| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 41 |
|
* |
| 42 |
– |
* Hxy.cpp |
| 43 |
– |
* OOPSE-2.0 |
| 44 |
– |
* |
| 42 |
|
* Created by Xiuquan Sun on 05/09/06. |
| 43 |
|
* @author Xiuquan Sun |
| 44 |
< |
* @version $Id: Hxy.cpp,v 1.4 2006-05-17 21:51:42 tim Exp $ |
| 44 |
> |
* @version $Id$ |
| 45 |
|
* |
| 46 |
|
*/ |
| 47 |
|
|
| 58 |
|
#include<stdlib.h> |
| 59 |
|
#include<math.h> |
| 60 |
|
|
| 61 |
< |
namespace oopse { |
| 61 |
> |
namespace OpenMD { |
| 62 |
|
|
| 63 |
|
Hxy::Hxy(SimInfo* info, const std::string& filename, const std::string& sele, int nbins_x, int nbins_y, int nrbins) |
| 64 |
|
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), nBinsX_(nbins_x), nBinsY_(nbins_y), nbins_(nrbins){ |
| 70 |
|
|
| 71 |
|
gridsample_.resize(nBinsX_*nBinsY_); |
| 72 |
|
gridZ_.resize(nBinsX_*nBinsY_); |
| 73 |
+ |
mag.resize(nBinsX_*nBinsY_); |
| 74 |
+ |
newmag.resize(nBinsX_*nBinsY_); |
| 75 |
|
|
| 76 |
|
sum_bin.resize(nbins_); |
| 77 |
|
avg_bin.resize(nbins_); |
| 82 |
|
errbin_sum_sq.resize(nbins_); |
| 83 |
|
errbin_sq.resize(nbins_); |
| 84 |
|
|
| 85 |
+ |
bin.resize(nbins_); |
| 86 |
+ |
samples.resize(nbins_); |
| 87 |
+ |
|
| 88 |
|
setOutputName(getPrefix(filename) + ".Hxy"); |
| 89 |
|
} |
| 90 |
|
|
| 91 |
+ |
Hxy::~Hxy(){ |
| 92 |
+ |
gridsample_.clear(); |
| 93 |
+ |
gridZ_.clear(); |
| 94 |
+ |
sum_bin.clear(); |
| 95 |
+ |
avg_bin.clear(); |
| 96 |
+ |
errbin_sum.clear(); |
| 97 |
+ |
errbin.clear(); |
| 98 |
+ |
sum_bin_sq.clear(); |
| 99 |
+ |
avg_bin_sq.clear(); |
| 100 |
+ |
errbin_sum_sq.clear(); |
| 101 |
+ |
errbin_sq.clear(); |
| 102 |
+ |
|
| 103 |
+ |
for(unsigned int i=0; i < bin.size(); i++) |
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+ |
bin[i].clear(); |
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+ |
for(unsigned int i=0; i < samples.size(); i++) |
| 106 |
+ |
samples[i].clear(); |
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+ |
|
| 108 |
+ |
mag.clear(); |
| 109 |
+ |
newmag.clear(); |
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+ |
} |
| 111 |
+ |
|
| 112 |
|
void Hxy::process() { |
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|
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
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DumpReader reader(info_, dumpFilename_); |
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|
int nFrames = reader.getNFrames(); |
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nProcessed_ = nFrames/step_; |
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|
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< |
std::vector<RealType> mag, newmag; |
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> |
for(unsigned int k=0; k < bin.size(); k++) |
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> |
bin[k].resize(nFrames); |
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> |
for(unsigned int k=0; k < samples.size(); k++) |
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> |
samples[k].resize(nFrames); |
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> |
|
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|
RealType lenX_, lenY_; |
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|
RealType gridX_, gridY_; |
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|
RealType halfBoxX_, halfBoxY_; |
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< |
int binNoX, binNoY; |
| 126 |
> |
|
| 127 |
|
RealType interpsum, value; |
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|
int ninterp, px, py, newp; |
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< |
int newx, newy, newindex, index; |
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> |
int newindex, index; |
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|
int new_i, new_j, new_index; |
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+ |
|
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|
RealType freq_x, freq_y, zero_freq_x, zero_freq_y, freq; |
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< |
