| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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, 234107 (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 |
*/ |
| 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 |
using namespace MATPACK; |
| 55 |
namespace OpenMD { |
| 56 |
|
| 57 |
BondOrderParameter::BondOrderParameter(SimInfo* info, |
| 58 |
const std::string& filename, |
| 59 |
const std::string& sele, |
| 60 |
double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
| 61 |
|
| 62 |
setOutputName(getPrefix(filename) + ".bo"); |
| 63 |
|
| 64 |
evaluator_.loadScriptString(sele); |
| 65 |
if (!evaluator_.isDynamic()) { |
| 66 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 67 |
} |
| 68 |
|
| 69 |
// Set up cutoff radius and order of the Legendre Polynomial: |
| 70 |
|
| 71 |
rCut_ = rCut; |
| 72 |
nBins_ = nbins; |
| 73 |
Qcount_.resize(lMax_+1); |
| 74 |
Wcount_.resize(lMax_+1); |
| 75 |
|
| 76 |
// Q can take values from 0 to 1 |
| 77 |
|
| 78 |
MinQ_ = 0.0; |
| 79 |
MaxQ_ = 1.1; |
| 80 |
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
| 81 |
|
| 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_ = -1.1; |
| 86 |
MaxW_ = 1.1; |
| 87 |
deltaW_ = (MaxW_ - MinW_) / nbins; |
| 88 |
|
| 89 |
// Make arrays for Wigner3jm |
| 90 |
RealType* THRCOF = new RealType[2*lMax_+1]; |
| 91 |
// Variables for Wigner routine |
| 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 = (RealType)l; |
| 98 |
for (int m1 = -l; m1 <= l; m1++) { |
| 99 |
m1Pass = (RealType)m1; |
| 100 |
|
| 101 |
std::pair<int,int> lm = std::make_pair(l, m1); |
| 102 |
|
| 103 |
// Zero work array |
| 104 |
for (int ii = 0; ii < 2*l + 1; ii++){ |
| 105 |
THRCOF[ii] = 0.0; |
| 106 |
} |
| 107 |
|
| 108 |
// Get Wigner coefficients |
| 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++) { |
| 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 |
|
| 138 |
void BondOrderParameter::initializeHistogram() { |
| 139 |
for (int bin = 0; bin < nBins_; bin++) { |
| 140 |
for (int l = 0; l <= lMax_; l++) { |
| 141 |
Q_histogram_[std::make_pair(bin,l)] = 0; |
| 142 |
W_histogram_[std::make_pair(bin,l)] = 0; |
| 143 |
} |
| 144 |
} |
| 145 |
} |
| 146 |
|
| 147 |
void BondOrderParameter::process() { |
| 148 |
Molecule* mol; |
| 149 |
Atom* atom; |
| 150 |
RigidBody* rb; |
| 151 |
int myIndex; |
| 152 |
SimInfo::MoleculeIterator mi; |
| 153 |
Molecule::RigidBodyIterator rbIter; |
| 154 |
Molecule::AtomIterator ai; |
| 155 |
StuntDouble* sd; |
| 156 |
Vector3d vec; |
| 157 |
RealType costheta; |
| 158 |
RealType phi; |
| 159 |
RealType r; |
| 160 |
std::map<std::pair<int,int>,ComplexType> q; |
| 161 |
std::vector<RealType> q_l; |
| 162 |
std::vector<RealType> q2; |
| 163 |
std::vector<ComplexType> w; |
| 164 |
std::vector<ComplexType> w_hat; |
| 165 |
std::map<std::pair<int,int>,ComplexType> QBar; |
| 166 |
std::vector<RealType> Q2; |
| 167 |
std::vector<RealType> Q; |
| 168 |
std::vector<ComplexType> W; |
| 169 |
std::vector<ComplexType> W_hat; |
| 170 |
int nBonds, Nbonds; |
| 171 |
SphericalHarmonic sphericalHarmonic; |
| 172 |
int i; |
| 173 |
|
| 174 |
DumpReader reader(info_, dumpFilename_); |
| 175 |
int nFrames = reader.getNFrames(); |
| 176 |
frameCounter_ = 0; |
| 177 |
|
| 178 |
q_l.resize(lMax_+1); |
| 179 |
q2.resize(lMax_+1); |
| 180 |
w.resize(lMax_+1); |
| 181 |
w_hat.resize(lMax_+1); |
