NAMD
Public Attributes | List of all members
PatchDataSOA Struct Reference

#include <NamdTypes.h>

Public Attributes

unsigned char * buffer
 
double * pos_x
 
double * pos_y
 
double * pos_z
 
float * charge
 
int32 * vdwType
 
int32 * partition
 
int32 * nonbondedGroupSize
 
int32 * hydrogenGroupSize
 
int32 * isWater
 
int32 * sortOrder
 
int32 * unsortOrder
 
int32 * id
 
int32 * exclId
 
int32 * sigId
 
int32 * atomFixed
 
int32 * groupFixed
 
double * vel_x
 Jim recommends double precision velocity. More...
 
double * vel_y
 
double * vel_z
 
double * fixedPosition_x
 
double * fixedPosition_y
 
double * fixedPosition_z
 
double * recipMass
 derived from mass More...
 
float * mass
 
float * langevinParam
 
int32 * status
 
int32 * transform_i
 
int32 * transform_j
 
int32 * transform_k
 
int32 * migrationGroupSize
 
float * rigidBondLength
 
float * langScalVelBBK2
 derived from langevinParam More...
 
float * langScalRandBBK2
 from langevinParam and recipMass More...
 
float * gaussrand_x
 fill with Gaussian distributed random numbers More...
 
float * gaussrand_y
 
float * gaussrand_z
 
double * f_normal_x
 
double * f_normal_y
 
double * f_normal_z
 
double * f_nbond_x
 
double * f_nbond_y
 
double * f_nbond_z
 
double * f_slow_x
 
double * f_slow_y
 
double * f_slow_z
 
double * f_global_x
 
double * f_global_y
 
double * f_global_z
 
double * f_saved_nbond_x
 
double * f_saved_nbond_y
 
double * f_saved_nbond_z
 
double * f_saved_slow_x
 
double * f_saved_slow_y
 
double * f_saved_slow_z
 
double * velNew_x
 temp storage for rigid bond constraints More...
 
double * velNew_y
 
double * velNew_z
 
double * posNew_x
 
double * posNew_y
 
double * posNew_z
 
size_t numBytes
 number of bytes allocated for soa_buffer More...
 
int32 numAtoms
 number of atoms More...
 
int32 maxAtoms
 max number of atoms available, multiple of MAXFACTOR More...
 

Detailed Description

Definition at line 363 of file NamdTypes.h.

Member Data Documentation

◆ atomFixed

int32* PatchDataSOA::atomFixed

Definition at line 383 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ buffer

unsigned char* PatchDataSOA::buffer

Definition at line 365 of file NamdTypes.h.

Referenced by PatchDataSOA_initialize(), and PatchDataSOA_set_buffer().

◆ charge

float* PatchDataSOA::charge

Definition at line 371 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), HomePatch::positionsReady_SOA(), Sequencer::rescaleSoluteCharges(), and Sequencer::runComputeObjects_SOA().

◆ exclId

int32* PatchDataSOA::exclId

Definition at line 381 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ f_global_x

double* PatchDataSOA::f_global_x

Definition at line 427 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ f_global_y

double* PatchDataSOA::f_global_y

Definition at line 428 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ f_global_z

double* PatchDataSOA::f_global_z

Definition at line 429 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ f_nbond_x

double* PatchDataSOA::f_nbond_x

Definition at line 421 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ f_nbond_y

double* PatchDataSOA::f_nbond_y

Definition at line 422 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ f_nbond_z

double* PatchDataSOA::f_nbond_z

Definition at line 423 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ f_normal_x

double* PatchDataSOA::f_normal_x

Definition at line 418 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::runComputeObjects_SOA(), ComputeGlobal::saveTotalForces(), and Sequencer::submitReductions_SOA().

◆ f_normal_y

double* PatchDataSOA::f_normal_y

Definition at line 419 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::runComputeObjects_SOA(), ComputeGlobal::saveTotalForces(), and Sequencer::submitReductions_SOA().

◆ f_normal_z

double* PatchDataSOA::f_normal_z

Definition at line 420 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::runComputeObjects_SOA(), ComputeGlobal::saveTotalForces(), and Sequencer::submitReductions_SOA().

◆ f_saved_nbond_x

double* PatchDataSOA::f_saved_nbond_x

saved nonbonded force

Definition at line 430 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and ComputeGlobal::saveTotalForces().

