| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <stdio.h> |
| 4 |
#include <stdlib.h> |
| 5 |
#include <string.h> |
| 6 |
#include <math.h> |
| 7 |
|
| 8 |
|
| 9 |
#include "params.h" |
| 10 |
#include "tcProps.h" |
| 11 |
#include "readWrite.h" |
| 12 |
#include "gofz.h" |
| 13 |
|
| 14 |
|
| 15 |
|
| 16 |
struct gofzStr{ |
| 17 |
double gofz[GOFZNBINS]; |
| 18 |
}; |
| 19 |
|
| 20 |
struct gofzStr gofzCorrs[5]; |
| 21 |
double gofzDl; |
| 22 |
int halfGzBins; |
| 23 |
|
| 24 |
void accumGofZ( struct atomCoord *atoms, double Hmat[3][3], double maxL ); |
| 25 |
|
| 26 |
double wrapMyZ( double z, double box ); |
| 27 |
|
| 28 |
void calcGofz(double startTime, struct atomCoord *atoms, |
| 29 |
char* outPrefix ){ |
| 30 |
|
| 31 |
// list of 'a priori' constants |
| 32 |
|
| 33 |
const int nLipAtoms = NL_ATOMS; |
| 34 |
const int nBonds = NBONDS; |
| 35 |
const int nLipids = NLIPIDS; |
| 36 |
const int nSSD = NSSD; |
| 37 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
| 38 |
|
| 39 |
// variables |
| 40 |
|
| 41 |
char outName[500]; |
| 42 |
FILE* outFile; |
| 43 |
int i, j, k; |
| 44 |
int startFrame, corrFrames, framesFinished; |
| 45 |
int startFound, percentComplete; |
| 46 |
|
| 47 |
double Hmat[3][3]; |
| 48 |
double maxL, halfMax; |
| 49 |
|
| 50 |
framesFinished = 0; |
| 51 |
|
| 52 |
startFound = 0; |
| 53 |
startFrame = -1; |
| 54 |
while( !startFound ){ |
| 55 |
|
| 56 |
startFrame++; |
| 57 |
|
| 58 |
if(startFrame >= nFrames){ |
| 59 |
|
| 60 |
fprintf( stderr, |
| 61 |
"Start Time, %G, was not found in the dump file.\n", |
| 62 |
startTime ); |
| 63 |
exit(0); |
| 64 |
} |
| 65 |
|
| 66 |
if(startTime <= frameTimes[startFrame]) |
| 67 |
startFound = 1; |
| 68 |
|
| 69 |
|
| 70 |
} |
| 71 |
|
| 72 |
corrFrames = nFrames - startFrame; |
| 73 |
|
| 74 |
maxL = scanSmallestZ( startFrame ); |
| 75 |
halfMax = maxL * 0.5; |
| 76 |
gofzDl = maxL / GOFZNBINS; |
| 77 |
halfGzBins = (GOFZNBINS-1)*0.5; |
| 78 |
|
| 79 |
for(i=0;i<GOFZNBINS;i++) |
| 80 |
for(j=0;j<5;j++) |
| 81 |
gofzCorrs[j].gofz[i] = 0.0; |
| 82 |
|
| 83 |
|
| 84 |
for(i=startFrame; i<nFrames; i++){ |
| 85 |
|
| 86 |
percentComplete = |
| 87 |
(int)( 100.0 * (double)framesFinished / (double) corrFrames ); |
| 88 |
|
| 89 |
fprintf( stdout, |
| 90 |
"\rg(z) corr %3d%% complete.", |
| 91 |
percentComplete ); |
| 92 |
fflush( stdout ); |
| 93 |
|
| 94 |
readFrame( i, atoms, Hmat ); |
| 95 |
|
| 96 |
accumGofZ( atoms, Hmat, maxL ); |
| 97 |
|
| 98 |
framesFinished++; |
| 99 |
} |
| 100 |
|
| 101 |
for(i=0;i<GOFZNBINS;i++) |
| 102 |
for(j=0;j<5;j++) |
| 103 |
gofzCorrs[j].gofz[i] /= corrFrames; |
| 104 |
|
| 105 |
sprintf( outName, "%s.gofz", outPrefix ); |
| 106 |
outFile = fopen( outName, "w" ); |
| 107 |
|
| 108 |
fprintf( outFile, |
| 109 |
"#z\tHEAD\tCH\tCH2\tCH3\tSSD\n"); |
| 110 |
for(i=0;i<GOFZNBINS;i++) |
| 111 |
