Merge pull request #494 from moritzgubler/property/hirshfeld

Add Hirshfeld charge analysis

Author: stigrj

CMakeLists.txt

@@ -58,6 +58,7 @@ include(${PROJECT_SOURCE_DIR}/cmake/downloaded/autocmake_code_coverage.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/mpi.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/omp.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/sad_basis.cmake)
+include(${PROJECT_SOURCE_DIR}/cmake/custom/hirshfeld.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/main.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/feature_summary.cmake)
 include(${PROJECT_SOURCE_DIR}/cmake/custom/tests.cmake)

cmake/custom/hirshfeld.cmake

@@ -0,0 +1,7 @@
+
+set(HIRSHFELD_SOURCE_DIR ${PROJECT_SOURCE_DIR}/share/hirshfeld CACHE STRING "Path to azora potentials")
+set(HIRSHFELD_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/${PROJECT_NAME}/hirshfeld)
+install(
+  DIRECTORY share/hirshfeld
+  DESTINATION share/${PROJECT_NAME}
+  )

doc/users/user_ref.rst

@@ -440,6 +440,12 @@ User input reference
 
     **Default** ``[]``
 
+   :hirshfeld_charges: Compute Hirshfeld charges. 
+  
+    **Type** ``bool``
+  
+    **Default** ``False``
+  
    :geometric_derivative: Compute geometric derivative. 
 
     **Type** ``bool``

python/mrchem/helpers.py

@@ -295,6 +295,12 @@ def write_scf_properties(user_dict, origin):
             "precision": user_dict["world_prec"],
             "smoothing": user_dict["Precisions"]["nuclear_prec"],
         }
+    if user_dict["Properties"]["hirshfeld_charges"]:
+        prop_dict["hirshfeld_charges"] = {}
+        prop_dict["hirshfeld_charges"]["hirshfeld-1"] = {
+            'precision': user_dict["world_prec"]
+        }
+
     return prop_dict
 
 

python/mrchem/input_parser/README.md

@@ -1,2 +1,2 @@
-This file was automatically generated by parselglossy on 2024-05-14
+This file was automatically generated by parselglossy on 2024-08-15
 Editing is *STRONGLY DISCOURAGED*

python/mrchem/input_parser/__init__.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2024-05-14
+# This file was automatically generated by parselglossy on 2024-08-15
 # Editing is *STRONGLY DISCOURAGED*

python/mrchem/input_parser/api.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2024-05-14
+# This file was automatically generated by parselglossy on 2024-08-15
 # Editing is *STRONGLY DISCOURAGED*
 
 from copy import deepcopy
@@ -359,6 +359,9 @@ def stencil() -> JSONDict:
                                         {   'default': [],
                                             'name': 'plot_orbitals',
                                             'type': 'List[int]'},
+                                        {   'default': False,
+                                            'name': 'hirshfeld_charges',
+                                            'type': 'bool'},
                                         {   'default': "user['GeometryOptimizer']['run']",
                                             'name': 'geometric_derivative',
                                             'type': 'bool'}],

python/mrchem/input_parser/cli.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2024-05-14
+# This file was automatically generated by parselglossy on 2024-08-15
 # Editing is *STRONGLY DISCOURAGED*
 
 import argparse

python/mrchem/input_parser/docs/user_ref.rst

@@ -440,6 +440,12 @@ User input reference
 
     **Default** ``[]``
 
+   :hirshfeld_charges: Compute Hirshfeld charges. 
+  
+    **Type** ``bool``
+  
+    **Default** ``False``
+  
    :geometric_derivative: Compute geometric derivative. 
 
     **Type** ``bool``

python/mrchem/input_parser/plumbing/lexer.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2024-05-14
+# This file was automatically generated by parselglossy on 2024-08-15
 # Editing is *STRONGLY DISCOURAGED*
 
 import json

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 <[email protected]>"

python/mrchem/input_parser/plumbing/pyparsing/actions.py

@@ -111,7 +111,6 @@ def with_attribute(*args, **attr_dict):
             <div type="graph">1,3 2,3 1,1</div>
             <div>this has no type</div>
             </div>
-
         '''
         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

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 '_')"""