| 182 |
|
| 183 |
Q2.resize(lMax_+1); |
| 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); |
| 191 |
frameCounter_++; |
| 192 |
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 193 |
|
| 194 |
if (evaluator_.isDynamic()) { |
| 195 |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 196 |
} |
| 197 |
|
| 198 |
// update the positions of atoms which belong to the rigidbodies |
| 199 |
|
| 200 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 201 |
mol = info_->nextMolecule(mi)) { |
| 202 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 203 |
rb = mol->nextRigidBody(rbIter)) { |
| 204 |
rb->updateAtoms(); |
| 205 |
} |
| 206 |
} |
| 207 |
|
| 208 |
// outer loop is over the selected StuntDoubles: |
| 209 |
|
| 210 |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 211 |
sd = seleMan_.nextSelected(i)) { |
| 212 |
|
| 213 |
myIndex = sd->getGlobalIndex(); |
| 214 |
nBonds = 0; |
| 215 |
|
| 216 |
for (int l = 0; l <= lMax_; l++) { |
| 217 |
for (int m = -l; m <= l; m++) { |
| 218 |
q[std::make_pair(l,m)] = 0.0; |
| 219 |
} |
| 220 |
} |
| 221 |
|
| 222 |
// inner loop is over all other atoms in the system: |
| 223 |
|
| 224 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 225 |
mol = info_->nextMolecule(mi)) { |
| 226 |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 227 |
atom = mol->nextAtom(ai)) { |
| 228 |
|
| 229 |
if (atom->getGlobalIndex() != myIndex) { |
| 230 |
|
| 231 |
vec = sd->getPos() - atom->getPos(); |
| 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)) |
| 238 |
// The spherical harmonics are wrt any arbitrary coordinate |
| 239 |
// system, we choose standard spherical coordinates |
| 240 |
|
| 241 |
r = vec.length(); |
| 242 |
|
| 243 |
// Check to see if neighbor is in bond cutoff |
| 244 |
|
| 245 |
if (r < rCut_) { |
| 246 |
costheta = vec.z() / r; |
| 247 |
phi = atan2(vec.y(), vec.x()); |
| 248 |
|
| 249 |
for (int l = 0; l <= lMax_; l++) { |
| 250 |
sphericalHarmonic.setL(l); |
| 251 |
for(int m = -l; m <= l; m++){ |
| 252 |
sphericalHarmonic.setM(m); |
| 253 |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
| 254 |
} |
| 255 |
} |
| 256 |
nBonds++; |
| 257 |
} |
| 258 |
} |
| 259 |
} |
| 260 |
} |
| 261 |
|
| 262 |
|
| 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 / (RealType)(2*l + 1)); |
| 270 |
} |
| 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++) { |
| 279 |
int m2 = m2Min[lm] + mmm; |
| 280 |
int m3 = -m1-m2; |
| 281 |
w[l] += w3j[lm][mmm] * q[lm] * |
| 282 |
q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
| 283 |
} |
| 284 |
} |
| 285 |
|
| 286 |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
| 287 |
} |
| 288 |
|
| 289 |
collectHistogram(q_l, w_hat); |
| 290 |
|
| 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)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
| 295 |
} |
| 296 |
} |
| 297 |
} |
| 298 |
} |
| 299 |
|
| 300 |
// Normalize Qbar2 |
| 301 |
for (int l = 0; l <= lMax_; l++) { |
| 302 |
for (int m = -l; m <= l; m++){ |
| 303 |
QBar[std::make_pair(l,m)] /= Nbonds; |
| 304 |
} |
| 305 |
} |
| 306 |
|
| 307 |
// Find second order invariant Q_l |
| 308 |
|
| 309 |
for (int l = 0; l <= lMax_; l++) { |
| 310 |
Q2[l] = 0.0; |
| 311 |
for (int m = -l; m <= l; m++){ |
| 312 |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
| 313 |
} |
