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 ){ |
12 |
|
13 |
myStamp = theStamp; |
14 |
nAtoms = myStamp->getNAtoms(); |
15 |
|
16 |
myConfig=NULL; |
17 |
|
18 |
myCoords = NULL; |
19 |
|
20 |
calcRefCoords(); |
21 |
} |
22 |
|
23 |
MoLocator::~MoLocator(){ |
24 |
|
25 |
if( myCoords != NULL ) delete[] myCoords; |
26 |
} |
27 |
|
28 |
void MoLocator::setConfig(SimState * theConfig){ |
29 |
|
30 |
myConfig = theConfig; |
31 |
haveConfig = true; |
32 |
} |
33 |
|
34 |
void MoLocator::placeMol( double pos[3], double A[3][3], Atom** atomArray, |
35 |
int atomIndex ){ |
36 |
|
37 |
int i,j,k; |
38 |
double r[3]; |
39 |
double ux, uy, uz, u, uSqr; |
40 |
|
41 |
AtomStamp* currAtom; |
42 |
DirectionalAtom* dAtom; |
43 |
|
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 |
|
52 |
for(i=0; i<nAtoms; i++){ |
53 |
|
54 |
currAtom = myStamp->getAtom( i ); |
55 |
j = atomIndex+i; |
56 |
|
57 |
if( currAtom->haveOrientation()){ |
58 |
|
59 |
dAtom = new DirectionalAtom( j, myConfig); |
60 |
atomArray[j] = dAtom; |
61 |
atomArray[j]->setCoords(void); |
62 |
|
63 |
ux = currAtom->getOrntX(); |
64 |
uy = currAtom->getOrntY(); |
65 |
uz = currAtom->getOrntZ(); |
66 |
|
67 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
68 |
|
69 |
u = sqrt( uSqr ); |
70 |
ux = ux / u; |
71 |
uy = uy / u; |
72 |
uz = uz / u; |
73 |
|
74 |
dAtom->setSUx( ux ); |
75 |
dAtom->setSUy( uy ); |
76 |
dAtom->setSUz( uz ); |
77 |
|
78 |
dAtom->setA( A ); |
79 |
|
80 |
dAtom->setJx( 0.0 ); |
81 |
dAtom->setJy( 0.0 ); |
82 |
dAtom->setJz( 0.0 ); |
83 |
|
84 |
} |
85 |
else{ |
86 |
atomArray[j] = new GeneralAtom( j, myConfig); |
87 |
atomArray[j]->setCoords(void); |
88 |
} |
89 |
|
90 |
atomArray[j]->setType( currAtom->getType() ); |
91 |
|
92 |
for(k=0; k<3; k++) r[k] = myCoords[(i*3)+k]; |
93 |
|
94 |
rotMe( r, A ); |
95 |
|
96 |
for(k=0; k<3; k++) r[k] += pos[k]; |
97 |
|
98 |
atomArray[j]->setX( r[0] ); |
99 |
atomArray[j]->setY( r[1] ); |
100 |
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 ); |
105 |
} |
106 |
} |
107 |
|
108 |
void MoLocator::calcRefCoords( void ){ |
109 |
|
110 |
int i,j,k; |
111 |
AtomStamp* currAtom; |
112 |
double centerX, centerY, centerZ; |
113 |
double smallX, smallY, smallZ; |
114 |
double bigX, bigY, bigZ; |
115 |
double dx, dy, dz; |
116 |
double dsqr; |
117 |
|
118 |
|
119 |
centerX = 0.0; |
120 |
centerY = 0.0; |
121 |
centerZ = 0.0; |
122 |
|
123 |
for(i=0; i<nAtoms; i++){ |
124 |
|
125 |
currAtom = myStamp->getAtom(i); |
126 |
if( !currAtom->havePosition() ){ |
127 |
sprintf( painCave.errMsg, |
128 |
"MoLocator error.\n" |
129 |
" Component %s, atom %s does not have a position specified.\n" |
130 |
" This means MoLocator cannot initalize it's position.\n", |
131 |
myStamp->getID(), |
132 |
currAtom->getType() ); |
133 |
painCave.isFatal = 1; |
134 |
simError(); |
135 |
} |
136 |
|
137 |
|
138 |
centerX += currAtom->getPosX(); |
139 |
centerY += currAtom->getPosY(); |
140 |
centerZ += currAtom->getPosZ(); |
141 |
} |
142 |
|
143 |
centerX /= nAtoms; |
144 |
centerY /= nAtoms; |
145 |
centerZ /= nAtoms; |
146 |
|
147 |
myCoords = new double[nAtoms*3]; |
148 |
|
149 |
j = 0; |
150 |
for(i=0; i<nAtoms; i++){ |
151 |
|
152 |
currAtom = myStamp->getAtom(i); |
153 |
j = i*3; |
154 |
|
155 |
myCoords[j] = currAtom->getPosX() - centerX; |
156 |
myCoords[j+1] = currAtom->getPosY() - centerY; |
157 |
myCoords[j+2] = currAtom->getPosZ() - centerZ; |
158 |
} |
159 |
|
160 |
smallX = myCoords[0]; |
161 |
smallY = myCoords[1]; |
162 |
smallZ = myCoords[2]; |
163 |
|
164 |
bigX = myCoords[0]; |
165 |
bigY = myCoords[1]; |
166 |
bigZ = myCoords[2]; |
167 |
|
168 |
j=0; |
169 |
for(i=1; i<nAtoms; i++){ |
170 |
j= i*3; |
171 |
|
172 |
if( myCoords[j] < smallX ) smallX = myCoords[j]; |
173 |
if( myCoords[j+1] < smallY ) smallY = myCoords[j+1]; |
174 |
if( myCoords[j+2] < smallZ ) smallZ = myCoords[j+2]; |
175 |
|
176 |
if( myCoords[j] > bigX ) bigX = myCoords[j]; |
177 |
if( myCoords[j+1] > bigY ) bigY = myCoords[j+1]; |
178 |
if( myCoords[j+2] > bigZ ) bigZ = myCoords[j+2]; |
179 |
} |
180 |
|
181 |
|
182 |
dx = bigX - smallX; |
183 |
dy = bigY - smallY; |
184 |
dz = bigZ - smallZ; |
185 |
|
186 |
dsqr = (dx * dx) + (dy * dy) + (dz * dz); |
187 |
maxLength = sqrt( dsqr ); |
188 |
} |
189 |
|
190 |
void MoLocator::rotMe( double r[3], double A[3][3] ){ |
191 |
|
192 |
double rt[3]; |
193 |
int i,j; |
194 |
|
195 |
for(i=0; i<3; i++) rt[i] = r[i]; |
196 |
|
197 |
for(i=0; i<3; i++){ |
198 |
r[i] = 0.0; |
199 |
for(j=0; j<3; j++){ |
200 |
r[i] += A[i][j] * rt[j]; |
201 |
} |
202 |
} |
203 |
} |