/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator 

   Original Version:
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov 

   See the README file in the top-level LAMMPS directory. 

   ----------------------------------------------------------------------- 

   USER-CUDA Package and associated modifications:
   https://sourceforge.net/projects/lammpscuda/ 

   Christian Trott, christian.trott@...1735...
   Lars Winterfeld, lars.winterfeld@...1735...
   Theoretical Physics II, University of Technology Ilmenau, Germany 

   See the README file in the USER-CUDA directory. 

   This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include "cuda.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "universe.h"
#include "input.h"
#include "error.h"
#include "cuda_neigh_list.h"
//#include "pre_binning_cu.h"
#include "binning_cu.h"
//#include "reverse_binning_cu.h"
#include <ctime>
#include <cmath>
#include "cuda_pair_cu.h"
#include "cuda_cu.h"

using namespace LAMMPS_NS;



Cuda::Cuda(LAMMPS *lmp) : Pointers(lmp)
{
	cuda_exists=true;
	lmp->cuda=this;
	if(universe->me==0)
	printf("# Using LAMMPS_CUDA \n");
	shared_data.me=universe->me;
	device_set=false;
	
	Cuda_Cuda_GetCompileSettings(&shared_data);
	
	if(shared_data.compile_settings.prec_glob!=sizeof(CUDA_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: Global Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_glob, sizeof(CUDA_FLOAT)/4);
	if(shared_data.compile_settings.prec_x!=sizeof(X_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: X Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_x, sizeof(X_FLOAT)/4);
	if(shared_data.compile_settings.prec_v!=sizeof(V_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: V Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_v, sizeof(V_FLOAT)/4);
	if(shared_data.compile_settings.prec_f!=sizeof(F_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: F Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_f, sizeof(F_FLOAT)/4);
	if(shared_data.compile_settings.prec_pppm!=sizeof(PPPM_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: PPPM Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_pppm, sizeof(PPPM_FLOAT)/4);
	if(shared_data.compile_settings.prec_fft!=sizeof(FFT_FLOAT)/4) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: FFT Precision: cuda %i cpp %i\n\n",shared_data.compile_settings.prec_fft, sizeof(FFT_FLOAT)/4);
    #ifdef FFT_CUFFT
      if(shared_data.compile_settings.cufft!=1) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: cufft: cuda %i cpp %i\n\n",shared_data.compile_settings.cufft, 1);
    #else	
      if(shared_data.compile_settings.cufft!=0) printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: cufft: cuda %i cpp %i\n\n",shared_data.compile_settings.cufft, 0);
    #endif
    
    if(shared_data.compile_settings.arch!=CUDA_ARCH)  printf("\n\n # CUDA WARNING: Compile Settings of cuda and cpp code differ! \n # CUDA WARNING: arch: cuda %i cpp %i\n\n",shared_data.compile_settings.cufft, CUDA_ARCH);
	
	cu_x          = 0;
	cu_v          = 0;
	cu_f          = 0;
	cu_tag        = 0;
	cu_type       = 0;
	cu_mask       = 0;
	cu_image      = 0;
	cu_xhold      = 0;
	cu_q          = 0;
	cu_rmass      = 0;
	cu_mass       = 0;
	cu_virial     = 0;
	cu_eatom      = 0;
	cu_vatom      = 0;
	cu_radius	  = 0;
	cu_density	  = 0;
	cu_omega	  = 0;
	cu_torque	  = 0;
	
	cu_special 	  = 0;
	cu_nspecial   = 0;
	
	cu_molecule   = 0;
	
	cu_x_type 	  = 0;
	x_type		  = 0;
	cu_v_radius	  = 0;
	v_radius	  = 0;
	cu_omega_rmass	  = 0;
	omega_rmass	  = 0;
	
	binned_id = 0;
	cu_binned_id  = 0;
	binned_idnew = 0;
	cu_binned_idnew = 0;
	
	cu_map_array = 0;
	
	copy_buffer=0;
	copy_buffersize=0;
	
	neighbor_decide_by_integrator=0;
	pinned=true;
	
	debugdata=0;
	new int[2*CUDA_MAX_DEBUG_SIZE];
	
	finished_setup = false;
	begin_setup = false;
	finished_run = false;

	setSharedDataZero();
	
	uploadtime=0;
	downloadtime=0;
	dotiming=false;

  dotestatom = false;
  testatom = 0;
	oncpu = true;

  self_comm = 0;
	MYDBG( printf("# CUDA: Cuda::Cuda Done...\n");)
	//cCudaData<double, float, yx >  
}

