Parameters.h

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#ifndef PARAMETERS
#define PARAMETERS
 
#include <cstdlib>
#include <cmath>
#include <cstdio>
#include <vector>
#include <iostream>
#include <fstream>
#include <map>
//#include <boost/variant.hpp>
#include <variant>
#if !__EMSCRIPTEN__ && __GNUC__ < 8
  #include <experimental/filesystem>
  namespace fs = std::experimental::filesystem ; 
#else
  #include <filesystem>
  namespace fs = std::filesystem ; 
#endif
 
#include "Typedefs.h"
#include "Tools.h"
#include "Xml.h"
#include "Vtk.h"
#include "RigidBody.h"
#include "Mesh.h"
#include "Boundaries.h"
#include "json_parser.h"
//#include "json.hpp"
//
#include <boost/random.hpp>
  
#ifdef EMSCRIPTEN
  #define STR_PROTECT(s) static_cast<const char*>(s "\0")
#else
  #define STR_PROTECT(s) s
#endif
 
//using json = nlohmann::json;
using json = nddem::json ; 
using namespace std ;
enum class ExportType {NONE=0, CSV=1, VTK=2, NETCDFF=4, XML=8, XMLbase64=16, CSVA=32, CSVCONTACT=64} ;
enum class ExportData {NONE=0, POSITION=0x1, VELOCITY=0x2, OMEGA=0x4, OMEGAMAG=0x8, ORIENTATION=0x10, COORDINATION=0x20, RADIUS=0x40, IDS=0x80, FN=0x100, FT=0x200, TORQUE=0x400, GHOSTMASK=0x800, GHOSTDIR=0x1000, BRANCHVECTOR=0x2000, FN_EL=0x4000, FN_VISC=0x8000, FT_EL=0x10000, FT_VISC=0x20000, FT_FRIC=0x40000, FT_FRICTYPE=0x80000, CONTACTPOSITION=0x100000, MASS=0x200000} ; 
inline ExportType & operator|=(ExportType & a, const ExportType b) {a= static_cast<ExportType>(static_cast<int>(a) | static_cast<int>(b)); return a ; }
inline ExportData & operator|=(ExportData & a, const ExportData b) {a= static_cast<ExportData>(static_cast<int>(a) | static_cast<int>(b)); return a ; }
inline ExportData   operator| (ExportData a, ExportData b) {auto c= static_cast<ExportData>(static_cast<int>(a) | static_cast<int>(b)); return c ; }
inline ExportData   operator~ (ExportData a) {auto c= static_cast<ExportData>(~static_cast<int>(a)); return c ; }
inline ExportData & operator&=(ExportData & a, const ExportData b) {a= static_cast<ExportData>(static_cast<int>(a) & static_cast<int>(b)); return a ; }
inline ExportData & operator>>= (ExportData& w, int u) {w=static_cast<ExportData>(static_cast<int>(w)>>u) ; return w ; }
inline ExportData & operator<<= (ExportData& w, int u) {w=static_cast<ExportData>(static_cast<int>(w)<<u) ; return w ; }
inline bool operator& (ExportType & a, ExportType b) {return (static_cast<int>(a) & static_cast<int>(b)) ; }
inline bool operator& (ExportData & a, ExportData b) {return (static_cast<int>(a) & static_cast<int>(b)) ; }
 
template <int d>
class Multiproc ;
 
template <typename T>
class number_gen {
public:
    void parse (std::string s) 
    {
      auto res = s.find(':') ; double val ; 
      if (res==std::string::npos)
      {
        val=stod(s) ; first=static_cast<T>(val) ; 
        isconst=true ; delta=0 ; 
        last = std::numeric_limits<T>::max() ; 
      }
      else
      {
        isconst=false ; 
        val=stod(s) ; first=static_cast<T>(val) ; 
        s=s.substr(res+1) ; res = s.find(':') ; 
        if (res==std::string::npos)
        {
          val=stod(s) ; last=static_cast<T>(val) ; 
          delta=1 ;
        }
        else
        {
          val=stod(s) ; delta=static_cast<T>(val) ; 
          s=s.substr(res+1) ; 
          val=stod(s) ; last=static_cast<T>(val) ; 
        }
      }
      iter=0 ; 
    }
    
    void reset () {iter = 0 ; }
    int niter() { return isconst?1:(floor((last-first)/delta)+1) ;  }
    T cur() {return first+delta*iter ; }
    std::optional<T> operator() (bool allow=false) 
    { 
      if (isconst)
      {
        if (iter>0 && !allow) return {} ; 
        else 
        {
          iter ++ ; 
          return first ; 
        }
      }
      else
      {
        T res = first+delta*iter ; 
        if (res>last && !allow) 
          return {} ;
        iter++ ; 
        return res ; 
      }
    }
private:
    int iter=0 ; 
    bool isconst = true ; 
    T first, last, delta=1 ; 
}; 
template <typename T>
std::istream & operator>> (std::istream & in, number_gen<T> & n) {std::string s; in >>s ; n.parse(s) ; return in ; }
 
template <int d>
class Parameters {
public :
    Parameters () {Parameters(0) ; }
    Parameters (int NN):
        N(5),           //number of particles
        tdump(100000000),       //dump data every these timesteps
        tinfo(100),
        T(5000),        //number of timesteps
        dt(0.0001),          //timestep
        rho(1),         //density (unit [M.L^(-d)]) WARNING UNUSED
        Kn(0.0001) ,    //Hooke stiffness
        Kt(0.00001) ,   //Tangential stiffness
        Gamman(0.0001), //Normal damping
        Gammat(0),      //Tangential damping
        Mu(0.5),        // Friction coefficient
        Mu_wall(0.5),        // Wall friction coefficient
        damping(0.0),
        forceinsphere(false), 
        cellsize(-1),
        contact_strategy(ContactStrategies::NAIVE), 
        //dumpkind(ExportType::NONE),    //How to dump: 0=nothing, 1=csv, 2=vtk
        //dumplist(ExportData::POSITION),
        Directory ("Output"),
        orientationtracking(true),
        wallforcecompute(false),
        wallforcerequested(false),
        wallforcecomputed(false),
        graddesc_gamma(0.1),
        graddesc_tol(1e-5)
        {
         reset_ND(NN) ;
        } 
 
    void reset_ND (int NN)
    {
     N=NN ; r.resize(N,0.5) ; //particle size
     m.resize(N, 1e-2); // Set the masses directly
     I.resize(N,1) ; //Momentum of inertia (particles are sphere)
     g.resize(d,0) ; // Initialise gravity
     Frozen.resize(N,false) ;
 
     Boundaries.resize(d) ; // Boundary type in [:,3]: 0=regular pbc, 1=wall}
    }
 
    int N; 
    int tdump ; 
    int tinfo ; 
    double T ; 
    double dt ; 
    double rho; 
    double Kn ; 
    double Kt ; 
    double Gamman; 
    double Gammat ; 
    double Mu ; 
    double Mu_wall; //< Wall friction
    double damping; //< Artificial rolling damping
    bool forceinsphere; //< Artificial rolling damping
    double cellsize ; 
    ContactModels ContactModel=HOOKE ; 
    ContactStrategies contact_strategy = NAIVE ; 
    vector <std::pair<ExportType,ExportData>> dumps ; 
    //ExportType dumpkind ;
    //ExportData dumplist ;
    vector <double> r ; 
    vector <double> m ; 
    vector <double> I ; 
    vector <double> g ; 
    vector <bool> Frozen ; 
    vector < Boundary<d> > Boundaries ; 
    string Directory ; 
    bool orientationtracking ; 
    bool wallforcecompute ; 
    bool wallforcerequested ; 
    bool wallforcecomputed ; 
    double graddesc_gamma ; 
    double graddesc_tol ; 
    bool contactforcedump ; 
    unsigned long int seed = 5489UL ; 
    double gravityrotateangle = 0.0; 
    RigidBodies_<d> RigidBodies ; 
    vector <Mesh<d>> Meshes ; 
    int n_restart=-1 ; 
    std::string restart_filename="" ; 
    unsigned char restart_flag ; 
    
    multimap<float, string> events ; 
    
    template <class Archive>
    void serialize(Archive &ar) {
        ar(N, tdump, tinfo, T, dt, rho, Kn, Kt, Gamman, Gammat, Mu, Mu_wall, damping, forceinsphere, cellsize, ContactModel, contact_strategy,
           dumps, r, m, I, g, Frozen, Boundaries, Directory, orientationtracking, wallforcecompute, wallforcerequested, wallforcecomputed, 
           graddesc_gamma, graddesc_tol, contactforcedump, seed, gravityrotateangle, RigidBodies, Meshes, events,
           n_restart, restart_filename, restart_flag 
           ) ; 
    }
 
