| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
< |
* BondOrderParameter.cpp |
| 33 |
< |
* OOPSE-4 |
| 34 |
< |
* |
| 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 |
> |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 41 |
|
* Created by J. Daniel Gezelter on 09/26/06. |
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|
* @author J. Daniel Gezelter |
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< |
* @version $Id: BOPofR.cpp,v 1.1 2007-04-11 23:27:20 chuckv Exp $ |
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> |
* @version $Id$ |
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* |
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*/ |
| 46 |
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|
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|
#include "io/DumpReader.hpp" |
| 50 |
|
#include "primitives/Molecule.hpp" |
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|
#include "utils/NumericConstant.hpp" |
| 52 |
+ |
#include "math/Wigner3jm.hpp" |
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+ |
#include "brains/Thermo.hpp" |
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|
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+ |
using namespace MATPACK; |
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+ |
namespace OpenMD { |
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|
|
| 57 |
– |
namespace oopse { |
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– |
|
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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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|
| 75 |
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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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+ |
|
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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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// Make arrays for Wigner3jm |
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< |
double* THRCOF = new double[2*lMax_+1]; |
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> |
RealType* THRCOF = new RealType[2*lMax_+1]; |
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// Variables for Wigner routine |
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< |
double lPass, m1Pass, m2m, m2M; |
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> |
RealType lPass, m1Pass, m2m, m2M; |
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int error, mSize; |
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mSize = 2*lMax_+1; |
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|
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for (int l = 0; l <= lMax_; l++) { |
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< |
lPass = (double)l; |
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> |
lPass = (RealType)l; |
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for (int m1 = -l; m1 <= l; m1++) { |
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< |
m1Pass = (double)m1; |
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> |
m1Pass = (RealType)m1; |
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|
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std::pair<int,int> lm = std::make_pair(l, m1); |
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|
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} |
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|
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// Get Wigner coefficients |
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Wigner3jm(&lPass, &lPass, &lPass, |
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< |
&m1Pass, &m2m, &m2M, |
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THRCOF, &mSize, &error); |
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> |
Wigner3jm(lPass, lPass, lPass, |
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> |
m1Pass, m2m, m2M, |
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> |
THRCOF, mSize, error); |
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|
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m2Min[lm] = (int)floor(m2m); |
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m2Max[lm] = (int)floor(m2M); |
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} |
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|
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delete [] THRCOF; |
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THRCOF = NULL; |
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> |
THRCOF = NULL; |
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|
|
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– |
|
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– |
for (int bin = 0; bin < nBins_; bin++) { |
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– |
QofR_[bin].resize(lMax_ + 1); |
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– |
WofR_[bin].resize(lMax_ + 1 ); |
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– |
RCount_[bin].resize(lMax_ + 1); |
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– |
|
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– |
for (int l = 0; l <= lMax_; l++) { |
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– |
QofR_[bin][l] = 0.0; |
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– |
WofR_[bin][l] = 0.0; |
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– |
RCount_[bin][l] = 1; |
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– |
} |
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– |
|
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– |
} |
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– |
|
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|
} |
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|
|
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|
BOPofR::~BOPofR() { |
| 145 |
|
} |
| 146 |
|
|
| 147 |
|
|
| 148 |
< |
void BOPofR::initalizeHistogram() { |
