Adds r2SCAN hybrids; r2SCAN-3c and B97-3c (psi4#2842)

* adds couple of r2scan based functionals * 3c update, + scan hybrid functionals * dft printing doi formatting * allow omitting default disp params; turn gcp on * cleanup * adds basis set files * add <optional> header * prevent r2scan3c dict from building; get new QCEngine * allow custom qcng in CI * py packaging wants to control us * right number * ok, setuptools via packaging wants to control us * they're working together * one back * more errors * fix bib * full spec * add some tests * touchups * check everything * fixup * fixups * condense another fctl * fixes --------- Co-authored-by: Lori A. Burns <[email protected]>
evangelistalab · Dec 5, 2023 · 6c81789 · 6c81789
1 parent 8e4ee09
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diff --git a/.azure-pipelines/azure-pipelines-linux.yml b/.azure-pipelines/azure-pipelines-linux.yml
@@ -41,7 +41,7 @@ jobs:
 
   pool:
     vmImage: $(vmImage)
-  
+
   steps:
   - bash: |
       [[ "${APT_REPOSITORY}" ]] && echo "Add Repo ${APT_REPOSITORY}" && sudo add-apt-repository "${APT_REPOSITORY}"
@@ -99,7 +99,6 @@ jobs:
         echo "  - psi4::gcp" >> env_p4env.yaml
         echo "  - psi4::dftd3" >> env_p4env.yaml
       fi
-      sed -i "s;- libxc-c;- psi4::libxc=5;g" env_p4env.yaml
       sed -i "s;- conda-forge/label/libint_dev;#- conda-forge/label/libint_dev;g" env_p4env.yaml
       sed -i "s;#- psi4/label/testing::libint2;- psi4/label/testing::libint=2.8.0dev2;g" env_p4env.yaml
       echo "\n<<<  env_p4env.yaml  >>>\n"
@@ -158,3 +157,5 @@ jobs:
       source activate p4env
       PYTHONPATH=stage/lib/ pytest -v -rws --durations=15 --durations-min=40 --strict-markers --color yes -n 2 -m "$PYTEST_MARKER_EXPR" stage/lib/psi4/tests/
     displayName: 'PyTest Tests'
+
+# setuptools v66 (vendors packaging v23) incompatible with arb. tarballs. thinks the branch names are versions
diff --git a/.azure-pipelines/azure-pipelines-windows.yml b/.azure-pipelines/azure-pipelines-windows.yml
@@ -275,6 +275,7 @@ jobs:
       # Build package
       - script: |
           set INSTALL_DIR=$(Build.BinariesDirectory)\install
+          conda config --set channel_priority flexible
           conda build --python %PYTHON_VERSION% ^
                       conda\win
           copy /y C:\tools\miniforge3\conda-bld\win-64\psi4-*.bz2 $(Build.ArtifactStagingDirectory)

diff --git a/codedeps.yaml b/codedeps.yaml
@@ -945,7 +945,7 @@ data:
       commit: 6.2.2
     #cmake:
     #  name: Libxc
-    #  constraint: 5.1.2  # two calls: catch v5, v6
+    #  constraint: 6.0.0
     #  target: Libxc::xc
       components:
         - C

diff --git a/doc/sphinxman/source/basissets_tables.rst b/doc/sphinxman/source/basissets_tables.rst
@@ -292,6 +292,12 @@ Appendix :ref:`apdx:basisElement`.
     +--------------+-------------+
     | def2-QZVPP   | def2-QZVPPD |
     +--------------+-------------+
+    | def2-mSVP    |             |
+    +--------------+-------------+
+    | def2-mTZVP   |             |
+    +--------------+-------------+
+    | def2-mTZVPP  |             |
+    +--------------+-------------+
 
