Merge pull request #44 from molssi-seamm/dev

Corrected the references in the ReaxFF files.

Author: seamm

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2025.5.26.1 -- Corrected the references in the ReaxFF files.
+   * The references in the ReaxFF forcefields included with the release were not
+     correctly formatted so were being ignored.
+
 2025.5.26 -- Updated the OPLS-AA forcefield file to allow personal versions
    * Updated the OPLS-AA forcefield to support an optional local user file
      'my_oplsaa.frc' to add to or override parameters in the main file.

forcefield_step/data/reaxff/CHLiOFSi_Yun_2017.frc

@@ -306,7 +306,7 @@ ReaxFF forcefield translated from Reax format
 Reactive MD-force field: C/H/O/Si/Li/F force field Apr 2017
 
 
-@article{10.1021/acs.jpclett.7b00898, 
+@bibtex @article{10.1021/acs.jpclett.7b00898, 
 year = {2017}, 
 title = {{Simulation Protocol for Prediction of a Solid-Electrolyte Interphase on the Silicon-based Anodes of a Lithium-Ion Battery: ReaxFF Reactive Force Field}}, 
 author = {Yun, Kang-Seop and Pai, Sung Jin and Yeo, Byung Chul and Lee, Kwang-Ryeol and Kim, Sun-Jae and Han, Sang Soo}, 

forcefield_step/data/reaxff/CHNOFSClNiPt_FC_2013.frc

@@ -443,7 +443,7 @@ From LAMMPS examples/reaxff/FC
 
 DATE: 2013-06-28 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Singh, Phys Rev B 87, 104114 (2013) COMMENT: Reactive MD-force field: Singh, Phys. Rev. B 87, 104114 (2013)
 
-@article{PhysRevB.87.104114,
+@bibtex @article{PhysRevB.87.104114,
   title = {Thermal properties of fluorinated graphene},
   author = {Singh, Sandeep Kumar and Srinivasan, S. Goverapet and Neek-Amal, M. and Costamagna, S. and van Duin, Adri C. T. and Peeters, F. M.},
   journal = {Phys. Rev. B},

forcefield_step/data/reaxff/CHNO_HNS_2014.frc

@@ -262,7 +262,7 @@ T.-R. Shan, R. R. Wixom, A. P. Thompson,
 "Atomistic Simulation of Nanoscale Void-Enhanced Initiation in Hexanitrostilbene",
 Proc. 15th International Detonation Symposium, pp. 962-969, SAND Number: SAND2014-15518J
 
-@techreport{shan2014nanoscale,
+@bibtex @techreport{shan2014nanoscale,
   title={Nanoscale Void-Enhanced Initiation in Hexanitrostilbene: Reactive Molecular Dynamics Simulations.},
   author={Shan, Tzu-Ray and Wixom, Ryan R and Thompson, Aidan Patrick},
   year={2014},

forcefield_step/data/reaxff/CHNO_RDX_2003.frc

@@ -251,7 +251,7 @@ N.B. Removed two angle terms
 2)   1  2  4   0.0000   0.0019   6.3000   0.0000   0.0000   0.0000   1.0400        
      This is the first of two lines for 1 2 4. LAMMPS takes the second...
 
-@article{PhysRevLett.91.098301,
+@bibtex @article{PhysRevLett.91.098301,
   title = {Shock Waves in High-Energy Materials: The Initial Chemical Events in Nitramine RDX},
   author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
   journal = {Phys. Rev. Lett.},

forcefield_step/data/reaxff/CHOFe_FeOH_2010.frc

@@ -245,7 +245,7 @@ imported from LAMMPS examples/reaxff/FeOH3
 
 DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Aryanpour, van Duin and Kubicki, J Phys Chem A, 114, 6298-6307 (2010) COMMENT Reactive MD-force field: Fe/O/water: Aryanpour, M.; van Duin, A. C. T.; Kubicki, J. D. J. Phys. Chem. A 2010, 114, 6298-6307
 
-@article{doi:10.1021/jp101332k,
+@bibtex @article{doi:10.1021/jp101332k,
 author = {Aryanpour, Masoud and van Duin, Adri C. T. and Kubicki, James D.},
 title = {Development of a Reactive Force Field for Iron−Oxyhydroxide Systems},
 journal = {The Journal of Physical Chemistry A},

forcefield_step/data/reaxff/CHOV_VOH_2008.frc

@@ -251,7 +251,7 @@ imported from LAMMPS examples/reaxff/voh
 
 DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Chenoweth et al, J Phys Chem C, 112, 14645-14654 (2008) COMMENT Reactive MD-force field: V/O/C/H potential: Chenoweth, K.; et al. J. Phys. Chem. C, 2008, 112, 14645-14654. 
 
