/* ---------------------------------------------------------------------- This is the ██╗ ██╗ ██████╗ ██████╗ ██████╗ ██╗ ██╗████████╗███████╗ ██║ ██║██╔════╝ ██╔════╝ ██╔════╝ ██║ ██║╚══██╔══╝██╔════╝ ██║ ██║██║ ███╗██║ ███╗██║ ███╗███████║ ██║ ███████╗ ██║ ██║██║ ██║██║ ██║██║ ██║██╔══██║ ██║ ╚════██║ ███████╗██║╚██████╔╝╚██████╔╝╚██████╔╝██║ ██║ ██║ ███████║ ╚══════╝╚═╝ ╚═════╝ ╚═════╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝ ╚══════╝® DEM simulation engine, released by DCS Computing Gmbh, Linz, Austria http://www.dcs-computing.com, office@dcs-computing.com LIGGGHTS® is part of CFDEM®project: http://www.liggghts.com | http://www.cfdem.com Core developer and main author: Christoph Kloss, christoph.kloss@dcs-computing.com LIGGGHTS® is open-source, distributed under the terms of the GNU Public License, version 2 or later. It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. You should have received a copy of the GNU General Public License along with LIGGGHTS®. If not, see http://www.gnu.org/licenses . See also top-level README and LICENSE files. LIGGGHTS® and CFDEM® are registered trade marks of DCS Computing GmbH, the producer of the LIGGGHTS® software and the CFDEM®coupling software See http://www.cfdem.com/terms-trademark-policy for details. ------------------------------------------------------------------------- Contributing author and copyright for this file: This file is from LAMMPS 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. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ #include #include #include "respa.h" #include "neighbor.h" #include "atom.h" #include "domain.h" #include "comm.h" #include "force.h" #include "pair.h" #include "bond.h" #include "angle.h" #include "dihedral.h" #include "improper.h" #include "kspace.h" #include "output.h" #include "update.h" #include "modify.h" #include "compute.h" #include "fix_respa.h" #include "timer.h" #include "memory.h" #include "error.h" #include "signal_handling.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ Respa::Respa(LAMMPS *lmp, int narg, char **arg) : Integrate(lmp, narg, arg) { if (narg < 1) error->all(FLERR,"Illegal run_style respa command"); nlevels = force->inumeric(FLERR,arg[0]); if (nlevels < 1) error->all(FLERR,"Respa levels must be >= 1"); if (narg < nlevels) error->all(FLERR,"Illegal run_style respa command"); loop = new int[nlevels]; for (int iarg = 1; iarg < nlevels; iarg++) { loop[iarg-1] = force->inumeric(FLERR,arg[iarg]); if (loop[iarg-1] <= 0) error->all(FLERR,"Illegal run_style respa command"); } loop[nlevels-1] = 1; // set level at which each force is computed // argument settings override defaults level_bond = level_angle = level_dihedral = level_improper = -1; level_pair = level_kspace = -1; level_inner = level_middle = level_outer = -1; int iarg = nlevels; while (iarg < narg) { if (strcmp(arg[iarg],"bond") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_bond = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else if (strcmp(arg[iarg],"angle") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_angle = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else if (strcmp(arg[iarg],"dihedral") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_dihedral = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else if (strcmp(arg[iarg],"improper") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_improper = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else if (strcmp(arg[iarg],"pair") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_pair = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else if (strcmp(arg[iarg],"inner") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal run_style respa command"); level_inner = force->inumeric(FLERR,arg[iarg+1]) - 1; cutoff[0] = force->numeric(FLERR,arg[iarg+2]); cutoff[1] = force->numeric(FLERR,arg[iarg+3]); iarg += 4; } else if (strcmp(arg[iarg],"middle") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal run_style respa command"); level_middle = force->inumeric(FLERR,arg[iarg+1]) - 1; cutoff[2] = force->numeric(FLERR,arg[iarg+2]); cutoff[3] = force->numeric(FLERR,arg[iarg+3]); iarg += 4; } else if (strcmp(arg[iarg],"outer") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_outer = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else if (strcmp(arg[iarg],"kspace") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal run_style respa command"); level_kspace = force->inumeric(FLERR,arg[iarg+1]) - 1; iarg += 2; } else error->all(FLERR,"Illegal run_style respa command"); } // cannot specify both pair and inner/middle/outer if (level_pair >= 0 && (level_inner >= 0 || level_middle >= 0 || level_outer >= 0)) error->all(FLERR,"Cannot set both respa pair and inner/middle/outer"); // if either inner and outer is specified, then both must be if ((level_inner >= 0 && level_outer == -1) || (level_outer >= 0 && level_inner == -1)) error->all(FLERR,"Must set both respa inner and outer"); // middle cannot be set without inner/outer if (level_middle >= 0 && level_inner == -1) error->all(FLERR,"Cannot set respa middle without inner/outer"); // set defaults if user did not specify level // bond to innermost level // angle same as bond, dihedral same as angle, improper same as dihedral // pair to outermost level if no inner/middle/outer // inner/middle/outer have no defaults // kspace same as pair or outer if (level_bond == -1) level_bond = 0; if (level_angle == -1) level_angle = level_bond; if (level_dihedral == -1) level_dihedral = level_angle; if (level_improper == -1) level_improper = level_dihedral; if (level_pair == -1 && level_inner == -1) level_pair = nlevels-1; if (level_kspace == -1 && level_pair >= 0) level_kspace = level_pair; if (level_kspace == -1 && level_pair == -1) level_kspace = level_outer; // print respa levels if (comm->me == 0) { if (screen) { fprintf(screen,"Respa levels:\n"); for (int i = 0; i < nlevels; i++) { fprintf(screen," %d =",i+1); if (level_bond == i) fprintf(screen," bond"); if (level_angle == i) fprintf(screen," angle"); if (level_dihedral == i) fprintf(screen," dihedral"); if (level_improper == i) fprintf(screen," improper"); if (level_pair == i) fprintf(screen," pair"); if (level_inner == i) fprintf(screen," pair-inner"); if (level_middle == i) fprintf(screen," pair-middle"); if (level_outer == i) fprintf(screen," pair-outer"); if (level_kspace == i) fprintf(screen," kspace"); fprintf(screen,"\n"); } } if (logfile) { fprintf(logfile,"Respa levels:\n"); for (int i = 0; i < nlevels; i++) { fprintf(logfile," %d =",i+1); if (level_bond == i) fprintf(logfile," bond"); if (level_angle == i) fprintf(logfile," angle"); if (level_dihedral == i) fprintf(logfile," dihedral"); if (level_improper == i) fprintf(logfile," improper"); if (level_pair == i) fprintf(logfile," pair"); if (level_inner == i) fprintf(logfile," pair-inner"); if (level_middle == i) fprintf(logfile," pair-middle"); if (level_outer == i) fprintf(logfile," pair-outer"); if (level_kspace == i) fprintf(logfile," kspace"); fprintf(logfile,"\n"); } } } // check that levels are in correct order if (level_angle < level_bond || level_dihedral < level_angle || level_improper < level_dihedral) error->all(FLERR,"Invalid order of forces within respa levels"); if (level_pair >= 0) { if (level_pair < level_improper || level_kspace < level_pair) error->all(FLERR,"Invalid order of forces within respa levels"); } if (level_pair == -1 && level_middle == -1) { if (level_inner < level_improper || level_outer < level_inner || level_kspace < level_outer) error->all(FLERR,"Invalid order of forces within respa levels"); } if (level_pair == -1 && level_middle >= 0) { if (level_inner < level_improper || level_middle < level_inner || level_outer < level_inner || level_kspace < level_outer) error->all(FLERR,"Invalid order of forces within respa levels"); } // warn if any levels are devoid of forces int flag = 0; for (int i = 0; i < nlevels; i++) if (level_bond != i && level_angle != i && level_dihedral != i && level_improper != i && level_pair != i && level_inner != i && level_middle != i && level_outer != i && level_kspace != i) flag = 1; if (flag && comm->me == 0) error->warning(FLERR,"One or more respa levels compute no forces"); // check cutoff consistency if inner/middle/outer are enabled if (level_inner >= 0 && cutoff[1] < cutoff[0]) error->all(FLERR,"Respa inner cutoffs are