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Author: ss0832

README.md

@@ -10,13 +10,13 @@ I also welcome contributions, bug reports, and pull requests to improve this too
 
 Note on Contributions: While bug reports and pull requests are welcome, please note that this is a personal project maintained in my spare time. Responses to issues and PRs may be delayed or not guaranteed. I appreciate your patience and understanding.
 
-Multifunctional geometry optimisation tools for quantum chemical calculations
+Multifunctional geometry optimization tools for quantum chemical calculations 
 
 This program implements many geometry optimization methods in Python for learning purposes.
 
 This program can also automatically calculate the transition-state structure from a single equilibrium geometry.
 
-Notice: This program has NOT been experimentally validated in laboratory settings. I release this code to enable community contributions and collaborative development. Use at your own discretion and validate results independently.
+**Notice:** This program has NOT been experimentally validated in laboratory settings. I release this code to enable community contributions and collaborative development. Use at your own discretion and validate results independently. 
 
 (Caution: Using Japanese to explain) Instructions on how to use: 
 - https://ss0832.github.io/
@@ -55,6 +55,7 @@ pip install -r requirements.txt
 cp test/config_autots_run_xtb_test.json .
 python run_autots.py aldol_rxn.xyz -cfg config_autots_run_xtb_test.json
 
+
 # Installation via environment.yml (Linux / conda-forge)
 
 ## 1. Download and install MultiOptPy:
@@ -72,12 +73,10 @@ python run_autots.py aldol_rxn.xyz -cfg config_autots_run_xtb_test.json
 ```
 
 ## Required Modules
-
 ```
 cd <directory of repository files>
 pip install -r requirements.txt
 ```
-
  - psi4 (Official page:https://psicode.org/) or PySCF 
  - numpy
  - matplotlib
@@ -89,7 +88,7 @@ Optional
  - tblite (If you use extended tight binding (xTB) method, this module is required.)
  - dxtb (same as above)
  - ASE 
-
+   
 ## References
 
 References are given in the source code.
@@ -99,20 +98,20 @@ 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 optmain.py SN2.xyz -ma 150 1 6
+python optmain.py SN2.xyz -ma 150 1 6 -pyscf -elec 0 -spin 0 -opt rsirfo_block_fsb -modelhess
 ```
 ```
-python optmain.py aldol_rxn.xyz -ma 95 1 5 50 3 11
+python optmain.py aldol_rxn.xyz -ma 95 1 5 50 3 11 -pyscf -elec 0 -spin 0 -opt rsirfo_block_fsb -modelhess
 ```
-For SADDLE calculation
+For SADDLE calculation 
 ```
-python optmain.py aldol_rxn_PT.xyz -xtb GFN2-xTB -opt rsirfo_bofill -order 1 -fc 5
+python optmain.py aldol_rxn_PT.xyz -xtb GFN2-xTB -opt RSIRFO_bofill -order 1 -fc 5
 ```
 
 For NEB method
 
 ```
-python nebmain.py aldol_rxn -xtb GFN2-xTB -ns 50 
+python nebmain.py aldol_rxn -xtb GFN2-xTB -ns 50 -adpred 1 -nd 0.5
 ```
 
 For iEIP method
@@ -157,8 +156,8 @@ Recommended optimization methods:
 
 - FIRE (Robust method)
 - TR_LBFGS (Limited-memory BFGS method with trust radius method, Faster convergence than FIRE without Hessian)
-- RSIRFO_FSB (can use quasi-Newton method)
-- RSIRFO_Bofill (for calculation of saddle point)
+- rsirfo_block_fsb 
+- rsirfo_block_bofill (for calculation of saddle point)
 
 `-ma`
 
@@ -311,11 +310,17 @@ Author of this program is ss0832.
 
