| 1 |
< |
#include <cstdlib> |
| 1 |
> |
#include <stdlib.h> |
| 2 |
|
|
| 3 |
|
|
| 4 |
|
#include "Molecule.hpp" |
| 12 |
|
myBonds = NULL; |
| 13 |
|
myBends = NULL; |
| 14 |
|
myTorsions = NULL; |
| 15 |
– |
|
| 15 |
|
} |
| 16 |
|
|
| 18 |
– |
|
| 19 |
– |
|
| 17 |
|
Molecule::~Molecule( void ){ |
| 18 |
|
int i; |
| 19 |
|
|
| 37 |
|
delete[] myTorsions; |
| 38 |
|
} |
| 39 |
|
|
| 43 |
– |
if( myExcludes != NULL ){ |
| 44 |
– |
for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i]; |
| 45 |
– |
delete[] myExcludes; |
| 46 |
– |
} |
| 40 |
|
} |
| 41 |
|
|
| 42 |
|
|
| 43 |
|
void Molecule::initialize( molInit &theInit ){ |
| 44 |
|
|
| 45 |
+ |
CutoffGroup* curCutoffGroup; |
| 46 |
+ |
vector<CutoffGroup*>::iterator iterCutoff; |
| 47 |
+ |
Atom* cutoffAtom; |
| 48 |
+ |
vector<Atom*>::iterator iterAtom; |
| 49 |
+ |
int atomIndex; |
| 50 |
+ |
|
| 51 |
|
nAtoms = theInit.nAtoms; |
| 52 |
|
nMembers = nAtoms; |
| 53 |
|
nBonds = theInit.nBonds; |
| 54 |
|
nBends = theInit.nBends; |
| 55 |
|
nTorsions = theInit.nTorsions; |
| 56 |
< |
nExcludes = theInit.nExcludes; |
| 56 |
> |
nRigidBodies = theInit.nRigidBodies; |
| 57 |
|
nOriented = theInit.nOriented; |
| 58 |
+ |
nCutoffGroups = theInit.nCutoffGroups; |
| 59 |
|
|
| 60 |
|
myAtoms = theInit.myAtoms; |
| 61 |
|
myBonds = theInit.myBonds; |
| 62 |
|
myBends = theInit.myBends; |
| 63 |
|
myTorsions = theInit.myTorsions; |
| 64 |
< |
myExcludes = theInit.myExcludes; |
| 65 |
< |
|
| 64 |
> |
myRigidBodies = theInit.myRigidBodies; |
| 65 |
> |
|
| 66 |
> |
myIntegrableObjects = theInit.myIntegrableObjects; |
| 67 |
> |
|
| 68 |
> |
for (int i = 0; i < myRigidBodies.size(); i++) |
| 69 |
> |
myRigidBodies[i]->calcRefCoords(); |
| 70 |
> |
|
| 71 |
> |
myCutoffGroups = theInit.myCutoffGroups; |
| 72 |
> |
|
| 73 |
> |
//creat a global index set of atoms which belong to cutoff group. |
| 74 |
> |
//it will be use to speed up the query whether an atom belongs to cutoff group or not |
| 75 |
> |
cutoffAtomSet.clear(); |
| 76 |
> |
|
| 77 |
> |
for(curCutoffGroup = beginCutoffGroup(iterCutoff); curCutoffGroup != NULL; |
| 78 |
> |
curCutoffGroup = nextCutoffGroup(iterCutoff)){ |
| 79 |
> |
|
| 80 |
> |
for(cutoffAtom = curCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; |
| 81 |
> |
cutoffAtom = curCutoffGroup->nextAtom(iterAtom)){ |
| 82 |
> |
#ifdef IS_MPI |
| 83 |
> |
atomIndex = cutoffAtom->getGlobalIndex(); |
| 84 |
> |
#else |
| 85 |
> |
atomIndex = cutoffAtom->getIndex(); |
| 86 |
> |
#endif |
| 87 |
> |
cutoffAtomSet.insert(atomIndex); |
| 88 |
> |
}// end for(cutoffAtom) |
| 89 |
> |