 |
 |

diff --git a/doc/sphinxman/source/bibliography.rst b/doc/sphinxman/source/bibliography.rst
@@ -725,3 +725,19 @@ Bibliography
    F. Weigend,
    *Phys. Chem. Chem. Phys.* **4**, 4285-4291 (2002).
    https://doi.org/10.1039/B204199P
+
+.. [Brandenburg:2018:b973c]
+   J. G. Brandenburg, C.Bannwarth, A. Hansen, S. Grimme,
+   *J. Chem. Phys.* **148**, 064104, (2018).
+   https://doi.org/10.1063/1.5012601
+
+.. [Muller:2023:014103]
+   M. M\ |u_dots|\ ller and A. Hansen and S. Grimme
+   *J. Chem. Phys.* **158**, 014103 (2023).
+   https://doi.org/10.1063/5.0133026
+
+.. [Grimme:2021:064103]
+   S. Grimme and A. Hansen and S. Ehlert and J.-M. Mewes
+   *J. Chem. Phys.* **154**, 064103 (2021).
+   https://doi.org/10.1063/5.0040021
+
diff --git a/doc/sphinxman/source/build_planning.rst b/doc/sphinxman/source/build_planning.rst
@@ -37,7 +37,9 @@ Compiling and Installing from Source
 .. warning:: As of v1.8, primary binary distribution has moved from
    the psi4 channel to the conda-forge channel. Neither install docs
    for users nor compile docs for developers have been updated yet to
-   reflect new patterns. Please consult :psicode:`psicode downloads
+   reflect new patterns. Please consult :source:`conda/psi4-path-advisor.py`
+   (extensive help menu at ``conda/psi4-path-advisor.py -h``)
+   or :psicode:`psicode downloads
    page <installs/latest/>` for the latest guides.
 
 This section fulfills the duty of every Linux project to have an INSTALL

diff --git a/doc/sphinxman/source/dftd3.rst b/doc/sphinxman/source/dftd3.rst
@@ -93,6 +93,7 @@ Installation
 * There are two implementations of DFTD3; see :ref:`table:empdispimpl` . The newer
   "s-dftd3" one is preferred, while the older "classic" one will work for the immediate future.
   |PSIfour| will automatically select whichever is available.
+  Starting with v1.9, only "s-dftd3" is supported, though the "classic" continues to work for many applications.
 
 * DFTD3 is available as a conda package for Linux and macOS and Windows.
 
@@ -222,6 +223,7 @@ available only through the ``DFTD3`` or ``DFTD4`` programs. Once installed, the
 ``dftd3``/|PSIfour| and ``dftd4``/|PSIfour| interfaces are transparent, and all corrections are
 interfaced exactly alike.
 The -D3 interface can use classic or simple-dftd3 programs interchangeably and will prefer the latter.
+Starting in v1.9, the classic program is no longer supported or tested, though it isn't deliberately disabled.
 
 Despite different defaults in these programs when run independently,
 when run through |PSIfour| as EmpiricalDispersion engine, each should
@@ -308,7 +310,7 @@ the ``dftd3``/|PSIfour| interface enables computations of three-body dispersion
 corrections. In ``DFT-D3``, three-body dispersion is approximated with the
 Axilrod-Teller-Muto model:
 
-.. math:: E_{disp}^{(3)}=-\frac{1}{6}\sum_{A\neqB\neqC}\frac{C_{9}^{ABC}(3\cos{\theta_a}\cos{\theta_b}\cos{\theta_c}+1)}{(r_{AB}r_{BC}r_{AC})^{3}}f_{damp}(\bar{r}_{ABC})
+.. math:: E_{disp}^{(3)}=-\frac{1}{6}\sum_{A\neq B\neq C}\frac{C_{9}^{ABC}(3\cos{\theta_a}\cos{\theta_b}\cos{\theta_c}+1)}{(r_{AB}r_{BC}r_{AC})^{3}}f_{damp}(\bar{r}_{ABC})
 
 where :math:`\theta_a` is the angle at atom A corresponding to the triangle formed by atoms A, B, and C,
 and :math:`\bar{r}_{ABC}` is the geometric mean of the corresponding atomic-pair distances.

diff --git a/doc/sphinxman/source/gcp.rst b/doc/sphinxman/source/gcp.rst
@@ -60,6 +60,8 @@ Installation
 * There are two implementations of gCP; see :ref:`table:empdispimpl` . The newer
   "mctc" one is preferred, while the older "classic" one will work for the immediate future.
   |PSIfour| will automatically select whichever is available.
+  Starting with v1.9, only "mctc-gcp" is supported, though the now untested
+  "classic" continues to work for many applications.
 
