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using namespace MATPACK; |
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namespace OpenMD { |
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< |
BOPofR::BOPofR(SimInfo* info, const std::string& filename, const std::string& sele, double rCut, |
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int nbins, RealType len) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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BOPofR::BOPofR(SimInfo* info, const std::string& filename, |
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const std::string& sele, double rCut, int nbins, |
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RealType len) : StaticAnalyser(info, filename), |
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selectionScript_(sele), |
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evaluator_(info), seleMan_(info) { |
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setOutputName(getPrefix(filename) + ".bo"); |
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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seleMan_.setSelectionSet(evaluator_.evaluate()); |
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} |
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// Set up cutoff radius and order of the Legendre Polynomial: |
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rCut_ = rCut; |
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nBins_ = nbins; |
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len_ = len; |
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deltaR_ = len_/nBins_; |
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RCount_.resize(nBins_); |
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WofR_.resize(nBins_); |
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QofR_.resize(nBins_); |
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for (int i = 0; i < nBins_; i++){ |
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RCount_[i] = 0; |
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WofR_[i] = 0; |
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QofR_[i] = 0; |
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} |
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for (int i = 0; i < nBins_; i++){ |
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RCount_[i] = 0; |
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WofR_[i] = 0; |
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QofR_[i] = 0; |
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} |
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// Make arrays for Wigner3jm |
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RealType* THRCOF = new RealType[2*lMax_+1]; |
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// Variables for Wigner routine |
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} |
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BOPofR::~BOPofR() { |
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/* |
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std::cerr << "Freeing stuff" << std::endl; |
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/* |
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std::cerr << "Freeing stuff" << std::endl; |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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w3j[std::make_pair(l,m)].clear(); |
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void BOPofR::initializeHistogram() { |
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for (int i = 0; i < nBins_; i++){ |
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RCount_[i] = 0; |
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WofR_[i] = 0; |
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QofR_[i] = 0; |
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} |
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for (int i = 0; i < nBins_; i++){ |
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RCount_[i] = 0; |
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WofR_[i] = 0; |
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QofR_[i] = 0; |
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} |
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} |
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void BOPofR::process() { |
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Molecule* mol; |
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Atom* atom; |
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collectHistogram(q_l, w_hat, distCOM); |
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// printf( "%s %18.10g %18.10g %18.10g %18.10g \n", sd->getType().c_str(),pos[0],pos[1],pos[2],real(w_hat[6])); |
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// printf( "%s %18.10g %18.10g %18.10g %18.10g \n", sd->getType().c_str(),pos[0],pos[1],pos[2],real(w_hat[6])); |
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} |
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} |
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writeOrderParameter(); |
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} |
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void BOPofR::collectHistogram(std::vector<RealType> q, |
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std::vector<ComplexType> what, RealType distCOM) { |
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IcosahedralOfR::IcosahedralOfR(SimInfo* info, const std::string& filename, |
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const std::string& sele, double rCut, |
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int nbins, RealType len) : BOPofR(info, |
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filename, |
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sele, rCut, |
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nbins, len) { |
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} |
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void IcosahedralOfR::collectHistogram(std::vector<RealType> q, |
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std::vector<ComplexType> what, |
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RealType distCOM) { |
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if ( distCOM < len_){ |
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// Figure out where this distance goes... |
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int whichBin = int(distCOM / deltaR_); |
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RCount_[whichBin]++; |
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if(real(what[6]) < -0.15){ |
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WofR_[whichBin]++; |
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WofR_[whichBin]++; |
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} |
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if(q[6] > 0.5){ |
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if(q[6] > 0.5){ |
