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CUDAMeasureRDF.cu File Reference

CUDA kernels for calculating radial distribution function histograms. More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <cuda.h>
#include "Inform.h"
#include "utilities.h"
#include "WKFThreads.h"
#include "WKFUtils.h"
#include "CUDAKernels.h"

Go to the source code of this file.


Compounds

struct rdfthrparms

Defines

#define NBLOCK 32
#define MAXBIN 1024
#define NCUDABLOCKS 256
#define NBLOCKHIST 64
#define NCONSTBLOCK 5440
#define THREADSPERWARP 32
#define WARP_LOG_SIZE 5
#define BIN_OVERFLOW_LIMIT 2147483648
#define ull2float __uint2float_rn

Functions

__global__ void init_hist (unsigned int *llhistg, int maxbin)
__global__ void init_hist_f (float *histdev)
__global__ void reimage_xyz (float *xyz, int natomsi, int natomsipad, float3 celld, float rmax)
__global__ void phantom_xyz (float *xyz, int natomsi, int natomsipad, float minxyz, float rmax)
void copycoordstoconstbuff (int natoms, const float *xyzh)
__device__ void addData (volatile unsigned int *s_WarpHist, unsigned int data, unsigned int threadTag)
__global__ void calculate_rdf (int usepbc, float *xyz, int natomsi, int natomsj, float3 celld, unsigned int *llhistg, int nbins, float rmin, float delr_inv)
__global__ void calculate_histogram (float *histdev, unsigned int *llhistg, int nbins)
void calculate_histogram_block (int usepbc, float *xyz, int natomsi, int natomsj, float3 celld, unsigned int *llhistg, int nbins, float rmin, float delr_inv, float *histdev, int nblockhist)
void * rdf_thread (void *voidparms)
int rdf_gpu (wkf_threadpool_t *devpool, int usepbc, int natoms1, float *xyz, int natoms2, float *xyz2, float *cell, float *hist, int nbins, float rmin, float delr)

Variables

__constant__ float xyzj [3 *NCONSTBLOCK]

Detailed Description

CUDA kernels for calculating radial distribution function histograms.

This work is described in the following paper:

"Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units - Radial Distribution Function Histogramming" Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer. Journal of Computational Physics, 230(9):3556-3569, 2011. http://dx.doi.org/10.1016/j.jcp.2011年01月04日8

Definition in file CUDAMeasureRDF.cu.

Define Documentation

#define BIN_OVERFLOW_LIMIT 2147483648

Definition at line 87 of file CUDAMeasureRDF.cu.

Referenced by rdf_thread.

#define MAXBIN 1024

Definition at line 55 of file CUDAMeasureRDF.cu.

Referenced by calculate_histogram, calculate_histogram_block, calculate_rdf, rdf_gpu, and rdf_thread.

#define NBLOCK 32

Definition at line 54 of file CUDAMeasureRDF.cu.

Referenced by calculate_histogram, calculate_rdf, init_hist, phantom_xyz, rdf_gpu, rdf_thread, and reimage_xyz.

#define NBLOCKHIST 64

Definition at line 77 of file CUDAMeasureRDF.cu.

Referenced by calculate_histogram, and rdf_gpu.

#define NCONSTBLOCK 5440

Definition at line 81 of file CUDAMeasureRDF.cu.

Referenced by rdf_gpu, and rdf_thread.

#define NCUDABLOCKS 256

Definition at line 72 of file CUDAMeasureRDF.cu.

Referenced by calculate_histogram, calculate_rdf, phantom_xyz, rdf_thread, and reimage_xyz.

#define THREADSPERWARP 32

Definition at line 84 of file CUDAMeasureRDF.cu.

Referenced by calculate_histogram, calculate_rdf, init_hist, and rdf_thread.

#define ull2float __uint2float_rn

Definition at line 578 of file CUDAMeasureRDF.cu.

Referenced by calculate_histogram.

#define WARP_LOG_SIZE 5

Definition at line 85 of file CUDAMeasureRDF.cu.

Referenced by calculate_rdf.

Function Documentation

__device__ void addData ( volatile unsigned int * s_WarpHist,
unsigned int data,
unsigned int threadTag
)

Definition at line 348 of file CUDAMeasureRDF.cu.

References data.

Referenced by calculate_rdf.

