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#include "UseTheForce/DUFF.hpp" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/charge_interface.h" |
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#include "UseTheForce/DarkSide/dipole_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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|
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namespace oopse { |
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|
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return new DUFF(); |
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} |
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|
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< |
//register createDUFF to ForceFieldCreator |
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> |
//register createDUFF to ForceFieldFactory |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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|
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|
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case "AtomTypes" : |
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result = DUFF::AtomTypeSection; |
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break; |
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case "DirectionalAtomTypes" : |
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result = DUFF::DirectionalAtomTypeSection; |
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break; |
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|
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case "BondTypes" : |
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result = DUFF::BondTypeSection; |
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std::string line; |
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char buffer[bufferSize]; |
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int lineNo = 0; |
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int atomIdent = 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
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ParseState currentSection = DUFF::UnknownSection; |
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|
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while(ffStream.getline(buffer, bufferSize)){ |
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|
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switch(currentSection) { |
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case DUFF::AtomTypeSection : |
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< |
parseAtomType(line, lineNo); |
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> |
parseAtomType(line, lineNo, atomIdent); |
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break; |
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|
96 |
+ |
case DUFF::DirectionalAtomTypeSection : |
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+ |
parseDirectionalAtomType(line, lineNo); |
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break; |
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|
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case DUFF::BondTypeSection : |
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parseBondType(line, lineNo); |
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break; |
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} |
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|
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|
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< |
void DUFF::parseAtomType(const std::string& line, int lineNo){ |
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> |
void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
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StringTokenizer tokenizer(line); |
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< |
|
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< |
if (tokenizer.countTokens() >= 4) { |
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atomTypeName = tokenizer.nextToken(); |
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mass = tokenizer.nextTokenAsFloat(); |
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< |
epsilon = tokenizer.nextTokenAsFloat(); |
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< |
sigma = tokenizer.nextTokenAsFloat(); |
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> |
int nTokens = tokenizer.countTokens(); |
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|
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< |
atomType = new AtomType(); |
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> |
//in AtomTypeSection, a line at least contains 5 tokens |
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> |
//atomTypeName, is Directional, isLJ, isCharge and mass |
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> |
if (nTokens < 5) { |
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|
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} else { |
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|
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std::string atomTypeName = tokenizer.nextToken(); |
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> |
bool isDirectional = tokenizer.nextTokenAsBool(); |
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> |
bool isLJ = tokenizer.nextTokenAsBool(); |
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> |
bool isCharge = tokenizer.nextTokenAsBool(); |
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> |
double mass = tokenizer.nextTokenAsDouble(); |
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> |
double epsilon; |
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> |
