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 1.7 2008-09-10 19:51:43 cli2 Exp $
 *
 */

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

namespace oopse{
  shapedLattice::shapedLattice(RealType 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<RealType> lc;
    lc.push_back(latticeConstant_);
    simpleLattice_->setLatticeConstant(lc);
    sitesComputed_ = false;
  }
    
  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_);  
    sitesComputed_ = false;  
  }

  void shapedLattice::setOrigin(Vector3d origin){
    origin_ = origin;
    simpleLattice_->setOrigin(origin_);
    sitesComputed_ = false;  
  }
  
  void shapedLattice::findSites(){

    sites_.clear();
    orientations_.clear();

    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];
              sites_.push_back(myPoint);
              orientations_.push_back(myOrt);
            }
          }
        }
      }
    }
    sitesComputed_ = true;
  }

  std::vector<Vector3d> shapedLattice::getSites() { 
    if (!sitesComputed_) {
      findSites();
    } 
    return sites_;
  }

  std::vector<Vector3d> shapedLattice::getOrientations() { 
    if (!sitesComputed_) {
      findSites();
    } 
    return orientations_;
  }
}
Revision:	3446
Committed:	Wed Sep 10 19:51:45 2008 UTC (15 years, 9 months ago) by cli2
File size:	4949 byte(s)
Log Message:	Inversion fixes and amber mostly working
#	User	Rev	Content
1	chuckv	2633	/* 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	cli2	3446	* @version $Id: shapedLattice.cpp,v 1.7 2008-09-10 19:51:43 cli2 Exp $
46	chuckv	2633	*
47			*/
48
49	cli2	3446	#include <cstdlib>
50	chuckv	2633	#include "lattice/shapedLattice.hpp"
51			#include "math/Vector3.hpp"
52			#include "brains/Register.hpp"
53			#include "lattice/LatticeFactory.hpp"
54
55			namespace oopse{
56	gezelter	3046	shapedLattice::shapedLattice(RealType latticeConstant,
57	chuckv	2633	std::string latticeType) {
58	gezelter	3046	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	chuckv	2633
67	gezelter	3046	//Set the lattice constant
68	tim	2759	std::vector<RealType> lc;
69	chuckv	2633	lc.push_back(latticeConstant_);
70	gezelter	3046	simpleLattice_->setLatticeConstant(lc);
71			sitesComputed_ = false;
72			}
73
74	chuckv	2633	void shapedLattice::setGridDimension(Vector3d dimension){
75			dimension_ = dimension;
76	gezelter	3046	// Find number of unit cells in each direction
77			beginNx_ = -(int) ceil(0.5*dimension_[0]/latticeConstant_) ;
78			beginNy_ = -(int) ceil(0.5*dimension_[1]/latticeConstant_) ;
79			beginNz_ = -(int) ceil(0.5*dimension_[2]/latticeConstant_) ;
80	chuckv	2673	endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_);
81	gezelter	3046	endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_);
82			endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_);
83			sitesComputed_ = false;
84	chuckv	2633	}
85	gezelter	3050
86			void shapedLattice::setOrigin(Vector3d origin){
87			origin_ = origin;
88			simpleLattice_->setOrigin(origin_);
89			sitesComputed_ = false;
90			}
91	chuckv	2633
92	gezelter	3046	void shapedLattice::findSites(){
93
94			sites_.clear();
95			orientations_.clear();
96
97			std::vector<Vector3d> latticePos;
98			std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt();
99			int numMolPerCell = simpleLattice_->getNumSitesPerCell();
100
101			for(int i = beginNx_; i < endNx_; i++) {
102			for(int j = beginNy_; j < endNy_; j++) {
103			for(int k = beginNz_; k < endNz_; k++) {
104			//get the position of the cell sites
105			simpleLattice_->getLatticePointsPos(latticePos, i, j, k);
106			for(int l = 0; l < numMolPerCell; l++) {
107			if (isInterior(latticePos[l])){
108			Vector3d myPoint = latticePos[l];
109			Vector3d myOrt = pointsOrt[l];
110			sites_.push_back(myPoint);
111			orientations_.push_back(myOrt);
112	chuckv	2633	}
113			}
114			}
115			}
116	gezelter	3046	}
117			sitesComputed_ = true;
118			}
119
120			std::vector<Vector3d> shapedLattice::getSites() {
121			if (!sitesComputed_) {
122			findSites();
123			}
124			return sites_;
125			}
126
127			std::vector<Vector3d> shapedLattice::getOrientations() {
128			if (!sitesComputed_) {
129			findSites();
130			}
131			return orientations_;
132			}
133	chuckv	2633	}