| 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 |
< |
* |
| 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: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $ |
| 43 |
> |
* @version $Id$ |
| 44 |
|
* |
| 45 |
|
*/ |
| 46 |
|
|
| 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, |
| 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 |
|
|
| 106 |
|
} |
| 107 |
|
|
| 108 |
|
// Get Wigner coefficients |
| 109 |
< |
Wigner3jm(&lPass, &lPass, &lPass, |
| 110 |
< |
&m1Pass, &m2m, &m2M, |
| 111 |
< |
THRCOF, &mSize, &error); |
| 112 |
< |
|
| 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 |
|
|
| 135 |
|
m2Max.clear(); |
| 136 |
|
} |
| 137 |
|
|
| 138 |
< |
void BondOrderParameter::initalizeHistogram() { |
| 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; |
| 157 |
|
RealType costheta; |
| 158 |
|
RealType phi; |
| 159 |
|
RealType r; |
| 158 |
– |
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(); |
| 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 |
|
} |
| 257 |
|
nBonds++; |
| 264 |
|
for (int l = 0; l <= lMax_; l++) { |
| 265 |
|
q2[l] = 0.0; |
| 266 |
|
for (int m = -l; m <= l; m++){ |
| 267 |
< |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
| 267 |
> |
q[std::make_pair(l,m)] /= (RealType)nBonds; |
| 268 |
> |
|
| 269 |
|
q2[l] += norm(q[std::make_pair(l,m)]); |
| 270 |
|
} |
| 271 |
|
q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
| 285 |
|
} |
| 286 |
|
} |
| 287 |
|
|
| 288 |
< |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
| 288 |
> |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
| 289 |
|
} |
| 290 |
|
|
| 291 |
|
collectHistogram(q_l, w_hat); |
| 330 |
|
} |
| 331 |
|
} |
| 332 |
|
|
| 333 |
< |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
| 333 |
> |
W_hat[l] = W[l] / pow(Q2[l], RealType(1.5)); |
| 334 |
|
} |
| 335 |
|
|
| 336 |
|
writeOrderParameter(Q, W_hat); |
