1 |
gezelter |
829 |
#include <stdlib.h> |
2 |
mmeineke |
426 |
|
3 |
|
|
|
4 |
|
|
#include "Molecule.hpp" |
5 |
chuckv |
438 |
#include "simError.h" |
6 |
mmeineke |
426 |
|
7 |
|
|
|
8 |
|
|
|
9 |
|
|
Molecule::Molecule( void ){ |
10 |
|
|
|
11 |
|
|
myAtoms = NULL; |
12 |
|
|
myBonds = NULL; |
13 |
|
|
myBends = NULL; |
14 |
|
|
myTorsions = NULL; |
15 |
gezelter |
1097 |
myRigidBodies = NULL; |
16 |
mmeineke |
426 |
|
17 |
|
|
} |
18 |
|
|
|
19 |
|
|
|
20 |
|
|
|
21 |
|
|
Molecule::~Molecule( void ){ |
22 |
|
|
int i; |
23 |
|
|
|
24 |
|
|
if( myAtoms != NULL ){ |
25 |
|
|
for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i]; |
26 |
|
|
delete[] myAtoms; |
27 |
|
|
} |
28 |
|
|
|
29 |
|
|
if( myBonds != NULL ){ |
30 |
|
|
for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i]; |
31 |
|
|
delete[] myBonds; |
32 |
|
|
} |
33 |
|
|
|
34 |
|
|
if( myBends != NULL ){ |
35 |
|
|
for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i]; |
36 |
|
|
delete[] myBends; |
37 |
|
|
} |
38 |
|
|
|
39 |
|
|
if( myTorsions != NULL ){ |
40 |
|
|
for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i]; |
41 |
|
|
delete[] myTorsions; |
42 |
|
|
} |
43 |
|
|
|
44 |
gezelter |
1097 |
if( myRigidBodies != NULL ){ |
45 |
|
|
for(i=0; i<nRigidBodies; i++) if(myRigidBodies[i] != NULL ) |
46 |
|
|
delete myRigidBodies[i]; |
47 |
|
|
delete[] myRigidBodies; |
48 |
mmeineke |
426 |
} |
49 |
gezelter |
1097 |
|
50 |
mmeineke |
426 |
} |
51 |
|
|
|
52 |
|
|
|
53 |
|
|
void Molecule::initialize( molInit &theInit ){ |
54 |
|
|
|
55 |
|
|
nAtoms = theInit.nAtoms; |
56 |
|
|
nMembers = nAtoms; |
57 |
|
|
nBonds = theInit.nBonds; |
58 |
|
|
nBends = theInit.nBends; |
59 |
|
|
nTorsions = theInit.nTorsions; |
60 |
gezelter |
1097 |
nRigidBodies = theInit.nRigidBodies; |
61 |
mmeineke |
426 |
nOriented = theInit.nOriented; |
62 |
|
|
|
63 |
|
|
myAtoms = theInit.myAtoms; |
64 |
|
|
myBonds = theInit.myBonds; |
65 |
|
|
myBends = theInit.myBends; |
66 |
|
|
myTorsions = theInit.myTorsions; |
67 |
gezelter |
1097 |
myRigidBodies = theInit.myRigidBodies; |
68 |
mmeineke |
426 |
|
69 |
|
|
} |
70 |
|
|
|
71 |
|
|
void Molecule::calcForces( void ){ |
72 |
|
|
|
73 |
|
|
int i; |
74 |
|
|
|
75 |
gezelter |
1097 |
for(i=0; i<nRigidBodies; i++) { |
76 |
|
|
myRigidBodies[i]->updateAtoms(); |
77 |
|
|
} |
78 |
|
|
|
79 |
mmeineke |
426 |
for(i=0; i<nBonds; i++){ |
80 |
|
|
myBonds[i]->calc_forces(); |