double sigma; |
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> |
double charge; |
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> |
nTokens -= 5; |
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|
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//parse epsilon and sigma |
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if (isLJ) { |
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if (nTokens >= 2) { |
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> |
epsilon = tokenizer.nextTokenAsDouble(); |
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> |
sigma = tokenizer.nextTokenAsDouble(); |
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> |
nTokens -= 2; |
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} else { |
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|
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} |
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} |
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> |
|
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> |
//parse charge |
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> |
if (isCharge) { |
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> |
if (nTokens >= 1) { |
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> |
charge = tokenizer.nextTokenAsDouble(); |
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> |
nTokens -= 1; |
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} else { |
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|
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} |
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} |
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> |
|
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> |
AtomType* atomType; |
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> |
if (isDirectional) { |
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atomType = new DirectionalAtomType(); |
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} else { |
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atomType = new AtomType(); |
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} |
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|
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atomType->setName(atomTypeName); |
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atomType->setMass(mass); |
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|
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//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
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atomType->setLennardJones(); |
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|
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< |
atomType->setIdent(ident); |
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< |
atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
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< |
atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
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> |
atomType->setIdent(ident); |
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|
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atomType->complete(); |
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//notify a new LJtype atom type is created |
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– |
newLJtype(&ident, &sigma, &epsilon, &status); |
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|
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< |
//add atom type to AtomTypeContainer |
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< |
addAtomType(atomTypeName, atomType); |
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< |
++ident; |
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> |
int setLJStatus; |
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|
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< |
} else { |
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< |
sprintf( painCave.errMsg, |
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< |
"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
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< |
"in line %d : %s\n", |
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< |
filename.c_str(), lineNo, line); |
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< |
painCave.severity = OOPSE_ERROR; |
217 |
< |
painCave.isFatal = 1; |
218 |
< |
simError(); |
211 |
> |
//notify a new LJtype atom type is created |
212 |
> |
if (isLJ) { |
213 |
> |
newLJtype(&ident, &sigma, &epsilon, &setLJStatus); |
214 |
> |
} |
215 |
> |
|
216 |
> |
int setChargeStatus; |
217 |
> |
if (isCharge) { |
218 |
> |
newChargeType(&ident, &charge, &setChargeStatus) |
219 |
> |
} |
220 |
> |
|
221 |
> |
if (setLJStatus && setChargeStatus) { |
222 |
> |
//add atom type to AtomTypeContainer |
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> |
addAtomType(atomTypeName, atomType); |
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> |
++ident; |
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> |
} else { |
226 |
> |
//error in notifying fortran |
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> |
delete atomType; |
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> |
} |
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} |
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+ |
|
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} |
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+ |
|
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|
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+ |
void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) { |
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+ |
