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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
| 11 |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
| 9 |
|
* notice, this list of conditions and the following disclaimer. |
| 10 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 11 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 12 |
|
* notice, this list of conditions and the following disclaimer in the |
| 13 |
|
* documentation and/or other materials provided with the |
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|
* distribution. |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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|
* |
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+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
| 33 |
+ |
* work. Good starting points are: |
| 34 |
+ |
* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 38 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
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* [4] Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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* |
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* sphericalLattice.cpp |
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* |
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* Created by Charles F. Vardeman II on 17 Feb 2006. |
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* Edited by Kelsey M. Stocker on 23 Feb 2012. |
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* @author Charles F. Vardeman II |
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* @version $Id: shapedLattice.cpp,v 1.3 2006-03-29 19:17:20 chuckv Exp $ |
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* @version $Id$ |
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* |
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*/ |
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|
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< |
|
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#include <cstdlib> |
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#include "lattice/shapedLattice.hpp" |
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#include "math/Vector3.hpp" |
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#include "brains/Register.hpp" |
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#include "lattice/LatticeFactory.hpp" |
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|
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namespace oopse{ |
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shapedLattice::shapedLattice(double latticeConstant, |
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namespace OpenMD{ |
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> |
shapedLattice::shapedLattice(RealType latticeConstant, |
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std::string latticeType) { |
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latticeConstant_ = latticeConstant; |
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latticeType_ = latticeType; |
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registerLattice(); |
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simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType); |
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if (simpleLattice_ == NULL){ |
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std::cerr << "shapedLattice:: Error creating lattice" << std::endl; |
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exit(1); |
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} |
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latticeConstant_ = latticeConstant; |
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latticeType_ = latticeType; |
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registerLattice(); |
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> |
simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType); |
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if (simpleLattice_ == NULL){ |
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std::cerr << "shapedLattice:: Error creating lattice" << std::endl; |
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exit(1); |
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} |
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|
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//Set the lattice constant |
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std::vector<double> lc; |
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//Set the lattice constant |
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std::vector<RealType> lc; |
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lc.push_back(latticeConstant_); |
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simpleLattice_->setLatticeConstant(lc); |
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} |
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|
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|
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|
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> |
simpleLattice_->setLatticeConstant(lc); |
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sitesComputed_ = false; |
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} |
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> |
|
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void shapedLattice::setGridDimension(Vector3d dimension){ |
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dimension_ = dimension; |
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// Find number of unit cells in each direction |
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beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ; |
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beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ; |
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beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ; |
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> |
// Find number of unit cells in each direction |
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> |
beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ; |
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> |
beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ; |
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> |
beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ; |
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|
endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_); |
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endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_); |
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endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); |
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> |
endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_); |
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> |
endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); |
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> |
std::cerr << "begin = " << beginNx_ << " " << beginNy_ << " " << beginNz_ << "\n"; |
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std::cerr << "end = " << endNx_ << " " << endNy_ << " " << endNz_ << "\n"; |
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sitesComputed_ = false; |
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} |
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+ |
|
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+ |
void shapedLattice::setOrigin(Vector3d origin){ |
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origin_ = origin; |
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simpleLattice_->setOrigin(origin_); |
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sitesComputed_ = false; |
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} |
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|
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< |
|
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< |
|
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< |
std::vector<Vector3d> shapedLattice::getPoints(){ |
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std::vector<Vector3d> latticePos; |
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|
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< |
|
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< |
std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt(); |
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< |
int numMolPerCell = simpleLattice_->getNumSitesPerCell(); |
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< |
for(int i = beginNx_; i < endNx_; i++) { |
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< |
for(int j = beginNy_; j < endNy_; j++) { |
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< |
for(int k = beginNz_; k < endNz_; k++) { |
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< |
//get the position of the cell sites |
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< |
simpleLattice_->getLatticePointsPos(latticePos, i, j, k); |
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< |
|
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< |
for(int l = 0; l < numMolPerCell; l++) { |
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< |
|
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< |
|
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< |
if (isInterior(latticePos[l])){ |
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< |
Vector3d myPoint = latticePos[l]; |
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< |
Vector3d myOrt = pointsOrt[l]; |
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coords_.push_back(myPoint); |
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< |
coordsOrt_.push_back(myOrt); |
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< |
} |
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> |
void shapedLattice::findSites(){ |
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> |
|
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> |
sites_.clear(); |
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> |
orientations_.clear(); |
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> |
|
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> |
std::vector<Vector3d> latticePos; |
| 101 |
> |
std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt(); |
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> |
int numMolPerCell = simpleLattice_->getNumSitesPerCell(); |
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> |
|
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> |
for(int i = beginNx_; i < endNx_; i++) { |
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> |
for(int j = beginNy_; j < endNy_; j++) { |
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> |
for(int k = beginNz_; k < endNz_; k++) { |
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> |
//get the position of the cell sites |
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> |
simpleLattice_->getLatticePointsPos(latticePos, i, j, k); |
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> |
for(int l = 0; l < numMolPerCell; l++) { |
| 110 |
> |
if (isInterior(latticePos[l])){ |
| 111 |
> |
Vector3d myPoint = latticePos[l]; |
| 112 |
> |
Vector3d myOrt = pointsOrt[l]; |
| 113 |
> |
sites_.push_back(myPoint); |
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> |
orientations_.push_back(myOrt); |
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|
} |
| 116 |
|
} |
| 117 |
|
} |
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|
} |
| 119 |
< |
|
| 120 |
< |
return coords_; |
| 121 |
< |
|
| 122 |
< |
} |
| 119 |
> |
} |
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> |
sitesComputed_ = true; |
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> |
} |
| 122 |
> |
|
| 123 |
> |
std::vector<Vector3d> shapedLattice::getSites() { |
| 124 |
> |
if (!sitesComputed_) { |
| 125 |
> |
findSites(); |
| 126 |
> |
} |
| 127 |
> |
return sites_; |
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> |
} |
| 129 |
> |
|
| 130 |
> |
std::vector<Vector3d> shapedLattice::getOrientations() { |
| 131 |
> |
if (!sitesComputed_) { |
| 132 |
> |
findSites(); |
| 133 |
> |
} |
| 134 |
> |
return orientations_; |
| 135 |
> |
} |
| 136 |
|
} |
