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root/group/trunk/OOPSE/libmdtools/Atom.cpp
Revision: 1167
Committed: Wed May 12 16:38:45 2004 UTC (20 years, 2 months ago) by tim
File size: 3146 byte(s)
Log Message: 
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file

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 1167 &ul);
52 gezelter 409 }
53 mmeineke 670 else{
54     sprintf( painCave.errMsg,
55     "Attempted to set Atom %d coordinates with an unallocated "
56 mmeineke 787 "SimState object.\n", index );
57 mmeineke 670 painCave.isFatal = 1;
58     simError();
59     }
60 gezelter 1097
61 mmeineke 670 hasCoords = true;
62 gezelter 1097
63 gezelter 409 }
64    
65 mmeineke 599 void Atom::getPos( double theP[3] ){
66    
67 mmeineke 670 if( hasCoords ){
68     theP[0] = pos[offsetX];
69     theP[1] = pos[offsetY];
70     theP[2] = pos[offsetZ];
71     }
72     else{
73    
74     sprintf( painCave.errMsg,
75     "Attempt to get Pos for atom %d before coords set.\n",
76     index );
77     painCave.isFatal = 1;
78     simError();
79     }
80 mmeineke 599 }
81    
82     void Atom::setPos( double theP[3] ){
83 gezelter 1097
84 mmeineke 670 if( hasCoords ){
85     pos[offsetX] = theP[0];
86     pos[offsetY] = theP[1];
87     pos[offsetZ] = theP[2];
88     }
89     else{
90    
91     sprintf( painCave.errMsg,
92     "Attempt to set Pos for atom %d before coords set.\n",
93     index );
94     painCave.isFatal = 1;
95     simError();
96     }
97 mmeineke 599 }
98    
99     void Atom::getVel( double theV[3] ){
100    
101 mmeineke 670 if( hasCoords ){
102     theV[0] = vel[offsetX];
103     theV[1] = vel[offsetY];
104     theV[2] = vel[offsetZ];
105     }
106     else{
107    
108     sprintf( painCave.errMsg,
109     "Attempt to get vel for atom %d before coords set.\n",
110     index );
111     painCave.isFatal = 1;
112     simError();
113     }
114    
115 mmeineke 599 }
116    
117     void Atom::setVel( double theV[3] ){
118    
119 mmeineke 670 if( hasCoords ){
120     vel[offsetX] = theV[0];
121     vel[offsetY] = theV[1];
122     vel[offsetZ] = theV[2];
123     }
124     else{
125    
126     sprintf( painCave.errMsg,
127     "Attempt to set vel for atom %d before coords set.\n",
128     index );
129     painCave.isFatal = 1;
130     simError();
131     }
132 mmeineke 599 }
133    
134     void Atom::getFrc( double theF[3] ){
135    
136 mmeineke 670 if( hasCoords ){
137     theF[0] = frc[offsetX];
138     theF[1] = frc[offsetY];
139     theF[2] = frc[offsetZ];
140     }
141     else{
142    
143     sprintf( painCave.errMsg,
144     "Attempt to get frc for atom %d before coords set.\n",
145     index );
146     painCave.isFatal = 1;
147     simError();
148     }
149 mmeineke 599 }
150    
151     void Atom::addFrc( double theF[3] ){
152    
153 mmeineke 670 if( hasCoords ){
154     frc[offsetX] += theF[0];
155     frc[offsetY] += theF[1];
156     frc[offsetZ] += theF[2];
157     }
158     else{
159    
160     sprintf( painCave.errMsg,
161     "Attempt to add frc for atom %d before coords set.\n",
162     index );
163     painCave.isFatal = 1;
164     simError();
165     }
166 mmeineke 599 }
167 mmeineke 670
168    
169 gezelter 1097 void Atom::zeroForces( void ){
170 mmeineke 670
171     if( hasCoords ){
172     frc[offsetX] = 0.0;
173     frc[offsetY] = 0.0;
174     frc[offsetZ] = 0.0;
175     }
176     else{
177    
178     sprintf( painCave.errMsg,
179     "Attempt to zero frc for atom %d before coords set.\n",
180     index );
181     painCave.isFatal = 1;
182     simError();
183     }
184     }
185 tim 1118