diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 83d34c306..503b87f4a 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -1,378 +1,378 @@ /* ---------------------------------------------------------------------- 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 <stdlib.h> #include <string.h> #include "fix_wall.h" #include "atom.h" #include "input.h" #include "variable.h" #include "domain.h" #include "lattice.h" #include "update.h" #include "modify.h" #include "respa.h" #include "error.h" #include "force.h" using namespace LAMMPS_NS; using namespace FixConst; enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5}; enum{NONE=0,EDGE,CONSTANT,VARIABLE}; /* ---------------------------------------------------------------------- */ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) + Fix(lmp, narg, arg), + nwall(0) { scalar_flag = 1; vector_flag = 1; global_freq = 1; extscalar = 1; extvector = 1; respa_level_support = 1; ilevel_respa = 0; // parse args - nwall = 0; int scaleflag = 1; fldflag = 0; int pbcflag = 0; for (int i = 0; i < 6; i++) xstr[i] = estr[i] = sstr[i] = NULL; int iarg = 3; while (iarg < narg) { if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) || (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) || (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) { if (iarg+5 > narg) error->all(FLERR,"Illegal fix wall command"); int newwall; if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO; else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI; else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO; else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI; else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO; else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI; for (int m = 0; (m < nwall) && (m < 6); m++) if (newwall == wallwhich[m]) error->all(FLERR,"Wall defined twice in fix wall command"); wallwhich[nwall] = newwall; if (strcmp(arg[iarg+1],"EDGE") == 0) { xstyle[nwall] = EDGE; int dim = wallwhich[nwall] / 2; int side = wallwhich[nwall] % 2; if (side == 0) coord0[nwall] = domain->boxlo[dim]; else coord0[nwall] = domain->boxhi[dim]; } else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) { xstyle[nwall] = VARIABLE; int n = strlen(&arg[iarg+1][2]) + 1; xstr[nwall] = new char[n]; strcpy(xstr[nwall],&arg[iarg+1][2]); } else { xstyle[nwall] = CONSTANT; coord0[nwall] = force->numeric(FLERR,arg[iarg+1]); } if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) { int n = strlen(&arg[iarg+2][2]) + 1; estr[nwall] = new char[n]; strcpy(estr[nwall],&arg[iarg+2][2]); estyle[nwall] = VARIABLE; } else { epsilon[nwall] = force->numeric(FLERR,arg[iarg+2]); estyle[nwall] = CONSTANT; } if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) { int n = strlen(&arg[iarg+3][2]) + 1; sstr[nwall] = new char[n]; strcpy(sstr[nwall],&arg[iarg+3][2]); sstyle[nwall] = VARIABLE; } else { sigma[nwall] = force->numeric(FLERR,arg[iarg+3]); sstyle[nwall] = CONSTANT; } cutoff[nwall] = force->numeric(FLERR,arg[iarg+4]); nwall++; iarg += 5; } else if (strcmp(arg[iarg],"units") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall command"); if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; else error->all(FLERR,"Illegal fix wall command"); iarg += 2; } else if (strcmp(arg[iarg],"fld") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall command"); if (strcmp(arg[iarg+1],"no") == 0) fldflag = 0; else if (strcmp(arg[iarg+1],"yes") == 0) fldflag = 1; else error->all(FLERR,"Illegal fix wall command"); iarg += 2; } else if (strcmp(arg[iarg],"pbc") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall command"); if (strcmp(arg[iarg+1],"yes") == 0) pbcflag = 1; else if (strcmp(arg[iarg+1],"no") == 0) pbcflag = 0; else error->all(FLERR,"Illegal fix wall command"); iarg += 2; } else error->all(FLERR,"Illegal fix wall command"); } size_vector = nwall; // error checks if (nwall == 0) error->all(FLERR,"Illegal fix wall command"); for (int m = 0; m < nwall; m++) if (cutoff[m] <= 0.0) error->all(FLERR,"Fix wall cutoff <= 0.0"); for (int m = 0; m < nwall; m++) if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2) error->all(FLERR,"Cannot use fix wall zlo/zhi for a 2d simulation"); if (!pbcflag) { for (int m = 0; m < nwall; m++) { if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic) error->all(FLERR,"Cannot use fix wall in periodic dimension"); if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic) error->all(FLERR,"Cannot use fix wall in periodic dimension"); if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic) error->all(FLERR,"Cannot use fix wall in periodic dimension"); } } // scale factors for wall position for CONSTANT and VARIABLE walls int flag = 0; for (int m = 0; m < nwall; m++) if (xstyle[m] != EDGE) flag = 1; if (flag) { if (scaleflag) { xscale = domain->lattice->xlattice; yscale = domain->lattice->ylattice; zscale = domain->lattice->zlattice; } else xscale = yscale = zscale = 1.0; for (int m = 0; m < nwall; m++) { if (xstyle[m] != CONSTANT) continue; if (wallwhich[m] < YLO) coord0[m] *= xscale; else if (wallwhich[m] < ZLO) coord0[m] *= yscale; else coord0[m] *= zscale; } } // set xflag if any wall positions are variable // set varflag if any wall positions or parameters are variable // set wstyle to VARIABLE if either epsilon or sigma is a variable varflag = xflag = 0; for (int m = 0; m < nwall; m++) { if (xstyle[m] == VARIABLE) xflag = 1; if (xflag || estyle[m] == VARIABLE || sstyle[m] == VARIABLE) varflag = 1; if (estyle[m] == VARIABLE || sstyle[m] == VARIABLE) wstyle[m] = VARIABLE; else wstyle[m] = CONSTANT; } eflag = 0; for (int m = 0; m <= nwall; m++) ewall[m] = 0.0; } /* ---------------------------------------------------------------------- */ FixWall::~FixWall() { for (int m = 0; m < nwall; m++) { delete [] xstr[m]; delete [] estr[m]; delete [] sstr[m]; } } /* ---------------------------------------------------------------------- */ int FixWall::setmask() { int mask = 0; // FLD implicit needs to invoke wall forces before pair style if (fldflag) mask |= PRE_FORCE; else mask |= POST_FORCE; mask |= THERMO_ENERGY; mask |= POST_FORCE_RESPA; mask |= MIN_POST_FORCE; return mask; } /* ---------------------------------------------------------------------- */ void FixWall::init() { for (int m = 0; m < nwall; m++) { if (xstyle[m] == VARIABLE) { xindex[m] = input->variable->find(xstr[m]); if (xindex[m] < 0) error->all(FLERR,"Variable name for fix wall does not exist"); if (!input->variable->equalstyle(xindex[m])) error->all(FLERR,"Variable for fix wall is invalid style"); } if (estyle[m] == VARIABLE) { eindex[m] = input->variable->find(estr[m]); if (eindex[m] < 0) error->all(FLERR,"Variable name for fix wall does not exist"); if (!input->variable->equalstyle(eindex[m])) error->all(FLERR,"Variable for fix wall is invalid style"); } if (sstyle[m] == VARIABLE) { sindex[m] = input->variable->find(sstr[m]); if (sindex[m] < 0) error->all(FLERR,"Variable name for fix wall does not exist"); if (!input->variable->equalstyle(sindex[m])) error->all(FLERR,"Variable for fix wall is invalid style"); } } // setup coefficients for (int m = 0; m < nwall; m++) precompute(m); if (strstr(update->integrate_style,"respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } } /* ---------------------------------------------------------------------- */ void FixWall::setup(int vflag) { if (strstr(update->integrate_style,"verlet")) { if (!fldflag) post_force(vflag); } else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); post_force_respa(vflag,ilevel_respa,0); ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); } } /* ---------------------------------------------------------------------- */ void FixWall::min_setup(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- only called if fldflag set, in place of post_force ------------------------------------------------------------------------- */ void FixWall::pre_force(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- */ void FixWall::post_force(int vflag) { eflag = 0; for (int m = 0; m <= nwall; m++) ewall[m] = 0.0; // coord = current position of wall // evaluate variables if necessary, wrap with clear/add // for epsilon/sigma variables need to re-invoke precompute() if (varflag) modify->clearstep_compute(); double coord; for (int m = 0; m < nwall; m++) { if (xstyle[m] == VARIABLE) { coord = input->variable->compute_equal(xindex[m]); if (wallwhich[m] < YLO) coord *= xscale; else if (wallwhich[m] < ZLO) coord *= yscale; else coord *= zscale; } else coord = coord0[m]; if (wstyle[m] == VARIABLE) { if (estyle[m] == VARIABLE) { epsilon[m] = input->variable->compute_equal(eindex[m]); if (epsilon[m] < 0.0) error->all(FLERR,"Variable evaluation in fix wall gave bad value"); } if (sstyle[m] == VARIABLE) { sigma[m] = input->variable->compute_equal(sindex[m]); if (sigma[m] < 0.0) error->all(FLERR,"Variable evaluation in fix wall gave bad value"); } precompute(m); } wall_particle(m,wallwhich[m],coord); } if (varflag) modify->addstep_compute(update->ntimestep + 1); } /* ---------------------------------------------------------------------- */ void FixWall::post_force_respa(int vflag, int ilevel, int iloop) { if (ilevel == ilevel_respa) post_force(vflag); } /* ---------------------------------------------------------------------- */ void FixWall::min_post_force(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- energy of wall interaction ------------------------------------------------------------------------- */ double FixWall::compute_scalar() { // only sum across procs one time if (eflag == 0) { MPI_Allreduce(ewall,ewall_all,nwall+1,MPI_DOUBLE,MPI_SUM,world); eflag = 1; } return ewall_all[0]; } /* ---------------------------------------------------------------------- components of force on wall ------------------------------------------------------------------------- */ double FixWall::compute_vector(int n) { // only sum across procs one time if (eflag == 0) { MPI_Allreduce(ewall,ewall_all,nwall+1,MPI_DOUBLE,MPI_SUM,world); eflag = 1; } return ewall_all[n+1]; } diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index b5c70037b..dba7cf703 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -1,228 +1,229 @@ /* ---------------------------------------------------------------------- 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 <stdlib.h> #include <string.h> #include "fix_wall_reflect.h" #include "atom.h" #include "comm.h" #include "update.h" #include "modify.h" #include "domain.h" #include "lattice.h" #include "input.h" #include "variable.h" #include "error.h" #include "force.h" using namespace LAMMPS_NS; using namespace FixConst; enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5}; enum{NONE=0,EDGE,CONSTANT,VARIABLE}; /* ---------------------------------------------------------------------- */ FixWallReflect::FixWallReflect(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) + Fix(lmp, narg, arg), + nwall(0) { if (narg < 4) error->all(FLERR,"Illegal fix wall/reflect command"); // parse args nwall = 0; int scaleflag = 1; int iarg = 3; while (iarg < narg) { if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) || (strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) || (strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall/reflect command"); int newwall; if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO; else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI; else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO; else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI; else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO; else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI; for (int m = 0; (m < nwall) && (m < 6); m++) if (newwall == wallwhich[m]) error->all(FLERR,"Wall defined twice in fix wall/reflect command"); wallwhich[nwall] = newwall; if (strcmp(arg[iarg+1],"EDGE") == 0) { wallstyle[nwall] = EDGE; int dim = wallwhich[nwall] / 2; int side = wallwhich[nwall] % 2; if (side == 0) coord0[nwall] = domain->boxlo[dim]; else coord0[nwall] = domain->boxhi[dim]; } else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) { wallstyle[nwall] = VARIABLE; int n = strlen(&arg[iarg+1][2]) + 1; varstr[nwall] = new char[n]; strcpy(varstr[nwall],&arg[iarg+1][2]); } else { wallstyle[nwall] = CONSTANT; coord0[nwall] = force->numeric(FLERR,arg[iarg+1]); } nwall++; iarg += 2; } else if (strcmp(arg[iarg],"units") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal wall/reflect command"); if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; else error->all(FLERR,"Illegal fix wall/reflect command"); iarg += 2; } else error->all(FLERR,"Illegal fix wall/reflect command"); } // error check if (nwall == 0) error->all(FLERR,"Illegal fix wall command"); for (int m = 0; m < nwall; m++) { if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic) error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension"); if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic) error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension"); if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic) error->all(FLERR,"Cannot use fix wall/reflect in periodic dimension"); } for (int m = 0; m < nwall; m++) if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2) error->all(FLERR, "Cannot use fix wall/reflect zlo/zhi for a 2d simulation"); // scale factors for CONSTANT and VARIABLE walls int flag = 0; for (int m = 0; m < nwall; m++) if (wallstyle[m] != EDGE) flag = 1; if (flag) { if (scaleflag) { xscale = domain->lattice->xlattice; yscale = domain->lattice->ylattice; zscale = domain->lattice->zlattice; } else xscale = yscale = zscale = 1.0; for (int m = 0; m < nwall; m++) { if (wallstyle[m] != CONSTANT) continue; if (wallwhich[m] < YLO) coord0[m] *= xscale; else if (wallwhich[m] < ZLO) coord0[m] *= yscale; else coord0[m] *= zscale; } } // set varflag if any wall positions are variable varflag = 0; for (int m = 0; m < nwall; m++) if (wallstyle[m] == VARIABLE) varflag = 1; } /* ---------------------------------------------------------------------- */ FixWallReflect::~FixWallReflect() { if (copymode) return; for (int m = 0; m < nwall; m++) if (wallstyle[m] == VARIABLE) delete [] varstr[m]; } /* ---------------------------------------------------------------------- */ int FixWallReflect::setmask() { int mask = 0; mask |= POST_INTEGRATE; mask |= POST_INTEGRATE_RESPA; return mask; } /* ---------------------------------------------------------------------- */ void FixWallReflect::init() { for (int m = 0; m < nwall; m++) { if (wallstyle[m] != VARIABLE) continue; varindex[m] = input->variable->find(varstr[m]); if (varindex[m] < 0) error->all(FLERR,"Variable name for fix wall/reflect does not exist"); if (!input->variable->equalstyle(varindex[m])) error->all(FLERR,"Variable for fix wall/reflect is invalid style"); } int nrigid = 0; for (int i = 0; i < modify->nfix; i++) if (modify->fix[i]->rigid_flag) nrigid++; if (nrigid && comm->me == 0) error->warning(FLERR,"Should not allow rigid bodies to bounce off " "relecting walls"); } /* ---------------------------------------------------------------------- */ void FixWallReflect::post_integrate() { int i,dim,side; double coord; // coord = current position of wall // evaluate variable if necessary, wrap with clear/add double **x = atom->x; double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; if (varflag) modify->clearstep_compute(); for (int m = 0; m < nwall; m++) { if (wallstyle[m] == VARIABLE) { coord = input->variable->compute_equal(varindex[m]); if (wallwhich[m] < YLO) coord *= xscale; else if (wallwhich[m] < ZLO) coord *= yscale; else coord *= zscale; } else coord = coord0[m]; dim = wallwhich[m] / 2; side = wallwhich[m] % 2; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { if (side == 0) { if (x[i][dim] < coord) { x[i][dim] = coord + (coord - x[i][dim]); v[i][dim] = -v[i][dim]; } } else { if (x[i][dim] > coord) { x[i][dim] = coord - (x[i][dim] - coord); v[i][dim] = -v[i][dim]; } } } } if (varflag) modify->addstep_compute(update->ntimestep + 1); } diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index 824f92eb8..f543c1217 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -1,367 +1,368 @@ /* ---------------------------------------------------------------------- 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 <stdlib.h> #include <string.h> #include "fix_wall_region.h" #include "atom.h" #include "atom_vec.h" #include "domain.h" #include "region.h" #include "force.h" #include "lattice.h" #include "update.h" #include "output.h" #include "respa.h" #include "error.h" using namespace LAMMPS_NS; using namespace FixConst; enum{LJ93,LJ126,COLLOID,HARMONIC}; /* ---------------------------------------------------------------------- */ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) + Fix(lmp, narg, arg), + idregion(NULL) { if (narg != 8) error->all(FLERR,"Illegal fix wall/region command"); scalar_flag = 1; vector_flag = 1; size_vector = 3; global_freq = 1; extscalar = 1; extvector = 1; respa_level_support = 1; ilevel_respa = 0; // parse args iregion = domain->find_region(arg[3]); if (iregion == -1) error->all(FLERR,"Region ID for fix wall/region does not exist"); int n = strlen(arg[3]) + 1; idregion = new char[n]; strcpy(idregion,arg[3]); if (strcmp(arg[4],"lj93") == 0) style = LJ93; else if (strcmp(arg[4],"lj126") == 0) style = LJ126; else if (strcmp(arg[4],"colloid") == 0) style = COLLOID; else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC; else error->all(FLERR,"Illegal fix wall/region command"); epsilon = force->numeric(FLERR,arg[5]); sigma = force->numeric(FLERR,arg[6]); cutoff = force->numeric(FLERR,arg[7]); if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region cutoff <= 0.0"); eflag = 0; ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0; } /* ---------------------------------------------------------------------- */ FixWallRegion::~FixWallRegion() { delete [] idregion; } /* ---------------------------------------------------------------------- */ int FixWallRegion::setmask() { int mask = 0; mask |= POST_FORCE; mask |= THERMO_ENERGY; mask |= POST_FORCE_RESPA; mask |= MIN_POST_FORCE; return mask; } /* ---------------------------------------------------------------------- */ void FixWallRegion::init() { // set index and check validity of region iregion = domain->find_region(idregion); if (iregion == -1) error->all(FLERR,"Region ID for fix wall/region does not exist"); // error checks for style COLLOID // insure all particles in group are extended particles if (style == COLLOID) { if (!atom->sphere_flag) error->all(FLERR,"Fix wall/region colloid requires atom style sphere"); double *radius = atom->radius; int *mask = atom->mask; int nlocal = atom->nlocal; int flag = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) if (radius[i] == 0.0) flag = 1; int flagall; MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); if (flagall) error->all(FLERR,"Fix wall/region colloid requires extended particles"); } // setup coefficients for each style if (style == LJ93) { coeff1 = 6.0/5.0 * epsilon * pow(sigma,9.0); coeff2 = 3.0 * epsilon * pow(sigma,3.0); coeff3 = 2.0/15.0 * epsilon * pow(sigma,9.0); coeff4 = epsilon * pow(sigma,3.0); double rinv = 1.0/cutoff; double r2inv = rinv*rinv; double r4inv = r2inv*r2inv; offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv; } else if (style == LJ126) { coeff1 = 48.0 * epsilon * pow(sigma,12.0); coeff2 = 24.0 * epsilon * pow(sigma,6.0); coeff3 = 4.0 * epsilon * pow(sigma,12.0); coeff4 = 4.0 * epsilon * pow(sigma,6.0); double r2inv = 1.0/(cutoff*cutoff); double r6inv = r2inv*r2inv*r2inv; offset = r6inv*(coeff3*r6inv - coeff4); } else if (style == COLLOID) { coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0); coeff2 = -2.0/3.0 * epsilon; coeff3 = epsilon * pow(sigma,6.0)/7560.0; coeff4 = epsilon/6.0; double rinv = 1.0/cutoff; double r2inv = rinv*rinv; double r4inv = r2inv*r2inv; offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv; } if (strstr(update->integrate_style,"respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } } /* ---------------------------------------------------------------------- */ void FixWallRegion::setup(int vflag) { if (strstr(update->integrate_style,"verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); post_force_respa(vflag,ilevel_respa,0); ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); } } /* ---------------------------------------------------------------------- */ void FixWallRegion::min_setup(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- */ void FixWallRegion::post_force(int vflag) { int i,m,n; double rinv,fx,fy,fz,tooclose; double **x = atom->x; double **f = atom->f; double *radius = atom->radius; int *mask = atom->mask; int nlocal = atom->nlocal; Region *region = domain->regions[iregion]; region->prematch(); int onflag = 0; // region->match() insures particle is in region or on surface, else error // if returned contact dist r = 0, is on surface, also an error // in COLLOID case, r <= radius is an error // initilize ewall after region->prematch(), // so a dynamic region can access last timestep values eflag = 0; ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { if (!region->match(x[i][0],x[i][1],x[i][2])) { onflag = 1; continue; } if (style == COLLOID) tooclose = radius[i]; else tooclose = 0.0; n = region->surface(x[i][0],x[i][1],x[i][2],cutoff); for (m = 0; m < n; m++) { if (region->contact[m].r <= tooclose) { onflag = 1; continue; } else rinv = 1.0/region->contact[m].r; if (style == LJ93) lj93(region->contact[m].r); else if (style == LJ126) lj126(region->contact[m].r); else if (style == COLLOID) colloid(region->contact[m].r,radius[i]); else harmonic(region->contact[m].r); ewall[0] += eng; fx = fwall * region->contact[m].delx * rinv; fy = fwall * region->contact[m].dely * rinv; fz = fwall * region->contact[m].delz * rinv; f[i][0] += fx; f[i][1] += fy; f[i][2] += fz; ewall[1] -= fx; ewall[2] -= fy; ewall[3] -= fz; } } if (onflag) error->one(FLERR,"Particle outside surface of region " "used in fix wall/region"); } /* ---------------------------------------------------------------------- */ void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop) { if (ilevel == ilevel_respa) post_force(vflag); } /* ---------------------------------------------------------------------- */ void FixWallRegion::min_post_force(int vflag) { post_force(vflag); } /* ---------------------------------------------------------------------- energy of wall interaction ------------------------------------------------------------------------- */ double FixWallRegion::compute_scalar() { // only sum across procs one time if (eflag == 0) { MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world); eflag = 1; } return ewall_all[0]; } /* ---------------------------------------------------------------------- components of force on wall ------------------------------------------------------------------------- */ double FixWallRegion::compute_vector(int n) { // only sum across procs one time if (eflag == 0) { MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world); eflag = 1; } return ewall_all[n+1]; } /* ---------------------------------------------------------------------- LJ 9/3 interaction for particle with wall compute eng and fwall = magnitude of wall force ------------------------------------------------------------------------- */ void FixWallRegion::lj93(double r) { double rinv = 1.0/r; double r2inv = rinv*rinv; double r4inv = r2inv*r2inv; double r10inv = r4inv*r4inv*r2inv; fwall = coeff1*r10inv - coeff2*r4inv; eng = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv - offset; } /* ---------------------------------------------------------------------- LJ 12/6 interaction for particle with wall compute eng and fwall = magnitude of wall force ------------------------------------------------------------------------- */ void FixWallRegion::lj126(double r) { double rinv = 1.0/r; double r2inv = rinv*rinv; double r6inv = r2inv*r2inv*r2inv; fwall = r6inv*(coeff1*r6inv - coeff2) * rinv; eng = r6inv*(coeff3*r6inv - coeff4) - offset; } /* ---------------------------------------------------------------------- colloid interaction for finite-size particle of rad with wall compute eng and fwall = magnitude of wall force ------------------------------------------------------------------------- */ void FixWallRegion::colloid(double r, double rad) { double new_coeff2 = coeff2*rad*rad*rad; double diam = 2.0*rad; double rad2 = rad*rad; double rad4 = rad2*rad2; double rad8 = rad4*rad4; double delta2 = rad2 - r*r; double rinv = 1.0/delta2; double r2inv = rinv*rinv; double r4inv = r2inv*r2inv; double r8inv = r4inv*r4inv; fwall = coeff1*(rad8*rad + 27.0*rad4*rad2*rad*pow(r,2.0) + 63.0*rad4*rad*pow(r,4.0) + 21.0*rad2*rad*pow(r,6.0))*r8inv - new_coeff2*r2inv; double r2 = 0.5*diam - r; double rinv2 = 1.0/r2; double r2inv2 = rinv2*rinv2; double r4inv2 = r2inv2*r2inv2; double r3 = r + 0.5*diam; double rinv3 = 1.0/r3; double r2inv3 = rinv3*rinv3; double r4inv3 = r2inv3*r2inv3; eng = coeff3*((-3.5*diam+r)*r4inv2*r2inv2*rinv2 + (3.5*diam+r)*r4inv3*r2inv3*rinv3) - coeff4*((-diam*r+r2*r3*(log(-r2)-log(r3)))* (-rinv2)*rinv3) - offset; } /* ---------------------------------------------------------------------- harmonic interaction for particle with wall compute eng and fwall = magnitude of wall force ------------------------------------------------------------------------- */ void FixWallRegion::harmonic(double r) { double dr = cutoff - r; fwall = 2.0*epsilon*dr; eng = epsilon*dr*dr; }