Merge branch 'master' into surface_forces

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

@@ -298,6 +298,12 @@ def write_scf_properties(user_dict, origin):
             "surface_integral_precision": user_dict["Forces"]["surface_integral_precision"],
             "radius_factor": user_dict["Forces"]["radius_factor"],
         }
+    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 2024-08-07
+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 2024-08-07
+# 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 2024-08-07
+# 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 2024-08-07
+# 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 2024-08-07
+# This file was automatically generated by parselglossy on 2024-08-15
 # Editing is *STRONGLY DISCOURAGED*
 
 import json

python/template.yml

@@ -403,6 +403,11 @@ sections:
         docstring: |
           Plot converged molecular orbitals from list of indices, negative index
           plots all orbitals.
+      - name: hirshfeld_charges
+        type: bool
+        default: false
+        docstring: |
+          Compute Hirshfeld charges.
   - name: Forces
     docstring: |
       Define parameters for the computation of forces.

share/hirshfeld/lda/Ag.density

@@ -0,0 +1,192 @@
+9.757819552000000172e-19 1.523042765000000072e+05
+2.948306927999999936e-05 1.520417942000000039e+05
+6.108217363999999779e-05 1.496829188000000140e+05
+9.494917828999999360e-05 1.465817964999999967e+05
+1.312468469000000089e-04 1.429753722000000125e+05
+1.701496233999999974e-04 1.392388728999999876e+05
+2.118444703999999986e-04 1.356978759999999893e+05
+2.565317673000000139e-04 1.323946336000000010e+05
+3.044262724000000196e-04 1.293210169000000024e+05
+3.557581554999999932e-04 1.264383687000000064e+05
+4.107741027999999928e-04 1.237116674000000057e+05
+4.697385021999999906e-04 1.211104409000000014e+05
+5.329347132000000244e-04 1.186097936000000045e+05
+6.006664277000000078e-04 1.161891530999999959e+05
+6.732591288999999939e-04 1.138315077000000019e+05
+7.510616540000000134e-04 1.115226235000000015e+05
+8.344478699000000034e-04 1.092504734999999928e+05
+9.238184682000000073e-04 1.070047808999999979e+05
+1.019602889000000012e-03 1.047766772000000055e+05
+1.122261384000000032e-03 1.025584389999999985e+05
+1.232287223000000072e-03 1.003432883000000002e+05
+1.350209064999999958e-03 9.812524145000000135e+04
+1.476593496999999968e-03 9.589899456999999529e+04
+1.612047747999999963e-03 9.365983877000000211e+04
+1.757222607000000084e-03 9.140359815000000526e+04
+1.912815546999999984e-03 8.912658662000000186e+04
+2.079574067999999994e-03 8.682558011999999871e+04
+2.258299285999999795e-03 8.449780143000000680e+04
+2.449849772999999984e-03 8.214091585999999370e+04
+2.655145678000000141e-03 7.975303608999999415e+04
+2.875173136999999851e-03 7.733273487000000023e+04
+3.110989004000000186e-03 7.487906449999999313e+04
+3.363725912999999956e-03 7.239158203000000503e+04
+3.634597709000000031e-03 6.987037919000000693e+04
+3.924905266000000038e-03 6.731611600999999791e+04
+4.236042714999999938e-03 6.473005705999999918e+04
+4.569504127000000200e-03 6.211410902999999962e+04
+4.926890661999999699e-03 5.947085831000000326e+04
+5.309918238000000193e-03 5.680360693000000174e+04
+5.720425739000000419e-03 5.411640516000000207e+04
+6.160383816000000387e-03 5.141407867000000260e+04
+6.631904313000000148e-03 4.870224801999999909e+04
+7.137250359999999794e-03 4.598733806000000186e+04
+7.678847190999999600e-03 4.327657452000000194e+04
+8.259293727999999710e-03 4.057796502999999939e+04
+8.881374997000000826e-03 3.790026183000000310e+04
+9.548075414000000566e-03 3.525290320000000065e+04
