| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#include "applications/staticProps/SpatialStatistics.hpp" |
| 44 |
#include "io/DumpReader.hpp" |
| 45 |
#include "primitives/Molecule.hpp" |
| 46 |
|
| 47 |
namespace OpenMD { |
| 48 |
|
| 49 |
SpatialStatistics::SpatialStatistics(SimInfo* info, const string& filename, |
| 50 |
const string& sele, int nbins) |
| 51 |
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), |
| 52 |
seleMan_(info), nBins_(nbins){ |
| 53 |
|
| 54 |
evaluator_.loadScriptString(sele); |
| 55 |
if (!evaluator_.isDynamic()) { |
| 56 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 57 |
} |
| 58 |
|
| 59 |
// Pre-load an OutputData for the count of objects: |
| 60 |
counts_ = new OutputData; |
| 61 |
counts_->units = "objects"; |
| 62 |
counts_->title = "Objects"; |
| 63 |
counts_->dataType = odtReal; |
| 64 |
counts_->dataHandling = odhTotal; |
| 65 |
counts_->accumulator.reserve(nBins_); |
| 66 |
for (int i = 0; i < nBins_; i++) |
| 67 |
counts_->accumulator.push_back( new Accumulator() ); |
| 68 |
|
| 69 |
setOutputName(getPrefix(filename) + ".spst"); |
| 70 |
} |
| 71 |
|
| 72 |
SpatialStatistics::~SpatialStatistics() { |
| 73 |
vector<OutputData*>::iterator i; |
| 74 |
OutputData* outputData; |
| 75 |
|
| 76 |
for(outputData = beginOutputData(i); outputData; |
| 77 |
outputData = nextOutputData(i)) { |
| 78 |
delete outputData; |
| 79 |
} |
| 80 |
data_.clear(); |
| 81 |
|
| 82 |
delete counts_; |
| 83 |
} |
| 84 |
|
| 85 |
|
| 86 |
void SpatialStatistics::process() { |
| 87 |
|
| 88 |
DumpReader reader(info_, dumpFilename_); |
| 89 |
int nFrames = reader.getNFrames(); |
| 90 |
nProcessed_ = nFrames/step_; |
| 91 |
|
| 92 |
for (int istep = 0; istep < nFrames; istep += step_) { |
| 93 |
reader.readFrame(istep); |
| 94 |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 95 |
processFrame(istep); |
| 96 |
} |
| 97 |
writeOutput(); |
| 98 |
} |
| 99 |
|
| 100 |
|
| 101 |
void SpatialStatistics::processFrame(int istep) { |
| 102 |
Molecule* mol; |
| 103 |
RigidBody* rb; |
| 104 |
StuntDouble* sd; |
| 105 |
SimInfo::MoleculeIterator mi; |
| 106 |
Molecule::RigidBodyIterator rbIter; |
| 107 |
int i; |
| 108 |
|
| 109 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 110 |
mol = info_->nextMolecule(mi)) { |
| 111 |
|
| 112 |
// change the positions of atoms which belong to the rigidbodies |
| 113 |
|
| 114 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 115 |
rb = mol->nextRigidBody(rbIter)) { |
| 116 |
rb->updateAtoms(); |
| 117 |
} |
| 118 |
} |
| 119 |
|
| 120 |
if (evaluator_.isDynamic()) { |
| 121 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 122 |
} |
| 123 |
|
| 124 |
// loop over the selected atoms: |
| 125 |
|
| 126 |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 127 |
sd = seleMan_.nextSelected(i)) { |
| 128 |
|
| 129 |
// figure out where that object is: |
| 130 |
|
| 131 |
Vector3d pos = sd->getPos(); |
| 132 |
|
| 133 |
int bin = getBin(pos); |
| 134 |
|
| 135 |
// forward the work of statistics on to the subclass: |
| 136 |
|
| 137 |
processStuntDouble( sd, bin ); |
| 138 |
|
| 139 |
dynamic_cast<Accumulator *>(counts_->accumulator[bin])->add(1); |
| 140 |
} |
| 141 |
} |
| 142 |
|
| 143 |
|
| 144 |
void SpatialStatistics::writeOutput() { |
| 145 |
|
| 146 |
vector<OutputData*>::iterator i; |
| 147 |
OutputData* outputData; |
| 148 |
|
| 149 |
ofstream outStream(outputFilename_.c_str()); |
| 150 |
if (outStream.is_open()) { |
| 151 |
|
| 152 |
//write title |
| 153 |
outStream << "# SPATIAL STATISTICS\n"; |
| 154 |
outStream << "#"; |
| 155 |
|
| 156 |
for(outputData = beginOutputData(i); outputData; |
| 157 |
outputData = nextOutputData(i)) { |
| 158 |
outStream << "\t" << outputData->title << |
| 159 |
"(" << outputData->units << ")"; |
| 160 |
// add some extra tabs for column alignment |
