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rename pair style lebedeva to lebedeva/z to be consistent with kolmolgorov/crespi/z

This commit is contained in:
Axel Kohlmeyer 2019-01-03 17:17:10 -05:00
parent abcba913ab
commit 7323179de3
12 changed files with 57 additions and 44 deletions
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1
doc/src/Commands_pair.txt
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@ -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,

1
doc/src/lammps.book
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@ -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

3
doc/src/pair_ilp_graphene_hbn.txt
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@ -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

1
doc/src/pair_kolmogorov_crespi_full.txt
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@ -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.

11
doc/src/pair_kolmogorov_crespi_z.txt
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@ -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

23
doc/src/pair_lebedeva.txt → doc/src/pair_lebedeva_z.txt
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@ -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

1
doc/src/pair_style.txt
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@ -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

1
doc/src/pairs.txt
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@ -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

24
examples/USER/misc/lebedeva/2particles.in
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@ -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

1
src/USER-MISC/README
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@ -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

22
src/USER-MISC/pair_lebedeva.cpp
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@ -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];

12
src/USER-MISC/pair_lebedeva.h
View File

@ -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 **);