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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@790 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-08-10 22:59:04 +00:00
parent 2736f0e9b8
commit a8bc4c1805
6 changed files with 4193 additions and 45 deletions
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4
src/MANYBODY/Install.csh
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@ -4,12 +4,14 @@ if ($1 == 1) then
cp style_manybody.h ..
cp pair_airebo.cpp ..
cp pair_eam.cpp ..
cp pair_eam_alloy.cpp ..
cp pair_eam_fs.cpp ..
cp pair_sw.cpp ..
cp pair_tersoff.cpp ..
cp pair_airebo.h ..
cp pair_eam.h ..
cp pair_eam_alloy.h ..
cp pair_eam_fs.h ..
@ -21,12 +23,14 @@ else if ($1 == 0) then
rm ../style_manybody.h
touch ../style_manybody.h
rm ../pair_airebo.cpp
rm ../pair_eam.cpp
rm ../pair_eam_alloy.cpp
rm ../pair_eam_fs.cpp
rm ../pair_sw.cpp
rm ../pair_tersoff.cpp
rm ../pair_airebo.h
rm ../pair_eam.h
rm ../pair_eam_alloy.h
rm ../pair_eam_fs.h

3999
src/MANYBODY/pair_airebo.cpp Normal file
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File diff suppressed because it is too large Load Diff

117
src/MANYBODY/pair_airebo.h Normal file
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@ -0,0 +1,117 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef PAIR_AIREBO_H
#define PAIR_AIREBO_H
#include "pair.h"
namespace LAMMPS_NS {
class PairAIREBO : public Pair {
public:
PairAIREBO(class LAMMPS *);
virtual ~PairAIREBO();
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void write_restart(FILE *) {}
void read_restart(FILE *) {}
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
void single(int, int, int, int, double, double, double, int, One &) {}
private:
int me;
int ljflag,torflag; // 0/1 if LJ,torsion terms included
int maxlocal; // size of numneigh, firstneigh arrays
int **pages; // neighbor list pages
int maxpage; // # of pages currently allocated
int pgsize; // size of neighbor page
int oneatom; // max # of neighbors for one atom
int npage; // current page in page list
int *map;
double cutlj; // user-specified LJ cutoff
double cutljrebosq; // cut for when to compute
// REBO neighs of ghost atoms
double **cutljsq; // LJ cutoffs for C,H types
double **lj1,**lj2,**lj3,**lj4; // pre-computed LJ coeffs for C,H types
double cut3rebo; // maximum distance for 3rd REBO neigh
int *REBO_numneigh; // # of pair neighbors for each atom
int **REBO_firstneigh; // ptr to 1st neighbor of each atom
double *nC,*nH; // sum of weighing fns with REBO neighs
double smin,Nmin,Nmax,NCmin,NCmax,thmin,thmax;
double rcmin[2][2],rcmax[2][2],rcmaxsq[2][2],rcmaxp[2][2];
double Q[2][2],alpha[2][2],A[2][2],rho[2][2],BIJc[2][2][3],Beta[2][2][3];
double rcLJmin[2][2],rcLJmax[2][2],rcLJmaxsq[2][2],bLJmin[2][2],bLJmax[2][2];
double epsilon[2][2],sigma[2][2],epsilonT[2][2];
// spline coefficients
double gCdom[5],gC1[4][6],gC2[4][6],gHdom[4],gH[3][6];
double pCCdom[2][2],pCHdom[2][2],pCC[4][4][16],pCH[4][4][16];
double piCCdom[3][2],piCHdom[3][2],piHHdom[3][2];
double piCC[4][4][9][64],piCH[4][4][9][64],piHH[4][4][9][64];
double Tijdom[3][2],Tijc[4][4][9][64];
// spline knot values
double PCCf[5][5],PCCdfdx[5][5],PCCdfdy[5][5],PCHf[5][5];
double PCHdfdx[5][5],PCHdfdy[5][5];
double piCCf[5][5][10],piCCdfdx[5][5][10];
double piCCdfdy[5][5][10],piCCdfdz[5][5][10];
double piCHf[5][5][10],piCHdfdx[5][5][10];
double piCHdfdy[5][5][10],piCHdfdz[5][5][10];
double piHHf[5][5][10],piHHdfdx[5][5][10];
double piHHdfdy[5][5][10],piHHdfdz[5][5][10];
double Tf[5][5][10],Tdfdx[5][5][10],Tdfdy[5][5][10],Tdfdz[5][5][10];
void REBO_neigh();
void FREBO(int, double **);
void FLJ(int, double **);
void TORSION(int, double **);
double bondorder(int, int, double *, double, double, double **);
double bondorderLJ(int, int, double *, double, double,
double *, double, double **);
double Sp(double, double, double, double &);
double Sp2(double, double, double, double &);
double gSpline(double, double, int, double *, double *);
double PijSpline(double, double, int, int, double *);
double piRCSpline(double, double, double, int, int, double *);
double TijSpline(double, double, double, double *);
double kronecker(int, int);
void add_pages(int);
void read_file(char *);
double Sp5th(double, double *, double *);
double Spbicubic(double, double, double *, double *);
double Sptricubic(double, double, double, double *, double *);
void spline_init();
void allocate();
};
}
#endif

