCH 48/50] change include --- src/qmoperators/one_electron/AZoraPotential.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/qmoperators/one_electron/AZoraPotential.cpp b/src/qmoperators/one_electron/AZoraPotential.cpp index 0b76e8e9b..3b2cb92ca 100644 --- a/src/qmoperators/one_electron/AZoraPotential.cpp +++ b/src/qmoperators/one_electron/AZoraPotential.cpp @@ -5,7 +5,7 @@ #include "chemistry/Nucleus.h" #include #include -#include +#include #include #include "utils/PolyInterpolator.h" #include "qmoperators/QMOperator.h" From fdae9976706e986374147014c2e436a52b30c1bc Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Tue, 22 Oct 2024 11:38:42 +0200 Subject: [PATCH 49/50] fix typo in code --- python/mrchem/helpers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/mrchem/helpers.py b/python/mrchem/helpers.py index a25c88c9a..de7731dc8 100644 --- a/python/mrchem/helpers.py +++ b/python/mrchem/helpers.py @@ -352,7 +352,7 @@ def write_rsp_calc(omega, user_dict, origin): rsp_calc["unperturbed"] = { "precision": user_dict["world_prec"], "localize": rsp_dict["localize"], - "fock_operator": (user_dict, wf_dict, origin), + "fock_operator": write_scf_fock(user_dict, wf_dict, origin), } guess_str = rsp_dict["guess_type"].lower() From 764eb22deb98208c9d88b034d78cf0041bfc00ae Mon Sep 17 00:00:00 2001 From: moritzgubler Date: Wed, 6 Nov 2024 13:03:33 +0100 Subject: [PATCH 50/50] add test --- tests/CMakeLists.txt | 1 + tests/he_azora_scf_lda/CMakeLists.txt | 10 + tests/he_azora_scf_lda/he.inp | 14 + tests/he_azora_scf_lda/reference/he.json | 372 +++++++++++++++++++++++ tests/he_azora_scf_lda/reference/he.out | 296 ++++++++++++++++++ tests/he_azora_scf_lda/test | 26 ++ 6 files changed, 719 insertions(+) create mode 100644 tests/he_azora_scf_lda/CMakeLists.txt create mode 100644 tests/he_azora_scf_lda/he.inp create mode 100644 tests/he_azora_scf_lda/reference/he.json create mode 100644 tests/he_azora_scf_lda/reference/he.out create mode 100755 tests/he_azora_scf_lda/test diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index 42e7f36e4..ed4f2f4b4 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -34,5 +34,6 @@ add_subdirectory(li_solv) add_subdirectory(h_pb) add_subdirectory(h_lpb) add_subdirectory(he_zora_scf_lda) +add_subdirectory(he_azora_scf_lda) add_subdirectory(cavity_input_parser) add_subdirectory(h2_pol_solv) diff --git a/tests/he_azora_scf_lda/CMakeLists.txt b/tests/he_azora_scf_lda/CMakeLists.txt new file mode 100644 index 000000000..18aa7bafe --- /dev/null +++ b/tests/he_azora_scf_lda/CMakeLists.txt @@ -0,0 +1,10 @@ +if(ENABLE_MPI) + set(_he_azora_scf_lda_launcher "${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} 1") +endif() + +add_integration_test( + NAME "He_AZORA_SCF_LDA" + LABELS "mrchem;he_azora_scf_lda;He_AZORA_SCF_LDA;energy;lda;scf;zora;azora;he;helium" + COST 100 + LAUNCH_AGENT ${_he_azora_scf_lda_launcher} + ) diff --git a/tests/he_azora_scf_lda/he.inp b/tests/he_azora_scf_lda/he.inp new file mode 100644 index 000000000..3e1d0da66 --- /dev/null +++ b/tests/he_azora_scf_lda/he.inp @@ -0,0 +1,14 @@ +world_prec = 1.0e-4 + +WaveFunction { + method = LDA + restricted = true + relativity = azora +} + + +Molecule { +$coords +He 0.0 0.0 0.0 +$end +} diff --git a/tests/he_azora_scf_lda/reference/he.json b/tests/he_azora_scf_lda/reference/he.json new file mode 100644 index 000000000..9b19c6480 --- /dev/null +++ b/tests/he_azora_scf_lda/reference/he.json @@ -0,0 +1,372 @@ +{ + "input": { + "constants": { + "N_a": 6.02214076e+23, + "angstrom2bohrs": 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": "he", + "r_rms": 3.5849373401e-05, + "xyz": [ + 0.0, + 0.0, + 0.0 + ] + } + ], + "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": -4 + }, + "printer": { + "file_name": "he", + "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 + } + }, + "zora_operator": { + "include_coulomb": false, + "include_nuclear": false, + "include_xc": false, + "isAZORA": true + } + }, + "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": "AZORA", + "restricted": true, + "rotate": true, + "screen": 12.0, + "type": "sad_gto", + "zeta": 0 + }, + "properties": { + "dipole_moment": { + "dip-1": { + "operator": "h_e_dip", + "precision": 0.0001, + "r_O": [ + 0.0, + 0.0, + 0.0 + ] + } + } + }, + "scf_solver": { + "checkpoint": false, + "energy_thrs": -1.0, + "environment": "None", + "external_field": "None", + "file_chk": "checkpoint/phi_scf", + "final_prec": 