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root/OpenMD/trunk/src/primitives/Atom.cpp
Revision: 3
Committed: Fri Sep 24 16:27:58 2004 UTC (20 years, 7 months ago) by tim
File size: 3163 byte(s)
Log Message: 
change the #include in source files

File Contents

# User Rev Content
1 gezelter 2 #include <iostream>
2    
3     using namespace std;
4    
5 tim 3 #include "utils/simError.h"
6     #include "primitives/Atom.hpp"
7 gezelter 2
8     Atom::Atom(int theIndex, SimState* theConfig) {
9    
10     objType = OT_ATOM;
11     myConfig = theConfig;
12     hasCoords = false;
13    
14     has_dipole = 0;
15     has_charge = 0;
16    
17     index = theIndex;
18     offset = 0;
19     offsetX = offset;
20     offsetY = offset+1;
21     offsetZ = offset+2;
22    
23     Axx = 0;
24     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     void Atom::setIndex(int theIndex) {
37     index = theIndex;
38     }
39    
40     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     &ul);
52     }
53     else{
54     sprintf( painCave.errMsg,
55     "Attempted to set Atom %d coordinates with an unallocated "
56     "SimState object.\n", index );
57     painCave.isFatal = 1;
58     simError();
59     }
60    
61     hasCoords = true;
62    
63     }
64    
65     void Atom::getPos( double theP[3] ){
66    
67     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     }
81    
82     void Atom::setPos( double theP[3] ){
83    
84     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     }
98    
99     void Atom::getVel( double theV[3] ){
100    
101     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     }
116    
117     void Atom::setVel( double theV[3] ){
118    
119     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     }
133    
134     void Atom::getFrc( double theF[3] ){
135    
136     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     }
150    
151     void Atom::addFrc( double theF[3] ){
152    
153     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     }
167    
168    
169     void Atom::zeroForces( void ){
170    
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