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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 |
| 10 |
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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 |
| 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 |
< |
* |
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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 |
|
* |
| 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 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
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* |
| 32 |
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* BondOrderParameter.cpp |
| 33 |
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* OOPSE-4 |
| 34 |
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* |
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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 |
> |
* |
| 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). * |
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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 "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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+ |
#include "math/Wigner3jm.hpp" |
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|
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using namespace MATPACK; |
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namespace OpenMD { |
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|
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– |
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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|
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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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|
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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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> |
THRCOF = NULL; |
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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::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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|
|
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< |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
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> |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
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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... |
| 323 |
|
int whichBin = distCOM / deltaR_; |
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< |
|
| 325 |
< |
|
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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++) { |
| 348 |
< |
|
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< |
osq << "\t" << (RealType)QofR_[i][l]/(RealType)RCount_[i][l]; |
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< |
} |
| 351 |
< |
osq << "\n"; |
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> |
if (RCount_[i] == 0){ |
| 348 |
> |
osq << "\t" << 0; |
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> |
osq << "\n"; |
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> |
}else{ |
| 351 |
> |
osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i]; |
| 352 |
> |
osq << "\n"; |
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> |
} |
| 354 |
|
} |
| 355 |
|
|
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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); |
| 371 |
|
osw << Rval; |
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< |
for (int l = 0; l <= lMax_; l++) { |
| 373 |
< |
|
| 374 |
< |
osw << "\t" << (RealType)WofR_[i][l]/(RealType)RCount_[i][l]; |
| 375 |
< |
} |
| 376 |
< |
osw << "\n"; |
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> |
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 |
|
|
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|
osw.close(); |
