MultiOptPy 1.20.4__py3-none-any.whl → 1.20.6__py3-none-any.whl

multioptpy/moleculardynamics.py

@@ -119,35 +119,45 @@ class MD:
 
 
     def exec_md(self, TM, geom_num_list, prev_geom_num_list, B_g, B_e, pre_B_g, iter):
+        # Initialize SHAKE constraint if applicable
         if iter == 0 and len(self.constraint_condition_list) > 0:
             self.class_SHAKE = SHAKE(TM.delta_timescale, self.constraint_condition_list)
-        if self.mdtype == "nosehoover" or self.mdtype == "nvt": 
+        
+        # Execute Thermostat / Integrator
+        if self.mdtype in ["nosehoover", "nvt"]: 
             new_geometry = TM.Nose_Hoover_thermostat(geom_num_list, B_g)
         elif self.mdtype == "nosehooverchain": 
             new_geometry = TM.Nose_Hoover_chain_thermostat(geom_num_list, B_g)
-        elif self.mdtype == "velocityverlet" or self.mdtype == "nve":
+        
+        elif self.mdtype in ["langevin", "baoab"]:
+            new_geometry = TM.Langevin_thermostat(geom_num_list, B_g)
+        
+        elif self.mdtype in ["velocityverlet", "nve"]:
             new_geometry = TM.Velocity_Verlet(geom_num_list, B_g, pre_B_g, iter)
         else:
             print("Unexpected method.", self.mdtype)
-            raise
+            raise ValueError(f"Unknown MD type: {self.mdtype}")
         
+        # Apply SHAKE constraints
         if iter > 0 and len(self.constraint_condition_list) > 0:
-            
             new_geometry, tmp_momentum_list = self.class_SHAKE.run(new_geometry, prev_geom_num_list, TM.momentum_list, TM.element_list)
             TM.momentum_list = copy.copy(tmp_momentum_list)
 
-        kinetic_ene = 0.0
-        
-        for i in range(len(geom_num_list)):
-            kinetic_ene += np.sum(TM.momentum_list[i] ** 2) / (2 * atomic_mass(TM.element_list[i]))
+        # [Optimization] Calculate kinetic energy using vectorized method in Thermostat
+        kinetic_ene = TM.calc_tot_kinetic_energy()
         
         tot_energy = B_e + kinetic_ene
         print("hamiltonian :", tot_energy, "hartree")
         
         self.tot_energy_list.append(tot_energy)
         
+        # Apply Periodic Boundary Condition
         if len(self.pbc_box) > 0:
             new_geometry = apply_periodic_boundary_condition(new_geometry, TM.element_list, self.pbc_box)
+            # Ensure new_geometry remains a numpy array after PBC application
+            if not isinstance(new_geometry, np.ndarray):
+                new_geometry = np.array(new_geometry, dtype=np.float64)
+
         return new_geometry
 
 
@@ -221,11 +231,9 @@ class MD:
         #-----------------------------------
         with open(self.BPA_FOLDER_DIRECTORY+"input.txt", "w") as f:
             f.write(str(vars(self.args)))
-        pre_B_g = []
-
-        for i in range(len(element_list)):
-            pre_B_g.append(np.array([0,0,0], dtype="float64"))
-        pre_B_g = np.array(pre_B_g, dtype="float64")
+        
+        # [Optimization] Efficient initialization of pre_B_g
+        pre_B_g = np.zeros((len(element_list), 3), dtype=np.float64)
 
         #-------------------------------------
         finish_frag = False

{multioptpy-1.20.4.dist-info → multioptpy-1.20.6.dist-info}/METADATA

@@ -1,21 +1,21 @@
 Metadata-Version: 2.4
 Name: MultiOptPy
-Version: 1.20.4
+Version: 1.20.6
 Summary: Multifunctional geometry optimization tools for quantum chemical calculations.
 Author-email: ss0832 <highlighty876@gmail.com>
-License: GPLv3
+License-Expression: GPL-3.0-or-later
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy~=2.2.0
+Requires-Dist: numpy>=2.2.0
 Requires-Dist: scipy>=1.13.0
-Requires-Dist: matplotlib~=3.10.0
+Requires-Dist: matplotlib>=3.10.0
 Requires-Dist: torch~=2.6.0
-Requires-Dist: pyscf~=2.9.0
-Requires-Dist: tblite~=0.4.0
+Requires-Dist: pyscf>=2.9.0
+Requires-Dist: tblite>=0.4.0
 Requires-Dist: ase~=3.26.0
 Requires-Dist: fairchem-core~=2.7.0
-Requires-Dist: sympy~=1.13.0
+Requires-Dist: sympy>=1.13.0
 Dynamic: license-file
 
