13 |
|
myStamp = theStamp; |
14 |
|
nAtoms = myStamp->getNAtoms(); |
15 |
|
|
16 |
– |
myConfig=NULL; |
17 |
– |
|
16 |
|
myCoords = NULL; |
17 |
|
|
18 |
|
calcRefCoords(); |
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]; |
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 ); |
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(); |
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() ); |
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 |
|
|