// Useful functions
    int set_boundaries() ;  
    //int init_particles(v2d & X, v2d & A) ;
    void perform_PBC(v1d & X, uint32_t & PBCFlags) ; 
    void perform_PBCLE_move() ;
    void perform_PBCLE (v1d & X, v1d & V, uint32_t & PBCFlag) ;
    bool perform_forceinsphere(v1d & X)
    {
      bool res = false ;
      if (! Boundaries[0].is_sphere())
      { printf("ERR: forceinsphere expect the sphere to be the first wall.") ; return false ; }
      
      double dst = 0 ; 
      for (int dd=0 ; dd<d ; dd++) dst += (X[dd]-Boundaries[0].center[dd])*(X[dd]-Boundaries[0].center[dd]) ; 
      if (dst > Boundaries[0].radius*Boundaries[0].radius || std::isnan(dst))
      {
        printf("%g ", dst) ; fflush(stdout) ;
        boost::random::mt19937 rng(++seed);
        boost::random::uniform_01<boost::mt19937> rand(rng) ;
        do {
            dst=0 ;
            for(int dd=0 ; dd < d ; dd++)
            {
              X[dd] = (rand()*Boundaries[0].radius*2-Boundaries[0].radius) + Boundaries[0].center[dd] ; 
              dst += (Boundaries[0].center[dd]-X[dd])*(Boundaries[0].center[dd]-X[dd]) ;
            }        
         } while ( dst > Boundaries[0].radius * Boundaries[0].radius) ;
        res = true ;
        printf("[INFO] Bringing back in sphere forcibly. \n"); fflush(stdout) ;
      }
      return res ;
    }
 
    void perform_MOVINGWALL() ; 
    int init_mass() ; 
    int init_inertia() ; 
 
    void do_nothing (double time __attribute__((unused))) {return;}
    double grav_intensity = 10, grav_omega=1 ; int grav_rotdim[2]={0,1} ;
    void do_gravityrotate (double deltatime) {gravityrotateangle += deltatime*grav_omega; g[grav_rotdim[0]]=grav_intensity*cos(gravityrotateangle); g[grav_rotdim[1]]=grav_intensity*sin(gravityrotateangle); return;}
    void (Parameters::*update_gravity) (double time) = &Parameters::do_nothing ;
 
    void load_datafile (char path[], v2d & X, v2d & V, v2d & Omega) ; 
    void check_events(float time, v2d & X, v2d & V, v2d & Omega) ; 
    void interpret_command (istream & in, v2d & X, v2d & V, v2d & Omega) ; 
    void interpret_command (string & in, v2d & X, v2d & V, v2d & Omega) ; 
 
    void remove_particle (int idx, v2d & X, v2d & V, v2d & A, v2d & Omega, v2d & F, v2d & FOld, v2d & Torque, v2d & TorqueOld) ; 
    void add_particle (/*v2d & X, v2d & V, v2d & A, v2d & Omega, v2d & F, v2d & FOld, v2d & Torque, v2d & TorqueOld*/) ; 
    void init_locations (char *line, v2d & X, char *extras) ; 
    void init_radii (char line[], v1d & r) ;  
 
    void display_info(int tint, v2d& V, v2d& Omega, v2d& F, v2d& Torque, int, int) ; 
    void quit_cleanly() ; 
    void finalise(); 
    void xml_header () ; 
    int dumphandling (int ti, double t, v2d &X, v2d &V, v1d &Vmag, v2d &A, v2d &Omega, v1d &OmegaMag, vector<uint32_t> &PBCFlags, v1d & Z, Multiproc<d> & MP) ; 
    int savecsvcontact (FILE * out, ExportData outflags, Multiproc<d> & MP, cv2d & X)
    {
     if (outflags & ExportData::IDS) fprintf(out, "id_i, id_j, ") ;
     if (outflags & ExportData::CONTACTPOSITION || outflags & ExportData::POSITION)
     {
         for (int dd = 0 ; dd<d ; dd++)
             fprintf(out, "x%d_i, ", dd) ;
         for (int dd = 0 ; dd<d ; dd++)
             fprintf(out, "x%d_j, ", dd) ;
     }
     if (outflags & ExportData::FN)
         for (int dd = 0 ; dd<d ; dd++)
             fprintf(out, "Fn%d_i, ", dd) ;
     if (outflags & ExportData::FT)
         for (int dd = 0 ; dd<d ; dd++)
             fprintf(out, "Ft%d_i, ", dd) ;
     if (outflags & ExportData::TORQUE)
     {
         for (int dd = 0 ; dd<d*(d-1)/2 ; dd++)
         {
             auto val = Tools<d>::MASIndex[dd] ;
             fprintf(out, "Torque%d:%d_i, ", val.first, val.second) ;
         }
         for (int dd = 0 ; dd<d*(d-1)/2 ; dd++)
         {
             auto val =  Tools<d>::MASIndex[dd] ;
             fprintf(out, "Torque%d:%d_j, ", val.first, val.second) ;
         }
     }
     if (outflags & ExportData::GHOSTMASK)
        fprintf(out, "GhostMask, ") ;
     if (outflags & ExportData::GHOSTDIR)
        fprintf(out, "GhostDir, ") ;
     if (outflags & ExportData::BRANCHVECTOR)
     {
         for (int dd = 0 ; dd<d ; dd++)
             fprintf(out, "lij%d, ", dd) ;
     }
 
     fseek (out, -2, SEEK_CUR) ;
     fprintf(out, "\n") ;
 
     for (auto & CLp : MP.CLp)
     {
         for (auto & contact: CLp.v)
         {
             if (outflags & ExportData::IDS)
                fprintf(out, "%d %d ", contact.i, contact.j) ;
             if (outflags & ExportData::CONTACTPOSITION || outflags & ExportData::POSITION)
             {
                 for (auto dd : X[contact.i])
                  fprintf(out, "%g ", dd) ;
                 for (auto dd : X[contact.j])
                  fprintf(out, "%g ", dd) ;
             }
             if (outflags & ExportData::FN)
                for (auto dd : contact.infos->Fn)
                  fprintf(out, "%g ", dd) ;
             if (outflags & ExportData::FT)
                for (auto dd : contact.infos->Ft)
                  fprintf(out, "%g ", dd) ;
 
             if (outflags & ExportData::TORQUE)
             {
                for (auto dd : contact.infos->Torquei)
                  fprintf(out, "%g ", dd) ;
                for (auto dd : contact.infos->Torquej)
                  fprintf(out, "%g ", dd) ;
             }
 
             if (outflags & ExportData::GHOSTMASK)
                 fprintf(out, "%d ", contact.ghost) ;
             if (outflags & ExportData::GHOSTDIR)
                 fprintf(out, "%d ", contact.ghostdir) ;
 
             if (outflags & ExportData::BRANCHVECTOR)
             {
                auto [loc,branch] = contact.compute_branchvector(X, *this) ; 
               
                for (int dd = 0 ; dd<d ; dd++) fprintf(out, "%g ", branch[dd]) ;
             }
         fprintf(out, "\n") ;
         }
     }
     return 0 ;
    }
 
 
// For Xml Writing
    XMLWriter * xmlout ;
} ;
/*****************************************************************************************************
 *                                                                                                   *
 *                                                                                                   *
 *                                                                                                   *
 * IMPLEMENTATIONS                                                                                   *
 *                                                                                                   *
 *                                                                                                   *
 *                                                                                                   *
 * ***************************************************************************************************/
double nan_or_double (istream & in)
{
  char c; std::string word ; 
  if (!in.good()) return std::numeric_limits<double>::quiet_NaN();
  while (isspace(c = in.peek())) in.get();
  if ( !isdigit(c) && c!='-' && c!='.') { in >> word ; return std::numeric_limits<double>::quiet_NaN(); }
  double x ; 
  in >> x;
  return x ; 
}
 
