MultiOptPy 1.21.0__tar.gz → 1.21.2__tar.gz

{multioptpy-1.21.0 → multioptpy-1.21.2/MultiOptPy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MultiOptPy
-Version: 1.21.0
+Version: 1.21.2
 Summary: Multifunctional geometry optimization tools for quantum chemical calculations.
 Author-email: ss0832 <highlighty876@gmail.com>
 License-Expression: GPL-3.0-or-later
@@ -20,6 +20,10 @@ Dynamic: license-file
 
 # MultiOptPy
 
+**Status: Maintenance Mode**
+This project is currently in maintenance mode following the release of version 1.21.0. Version 1.21.0 represents the most recent stable release, incorporating the latest structural optimization algorithms and interface modifications developed within this framework. Active development of new functionalities is suspended. Future updates may be limited to specific bug fixes or dependency adjustments, and the frequency of these updates is undetermined. The repository remains accessible under the GNU Affero General Public License v3.0. Users seeking to implement new features or modify existing algorithms are advised to fork the codebase for independent development.
+
+
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1wpW8YO8r9gq20GACyzdaEsFK4Va1JQs4?usp=sharing) (Test 1, only use GFN2-xTB)
 
 
@@ -29,7 +33,7 @@ Dynamic: license-file
 [![Buy Me A Coffee](https://img.shields.io/badge/Buy%20Me%20a%20Coffee-ffdd00?style=for-the-badge&logo=buy-me-a-coffee&logoColor=black)](https://buymeacoffee.com/ss0832)
 
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/multioptpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/multioptpy)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18529521.svg)](https://doi.org/10.5281/zenodo.18529521)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18811289.svg)](https://doi.org/10.5281/zenodo.18811289)
 
 
 
@@ -156,8 +160,12 @@ References are given in the source code.
 
 ## Usage
 
-After downloading the repository using git clone or similar commands, move to the generated directory and run the following:
-python command
+1. Download the repository using git clone or similar commands, and navigate to the generated directory.
+
+2. Copy the corresponding .xyz file from the test directory and the .py file from the scripts directory.
+
+3. Run the following Python command:
+
 ```
 python optmain.py SN2.xyz -ma 150 1 6 -pyscf -elec 0 -spin 0 -opt rsirfo_block_fsb -modelhess
 ```
@@ -226,6 +234,12 @@ For relaxed scan (Similar to functions implemented in Gaussian)
 ```
 python relaxed_scan.py SN2.xyz -nsample 8 -scan bond 1,2 1.3,2.6 -elec -1 -spin 0 -xtb GFN2-xTB -opt crsirfo_block_fsb -modelhess
 ```
+For reaction network exploration
+```
+python run_mapper.py mapper_test.xyz -cfg config_mapper_test.json
+```
+Test of run_mapping.py (https://github.com/ss0832/mop_mapper_test/).
+
 ## Options
 (optmain.py)
 
@@ -412,15 +426,15 @@ If you use MultiOptPy in your research, please cite it as follows:
   author       = {ss0832},
   title        = {MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations},
   month        = dec,
-  year         = 2025,
+  year         = 2026,
   publisher    = {Zenodo},
-  version      = {v1.20.8},
-  doi          = {10.5281/zenodo.18529521},
-  url          = {https://doi.org/10.5281/zenodo.18529521}
+  version      = {v1.21.1},
+  doi          = {10.5281/zenodo.18811289},
+  url          = {https://doi.org/10.5281/zenodo.18811289}
 }
 ```
 ```
-ss0832. (2025). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.20.8). Zenodo. https://doi.org/10.5281/zenodo.18529521
+ss0832. (2026). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.21.1). Zenodo. https://doi.org/10.5281/zenodo.18811289
 ```
 
 ## Setting Up an Environment for Using NNP(UMA) on Windows 11
@@ -491,3 +505,4 @@ This enables **MultiOptPy** to use the **uma-s-1p1 NNP model**.
 conda env create -f environment_win11uma.yml
 conda activate test_mop_win11_uma
 ```
+