| 314 |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 315 |
} |
| 316 |
|
| 317 |
// Find Third Order Invariant W_l |
| 318 |
|
| 319 |
for (int l = 0; l <= lMax_; l++) { |
| 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++) { |
| 324 |
int m2 = m2Min[lm] + mmm; |
| 325 |
int m3 = -m1-m2; |
| 326 |
W[l] += w3j[lm][mmm] * QBar[lm] * |
| 327 |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
| 328 |
} |
| 329 |
} |
| 330 |
|
| 331 |
W_hat[l] = W[l] / pow(Q2[l], RealType(1.5)); |
| 332 |
} |
| 333 |
|
| 334 |
writeOrderParameter(Q, W_hat); |
| 335 |
} |
| 336 |
|
| 337 |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
| 338 |
std::vector<ComplexType> what) { |
| 339 |
|
| 340 |
for (int l = 0; l <= lMax_; l++) { |
| 341 |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
| 342 |
int qbin = int((q[l] - MinQ_) / deltaQ_); |
| 343 |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
| 344 |
Qcount_[l]++; |
| 345 |
} else { |
| 346 |
sprintf( painCave.errMsg, |
| 347 |
"q_l value outside reasonable range\n"); |
| 348 |
painCave.severity = OPENMD_ERROR; |
| 349 |
painCave.isFatal = 1; |
| 350 |
simError(); |
| 351 |
} |
| 352 |
} |
| 353 |
|
| 354 |
for (int l = 0; l <= lMax_; l++) { |
| 355 |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
| 356 |
int wbin = int((real(what[l]) - MinW_) / deltaW_); |
| 357 |
W_histogram_[std::make_pair(wbin,l)] += 1; |
| 358 |
Wcount_[l]++; |
| 359 |
} else { |
| 360 |
sprintf( painCave.errMsg, |
| 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 |
} |
| 366 |
} |
| 367 |
|
| 368 |
} |
| 369 |
|
| 370 |
|
| 371 |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
| 372 |
std::vector<ComplexType> What) { |
| 373 |
|
| 374 |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
| 375 |
|
| 376 |
if (osq.is_open()) { |
| 377 |
|
| 378 |
osq << "# Bond Order Parameters\n"; |
| 379 |
osq << "# selection: (" << selectionScript_ << ")\n"; |
| 380 |
osq << "# \n"; |
| 381 |
for (int l = 0; l <= lMax_; l++) { |
| 382 |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
| 383 |
} |
| 384 |
// Normalize by number of frames and write it out: |
| 385 |
for (int i = 0; i < nBins_; ++i) { |
| 386 |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 387 |
osq << Qval; |
| 388 |
for (int l = 0; l <= lMax_; l++) { |
| 389 |
|
| 390 |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
| 391 |
} |
| 392 |
osq << "\n"; |
| 393 |
} |
| 394 |
|
| 395 |
osq.close(); |
| 396 |
|
| 397 |
} else { |
| 398 |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 399 |
(getOutputFileName() + "q").c_str()); |
| 400 |
painCave.isFatal = 1; |
| 401 |
simError(); |
| 402 |
} |
| 403 |
|
| 404 |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
| 405 |
|
| 406 |
if (osw.is_open()) { |
| 407 |
osw << "# Bond Order Parameters\n"; |
| 408 |
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 409 |
osw << "# \n"; |
| 410 |
for (int l = 0; l <= lMax_; l++) { |
| 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 |
|
| 419 |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
| 420 |
} |
| 421 |
osw << "\n"; |
| 422 |
} |
| 423 |
|
| 424 |
osw.close(); |
| 425 |
} else { |
| 426 |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 427 |
(getOutputFileName() + "w").c_str()); |
| 428 |
painCave.isFatal = 1; |
| 429 |
simError(); |
| 430 |
} |
| 431 |
|
| 432 |
} |
| 433 |
} |
