(a8bc4c18) · Commits · 郑智淋 / lammps

src/MANYBODY/Install.csh

+4 −0

Original line number	Diff line number	Diff line
		@@ -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

src/MANYBODY/pair_airebo.cpp

0 → 100644

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Preview size limit exceeded, changes collapsed.

src/MANYBODY/pair_airebo.h

0 → 100644

+117 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		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

src/MANYBODY/style_manybody.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -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)

src/neighbor.cpp

+70 −45

Original line number	Diff line number	Diff line
		@@ -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
		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;
		@@ -1017,6 +1028,11 @@ void Neighbor::setup_bins()
		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);

		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;

		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 (1.0mbinxmbiny*mbinz > INT_MAX)
		error->all("Domain too large for neighbor bins");

		// memory for bin ptrs

		mbins = mbinxmbinymbinz;
		@@ -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;
		}
		*/
		}

		/* ----------------------------------------------------------------------

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