refine the code and documentation

doc/src/Eqs/pair_ilp_graphene_hbn.tex

@@ -0,0 +1,42 @@
+\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
+\pdfoutput=1
+\bibliographystyle{apsrev4}
+\usepackage{color}
+\usepackage{dcolumn} %Align table columns on decimal point
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage{amsthm}
+\usepackage{graphicx}
+\usepackage[pdftex]{hyperref}
+\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
+\usepackage[all]{hypcap}
+\newcommand{\red}{\color{red}}
+\newcommand{\blue}{\color{blue}}
+\definecolor{green}{rgb}{0,0.5,0}
+\newcommand{\green}{\color{green}}
+\newcommand{\white}{\color{white}}
+%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
+\thickmuskip=0.5\thickmuskip %shorter spaces in math
+%
+\begin{document}
+%
+\begingroup
+\Large
+\begin{eqnarray*}
+  E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
+  V_{ij} & = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} 
+               \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - 
+                \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
+                \cdot \frac{C_6}{r^6_{ij}} \right \}\\[15pt]
+  \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\[15pt]
+  \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\[15pt]
+  f(\rho) & = &  C e^{ -( \rho / \delta )^2 }\\[15pt]
+  {\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+                          70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
+                          84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
+                          35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
+\end{eqnarray*}
+\endgroup
+%
+\end{document}
+%

doc/src/pair_ilp_graphene_hbn.txt

@@ -30,12 +30,12 @@ pair_coeff  2 2 coul/shield 0.69
 
 [Description:]
 
-The {ILP/graphene/hBN} style computes the registry-dependent interlayer
+The {ilp/graphene/hbn} style computes the registry-dependent interlayer
 potential (RDILP) potential as described in "(Leven)"_#Leven and
 "(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
 in "(Kolmogorov)"_#Kolmogorov2.
 
-:c,image(Eqs/pair_ilp_gr_hBN.jpg)
+:c,image(Eqs/pair_ilp_graphene_hbn.jpg)
 
 Where Tap(r_ij) is the taper function which provides a continuous
 cutoff (up to third derivative) for interatomic separations larger than

potentials/CC.KC-full

@@ -0,0 +1,8 @@
+# Kolmogorov-Crespi Potential
+#
+# Cite as A.N. Kolmogorov & V. H. Crespi, 
+# Registry-dependent interlayer potential for graphitic systems
+# Physical Review B 71, 235415 (2005)
+# 
+#      z0     C0     C2      C4       C    delta  lambda      A     S	rcut
+C  C  3.34  15.71  12.29   4.933   3.030   0.578   3.629   10.238  1.0  2.0

src/USER-MISC/pair_ilp_graphene_hbn.cpp

@@ -321,9 +321,9 @@ void PairILPGrapheneHBN::calc_normal()
     memory->destroy(dnormal);
     memory->destroy(dnormdri);
     nmax = atom->nmax;
-    memory->create(normal,nmax,3,"ILP:normal");
-    memory->create(dnormdri,3,3,nmax,"ILP:dnormdri");
-    memory->create(dnormal,3,3,3,nmax,"ILP:dnormal");
+    memory->create(normal,nmax,3,"ILPGrapheneHBN:normal");
+    memory->create(dnormdri,3,3,nmax,"ILPGrapheneHBN:dnormdri");
+    memory->create(dnormal,3,3,3,nmax,"ILPGrapheneHBN:dnormal");
   }
 
   inum = list->inum;
@@ -667,10 +667,7 @@ void PairILPGrapheneHBN::init_style()
 
 
 /* ----------------------------------------------------------------------
-   create ILP neighbor list from main neighbor list
-   ILP neighbor list stores neighbors of ghost atoms
-   ILP_numneigh for calcualting normals and
-   ILP_pair_numneigh for calculating force
+   create ILP neighbor list from main neighbor list to calcualte normals
 ------------------------------------------------------------------------- */
 
 void PairILPGrapheneHBN::ILP_neigh()
@@ -687,8 +684,8 @@ void PairILPGrapheneHBN::ILP_neigh()
     maxlocal = atom->nmax;
     memory->destroy(ILP_numneigh);
     memory->sfree(ILP_firstneigh);
-    memory->create(ILP_numneigh,maxlocal,"ILP:numneigh");
-    ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILP:firstneigh");
+    memory->create(ILP_numneigh,maxlocal,"ILPGrapheneHBN:numneigh");
+    ILP_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),"ILPGrapheneHBN:firstneigh");
   }
 
   allnum = list->inum + list->gnum;
@@ -730,6 +727,7 @@ void PairILPGrapheneHBN::ILP_neigh()
 
     ILP_firstneigh[i] = neighptr;
     ILP_numneigh[i] = n;
+    if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals");
     ipage->vgot(n);
     if (ipage->status())
       error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

src/USER-MISC/pair_kolmogorov_crespi_full.cpp

@@ -671,10 +671,7 @@ void PairKolmogorovCrespiFull::init_style()
 
 
 /* ----------------------------------------------------------------------
-   create KC neighbor list from main neighbor list
-   KC neighbor list stores neighbors of ghost atoms
-   KC_numneigh for calcualting normals and
-   KC_pair_numneigh for calculating force
+ create neighbor list from main neighbor list for calculating the normals
 ------------------------------------------------------------------------- */
 
 void PairKolmogorovCrespiFull::KC_neigh()
@@ -735,6 +732,7 @@ void PairKolmogorovCrespiFull::KC_neigh()
 
     KC_firstneigh[i] = neighptr;
     KC_numneigh[i] = n;
+    if (n > 3) error->all(FLERR,"There are too many neighbors for some atoms, please reduce the cutoff for normals");
     ipage->vgot(n);
     if (ipage->status())
       error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");