| 34 |
|
* |
| 35 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 37 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 38 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
> |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 40 |
|
* |
| 40 |
– |
* |
| 41 |
|
* NanoVolume.cpp |
| 42 |
|
* |
| 43 |
|
* Created by Charles F. Vardeman II on 14 Dec 2006. |
| 47 |
|
*/ |
| 48 |
|
|
| 49 |
|
#include "applications/staticProps/NanoVolume.hpp" |
| 50 |
+ |
#if defined(HAVE_QHULL) |
| 51 |
|
#include "math/ConvexHull.hpp" |
| 52 |
|
#include "math/AlphaHull.hpp" |
| 53 |
+ |
#endif |
| 54 |
|
#include "utils/simError.h" |
| 55 |
|
#include "io/DumpReader.hpp" |
| 56 |
|
#include "primitives/Molecule.hpp" |
| 61 |
|
NanoVolume::NanoVolume(SimInfo* info, |
| 62 |
|
const std::string& filename, |
| 63 |
|
const std::string& sele) |
| 64 |
< |
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) { |
| 64 |
> |
: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), |
| 65 |
> |
seleMan_(info) { |
| 66 |
> |
|
| 67 |
|
setOutputName(getPrefix(filename) + ".avol"); |
| 68 |
+ |
|
| 69 |
+ |
osq.open(getOutputFileName().c_str()); |
| 70 |
|
|
| 71 |
|
evaluator_.loadScriptString(sele); |
| 72 |
|
if (!evaluator_.isDynamic()) { |
| 73 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 74 |
|
} |
| 75 |
|
frameCounter_ = 0; |
| 70 |
– |
totalVolume_ = 0.0; |
| 76 |
|
} |
| 77 |
|
|
| 78 |
|
void NanoVolume::process() { |
| 79 |
|
#if defined(HAVE_QHULL) |
| 80 |
|
Molecule* mol; |
| 76 |
– |
Atom* atom; |
| 81 |
|
RigidBody* rb; |
| 78 |
– |
int myIndex; |
| 82 |
|
SimInfo::MoleculeIterator mi; |
| 83 |
|
Molecule::RigidBodyIterator rbIter; |
| 81 |
– |
Molecule::AtomIterator ai; |
| 84 |
|
StuntDouble* sd; |
| 85 |
|
Vector3d vec; |
| 86 |
< |
int i,j; |
| 86 |
> |
int i; |
| 87 |
|
|
| 88 |
< |
#ifdef HAVE_QHULL |
| 89 |
< |
//ConvexHull* thishull = new ConvexHull(); |
| 90 |
< |
AlphaHull* thishull = new AlphaHull(2.0); |
| 89 |
< |
#endif |
| 90 |
< |
|
| 88 |
> |
AlphaHull* thishull = new AlphaHull(2.0); |
| 89 |
> |
//ConvexHull* thishull = new ConvexHull(); |
| 90 |
> |
|
| 91 |
|
DumpReader reader(info_, dumpFilename_); |
| 92 |
|
int nFrames = reader.getNFrames(); |
| 93 |
|
frameCounter_ = 0; |
| 98 |
|
reader.readFrame(istep); |
| 99 |
|
frameCounter_++; |
| 100 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 101 |
+ |
RealType time = currentSnapshot_->getTime(); |
| 102 |
|
|
| 103 |
|
// Clear pos vector between each frame. |
| 104 |
|
theAtoms_.clear(); |
| 107 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 108 |
|
} |
| 109 |
|
|
| 110 |
< |
// update the positions of atoms which belong to the rigidbodies |
| 110 |
> |
// update the positions of atoms which belong to the rigid bodies |
| 111 |
|
|
| 112 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 113 |
|
mol = info_->nextMolecule(mi)) { |
| 120 |
|
// outer loop is over the selected StuntDoubles: |
| 121 |
|
|
| 122 |
|
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 123 |
< |
sd = seleMan_.nextSelected(i)) { |
| 124 |
< |
|
| 124 |
< |
theAtoms_.push_back(sd); |
| 125 |
< |
myIndex = sd->getGlobalIndex(); |
| 126 |
< |
|
| 123 |
> |
sd = seleMan_.nextSelected(i)) { |
| 124 |
> |
theAtoms_.push_back(sd); |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
/* |
| 127 |
> |
/* variant below for signle atoms, not StuntDoubles: |
| 128 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 129 |
< |
mol = info_->nextMolecule(mi)) { |
| 130 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 131 |
< |
atom = mol->nextAtom(ai)) { |
| 132 |
< |
theAtoms_.push_back(atom); |
| 133 |
< |
} |
| 134 |
< |
} |
| 129 |
> |
mol = info_->nextMolecule(mi)) { |
| 130 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 131 |
> |
atom = mol->nextAtom(ai)) { |
| 132 |
> |
theAtoms_.push_back(atom); |
| 133 |
> |
} |
| 134 |
> |
} |
| 135 |
|
*/ |
| 136 |
+ |
|
| 137 |
|
// Generate convex hull for this frame. |
| 138 |
|
thishull->computeHull(theAtoms_); |
| 139 |
< |
// totalVolume_ += hull->getVolume(); |
| 141 |
< |
} |
| 142 |
< |
//RealType avgVolume = totalVolume_/(RealType) frameCounter_; |
| 143 |
< |
//std::cout.precision(7); |
| 144 |
< |
//std::cout << avgVolume << std::endl; |
| 145 |
< |
/* |
| 146 |
< |
std::ofstream osq(getOutputFileName().c_str()); |
| 147 |
< |
osq.precision(7); |
| 148 |
< |
if (osq.is_open()){ |
| 149 |
< |
osq << avgVolume << std::endl; |
| 139 |
> |
RealType volume = thishull->getVolume(); |
| 140 |
|
|
| 141 |
+ |
osq.precision(7); |
| 142 |
+ |
if (osq.is_open()){ |
| 143 |
+ |
osq << time << "\t" << volume << std::endl; |
| 144 |
+ |
} |
| 145 |
|
} |
| 146 |
|
osq.close(); |
| 147 |
< |
*/ |
| 147 |
> |
|
| 148 |
|
#else |
| 149 |
|
sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n"); |
| 150 |
|
painCave.isFatal = 1; |
| 151 |
|
simError(); |
| 158 |
– |
|
| 152 |
|
#endif |
| 153 |
|
|
| 154 |
|
} |