 # MultiOptPy
@@ -29,7 +29,7 @@ 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.17970774.svg)](https://doi.org/10.5281/zenodo.17970774)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17973395.svg)](https://doi.org/10.5281/zenodo.17973395)
 
 If this tool helped your studies, education, or saved your time, I'd appreciate a coffee!
 Your support serves as a great encouragement for this personal project and fuels my next journey.
@@ -80,9 +80,9 @@ conda create -n test_mop python=3.12.7
 conda activate test_mop
 
 ## 3. Download and install MultiOptPy:
-wget https://github.com/ss0832/MultiOptPy/archive/refs/tags/v1.20.3.zip
-unzip v1.20.3.zip
-cd MultiOptPy-1.20.3
+wget https://github.com/ss0832/MultiOptPy/archive/refs/tags/v1.20.5.zip
+unzip v1.20.5.zip
+cd MultiOptPy-1.20.5
 pip install -r requirements.txt
 
 ## 4. Copy the test configuration file and run the AutoTS workflow:
@@ -107,10 +107,10 @@ python run_autots.py aldol_rxn.xyz -cfg config_autots_run_xtb_test.json
 # Installation via pip (Linux)
 conda create -n <env-name> python=3.12 pip
 conda activate <env-name>
-pip install git+https://github.com/ss0832/MultiOptPy.git@v1.20.3
-wget https://github.com/ss0832/MultiOptPy/archive/refs/tags/v1.20.3.zip
-unzip v1.20.3.zip
-cd MultiOptPy-1.20.3
+pip install git+https://github.com/ss0832/MultiOptPy.git@v1.20.5
+wget https://github.com/ss0832/MultiOptPy/archive/refs/tags/v1.20.5.zip
+unzip v1.20.5.zip
+cd MultiOptPy-1.20.5
 
 ## 💻 Command Line Interface (CLI) Functionality (v1.20.2)
 # The following eight core functionalities are available as direct executable commands in your terminal after installation:
@@ -157,7 +157,7 @@ References are given in the source code.
 After downloading the repository using git clone or similar commands, move to the generated directory and run the following:
 python command
 ```
-python optmain.py SN2.xyz -ma 150 1 6 -pyscf -elec 0 -spin 0 -opt rsirfo_block_fsb -modelhess
+python optmain.py SN2.xyz -ma 150 1 6 -pyscf -elec -1 -spin 0 -opt rsirfo_block_fsb -modelhess
 ```
 CLI command (arbitrary directory)
 ```
@@ -412,13 +412,13 @@ If you use MultiOptPy in your research, please cite it as follows:
   month        = dec,
   year         = 2025,
   publisher    = {Zenodo},
-  version      = {v1.20.3},
-  doi          = {10.5281/zenodo.17970774},
-  url          = {https://doi.org/10.5281/zenodo.17970774}
+  version      = {v1.20.4},
+  doi          = {10.5281/zenodo.17973395},
+  url          = {https://doi.org/10.5281/zenodo.17973395}
 }
 ```
 ```
-ss0832. (2025). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.20.3). Zenodo. https://doi.org/10.5281/zenodo.17970774
+ss0832. (2025). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.20.4). Zenodo. https://doi.org/10.5281/zenodo.17973395
 ```
 
