[pull] master from MRChemSoft:master

.circleci/config.yml

@@ -48,29 +48,40 @@ variables:
       shell: /bin/bash
       command: |
         cd build
-        ctest --output-on-failure --verbose
+        ctest -N \
+          | sed -n 's/.*Test #[0-9]\+: \(.*\)/\1/p' \
+          | circleci tests split \
+          | tr '\n' '|' \
+          | sed 's/|$//' \
+          | xargs -I {} ctest  --verbose --output-on-failure -R "{}"
 
 jobs:
   serial-py3:
+    parallelism: 4 
     <<: *ubuntu-2204
     steps:
-      - checkout
+      - checkout:
+         method: blobless
       - *configure-serial
       - *build
       - *tests
   omp-py3:
+    parallelism: 4 
     <<: *ubuntu-2204
     environment:
       - OMP_NUM_THREADS: '2'
     steps:
-      - checkout
+      - checkout:
+         method: blobless
       - *configure-omp
       - *build
       - *tests
   mpi-py3:
+    parallelism: 4 
     <<: *ubuntu-2204
     steps:
-      - checkout
+      - checkout:
+         method: blobless
       - *configure-mpi
       - *build
       - *tests

.github/workflows/build-test.yml

@@ -26,7 +26,16 @@ jobs:
         os: [ubuntu-latest] #, macos-12]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+
+    - name: Cache conda
+      uses: actions/cache@v4
+      env:
+        CACHE_NUMBER: 0  # Increase this value to reset cache if .github/mrchem-gha.yml has not changed
+      with:
+        path: ~/conda_pkgs_dir
+        key:
+          ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/mrchem-gha.yml') }}
 
     - uses: conda-incubator/setup-miniconda@v3
       with:
@@ -35,7 +44,7 @@ jobs:
           activate-environment: mrchem-gha
           environment-file: .github/mrchem-gha.yml
           channel-priority: true
-          python-version: 3.9
+          python-version: 3.11
           use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
 
     - name: Configure

doc/users/manual.rst

@@ -43,3 +43,4 @@ in more detail in the sections below.
    qcengine
    program_json
    geometry_optimization.rst
+   pseudopotentials.rst

doc/users/na_pp.inp

@@ -0,0 +1,27 @@
+world_prec = 1e-04
+world_unit = bohr
+
+Pseudopotential {
+$pp_files
+{
+"Na": "psppar.Na"
+}
+$end
+}
+
+SCF {
+    initial_mixing_steps = 2
+}
+
+Molecule {
+charge = 0
+multiplicity = 2
+$coords
+Na 0.0 0.0 0.0
+$end
+}
+
+WaveFunction {
+  method = pbe
+  restricted = false
+}

