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root/group/trunk/OOPSE/utils/MoLocator.cpp
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Comparing trunk/OOPSE/utils/MoLocator.cpp (file contents):
Revision 503 by mmeineke, Wed Apr 16 21:11:37 2003 UTC vs.
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC

# Line 1 | Line 1
1 + #include <iostream>
2 +
3   #include <cstdlib>
4   #include <cmath>
5  
6 + #include "simError.h"
7 +
8   #include "MoLocator.hpp"
9  
10  
11 < MoLocator::MoLocator( MoleCuleStamp* theStamp ){
11 > MoLocator::MoLocator( MoleculeStamp* theStamp ){
12  
13    myStamp = theStamp;
14    nAtoms = myStamp->getNAtoms();
# Line 19 | Line 23 | MoLocator::~MoLocator(){
23    if( myCoords != NULL ) delete[] myCoords;
24   }
25  
26 < void MoLocator::placeMol( double pos[3], double A[3][3], Atom** atomArray){
26 > void MoLocator::placeMol( double pos[3], double A[3][3], Atom** atomArray,
27 >                          int atomIndex ){
28    
29    int i,j,k;
30    double r[3];
31 +  double ux, uy, uz, u, uSqr;
32    
33    AtomStamp* currAtom;
34    DirectionalAtom* dAtom;
35    
36 +  for(i=0; i<nAtoms; i++){
37 +    
38 +    currAtom = myStamp->getAtom( i );
39 +    j = atomIndex+i;
40 +
41 +    if( currAtom->haveOrientation()){
42 +      
43 +      dAtom = new DirectionalAtom( j );
44 +      atomArray[j] = dAtom;
45 +      
46 +      ux = currAtom->getOrntX();
47 +      uy = currAtom->getOrntY();
48 +      uz = currAtom->getOrntZ();
49 +      
50 +      uSqr = (ux * ux) + (uy * uy) + (uz * uz);
51 +      
52 +      u = sqrt( uSqr );
53 +      ux = ux / u;
54 +      uy = uy / u;
55 +      uz = uz / u;
56 +      
57 +      dAtom->setSUx( ux );
58 +      dAtom->setSUy( uy );
59 +      dAtom->setSUz( uz );
60 +      
61 +      dAtom->setA( A );
62 +      
63 +      dAtom->setJx( 0.0 );
64 +      dAtom->setJy( 0.0 );
65 +      dAtom->setJz( 0.0 );
66 +      
67 +    }
68 +    else{
69 +      atomArray[j] = new GeneralAtom( j );
70 +    }
71 +    
72 +    atomArray[j]->setType( currAtom->getType() );
73 +    
74 +    for(k=0; k<3; k++) r[k] = myCoords[(i*3)+k];
75 +
76 +    rotMe( r, A );
77 +
78 +    for(k=0; k<3; k++) r[k] += pos[k];
79 +
80 +    atomArray[j]->setX( r[0] );
81 +    atomArray[j]->setY( r[1] );
82 +    atomArray[j]->setZ( r[2] );
83 +
84 +    atomArray[j]->set_vx( 0.0 );
85 +    atomArray[j]->set_vy( 0.0 );
86 +    atomArray[j]->set_vz( 0.0 );
87 +  }
88   }
89  
90   void MoLocator::calcRefCoords( void ){
# Line 43 | Line 101 | void MoLocator::calcRefCoords( void ){
101    centerX = 0.0;
102    centerY = 0.0;
103    centerZ = 0.0;
104 <  for(i=0; <nAtoms; i++){
104 >  for(i=0; i<nAtoms; i++){
105      
106      currAtom = myStamp->getAtom(i);
107 +    if( !currAtom->havePosition() ){
108 +      sprintf( painCave.errMsg,
109 +               "MoLocator error.\n"
110 +               "  Component %s, atom %s does not have a position specified.\n"
111 +               "  This means MoLocator cannot initalize it's position.\n",
112 +               myStamp->getID(),
113 +               currAtom->getType() );
114 +      painCave.isFatal = 1;
115 +      simError();
116 +    }
117 +
118      
119      centerX += currAtom->getPosX();
120      centerY += currAtom->getPosY();
# Line 59 | Line 128 | void MoLocator::calcRefCoords( void ){
128    myCoords = new double[nAtoms*3];
129  
130    j = 0;
131 <  for(i=0; <nAtoms; i++){
131 >  for(i=0; i<nAtoms; i++){
132      
133      currAtom = myStamp->getAtom(i);
134      j = i*3;
# Line 104 | Line 173 | void MoLocator::rotMe( double r[3], double A[3][3] ){
173    double rt[3];
174    int i,j;
175  
176 <  for(i=0; i<3 i++) rt[i] = r[i];
176 >  for(i=0; i<3; i++) rt[i] = r[i];
177  
178    for(i=0; i<3; i++){
179      r[i] = 0.0;
# Line 113 | Line 182 | void MoLocator::rotMe( double r[3], double A[3][3] ){
182      }
183    }
184   }
116 –      

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