RealType maxfreqx, maxfreqy, maxfreq, dfreq; |
| 133 |
> |
RealType maxfreqx, maxfreqy, maxfreq; |
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> |
|
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|
int whichbin; |
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< |
int nMolecules; |
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> |
|
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> |
std::fill(sum_bin.begin(), sum_bin.end(), 0.0); |
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> |
std::fill(avg_bin.begin(), avg_bin.end(), 0.0); |
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> |
std::fill(errbin_sum.begin(), errbin_sum.end(), 0.0); |
| 140 |
> |
std::fill(errbin.begin(), errbin.end(), 0.0); |
| 141 |
> |
std::fill(sum_bin_sq.begin(), sum_bin_sq.end(), 0.0); |
| 142 |
> |
std::fill(avg_bin_sq.begin(), avg_bin_sq.end(), 0.0); |
| 143 |
> |
std::fill(errbin_sum_sq.begin(), errbin_sum_sq.end(), 0.0); |
| 144 |
> |
std::fill(errbin_sq.begin(), errbin_sq.end(), 0.0); |
| 145 |
|
|
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+ |
for(unsigned int i=0; i < bin.size(); i++) |
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+ |
std::fill(bin[i].begin(), bin[i].end(), 0.0); |
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+ |
|
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+ |
for(unsigned int i=0; i < samples.size(); i++) |
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+ |
std::fill(samples[i].begin(), samples[i].end(), 0); |
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+ |
|
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|
for (int istep = 0; istep < nFrames; istep += step_) { |
| 153 |
|
|
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|
reader.readFrame(istep); |
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|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 113 |
– |
nMolecules = info_->getNGlobalMolecules(); |
| 156 |
|
|
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|
Mat3x3d hmat = currentSnapshot_->getHmat(); |
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|
|
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|
fftwnd_plan p; |
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|
#endif |
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|
fftw_complex *in, *out; |
| 123 |
– |
|
| 165 |
|
|
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|
in = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) * (nBinsX_*nBinsY_)); |
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|
out = (fftw_complex*) fftw_malloc(sizeof(fftw_complex) *(nBinsX_*nBinsY_)); |
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|
#else |
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|
p = fftw2d_create_plan(nBinsX_, nBinsY_, FFTW_FORWARD, FFTW_ESTIMATE); |
| 174 |
|
#endif |
| 175 |
< |
|
| 175 |
> |
|
| 176 |
> |
std::fill(gridsample_.begin(), gridsample_.end(), 0); |
| 177 |
> |
std::fill(gridZ_.begin(), gridZ_.end(), 0.0); |
| 178 |
> |
std::fill(mag.begin(), mag.end(), 0.0); |
| 179 |
> |
std::fill(newmag.begin(), newmag.end(), 0.0); |
| 180 |
> |
|
| 181 |
|
int i, j; |
| 182 |
|
|
| 137 |
– |
gridsample_.clear(); |
| 138 |
– |
gridZ_.clear(); |
| 139 |
– |
sum_bin.clear(); |
| 140 |
– |
avg_bin.clear(); |
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– |
errbin_sum.clear(); |
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– |
errbin.clear(); |
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– |
sum_bin_sq.clear(); |
| 144 |
– |
avg_bin_sq.clear(); |
| 145 |
– |
errbin_sum_sq.clear(); |
| 146 |
– |
errbin_sq.clear(); |
| 147 |
– |
|
| 148 |
– |
mag.resize(nBinsX_*nBinsY_); |
| 149 |
– |
newmag.resize(nBinsX_*nBinsY_); |
| 150 |
– |
mag.clear(); |
| 151 |
– |
newmag.clear(); |
| 152 |
– |
|
| 183 |
|
StuntDouble* sd; |
| 184 |
|
|
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|
lenX_ = hmat(0,0); |
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|
gridX_ = lenX_ /(nBinsX_); |
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|