0.0001, + "helmholtz_prec": -1.0, + "kain": 5, + "localize": false, + "max_iter": 100, + "method": "DFT (SVWN5)", + "orbital_thrs": 0.001, + "relativity": "AZORA", + "rotation": 0, + "start_prec": 0.0001 + } + }, + "schema_name": "mrchem_input", + "schema_version": 1 + }, + "output": { + "properties": { + "center_of_mass": [ + 0.0, + 0.0, + 0.0 + ], + "charge": 0, + "dipole_moment": { + "dip-1": { + "magnitude": 1.5414130052328172e-12, + "r_O": [ + 0.0, + 0.0, + 0.0 + ], + "vector": [ + 0.0, + 0.0, + 0.0 + ], + "vector_el": [ + 0.0, + 0.0, + 0.0 + ], + "vector_nuc": [ + 0.0, + 0.0, + 0.0 + ] + } + }, + "geometry": [ + { + "symbol": "He", + "xyz": [ + 0.0, + 0.0, + 0.0 + ] + } + ], + "multiplicity": 1, + "orbital_energies": { + "energy": [ + -0.570464666039006 + ], + "occupation": [ + 2.0 + ], + "spin": [ + "p" + ], + "sum_occupied": -1.140929332078012 + }, + "scf_energy": { + "E_ee": 1.9962222364216329, + "E_eext": 0.0, + "E_el": -2.835003921655858, + "E_en": -6.625820552295827, + "E_kin": 2.7679525130939138, + "E_next": 0.0, + "E_nn": 0.0, + "E_nuc": 0.0, + "E_tot": -2.835003921655858, + "E_x": 0.0, + "E_xc": -0.9733581188755775, + "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": 2.0262673615492934, + "E_eext": 0.0, + "E_el": -2.8061198579393087, + "E_en": -6.595209258134876, + "E_kin": 2.7470772638332845, + "E_next": 0.0, + "E_nn": 0.0, + "E_nuc": 0.0, + "E_tot": -2.8061198579393087, + "E_x": 0.0, + "E_xc": -0.9842552251870108, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + }, + "scf_solver": { + "converged": true, + "cycles": [ + { + "energy_terms": { + "E_ee": 1.973384349083191, + "E_eext": 0.0, + "E_el": -2.8339954491064434, + "E_en": -6.528192694988571, + "E_kin": 2.683318941139394, + "E_next": 0.0, + "E_nn": 0.0, + "E_nuc": 0.0, + "E_tot": -2.8339954491064434, + "E_x": 0.0, + "E_xc": -0.9625060443404567, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + }, + "energy_total": -2.8339954491064434, + "energy_update": 0.027875591167134672, + "mo_residual": 0.0708364444278362, + "wall_time": 1.743911586 + }, + { + "energy_terms": { + "E_ee": 1.994312226962929, + "E_eext": 0.0, + "E_el": -2.8349265026797847, + "E_en": -6.6081583679284135, + "E_kin": 2.7511471759544044, + "E_next": 0.0, + "E_nn": 0.0, + "E_nuc": 0.0, + "E_tot": -2.8349265026797847, + "E_x": 0.0, + "E_xc": -0.9722275376687047, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + }, + "energy_total": -2.8349265026797847, + "energy_update": 0.0009310535733413339, + "mo_residual": 0.008304451068131975, + "wall_time": 1.454814606 + }, + { + "energy_terms": { + "E_ee": 1.9954809275242602, + "E_eext": 0.0, + "E_el": -2.834996526943462, + "E_en": -6.620132609175466, + "E_kin": 2.7626021706049264, + "E_next": 0.0, + "E_nn": 0.0, + "E_nuc": 0.0, + "E_tot": -2.834996526943462, + "E_x": 0.0, + "E_xc": -0.9729470158971822, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + }, + "energy_total": -2.834996526943462, + "energy_update": 7.002426367730408e-05, + "mo_residual": 0.0016099564962614482, + "wall_time": 1.523955258 + }, + { + "energy_terms": { + "E_ee": 1.9962222364216329, + "E_eext": 0.0, + "E_el": -2.835003921655858, + "E_en": -6.625820552295827, + "E_kin": 2.7679525130939138, + "E_next": 0.0, + "E_nn": 0.0, + "E_nuc": 0.0, + "E_tot": -2.835003921655858, + "E_x": 0.0, + "E_xc": -0.9733581188755775, + "Er_el": 0.0, + "Er_nuc": 0.0, + "Er_tot": 0.0 + }, + "energy_total": -2.835003921655858, + "energy_update": 7.394712395747405e-06, + "mo_residual": 0.0005919718940979519, + "wall_time": 1.566191235 + } + ], + "wall_time": 6.289502326 + }, + "success": true + }, + "schema_name": "mrchem_output", + "schema_version": 1, + "success": true + } +} diff --git a/tests/he_azora_scf_lda/reference/he.out b/tests/he_azora_scf_lda/reference/he.out new file mode 100644 index 000000000..8bc4fec38 --- /dev/null +++ b/tests/he_azora_scf_lda/reference/he.out @@ -0,0 +1,296 @@ + + +*************************************************************************** +*** *** +*** *** +*** __ __ ____ ____ _ *** +*** | \/ | _ \ / ___| |__ ___ _ __ ___ *** +*** | |\/| | |_) | | | '_ \ / _ \ '_ ` _ \ *** +*** | | | | _ <| |___| | | | __/ | | | | | *** +*** |_| |_|_| \_\\____|_| |_|\___|_| |_| |_| *** +*** *** +*** VERSION 1.2.0-alpha *** +*** *** +*** Git branch azora_all_potentials *** +*** Git commit hash fdae9976706e98637414 *** +*** Git commit author moritzgubler *** +*** Git commit