 
template <int d>
int Parameters<d>::set_boundaries()
{
    for (int i=0 ; i<d ; i++)
    {
        Boundaries[i].xmin= 0 ;
        Boundaries[i].xmax= 1 ;
        Boundaries[i].delta=1 ; //Precomputed to increase speed
        Boundaries[i].Type = WallType::PBC ; // PBC by default
    }
    //np.savetxt('Boundaries.csv', Boundaries , delimiter=',', fmt='%.6g', header='Low,High,Size,Type', comments='')
    return 0 ;
}
//----------------------------------------------------
template <int d>
void Parameters<d>::perform_PBC (v1d & X, uint32_t & PBCFlag)
{
 for (size_t j=0 ; j<Boundaries.size() ; j++)
 {
   if (Boundaries[j].Type== WallType::PBC) //PBC
   {
    if      (X[j]<Boundaries[j].xmin) {X[j] += Boundaries[j].delta ; PBCFlag |= (1<<j) ;}
    else if (X[j]>Boundaries[j].xmax) {X[j] -= Boundaries[j].delta ; PBCFlag |= (1<<j) ;}
   }
 }
}
//----------------------------------------------------
template <int d>
void Parameters<d>::perform_PBCLE (v1d & X, v1d & V, uint32_t & PBCFlag)
{
    if (Boundaries[0].Type == WallType::PBC_LE)
    {
        if      (X[0]<Boundaries[0].xmin)
        {
            X[0] += Boundaries[0].delta ; PBCFlag |= 1 ;
            X[1] += Boundaries[0].displacement ;
            V[1] += Boundaries[0].delta*Boundaries[0].vel ; ;
        }
        else if (X[0]>Boundaries[0].xmax)
        {
            X[0] -= Boundaries[0].delta ; PBCFlag |= 1 ;
            X[1] -= Boundaries[0].displacement ;
            V[1] -= Boundaries[0].delta*Boundaries[0].vel ; ;
        }
 
        if ( X[1]<Boundaries[1].xmin) {X[1]+=Boundaries[1].delta ; PBCFlag |= 2 ; }
        if ( X[1]>Boundaries[1].xmax) {X[1]-=Boundaries[1].delta ; PBCFlag |= 2 ; }
    }
}
//----------------------------------------------------
template <int d>
void Parameters<d>::perform_PBCLE_move ()
{
    if (Boundaries[0].Type==WallType::PBC_LE)
    {
        Boundaries[0].displacement += dt*Boundaries[0].vel*Boundaries[0].delta ;
        if (Boundaries[0].displacement>Boundaries[1].xmax)
            Boundaries[0].displacement -= Boundaries[1].delta ;
    }
}
//----------------------------------------------------
template <int d>
void Parameters<d>::perform_MOVINGWALL ()
{
 for (size_t j=0 ; j<Boundaries.size() ; j++)
 {
  if (Boundaries[j].Type == WallType::MOVINGWALL)
  {
    Boundaries[j].xmin += Boundaries[j].velmin * dt ;
    Boundaries[j].xmax += Boundaries[j].velmax * dt ;
  }
 }
}
//-----------------------------------------------------
/*int Parameters::init_particles(v2d & X, v2d & A)
{
 boost::random::mt19937 rng;
 boost::random::uniform_01<boost::mt19937> rand(rng) ;
 for (int i=0 ; i<N ; i++)
   for (int dd=0 ; dd<d ; dd++)
   {
     X[i][dd]=rand()*(Boundaries[dd][2]-Boundaries[dd][3]*2*r[i])+(Boundaries[dd][0]+Boundaries[dd][3]*r[i]);//avoid too much overlap with walls
     //m[i]=volume(r[i])*rho ;
 
   }
 //X[0][5]=0.14 ;
 //V[0][:]=np.zeros((1,d))+0.0001*unitvec(0) ;
 //X[1][:]=np.ones((1,d))*0.7 ; X[1,5]=0.2 ; X[1,4]=0.71 ;
 //X[1][:]=np.array([0.21,0.21,0.9,0.2]) ;
 return 0 ;
}*/
template <int d>
int Parameters<d>::init_mass ()
{
 for (int i=0 ; i<N ; i++)
   m[i]=rho*Tools<d>::Volume(r[i]) ;
return 0 ;
}
 
template <int d>
int Parameters<d>::init_inertia ()
{
 for (int i=0; i<N ; i++)
 {
   I[i]=Tools<d>::InertiaMomentum (r[i], rho) ;
 }
 return 0 ;
}
//---------------------------------------------------
template <int d>
void Parameters<d>::load_datafile (char path[], v2d & X, v2d & V, v2d & Omega)
{
  ifstream in ;
 
  in.open(path) ;
  if (!in.is_open()) { printf("[Input] file cannot be open\n"); return ;}
 
  while (! in.eof())
  {
    interpret_command(in, X, V, Omega) ;
  }
 
  for (auto v : dumps)
    if (v.first==ExportType::XML || v.first==ExportType::XMLbase64)
      xmlout= new XMLWriter(Directory+"/dump.xml") ;
 
  in.close() ;
  // Self copy :)
  fs::path p (path) ;
  fs::path pcp (Directory+"/in") ;// pcp/= p.filename() ;
  copy_file(p,pcp, fs::copy_options::overwrite_existing);
}
//-------------------------------------------------
template <int d>
void Parameters<d>::check_events(float time, v2d & X, v2d & V, v2d & Omega)
{
  while (events.size()>0 && events.begin()->first < time)
  {
    stringstream command ; command.str(events.begin()->second) ;
    printf("\nThe following event is implemented now: %s\n", events.begin()->second.c_str()) ;
    interpret_command(command, X,V,Omega) ;
    events.erase(events.begin()) ;
  }
 
}
//------------------------------------------------------
std::istream& operator>>(std::istream& in, std::variant<int*,double*,bool*> v)
{
  printf("SETTING variable %ld\n", v.index());
  switch(v.index())
  {
    case 0: in >> *(std::get<int*>(v)) ; break ;
    case 1: in >> *(std::get<double*>(v)); break ;
    case 2: in >> *(std::get<bool*>(v)); break ;
  }
  return(in) ;}
//------------------------------------------------------
template <int d>
void Parameters<d>::interpret_command (string &in, v2d & X, v2d & V, v2d & Omega)
{
    stringstream B(in) ;
    return (interpret_command(B, X, V, Omega)) ;
}
template <int d>
void Parameters<d>::interpret_command (istream & in, v2d & X, v2d & V, v2d & Omega)
{
  map <string, std::variant<int*,double*,bool*>> SetValueMap = {
     {"Kn",&Kn},
     {"Kt",&Kt},
     {"GammaN",&Gamman},
     {"GammaT",&Gammat},
     {"rho",&rho},
     {"Mu",&Mu},
     {"Mu_wall",&Mu_wall},
     {"damping",&damping},
     {"T",&T},
     {"tdump",&tdump},
     {"orientationtracking",&orientationtracking},
     {"tinfo",&tinfo},
     {"dt",&dt},
     //{"skin", &skin},
     {"gradientdescent_gamma", &graddesc_gamma},
     {"gradientdescent_tol", &graddesc_tol},
     {"cell_size", &cellsize},
     {"forceinsphere", &forceinsphere}
  } ;
 
// Lambda definitions
 auto discard_line = [&](){char line [5000] ; in.getline(line, 5000) ; } ;
 auto read_event = [&](){float time ; char line [5000] ; in >> time ; in.getline (line, 5000) ; events.insert(make_pair(time,line)) ; printf("[INFO] Registering an event: %g -> %s\n", time, line) ;} ;
 auto doauto = [&]() { char line [5000] ; in>>line ;
   if (!strcmp(line, "mass")) init_mass() ;
   else if (!strcmp(line, "rho"))
   {
     rho= m[0]/Tools<d>::Volume(r[0]) ;
     printf("[INFO] Using first particle mass to set rho: %g [M].[L]^-%d\n", rho, d) ;
   }
   else if (!strcmp(line, "inertia")) init_inertia() ;
   else if (!strcmp(line, "location"))
   {
     in >> line ;
     char extras[5000]; in.getline(extras, 5000) ; 
     init_locations(line, X, extras) ;
     printf("[INFO] Set all particle locations\n") ;
   }
   else if (!strcmp(line, "radius"))
   {
     in.getline(line, 5000) ;
     init_radii(line, r) ;
     printf("[INFO] Set all particle radii\n") ;
   }
   else printf("[WARN] Unknown auto command in input script\n") ;
   printf("[INFO] Doing an auto \n") ;
   } ;
 auto setvalue = [&]() { char line[5000] ; in >> line ;
   try {
     in >> SetValueMap.at(line) ;
   }
   catch (const std::out_of_range & e) {
     if (!strcmp(line, "dumps"))
     {
       string word ;
       in>>word ;
       ExportType dumpkind=ExportType::NONE ;
       if (word=="CSV") dumpkind = ExportType::CSV ;
       else if (word=="VTK") dumpkind = ExportType::VTK ;
       else if (word=="NETCDFF") dumpkind = ExportType::NETCDFF ;
       else if (word=="XML") dumpkind = ExportType::XML ;
       else if (word=="XMLbase64") dumpkind = ExportType::XMLbase64 ;
       else if (word=="CSVA") dumpkind = ExportType::CSVA ;
       else if (word=="CONTACTFORCES") {dumpkind = ExportType::CSVCONTACT ; contactforcedump = true ; }
       else if (word=="WALLFORCE") {wallforcecompute = true ; goto LABEL_leave ;} //Jumps at the end of the section
       else {printf("Unknown dump type\n") ; }
 
