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/* ----------------------------------------------------------------------
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:
Christoph Kloss (JKU Linz, DCS Computing GmbH, Linz)
Richard Berger (JKU Linz)
Copyright 2012- DCS Computing GmbH, Linz
Copyright 2009-2015 JKU Linz
------------------------------------------------------------------------- */
#include <cmath>
#include <algorithm>
#include <stdlib.h>
#include <string.h>
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "update.h"
#include "comm.h"
#include "modify.h"
#include "domain.h"
#include "random_park.h"
#include "memory.h"
#include "error.h"
#include "fix_multisphere.h"
#include "fix_particledistribution_discrete.h"
#include "fix_template_sphere.h"
#include "fix_property_atom.h"
#include "irregular.h"
#include "fix_insert.h"
#include "math_extra_liggghts.h"
#include "mpi_liggghts.h"
#include "vector_liggghts.h"
#include "probability_distribution.h"
#include "region_neighbor_list.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define EPSILON 0.001
#define LMP_DEBUGMODE_FIXINSERT false //(667 == update->ntimestep)// true
#define LMP_DEBUG_OUT_FIXINSERT screen
/* ---------------------------------------------------------------------- */
FixInsert::FixInsert(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
neighList(*new RegionNeighborList<interpolate_no>(lmp))
{
if (narg < 7) error->fix_error(FLERR,this,"not enough arguments");
restart_global = 1;
setup_flag = false;
fix_distribution = NULL;
fix_multisphere = NULL;
multisphere = NULL;
compress_flag = false ;
// required args
iarg = 3;
if(strcmp(arg[iarg++],"seed")) error->fix_error(FLERR,this,"expecting keyword 'seed'");
// random number generator, seed depends on proc
random = new RanPark(lmp, arg[iarg++], true);
seed = random->getSeed();
if (seed <= 0) error->fix_error(FLERR,this,"illegal seed");
// set defaults
init_defaults();
// parse args
#ifdef SUPERQUADRIC_ACTIVE_FLAG
check_obb_flag = 1;
#endif
bool hasargs = true;
while(iarg < narg && hasargs)
{
hasargs = false;
if(strcmp(arg[iarg],"distributiontemplate") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
int ifix = modify->find_fix(arg[iarg+1]);
if(ifix < 0 || strncmp(modify->fix[ifix]->style,"particledistribution/discrete",29))
error->fix_error(FLERR,this,"Fix insert requires you to define a valid ID for a fix of type particledistribution/discrete");
fix_distribution = static_cast<FixParticledistributionDiscrete*>(modify->fix[ifix]);
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"maxattempt") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
maxattempt = atoi(arg[iarg+1]);
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"nparticles") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"INF") == 0)
ninsert_exists = 0;
else ninsert = atof(arg[iarg+1]);
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"mass") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"INF") == 0)
ninsert_exists = 0;
else massinsert = atof(arg[iarg+1]);
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"massrate") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
massflowrate = atof(arg[iarg+1]);
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"particlerate") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
nflowrate = atof(arg[iarg+1]);
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"insert_every_time") == 0 || strcmp(arg[iarg],"insert_every") == 0 || strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"once") == 0) insert_every = 0;
else if(strcmp(arg[iarg],"insert_every_time") == 0)
{
if(!update->timestep_set)
error->fix_error(FLERR,this,"need so set 'timestep' before");
insert_every = static_cast<int>(atof(arg[iarg+1])/update->dt);
}
else
insert_every = atoi(arg[iarg+1]);
if(insert_every < 0) error->fix_error(FLERR,this,"insert_every must be >= 0");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
first_ins_step = atoi(arg[iarg+1]);
