src/lattice/shapedLattice.cpp

/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 *
 *  sphericalLattice.cpp
 *
 *  Created by Charles F. Vardeman II on 17 Feb 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: shapedLattice.cpp,v 1.3 2006-03-29 19:17:20 chuckv Exp $
 *
 */


#include "lattice/shapedLattice.hpp"
#include "math/Vector3.hpp"
#include "brains/Register.hpp"
#include "lattice/LatticeFactory.hpp"

namespace oopse{
        shapedLattice::shapedLattice(double latticeConstant, 
                               std::string latticeType) {
                latticeConstant_ = latticeConstant;
                latticeType_ = latticeType;
                registerLattice();
                simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType);
                if (simpleLattice_ == NULL){
                        std::cerr << "shapedLattice:: Error creating lattice" << std::endl;
                        exit(1);
                }
                
                //Set the lattice constant
    std::vector<double> lc;
    lc.push_back(latticeConstant_);
                simpleLattice_->setLatticeConstant(lc);
        }
        
  
  void shapedLattice::setGridDimension(Vector3d dimension){
    dimension_ = dimension;
                // Find number of unit cells in each direction
                beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ;
                beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ;
                beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ;    
    endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_);
                endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_);
                endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_);    
  }
  
  
    std::vector<Vector3d> shapedLattice::getPoints(){
                        std::vector<Vector3d> latticePos;
                        
      
      std::vector<Vector3d> pointsOrt =  simpleLattice_->getLatticePointsOrt();
      int numMolPerCell = simpleLattice_->getNumSitesPerCell(); 
      for(int i = beginNx_; i < endNx_; i++) {     
        for(int j = beginNy_; j < endNy_; j++) {       
          for(int k = beginNz_; k < endNz_; k++) {
            //get the position of the cell sites
            simpleLattice_->getLatticePointsPos(latticePos, i, j, k);
            
            for(int l = 0; l < numMolPerCell; l++) {
              
              
              if (isInterior(latticePos[l])){
                Vector3d myPoint = latticePos[l];
                Vector3d myOrt = pointsOrt[l];
                coords_.push_back(myPoint);
                coordsOrt_.push_back(myOrt);
              }
            }
          }
        }
      }
      
      return coords_;
      
                }       
}
Revision:	923
Committed:	Wed Mar 29 19:17:20 2006 UTC (19 years, 1 month ago) by chuckv
File size:	4455 byte(s)
Log Message:	Fixed latticeOrt in shapedlatice and latticebuilder.
#	User	Rev	Content
1	chuckv	905	/* 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	chuckv	923	* @version $Id: shapedLattice.cpp,v 1.3 2006-03-29 19:17:20 chuckv Exp $
46	chuckv	905	*
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(double 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<double> 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	chuckv	919	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	chuckv	905	}
85
86
87
88	chuckv	919	std::vector<Vector3d> shapedLattice::getPoints(){
89	chuckv	905	std::vector<Vector3d> latticePos;
90
91	chuckv	923
92			std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt();
93	chuckv	905	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	chuckv	919
103	chuckv	905	if (isInterior(latticePos[l])){
104	chuckv	919	Vector3d myPoint = latticePos[l];
105	chuckv	923	Vector3d myOrt = pointsOrt[l];
106	chuckv	919	coords_.push_back(myPoint);
107	chuckv	923	coordsOrt_.push_back(myOrt);
108	chuckv	905	}
109			}
110			}
111			}
112			}
113
114			return coords_;
115
116			}
117			}