2
src/MANYBODY/style_manybody.h
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@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#ifdef PairInclude
#include "pair_airebo.h"
#include "pair_eam.h"
#include "pair_eam_alloy.h"
#include "pair_eam_fs.h"
@ -20,6 +21,7 @@
#endif
#ifdef PairClass
PairStyle(airebo,PairAIREBO)
PairStyle(eam,PairEAM)
PairStyle(eam/alloy,PairEAMAlloy)
PairStyle(eam/fs,PairEAMFS)

115
src/neighbor.cpp
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@ -44,6 +44,7 @@ using namespace LAMMPS_NS;
#define SMALL 1.0e-6
#define EXDELTA 1
#define BIG 1.0e20
#define CUT2BIN_RATIO 100
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -239,6 +240,7 @@ void Neighbor::init()
int i,j,m,n;
ncalls = ndanger = 0;
dimension = domain->dimension;
triclinic = domain->triclinic;
// error check
@ -520,19 +522,19 @@ void Neighbor::init()
} else if (style == BIN) {
if (force->newton_pair == 0) {
half_build = &Neighbor::granular_bin_no_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton;
} else if (triclinic) {
half_build = &Neighbor::granular_bin_newton_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
} else {
half_build = &Neighbor::granular_bin_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton;
else
half_stencil = &Neighbor::stencil_half_2d_newton;
@ -547,19 +549,19 @@ void Neighbor::init()
} else if (style == BIN) {
if (force->newton_pair == 0) {
half_build = &Neighbor::respa_bin_no_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton;
} else if (triclinic) {
half_build = &Neighbor::respa_bin_newton_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
} else {
half_build = &Neighbor::respa_bin_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton;
else
half_stencil = &Neighbor::stencil_half_2d_newton;
@ -582,7 +584,7 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else {
half_build = &Neighbor::half_bin_no_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton;
@ -593,13 +595,13 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else if (triclinic) {
half_build = &Neighbor::half_bin_newton_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_tri;
} else {
half_build = &Neighbor::half_bin_newton;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton;
else
half_stencil = &Neighbor::stencil_half_2d_newton;
@ -612,7 +614,7 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else {
half_build = &Neighbor::half_bin_no_newton_multi;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_no_newton_multi;
else
half_stencil = &Neighbor::stencil_half_2d_no_newton_multi;
@ -623,13 +625,13 @@ void Neighbor::init()
half_stencil = &Neighbor::stencil_none;
} else if (triclinic) {
half_build = &Neighbor::half_bin_newton_multi_tri;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_multi_tri;
else
half_stencil = &Neighbor::stencil_half_2d_newton_multi_tri;
} else {
half_build = &Neighbor::half_bin_newton_multi;
if (domain->dimension == 3)
if (dimension == 3)
half_stencil = &Neighbor::stencil_half_3d_newton_multi;
else
half_stencil = &Neighbor::stencil_half_2d_newton_multi;
@ -644,13 +646,13 @@ void Neighbor::init()
if (style == NSQ) full_build = &Neighbor::full_nsq;
else if (style == BIN) {
full_build = &Neighbor::full_bin;
if (domain->dimension == 3)
if (dimension == 3)
full_stencil = &Neighbor::stencil_full_3d;
else
full_stencil = &Neighbor::stencil_full_2d;
} else {
full_build = &Neighbor::full_bin_multi;
if (domain->dimension == 3)
if (dimension == 3)
full_stencil = &Neighbor::stencil_full_3d_multi;
else
full_stencil = &Neighbor::stencil_full_2d_multi;
@ -922,16 +924,19 @@ void Neighbor::build_full()
/* ----------------------------------------------------------------------
setup neighbor binning parameters
bin numbering is global: 0 = 0.0 to binsize, 1 = binsize to 2*binsize
nbin-1 = bbox-binsize to binsize
nbin = bbox to bbox+binsize
-1,-2,etc = -binsize to 0.0, -2*size to -size, etc
bin numbering in each dimension is global:
0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
nbin-1,nbin,etc = bbox-binsize to binsize, bbox to bbox+binsize, etc
-1,-2,etc = -binsize to 0.0, -2*size to -size, etc
code will work for any binsize
since next(xyz) and stencil extend as far as necessary
binsize = 1/2 of cutoff is roughly optimal
for orthogonal boxes, prd must be filled exactly by integer # of bins
so procs on both sides of PBC see same bin boundary
for triclinic, tilted simulation box cannot contain integer # of bins
for orthogonal boxes:
a dim must be filled exactly by integer # of bins
in periodic, procs on both sides of PBC must see same bin boundary
in non-periodic, coord2bin() still assumes this by use of nbin xyz
for triclinic boxes:
tilted simulation box cannot contain integer # of bins