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QofR_[whichBin]++; |
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} |
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} |
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} |
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} |
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} |
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< |
void BOPofR::writeOrderParameter() { |
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> |
FCCOfR::FCCOfR(SimInfo* info, const std::string& filename, |
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> |
const std::string& sele, double rCut, |
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> |
int nbins, RealType len) : BOPofR(info, filename, sele, rCut, |
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> |
nbins, len) {} |
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> |
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> |
void FCCOfR::collectHistogram(std::vector<RealType> q, |
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> |
std::vector<ComplexType> what, |
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> |
RealType distCOM) { |
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> |
|
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> |
if ( distCOM < len_){ |
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> |
// Figure out where this distance goes... |
| 361 |
> |
int whichBin = int(distCOM / deltaR_); |
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> |
RCount_[whichBin]++; |
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> |
|
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> |
if(real(what[4]) < -0.12){ |
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> |
WofR_[whichBin]++; |
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> |
} |
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> |
} |
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> |
} |
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> |
|
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> |
void IcosahedralOfR::writeOrderParameter() { |
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std::ofstream osq((getOutputFileName() + "qr").c_str()); |
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if (osq.is_open()) { |
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// Normalize by number of frames and write it out: |
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< |
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> |
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for (int i = 0; i < nBins_; ++i) { |
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RealType Rval = (i + 0.5) * deltaR_; |
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osq << Rval; |
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< |
if (RCount_[i] == 0){ |
| 382 |
< |
osq << "\t" << 0; |
| 383 |
< |
osq << "\n"; |
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< |
}else{ |
| 385 |
< |
osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i]; |
| 386 |
< |
osq << "\n"; |
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< |
} |
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> |
if (RCount_[i] == 0){ |
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> |
osq << "\t" << 0; |
| 383 |
> |
osq << "\n"; |
| 384 |
> |
}else{ |
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> |
osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i]; |
| 386 |
> |
osq << "\n"; |
| 387 |
> |
} |
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} |
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< |
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| 389 |
> |
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osq.close(); |
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< |
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| 391 |
> |
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| 392 |
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} else { |
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sprintf(painCave.errMsg, "BOPofR: unable to open %s\n", |
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(getOutputFileName() + "q").c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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< |
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| 398 |
> |
|
| 399 |
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std::ofstream osw((getOutputFileName() + "wr").c_str()); |
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< |
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| 400 |
> |
|
| 401 |
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if (osw.is_open()) { |
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// Normalize by number of frames and write it out: |
| 403 |
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for (int i = 0; i < nBins_; ++i) { |
| 404 |
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RealType Rval = deltaR_ * (i + 0.5); |
| 405 |
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osw << Rval; |
| 406 |
< |
if (RCount_[i] == 0){ |
| 407 |
< |
osw << "\t" << 0; |
| 408 |
< |
osw << "\n"; |
| 409 |
< |
}else{ |
| 410 |
< |
osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i]; |
| 411 |
< |
osw << "\n"; |
| 412 |
< |
} |
| 406 |
> |
if (RCount_[i] == 0){ |
| 407 |
> |
osw << "\t" << 0; |
| 408 |
> |
osw << "\n"; |
| 409 |
> |
}else{ |
| 410 |
> |
osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i]; |
| 411 |
> |
osw << "\n"; |
| 412 |
> |
} |
| 413 |
|
} |
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< |
|
| 414 |
> |
|
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osw.close(); |
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} else { |
| 417 |
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sprintf(painCave.errMsg, "BOPofR: unable to open %s\n", |
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} |
| 423 |
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|
| 424 |
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} |
| 425 |
+ |
void FCCOfR::writeOrderParameter() { |
| 426 |
+ |
|
| 427 |
+ |
std::ofstream osw((getOutputFileName() + "wr").c_str()); |
| 428 |
+ |
|
| 429 |
+ |
if (osw.is_open()) { |
| 430 |
+ |
// Normalize by number of frames and write it out: |
| 431 |
+ |
for (int i = 0; i < nBins_; ++i) { |
| 432 |
+ |
RealType Rval = deltaR_ * (i + 0.5); |
| 433 |
+ |
osw << Rval; |
| 434 |
+ |
if (RCount_[i] == 0){ |
| 435 |
+ |
osw << "\t" << 0; |
| 436 |
+ |
osw << "\n"; |
| 437 |
+ |
}else{ |
| 438 |
+ |
osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i]; |
| 439 |
+ |
osw << "\n"; |
| 440 |
+ |
} |
| 441 |
+ |
} |
| 442 |
+ |
|
| 443 |
+ |
osw.close(); |
| 444 |
+ |
} else { |
| 445 |
+ |
sprintf(painCave.errMsg, "BOPofR: unable to open %s\n", |
| 446 |
+ |
(getOutputFileName() + "w").c_str()); |
| 447 |
+ |
painCave.isFatal = 1; |
| 448 |
+ |
simError(); |
| 449 |
+ |
|
| 450 |
+ |
} |
| 451 |
+ |
|
| 452 |
+ |
} |
| 453 |
|
} |
