| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
+ |
* |
| 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" |
| 54 |
– |
#include "math/SphericalHarmonic.hpp" |
| 52 |
|
|
| 53 |
< |
namespace oopse { |
| 53 |
> |
namespace OpenMD { |
| 54 |
|
|
| 55 |
|
BondOrderParameter::BondOrderParameter(SimInfo* info, |
| 56 |
|
const std::string& filename, |
| 57 |
|
const std::string& sele, |
| 58 |
< |
double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
| 58 |
> |
double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
| 59 |
|
|
| 60 |
|
setOutputName(getPrefix(filename) + ".bo"); |
| 61 |
|
|
| 66 |
|
|
| 67 |
|
// Set up cutoff radius and order of the Legendre Polynomial: |
| 68 |
|
|
| 72 |
– |
lNumber_ = lNumber; |
| 69 |
|
rCut_ = rCut; |
| 70 |
< |
mSize_ = 2*lNumber_+1; |
| 70 |
> |
nBins_ = nbins; |
| 71 |
> |
Qcount_.resize(lMax_+1); |
| 72 |
> |
Wcount_.resize(lMax_+1); |
| 73 |
|
|
| 74 |
|
// Q can take values from 0 to 1 |
| 75 |
|
|
| 76 |
|
MinQ_ = 0.0; |
| 77 |
< |
MaxQ_ = 3.0; |
| 77 |
> |
MaxQ_ = 1.1; |
| 78 |
|
deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
| 81 |
– |
Q_histogram_.resize(nbins); |
| 79 |
|
|
| 80 |
|
// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
| 81 |
|
// use values for MinW_ and MaxW_ that are slightly larger than this: |
| 82 |
|
|
| 83 |
< |
MinW_ = -0.18; |
| 84 |
< |
MaxW_ = 0.18; |
| 83 |
> |
MinW_ = -1.1; |
| 84 |
> |
MaxW_ = 1.1; |
| 85 |
|
deltaW_ = (MaxW_ - MinW_) / nbins; |
| 89 |
– |
W_histogram_.resize(nbins); |
| 86 |
|
|
| 87 |
< |
} |
| 87 |
> |
// Make arrays for Wigner3jm |
| 88 |
> |
double* THRCOF = new double[2*lMax_+1]; |
| 89 |
> |
// Variables for Wigner routine |
| 90 |
> |
double lPass, m1Pass, m2m, m2M; |
| 91 |
> |
int error, mSize; |
| 92 |
> |
mSize = 2*lMax_+1; |
| 93 |
|
|
| 94 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 95 |
+ |
lPass = (double)l; |
| 96 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
| 97 |
+ |
m1Pass = (double)m1; |
| 98 |
+ |
|
| 99 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
| 100 |
+ |
|
| 101 |
+ |
// Zero work array |
| 102 |
+ |
for (int ii = 0; ii < 2*l + 1; ii++){ |
| 103 |
+ |
THRCOF[ii] = 0.0; |
| 104 |
+ |
} |
| 105 |
+ |
|
| 106 |
+ |
// Get Wigner coefficients |
| 107 |
+ |
Wigner3jm(&lPass, &lPass, &lPass, |
| 108 |
+ |
&m1Pass, &m2m, &m2M, |
| 109 |
+ |
THRCOF, &mSize, &error); |
| 110 |
+ |
|
| 111 |
+ |
m2Min[lm] = (int)floor(m2m); |
| 112 |
+ |
m2Max[lm] = (int)floor(m2M); |
| 113 |
+ |
|
| 114 |
+ |
for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) { |
| 115 |
+ |
w3j[lm].push_back(THRCOF[mmm]); |
| 116 |
+ |
} |
| 117 |
+ |
} |
| 118 |
+ |
} |
| 119 |
+ |
delete [] THRCOF; |
| 120 |
+ |
THRCOF = NULL; |
| 121 |
+ |
} |
| 122 |
+ |
|
| 123 |
|
BondOrderParameter::~BondOrderParameter() { |
| 124 |
|
Q_histogram_.clear(); |
| 125 |
|
W_histogram_.clear(); |
| 126 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 127 |
+ |
for (int m = -l; m <= l; m++) { |
| 128 |
+ |
w3j[std::make_pair(l,m)].clear(); |
| 129 |
+ |
} |
| 130 |
+ |
} |
| 131 |
+ |
w3j.clear(); |
| 132 |
+ |
m2Min.clear(); |
| 133 |
+ |
m2Max.clear(); |
| 134 |
|
} |
| 135 |
