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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
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< |
* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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< |
* 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 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
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|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
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* distribution. |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* BondOrderParameter.cpp |
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* OOPSE-4 |
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> |
* 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 |
> |
* |
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> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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> |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
> |
* [4] Vardeman & Gezelter, in progress (2009). |
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* |
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* 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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*/ |
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|
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#include "utils/NumericConstant.hpp" |
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|
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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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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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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} |
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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() { |
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|
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|
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void BOPofR::initalizeHistogram() { |
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< |
for (int bin = 0; bin < nBins_; bin++) { |
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< |
QofR_[bin].resize(lMax_); |
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< |
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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< |
} |
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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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|
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|
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|
} |
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|
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|
collectHistogram(q_l, w_hat, distCOM); |
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< |
if(real(w_hat[6]) < -0.1){ |
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< |
std::cout << real(w_hat[6]) << pos << std::endl; |
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} |
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> |
|
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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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|
} |
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|
|
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|
if ( distCOM < len_){ |
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// Figure out where this distance goes... |
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|
int whichBin = distCOM / deltaR_; |
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< |
|
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< |
|
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< |
for (int l = 0; l <= lMax_; l++) { |
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< |
RCount_[whichBin][l]++; |
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< |
QofR_[whichBin][l]=q[l]; |
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< |
WofR_[whichBin][l]=real(what[l]); |
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> |
RCount_[whichBin]++; |
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> |
|
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> |
if(real(what[6]) < -0.15){ |
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> |
WofR_[whichBin]++; |
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|
} |
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< |
|
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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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|
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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< |
for (int l = 0; l <= lMax_; l++) { |
| 347 |
< |
|
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< |
osq << "\t" << (RealType)QofR_[i][l]/(RealType)RCount_[i][l]; |
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< |
} |
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< |
osq << "\n"; |
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> |
if (RCount_[i] == 0){ |
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> |
osq << "\t" << 0; |
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> |
osq << "\n"; |
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> |
}else{ |
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> |
osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i]; |
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> |
osq << "\n"; |
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> |
} |
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|
} |
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|
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|
osq.close(); |
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|
for (int i = 0; i < nBins_; ++i) { |
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|
RealType Rval = deltaR_ * (i + 0.5); |
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|
osw << Rval; |
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< |
for (int l = 0; l <= lMax_; l++) { |
| 372 |
< |
|
| 373 |
< |
osw << "\t" << (RealType)WofR_[i][l]/(RealType)RCount_[i][l]; |
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< |
} |
| 375 |
< |
osw << "\n"; |
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> |
if (RCount_[i] == 0){ |
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> |
osw << "\t" << 0; |
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> |
osw << "\n"; |
| 374 |
> |
}else{ |
| 375 |
> |
osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i]; |
| 376 |
> |
osw << "\n"; |
| 377 |
> |
} |
| 378 |
|
} |
| 379 |
|
|
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|
osw.close(); |