date Tue Oct 22 11:38:42 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 : [ 16.00000 16.00000 16.00000 ] + scaling factor : [ 1.00000 1.00000 1.00000 ] + lower bounds : [ -16.00000 -16.00000 -16.00000 ] + upper bounds : [ 16.00000 16.00000 16.00000 ] + total length : [ 32.00000 32.00000 32.00000 ] +=========================================================================== + + + +*************************************************************************** +*** *** +*** Initializing Molecule *** +*** *** +*************************************************************************** + + +=========================================================================== + Molecule +--------------------------------------------------------------------------- + Charge : 0 + Multiplicity : 1 +--------------------------------------------------------------------------- + N Atom : x y z +--------------------------------------------------------------------------- + 0 He : 0.000000 0.000000 0.000000 +--------------------------------------------------------------------------- + Center of mass : 0.000000 0.000000 0.000000 +=========================================================================== + + + +*************************************************************************** +*** *** +*** Computing Initial Guess Wavefunction *** +*** *** +*************************************************************************** + + +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Calculation : Compute initial orbitals + Method : Diagonalize SAD Hamiltonian + Precision : 1.00000e-03 + Screening : 1.20000e+01 StdDev + Restricted : True + Functional : LDA (SVWN5) + AO basis : 3-21G +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +=========================================================================== + Molecular Orbitals +--------------------------------------------------------------------------- + Alpha electrons : 1 + Beta electrons : 1 + Total electrons : 2 +--------------------------------------------------------------------------- + n Occ Spin : Norm +--------------------------------------------------------------------------- + 0 2 p : 9.999999998814e-01 +=========================================================================== + + +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Calculation : Compute initial energy + Method : DFT (SVWN5) + Relativity : AZORA + Environment : None + External fields : None + Precision : 1.00000e-03 + Localization : Off +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +=========================================================================== + Molecular Energy (initial) +--------------------------------------------------------------------------- + Kinetic energy : (au) 2.747077263833 + E-N energy : (au) -6.595209258135 + Coulomb energy : (au) 2.026267361549 + Exchange energy : (au) 0.000000000000 + X-C energy : (au) -0.984255225187 + N-N energy : (au) 0.000000000000 +--------------------------------------------------------------------------- + Electronic energy : (au) -2.806119857939 + Nuclear energy : (au) 0.000000000000 +--------------------------------------------------------------------------- + Total energy : (au) -2.806119857939e+00 + : (kcal/mol) -1.760866796213e+03 + : (kJ/mol) -7.367466675357e+03 + : (eV) -7.635841130692e+01 +=========================================================================== + + +=========================================================================== + Orbital Energies (initial) +--------------------------------------------------------------------------- + n Occ Spin : Epsilon +--------------------------------------------------------------------------- + 0 2 p : (au) -0.542683110301 +--------------------------------------------------------------------------- + Sum occupied : (au) -1.085366220603 +=========================================================================== + + + +*************************************************************************** +*** *** +*** Computing Ground State Wavefunction *** +*** *** +*************************************************************************** + + +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Calculation : Optimize ground state orbitals + Method : DFT (SVWN5) + Relativity : AZORA + Environment : None + External fields : None + Checkpointing : Off + Max iterations : 100 + KAIN solver : 5 + Localization : Off + Diagonalization : First two iterations + Start precision : 1.00000e-04 + Final precision : 1.00000e-04 + Helmholtz precision : Dynamic + Energy threshold : Off + Orbital threshold : 1.00000e-03 +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +=========================================================================== + Iter MO residual Total energy Update +--------------------------------------------------------------------------- + 0 1.000000e+00 -2.806119857939 -2.806120e+00 + 1 7.083644e-02 -2.833995449106 -2.787559e-02 + 2 8.304451e-03 -2.834926502680 -9.310536e-04 + 3 1.609956e-03 -2.834996526943 -7.002426e-05 + 4 5.919719e-04 -2.835003921656 -7.394712e-06 +--------------------------------------------------------------------------- + SCF converged in 4 iterations! +=========================================================================== + + + +*************************************************************************** +*** *** +*** Printing Molecular Properties *** +*** *** +*************************************************************************** + + +=========================================================================== + Molecule +--------------------------------------------------------------------------- + Charge : 0 + Multiplicity : 1 +--------------------------------------------------------------------------- + N Atom : x y z +--------------------------------------------------------------------------- + 0 He : 0.000000 0.000000 0.000000 +--------------------------------------------------------------------------- + Center of mass : 0.000000 0.000000 0.000000 +=========================================================================== + + +=========================================================================== + Molecular Energy (final) +--------------------------------------------------------------------------- + Kinetic energy : (au) 2.767952513094 + E-N energy : (au) -6.625820552296 + Coulomb energy : (au) 1.996222236422 + Exchange energy : (au) 0.000000000000 + X-C energy : (au) -0.973358118876 + N-N energy : (au) 0.000000000000 +--------------------------------------------------------------------------- + Electronic energy : (au) -2.835003921656 + Nuclear energy : (au) 0.000000000000 +--------------------------------------------------------------------------- + Total energy : (au) -2.835003921656e+00 + : (kcal/mol) -1.778991819845e+03 + : (kJ/mol) -7.443301774231e+03 + : (eV) -7.714438672107e+01 +=========================================================================== + + +=========================================================================== + Orbital Energies (final) +--------------------------------------------------------------------------- + n Occ Spin : Epsilon +--------------------------------------------------------------------------- + 0 2 p : (au) -0.570464666039 +--------------------------------------------------------------------------- + Sum occupied : (au) -1.140929332078 +=========================================================================== + + +=========================================================================== + Dipole Moment (dip-1) +--------------------------------------------------------------------------- + r_O : 0.000000 0.000000 0.000000 +--------------------------------------------------------------------------- + Electronic vector : 0.000000 0.000000 0.000000 + Magnitude : (au) 0.000000 + : (Debye) 0.000000 +--------------------------------------------------------------------------- + Nuclear vector : -0.000000 -0.000000 -0.000000 + Magnitude : (au) 0.000000 + : (Debye) 0.000000 +--------------------------------------------------------------------------- + Total vector : -0.000000 -0.000000 -0.000000 + Magnitude : (au) 0.000000 + : (Debye) 0.000000 +=========================================================================== + + + + +*************************************************************************** +*** *** +*** Exiting MRChem *** +*** *** +*** Wall time : 0h 0m 7s *** +*** *** +*************************************************************************** + + diff --git a/tests/he_azora_scf_lda/test b/tests/he_azora_scf_lda/test new file mode 100755 index 000000000..29564cb9d --- /dev/null +++ b/tests/he_azora_scf_lda/test @@ -0,0 +1,26 @@ +#!/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), +} + +ierr = run(options, input_file="he", filters=filters) + +sys.exit(ierr)