{multioptpy-1.21.0 → multioptpy-1.21.2}/MultiOptPy.egg-info/SOURCES.txt

@@ -8,7 +8,6 @@ MultiOptPy.egg-info/entry_points.txt
 MultiOptPy.egg-info/requires.txt
 MultiOptPy.egg-info/top_level.txt
 multioptpy/__init__.py
-multioptpy/entrypoints.py
 multioptpy/fileio.py
 multioptpy/ieip.py
 multioptpy/interface.py
@@ -46,6 +45,13 @@ multioptpy/Constraint/constraint_condition.py
 multioptpy/Coordinate/__init__.py
 multioptpy/Coordinate/polar_coordinate.py
 multioptpy/Coordinate/redundant_coordinate.py
+multioptpy/Entrypoints/__init__.py
+multioptpy/Entrypoints/autots.py
+multioptpy/Entrypoints/conformation_search.py
+multioptpy/Entrypoints/core.py
+multioptpy/Entrypoints/mapper.py
+multioptpy/Entrypoints/orientation_search.py
+multioptpy/Entrypoints/relaxed_scan.py
 multioptpy/IRC/__init__.py
 multioptpy/IRC/converge_criteria.py
 multioptpy/IRC/dvv.py
@@ -109,19 +115,10 @@ multioptpy/ModelHessian/swartd2.py
 multioptpy/ModelHessian/swartd3.py
 multioptpy/ModelHessian/swartd4.py
 multioptpy/ModelHessian/tshess.py
-multioptpy/Optimizer/QHAdam.py
 multioptpy/Optimizer/__init__.py
 multioptpy/Optimizer/abc_fire.py
 multioptpy/Optimizer/adabelief.py
-multioptpy/Optimizer/adabound.py
-multioptpy/Optimizer/adadelta.py
-multioptpy/Optimizer/adaderivative.py
-multioptpy/Optimizer/adadiff.py
-multioptpy/Optimizer/adafactor.py
 multioptpy/Optimizer/adam.py
-multioptpy/Optimizer/adamax.py
-multioptpy/Optimizer/adamod.py
-multioptpy/Optimizer/adamw.py
 multioptpy/Optimizer/adiis.py
 multioptpy/Optimizer/afire_neb.py
 multioptpy/Optimizer/block_hessian_update.py
@@ -134,7 +131,6 @@ multioptpy/Optimizer/crsirfo.py
 multioptpy/Optimizer/dic_rsirfo.py
 multioptpy/Optimizer/ediis.py
 multioptpy/Optimizer/eve.py
-multioptpy/Optimizer/fastadabelief.py
 multioptpy/Optimizer/fire.py
 multioptpy/Optimizer/fire2.py
 multioptpy/Optimizer/fire_neb.py
@@ -147,7 +143,6 @@ multioptpy/Optimizer/gpr_step.py
 multioptpy/Optimizer/gradientdescent.py
 multioptpy/Optimizer/gradientdescent_neb.py
 multioptpy/Optimizer/hessian_update.py
-multioptpy/Optimizer/hybrid_rfo.py
 multioptpy/Optimizer/kdiis.py
 multioptpy/Optimizer/lars.py
 multioptpy/Optimizer/lbfgs.py
@@ -156,25 +151,19 @@ multioptpy/Optimizer/linesearch.py
 multioptpy/Optimizer/lookahead.py
 multioptpy/Optimizer/mf_rsirfo.py
 multioptpy/Optimizer/mode_following.py
-multioptpy/Optimizer/nadam.py
 multioptpy/Optimizer/newton.py
 multioptpy/Optimizer/prodigy.py
 multioptpy/Optimizer/purtubation.py
 multioptpy/Optimizer/quickmin_neb.py
 multioptpy/Optimizer/radam.py
 multioptpy/Optimizer/rfo_neb.py
-multioptpy/Optimizer/ric_rfo.py
 multioptpy/Optimizer/rl_step.py
-multioptpy/Optimizer/rmspropgrave.py
 multioptpy/Optimizer/rsirfo.py
 multioptpy/Optimizer/rsprfo.py
-multioptpy/Optimizer/sadam.py
-multioptpy/Optimizer/samsgrad.py
 multioptpy/Optimizer/tr_lbfgs.py
 multioptpy/Optimizer/trim.py
 multioptpy/Optimizer/trust_radius.py
 multioptpy/Optimizer/trust_radius_neb.py
-multioptpy/Optimizer/yogi.py
 multioptpy/OtherMethod/__init__.py
 multioptpy/OtherMethod/addf.py
 multioptpy/OtherMethod/dimer.py
@@ -245,6 +234,7 @@ multioptpy/Utils/bond_connectivity.py
 multioptpy/Utils/calc_tools.py
 multioptpy/Utils/oniom.py
 multioptpy/Utils/pbc.py
+multioptpy/Utils/rcmc.py
 multioptpy/Utils/riemann_curvature.py
 multioptpy/Utils/symmetry_analyzer.py
 multioptpy/Visualization/__init__.py