◆ f_saved_nbond_y

double* PatchDataSOA::f_saved_nbond_y

saved nonbonded force

Definition at line 431 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and ComputeGlobal::saveTotalForces().

◆ f_saved_nbond_z

double* PatchDataSOA::f_saved_nbond_z

saved nonbonded force

Definition at line 432 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and ComputeGlobal::saveTotalForces().

◆ f_saved_slow_x

double* PatchDataSOA::f_saved_slow_x

saved slow force

Definition at line 433 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and ComputeGlobal::saveTotalForces().

◆ f_saved_slow_y

double* PatchDataSOA::f_saved_slow_y

saved slow force

Definition at line 434 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and ComputeGlobal::saveTotalForces().

◆ f_saved_slow_z

double* PatchDataSOA::f_saved_slow_z

saved slow force

Definition at line 435 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and ComputeGlobal::saveTotalForces().

◆ f_slow_x

double* PatchDataSOA::f_slow_x

Definition at line 424 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ f_slow_y

double* PatchDataSOA::f_slow_y

Definition at line 425 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ f_slow_z

double* PatchDataSOA::f_slow_z

Definition at line 426 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ fixedPosition_x

double* PatchDataSOA::fixedPosition_x

Definition at line 390 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ fixedPosition_y

double* PatchDataSOA::fixedPosition_y

Definition at line 391 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ fixedPosition_z

double* PatchDataSOA::fixedPosition_z

Definition at line 392 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ gaussrand_x

float* PatchDataSOA::gaussrand_x

fill with Gaussian distributed random numbers

Definition at line 413 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), and PatchDataSOA_set_buffer().

◆ gaussrand_y

float* PatchDataSOA::gaussrand_y

Definition at line 414 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), and PatchDataSOA_set_buffer().

◆ gaussrand_z

float* PatchDataSOA::gaussrand_z

Definition at line 415 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), and PatchDataSOA_set_buffer().

◆ groupFixed

int32* PatchDataSOA::groupFixed

Definition at line 384 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ hydrogenGroupSize

int32* PatchDataSOA::hydrogenGroupSize

Definition at line 375 of file NamdTypes.h.

Referenced by Sequencer::berendsenPressure_SOA(), HomePatch::buildRattleList_SOA(), HomePatch::doGroupSizeCheck_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), PatchDataSOA_set_buffer(), HomePatch::positionsReady_SOA(), HomePatch::rattle1_SOA(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ id

int32* PatchDataSOA::id

Definition at line 380 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ isWater

int32* PatchDataSOA::isWater

Definition at line 376 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ langevinParam

float* PatchDataSOA::langevinParam

Definition at line 396 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), and PatchDataSOA_set_buffer().

◆ langScalRandBBK2

float* PatchDataSOA::langScalRandBBK2

from langevinParam and recipMass

Definition at line 410 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), and PatchDataSOA_set_buffer().

◆ langScalVelBBK2

float* PatchDataSOA::langScalVelBBK2

derived from langevinParam

Definition at line 409 of file NamdTypes.h.

Referenced by Sequencer::integrate_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), and PatchDataSOA_set_buffer().

◆ mass

float* PatchDataSOA::mass

Definition at line 395 of file NamdTypes.h.

Referenced by Sequencer::berendsenPressure_SOA(), HomePatch::buildRattleList_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ maxAtoms

int32 PatchDataSOA::maxAtoms

max number of atoms available, multiple of MAXFACTOR

Definition at line 447 of file NamdTypes.h.

Referenced by PatchDataSOA_initialize(), PatchDataSOA_set_buffer(), and PatchDataSOA_set_size().

◆ migrationGroupSize

int32* PatchDataSOA::migrationGroupSize

Definition at line 404 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ nonbondedGroupSize

int32* PatchDataSOA::nonbondedGroupSize

Definition at line 374 of file NamdTypes.h.

Referenced by HomePatch::doGroupSizeCheck_SOA(), PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ numAtoms

int32 PatchDataSOA::numAtoms

number of atoms

Definition at line 446 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::berendsenPressure_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), Sequencer::maximumMove_SOA(), PatchDataSOA_initialize(), PatchDataSOA_set_size(), Sequencer::runComputeObjects_SOA(), Sequencer::stochRescaleVelocities_SOA(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ numBytes

size_t PatchDataSOA::numBytes

number of bytes allocated for soa_buffer

Definition at line 445 of file NamdTypes.h.