-@article{doi:10.1021/jp802134x,
+@bibtex @article{doi:10.1021/jp802134x,
 author = {Chenoweth, Kimberly and van Duin, Adri C. T. and Persson, Petter and Cheng, Mu-Jeng and Oxgaard, Jonas and Goddard, William A. III},
 title = {Development and Application of a ReaxFF Reactive Force Field for Oxidative Dehydrogenation on Vanadium Oxide Catalysts},
 journal = {The Journal of Physical Chemistry C},

forcefield_step/data/reaxff/CHO_cho_2008.frc

@@ -210,7 +210,7 @@ ReaxFF forcefield translated from Reax format
 
 DATE: 2011-02-18 DATE: 2010-11-03 DATE: 2010-02-19 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Chenoweth, van Duin and Goddard, J Phys Chem A, 112, 1040-1053 (2008) COMMENT: Reactive MD-force field c/h/o combustion force field: Chenoweth, K.; van Duin, A.C.T.; Goddard, W.A. J. Phys. Chem. A 2008, 112, 1040-1053.
 
-@article{doi:10.1021/jp709896w,
+@bibtex @article{doi:10.1021/jp709896w,
 author = {Chenoweth, Kimberly and van Duin, Adri C. T. and Goddard, William A.},
 title = {ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation},
 journal = {The Journal of Physical Chemistry A},

forcefield_step/data/reaxff/CLiSi_Guifo_2023.frc

@@ -170,7 +170,7 @@ ReaxFF forcefield translated from Reax format
 
 Reactive MD-force field: Li/Si/C force field Volkswagen Jan 12, 2022
 
-@article{10.1021/acs.jpcc.2c07773, 
+@bibtex @article{10.1021/acs.jpcc.2c07773, 
 year = {2023}, 
 title = {{Development and Validation of a ReaxFF Reactive Force Field for Modeling Silicon–Carbon Composite Anode Materials in Lithium-Ion Batteries}}, 
 author = {Guifo, Stéphane B. Olou’ou and Mueller, Jonathan E. and Duin, Diana van and Talkhoncheh, Mahdi K. and Duin, Adri C. T. van and Henriques, David and Markus, Torsten}, 

forcefield_step/data/reaxff/HBNO_AB_2010.frc

@@ -236,7 +236,7 @@ import from LAMMPS examples/reaxff/AB
 
 DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Weismiller, van Duin,  Lee, Yetter, J Phys Chem A, 114, 5485-5492 (2010) COMMENT: Reactive MD-force field for Ammonia Borane: Weismiller, M.R.; van Duin, A.C.T.; Lee, J.; Yetter, R.A. J. Phys. Chem. A 2010, 114, 5485-5492
 
-@article{doi:10.1021/jp100136c,
+@bibtex @article{doi:10.1021/jp100136c,
 author = {Weismiller, Michael R. and van Duin, Adri C. T. and Lee, Jongguen and Yetter, Richard A.},
 title = {ReaxFF Reactive Force Field Development and Applications for Molecular Dynamics Simulations of Ammonia Borane Dehydrogenation and Combustion},
 journal = {The Journal of Physical Chemistry A},

forcefield_step/data/reaxff/HOAu_AuO_2010.frc

@@ -192,7 +192,7 @@ ReaxFF forcefield translated from Reax format
 
 DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Joshi et al, J Mat Chem, 20, 10431-10437 (2010) COMMENT: Reactive MD-force field: Au-Au: Keith, J. A. et al. Phys Rev B 2010, 81, 235404; Joshi, K. et al., J. Mat. Chem 2010, 20, 10431-10437
 
-@article{PhysRevB.81.235404,
+@bibtex @article{PhysRevB.81.235404,
   title = {Reactive forcefield for simulating gold surfaces and nanoparticles},
   author = {Keith, John A. and Fantauzzi, Donato and Jacob, Timo and van Duin, Adri C. T.},
   journal = {Phys. Rev. B},
@@ -207,7 +207,7 @@ DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Joshi
   url = {https://link.aps.org/doi/10.1103/PhysRevB.81.235404}
 }
 
-@Article{C0JM01556C,
+@bibtex @article{C0JM01556C,
 author ="Joshi, Kaushik and van Duin, Adri C. T. and Jacob, Timo",
 title  ="Development of a ReaxFF description of gold oxides and initial application to cold welding of partially oxidized gold surfaces",
 journal  ="J. Mater. Chem.",

forcefield_step/data/reaxff/HOZn_ZNOH_2010.frc

@@ -182,7 +182,7 @@ Import from LAMMPS examples/reaxff/ZnOH2
 
 DATE: 2011-02-18 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Raymand, van Duin, Spangberg, Goddard and Hermansson, Surf Sci, 604, 741-752 (2010) COMMENT: Reactive MD-force field: water/zinc: Raymand, D.; van Duin, A. C. T.; Spangberg, D.; Goddard, W. A.; Hermansson, K. Surface Science 2010, 604, 9-10, 741-752.
 
-@article{RAYMAND2010741,
+@bibtex @article{RAYMAND2010741,
 title = {Water adsorption on stepped ZnO surfaces from MD simulation},
 journal = {Surface Science},
 volume = {604},