From 7323179de33278b687b17a4e89998f4b9dda8a21 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 3 Jan 2019 17:17:10 -0500
Subject: [PATCH] rename pair style lebedeva to lebedeva/z to be consistent
with kolmolgorov/crespi/z
---
doc/src/Commands_pair.txt | 1 +
doc/src/lammps.book | 1 +
doc/src/pair_ilp_graphene_hbn.txt | 3 ++-
doc/src/pair_kolmogorov_crespi_full.txt | 1 +
doc/src/pair_kolmogorov_crespi_z.txt | 11 +++++----
...{pair_lebedeva.txt => pair_lebedeva_z.txt} | 23 ++++++++++--------
doc/src/pair_style.txt | 1 +
doc/src/pairs.txt | 1 +
examples/USER/misc/lebedeva/2particles.in | 24 +++++++++----------
src/USER-MISC/README | 1 +
src/USER-MISC/pair_lebedeva.cpp | 22 ++++++++---------
src/USER-MISC/pair_lebedeva.h | 12 +++++-----
12 files changed, 57 insertions(+), 44 deletions(-)
rename doc/src/{pair_lebedeva.txt => pair_lebedeva_z.txt} (69%)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 2691ccaebf..46f4950ad7 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -107,6 +107,7 @@ OPT.
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lcbop"_pair_lcbop.html,
+"lebedeva/z"_pair_lebedeva_z.html,
"lennard/mdf"_pair_mdf.html,
"line/lj"_pair_line_lj.html,
"list"_pair_list.html,
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index d752d2a929..a1bbaf896e 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -585,6 +585,7 @@ pair_kim.html
pair_kolmogorov_crespi_full.html
pair_kolmogorov_crespi_z.html
pair_lcbop.html
+pair_lebedeva_z.html
pair_line_lj.html
pair_list.html
pair_lj.html
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index a8d74dca0f..76dda14ec6 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -10,7 +10,7 @@ pair_style ilp/graphene/hbn command :h3
[Syntax:]
-pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre
+pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the taper function
@@ -110,6 +110,7 @@ units, if your simulation does not use {metal} units.
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
+"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
"pair_style pair_coul_shield"_pair_coul_shield.html.
[Default:] tap_flag = 1
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index a13825abe5..6d76a24bdb 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -100,6 +100,7 @@ units.
"pair_coeff"_pair_coeff.html,
"pair_none"_pair_none.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index a494c927b8..aabb3460e7 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -10,7 +10,7 @@ pair_style kolmogorov/crespi/z command :h3
[Syntax:]
-pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre
+pair_style \[hybrid/overlay ...\] kolmogorov/crespi/z cutoff :pre
[Examples:]
@@ -56,9 +56,12 @@ package"_Build_package.html doc page for more info.
[Related commands:]
-"pair_coeff"_pair_coeff.html
-"pair_none"_pair_none.html
-"pair_style hybrid/overlay"_pair_hybrid.html
+"pair_coeff"_pair_coeff.html,
+"pair_none"_pair_none.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
+"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"pair_style lebedeva/z"_pair_lebedeva_z.html
[Default:] none
diff --git a/doc/src/pair_lebedeva.txt b/doc/src/pair_lebedeva_z.txt
similarity index 69%
rename from doc/src/pair_lebedeva.txt
rename to doc/src/pair_lebedeva_z.txt
index 6b9eabc611..9eab56d0d9 100644
--- a/doc/src/pair_lebedeva.txt
+++ b/doc/src/pair_lebedeva_z.txt
@@ -6,25 +6,25 @@
:line
-pair_style lebedeva command :h3
+pair_style lebedeva/z command :h3
[Syntax:]
-pair_style hybrid/overlay lebedeva cutoff :pre
+pair_style \[hybrid/overlay ...\] lebedeva/z cutoff :pre
[Examples:]
-pair_style hybrid/overlay lebedeva 20.0
+pair_style hybrid/overlay lebedeva/z 20.0
pair_coeff * * none
-pair_coeff 1 2 lebedeva CC.Lebedeva C C :pre
+pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
-pair_style hybrid/overlay rebo lebedeva 14.0
+pair_style hybrid/overlay rebo lebedeva/z 14.0
pair_coeff * * rebo CH.airebo C C
-pair_coeff 1 2 lebedeva CC.Lebedeva C C :pre
+pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre
[Description:]
-The {lebedeva} style computes the Lebedeva interaction
+The {lebedeva/z} style computes the Lebedeva interaction
potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made,
which is to take all normals along the z-axis.