| 149 |
< |
for (int bin = 0; bin < nBins_; bin++) { |
| 150 |
< |
QofR_[bin].resize(lMax_); |
| 151 |
< |
WofR_[bin].resize(lMax_); |
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< |
RCount_[bin].resize(lMax_); |
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< |
for (int l = 0; l <= lMax_; l++) { |
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< |
QofR_[bin][l] = 0; |
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< |
WofR_[bin][l] = 0; |
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< |
RCount_[bin][l] = 0; |
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< |
} |
| 167 |
< |
} |
| 148 |
> |
void BOPofR::initializeHistogram() { |
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> |
for (int i = 0; i < nBins_; i++){ |
| 150 |
> |
RCount_[i] = 0; |
| 151 |
> |
WofR_[i] = 0; |
| 152 |
> |
QofR_[i] = 0; |
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> |
} |
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|
} |
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|
|
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|
|
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|
RealType costheta; |
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|
RealType phi; |
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|
RealType r; |
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– |
RealType dist; |
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Vector3d rCOM; |
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RealType distCOM; |
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|
Vector3d pos; |
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std::vector<RealType> q2; |
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|
std::vector<ComplexType> w; |
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|
std::vector<ComplexType> w_hat; |
| 194 |
– |
std::map<std::pair<int,int>,ComplexType> QBar; |
| 179 |
|
std::vector<RealType> Q2; |
| 180 |
|
std::vector<RealType> Q; |
| 181 |
|
std::vector<ComplexType> W; |
| 182 |
|
std::vector<ComplexType> W_hat; |
| 183 |
< |
int nBonds, Nbonds; |
| 183 |
> |
int nBonds; |
| 184 |
|
SphericalHarmonic sphericalHarmonic; |
| 185 |
< |
int i, j; |
| 186 |
< |
|
| 185 |
> |
int i; |
| 186 |
> |
|
| 187 |
|
DumpReader reader(info_, dumpFilename_); |
| 188 |
|
int nFrames = reader.getNFrames(); |
| 189 |
|
frameCounter_ = 0; |
| 190 |
|
|
| 191 |
+ |
Thermo thermo(info_); |
| 192 |
+ |
|
| 193 |
|
q_l.resize(lMax_+1); |
| 194 |
|
q2.resize(lMax_+1); |
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|
w.resize(lMax_+1); |
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Q.resize(lMax_+1); |
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W.resize(lMax_+1); |
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|
W_hat.resize(lMax_+1); |
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– |
Nbonds = 0; |
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|
|
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|
for (int istep = 0; istep < nFrames; istep += step_) { |
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|
reader.readFrame(istep); |
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|
frameCounter_++; |
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|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 207 |
< |
CenterOfMass = info_->getCom(); |
| 207 |
> |
CenterOfMass = thermo.getCom(); |
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|
if (evaluator_.isDynamic()) { |
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|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 210 |
|
} |
| 302 |
|
} |
| 303 |
|
} |
| 304 |
|
|
| 305 |
< |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
| 305 |
> |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
| 306 |
|
} |
| 307 |
|
|
| 308 |
|
collectHistogram(q_l, w_hat, distCOM); |
| 309 |
< |
if(real(w_hat[6]) < -0.1){ |
| 310 |
< |
std::cout << real(w_hat[6]) << pos << std::endl; |
| 311 |
< |
} |
| 309 |
> |
|
| 310 |
> |
// 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])); |
| 311 |
> |
|
| 312 |
|
} |
| 313 |
|
} |
| 314 |
|
|
| 320 |
|
|
| 321 |
|
if ( distCOM < len_){ |
| 322 |
|
// Figure out where this distance goes... |
| 323 |
< |
int whichBin = distCOM / deltaR_; |
| 324 |
< |
|
| 325 |
< |
|
| 326 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 327 |
< |
RCount_[whichBin][l]++; |
| 343 |
< |
QofR_[whichBin][l]=q[l]; |
| 344 |
< |
WofR_[whichBin][l]=real(what[l]); |
| 323 |
> |
int whichBin = int(distCOM / deltaR_); |
| 324 |
> |
RCount_[whichBin]++; |
| 325 |
> |
|
| 326 |
> |
if(real(what[6]) < -0.15){ |
| 327 |
> |
WofR_[whichBin]++; |
| 328 |
|
} |
| 329 |
< |
|
| 329 |
> |
if(q[6] > 0.5){ |
| 330 |
> |
QofR_[whichBin]++; |
| 331 |
> |
} |
| 332 |
|
} |
| 333 |
|
|
| 334 |
|
} |
| 344 |
|
for (int i = 0; i < nBins_; ++i) { |
| 345 |
|
RealType Rval = (i + 0.5) * deltaR_; |
| 346 |
|
osq << Rval; |
| 347 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 348 |
< |
|
| 349 |
< |
osq << "\t" << (RealType)QofR_[i][l]/(RealType)RCount_[i][l]; |
| 350 |
< |
} |
| 351 |
< |
osq << "\n"; |
| 347 |
> |
if (RCount_[i] == 0){ |
| 348 |
> |
osq << "\t" << 0; |
| 349 |
> |
osq << "\n"; |
| 350 |
> |
}else{ |
| 351 |
> |
osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i]; |
| 352 |
> |
osq << "\n"; |
| 353 |
> |
} |
| 354 |
|
} |
| 355 |
|
|
| 356 |
|
osq.close(); |
| 369 |
|
for (int i = 0; i < nBins_; ++i) { |
| 370 |
|
RealType Rval = deltaR_ * (i + 0.5); |
| 371 |
|
osw << Rval; |
| 372 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 373 |
< |
|
| 374 |
< |
osw << "\t" << (RealType)WofR_[i][l]/(RealType)RCount_[i][l]; |
| 375 |
< |
} |
| 376 |
< |
osw << "\n"; |
| 372 |
> |
if (RCount_[i] == 0){ |
| 373 |
> |
osw << "\t" << 0; |
| 374 |
> |
osw << "\n"; |
| 375 |
> |
}else{ |
| 376 |
> |
osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i]; |
| 377 |
> |
osw << "\n"; |
| 378 |
> |
} |
| 379 |
|
} |
| 380 |
|
|
| 381 |
|
osw.close(); |
