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root/group/trunk/OOPSE/libmdtools/Atom.cpp
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Comparing trunk/OOPSE/libmdtools/Atom.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 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 54 | 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  
66 – // void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
67 – //                    double* Atrq, double* AAmat, double* Amu,
68 – //                    double* Aul) {
69 –
70 – //   int nNew = nElements+nAdded;
71 –
72 – //   double* new_pos = new double[nNew*3];
73 – //   double* new_vel = new double[nNew*3];
74 – //   double* new_frc = new double[nNew*3];
75 – //   double* new_trq = new double[nNew*3];
76 – //   double* new_Amat = new double[nNew*9];
77 – //   double* new_mu = new double[nNew];
78 – //   double* new_ul = new double[nNew*3];
79 – //   int i, j;
80 –  
81 – //   for (i = 0; i < 3*nElements; i++) {
82 – //     new_pos[i] = pos[i];
83 – //     new_vel[i] = vel[i];
84 – //     new_frc[i] = frc[i];
85 – //     new_trq[i] = trq[i];
86 – //     new_ul[i] = ul[i];
87 – //   }
88 –
89 – //   for(i = 0; i < 3*nAdded; i++) {
90 – //     j = i + 3*nElements;
91 – //     new_pos[j] = Apos[i];
92 – //     new_vel[j] = Avel[i];
93 – //     new_frc[j] = Afrc[i];
94 – //     new_trq[j] = Atrq[i];
95 – //     new_ul[j] = Aul[i];
96 – //   }
97 –
98 – //   for (i = 0; i < 9*nElements; i++) {
99 – //     new_Amat[i] = Amat[i];
100 – //   }
101 –
102 – //   for(i = 0; i < 9*nAdded; i++) {
103 – //     j = i + 9*nElements;
104 – //     new_Amat[j] = AAmat[i];
105 – //   }
106 –
107 – //   for (i = 0; i < nElements; i++) {
108 – //     new_mu[i] = mu[i];
109 – //   }
110 –
111 – //   for(i = 0; i < nAdded; i++) {
112 – //     j = i + nElements;
113 – //     new_mu[j] = Amu[i];
114 – //   }
115 –
116 – //   delete[] pos;
117 – //   delete[] vel;
118 – //   delete[] frc;
119 – //   delete[] trq;
120 – //   delete[] Amat;
121 – //   delete[] mu;
122 –
123 – //   pos = new_pos;
124 – //   vel = new_vel;
125 – //   frc = new_frc;
126 – //   trq = new_trq;
127 – //   ul = new_ul;
128 – //   Amat = new_Amat;
129 – //   mu = new_mu;
130 –
131 – //   nElements = nNew;
132 – // }
133 –
134 – // void Atom::deleteAtom(int theIndex) {
135 – //   deleteRange(theIndex, theIndex);
136 – // }
137 –
138 – // void Atom::deleteRange(int startIndex, int stopIndex) {
139 –
140 – //   int nNew = nElements-(stopIndex-startIndex+1);
141 –
142 – //   double* new_pos = new double[nNew*3];
143 – //   double* new_vel = new double[nNew*3];
144 – //   double* new_frc = new double[nNew*3];
145 – //   double* new_trq = new double[nNew*3];
146 – //   double* new_Amat = new double[nNew*9];
147 – //   double* new_mu = new double[nNew];
148 – //   double* new_ul = new double[nNew*3];
149 – //   int i, j;
150 –  
151 – //   for (i = 0; i < 3*startIndex; i++) {
152 – //     new_pos[i] = pos[i];
153 – //     new_vel[i] = vel[i];
154 – //     new_frc[i] = frc[i];
155 – //     new_trq[i] = trq[i];
156 – //     new_ul[i] = ul[i];
157 – //   }
158 –
159 – //   for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
160 – //     j = i - 3*startIndex + 1;
161 – //     new_pos[j] = pos[i];
162 – //     new_vel[j] = vel[i];
163 – //     new_frc[j] = frc[i];
164 – //     new_trq[j] = trq[i];
165 – //     new_ul[j] = ul[i];
166 – //   }
167 –
168 – //   for (i = 0; i < 9*startIndex; i++) {
169 – //     new_Amat[i] = Amat[i];
170 – //   }
171 –
172 – //   for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
173 – //     j = i - 9*startIndex + 1;
174 – //     new_Amat[j] = Amat[i];
175 – //   }
176 –
177 – //   for (i = 0; i < startIndex; i++) {
178 – //     new_mu[i] = mu[i];
179 – //   }
180 –
181 – //   for(i = (stopIndex+1); i < nElements; i++) {
182 – //     j = i - startIndex + 1;
183 – //     new_mu[j] = mu[i];
184 – //   }
185 –
186 – //   delete[] pos;
187 – //   delete[] vel;
188 – //   delete[] frc;
189 – //   delete[] trq;
190 – //   delete[] Amat;
191 – //   delete[] mu;
192 –
193 – //   pos = new_pos;
194 – //   vel = new_vel;
195 – //   frc = new_frc;
196 – //   trq = new_trq;
197 – //   ul = new_ul;
198 – //   Amat = new_Amat;
199 – //   mu = new_mu;
200 –
201 – //   nElements = nNew;
202 – // }
203 –
204 –
65   void Atom::getPos( double theP[3] ){
66    
67    if( hasCoords ){
# Line 220 | 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 306 | Line 166 | void GeneralAtom::zeroForces( void ){
166   }
167  
168  
169 < void GeneralAtom::zeroForces( void ){
169 > void Atom::zeroForces( void ){
170    
311 –  
171    if( hasCoords ){
172      frc[offsetX] = 0.0;
173      frc[offsetY] = 0.0;
# Line 323 | Line 182 | void GeneralAtom::zeroForces( void ){
182      simError();
183    }
184   }
185 +

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