25 |
|
|
26 |
|
#include "UseTheForce/DUFF.hpp" |
27 |
|
#include "UseTheForce/DarkSide/lj_interface.h" |
28 |
+ |
#include "UseTheForce/DarkSide/charge_interface.h" |
29 |
+ |
#include "UseTheForce/DarkSide/dipole_interface.h" |
30 |
+ |
#include "UseTheForce/DarkSide/sticky_interface.h" |
31 |
|
|
32 |
|
namespace oopse { |
33 |
|
|
36 |
|
return new DUFF(); |
37 |
|
} |
38 |
|
|
39 |
< |
//register createDUFF to ForceFieldCreator |
39 |
> |
//register createDUFF to ForceFieldFactory |
40 |
|
ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
41 |
|
|
42 |
|
|
47 |
|
case "AtomTypes" : |
48 |
|
result = DUFF::AtomTypeSection; |
49 |
|
break; |
50 |
+ |
case "DirectionalAtomTypes" : |
51 |
+ |
result = DUFF::DirectionalAtomTypeSection; |
52 |
+ |
break; |
53 |
|
|
54 |
|
case "BondTypes" : |
55 |
|
result = DUFF::BondTypeSection; |
76 |
|
std::string line; |
77 |
|
char buffer[bufferSize]; |
78 |
|
int lineNo = 0; |
79 |
+ |
int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
80 |
|
ParseState currentSection = DUFF::UnknownSection; |
81 |
|
|
82 |
|
while(ffStream.getline(buffer, bufferSize)){ |
90 |
|
|
91 |
|
switch(currentSection) { |
92 |
|
case DUFF::AtomTypeSection : |
93 |
< |
parseAtomType(line, lineNo); |
93 |
> |
parseAtomType(line, lineNo, atomIdent); |
94 |
|
break; |
95 |
|
|
96 |
+ |
case DUFF::DirectionalAtomTypeSection : |
97 |
+ |
parseDirectionalAtomType(line, lineNo); |
98 |
+ |
break; |
99 |
+ |
|
100 |
|
case DUFF::BondTypeSection : |
101 |
|
parseBondType(line, lineNo); |
102 |
|
break; |
146 |
|
delete ffStream; |
147 |
|
} |
148 |
|
|
149 |
< |
|
139 |
< |
void DUFF::parseAtomType(const std::string& line, int lineNo){ |
149 |
> |
void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
150 |
|
StringTokenizer tokenizer(line); |
151 |
< |
|
142 |
< |
if (tokenizer.countTokens() >= 4) { |
143 |
< |
atomTypeName = tokenizer.nextToken(); |
144 |
< |
mass = tokenizer.nextTokenAsFloat(); |
145 |
< |
epsilon = tokenizer.nextTokenAsFloat(); |
146 |
< |
sigma = tokenizer.nextTokenAsFloat(); |
151 |
> |
int nTokens = tokenizer.countTokens(); |
152 |
|
|
153 |
< |
atomType = new AtomType(); |
153 |
> |
//in AtomTypeSection, a line at least contains 5 tokens |
154 |
> |
//atomTypeName, is Directional, isLJ, isCharge and mass |
155 |
> |
if (nTokens < 5) { |
156 |
> |
|
157 |
> |
} else { |
158 |
> |
|
159 |
> |
std::string atomTypeName = tokenizer.nextToken(); |
160 |
> |
bool isDirectional = tokenizer.nextTokenAsBool(); |
161 |
> |
bool isLJ = tokenizer.nextTokenAsBool(); |
162 |
> |
bool isCharge = tokenizer.nextTokenAsBool(); |
163 |
> |
double mass = tokenizer.nextTokenAsDouble(); |
164 |
> |
double epsilon; |
165 |
> |
double sigma; |
166 |
> |
double charge; |
