Merge branch 'main' into jack

Author: Jacklaw441

.DS_Store

@@ -4,37 +4,42 @@
 How to reference EFP
 ********************
 
-* The paper describing the original implementation of EFP1 (EFP version for water solvent) method in GAMESS:
-`The first EFP paper (1996) <https://doi.org/10.1063/1.472045>`_
+* The original implementation of EFP1 (EFP version for water solvent) method in GAMESS:
+  
+  `The first EFP paper (1996) <https://doi.org/10.1063/1.472045>`_
 
- Paul N. Day, Jan H. Jensen, Mark S. Gordon, Simon P. Webb, Walter J. Stevens, Morris Krauss, David Garmer, Harold Basch, Drora Cohen. An effective fragment method for modeling solvent effects in quantum mechanical calculations. J. Chem. Phys. **1996**, 105 (5), 1968–1986.
+  Paul N. Day, Jan H. Jensen, Mark S. Gordon, Simon P. Webb, Walter J. Stevens, Morris Krauss, David Garmer, Harold Basch, Drora Cohen. An effective fragment method for modeling solvent effects in quantum mechanical calculations. J. Chem. Phys. **1996**, 105 (5), 1968–1986.
 
 * The original description of the EFP2 (general EFP) model:
-`2001 Feature Article <https://doi.org/10.1021/jp002747h>`_
+  
+  `2001 Feature Article <https://doi.org/10.1021/jp002747h>`_
+  
+  Mark S. Gordon, Mark A. Freitag, Pradipta Bandyopadhyay, Jan H. Jensen, Visvaldas Kairys, and Walter J. Stevens. The Effective Fragment Potential Method:  A QM-Based MM Approach to Modeling Environmental Effects in Chemistry. J. Phys. Chem. A **2001** 105 (2), 293-307
 
- Mark S. Gordon, Mark A. Freitag, Pradipta Bandyopadhyay, Jan H. Jensen, Visvaldas Kairys, and Walter J. Stevens. The Effective Fragment Potential Method:  A QM-Based MM Approach to Modeling Environmental Effects in Chemistry. J. Phys. Chem. A **2001** 105 (2), 293-307
-
-* A more recent review of the EFP2 model:
-`2013 review of EFP2 developments <http://dx.doi.org/10.1146/annurev-physchem-040412-110031>`_
-
- Mark S. Gordon,  Quentin A. Smith, Peng Xu, Lyudmila V. Slipchenko. Accurate First Principles Model Potentials for Intermolecular Interactions. Ann. Rev. Phys. Chem. **2013** 64, 553-578.
+* A more recent review of the EFP2 model: 
+  
+  `2013 review of EFP2 developments <http://dx.doi.org/10.1146/annurev-physchem-040412-110031>`_
+  
+  Mark S. Gordon,  Quentin A. Smith, Peng Xu, Lyudmila V. Slipchenko. Accurate First Principles Model Potentials for Intermolecular Interactions. Ann. Rev. Phys. Chem. **2013** 64, 553-578.
 
 * Excited states QM/EFP models in GAMESS:
-`2011 review of excited state QM/EFP models and applications <http://dx.doi.org/10.1021/jz200947j>`_
-
- Albert DeFusco, Noriyuki Minezawa, Lyudmila V. Slipchenko, Federico Zahariev, and Mark S. Gordon. Modeling Solvent Effects on Electronic Excited States. J. Phys. Chem. Lett. **2011** 2 (17), 2184-2192.
+  
+  `2011 review of excited state QM/EFP models and applications <http://dx.doi.org/10.1021/jz200947j>`_
+  
+  Albert DeFusco, Noriyuki Minezawa, Lyudmila V. Slipchenko, Federico Zahariev, and Mark S. Gordon. Modeling Solvent Effects on Electronic Excited States. J. Phys. Chem. Lett. **2011** 2 (17), 2184-2192.
 
 * CIS, CIS(D) and EOM-CCSD /EFP models in Q-Chem:
-`EOM-CCSD and CIS(D) QM/EFP models <http://dx.doi.org/10.1021/jp101797a>`_
-
- Lyudmila V. Slipchenko. Solvation of the Excited States of Chromophores in Polarizable Environment: Orbital Relaxation versus Polarization. J. Phys. Chem. A **2010** 114 (33), 8824-8830.
+  
+  `EOM-CCSD and CIS(D) QM/EFP models <http://dx.doi.org/10.1021/jp101797a>`_
+  
+  Lyudmila V. Slipchenko. Solvation of the Excited States of Chromophores in Polarizable Environment: Orbital Relaxation versus Polarization. J. Phys. Chem. A **2010** 114 (33), 8824-8830.
 
 * If you use LibEFP library and/or EFP implementation in Q-Chem, please cite:
-
-`Original LibEFP paper <http://dx.doi.org/10.1002/jcc.23375>`_
-
- Ilya A. Kaliman, Lyudmila V. Slipchenko. LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library. J. Comput. Chem. **2013** 34, 2284–2292.
-
-`Parallel implementation of LibEFP <http://dx.doi.org/10.1002/jcc.23772>`_
-
- Ilya A. Kaliman, Lyudmila V. Slipchenko. Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library. J. Comput. Chem. **2015** 36, 129–135.
+  
+  `Original LibEFP paper <http://dx.doi.org/10.1002/jcc.23375>`_
+  
+  Ilya A. Kaliman, Lyudmila V. Slipchenko. LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library. J. Comput. Chem. **2013** 34, 2284–2292.
+  
+  `Parallel implementation of LibEFP <http://dx.doi.org/10.1002/jcc.23772>`_
+  
+  Ilya A. Kaliman, Lyudmila V. Slipchenko. Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library. J. Comput. Chem. **2015** 36, 129–135.

examples/parameters/.DS_Store doc/.DS_Storeexamples/parameters/.DS_Store renamed to doc/.DS_Store

@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'EFP documentation'
-copyright = '2020-2024'
+copyright = '2020-2025'
 author = 'Lyudmila Slipchenko'
 
 # The full version, including alpha/beta/rc tags
@@ -30,6 +30,9 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
+#extensions = [
+#    'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme',
+#]
 extensions = [
     'sphinx.ext.autosectionlabel', 'sphinx_rtd_theme', 'sphinx_panels',
 ]