}//end for(curCutoffGroup) |
| 90 |
> |
|
| 91 |
|
} |
| 92 |
|
|
| 93 |
|
void Molecule::calcForces( void ){ |
| 94 |
|
|
| 95 |
|
int i; |
| 96 |
+ |
double com[3]; |
| 97 |
|
|
| 98 |
+ |
for(i=0; i<myRigidBodies.size(); i++) { |
| 99 |
+ |
myRigidBodies[i]->updateAtoms(); |
| 100 |
+ |
} |
| 101 |
+ |
|
| 102 |
+ |
//calculate the center of mass of the molecule |
| 103 |
+ |
//getCOM(com); |
| 104 |
+ |
//for(int i = 0; i < nAtoms; i ++) |
| 105 |
+ |
// myAtoms[i]->setRc(com); |
| 106 |
+ |
|
| 107 |
+ |
|
| 108 |
|
for(i=0; i<nBonds; i++){ |
| 109 |
|
myBonds[i]->calc_forces(); |
| 110 |
|
} |
| 116 |
|
for(i=0; i<nTorsions; i++){ |
| 117 |
|
myTorsions[i]->calc_forces(); |
| 118 |
|
} |
| 119 |
+ |
|
| 120 |
+ |
// Rigid Body forces and torques are done after the fortran force loop |
| 121 |
+ |
|
| 122 |
|
} |
| 123 |
|
|
| 124 |
|
|
| 126 |
|
|
| 127 |
|
int i; |
| 128 |
|
double myPot = 0.0; |
| 129 |
+ |
|
| 130 |
+ |
for(i=0; i<myRigidBodies.size(); i++) { |
| 131 |
+ |
myRigidBodies[i]->updateAtoms(); |
| 132 |
+ |
} |
| 133 |
|
|
| 134 |
|
for(i=0; i<nBonds; i++){ |
| 135 |
|
myPot += myBonds[i]->get_potential(); |
| 161 |
|
for(i=0; i<nTorsions; i++){ |
| 162 |
|
myTorsions[i]->printMe(); |
| 163 |
|
} |
| 164 |
+ |
|
| 165 |
|
} |
| 166 |
|
|
| 167 |
|
void Molecule::moveCOM(double delta[3]){ |
| 168 |
< |
double x, y, z; |
| 169 |
< |
int i; |
| 168 |
> |
double aPos[3]; |
| 169 |
> |
int i, j; |
| 170 |
|
|
| 171 |
< |
for(i=0; i<nAtoms; i++) { |
| 172 |
< |
if(myAtoms[i] != NULL ) { |
| 171 |
> |
for(i=0; i<myIntegrableObjects.size(); i++) { |
| 172 |
> |
if(myIntegrableObjects[i] != NULL ) { |
| 173 |
> |
|
| 174 |
> |
myIntegrableObjects[i]->getPos( aPos ); |
| 175 |
> |
|
| 176 |
> |
for (j=0; j< 3; j++) |
| 177 |
> |
aPos[j] += delta[j]; |
| 178 |
|
|
| 179 |
< |
x = myAtoms[i]->getX() + delta[0]; |
| 180 |
< |
y = myAtoms[i]->getY() + delta[1]; |
| 181 |
< |
z = myAtoms[i]->getZ() + delta[2]; |
| 179 |
> |
myIntegrableObjects[i]->setPos( aPos ); |
| 180 |
> |
} |
| 181 |
> |
} |
| 182 |
|
|
| 183 |
< |
myAtoms[i]->setX(x); |
| 184 |
< |
myAtoms[i]->setY(y); |
| 185 |
< |
myAtoms[i]->setZ(z); |
| 183 |
> |
for(i=0; i<myRigidBodies.size(); i++) { |
| 184 |
> |
|
| 185 |
> |
myRigidBodies[i]->getPos( aPos ); |
| 186 |
> |
|
| 187 |
> |
for (j=0; j< 3; j++) |
| 188 |
> |
aPos[j] += delta[j]; |
| 189 |
> |
|
| 190 |
> |
myRigidBodies[i]->setPos( aPos ); |
| 191 |
|
} |
| 192 |
+ |
} |
| 193 |
+ |
|
| 194 |
+ |
void Molecule::atoms2rigidBodies( void ) { |
| 195 |
+ |
int i; |
| 196 |
+ |
for (i = 0; i < myRigidBodies.size(); i++) { |
| 197 |
+ |