Cuda::~Cuda()
{
	
	print_timings();
	
	if(universe->me==0) printf("# CUDA: Free memory...\n");
	
	delete cu_q;
	delete cu_x;
	delete cu_v;
	delete cu_f;
	delete cu_tag;
	delete cu_type;
	delete cu_mask;
	delete cu_image;
	delete cu_xhold;
	delete cu_mass;
	delete cu_rmass;
	delete cu_virial;
	delete cu_eng_vdwl;
	delete cu_eng_coul;
	delete cu_eatom;
	delete cu_vatom;
	delete cu_radius;
	delete cu_density;
	delete cu_omega;
	delete cu_torque;
	delete cu_molecule;
	
	delete cu_x_type;
	delete [] x_type;
	delete cu_v_radius;
	delete [] v_radius;
	delete cu_omega_rmass;
	delete [] omega_rmass;
	
	delete cu_map_array;
	
	std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
	while(p != neigh_lists.end())
	{
		delete p->second;
		++p;
	}
}

void Cuda::accelerator(int narg, char** arg)
{
	if(device_set) return;
	if(universe->me==0)
	printf("# CUDA: Activate GPU \n");
	
	int* devicelist=NULL;
	int pppn=2;
    for(int i=0;i<narg;i++)
	{
	  if(strcmp(arg[i],"gpu/node")==0) 
	  {
	    if(++i==narg) 
	      error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'gpu/node' option."); 
	    pppn=atoi(arg[i]);
	  } 

	  if(strcmp(arg[i],"gpu/node/special")==0) 
	  {
	    if(++i==narg) 
	      error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting number of GPUs to be used per node after keyword 'gpu/node/special'."); 
	    pppn=atoi(arg[i]);
	    if(pppn<1) error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting number of GPUs to be used per node after keyword 'gpu/node special'."); 
	    if(i+pppn==narg) 
	      error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting list of device ids after keyword 'gpu/node special'."); 
	    devicelist=new int[pppn];
	    for(int k=0;k<pppn;k++)
	      {i++;devicelist[k]=atoi(arg[i]);}
	  }

	  if(strcmp(arg[i],"pinned")==0) 
	  {
	  	if(++i==narg) 
	  	  error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'pinned' option."); 
	    pinned=atoi(arg[i])==0?false:true;
            if((pinned==false)&&(universe->me==0)) printf(" #CUDA: Pinned memory is not used for communication\n");
	  }

	  if(strcmp(arg[i],"timing")==0) 
	  {
	  	dotiming=true;
	  }

	  if(strcmp(arg[i],"suffix")==0) 
	  {
	  	if(++i==narg) 
	  	  error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a string after 'suffix' option."); 
	  	strcpy(lmp->suffix,arg[i]);
	  }

	  if(strcmp(arg[i],"overlap_comm")==0) 
	  {
	  	shared_data.overlap_comm=1;
	  }

	  if(strcmp(arg[i],"test")==0) 
	  {
	  	if(++i==narg) 
	  	  error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'test' option."); 
	    testatom=atof(arg[i]);
	    dotestatom=true;
	  }

	  if(strcmp(arg[i],"override/bpa")==0) 
	  {
	  	if(++i==narg) 
	  	  error->all(FLERR,"Invalid Options for 'accelerator' command. Expecting a number after 'override/bpa' option."); 
	      shared_data.pair.override_block_per_atom = atoi(arg[i]);
	  }
	}

	CudaWrapper_Init(0, (char**)0,universe->me,pppn,devicelist);
	//if(shared_data.overlap_comm)
	  	CudaWrapper_AddStreams(3);
	cu_x          = 0;
	cu_v          = 0;
	cu_f          = 0;
	cu_tag        = 0;
	cu_type       = 0;
	cu_mask       = 0;
	cu_image      = 0;
	cu_xhold      = 0;
	cu_q          = 0;
	cu_rmass      = 0;
	cu_mass       = 0;
	cu_virial     = 0;
	cu_eatom      = 0;
	cu_vatom      = 0;
	cu_radius	    = 0;
	cu_density	  = 0;
	cu_omega	    = 0;
	cu_torque	    = 0;
	
	cu_special 	  = 0;
	cu_nspecial   = 0;
	
	cu_molecule   = 0;
	
	cu_x_type 	  = 0;
	cu_v_radius	  = 0;
	cu_omega_rmass	  = 0;
	
	cu_binned_id  = 0;
	cu_binned_idnew = 0;
	device_set=true;
	allocate();
	delete devicelist;
}

void Cuda::setSharedDataZero()
{
	MYDBG(printf("# CUDA: Cuda::setSharedDataZero ...\n");)
	shared_data.atom.nlocal = 0;
	shared_data.atom.nghost = 0;
	shared_data.atom.nall = 0;
	shared_data.atom.nmax = 0;
	shared_data.atom.ntypes = 0;
	shared_data.atom.q_flag = 0;
	shared_data.atom.need_eatom = 0;
	shared_data.atom.need_vatom = 0;
  shared_data.atom.update_nmax = 1;
  shared_data.atom.update_nlocal = 1;
  shared_data.atom.update_neigh = 1;
	
