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MeasureQCP.C File Reference

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "Measure.h"
#include "AtomSel.h"
#include "utilities.h"
#include "ResizeArray.h"
#include "MoleculeList.h"
#include "Inform.h"
#include "Timestep.h"
#include "CUDAAccel.h"
#include "CUDAMeasureQCP.h"
#include "VMDApp.h"
#include "WKFThreads.h"
#include "WKFUtils.h"

Go to the source code of this file.

Compounds

struct  qcprmsdthreadparms

Defines

#define VMDQCPUSESSE   1
#define VMDQCPUSETHRPOOL   1

Functions

double InnerProductSOA (double *A, float *crdx1, float *crdy1, float *crdz1, float *crdx2, float *crdy2, float *crdz2, const int cnt, const float *weight)
void com_soa (int cnt, float *&soax, float *&soay, float *&soaz, double &comx, double &comy, double &comz, const float *weight)
int center_convert_soa (const AtomSel *sel, int num, const float *framepos, const float *weight, float *&soax, float *&soay, float *&soaz)
int center_convert_single_soa (const AtomSel *sel, int num, const float *framepos, const float *weight, float *soax, float *soay, float *soaz)
int measure_rmsd_qcp (VMDApp *app, const AtomSel *sel1, const AtomSel *sel2, int num, const float *framepos1, const float *framepos2, float *weight, float *rmsd)
int idx2sub_tril (long N, long ind, long *J, long *I)
void * measure_rmsdmat_qcp_thread (void *voidparms)
int measure_rmsdmat_qcp (VMDApp *app, const AtomSel *sel, MoleculeList *mlist, int num, float *weight, int first, int last, int step, float *rmsdmat)
int measure_rmsdmat_qcp_ooc (VMDApp *app, const AtomSel *sel, MoleculeList *mlist, int nfiles, const char **trjfileset, int num, float *weight, int first, int last, int step, int &framecount, float *&rmsdmat)
int FastCalcRMSDAndRotation (double *rot, double *A, float *rmsd, double E0, int len, double minScore)

Define Documentation

#define VMDQCPUSESSE   1
 

Definition at line 28 of file MeasureQCP.C.

#define VMDQCPUSETHRPOOL   1
 

Definition at line 34 of file MeasureQCP.C.

Function Documentation

int center_convert_single_soa (  const AtomSel *    sel,
int    num,
const float *    framepos,
const float *    weight,
float *    soax,
float *    soay,
float *    soaz
) 
 

Definition at line 797 of file MeasureQCP.C.

References AtomSel::firstsel, num, AtomSel::on, and AtomSel::selected.

Referenced by measure_rmsdmat_qcp, and measure_rmsdmat_qcp_ooc.

int center_convert_soa (  const AtomSel *    sel,
int    num,
const float *    framepos,
const float *    weight,
float *&    soax,
float *&    soay,
float *&    soaz
) 
 

Definition at line 735 of file MeasureQCP.C.

References com_soa, AtomSel::firstsel, num, AtomSel::on, and AtomSel::selected.

Referenced by measure_rmsd_qcp.

void com_soa (  int    cnt,
float *&    soax,
float *&    soay,
float *&    soaz,
double &    comx,
double &    comy,
double &    comz,
const float *    weight
) 
 

Definition at line 695 of file MeasureQCP.C.

References NULL.

Referenced by center_convert_soa.

int FastCalcRMSDAndRotation (  double *    rot,
double *    A,
float *    rmsd,
double    E0,
int    len,
double    minScore
) 
 

Definition at line 1432 of file MeasureQCP.C.

Referenced by measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsdmat_qcp_thread, and qcp_soa_gpu.

int idx2sub_tril (  long    N,
long    ind,
long *    J,
long *    I
)  [static]
 

Definition at line 918 of file MeasureQCP.C.

Referenced by measure_rmsdmat_qcp_thread.

double InnerProductSOA (  double *    A,
float *    crdx1,
float *    crdy1,
float *    crdz1,
float *    crdx2,
float *    crdy2,
float *    crdz2,
const int    cnt,
const float *    weight
)  [static]
 

Definition at line 328 of file MeasureQCP.C.

References NULL.

Referenced by measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsdmat_qcp_thread, and qcp_soa_gpu.

int measure_rmsd_qcp (  VMDApp *    app,
const AtomSel *    sel1,
const AtomSel *    sel2,
int    num,
const float *    framepos1,
const float *    framepos2,
float *    weight,
float *    rmsd
) 
 

Definition at line 846 of file MeasureQCP.C.