multioptpy-1.21.2/MultiOptPy.egg-info/entry_points.txt

@@ -0,0 +1,11 @@
+[console_scripts]
+confsearch = multioptpy.Entrypoints:run_confsearch
+ieipmain = multioptpy.Entrypoints:run_ieipmain
+mdmain = multioptpy.Entrypoints:run_mdmain
+nebmain = multioptpy.Entrypoints:run_nebmain
+optmain = multioptpy.Entrypoints:run_optmain
+orientsearch = multioptpy.Entrypoints:run_orientsearch
+relaxedscan = multioptpy.Entrypoints:run_relaxedscan
+run_autots = multioptpy.Entrypoints:run_autots
+run_mapper = multioptpy.Entrypoints:run_mapper
+run_rcmc = multioptpy.Entrypoints:run_rcmc

{multioptpy-1.21.0/MultiOptPy.egg-info → multioptpy-1.21.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MultiOptPy
-Version: 1.21.0
+Version: 1.21.2
 Summary: Multifunctional geometry optimization tools for quantum chemical calculations.
 Author-email: ss0832 <highlighty876@gmail.com>
 License-Expression: GPL-3.0-or-later
@@ -20,6 +20,10 @@ Dynamic: license-file
 
 # MultiOptPy
 
+**Status: Maintenance Mode**
+This project is currently in maintenance mode following the release of version 1.21.0. Version 1.21.0 represents the most recent stable release, incorporating the latest structural optimization algorithms and interface modifications developed within this framework. Active development of new functionalities is suspended. Future updates may be limited to specific bug fixes or dependency adjustments, and the frequency of these updates is undetermined. The repository remains accessible under the GNU Affero General Public License v3.0. Users seeking to implement new features or modify existing algorithms are advised to fork the codebase for independent development.
+
+
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1wpW8YO8r9gq20GACyzdaEsFK4Va1JQs4?usp=sharing) (Test 1, only use GFN2-xTB)
 
 
@@ -29,7 +33,7 @@ Dynamic: license-file
 [![Buy Me A Coffee](https://img.shields.io/badge/Buy%20Me%20a%20Coffee-ffdd00?style=for-the-badge&logo=buy-me-a-coffee&logoColor=black)](https://buymeacoffee.com/ss0832)
 
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/multioptpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/multioptpy)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18529521.svg)](https://doi.org/10.5281/zenodo.18529521)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18811289.svg)](https://doi.org/10.5281/zenodo.18811289)
 
 
 
@@ -156,8 +160,12 @@ References are given in the source code.
 