doc/users/pseudopotentials.rst

@@ -0,0 +1,108 @@
+---------------------------------
+Pseudopotential calculations
+---------------------------------
+
+MRChem supports Goedecker-Teter-Hutter (GTH) pseudopotentials, which replace
+core electrons with an effective potential. This reduces the number of electrons
+that need to be treated explicitly, which can significantly lower the
+computational cost..
+
+Setting up a pseudopotential calculation
+----------------------------------------
+
+A pseudopotential calculation is set up by adding a ``Pseudopotential`` section
+to the input file. The ``pp_files`` keyword is a JSON string that maps elements
+(or atom indices) to pseudopotential parameter files. Here is an example for a
+sodium atom:
+
+.. include:: na_pp.inp
+    :literal:
+
+The pseudopotential parameter file (here ``psppar.Na``) must be present in
+the working directory when the calculation is launched. These files follow the
+PSPPAR format used by BigDFT and contain the local potential
+parameters, non-local projectors and optionally non-linear core correction
+(NLCC) data.
+
+Assigning pseudopotentials
+--------------------------
+
+The ``pp_files`` keyword accepts a JSON dictionary. Keys can be either element
+symbols or atom indices (1-based). This allows flexible assignment:
+
+**By element** -- all atoms of that element use the same pseudopotential::
+
+    $pp_files
+    {
+    "Na": "psppar.Na",
+    "Cl": "psppar.Cl"
+    }
+    $end
+
+**By index** -- specific atoms can be assigned individually::
+
+    $pp_files
+    {
+    "1": "psppar.Na",
+    "2": "psppar.Cl"
+    }
+    $end
+
+**Mixed all-electron and pseudopotential** -- setting an empty string or
+``"none"`` for an element will use the all-electron description for that
+element::
+
+    $pp_files
+    {
+    "Na": "psppar.Na",
+    "O": "none"
+    }
+    $end
+
+Atoms that are not mentioned in ``pp_files`` at all will also default to
+all-electron treatment.
+
+Pseudopotential precision
+-------------------------
+
+The precision of the pseudopotential construction is controlled by
+``pp_prec``, which defaults to ``world_prec``. In most cases the default
+is sufficient, but it can be set explicitly if needed::
+
+    Pseudopotential {
+    $pp_files
+    {
+    "Na": "psppar.Na"
+    }
+    $end
+      pp_prec = 1.0e-6
+    }
+
+PSPPAR file format
+------------------
+
+The pseudopotential parameter files use the format from the BigDFT/Goedecker
+pseudopotential library. A typical file looks like this::
+
+    spin-polarized 1       2.840       5.800  ...
+     11.000  1.000  20240517                        zatom, zion, date
+       12   -101130  1 0 2002 0                     pspcod, ixc, lmax, ...
+        0.7499...    2 -0.7392...  -0.1720...       rloc nloc c1 .. cnloc
+       2                                            nsep
+       0.7125...  2  0.3650...  -0.1023...          s-projector
+                         0.7522...
+       0.9000...  1  0.4314...                      p-projector
+                         0.0000...
+        0.5941...     0.3564...                     rcore, qcore (nlcc)
+
+The key quantities read from this file are:
+
+- ``zion``: ionic charge (number of valence electrons)
+- ``rloc``, ``nloc``, ``c1..cnloc``: local pseudopotential parameters
+- ``nsep``: number of non-local (separable) projector channels
+- For each channel: projector radius, dimension, and h-matrix elements
+- Optional NLCC parameters: ``rcore`` and ``qcore``
+
+GTH pseudopotential files for most elements can be obtained from the
+`CP2K GTH pseudopotential repository <https://github.com/cp2k/cp2k/tree/master/data>`_.
+or from here: https://github.com/OpenCPMD/GTH-pseudopotentials/tree/main

doc/users/schema_input.json

@@ -130,7 +130,8 @@
       "final_prec": float,                   # Final precision for solver
       "helmholtz_prec": float,               # Precision for Helmholtz operators
       "orbital_thrs": float,                 # Convergence threshold orbitals
-      "energy_thrs":float                    # Convergence threshold energy
+      "energy_thrs": float,                  # Convergence threshold energy
+      "deltascf_method": string              # Name of DeltaSCF method
     },
     "properties": {                          # Collection of properties to compute
       "dipole_moment": {                     # Collection of dipole moments

doc/users/user_inp.rst

@@ -380,6 +380,7 @@ The optimization is controlled by the following keywords (defaults shown):
       final_prec = -1.0                     # Dynamic precision, final value
       orbital_thrs = 10 * world_prec        # Convergence threshold orbitals
       energy_thrs = -1.0                    # Convergence threshold energy
+      deltascf_method = none                # Method to use for a DeltaSCF calculation
     }
 
 If ``run = false`` no SCF is performed, and the properties are computed directly
@@ -408,6 +409,9 @@ This means that the number of correct digits in the total energy will be
 saturated well before this point, and one should rather use the ``energy_thrs``
 keyword in this case in order to save a few iterations.
 