< |
|
| 135 |
> |
|
| 136 |
|
void BondOrderParameter::initalizeHistogram() { |
| 137 |
< |
std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
| 138 |
< |
std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
| 137 |
> |
for (int bin = 0; bin < nBins_; bin++) { |
| 138 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 139 |
> |
Q_histogram_[std::make_pair(bin,l)] = 0; |
| 140 |
> |
W_histogram_[std::make_pair(bin,l)] = 0; |
| 141 |
> |
} |
| 142 |
> |
} |
| 143 |
|
} |
| 144 |
|
|
| 145 |
|
void BondOrderParameter::process() { |
| 156 |
|
RealType phi; |
| 157 |
|
RealType r; |
| 158 |
|
RealType dist; |
| 159 |
< |
std::map<int,ComplexType> q_lm; |
| 160 |
< |
std::map<int,ComplexType> QBar_lm; |
| 161 |
< |
RealType QSq_l; |
| 162 |
< |
RealType Q_l; |
| 163 |
< |
ComplexType W_l; |
| 164 |
< |
ComplexType W_l_hat; |
| 159 |
> |
std::map<std::pair<int,int>,ComplexType> q; |
| 160 |
> |
std::vector<RealType> q_l; |
| 161 |
> |
std::vector<RealType> q2; |
| 162 |
> |
std::vector<ComplexType> w; |
| 163 |
> |
std::vector<ComplexType> w_hat; |
| 164 |
> |
std::map<std::pair<int,int>,ComplexType> QBar; |
| 165 |
> |
std::vector<RealType> Q2; |
| 166 |
> |
std::vector<RealType> Q; |
| 167 |
> |
std::vector<ComplexType> W; |
| 168 |
> |
std::vector<ComplexType> W_hat; |
| 169 |
|
int nBonds, Nbonds; |
| 170 |
|
SphericalHarmonic sphericalHarmonic; |
| 171 |
|
int i, j; |
| 126 |
– |
// Make arrays for Wigner3jm |
| 127 |
– |
double* THRCOF = new double[mSize_]; |
| 128 |
– |
// Variables for Wigner routine |
| 129 |
– |
double l_ = (double)lNumber_; |
| 130 |
– |
double m1Pass, m2Min, m2Max; |
| 131 |
– |
int error, m1, m2, m3; |
| 172 |
|
|
| 133 |
– |
// Set the l for the spherical harmonic, it doesn't change |
| 134 |
– |
sphericalHarmonic.setL(lNumber_); |
| 135 |
– |
|
| 173 |
|
DumpReader reader(info_, dumpFilename_); |
| 174 |
|
int nFrames = reader.getNFrames(); |
| 175 |
|
frameCounter_ = 0; |
| 176 |
|
|
| 177 |
+ |
q_l.resize(lMax_+1); |
| 178 |
+ |
q2.resize(lMax_+1); |
| 179 |
+ |
w.resize(lMax_+1); |
| 180 |
+ |
w_hat.resize(lMax_+1); |
| 181 |
+ |
|
| 182 |
+ |
Q2.resize(lMax_+1); |
| 183 |
+ |
Q.resize(lMax_+1); |
| 184 |
+ |
W.resize(lMax_+1); |
| 185 |
+ |
W_hat.resize(lMax_+1); |
| 186 |
+ |
Nbonds = 0; |
| 187 |
+ |
|
| 188 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
| 189 |
|
reader.readFrame(istep); |
| 190 |
|
frameCounter_++; |
| 211 |
|
|
| 212 |
|
myIndex = sd->getGlobalIndex(); |
| 213 |
|
nBonds = 0; |
| 214 |
< |
for (int m = -lNumber_; m <= lNumber_; m++) { |
| 215 |
< |
q_lm[m] = 0.0; |
| 214 |
> |
|
| 215 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 216 |
> |
for (int m = -l; m <= l; m++) { |
| 217 |
> |
q[std::make_pair(l,m)] = 0.0; |
| 218 |
> |
} |
| 219 |
|
} |
| 220 |
|
|
| 221 |
|
// inner loop is over all other atoms in the system: |
| 228 |
|
if (atom->getGlobalIndex() != myIndex) { |
| 229 |
|
|
| 230 |
|
vec = sd->getPos() - atom->getPos(); |
| 231 |
< |
currentSnapshot_->wrapVector(vec); |
| 231 |
> |
|
| 232 |
> |
if (usePeriodicBoundaryConditions_) |
| 233 |
> |
currentSnapshot_->wrapVector(vec); |
| 234 |
|
|
| 235 |
|
// Calculate "bonds" and build Q_lm(r) where |
