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root/group/trunk/OOPSE/utils/sysbuilder/MoLocator.cpp
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Comparing trunk/OOPSE/utils/sysbuilder/MoLocator.cpp (file contents):
Revision 678 by chuckv, Mon Aug 11 22:12:31 2003 UTC vs.
Revision 825 by mmeineke, Mon Oct 27 22:08:36 2003 UTC

# Line 13 | Line 13 | MoLocator::MoLocator( MoleculeStamp* theStamp ){
13    myStamp = theStamp;
14    nAtoms = myStamp->getNAtoms();
15  
16 –  myConfig=NULL;
17 –  
16    myCoords = NULL;
17    
18    calcRefCoords();
# Line 25 | Line 23 | MoLocator::~MoLocator(){
23    if( myCoords != NULL ) delete[] myCoords;
24   }
25  
28 – void MoLocator::setConfig(SimState * theConfig){
29 –
30 –        myConfig = theConfig;
31 –        haveConfig = true;
32 – }
33 –
26   void MoLocator::placeMol( double pos[3], double A[3][3], Atom** atomArray,
27 <                          int atomIndex ){
27 >                          int atomIndex, SimState* myConfig ){
28  
29    int i,j,k;
30    double r[3];
# Line 40 | Line 32 | void MoLocator::placeMol( double pos[3], double A[3][3
32    
33    AtomStamp* currAtom;
34    DirectionalAtom* dAtom;
35 +  double vel[3];
36 +  for(i=0;i<3;i++)vel[i]=0.0;
37  
44 –
45 – if( !haveConfig ){
46 –        sprintf(painCave.errMsg,
47 –                "attempt to placeMol without setting the SimState in the MoLocator.\n",);
48 –        painCave.isFatal = 1;
49 –        simError(void);
50 – }
51 –  
38    for(i=0; i<nAtoms; i++){
39      
40      currAtom = myStamp->getAtom( i );
# Line 58 | Line 44 | if( !haveConfig ){
44        
45        dAtom = new DirectionalAtom( j, myConfig);
46        atomArray[j] = dAtom;
47 <          atomArray[j]->setCoords(void);
47 >      atomArray[j]->setCoords();
48            
49        ux = currAtom->getOrntX();
50        uy = currAtom->getOrntY();
# Line 84 | Line 70 | if( !haveConfig ){
70      }
71      else{
72        atomArray[j] = new GeneralAtom( j, myConfig);
73 <          atomArray[j]->setCoords(void);
73 >      atomArray[j]->setCoords();
74      }
75      
76      atomArray[j]->setType( currAtom->getType() );
# Line 95 | Line 81 | if( !haveConfig ){
81  
82      for(k=0; k<3; k++) r[k] += pos[k];
83  
84 <    atomArray[j]->setX( r[0] );
85 <    atomArray[j]->setY( r[1] );
86 <    atomArray[j]->setZ( r[2] );
101 <
102 <    atomArray[j]->set_vx( 0.0 );
103 <    atomArray[j]->set_vy( 0.0 );
104 <    atomArray[j]->set_vz( 0.0 );
84 >    atomArray[j]->setPos( r );
85 >        
86 >    atomArray[j]->setVel( vel );;
87    }
88   }
89  
# Line 201 | Line 183 | void MoLocator::rotMe( double r[3], double A[3][3] ){
183      }
184    }
185   }
186 +
187 + void getRandomRot( double rot[3][3] ){
188 +
189 +  double theta, phi, psi;
190 +  double cosTheta;
191 +
192 +  // select random phi, psi, and cosTheta
193 +
194 +  phi = 2.0 * M_PI * drand48();
195 +  psi = 2.0 * M_PI * drand48();
196 +  cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1
197 +
198 +  theta = acos( cosTheta );
199 +
200 +  getEulerRot( theta, phi, psi, rot );
201 + }
202 +
203 +
204 + void getEulerRot( double theta, double phi, double psi, double rot[3][3] ){
205 +
206 +  rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
207 +  rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
208 +  rot[0][2] = sin(theta) * sin(psi);
209 +  
210 +  rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
211 +  rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
212 +  rot[1][2] = sin(theta) * cos(psi);
213 +
214 +  rot[2][0] = sin(phi) * sin(theta);
215 +  rot[2][1] = -cos(phi) * sin(theta);
216 +  rot[2][2] = cos(theta);  
217 + }
218 +

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