+1.026259302000000033e-02 3.264593126000000120e+04
+1.102835475000000023e-02 3.008988382999999885e+04
+1.184903271999999952e-02 2.759565880000000107e+04
+1.272856177000000061e-02 2.517435019000000102e+04
+1.367115812999999958e-02 2.283705631999999969e+04
+1.468133953000000033e-02 2.059466170000000056e+04
+1.576394662000000016e-02 1.845759590000000026e+04
+1.692416597999999925e-02 1.643557449999999881e+04
+1.816755471999999955e-02 1.453732915999999932e+04
+1.950006681000000103e-02 1.277033582999999999e+04
+2.092808128000000004e-02 1.114055203000000074e+04
+2.245843238000000061e-02 9.652175733000000037e+03
+2.409844187000000082e-02 8.307439661000000342e+03
+2.585595355999999873e-02 7.106455033999999614e+03
+2.773937027000000083e-02 6.047118687999999565e+03
+2.975769337999999847e-02 5.125095736000000215e+03
+3.192056508999999848e-02 4.333887329000000136e+03
+3.423831363999999683e-02 3.664989112000000205e+03
+3.672200169999999958e-02 3.108140840000000026e+03
+3.938347802000000120e-02 2.651661607999999887e+03
+4.223543269999999877e-02 2.282858655999999883e+03
+4.529145625000000064e-02 1.988491209999999910e+03
+4.856610263000000344e-02 1.755265086999999994e+03
+5.207495670000000104e-02 1.570329451000000063e+03
+5.583470614000000248e-02 1.421744783999999981e+03
+5.986321827999999817e-02 1.298891374999999925e+03
+6.417962215000000414e-02 1.192790610000000015e+03
+6.880439593999999881e-02 1.096316974999999957e+03
+7.375946032999999846e-02 1.004286765999999943e+03
+7.906827805999999681e-02 9.134191858000000366e+02
+8.475595998000000353e-02 8.221761014999999588e+02
+9.084937804999999866e-02 7.304971021000000064e+02
+9.737728576000000136e-02 6.394555661000000555e+02
+1.043704461999999944e-01 5.508682529000000159e+02
+1.118617684000000057e-01 4.668946616999999719e+02
+1.198864523999999959e-01 3.896625981999999908e+02
+1.284821429999999931e-01 3.209529039999999895e+02
+1.376890936999999870e-01 2.619693740000000162e+02
+1.475503401000000103e-01 2.132100816999999893e+02
+1.581118841999999969e-01 1.744445738999999946e+02
+1.694228892999999903e-01 1.447889552000000037e+02
+1.815358867999999903e-01 1.228593084000000033e+02
+1.945069947999999993e-01 1.069749204999999961e+02
+2.083961485999999974e-01 9.537795108999999627e+01
+2.232673444999999923e-01 8.643647581000000457e+01
+2.391888970999999919e-01 7.880326585000000250e+01
+2.562337091999999927e-01 7.151223903999999720e+01
+2.744795564999999993e-01 6.400642766999999367e+01
+2.940093859999999837e-01 5.610331177999999852e+01
+3.149116285999999931e-01 4.791315583000000089e+01
+3.372805261999999860e-01 3.973173538000000349e+01
+3.612164733000000072e-01 3.192973074000000011e+01
+3.868263726000000235e-01 2.485753002999999950e+01
+4.142240039999999790e-01 1.877770715000000123e+01
+4.435304078000000261e-01 1.382996544999999955e+01
+4.748742793999999878e-01 1.002662298000000085e+01
+5.083923767000000371e-01 7.271887265000000156e+00
+5.442299368999999887e-01 5.395641005999999962e+00
+5.825411029000000518e-01 4.192113531999999587e+00
+6.234893558999999863e-01 3.455236795999999888e+00
+6.672479531999999658e-01 3.005120749000000036e+00
+7.140003673999999467e-01 2.703221257000000044e+00
+7.639407244000000485e-01 2.456625939999999897e+00
+8.172742367999999979e-01 2.213857894000000215e+00
+8.742176267000000278e-01 1.955518292999999908e+00
+9.349995357000000507e-01 1.683090725000000010e+00
+9.998609135999999564e-01 1.408563352000000046e+00
+1.069055381999999943e+00 1.146493900000000066e+00
+1.142849564999999901e+00 9.090755313999999698e-01
+1.221523375999999939e+00 7.039293283999999984e-01
+1.305370262000000059e+00 5.338851217000000204e-01
+1.394697379999999987e+00 3.979019997000000086e-01
+1.489825715999999911e+00 2.924116880000000029e-01
