| 15 |
|
visitorName = "ZConsVisitor"; |
| 16 |
|
|
| 17 |
|
//retrieve tolerance for z-constraint molecuels |
| 18 |
< |
data = info->getProperty(ZCONSTOL_ID); |
| 18 |
> |
data = info->getPropertyByName(ZCONSTOL_ID); |
| 19 |
|
|
| 20 |
|
if (!data){ |
| 21 |
|
cerr << "Can not get zconstraint tolerance from SimInfo" << endl; |
| 36 |
|
} |
| 37 |
|
|
| 38 |
|
//retrieve sample time of z-contraint |
| 39 |
< |
data = info->getProperty(ZCONSTIME_ID); |
| 39 |
> |
data = info->getPropertyByName(ZCONSTIME_ID); |
| 40 |
|
|
| 41 |
|
if (!data){ |
| 42 |
|
cerr << "Can not get zcons time from SimInfo" << endl; |
| 57 |
|
} |
| 58 |
|
|
| 59 |
|
//retrieve index of z-constraint molecules |
| 60 |
< |
data = info->getProperty(ZCONSPARADATA_ID); |
| 60 |
> |
data = info->getPropertyByName(ZCONSPARADATA_ID); |
| 61 |
|
if (!data){ |
| 62 |
|
cerr << "Can not get index of z-constraint molecules from SimInfo" << endl; |
| 63 |
|
haveZcons = false; |
| 95 |
|
}//end if (!data |
| 96 |
|
|
| 97 |
|
//retrieve output filename of z force |
| 98 |
< |
data = info->getProperty(ZCONSFILENAME_ID); |
| 98 |
> |
data = info->getPropertyByName(ZCONSFILENAME_ID); |
| 99 |
|
if (!data){ |
| 100 |
|
cerr << "Can not get filename of z-constraint output from SimInfo" << endl; |
| 101 |
|
haveZcons = false; |
| 130 |
|
|
| 131 |
|
void ZConsVisitor::visit(Atom* atom){ |
| 132 |
|
string prefix; |
| 133 |
< |
if(isZconstraint(atom->getIndex(), prefix)) |
| 133 |
> |
if(isZconstraint(atom->getLocalIndex(), prefix)) |
| 134 |
|
internalVisit(atom, prefix); |
| 135 |
|
} |
| 136 |
|
|
| 137 |
|
void ZConsVisitor::visit(DirectionalAtom* datom){ |
| 138 |
|
string prefix; |
| 139 |
|
|
| 140 |
< |
if(isZconstraint(datom->getIndex(), prefix)) |
| 140 |
> |
if(isZconstraint(datom->getLocalIndex(), prefix)) |
| 141 |
|
internalVisit(datom, prefix); |
| 142 |
|
} |
| 143 |
|
|
| 147 |
|
|
| 148 |
|
atoms = rb->getAtoms(); |
| 149 |
|
|
| 150 |
< |
if(isZconstraint(atoms[0]->getIndex(), prefix)) |
| 150 |
> |
if(isZconstraint(atoms[0]->getLocalIndex(), prefix)) |
| 151 |
|
internalVisit(rb, prefix); |
| 152 |
|
} |
| 153 |
|
|
| 155 |
|
Molecule* mols; |
| 156 |
|
mols = info->molecules; |
| 157 |
|
for(int i =0; i < info->n_mol; i++) |
| 158 |
< |
if(index == mols[i].getMyIndex()) |
| 158 |
> |
if(index == mols[i].getGlobalIndex()) |
| 159 |
|
return &mols[i]; |
| 160 |
|
|
| 161 |
|
return NULL; |
| 163 |
|
|
| 164 |
|
void ZConsVisitor::update(){ |
| 165 |
|
Molecule* mol; |
| 166 |
< |
double com[3]; |
| 166 |
> |
Vector3d com; |
| 167 |
|
ZConsState state; |
| 168 |
< |
Atom** atoms; |
| 169 |
< |
int natoms; |
| 168 |
> |
//Atom** atoms; |
| 169 |
> |
//int natoms; |
| 170 |
|
|
| 171 |
|
getZconsPos(info->currentTime); |
| 172 |
|
|
| 173 |
|
for(size_t i = 0; i < zconsMol.size(); i++){ |
| 174 |
< |
zconsMol[i]->getCOM(com); |
| 174 |
> |
com = zconsMol[i]->getCom(); |
| 175 |
|
|
| 176 |
|
if(fabs(com[2] - zconsPos[i]) < zconsTol) |
| 177 |
|
state = zsFixed; |
| 179 |
|
state = zsMoving; |
| 180 |
|
|
| 181 |
|
//update the state of zconstraint atom |
| 182 |
< |
natoms = zconsMol[i]->getNAtoms(); |
| 183 |
< |
atoms = zconsMol[i]->getMyAtoms(); |
| 184 |
< |
for(int j =0; j < natoms; j++) |
| 185 |
< |
zconsState[atoms[j]->getIndex()] = state; |
| 182 |
> |
//natoms = zconsMol[i]->getNAtoms(); |
| 183 |
> |
//atoms = zconsMol[i]->getMyAtoms(); |
| 184 |
> |
//for(int j =0; j < natoms; j++) |
| 185 |
> |
// zconsState[atoms[j]->getLocalIndex()] = state; |
| 186 |
> |
|
| 187 |
> |
std::vector<Atom*>::iterator j; |
| 188 |
> |
for (Atom* atom = zconsMol[i]->beginAtom(j); atom != NULL; atom = zconsMol[i]->nextAtom(j)) { |
| 189 |
> |
zconsState[atom->getLocalIndex()] = state; |
| 190 |
> |
} |
| 191 |
|
} |
| 192 |
|
|
| 193 |
|
} |
| 220 |
|
|
| 221 |
|
|
| 222 |
|
//if there is not atom data, just skip it |
| 223 |
< |
data = sd->getProperty("ATOMDATA"); |
| 223 |
> |
data = sd->getPropertyByName("ATOMDATA"); |
| 224 |
|
if(data != NULL){ |
| 225 |
|
atomData = dynamic_cast<AtomData*>(data); |
| 226 |
|
if(atomData == NULL) |
| 272 |
|
result += buffer; |
| 273 |
|
|
| 274 |
|
for(size_t i = 0; i < zconsMol.size(); ++i){ |
| 275 |
< |
sprintf(buffer ,"zconstraint molecule[%d] = %d\n", i, zconsMol[i]->getMyIndex()); |
| 275 |
> |
sprintf(buffer ,"zconstraint molecule[%d] = %d\n", i, zconsMol[i]->getGlobalIndex()); |
| 276 |
|
result += buffer; |
| 277 |
|
|
| 278 |
|
} |