 ## Usage
 
-After downloading the repository using git clone or similar commands, move to the generated directory and run the following:
-python command
+1. Download the repository using git clone or similar commands, and navigate to the generated directory.
+
+2. Copy the corresponding .xyz file from the test directory and the .py file from the scripts directory.
+
+3. Run the following Python command:
+
 ```
 python optmain.py SN2.xyz -ma 150 1 6 -pyscf -elec 0 -spin 0 -opt rsirfo_block_fsb -modelhess
 ```
@@ -226,6 +234,12 @@ For relaxed scan (Similar to functions implemented in Gaussian)
 ```
 python relaxed_scan.py SN2.xyz -nsample 8 -scan bond 1,2 1.3,2.6 -elec -1 -spin 0 -xtb GFN2-xTB -opt crsirfo_block_fsb -modelhess
 ```
+For reaction network exploration
+```
+python run_mapper.py mapper_test.xyz -cfg config_mapper_test.json
+```
+Test of run_mapping.py (https://github.com/ss0832/mop_mapper_test/).
+
 ## Options
 (optmain.py)
 
@@ -412,15 +426,15 @@ If you use MultiOptPy in your research, please cite it as follows:
   author       = {ss0832},
   title        = {MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations},
   month        = dec,
-  year         = 2025,
+  year         = 2026,
   publisher    = {Zenodo},
-  version      = {v1.20.8},
-  doi          = {10.5281/zenodo.18529521},
-  url          = {https://doi.org/10.5281/zenodo.18529521}
+  version      = {v1.21.1},
+  doi          = {10.5281/zenodo.18811289},
+  url          = {https://doi.org/10.5281/zenodo.18811289}
 }
 ```
 ```
-ss0832. (2025). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.20.8). Zenodo. https://doi.org/10.5281/zenodo.18529521
+ss0832. (2026). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.21.1). Zenodo. https://doi.org/10.5281/zenodo.18811289
 ```
 
 ## Setting Up an Environment for Using NNP(UMA) on Windows 11
@@ -491,3 +505,4 @@ This enables **MultiOptPy** to use the **uma-s-1p1 NNP model**.
 conda env create -f environment_win11uma.yml
 conda activate test_mop_win11_uma
 ```
+

{multioptpy-1.21.0 → multioptpy-1.21.2}/README.md

@@ -1,5 +1,9 @@
 # MultiOptPy
 
+**Status: Maintenance Mode**
+This project is currently in maintenance mode following the release of version 1.21.0. Version 1.21.0 represents the most recent stable release, incorporating the latest structural optimization algorithms and interface modifications developed within this framework. Active development of new functionalities is suspended. Future updates may be limited to specific bug fixes or dependency adjustments, and the frequency of these updates is undetermined. The repository remains accessible under the GNU Affero General Public License v3.0. Users seeking to implement new features or modify existing algorithms are advised to fork the codebase for independent development.
+
+
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1wpW8YO8r9gq20GACyzdaEsFK4Va1JQs4?usp=sharing) (Test 1, only use GFN2-xTB)
 
 
@@ -9,7 +13,7 @@
 [![Buy Me A Coffee](https://img.shields.io/badge/Buy%20Me%20a%20Coffee-ffdd00?style=for-the-badge&logo=buy-me-a-coffee&logoColor=black)](https://buymeacoffee.com/ss0832)
 
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/multioptpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/multioptpy)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18529521.svg)](https://doi.org/10.5281/zenodo.18529521)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18811289.svg)](https://doi.org/10.5281/zenodo.18811289)
 
 
 
@@ -136,8 +140,12 @@ References are given in the source code.
 
 ## Usage
 
-After downloading the repository using git clone or similar commands, move to the generated directory and run the following:
-python command
+1. Download the repository using git clone or similar commands, and navigate to the generated directory.
+
+2. Copy the corresponding .xyz file from the test directory and the .py file from the scripts directory.
+
+3. Run the following Python command:
+
 ```
 python optmain.py SN2.xyz -ma 150 1 6 -pyscf -elec 0 -spin 0 -opt rsirfo_block_fsb -modelhess
 ```
@@ -206,6 +214,12 @@ For relaxed scan (Similar to functions implemented in Gaussian)
 ```
 python relaxed_scan.py SN2.xyz -nsample 8 -scan bond 1,2 1.3,2.6 -elec -1 -spin 0 -xtb GFN2-xTB -opt crsirfo_block_fsb -modelhess
 ```
+For reaction network exploration
+```
+python run_mapper.py mapper_test.xyz -cfg config_mapper_test.json
+```
+Test of run_mapping.py (https://github.com/ss0832/mop_mapper_test/).
+
 ## Options
 (optmain.py)
 
