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root/group/trunk/OOPSE/libmdtools/Atom.cpp
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Comparing trunk/OOPSE/libmdtools/Atom.cpp (file contents):
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC vs.
Revision 1126 by tim, Tue Apr 20 05:39:38 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;
13 >
14    has_dipole = 0;
15 <  is_VDW = 0;
16 <  is_LJ = 0;
15 >  has_charge = 0;
16    
17    index = theIndex;
18    offset = 0;
# Line 42 | Line 41 | void Atom::setCoords(void){
41  
42    if( myConfig->isAllocated() ){
43  
45 –
44      myConfig->getAtomPointers( index,
45                       &pos,
46                       &vel,
# Line 55 | Line 53 | void Atom::setCoords(void){
53    else{
54      sprintf( painCave.errMsg,
55               "Attempted to set Atom %d  coordinates with an unallocated "
56 <             "SimState object.\n" );
56 >             "SimState object.\n", index );
57      painCave.isFatal = 1;
58      simError();
59    }
60 <
60 >  
61    hasCoords = true;
62 <
62 >  
63   }
64  
67 – // void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
68 – //                    double* Atrq, double* AAmat, double* Amu,
69 – //                    double* Aul) {
70 –
71 – //   int nNew = nElements+nAdded;
72 –
73 – //   double* new_pos = new double[nNew*3];
74 – //   double* new_vel = new double[nNew*3];
75 – //   double* new_frc = new double[nNew*3];
76 – //   double* new_trq = new double[nNew*3];
77 – //   double* new_Amat = new double[nNew*9];
78 – //   double* new_mu = new double[nNew];
79 – //   double* new_ul = new double[nNew*3];
80 – //   int i, j;
81 –  
82 – //   for (i = 0; i < 3*nElements; i++) {
83 – //     new_pos[i] = pos[i];
84 – //     new_vel[i] = vel[i];
85 – //     new_frc[i] = frc[i];
86 – //     new_trq[i] = trq[i];
87 – //     new_ul[i] = ul[i];
88 – //   }
89 –
90 – //   for(i = 0; i < 3*nAdded; i++) {
91 – //     j = i + 3*nElements;
92 – //     new_pos[j] = Apos[i];
93 – //     new_vel[j] = Avel[i];
94 – //     new_frc[j] = Afrc[i];
95 – //     new_trq[j] = Atrq[i];
96 – //     new_ul[j] = Aul[i];
97 – //   }
98 –
99 – //   for (i = 0; i < 9*nElements; i++) {
100 – //     new_Amat[i] = Amat[i];
101 – //   }
102 –
103 – //   for(i = 0; i < 9*nAdded; i++) {
104 – //     j = i + 9*nElements;
105 – //     new_Amat[j] = AAmat[i];
106 – //   }
107 –
108 – //   for (i = 0; i < nElements; i++) {
109 – //     new_mu[i] = mu[i];
110 – //   }
111 –
112 – //   for(i = 0; i < nAdded; i++) {
113 – //     j = i + nElements;
114 – //     new_mu[j] = Amu[i];
115 – //   }
116 –
117 – //   delete[] pos;
118 – //   delete[] vel;
119 – //   delete[] frc;
120 – //   delete[] trq;
121 – //   delete[] Amat;
122 – //   delete[] mu;
123 –
124 – //   pos = new_pos;
125 – //   vel = new_vel;
126 – //   frc = new_frc;
127 – //   trq = new_trq;
128 – //   ul = new_ul;
129 – //   Amat = new_Amat;
130 – //   mu = new_mu;
131 –
132 – //   nElements = nNew;
133 – // }
134 –
135 – // void Atom::deleteAtom(int theIndex) {
136 – //   deleteRange(theIndex, theIndex);
137 – // }
138 –
139 – // void Atom::deleteRange(int startIndex, int stopIndex) {
140 –
141 – //   int nNew = nElements-(stopIndex-startIndex+1);
142 –
143 – //   double* new_pos = new double[nNew*3];
144 – //   double* new_vel = new double[nNew*3];
145 – //   double* new_frc = new double[nNew*3];
146 – //   double* new_trq = new double[nNew*3];
147 – //   double* new_Amat = new double[nNew*9];
148 – //   double* new_mu = new double[nNew];
149 – //   double* new_ul = new double[nNew*3];
150 – //   int i, j;
151 –  
152 – //   for (i = 0; i < 3*startIndex; i++) {
153 – //     new_pos[i] = pos[i];
154 – //     new_vel[i] = vel[i];
155 – //     new_frc[i] = frc[i];
156 – //     new_trq[i] = trq[i];
157 – //     new_ul[i] = ul[i];
158 – //   }
159 –
160 – //   for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
161 – //     j = i - 3*startIndex + 1;
162 – //     new_pos[j] = pos[i];
163 – //     new_vel[j] = vel[i];
164 – //     new_frc[j] = frc[i];
165 – //     new_trq[j] = trq[i];
166 – //     new_ul[j] = ul[i];
167 – //   }
168 –
169 – //   for (i = 0; i < 9*startIndex; i++) {
170 – //     new_Amat[i] = Amat[i];
171 – //   }
172 –
173 – //   for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
174 – //     j = i - 9*startIndex + 1;
175 – //     new_Amat[j] = Amat[i];
176 – //   }
177 –
178 – //   for (i = 0; i < startIndex; i++) {
179 – //     new_mu[i] = mu[i];
180 – //   }
181 –
182 – //   for(i = (stopIndex+1); i < nElements; i++) {
183 – //     j = i - startIndex + 1;
184 – //     new_mu[j] = mu[i];
185 – //   }
186 –
187 – //   delete[] pos;
188 – //   delete[] vel;
189 – //   delete[] frc;
190 – //   delete[] trq;
191 – //   delete[] Amat;
192 – //   delete[] mu;
193 –
194 – //   pos = new_pos;
195 – //   vel = new_vel;
196 – //   frc = new_frc;
197 – //   trq = new_trq;
198 – //   ul = new_ul;
199 – //   Amat = new_Amat;
200 – //   mu = new_mu;
201 –
202 – //   nElements = nNew;
203 – // }
204 –
205 –
65   void Atom::getPos( double theP[3] ){
66    
67    if( hasCoords ){
# Line 221 | Line 80 | void Atom::setPos( double theP[3] ){
80   }
81  
82   void Atom::setPos( double theP[3] ){
83 <  
83 >
84    if( hasCoords ){
85      pos[offsetX] = theP[0];
86      pos[offsetY] = theP[1];
# Line 307 | Line 166 | void GeneralAtom::zeroForces( void ){
166   }
167  
168  
169 < void GeneralAtom::zeroForces( void ){
169 > void Atom::zeroForces( void ){
170    
312 –  
171    if( hasCoords ){
172      frc[offsetX] = 0.0;
173      frc[offsetY] = 0.0;
# Line 324 | Line 182 | void GeneralAtom::zeroForces( void ){
182      simError();
183    }
184   }
185 +

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