gridY_ = lenY_ /(nBinsY_); |
| 190 |
|
|
| 191 |
< |
RealType halfBoxX_ = lenX_ / 2.0; |
| 192 |
< |
RealType halfBoxY_ = lenY_ / 2.0; |
| 191 |
> |
halfBoxX_ = lenX_ / 2.0; |
| 192 |
> |
halfBoxY_ = lenY_ / 2.0; |
| 193 |
|
|
| 194 |
|
if (evaluator_.isDynamic()) { |
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|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
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|
//wrap the stuntdoubles into a cell |
| 199 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
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|
Vector3d pos = sd->getPos(); |
| 201 |
< |
currentSnapshot_->wrapVector(pos); |
| 201 |
> |
if (usePeriodicBoundaryConditions_) |
| 202 |
> |
currentSnapshot_->wrapVector(pos); |
| 203 |
|
sd->setPos(pos); |
| 204 |
< |
} |
| 204 |
> |
} |
| 205 |
|
|
| 206 |
|
//determine which atom belongs to which grid |
| 207 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { |
| 208 |
|
Vector3d pos = sd->getPos(); |
| 209 |
|
//int binNo = (pos.z() /deltaR_) - 1; |
| 210 |
< |
int binNoX = (pos.x() + halfBoxX_) /gridX_; |
| 211 |
< |
int binNoY = (pos.y() + halfBoxY_) /gridY_; |
| 210 |
> |
int binNoX = (int) ((pos.x() + halfBoxX_) / gridX_); |
| 211 |
> |
int binNoY = (int) ((pos.y() + halfBoxY_) / gridY_); |
| 212 |
|
//std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = " << deltaR_ << " binNo = " << binNo << "\n"; |
| 213 |
|
gridZ_[binNoX*nBinsY_+binNoY] += pos.z(); |
| 214 |
|
gridsample_[binNoX*nBinsY_+binNoY]++; |
| 217 |
|
// FFT stuff depends on nx and ny, so delay allocation until we have |
| 218 |
|
// that information |
| 219 |
|
|
| 189 |
– |
for (i=0; i< nBinsX_; i++) { |
| 190 |
– |
for(j=0; j< nBinsY_; j++) { |
| 191 |
– |
newindex = i*nBinsY_ + j; |
| 192 |
– |
mag[newindex] = 0.0; |
| 193 |
– |
newmag[newindex] = 0.0; |
| 194 |
– |
} |
| 195 |
– |
} |
| 196 |
– |
|
| 220 |
|
for(i = 0; i < nBinsX_; i++){ |
| 221 |
|
for(j = 0; j < nBinsY_; j++){ |
| 222 |
|
newindex = i * nBinsY_ + j; |
| 290 |
|
c_im(in[newindex]) = 0.0; |
| 291 |
|
} |
| 292 |
|
} |
| 293 |
+ |
|
| 294 |
|
#ifdef HAVE_FFTW3_H |
| 295 |
|
fftw_execute(p); |
| 296 |
|
#else |
| 303 |
|
mag[newindex] = pow(c_re(out[newindex]),2) + pow(c_im(out[newindex]),2); |
| 304 |
|
} |
| 305 |
|
} |
| 306 |
+ |
|
| 307 |
|
#ifdef HAVE_FFTW3_H |
| 308 |
|
fftw_destroy_plan(p); |
| 309 |
|
#else |
| 383 |
|
|
| 384 |
|
for ( i = 0; i < nbins_; i++) { |
| 385 |
|
if ( samples[i][istep] > 0) { |
| 386 |
< |
bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nMolecules; |
| 386 |
> |
bin[i][istep] = 4.0 * sqrt(bin[i][istep] / (RealType)samples[i][istep]) / (RealType)nBinsX_ / (RealType)nBinsY_; |
| 387 |
|
} |
| 388 |
|
} |
| 364 |
– |
|
| 389 |
|
} |
| 390 |
< |
|
| 390 |
> |
|
| 391 |
|
for (int i = 0; i < nbins_; i++) { |
| 392 |
|
for (int j = 0; j < nFrames; j++) { |
| 393 |
|
sum_bin[i] += bin[i][j]; |
| 402 |
|
errbin[i] = sqrt( errbin_sum[i] / (RealType)nFrames ); |
| 403 |
|
errbin_sq[i] = sqrt( errbin_sum_sq[i] / (RealType)nFrames ); |
| 404 |
|
} |
| 405 |
< |
|
| 405 |
> |
|
| 406 |
|
printSpectrum(); |
| 407 |
+ |
|
| 408 |
|
#else |
| 409 |
|
sprintf(painCave.errMsg, "Hxy: FFTW support was not compiled in!\n"); |
| 410 |
|
painCave.isFatal = 1; |
| 411 |
|
simError(); |
| 412 |
|
|
| 413 |
|
#endif |
| 414 |
< |
|
| 390 |
< |
} |
| 414 |
> |
} |
| 415 |
|
|
| 416 |
|
void Hxy::printSpectrum() { |
| 417 |
|
std::ofstream rdfStream(outputFilename_.c_str()); |
| 418 |
|
if (rdfStream.is_open()) { |
| 419 |
< |
|
| 420 |
< |
for (int i = 0; i < nbins_; i++) { |
| 419 |
> |
|
| 420 |
> |
for (int i = 0; i < nbins_; ++i) { |
| 421 |
|
if ( avg_bin[i] > 0 ){ |
| 422 |
< |
rdfStream << i*dfreq << "\t" |
| 422 |
> |
rdfStream << (RealType)i * dfreq << "\t" |
| 423 |
|
<<pow(avg_bin[i], 2)<<"\t" |
| 424 |
|
<<errbin_sq[i]<<"\t" |
| 425 |
|
<<avg_bin[i]<<"\t" |
| 432 |
|
painCave.isFatal = 1; |
| 433 |
|
simError(); |
| 434 |
|
} |
| 435 |
< |
|
| 435 |
> |
|
| 436 |
|
rdfStream.close(); |
| 437 |
+ |
|
| 438 |
|
} |
| 439 |
|
|
| 440 |
|
} |