| 161 |
if (outputData->dataType == odtVector3) outStream << "\t\t"; |
| 162 |
} |
| 163 |
|
| 164 |
outStream << std::endl; |
| 165 |
|
| 166 |
outStream.precision(8); |
| 167 |
|
| 168 |
for (int j = 0; j < nBins_; j++) { |
| 169 |
|
| 170 |
int counts = counts_->accumulator[j]->count(); |
| 171 |
|
| 172 |
if (counts > 0) { |
| 173 |
for(outputData = beginOutputData(i); outputData; |
| 174 |
outputData = nextOutputData(i)) { |
| 175 |
|
| 176 |
int n = outputData->accumulator[j]->count(); |
| 177 |
if (n != 0) { |
| 178 |
writeData( outStream, outputData, j ); |
| 179 |
} |
| 180 |
} |
| 181 |
outStream << std::endl; |
| 182 |
} |
| 183 |
} |
| 184 |
|
| 185 |
outStream << "#######################################################\n"; |
| 186 |
outStream << "# Standard Deviations in those quantities follow:\n"; |
| 187 |
outStream << "#######################################################\n"; |
| 188 |
|
| 189 |
for (int j = 0; j < nBins_; j++) { |
| 190 |
int counts = counts_->accumulator[j]->count(); |
| 191 |
if (counts > 0) { |
| 192 |
|
| 193 |
outStream << "#"; |
| 194 |
for(outputData = beginOutputData(i); outputData; |
| 195 |
outputData = nextOutputData(i)) { |
| 196 |
|
| 197 |
int n = outputData->accumulator[j]->count(); |
| 198 |
if (n != 0) { |
| 199 |
writeStdDev( outStream, outputData, j ); |
| 200 |
} |
| 201 |
} |
| 202 |
outStream << std::endl; |
| 203 |
} |
| 204 |
} |
| 205 |
|
| 206 |
outStream.flush(); |
| 207 |
outStream.close(); |
| 208 |
|
| 209 |
} else { |
| 210 |
sprintf(painCave.errMsg, "SpatialStatistics: unable to open %s\n", |
| 211 |
outputFilename_.c_str()); |
| 212 |
painCave.isFatal = 1; |
| 213 |
simError(); |
| 214 |
} |
| 215 |
} |
| 216 |
|
| 217 |
|
| 218 |
void SpatialStatistics::writeData(ostream& os, OutputData* dat, |
| 219 |
unsigned int bin) { |
| 220 |
assert(int(bin) < nBins_); |
| 221 |
int n = dat->accumulator[bin]->count(); |
| 222 |
if (n == 0) return; |
| 223 |
|
| 224 |
RealType r; |
| 225 |
Vector3d v; |
| 226 |
|
| 227 |
if( dat->dataType == odtReal ) { |
| 228 |
dynamic_cast<Accumulator*>(dat->accumulator[bin])->getAverage(r); |
| 229 |
if (isinf(r) || isnan(r) ) { |
| 230 |
sprintf( painCave.errMsg, |
| 231 |
"SpatialStatistics detected a numerical error writing:\n" |
| 232 |
"\t%s for bin %d", |
| 233 |
dat->title.c_str(), bin); |
| 234 |
painCave.isFatal = 1; |
| 235 |
simError(); |
| 236 |
} |
| 237 |
if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count(); |
| 238 |
os << "\t" << r; |
| 239 |
|
| 240 |
} else if ( dat->dataType == odtVector3 ) { |
| 241 |
dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getAverage(v); |
| 242 |
if (isinf(v[0]) || isnan(v[0]) || |
| 243 |
isinf(v[1]) || isnan(v[1]) || |
| 244 |
isinf(v[2]) || isnan(v[2]) ) { |
| 245 |
sprintf( painCave.errMsg, |
| 246 |
"SpatialStatistics detected a numerical error writing:\n" |
| 247 |
"\t%s for bin %d", |
| 248 |
dat->title.c_str(), bin); |
| 249 |
painCave.isFatal = 1; |
| 250 |
simError(); |
| 251 |
} |
| 252 |
if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count(); |
| 253 |
os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2]; |
| 254 |
} |
| 255 |
} |
| 256 |
|
| 257 |
void SpatialStatistics::writeStdDev(ostream& os, OutputData* dat, |
| 258 |
unsigned int bin) { |
| 259 |
assert(int(bin) < nBins_); |
| 260 |
int n = dat->accumulator[bin]->count(); |
| 261 |
if (n == 0) return; |
| 262 |
|
| 263 |
RealType r; |
| 264 |
Vector3d v; |
| 265 |
|
| 266 |
if( dat->dataType == odtReal ) { |
| 267 |
dynamic_cast<Accumulator*>(dat->accumulator[bin])->getStdDev(r); |
| 268 |
if (isinf(r) || isnan(r) ) { |
| 269 |
sprintf( painCave.errMsg, |
| 270 |
"SpatialStatistics detected a numerical error writing:\n" |
| 271 |
"\tstandard deviation of %s for bin %d", |
| 272 |
