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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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#include <mkl_lapack64.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 "directorWhole.h" |
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|
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struct directStr{ |
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double u[3]; |
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double order; |
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double time; |
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}; |
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|
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struct directStr* directorWhole; |
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|
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void accumDWFrame( int index, struct atomCoord *atoms ); |
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|
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void calcDirWholeCorr(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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|
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corrFrames = nFrames - startFrame; |
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directorWhole = (struct directStr*)calloc(corrFrames, |
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sizeof(struct directStr)); |
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|
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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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"\rDirector bilayer 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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directorWhole[i-startFrame].time = frameTimes[i]; |
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|
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accumDWFrame( i-startFrame, atoms ); |
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|
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framesFinished++; |
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} |
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|
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sprintf( outName, "%s.dirWhole", outPrefix ); |
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outFile = fopen( outName, "w" ); |
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|
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fprintf( outFile, |
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"#time\torderParam\tx\ty\tz\n"); |
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|
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for(i=0;i<corrFrames;i++){ |
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fprintf( outFile, |
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"%6G\t%6G\t%6G\t%6G\t%6G\n", |
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directorWhole[i].time, |
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directorWhole[i].order, |
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directorWhole[i].u[0], |
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directorWhole[i].u[1], |
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directorWhole[i].u[2]); |
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} |
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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)framesFinished / (double) corrFrames ); |
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|
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fprintf( stdout, |
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"\rDirector bilayer 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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|
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void accumDWFrame( int index, 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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const double oneThird = 1.0 / 3.0; |
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|
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int i,j,k,l,m,n; |
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int lWork; |
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int nfilled; |
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int ndiag; |
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int ifail; |
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|
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double oMat[3][3]; |
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double iMat[3][3]; |
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double matWrap[9]; |
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double com[3]; |
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double totMass; |
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double lenPrinc, distl; |
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|
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struct uVect{ |
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double u[3]; |
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}; |
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struct uVect principal[nLipids]; |
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|
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|
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double evals[3]; |
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double work[9]; |
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double *u; |
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double smallest, max; |
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int which; |
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|
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char job, uplo; |
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|
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job = 'V'; |
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uplo = 'U'; |
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nfilled = 3; |
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ndiag = 3; |
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lWork = 9; |
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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) |
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oMat[i][j] = 0.0; |
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|
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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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// find the moment of inertia |
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|
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for(j=0;j<3;j++) |
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for(l=0;l<3;l++) |
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iMat[j][l] = 0.0; |
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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++) com[m] = 0.0; |
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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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com[m] += atoms[l].mass * atoms[l].pos[m]; |
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|
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totMass += atoms[l].mass; |
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} |
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for(m=0;m<3;m++) com[m] /= totMass; |
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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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|
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distl = 0.0; |
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for(m=0; m<3;m++) |
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distl += (atoms[l].pos[m]-com[m])*(atoms[l].pos[m]-com[m]); |
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|
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for(m=0; m<3; m++) |
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iMat[m][m] += atoms[l].mass * distl; |
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|
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for(m=0;m<3;m++) |
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for(n=0;n<3;n++) |
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iMat[m][n] -= atoms[l].mass * ( atoms[l].pos[m] - com[m] ) * |
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( atoms[l].pos[n] - com[n] ); |
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|
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|
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} |
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|
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// fprintf(stderr, "iMat (before) = %6G, %6G, %6G\n" |
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// " %6G, %6G, %6G\n" |
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// " %6G, %6G, %6G\n\n", |
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// iMat[0][0], iMat[0][1], iMat[0][2], |
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// iMat[1][0], iMat[1][1], iMat[1][2], |
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// iMat[2][0], iMat[2][1], iMat[2][2]); |
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|
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// matWrap to fortran convention |
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|
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for(j=0;j<3;j++) |
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for(l=0;l<3;l++) |
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matWrap[l+3*j] = iMat[l][j]; |
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|
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ifail = 0; |
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dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail); |
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|
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if (ifail) { |
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fprintf(stderr, "dsyev screwed something up!\n"); |
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exit(0); |
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} |
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|
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// matWrap from fortran convention |
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|
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for(j=0;j<3;j++) |
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for(l=0;l<3;l++) |
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iMat[l][j] = matWrap[l+3*j]; |
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|
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// fprintf(stderr, "evals = %6G, %6G, %6G\n\n", |
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// evals[0], evals[1], evals[2]); |
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|
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// fprintf(stderr, "iMat (after) = %6G, %6G, %6G\n" |
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// " %6G, %6G, %6G\n" |
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// " %6G, %6G, %6G\n\n", |
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// iMat[0][0], iMat[0][1], iMat[0][2], |
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// iMat[1][0], iMat[1][1], iMat[1][2], |
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// iMat[2][0], iMat[2][1], iMat[2][2]); |
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|
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|
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|
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smallest = fabs(evals[0]); |
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which = 0; |
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for(j=0;j<3;j++){ |
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if( fabs(evals[j]) < smallest ){ |
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which = j; |
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smallest = fabs(evals[j]); |
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} |
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} |
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|
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lenPrinc = 0.0; |
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for(j=0;j<3;j++) |
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lenPrinc += iMat[j][which] * iMat[j][which]; |
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lenPrinc = sqrt( lenPrinc ); |
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|
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for(j=0;j<3;j++) |
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principal[i].u[j] = iMat[j][which]/lenPrinc; |
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|
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|
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|
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|
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|
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// find the director of the bilayer |
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|
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u = principal[i].u; |
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|
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oMat[0][0] += u[0] * u[0] - oneThird; |
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oMat[0][1] += u[0] * u[1]; |
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oMat[0][2] += u[0] * u[2]; |
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|
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oMat[1][0] += u[1] * u[0]; |
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oMat[1][1] += u[1] * u[1] - oneThird; |
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oMat[1][2] += u[1] * u[2]; |
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|
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oMat[2][0] += u[2] * u[0]; |
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oMat[2][1] += u[2] * u[1]; |
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oMat[2][2] += u[2] * u[2] - oneThird; |
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} |
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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) |
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oMat[i][j] /= (double)nLipids; |
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|
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// matWrap to fortran convention |
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|
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for(j=0;j<3;j++) |
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for(l=0;l<3;l++) |
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matWrap[l+3*j] = oMat[l][j]; |
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|
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ifail = 0; |
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dsyev(&job, &uplo, &nfilled, matWrap, &ndiag, evals, work, &lWork, &ifail); |
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|
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if (ifail) { |
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fprintf(stderr, "dsyev screwed something up!\n"); |
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exit(0); |
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} |
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|
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// matWrap from fortran convention |
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|
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for(j=0;j<3;j++) |
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for(l=0;l<3;l++) |
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oMat[l][j] = matWrap[l+3*j]; |
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|
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max = 0.0; |
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for (i=0; i<3;i++) { |
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if (fabs(evals[i]) > max) { |
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which = i; |
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max = fabs(evals[i]); |
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} |
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} |
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|
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for (i = 0; i < 3; i++) { |
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directorWhole[index].u[i] = oMat[i][which]; |
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} |
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|
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directorWhole[index].order = 1.5 * max; |
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|
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// fprintf(stderr, |
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// "frame[%d] => order = %6G; < %6G, %6G, %6G >\n", |
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// index, |
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// directorWhole[index].order, |
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// directorWhole[index].u[0], |
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// directorWhole[index].u[1], |
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// directorWhole[index].u[2] ); |
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|
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// fprintf(stdout, |
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// "%6g\t%6G\n", |
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// directorWhole[index].time, |
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// directorWhole[index].order); |
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} |
