| 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 $Id$ |
| 49 |
|
#include "io/DumpReader.hpp" |
| 50 |
|
#include "primitives/Molecule.hpp" |
| 51 |
|
#include "utils/NumericConstant.hpp" |
| 52 |
+ |
#include "math/Wigner3jm.hpp" |
| 53 |
+ |
#include "brains/Thermo.hpp" |
| 54 |
|
|
| 55 |
< |
|
| 55 |
> |
using namespace MATPACK; |
| 56 |
|
namespace OpenMD { |
| 57 |
|
|
| 58 |
|
BOPofR::BOPofR(SimInfo* info, const std::string& filename, const std::string& sele, double rCut, |
| 83 |
|
} |
| 84 |
|
|
| 85 |
|
// Make arrays for Wigner3jm |
| 86 |
< |
double* THRCOF = new double[2*lMax_+1]; |
| 86 |
> |
RealType* THRCOF = new RealType[2*lMax_+1]; |
| 87 |
|
// Variables for Wigner routine |
| 88 |
< |
double lPass, m1Pass, m2m, m2M; |
| 88 |
> |
RealType lPass, m1Pass, m2m, m2M; |
| 89 |
|
int error, mSize; |
| 90 |
|
mSize = 2*lMax_+1; |
| 91 |
|
|
| 92 |
|
for (int l = 0; l <= lMax_; l++) { |
| 93 |
< |
lPass = (double)l; |
| 93 |
> |
lPass = (RealType)l; |
| 94 |
|
for (int m1 = -l; m1 <= l; m1++) { |
| 95 |
< |
m1Pass = (double)m1; |
| 95 |
> |
m1Pass = (RealType)m1; |
| 96 |
|
|
| 97 |
|
std::pair<int,int> lm = std::make_pair(l, m1); |
| 98 |
|
|
| 102 |
|
} |
| 103 |
|
|
| 104 |
|
// Get Wigner coefficients |
| 105 |
< |
Wigner3jm(&lPass, &lPass, &lPass, |
| 106 |
< |
&m1Pass, &m2m, &m2M, |
| 107 |
< |
THRCOF, &mSize, &error); |
| 105 |
> |
Wigner3jm(lPass, lPass, lPass, |
| 106 |
> |
m1Pass, m2m, m2M, |
| 107 |
> |
THRCOF, mSize, error); |
| 108 |
|
|
| 109 |
|
m2Min[lm] = (int)floor(m2m); |
| 110 |
|
m2Max[lm] = (int)floor(m2M); |
| 145 |
|
} |
| 146 |
|
|
| 147 |
|
|
| 148 |
< |
void BOPofR::initalizeHistogram() { |
| 148 |
> |
void BOPofR::initializeHistogram() { |
| 149 |
|
for (int i = 0; i < nBins_; i++){ |
| 150 |
|
RCount_[i] = 0; |
| 151 |
|
WofR_[i] = 0; |
| 167 |
|
RealType costheta; |
| 168 |
|
RealType phi; |
| 169 |
|
RealType r; |
| 168 |
– |
RealType dist; |
| 170 |
|
Vector3d rCOM; |
| 171 |
|
RealType distCOM; |
| 172 |
|
Vector3d pos; |
| 183 |
|
std::vector<ComplexType> W_hat; |
| 184 |
|
int nBonds, Nbonds; |
| 185 |
|
SphericalHarmonic sphericalHarmonic; |
| 186 |
< |
int i, j; |
| 187 |
< |
|
| 186 |
> |
int i; |
| 187 |
> |
|
| 188 |
|
DumpReader reader(info_, dumpFilename_); |
| 189 |
|
int nFrames = reader.getNFrames(); |
| 190 |
|
frameCounter_ = 0; |
| 191 |
|
|
| 192 |
+ |
Thermo thermo(info_); |
| 193 |
+ |
|
| 194 |
|
q_l.resize(lMax_+1); |
| 195 |
|
q2.resize(lMax_+1); |
| 196 |
|
w.resize(lMax_+1); |
| 206 |
|
reader.readFrame(istep); |
| 207 |
|
frameCounter_++; |
| 208 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 209 |
< |
CenterOfMass = info_->getCom(); |
| 209 |
> |
CenterOfMass = thermo.getCom(); |
| 210 |
|
if (evaluator_.isDynamic()) { |
| 211 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 212 |
|
} |
| 304 |
|
} |
| 305 |
|
} |
| 306 |
|
|
| 307 |
< |
w_hat[l] = w[l] / pow(q2[l], 1.5); |
| 307 |
> |
w_hat[l] = w[l] / pow(q2[l], RealType(1.5)); |
| 308 |
|
} |
| 309 |
|
|
| 310 |
|
collectHistogram(q_l, w_hat, distCOM); |