 * gCP is available as a conda package for Linux and macOS and Windows.
 
@@ -98,15 +100,19 @@ Running gCP
 ~~~~~~~~~~~
 
 At present there is a limited interface to gCP that is used
-only to implement the "HF-3c" [Sure:2013:1672]_ and "PBEh-3c"
-[Grimme:2015:054107]_ methods (both energy and gradient). The interface
-can use classic or mctc-gcp executables interchangeably and will prefer the latter.
-A :ref:`DFTD3 <sec:dftd3>` executable, classic or simple-dftd3,
-must also be available for these methods to
-run. Unlike every other method in |PSIfour|, if a basis set has not been
-set, these will default to their intended basis sets: MINIX for HF-3c
-and def2-mSVP for PBEh-3c. If a basis has previously been set, but you
-want to use the default basis, use the slash syntax to "empty" the basis
+only to implement the "HF-3c" [Sure:2013:1672]_, "PBEh-3c"
+[Grimme:2015:054107]_, "B97-3c" [Brandenburg:2018:b973c]_, "r2SCAN-3c" [Grimme:2021:064103]_,
+and "wB97X-3c" [Muller:2023:014103]_ methods (both energy and gradient).
+The interface can use classic or mctc-gcp executables but only the latter implements "B97-3c" and "r2SCAN-3c".
+The newest wB97X-3c method doesn't use a gcp correction (it does use ECPs down to first row elements)
+but is listed here for completeness of the "3c" family.
+A :ref:`DFTD3 <sec:dftd3>` executable, classic or simple-dftd3, must also be available for
+the HF-3c, PBEh-3c, or B97-3c methods to run.
+A :ref:`DFTD4 <sec:dftd3>` python module must also be available for
+the r2SCAN-3c or wB97X-3c methods to run.
+These method are defined with their own basis set and thus no basis set should be set by the user.
+|PSIfour| will select the intended basis sets: HF-3c/MINIX, PBEh-3c/def2-mSVP, B97-3c/def2-mTZVP, r2SCAN-3c/def2-mTZVPP, wB97X-3c/vDZP.
+If a basis has previously been set for another calculation, use the slash syntax to "empty" the basis
 option for the scope of the current calculation, ``energy("hf3c/")``.
 
 A few practical examples:
@@ -119,15 +125,10 @@ A few practical examples:
 
    optimize('pbeh3c')
 
-* HF-3c with non-standard basis ::
+* r2SCAN-3c with default basis after basis set ::
 
    set basis cc-pvdz
-   energy('hf3c')
-
-* PBEh-3c with default basis after basis set ::
-
-   set basis cc-pvdz
-   energy('pbeh3c/')
+   energy('r2scan3c/')
 
 If only BSSE/basis set corrections (rather than total energies) are of
 interest, the ``gcp`` program can be run independently of the scf

diff --git a/doc/sphinxman/source/introduction.rst b/doc/sphinxman/source/introduction.rst
@@ -596,12 +596,11 @@ Architectures
     principle, it should work on any Unix system. The latest version of the
     |PSIfour| program package may be obtained at `psicode.org <http://psicode.org>`_.
     The package is available as a binary (:ref:`Installing from Binary
-    <sec:conda>`) for Linux, macOS (not arm64), or Windows (both native and via Windows Subsystem for
+    <sec:conda>`) for Linux, macOS (both Intel and Apple Silicon), or Windows (both native and via Windows Subsystem for
     Linux aka `Bash on Ubuntu on Windows
     <https://docs.microsoft.com/en-us/windows/wsl/about>`_)
     or as source code (git repository or zipped archive from
     https://github.com/psi4/psi4.
-    At least initially, |PSIfour| 1.7 will not have binary packages for Mac.
 Compilers
     |PSIfour| has been successfully compiled using Intel, GCC, and Clang
     compilers. :ref:`Compiler requirements <faq:approvedcxx>` are primarily
@@ -620,9 +619,10 @@ Python
     |PSIfour| 1.6 supports Python 3.8, 3.9, and 3.10.
     |PSIfour| 1.7 supports Python 3.8, 3.9, 3.10, and 3.11 (no binary packages for 3.11).
