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Comparing trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (file contents):
Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41   #include "applications/hydrodynamics/ShapeBuilder.hpp"
42 < #include "applications/hydrodynamics/Spheric.hpp"
43 < #include "applications/hydrodynamics/Ellipsoid.hpp"
42 > #include "hydrodynamics/Sphere.hpp"
43 > #include "hydrodynamics/Ellipsoid.hpp"
44   #include "applications/hydrodynamics/CompositeShape.hpp"
45 < namespace oopse {
46 <
47 < Shape* ShapeBuilder::createShape(StuntDouble* sd) {
45 > namespace OpenMD {
46 >  
47 >  Shape* ShapeBuilder::createShape(StuntDouble* sd) {
48      Shape* currShape = NULL;
49 <            if (sd->isDirectionalAtom()) {
50 <              currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
51 <            } else if (sd->isAtom()) {
52 <                currShape = internalCreateShape(static_cast<Atom*>(sd));
53 <            } else if (sd->isRigidBody()) {
54 <                currShape = internalCreateShape(static_cast<RigidBody*>(sd));
55 <            }
56 <            
57 <
58 <        
59 <        return currShape;
60 <
61 < }
62 <
63 < Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
49 >    if (sd->isDirectionalAtom()) {
50 >      currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
51 >    } else if (sd->isAtom()) {
52 >      currShape = internalCreateShape(static_cast<Atom*>(sd));
53 >    } else if (sd->isRigidBody()) {
54 >      currShape = internalCreateShape(static_cast<RigidBody*>(sd));
55 >    }      
56 >    return currShape;  
57 >  }
58 >  
59 >  Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
60      AtomType* atomType = atom->getAtomType();
61      Shape* currShape = NULL;
62      if (atomType->isLennardJones()){
63 <        GenericData* data = atomType->getPropertyByName("LennardJones");
64 <        if (data != NULL) {
65 <            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
66 <
67 <            if (ljData != NULL) {
68 <                LJParam ljParam = ljData->getData();
69 <                currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
63 >      GenericData* data = atomType->getPropertyByName("LennardJones");
64 >      if (data != NULL) {
65 >        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
66 >        
67 >        if (ljData != NULL) {
68 >          LJParam ljParam = ljData->getData();
69 >          currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
70          } else {
71 <            sprintf( painCave.errMsg,
72 <            "Can not cast GenericData to LJParam\n");
73 <            painCave.severity = OOPSE_ERROR;
74 <            painCave.isFatal = 1;
75 <            simError();          
76 <            }      
77 <        }
78 <
71 >          sprintf( painCave.errMsg,
72 >                   "Can not cast GenericData to LJParam\n");
73 >          painCave.severity = OPENMD_ERROR;
74 >          painCave.isFatal = 1;
75 >          simError();          
76 >        }      
77 >      }
78 >    } else {
79 >      int obanum = etab.GetAtomicNum((atom->getType()).c_str());
80 >      if (obanum != 0) {
81 >        currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
82 >      } else {
83 >        sprintf( painCave.errMsg,
84 >                 "Could not find atom type in default element.txt\n");
85 >        painCave.severity = OPENMD_ERROR;
86 >        painCave.isFatal = 1;
87 >        simError();          
88 >      }
89      }
84 –
90      return currShape;
91 < }
92 <
93 < Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
91 >  }
92 >  
93 >  Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
94      AtomType* atomType = datom->getAtomType();
95      Shape* currShape = NULL;
96      if (atomType->isGayBerne()) {
97 <        DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
98 <
99 <        GenericData* data = dAtomType->getPropertyByName("GayBerne");
100 <        if (data != NULL) {
101 <            GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
102 <
103 <            if (gayBerneData != NULL) {  
104 <                GayBerneParam gayBerneParam = gayBerneData->getData();
105 <                currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
106 <            } else {
102 <                sprintf( painCave.errMsg,
103 <                       "Can not cast GenericData to GayBerneParam\n");
104 <                painCave.severity = OOPSE_ERROR;
105 <                painCave.isFatal = 1;
106 <                simError();  
107 <            }
97 >      DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
98 >      
99 >      GenericData* data = dAtomType->getPropertyByName("GayBerne");
100 >      if (data != NULL) {
101 >        GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
102 >        
103 >        if (gayBerneData != NULL) {  
104 >          GayBerneParam gayBerneParam = gayBerneData->getData();
105 >          currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0,
106 >                                    gayBerneParam.GB_d/2.0, datom->getA());
107          } else {
108 <          sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
109 <          painCave.severity = OOPSE_ERROR;
110 <          painCave.isFatal = 1;
111 <          simError();    
112 <        }            
108 >          sprintf( painCave.errMsg,
109 >                   "Can not cast GenericData to GayBerneParam\n");
110 >          painCave.severity = OPENMD_ERROR;
111 >          painCave.isFatal = 1;
112 >          simError();  
113 >        }
114 >      } else {
115 >        sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
116 >        painCave.severity = OPENMD_ERROR;
117 >        painCave.isFatal = 1;
118 >        simError();    
119 >      }            
120 >    } else if (atomType->isLennardJones()) {
121 >      GenericData* data = atomType->getPropertyByName("LennardJones");
122 >      if (data != NULL) {
123 >        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
124 >        
125 >        if (ljData != NULL) {
126 >          LJParam ljParam = ljData->getData();
127 >          currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
128 >        } else {
129 >          sprintf( painCave.errMsg,
130 >                   "Can not cast GenericData to LJParam\n");
131 >          painCave.severity = OPENMD_ERROR;
132 >          painCave.isFatal = 1;
133 >          simError();          
134 >        }      
135 >      } else {
136 >        int obanum = etab.GetAtomicNum((datom->getType()).c_str());
137 >        if (obanum != 0) {
138 >          currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
139 >        } else {
140 >          sprintf( painCave.errMsg,
141 >                   "Could not find atom type in default element.txt\n");
142 >          painCave.severity = OPENMD_ERROR;
143 >          painCave.isFatal = 1;
144 >          simError();          
145 >        }
146 >      }      
147      }
148      return currShape;
149 < }
117 < Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
149 >  }
150  
151 <        std::vector<Atom*>::iterator ai;
152 <        CompositeShape* compositeShape = new CompositeShape;
153 <        Atom* atom;
154 <        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
155 <            Shape* currShape = NULL;
156 <            if (atom->isDirectionalAtom()){
157 <                currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
158 <            }else if (atom->isAtom()){
159 <                currShape =  internalCreateShape(static_cast<Atom*>(atom));
160 <            }
161 <            if (currShape != NULL)
162 <                compositeShape->addShape(currShape);
163 <        }
164 <
165 <        return compositeShape;
151 >  Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
152 >    
153 >    std::vector<Atom*>::iterator ai;
154 >    CompositeShape* compositeShape = new CompositeShape;
155 >    Atom* atom;
156 >    for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
157 >      Shape* currShape = NULL;
158 >      if (atom->isDirectionalAtom()){
159 >        currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
160 >      }else if (atom->isAtom()){
161 >        currShape =  internalCreateShape(static_cast<Atom*>(atom));
162 >      }
163 >      if (currShape != NULL)
164 >        compositeShape->addShape(currShape);
165 >    }
166 >    
167 >    return compositeShape;
168 >  }  
169   }
135 –
136 – }

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