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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 |
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* the article in which the program was described (Matthew |
| 13 |
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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," |
| 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 |
|
* |
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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 |
| 13 |
|
* 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). |
| 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). |
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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: BondOrderParameter.cpp,v 1.18 2006-09-26 16:08:44 gezelter Exp $ |
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* @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $ |
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* |
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*/ |
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|
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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BondOrderParameter::BondOrderParameter(SimInfo* info, |
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const std::string& filename, |
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// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
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// use values for MinW_ and MaxW_ that are slightly larger than this: |
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|
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< |
MinW_ = -0.25; |
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< |
MaxW_ = 0.25; |
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> |
MinW_ = -1.1; |
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> |
MaxW_ = 1.1; |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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|
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// Make arrays for Wigner3jm |
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for (int ii = 0; ii < 2*l + 1; ii++){ |
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THRCOF[ii] = 0.0; |
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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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m2Min[lm] = (int)floor(m2m); |
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m2Max[lm] = (int)floor(m2M); |
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|
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< |
for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
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> |
for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) { |
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w3j[lm].push_back(THRCOF[mmm]); |
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} |
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} |
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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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if (atom->getGlobalIndex() != myIndex) { |
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|
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vec = sd->getPos() - atom->getPos(); |
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< |
currentSnapshot_->wrapVector(vec); |
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> |
|
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> |
if (usePeriodicBoundaryConditions_) |
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> |
currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
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// Q_lm = Y_lm(theta(r),phi(r)) |
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} |
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|
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|
|
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– |
for (int l = 0; l <= lMax_; l++) { |
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– |
q_l[l] = 0.0; |
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– |
for(int m = -l; m <= l; m++) { |
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– |
q_l[l] += norm(q[std::make_pair(l,m)]); |
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– |
} |
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– |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
| 268 |
– |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
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– |
} |
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– |
|
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– |
// Find second order invariant Q_l |
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– |
|
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|
for (int l = 0; l <= lMax_; l++) { |
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q2[l] = 0.0; |
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for (int m = -l; m <= l; m++){ |
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+ |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
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|
q2[l] += norm(q[std::make_pair(l,m)]); |
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|
} |
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< |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
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< |
(RealType)(2*l + 1))/(RealType)nBonds; |
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> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
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|
} |
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< |
|
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> |
|
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|
// Find Third Order Invariant W_l |
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|
|
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|
for (int l = 0; l <= lMax_; l++) { |
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w[l] = 0.0; |
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for (int m1 = -l; m1 <= l; m1++) { |
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std::pair<int,int> lm = std::make_pair(l, m1); |
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< |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
| 277 |
> |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
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|
int m2 = m2Min[lm] + mmm; |
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int m3 = -m1-m2; |
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w[l] += w3j[lm][mmm] * q[lm] * |
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Nbonds += nBonds; |
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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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< |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
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> |
QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
| 294 |
|
} |
| 295 |
|
} |
| 296 |
|
} |
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W[l] = 0.0; |
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for (int m1 = -l; m1 <= l; m1++) { |
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std::pair<int,int> lm = std::make_pair(l, m1); |
| 322 |
< |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
| 322 |
> |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
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|
int m2 = m2Min[lm] + mmm; |
| 324 |
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int m3 = -m1-m2; |
| 325 |
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W[l] += w3j[lm][mmm] * QBar[lm] * |
| 344 |
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} else { |
| 345 |
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sprintf( painCave.errMsg, |
| 346 |
|
"q_l value outside reasonable range\n"); |
| 347 |
< |
painCave.severity = OOPSE_ERROR; |
| 347 |
> |
painCave.severity = OPENMD_ERROR; |
| 348 |
|
painCave.isFatal = 1; |
| 349 |
|
simError(); |
| 350 |
|
} |
| 357 |
|
Wcount_[l]++; |
| 358 |
|
} else { |
| 359 |
|
sprintf( painCave.errMsg, |
| 360 |
< |
"Re[w_hat] value outside reasonable range\n"); |
| 361 |
< |
painCave.severity = OOPSE_ERROR; |
| 360 |
> |
"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
| 361 |
> |
painCave.severity = OPENMD_ERROR; |
| 362 |
|
painCave.isFatal = 1; |
| 363 |
|
simError(); |
| 364 |
|
} |
| 385 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 386 |
|
osq << Qval; |
| 387 |
|
for (int l = 0; l <= lMax_; l++) { |
| 388 |
< |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / |
| 389 |
< |
(RealType)Qcount_[l]; |
| 388 |
> |
|
| 389 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
| 390 |
|
} |
| 391 |
|
osq << "\n"; |
| 392 |
|
} |
| 407 |
|
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 408 |
|
osw << "# \n"; |
| 409 |
|
for (int l = 0; l <= lMax_; l++) { |
| 410 |
< |
osw << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
| 410 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
| 411 |
|
} |
| 412 |
|
// Normalize by number of frames and write it out: |
| 413 |
|
for (int i = 0; i < nBins_; ++i) { |
| 414 |
|
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
| 415 |
|
osw << Wval; |
| 416 |
|
for (int l = 0; l <= lMax_; l++) { |
| 417 |
< |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / |
| 418 |
< |
(RealType)Wcount_[l]; |
| 417 |
> |
|
| 418 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
| 419 |
|
} |
| 420 |
|
osw << "\n"; |
| 421 |
|
} |
