| 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. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 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] 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. |
| 42 |
+ |
* @author J. Daniel Gezelter |
| 43 |
+ |
* @version $Id$ |
| 44 |
+ |
* |
| 45 |
|
*/ |
| 41 |
– |
|
| 42 |
– |
|
| 43 |
– |
/* Creates orientational bond order parameters as outlined by |
| 44 |
– |
* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti |
| 45 |
– |
* Phys Rev B, 28,784,1983 |
| 46 |
– |
* |
| 47 |
– |
*/ |
| 46 |
|
|
| 47 |
|
#include "applications/staticProps/BondOrderParameter.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
#include "io/DumpReader.hpp" |
| 50 |
|
#include "primitives/Molecule.hpp" |
| 51 |
|
#include "utils/NumericConstant.hpp" |
| 52 |
+ |
#include "math/Wigner3jm.hpp" |
| 53 |
|
|
| 54 |
< |
namespace oopse { |
| 54 |
> |
using namespace MATPACK; |
| 55 |
> |
namespace OpenMD { |
| 56 |
|
|
| 57 |
|
BondOrderParameter::BondOrderParameter(SimInfo* info, |
| 58 |
|
const std::string& filename, |
| 82 |
|
// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
| 83 |
|
// use values for MinW_ and MaxW_ that are slightly larger than this: |
| 84 |
|
|
| 85 |
< |
MinW_ = -0.25; |
| 86 |
< |
MaxW_ = 0.25; |
| 85 |
> |
MinW_ = -1.1; |
| 86 |
> |
MaxW_ = 1.1; |
| 87 |
|
deltaW_ = (MaxW_ - MinW_) / nbins; |
| 88 |
|
|
| 89 |
|
// Make arrays for Wigner3jm |
| 90 |
< |
double* THRCOF = new double[2*lMax_+1]; |
| 90 |
> |
RealType* THRCOF = new RealType[2*lMax_+1]; |
| 91 |
|
// Variables for Wigner routine |
| 92 |
< |
double lPass, m1Pass, m2m, m2M; |
| 92 |
> |
RealType lPass, m1Pass, m2m, m2M; |
| 93 |
|
int error, mSize; |
| 94 |
|
mSize = 2*lMax_+1; |
| 95 |
|
|
| 96 |
|
for (int l = 0; l <= lMax_; l++) { |
| 97 |
< |
lPass = (double)l; |
| 97 |
> |
lPass = (RealType)l; |
| 98 |
|
for (int m1 = -l; m1 <= l; m1++) { |
| 99 |
< |
m1Pass = (double)m1; |
| 99 |
> |
m1Pass = (RealType)m1; |
| 100 |
|
|
| 101 |
|
std::pair<int,int> lm = std::make_pair(l, m1); |
| 102 |
|
|
| 104 |
|
for (int ii = 0; ii < 2*l + 1; ii++){ |
| 105 |
|
THRCOF[ii] = 0.0; |
| 106 |
|
} |
| 107 |
< |
|
| 107 |
> |
|
| 108 |
|
// Get Wigner coefficients |
| 109 |
< |
Wigner3jm(&lPass, &lPass, &lPass, |
| 110 |
< |
&m1Pass, &m2m, &m2M, |
| 111 |
< |
THRCOF, &mSize, &error); |
| 109 |
> |
Wigner3jm(lPass, lPass, lPass, |
| 110 |
> |
m1Pass, m2m, m2M, |
| 111 |
> |
THRCOF, mSize, error); |
| 112 |
|
|
| 113 |
|
m2Min[lm] = (int)floor(m2m); |
| 114 |
|
m2Max[lm] = (int)floor(m2M); |
| 115 |
|
|
| 116 |
< |
for (int mmm = 0; mmm < (int)(m2M - m2m); mmm++) { |
| 116 |
> |
for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) { |
| 117 |
|
w3j[lm].push_back(THRCOF[mmm]); |
| 118 |
|
} |
| 119 |
|
} |
| 120 |
|
} |
| 121 |
+ |
delete [] THRCOF; |
| 122 |
+ |
THRCOF = NULL; |
| 123 |
|
} |
| 124 |
|
|
| 125 |
|
BondOrderParameter::~BondOrderParameter() { |
| 126 |
|
Q_histogram_.clear(); |