if(first_ins_step < update->ntimestep + 1 && !modify->fix_restart_in_progress())
error->fix_error(FLERR,this,"'start' step can not be before current step");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"overlapcheck") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"yes")==0) check_ol_flag = 1;
else if(strcmp(arg[iarg+1],"no")==0) check_ol_flag = 0;
else error->fix_error(FLERR,this,"");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"all_in") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"yes")==0) all_in_flag = 1;
else if(strcmp(arg[iarg+1],"no")==0) all_in_flag = 0;
else error->fix_error(FLERR,this,"");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"set_property") == 0) {
if (iarg+3 > narg) error->fix_error(FLERR,this,"");
int n = strlen(arg[iarg+1]) + 1;
property_name = new char[n];
strcpy(property_name,arg[iarg+1]);
fix_property_value = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
hasargs = true;
} else if (strcmp(arg[iarg],"random_distribute") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"uncorrelated")==0) exact_number = 0;
else if(strcmp(arg[iarg+1],"exact")==0) exact_number = 1;
else error->fix_error(FLERR,this,"");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"verbose") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"no")==0) print_stats_during_flag = 0;
else if(strcmp(arg[iarg+1],"yes")==0) print_stats_during_flag = 1;
else error->fix_error(FLERR,this,"");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"compress_tags") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"not enough arguments for compress_tags");
if(0 == strcmp(arg[iarg+1],"yes"))
compress_flag = true;
else if(0 == strcmp(arg[iarg+1],"no"))
compress_flag = false;
else
error->fix_error(FLERR,this,"expecting 'yes' or 'no' after 'compress_tags'");
iarg += 2;
hasargs = true;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+5 > narg) error->fix_error(FLERR,this,"not enough keyword for 'vel'");
if (strcmp(arg[iarg+1],"constant") == 0) {
v_insert[0] = atof(arg[iarg+2]);
v_insert[1] = atof(arg[iarg+3]);
v_insert[2] = atof(arg[iarg+4]);
iarg += 5;
} else if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+8 > narg) error->fix_error(FLERR,this,"not enough keyword for 'uniform'");
v_randomSetting = RANDOM_UNIFORM;
v_insert[0] = atof(arg[iarg+2]);
v_insert[1] = atof(arg[iarg+3]);
v_insert[2] = atof(arg[iarg+4]);
v_insertFluct[0] = atof(arg[iarg+5]);
v_insertFluct[1] = atof(arg[iarg+6]);
v_insertFluct[2] = atof(arg[iarg+7]);
iarg += 8;
} else if (strcmp(arg[iarg+1],"gaussian") == 0) {
if (iarg+8 > narg) error->fix_error(FLERR,this,"not enough keyword for 'gaussian'");
v_randomSetting = RANDOM_GAUSSIAN;
v_insert[0] = atof(arg[iarg+2]);
v_insert[1] = atof(arg[iarg+3]);
v_insert[2] = atof(arg[iarg+4]);
v_insertFluct[0] = atof(arg[iarg+5]);
v_insertFluct[1] = atof(arg[iarg+6]);
v_insertFluct[2] = atof(arg[iarg+7]);
iarg += 8;
} else
error->fix_error(FLERR,this,"expecting keyword 'constant' or 'uniform' or 'gaussian' after keyword 'vel'");
hasargs = true;
} else if (strcmp(arg[iarg],"omega") == 0) {
if (iarg+5 > narg) error->fix_error(FLERR,this,"");
if (strcmp(arg[iarg+1],"constant") == 0)
{
omega_insert[0] = atof(arg[iarg+2]);
omega_insert[1] = atof(arg[iarg+3]);
omega_insert[2] = atof(arg[iarg+4]);
} else error->fix_error(FLERR,this,"expecting keyword 'constant' after keyword 'omega'");
iarg += 5;
hasargs = true;
} else if (strcmp(arg[iarg],"orientation") == 0) {
if (iarg+2 > narg)
error->fix_error(FLERR,this,"not enough arguments for 'orientation'");
iarg++;
if(strcmp(arg[iarg],"random") == 0)
{
quat_random_ = true;
iarg++;
}
else if(strcmp(arg[iarg],"template") == 0)
{
quat_random_ = false;
iarg++;
}
else if (strcmp(arg[iarg],"constant") == 0)
{
iarg++;
if (iarg+4 > narg) error->fix_error(FLERR,this,"");
quat_insert[0] = atof(arg[iarg++]);
quat_insert[1] = atof(arg[iarg++]);
quat_insert[2] = atof(arg[iarg++]);
quat_insert[3] = atof(arg[iarg++]);