@@ -392,15 +406,15 @@ If you use MultiOptPy in your research, please cite it as follows:
   author       = {ss0832},
   title        = {MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations},
   month        = dec,
-  year         = 2025,
+  year         = 2026,
   publisher    = {Zenodo},
-  version      = {v1.20.8},
-  doi          = {10.5281/zenodo.18529521},
-  url          = {https://doi.org/10.5281/zenodo.18529521}
+  version      = {v1.21.1},
+  doi          = {10.5281/zenodo.18811289},
+  url          = {https://doi.org/10.5281/zenodo.18811289}
 }
 ```
 ```
-ss0832. (2025). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.20.8). Zenodo. https://doi.org/10.5281/zenodo.18529521
+ss0832. (2026). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.21.1). Zenodo. https://doi.org/10.5281/zenodo.18811289
 ```
 
 ## Setting Up an Environment for Using NNP(UMA) on Windows 11
@@ -471,3 +485,4 @@ This enables **MultiOptPy** to use the **uma-s-1p1 NNP model**.
 conda env create -f environment_win11uma.yml
 conda activate test_mop_win11_uma
 ```
+

{multioptpy-1.21.0 → multioptpy-1.21.2}/multioptpy/Calculator/ase_calculation_tools.py

@@ -80,7 +80,7 @@ class Calculation:
         self.FUNCTIONAL = kwarg.get("FUNCTIONAL", "PBE")
         self.BASIS_SET = kwarg.get("BASIS_SET", "6-31G(d)")
         self.FC_COUNT = kwarg.get("FC_COUNT", 1)
-        self.BPA_FOLDER_DIRECTORY = kwarg.get("BPA_FOLDER_DIRECTORY", None)
+        self.BPA_FOLDER_DIRECTORY = kwarg.get("BPA_FOLDER_DIRECTORY", "./")
         self.Model_hess = kwarg.get("Model_hess", None)
         self.unrestrict = kwarg.get("unrestrict", None)
         self.software_type = kwarg.get("software_type", None)

{multioptpy-1.21.0 → multioptpy-1.21.2}/multioptpy/Calculator/pyscf_calculation_tools.py

@@ -42,7 +42,7 @@ class Calculation:
         self.SET_MEMORY = kwarg.get("SET_MEMORY", "4GB")
         self.FUNCTIONAL = kwarg.get("FUNCTIONAL", "b3lyp")
         self.FC_COUNT = kwarg.get("FC_COUNT", 1)
-        self.BPA_FOLDER_DIRECTORY = kwarg.get("BPA_FOLDER_DIRECTORY", None)
+        self.BPA_FOLDER_DIRECTORY = kwarg.get("BPA_FOLDER_DIRECTORY", "./")
         self.Model_hess = kwarg.get("Model_hess", None)
         self.electronic_charge = kwarg.get("electronic_charge", 0)
         self.spin_multiplicity = kwarg.get("spin_multiplicity", 1)

{multioptpy-1.21.0 → multioptpy-1.21.2}/multioptpy/Calculator/tblite_calculation_tools.py