| 236 |
|
// Q_lm = Y_lm(theta(r),phi(r)) |
| 244 |
|
if (r < rCut_) { |
| 245 |
|
costheta = vec.z() / r; |
| 246 |
|
phi = atan2(vec.y(), vec.x()); |
| 247 |
< |
|
| 248 |
< |
for(int m = -lNumber_; m <= lNumber_; m++){ |
| 249 |
< |
sphericalHarmonic.setM(m); |
| 250 |
< |
q_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
| 247 |
> |
|
| 248 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 249 |
> |
sphericalHarmonic.setL(l); |
| 250 |
> |
for(int m = -l; m <= l; m++){ |
| 251 |
> |
sphericalHarmonic.setM(m); |
| 252 |
> |
q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
| 253 |
> |
|
| 254 |
> |
} |
| 255 |
|
} |
| 256 |
|
nBonds++; |
| 257 |
|
} |
| 258 |
|
} |
| 259 |
|
} |
| 260 |
|
} |
| 261 |
< |
RealType ql = 0.0; |
| 262 |
< |
for(int m=-lNumber_; m<=lNumber_; m++) { |
| 263 |
< |
ql += norm(QBar_lm[m]); |
| 264 |
< |
} |
| 265 |
< |
ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1); |
| 266 |
< |
collectHistogram(sqrt(ql)/(RealType)nBonds); |
| 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 |
|
|
| 268 |
+ |
q2[l] += norm(q[std::make_pair(l,m)]); |
| 269 |
+ |
} |
| 270 |
+ |
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 271 |
+ |
} |
| 272 |
+ |
|
| 273 |
+ |
// Find Third Order Invariant W_l |
| 274 |
+ |
|
| 275 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 276 |
+ |
w[l] = 0.0; |
| 277 |
+ |
for (int m1 = -l; m1 <= l; m1++) { |
| 278 |
+ |
std::pair<int,int> lm = std::make_pair(l, m1); |
| 279 |
+ |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
| 280 |
+ |
int m2 = m2Min[lm] + mmm; |
| 281 |
+ |
int m3 = -m1-m2; |
| 282 |
+ |
w[l] += w3j[lm][mmm] * q[lm] * |
| 283 |
+ |
q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; |
| 284 |
+ |
} |
| 285 |
+ |
} |
| 286 |
+ |
|
| 287 |
+ |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
| 288 |
+ |
} |
| 289 |
+ |
|
| 290 |
+ |
collectHistogram(q_l, w_hat); |
| 291 |
+ |
|
| 292 |
|
Nbonds += nBonds; |
| 293 |
< |
for (int m=-lNumber_; m<=lNumber_; m++) { |
| 294 |
< |
QBar_lm[m] += q_lm[m]; |
| 293 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 294 |
> |
for (int m = -l; m <= l; m++) { |
| 295 |
> |
QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; |
| 296 |
> |
} |
| 297 |
|
} |
| 298 |
|
} |
| 299 |
|
} |
| 300 |
< |
|
| 300 |
> |
|
| 301 |
|
// Normalize Qbar2 |
| 302 |
< |
for (int m = -lNumber_;m <= lNumber_; m++){ |
| 303 |
< |
QBar_lm[m] /= Nbonds; |
| 302 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 303 |
> |
for (int m = -l; m <= l; m++){ |
| 304 |
> |
QBar[std::make_pair(l,m)] /= Nbonds; |
| 305 |
> |
} |
| 306 |
|
} |
| 307 |
|
|
| 308 |
|
// Find second order invariant Q_l |
| 309 |
|
|
| 310 |
< |
QSq_l = 0.0; |
| 311 |
< |
for (int m = -lNumber_; m <= lNumber_; m++){ |
| 312 |
< |
QSq_l += norm(QBar_lm[m]); |
| 310 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 311 |
> |
Q2[l] = 0.0; |
| 312 |
> |
for (int m = -l; m <= l; m++){ |
| 313 |
> |
Q2[l] += norm(QBar[std::make_pair(l,m)]); |
| 314 |
> |
} |
| 315 |
> |
Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 316 |
|
} |
| 317 |
|
|
| 230 |
– |
std::cout << "qsl = " << QSq_l << "\n"; |
