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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4]  Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *
 *  sphericalLattice.cpp
 *
 *  Created by Charles F. Vardeman II on 17 Feb 2006.
 *  Edited by Kelsey M. Stocker on 23 Feb 2012.
 *  @author  Charles F. Vardeman II
 *  @version $Id$
 *
 */

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

namespace OpenMD{
  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_);  
    std::cerr << "begin = " << beginNx_ << " " << beginNy_ << " " << beginNz_ << "\n";
    std::cerr << "end = " << endNx_ << " " << endNy_ << " " << endNz_ << "\n";
    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:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	5206 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	905	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	905	* notice, this list of conditions and the following disclaimer in the
13			* documentation and/or other materials provided with the
14			* distribution.
15			*
16			* This software is provided "AS IS," without a warranty of any
17			* kind. All express or implied conditions, representations and
18			* warranties, including any implied warranty of merchantability,
19			* fitness for a particular purpose or non-infringement, are hereby
20			* excluded. The University of Notre Dame and its licensors shall not
21			* be liable for any damages suffered by licensee as a result of
22			* using, modifying or distributing the software or its
23			* derivatives. In no event will the University of Notre Dame or its
24			* licensors be liable for any lost revenue, profit or data, or for
25			* direct, indirect, special, consequential, incidental or punitive
26			* damages, however caused and regardless of the theory of liability,
27			* arising out of the use of or inability to use software, even if the
28			* University of Notre Dame has been advised of the possibility of
29			* such damages.
30			*
31	gezelter	1390	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32			* research, please cite the appropriate papers when you publish your
33			* work. Good starting points are:
34			*
35			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	kstocke1	1701	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39			* [4] Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	chuckv	905	*
41			* sphericalLattice.cpp
42			*
43			* Created by Charles F. Vardeman II on 17 Feb 2006.
44	kstocke1	1701	* Edited by Kelsey M. Stocker on 23 Feb 2012.
45	chuckv	905	* @author Charles F. Vardeman II
46	gezelter	1442	* @version $Id$
47	chuckv	905	*
48			*/
49
50	cli2	1290	#include <cstdlib>
51	chuckv	905	#include "lattice/shapedLattice.hpp"
52			#include "math/Vector3.hpp"
53			#include "brains/Register.hpp"
54			#include "lattice/LatticeFactory.hpp"
55
56	gezelter	1390	namespace OpenMD{
57	gezelter	1070	shapedLattice::shapedLattice(RealType latticeConstant,
58	chuckv	905	std::string latticeType) {
59	gezelter	1070	latticeConstant_ = latticeConstant;
60			latticeType_ = latticeType;
61			registerLattice();
62			simpleLattice_ = LatticeFactory::getInstance()->createLattice(latticeType);
63			if (simpleLattice_ == NULL){
64			std::cerr << "shapedLattice:: Error creating lattice" << std::endl;
65			exit(1);
66			}
67	chuckv	905
68	gezelter	1070	//Set the lattice constant
69	tim	963	std::vector<RealType> lc;
70	chuckv	905	lc.push_back(latticeConstant_);
71	gezelter	1070	simpleLattice_->setLatticeConstant(lc);
72			sitesComputed_ = false;
73			}
74
75	chuckv	905	void shapedLattice::setGridDimension(Vector3d dimension){
76			dimension_ = dimension;
77	gezelter	1070	// 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	chuckv	919	endNx_ = (int) ceil(0.5*dimension_[0]/latticeConstant_);
82	gezelter	1070	endNy_ = (int) ceil(0.5*dimension_[1]/latticeConstant_);
83			endNz_ = (int) ceil(0.5*dimension_[2]/latticeConstant_);
84	kstocke1	1701	std::cerr << "begin = " << beginNx_ << " " << beginNy_ << " " << beginNz_ << "\n";
85			std::cerr << "end = " << endNx_ << " " << endNy_ << " " << endNz_ << "\n";
86	gezelter	1070	sitesComputed_ = false;
87	chuckv	905	}
88	gezelter	1074
89			void shapedLattice::setOrigin(Vector3d origin){
90			origin_ = origin;
91			simpleLattice_->setOrigin(origin_);
92			sitesComputed_ = false;
93			}
94	chuckv	905
95	gezelter	1070	void shapedLattice::findSites(){
96
97			sites_.clear();
98			orientations_.clear();
99
100			std::vector<Vector3d> latticePos;
101			std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt();
102			int numMolPerCell = simpleLattice_->getNumSitesPerCell();
103
104			for(int i = beginNx_; i < endNx_; i++) {
105			for(int j = beginNy_; j < endNy_; j++) {
106			for(int k = beginNz_; k < endNz_; k++) {
107			//get the position of the cell sites
108			simpleLattice_->getLatticePointsPos(latticePos, i, j, k);
109			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);
114			orientations_.push_back(myOrt);
115	chuckv	905	}
116			}
117			}
118			}
119	gezelter	1070	}
120			sitesComputed_ = true;
121			}
122
123			std::vector<Vector3d> shapedLattice::getSites() {
124			if (!sitesComputed_) {
125			findSites();
126			}
127			return sites_;
128			}
129
130			std::vector<Vector3d> shapedLattice::getOrientations() {
131			if (!sitesComputed_) {
132			findSites();
133			}
134			return orientations_;
135			}
136	chuckv	905	}