       { // New section so g++ doesn't complains about the goto ...
       in>>word ;
       if (word != "with") printf("ERR: expecting keyword 'with'\n") ;
       int nbparam ;
       ExportData dumplist = ExportData::NONE ;
       in>>nbparam ;
       for (int i=0 ; i<nbparam ; i++)
       {
         in>>word ;
         if (word=="Position") dumplist |= ExportData::POSITION ;
         else if (word =="Velocity") dumplist |= ExportData::VELOCITY ;
         else if (word =="Omega") dumplist |= ExportData::OMEGA ;
         else if (word =="OmegaMag") dumplist |= ExportData::OMEGAMAG ;
         else if (word =="Orientation")
         {
           orientationtracking=true ;
           dumplist |= ExportData::ORIENTATION ;
         }
         else if (word =="Coordination") dumplist |= ExportData::COORDINATION ;
         else if (word =="Radius") dumplist |= ExportData::RADIUS ;
         else if (word =="Mass") dumplist |= ExportData::MASS ;
         
         else if (word =="Ids") dumplist |= ExportData::IDS ; // Contact properties
         else if (word =="Fn") dumplist |= ExportData::FN ;
         else if (word =="Ft") dumplist |= ExportData::FT ;
         else if (word =="Torque") dumplist |= ExportData::TORQUE ;
         else if (word =="Branch") dumplist |= ExportData::BRANCHVECTOR ;
         else if (word =="Fn_el") dumplist |= ExportData::FN_EL ;
         else if (word =="Fn_visc") dumplist |= ExportData::FN_VISC ;
         else if (word =="Ft_el") dumplist |= ExportData::FT_EL ;
         else if (word =="Ft_visc") dumplist |= ExportData::FT_VISC ;
         else if (word =="Ft_fric") dumplist |= ExportData::FT_FRIC ;
         else if (word =="Ft_frictype") dumplist |= ExportData::FT_FRICTYPE ;
         else if (word =="Ghost_mask") dumplist |= ExportData::GHOSTMASK ;
         else if (word =="Ghost_direction") dumplist |= ExportData::GHOSTDIR;
           
         else printf("Unknown asked data %s\n", word.c_str()) ;
       }
       
       if (dumplist & (ExportData::GHOSTMASK | ExportData::GHOSTDIR | ExportData::FT_FRICTYPE | ExportData::CONTACTPOSITION | ExportData::FN | ExportData::FT | ExportData::BRANCHVECTOR | ExportData::FN_EL | ExportData::FN_VISC | ExportData::FT_EL | ExportData::FT_VISC | ExportData::FT_FRIC)) dumplist |= ExportData::IDS ; 
       /*if constexpr (!SAVE_FORCE_COMPONENTS)
       {
         if (dumplist & (ExportData::FN_EL | ExportData::FN_VISC | ExportData::FT_EL | ExportData::FT_VISC | ExportData::FT_FRIC | ExportData::FT_FRICTYPE))
         {
           printf("WARN: NDDEM was compiled without support for force subcomponents exporting. Removing from the dump output.") ; 
           dumplist &= ~(ExportData::FN_EL | ExportData::FN_VISC | ExportData::FT_EL | ExportData::FT_VISC | ExportData::FT_FRIC | ExportData::FT_FRICTYPE) ; 
         }
       }*/
 
       dumps.push_back(make_pair(dumpkind,dumplist)) ;
       }
       LABEL_leave: ; // Goto label (I know, not beautiful, but makes sense here really)
     }
     else
       printf("[ERROR] Unknown parameter to set\n") ;
   }
 } ; // END of the setvalue lambda
 
// Function mapping
 map<string, function<void()>> Lvl0 ;
 Lvl0["event"] = read_event ;
 Lvl0["CG"] = discard_line ; // Discard CoarseGraining functions in DEM
 Lvl0["set"] = setvalue ;
 Lvl0["auto"] = doauto ;
 
 Lvl0["directory"] = [&](){in>>Directory ; if (! fs::exists(Directory)) fs::create_directory(Directory); };
 Lvl0["dimensions"] = [&](){int nn; int dd ; in>>dd>>nn ; if (N!=nn || d!=dd) {printf("[ERROR] Dimension of number of particles not matching the input file requirements d=%d N=%d\n", d, N) ; std::exit(2) ; }} ;
 Lvl0["location"] = [&]()
 {
   number_gen<int> ids ; number_gen<double> locs[d] ; 
   in >> ids ; for (int i=0 ; i<d ; i++) in >> locs[i] ;
   
   auto id=ids() ; 
   while (id.has_value()) 
   {
    for (int i=0 ; id.has_value() && i<d ; i++)
      X[id.value()][i]= locs[i](true).value() ;
    id = ids() ; 
   }
   //try { while (1) for (int i=0, id=ids() ; i<d; i++) X[id][i]= locs[i](true) ; } catch(...) {}
   //int id ; in>>id ; for (int i=0 ; i<d ; i++) {in >> X[id][i] ;} 
   //for (int i=0, id=ids(); i<d ; i++) { X[id][i]= locs[i]() ;} 
   printf("[INFO] Changing particle location.\n") ; 
  
 } ;
 Lvl0["velocity"] = [&](){int id ; in>>id ; for (int i=0 ; i<d ; i++) {in >> V[id][i] ;} printf("[INFO] Changing particle velocity.\n") ; } ;
 Lvl0["omega"]    = [&](){int id ; in>>id ; for (int i=0 ; i<d*(d-1)/2 ; i++) {in >> Omega[id][i] ;} printf("[INFO] Changing particle angular velocity.\n") ; } ;
 Lvl0["freeze"]   = [&](){int id ; in>>id ; Frozen[id]=true ; printf("[INFO] Freezing particle.\n") ;} ;
 Lvl0["radius"]   = [&](){int id ; double radius ; in>>id>>radius ; if(id==-1) r = v1d(N,radius) ; else r[id]=radius ; printf("[INFO] Set radius of particle.\n") ;} ;
 Lvl0["mass"]     = [&](){int id ; double mass ;   in>>id>>mass   ; if(id==-1) m = v1d(N,mass  ) ; else r[id]=mass   ; printf("[INFO] Set mass of particle.\n") ;} ;
 Lvl0["gravity"]  = [&](){for (int i=0 ; i<d ; i++) {in >> g[i] ;} printf("[INFO] Changing gravity.\n") ; } ;
 Lvl0["ContactModel"] = [&](){ std::string s ; in >> s ; if (s=="Hertz") {ContactModel=ContactModels::HERTZ ;printf("[INFO] Using Hertz model\n") ;} else ContactModel=ContactModels::HOOKE ; } ;
 Lvl0["ContactStrategy"] = [&](){ std::string s ; in >> s ; if (s=="naive") {contact_strategy = ContactStrategies::NAIVE ; } 
                                                            else if (s=="cells") {contact_strategy = ContactStrategies::CELLS  ; } 
                                                            else if (s=="octree") {contact_strategy = ContactStrategies::OCTREE ; }
                                                            else {printf("[WARN] Unknown contact strategy\n") ; }} ;
 Lvl0["gravityangle"] = [&](){ double intensity, angle ; in >> intensity >> angle ;
    Tools<d>::setzero(g) ;
    g[0] = -intensity * cos(angle / 180. * M_PI) ;
    g[1] = intensity * sin(angle / 180. * M_PI) ;
    printf("[INFO] Changing gravity angle in degree between x0 and x1.\n") ;
    } ;
 Lvl0["gravityrotate"] = [&] () {
     update_gravity =&Parameters::do_gravityrotate;
     Tools<d>::setzero(g) ;
     in >> grav_intensity >> grav_omega >> grav_rotdim[0] >> grav_rotdim[1] ;
     printf("[INFO] Setting up a rotating gravity\n") ;
    } ;
 Lvl0["boundary"] = [&](){size_t id ; in>>id ;
    if (id>=Boundaries.size()) {Boundaries.resize(id+1) ;}
    char line [5000] ; in>>line ;
    if (!strcmp(line, "PBC")) 
      Boundaries[id].Type=WallType::PBC ;
    else if (!strcmp(line, "WALL")) 
      Boundaries[id].Type=WallType::WALL ;
    else if (!strcmp(line, "MOVINGWALL")) 
      Boundaries[id].Type=WallType::MOVINGWALL ;
    else if (!strcmp(line, "SPHERE")) 
      Boundaries[id].Type=WallType::SPHERE ; 
    else if (!strcmp(line, "HEMISPHERE")) 
      Boundaries[id].Type=WallType::HEMISPHERE ; 
    else if (!strcmp(line, "AXIALCYLINDER")) 
      Boundaries[id].Type=WallType::AXIALCYLINDER ;
    else if (!strcmp(line, "ROTATINGSPHERE")) 
      Boundaries[id].Type=WallType::ROTATINGSPHERE ; 
    else if (!strcmp(line, "PBCLE")) 
    {
      assert((id==0)) ;
      Boundaries[id].Type=WallType::PBC_LE ; 
    }
    else if (!strcmp(line, "ELLIPSE")) 
      Boundaries[id].Type=WallType::ELLIPSE ; 
    else if (!strcmp(line, "REMOVE")) 
      { Boundaries.erase(Boundaries.begin() + id); return ; }
    else printf("[WARN] Unknown boundary condition, unchanged.\n") ;
    