References center_convert_soa, FastCalcRMSDAndRotation, InnerProductSOA, MEASURE_ERR_MISMATCHEDCNT, MEASURE_ERR_NOSEL, MEASURE_ERR_NOWEIGHT, MEASURE_NOERR, NULL, num, AtomSel::num_atoms, and AtomSel::selected.

Referenced by py_rmsd_q, and vmd_measure_rmsd_qcp.

int measure_rmsdmat_qcp (  VMDApp *    app,
const AtomSel *    sel,
MoleculeList *    mlist,
int    num,
float *    weight,
int    first,
int    last,
int    step,
float *    rmsdmat
) 
 

Definition at line 1068 of file MeasureQCP.C.

References center_convert_single_soa, qcprmsdthreadparms::crds, wkf_tasktile_struct::end, FastCalcRMSDAndRotation, qcprmsdthreadparms::first, qcprmsdthreadparms::framecrdsz, DrawMolecule::get_frame, InnerProductSOA, qcprmsdthreadparms::last, MEASURE_ERR_BADFRAMERANGE, MEASURE_ERR_NOSEL, MEASURE_NOERR, measure_rmsdmat_qcp_thread, MoleculeList::mol_from_id, AtomSel::molid, num, AtomSel::num_atoms, DrawMolecule::numframes, qcprmsdthreadparms::padcnt, qcprmsdthreadparms::rmsdmat, qcprmsdthreadparms::sel, AtomSel::selected, wkf_tasktile_struct::start, qcprmsdthreadparms::step, VMDApp::thrpool, wkf_thread_numprocessors, wkf_threadlaunch, wkf_threadpool_launch, wkf_threadpool_sched_dynamic, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_timenow, and wkf_timerhandle.

Referenced by py_rmsdmat_q, and vmd_measure_rmsdmat_qcp.

int measure_rmsdmat_qcp_ooc (  VMDApp *    app,
const AtomSel *    sel,
MoleculeList *    mlist,
int    nfiles,
const char **    trjfileset,
int    num,
float *    weight,
int    first,
int    last,
int    step,
int &    framecount,
float *&    rmsdmat
) 
 

Definition at line 1249 of file MeasureQCP.C.

References center_convert_single_soa, qcprmsdthreadparms::crds, VMDApp::cuda, wkf_tasktile_struct::end, qcprmsdthreadparms::first, qcprmsdthreadparms::framecrdsz, CUDAAccel::get_cuda_devpool, DrawMolecule::get_frame, qcprmsdthreadparms::last, MEASURE_ERR_BADFRAMERANGE, MEASURE_ERR_NOSEL, MEASURE_NOERR, measure_rmsdmat_qcp_thread, MoleculeList::mol_from_id, AtomSel::molid, num, DrawMolecule::numframes, qcprmsdthreadparms::padcnt, qcp_soa_gpu_ooc, qcprmsdthreadparms::rmsdmat, qcprmsdthreadparms::sel, AtomSel::selected, wkf_tasktile_struct::start, qcprmsdthreadparms::step, VMDApp::thrpool, wkf_thread_numprocessors, wkf_threadlaunch, wkf_threadpool_launch, wkf_threadpool_sched_dynamic, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_timenow, and wkf_timerhandle.

Referenced by vmd_measure_rmsdmat_qcp_ooc.

void* measure_rmsdmat_qcp_thread (  void *    voidparms )  [static]
 

Definition at line 959 of file MeasureQCP.C.

References qcprmsdthreadparms::crds, wkf_tasktile_struct::end, FastCalcRMSDAndRotation, qcprmsdthreadparms::first, qcprmsdthreadparms::framecrdsz, idx2sub_tril, InnerProductSOA, qcprmsdthreadparms::last, NULL, qcprmsdthreadparms::rmsdmat, qcprmsdthreadparms::sel, AtomSel::selected, wkf_tasktile_struct::start, qcprmsdthreadparms::step, WKF_SCHED_DONE, wkf_threadlaunch_getdata, wkf_threadlaunch_getid, wkf_threadlaunch_next_tile, wkf_threadpool_next_tile, wkf_threadpool_worker_getdata, and wkf_threadpool_worker_getid.

Referenced by measure_rmsdmat_qcp, and measure_rmsdmat_qcp_ooc.

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