update pot list

Author: Cavenfish

docs/src/potentials/potList.md

@@ -2,18 +2,103 @@
 
 YASS contains a few potentials.
 
+## Leonard Jones Potential
+
+```julia
+# Example vars for Au
+d = Dict(
+  "epsilon" => 0.2297,
+  "sigma" => 2.95,
+  "rs" => 19.0,
+  "rc" => 20.0
+)
+
+calc = LJ(d)
+```
+
 ## CO Potentials
 
 ### MvHff
 
-CO-CO Potential from van Hemert et al. 2015
+Based on:
+van Hemert, Marc C., Junko Takahashi, and Ewine F. van Dishoeck. "Molecular
+dynamics study of the photodesorption of CO ice." The Journal of Physical
+Chemistry A 119.24 (2015): 6354-6369.
+
+Link:
+https://pubs.acs.org/doi/full/10.1021/acs.jpca.5b02611
+
+```julia
+calc = MvHff()
+```
 
 ### HGNN
 
-CO-CO Potential from Chen et al. 2020
+Based on:
+Chen, Jun, et al. "Energy transfer between vibrationally excited carbon monoxide
+based on a highly accurate six-dimensional potential energy surface." The 
+Journal of Chemical Physics 153.5 (2020).
+
+Link:
+https://pubs.aip.org/aip/jcp/article/153/5/054310/1065758
+
+```julia
+calc = HGNN()
+```
 
 ## H$_2$O Potentials
 
 ### TIP4P/2005f
 
-### SPC-F
+Based on:
+González, M. A., & Abascal, J. L. (2011). A flexible model for water based on
+TIP4P/2005. The Journal of chemical physics, 135(22).
+
+Link:
+https://pubs.aip.org/aip/jcp/article/135/22/224516/190786
+
+```julia
+calc = TIP4Pf()
+```
+
+### Simple Point Charge Models
+
+#### SPC/F
+
+Based on:
+Toukan, Kahled, and Aneesur Rahman. "Molecular-dynamics study of atomic
+motions in water." Physical Review B 31.5 (1985): 2643.
+
+Link:
+https://journals.aps.org/prb/abstract/10.1103/PhysRevB.31.2643
+
+```julia
+calc = SPC("SPC/F")
+```
+
+#### SPC/Fd
+
+Based on:
+Dang, Liem X., and B. Montgomery Pettitt. "Simple intramolecular model
+potentials for water." Journal of physical chemistry 91.12 (1987): 3349-3354.
+
+Link:
+https://doi.org/10.1021/j100296a048
+
+```julia
+calc = SPC("SPC/Fd")
+```
+
+#### SPC/Fw
+
+Based on:
+Wu, Yujie, Harald L. Tepper, and Gregory A. Voth. "Flexible simple
+point-charge water model with improved liquid-state properties." The Journal
+of chemical physics 124.2 (2006).
+
+Link:
+https://doi.org/10.1063/1.2136877
+
+```julia
+calc = SPC("SPC/Fw")
+```