     |PSIfour| 1.8 supports Python 3.8, 3.9, 3.10, and 3.11.
+    |PSIfour| 1.9 supports Python 3.8, 3.9, 3.10, 3.11, and 3.12.
     The future plan is to (1) be compatible with 3.8 and above until there is a good reason to drop
     older versions but (2) only build and test for versions conda-forge supports.
-    The current master supports 3.8, 3.9, 3.10, and 3.11.
+    The current master supports 3.8, 3.9, 3.10, 3.11, and 3.12.
 
 .. index:: license
 
@@ -761,7 +761,8 @@ For more tables with capabilities details:
     +-------------------------+-------------------+-------------------+------------+------------+------------+------------+
     | ❖ with :ref:`DFTD3, DFTD4<sec:dftd3>`, and :ref:`gCP<sec:gcp>`                                                      |
     +-------------------------+-------------------+-------------------+------------+------------+------------+------------+
-    | HF-3c, PBEh-3c          | R/U/ROHF, R/UKS   |                   | E/G        |            |            |            |
+    | HF-3c, PBEh-3c, B97-3C, | R/U/ROHF, R/UKS   |                   | E/G        |            |            |            |
+    | r2SCAN-3c, wB97X-3c     |                   |                   |            |            |            |            |
     +-------------------------+-------------------+-------------------+------------+------------+------------+------------+
     | DFT-D3, DFT-D4          | RKS/UKS           |                   | E/G        |            |            |            |
     +-------------------------+-------------------+-------------------+------------+------------+------------+------------+

diff --git a/external/upstream/libxc/CMakeLists.txt b/external/upstream/libxc/CMakeLists.txt
@@ -1,8 +1,4 @@
 find_package(Libxc 6.0.0 CONFIG QUIET COMPONENTS C)
-if(NOT ${Libxc_FOUND})
-    # LibxcConfig.cmake encodes searching only within major version, so need two calls to allow v5 or v6
-    find_package(Libxc 5.1.2 CONFIG QUIET COMPONENTS C)
-endif()
 
 if(${Libxc_FOUND})
     get_property(_loc TARGET Libxc::xc PROPERTY LOCATION)

diff --git a/external/upstream/qcengine/CMakeLists.txt b/external/upstream/qcengine/CMakeLists.txt
@@ -31,6 +31,9 @@ else()
     # Note: Without downgrading setuptools or `sed`ing "git_refnames" (_version.py for versioneer-generated),
     #   pip will strenuously resist ("Invalid version: <branch or commit>") arbitrary branch or commit refs from GH.
     #   Make a proper PEP440 tag (e.g., `git tag -a v0.26.0.dev1 -m "v0.26.0.dev1"`), push it, and use in URL below.
+    #
+    #   With downgrading to (setuptools"<66.0.0" packaging"<23.0" ; former vendors latter), one can use arbitrary
+    #   branch or commit tarballs without the tagging procedure described above.
 
     ExternalProject_Add(qcengine_external
         DEPENDS qcelemental_external

diff --git a/psi4/CMakeLists.txt b/psi4/CMakeLists.txt
@@ -223,10 +223,7 @@ else()
     message(STATUS "Disabled BrianQC ${BrianQC_DIR}")
 endif()
 
-find_package(Libxc 6.0.0 CONFIG QUIET COMPONENTS C)
-if(NOT ${Libxc_FOUND})
-    find_package(Libxc 5.1.2 CONFIG REQUIRED COMPONENTS C)
-endif()
+find_package(Libxc 6.0.0 CONFIG REQUIRED COMPONENTS C)
 get_property(_loc TARGET Libxc::xc PROPERTY LOCATION)
 list(APPEND _addons ${_loc})
 message(STATUS "${Cyan}Using Libxc${ColourReset}: ${_loc} (version ${Libxc_VERSION})")

diff --git a/psi4/driver/driver.py b/psi4/driver/driver.py
@@ -140,10 +140,16 @@ def energy(name, **kwargs):
     +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