@@ -50,9 +50,12 @@ package"_Build_package.html doc page for more info.
[Related commands:]
-"pair_coeff"_pair_coeff.html
-"pair_none"_pair_none.html
-"pair_style hybrid/overlay"_pair_hybrid.html
+"pair_coeff"_pair_coeff.html,
+"pair_style none"_pair_none.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html,
+"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html.
[Default:] none
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index ea746f8943..714ec55d2e 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -174,6 +174,7 @@ accelerated styles exist.
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
+"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis
"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
"line/lj"_pair_line_lj.html - LJ potential between line segments
"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 7a7ad86d0d..2810252402 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -50,6 +50,7 @@ Pair Styles :h1
pair_kolmogorov_crespi_full
pair_kolmogorov_crespi_z
pair_lcbop
+ pair_lebedeva_z
pair_line_lj
pair_list
pair_lj
diff --git a/examples/USER/misc/lebedeva/2particles.in b/examples/USER/misc/lebedeva/2particles.in
index 2a9851f383..81cca2e473 100644
--- a/examples/USER/misc/lebedeva/2particles.in
+++ b/examples/USER/misc/lebedeva/2particles.in
@@ -1,4 +1,4 @@
-# After running LAMMPS with this input script a number of dump files is created.
+# After running LAMMPS with this input script a number of dump files is created.
# To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat,
@@ -8,17 +8,17 @@
# Email: softquake@gmail.com
-# ---------- Start simulation ---------------------
+# ---------- Start simulation ---------------------
clear
-units metal
-dimension 3
-boundary f f f
-atom_style atomic
+units metal
+dimension 3
+boundary f f f
+atom_style atomic
# ========================== Create Atomistic Structure ===========================
region whole block 0 20 0 20 0 10
-create_box 2 whole
+create_box 2 whole
read_data 2particles.dat add append
@@ -27,22 +27,22 @@ group graphite type 1 2
group graphene1 type 1
group graphene2 type 2
-pair_style hybrid/overlay lebedeva 20
+pair_style hybrid/overlay lebedeva/z 20
pair_coeff * * none
-pair_coeff 1 2 lebedeva CC.Lebedeva C C
+pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
mass 1 12.01 # Carbon
mass 2 12.01 # Carbon
-neighbor 0.3 bin
-neigh_modify delay 1 check yes
+neighbor 0.3 bin
+neigh_modify delay 1 check yes
compute peratom all pe/atom
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3
-thermo 10
+thermo 10
thermo_style custom step pe press temp
thermo_modify lost ignore
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index cf948df233..13e406d42f 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -71,6 +71,7 @@ pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
+pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), softquake at gmail dot com, 4 Jan 19
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
diff --git a/src/USER-MISC/pair_lebedeva.cpp b/src/USER-MISC/pair_lebedeva.cpp
index 16305e84cd..b7773c80b0 100644
--- a/src/USER-MISC/pair_lebedeva.cpp
+++ b/src/USER-MISC/pair_lebedeva.cpp
@@ -17,7 +17,7 @@
e-mail: softquake at gmail dot com
Writing this was based on C code of Kolmogorov-Crespi potential
of Jaap Kroes and others.
-
+
This is potential described in
[Lebedeva et al., Physica E, 44(6), 949-954, 2012.]