 ## Setting Up an Environment for Using NNP(UMA) on Windows 11

{multioptpy-1.20.4.dist-info → multioptpy-1.20.6.dist-info}/RECORD

@@ -1,15 +1,15 @@
 multioptpy/__init__.py,sha256=OJ7BAhHT2pWsIdC5wZfhCA5J8zW-odvaym9ySpPZ3Hw,125
-multioptpy/entrypoints.py,sha256=rizxMJSbFq2aAKpcsPIy1CTIh_ZCGkDpCEEkvMOy6uc,39130
+multioptpy/entrypoints.py,sha256=JeAlyVHVGmPXRT9pIMdL5CfKRw6WZgzlYd02hZY8xK4,58482
 multioptpy/fileio.py,sha256=BJVhls9P_GU-ZB_nZgTgUPejru8-lJ1Qi-typHsG0WY,27175
-multioptpy/ieip.py,sha256=7zjvxW76k-5-tdgCpW0u4QzQBQtrLkcTYzNauhTX0qA,16182
-multioptpy/interface.py,sha256=t0wzrHhMxn4gV65NHoQ4_zbAVd6tCX0U87Z6sjvIXXc,81835
+multioptpy/ieip.py,sha256=XjN3ii1xVclXdSVb6g1gO1Q_7VtOBFR9jK7MjdFZrFM,16786
+multioptpy/interface.py,sha256=Xohjpk1ofcEmDygGg93dRh9Dzha6VjbtcefmcoXqoZE,82013
 multioptpy/irc.py,sha256=lTb1atfC5_QgW9a7FqQC-e-CXlTEhi1lms-zie_dEhI,20777
-multioptpy/moleculardynamics.py,sha256=FGA2fulBbNx26gCUSoauaOMoT0dIIddemXEiAoHC6p0,20359
+multioptpy/moleculardynamics.py,sha256=qSrHtQYZXIK-ji7HyZeReAjLhrB2k_1DrO6iOTuudog,20816
 multioptpy/neb.py,sha256=eQQsB8HrDOZ4rlvHOUIwfR52QNDvuhvH1am5h6K7Ho0,59339
 multioptpy/optimization.py,sha256=FBMueS5ChGCZvCHsY7S8hCLf4nrWvjNMcEfWfj8vIdU,101480
 multioptpy/optimizer.py,sha256=Nm6uDEMiv9u5_CPdhQYqGzwmCqHNzDIdYeYIn9z5EwM,42047
 multioptpy/Calculator/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-multioptpy/Calculator/ase_calculation_tools.py,sha256=gJsqUhv_JVv5_OrHbOD3IvSdfkJuRz4pQ14a_xmkknA,20143
+multioptpy/Calculator/ase_calculation_tools.py,sha256=TxLpUsXM2Cg3U4jUfquZzq6IhGz7FbLj1GO8nWijzzw,20830
 multioptpy/Calculator/dxtb_calculation_tools.py,sha256=s3LTuypTsfZEIrnkuOQUOCegfh9LCyUG0tI3zzYiliQ,16492
 multioptpy/Calculator/emt_calculation_tools.py,sha256=aq4I3yM0_A7PFCX2sB5qHfEoij2LP0cqYu_BQkMztMQ,21762
 multioptpy/Calculator/gpaw_calculation_tools.py,sha256=P2a8YSCzHvgSdvPS_HQo-liLkVBQ1ePr4tooHJm2aL4,8079
@@ -25,10 +25,11 @@ multioptpy/Calculator/ase_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm
 multioptpy/Calculator/ase_tools/fairchem.py,sha256=n7sZVEik1iw-gjTXyUx6uGQbJhn9FhhCJXatKQGK8oY,1627
 multioptpy/Calculator/ase_tools/gamess.py,sha256=OvRD5TGze--x-ZKqLPUAC78UwVlZwLDf-B4VoHrjp9I,904
 multioptpy/Calculator/ase_tools/gaussian.py,sha256=y4r64zX2o5zORUDt_h6SmnsBQ3wM8WQr7zP1XVmcw74,7829
+multioptpy/Calculator/ase_tools/gxtb_dev.py,sha256=cBWenNu4PYtgQ-kelwmMqJ0FK4WxnCd-IGOA_BxX-y0,1529
 multioptpy/Calculator/ase_tools/mace.py,sha256=AsyUkTFrOI-kSnDT4d7ehViQfCRT5fG8wdYUTn56RCw,928
 multioptpy/Calculator/ase_tools/mopac.py,sha256=RUMNikbmVxIvoTi4H8JU3fXY2vBu6BzPxcv0NPd_L-k,723
 multioptpy/Calculator/ase_tools/nwchem.py,sha256=0NPIaX1_mzkzLh_r9e3WJA6fEiNrksEbXFwbATHkNuw,1162