+1.591090115000000083e+00 2.126062447000000022e-01
+1.698839229000000062e+00 1.534291822999999944e-01
+1.813435356000000054e+00 1.102081240999999989e-01
+1.935254178000000103e+00 7.897259099999999477e-02
+2.064684356999999970e+00 5.654394867999999741e-02
+2.202127009999999885e+00 4.048720642999999869e-02
+2.347995024999999902e+00 2.899659300999999842e-02
+2.502712219999999821e+00 2.076325356000000011e-02
+2.666712334000000073e+00 1.485227790000000041e-02
+2.840437840999999963e+00 1.060085761999999925e-02
+3.024338574000000168e+00 7.539875439000000117e-03
+3.218870163000000062e+00 5.336412262999999830e-03
+3.424492284999999914e+00 3.752918398000000197e-03
+3.641666713999999860e+00 2.618758055999999886e-03
+3.870855197000000025e+00 1.810538061999999960e-03
+4.112517146000000068e+00 1.238508779000000067e-03
+4.367107168999999622e+00 8.371096931999999491e-04
+4.635072451000000093e+00 5.583369475999999752e-04
+4.916850017999999878e+00 3.670396824999999771e-04
+5.212863895999999997e+00 2.375439438000000116e-04
+5.523522203999999824e+00 1.511980480999999875e-04
+5.849214221000000435e+00 9.456409337000000264e-05
+6.190307454000000043e+00 5.806880856999999742e-05
+6.547144754999999705e+00 3.498709335000000064e-05
+6.920041535000000188e+00 2.067212689000000060e-05
+7.309283114000000303e+00 1.197262152999999948e-05
+7.715122245999999961e+00 6.794884612999999926e-06
+8.137776880000000546e+00 3.778066713000000148e-06
+8.577428181000000151e+00 2.057775851000000190e-06
+9.034218857000000824e+00 1.097867775999999897e-06
+9.508251819999999910e+00 5.737740055000000066e-07
+9.999589214000000226e+00 2.937751702000000197e-07
+1.050825181999999991e+01 1.473815478999999957e-07
+1.103421885999999930e+01 7.246330984999999878e-08
+1.157742818000000007e+01 3.492636334000000220e-08
+1.213777688000000055e+01 1.650741516000000083e-08
+1.271512225000000029e+01 7.653154724000000721e-09
+1.330928311000000086e+01 3.481734177999999846e-09
+1.392004153999999971e+01 1.554939321000000024e-09
+1.454714474999999929e+01 6.819815759999999858e-10
+1.519030745000000060e+01 2.938734313000000151e-10
+1.584921422000000035e+01 1.244718580999999944e-10
+1.652352219999999861e+01 5.184497144999999777e-11
+1.721286389999999855e+01 2.124585587000000071e-11
+1.791685001999999827e+01 8.570118196999999701e-12
+1.863507244999999912e+01 3.404567056999999995e-12
+1.936710717000000059e+01 1.332664646000000083e-12
+2.011251714999999862e+01 5.142665289999999762e-13
+2.087085520000000116e+01 1.957450493999999878e-13
+2.164166670999999909e+01 7.352864828000000048e-14
+2.242449227999999906e+01 2.727182623999999954e-14
+2.321887016000000159e+01 9.992907137000000461e-15
+2.402433857000000117e+01 3.619227663000000029e-15
+2.484043783999999988e+01 1.296314274000000055e-15
+2.566671232999999930e+01 4.593981749000000114e-16
+2.650271221999999938e+01 1.611699895000000057e-16
+2.734799501999999904e+01 5.600262308999999821e-17
+2.820212701000000166e+01 1.928291664000000121e-17
+2.906468436000000111e+01 6.582324843999999742e-18
+2.993525418000000116e+01 2.228573896999999900e-18
+3.081343535999999972e+01 7.486989882000000039e-19
+3.169883923000000081e+01 2.496924974999999901e-19
+3.259109011999999694e+01 8.269867731000000155e-20
+3.348982571999999891e+01 2.721161850999999793e-20
+3.439469737999999666e+01 8.898496541999999646e-21
+3.530537025999999656e+01 2.892773866000000155e-21
+3.622152338000000071e+01 9.346546237999999768e-22
+3.714284956000000193e+01 3.002299288000000055e-22
+3.806905538000000178e+01 9.535441064000000394e-23
+3.899986091000000243e+01 3.050448574999999784e-23
+3.993499953999999974e+01 8.579306635000000353e-24
+4.087421762999999686e+01 2.314697128000000104e-24