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root/OpenMD/branches/development/src/lattice/shapedLattice.cpp

Comparing:
trunk/src/lattice/shapedLattice.cpp (file contents), Revision 905 by chuckv, Fri Mar 17 16:11:30 2006 UTC vs.
branches/development/src/lattice/shapedLattice.cpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	Line 5 | Line 5
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
8	>	* 1. Redistributions of source code must retain the above copyright
9		*    notice, this list of conditions and the following disclaimer.
10		*
11	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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: shapedLattice.cpp,v 1.1 2006-03-17 16:10:19 chuckv Exp $
46	>	*  @version $Id$
47		*
48		*/
49
50	<
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	<	namespace oopse{
57	<	shapedLattice::shapedLattice(double latticeConstant,
58	<	std::string latticeType) {
59	<	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	<	}
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<double> lc;
68	>	//Set the lattice constant
69	>	std::vector<RealType> lc;
70		lc.push_back(latticeConstant_);
71	<	simpleLattice_->setLatticeConstant(lc);
72	<	origin_[0]=0.0;
73	<	origin_[1]=0.0;
74	<	origin_[2]=0.0;
74	<	}
75	<
76	<
77	<
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(dimension_[0]/latticeConstant_) ;
79	<	beginNy_ = -(int) ceil(dimension_[1]/latticeConstant_) ;
80	<	beginNz_ = -(int) ceil(dimension_[2]/latticeConstant_) ;
81	<	endNx_ = (int) ceil(dimension_[0]/latticeConstant_);
82	<	endNy_ = (int) ceil(dimension_[1]/latticeConstant_);
83	<	endNz_ = (int) ceil(dimension_[2]/latticeConstant_);
84	<
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	>	std::cerr << "begin = " << beginNx_ << " " << beginNy_ << " " << beginNz_ << "\n";
85	>	std::cerr << "end = " << endNx_ << " " << endNy_ << " " << endNz_ << "\n";
86	>	sitesComputed_ = false;
87		}
88	<
89	<
91	<
92	<	void shapedLattice::setGridDimension(Vector3d dimension, Vector3d origin){
93	<	dimension_ = dimension;
88	>
89	>	void shapedLattice::setOrigin(Vector3d origin){
90		origin_ = origin;
91	<	// Find number of unit cells in each direction
92	<	beginNx_ = -(int) ceil(dimension_[0]/latticeConstant_) + (int) floor(origin[0]);
97	<	beginNy_ = -(int) ceil(dimension_[1]/latticeConstant_) + (int) floor(origin[1]);
98	<	beginNz_ = -(int) ceil(dimension_[2]/latticeConstant_) + (int) floor(origin[2]);
99	<	endNx_ = (int) ceil(dimension_[0]/latticeConstant_) + (int) floor(origin[0]);
100	<	endNy_ = (int) ceil(dimension_[1]/latticeConstant_) + (int) floor(origin[1]);
101	<	endNz_ = (int) ceil(dimension_[2]/latticeConstant_) + (int) floor(origin[2]);
102	<
91	>	simpleLattice_->setOrigin(origin_);
92	>	sitesComputed_ = false;
93		}
94
95	<	std::vector<Vector3d> shapedLattice::getPoints(){
96	<	std::vector<Vector3d> latticePos;
97	<
98	<	int numMolPerCell = simpleLattice_->getNumSitesPerCell();
99	<	for(int i = beginNx_; i < endNx_; i++) {
100	<	for(int j = beginNy_; j < endNy_; j++) {
101	<	for(int k = beginNz_; k < endNz_; k++) {
102	<	//get the position of the cell sites
103	<	simpleLattice_->getLatticePointsPos(latticePos, i, j, k);
104	<
105	<	for(int l = 0; l < numMolPerCell; l++) {
106	<
107	<	if (isInterior(latticePos[l])){
108	<	coords_.push_back(latticePos[l]);
109	<	}
95	>	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		}
116		}
117		}
118		}
119	<
120	<	return coords_;
121	<
122	<	}
119	>	}
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		}

Comparing:
trunk/src/lattice/shapedLattice.cpp (property svn:keywords), Revision 905 by chuckv, Fri Mar 17 16:11:30 2006 UTC vs.
branches/development/src/lattice/shapedLattice.cpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

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