-multioptpy/Calculator/ase_tools/orca.py,sha256=-9D5bqzQzn9IkvbYGC-OJtJKbneGKFKQVBcOhldvfw8,1026
+multioptpy/Calculator/ase_tools/orca.py,sha256=JjTCvW3YT1KwaImkIxyd8FcUgz8BHO5ZFGHqiX3lJKc,10141
 multioptpy/Calculator/ase_tools/pygfn0.py,sha256=N-Rrtu8wvduPxRSGQMYK9LmQiWCtfCbkBOTXjhHK-gE,1468
 multioptpy/Constraint/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 multioptpy/Constraint/constraint_condition.py,sha256=wS14fYCzP1V4_d1HLElW3a6fxKfEEX3EjxPvvbRPhZ8,44202
@@ -52,7 +53,7 @@ multioptpy/Interpolation/linear_interpolation.py,sha256=9Nu3znsNKGWoYZ0gEWhhrwEi
 multioptpy/Interpolation/savitzky_golay_interpolation.py,sha256=MVUT8Rbe_8oN11FAPu99LeeJwOZ-C23wnLwiOo9f8Lc,12483
 multioptpy/Interpolation/spline_interpolation.py,sha256=n_HK4TDri2owAwcW_zyIxnZKpO96WcV8IvLhm0QPuB0,14746
 multioptpy/MD/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-multioptpy/MD/thermostat.py,sha256=CBC_LLuOqum6Gvk2uK23zUKF0qb8tjHhzi6CziJkQUs,8205
+multioptpy/MD/thermostat.py,sha256=z7WqlR7wzvSRk2IHXTHeWJj-PTW4083viEjNWLXIJd8,12232
 multioptpy/MEP/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 multioptpy/MEP/pathopt_bneb_force.py,sha256=k9ld8UJaWWOoU6yjTPGpE1kyx7V69W2k0QR23_lSnys,23826
 multioptpy/MEP/pathopt_dmf_force.py,sha256=69yCYIAIWyJmz6ouS6tZ5i7KVIyWwxEmwq_aqFUCSq8,21014
@@ -77,7 +78,7 @@ multioptpy/ModelHessian/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 multioptpy/ModelHessian/approx_hessian.py,sha256=efF8FA7lqBuw8h4DmkfU7T78yZiS5tQ_FhMm0CAseYE,6717
 multioptpy/ModelHessian/calc_params.py,sha256=aWkXqqyYpg5_qemflM2oIkFA8g-h3wTiE_C_a5dkLxc,7645
 multioptpy/ModelHessian/fischer.py,sha256=pdXmOMGF4Ie8cA3qN-KuyhJl_cuetvmpoI9t0fE3tNE,11011
-multioptpy/ModelHessian/fischerd3.py,sha256=zdmdEOqCWseY9VrroOZY9kOOIeBfJkhWlwDIBrgJwVI,16266
+multioptpy/ModelHessian/fischerd3.py,sha256=QWS-vWkHEzPLiMl8bAhd5A9BV1fKj8ym7GVVdZ8fg5M,13450
 multioptpy/ModelHessian/fischerd4.py,sha256=GuSwCjzMV8g6BHvX0DJjHr_8AfjVdrfNn5DO_BEdDj4,17070
 multioptpy/ModelHessian/gfn0xtb.py,sha256=xUipDBP_o9Y9bJ74RehCY06kroueStc0MsSm1llg638,27051
 multioptpy/ModelHessian/gfnff.py,sha256=INsTLJ2c7wEqk0mxn_lURsQ2JsT8dM6JClR2etEein8,31162
@@ -151,8 +152,8 @@ multioptpy/Optimizer/rfo_neb.py,sha256=gtgkW8ImC_-QZGpsYHmBgvstkoPuGedNUG6BFrfvM
 multioptpy/Optimizer/ric_rfo.py,sha256=xSDYTkOxQ8MytlSYo0z49Grd9-ZPcaJFbmHuqs7ePwI,33884
 multioptpy/Optimizer/rl_step.py,sha256=XARDUifWoVmcoXXbVvmVGxvNEyLA1DtfENGnliUuuTg,27344
 multioptpy/Optimizer/rmspropgrave.py,sha256=xUDXB1NKLljfc39NWXqc2-5NC-ux9bt58NpYlXb7LnM,2327
-multioptpy/Optimizer/rsirfo.py,sha256=wSiueMmcpP2ZTpOl8ziHvv2ijuzhT0M9qle_DMkLOY4,76994
-multioptpy/Optimizer/rsprfo.py,sha256=P_wQttq6cZ7XJvfkYIuW1IRpZBqImMgfCmpNwRCWPiI,49316
