From 8287969efa327bc5096118df84ffe8d0fdfa6c4e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 20 Oct 2011 15:10:28 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7155 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/ASPHERE/Install.sh | 16 +- src/ASPHERE/pair_line.cpp | 444 -------------------------- src/ASPHERE/pair_line.h | 61 ---- src/ASPHERE/pair_tri.cpp | 637 -------------------------------------- src/ASPHERE/pair_tri.h | 61 ---- 5 files changed, 8 insertions(+), 1211 deletions(-) delete mode 100644 src/ASPHERE/pair_line.cpp delete mode 100644 src/ASPHERE/pair_line.h delete mode 100644 src/ASPHERE/pair_tri.cpp delete mode 100644 src/ASPHERE/pair_tri.h diff --git a/src/ASPHERE/Install.sh b/src/ASPHERE/Install.sh index 2f6f974332..1cc7a4b61d 100644 --- a/src/ASPHERE/Install.sh +++ b/src/ASPHERE/Install.sh @@ -12,9 +12,9 @@ if (test $1 = 1) then cp fix_nve_tri.cpp .. cp fix_nvt_asphere.cpp .. cp pair_gayberne.cpp .. - cp pair_line.cpp .. + cp pair_line_lj.cpp .. cp pair_resquared.cpp .. - cp pair_tri.cpp .. + cp pair_tri_Lj.cpp .. cp compute_erotate_asphere.h .. cp compute_temp_asphere.h .. @@ -26,9 +26,9 @@ if (test $1 = 1) then cp fix_nve_tri.h .. cp fix_nvt_asphere.h .. cp pair_gayberne.h .. - cp pair_line.h .. + cp pair_line_lj.h .. cp pair_resquared.h .. - cp pair_tri.h .. + cp pair_tri_lj.h .. elif (test $1 = 0) then @@ -42,9 +42,9 @@ elif (test $1 = 0) then rm -f ../fix_nve_tri.cpp rm -f ../fix_nvt_asphere.cpp rm -f ../pair_gayberne.cpp - rm -f ../pair_line.cpp + rm -f ../pair_line_lj.cpp rm -f ../pair_resquared.cpp - rm -f ../pair_tri.cpp + rm -f ../pair_tri_lj.cpp rm -f ../compute_erotate_asphere.h rm -f ../compute_temp_asphere.h @@ -56,8 +56,8 @@ elif (test $1 = 0) then rm -f ../fix_nve_tri.h rm -f ../fix_nvt_asphere.h rm -f ../pair_gayberne.h - rm -f ../pair_line.h + rm -f ../pair_line_lj.h rm -f ../pair_resquared.h - rm -f ../pair_tri.h + rm -f ../pair_tri_lj.h fi diff --git a/src/ASPHERE/pair_line.cpp b/src/ASPHERE/pair_line.cpp deleted file mode 100644 index 4a3902c888..0000000000 --- a/src/ASPHERE/pair_line.cpp +++ /dev/null @@ -1,444 +0,0 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#include "math.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "pair_line.h" -#include "atom.h" -#include "atom_vec_line.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -#define DELTA 10000 - -/* ---------------------------------------------------------------------- */ - -PairLine::PairLine(LAMMPS *lmp) : Pair(lmp) -{ - avec = (AtomVecLine *) atom->style_match("line"); - if (!avec) error->all(FLERR,"Pair line requires atom style line"); - - dmax = nmax = 0; - discrete = NULL; - dnum = dfirst = NULL; - - single_enable = 0; -} - -/* ---------------------------------------------------------------------- */ - -PairLine::~PairLine() -{ - memory->sfree(discrete); - memory->destroy(dnum); - memory->destroy(dfirst); - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairLine::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - int ni,nj,npi,npj,ifirst,jfirst; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj; - double xi[2],xj[2],fi[2],fj[2],dxi,dxj,dyi,dyj,ti,tj; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - double **torque = atom->torque; - int *line = atom->line; - int *type = atom->type; - int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // grow discrete list if necessary and initialize - - if (nall > nmax) { - memory->destroy(dnum); - memory->destroy(dfirst); - memory->create(dnum,nall,"pair:dnum"); - memory->create(dfirst,nall,"pair:dfirst"); - } - for (i = 0; i < nall; i++) dnum[i] = 0; - ndiscrete = 0; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq >= cutsq[itype][jtype]) continue; - - // line/line interactions = NxN particles - - evdwl = 0.0; - if (line[i] >= 0 && line[j] >= 0) { - if (dnum[i] == 0) discretize(i,sigma[itype][itype]); - npi = dnum[i]; - ifirst = dfirst[i]; - if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]); - npj = dnum[j]; - jfirst = dfirst[j]; - - for (ni = 0; ni < npi; ni++) { - dxi = discrete[ifirst+ni].dx; - dyi = discrete[ifirst+ni].dy; - - for (nj = 0; nj < npj; nj++) { - dxj = discrete[jfirst+nj].dx; - dyj = discrete[jfirst+nj].dy; - - xi[0] = x[i][0] + dxi; - xi[1] = x[i][1] + dyi; - xj[0] = x[j][0] + dxj; - xj[1] = x[j][1] + dyj; - - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - rsq = delx*delx + dely*dely; - - sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma); - sig3 = sig*sig*sig; - term2 = 24.0*epsilon[itype][jtype] * sig3*sig3; - term1 = 2.0 * term2 * sig3*sig3; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (term1*r6inv - term2); - fpair = forcelj*r2inv; - - if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0); - - fi[0] = delx*fpair; - fi[1] = dely*fpair; - f[i][0] += fi[0]; - f[i][1] += fi[1]; - torque[i][2] += dxi*fi[1] - dyi*fi[0]; - - if (newton_pair || j < nlocal) { - fj[0] = -delx*fpair; - fj[1] = -dely*fpair; - f[j][0] += fj[0]; - f[j][1] += fj[1]; - torque[j][2] += dxj*fj[1] - dyj*fj[0]; - } - } - } - - // line/particle interaction = Nx1 particles - // convert line into Np particles based on sigma and line length - - } else if (line[i] >= 0) { - if (dnum[i] == 0) discretize(i,sigma[itype][itype]); - npi = dnum[i]; - ifirst = dfirst[i]; - - for (ni = 0; ni < npi; ni++) { - dxi = discrete[ifirst+ni].dx; - dyi = discrete[ifirst+ni].dy; - - xi[0] = x[i][0] + dxi; - xi[1] = x[i][1] + dyi; - xj[0] = x[j][0]; - xj[1] = x[j][1]; - - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - rsq = delx*delx + dely*dely; - - sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]); - sig3 = sig*sig*sig; - term2 = 24.0*epsilon[itype][jtype] * sig3*sig3; - term1 = 2.0 * term2 * sig3*sig3; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (term1*r6inv - term2); - fpair = forcelj*r2inv; - - if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0); - - fi[0] = delx*fpair; - fi[1] = dely*fpair; - f[i][0] += fi[0]; - f[i][1] += fi[1]; - torque[i][2] += dxi*fi[1] - dyi*fi[0]; - - if (newton_pair || j < nlocal) { - fj[0] = -delx*fpair; - fj[1] = -dely*fpair; - f[j][0] += fj[0]; - f[j][1] += fj[1]; - } - } - - // particle/line interaction = Nx1 particles - // convert line into Np particles based on sigma and line length - - } else if (line[j] >= 0) { - if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]); - npj = dnum[j]; - jfirst = dfirst[j]; - - for (nj = 0; nj < npj; nj++) { - dxj = discrete[jfirst+nj].dx; - dyj = discrete[jfirst+nj].dy; - - xi[0] = x[i][0]; - xi[1] = x[i][1]; - xj[0] = x[j][0] + dxj; - xj[1] = x[j][1] + dyj; - - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - rsq = delx*delx + dely*dely; - - sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma); - sig3 = sig*sig*sig; - term2 = 24.0*epsilon[itype][jtype] * sig3*sig3; - term1 = 2.0 * term2 * sig3*sig3; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (term1*r6inv - term2); - fpair = forcelj*r2inv; - - if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0); - - fi[0] = delx*fpair; - fi[1] = dely*fpair; - f[i][0] += fi[0]; - f[i][1] += fi[1]; - - if (newton_pair || j < nlocal) { - f[j][0] += fj[0]; - f[j][1] += fj[1]; - fj[0] = -delx*fpair; - fj[1] = -dely*fpair; - torque[j][2] += dxj*fj[1] - dyj*fj[0]; - } - } - - // particle/particle