    Boundaries[id].read_line(in) ; 
    
    printf("[INFO] Changing BC.\n") ;
   };
 Lvl0["rigid"] = [&] () 
 {
   size_t id, npart ; in >> id ;
   if (RigidBodies.RB.size()<id+1) RigidBodies.RB.resize(id+1) ; 
   string s ; in>>s ; 
   
   if (s=="set")
   {
      in >> npart ; 
      std::vector<int> ids ; int tmp ; 
      for (size_t i=0 ; i<npart ; i++)
      {
        in >> tmp ; 
        ids.push_back(tmp) ; 
      }
      RigidBodies.RB[id].setparticles(ids, X, m) ; 
   }
   else if (s=="gravity")
   {
     in >> s ;
     if (s=="on") RigidBodies.RB[id].cancelgravity = false ; 
     else if (s=="off") RigidBodies.RB[id].cancelgravity = true ;
   }
   else if (s=="addforce")
   {
     for (int dd=0 ; dd<d ; dd++)
       in >> RigidBodies.RB[id].addforce[dd] ; //= nan_or_double(in) ; 
   }
   else if (s=="velocity")
   {
     for (int dd=0 ; dd<d ; dd++)
       RigidBodies.RB[id].setvel[dd] = nan_or_double(in) ;
     printf("%g %g\n", RigidBodies.RB[0].setvel[0], RigidBodies.RB[0].setvel[1]) ; 
   }
   
   printf("[INFO] Defining a rigid body.\n") ;
 };
 Lvl0["mesh"] = [&] () 
 {
   string s ; in>>s ; 
   json j;
   if (s=="file" || s=="string")
   {
     if (s=="file") 
     {
      in >> s ;
      std::ifstream i(s.c_str());
      if (i.is_open()==false) {printf("Cannot find the json file provided as argument\n") ; return ; }
      i >> j; 
     }
     else 
     {
      std::getline(in, s) ;
      j=json::parse(s) ; 
     }
    //try 
    { 
      if (j["dimension"].get<int>()!=d) {printf("Incorrect dimension in the json Mesh file: %d, expecting %d.\n", j["dimension"].get<int>(),d) ; return ;}
      for (auto & v: j["objects"])
      {                
        Meshes.push_back({v[STR_PROTECT("dimensionality")].get<int>(), v["vertices"].get<std::vector<std::vector<double>>>()}) ;  
                
        printf("[INFO] Mesh object added.\n") ; 
      }      
    }
   }
   else if (s=="translate")
   {
     std::vector<double> t(d,0) ; 
     for (int i=0 ; i<d ; i++) in>>t[i] ; 
     for (auto &v: Meshes) v.translate(t) ; 
   }
   else if (s=="rotate")
   {
     std::vector<double> r(d*d, 0) ; 
     for (int i=0 ; i<d*d ; i++) in >> r[i] ; 
     for (auto &v: Meshes) v.rotate(r) ; 
   }
   else if (s=="remove")
   {
    int id ; 
    in >> id ;
    Meshes.erase(Meshes.begin()+id) ; 
   }
   else if (s=="export")
   {
     in >> s ; 
     FILE * out = fopen(s.c_str(), "w") ; 
     if (out==NULL) printf("[WARN] Cannot open file to export mesh") ; 
     else
     {
       fprintf(out, "{\n \"dimension\": %d, \n \"objects\":[\n", d) ; 
       for (size_t i=0 ; i<Meshes.size() ; i++)
       {
         auto res = Meshes[i].export_json() ; 
         fprintf(out, "%s", res.c_str()) ;
         if (i<Meshes.size()-1) fprintf(out, ",\n") ; 
       }
       fprintf(out, "\n]}") ; 
       fclose(out) ; 
     }
     //for (auto & v: Meshes) v.disp() ; 
   }
   else
     printf("[WARN] Unknown mesh subcommand\n") ; 
   
 };
 Lvl0["restart"] = [&] () {
   restart_flag=0 ;
   std::string s ; in >> s ; 
   if (s=="ignore")
     restart_flag |= (1<<1) ; 
   else if (s=="force") 
     restart_flag |= (2<<1) ; 
  
   in >> s ; 
   if (s=="keepall")
     restart_flag |= 1 ; 
   
   in >> n_restart ; 
   in >> restart_filename ;   
 } ; 
 
 
// Processing
 string line ;
 in>>line;
 if (line[0]=='#') {discard_line() ; return  ;}
 try {Lvl0.at(line)() ; }
 catch (const std::out_of_range & e) { printf("LVL0 command unknown: %s\n", line.c_str()) ; discard_line() ; }
 
}
//================================================================================================================================================
 
//=====================================
template <int d>
void Parameters<d>::remove_particle (int idx, v2d & X, v2d & V, v2d & A, v2d & Omega, v2d & F, v2d & FOld, v2d & Torque, v2d & TorqueOld)
{
    printf("WARN: it is probably a bad idea to use remove particle which hasn't been tested ... \n") ;
    X.erase (X.begin()+idx) ; V.erase (V.begin()+idx) ;
    A.erase (A.begin()+idx) ; Omega.erase (Omega.begin()+idx) ;
    F.erase (F.begin()+idx) ; FOld.erase (FOld.begin()+idx) ;
    Torque.erase (Torque.begin()+idx) ; TorqueOld.erase (TorqueOld.begin()+idx) ;
    I.erase(I.begin()+idx) ; m.erase(m.begin()+idx) ; r.erase(r.begin()+idx) ;
    Frozen.erase(Frozen.begin()+idx) ;
    N-- ;
}
//--------------------
template <int d>
void Parameters<d>::add_particle (/*v2d & X, v2d & V, v2d & A, v2d & Omega, v2d & F, v2d & FOld, v2d & Torque, v2d & TorqueOld*/)
{
    printf("add_particle NOT IMPLEMENTED YET\n") ;
}
//----------------
template <int d>
void Parameters<d>::init_locations (char *line, v2d & X, char *extras)
{
    boost::random::mt19937 rng(seed);
    boost::random::uniform_01<boost::mt19937> rand(rng) ;
    if (!strcmp(line, "square"))
    {
        auto m = *(std::max_element(r.begin(), r.end())) ;
        printf("%g\n", m) ;
        int dd ;
        for (dd=0 ; dd<d ; dd++) X[0][dd]=Boundaries[dd].xmin+m ;
        for (int i=1 ; i<N ; i++)
        {
            X[i]=X[i-1] ;
            for (dd=0 ; dd<d ; dd++)
            {
                X[i][dd] += 2*m ;
                if (X[i][dd] > Boundaries[dd].xmax-m)
                    X[i][dd] = Boundaries[dd].xmin+m ;
                else
                    break ;
            }
            if (dd==d) {printf("WARN: cannot affect all particles on the square lattice, not enough space in the simulation box\n") ; break ; }
        }
    }
    else if (!strcmp(line, "randomsquare"))
    {
        auto m = *(std::max_element(r.begin(), r.end())) ;
        printf("%g\n", m) ;
        int dd ;
        for (dd=0 ; dd<d ; dd++) X[0][dd]=Boundaries[dd].xmin+m ;
        for (int i=1 ; i<N ; i++)
        {
            X[i]=X[i-1] ;
            for (dd=0 ; dd<d ; dd++)
            {
                X[i][dd] += 2*m ;
                if (X[i][dd] > Boundaries[dd].xmax-m)
                    X[i][dd] = Boundaries[dd].xmin+m + 0.1*m*(rand()-0.5) ;
                else
                    break ;
            }
            if (dd==d) {printf("WARN: cannot affect all particles on the square lattice, not enough space in the simulation box\n") ; break ; }
        }
    }
    else if (!strcmp(line, "randomdrop"))
    {
 