81 |
|
|
} |
82 |
|
|
|
83 |
|
|
for(i=0; i<nBends; i++){ |
84 |
|
|
myBends[i]->calc_forces(); |
85 |
|
|
} |
86 |
|
|
|
87 |
|
|
for(i=0; i<nTorsions; i++){ |
88 |
|
|
myTorsions[i]->calc_forces(); |
89 |
|
|
} |
90 |
gezelter |
1097 |
|
91 |
|
|
// Rigid Body forces and torques are done after the fortran force loop |
92 |
|
|
|
93 |
mmeineke |
426 |
} |
94 |
|
|
|
95 |
|
|
|
96 |
mmeineke |
428 |
double Molecule::getPotential( void ){ |
97 |
mmeineke |
426 |
|
98 |
|
|
int i; |
99 |
|
|
double myPot = 0.0; |
100 |
|
|
|
101 |
|
|
for(i=0; i<nBonds; i++){ |
102 |
|
|
myPot += myBonds[i]->get_potential(); |
103 |
|
|
} |
104 |
|
|
|
105 |
|
|
for(i=0; i<nBends; i++){ |
106 |
|
|
myPot += myBends[i]->get_potential(); |
107 |
|
|
} |
108 |
|
|
|
109 |
|
|
for(i=0; i<nTorsions; i++){ |
110 |
|
|
myPot += myTorsions[i]->get_potential(); |
111 |
|
|
} |
112 |
|
|
|
113 |
|
|
return myPot; |
114 |
|
|
} |
115 |
mmeineke |
435 |
|
116 |
|
|
void Molecule::printMe( void ){ |
117 |
|
|
|
118 |
|
|
int i; |
119 |
|
|
|
120 |
|
|
for(i=0; i<nBonds; i++){ |
121 |
|
|
myBonds[i]->printMe(); |
122 |
|
|
} |
123 |
|
|
|
124 |
|
|
for(i=0; i<nBends; i++){ |
125 |
|
|
myBends[i]->printMe(); |
126 |
|
|
} |
127 |
|
|
|
128 |
|
|
for(i=0; i<nTorsions; i++){ |
129 |
|
|
myTorsions[i]->printMe(); |
130 |
|
|
} |
131 |
gezelter |
1097 |
|
132 |
mmeineke |
435 |
} |
133 |
gezelter |
446 |
|
134 |
mmeineke |
449 |
void Molecule::moveCOM(double delta[3]){ |
135 |
gezelter |
610 |
double aPos[3]; |
136 |
|
|
int i, j; |
137 |
gezelter |
446 |
|
138 |
|
|
for(i=0; i<nAtoms; i++) { |
139 |
|
|
if(myAtoms[i] != NULL ) { |
140 |
gezelter |
610 |
|
141 |
|
|
myAtoms[i]->getPos( aPos ); |
142 |
|
|
|
143 |
|
|
for (j=0; j< 3; j++) |
144 |
|
|
aPos[j] += delta[j]; |
145 |
gezelter |
446 |
|
146 |
gezelter |
610 |
myAtoms[i]->setPos( aPos ); |
147 |
gezelter |
446 |
} |
148 |
|
|
} |
149 |
gezelter |
1097 |
|
150 |
|
|
for(i=0; i<nRigidBodies; i++) { |
151 |
|
|
|
152 |
|
|
if (myRigidBodies[i] != NULL) { |
153 |
|
|
|
154 |
|
|
myRigidBodies[i]->getPos( aPos ); |
155 |
|
|
|
156 |
|
|
for (j=0; j< 3; j++) |
157 |
|
|
aPos[j] += delta[j]; |
158 |
|
|
|
159 |
|
|
myRigidBodies[i]->setPos( aPos ); |
160 |
|
|
} |
161 |
|
|
} |
162 |
gezelter |
446 |
} |
163 |
|
|
|
164 |
gezelter |
1097 |
void Molecule::atoms2rigidBodies( void ) { |
165 |
|
|
int i; |
166 |
|
|
for (i = 0; i < nRigidBodies; i++) { |