@@ -36,7 +36,7 @@ class Calculation:
         self.START_FILE = kwarg.get("START_FILE", None)
         self.N_THREAD = kwarg.get("N_THREAD", 1)
         self.SET_MEMORY = kwarg.get("SET_MEMORY", "2GB")
-        self.FUNCTIONAL = kwarg.get("FUNCTIONAL", None) # Used for method selection if needed
+        self.FUNCTIONAL = kwarg.get("FUNCTIONAL", None)
         self.FC_COUNT = kwarg.get("FC_COUNT", 1)
         self.BPA_FOLDER_DIRECTORY = kwarg.get("BPA_FOLDER_DIRECTORY", "./")
         self.Model_hess = kwarg.get("Model_hess", None)
@@ -45,14 +45,19 @@ class Calculation:
         self.hessian_flag = False
         self.cpcm_solv_model = kwarg.get("cpcm_solv_model", None)
         self.alpb_solv_model = kwarg.get("alpb_solv_model", None)
-        self.method = kwarg.get("method", "GFN2-xTB") # Default method
+        self.method = kwarg.get("method", "GFN2-xTB")
         self.verbosity = 0
         self.numerical_delivative_delta = 0.0001
 
+        # --- OPTIMIZATION: Enforce Thread Count for tblite/OpenMP ---
+        os.environ["OMP_NUM_THREADS"] = str(self.N_THREAD)
+        os.environ["MKL_NUM_THREADS"] = str(self.N_THREAD)
+        os.environ["OPENBLAS_NUM_THREADS"] = str(self.N_THREAD)
+
     def _get_calculator(self, positions_bohr, element_numbers, charge, uhf):
         """Internal helper to create Calculator instance"""
         calc = Calculator(self.method, element_numbers, positions_bohr, charge=charge, uhf=uhf)
-        calc.set("max-iter", 500) # Or dynamic based on atoms
+        calc.set("max-iter", 500)
         calc.set("verbosity", self.verbosity)
         
         if self.cpcm_solv_model is not None:
@@ -65,92 +70,68 @@ class Calculation:
     def run_calculation(self, positions_bohr, element_number_list, charge_mult):
         """
         Execute TBLite calculation for a single geometry.
-        
-        Args:
-            positions_bohr (np.ndarray): Coordinates in Bohr.
-            element_number_list (np.ndarray): Array of atomic numbers.
-            charge_mult (list): [charge, multiplicity].
-            
-        Returns:
-            tuple: (energy, gradient)
         """
         charge = int(charge_mult[0])
         mult = int(charge_mult[1])
-        # xTB logic: uhf is number of unpaired electrons (mult - 1)
         uhf = max(mult - 1, 0)
         
-        # Override uhf if unrestrict flag is set but mult is 1 (though usually 0 for singlet)
         if self.unrestrict and uhf == 0:
-             # Logic depends on specific needs, usually 0 is fine for RHF/RKS equivalent
              pass
 
         calc = self._get_calculator(positions_bohr, element_number_list, charge, uhf)
         
-        # Execute
         res = calc.singlepoint()
         e = float(res.get("energy"))
         g = res.get("gradient") # Hartree/Bohr
         
-        np.save(self.BPA_FOLDER_DIRECTORY+"raw_grad.npy", g)
-        
-        self.res = res # Store full result for later access to orbitals, etc.
+        np.save(os.path.join(self.BPA_FOLDER_DIRECTORY, "raw_grad.npy"), g)
+        self.res = res 
         
         return e, g
 
     def numerical_hessian(self, geom_num_list, element_number_list, electric_charge_and_multiplicity):
         """
         Compute numerical Hessian using finite difference of gradients.
+        (Highly optimized O(N) evaluation with 1D loop and in-place modification)
         """
         n_atoms = len(geom_num_list)
         hessian = np.zeros((3 * n_atoms, 3 * n_atoms))
         