        for (int i=0 ; i<N ; i++)
        {
         for(int dd=0 ; dd < d ; dd++)
         {
           if (Boundaries[dd].Type==WallType::PBC)
             X[i][dd] = rand()*Boundaries[dd].delta + Boundaries[dd].xmin ;
           else
             X[i][dd] = rand()*(Boundaries[dd].delta-2*r[i]) + Boundaries[dd].xmin + r[i] ;
         }
        }
    }
    else if (!strcmp(line, "insphere"))
    {
        //printf("Location::insphere assumes that wall #d is a sphere") ; fflush(stdout) ;
        auto w = std::find_if(Boundaries.begin(), Boundaries.end(), [](auto u){return (u.Type==WallType::SPHERE || u.Type==WallType::ROTATINGSPHERE) ; }) ; 
        if ( w == Boundaries.end()) {printf("ERR: the spherical wall cannot be found\n") ; fflush(stdout) ; } 
        int id = w-Boundaries.begin() ; 
        
        for (int i=0 ; i<N ; i++)
        {
         double dst=0 ;
         printf(".") ; fflush(stdout);
         do {
            dst=0 ;
            for(int dd=0 ; dd < d ; dd++)
            {
              X[i][dd] = (rand()*Boundaries[id].radius*2-Boundaries[id].radius) + Boundaries[id].center[dd] ; 
              dst += (Boundaries[id].center[dd]-X[i][dd])*(Boundaries[id].center[dd]-X[i][dd]) ;
            }
         } while ( sqrt(dst) > (Boundaries[id].radius-2*r[i])) ;
        }
    }  
    else if (!strcmp(line, "incylinder"))
    {
        //printf("Location::insphere assumes that wall #d is a sphere") ; fflush(stdout) ;
        auto w = std::find_if(Boundaries.begin(), Boundaries.end(), [](auto u){return (u.Type==WallType::AXIALCYLINDER) ; }) ; 
        if ( w== Boundaries.end()) {printf("ERR: the cylinder wall cannot be found\n") ; fflush(stdout) ; } 
        int id = w-Boundaries.begin() ; 
        
        for (int i=0 ; i<N ; i++)
        {
         double dst=0 ;
         printf(".") ; fflush(stdout);
         do {
            dst=0 ;
            for(int dd=0 ; dd < d ; dd++)
            {
              if (dd == Boundaries[id].axis)
              {
                X[i][dd] = rand() * (Boundaries[Boundaries[id].axis].delta-2*r[i]) + Boundaries[Boundaries[id].axis].xmin + r[i] ; 
              }
              else 
              {
                X[i][dd] = (rand()*Boundaries[id].radius*2-Boundaries[id].radius) ; 
                dst += X[i][dd]*X[i][dd] ;
              }
            }
         } while ( sqrt(dst) > (Boundaries[id].radius-2*r[i])) ;
        }
    }
    else if (!strcmp(line, "roughinclineplane"))
    {
      printf("Location::roughinclineplane assumes a plane of normal [1,0,0...] at location 0 along the 1st dimension.") ; fflush(stdout) ;
      auto m = *(std::max_element(r.begin(), r.end())) ; // Max radius
      double delta=0.1*m ;
      for (int dd=0 ; dd<d ; dd++) X[0][dd]=Boundaries[dd].xmin+m+delta ;
      Frozen[0]=true ;
      for (int i=1 ; i<N ; i++)
      {
        X[i]=X[i-1] ;
        for (int dd=d-1 ; dd>=0 ; dd--)
        {
          X[i][dd] += 2*m+2*delta ;
          if (X[i][dd]>Boundaries[dd].xmax-m-delta)
            X[i][dd] = Boundaries[dd].xmin+m+delta ;
          else
            break ;
        }
        if (X[i][0]==Boundaries[0].xmin+m+delta) Frozen[i]=true ;
        // randomize the previous grain
        for (int dd=0 ; dd<d ; dd++)
          X[i-1][dd] += (rand()-0.5)*2*delta ;
      }
    }
    else if (!strcmp(line, "smallroughinclineplane"))
    {
      printf("Location::smallroughinclineplane assumes a plane of normal [1,0,0...] at location 0 along the 1st dimension. The frozen particles are forced to be the smallest particle radius\n") ; fflush(stdout) ;
      auto r_max = *(std::max_element(r.begin(), r.end())) ; // Max radius
      auto r_min = *(std::min_element(r.begin(), r.end())) ; // Max radius
      double m = r_max;
      double delta=0.1*r_max ;
      int i_bottom_layer = 1;
      for (int dd=1 ; dd<d ; dd++) 
        i_bottom_layer *= floor(Boundaries[dd].delta/(2*r_min+0.2*r_min))  ;
      printf("BOTTOM LAYER NUMBER: %d\n", i_bottom_layer);
      // for (int dd=1 ; dd<d ; dd++) X[0][dd]=Boundaries[dd].xmin+r_max+delta ; // skip first dimension
      Frozen[0]=true ;
      r[0] = r_min;
      for (int i=1 ; i<N ; i++)
      {
        X[i]=X[i-1] ;
        if (i < i_bottom_layer ) {
          Frozen[i]=true ;
          r[i] = r_min;
          m = r_min;
          delta = 0.1*r_min;
        } else {
          m = r_max;
          delta = 0.1*r_max;
        }
        for (int dd=d-1 ; dd>=0 ; dd--)
        {
          X[i][dd] += 2*m+2*delta ;
          if (X[i][dd]>Boundaries[dd].xmax-m-delta)
            if (i < i_bottom_layer ) {
              X[i][dd] = 0 ;
            } else {
              X[i][dd] = Boundaries[dd].xmin+m+delta ;
            }
          else
            break ;
        }
        // randomize this grain EXCEPT if it is a boundary particle
        for (int dd=0 ; dd<d ; dd++) {
          if (i >= i_bottom_layer) {
            X[i][dd] += (rand()-0.5)*2*delta ;
          }
        }
      }
      // add some randomness to boundary particles in first dimension only
      for (int i=1 ; i<i_bottom_layer ; i++)
      {
        X[i][0] += rand()*2*delta;
      }
    }
    else if (!strcmp(line, "roughinclineplane2"))
    {
      printf("Location::roughinclineplane assumes a plane of normal [1,0,0...] at location 0 along the 1st dimension.") ; fflush(stdout) ;
      auto m = *(std::max_element(r.begin(), r.end())) ; // Max radius
      double delta=0.1*m ; int ddd ;
      for (int dd=0 ; dd<d ; dd++) X[0][dd]=Boundaries[dd].xmin+m ;
      Frozen[0]=true ; bool bottomlayer=true ;
      for (int i=1 ; i<N ; i++)
      {
        X[i]=X[i-1] ;
        for (ddd=d-1 ; ddd>=0 ; ddd--)
        {
          if (bottomlayer)
          {
            X[i][ddd]+= 2*m ;
            if (X[i][ddd]>Boundaries[ddd].xmax-m)
              X[i][ddd] = Boundaries[ddd].xmin+m ;
            else
              break ;
          }
          else
          {
            X[i][ddd] += 2*m+2*delta ;
            if (X[i][ddd]>Boundaries[ddd].xmax-m-delta)
              X[i][ddd] = Boundaries[ddd].xmin+m+delta ;
            else
              break ;
          }
        }
        if (ddd==0) bottomlayer=false ;
        if (bottomlayer)
        {
          Frozen[i-1]=true ;
          X[i-1][0] += rand()*delta ; // Randomness only on x0, and only >r (above the bottom wall)
        }
        else
        {
          for (int dd=0 ; dd<d ; dd++)
            X[i-1][dd] += (rand()-0.5)*2*delta ;
        }
      }
    }
    else if (!strcmp(line, "quasicrystal"))
    {
        auto m = *(std::max_element(r.begin(), r.end())) ; // largest radius
        printf("%g\n", m) ;
        int dd ;
        // X is an array of particle locations
        for (dd=0 ; dd<d ; dd++) { X[0][dd]=Boundaries[dd].xmin+m ; } // d is number of dimensions, dd is its index
        for (int i=1 ; i<N ; i++) // number of particles
        {
            X[i]=X[i-1] ; // get previous particle location
            for (dd=0 ; dd<d ; dd++) // iterate over dimensions
            {
                X[i][dd] += 2*m ; // add a diameter
                if (X[i][dd]>Boundaries[dd].xmax-m) // if too close to 'right'
                    X[i][dd] = Boundaries[dd].xmin+m ; // bring back to 'left'
                else
                    break ;
            }
            if (dd==d) {printf("WARN: cannot affect all particles on the square lattice, not enough space in the simulation box\n") ; break ; }
        }
    }
    else if (!strcmp(line, "fromfile"))
    {
      while (*extras == ' ') extras++ ; 
      std::ifstream in(extras); // Open the file
    