  shared_data.pair.cudable_force = 0;
	shared_data.pair.collect_forces_later = 0;
	shared_data.pair.use_block_per_atom = 0;
	shared_data.pair.override_block_per_atom = -1;
	shared_data.pair.cut = 0;
	shared_data.pair.cutsq = 0;
	shared_data.pair.cut_inner = 0;
	shared_data.pair.cut_coul = 0;
	shared_data.pair.special_lj = 0;
	shared_data.pair.special_coul = 0;
	
	shared_data.pair.neighall = false;
	
	shared_data.pppm.cudable_force = 0;
	
	shared_data.buffersize = 0;
	shared_data.buffer_new = 1;
	shared_data.buffer = NULL;
	
	shared_data.comm.comm_phase=0;
	shared_data.overlap_comm=0;

	shared_data.comm.buffer = NULL;
	shared_data.comm.buffer_size=0;
	shared_data.comm.overlap_split_ratio=0;
   // setTimingsZero();
}

void Cuda::allocate()
{
	accelerator(0,NULL);
	MYDBG(printf("# CUDA: Cuda::allocate ...\n");)
	if(not cu_virial)
	{
	  cu_virial    = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.virial , 6);
	  cu_eng_vdwl  = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.eng_vdwl ,1);
	  cu_eng_coul  = new cCudaData<double, ENERGY_FLOAT, x > (NULL, & shared_data.pair.eng_coul ,1);
	  cu_extent 	 = new cCudaData<double, double, x> (extent, 6);
	  shared_data.flag = CudaWrapper_AllocCudaData(sizeof(int));
	  int size=2*CUDA_MAX_DEBUG_SIZE;
	  debugdata = new int[size];
	  cu_debugdata    = new cCudaData<int, int, x > (debugdata , size);
	  shared_data.debugdata=cu_debugdata->dev_data();
	}
	checkResize();
	setSystemParams();
	MYDBG(printf("# CUDA: Cuda::allocate done...\n");)
}

void Cuda::setSystemParams()
{
    MYDBG(printf("# CUDA: Cuda::setSystemParams ...\n");)
	shared_data.atom.nlocal = atom->nlocal;
	shared_data.atom.nghost = atom->nghost;
	shared_data.atom.nall = atom->nlocal + atom->nghost;
	shared_data.atom.ntypes = atom->ntypes;
	shared_data.atom.q_flag = atom->q_flag;
	shared_data.atom.rmass_flag = atom->rmass_flag;
    MYDBG(printf("# CUDA: Cuda::setSystemParams done ...\n");)
}

void Cuda::setDomainParams()
{
    MYDBG(printf("# CUDA: Cuda::setDomainParams ...\n");)
 	cuda_shared_domain* cu_domain = &shared_data.domain;
 
    cu_domain->triclinic = domain->triclinic;
	for(short i=0; i<3; ++i)
	{
		cu_domain->periodicity[i] = domain->periodicity[i];
		cu_domain->sublo[i] = domain->sublo[i];
		cu_domain->subhi[i] = domain->subhi[i];
		cu_domain->boxlo[i] = domain->boxlo[i];
		cu_domain->boxhi[i] = domain->boxhi[i];
		cu_domain->prd[i] = domain->prd[i];
	}
	if(domain->triclinic)
    {
	  for(short i=0; i<3; ++i)
	  {
	    cu_domain->boxlo_lamda[i] = domain->boxlo_lamda[i];
	    cu_domain->boxhi_lamda[i] = domain->boxhi_lamda[i];
	    cu_domain->prd_lamda[i] = domain->prd_lamda[i];
	  }
	  cu_domain->xy = domain->xy;
	  cu_domain->xz = domain->xz;
	  cu_domain->yz = domain->yz;
	}

    for(int i=0;i<6;i++) 
	{
	  cu_domain->h[i]=domain->h[i];
	  cu_domain->h_inv[i]=domain->h_inv[i];
	  cu_domain->h_rate[i]=domain->h_rate[i];
	}
	
	cu_domain->update=2;
    MYDBG(printf("# CUDA: Cuda::setDomainParams done ...\n");)
}

void Cuda::checkResize()
{
    MYDBG(printf("# CUDA: Cuda::checkResize ...\n");)
    accelerator(0,NULL);
	cuda_shared_atom* cu_atom = & shared_data.atom;
	cuda_shared_pair* cu_pair = & shared_data.pair;
	cu_atom->q_flag      = atom->q_flag;
	cu_atom->rmass_flag  = atom->rmass ? 1 : 0;
	cu_atom->nall = atom->nlocal + atom->nghost;
	cu_atom->nlocal      = atom->nlocal;
	cu_atom->nghost      = atom->nghost;
	