invalid"); if (level_middle >= 0 && (cutoff[3] < cutoff[2] || cutoff[2] < cutoff[1])) error->all(FLERR,"Respa middle cutoffs are invalid"); // set outer pair of cutoffs to inner pair if middle is not enabled if (level_inner >= 0 && level_middle < 0) { cutoff[2] = cutoff[0]; cutoff[3] = cutoff[1]; } // allocate other needed arrays newton = new int[nlevels]; step = new double[nlevels]; } /* ---------------------------------------------------------------------- */ Respa::~Respa() { delete [] loop; delete [] newton; delete [] step; } /* ---------------------------------------------------------------------- initialization before run ------------------------------------------------------------------------- */ void Respa::init() { Integrate::init(); // warn if no fixes if (modify->nfix == 0 && comm->me == 0) error->warning(FLERR,"No fixes defined, atoms won't move"); // create fix needed for storing atom-based respa level forces // will delete it at end of run char **fixarg = new char*[4]; fixarg[0] = (char *) "RESPA"; fixarg[1] = (char *) "all"; fixarg[2] = (char *) "RESPA"; fixarg[3] = new char[8]; sprintf(fixarg[3],"%d",nlevels); modify->add_fix(4,fixarg); delete [] fixarg[3]; delete [] fixarg; fix_respa = (FixRespa *) modify->fix[modify->nfix-1]; // insure respa inner/middle/outer is using Pair class that supports it if (level_inner >= 0) if (force->pair && force->pair->respa_enable == 0) error->all(FLERR,"Pair style does not support rRESPA inner/middle/outer"); // virial_style = 1 (explicit) since never computed implicitly like Verlet virial_style = 1; // setup lists of computes for global and per-atom PE and pressure ev_setup(); // detect if fix omp is present and will clear force arrays int ifix = modify->find_fix("package_omp"); if (ifix >= 0) external_force_clear = 1; // set flags for what arrays to clear in force_clear() // need to clear additionals arrays if they exist torqueflag = 0; if (atom->torque_flag) torqueflag = 1; erforceflag = 0; if (atom->erforce_flag) erforceflag = 1; e_flag = 0; if (atom->e_flag) e_flag = 1; rho_flag = 0; if (atom->rho_flag) rho_flag = 1; // step[] = timestep for each level step[nlevels-1] = update->dt; for (int ilevel = nlevels-2; ilevel >= 0; ilevel--) step[ilevel] = step[ilevel+1]/loop[ilevel]; // set newton flag for each level for (int ilevel = 0; ilevel < nlevels; ilevel++) { newton[ilevel] = 0; if (force->newton_bond) { if (level_bond == ilevel || level_angle == ilevel || level_dihedral == ilevel || level_improper == ilevel) newton[ilevel] = 1; } if (force->newton_pair) { if (level_pair == ilevel || level_inner == ilevel || level_middle == ilevel || level_outer == ilevel) newton[ilevel] = 1; } } // orthogonal vs triclinic simulation box triclinic = domain->triclinic; } /* ---------------------------------------------------------------------- setup before run ------------------------------------------------------------------------- */ void Respa::setup() { if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n"); update->setupflag = 1; // setup domain, communication and neighboring // acquire ghosts // build neighbor lists atom->setup(); modify->setup_pre_exchange(); if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); domain->reset_box(); comm->setup(); if (neighbor->style) neighbor->setup_bins(); comm->exchange(); if (atom->sortfreq > 0) atom->sort(); comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); neighbor->build(); neighbor->ncalls = 0; // compute all forces ev_set(update->ntimestep); for (int ilevel = 0; ilevel < nlevels; ilevel++) { force_clear(newton[ilevel]); modify->setup_pre_force_respa(vflag,ilevel); if (level_pair == ilevel && pair_compute_flag) force->pair->compute(eflag,vflag); if (level_inner == ilevel && pair_compute_flag) force->pair->compute_inner(); if (level_middle == ilevel && pair_compute_flag) force->pair->compute_middle(); if (level_outer == ilevel && pair_compute_flag) force->pair->compute_outer(eflag,vflag); if (level_bond == ilevel && force->bond) force->bond->compute(eflag,vflag); if (level_angle == ilevel && force->angle) force->angle->compute(eflag,vflag); if (level_dihedral == ilevel && force->dihedral) force->dihedral->compute(eflag,vflag); if (level_improper == ilevel && force->improper) force->improper->compute(eflag,vflag); if (level_kspace == ilevel && force->kspace) { force->kspace->setup(); if (kspace_compute_flag) force->kspace->compute(eflag,vflag); } if (newton[ilevel]) comm->reverse_comm(); copy_f_flevel(ilevel); } modify->setup(vflag); sum_flevel_f(); output->setup(); update->setupflag = 0; } /* ---------------------------------------------------------------------- setup without output flag = 0 = just force calculation flag = 1 = reneighbor and force calculation ------------------------------------------------------------------------- */ void Respa::setup_minimal(int flag) { update->setupflag = 1; // setup domain, communication and neighboring // acquire ghosts // build neighbor lists if (flag) { modify->setup_pre_exchange(); if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); domain->reset_box(); comm->setup(); if (neighbor->style) neighbor->setup_bins(); comm->exchange(); comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); domain->image_check(); domain->box_too_small_check(); modify->setup_pre_neighbor(); neighbor->build(); neighbor->ncalls = 0; } // compute all forces ev_set(update->ntimestep); for (int ilevel = 0; ilevel < nlevels; ilevel++) { force_clear(newton[ilevel]); modify->setup_pre_force_respa(vflag,ilevel); if (level_pair == ilevel && pair_compute_flag) force->pair->compute(eflag,vflag); if (level_inner == ilevel && pair_compute_flag) force->pair->compute_inner(); if (level_middle == ilevel && pair_compute_flag) force->pair->compute_middle(); if (level_outer == ilevel && pair_compute_flag) force->pair->compute_outer(eflag,vflag); if (level_bond == ilevel && force->bond) force->bond->compute(eflag,vflag); if (level_angle == ilevel && force->angle) force->angle->compute(eflag,vflag); if (level_dihedral == ilevel && force->dihedral) force->dihedral->compute(eflag,vflag); if (level_improper == ilevel && force->improper) force->improper->compute(eflag,vflag); if (level_kspace == ilevel && force->kspace) { force->kspace->setup(); if (kspace_compute_flag) force->kspace->compute(eflag,vflag); } if (newton[ilevel]) comm->reverse_comm(); copy_f_flevel(ilevel); } modify->setup(vflag); sum_flevel_f(); update->setupflag = 0; } /* ---------------------------------------------------------------------- run for N steps ------------------------------------------------------------------------- */ void Respa::run(int n) { bigint ntimestep; for (int i = 0; i < n; i++) { ntimestep = ++update->ntimestep; ev_set(ntimestep); recurse(nlevels-1); if (modify->n_end_of_step) modify->end_of_step(); if (ntimestep == output->next) { timer->stamp(); sum_flevel_f(); output->write(update->ntimestep); timer->stamp(TIME_OUTPUT); } if (SignalHandler::request_quit && !SignalHandler::request_write_restart) break; } } /* ---------------------------------------------------------------------- delete rRESPA fix at end of run, so its atom arrays won't persist ------------------------------------------------------------------------- */ void Respa::cleanup() { modify->post_run(); modify->delete_fix("RESPA"); domain->box_too_small_check(); update->update_time(); } /* ---------------------------------------------------------------------- */ void Respa::reset_dt() { step[nlevels-1] = update->dt; for (int ilevel = nlevels-2; ilevel >= 0; ilevel--) step[ilevel] = step[ilevel+1]/loop[ilevel]; } /* ---------------------------------------------------------------------- */ void Respa::recurse(int ilevel) { copy_flevel_f(ilevel); for (int iloop = 0; iloop < loop[ilevel]; iloop++) { modify->initial_integrate_respa(vflag,ilevel,iloop); if (modify->n_post_integrate_respa) modify->post_integrate_respa(ilevel,iloop); if (ilevel) recurse(ilevel-1); // at outermost level, check on rebuilding neighbor list // at innermost level, communicate // at middle levels, do nothing if (ilevel == nlevels-1) { int nflag = neighbor->decide(); if (nflag) { if (modify->n_pre_exchange) modify->pre_exchange(); if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); if (domain->box_change) { domain->reset_box(); comm->setup(); if (neighbor->style) neighbor->setup_bins(); } timer->stamp(); comm->exchange(); if (atom->sortfreq > 0 && update->ntimestep >= atom->nextsort) atom->sort(); comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); timer->stamp(TIME_COMM); if (modify->n_pre_neighbor) modify->pre_neighbor(); neighbor->build(); timer->stamp(TIME_NEIGHBOR); } else if (ilevel == 0) { timer->stamp(); comm->forward_comm(); timer->stamp(TIME_COMM); } } else if (ilevel == 0) { timer->stamp(); comm->forward_comm(); timer->stamp(TIME_COMM); } // force computations // important that ordering is same as Verlet // so that any order dependencies are the same // when potentials are invoked at same level force_clear(newton[ilevel]); if (modify->n_pre_force_respa) modify->pre_force_respa(vflag,ilevel,iloop); timer->stamp(); if (level_pair == ilevel && pair_compute_flag) { force->pair->compute(eflag,vflag); timer->stamp(TIME_PAIR); } if (level_inner == ilevel && pair_compute_flag) { force->pair->compute_inner(); timer->stamp(TIME_PAIR); } if (level_middle == ilevel && pair_compute_flag) { force->pair->compute_middle(); timer->stamp(TIME_PAIR); } if (level_outer == ilevel && pair_compute_flag) { force->pair->compute_outer(eflag,vflag); timer->stamp(TIME_PAIR); } if (level_bond == ilevel && force->bond) { force->bond->compute(eflag,vflag); timer->stamp(TIME_BOND); } if (level_angle == ilevel && force->angle) { force->angle->compute(eflag,vflag); timer->stamp(TIME_BOND); } if (level_dihedral == ilevel && force->dihedral) { force->dihedral->compute(eflag,vflag); timer->stamp(TIME_BOND); } if (level_improper == ilevel && force->improper) { force->improper->compute(eflag,vflag); timer->stamp(TIME_BOND); } if (level_kspace == ilevel && kspace_compute_flag) { force->kspace->compute(eflag,vflag); timer->stamp(TIME_KSPACE); } if (newton[ilevel]) { comm->reverse_comm(); timer->stamp(TIME_COMM); } if (modify->n_post_force_respa) modify->post_force_respa(vflag,ilevel,iloop); modify->final_integrate_respa(ilevel,iloop); } copy_f_flevel(ilevel); } /* ---------------------------------------------------------------------- clear force on own & ghost atoms ------------------------------------------------------------------------- */ void Respa::force_clear(int newtonflag) { if (external_force_clear) return; // clear global force array // nall includes ghosts only if newton flag is set int nall; if (newtonflag) nall = atom->nlocal + atom->nghost; else nall = atom->nlocal; size_t nbytes = sizeof(double) * nall; if (nbytes > 0 ) { memset(&(atom->f[0][0]),0,3*nbytes); if (torqueflag) memset(&(atom->torque[0][0]),0,3*nbytes); if (erforceflag) memset(&(atom->erforce[0]), 0, nbytes); if (e_flag) memset(&(atom->de[0]), 0, nbytes); if (rho_flag) memset(&(atom->drho[0]), 0, nbytes); } } /* ---------------------------------------------------------------------- copy force components from atom->f to FixRespa->f_level ------------------------------------------------------------------------- */ void Respa::copy_f_flevel(int ilevel) { double ***f_level = fix_respa->f_level; double **f = atom->f; int n = atom->nlocal; for (int i = 0; i < n; i++) { f_level[i][ilevel][0] = f[i][0]; f_level[i][ilevel][1] = f[i][1]; f_level[i][ilevel][2] = f[i][2]; } } /* ---------------------------------------------------------------------- copy force components from FixRespa->f_level to atom->f ------------------------------------------------------------------------- */ void Respa::copy_flevel_f(int ilevel) { double ***f_level = fix_respa->f_level; double **f = atom->f; int n = atom->nlocal; for (int i = 0; i < n; i++) { f[i][0] = f_level[i][ilevel][0]; f[i][1] = f_level[i][ilevel][1]; f[i][2] = f_level[i][ilevel][2]; } } /* ---------------------------------------------------------------------- sum all force components from FixRespa->f_level to create full atom->f ------------------------------------------------------------------------- */ void Respa::sum_flevel_f() { copy_flevel_f(0); double ***f_level = fix_respa->f_level; double **f = atom->f; int n = atom->nlocal; for (int ilevel = 1; ilevel < nlevels; ilevel++) { for (int i = 0; i < n; i++) { f[i][0] += f_level[i][ilevel][0]; f[i][1] += f_level[i][ilevel][1]; f[i][2] += f_level[i][ilevel][2]; } } }