      if (!in) { std::cerr << "Failed to open the file." << std::endl; return;}
      while (!in.eof())
      {
        int idx  ; 
        in >> idx ;
        for (int dd=0 ; dd<d ; dd++)
          in >> X[idx][dd] ; 
        in >> r[idx] ; 
      }
    }
    else
        printf("ERR: undefined initial location function.\n") ;
}
//-----------------------------
template <int d>
void Parameters<d>::init_radii (char line[], v1d & r)
{
  std::istringstream s(line) ;
  std::string word ;
  double minr, maxr, fraction, fuzz ;
  boost::random::mt19937 rng(seed);
  boost::random::uniform_01<boost::mt19937> rand(rng) ;
 
  s >> word ;
  printf("[%s]\n", word.c_str()) ;
  if (word == "uniform")
  {
    s >> minr ; s >> maxr ;
    for (auto & v : r) v = rand()*(maxr-minr)+minr ;
  }
  else if (word == "bidisperse")
  {
    s >> minr ; s >> maxr ;
    s >> fraction ;
 
    double Vs=Tools<d>::Volume(minr) ;
    double Vl=Tools<d>::Volume(maxr) ;
    double f = fraction*Vs/((1-fraction)*Vl+fraction*Vs) ;
 
    for (auto & v : r) v = (rand()<f?maxr:minr) ;
 
  }
  else if (word == "bidisperse_fuzzy")
  {
    s >> minr ; s >> maxr ;
    s >> fraction ;
    s >> fuzz ;
 
    double Vs=Tools<d>::Volume(minr) ;
    double Vl=Tools<d>::Volume(maxr) ;
    double f = fraction*Vs/((1-fraction)*Vl+fraction*Vs) ;
 
    for (auto & v : r)
    {
      v = (rand()<f?maxr:minr) ;
      v = v + (rand()*2-1)*(fuzz*v) ;
    }
  }
  else
    printf("WARN: unknown radius distribution automatic creation. Nothing done ...\n") ;
}
 
 
//======================================
template <int d>
void Parameters<d>::display_info(int tint, v2d& V, v2d& Omega, v2d& F, v2d& Torque, int nct, int ngst)
{
static bool first=true ;
static double Rmax, mmax ;
if (first)
{
 Rmax=*max_element(r.begin(), r.end()) ;
 mmax=*max_element(m.begin(), m.end()) ;
 //printf("\e[10S\e[9A") ;
}
 
//printf("\e[s%c\n", letters[tint%4]) ;
//printf("\033%c %c\n", 0x37, letters[tint%4]) ;
if (tint%tinfo==0)
{
  //for (int i=0 ; i<(tint*100)/int(T/dt) ; i++) printf("#") ;
  //printf("%d %d %d ",tint, T, (tint*100)/T) ;
 if (!first) printf("\e[8A") ;
 printf("\e[80G") ;
 printf("\n\e[80G NContacts: %d | Nghosts: %d \n", nct, ngst) ;
 
 double Vmax=Tools<d>::norm(*max_element(V.begin(), V.end(), [](cv1d &a, cv1d &b) {return (Tools<d>::normsq(a)<Tools<d>::normsq(b)) ;})) ;
 double Omegamax=Tools<d>::skewnorm(*max_element(Omega.begin(), Omega.end(), [](cv1d &a, cv1d &b) {return (Tools<d>::skewnormsq(a)<Tools<d>::skewnormsq(b)) ;})) ;
 double Torquemax=Tools<d>::skewnorm(*max_element(Torque.begin(), Torque.end(), [](cv1d &a, cv1d &b) {return (Tools<d>::skewnormsq(a)<Tools<d>::skewnormsq(b)) ;})) ;
 double Fmax=Tools<d>::norm(*max_element(F.begin(), F.end(), [](cv1d &a, cv1d &b) {return (Tools<d>::normsq(a)<Tools<d>::normsq(b)) ;})) ;
 
 printf("\n") ;
 printf("\e[80G Max V: %15g | V dt / R      = %15g \n", Vmax, Vmax*dt/Rmax) ;
 printf("\e[80G Max O: %15g | Omega dt      = %15g \n", Omegamax, Omegamax*dt) ;
 printf("\e[80G Max F: %15g | F dt dt / m r = %15g \n", Fmax, Fmax*dt*dt/(mmax*Rmax)) ;
 printf("\e[80G Max M: %15g | M dt / m R R  = %15g \n", Torquemax, Torquemax*dt/(mmax*Rmax*Rmax)) ;
 printf("\e[80G                        | g dt dt / R   = %15g \n", Tools<d>::norm(g)*dt*dt/Rmax) ;
 
//printf("\e[u") ;
//printf("\\033%c", 0x38) ;
printf("\e[0G") ;
fflush(stdout) ;
}
if (first) first=false ;
}
//------------------------------------------
template <int d>
void Parameters<d>::xml_header ()
{
   xmlout->openbranch("boundaries", {make_pair("length", to_string(d*2))}) ;
   if (Boundaries[0].Type==WallType::ROTATINGSPHERE)
     for (int i=0 ; i<d ; i++) xmlout->fic << Boundaries[0].center[d]-Boundaries[0].radius << " " << Boundaries[0].center[d]+Boundaries[0].radius  << " " ;
   else
     for (int i=0 ; i<d ; i++) xmlout->fic << Boundaries[i].xmin << " " << Boundaries[i].xmax << " " ;
   xmlout->closebranch() ;
 
   xmlout->openbranch("radius", {make_pair("length", to_string(N))}) ;
   for (auto v: r) xmlout->fic << v << " " ;
   xmlout->closebranch() ;
}
 
//-----------------------------------------
template <int d>
void Parameters<d>::quit_cleanly()
{
  for (auto v : dumps)
    if ((v.first == ExportType::XML) || (v.first == ExportType::XMLbase64))
      xmlout->emergencyclose() ;
}
template <int d>
void Parameters<d>::finalise()
{
  for (auto v : dumps)
    if ((v.first == ExportType::XML) || (v.first == ExportType::XMLbase64))
      xmlout->close() ;
}
 
 
//========================================
template <int d>
int Parameters<d>::dumphandling (int ti, double t, v2d &X, v2d &V, v1d &Vmag, v2d &A, v2d &Omega, v1d &OmegaMag, vector<uint32_t> &PBCFlags, v1d & Z, Multiproc<d> & MP)
{
  static bool xmlstarted=false ;
 
  for (auto v : dumps)
  {
    if (v.first==ExportType::CSV)
    {
      char path[500] ; sprintf(path, "%s/dump-%05d.csv", Directory.c_str(), ti) ;
      Tools<d>::norm(Vmag, V) ; Tools<d>::norm(OmegaMag, Omega) ;
      if ( v.second & ExportData::VELOCITY)
      {
         Tools<d>::savecsv(path, X, V, r, PBCFlags, Vmag, OmegaMag, Z) ; //These are always written for CSV, independent of the dumplist
      }
      else
      {
          Tools<d>::savecsv(path, X, r, PBCFlags, Vmag, OmegaMag, Z) ; //These are always written for CSV, independent of the dumplist
      }
      if (v.second & ExportData::ORIENTATION)
      {
        char path[500] ; sprintf(path, "%s/dumpA-%05d.csv", Directory.c_str(), ti) ;
        Tools<d>::savecsv(path, A) ;
      }
    }
 
 
    if (v.first == ExportType::CSVCONTACT)
    {
     char path[500] ; sprintf(path, "%s/dumpcontactforce-%05d.csv", Directory.c_str(), ti) ;
     FILE * out = fopen(path, "w") ;
     if (out == NULL) {printf("[ERR] Cannot open file for contact force writing.\n") ; fflush(stdout) ; return 1 ; }
     savecsvcontact(out, v.second, MP, X) ;
     fclose(out) ;
    }
 
    if (v.first == ExportType::VTK)
    {
        v2d tmp ;
        char path[500] ; sprintf(path, "%s/dump-%05d.vtk", Directory.c_str(), ti) ;
        