} else error->fix_error(FLERR,this,"expecting 'random', template' or 'constant' after keyword 'quat'");
hasargs = true;
}
#ifdef SUPERQUADRIC_ACTIVE_FLAG
else if (strcmp(arg[iarg],"check_obb") == 0) {
if (iarg+2 > narg) error->fix_error(FLERR,this,"");
if(strcmp(arg[iarg+1],"yes")==0) check_obb_flag = 1;
else if(strcmp(arg[iarg+1],"no")==0) check_obb_flag = 0;
else error->fix_error(FLERR,this,"");
if(check_ol_flag==0) check_obb_flag = 0;
iarg += 2;
hasargs = true;
}
#endif
else if(strcmp(style,"insert") == 0) error->fix_error(FLERR,this,"unknown keyword");
}
// memory not allocated initially
ninsert_this_max_local = 0;
// check for missing or contradictory settings
sanity_check();
//min/max type to be inserted, need that to check if material properties defined for all materials
type_max = fix_distribution->max_type();
type_min = fix_distribution->min_type();
// allgather arrays
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
recvcounts = new int[nprocs];
displs = new int[nprocs];
// set next reneighbor
force_reneighbor = 1;
next_reneighbor = first_ins_step;
most_recent_ins_step = -1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
print_stats_start_flag = 1;
irregular = new Irregular(lmp);
// calc max insertion radius
int ntypes = atom->ntypes;
maxrad = 0.;
minrad = 1000.;
for(int i = 1; i <= ntypes; i++)
{
maxrad = std::max(maxrad,max_rad(i));
minrad = std::min(minrad,min_rad(i));
}
}
/* ---------------------------------------------------------------------- */
FixInsert::~FixInsert()
{
delete random;
delete [] recvcounts;
delete [] displs;
delete &neighList;
if(property_name) delete []property_name;
if(irregular) delete irregular;
irregular = 0;
}
/* ---------------------------------------------------------------------- */
void FixInsert::setup(int vflag)
{
// do this only once
if(setup_flag) return;
else setup_flag = true;
// calculate ninsert, insert_every, ninsert_per
calc_insertion_properties();
// calc last step of insertion
if(ninsert_exists)
{
if(ninsert <= ninsert_per)
final_ins_step = first_ins_step;
else
final_ins_step = first_ins_step +
static_cast<int>(static_cast<double>(ninsert)/ninsert_per) * static_cast<double>(insert_every);
if(final_ins_step < 0)
error->fix_error(FLERR,this,"Particle insertion: Overflow - need too long for particle insertion. "
"Please decrease # particles to insert or increase insertion rate");
if(ninsert < 0)
error->fix_error(FLERR,this,"Particle insertion: Overflow - too many particles for particle insertion. "
"Please decrease # particles to insert.");
}
else
final_ins_step = -1;
// print statistics
print_stats_start();
}
/* ---------------------------------------------------------------------- */
void FixInsert::init_defaults()
{
// default is that total # of particles to insert by this command is known
ninsert_exists = 1;
ninsert = ninserted = 0;
massinsert = massinserted = 0.;
nflowrate = massflowrate = 0.;
insert_every = -1;
ninsert_per = 0.;
// 1st insertion on next timestep is default
first_ins_step = update->ntimestep + 1;
maxattempt = 50;
check_ol_flag = 1;
all_in_flag = 0;
exact_number = 1;
v_randomSetting = RANDOM_CONSTANT;
vectorZeroize3D(v_insert);
vectorZeroize3D(v_insertFluct);
vectorZeroize3D(omega_insert);
quatIdentity4D(quat_insert);
quat_random_ = false;
print_stats_during_flag = 1;
warn_boxentent = true;
property_name = 0;
fix_property = 0;
fix_property_value = 0.;
}
/* ---------------------------------------------------------------------- */
void FixInsert::sanity_check()
{
if(fix_distribution == NULL)
error->fix_error(FLERR,this,"have to define a 'distributiontemplate'");
if(MathExtraLiggghts::abs(vectorMag4DSquared(quat_insert)-1.) > 1e-10)
error->fix_error(FLERR,this,"quaternion not valid");
if(ninsert > 0 && massinsert > 0.)
error->fix_error(FLERR,this,"must not define both 'nparticles' and 'mass'");
if(nflowrate > 0. && massflowrate > 0.)
error->fix_error(FLERR,this,"must not define both 'particlerate' and 'massrate'");
if(insert_every == 0 && (massflowrate > 0. || nflowrate > 0.))