	// do we have more atoms to upload than currently allocated memory on device? (also true if nothing yet allocated)
	if(atom->nmax > cu_atom->nmax || cu_tag == NULL)
	{
		delete cu_x;               cu_x         = new cCudaData<double, X_FLOAT, yx> ((double*)atom->x , & cu_atom->x        , atom->nmax, 3,0,true); //cu_x->set_buffer(&(shared_data.buffer),&(shared_data.buffersize),true);
		delete cu_v;               cu_v         = new cCudaData<double, V_FLOAT, yx> ((double*)atom->v, & cu_atom->v         , atom->nmax, 3);
		delete cu_f;               cu_f         = new cCudaData<double, F_FLOAT, yx> ((double*)atom->f, & cu_atom->f         , atom->nmax, 3,0,true);
		delete cu_tag;             cu_tag       = new cCudaData<int   , int    , x > (atom->tag       , & cu_atom->tag       , atom->nmax   );
		delete cu_type;            cu_type      = new cCudaData<int   , int    , x > (atom->type      , & cu_atom->type      , atom->nmax   );
		delete cu_mask;            cu_mask      = new cCudaData<int   , int    , x > (atom->mask      , & cu_atom->mask      , atom->nmax   );
		delete cu_image;           cu_image     = new cCudaData<int   , int    , x > (atom->image     , & cu_atom->image     , atom->nmax   );

		if(atom->rmass)
			{delete cu_rmass;      cu_rmass     = new cCudaData<double, V_FLOAT, x > (atom->rmass     , & cu_atom->rmass     , atom->nmax  );}

		if(cu_atom->q_flag)
			{delete cu_q;          cu_q         = new cCudaData<double, F_FLOAT, x > ((double*)atom->q, & cu_atom->q         , atom->nmax  );}// cu_q->set_buffer(&(copy_buffer),&(copy_buffersize),true);}

		if(atom->radius)
		{
			delete cu_radius;     cu_radius    = new cCudaData<double, X_FLOAT, x > (atom->radius    , & cu_atom->radius     , atom->nmax  );
		    delete cu_v_radius;   cu_v_radius  = new cCudaData<V_FLOAT, V_FLOAT, x> (v_radius , & cu_atom->v_radius      , atom->nmax*4);
		    delete cu_omega_rmass;   cu_omega_rmass  = new cCudaData<V_FLOAT, V_FLOAT, x> (omega_rmass , & cu_atom->omega_rmass      , atom->nmax*4);
		}

		if(atom->omega)
			{delete cu_omega;      cu_omega     = new cCudaData<double, V_FLOAT, yx > (((double*) atom->omega)    , & cu_atom->omega     , atom->nmax,3  );}

		if(atom->torque)
			{delete cu_torque;     cu_torque    = new cCudaData<double, F_FLOAT, yx > (((double*) atom->torque)   , & cu_atom->torque     , atom->nmax,3  );}

		if(atom->special)
			{delete cu_special;     cu_special    = new cCudaData<int, int, yx > (((int*) &(atom->special[0][0]))   , & cu_atom->special     , atom->nmax,atom->maxspecial  ); shared_data.atom.maxspecial=atom->maxspecial;}
		if(atom->nspecial)
			{delete cu_nspecial;     cu_nspecial    = new cCudaData<int, int, yx > (((int*) atom->nspecial)  , & cu_atom->nspecial     , atom->nmax,3  );}
		if(atom->molecule)
			{delete cu_molecule;     cu_molecule    = new cCudaData<int, int, x > (((int*) atom->molecule)  , & cu_atom->molecule     , atom->nmax  );}
		shared_data.atom.special_flag = neighbor->special_flag;
		shared_data.atom.molecular = atom->molecular;
		   
    cu_atom->update_nmax = 2;
    cu_atom->nmax        = atom->nmax;
	    
		delete cu_x_type;           cu_x_type   = new cCudaData<X_FLOAT, X_FLOAT, x> (x_type , & cu_atom->x_type      , atom->nmax*4);
	}

	if(((cu_xhold==NULL)||(cu_xhold->get_dim()[0]<neighbor->maxhold))&&neighbor->xhold)
	{
		delete cu_xhold;           cu_xhold     = new cCudaData<double, X_FLOAT, yx> ((double*)neighbor->xhold, & cu_atom->xhold         , neighbor->maxhold, 3);
		shared_data.atom.maxhold=neighbor->maxhold;
	}
	
	if(atom->mass && !cu_mass) 
	{cu_mass      = new cCudaData<double, V_FLOAT, x > (atom->mass      , & cu_atom->mass      , atom->ntypes+1);}
	cu_atom->mass_host   = atom->mass;
	
	if(atom->map_style==1)
	{
	  if((cu_map_array==NULL))
	  {
	  	cu_map_array   = new cCudaData<int, int, x > (atom->get_map_array()   , & cu_atom->map_array     , atom->get_map_size()  );
	  }
	  else
	  if(cu_map_array->dev_size()/sizeof(int)<atom->get_map_size())
	  {
	    delete cu_map_array;
      cu_map_array   = new cCudaData<int, int, x > (atom->get_map_array()   , & cu_atom->map_array     , atom->get_map_size()  );
	  }
	}
	
