ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Atom.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Atom.cpp (file contents):
Revision 410 by gezelter, Wed Mar 26 21:23:00 2003 UTC vs.
Revision 1125 by gezelter, Mon Apr 19 22:13:01 2004 UTC

# Line 1 | Line 1
1 + #include <iostream>
2 +
3 + using namespace std;
4 +
5 + #include "simError.h"
6   #include "Atom.hpp"
7  
8 < Atom::Atom(int theIndex) {
9 <  c_n_hyd = 0;
8 > Atom::Atom(int theIndex, SimState* theConfig) {
9 >
10 >  objType = OT_ATOM;
11 >  myConfig = theConfig;
12 >  hasCoords = false;
13 >
14    has_dipole = 0;
15 <  is_VDW = 0;
7 <  is_LJ = 0;
15 >  has_charge = 0;
16    
17    index = theIndex;
18 <  offset = 3 * index;
18 >  offset = 0;
19    offsetX = offset;
20    offsetY = offset+1;
21    offsetZ = offset+2;
22    
23 <  Axx = index*9;
23 >  Axx = 0;
24    Axy = Axx+1;
25    Axz = Axx+2;
26    
# Line 25 | Line 33 | void Atom::createArrays (int nElements) {
33    Azz = Axx+8;
34   }
35  
36 < void Atom::createArrays (int nElements) {
37 <  int i;
30 <  
31 <  pos = new double[nElements*3];
32 <  vel = new double[nElements*3];
33 <  frc = new double[nElements*3];
34 <  trq = new double[nElements*3];
35 <  Amat = new double[nElements*9];
36 <  mu = new double[nElements];
37 <  ul = new double[nElements*3];
38 <  
39 <  // init directional values to zero
40 <  
41 <  for( i=0; i<nElements; i++){
42 <    trq[i] = 0.0;
43 <    trq[i+1] = 0.0;
44 <    trq[i+2] = 0.0;
45 <    
46 <    Amat[i] = 1.0;
47 <    Amat[i+1] = 0.0;
48 <    Amat[i+2] = 0.0;
49 <    
50 <    Amat[i+3] = 0.0;
51 <    Amat[i+4] = 1.0;
52 <    Amat[i+5] = 0.0;
53 <    
54 <    Amat[i+6] = 0.0;
55 <    Amat[i+7] = 0.0;
56 <    Amat[i+8] = 1.0;
57 <    
58 <    mu[i] = 0.0;    
59 <    
60 <    ul[i] = 1.0;
61 <    ul[i+1] = 0.0;
62 <    ul[i+2] = 0.0;
63 <  }
36 > void Atom::setIndex(int theIndex) {
37 >  index = theIndex;
38   }
39  
40 < void Atom::destroyArrays(void) {
67 <  delete[] pos;
68 <  delete[] vel;
69 <  delete[] frc;
70 <  delete[] trq;
71 <  delete[] Amat;
72 <  delete[] mu;
73 < }
40 > void Atom::setCoords(void){
41  
42 < void Atom::setIndex(int theIndex) {
43 <  index = theIndex;
44 <  offset = index*3;
45 <  offsetX = offset;
46 <  offsetY = offset+1;
47 <  offsetZ = offset+2;
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 <  Axx = index*9;
83 <  Axy = Axx+1;
84 <  Axz = Axx+2;
61 >  hasCoords = true;
62    
86 –  Ayx = Axx+3;
87 –  Ayy = Axx+4;
88 –  Ayz = Axx+5;
89 –  
90 –  Azx = Axx+6;
91 –  Azy = Axx+7;
92 –  Azz = Axx+8;
63   }
64  
65 < void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
96 <                   double* Atrq, double* AAmat, double* Amu,
97 <                   double* Aul) {
98 <
99 <  int nNew = nElements+nAdded;
100 <
101 <  double* new_pos = new double[nNew*3];
102 <  double* new_vel = new double[nNew*3];
103 <  double* new_frc = new double[nNew*3];
104 <  double* new_trq = new double[nNew*3];
105 <  double* new_Amat = new double[nNew*9];
106 <  double* new_mu = new double[nNew];
107 <  double* new_ul = new double[nNew*3];
108 <  int i, j;
65 > void Atom::getPos( double theP[3] ){
66    
67 <  for (i = 0; i < 3*nElements; i++) {
68 <    new_pos[i] = pos[i];
69 <    new_vel[i] = vel[i];
70 <    new_frc[i] = frc[i];
114 <    new_trq[i] = trq[i];
115 <    new_ul[i] = ul[i];
67 >  if( hasCoords ){
68 >    theP[0] = pos[offsetX];
69 >    theP[1] = pos[offsetY];
70 >    theP[2] = pos[offsetZ];
71    }
72 +  else{
73  
74 <  for(i = 0; i < 3*nAdded; i++) {