error->fix_error(FLERR,this,"must not define 'particlerate' or 'massrate' for 'insert_every' = 0");
if(0 == comm->me)
{
std::vector<int> seeds;
seeds.push_back(random->state());
seeds.push_back(fix_distribution->random_state());
for(int itemplate = 0; itemplate < fix_distribution->n_particletemplates(); itemplate++)
{
seeds.push_back(fix_distribution->particletemplates()[itemplate]->random_insertion_state());
}
std::sort(seeds.begin(),seeds.end());
if(std::unique(seeds.begin(),seeds.end()) !=seeds.end() )
{
char errstr[1024];
sprintf(errstr,"Fix %s, ID %s: Random number generation: It is required that all the random seeds of this fix insert/*, \n"
" the random seed of particle distribution fix (id %s) template and all random seeds of the \n"
" fix particletemplate/* commands used by particle distribution fix (id %s) are different\n"
" Hint: possible valid (different) seeds would be the following numbers:\n"
" 15485863, 15485867, 32452843, 32452867, 49979687, 49979693, 67867967, 67867979, 86028121, 86028157",
style,id,fix_distribution->id,fix_distribution->id);
if(input->seed_check_throw_error())
error->one(FLERR,errstr);
else
error->warning(FLERR,errstr);
}
}
}
/* ---------------------------------------------------------------------- */
void FixInsert::print_stats_start()
{
if (me == 0 && print_stats_start_flag) {
if(ninsert_exists)
{
if (screen)
fprintf(screen ,"INFO: Particle insertion %s: %f particles every %d steps - particle rate %f (mass rate %e)\n"
" %d particles (mass %e) within %d steps\n",
id,ninsert_per,insert_every,nflowrate,massflowrate,ninsert,massinsert,final_ins_step-first_ins_step);
if (logfile)
fprintf(logfile,"INFO: Particle insertion %s: %f particles every %d steps - particle rate %f, (mass rate %e)\n"
" %d particles (mass %e) within %d steps\n",
id,ninsert_per,insert_every,nflowrate,massflowrate,ninsert,massinsert,final_ins_step-first_ins_step);
}
else if(massflowrate > 0.)
{
if (screen)
fprintf(screen ,"INFO: Particle insertion %s: %f particles every %d steps - particle rate %f (mass rate %e)\n",
id,ninsert_per,insert_every,nflowrate,massflowrate);
if (logfile)
fprintf(logfile,"INFO: Particle insertion %s: %f particles every %d steps - particle rate %f, (mass rate %e)\n",
id,ninsert_per,insert_every,nflowrate,massflowrate);
}
else
{
if (screen)
fprintf(screen ,"INFO: Particle insertion %s: inserting every %d steps\n",id,insert_every);
if (logfile)
fprintf(logfile ,"INFO: Particle insertion %s: inserting every %d steps\n",id,insert_every);
}
}
}
/* ---------------------------------------------------------------------- */
void FixInsert::print_stats_during(int ninsert_this, double mass_inserted_this)
{
bigint step = update->ntimestep;
if (me == 0 && print_stats_during_flag)
{
if (screen)
fprintf(screen ,"INFO: Particle insertion %s: inserted %d particle templates (mass %e) at step " BIGINT_FORMAT "\n"
" - a total of %d particle templates (mass %e) inserted so far.\n",
id,ninsert_this,mass_inserted_this,step,ninserted,massinserted);
if (logfile)
fprintf(logfile,"INFO: Particle insertion %s: inserted %d particle templates (mass %e) at step " BIGINT_FORMAT "\n"
" - a total of %d particle templates (mass %e) inserted so far.\n",
id,ninsert_this,mass_inserted_this,step,ninserted,massinserted);
}
}
/* ---------------------------------------------------------------------- */
int FixInsert::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixInsert::init()
{
int ntimestep = update->ntimestep;
if (!atom->radius_flag || !atom->rmass_flag)
error->fix_error(FLERR,this,"Fix insert requires atom attributes radius, rmass");
if (domain->triclinic)
error->fix_error(FLERR,this,"Cannot use with triclinic box");
if (domain->dimension != 3)
error->fix_error(FLERR,this,"Can use fix insert for 3d simulations only");
fix_multisphere = static_cast<FixMultisphere*>(modify->find_fix_style("multisphere", 0));
if(!fix_multisphere) multisphere = NULL;
else multisphere = &fix_multisphere->data();
// in case of new fix insert in a restarted simulation, have to add current time-step
if(next_reneighbor > 0 && next_reneighbor < ntimestep)
{
error->fix_error(FLERR,this,"'start' step can not be before current step");