+multioptpy/Optimizer/rsirfo.py,sha256=IjJ2BDu0QL4cFWi04BBmTU5N7xPqnAIf2jkkO3GV8OM,81810
+multioptpy/Optimizer/rsprfo.py,sha256=MZs8yBO3z-jhBAxZYR1WaG5DOWEoBC_uYrHqourYh70,56180
 multioptpy/Optimizer/sadam.py,sha256=7FjyALhYqHCOKXrN06tzCiCuS1SWKIPh1bJEdORYXMk,1865
 multioptpy/Optimizer/samsgrad.py,sha256=QGL-Pv6A4pvgOAI-BGyNqci7X-GH2J98Wm2xsoJa2Zc,2016
 multioptpy/Optimizer/tr_lbfgs.py,sha256=3GK1meULSBkuCyJkJ7AvEBzq2cFu8sr6dx3GIePrlAw,26949
@@ -166,6 +167,7 @@ multioptpy/OtherMethod/dimer.py,sha256=54oqeExIqP_PPBpaZAwo59X11n6k1BgttpYIGKnJ7
 multioptpy/OtherMethod/elastic_image_pair.py,sha256=YSXjfrmHRRnl5YZ5JVZMLsDSCyfY911Q2F5qp6dj1rQ,33586
 multioptpy/OtherMethod/modelfunction.py,sha256=GX_YvA8rOzcKeaZcth6L-S0q9wdsTLA07E9sjOaFyRU,26168
 multioptpy/OtherMethod/newton_traj.py,sha256=gozEqyOCpD4zbYMf3IwPKIMC7v4D7ddXCu1MUz8tzxE,20154
+multioptpy/OtherMethod/spring_pair_method.py,sha256=6YdLCIO-OOt_Mzzf8JFFtWVYAIa1Tsdi1VCxEbbPuto,15577
 multioptpy/OtherMethod/twopshs.py,sha256=GmBLKTNK-HqFpVmGgwmrtw9-IOf_hPYlUTslx95Sl20,49969
 multioptpy/PESAnalyzer/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 multioptpy/PESAnalyzer/calc_irc_curvature.py,sha256=YVZBydXcYLfO0Y8ZYGS7WXokkORfVQaO6zPbXwhQJt4,4986
@@ -241,9 +243,9 @@ multioptpy/Wrapper/ieip_wrapper.py,sha256=H0Fa7x5mzyFu5rnig7GdcZGX9LFclzRxDuREX5
 multioptpy/Wrapper/md_wrapper.py,sha256=EGQKY8BwBbjWkXxKQGlelzht872OsUp9GmyxPDgWav4,3050
 multioptpy/Wrapper/neb_wrapper.py,sha256=ZOyHhuSDKA5hABnQB7PYPfbQ9OyaAj9KKBeKu_HLiY4,3254
 multioptpy/Wrapper/optimize_wrapper.py,sha256=b5DoiSb5Y4YjzYaSfxNa4A5QMn7_UzAvActPOpL78Ok,2667
-multioptpy-1.20.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-multioptpy-1.20.4.dist-info/METADATA,sha256=dG63R9Y4sXhoGbAjwINFbLarxvbM4eqBR81Y_pkyrPo,16690
-multioptpy-1.20.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-multioptpy-1.20.4.dist-info/entry_points.txt,sha256=u2Y0tgYMu7UyZumhLCfoME92lCQXhurAAsixL_B3caw,404
-multioptpy-1.20.4.dist-info/top_level.txt,sha256=_MXQNcS1xJbRbGnYUM-F_G-PlLK7wTIkuqx-EvfAhRc,11
-multioptpy-1.20.4.dist-info/RECORD,,
+multioptpy-1.20.6.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+multioptpy-1.20.6.dist-info/METADATA,sha256=wPARwptr8gTPYvTEG3kamkh_rOecyhJbNndyInlmngc,16713
+multioptpy-1.20.6.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+multioptpy-1.20.6.dist-info/entry_points.txt,sha256=u2Y0tgYMu7UyZumhLCfoME92lCQXhurAAsixL_B3caw,404
+multioptpy-1.20.6.dist-info/top_level.txt,sha256=_MXQNcS1xJbRbGnYUM-F_G-PlLK7wTIkuqx-EvfAhRc,11
+multioptpy-1.20.6.dist-info/RECORD,,

{multioptpy-1.20.4.dist-info → multioptpy-1.20.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any