75 <    j = i + 3*nElements;
76 <    new_pos[j] = Apos[i];
77 <    new_vel[j] = Avel[i];
78 <    new_frc[j] = Afrc[i];
123 <    new_trq[j] = Atrq[i];
124 <    new_ul[j] = Aul[i];
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 <  for (i = 0; i < 9*nElements; i++) {
128 <    new_Amat[i] = Amat[i];
129 <  }
82 > void Atom::setPos( double theP[3] ){
83  
84 <  for(i = 0; i < 9*nAdded; i++) {
85 <    j = i + 9*nElements;
86 <    new_Amat[j] = AAmat[i];
84 >  if( hasCoords ){
85 >    pos[offsetX] = theP[0];
86 >    pos[offsetY] = theP[1];
87 >    pos[offsetZ] = theP[2];
88    }
89 +  else{
90  
91 <  for (i = 0; i < nElements; i++) {
92 <    new_mu[i] = mu[i];
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 <  for(i = 0; i < nAdded; i++) {
100 <    j = i + nElements;
101 <    new_mu[j] = Amu[i];
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  
145 –  delete[] pos;
146 –  delete[] vel;
147 –  delete[] frc;
148 –  delete[] trq;
149 –  delete[] Amat;
150 –  delete[] mu;
151 –
152 –  pos = new_pos;
153 –  vel = new_vel;
154 –  frc = new_frc;
155 –  trq = new_trq;
156 –  ul = new_ul;
157 –  Amat = new_Amat;
158 –  mu = new_mu;
159 –
160 –  nElements = nNew;
115   }
116  
117 < void Atom::deleteAtom(int theIndex) {
118 <  deleteRange(theIndex, theIndex);
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::deleteRange(int startIndex, int stopIndex) {
168 <
169 <  int nNew = nElements-(stopIndex-startIndex+1);
170 <
171 <  double* new_pos = new double[nNew*3];
172 <  double* new_vel = new double[nNew*3];
173 <  double* new_frc = new double[nNew*3];
174 <  double* new_trq = new double[nNew*3];
175 <  double* new_Amat = new double[nNew*9];
176 <  double* new_mu = new double[nNew];
177 <  double* new_ul = new double[nNew*3];
178 <  int i, j;
134 > void Atom::getFrc( double theF[3] ){
135    
136 <  for (i = 0; i < 3*startIndex; i++) {
137 <    new_pos[i] = pos[i];
138 <    new_vel[i] = vel[i];
139 <    new_frc[i] = frc[i];
184 <    new_trq[i] = trq[i];
185 <    new_ul[i] = ul[i];
136 >  if( hasCoords ){
137 >    theF[0] = frc[offsetX];
138 >    theF[1] = frc[offsetY];
139 >    theF[2] = frc[offsetZ];
140    }
141 <
142 <  for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
143 <    j = i - 3*startIndex + 1;
144 <    new_pos[j] = pos[i];
145 <    new_vel[j] = vel[i];
146 <    new_frc[j] = frc[i];
147 <    new_trq[j] = trq[i];
194 <    new_ul[j] = ul[i];
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 <  for (i = 0; i < 9*startIndex; i++) {
152 <    new_Amat[i] = Amat[i];
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 <
159 <  for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
160 <    j = i - 9*startIndex + 1;
161 <    new_Amat[j] = Amat[i];
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  
206 –  for (i = 0; i < startIndex; i++) {
207 –    new_mu[i] = mu[i];
208 –  }
168  
169 <  for(i = (stopIndex+1); i < nElements; i++) {
170 <    j = i - startIndex + 1;
171 <    new_mu[j] = mu[i];
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  
186 <  delete[] pos;
187 <  delete[] vel;
217 <  delete[] frc;
218 <  delete[] trq;
219 <  delete[] Amat;
220 <  delete[] mu;
221 <
222 <  pos = new_pos;
223 <  vel = new_vel;
224 <  frc = new_frc;
225 <  trq = new_trq;
226 <  ul = new_ul;
227 <  Amat = new_Amat;
228 <  mu = new_mu;
229 <
230 <  nElements = nNew;
186 > void Atom::accept(BaseVisitor* v){
187 >  v->visit(this);
188   }
189 +

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines