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root/group/trunk/OOPSE/libmdtools/Atom.cpp
Revision: 1136
Committed: Tue Apr 27 16:26:44 2004 UTC (20 years, 4 months ago) by tim
File size: 3783 byte(s)
Log Message: 
add center of mass of the molecule and massRation into atom class

File Contents

# User Rev Content
1 mmeineke 561 #include <iostream>
2    
3     using namespace std;
4    
5 mmeineke 670 #include "simError.h"
6 gezelter 409 #include "Atom.hpp"
7    
8 mmeineke 670 Atom::Atom(int theIndex, SimState* theConfig) {
9 gezelter 1097
10     objType = OT_ATOM;
11 mmeineke 670 myConfig = theConfig;
12     hasCoords = false;
13 mmeineke 707
14 gezelter 409 has_dipole = 0;
15 gezelter 1125 has_charge = 0;
16 gezelter 409
17     index = theIndex;
18 mmeineke 670 offset = 0;
19 gezelter 409 offsetX = offset;
20     offsetY = offset+1;
21     offsetZ = offset+2;
22    
23 mmeineke 670 Axx = 0;
24 gezelter 409 Axy = Axx+1;
25     Axz = Axx+2;
26    
27     Ayx = Axx+3;
28     Ayy = Axx+4;
29     Ayz = Axx+5;
30    
31     Azx = Axx+6;
32     Azy = Axx+7;
33     Azz = Axx+8;
34     }
35    
36 mmeineke 670 void Atom::setIndex(int theIndex) {
37     index = theIndex;
38     }
39 mmeineke 413
40 mmeineke 670 void Atom::setCoords(void){
41    
42     if( myConfig->isAllocated() ){
43    
44     myConfig->getAtomPointers( index,
45     &pos,
46     &vel,
47     &frc,
48     &trq,
49     &Amat,
50     &mu,
51 tim 1136 &ul,
52     &rc,
53     &massRatio);
54 gezelter 409 }
55 mmeineke 670 else{
56     sprintf( painCave.errMsg,
57     "Attempted to set Atom %d coordinates with an unallocated "
58 mmeineke 787 "SimState object.\n", index );
59 mmeineke 670 painCave.isFatal = 1;
60     simError();
61     }
62 gezelter 1097
63 mmeineke 670 hasCoords = true;
64 gezelter 1097
65 gezelter 409 }
66    
67 mmeineke 599 void Atom::getPos( double theP[3] ){
68    
69 mmeineke 670 if( hasCoords ){
70     theP[0] = pos[offsetX];
71     theP[1] = pos[offsetY];
72     theP[2] = pos[offsetZ];
73     }
74     else{
75    
76     sprintf( painCave.errMsg,
77     "Attempt to get Pos for atom %d before coords set.\n",
78     index );
79     painCave.isFatal = 1;
80     simError();
81     }
82 mmeineke 599 }
83    
84     void Atom::setPos( double theP[3] ){
85 gezelter 1097
86 mmeineke 670 if( hasCoords ){
87     pos[offsetX] = theP[0];
88     pos[offsetY] = theP[1];
89     pos[offsetZ] = theP[2];
90     }
91     else{
92    
93     sprintf( painCave.errMsg,
94     "Attempt to set Pos for atom %d before coords set.\n",
95     index );
96     painCave.isFatal = 1;
97     simError();
98     }
99 mmeineke 599 }
100    
101     void Atom::getVel( double theV[3] ){
102    
103 mmeineke 670 if( hasCoords ){
104     theV[0] = vel[offsetX];
105     theV[1] = vel[offsetY];
106     theV[2] = vel[offsetZ];
107     }
108     else{
109    
110     sprintf( painCave.errMsg,
111     "Attempt to get vel for atom %d before coords set.\n",
112     index );
113     painCave.isFatal = 1;
114     simError();
115     }
116    
117 mmeineke 599 }
118    
119     void Atom::setVel( double theV[3] ){
120    
121 mmeineke 670 if( hasCoords ){
122     vel[offsetX] = theV[0];
123     vel[offsetY] = theV[1];
124     vel[offsetZ] = theV[2];
125     }
126     else{
127    
128     sprintf( painCave.errMsg,
129     "Attempt to set vel for atom %d before coords set.\n",
130     index );
131     painCave.isFatal = 1;
132     simError();
133     }
134 mmeineke 599 }
135    
136     void Atom::getFrc( double theF[3] ){
137    
138 mmeineke 670 if( hasCoords ){
139     theF[0] = frc[offsetX];
140     theF[1] = frc[offsetY];
141     theF[2] = frc[offsetZ];
142     }
143     else{
144    
145     sprintf( painCave.errMsg,
146     "Attempt to get frc for atom %d before coords set.\n",
147     index );
148     painCave.isFatal = 1;
149     simError();
150     }
151 mmeineke 599 }
152    
153     void Atom::addFrc( double theF[3] ){
154    
155 mmeineke 670 if( hasCoords ){
156     frc[offsetX] += theF[0];
157     frc[offsetY] += theF[1];
158     frc[offsetZ] += theF[2];
159     }
160     else{
161    
162     sprintf( painCave.errMsg,
163     "Attempt to add frc for atom %d before coords set.\n",
164     index );
165     painCave.isFatal = 1;
166     simError();
167     }
168 mmeineke 599 }
169 mmeineke 670
170    
171 gezelter 1097 void Atom::zeroForces( void ){
172 mmeineke 670
173     if( hasCoords ){
174     frc[offsetX] = 0.0;
175     frc[offsetY] = 0.0;
176     frc[offsetZ] = 0.0;
177     }
178     else{
179    
180     sprintf( painCave.errMsg,
181     "Attempt to zero frc for atom %d before coords set.\n",
182     index );
183     painCave.isFatal = 1;
184     simError();
185     }
186     }
187 tim 1118
188 tim 1136 void Atom::getRc(double theRc[3]){
189    
190     if( hasCoords ){
191     theRc[0] = rc[offsetX];
192     theRc[1] = rc[offsetY];
193     theRc[2] = rc[offsetZ];
194     }
195     else{
196    
197     sprintf( painCave.errMsg,
198     "Attempt to get rc for atom %d before coords set.\n",
199     index );
200     painCave.isFatal = 1;
201     simError();
202     }
203    
204     }
205    
206     void Atom::setRc(double theRc[3]){
207     if( hasCoords ){
208     rc[offsetX] = theRc[0] ;
209     rc[offsetY] = theRc[1];
210     rc[offsetZ] = theRc[2];
211     }
212     else{
213    
214     sprintf( painCave.errMsg,
215     "Attempt to set rc for atom %d before coords set.\n",
216     index );
217     painCave.isFatal = 1;
218     }
219     }