StringTokenizer tokenizer(line); |
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int nTokens = tokenizer.countTokens(); |
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|
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//in irectionalAtomTypeSection, a line at least contains 6 tokens |
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//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
240 |
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if (nTokens < 6) { |
241 |
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|
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} else { |
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|
244 |
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|
245 |
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std::string atomTypeName = tokenizer.nextToken(); |
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bool isDipole = tokenizer.nextTokenAsBool(); |
247 |
+ |
bool isSticky = tokenizer.nextTokenAsBool(); |
248 |
+ |
double Ixx = tokenizer.nextTokenAsDouble(); |
249 |
+ |
double Iyy = tokenizer.nextTokenAsDouble(); |
250 |
+ |
double Izz = tokenizer.nextTokenAsDouble(); |
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nTokens -= 6; |
252 |
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|
253 |
+ |
AtomType* atomType = getAtomType(atomTypeName); |
254 |
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if (atomType == NULL) { |
255 |
+ |
|
256 |
+ |
} |
257 |
+ |
|
258 |
+ |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
259 |
+ |
if (dAtomType == NULL) { |
260 |
+ |
|
261 |
+ |
|
262 |
+ |
} |
263 |
+ |
|
264 |
+ |
dAtomType->setDipole(isDipole); |
265 |
+ |
dAtomType->setSticky(isSticky); |
266 |
+ |
|
267 |
+ |
Mat3x3d inertialMat; |
268 |
+ |
inertialMat(0, 0) = Ixx; |
269 |
+ |
inertialMat(1, 1) = Ixx; |
270 |
+ |
inertialMat(2, 2) = Ixx; |
271 |
+ |
dAtomType->setI(inertialMat); |
272 |
+ |
|
273 |
+ |
//read dipole moment |
274 |
+ |
double dipole; |
275 |
+ |
if (isDipole) { |
276 |
+ |
if (nTokens >= 1) { |
277 |
+ |
dipole = tokenizer.nextTokenAsDouble(); |
278 |
+ |
nTokens -= 1; |
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+ |
} else { |
280 |
+ |
|
281 |
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} |
282 |
+ |
} |
283 |
+ |
|
284 |
+ |
//read sticky parameters |
285 |
+ |
double w0; |
286 |
+ |
double v0; |
287 |
+ |
double v0p; |
288 |
+ |
double rl; |
289 |
+ |
double ru; |
290 |
+ |
double rlp; |
291 |
+ |
double rup; |
292 |
+ |
if (isSticky) { |
293 |
+ |
if (nTokens >= 7) { |
294 |
+ |
w0 = tokenizer.nextTokenAsDouble(); |
295 |
+ |
v0 = tokenizer.nextTokenAsDouble(); |
296 |
+ |
v0p = tokenizer.nextTokenAsDouble(); |
297 |
+ |
rl = tokenizer.nextTokenAsDouble(); |
298 |
+ |
ru = tokenizer.nextTokenAsDouble(); |
299 |
+ |
rlp = tokenizer.nextTokenAsDouble(); |
300 |
+ |
rup = tokenizer.nextTokenAsDouble(); |
301 |
+ |
nTokens -= 7; |
302 |
+ |
} else { |
303 |
+ |
|
304 |
+ |
} |
305 |
+ |
} |
306 |
+ |
|
307 |
+ |
|
308 |
+ |
//notify fotran a newDipoleType is created |
309 |
+ |
int ident = dAtomType->getIdent(); |
310 |
+ |
int setDipoleStatus; |
311 |
+ |
if (isDipole) { |
312 |
+ |
newDipoleType(&ident, &dipole, &setDipoleStatus); |
313 |
+ |
} |
314 |
+ |
|
315 |
+ |
//notify fotran a StickyType is created |
316 |
+ |
int setStickyStatus; |
317 |
+ |
if (isSticky) { |
318 |
+ |
makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
319 |
+ |
} |
320 |
+ |
|
321 |
+ |
|
322 |
+ |
if (!setDipoleStatus || !setStickyStatus) { |
323 |
+ |
|
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
} |
327 |
|
} |
328 |
|
|
329 |
|
void DUFF::parseBondType(const std::string& line, int lineNo){ |
407 |
|
for (int i = 0; i < nPairs; ++i) { |
408 |
|
power = tokenizer.nextTokenAsInt(); |
409 |
|
coefficient = tokenizer.nextTokenAsDouble(); |
410 |
< |
|
260 |
< |
if (power < 0) { |
261 |
< |
|
262 |
< |
} else { |
263 |
< |
pbt->setCoefficient(power, coefficient); |
264 |
< |
} |
410 |
> |
pbt->setCoefficient(power, coefficient); |
411 |
|
} |
412 |
|
} |
413 |
|
|
520 |
|
for (int i = 0; i < nPairs; ++i) { |
521 |
|
power = tokenizer.nextTokenAsInt(); |
522 |
|
coefficient = tokenizer.nextTokenAsDouble(); |
523 |
< |
|
378 |
< |
if (power < 0) { |
379 |
< |
|
380 |
< |
} else { |
381 |
< |
pbt->setCoefficient(power, coefficient); |
382 |
< |
} |
523 |
> |
pbt->setCoefficient(power, coefficient); |
524 |
|
} |
525 |
|
} |
526 |
|
|
604 |
|
for (int i = 0; i < nPairs; ++i) { |
605 |
|
power = tokenizer.nextTokenAsInt(); |
606 |
|
coefficient = tokenizer.nextTokenAsDouble(); |
607 |
< |
|
467 |
< |
if (power < 0) { |
468 |
< |
|
469 |
< |
} else { |
470 |
< |
pbt->setCoefficient(power, coefficient); |
471 |
< |
} |
607 |
> |
pbt->setCoefficient(power, coefficient); |
608 |
|
} |
609 |
|
} |
610 |
|
|
616 |
|
} else { |
617 |
|
int nSets = nTokens / 3; |
618 |
|
|
483 |
– |
double kchi; |
484 |
– |
int n; |
485 |
– |
double delta; |
619 |
|
CharmmTorsionType* ctt = new CharmmTorsionType(); |
620 |
|
|
621 |
|
for (int i = 0; i < nSets; ++i) { |
622 |
< |
kchi = tokenizer.nextTokenAsDouble(); |
623 |
< |
n = tokenizer.nextTokenAsInt(); |
624 |
< |
delta = tokenizer.nextTokenAsDouble(); |
622 |
> |
double kchi = tokenizer.nextTokenAsDouble(); |
623 |
> |
int n = tokenizer.nextTokenAsInt(); |
624 |
> |
double delta = tokenizer.nextTokenAsDouble(); |
625 |
|
|
626 |
< |
if (n < 0 || n > 6) { |
494 |
< |
|
495 |
< |
} else { |
496 |
< |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
497 |
< |
} |
626 |
> |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
627 |
|
} |
628 |
|
} |
629 |
|
default: |
636 |
|
} |
637 |
|
|
638 |
|
} //end namespace oopse |
510 |
– |
|