| 45 |
|
* |
| 46 |
|
* Created by Charles F. Vardeman II on 14 Dec 2006. |
| 47 |
|
* @author Charles F. Vardeman II |
| 48 |
< |
* @version $Id: NanoVolume.cpp,v 1.4 2007-12-06 20:04:01 cpuglis Exp $ |
| 48 |
> |
* @version $Id: NanoVolume.cpp,v 1.7 2008-09-14 01:32:23 chuckv Exp $ |
| 49 |
|
* |
| 50 |
|
*/ |
| 51 |
|
|
| 52 |
|
#include "applications/staticProps/NanoVolume.hpp" |
| 53 |
|
#include "math/ConvexHull.hpp" |
| 54 |
+ |
//#include "math/AlphaShape.hpp" |
| 55 |
|
#include "utils/simError.h" |
| 56 |
|
#include "io/DumpReader.hpp" |
| 57 |
|
#include "primitives/Molecule.hpp" |
| 74 |
|
} |
| 75 |
|
|
| 76 |
|
void NanoVolume::process() { |
| 77 |
< |
#if defined(HAVE_CGAL) |
| 77 |
> |
#if defined(HAVE_CGAL) || defined(HAVE_QHULL) |
| 78 |
|
Molecule* mol; |
| 79 |
|
Atom* atom; |
| 80 |
|
RigidBody* rb; |
| 86 |
|
Vector3d vec; |
| 87 |
|
int i,j; |
| 88 |
|
|
| 89 |
< |
ConvexHull* hull = new ConvexHull(); |
| 89 |
> |
#ifdef HAVE_QHULL |
| 90 |
> |
ConvexHull* thishull = new ConvexHull(); |
| 91 |
> |
#endif |
| 92 |
> |
#ifdef HAVE_CGAL |
| 93 |
> |
// AlphaShape* hull = new AlphaShape(); |
| 94 |
> |
ConvexHull* thishull = new ConvexHull(); |
| 95 |
> |
#endif |
| 96 |
|
|
| 97 |
|
DumpReader reader(info_, dumpFilename_); |
| 98 |
|
int nFrames = reader.getNFrames(); |
| 99 |
|
frameCounter_ = 0; |
| 100 |
|
|
| 101 |
< |
pos_.reserve(info_->getNGlobalAtoms()); |
| 101 |
> |
theAtoms_.reserve(info_->getNGlobalAtoms()); |
| 102 |
|
|
| 103 |
|
for (int istep = 0; istep < nFrames; istep += step_) { |
| 104 |
|
reader.readFrame(istep); |
| 106 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 107 |
|
|
| 108 |
|
// Clear pos vector between each frame. |
| 109 |
< |
pos_.clear(); |
| 109 |
> |
theAtoms_.clear(); |
| 110 |
|
|
| 111 |
|
if (evaluator_.isDynamic()) { |
| 112 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 123 |
|
} |
| 124 |
|
|
| 125 |
|
// outer loop is over the selected StuntDoubles: |
| 126 |
< |
|
| 126 |
> |
/* |
| 127 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 128 |
< |
sd = seleMan_.nextSelected(i)) { |
| 128 |
> |
sd = seleMan_.nextSelected(i)) { |
| 129 |
|
|
| 130 |
|
pos_.push_back(sd->getPos()); |
| 131 |
|
myIndex = sd->getGlobalIndex(); |
| 132 |
|
|
| 133 |
|
} |
| 134 |
+ |
*/ |
| 135 |
+ |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 136 |
+ |
mol = info_->nextMolecule(mi)) { |
| 137 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 138 |
+ |
atom = mol->nextAtom(ai)) { |
| 139 |
+ |
theAtoms_.push_back(atom); |
| 140 |
+ |
} |
| 141 |
+ |
} |
| 142 |
+ |
|
| 143 |
|
// Generate convex hull for this frame. |
| 144 |
< |
hull->genHull(pos_); |
| 145 |
< |
totalVolume_ += hull->getVolume(); |
| 144 |
> |
thishull->computeHull(theAtoms_); |
| 145 |
> |
// totalVolume_ += hull->getVolume(); |
| 146 |
|
} |
| 147 |
< |
RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
| 147 |
> |
//RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
| 148 |
|
//std::cout.precision(7); |
| 149 |
|
//std::cout << avgVolume << std::endl; |
| 150 |
< |
|
| 150 |
> |
/* |
| 151 |
|
std::ofstream osq(getOutputFileName().c_str()); |
| 152 |
|
osq.precision(7); |
| 153 |
|
if (osq.is_open()){ |
| 155 |
|
|
| 156 |
|
} |
| 157 |
|
osq.close(); |
| 158 |
+ |
*/ |
| 159 |
|
#else |
| 160 |
< |
sprintf(painCave.errMsg, "NanoVolume: CGAL support was not compiled in!\n"); |
| 160 |
> |
sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n"); |
| 161 |
|
painCave.isFatal = 1; |
| 162 |
|
simError(); |
| 163 |
+ |
|
| 164 |
|
#endif |
| 165 |
+ |
|
| 166 |
|
} |
