applications/nanoparticleBuilder/sphericalNanoparticle.cpp

/*
 *  sphericalNanoparticle.cpp
 *  OOPSE-2.0
 *
 *  Created by Charles F. Vardeman II on 9/28/05.
 *  Copyright 2005 __MyCompanyName__. All rights reserved.
 * Copyright (c) 2005 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.
 */

#include "sphericalNanoparticle.hpp"
#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <iostream>
#include <string>
#include <map>
#include <fstream>

#include "config.h"


#include "lattice/LatticeFactory.hpp"
#include "utils/MoLocator.hpp"
#include "lattice/Lattice.hpp"
#include "brains/Register.hpp"
#include "brains/SimInfo.hpp"
#include "brains/SimCreator.hpp"
#include "io/DumpWriter.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "utils/StringUtils.hpp"

using namespace std;
using namespace oopse;

sphericalNanoparticle::sphericalNanoparticle(double radius, int latticeConstant){
  
  particleRadius_ = radius;
  particleDiameter_ = 2.0 * radius;
  latticeConstant_ = latticeConstant;
  
  // Number of Unit Cells in Length first
  ny_ = (int)(particleDiameter/latticeConstant);
  // Number of unit cells in Width
  nx_ = (int)(particleDiameter/latticeConstant);
  nz_ = (int)(particleDiameter/latticeConstant);
}

int sphericalNanoparticle::getNMol(Lattice& simpleLat){
  int numMol;
  int numMolPerCell
    std::vector<Vector3d> latticePos;
  
  numMol = 0;
  numMolPerCell = simpleLat->getNumSitesPerCell();
  for(int i = -nx_; i < nx_; i++) {     
    for(int j = -ny_; j < ny_; j++) {       
      for(int k = -nz_; k < nz_; k++) {
        simpleLat->getLatticePointsPos(latticePos, i, j, k);
        
        for(int l = 0; l < numMolPerCell; l++) {
          rx = latticePos[l][0];
          ry = latticePos[l][1];
          rz = latticePos[l][2];
          dist = sqrt(rx*rx + ry*ry + rz*rz)
            if (dist <= particleRadius){
              numMol++;
            }
        }
      }
    }
  }
  
  return numMol;
}

int sphericalNanoparticle::getNMol(Lattice &simpleLat, int nComponents, double &shellRadius,int &numSites){
  int numMol;
  int numMolPerCell
    std::vector<Vector3d> latticePos;
  
  numMol = 0;
  numMolPerCell = simpleLat->getNumSitesPerCell();
  for(int i = -nx_; i < nx_; i++) {     
    for(int j = -ny_; j < ny_; j++) {       
      for(int k = -nz_; k < nz_; k++) {
        simpleLat->getLatticePointsPos(latticePos, i, j, k);
        
        for(int l = 0; l < numMolPerCell; l++) {
          rx = latticePos[l][0];
          ry = latticePos[l][1];
          rz = latticePos[l][2];
          dist = sqrt(rx*rx + ry*ry + rz*rz)
            if (dist <= particleRadius){
              for (int l = 0; l< nComponents -1;l++){
                if (dist <= shellRadius[l]{
                  numMol++;
                }
            }
        }
      }
    }
  }
  