interaction = 1x1 particles - - } else { - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - fpair = forcelj*r2inv; - - if (eflag) - evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairLine::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairLine::settings(int narg, char **arg) -{ - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - - cut_global = force->numeric(arg[0]); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i+1; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairLine::coeff(int narg, char **arg) -{ - if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(arg[0],atom->ntypes,ilo,ihi); - force->bounds(arg[1],atom->ntypes,jlo,jhi); - - double epsilon_one = force->numeric(arg[2]); - double sigma_one = force->numeric(arg[3]); - - double cut_one = cut_global; - if (narg == 5) cut_one = force->numeric(arg[4]); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - epsilon[i][j] = epsilon_one; - sigma[i][j] = sigma_one; - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairLine::init_one(int i, int j) -{ - if (setflag[i][j] == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); - } - - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - - epsilon[j][i] = epsilon[i][j]; - sigma[j][i] = sigma[i][j]; - lj1[j][i] = lj1[i][j]; - lj2[j][i] = lj2[i][j]; - lj3[j][i] = lj3[i][j]; - lj4[j][i] = lj4[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - discretize line segment I into N sub-segments no more than sigma in length - store new discrete particles in Discrete list -------------------------------------------------------------------------- */ - -void PairLine::discretize(int i, double sigma) -{ - AtomVecLine::Bonus *bonus = avec->bonus; - double length = bonus[atom->line[i]].length; - double theta = bonus[atom->line[i]].theta; - int n = static_cast (length/sigma) + 1; - dnum[i] = n; - dfirst[i] = ndiscrete; - - if (ndiscrete + n > dmax) { - dmax += DELTA; - discrete = (Discrete *) - memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete"); - } - - double *x = atom->x[i]; - sigma = length/n; - double delta; - - for (int m = 0; m < n; m++) { - delta = -0.5 + (2*m+1)/(2.0*n); - discrete[ndiscrete].dx = delta*length*cos(theta); - discrete[ndiscrete].dy = delta*length*sin(theta); - discrete[ndiscrete].sigma = sigma; - ndiscrete++; - } -} diff --git a/src/ASPHERE/pair_line.h b/src/ASPHERE/pair_line.h deleted file mode 100644 index 6598bfe6c1..0000000000 --- a/src/ASPHERE/pair_line.h +++ /dev/null @@ -1,61 +0,0 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(line,PairLine) - -#else - -#ifndef LMP_PAIR_LINE_H -#define LMP_PAIR_LINE_H - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairLine : public Pair { - public: - PairLine(class LAMMPS *); - ~PairLine(); - void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - double init_one(int, int); - - protected: - double cut_global; - double **cut; - double **epsilon,**sigma; - double **lj1,**lj2,**lj3,**lj4; - class AtomVecLine *avec; - - struct Discrete { - double dx,dy; - double sigma; - }; - Discrete *discrete; // list of all discretes for all lines - int ndiscrete; // number of discretes in list - int dmax; // allocated size of discrete list - int *dnum; // number of discretes per line, 0 if uninit - int *dfirst; // index of first discrete per each line - int nmax; // allocated size of dnum,dfirst vectors - - void allocate(); - void discretize(int, double); -}; - -} - -#endif -#endif diff --git a/src/ASPHERE/pair_tri.cpp b/src/ASPHERE/pair_tri.cpp deleted file mode 100644 index 0a40b8fb06..0000000000 --- a/src/ASPHERE/pair_tri.cpp +++ /dev/null @@ -1,637 +0,0 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#include "math.