myRigidBodies[i]->calcForcesAndTorques(); |
| 198 |
|
} |
| 199 |
|
} |
| 200 |
|
|
| 201 |
|
void Molecule::getCOM( double COM[3] ) { |
| 202 |
|
|
| 203 |
|
double mass, mtot; |
| 204 |
< |
int i; |
| 204 |
> |
double aPos[3]; |
| 205 |
> |
int i, j; |
| 206 |
|
|
| 207 |
< |
COM[0] = 0.0; |
| 208 |
< |
COM[1] = 0.0; |
| 209 |
< |
COM[2] = 0.0; |
| 207 |
> |
for (j=0; j<3; j++) |
| 208 |
> |
COM[j] = 0.0; |
| 209 |
> |
|
| 210 |
|
mtot = 0.0; |
| 211 |
|
|
| 212 |
< |
for (i=0; i < nAtoms; i++) { |
| 213 |
< |
if (myAtoms[i] != NULL) { |
| 212 |
> |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 213 |
> |
if (myIntegrableObjects[i] != NULL) { |
| 214 |
|
|
| 215 |
< |
mass = myAtoms[i]->getMass(); |
| 215 |
> |
mass = myIntegrableObjects[i]->getMass(); |
| 216 |
|
mtot += mass; |
| 217 |
< |
COM[0] += myAtoms[i]->getX() * mass; |
| 218 |
< |
COM[1] += myAtoms[i]->getY() * mass; |
| 158 |
< |
COM[2] += myAtoms[i]->getZ() * mass; |
| 217 |
> |
|
| 218 |
> |
myIntegrableObjects[i]->getPos( aPos ); |
| 219 |
|
|
| 220 |
+ |
for( j = 0; j < 3; j++) |
| 221 |
+ |
COM[j] += aPos[j] * mass; |
| 222 |
+ |
|
| 223 |
|
} |
| 224 |
|
} |
| 225 |
|
|
| 226 |
< |
COM[0] /= mtot; |
| 227 |
< |
COM[1] /= mtot; |
| 228 |
< |
COM[2] /= mtot; |
| 226 |
> |
for (j = 0; j < 3; j++) |
| 227 |
> |
COM[j] /= mtot; |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
double Molecule::getCOMvel( double COMvel[3] ) { |
| 231 |
> |
|
| 232 |
> |
double mass, mtot; |
| 233 |
> |
double aVel[3]; |
| 234 |
> |
int i, j; |
| 235 |
> |
|
| 236 |
> |
|
| 237 |
> |
for (j=0; j<3; j++) |
| 238 |
> |
COMvel[j] = 0.0; |
| 239 |
> |
|
| 240 |
> |
mtot = 0.0; |
| 241 |
> |
|
| 242 |
> |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 243 |
> |
if (myIntegrableObjects[i] != NULL) { |
| 244 |
> |
|
| 245 |
> |
mass = myIntegrableObjects[i]->getMass(); |
| 246 |
> |
mtot += mass; |
| 247 |
> |
|
| 248 |
> |
myIntegrableObjects[i]->getVel(aVel); |
| 249 |
> |
|
| 250 |
> |
for (j=0; j<3; j++) |
| 251 |
> |
COMvel[j] += aVel[j]*mass; |
| 252 |
> |
|
| 253 |
> |
} |
| 254 |
> |
} |
| 255 |
> |
|
| 256 |
> |
for (j=0; j<3; j++) |
| 257 |
> |
COMvel[j] /= mtot; |
| 258 |
|
|
| 259 |
< |
return COM; |
| 259 |
> |
return mtot; |
| 260 |
> |
|
| 261 |
|
} |
| 262 |
+ |
|
| 263 |
+ |
double Molecule::getTotalMass() |
| 264 |
+ |
{ |
| 265 |
+ |
|
| 266 |
+ |
double totalMass; |
| 267 |
+ |
|
| 268 |
+ |
totalMass = 0; |
| 269 |
+ |
for(int i =0; i < myIntegrableObjects.size(); i++){ |
| 270 |
+ |
totalMass += myIntegrableObjects[i]->getMass(); |
| 271 |
+ |
} |
| 272 |
+ |
|
| 273 |
+ |
return totalMass; |
| 274 |
+ |
} |