167 |
|
|
if (myRigidBodies[i] != NULL) { |
168 |
|
|
myRigidBodies[i]->calcForcesAndTorques(); |
169 |
|
|
} |
170 |
|
|
} |
171 |
|
|
} |
172 |
|
|
|
173 |
mmeineke |
449 |
void Molecule::getCOM( double COM[3] ) { |
174 |
gezelter |
446 |
|
175 |
|
|
double mass, mtot; |
176 |
gezelter |
610 |
double aPos[3]; |
177 |
|
|
int i, j; |
178 |
gezelter |
446 |
|
179 |
gezelter |
610 |
for (j=0; j<3; j++) |
180 |
|
|
COM[j] = 0.0; |
181 |
|
|
|
182 |
gezelter |
446 |
mtot = 0.0; |
183 |
|
|
|
184 |
|
|
for (i=0; i < nAtoms; i++) { |
185 |
|
|
if (myAtoms[i] != NULL) { |
186 |
|
|
|
187 |
|
|
mass = myAtoms[i]->getMass(); |
188 |
|
|
mtot += mass; |
189 |
gezelter |
610 |
|
190 |
|
|
myAtoms[i]->getPos( aPos ); |
191 |
gezelter |
446 |
|
192 |
gezelter |
610 |
for( j = 0; j < 3; j++) |
193 |
|
|
COM[j] += aPos[j] * mass; |
194 |
|
|
|
195 |
gezelter |
446 |
} |
196 |
|
|
} |
197 |
|
|
|
198 |
gezelter |
610 |
for (j = 0; j < 3; j++) |
199 |
|
|
COM[j] /= mtot; |
200 |
gezelter |
446 |
} |
201 |
gezelter |
468 |
|
202 |
gezelter |
475 |
double Molecule::getCOMvel( double COMvel[3] ) { |
203 |
gezelter |
468 |
|
204 |
gezelter |
475 |
double mass, mtot; |
205 |
gezelter |
607 |
double aVel[3]; |
206 |
|
|
int i, j; |
207 |
gezelter |
468 |
|
208 |
gezelter |
607 |
|
209 |
|
|
for (j=0; j<3; j++) |
210 |
|
|
COMvel[j] = 0.0; |
211 |
|
|
|
212 |
gezelter |
468 |
mtot = 0.0; |
213 |
|
|
|
214 |
|
|
for (i=0; i < nAtoms; i++) { |
215 |
|
|
if (myAtoms[i] != NULL) { |
216 |
mmeineke |
489 |
|
217 |
gezelter |
468 |
mass = myAtoms[i]->getMass(); |
218 |
|
|
mtot += mass; |
219 |
|
|
|
220 |
gezelter |
607 |
myAtoms[i]->getVel(aVel); |
221 |
|
|
|
222 |
|
|
for (j=0; j<3; j++) |
223 |
|
|
COMvel[j] += aVel[j]*mass; |
224 |
|
|
|
225 |
gezelter |
468 |
} |
226 |
|
|
} |
227 |
|
|
|
228 |
gezelter |
607 |
for (j=0; j<3; j++) |
229 |
|
|
COMvel[j] /= mtot; |
230 |
gezelter |
468 |
|
231 |
gezelter |
475 |
return mtot; |
232 |
|
|
|
233 |
gezelter |
468 |
} |
234 |
tim |
658 |
|
235 |
|
|
double Molecule::getTotalMass() |
236 |
|
|
{ |
237 |
|
|
int natoms; |
238 |
|
|
Atom** atoms; |
239 |
|
|
double totalMass; |
240 |
|
|
|
241 |
|
|
natoms = getNAtoms(); |
242 |
|
|
atoms = getMyAtoms(); |
243 |
|
|
totalMass = 0; |
244 |
|
|
for(int i =0; i < natoms; i++){ |
245 |
|
|
totalMass += atoms[i]->getMass(); |
246 |
|
|
} |
247 |
|
|
|
248 |
|
|
return totalMass; |
249 |
|
|
} |