}
if(property_name)
{
fix_property = static_cast<FixPropertyAtom*>(modify->find_fix_property(property_name,"property/atom","scalar",1,1,this->style,true));
}
}
/* ---------------------------------------------------------------------- */
void FixInsert::reset_timestep(bigint newstep,bigint oldstep)
{
next_reneighbor += (newstep-oldstep);
}
/* ---------------------------------------------------------------------- */
int FixInsert::min_type()
{
return type_min;
}
/* ---------------------------------------------------------------------- */
int FixInsert::max_type()
{
return type_max;
}
/* ---------------------------------------------------------------------- */
double FixInsert::max_rad(int type)
{
return fix_distribution->max_rad(type);
}
/* ---------------------------------------------------------------------- */
double FixInsert::min_rad(int type)
{
return fix_distribution->min_rad(type);
}
/* ---------------------------------------------------------------------- */
double FixInsert::max_r_bound()
{
return fix_distribution->max_r_bound();
}
/* ---------------------------------------------------------------------- */
double FixInsert::extend_cut_ghost()
{
if(!fix_multisphere)
return 0.;
return 2.*fix_distribution->max_r_bound();
}
/* ---------------------------------------------------------------------- */
int FixInsert::calc_ninsert_this()
{
if(ninsert_per == 0.) error->fix_error(FLERR,this,"ninsert_per == 0.");
// number of bodies to insert this timestep
int ninsert_this = static_cast<int>(ninsert_per + random->uniform());
if (ninsert_exists && ninserted + ninsert_this > ninsert) ninsert_this = ninsert - ninserted;
return ninsert_this;
}
/* ----------------------------------------------------------------------
perform particle insertion
------------------------------------------------------------------------- */
void FixInsert::pre_exchange()
{
int ninsert_this, ninsert_this_local; // global and local # bodies to insert this time-step
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep || most_recent_ins_step == update->ntimestep) return;
most_recent_ins_step = update->ntimestep;
// things to be done before inserting new particles
if(!pre_insert())
return;
// number of particles to insert this timestep
ninsert_this = calc_ninsert_this();
// limit to max number of particles that shall be inserted
// to avoid that max # may be slightly exceeded by random processes
// in fix_distribution->randomize_list, set exact_number to 1
if (ninsert_exists && ninserted + ninsert_this >= ninsert)
{
ninsert_this = ninsert - ninserted;
if(ninsert_this < 0)
ninsert_this = 0;
exact_number = 1;
}
// distribute ninsert_this across processors
ninsert_this_local = distribute_ninsert_this(ninsert_this);
// re-allocate list if necessary
if(ninsert_this_local > ninsert_this_max_local)
{
init_list(ninsert_this_local);
ninsert_this_max_local = ninsert_this_local;
}
// generate list of insertions
// number of inserted particles can change if exact_number = 0
ninsert_this_local = generate_list(ninsert_this_local,groupbit,exact_number);
MPI_Sum_Scalar(ninsert_this_local,ninsert_this,world);
if(ninsert_this == 0)
{
// warn if flowrate should be fulfilled
if((nflowrate > 0. || massflowrate > 0.) && comm->me == 0)
error->warning(FLERR,"Particle insertion: Inserting no particle - check particle insertion settings");
// schedule next insertion
if (insert_every && (!ninsert_exists || ninserted < ninsert))
next_reneighbor += insert_every;
else if(0 == insert_every)
next_reneighbor = -1;
return;
}
else if(ninsert_this < 0)
{
error->fix_error(FLERR,this,"Particle insertion: Internal error");
}
double min_subbox_extent;
int min_dim;
domain->min_subbox_extent(min_subbox_extent,min_dim);
if(warn_boxentent && min_subbox_extent < 2.2 *max_r_bound())
{
char msg[256];
sprintf(msg,"Particle insertion on proc %d: sub-domain is smaller than the bounding radius of insert particles to insert: \nMax. bounding "
"sphere diameter is %f, sub-domain extent in %s direction is only %f ",
comm->me,2.*max_r_bound(),0==min_dim?"x":(1==min_dim?"y":"z"),min_subbox_extent);
error->warning(FLERR,msg);
}
// warn if max # insertions exceeded by random processes
