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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 <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 "scdCorr.h" |
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|
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double scdParamTot[9]; |
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|
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void accumScdFrame( struct atomCoord* atoms ); |
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void scdSet( int index, struct atomCoord* atoms, double *Sxx, |
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double *Syy, int nLipid, int a, int b, int c ); |
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|
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void calcScdCorr( double startTime, struct atomCoord* atoms, |
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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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FILE* outFile; |
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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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|
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double Hmat[3][3]; |
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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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corrFrames = nFrames - startFrame; |
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|
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for(i=0;i<9;i++) |
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scdParamTot[i] = 0.0; |
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|
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for(i=startFrame; i<nFrames; i++){ |
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|
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percentComplete = |
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(int)( 100.0 * (double)framesFinished / (double) corrFrames ); |
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|
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fprintf( stdout, |
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"\rScd corr %3d%% complete.", |
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percentComplete ); |
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fflush( stdout ); |
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|
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readFrame( i, atoms, Hmat ); |
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|
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accumScdFrame( atoms ); |
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|
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framesFinished++; |
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} |
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|
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for(i=0;i<9;i++) |
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scdParamTot[i] /= (double)corrFrames; |
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sprintf( outName, "%s.scdCorr", outPrefix ); |
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outFile = fopen( outName, "w" ); |
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|
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fprintf( outFile, |
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"#C_num\tScd\n" ); |
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for(i=1;i<8;i++) |
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fprintf( outFile, |
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"%d\t%G\n", |
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i+1, |
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scdParamTot[i] ); |
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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)framesFinished / (double) corrFrames ); |
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|
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fprintf( stdout, |
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"\rScd corr %3d%% complete.\n" |
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"done.\n", |
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percentComplete ); |
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fflush( stdout ); |
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} |
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|
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void accumScdFrame( struct atomCoord* atoms ){ |
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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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int index; |
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int i,j,k; |
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|
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double scdParam[9]; |
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double Sxx[9]; |
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double Syy[9]; |
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for(i=0;i<9;i++){ |
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Sxx[i] = 0.0; |
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Syy[i] = 0.0; |
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} |
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|
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for(i=0;i<nLipids;i++){ |
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// Sxx average first |
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// chain 1 |
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|
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scdSet( 1, atoms, Sxx, Syy, i, 2, 3, 4 ); |
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scdSet( 2, atoms, Sxx, Syy, i, 3, 4, 5 ); |
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scdSet( 3, atoms, Sxx, Syy, i, 4, 5, 6 ); |
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scdSet( 4, atoms, Sxx, Syy, i, 5, 6, 7 ); |
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scdSet( 5, atoms, Sxx, Syy, i, 6, 7, 8 ); |
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scdSet( 6, atoms, Sxx, Syy, i, 7, 8, 9 ); |
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scdSet( 7, atoms, Sxx, Syy, i, 8, 9, 10 ); |
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|
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// chain 2 |
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|
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scdSet( 1, atoms, Sxx, Syy, i, 2, 11, 12 ); |
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scdSet( 2, atoms, Sxx, Syy, i, 11, 12, 13 ); |
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scdSet( 3, atoms, Sxx, Syy, i, 12, 13, 14 ); |
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scdSet( 4, atoms, Sxx, Syy, i, 13, 14, 15 ); |
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scdSet( 5, atoms, Sxx, Syy, i, 14, 15, 16 ); |
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scdSet( 6, atoms, Sxx, Syy, i, 15, 16, 17 ); |
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scdSet( 7, atoms, Sxx, Syy, i, 16, 17, 18 ); |
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} |
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|
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// take the average of the frame |
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|
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Sxx[0] /= 2*nLipids; |
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for(i=1;i<9;i++) |
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Sxx[i] /= 4*nLipids; |
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|
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Syy[0] /= 2*nLipids; |
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for(i=1;i<9;i++) |
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Syy[i] /= 4*nLipids; |
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|
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for(i=0;i<9;i++) |
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scdParam[i] = 2.0*Sxx[i]/3.0 + Syy[i]/3.0; |
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|
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// accumulate into the running average |
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for(i=0;i<9;i++) |
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scdParamTot[i] += scdParam[i]; |
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|
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|
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} |
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|
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void scdSet( int index, struct atomCoord* atoms, double *Sxx, |
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double *Syy, int nLipid, int a, int b, int c ){ |
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|
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int i,k; |
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double dist,dSqr; |
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double molX[3]; |
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double molY[3]; |
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double molZ[3]; |
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double temp[3]; |
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k = nLipid*NL_ATOMS; |
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a += k; |
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b += k; |
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c += k; |
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// calc the molecular z axis |
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for(i=0;i<3;i++) |
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molZ[i] = atoms[c].pos[i] - atoms[a].pos[i]; |
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dSqr = 0.0; |
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for(i=0;i<3;i++) |
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dSqr += molZ[i] * molZ[i]; |
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dist = sqrt(dSqr); |
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for(i=0;i<3;i++) |
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molZ[i] /= dist; |
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// calc the temp vector |
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for(i=0;i<3;i++) |
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temp[i] = atoms[a].pos[i] - atoms[b].pos[i]; |
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|
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dSqr = 0.0; |
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for(i=0;i<3;i++) |
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dSqr += temp[i] * temp[i]; |
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dist = sqrt(dSqr); |
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for(i=0;i<3;i++) |
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temp[i] /= dist; |
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// calc the molecular x axis ( x = temp cross z ) |
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molX[0] = temp[1]*molZ[2] - molZ[1]*temp[2]; |
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molX[1] = temp[2]*molZ[0] - molZ[2]*temp[0]; |
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molX[2] = temp[0]*molZ[1] - molZ[0]*temp[1]; |
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// calc the y axis ( y = z cross x ) |
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molY[0] = molZ[1]*molX[2] - molX[1]*molZ[2]; |
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molY[1] = molZ[2]*molX[0] - molX[2]*molZ[0]; |
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molY[2] = molZ[0]*molX[1] - molX[0]*molZ[1]; |
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// calculate the Sxx and Syy params |
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Sxx[index] += 3 * molX[2] * molX[2] - 1; |
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Syy[index] += 3 * molY[2] * molY[2] - 1; |
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} |