     | qchf                    | quadratically-convergent HF                                                                                                           |
     +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
-    | hf3c                    | HF with dispersion, BSSE, and basis set corrections :ref:`[manual] <sec:gcp>`                                                         |
+    | hf3c                    | HF with dispersion, BSSE, SRB, and basis set corrections :ref:`[manual] <sec:gcp>`                                                    |
     +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
     | pbeh3c                  | PBEh with dispersion, BSSE, and basis set corrections :ref:`[manual] <sec:gcp>`                                                       |
     +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
+    | b973c                   | B97(GGA) with dispersion, SRB, and basis set corrections :ref:`[manual] <sec:gcp>`                                                    |
+    +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
+    | r2scan3c                | r2SCAN with dispersion, BSSE, and basis set corrections :ref:`[manual] <sec:gcp>`                                                     |
+    +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
+    | wb97x3c                 | wB97X with dispersion and basis set corrections :ref:`[manual] <sec:gcp>`                                                             |
+    +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
     | dct                     | density cumulant (functional) theory :ref:`[manual] <sec:dct>`                                                                        |
     +-------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
     | mp2                     | 2nd-order |MollerPlesset| perturbation theory (MP2) :ref:`[manual] <sec:dfmp2>` :ref:`[details] <dd_mp2>`                             |

diff --git a/psi4/driver/driver_util.py b/psi4/driver/driver_util.py
@@ -261,6 +261,8 @@ def _alternative_methods_message(method_name: str, dertype: str, *, messages: Di
         stats = messages[0]
         conditions2 = [stats[k][1] for k in ["method_type", "reference", "fcae", "qc_module"]]
         return f"Method={stats['method']} is not available for {dertype} derivative level under conditions {', '.join(conditions2)}. See {stats['link']}.{alternatives}"
+    elif "-d" in method_name or "3c" in method_name:
+        return f"""Method={method_name} is not available for {dertype} derivative level. Some methods need dftd4-python>=3.5.0 and gcp-correction installed. Please `conda install "dftd4-python>=3.5" gcp-correction -c conda-forge` .{alternatives}"""
     else:
         return f"Method={method_name} is not available for {dertype} derivative level.{alternatives}"
 

diff --git a/psi4/driver/procrouting/dft/dft_builder.py b/psi4/driver/procrouting/dft/dft_builder.py
@@ -82,7 +82,7 @@
 import collections
 import copy
 
-from qcengine.programs.empirical_dispersion_resources import dashcoeff, get_dispersion_aliases
+from qcengine.programs.empirical_dispersion_resources import dashcoeff, get_dispersion_aliases, new_d4_api
 
 from psi4 import core
 
@@ -97,6 +97,9 @@
 dict_functionals.update(hyb_functionals.functional_list)
 dict_functionals.update(dh_functionals.functional_list)
 
+# remove r2scan-3c from dictionary if dftd4 <= v3.5.0
+if new_d4_api is False:
+    dict_functionals.pop("r2scan3c")
 
 def get_functional_aliases(functional_dict):
     if "alias" in functional_dict:
@@ -125,6 +128,10 @@ def get_functional_aliases(functional_dict):
         for formal in functional_aliases:
             # "bless" the original functional dft/*_functionals dispersion definition including aliases
             dashcoeff_supplement[disp['type']]['definitions'][formal] = disp
+            # add omitted default parameters of the dispersion correction
+            for p,val in dashcoeff[disp['type']]['default'].items():
+                if p not in dashcoeff_supplement[disp['type']]['definitions'][formal]['params'].keys():
+                    dashcoeff_supplement[disp['type']]['definitions'][formal]['params'][p]=val
             # generate dispersion aliases for every functional alias
             for nominal_dispersion_level, resolved_dispersion_level in _dispersion_aliases.items():
                 if resolved_dispersion_level == disp["type"]:
@@ -235,7 +242,7 @@ def check_consistency(func_dictionary):
         allowed_params = sorted(dashcoeff[_dispersion_aliases[disp["type"]]]["default"].keys())
         if "params" not in disp or sorted(disp["params"].keys()) != allowed_params:
             raise ValidationError(
-                f"SCF: Dispersion params ({list(disp['params'].keys())}) must include all ({allowed_params})")
+                f"SCF: Dispersion params for {name} ({list(disp['params'].keys())}) must include all ({allowed_params})")
     # 3d) check formatting for dispersion citation
         if "citation" in disp:
             cit = disp["citation"]
@@ -258,7 +265,11 @@ def build_superfunctional_from_dictionary(func_dictionary, npoints, deriv, restr
     if "xc_functionals" in func_dictionary:
         for xc_key in func_dictionary["xc_functionals"]:
             xc_name = ("XC_" + xc_key).upper()
-        sup = core.SuperFunctional.XC_build(xc_name, restricted)
+            xc_params = func_dictionary["xc_functionals"][xc_key]
+            if "tweak" in xc_params:
+                sup = core.SuperFunctional.XC_build(xc_name, restricted, xc_params["tweak"])
+            else:
+                sup = core.SuperFunctional.XC_build(xc_name, restricted)
         descr = "    " + func_dictionary["name"] + " "
         if sup.is_gga():
             if sup.x_alpha() > 0:
@@ -382,7 +393,7 @@ def build_superfunctional_from_dictionary(func_dictionary, npoints, deriv, restr
         sup.set_citation(func_dictionary["citation"])
     if "description" in func_dictionary:
         if "doi" in func_dictionary:
-            sup.set_description(func_dictionary["description"] + "(" + func_dictionary["doi"] + ")")
+            sup.set_description(func_dictionary["description"].replace("\n", "") + "  (" + func_dictionary["doi"].lstrip() + ")")
         else:
             sup.set_description(func_dictionary["description"])
 

diff --git a/psi4/driver/procrouting/dft/gga_functionals.py b/psi4/driver/procrouting/dft/gga_functionals.py
@@ -351,6 +351,28 @@
     '    BP86 GGA XC Functional based on VWN5 corr. & more accurate ftilde value\n',
 })
 
+# B97-3c = modified B97(GGA) + D3BJ + SRB(through mctc-gcp)
+funcs.append({
+    "name": "B973c",
+    "alias": ["B97-3c"],
+    "xc_functionals": {
+        "GGA_XC_B97_3C": {}
+    },
+    "description": '    B97-3c GGA-based 3C composite method with a TZ basis set, D3 and short-range basis set correction.\n',
+    "citation": '     J. G. Brandenburg, C.Bannwarth, A. Hansen, S. Grimme J. Chem. Phys. 148, 064104, 2018\n',
+    "doi": "10.1063/1.5012601",
+    "dispersion": {
+        "type": "d3bjatm",
+        "params": {
+            's6': 1.000,
+            's8': 1.500,
+            'a1': 0.370,
+            'a2': 4.100,
+        },
+    },
+})
+
+
 functional_list = {}
 for functional in funcs:
     functional_list[functional["name"].lower()] = functional