dat->title.c_str(), bin); |
| 273 |
painCave.isFatal = 1; |
| 274 |
simError(); |
| 275 |
} |
| 276 |
if (dat->dataHandling == odhTotal) r *= dat->accumulator[bin]->count(); |
| 277 |
os << "\t" << r; |
| 278 |
|
| 279 |
} else if ( dat->dataType == odtVector3 ) { |
| 280 |
dynamic_cast<VectorAccumulator*>(dat->accumulator[bin])->getStdDev(v); |
| 281 |
if (isinf(v[0]) || isnan(v[0]) || |
| 282 |
isinf(v[1]) || isnan(v[1]) || |
| 283 |
isinf(v[2]) || isnan(v[2]) ) { |
| 284 |
sprintf( painCave.errMsg, |
| 285 |
"SpatialStatistics detected a numerical error writing:\n" |
| 286 |
"\tstandard deviation of %s for bin %d", |
| 287 |
dat->title.c_str(), bin); |
| 288 |
painCave.isFatal = 1; |
| 289 |
simError(); |
| 290 |
} |
| 291 |
if (dat->dataHandling == odhTotal) v *= dat->accumulator[bin]->count(); |
| 292 |
os << "\t" << v[0] << "\t" << v[1] << "\t" << v[2]; |
| 293 |
} |
| 294 |
} |
| 295 |
|
| 296 |
|
| 297 |
OutputData* SpatialStatistics::beginOutputData(vector<OutputData*>::iterator& i) { |
| 298 |
i = data_.begin(); |
| 299 |
return i != data_.end()? *i : NULL; |
| 300 |
} |
| 301 |
|
| 302 |
OutputData* SpatialStatistics::nextOutputData(vector<OutputData*>::iterator& i){ |
| 303 |
++i; |
| 304 |
return i != data_.end()? *i: NULL; |
| 305 |
} |
| 306 |
|
| 307 |
|
| 308 |
SlabStatistics::SlabStatistics(SimInfo* info, const string& filename, |
| 309 |
const string& sele, int nbins) : |
| 310 |
SpatialStatistics(info, filename, sele, nbins) { |
| 311 |
|
| 312 |
z_ = new OutputData; |
| 313 |
z_->units = "Angstroms"; |
| 314 |
z_->title = "Z"; |
| 315 |
z_->dataType = odtReal; |
| 316 |
z_->dataHandling = odhAverage; |
| 317 |
z_->accumulator.reserve(nbins); |
| 318 |
for (int i = 0; i < nbins; i++) |
| 319 |
z_->accumulator.push_back( new Accumulator() ); |
| 320 |
data_.push_back(z_); |
| 321 |
} |
| 322 |
|
| 323 |
void SlabStatistics::processFrame(int istep) { |
| 324 |
RealType z; |
| 325 |
hmat_ = currentSnapshot_->getHmat(); |
| 326 |
for (int i = 0; i < nBins_; i++) { |
| 327 |
z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2); |
| 328 |
dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z); |
| 329 |
} |
| 330 |
volume_ = currentSnapshot_->getVolume(); |
| 331 |
|
| 332 |
SpatialStatistics::processFrame(istep); |
| 333 |
} |
| 334 |
|
| 335 |
int SlabStatistics::getBin(Vector3d pos) { |
| 336 |
currentSnapshot_->wrapVector(pos); |
| 337 |
// which bin is this stuntdouble in? |
| 338 |
// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)] |
| 339 |
// Shift molecules by half a box to have bins start at 0 |
| 340 |
// The modulo operator is used to wrap the case when we are |
| 341 |
// beyond the end of the bins back to the beginning. |
| 342 |
return int(nBins_ * (pos.z() / hmat_(2,2) + 0.5)) % nBins_; |
| 343 |
} |
| 344 |
|
| 345 |
|
| 346 |
ShellStatistics::ShellStatistics(SimInfo* info, const string& filename, |
| 347 |
const string& sele, int nbins) : |
| 348 |
SpatialStatistics(info, filename, sele, nbins){ |
| 349 |
|
| 350 |
coordinateOrigin_ = V3Zero; |
| 351 |
binWidth_ = 1.0; |
| 352 |
|
| 353 |
r_ = new OutputData; |
| 354 |
r_->units = "Angstroms"; |
| 355 |
r_->title = "R"; |
| 356 |
r_->dataType = odtReal; |
| 357 |
r_->dataHandling = odhAverage; |
| 358 |
r_->accumulator.reserve(nbins); |
| 359 |
for (int i = 0; i < nbins; i++) |
| 360 |
r_->accumulator.push_back( new Accumulator() ); |
| 361 |
data_.push_back(r_); |
| 362 |
|
| 363 |
for (int i = 0; i < nbins; i++) { |
| 364 |
RealType r = (((RealType)i + 0.5) * binWidth_); |
| 365 |
dynamic_cast<Accumulator*>(r_->accumulator[i])->add(r); |
| 366 |
} |
| 367 |
} |
| 368 |
|
| 369 |
int ShellStatistics::getBin(Vector3d pos) { |
| 370 |
Vector3d rPos = pos - coordinateOrigin_; |
| 371 |
return int(rPos.length() / binWidth_); |
| 372 |
} |
| 373 |
} |
| 374 |
|