         charge = int(electric_charge_and_multiplicity[0])
-        uhf = int(electric_charge_and_multiplicity[1]) - 1
-
-        # Pre-calculation setup
-        # Note: Optimization opportunity - parallelize this loop if possible in future
-        count = 0
-        for atom_num in range(n_atoms):
-            for i in range(3): # x, y, z
-                for atom_num_2 in range(n_atoms):
-                    for j in range(3):
-                        # Symmetric check to avoid double calculation
-                        if count > 3 * atom_num_2 + j:
-                            continue
-                        
-                        tmp_grad = []
-                        for direction in [1, -1]:
-                            # Perturb geometry
-                            perturbed_geom = copy.copy(geom_num_list)
-                            perturbed_geom[atom_num][i] += direction * self.numerical_delivative_delta
-                            
-                            calc = self._get_calculator(perturbed_geom, element_number_list, charge, uhf)
-                            res = calc.singlepoint()
-                            g = res.get("gradient")
-                            tmp_grad.append(g[atom_num_2][j])
-                        
-                        # Central difference
-                        val = (tmp_grad[0] - tmp_grad[1]) / (2 * self.numerical_delivative_delta)
-                        hessian[3*atom_num+i][3*atom_num_2+j] = val
-                        hessian[3*atom_num_2+j][3*atom_num+i] = val
-                        
-                count += 1
+        uhf = max(int(electric_charge_and_multiplicity[1]) - 1, 0)
+        delta = self.numerical_delivative_delta
+        
+        
+        geom = np.array(geom_num_list, dtype=float)
+
+        for j in range(3 * n_atoms):
+            atom = j // 3
+            coord = j % 3
+
+            
+            geom[atom, coord] += delta
+            calc_plus = self._get_calculator(geom, element_number_list, charge, uhf)
+            grad_plus = calc_plus.singlepoint().get("gradient").flatten()
+
+           
+            geom[atom, coord] -= 2 * delta
+            calc_minus = self._get_calculator(geom, element_number_list, charge, uhf)
+            grad_minus = calc_minus.singlepoint().get("gradient").flatten()
+
+           
+            geom[atom, coord] += delta
+
+          
+            hessian[:, j] = (grad_plus - grad_minus) / (2 * delta)
+
+        
+        hessian = (hessian + hessian.T) / 2.0
         return hessian
 
     def calc_exact_hess(self, positions_bohr, element_number_list, charge_mult):
-        """
-        Calculate Exact Hessian (Numerical) and project out TR modes.
-        """
-        # Compute raw numerical Hessian
         exact_hess = self.numerical_hessian(positions_bohr, element_number_list, charge_mult)
-        np.save(self.BPA_FOLDER_DIRECTORY+"raw_hessian.npy", exact_hess)
-        # Project out Translation/Rotation
-        # Note: Calculationtools usually expects Bohr for projection if hessian is in au?
-        # Re-checking previous context: `project_out_hess_tr_and_rot_for_coord` seems to handle it.
-        # It takes `positions` which here are in Bohr.
+        np.save(os.path.join(self.BPA_FOLDER_DIRECTORY, "raw_hessian.npy"), exact_hess)
         
-        # Ensure element_number_list is a list for the tool if needed, or array
-        # The original code passed `element_number_list.tolist()`
         elem_list_arg = element_number_list.tolist() if isinstance(element_number_list, np.ndarray) else element_number_list
         
         exact_hess = Calculationtools().project_out_hess_tr_and_rot_for_coord(

multioptpy-1.21.2/multioptpy/Entrypoints/__init__.py

@@ -0,0 +1,25 @@
+from multioptpy.Entrypoints.core import (
+    run_optmain,
+    run_ieipmain,
+    run_mdmain,
+    run_nebmain,
+    run_rcmc,
+)
+from multioptpy.Entrypoints.relaxed_scan import run_relaxedscan
+from multioptpy.Entrypoints.orientation_search import run_orientsearch
+from multioptpy.Entrypoints.autots import run_autots
+from multioptpy.Entrypoints.conformation_search import run_confsearch
+from multioptpy.Entrypoints.mapper import run_mapper
+
+__all__ = [
+    "run_optmain",
+    "run_ieipmain",
+    "run_mdmain",
+    "run_nebmain",
+    "run_relaxedscan",
+    "run_orientsearch",
+    "run_autots",
+    "run_confsearch",
+    "run_mapper",
+    "run_rcmc",
+]