+There is also the possibility to run a DeltaSCF calculation using either the
+``MOM`` or ``IMOM`` method.
+
 .. note::
 
     It is usually not feasible to converge the orbitals *beyond* the overall

doc/users/user_ref.rst

@@ -231,12 +231,24 @@ User input reference
 
     **Default** ``-1``
 
-   :omp_threads: Force the number of omp threads (leave default is better). 
+   :bank_per_node: Number of MPI processes per node exclusively dedicated to manage orbital bank. 
 
     **Type** ``int``
 
     **Default** ``-1``
 
+   :omp_threads: Force the number of omp threads for worker processes (leave default is better). 
+
+    **Type** ``int``
+
+    **Default** ``-1``
+
+   :use_omp_num_threads: This will use the environment variable OMP_NUM_THREADS to determine the average number of threads for OMP (bank will use 1, workers may use more). 
+
+    **Type** ``bool``
+
+    **Default** ``False``
+
  :Basis: Define polynomial basis. 
 
   :red:`Keywords`
@@ -353,6 +365,21 @@ User input reference
     **Predicates**
       - ``value.lower() in ['point_like', 'point_parabola', 'point_minimal', 'finite_gaussian', 'finite_sphere']``
 
+ :Pseudopotential: Define the pseudopotentials. 
+
+  :red:`Keywords`
+   :pp_files: Json string of pseudopotential files. The key can be the element symbol or a number. When the key is an element symbol, all atoms of that element will use the given pseudopotential. When the key is a number (index is 1 based), the corresponding atom will use the given pseudopotential. When the value is an empty string, an all electron calculation will  be performed for the corresponding atom or element. 
+
+    **Type** ``str``
+
+    **Default** ``{}``
+
+   :pp_prec: Precision parameter used in construction of pseudopotentials. 
+
+    **Type** ``float``
+
+    **Default** ``user['world_prec']``
+
  :ZORA: Define required parameters for the ZORA Hamiltonian. 
 
   :red:`Keywords`
@@ -656,7 +683,7 @@ User input reference
 
     **Default** ``initial_guess/y_b``
 
-   :cube_vectors: Directory where cube vectors are stored for mrchem calculation. 
+   :cube_vectors: Directory where cube vectors are stored for MRChem calculation. 
 
     **Type** ``str``
 
@@ -728,14 +755,32 @@ User input reference
 
     **Default** ``-1.0``
 
-   :guess_type: Type of initial guess for ground state orbitals. ``chk`` restarts a previous calculation which was dumped using the ``write_checkpoint`` keyword. This will load MRA and electron spin configuration directly from the checkpoint files, which are thus required to be identical in the two calculations. ``mw`` will start from final orbitals in a previous calculation written using the ``write_orbitals`` keyword. The orbitals will be re-projected into the new computational setup, which means that the electron spin configuration and MRA can be different in the two calculations. ``gto`` reads precomputed GTO orbitals (requires extra non-standard input files for basis set and MO coefficients). ``core`` and ``sad`` will diagonalize the Fock matrix in the given AO basis (SZ, DZ, TZ or QZ) using a Core or Superposition of Atomic Densities Hamiltonian, respectively. ``cube`` will start from orbitals saved in cubefiles from external calculations. 
+   :guess_type: Type of initial guess for ground state orbitals. ``chk`` restarts a previous calculation which was dumped using the ``write_checkpoint`` keyword. This will load MRA and electron spin configuration directly from the checkpoint files, which are thus required to be identical in the two calculations. ``mw`` will start from final orbitals in a previous calculation written using the ``write_orbitals`` keyword. The orbitals will be re-projected into the new computational setup, which means that the electron spin configuration and MRA can be different in the two calculations. ``gto`` reads precomputed GTO orbitals (requires extra non-standard input files for basis set and MO coefficients). ``core`` and ``sad`` will diagonalize the Fock matrix in the given AO basis (SZ, DZ, TZ or QZ) using a Core or Superposition of Atomic Densities Hamiltonian, respectively. ``cube`` will start from orbitals saved in cubefiles from external calculations. ``nao`` will start from orbitals saved in NAO format from external calculations.  It also allows for some mixing iterations to converge the initial guess within the nao basis. 
 