 GNU Affero General Public License v3.0
 
+
+## Contact
+
+highlighty876[at]gmail.com
+
 ## Citation
 
 ss0832. (2025). MultiOptPy: Multifunctional geometry optimization tools for quantum chemical calculations (v1.20.0). Zenodo. https://doi.org/10.5281/zenodo.17759573
 
 
+
 ## Setting Up an Environment for Using NNP(UMA) on Windows 11
 
 ### 1. Install Anaconda
@@ -378,7 +383,9 @@ This enables **MultiOptPy-v1.20.0-rc.4** to use the **uma-s-1p1 NNP model**.
 - arXiv preprint arXiv:2505.08762 (2025).
 - https://github.com/facebookresearch/fairchem
 
-## Contact
-
-highlighty876[at]gmail.com
+## Create environment for Win11 / UMA(NNP) using conda
 
+```
+conda env create -f environment_win11uma.yml
+conda activate test_mop_win11_uma
+```

environment_win11uma.yml

@@ -0,0 +1,105 @@
+name: test_mop_win11_uma
+channels:
+ - conda-forge
+ - defaults
+dependencies:
+ - python=3.12.7
+ - pip
+ - setuptools
+ - wheel
+ - pip:
+     - absl-py==2.3.1
+     - annotated-types==0.7.0
+     - antlr4-python3-runtime==4.9.3
+     - ase==3.26.0
+     - ase-db-backends==0.10.0
+     - bibtexparser==1.4.3
+     - certifi==2025.8.3
+     - cffi==1.17.1
+     - charset-normalizer==3.4.2
+     - click==8.2.1
+     - cloudpickle==3.1.1
+     - clusterscope==0.0.12
+     - colorama==0.4.6
+     - contourpy==1.3.3
+     - cryptography==45.0.6
+     - cycler==0.12.1
+     - e3nn==0.5.6
+     - fairchem-core==2.7.1
+     - filelock==3.18.0
+     - fonttools==4.59.0
+     - fsspec==2025.7.0
+     - gitdb==4.0.12
+     - gitpython==3.1.45
+     - grpcio==1.74.0
+     - huggingface-hub==0.34.3
+     - hydra-core==1.3.2
+     - idna==3.10
+     - jax==0.7.2
+     - jaxlib==0.7.2
+     - jinja2==3.1.6
+     - joblib==1.5.1
+     - kiwisolver==1.4.8
+     - llvmlite==0.44.0
+     - lmdb==1.7.3
+     - markdown==3.8.2
+     - markupsafe==3.0.2
+     - matplotlib==3.10.5
+     - ml-dtypes==0.5.3
+     - monty==2025.3.3
+     - mpmath==1.3.0
+     - mypy-extensions==1.1.0
+     - narwhals==2.0.1
+     - networkx==3.5
+     - numba==0.61.2
+     - numpy==2.2.6
+     - omegaconf==2.3.0
+     - opt-einsum==3.4.0
+     - opt-einsum-fx==0.1.4
+     - orjson==3.11.1
+     - packaging==25.0
+     - palettable==3.3.3
+     - pandas==2.3.1
+     - pillow==11.3.0
+     - platformdirs==4.3.8
+     - plotly==6.2.0
+     - protobuf==6.31.1
+     - psutil==7.0.0
+     - psycopg2-binary==2.9.10
+     - pycparser==2.22
+     - pydantic==2.11.7
+     - pydantic-core==2.33.2
+     - pygfn0==0.0.3
+     - pymatgen==2025.10.7
+     - pymysql==1.1.1
+     - pyparsing==3.2.3
+     - pyre-extensions==0.0.32
+     - python-dateutil==2.9.0.post0
+     - pytz==2025.2
+     - pyyaml==6.0.2
+     - requests==2.32.4
+     - ruamel-yaml==0.18.14
+     - ruamel-yaml-clib==0.2.12
+     - scipy==1.16.3
+     - sella==2.3.5
+     - sentry-sdk==2.34.1
+     - six==1.17.0
+     - smmap==5.0.2
+     - spglib==2.6.0
+     - submitit==1.5.3
+     - sympy==1.13.1
+     - tabulate==0.9.0
+     - tensorboard==2.20.0
+     - tensorboard-data-server==0.7.2
+     - torch==2.6.0
+     - torchtnt==0.2.4
+     - tqdm==4.67.1
+     - typing-extensions==4.14.1
+     - typing-inspect==0.9.0
+     - typing-inspection==0.4.1
+     - tzdata==2025.2
+     - uncertainties==3.2.3
+     - urllib3==2.5.0
+     - wandb==0.21.0
+     - websockets==15.0.1
+     - werkzeug==3.1.3