	
	// if any of the host pointers have changed (e.g. re-allocated somewhere else), set to correct pointer
	if(cu_x   ->get_host_data() != atom->x)    cu_x   ->set_host_data((double*) (atom->x));
	if(cu_v   ->get_host_data() != atom->v)    cu_v   ->set_host_data((double*) (atom->v));
	if(cu_f   ->get_host_data() != atom->f)    cu_f   ->set_host_data((double*) (atom->f));
	if(cu_tag ->get_host_data() != atom->tag)  cu_tag ->set_host_data(atom->tag);
	if(cu_type->get_host_data() != atom->type) cu_type->set_host_data(atom->type);
	if(cu_mask->get_host_data() != atom->mask) cu_mask->set_host_data(atom->mask);
	if(cu_image->get_host_data() != atom->image) cu_mask->set_host_data(atom->image);
	
	if(cu_xhold)
	if(cu_xhold->get_host_data()!= neighbor->xhold) cu_xhold->set_host_data((double*)(neighbor->xhold));
	
	if(atom->rmass)
	if(cu_rmass->get_host_data() != atom->rmass) cu_rmass->set_host_data((double*) (atom->rmass));

	if(cu_atom->q_flag)
	if(cu_q->get_host_data() != atom->q) cu_q->set_host_data((double*) (atom->q));
	
	if(atom->radius)
	if(cu_radius->get_host_data() != atom->radius) cu_radius->set_host_data((double*) (atom->radius));

	if(atom->omega)
	if(cu_omega->get_host_data() != atom->omega) cu_omega->set_host_data((double*) (atom->omega));

	if(atom->torque)
	if(cu_torque->get_host_data() != atom->torque) cu_torque->set_host_data((double*) (atom->torque));

	if(atom->special)
	if(cu_special->get_host_data() != atom->special)
			{delete cu_special;     cu_special    = new cCudaData<int, int, yx > (((int*) atom->special)   , & cu_atom->special     , atom->nmax,atom->maxspecial  ); shared_data.atom.maxspecial=atom->maxspecial;}
	
	if(atom->nspecial)
	if(cu_nspecial->get_host_data() != atom->nspecial) cu_nspecial->set_host_data((int*) (atom->nspecial));

	if(atom->molecule)
	if(cu_molecule->get_host_data() != atom->molecule) cu_molecule->set_host_data((int*) (atom->molecule));

	if(force)
	if(cu_virial   ->get_host_data() != force->pair->virial)    cu_virial   ->set_host_data(force->pair->virial);
	if(force)
	if(cu_eng_vdwl ->get_host_data() != &force->pair->eng_vdwl)    cu_eng_vdwl  ->set_host_data(&force->pair->eng_vdwl);
	if(force)
	if(cu_eng_coul ->get_host_data() != &force->pair->eng_coul)    cu_eng_coul   ->set_host_data(&force->pair->eng_coul);

 	cu_atom->update_nlocal = 2;
	MYDBG(printf("# CUDA: Cuda::checkResize done...\n");)
}

void Cuda::evsetup_eatom_vatom(int eflag_atom,int vflag_atom)
{
    if(eflag_atom)
    {
    	if(not cu_eatom) 
    		cu_eatom         = new cCudaData<double, ENERGY_FLOAT, x > (force->pair->eatom, & (shared_data.atom.eatom)         , atom->nmax  );// cu_eatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
    	if(cu_eatom->get_dim()[0]!=atom->nmax)
    	{
    	  //delete cu_eatom;
        //cu_eatom         = new cCudaData<double, ENERGY_FLOAT, x > (force->pair->eatom, & (shared_data.atom.eatom)         , atom->nmax  );// cu_eatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
    	  shared_data.atom.update_nmax=2;
    	}