if (ninsert_exists && ninserted + ninsert_this > ninsert)
{
error->warning(FLERR,"INFO: Particle insertion: Number of particles to insert was slightly exceeded by random process");
}
// fill xnear array with particles to check overlap against
// add particles in insertion volume to xnear list
neighList.reset();
if(check_ol_flag)
load_xnear(ninsert_this_local);
// insertion counters in this step
int ninserted_this = 0, ninserted_spheres_this = 0;
int ninserted_this_local = 0, ninserted_spheres_this_local = 0;
double mass_inserted_this = 0.;
double mass_inserted_this_local = 0.;
// randomize insertion positions and set v, omega
// also performs overlap check via xnear if requested
// returns # bodies and # spheres that could actually be inserted
x_v_omega(ninsert_this_local,ninserted_this_local,ninserted_spheres_this_local,mass_inserted_this_local);
// actual particle insertion
fix_distribution->pre_insert(ninserted_this_local,fix_property,fix_property_value);
ninserted_spheres_this_local = fix_distribution->insert(ninserted_this_local);
// warn if max # insertions exceeded by random processes
if (ninsert_exists && ninserted + ninsert_this > ninsert)
{
error->warning(FLERR,"INFO: Particle insertion: Number of particles to insert was slightly exceeded by random process");
}
// set tag # of new particles beyond all previous atoms, reset global natoms
// if global map exists, reset it now instead of waiting for comm
// since deleting atoms messes up ghosts
int step = update->ntimestep;
if (atom->tag_enable)
{
//force all tags to be reset by setting them to zero
if(compress_flag)
{
if(comm->me == 0)
printf("FixInsertStream: resetting tags @ step %d. \n", step);
int *tag = atom->tag;
for (int i = 0; i < atom->nlocal; i++)
tag[i] = 0;
}
atom->tag_extend();
atom->natoms += static_cast<double>(ninserted_spheres_this);
if (atom->map_style)
{
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
}
// give particle distributions the chance to do some wrap-up
fix_distribution->finalize_insertion();
// give derived classes the chance to do some wrap-up
finalize_insertion(ninserted_spheres_this_local);
// tally stats
MPI_Sum_Scalar(ninserted_this_local,ninserted_this,world);
ninserted += ninserted_this;
MPI_Sum_Scalar(mass_inserted_this_local,mass_inserted_this,world);
massinserted += mass_inserted_this;
print_stats_during(ninserted_this,mass_inserted_this);
if(ninserted_this < ninsert_this && comm->me == 0)
error->warning(FLERR,"Particle insertion: Less insertions than requested");
if (irregular->migrate_check())
irregular->migrate_atoms();
// next timestep to insert
if (insert_every && (!ninsert_exists || ninserted < ninsert)) next_reneighbor += insert_every;
else next_reneighbor = 0;
}
/* ----------------------------------------------------------------------
distribute insertions across processors
------------------------------------------------------------------------- */
int FixInsert::distribute_ninsert_this(int ninsert_this)
{
int me, nprocs, ngap, ninsert_this_local, *ninsert_this_local_all;
double fraction_local, fraction_local_all_sum, *fraction_local_all, *remainder, r, rsum;
me = comm->me;
nprocs = comm->nprocs;
fraction_local = insertion_fraction();
if(!exact_number)
return static_cast<int>(fraction_local*static_cast<double>(ninsert_this) + random->uniform());
// for exact_number==1, have to allgather to exactly match ninsert_this
fraction_local_all = new double[nprocs];
remainder = new double[nprocs];
ninsert_this_local_all = new int[nprocs];
// allgather local fractions
MPI_Allgather(&fraction_local,1,MPI_DOUBLE,fraction_local_all,1,MPI_DOUBLE,world);
// proc0 calculates ninsert_this_local for all processes
if(me == 0)
{
// remove fractions < 2% / nprocs
// have to normalize so not all portions get cancelled away for higher proc counts
// normalize fraction_local_all so sum across processors is 1
double lower_thresh = 0.02 / static_cast<double>(nprocs);
fraction_local_all_sum = 0.;
for(int iproc = 0; iproc < nprocs; iproc++)
{
if(fraction_local_all[iproc] < lower_thresh)
fraction_local_all[iproc] = 0.;
fraction_local_all_sum += fraction_local_all[iproc];
}
if(fraction_local_all_sum == 0.)
