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#define _FILE_OFFSET_BITS 64 |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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|
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|
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#include "params.h" |
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#include "tcProps.h" |
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#include "readWrite.h" |
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#include "rmsd.h" |
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|
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struct frameStruct{ |
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struct atomCoord atoms[NL_ATOMS*NLIPIDS+NSSD]; |
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double time; |
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double Hmat[3][3]; |
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}; |
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|
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struct binStruct{ |
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double rmsd; |
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int nValues; |
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}; |
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|
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struct binStruct rmsdCorr[RMSDBINS]; |
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|
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struct frameStruct* myFrames; |
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|
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void calcRMSDpair( int bin, int i, int j, enum atomNames rType ); |
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|
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void rmsd( enum atomNames rType, double startTime, char* outPrefix ){ |
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|
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// list of 'a priori' constants |
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|
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const int nLipAtoms = NL_ATOMS; |
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const int nBonds = NBONDS; |
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const int nLipids = NLIPIDS; |
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const int nSSD = NSSD; |
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const int nAtoms = nLipAtoms * nLipids + nSSD; |
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|
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// variables |
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|
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char outName[500]; |
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|
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FILE* outFile; |
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|
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int i, j, k; |
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int startFrame, corrFrames, framesFinished; |
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int startFound, percentComplete; |
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int index; |
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int nCounts; |
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int bin; |
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|
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double Hmat[3][3]; |
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double diffTime; |
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double rmsdDt; |
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double timeOut, outVal; |
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|
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framesFinished = 0; |
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|
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startFound = 0; |
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startFrame = -1; |
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while( !startFound ){ |
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|
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startFrame++; |
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|
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if(startFrame >= nFrames){ |
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|
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fprintf( stderr, |
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"Start Time, %G, was not found in the dump file.\n", |
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startTime ); |
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exit(0); |
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} |
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|
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if(startTime <= frameTimes[startFrame]) |
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startFound = 1; |
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|
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|
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} |
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|
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corrFrames = nFrames - startFrame; |
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myFrames = (struct frameStruct*)calloc(corrFrames, |
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sizeof(struct frameStruct)); |
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|
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index=0; |
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for(i=startFrame;i<nFrames;i++){ |
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|
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if( index >= corrFrames ){ |
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fprintf( stderr, |
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"Error, number of frames, %d, exceeds corrFrames, %d.\n", |
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index, |
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corrFrames ); |
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} |
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|
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myFrames[index].time = frameTimes[i]; |
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readFrame(i, myFrames[index].atoms, myFrames[index].Hmat ); |
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} |
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|
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// initialize the counts and the correlation |
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|
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nCounts = 0; |
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for(i=0;i<(corrFrames-1);i++) |
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for(j=i+1;j<corrFrames;j++) |
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nCounts++; |
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|
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for(i=0;i<RMSDBINS;i++){ |
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rmsdCorr[i].rmsd = 0.0; |
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rmsdCorr[i].nValues = 0; |
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} |
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|
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rmsdDt = (myFrames[corrFrames-1].time - myFrames[0].time) / RMSDBINS; |
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|
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// perform the calculation |
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|
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index = 0; |
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for(i=0;i<(corrFrames-1);i++){ |
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for(j=i+1;j<corrFrames;j++){ |
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|
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diffTime = myFrames[j].time - myFrames[i].time; |
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if( diffTime > 0.0 ){ |
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|
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percentComplete = |
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(int)( 100.0 * (double)index / (double) nCounts ); |
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|
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fprintf( stdout, |
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"\rRMSD corr %3d%% complete.", |
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percentComplete ); |
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fflush( stdout ); |
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|
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bin = (int)(diffTime / rmsdDt); |
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if( bin < RMSDBINS) |
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calcRMSDpair( bin, i, j, rType ); |
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} |
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|
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index++; |
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} |
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} |
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|
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// print out the correlation |
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|
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sprintf( outName, "%s.rmsd", outPrefix ); |
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outFile = fopen( outName, "w" ); |
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|
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fprintf( outFile, |
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"#time\trmsd\n"); |
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|
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for(i=0;i<RMSDBINS;i++){ |
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|
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if(rmsdCorr[i].nValues){ |
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|
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timeOut = (2.0*(double)i+1.0)*rmsdDt*0.5; |
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outVal = rmsdCorr[i].rmsd / (double)rmsdCorr[i].nValues; |
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|
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fprintf( outFile, |
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"%6G\t%6G\n", |
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timeOut, outVal ); |
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} |
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} |
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|
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fflush(outFile); |
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fclose(outFile); |
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|
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percentComplete = |
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(int)( 100.0 * (double)index / (double) nCounts ); |
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|
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fprintf( stdout, |
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"\rRMSD corr %3d%% complete.", |
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percentComplete ); |
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fflush( stdout ); |
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|
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free( myFrames ); |
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myFrames = NULL; |
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} |
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|
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|
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void calcRMSDpair( int bin, int frameI, int frameJ, enum atomNames rType ){ |
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|
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struct atomCoord* atomsI; |
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struct atomCoord* atomsJ; |
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|
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int i,j,k,l,m,n; |
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int nAccums; |
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|
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double d[3]; |
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double dSqr; |
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double comI[3]; |
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double comJ[3]; |
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double totMass; |
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double accum; |
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|
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|
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|
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// list of 'a priori' constants |
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|
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const int nLipAtoms = NL_ATOMS; |
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const int nBonds = NBONDS; |
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const int nLipids = NLIPIDS; |
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const int nSSD = NSSD; |
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const int nAtoms = nLipAtoms * nLipids + nSSD; |
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|
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|
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atomsI = myFrames[frameI].atoms; |
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atomsJ = myFrames[frameJ].atoms; |
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|
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if( rType != COM ){ |
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nAccums = 0; |
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for(i=0;i<nAtoms;i++){ |
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|
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if (atomsI[i].type == rType){ |
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|
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for(j=0;j<3;j++) |
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d[j] = atomsJ[i].pos[j] - atomsI[i].pos[j]; |
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|
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dSqr = 0.0; |
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for(j=0;j<3;j++) |
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dSqr += d[j] * d[j]; |
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|
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accum += sqrt(dSqr); |
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nAccums++; |
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} |
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} |
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} |
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else{ |
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|
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nAccums = 0; |
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for(i=0;i<nLipids;i++){ |
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|
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k = i*nLipAtoms; |
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|
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// com calc |
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|
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totMass = 0.0; |
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for(m=0;m<3;m++){ |
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comI[m] = 0.0; |
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comJ[m] = 0.0; |
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} |
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for(j=0;j<nLipAtoms;j++){ |
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l=k+j; |
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|
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for(m=0;m<3;m++){ |
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comI[m] += atomsI[l].mass * atomsI[l].pos[m]; |
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comJ[m] += atomsJ[l].mass * atomsJ[l].pos[m]; |
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|
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totMass += atomsI[l].mass; |
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} |
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for(m=0;m<3;m++){ |
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comI[m] /= totMass; |
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comJ[m] /= totMass; |
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} |
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} |
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|
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for(j=0;j<3;j++) |
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d[j] = comJ[j] - comI[j]; |
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|
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dSqr = 0.0; |
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for(j=0;j<3;j++) |
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dSqr += d[j] * d[j]; |
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|
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accum += sqrt(dSqr); |
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nAccums++; |
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} |
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} |
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|
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accum /= (double)nAccums; |
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rmsdCorr[bin].rmsd += accum; |
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rmsdCorr[bin].nValues++; |
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} |
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