HomePatch.h File Reference

#include "charm++.h"
#include "NamdTypes.h"
#include "Patch.h"
#include "PatchMap.h"
#include "MigrateAtomsMsg.h"
#include "main.h"
#include "common.h"
#include "Migration.h"
#include "Settle.h"
#include <string>
#include <map>

Go to the source code of this file.

Classes
class	HomePatch
struct	HomePatch::RattleList
struct	HomePatch::checkpoint_t

Macros
#define	TIMER_INIT(T, TYPE)   do { } while(0)
#define	TIMER_INIT_WIDTH(T, TYPE, WIDTH)   do{ } while(0)
#define	TIMER_START(T, TYPE)   do { } while(0)
#define	TIMER_STOP(T, TYPE)   do { } while(0)
#define	TIMER_DONE(T)   do { } while(0)
#define	TIMER_REPORT(T)   do { } while(0)

Enumerations
enum	{ MAXFACTOR = 32 }

Functions
void	PatchDataSOA_initialize (PatchDataSOA *p)
size_t	PatchDataSOA_set_size (PatchDataSOA *p, int natoms, int pad=MAXFACTOR)
void	PatchDataSOA_set_buffer (PatchDataSOA *p, void *mybuffer)

Macro Definition Documentation

TIMER_DONE

#define TIMER_DONE

(

T

)

do { } while(0)

Definition at line 266 of file HomePatch.h.

Referenced by Sequencer::integrate(), and Sequencer::integrate_SOA().

TIMER_INIT

#define TIMER_INIT	(		T,
			TYPE
	)		do { } while(0)

Definition at line 262 of file HomePatch.h.

TIMER_INIT_WIDTH

#define TIMER_INIT_WIDTH	(		T,
			TYPE,
			WIDTH
	)		do{ } while(0)

Definition at line 263 of file HomePatch.h.

Referenced by Sequencer::integrate(), and Sequencer::integrate_SOA().

TIMER_REPORT

#define TIMER_REPORT

(

T

)

do { } while(0)

Definition at line 267 of file HomePatch.h.

Referenced by Sequencer::integrate(), and Sequencer::integrate_SOA().

TIMER_START

#define TIMER_START	(		T,
			TYPE
	)		do { } while(0)

Definition at line 264 of file HomePatch.h.

Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2(), and Sequencer::langevinVelocitiesBBK2_SOA().

TIMER_STOP

#define TIMER_STOP	(		T,
			TYPE
	)		do { } while(0)

Definition at line 265 of file HomePatch.h.

Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2(), and Sequencer::langevinVelocitiesBBK2_SOA().

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
MAXFACTOR	pad length of arrays up to this next multiple

Definition at line 295 of file HomePatch.h.

     {
#ifdef NAMD_CUDA
  MAXFACTOR = 32  
#else
  //TODO:HIP verify
  MAXFACTOR = 32
#endif
};

Function Documentation

PatchDataSOA_initialize()

void PatchDataSOA_initialize

(

PatchDataSOA *

p

)

Initialize fundamental parts of PatchDataSOA.

Definition at line 2366 of file HomePatch.C.

References PatchDataSOA::buffer, PatchDataSOA::maxAtoms, PatchDataSOA::numAtoms, and PatchDataSOA::numBytes.

                                              {
  p->buffer = NULL;
  p->numBytes = 0;
  p->numAtoms = 0;
  p->maxAtoms = 0;
}

PatchDataSOA_set_buffer()

void PatchDataSOA_set_buffer	(	PatchDataSOA *	p,
		void *	mybuffer
	)

Caller provides the buffer space to be used. Set all pointers relative to this provided address, pointing into the buffer space.

Definition at line 2397 of file HomePatch.C.