error->one(FLERR,"Internal error distributing particles to processes");
for(int iproc = 0; iproc < nprocs; iproc++)
fraction_local_all[iproc] /= fraction_local_all_sum;
rsum = 0.;
for(int iproc = 0; iproc < nprocs; iproc++)
{
ninsert_this_local_all[iproc] = static_cast<int>(fraction_local_all[iproc]*static_cast<double>(ninsert_this));
remainder[iproc] = fraction_local_all[iproc]*static_cast<double>(ninsert_this) - ninsert_this_local_all[iproc];
rsum += remainder[iproc];
}
ngap = round(rsum);
for(int i = 0; i < ngap; i++)
{
r = random->uniform() * static_cast<double>(ngap);
int iproc = 0;
rsum = remainder[iproc];
while(iproc < (nprocs-1) && rsum < r)
{
iproc++;
rsum += remainder[iproc];
}
ninsert_this_local_all[iproc]++;
}
}
// Bcast the result
MPI_Bcast(ninsert_this_local_all,nprocs, MPI_INT,0,world);
ninsert_this_local = ninsert_this_local_all[me];
delete []fraction_local_all;
delete []remainder;
delete []ninsert_this_local_all;
return ninsert_this_local;
}
/* ----------------------------------------------------------------------
fill neighbor list with nearby particles
------------------------------------------------------------------------- */
int FixInsert::load_xnear(int ninsert_this_local)
{
// load up neighbor list with local and ghosts
double **x = atom->x;
double *radius = atom->radius;
const int nall = atom->nlocal + atom->nghost;
BoundingBox bb = getBoundingBox();
neighList.reset();
#ifdef SUPERQUADRIC_ACTIVE_FLAG
neighList.set_obb_flag(check_obb_flag);
#endif
if(neighList.setBoundingBox(bb, maxrad,true,true))
{
for (int i = 0; i < nall; ++i)
{
if (is_nearby(i) && neighList.isInBoundingBox(x[i]) )
{
#ifdef SUPERQUADRIC_ACTIVE_FLAG
if(atom->superquadric_flag and check_obb_flag)
neighList.insert_superquadric(x[i], radius[i], atom->quaternion[i], atom->shape[i], atom->blockiness[i]);
else
neighList.insert(x[i], radius[i]);
#else
neighList.insert(x[i], radius[i]);
#endif
}
}
}
return neighList.count();
}
/* ----------------------------------------------------------------------
generate random velocity based on random setting
------------------------------------------------------------------------- */
void FixInsert::generate_random_velocity(double * velocity) {
switch(v_randomSetting) {
case RANDOM_UNIFORM:
velocity[0] = v_insert[0] + v_insertFluct[0] * 2.0 * (random->uniform()-0.50);
velocity[1] = v_insert[1] + v_insertFluct[1] * 2.0 * (random->uniform()-0.50);
velocity[2] = v_insert[2] + v_insertFluct[2] * 2.0 * (random->uniform()-0.50);
break;
case RANDOM_GAUSSIAN:
velocity[0] = v_insert[0] + v_insertFluct[0] * random->gaussian();
velocity[1] = v_insert[1] + v_insertFluct[1] * random->gaussian();
velocity[2] = v_insert[2] + v_insertFluct[2] * random->gaussian();
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixInsert::write_restart(FILE *fp)
{
int n = 0;
double list[5];
list[n++] = static_cast<double>(random->state());
list[n++] = static_cast<double>(ninserted);
list[n++] = static_cast<double>(first_ins_step);
list[n++] = static_cast<double>(next_reneighbor);
list[n++] = massinserted;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixInsert::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
bigint next_reneighbor_re;
seed = static_cast<int> (list[n++]) + comm->me;
ninserted = static_cast<int> (list[n++]);
first_ins_step = static_cast<int> (list[n++]);
next_reneighbor_re = static_cast<bigint> (list[n++]);
massinserted = list[n++];
random->reset(seed);
// in order to be able to continue pouring with increased number of particles
// if insert was already finished in run to be restarted
if(next_reneighbor_re != 0) next_reneighbor = next_reneighbor_re;
}
/* ----------------------------------------------------------------------
output
------------------------------------------------------------------------- */
double FixInsert::compute_vector(int index)
{
if(index == 0) return static_cast<double>(ninserted);
if(index == 1) return massinserted;
return 0.0;
}
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