| 231 |
– |
Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
| 232 |
– |
|
| 318 |
|
// Find Third Order Invariant W_l |
| 319 |
|
|
| 320 |
< |
W_l = 0.0; |
| 321 |
< |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
| 322 |
< |
// Zero work array |
| 323 |
< |
for (int ii = 0; ii < mSize_; ii++){ |
| 324 |
< |
THRCOF[ii] = 0.0; |
| 320 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 321 |
> |
W[l] = 0.0; |
| 322 |
> |
for (int m1 = -l; m1 <= l; m1++) { |
| 323 |
> |
std::pair<int,int> lm = std::make_pair(l, m1); |
| 324 |
> |
for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { |
| 325 |
> |
int m2 = m2Min[lm] + mmm; |
| 326 |
> |
int m3 = -m1-m2; |
| 327 |
> |
W[l] += w3j[lm][mmm] * QBar[lm] * |
| 328 |
> |
QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; |
| 329 |
> |
} |
| 330 |
|
} |
| 241 |
– |
// Get Wigner coefficients |
| 242 |
– |
m1Pass = (double)m1; |
| 331 |
|
|
| 332 |
< |
Wigner3jm(&l_, &l_, &l_, |
| 245 |
< |
&m1Pass, &m2Min, &m2Max, |
| 246 |
< |
THRCOF, &mSize_, &error); |
| 247 |
< |
|
| 248 |
< |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
| 249 |
< |
m2 = (int)floor(m2Min) + mmm; |
| 250 |
< |
m3 = -m1-m2; |
| 251 |
< |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
| 252 |
< |
} |
| 332 |
> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
| 333 |
|
} |
| 334 |
|
|
| 335 |
< |
W_l_hat = W_l / pow(QSq_l, 1.5); |
| 256 |
< |
|
| 257 |
< |
writeOrderParameter(Q_l, real(W_l_hat)); |
| 335 |
> |
writeOrderParameter(Q, W_hat); |
| 336 |
|
} |
| 337 |
|
|
| 338 |
< |
void BondOrderParameter::collectHistogram(RealType q_l) { |
| 338 |
> |
void BondOrderParameter::collectHistogram(std::vector<RealType> q, |
| 339 |
> |
std::vector<ComplexType> what) { |
| 340 |
|
|
| 341 |
< |
if (q_l >= MinQ_ && q_l < MaxQ_) { |
| 342 |
< |
int qbin = (q_l - MinQ_) / deltaQ_; |
| 343 |
< |
Q_histogram_[qbin] += 1; |
| 344 |
< |
Qcount_++; |
| 345 |
< |
sumQ_ += q_l; |
| 346 |
< |
sumQ2_ += q_l * q_l; |
| 347 |
< |
} else { |
| 348 |
< |
sprintf( painCave.errMsg, |
| 349 |
< |
"q_l value outside reasonable range\n"); |
| 350 |
< |
painCave.severity = OOPSE_ERROR; |
| 351 |
< |
painCave.isFatal = 1; |
| 352 |
< |
simError(); |
| 341 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 342 |
> |
if (q[l] >= MinQ_ && q[l] < MaxQ_) { |
| 343 |
> |
int qbin = (q[l] - MinQ_) / deltaQ_; |
| 344 |
> |
Q_histogram_[std::make_pair(qbin,l)] += 1; |
| 345 |
> |
Qcount_[l]++; |
| 346 |
> |
} else { |
| 347 |
> |
sprintf( painCave.errMsg, |
| 348 |
> |
"q_l value outside reasonable range\n"); |
| 349 |
> |
painCave.severity = OPENMD_ERROR; |
| 350 |
> |
painCave.isFatal = 1; |
| 351 |
> |
simError(); |
| 352 |
> |
} |
| 353 |
|
} |
| 354 |
|
|
| 355 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 356 |
+ |
if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { |
| 357 |
+ |
int wbin = (real(what[l]) - MinW_) / deltaW_; |
| 358 |
+ |
W_histogram_[std::make_pair(wbin,l)] += 1; |
| 359 |
+ |
Wcount_[l]++; |
| 360 |
+ |
} else { |
| 361 |
+ |
sprintf( painCave.errMsg, |
| 362 |
+ |
"Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); |
| 363 |
+ |
painCave.severity = OPENMD_ERROR; |