stencil & neigh list built differently to account for this
mbinlo = lowest global bin any of my ghost atoms could fall into
mbinhi = highest global bin any of my ghost atoms could fall into
@ -979,36 +984,42 @@ void Neighbor::setup_bins()
bbox[1] = bboxhi[1] - bboxlo[1];
bbox[2] = bboxhi[2] - bboxlo[2];
// optimal bin size is roughly 1/2 the cutoff
// for BIN style, binsize = 1/2 of max neighbor cutoff
// for MULTI style, binsize = 1/2 of min neighbor cutoff
// special case of all cutoffs = 0.0, binsize = box size
double binsize;
if (style == BIN) binsize = 0.5*cutneighmax;
else binsize = 0.5*cutneighmin;
if (binsize == 0.0) binsize = bbox[0];
double binsize_optimal;
if (style == BIN) binsize_optimal = 0.5*cutneighmax;
else binsize_optimal = 0.5*cutneighmin;
if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
double binsizeinv = 1.0/binsize_optimal;
// test for too many global bins in any dimension due to huge domain
// test for too many global bins in any dimension due to huge global domain
double binsizeinv = 1.0/binsize;
if (bbox[0]*binsizeinv > INT_MAX || bbox[1]*binsizeinv > INT_MAX ||
bbox[2]*binsizeinv > INT_MAX)
error->all("Domain too large for neighbor bins");
// divide box into bins
// optimal size is roughly 1/2 the cutoff
// use one bin even if cutoff >> bbox
// create actual bins
// always have one bin even if cutoff > bbox
// for 2d, nbinz = 1
nbinx = static_cast<int> (bbox[0]*binsizeinv);
nbiny = static_cast<int> (bbox[1]*binsizeinv);
if (domain->dimension == 3)
nbinz = static_cast<int> (bbox[2]*binsizeinv);
if (dimension == 3) nbinz = static_cast<int> (bbox[2]*binsizeinv);
else nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
// compute actual bin size for nbins to fit into box exactly
// error if actual bin size << cutoff, since will create a zillion bins
// this happens when nbin = 1 and box size << cutoff
// typically due to non-periodic, flat system in a particular dim
// in that extreme case, should use NSQ not BIN neighbor style
binsizex = bbox[0]/nbinx;
binsizey = bbox[1]/nbiny;
binsizez = bbox[2]/nbinz;
@ -1016,7 +1027,12 @@ void Neighbor::setup_bins()
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
bininvz = 1.0 / binsizez;
if (binsize_optimal*bininvx > CUT2BIN_RATIO ||
binsize_optimal*bininvy > CUT2BIN_RATIO ||
binsize_optimal*bininvz > CUT2BIN_RATIO)
error->all("Cannot use neighbor bins - box size << cutoff");
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in
// coord = lowest and highest values of coords for my ghost atoms
// static_cast(-1.5) = -1, so subract additional -1
@ -1037,13 +1053,16 @@ void Neighbor::setup_bins()
coord = bsubboxhi[1] + SMALL*bbox[1];
mbinyhi = static_cast<int> ((coord-bboxlo[1])*bininvy);
coord = bsubboxlo[2] - SMALL*bbox[2];
mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
coord = bsubboxhi[2] + SMALL*bbox[2];
mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (dimension == 3) {
coord = bsubboxlo[2] - SMALL*bbox[2];
mbinzlo = static_cast<int> ((coord-bboxlo[2])*bininvz);
if (coord < bboxlo[2]) mbinzlo = mbinzlo - 1;
coord = bsubboxhi[2] + SMALL*bbox[2];
mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz);
}
// extend bins by 1 to insure stencil extent is included
// if 2d, only 1 bin in z
mbinxlo = mbinxlo - 1;
mbinxhi = mbinxhi + 1;
@ -1053,15 +1072,12 @@ void Neighbor::setup_bins()
mbinyhi = mbinyhi + 1;
mbiny = mbinyhi - mbinylo + 1;
mbinzlo = mbinzlo - 1;
mbinzhi = mbinzhi + 1;
if (dimension == 3) {
mbinzlo = mbinzlo - 1;
mbinzhi = mbinzhi + 1;
} else mbinzlo = mbinzhi = 0;
mbinz = mbinzhi - mbinzlo + 1;
// test for too many total local bins due to huge domain
if (1.0*mbinx*mbiny*mbinz > INT_MAX)
error->all("Domain too large for neighbor bins");
// memory for bin ptrs
mbins = mbinx*mbiny*mbinz;
@ -1081,6 +1097,7 @@ void Neighbor::setup_bins()
if (sy*binsizey < cutneighmax) sy++;
int sz = static_cast<int> (cutneighmax*bininvz);
if (sz*binsizez < cutneighmax) sz++;
if (dimension == 2) sz = 0;
// allocate stencil memory and create stencil(s)
// check half/full instead of half_every/full_every so stencils will be
@ -1456,6 +1473,14 @@ void Neighbor::bin_atoms()
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
/*
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
*/
}
/* ----------------------------------------------------------------------

1
src/neighbor.h
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@ -120,6 +120,7 @@ class Neighbor : protected Pointers {
double binsizex,binsizey,binsizez; // bin sizes and inverse sizes
double bininvx,bininvy,bininvz;
int dimension; // 2/3 for 2d/3d
int triclinic; // 0 if domain is orthog, 1 if triclinic
double *bboxlo,*bboxhi; // copy of full domain bounding box