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "pair_tri.h" -#include "math_extra.h" -#include "atom.h" -#include "atom_vec_tri.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -#define DELTA 20 - -/* ---------------------------------------------------------------------- */ - -PairTri::PairTri(LAMMPS *lmp) : Pair(lmp) -{ - avec = (AtomVecTri *) atom->style_match("tri"); - if (!avec) error->all(FLERR,"Pair tri requires atom style tri"); - - dmax = nmax = 0; - discrete = NULL; - dnum = dfirst = NULL; - - single_enable = 0; -} - -/* ---------------------------------------------------------------------- */ - -PairTri::~PairTri() -{ - memory->sfree(discrete); - memory->destroy(dnum); - memory->destroy(dfirst); - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairTri::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - int ni,nj,npi,npj,ifirst,jfirst; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj; - double dxi,dxj,dyi,dyj,dzi,dzj; - double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3],p[3][3]; - double dc1[3],dc2[3],dc3[3]; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - AtomVecTri::Bonus *bonus = avec->bonus; - double **x = atom->x; - double **f = atom->f; - double **torque = atom->torque; - int *tri = atom->tri; - int *type = atom->type; - int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // grow discrete list if necessary and initialize - - if (nall > nmax) { - memory->destroy(dnum); - memory->destroy(dfirst); - memory->create(dnum,nall,"pair:dnum"); - memory->create(dfirst,nall,"pair:dfirst"); - } - for (i = 0; i < nall; i++) dnum[i] = 0; - ndiscrete = 0; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq >= cutsq[itype][jtype]) continue; - - // tri/tri interactions = NxN particles - // c1,c2,c3 = corner pts of triangle I or J - - evdwl = 0.0; - if (tri[i] >= 0 && tri[j] >= 0) { - if (dnum[i] == 0) { - MathExtra::quat_to_mat(bonus[tri[i]].quat,p); - MathExtra::matvec(p,bonus[tri[i]].c1,dc1); - MathExtra::matvec(p,bonus[tri[i]].c2,dc2); - MathExtra::matvec(p,bonus[tri[i]].c3,dc3); - dfirst[i] = ndiscrete; - discretize(i,sigma[itype][itype],dc1,dc2,dc3); - dnum[i] = ndiscrete - dfirst[i]; - } - npi = dnum[i]; - ifirst = dfirst[i]; - - if (dnum[j] == 0) { - MathExtra::quat_to_mat(bonus[tri[j]].quat,p); - MathExtra::matvec(p,bonus[tri[j]].c1,dc1); - MathExtra::matvec(p,bonus[tri[j]].c2,dc2); - MathExtra::matvec(p,bonus[tri[j]].c3,dc3); - dfirst[j] = ndiscrete; - discretize(j,sigma[jtype][jtype],dc1,dc2,dc3); - dnum[j] = ndiscrete - dfirst[j]; - } - npj = dnum[j]; - jfirst = dfirst[j]; - - for (ni = 0; ni < npi; ni++) { - dxi = discrete[ifirst+ni].dx; - dyi = discrete[ifirst+ni].dy; - dzi = discrete[ifirst+ni].dz; - - for (nj = 0; nj < npj; nj++) { - dxj = discrete[jfirst+nj].dx; - dyj = discrete[jfirst+nj].dy; - dzj = discrete[jfirst+nj].dz; - - xi[0] = x[i][0] + dxi; - xi[1] = x[i][1] + dyi; - xi[2] = x[i][2] + dzi; - xj[0] = x[j][0] + dxj; - xj[1] = x[j][1] + dyj; - xj[2] = x[j][2] + dzj; - - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - delz = xi[2] - xj[2]; - rsq = delx*delx + dely*dely + delz*delz; - - sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma); - sig3 = sig*sig*sig; - term2 = 24.0*epsilon[itype][jtype] * sig3*sig3; - term1 = 2.0 * term2 * sig3*sig3; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (term1*r6inv - term2); - fpair = forcelj*r2inv; - - if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0); - - fi[0] = delx*fpair; - fi[1] = dely*fpair; - fi[2] = delz*fpair; - f[i][0] += fi[0]; - f[i][1] += fi[1]; - f[i][2] += fi[2]; - ti[0] = dyi*fi[2] - dzi*fi[1]; - ti[1] = dzi*fi[0] - dxi*fi[2]; - ti[2] = dxi*fi[1] - dyi*fi[0]; - torque[i][0] += ti[0]; - torque[i][1] += ti[1]; - torque[i][2] += ti[2]; - - if (newton_pair || j < nlocal) { - fj[0] = -delx*fpair; - fj[1] = -dely*fpair; - fj[2] = -delz*fpair; - f[j][0] += fj[0]; - f[j][1] += fj[1]; - f[j][2] += fj[2]; - tj[0] = dyj*fj[2] - dzj*fj[1]; - tj[1] = dzj*fj[0] - dxj*fj[2]; - tj[2] = dxj*fj[1] - dyj*fj[0]; - torque[j][0] += tj[0]; - torque[j][1] += tj[1]; - torque[j][2] += tj[2]; - } - } - } - - // tri/particle interaction = Nx1 particles - // c1,c2,c3 = corner pts of triangle I - - } else if (tri[i] >= 0) { - - if (dnum[i] == 0) { - MathExtra::quat_to_mat(bonus[tri[i]].quat,p); - MathExtra::matvec(p,bonus[tri[i]].c1,dc1); - MathExtra::matvec(p,bonus[tri[i]].c2,dc2); - MathExtra::matvec(p,bonus[tri[i]].c3,dc3); - dfirst[i] = ndiscrete; - discretize(i,sigma[itype][itype],dc1,dc2,dc3); - dnum[i] = ndiscrete - dfirst[i]; - } - npi = dnum[i]; - ifirst = dfirst[i]; - - for (ni = 0; ni < npi; ni++) { - dxi = discrete[ifirst+ni].dx; - dyi = discrete[ifirst+ni].dy; - dzi = discrete[ifirst+ni].dz; - - xi[0] = x[i][0] + dxi; - xi[1] = x[i][1] + dyi; - xi[2] = x[i][2] + dzi; - xj[0] = x[j][0]; - xj[1] = x[j][1]; - xj[2] = x[j][2]; - - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - delz = xi[2] - xj[2]; - rsq = delx*delx + dely*dely + delz*delz; - - sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]); - sig3 = sig*sig*sig; - term2 = 24.0*epsilon[itype][jtype] * sig3*sig3; - term1 = 2.0 * term2 * sig3*sig3; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (term1*r6inv - term2); - fpair = forcelj*r2inv; - - if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0); - - fi[0] = delx*fpair; - fi[1] = dely*fpair; - fi[2] = delz*fpair; - f[i][0] += fi[0]; - f[i][1] += fi[1]; - f[i][2] += fi[2]; - ti[0] = dyi*fi[2] - dzi*fi[1]; - ti[1] = dzi*fi[0] - dxi*fi[2]; - ti[2] = dxi*fi[1] - dyi*fi[0]; - torque[i][2] += ti[0]; - torque[i][1] += ti[1]; - torque[i][2] += ti[2]; - - if (newton_pair || j < nlocal) { - fj[0] = -delx*fpair; - fj[1] = -dely*fpair; - fj[2] = -delz*fpair; - f[j][0] += fj[0]; - f[j][1] += fj[1]; - f[j][2] += fj[2]; - } - } - - // particle/tri interaction = Nx1 particles - // c1,c2,c3 = corner pts of triangle J - - } else if (tri[j] >= 0) { - if (dnum[j] == 0) { - MathExtra::quat_to_mat(bonus[tri[j]].quat,p); - MathExtra::matvec(p,bonus[tri[j]].c1,dc1); - MathExtra::matvec(p,bonus[tri[j]].c2,dc2); - MathExtra::matvec(p,bonus[tri[j]].c3,dc3); - dfirst[j] = ndiscrete; - discretize(j,sigma[jtype][jtype],dc1,dc2,dc3); - dnum[j] = ndiscrete - dfirst[j]; - } - npj = dnum[j]; - jfirst = dfirst[j]; - - for (nj = 0; nj < npj; nj++) { - dxj = discrete[jfirst+nj].dx; - dyj = discrete[jfirst+nj].dy; - dzj = discrete[jfirst+nj].dz; - - xi[0] = x[i][0]; - xi[1] = x[i][1]; - xi[2] = x[i][2]; - xj[0] = x[j][0] + dxj; - xj[1] = x[j][1] + dyj; - xj[2] = x[j][2] + dzj; - - delx = xi[0] - xj[0]; - dely = xi[1] - xj[1]; - delz = xi[2] - xj[2]; - rsq = delx*delx + dely*dely + delz*delz; - - sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma); - sig3 = sig*sig*sig; - term2 = 24.0*epsilon[itype][jtype] * sig3*sig3; - term1 = 2.0 * term2 * sig3*sig3; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (term1*r6inv - term2); - fpair = forcelj*r2inv; - - if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0); - - fi[0] = delx*fpair; - fi[1] = dely*fpair; - fi[2] = delz*fpair; - f[i][0] += fi[0]; - f[i][1] += fi[1]; - f[i][2] += fi[2]; - - if (newton_pair || j < nlocal) { - fj[0] = -delx*fpair; - fj[1] = -dely*fpair; - fj[2] = -delz*fpair; - f[j][0] += fj[0]; - f[j][1] += fj[1]; - f[j][2] += fj[2]; - tj[0] = dyj*fj[2] - dzj*fj[1]; - tj[1] = dzj*fj[0] - dxj*fj[2]; - tj[2] = dxj*fj[1] - dyj*fj[0]; - torque[j][0] += tj[0]; - torque[j][1] += tj[1]; - torque[j][2] += tj[2]; - } - } - - // particle/particle interaction = 1x1 particles - - } else { - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - fpair = forcelj*r2inv; - - if (eflag) - evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairTri::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairTri::settings(int narg, char **arg) -{ - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - - cut_global = force->numeric(arg[0]); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i+1; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairTri::coeff(int narg, char **arg) -{ - if (narg < 4 || narg > 5) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(arg[0],atom->ntypes,ilo,ihi); - force->bounds(arg[1],atom->ntypes,jlo,jhi); - - double epsilon_one = force->numeric(arg[2]); - double sigma_one = force->numeric(arg[3]); - - double cut_one = cut_global; - if (narg == 5) cut_one = force->numeric(arg[4]); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - epsilon[i][j] = epsilon_one; - sigma[i][j] = sigma_one; - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairTri::init_one(int i, int j) -{ - if (setflag[i][j] == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); - } - - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - - epsilon[j][i] = epsilon[i][j]; - sigma[j][i] = sigma[i][j]; - lj1[j][i] = lj1[i][j]; - lj2[j][i] = lj2[i][j]; - lj3[j][i] = lj3[i][j]; - lj4[j][i] = lj4[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - recursively discretize triangle I with displaced corners c1,c2,c3 - into N sub-tris no more than sigma in size - recurse by making 2 tris via bisecting longest side - store new discrete particles in Discrete list -------------------------------------------------------------------------- */ - -void PairTri::discretize(int i, double sigma, - double *c1, double *c2, double *c3) -{ - double c1c2[3],c2c3[3],c1c3[3]; - - double centroid[3],dc1[3],dc2[3],dc3[3]; - - centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0; - centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0; - centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0; - - MathExtra::sub3(c1,centroid,dc1); - MathExtra::sub3(c2,centroid,dc2); - MathExtra::sub3(c3,centroid,dc3); - - double sigmasq = 0.25 * sigma*sigma; - double len1sq = MathExtra::lensq3(dc1); - double len2sq = MathExtra::lensq3(dc2); - double len3sq = MathExtra::lensq3(dc3); - - // if sigma sphere overlaps all corner points, add particle at centroid - - if (len1sq <= sigmasq && len2sq <= sigmasq & len3sq <= sigmasq) { - if (ndiscrete == dmax) { - dmax += DELTA; - discrete = (Discrete *) - memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete"); - } - discrete[ndiscrete].dx = centroid[0]; - discrete[ndiscrete].dy = centroid[1]; - discrete[ndiscrete].dz = centroid[2]; - sigmasq = MAX(len1sq,len2sq); - sigmasq = MAX(sigmasq,len3sq); - discrete[ndiscrete].sigma = 2.0 * sqrt(sigmasq); - ndiscrete++; - return; - } - - // else break triangle into 2 sub-triangles and recurse - - double c12[3],c23[3],c13[3],mid[3]; - - MathExtra::sub3(c2,c3,c23); - len1sq = MathExtra::lensq3(c23); - MathExtra::sub3(c1,c3,c13); - len2sq = MathExtra::lensq3(c13); - MathExtra::sub3(c1,c2,c12); - len3sq = MathExtra::lensq3(c12); - - double maxsq = MAX(len1sq,len2sq); - maxsq = MAX(maxsq,len3sq); - - if (len1sq == maxsq) { - MathExtra::add3(c2,c3,mid); - MathExtra::scale3(0.5,mid); - discretize(i,sigma,c1,c2,mid); - discretize(i,sigma,c1,c3,mid); - } else if (len2sq == maxsq) { - MathExtra::add3(c1,c3,mid); - MathExtra::scale3(0.5,mid); - discretize(i,sigma,c2,c1,mid); - discretize(i,sigma,c2,c3,mid); - } else { - MathExtra::add3(c1,c2,mid); - MathExtra::scale3(0.5,mid); - discretize(i,sigma,c3,c1,mid); - discretize(i,sigma,c3,c2,mid); - } -} - -/* ---------------------------------------------------------------------- - recursively discretize triangle I with displaced corners c1,c2,c3 - into N sub-tris no more than sigma in size - recurse by making 6 tris via centroid - store new discrete particles in Discrete list -------------------------------------------------------------------------- */ - -/* -void PairTri::discretize(int i, double sigma, - double *c1, double *c2, double *c3) -{ - double centroid[3],dc1[3],dc2[3],dc3[3]; - - centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0; - centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0; - centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0; - - MathExtra::sub3(c1,centroid,dc1); - MathExtra::sub3(c2,centroid,dc2); - MathExtra::sub3(c3,centroid,dc3); - - double sigmasq = 0.25 * sigma*sigma; - double len1sq = MathExtra::lensq3(dc1); - double len2sq = MathExtra::lensq3(dc2); - double len3sq = MathExtra::lensq3(dc3); - - // if sigma sphere overlaps all corner points, add particle at centroid - - if (len1sq <= sigmasq && len2sq <= sigmasq & len3sq <= sigmasq) { - if (ndiscrete == dmax) { - dmax += DELTA; - discrete = (Discrete *) - memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete"); - } - discrete[ndiscrete].dx = centroid[0]; - discrete[ndiscrete].dy = centroid[1]; - discrete[ndiscrete].dz = centroid[2]; - sigmasq = MAX(len1sq,len2sq); - sigmasq = MAX(sigmasq,len3sq); - discrete[ndiscrete].sigma = 2.0 * sqrt(sigmasq); - ndiscrete++; - return; - } - - // else break triangle into 6 sub-triangles and recurse - - double c1c2mid[3],c2c3mid[3],c1c3mid[3]; - - MathExtra::add3(c1,c2,c1c2mid); - MathExtra::scale3(0.5,c1c2mid); - MathExtra::add3(c2,c3,c2c3mid); - MathExtra::scale3(0.5,c2c3mid); - MathExtra::add3(c1,c3,c1c3mid); - MathExtra::scale3(0.5,c1c3mid); - - discretize(i,sigma,c1,c1c2mid,centroid); - discretize(i,sigma,c1,c1c3mid,centroid); - discretize(i,sigma,c2,c2c3mid,centroid); - discretize(i,sigma,c2,c1c2mid,centroid); - discretize(i,sigma,c3,c1c3mid,centroid); - discretize(i,sigma,c3,c2c3mid,centroid); -} - -*/ diff --git a/src/ASPHERE/pair_tri.h b/src/ASPHERE/pair_tri.h deleted file mode 100644 index fd1fe08bac..0000000000 --- a/src/ASPHERE/pair_tri.h +++ /dev/null @@ -1,61 +0,0 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(tri,PairTri) - -#else - -#ifndef LMP_PAIR_TRI_H -#define LMP_PAIR_TRI_H - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairTri : public Pair { - public: - PairTri(class LAMMPS *); - ~PairTri(); - void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - double init_one(int, int); - - protected: - double cut_global; - double **cut; - double **epsilon,**sigma; - double **lj1,**lj2,**lj3,**lj4; - class AtomVecTri *avec; - - struct Discrete { - double dx,dy,dz; - double sigma; - }; - Discrete *discrete; // list of all discretes for all lines - int ndiscrete; // number of discretes in list - int dmax; // allocated size of discrete list - int *dnum; // number of discretes per line, 0 if uninit - int *dfirst; // index of first discrete per each line - int nmax; // allocated size of dnum,dfirst vectors - - void allocate(); - void discretize(int, double, double *, double *, double *); -}; - -} - -#endif -#endif