Option to disable rotation in initial guess (#486)

* added option to disable rotation of orbitals before calculating the initial guess energy

* small typo

* added rotate option to schema_input.json

* fixed small typos

* remove temporary files generated by updating the input parser

* update .gitignore file

* Revert "update .gitignore file"

This reverts commit 166c32d.

* Revert "remove temporary files generated by updating the input parser"

This reverts commit 8240e30.

* throw warning when trying to run update_input_parser.py while python/mrchem/input_parser/plumbing/pyparsing already exists

doc/users/schema_input.json

@@ -101,6 +101,7 @@
       "zeta": int,                           # Zeta quality for AO basis
       "method": string,                      # Name of method for initial energy
       "localize": bool,                      # Use localized orbitals
+      "rotate": bool,                        # Rotate orbitals in initial guess
       "restricted": bool,                    # Use spin restricted orbitals
       "relativity": string,                  # Name of relativistic method
       "screen": float,                       # Screening used in GTO evaluations

doc/users/user_inp.rst

@@ -449,6 +449,7 @@ The ``core`` and ``sad`` guesses are fully specified with the following keywords
       guess_prec = 1.0e-3                   # Numerical precision used in guess
       guess_type = sad_gto                  # Type of inital guess (chk, mw, cube, core_XX, sad_XX)
       guess_screen = 12.0                   # Number of StdDev before a GTO is set to zero (sad_gto)
+      guess_rotate = true                   # Localize/Diagonalize guess orbitals before calculating the initial guess energy
     }
 
 Checkpointing

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. 
@@ -722,6 +722,12 @@ User input reference
     **Predicates**
       - ``value[-1] != '/'``
 
+   :guess_rotate: Localize/Diagonalize the initial guess orbitals before calculating the initial guess energy. 
+
+    **Type** ``bool``
+
+    **Default** ``True``
+
    :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``
@@ -12209,4 +12215,4 @@ User input reference
         **Type** ``float``
 
         **Default** ``0.00011186082063``
-
+

python/README.md

@@ -12,6 +12,7 @@ To run the script:
 
 ```bash
 $ cd python/mrchem
+$ rm -r input_parser/plumbing/pyparsing
 $ python update_input_parser.py
 ```
 
@@ -24,7 +25,7 @@ This does three things:
 Each of these steps can be deactivated by appropriate flags. For help on running the script, run
 
 ```bash
-$ cd python
+$ cd python/mrchem
 $ python update_input_parser.py -h
 ```
 
@@ -33,7 +34,8 @@ If the `Constants` and `Elements` input sections are unchanged, you can update t
 The utility script can also do this, by specifying the flag `--skip-template`:
 
 ```bash
-$ cd python
+$ cd python/mrchem
+$ rm -r input_parser/plumbing/pyparing
 $ python update_input_parser --skip-template
 ```
 
@@ -43,6 +45,7 @@ You can also perform these steps manually without using the utility script:
 
 ```bash
 $ cd python
+$ rm -r mrchem/input_parser/plumbing/pyparsing
 $ parselglossy generate --template template.yml --docfile user_ref.rst --doc-header="User input reference" --target="mrchem/input_parser"
 $ cp mrchem/input_parser/docs/user_ref.rst ../doc/users/user_ref.rst
 ```

python/mrchem/helpers.py

@@ -224,6 +224,7 @@ def write_scf_guess(user_dict, wf_dict):
         "external_field": wf_dict["external_name"],
         "screen": scf_dict["guess_screen"],
         "localize": scf_dict["localize"],
+        "rotate": scf_dict["guess_rotate"],
         "restricted": user_dict["WaveFunction"]["restricted"],
         "file_chk": f"{scf_dict['path_checkpoint']}/phi_scf",
         "file_basis": file_dict["guess_basis"],

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 2024-05-14
 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 2024-01-29
+# This file was automatically generated by parselglossy on 2024-05-14
 # 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 2024-02-08
+# This file was automatically generated by parselglossy on 2024-05-14
 # Editing is *STRONGLY DISCOURAGED*
 
 from copy import deepcopy
@@ -510,6 +510,9 @@ def stencil() -> JSONDict:
                                             'name': 'path_orbitals',
                                             'predicates': ["value[-1] != '/'"],
                                             'type': 'str'},
+                                        {   'default': True,
+                                            'name': 'guess_rotate',
+                                            'type': 'bool'},
                                         {   'default': "user['GeometryOptimizer']['use_previous_guess']",
                                             'name': 'write_orbitals',
                                             'type': 'bool'},

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 2024-05-14
 # Editing is *STRONGLY DISCOURAGED*
 
 import argparse

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`
@@ -716,6 +722,12 @@ User input reference
     **Predicates**
       - ``value[-1] != '/'``
 
+   :guess_rotate: Localize/Diagonalize the initial guess orbitals before calculating the initial guess energy. 
+
+    **Type** ``bool``
+
+    **Default** ``True``
+
    :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``

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 2024-05-14
 # Editing is *STRONGLY DISCOURAGED*
 
 import json

python/mrchem/update_input_parser.py

@@ -220,20 +220,24 @@ def update_periodic_table():
 
 def run_parselglossy():
     os.chdir(root)
-    cmd = [
-        "parselglossy",
-        "generate",
-        "--template",
-        "template.yml",
-        "--docfile",
-        "user_ref.rst",
-        "--doc-header",
-        "User input reference",
-        "--target",
-        target,
-    ]
+    pyparsing_path = target.joinpath("plumbing", "pyparsing")
+    if os.path.isdir(pyparsing_path):
+        print(f"{pyparsing_path} already exists. Please delete this directory to run the script.")
+    else:
+        cmd = [
+            "parselglossy",
+            "generate",
+            "--template",
+            "template.yml",
+            "--docfile",
+            "user_ref.rst",
+            "--doc-header",
+            "User input reference",
+            "--target",
+            target,
+        ]
 
-    subprocess.call(cmd)
+        subprocess.call(cmd)
 
 
 def update_doc():

python/template.yml

@@ -711,6 +711,11 @@ sections:
           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".
+      - name: guess_rotate
+        type: bool
+        default: true
+        docstring: |
+          Localize/Diagonalize the initial guess orbitals before calculating the initial guess energy.
   - name: Response
     docstring: |
       Includes parameters related to the response SCF optimization.

src/driver.cpp

@@ -405,6 +405,7 @@ bool driver::scf::guess_energy(const json &json_guess, Molecule &mol, FockBuilde
     auto environment = json_guess["environment"];
     auto external_field = json_guess["external_field"];
     auto localize = json_guess["localize"];
+    auto rotate = json_guess["rotate"];
 
     mrcpp::print::separator(0, '~');
     print_utils::text(0, "Calculation    ", "Compute initial energy");
@@ -425,14 +426,14 @@ bool driver::scf::guess_energy(const json &json_guess, Molecule &mol, FockBuilde
     auto &F_mat = mol.getFockMatrix();
 
     F_mat = ComplexMatrix::Zero(Phi.size(), Phi.size());
-    if (localize) orbital::localize(prec, Phi, F_mat);
+    if (localize && rotate) orbital::localize(prec, Phi, F_mat);
 
     F.setup(prec);
     F_mat = F(Phi, Phi);
     mol.getSCFEnergy() = F.trace(Phi, nucs);
     F.clear();
 
-    if (not localize) orbital::diagonalize(prec, Phi, F_mat);
+    if (not localize && rotate) orbital::diagonalize(prec, Phi, F_mat);
     if (plevel == 1) mrcpp::print::footer(1, t_scf, 2);
 
     Timer t_eps;