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Comparing trunk/OOPSE-2.0/src/types/AtomStamp.hpp (file contents):
Revision 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2483 by tim, Mon Dec 5 18:23:30 2005 UTC

# Line 1 | Line 1
1 < /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 < *
4 < * The University of Notre Dame grants you ("Licensee") a
5 < * non-exclusive, royalty free, license to use, modify and
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
19 < *    notice, this list of conditions and the following disclaimer.
20 < *
21 < * 3. Redistributions in binary form must reproduce the above copyright
22 < *    notice, this list of conditions and the following disclaimer in the
23 < *    documentation and/or other materials provided with the
24 < *    distribution.
25 < *
26 < * This software is provided "AS IS," without a warranty of any
27 < * kind. All express or implied conditions, representations and
28 < * warranties, including any implied warranty of merchantability,
29 < * fitness for a particular purpose or non-infringement, are hereby
30 < * excluded.  The University of Notre Dame and its licensors shall not
31 < * be liable for any damages suffered by licensee as a result of
32 < * using, modifying or distributing the software or its
33 < * derivatives. In no event will the University of Notre Dame or its
34 < * licensors be liable for any lost revenue, profit or data, or for
35 < * direct, indirect, special, consequential, incidental or punitive
36 < * damages, however caused and regardless of the theory of liability,
37 < * arising out of the use of or inability to use software, even if the
38 < * University of Notre Dame has been advised of the possibility of
39 < * such damages.
40 < */
41 <
42 < #ifndef TYPES_ATOMSTAMP_HPP
43 < #define TYPES_ATOMSTAMP_HPP
44 <
45 < #include "io/LinkedAssign.hpp"
46 <
47 < class AtomStamp{
48 <  
49 < public:
50 <  AtomStamp();
51 <  ~AtomStamp();
52 <
53 <  void setPosition( double x, double y, double z );
54 <  void setOrientation( double phi, double theta, double psi );
55 <  char* assignString( char* lhs, char* rhs );
56 <  char* assignDouble( char* lhs, double rhs );
57 <  char* assignInt( char* lhs, int rhs );
58 <  char* checkMe( void );
59 <
60 <  char* getType( void ) { return type; }
61 <  short int havePosition( void ) { return have_position; }
62 <  short int haveOrientation( void ) { return have_orientation; }
63 <  double getPosX( void ) { return pos[0]; }
64 <  double getPosY( void ) { return pos[1]; }
65 <  double getPosZ( void ) { return pos[2]; }
66 <  double getEulerPhi( void )   { return ornt[0]; }
67 <  double getEulerTheta( void ) { return ornt[1]; }
68 <  double getEulerPsi( void )   { return ornt[2]; }
69 <  
70 <
71 < private:
72 <
73 <  double pos[3]; //the position vector
74 <  short int have_position; // boolean for positions
75 <  double ornt[3]; // the Euler angles
76 <  short int have_orientation;
77 <  char type[100]; // the type name of the atom
78 <  short int have_type;
79 <  
80 <  LinkedAssign* unhandled; // the list of unhandled assignments
81 <  short int have_extras;
82 < };
83 <
84 < #endif
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 > *
4 > * The University of Notre Dame grants you ("Licensee") a
5 > * non-exclusive, royalty free, license to use, modify and
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
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41 >
42 > #ifndef TYPES_ATOMSTAMP_HPP
43 > #define TYPES_ATOMSTAMP_HPP
44 >
45 > #include <set>
46 > #include <vector>
47 >
48 > #include "types/DataHolder.hpp"
49 > namespace oopse {
50 >
51 > class AtomStamp  : public DataHolder {
52 >    DeclareParameter(Type, std::string);
53 >    public:
54 >        AtomStamp(int index);
55 >    public:
56 >
57 >      bool setPosition(const std::vector<double>& pos);
58 >      bool setOrientation(const std::vector<double>& ort);
59 >      bool havePosition() { return havePos_; }
60 >      bool haveOrientation() { return haveOrt_; }      
61 >      double getPosX() { return position_[0]; }
62 >      double getPosY() { return position_[1]; }
63 >      double getPosZ() { return position_[2]; }
64 >      double getEulerPhi()   { return orientation_[0]; }
65 >      double getEulerTheta() { return orientation_[1]; }
66 >      double getEulerPsi()   { return orientation_[2]; }
67 >      int getIndex() { return index_;}
68 >      virtual void validate();
69 >      typedef std::set<int>::iterator AtomIter;
70 >      typedef std::vector<int>::iterator BondIter;
71 >      int getFirstBonedAtom(AtomIter& ai) {
72 >        ai = bondedAtoms_.begin();
73 >        return ai != bondedAtoms_.end() ? *ai : -1;
74 >      }
75 >      
76 >      int getNextBonedAtom(AtomIter& ai) {
77 >        ++ai;
78 >        return ai != bondedAtoms_.end() ? *ai : -1;
79 >      }
80 >      
81 >      int getFirstBond(BondIter& bi) {
82 >        bi = bonds_.begin();
83 >        return bi != bonds_.end()? *bi: -1;
84 >      }
85 >      int getNextBond(BondIter& bi) {
86 >        ++bi;
87 >        return bi != bonds_.end()? *bi: -1;
88 >      }
89 >      
90 >      void addBond(int bondIndex) {bonds_.push_back(bondIndex);}
91 >      void addBondedAtom(int atomIndex) {bondedAtoms_.insert(atomIndex);}
92 >    private:
93 >        Vector3d position_;
94 >        Vector3d orientation_;
95 >        bool havePos_;
96 >        bool haveOrt_;
97 >        int index_;
98 >        std::vector<int> bonds_;
99 >        std::set<int> bondedAtoms_;
100 > };
101 >
102 > }
103 > #endif

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