fprintf( outFile, |
| 112 |
"%6G\t%6G\t%6G\t%6G\t%6G\t%6G\n", |
| 113 |
-halfMax + i*gofzDl, |
| 114 |
gofzCorrs[HEAD].gofz[i], |
| 115 |
gofzCorrs[CH].gofz[i], |
| 116 |
gofzCorrs[CH2].gofz[i], |
| 117 |
gofzCorrs[CH3].gofz[i], |
| 118 |
gofzCorrs[SSD].gofz[i] ); |
| 119 |
|
| 120 |
fflush(outFile); |
| 121 |
fclose(outFile); |
| 122 |
|
| 123 |
|
| 124 |
percentComplete = |
| 125 |
(int)( 100.0 * (double)framesFinished / (double) corrFrames ); |
| 126 |
|
| 127 |
fprintf( stdout, |
| 128 |
"\rg(z) corr %3d%% complete.\n" |
| 129 |
"done.\n", |
| 130 |
percentComplete ); |
| 131 |
fflush( stdout ); |
| 132 |
} |
| 133 |
|
| 134 |
void accumGofZ( struct atomCoord *atoms, double Hmat[3][3], double maxL ){ |
| 135 |
|
| 136 |
// list of 'a priori' constants |
| 137 |
|
| 138 |
const int nLipAtoms = NL_ATOMS; |
| 139 |
const int nBonds = NBONDS; |
| 140 |
const int nLipids = NLIPIDS; |
| 141 |
const int nSSD = NSSD; |
| 142 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
| 143 |
|
| 144 |
int i,j,k,l; |
| 145 |
int bin; |
| 146 |
|
| 147 |
double totMass; |
| 148 |
double comZ; |
| 149 |
double halfMax; |
| 150 |
double wrapZ; |
| 151 |
double scale; |
| 152 |
double volume, density, densCons; |
| 153 |
|
| 154 |
struct gofzStr tempCorrs[5]; |
| 155 |
|
| 156 |
for(i=0;i<GOFZNBINS;i++) |
| 157 |
for(j=0;j<5;j++) |
| 158 |
tempCorrs[j].gofz[i] = 0.0; |
| 159 |
|
| 160 |
// calculate comZ; |
| 161 |
|
| 162 |
totMass = 0.0; |
| 163 |
comZ = 0.0; |
| 164 |
for(i=0;i<nAtoms;i++){ |
| 165 |
comZ += atoms[i].pos[2]*atoms[i].mass; |
| 166 |
totMass += atoms[i].mass; |
| 167 |
} |
| 168 |
|
| 169 |
comZ /= totMass; |
| 170 |
|
| 171 |
halfMax = maxL * 0.5; |
| 172 |
|
| 173 |
// calc the gofZ; |
| 174 |
|
| 175 |
for(i=0;i<nAtoms;i++){ |
| 176 |
|
| 177 |
wrapZ = wrapMyZ( (atoms[i].pos[2] - comZ), Hmat[2][2] ); |
| 178 |
|
| 179 |
if(fabs(wrapZ) < halfMax ){ |
| 180 |
|
| 181 |
scale = wrapZ / halfMax; |
| 182 |
bin = (int)( (scale*halfGzBins) + halfGzBins ); |
| 183 |
|
| 184 |
tempCorrs[atoms[i].type].gofz[bin] += 1.0; |
| 185 |
} |
| 186 |
} |
| 187 |
|
| 188 |
volume = Hmat[0][0] * Hmat[1][1] * Hmat[2][2]; |
| 189 |
density = (double)nAtoms / volume; |
| 190 |
|
| 191 |
densCons = Hmat[0][0] * Hmat[1][1] * gofzDl * density; |
| 192 |
|
| 193 |
for(i=0;i<GOFZNBINS;i++) |
| 194 |
for(j=0;j<5;j++) |
| 195 |
tempCorrs[j].gofz[i] /= densCons; |
| 196 |
|
| 197 |
|
| 198 |
for(i=0;i<GOFZNBINS;i++) |
| 199 |
for(j=0;j<5;j++) |
| 200 |
gofzCorrs[j].gofz[i] += tempCorrs[j].gofz[i]; |
| 201 |
} |
| 202 |
|
| 203 |
|
| 204 |
double wrapMyZ( double z, double box ){ |
| 205 |
|
| 206 |
double scale, round; |
| 207 |
|
| 208 |
scale = z / box; |
| 209 |
|
| 210 |
round = ( scale >= 0 ) ? floor( scale + 0.5 ) : ceil( scale - 0.5 ); |
| 211 |
|
| 212 |
scale -= round; |
| 213 |
|
| 214 |
return scale*box; |
| 215 |
} |
