From 7323179de33278b687b17a4e89998f4b9dda8a21 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer 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 **);