| 364 |
+ |
painCave.isFatal = 1; |
| 365 |
+ |
simError(); |
| 366 |
+ |
} |
| 367 |
+ |
} |
| 368 |
+ |
|
| 369 |
|
} |
| 370 |
|
|
| 371 |
|
|
| 372 |
< |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
| 372 |
> |
void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, |
| 373 |
> |
std::vector<ComplexType> What) { |
| 374 |
> |
|
| 375 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
| 376 |
|
|
| 377 |
< |
std::ofstream os(getOutputFileName().c_str()); |
| 282 |
< |
|
| 283 |
< |
if (os.is_open()) { |
| 377 |
> |
if (osq.is_open()) { |
| 378 |
|
|
| 379 |
< |
os << "# Bond Order Parameters\n"; |
| 380 |
< |
os << "# selection: (" << selectionScript_ << ")\n"; |
| 381 |
< |
os << "# \n"; |
| 382 |
< |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
| 383 |
< |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
| 379 |
> |
osq << "# Bond Order Parameters\n"; |
| 380 |
> |
osq << "# selection: (" << selectionScript_ << ")\n"; |
| 381 |
> |
osq << "# \n"; |
| 382 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 383 |
> |
osq << "# <Q_" << l << ">: " << Q[l] << "\n"; |
| 384 |
> |
} |
| 385 |
|
// Normalize by number of frames and write it out: |
| 386 |
< |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
| 387 |
< |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 388 |
< |
osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
| 386 |
> |
for (int i = 0; i < nBins_; ++i) { |
| 387 |
> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
| 388 |
> |
osq << Qval; |
| 389 |
> |
for (int l = 0; l <= lMax_; l++) { |
| 390 |
> |
|
| 391 |
> |
osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; |
| 392 |
> |
} |
| 393 |
> |
osq << "\n"; |
| 394 |
|
} |
| 395 |
|
|
| 396 |
< |
os.close(); |
| 396 |
> |
osq.close(); |
| 397 |
|
|
| 398 |
|
} else { |
| 399 |
|
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 400 |
< |
getOutputFileName().c_str()); |
| 400 |
> |
(getOutputFileName() + "q").c_str()); |
| 401 |
|
painCave.isFatal = 1; |
| 402 |
|
simError(); |
| 403 |
|
} |
| 404 |
+ |
|
| 405 |
+ |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
| 406 |
+ |
|
| 407 |
+ |
if (osw.is_open()) { |
| 408 |
+ |
osw << "# Bond Order Parameters\n"; |
| 409 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
| 410 |
+ |
osw << "# \n"; |
| 411 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 412 |
+ |
osw << "# <W_" << l << ">: " << real(What[l]) << "\t" << imag(What[l]) << "\n"; |
| 413 |
+ |
} |
| 414 |
+ |
// Normalize by number of frames and write it out: |
| 415 |
+ |
for (int i = 0; i < nBins_; ++i) { |
| 416 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
| 417 |
+ |
osw << Wval; |
| 418 |
+ |
for (int l = 0; l <= lMax_; l++) { |
| 419 |
+ |
|
| 420 |
+ |
osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; |
| 421 |
+ |
} |
| 422 |
+ |
osw << "\n"; |
| 423 |
+ |
} |
| 424 |
+ |
|
| 425 |
+ |
osw.close(); |
| 426 |
+ |
} else { |
| 427 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
| 428 |
+ |
(getOutputFileName() + "w").c_str()); |
| 429 |
+ |
painCave.isFatal = 1; |
| 430 |
+ |
simError(); |
| 431 |
+ |
} |
| 432 |
+ |
|
| 433 |
|
} |
| 434 |
|
} |