    	cu_eatom->set_host_data(force->pair->eatom); 
		  cu_eatom->memset_device(0);
    }
    if(vflag_atom)
    {	
    	if(not cu_vatom) 
    		cu_vatom         = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)force->pair->vatom, & (shared_data.atom.vatom)         , atom->nmax ,6 );// cu_vatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
      if(cu_vatom->get_dim()[0]!=atom->nmax)
      {
        //delete cu_vatom;
        //cu_vatom         = new cCudaData<double, ENERGY_FLOAT, yx > ((double*)force->pair->vatom, & (shared_data.atom.vatom)         , atom->nmax ,6 );// cu_vatom->set_buffer(&(copy_buffer),&(copy_buffersize),true);}
        shared_data.atom.update_nmax=2;
      }
    	cu_vatom->set_host_data((double*)force->pair->vatom); 
		  cu_vatom->memset_device(0);
    }
}

void Cuda::uploadAll()
{
	MYDBG(printf("# CUDA: Cuda::uploadAll() ... start\n");)
	timespec starttime;
	timespec endtime;

	if(atom->nmax!=shared_data.atom.nmax) checkResize();
	clock_gettime(CLOCK_REALTIME,&starttime);
	cu_x   ->upload();
	cu_v   ->upload();
	cu_f   ->upload();
	cu_tag ->upload();
	cu_type->upload();
	cu_mask->upload();
	cu_image->upload();
	if(shared_data.atom.q_flag) cu_q    ->upload();
	
	if(atom->rmass)             cu_rmass->upload();

	if(atom->radius)            cu_radius->upload();
	if(atom->omega)             cu_omega->upload();
	if(atom->torque)            cu_torque->upload();
	if(atom->special)           cu_special->upload();
	if(atom->nspecial)          cu_nspecial->upload();
	if(atom->molecule)          cu_molecule->upload();
	if(cu_eatom) cu_eatom->upload();
	if(cu_vatom) cu_vatom->upload();

	clock_gettime(CLOCK_REALTIME,&endtime);
	uploadtime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
	CUDA_IF_BINNING(Cuda_PreBinning(& shared_data);)
	CUDA_IF_BINNING(Cuda_Binning   (& shared_data);)
	
	shared_data.atom.triggerneighsq=neighbor->triggersq;
	MYDBG(printf("# CUDA: Cuda::uploadAll() ... end\n");)
}

void Cuda::downloadAll()
{
	MYDBG(printf("# CUDA: Cuda::downloadAll() ... start\n");)
	timespec starttime;
	timespec endtime;

	if(atom->nmax!=shared_data.atom.nmax) checkResize();

	CUDA_IF_BINNING( Cuda_ReverseBinning(& shared_data); )
	clock_gettime(CLOCK_REALTIME,&starttime);
	cu_x   ->download();
	cu_v   ->download();
	cu_f   ->download();
	cu_type->download();
	cu_tag ->download();
	cu_mask->download();
	cu_image->download();

	//if(shared_data.atom.need_eatom) cu_eatom->download();
	//if(shared_data.atom.need_vatom) cu_vatom->download();

	if(shared_data.atom.q_flag) cu_q    ->download();
	if(atom->rmass)             cu_rmass->download();
	
	if(atom->radius)            cu_radius->download();
	if(atom->omega)             cu_omega->download();
	if(atom->torque)            cu_torque->download();
	if(atom->special)           cu_special->download();
	if(atom->nspecial)          cu_nspecial->download();
	if(atom->molecule)          cu_molecule->download();
	if(cu_eatom) cu_eatom->download();
	if(cu_vatom) cu_vatom->download();
	
	clock_gettime(CLOCK_REALTIME,&endtime);
	downloadtime+=(endtime.tv_sec-starttime.tv_sec+1.0*(endtime.tv_nsec-starttime.tv_nsec)/1000000000);
	MYDBG(printf("# CUDA: Cuda::downloadAll() ... end\n");)
}

void Cuda::downloadX()
{
	Cuda_Pair_RevertXType(& this->shared_data);
	cu_x->download();
}

CudaNeighList* Cuda::registerNeighborList(class NeighList* neigh_list)
{
	MYDBG(printf("# CUDA: Cuda::registerNeighborList() ... start a\n");)
	std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.find(neigh_list);

	if(p != neigh_lists.end()) return p->second;
	else
	{
		CudaNeighList* neigh_list_cuda = new CudaNeighList(lmp, neigh_list);
		neigh_lists.insert(std::pair<NeighList*, CudaNeighList*>(neigh_list, neigh_list_cuda));
		return neigh_list_cuda;
	}
	MYDBG(printf("# CUDA: Cuda::registerNeighborList() ... end b\n");)
}

void Cuda::uploadAllNeighborLists()
{
	MYDBG(printf("# CUDA: Cuda::uploadAllNeighborList() ... start\n");)
	std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
	while(p != neigh_lists.end())
	{
		p->second->nl_upload();
		if(not (p->second->neigh_list->cuda_list->build_cuda))
		for(int i=0;i<atom->nlocal;i++)
		p->second->sneighlist.maxneighbors=MAX(p->second->neigh_list->numneigh[i],p->second->sneighlist.maxneighbors) ;
		++p;
	}
	MYDBG(printf("# CUDA: Cuda::uploadAllNeighborList() ... done\n");)
}

