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"

using namespace std;
namespace OpenMD{
  shapedLattice::shapedLattice(RealType latticeConstant, 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:	1977
Committed:	Wed Mar 12 21:35:23 2014 UTC (11 years, 1 month ago) by gezelter
File size:	5019 byte(s)
Log Message:	Removed some scary errors that are really supposed to be OPENMD_INFO messages
#	Content
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. Redistributions of source code must retain the above copyright
9	* notice, this list of conditions and the following disclaimer.
10	*
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
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	* 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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	* [4] Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	*
41	* sphericalLattice.cpp
42	*
43	* Created by Charles F. Vardeman II on 17 Feb 2006.
44	* Edited by Kelsey M. Stocker on 23 Feb 2012.
45	* @author Charles F. Vardeman II
46	* @version $Id$
47	*
48	*/
49
50	#include <cstdlib>
51	#include "lattice/shapedLattice.hpp"
52	#include "math/Vector3.hpp"
53	#include "brains/Register.hpp"
54	#include "lattice/LatticeFactory.hpp"
55
56	using namespace std;
57	namespace OpenMD{
58	shapedLattice::shapedLattice(RealType latticeConstant, string latticeType)
59	: latticeConstant_(latticeConstant), latticeType_(latticeType) {
60
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
68	//Set the lattice constant
69	std::vector<RealType> lc;
70	lc.push_back(latticeConstant_);
71	simpleLattice_->setLatticeConstant(lc);
72	sitesComputed_ = false;
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	sitesComputed_ = false;
85	}
86
87	void shapedLattice::setOrigin(Vector3d origin){
88	origin_ = origin;
89	simpleLattice_->setOrigin(origin_);
90	sitesComputed_ = false;
91	}
92
93	void shapedLattice::findSites(){
94
95	sites_.clear();
96	orientations_.clear();
97
98	std::vector<Vector3d> latticePos;
99	std::vector<Vector3d> pointsOrt = simpleLattice_->getLatticePointsOrt();
100	int numMolPerCell = simpleLattice_->getNumSitesPerCell();
101
102	for(int i = beginNx_; i < endNx_; i++) {
103	for(int j = beginNy_; j < endNy_; j++) {
104	for(int k = beginNz_; k < endNz_; k++) {
105	//get the position of the cell sites
106	simpleLattice_->getLatticePointsPos(latticePos, i, j, k);
107	for(int l = 0; l < numMolPerCell; l++) {
108	if (isInterior(latticePos[l])){
109	Vector3d myPoint = latticePos[l];
110	Vector3d myOrt = pointsOrt[l];
111	sites_.push_back(myPoint);
112	orientations_.push_back(myOrt);
113	}
114	}
115	}
116	}
117	}
118	sitesComputed_ = true;
119	}
120
121	std::vector<Vector3d> shapedLattice::getSites() {
122	if (!sitesComputed_) {
123	findSites();
124	}
125	return sites_;
126	}
127
128	std::vector<Vector3d> shapedLattice::getOrientations() {
129	if (!sitesComputed_) {
130	findSites();
131	}
132	return orientations_;
133	}
134	}