        FILE * out = vtkwriter::open (path, d) ; 
        vtkwriter::write_points(out, X, d) ; 
        
        vector<std::pair<ExportData, int>> mapping ; 
        vector<vector<double>> contactdata ; 
        if (v.second & (ExportData::IDS | ExportData::GHOSTMASK | ExportData::GHOSTDIR | ExportData::FT_FRICTYPE | ExportData::CONTACTPOSITION | ExportData::FN | ExportData::FT | ExportData::BRANCHVECTOR | ExportData::FN_EL | ExportData::FN_VISC | ExportData::FT_EL | ExportData::FT_VISC | ExportData::FT_FRIC))
        {
          std::tie(mapping, contactdata) = MP.contacts2array(v.second, X, *this) ;
          if (mapping[0].first != ExportData::IDS) printf("ERR: something went wrong in writing contact data in the vtk file %X\n", static_cast<unsigned int>(mapping[0].first)) ; 
          vtkwriter::write_contactlines (out, contactdata) ; 
        }
        
        vtkwriter::start_pointdata(out, X) ; 
        vtkwriter::write_dimension_data(out, X, r, d, Boundaries) ;
                
        vector <TensorInfos> val;
        if (v.second & ExportData::VELOCITY) vtkwriter::write_data(out, {"Velocity", TensorType::VECTOR, &V}, d) ;
        if (v.second & ExportData::OMEGA)    vtkwriter::write_data(out, {"Omega", TensorType::SKEWTENSOR, &Omega}, d) ;
        if (v.second & ExportData::OMEGAMAG)  {tmp.push_back(OmegaMag) ; vtkwriter::write_data(out, {"OmegaMag", TensorType::SCALAR, &tmp}, d) ;}
        if (v.second & ExportData::ORIENTATION) vtkwriter::write_data(out, {"ORIENTATION", TensorType::TENSOR, &A}, d) ;
        if (v.second & ExportData::RADIUS) {tmp.push_back(r) ; vtkwriter::write_data(out, {"RADIUS", TensorType::SCALAR, &tmp}, d) ;}
        if (v.second & ExportData::MASS) {tmp.push_back(m) ; vtkwriter::write_data(out, {"MASS", TensorType::SCALAR, &tmp}, d) ;}
        if (v.second & ExportData::COORDINATION) {tmp.push_back(Z) ; vtkwriter::write_data(out, {"Coordination", TensorType::SCALAR, &tmp}, d) ;  }
        if (v.second & ExportData::IDS) {
            vector<double> tmpid (N, 0) ;
            for (int i=0 ; i<N ; i++)
                tmpid[i]=i ;
            tmp.push_back(tmpid) ; vtkwriter::write_data(out, {"Id", TensorType::SCALAR, &tmp}, d) ;
        }
        
        if (mapping.size()>1)
        { 
          vtkwriter::start_celldata(out, X.size(), contactdata.size());
          
          for (auto & v:mapping)
          {
            switch(v.first){
              case ExportData::CONTACTPOSITION : vtkwriter::write_celldata (out, "Locations", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FN : vtkwriter::write_celldata (out, "NormalForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FT : vtkwriter::write_celldata (out, "TangentialForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::BRANCHVECTOR : vtkwriter::write_celldata (out, "BranchVector", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FN_EL : vtkwriter::write_celldata (out, "ElasticNormalForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FN_VISC : vtkwriter::write_celldata (out, "ViscousNormalForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FT_EL : vtkwriter::write_celldata (out, "ElasticTangentialForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FT_VISC : vtkwriter::write_celldata (out, "VisousTangentialForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FT_FRIC : vtkwriter::write_celldata (out, "FrictionForce", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::FT_FRICTYPE : vtkwriter::write_celldata (out, "FrictionActivated", contactdata, TensorType::VECTOR, v.second, N, d) ; break ; 
              case ExportData::GHOSTMASK : vtkwriter::write_celldata (out, "GhostMask", contactdata, TensorType::SCALARMASK, v.second, N, d) ; break ; 
              case ExportData::GHOSTDIR : vtkwriter::write_celldata (out, "GhostDirection", contactdata, TensorType::SCALARMASK, v.second, N, d) ; break ; 
              default: break ; 
            }
          }
        }       
        
        vtkwriter::close(out) ; 
        //Tools<d>::savevtk(path, N, Boundaries, X, r, {}) ;
    }
 
    if (v.first == ExportType::NETCDFF)
          printf("WARN: netcdf writing hasn't been tested and therefore is not plugged in\n") ;
 
    if (v.first == ExportType::XML)
    {
      if (xmlstarted==false)
      {
        char path[500] ; sprintf(path, "%s/dump.xml", Directory.c_str()) ;
        xmlout->header(d, path) ;
        xml_header() ;
        xmlstarted=true ;
      }
      xmlout->startTS(t);
      if (v.second & ExportData::POSITION) xmlout->writeArray("Position", &X, ArrayType::particles, EncodingType::ascii);
      if (v.second & ExportData::VELOCITY) xmlout->writeArray("Velocity", &V, ArrayType::particles, EncodingType::ascii);
      if (v.second & ExportData::OMEGA)    xmlout->writeArray("Omega", &Omega, ArrayType::particles, EncodingType::ascii);
      if (v.second & ExportData::OMEGAMAG)
          printf("Omega Mag not implemented yet\n");
      if (v.second & ExportData::ORIENTATION) xmlout->writeArray("Orientation", &A, ArrayType::particles, EncodingType::ascii);
      if (v.second & ExportData::COORDINATION) xmlout->writeArray("Coordination", &Z, ArrayType::particles, EncodingType::ascii);
      
      if (v.second & (ExportData::IDS | ExportData::GHOSTMASK | ExportData::GHOSTDIR | ExportData::FT_FRICTYPE | ExportData::CONTACTPOSITION | ExportData::FN | ExportData::FT | ExportData::BRANCHVECTOR | ExportData::FN_EL | ExportData::FN_VISC | ExportData::FT_EL | ExportData::FT_VISC | ExportData::FT_FRIC))
      { 
        auto [mapping, tmp] = MP.contacts2array(v.second, X, *this) ;
        for (auto & v:mapping)
        {
          switch(v.first){
            case ExportData::IDS: xmlout->writeArray("Ids", &tmp, v.second, 2, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::CONTACTPOSITION : xmlout->writeArray("Locations", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FN : xmlout->writeArray("Normal force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FT : xmlout->writeArray("Tangential force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::BRANCHVECTOR : xmlout->writeArray("Branch vector", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FN_EL : xmlout->writeArray("Elastic normal force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FN_VISC : xmlout->writeArray("Viscous normal force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FT_EL : xmlout->writeArray("Elastic tangential force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FT_VISC : xmlout->writeArray("Visous tangential force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FT_FRIC : xmlout->writeArray("Friction force", &tmp, v.second, d, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::FT_FRICTYPE : xmlout->writeArray("Friction activated", &tmp, v.second, 1, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::GHOSTMASK : xmlout->writeArray("Ghost mask", &tmp, v.second, 1, ArrayType::contacts, EncodingType::ascii) ; break ;
            case ExportData::GHOSTDIR : xmlout->writeArray("Ghost direction", &tmp, v.second, 1, ArrayType::contacts, EncodingType::ascii) ; break ;
            default: break ; 
          }
        }
      }
      
//         case ExportData::POSITION: res.push_back(loc) ; break ; 
//         case ExportData::FN: res.push_back(contact.infos->Fn) ; break ;
//         case ExportData::FT: res.push_back(contact.infos->Ft) ; break ;
//         case ExportData::GHOSTMASK: res.push_back(contact.infos->ghost) ; break ;
//         case ExportData::GHOSTDIR : res.push_back(contact.infos->ghostdir) ; break ;
//         case ExportData::BRANCHVECTOR: res.push_back(branch) ; break ;
      xmlout->stopTS();
    }
 
    if (v.first == ExportType::XMLbase64)
    {
      if (xmlstarted==false)
      {
        char path[500] ; sprintf(path, "%s/dump.xml", Directory.c_str()) ;
        xmlout->header(d, path) ;
        xml_header() ;
        xmlstarted=true ;
      }
      xmlout->startTS(t);
      if (v.second & ExportData::POSITION) xmlout->writeArray("Position", &X, ArrayType::particles, EncodingType::base64);
      if (v.second & ExportData::VELOCITY) xmlout->writeArray("Velocity", &V, ArrayType::particles, EncodingType::base64);
      if (v.second & ExportData::OMEGA)    xmlout->writeArray("Omega", &Omega, ArrayType::particles, EncodingType::base64);
      if (v.second & ExportData::OMEGAMAG)
          printf("Omega Mag not implemented yet\n");
      if (v.second & ExportData::ORIENTATION) xmlout->writeArray("Orientation", &A, ArrayType::particles, EncodingType::base64);
      if (v.second & ExportData::COORDINATION) xmlout->writeArray("Orientation", &Z, ArrayType::particles, EncodingType::base64);
      xmlout->stopTS();
    }
 
  }
return 0 ;
}
 
#endif