| 1 |
#include <stdlib.h> |
| 2 |
#include <math.h> |
| 3 |
#include <vector> |
| 4 |
|
| 5 |
#include "simError.h" |
| 6 |
#include "AllCorr.hpp" |
| 7 |
|
| 8 |
|
| 9 |
AllCorr::AllCorr(){ |
| 10 |
|
| 11 |
pairCorrs = NULL; |
| 12 |
haveFrames = false; |
| 13 |
pairCorrSet = false; |
| 14 |
haveLength = false; |
| 15 |
haveNbins = false; |
| 16 |
} |
| 17 |
|
| 18 |
AllCorr::~AllCorr(){ |
| 19 |
int i; |
| 20 |
|
| 21 |
if( pairCorrs != NULL ){ |
| 22 |
for(i=0; i<nPairs; i++) |
| 23 |
delete pairCorrs[i]; |
| 24 |
delete[] pairCorrs; |
| 25 |
} |
| 26 |
} |
| 27 |
|
| 28 |
void AllCorr::setMaxLength( double theLength ){ |
| 29 |
maxLength = theLength; |
| 30 |
haveLength = true; |
| 31 |
} |
| 32 |
|
| 33 |
void AllCorr::setNbins( int theNbins ){ |
| 34 |
nBins = theNbins; |
| 35 |
haveNbins = true; |
| 36 |
} |
| 37 |
|
| 38 |
void AllCorr::setFrames( SimInfo* theInfoArray, int theNframes, |
| 39 |
DumpReader* theReader ){ |
| 40 |
int i; |
| 41 |
|
| 42 |
|
| 43 |
infoArray = theInfoArray; |
| 44 |
nFrames = theNframes; |
| 45 |
reader = theReader; |
| 46 |
|
| 47 |
nAtoms = infoArray[0].n_atoms; |
| 48 |
|
| 49 |
|
| 50 |
// allocate the first frame's atom arrays |
| 51 |
|
| 52 |
(infoArray[0].getConfiguration())->createArrays(infoArray[0].n_atoms); |
| 53 |
for (i = 0; i < infoArray[0].n_atoms; i++) |
| 54 |
infoArray[0].atoms[i]->setCoords(); |
| 55 |
|
| 56 |
// read in the first frame's positions |
| 57 |
|
| 58 |
reader->readFrame( &(infoArray[0]), 0 ); |
| 59 |
|
| 60 |
if( !haveLength ){ |
| 61 |
maxLength = infoArray[0].getMaxCutoff(); |
| 62 |
haveLength = true; |
| 63 |
} |
| 64 |
|
| 65 |
haveFrames = true; |
| 66 |
} |
| 67 |
|
| 68 |
void AllCorr::setPairCorrList( vector <PairCorrList> &theList ){ |
| 69 |
|
| 70 |
int i; |
| 71 |
char pair1[PCL_NAME_LENGTH]; |
| 72 |
char pair2[PCL_NAME_LENGTH]; |
| 73 |
|
| 74 |
if( !haveFrames ){ |
| 75 |
sprintf( painCave.errMsg, |
| 76 |
"\n" |
| 77 |
"AllCorr Error: attempt to create the pair correlations without" |
| 78 |
" first setting the Frames\n" ); |
| 79 |
painCave.isFatal = 1; |
| 80 |
simError(); |
| 81 |
} |
| 82 |
|
| 83 |
if( !haveNbins ){ |
| 84 |
sprintf( painCave.errMsg, |
| 85 |
"\n" |
| 86 |
"AllCorr Error: attempt to create the pair correlations without" |
| 87 |
" first setting nBins\n" ); |
| 88 |
painCave.isFatal = 1; |
| 89 |
simError(); |
| 90 |
} |
| 91 |
|
| 92 |
|
| 93 |
nPairs = (int)theList.size(); |
| 94 |
pairCorrs = new PairCorrType*[nPairs]; |
| 95 |
|
| 96 |
for(i=0;i<nPairs;i++){ |
| 97 |
|
| 98 |
theList[i].getAtom1( pair1 ); |
| 99 |
theList[i].getAtom2( pair2 ); |
| 100 |
|
| 101 |
switch( theList[i].getType() ){ |
| 102 |
|
| 103 |
case gofr: |
| 104 |
pairCorrs[i] = new GofR(pair1, pair2, nAtoms, nBins); |
| 105 |
break; |
| 106 |
|
| 107 |
default: |
| 108 |
|
| 109 |
sprintf( painCave.errMsg, |
| 110 |
"AllCorr Error: Unrecognized pair corr type in " |
| 111 |
" setPairCorrList()->theList[%d]\n", |
| 112 |
i ); |
| 113 |
painCave.isFatal = 1; |
| 114 |
simError(); |
| 115 |
break; |