__global__ void calculate_histogram ( float * histdev,
unsigned int * llhistg,
int nbins
)

Definition at line 585 of file CUDAMeasureRDF.cu.

References MAXBIN, NBLOCK, NBLOCKHIST, NCUDABLOCKS, THREADSPERWARP, and ull2float.

void calculate_histogram_block ( int usepbc,
float * xyz,
int natomsi,
int natomsj,
float3 celld,
unsigned int * llhistg,
int nbins,
float rmin,
float delr_inv,
float * histdev,
int nblockhist
)

Definition at line 661 of file CUDAMeasureRDF.cu.

References MAXBIN.

Referenced by rdf_thread.

__global__ void calculate_rdf ( int usepbc,
float * xyz,
int natomsi,
int natomsj,
float3 celld,
unsigned int * llhistg,
int nbins,
float rmin,
float delr_inv
)

Definition at line 367 of file CUDAMeasureRDF.cu.

References addData, MAXBIN, NBLOCK, NCUDABLOCKS, THREADSPERWARP, WARP_LOG_SIZE, and xyzj.

void copycoordstoconstbuff ( int natoms,
const float * xyzh
)

Definition at line 335 of file CUDAMeasureRDF.cu.

References xyzj.

Referenced by rdf_thread.

__global__ void init_hist ( unsigned int * llhistg,
int maxbin
)

Definition at line 93 of file CUDAMeasureRDF.cu.

References NBLOCK, and THREADSPERWARP.

__global__ void init_hist_f ( float * histdev )

Definition at line 154 of file CUDAMeasureRDF.cu.

__global__ void phantom_xyz ( float * xyz,
int natomsi,
int natomsipad,
float minxyz,
float rmax
)

Definition at line 252 of file CUDAMeasureRDF.cu.

References NBLOCK, and NCUDABLOCKS.

int rdf_gpu ( wkf_threadpool_t * devpool,
int usepbc,
int natoms1,
float * xyz,
int natoms2,
float * xyz2,
float * cell,
float * hist,
int nbins,
float rmin,
float delr
)

Definition at line 912 of file CUDAMeasureRDF.cu.

References rdfthrparms::cell, rdfthrparms::delr, wkf_tasktile_struct::end, rdfthrparms::histarray, MAXBIN, rdfthrparms::natoms1, rdfthrparms::natoms2, rdfthrparms::nbins, NBLOCK, NBLOCKHIST, rdfthrparms::nblockhist, rdfthrparms::nblocks, NCONSTBLOCK, rdfthrparms::nhblock, NULL, rdf_thread, rdfthrparms::rmin, wkf_tasktile_struct::start, rdfthrparms::usepbc, wkf_threadpool_get_workercount, wkf_threadpool_launch, wkf_threadpool_sched_dynamic, rdfthrparms::xyz, and rdfthrparms::xyz2array.

Referenced by measure_rdf.

void* rdf_thread ( void * voidparms ) [static]

Definition at line 713 of file CUDAMeasureRDF.cu.

References BIN_OVERFLOW_LIMIT, calculate_histogram_block, rdfthrparms::cell, copycoordstoconstbuff, rdfthrparms::delr, wkf_tasktile_struct::end, rdfthrparms::histarray, MAXBIN, rdfthrparms::natoms1, rdfthrparms::natoms2, rdfthrparms::nbins, NBLOCK, rdfthrparms::nblockhist, NCONSTBLOCK, NCUDABLOCKS, rdfthrparms::nhblock, NULL, rdfthrparms::rmin, wkf_tasktile_struct::start, THREADSPERWARP, rdfthrparms::usepbc, WKF_SCHED_DONE, wkf_threadpool_next_tile, wkf_threadpool_worker_getdata, wkf_threadpool_worker_getid, rdfthrparms::xyz, and rdfthrparms::xyz2array.

Referenced by rdf_gpu.

__global__ void reimage_xyz ( float * xyz,
int natomsi,
int natomsipad,
float3 celld,
float rmax
)

Definition at line 166 of file CUDAMeasureRDF.cu.

References NBLOCK, and NCUDABLOCKS.

Variable Documentation

__constant__ float xyzj[3*NCONSTBLOCK] [static]

Definition at line 331 of file CUDAMeasureRDF.cu.

Referenced by calculate_rdf, and copycoordstoconstbuff.

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