     **Type** ``str``
 
     **Default** ``sad_gto``
 
     **Predicates**
-      - ``value.lower() in ['mw', 'chk', 'gto', 'core_sz', 'core_dz', 'core_tz', 'core_qz', 'sad_sz', 'sad_dz', 'sad_tz', 'sad_qz', 'sad_gto', 'cube']``
+      - ``value.lower() in ['mw', 'chk', 'gto', 'core_sz', 'core_dz', 'core_tz', 'core_qz', 'sad_sz', 'sad_dz', 'sad_tz', 'sad_qz', 'sad_gto', 'cube', 'nao']``
+
+   :nao_directory: Directory where NAO orbitals are stored for MRChem calculation. 
+
+    **Type** ``str``
+
+    **Default** ``none``
+
+   :initial_mixing_steps: Number of mixing iterations to converge the initial guess within the nao basis. 
+
+    **Type** ``int``
+
+    **Default** ``4``
+
+   :initial_mixing_step_size: Step size for the mixing iterations to converge the initial guess within the nao basis. 
+
+    **Type** ``float``
+
+    **Default** ``0.4``
 
    :write_checkpoint: Write orbitals to disk in each iteration, file name ``<path_checkpoint>/phi_scf_idx_<0..N>``. Can be used as ``chk`` initial guess in subsequent calculations. Note: must be given in quotes if there are slashes in the path "path/to/checkpoint". 
 
@@ -752,6 +797,12 @@ User input reference
     **Predicates**
       - ``value[-1] != '/'``
 
+   :write_orbitals_txt: Write final orbitals to disk, in text format, file name ``<path_orbitals>/phi_<p/a/b>_scf_idx_<0..Np/Na/Nb>``. Can be used as ``mw`` initial guess in subsequent calculations. 
+
+    **Type** ``bool``
+
+    **Default** ``False``
+
    :path_orbitals: Path to where converged orbitals will be written in connection with the ``write_orbitals`` keyword. Note: must be given in quotes if there are slashes in the path "path/to/orbitals". 
 
     **Type** ``str``
@@ -767,6 +818,12 @@ User input reference
 
     **Default** ``True``
 
+   :deltascf_method: Method to use for a DeltaSCF calculation. Options are ``none`` for a normal SCF run, ``MOM`` for a run using the MOM method and ``IMOM`` for a run using the IMOM method. 
+
+    **Type** ``str``
+
+    **Default** ``none``
+
    :write_orbitals: Write final orbitals to disk, file name ``<path_orbitals>/phi_<p/a/b>_scf_idx_<0..Np/Na/Nb>``. Can be used as ``mw`` initial guess in subsequent calculations. 
 
     **Type** ``bool``
@@ -1071,6 +1128,15 @@ User input reference
 
     **Default** ``0.005``
 
+ :OrbitalOccupancies: Modify the default orbital occupancies in order to perform a DeltaSCF calculation. 
+
+  :red:`Keywords`
+   :occupancies: List of orbitals, i, for which the default occupancy, f, should be overwritten, written as a list in the format "i f_up f_down", where the orbitals are indexed from zero. 
+
+    **Type** ``str``
+
+    **Default** ````
+
  :Constants: Physical and mathematical constants used by MRChem
 
   :red:`Keywords`
@@ -12254,4 +12320,4 @@ User input reference
         **Type** ``float``
 
         **Default** ``0.00011186082063``
-
+

external/upstream/fetch_eigen3.cmake

@@ -1,4 +1,4 @@
-find_package(Eigen3 3.4 CONFIG QUIET
+find_package(Eigen3 CONFIG QUIET
   NO_CMAKE_PATH
   NO_CMAKE_PACKAGE_REGISTRY
   )