| 116 |
} |
| 117 |
} |
| 118 |
|
| 119 |
pairCorrSet = true; |
| 120 |
} |
| 121 |
|
| 122 |
void AllCorr::initCorrelations( char* theOutPrefix, bool theIsSeparateOut, |
| 123 |
bool theHavePairCorrs, |
| 124 |
bool theHaveStaticCorrs ){ |
| 125 |
int i; |
| 126 |
atomName* theNames = new atomName[nAtoms]; |
| 127 |
|
| 128 |
havePairCorrs = theHavePairCorrs; |
| 129 |
haveStaticCorrs = theHaveStaticCorrs; |
| 130 |
|
| 131 |
if( havePairCorrs){ |
| 132 |
|
| 133 |
if(!pairCorrSet){ |
| 134 |
sprintf( painCave.errMsg, |
| 135 |
"AllCorr error: Attempt to initialize pair correlations " |
| 136 |
" without first setting the pair correlation list.\n" ); |
| 137 |
painCave.isFatal = 1; |
| 138 |
simError(); |
| 139 |
} |
| 140 |
|
| 141 |
for(i=0;i<nAtoms;i++){ |
| 142 |
|
| 143 |
strcpy(theNames[i].name, infoArray[0].atoms[i]->getType() ); |
| 144 |
} |
| 145 |
|
| 146 |
for(i=0;i<nPairs;i++){ |
| 147 |
pairCorrs[i]->initCorr(maxLength, theNames ); |
| 148 |
} |
| 149 |
} |
| 150 |
|
| 151 |
if( haveStaticCorrs ){ |
| 152 |
|
| 153 |
// empty for now |
| 154 |
} |
| 155 |
|
| 156 |
strcpy(outPrefix, theOutPrefix); |
| 157 |
isSeparateOut = theIsSeparateOut; |
| 158 |
} |
| 159 |
|
| 160 |
|
| 161 |
void AllCorr::calcCorrelations(){ |
| 162 |
|
| 163 |
SimInfo* currInfo; |
| 164 |
int i,j,k,l; |
| 165 |
double rij[3], rDist, uHatI[3], uHatJ[3]; |
| 166 |
double* grndOut = NULL; |
| 167 |
double dSqr, ri[3], rj[3]; |
| 168 |
DirectionalAtom* dAtom; |
| 169 |
double frameVolume; |
| 170 |
|
| 171 |
|
| 172 |
for(k=0; k<nFrames; k++){ |
| 173 |
|
| 174 |
currInfo = &(infoArray[k]); |
| 175 |
|
| 176 |
// skip the first frame, as it is already initialized |
| 177 |
if( k != 0 ){ |
| 178 |
|
| 179 |
// allocate the frame's atom arrays |
| 180 |
|
| 181 |
(currInfo->getConfiguration())->createArrays(currInfo->n_atoms); |
| 182 |
for (i = 0; i < currInfo->n_atoms; i++) |
| 183 |
currInfo->atoms[i]->setCoords(); |
| 184 |
|
| 185 |
// read in the frame's positions |
| 186 |
|
| 187 |
reader->readFrame( &(infoArray[k]), 0 ); |
| 188 |
} |
| 189 |
|
| 190 |
frameVolume = currInfo->boxVol; |
| 191 |
this->setFrameVolume( frameVolume ); |
| 192 |
|
| 193 |
if(havePairCorrs){ |
| 194 |
|
| 195 |
// do the pair loop |
| 196 |
|
| 197 |
for(i=0;i<(nAtoms-1);i++){ |
| 198 |
|
| 199 |
if( this->matchI(i) ){ |
| 200 |
|
| 201 |
for(j=i+1;j<nAtoms;j++){ |
| 202 |
|
| 203 |
if( this->matchJ(j) ){ |
| 204 |
|
| 205 |
// calc rdist and rij; |
| 206 |
|
| 207 |
currInfo->atoms[i]->getPos( ri ); |
| 208 |
|
| 209 |
currInfo->atoms[j]->getPos( rj ); |
| 210 |
|
| 211 |
for(l=0;l<3;l++) |
| 212 |
rij[l] = rj[l] - ri[l]; |
| 213 |
|
| 214 |
currInfo->wrapVector( rij ); |
| 215 |
|
| 216 |
dSqr=0; |
| 217 |
for(l=0;l<3;l++) |
| 218 |
dSqr += rij[l] * rij[l]; |
| 219 |
|
| 220 |
rDist = sqrt( dSqr ); |
| 221 |
|
| 222 |
if( currInfo->atoms[i]->isDirectional() ){ |
| 223 |
|
| 224 |
dAtom = (DirectionalAtom*)currInfo->atoms[i]; |
| 225 |
dAtom->getU( uHatI ); |
| 226 |
|
| 227 |
if( currInfo->atoms[j]->isDirectional() ){ |
