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root/group/trunk/OOPSE/libmdtools/Atom.cpp
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Comparing trunk/OOPSE/libmdtools/Atom.cpp (file contents):
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 6 | Line 6 | Atom::Atom(int theIndex, SimState* theConfig) {
6   #include "Atom.hpp"
7  
8   Atom::Atom(int theIndex, SimState* theConfig) {
9 <  
9 >
10 >  objType = OT_ATOM;
11    myConfig = theConfig;
12    hasCoords = false;
13  
13 –  c_n_hyd = 0;
14    has_dipole = 0;
15 –  is_VDW = 0;
16 –  is_LJ = 0;
17 –  is_charged = 0;
15    
16    index = theIndex;
17    offset = 0;
# Line 43 | Line 40 | void Atom::setCoords(void){
40  
41    if( myConfig->isAllocated() ){
42  
46 –
43      myConfig->getAtomPointers( index,
44                       &pos,
45                       &vel,
# Line 60 | Line 56 | void Atom::setCoords(void){
56      painCave.isFatal = 1;
57      simError();
58    }
59 <
59 >  
60    hasCoords = true;
61 <
61 >  
62   }
63  
68 – // void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
69 – //                    double* Atrq, double* AAmat, double* Amu,
70 – //                    double* Aul) {
71 –
72 – //   int nNew = nElements+nAdded;
73 –
74 – //   double* new_pos = new double[nNew*3];
75 – //   double* new_vel = new double[nNew*3];
76 – //   double* new_frc = new double[nNew*3];
77 – //   double* new_trq = new double[nNew*3];
78 – //   double* new_Amat = new double[nNew*9];
79 – //   double* new_mu = new double[nNew];
80 – //   double* new_ul = new double[nNew*3];
81 – //   int i, j;
82 –  
83 – //   for (i = 0; i < 3*nElements; i++) {
84 – //     new_pos[i] = pos[i];
85 – //     new_vel[i] = vel[i];
86 – //     new_frc[i] = frc[i];
87 – //     new_trq[i] = trq[i];
88 – //     new_ul[i] = ul[i];
89 – //   }
90 –
91 – //   for(i = 0; i < 3*nAdded; i++) {
92 – //     j = i + 3*nElements;
93 – //     new_pos[j] = Apos[i];
94 – //     new_vel[j] = Avel[i];
95 – //     new_frc[j] = Afrc[i];
96 – //     new_trq[j] = Atrq[i];
97 – //     new_ul[j] = Aul[i];
98 – //   }
99 –
100 – //   for (i = 0; i < 9*nElements; i++) {
101 – //     new_Amat[i] = Amat[i];
102 – //   }
103 –
104 – //   for(i = 0; i < 9*nAdded; i++) {
105 – //     j = i + 9*nElements;
106 – //     new_Amat[j] = AAmat[i];
107 – //   }
108 –
109 – //   for (i = 0; i < nElements; i++) {
110 – //     new_mu[i] = mu[i];
111 – //   }
112 –
113 – //   for(i = 0; i < nAdded; i++) {
114 – //     j = i + nElements;
115 – //     new_mu[j] = Amu[i];
116 – //   }
117 –
118 – //   delete[] pos;
119 – //   delete[] vel;
120 – //   delete[] frc;
121 – //   delete[] trq;
122 – //   delete[] Amat;
123 – //   delete[] mu;
124 –
125 – //   pos = new_pos;
126 – //   vel = new_vel;
127 – //   frc = new_frc;
128 – //   trq = new_trq;
129 – //   ul = new_ul;
130 – //   Amat = new_Amat;
131 – //   mu = new_mu;
132 –
133 – //   nElements = nNew;
134 – // }
135 –
136 – // void Atom::deleteAtom(int theIndex) {
137 – //   deleteRange(theIndex, theIndex);
138 – // }
139 –
140 – // void Atom::deleteRange(int startIndex, int stopIndex) {
141 –
142 – //   int nNew = nElements-(stopIndex-startIndex+1);
143 –
144 – //   double* new_pos = new double[nNew*3];
145 – //   double* new_vel = new double[nNew*3];
146 – //   double* new_frc = new double[nNew*3];
147 – //   double* new_trq = new double[nNew*3];
148 – //   double* new_Amat = new double[nNew*9];
149 – //   double* new_mu = new double[nNew];
150 – //   double* new_ul = new double[nNew*3];
151 – //   int i, j;
152 –  
153 – //   for (i = 0; i < 3*startIndex; i++) {
154 – //     new_pos[i] = pos[i];
155 – //     new_vel[i] = vel[i];
156 – //     new_frc[i] = frc[i];
157 – //     new_trq[i] = trq[i];
158 – //     new_ul[i] = ul[i];
159 – //   }
160 –
161 – //   for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
162 – //     j = i - 3*startIndex + 1;
163 – //     new_pos[j] = pos[i];
164 – //     new_vel[j] = vel[i];
165 – //     new_frc[j] = frc[i];
166 – //     new_trq[j] = trq[i];
167 – //     new_ul[j] = ul[i];
168 – //   }
169 –
170 – //   for (i = 0; i < 9*startIndex; i++) {
171 – //     new_Amat[i] = Amat[i];
172 – //   }
173 –
174 – //   for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
175 – //     j = i - 9*startIndex + 1;
176 – //     new_Amat[j] = Amat[i];
177 – //   }
178 –
179 – //   for (i = 0; i < startIndex; i++) {
180 – //     new_mu[i] = mu[i];
181 – //   }
182 –
183 – //   for(i = (stopIndex+1); i < nElements; i++) {
184 – //     j = i - startIndex + 1;
185 – //     new_mu[j] = mu[i];
186 – //   }
187 –
188 – //   delete[] pos;
189 – //   delete[] vel;
190 – //   delete[] frc;
191 – //   delete[] trq;
192 – //   delete[] Amat;
193 – //   delete[] mu;
194 –
195 – //   pos = new_pos;
196 – //   vel = new_vel;
197 – //   frc = new_frc;
198 – //   trq = new_trq;
199 – //   ul = new_ul;
200 – //   Amat = new_Amat;
201 – //   mu = new_mu;
202 –
203 – //   nElements = nNew;
204 – // }
205 –
206 –
64   void Atom::getPos( double theP[3] ){
65    
66    if( hasCoords ){
# Line 222 | Line 79 | void Atom::setPos( double theP[3] ){
79   }
80  
81   void Atom::setPos( double theP[3] ){
82 <  
82 >
83    if( hasCoords ){
84      pos[offsetX] = theP[0];
85      pos[offsetY] = theP[1];
# Line 308 | Line 165 | void GeneralAtom::zeroForces( void ){
165   }
166  
167  
168 < void GeneralAtom::zeroForces( void ){
168 > void Atom::zeroForces( void ){
169    
313 –  
170    if( hasCoords ){
171      frc[offsetX] = 0.0;
172      frc[offsetY] = 0.0;

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