void Cuda::downloadAllNeighborLists()
{
	MYDBG(printf("# CUDA: Cuda::downloadAllNeighborList() ... start\n");)
	std::map<NeighList*, CudaNeighList*>::iterator p = neigh_lists.begin();
	while(p != neigh_lists.end())
	{
		p->second->nl_download();
		++p;
	}
}

void Cuda::update_xhold(int &maxhold,double* xhold)
{
     if(this->shared_data.atom.maxhold<atom->nmax)
     {
        maxhold = atom->nmax;
		delete this->cu_xhold;           this->cu_xhold     = new cCudaData<double, X_FLOAT, yx> ((double*)xhold, & this->shared_data.atom.xhold         , maxhold, 3);
     }
     this->shared_data.atom.maxhold=maxhold;
 	 CudaWrapper_CopyData(this->cu_xhold->dev_data(),this->cu_x->dev_data(),3*atom->nmax*sizeof(X_FLOAT));
}

void Cuda::setTimingsZero()
{
	shared_data.cuda_timings.test1=0;
	shared_data.cuda_timings.test2=0;
	
	//communication
	shared_data.cuda_timings.comm_forward_total = 0;
	shared_data.cuda_timings.comm_forward_mpi_upper = 0;
	shared_data.cuda_timings.comm_forward_mpi_lower = 0;
	shared_data.cuda_timings.comm_forward_kernel_pack = 0;
	shared_data.cuda_timings.comm_forward_kernel_unpack = 0;
	shared_data.cuda_timings.comm_forward_upload = 0;
	shared_data.cuda_timings.comm_forward_download = 0;

	shared_data.cuda_timings.comm_exchange_total = 0;
	shared_data.cuda_timings.comm_exchange_mpi = 0;
	shared_data.cuda_timings.comm_exchange_kernel_pack = 0;
	shared_data.cuda_timings.comm_exchange_kernel_unpack = 0;
	shared_data.cuda_timings.comm_exchange_kernel_fill = 0;
	shared_data.cuda_timings.comm_exchange_cpu_pack= 0;
	shared_data.cuda_timings.comm_exchange_upload = 0;
	shared_data.cuda_timings.comm_exchange_download = 0;

	shared_data.cuda_timings.comm_border_total = 0;
	shared_data.cuda_timings.comm_border_mpi = 0;
	shared_data.cuda_timings.comm_border_kernel_pack = 0;
	shared_data.cuda_timings.comm_border_kernel_unpack = 0;
	shared_data.cuda_timings.comm_border_kernel_buildlist = 0;
	shared_data.cuda_timings.comm_border_kernel_self = 0;
	shared_data.cuda_timings.comm_border_upload = 0;
	shared_data.cuda_timings.comm_border_download = 0;
	
	//pair forces
	shared_data.cuda_timings.pair_xtype_conversion = 0;
	shared_data.cuda_timings.pair_kernel = 0;
	shared_data.cuda_timings.pair_virial = 0;
	shared_data.cuda_timings.pair_force_collection = 0;
	
	//neighbor
	shared_data.cuda_timings.neigh_bin = 0;
	shared_data.cuda_timings.neigh_build = 0;
	shared_data.cuda_timings.neigh_special = 0;
	
	//PPPM
 	shared_data.cuda_timings.pppm_particle_map = 0;
  shared_data.cuda_timings.pppm_make_rho = 0;
  shared_data.cuda_timings.pppm_brick2fft = 0;
  shared_data.cuda_timings.pppm_poisson = 0;
  shared_data.cuda_timings.pppm_fillbrick = 0;
  shared_data.cuda_timings.pppm_fieldforce = 0;
  shared_data.cuda_timings.pppm_compute = 0;
	
	CudaWrapper_CheckUploadTime(true);
	CudaWrapper_CheckDownloadTime(true);
	CudaWrapper_CheckCPUBufUploadTime(true);
	CudaWrapper_CheckCPUBufDownloadTime(true);	
}

void Cuda::print_timings()
{
	if(universe->me!=0) return;
	if(not dotiming) return;
	printf("\n # CUDA: Special timings\n\n");
	printf("\n Transfer Times\n");
	printf(" PCIe Upload:  \t %lf s\n",CudaWrapper_CheckUploadTime());
	printf(" PCIe Download:\t %lf s\n",CudaWrapper_CheckDownloadTime());
	printf(" CPU Tempbbuf Upload:   \t %lf \n",CudaWrapper_CheckCPUBufUploadTime());
	printf(" CPU Tempbbuf Download: \t %lf \n",CudaWrapper_CheckCPUBufDownloadTime());
	