| 228 |
|
| 229 |
dAtom = (DirectionalAtom*)currInfo->atoms[j]; |
| 230 |
dAtom->getU( uHatJ ); |
| 231 |
|
| 232 |
this->pairCorrelate( rij, rDist, uHatI, uHatJ ); |
| 233 |
} |
| 234 |
else{ |
| 235 |
|
| 236 |
this->pairCorrelate( rij, rDist, uHatI, grndOut ); |
| 237 |
} |
| 238 |
} |
| 239 |
else if( currInfo->atoms[j]->isDirectional() ){ |
| 240 |
|
| 241 |
dAtom = (DirectionalAtom*)currInfo->atoms[j]; |
| 242 |
dAtom->getU( uHatJ ); |
| 243 |
|
| 244 |
this->pairCorrelate( rij, rDist, grndOut, uHatJ ); |
| 245 |
} |
| 246 |
else{ |
| 247 |
this->pairCorrelate( rij, rDist, grndOut, grndOut ); |
| 248 |
} |
| 249 |
} |
| 250 |
} |
| 251 |
} |
| 252 |
} |
| 253 |
} |
| 254 |
|
| 255 |
if( haveStaticCorrs ){ |
| 256 |
|
| 257 |
// empty for now |
| 258 |
|
| 259 |
} |
| 260 |
|
| 261 |
// accumulate the averages for this frame |
| 262 |
|
| 263 |
this->accumulateFrame(); |
| 264 |
|
| 265 |
// de-allocate the frame |
| 266 |
|
| 267 |
(currInfo->getConfiguration())->destroyArrays(); |
| 268 |
} |
| 269 |
|
| 270 |
this->writeCorrs(); |
| 271 |
} |
| 272 |
|
| 273 |
bool AllCorr::matchI(int i){ |
| 274 |
|
| 275 |
int k; |
| 276 |
bool result; |
| 277 |
|
| 278 |
result = false; |
| 279 |
|
| 280 |
for(k=0;k<nPairs;k++) |
| 281 |
result = (result || pairCorrs[k]->matchI(i) ); |
| 282 |
|
| 283 |
return result; |
| 284 |
} |
| 285 |
|
| 286 |
bool AllCorr::matchJ(int j){ |
| 287 |
|
| 288 |
int k; |
| 289 |
bool result; |
| 290 |
|
| 291 |
result = false; |
| 292 |
|
| 293 |
for(k=0;k<nPairs;k++) |
| 294 |
result = (result || pairCorrs[k]->matchJ(j) ); |
| 295 |
|
| 296 |
return result; |
| 297 |
} |
| 298 |
|
| 299 |
void AllCorr::pairCorrelate( double Rij[3], double dist, |
| 300 |
double uHatI[3], double uHatJ[3] ){ |
| 301 |
|
| 302 |
int i; |
| 303 |
|
| 304 |
for(i=0;i<nPairs;i++) |
| 305 |
pairCorrs[i]->correlate( Rij, dist, uHatI, uHatJ ); |
| 306 |
} |
| 307 |
|
| 308 |
void AllCorr::setFrameVolume( double theVolume ){ |
| 309 |
|
| 310 |
int i; |
| 311 |
|
| 312 |
if( havePairCorrs ){ |
| 313 |
|
| 314 |
for(i=0;i<nPairs;i++) |
| 315 |
pairCorrs[i]->setFrameVolume( theVolume ); |
| 316 |
} |
| 317 |
|
| 318 |
if( haveStaticCorrs ){ |
| 319 |
|
| 320 |
// empty for now |
| 321 |
} |
| 322 |
} |
| 323 |
|
| 324 |
void AllCorr::accumulateFrame( void ){ |
| 325 |
|
| 326 |
int i; |
| 327 |
|
| 328 |
if( havePairCorrs ){ |
| 329 |
|
| 330 |
for(i=0;i<nPairs;i++) |
| 331 |
pairCorrs[i]->accumulateFrame(); |
| 332 |
} |
| 333 |
|
| 334 |
if( haveStaticCorrs ){ |
| 335 |
|
| 336 |
// empty for now |
| 337 |
} |
| 338 |
} |
| 339 |
|
| 340 |
void AllCorr::writeCorrs( void ){ |
| 341 |
int i; |
| 342 |
|
| 343 |
if( isSeparateOut ){ |
| 344 |
|
| 345 |
if( havePairCorrs ){ |
| 346 |
|
| 347 |
for(i=0;i<nPairs;i++) |
| 348 |
pairCorrs[i]->writeCorr( outPrefix ); |
| 349 |
} |
| 350 |
|
| 351 |
if( haveStaticCorrs ){ |
| 352 |
|
| 353 |
// empty for now |
| 354 |
} |
| 355 |
|
| 356 |
} |
| 357 |
else{ |
| 358 |
|
| 359 |
// empty for now |
| 360 |
} |
| 361 |
|
| 362 |
} |