| 127 |
|
W_histogram_.clear(); |
| 128 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 129 |
+ |
for (int m = -l; m <= l; m++) { |
| 130 |
+ |
w3j[std::make_pair(l,m)].clear(); |
| 131 |
+ |
} |
| 132 |
+ |
} |
| 133 |
+ |
w3j.clear(); |
| 134 |
+ |
m2Min.clear(); |
| 135 |
+ |
m2Max.clear(); |
| 136 |
|
} |
| 137 |
< |
|
| 137 |
> |
|
| 138 |
|
void BondOrderParameter::initalizeHistogram() { |
| 139 |
|
for (int bin = 0; bin < nBins_; bin++) { |
| 140 |
|
for (int l = 0; l <= lMax_; l++) { |
| 157 |
|
RealType costheta; |
| 158 |
|
RealType phi; |
| 159 |
|
RealType r; |
| 150 |
– |
RealType dist; |
| 160 |
|
std::map<std::pair<int,int>,ComplexType> q; |
| 161 |
|
std::vector<RealType> q_l; |
| 162 |
|
std::vector<RealType> q2; |
| 169 |
|
std::vector<ComplexType> W_hat; |
| 170 |
|
int nBonds, Nbonds; |
| 171 |
|
SphericalHarmonic sphericalHarmonic; |
| 172 |
< |
int i, j; |
| 172 |
> |
int i; |
| 173 |
|
|
| 174 |
|
DumpReader reader(info_, dumpFilename_); |
| 175 |
|
int nFrames = reader.getNFrames(); |
| 184 |
|
Q.resize(lMax_+1); |
| 185 |
|
W.resize(lMax_+1); |
| 186 |
|
W_hat.resize(lMax_+1); |
| 187 |
+ |
Nbonds = 0; |
| 188 |
|
|
| 189 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
| 190 |
|
reader.readFrame(istep); |
| 229 |
|
if (atom->getGlobalIndex() != myIndex) { |
| 230 |
|
|
| 231 |
|
vec = sd->getPos() - atom->getPos(); |
| 232 |
< |
currentSnapshot_->wrapVector(vec); |
| 232 |
> |
|
| 233 |
> |
if (usePeriodicBoundaryConditions_) |
| 234 |
> |
currentSnapshot_->wrapVector(vec); |
| 235 |
|
|
| 236 |
|
// Calculate "bonds" and build Q_lm(r) where |
| 237 |
|
// Q_lm = Y_lm(theta(r),phi(r)) |
| 260 |
|
} |
| 261 |
|
|
| 262 |
|
|
| 251 |
– |
for (int l = 0; l <= lMax_; l++) { |
| 252 |
– |
q_l[l] = 0.0; |
| 253 |
– |
for(int m = -l; m <= l; m++) { |
| 254 |
– |
q_l[l] += norm(q[std::make_pair(l,m)]); |
| 255 |
– |
} |
| 256 |
– |
q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
| 257 |
– |
q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
| 258 |
– |
} |
| 259 |
– |
|
| 260 |
– |
// Find second order invariant Q_l |
| 261 |
– |
|
| 263 |
|
for (int l = 0; l <= lMax_; l++) { |
| 264 |
|
q2[l] = 0.0; |
| 265 |
|
for (int m = -l; m <= l; m++){ |
| 266 |
+ |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
| 267 |
|
q2[l] += norm(q[std::make_pair(l,m)]); |
| 268 |
|
} |
| 269 |
< |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / |
| 268 |
< |
(RealType)(2*l + 1))/(RealType)nBonds; |
| 269 |
> |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 270 |
|
} |
| 271 |
< |
|
| 271 |
> |
|
| 272 |
|
// Find Third Order Invariant W_l |
| 273 |
|
|
| 274 |
|
for (int l = 0; l <= lMax_; l++) { |
| 275 |
|
w[l] = 0.0; |
| 276 |
|
for (int m1 = -l; m1 <= l; m1++) { |
| 277 |
|
std::pair<int,int> lm = std::make_pair(l, m1); |
| 278 |
< |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
| 278 |
> |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
| 279 |
|