------------------------------------------------------------------------- */
@@ -41,7 +41,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairLebedeva::PairLebedeva(LAMMPS *lmp) : Pair(lmp)
+PairLebedevaZ::PairLebedevaZ(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
@@ -59,7 +59,7 @@ PairLebedeva::PairLebedeva(LAMMPS *lmp) : Pair(lmp)
/* ---------------------------------------------------------------------- */
-PairLebedeva::~PairLebedeva()
+PairLebedevaZ::~PairLebedevaZ()
{
if (allocated) {
memory->destroy(setflag);
@@ -78,7 +78,7 @@ PairLebedeva::~PairLebedeva()
/* ---------------------------------------------------------------------- */
-void PairLebedeva::compute(int eflag, int vflag)
+void PairLebedevaZ::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,der;
@@ -122,7 +122,7 @@ void PairLebedeva::compute(int eflag, int vflag)
rhosq = delx*delx + dely*dely;
rho = sqrt(rhosq);
rsq = rhosq + delz*delz;
-
+
if (rsq < cutsq[itype][jtype]) {
int iparam_ij = elem2param[map[itype]][map[jtype]];
@@ -173,7 +173,7 @@ void PairLebedeva::compute(int eflag, int vflag)
allocate all arrays
------------------------------------------------------------------------- */
-void PairLebedeva::allocate()
+void PairLebedevaZ::allocate()
{
allocated = 1;
int n = atom->ntypes;
@@ -193,7 +193,7 @@ void PairLebedeva::allocate()
global settings
------------------------------------------------------------------------- */
-void PairLebedeva::settings(int narg, char **arg)
+void PairLebedevaZ::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
if (strcmp(force->pair_style,"hybrid/overlay")!=0)
@@ -215,7 +215,7 @@ void PairLebedeva::settings(int narg, char **arg)
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
-void PairLebedeva::coeff(int narg, char **arg)
+void PairLebedevaZ::coeff(int narg, char **arg)
{
int i,j,n;
@@ -258,7 +258,7 @@ void PairLebedeva::coeff(int narg, char **arg)
read_file(arg[2]);
-
+
double cut_one = cut_global;
int count = 0;
@@ -278,7 +278,7 @@ void PairLebedeva::coeff(int narg, char **arg)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairLebedeva::init_one(int i, int j)
+double PairLebedevaZ::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
@@ -296,7 +296,7 @@ double PairLebedeva::init_one(int i, int j)
read Lebedeva potential file
------------------------------------------------------------------------- */
-void PairLebedeva::read_file(char *filename)
+void PairLebedevaZ::read_file(char *filename)
{
int params_per_line = 12;
char **words = new char*[params_per_line+1];
diff --git a/src/USER-MISC/pair_lebedeva.h b/src/USER-MISC/pair_lebedeva.h
index 66e759d202..ae229e0541 100644
--- a/src/USER-MISC/pair_lebedeva.h
+++ b/src/USER-MISC/pair_lebedeva.h
@@ -13,21 +13,21 @@
#ifdef PAIR_CLASS
-PairStyle(lebedeva,PairLebedeva)
+PairStyle(lebedeva/z,PairLebedevaZ)
#else
-#ifndef LMP_PAIR_LEBEDEVA_H
-#define LMP_PAIR_LEBEDEVA_H
+#ifndef LMP_PAIR_LEBEDEVA_Z_H
+#define LMP_PAIR_LEBEDEVA_Z_H
#include "pair.h"
namespace LAMMPS_NS {
-class PairLebedeva : public Pair {
+class PairLebedevaZ : public Pair {
public:
- PairLebedeva(class LAMMPS *);
- virtual ~PairLebedeva();
+ PairLebedevaZ(class LAMMPS *);
+ virtual ~PairLebedevaZ();
virtual void compute(int, int);
void settings(int, char **);
--
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