| 1 |
/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. |
| 2 |
* |
| 3 |
* The University of Notre Dame grants you ("Licensee") a |
| 4 |
* non-exclusive, royalty free, license to use, modify and |
| 5 |
* redistribute this software in source and binary code form, provided |
| 6 |
* that the following conditions are met: |
| 7 |
* |
| 8 |
* 1. Acknowledgement of the program authors must be made in any |
| 9 |
* publication of scientific results based in part on use of the |
| 10 |
* program. An acceptable form of acknowledgement is citation of |
| 11 |
* the article in which the program was described (Matthew |
| 12 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 13 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 14 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 15 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 16 |
* |
| 17 |
* 2. Redistributions of source code must retain the above copyright |
| 18 |
* notice, this list of conditions and the following disclaimer. |
| 19 |
* |
| 20 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 21 |
* notice, this list of conditions and the following disclaimer in the |
| 22 |
* documentation and/or other materials provided with the |
| 23 |
* distribution. |
| 24 |
* |
| 25 |
* This software is provided "AS IS," without a warranty of any |
| 26 |
* kind. All express or implied conditions, representations and |
| 27 |
* warranties, including any implied warranty of merchantability, |
| 28 |
* fitness for a particular purpose or non-infringement, are hereby |
| 29 |
* excluded. The University of Notre Dame and its licensors shall not |
| 30 |
* be liable for any damages suffered by licensee as a result of |
| 31 |
* using, modifying or distributing the software or its |
| 32 |
* derivatives. In no event will the University of Notre Dame or its |
| 33 |
* licensors be liable for any lost revenue, profit or data, or for |
| 34 |
* direct, indirect, special, consequential, incidental or punitive |
| 35 |
* damages, however caused and regardless of the theory of liability, |
| 36 |
* arising out of the use of or inability to use software, even if the |
| 37 |
* University of Notre Dame has been advised of the possibility of |
| 38 |
* such damages. |
| 39 |
* |
| 40 |
* |
| 41 |
* sphericalLattice.cpp |
| 42 |
* |
| 43 |
* Created by Charles F. Vardeman II on 17 Feb 2006. |
| 44 |
* @author Charles F. Vardeman II |
| 45 |
* @version $Id: shapedLattice.cpp,v 1.4 2006-05-17 21:51:42 tim Exp $ |
| 46 |
* |
| 47 |
*/ |
| 48 |
|
| 49 |
|
| 50 |
#include "lattice/shapedLattice.hpp" |
| 51 |
#include "math/Vector3.hpp" |
| 52 |
#include "brains/Register.hpp" |
| 53 |
#include "lattice/LatticeFactory.hpp" |
| 54 |
|
| 55 |
namespace oopse{ |
| 56 |
shapedLattice::shapedLattice(RealType latticeConstant, |
| 57 |
std::string latticeType) { |
| 58 |
latticeConstant_ = latticeConstant; |
| 59 |
latticeType_ = latticeType; |
| 60 |
registerLattice(); |
| 61 |
simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType); |
| 62 |
if (simpleLattice_ == NULL){ |
| 63 |
std::cerr << "shapedLattice:: Error creating lattice" << std::endl; |
| 64 |
exit(1); |
| 65 |
} |
| 66 |
|
| 67 |
//Set the lattice constant |
| 68 |
std::vector<RealType> lc; |
| 69 |
lc.push_back(latticeConstant_); |
| 70 |
simpleLattice_->setLatticeConstant(lc); |
| 71 |
} |
| 72 |
|
| 73 |
|
| 74 |
|
| 75 |
void shapedLattice::setGridDimension(Vector3d dimension){ |
| 76 |
dimension_ = dimension; |
| 77 |
// Find number of unit cells in each direction |
| 78 |
beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ; |
| 79 |
beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ; |
| 80 |
beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ; |
| 81 |
endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_); |
| 82 |
endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_); |
| 83 |
endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_); |
| 84 |
} |
| 85 |
|
| 86 |
|
| 87 |
|
| 88 |
std::vector<Vector3d> shapedLattice::getPoints(){ |
| 89 |
std::vector<Vector3d> latticePos; |
| 90 |
|
| 91 |
|
| 92 |
std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt(); |
| 93 |
int numMolPerCell = simpleLattice_->getNumSitesPerCell(); |
| 94 |
for(int i = beginNx_; i < endNx_; i++) { |
| 95 |
for(int j = beginNy_; j < endNy_; j++) { |
| 96 |
for(int k = beginNz_; k < endNz_; k++) { |
| 97 |
//get the position of the cell sites |
| 98 |
simpleLattice_->getLatticePointsPos(latticePos, i, j, k); |
| 99 |
|
| 100 |
for(int l = 0; l < numMolPerCell; l++) { |
| 101 |
|
| 102 |
|
| 103 |
if (isInterior(latticePos[l])){ |
| 104 |
Vector3d myPoint = latticePos[l]; |
| 105 |
Vector3d myOrt = pointsOrt[l]; |
| 106 |
coords_.push_back(myPoint); |
| 107 |
coordsOrt_.push_back(myOrt); |
| 108 |
} |
| 109 |
} |
| 110 |
} |
| 111 |
} |
| 112 |
} |
| 113 |
|
| 114 |
return coords_; |
| 115 |
|
| 116 |
} |
| 117 |
} |