167 |
> |
nTokens -= 5; |
168 |
> |
|
169 |
> |
//parse epsilon and sigma |
170 |
> |
if (isLJ) { |
171 |
> |
if (nTokens >= 2) { |
172 |
> |
epsilon = tokenizer.nextTokenAsDouble(); |
173 |
> |
sigma = tokenizer.nextTokenAsDouble(); |
174 |
> |
nTokens -= 2; |
175 |
> |
} else { |
176 |
> |
|
177 |
> |
} |
178 |
> |
} |
179 |
> |
|
180 |
> |
//parse charge |
181 |
> |
if (isCharge) { |
182 |
> |
if (nTokens >= 1) { |
183 |
> |
charge = tokenizer.nextTokenAsDouble(); |
184 |
> |
nTokens -= 1; |
185 |
> |
} else { |
186 |
> |
|
187 |
> |
} |
188 |
> |
} |
189 |
> |
|
190 |
> |
AtomType* atomType; |
191 |
> |
if (isDirectional) { |
192 |
> |
atomType = new DirectionalAtomType(); |
193 |
> |
} else { |
194 |
> |
atomType = new AtomType(); |
195 |
> |
} |
196 |
> |
|
197 |
|
atomType->setName(atomTypeName); |
198 |
|
atomType->setMass(mass); |
199 |
|
|
200 |
< |
//by default, all of the properties in AtomTypeProperties is set to 0 |
201 |
< |
//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
202 |
< |
atomType->setLennardJones(); |
200 |
> |
if (isLJ) { |
201 |
> |
atomType->setLennardJones(); |
202 |
> |
} |
203 |
|
|
204 |
< |
atomType->setIdent(ident); |
205 |
< |
atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
206 |
< |
atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
204 |
> |
if (isCharge) { |
205 |
> |
atomType->setCharge(); |
206 |
> |
} |
207 |
> |
|
208 |
> |
atomType->setIdent(ident); |
209 |
> |
|
210 |
|
atomType->complete(); |
160 |
– |
//notify a new LJtype atom type is created |
161 |
– |
newLJtype(&ident, &sigma, &epsilon, &status); |
211 |
|
|
212 |
< |
//add atom type to AtomTypeContainer |
164 |
< |
addAtomType(atomTypeName, atomType); |
165 |
< |
++ident; |
212 |
> |
int setLJStatus; |
213 |
|
|
214 |
< |
} else { |
215 |
< |
sprintf( painCave.errMsg, |
216 |
< |
"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
217 |
< |
"in line %d : %s\n", |
218 |
< |
filename.c_str(), lineNo, line); |
219 |
< |
painCave.severity = OOPSE_ERROR; |
220 |
< |
painCave.isFatal = 1; |
221 |
< |
simError(); |
214 |
> |
//notify a new LJtype atom type is created |
215 |
> |
if (isLJ) { |
216 |
> |
newLJtype(&ident, &sigma, &epsilon, &setLJStatus); |
217 |
> |
} |
218 |
> |
|
219 |
> |
int setChargeStatus; |
220 |
> |
if (isCharge) { |
221 |
> |
newChargeType(&ident, &charge, &setChargeStatus) |
222 |
> |
} |
223 |
> |
|
224 |
> |
if (setLJStatus && setChargeStatus) { |
225 |
> |
//add atom type to AtomTypeContainer |
226 |
> |
addAtomType(atomTypeName, atomType); |
227 |
> |
++ident; |
228 |
> |
} else { |
229 |
> |
//error in notifying fortran |
230 |
> |
delete atomType; |
231 |
> |
} |
232 |
|
} |
233 |
+ |
|
234 |
+ |
} |
235 |
+ |
|
236 |
+ |
|
237 |
+ |
