| 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 |
< |
* BondOrderParameter.cpp |
| 33 |
< |
* OOPSE-4 |
| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
* |
| 41 |
|
* Created by J. Daniel Gezelter on 09/26/06. |
| 42 |
|
* @author J. Daniel Gezelter |
| 43 |
< |
* @version $Id: BOPofR.cpp,v 1.1 2007-04-11 23:27:20 chuckv Exp $ |
| 43 |
> |
* @version $Id: BOPofR.cpp,v 1.4 2009-11-25 20:01:58 gezelter Exp $ |
| 44 |
|
* |
| 45 |
|
*/ |
| 46 |
|
|
| 51 |
|
#include "utils/NumericConstant.hpp" |
| 52 |
|
|
| 53 |
|
|
| 54 |
< |
namespace oopse { |
| 54 |
> |
namespace OpenMD { |
| 55 |
|
|
| 56 |
|
BOPofR::BOPofR(SimInfo* info, const std::string& filename, const std::string& sele, double rCut, |
| 57 |
|
int nbins, RealType len) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
| 73 |
|
RCount_.resize(nBins_); |
| 74 |
|
WofR_.resize(nBins_); |
| 75 |
|
QofR_.resize(nBins_); |
| 76 |
+ |
|
| 77 |
+ |
for (int i = 0; i < nBins_; i++){ |
| 78 |
+ |
RCount_[i] = 0; |
| 79 |
+ |
WofR_[i] = 0; |
| 80 |
+ |
QofR_[i] = 0; |
| 81 |
+ |
} |
| 82 |
|
|
| 83 |
|
// Make arrays for Wigner3jm |
| 84 |
|
double* THRCOF = new double[2*lMax_+1]; |
| 114 |
|
} |
| 115 |
|
|
| 116 |
|
delete [] THRCOF; |
| 117 |
< |
THRCOF = NULL; |
| 117 |
> |
THRCOF = NULL; |
| 118 |
|
|
| 116 |
– |
|
| 117 |
– |
for (int bin = 0; bin < nBins_; bin++) { |
| 118 |
– |
QofR_[bin].resize(lMax_ + 1); |
| 119 |
– |
WofR_[bin].resize(lMax_ + 1 ); |
| 120 |
– |
RCount_[bin].resize(lMax_ + 1); |
| 121 |
– |
|
| 122 |
– |
for (int l = 0; l <= lMax_; l++) { |
| 123 |
– |
QofR_[bin][l] = 0.0; |
| 124 |
– |
WofR_[bin][l] = 0.0; |
| 125 |
– |
RCount_[bin][l] = 1; |
| 126 |
– |
} |
| 127 |
– |
|
| 128 |
– |
} |
| 129 |
– |
|
| 119 |
|
} |
| 120 |
|
|
| 121 |
|
BOPofR::~BOPofR() { |
| 144 |
|
|
| 145 |
|
|
| 146 |
|
void BOPofR::initalizeHistogram() { |
| 147 |
< |
for (int bin = 0; bin < nBins_; bin++) { |
| 148 |
< |
QofR_[bin].resize(lMax_); |
| 149 |
< |
WofR_[bin].resize(lMax_); |
| 150 |
< |
RCount_[bin].resize(lMax_); |
| 151 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 163 |
< |
QofR_[bin][l] = 0; |
| 164 |
< |
WofR_[bin][l] = 0; |
| 165 |
< |
RCount_[bin][l] = 0; |
| 166 |
< |
} |
| 167 |
< |
} |
| 147 |
> |
for (int i = 0; i < nBins_; i++){ |
| 148 |
> |
RCount_[i] = 0; |
| 149 |
> |
WofR_[i] = 0; |
| 150 |
> |
QofR_[i] = 0; |
| 151 |
> |
} |
| 152 |
|
} |
| 153 |
|
|
| 154 |
|
|
| 305 |
|
} |
| 306 |
|
|
| 307 |
|
collectHistogram(q_l, w_hat, distCOM); |
| 308 |
< |
if(real(w_hat[6]) < -0.1){ |
| 309 |
< |
std::cout << real(w_hat[6]) << pos << std::endl; |
| 310 |
< |
} |
| 308 |
> |
|
| 309 |
> |
// 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])); |
| 310 |
> |
|
| 311 |
|
} |
| 312 |
|
} |
| 313 |
|
|
| 320 |
|
if ( distCOM < len_){ |
| 321 |
|
// Figure out where this distance goes... |
| 322 |
|
int whichBin = distCOM / deltaR_; |
| 323 |
< |
|
| 324 |
< |
|
| 325 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 326 |
< |
RCount_[whichBin][l]++; |
| 343 |
< |
QofR_[whichBin][l]=q[l]; |
| 344 |
< |
WofR_[whichBin][l]=real(what[l]); |
| 323 |
> |
RCount_[whichBin]++; |
| 324 |
> |
|
| 325 |
> |
if(real(what[6]) < -0.15){ |
| 326 |
> |
WofR_[whichBin]++; |
| 327 |
|
} |
| 328 |
< |
|
| 328 |
> |
if(q[6] > 0.5){ |
| 329 |
> |
QofR_[whichBin]++; |
| 330 |
> |
} |
| 331 |
|
} |
| 332 |
|
|
| 333 |
|
} |
| 343 |
|
for (int i = 0; i < nBins_; ++i) { |
| 344 |
|
RealType Rval = (i + 0.5) * deltaR_; |
| 345 |
|
osq << Rval; |
| 346 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 347 |
< |
|
| 348 |
< |
osq << "\t" << (RealType)QofR_[i][l]/(RealType)RCount_[i][l]; |
| 349 |
< |
} |
| 350 |
< |
osq << "\n"; |
| 346 |
> |
if (RCount_[i] == 0){ |
| 347 |
> |
osq << "\t" << 0; |
| 348 |
> |
osq << "\n"; |
| 349 |
> |
}else{ |
| 350 |
> |
osq << "\t" << (RealType)QofR_[i]/(RealType)RCount_[i]; |
| 351 |
> |
osq << "\n"; |
| 352 |
> |
} |
| 353 |
|
} |
| 354 |
|
|
| 355 |
|
osq.close(); |
| 368 |
|
for (int i = 0; i < nBins_; ++i) { |
| 369 |
|
RealType Rval = deltaR_ * (i + 0.5); |
| 370 |
|
osw << Rval; |
| 371 |
< |
for (int l = 0; l <= lMax_; l++) { |
| 372 |
< |
|
| 373 |
< |
osw << "\t" << (RealType)WofR_[i][l]/(RealType)RCount_[i][l]; |
| 374 |
< |
} |
| 375 |
< |
osw << "\n"; |
| 371 |
> |
if (RCount_[i] == 0){ |
| 372 |
> |
osw << "\t" << 0; |
| 373 |
> |
osw << "\n"; |
| 374 |
> |
}else{ |
| 375 |
> |
osw << "\t" << (RealType)WofR_[i]/(RealType)RCount_[i]; |
| 376 |
> |
osw << "\n"; |
| 377 |
> |
} |
| 378 |
|
} |
| 379 |
|
|
| 380 |
|
osw.close(); |