References PatchDataSOA::atomFixed, PatchDataSOA::buffer, PatchDataSOA::charge, PatchDataSOA::exclId, PatchDataSOA::f_global_x, PatchDataSOA::f_global_y, PatchDataSOA::f_global_z, PatchDataSOA::f_nbond_x, PatchDataSOA::f_nbond_y, PatchDataSOA::f_nbond_z, PatchDataSOA::f_normal_x, PatchDataSOA::f_normal_y, PatchDataSOA::f_normal_z, PatchDataSOA::f_saved_nbond_x, PatchDataSOA::f_saved_nbond_y, PatchDataSOA::f_saved_nbond_z, PatchDataSOA::f_saved_slow_x, PatchDataSOA::f_saved_slow_y, PatchDataSOA::f_saved_slow_z, PatchDataSOA::f_slow_x, PatchDataSOA::f_slow_y, PatchDataSOA::f_slow_z, PatchDataSOA::fixedPosition_x, PatchDataSOA::fixedPosition_y, PatchDataSOA::fixedPosition_z, PatchDataSOA::gaussrand_x, PatchDataSOA::gaussrand_y, PatchDataSOA::gaussrand_z, PatchDataSOA::groupFixed, PatchDataSOA::hydrogenGroupSize, PatchDataSOA::id, PatchDataSOA::isWater, PatchDataSOA::langevinParam, PatchDataSOA::langScalRandBBK2, PatchDataSOA::langScalVelBBK2, PatchDataSOA::mass, PatchDataSOA::maxAtoms, PatchDataSOA::migrationGroupSize, PatchDataSOA::nonbondedGroupSize, Node::Object(), PatchDataSOA::partition, PatchDataSOA::pos_x, PatchDataSOA::pos_y, PatchDataSOA::pos_z, PatchDataSOA::posNew_x, PatchDataSOA::posNew_y, PatchDataSOA::posNew_z, PatchDataSOA::recipMass, PatchDataSOA::rigidBondLength, PatchDataSOA::sigId, Node::simParameters, simParams, PatchDataSOA::sortOrder, PatchDataSOA::status, PatchDataSOA::transform_i, PatchDataSOA::transform_j, PatchDataSOA::transform_k, PatchDataSOA::unsortOrder, PatchDataSOA::vdwType, PatchDataSOA::vel_x, PatchDataSOA::vel_y, PatchDataSOA::vel_z, PatchDataSOA::velNew_x, PatchDataSOA::velNew_y, and PatchDataSOA::velNew_z.

      {
  const SimParameters *simParams = Node::Object()->simParameters;
  p->buffer = (unsigned char *) mybuffer;
  unsigned char *t = p->buffer;
  p->pos_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->pos_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->pos_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->charge = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->vdwType = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->partition = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->nonbondedGroupSize = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->hydrogenGroupSize = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->isWater = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->sortOrder = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->unsortOrder = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->id = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->exclId = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->sigId = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->atomFixed = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->groupFixed = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->vel_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->vel_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->vel_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->fixedPosition_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->fixedPosition_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->fixedPosition_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->recipMass = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->mass = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->langevinParam = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->status = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->transform_i = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->transform_j = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->transform_k = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->migrationGroupSize = (int *) t;
  t += p->maxAtoms * sizeof(int);
  p->rigidBondLength = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->langScalVelBBK2 = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->langScalRandBBK2 = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->gaussrand_x = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->gaussrand_y = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->gaussrand_z = (float *) t;
  t += p->maxAtoms * sizeof(float);
  p->f_normal_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_normal_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_normal_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_nbond_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_nbond_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_nbond_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_slow_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_slow_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_slow_z = (double *) t;
  t += p->maxAtoms * sizeof(float);
  if (simParams->colvarsOn || simParams->tclForcesOn || (simParams->IMDon && ! (simParams->IMDignore || simParams->IMDignoreForces))){
    p->f_global_x = (double *) t;
    t += p->maxAtoms * sizeof(double);
    p->f_global_y = (double *) t;
    t += p->maxAtoms * sizeof(double);
    p->f_global_z = (double *) t;
    t += p->maxAtoms * sizeof(double);
  }
  p->f_saved_nbond_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_saved_nbond_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_saved_nbond_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_saved_slow_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_saved_slow_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->f_saved_slow_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->velNew_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->velNew_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->velNew_z = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->posNew_x = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->posNew_y = (double *) t;
  t += p->maxAtoms * sizeof(double);
  p->posNew_z = (double *) t;
}

PatchDataSOA_set_size()

size_t PatchDataSOA_set_size	(	PatchDataSOA *	p,
		int	natoms,
		int	pad = MAXFACTOR
	)

Set sizes based on number of atoms and padding factor. Sets internally numAtoms, maxAtoms, and numBytes. Returns numBytes.

Definition at line 2373 of file HomePatch.C.

References PatchDataSOA::maxAtoms, PatchDataSOA::numAtoms, PatchDataSOA::numBytes, Node::Object(), Node::simParameters, and simParams.

      {
  if (natoms > p->maxAtoms) {
    // maxAtoms extends numAtoms to next multiple of padding
    p->maxAtoms = ((natoms + padding - 1) / padding) * padding;
    // set numBytes to allow each array to have maxAtoms space
    // count up total number of double, float, and int arrays
    // XXX TODO : these magic numbers are bad for maintability
    const SimParameters *simParams = Node::Object()->simParameters;
    // XXX TODO: For Colvars, tclForces, IMD or any GlobalMaster
    // client that requires the global forces, we need extra 3 buffers
    // to save the x, y and z components of the forces, and therefore
    // the number of double fields should be increased by 3 (from 31 to 34).
    int numdoubles = (simParams->colvarsOn || simParams->tclForcesOn || simParams->IMDon) ? 34: 31;
    p->numBytes = p->maxAtoms *
      (numdoubles * sizeof(double) + 9*sizeof(float) + 17*sizeof(int));
  }
  p->numAtoms = natoms;
  return p->numBytes;
}