int m2 = m2Min[lm] + mmm; |
| 280 |
|
int m3 = -m1-m2; |
| 281 |
|
w[l] += w3j[lm][mmm] * q[lm] * |
| 283 |
|
} |
| 284 |
|
} |
| 285 |
|
|
| 286 |
< |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
| 286 |
> |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
| 287 |
|
} |
| 288 |
|
|
| 289 |
|
collectHistogram(q_l, w_hat); |
| 291 |
|
Nbonds += nBonds; |
| 292 |
|
for (int l = 0; l <= lMax_; l++) { |
| 293 |
|
for (int m = -l; m <= l; m++) { |
| 294 |
< |
QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
| 294 |
> |
QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
| 295 |
|
} |
| 296 |
|
} |
| 297 |
|
} |
| 320 |
|
W[l] = 0.0; |
| 321 |
|
for (int m1 = -l; m1 <= l; m1++) { |
| 322 |
|
std::pair<int,int> lm = std::make_pair(l, m1); |
| 323 |
< |
for (int mmm = 0; mmm < (m2Max[lm] - m2Min[lm]); mmm++) { |
| 323 |
> |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
| 324 |
|
int m2 = m2Min[lm] + mmm; |
| 325 |
|
int m3 = -m1-m2; |
| 326 |
|
W[l] += w3j[lm][mmm] * QBar[lm] * |
| 328 |
|
} |
| 329 |
|
} |
| 330 |
|
|
| 331 |
< |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
| 331 |
> |
W_hat[l] = W[l] / pow(Q2[l], RealType(1.5)); |
| 332 |
|
} |
| 333 |
|
|
| 334 |
|
writeOrderParameter(Q, W_hat); |
| 345 |
|
} else { |
| 346 |
|
sprintf( painCave.errMsg, |
| 347 |
|
"q_l value outside reasonable range\n"); |
| 348 |
< |
painCave.severity = OOPSE_ERROR; |
| 348 |
> |
painCave.severity = OPENMD_ERROR; |
| 349 |
|
painCave.isFatal = 1; |
| 350 |
|
simError(); |
| 351 |
|
} |
| 358 |
|
Wcount_[l]++; |
| 359 |
|
} else { |
| 360 |
|
sprintf( painCave.errMsg, |
| 361 |
< |
"Re[w_hat] value outside reasonable range\n"); |
| 362 |
< |
painCave.severity = OOPSE_ERROR; |
| 361 |
> |
"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
| 362 |
> |
painCave.severity = OPENMD_ERROR; |
| 363 |
|
painCave.isFatal = 1; |
| 364 |
|
simError(); |
| 365 |
|
} |
| 386 |
|
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 387 |
|
osq << Qval; |
| 388 |
|
for (int l = 0; l <= lMax_; l++) { |
| 389 |
< |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
| 389 |
> |
|
| 390 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
| 391 |
|
} |
| 392 |
|
osq << "\n"; |
| 393 |
|
} |
| 408 |
|
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 409 |
|
osw << "# \n"; |
| 410 |
|
for (int l = 0; l <= lMax_; l++) { |
| 411 |
< |
osw << "# <W_" << l << ">: " << real(What[l]) << "\n"; |
| 411 |
> |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
| 412 |
|
} |
| 413 |
|
// Normalize by number of frames and write it out: |
| 414 |
|
for (int i = 0; i < nBins_; ++i) { |
| 415 |
|
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
| 416 |
|
osw << Wval; |
| 417 |
|
for (int l = 0; l <= lMax_; l++) { |
| 418 |
< |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)] / (RealType)Wcount_[l]; |
| 418 |
> |
|
| 419 |
> |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
| 420 |
|
} |
| 421 |
|
osw << "\n"; |
| 422 |
|
} |