	printf("\n Communication \n");
    
	printf(" Forward Total           \t %lf \n",shared_data.cuda_timings.comm_forward_total);
	printf(" Forward MPI Upper Bound \t %lf \n",shared_data.cuda_timings.comm_forward_mpi_upper);
	printf(" Forward MPI Lower Bound \t %lf \n",shared_data.cuda_timings.comm_forward_mpi_lower);
	printf(" Forward Kernel Pack     \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_pack);
	printf(" Forward Kernel Unpack   \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_unpack);
	printf(" Forward Kernel Self     \t %lf \n",shared_data.cuda_timings.comm_forward_kernel_self);
	printf(" Forward Upload          \t %lf \n",shared_data.cuda_timings.comm_forward_upload);
	printf(" Forward Download        \t %lf \n",shared_data.cuda_timings.comm_forward_download);
	printf(" Forward Overlap Split Ratio\t %lf \n",shared_data.comm.overlap_split_ratio);
	printf("\n");

	printf(" Exchange Total          \t %lf \n",shared_data.cuda_timings.comm_exchange_total);
	printf(" Exchange MPI            \t %lf \n",shared_data.cuda_timings.comm_exchange_mpi);
	printf(" Exchange Kernel Pack    \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_pack);
	printf(" Exchange Kernel Unpack  \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_unpack);
  printf(" Exchange Kernel Fill    \t %lf \n",shared_data.cuda_timings.comm_exchange_kernel_fill);
  printf(" Exchange CPU Pack	     \t %lf \n",shared_data.cuda_timings.comm_exchange_cpu_pack);
	printf(" Exchange Upload         \t %lf \n",shared_data.cuda_timings.comm_exchange_upload);
	printf(" Exchange Download       \t %lf \n",shared_data.cuda_timings.comm_exchange_download);
	printf("\n");

	printf(" Border Total            \t %lf \n",shared_data.cuda_timings.comm_border_total);
	printf(" Border MPI              \t %lf \n",shared_data.cuda_timings.comm_border_mpi);
	printf(" Border Kernel Pack      \t %lf \n",shared_data.cuda_timings.comm_border_kernel_pack);
	printf(" Border Kernel Unpack    \t %lf \n",shared_data.cuda_timings.comm_border_kernel_unpack);
	printf(" Border Kernel Self      \t %lf \n",shared_data.cuda_timings.comm_border_kernel_self);
	printf(" Border Kernel BuildList \t %lf \n",shared_data.cuda_timings.comm_border_kernel_buildlist);
	printf(" Border Upload           \t %lf \n",shared_data.cuda_timings.comm_border_upload);
	printf(" Border Download 	     \t %lf \n",shared_data.cuda_timings.comm_border_download);
	printf("\n");
	
	//pair forces
	printf(" Pair XType Conversion   \t %lf \n",shared_data.cuda_timings.pair_xtype_conversion );
	printf(" Pair Kernel             \t %lf \n",shared_data.cuda_timings.pair_kernel );
	printf(" Pair Virial             \t %lf \n",shared_data.cuda_timings.pair_virial );
	printf(" Pair Force Collection   \t %lf \n",shared_data.cuda_timings.pair_force_collection );
	printf("\n");
	
	//neighbor
	printf(" Neighbor Binning        \t %lf \n",shared_data.cuda_timings.neigh_bin );
	printf(" Neighbor Build          \t %lf \n",shared_data.cuda_timings.neigh_build );
	printf(" Neighbor Special        \t %lf \n",shared_data.cuda_timings.neigh_special );	
	printf("\n");
	
	//pppm
	if(force->kspace)
	{
	printf(" PPPM Total              \t %lf \n",shared_data.cuda_timings.pppm_compute );
	printf(" PPPM Particle Map       \t %lf \n",shared_data.cuda_timings.pppm_particle_map );
	printf(" PPPM Make Rho           \t %lf \n",shared_data.cuda_timings.pppm_make_rho );
	printf(" PPPM Brick2fft          \t %lf \n",shared_data.cuda_timings.pppm_brick2fft );
	printf(" PPPM Poisson            \t %lf \n",shared_data.cuda_timings.pppm_poisson );
	printf(" PPPM Fillbrick          \t %lf \n",shared_data.cuda_timings.pppm_fillbrick );
	printf(" PPPM Fieldforce         \t %lf \n",shared_data.cuda_timings.pppm_fieldforce );
	printf("\n");
	}	

	printf(" Debug Test 1            \t %lf \n",shared_data.cuda_timings.test1);
	printf(" Debug Test 2            \t %lf \n",shared_data.cuda_timings.test2);
	
	printf("\n");
}