  return numMol;
}


void sphericalNanoparticle::buildSphericalNanoparticle(Molecule* ){
  
  
}

Revision:	2566
Committed:	Fri Jan 13 21:57:48 2006 UTC (18 years, 5 months ago) by chuckv
File size:	4908 byte(s)
Log Message:	Removed MixingRule from Globals. Handled by forceField now.
#	User	Rev	Content
1	chuckv	2352	/*
2			* sphericalNanoparticle.cpp
3			* OOPSE-2.0
4			*
5			* Created by Charles F. Vardeman II on 9/28/05.
6			* Copyright 2005 __MyCompanyName__. All rights reserved.
7			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
8			*
9			* The University of Notre Dame grants you ("Licensee") a
10			* non-exclusive, royalty free, license to use, modify and
11			* redistribute this software in source and binary code form, provided
12			* that the following conditions are met:
13			*
14			* 1. Acknowledgement of the program authors must be made in any
15			* publication of scientific results based in part on use of the
16			* program. An acceptable form of acknowledgement is citation of
17			* the article in which the program was described (Matthew
18			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
19			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
20			* Parallel Simulation Engine for Molecular Dynamics,"
21			* J. Comput. Chem. 26, pp. 252-271 (2005))
22			*
23			* 2. Redistributions of source code must retain the above copyright
24			* notice, this list of conditions and the following disclaimer.
25			*
26			* 3. Redistributions in binary form must reproduce the above copyright
27			* notice, this list of conditions and the following disclaimer in the
28			* documentation and/or other materials provided with the
29			* distribution.
30			*
31			* This software is provided "AS IS," without a warranty of any
32			* kind. All express or implied conditions, representations and
33			* warranties, including any implied warranty of merchantability,
34			* fitness for a particular purpose or non-infringement, are hereby
35			* excluded. The University of Notre Dame and its licensors shall not
36			* be liable for any damages suffered by licensee as a result of
37			* using, modifying or distributing the software or its
38			* derivatives. In no event will the University of Notre Dame or its
39			* licensors be liable for any lost revenue, profit or data, or for
40			* direct, indirect, special, consequential, incidental or punitive
41			* damages, however caused and regardless of the theory of liability,
42			* arising out of the use of or inability to use software, even if the
43			* University of Notre Dame has been advised of the possibility of
44			* such damages.
45			*/
46
47			#include "sphericalNanoparticle.hpp"
48			#include <cstdlib>
49			#include <cstdio>
50			#include <cstring>
51			#include <cmath>
52			#include <iostream>
53			#include <string>
54			#include <map>
55			#include <fstream>
56
57			#include "config.h"
58
59
60			#include "lattice/LatticeFactory.hpp"
61			#include "utils/MoLocator.hpp"
62			#include "lattice/Lattice.hpp"
63			#include "brains/Register.hpp"
64			#include "brains/SimInfo.hpp"
65			#include "brains/SimCreator.hpp"
66			#include "io/DumpWriter.hpp"
67			#include "math/Vector3.hpp"
68			#include "math/SquareMatrix3.hpp"
69			#include "utils/StringUtils.hpp"
70
71			using namespace std;
72			using namespace oopse;
73
74	chuckv	2566	sphericalNanoparticle::sphericalNanoparticle(double radius, int latticeConstant){
75	chuckv	2352
76	chuckv	2566	particleRadius_ = radius;
77			particleDiameter_ = 2.0 * radius;
78			latticeConstant_ = latticeConstant;
79	chuckv	2352
80			// Number of Unit Cells in Length first
81			ny_ = (int)(particleDiameter/latticeConstant);
82			// Number of unit cells in Width
83			nx_ = (int)(particleDiameter/latticeConstant);
84			nz_ = (int)(particleDiameter/latticeConstant);
85			}
86
87			int sphericalNanoparticle::getNMol(Lattice& simpleLat){
88			int numMol;
89			int numMolPerCell
90			std::vector<Vector3d> latticePos;
91
92			numMol = 0;
93			numMolPerCell = simpleLat->getNumSitesPerCell();
94			for(int i = -nx_; i < nx_; i++) {
95			for(int j = -ny_; j < ny_; j++) {
96			for(int k = -nz_; k < nz_; k++) {
97			simpleLat->getLatticePointsPos(latticePos, i, j, k);
98
99			for(int l = 0; l < numMolPerCell; l++) {
100			rx = latticePos[l][0];
101			ry = latticePos[l][1];
102			rz = latticePos[l][2];
103			dist = sqrt(rxrx + ryry + rz*rz)
104			if (dist <= particleRadius){
105			numMol++;
106			}
107			}
108			}
109			}
110			}
111
112			return numMol;
113			}
114
115			int sphericalNanoparticle::getNMol(Lattice &simpleLat, int nComponents, double &shellRadius,int &numSites){
116			int numMol;
117			int numMolPerCell
118			std::vector<Vector3d> latticePos;
119
120			numMol = 0;
121			numMolPerCell = simpleLat->getNumSitesPerCell();
122			for(int i = -nx_; i < nx_; i++) {
123			for(int j = -ny_; j < ny_; j++) {
124			for(int k = -nz_; k < nz_; k++) {
125			simpleLat->getLatticePointsPos(latticePos, i, j, k);
126
127			for(int l = 0; l < numMolPerCell; l++) {
128			rx = latticePos[l][0];
129			ry = latticePos[l][1];
130			rz = latticePos[l][2];
131			dist = sqrt(rxrx + ryry + rz*rz)
132			if (dist <= particleRadius){
133			for (int l = 0; l< nComponents -1;l++){
134			if (dist <= shellRadius[l]{
135			numMol++;
136			}
137			}
138			}
139			}
140			}
141			}
142
143			return numMol;
144			}
145
146
147
148
149			void sphericalNanoparticle::buildSphericalNanoparticle(Molecule* ){
150
151
152
153
154
155			}
156