Referenced by PatchDataSOA_initialize(), and PatchDataSOA_set_size().

◆ partition

int32* PatchDataSOA::partition

Definition at line 373 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ pos_x

double* PatchDataSOA::pos_x

Definition at line 367 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::berendsenPressure_SOA(), HomePatch::buildRattleList_SOA(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), PatchDataSOA_set_buffer(), HomePatch::positionsReady_SOA(), HomePatch::rattle1_SOA(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ pos_y

double* PatchDataSOA::pos_y

Definition at line 368 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::berendsenPressure_SOA(), HomePatch::buildRattleList_SOA(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), PatchDataSOA_set_buffer(), HomePatch::positionsReady_SOA(), HomePatch::rattle1_SOA(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ pos_z

double* PatchDataSOA::pos_z

Definition at line 369 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::berendsenPressure_SOA(), HomePatch::buildRattleList_SOA(), HomePatch::doGroupSizeCheck_SOA(), HomePatch::doMarginCheck_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), PatchDataSOA_set_buffer(), HomePatch::positionsReady_SOA(), HomePatch::rattle1_SOA(), Sequencer::runComputeObjects_SOA(), and Sequencer::submitReductions_SOA().

◆ posNew_x

double* PatchDataSOA::posNew_x

Definition at line 441 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::rattle1_SOA().

◆ posNew_y

double* PatchDataSOA::posNew_y

Definition at line 442 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::rattle1_SOA().

◆ posNew_z

double* PatchDataSOA::posNew_z

Definition at line 443 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::rattle1_SOA().

◆ recipMass

double* PatchDataSOA::recipMass

derived from mass

Definition at line 394 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), HomePatch::buildRattleList_SOA(), Sequencer::integrate_SOA(), and PatchDataSOA_set_buffer().

◆ rigidBondLength

float* PatchDataSOA::rigidBondLength

Definition at line 406 of file NamdTypes.h.

Referenced by HomePatch::buildRattleList_SOA(), and PatchDataSOA_set_buffer().

◆ sigId

int32* PatchDataSOA::sigId

Definition at line 382 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ sortOrder

int32* PatchDataSOA::sortOrder

Definition at line 378 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ status

int32* PatchDataSOA::status

Definition at line 398 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ transform_i

int32* PatchDataSOA::transform_i

Definition at line 400 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ transform_j

int32* PatchDataSOA::transform_j

Definition at line 401 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ transform_k

int32* PatchDataSOA::transform_k

Definition at line 402 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer().

◆ unsortOrder

int32* PatchDataSOA::unsortOrder

Definition at line 379 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ vdwType

int32* PatchDataSOA::vdwType

Definition at line 372 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::positionsReady_SOA().

◆ vel_x

double* PatchDataSOA::vel_x

Jim recommends double precision velocity.

Definition at line 386 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), Sequencer::maximumMove_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::stochRescaleVelocities_SOA(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ vel_y

double* PatchDataSOA::vel_y

Definition at line 387 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), Sequencer::maximumMove_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::stochRescaleVelocities_SOA(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ vel_z

double* PatchDataSOA::vel_z

Definition at line 388 of file NamdTypes.h.

Referenced by Sequencer::addForceToMomentum_SOA(), Sequencer::addVelocityToPosition_SOA(), Sequencer::integrate_SOA(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), Sequencer::maximumMove_SOA(), PatchDataSOA_set_buffer(), HomePatch::rattle1_SOA(), Sequencer::stochRescaleVelocities_SOA(), Sequencer::submitHalfstep_SOA(), and Sequencer::submitReductions_SOA().

◆ velNew_x

double* PatchDataSOA::velNew_x

temp storage for rigid bond constraints

Definition at line 438 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::rattle1_SOA().

◆ velNew_y

double* PatchDataSOA::velNew_y

Definition at line 439 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::rattle1_SOA().

◆ velNew_z

double* PatchDataSOA::velNew_z

Definition at line 440 of file NamdTypes.h.

Referenced by PatchDataSOA_set_buffer(), and HomePatch::rattle1_SOA().

The documentation for this struct was generated from the following file:
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