void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) { |
238 |
+ |
StringTokenizer tokenizer(line); |
239 |
+ |
int nTokens = tokenizer.countTokens(); |
240 |
+ |
|
241 |
+ |
//in DirectionalAtomTypeSection, a line at least contains 6 tokens |
242 |
+ |
//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
243 |
+ |
if (nTokens < 6) { |
244 |
+ |
std::cerr << "Not enought tokens" << std::endl; |
245 |
+ |
} else { |
246 |
+ |
|
247 |
+ |
|
248 |
+ |
std::string atomTypeName = tokenizer.nextToken(); |
249 |
+ |
bool isDipole = tokenizer.nextTokenAsBool(); |
250 |
+ |
bool isSticky = tokenizer.nextTokenAsBool(); |
251 |
+ |
double Ixx = tokenizer.nextTokenAsDouble(); |
252 |
+ |
double Iyy = tokenizer.nextTokenAsDouble(); |
253 |
+ |
double Izz = tokenizer.nextTokenAsDouble(); |
254 |
+ |
nTokens -= 6; |
255 |
+ |
|
256 |
+ |
AtomType* atomType = getAtomType(atomTypeName); |
257 |
+ |
if (atomType == NULL) { |
258 |
+ |
|
259 |
+ |
} |
260 |
+ |
|
261 |
+ |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
262 |
+ |
if (dAtomType == NULL) { |
263 |
+ |
|
264 |
+ |
|
265 |
+ |
} |
266 |
+ |
|
267 |
+ |
if (isDipole) { |
268 |
+ |
dAtomType->setDipole(); |
269 |
+ |
} |
270 |
+ |
|
271 |
+ |
if (isSticky) { |
272 |
+ |
dAtomType->setSticky(); |
273 |
+ |
} |
274 |
+ |
|
275 |
+ |
Mat3x3d inertialMat; |
276 |
+ |
inertialMat(0, 0) = Ixx; |
277 |
+ |
inertialMat(1, 1) = Iyy; |
278 |
+ |
inertialMat(2, 2) = Izz; |
279 |
+ |
dAtomType->setI(inertialMat); |
280 |
+ |
|
281 |
+ |
//read dipole moment |
282 |
+ |
double dipole; |
283 |
+ |
if (isDipole) { |
284 |
+ |
if (nTokens >= 1) { |
285 |
+ |
dipole = tokenizer.nextTokenAsDouble(); |
286 |
+ |
nTokens -= 1; |
287 |
+ |
} else { |
288 |
+ |
|
289 |
+ |
} |
290 |
+ |
} |
291 |
+ |
|
292 |
+ |
//read sticky parameters |
293 |
+ |
double w0; |
294 |
+ |
double v0; |
295 |
+ |
double v0p; |
296 |
+ |
double rl; |
297 |
+ |
double ru; |
298 |
+ |
double rlp; |
299 |
+ |
double rup; |
300 |
+ |
if (isSticky) { |
301 |
+ |
if (nTokens >= 7) { |
302 |
+ |
w0 = tokenizer.nextTokenAsDouble(); |
303 |
+ |
v0 = tokenizer.nextTokenAsDouble(); |
304 |
+ |
v0p = tokenizer.nextTokenAsDouble(); |
305 |
+ |
rl = tokenizer.nextTokenAsDouble(); |
306 |
+ |
ru = tokenizer.nextTokenAsDouble(); |
307 |
+ |
rlp = tokenizer.nextTokenAsDouble(); |
308 |
+ |
rup = tokenizer.nextTokenAsDouble(); |
309 |
+ |
nTokens -= 7; |
310 |
+ |
} else { |
311 |
+ |
|
312 |
+ |
} |
313 |
+ |
} |
314 |
+ |
|
315 |
+ |
|
316 |
+ |
//notify fotran a newDipoleType is created |
317 |
+ |
int ident = dAtomType->getIdent(); |
318 |
+ |
int setDipoleStatus; |
319 |
+ |
if (isDipole) { |
320 |
+ |
newDipoleType(&ident, &dipole, &setDipoleStatus); |
321 |
+ |
} |
322 |
+ |
|
323 |
+ |
//notify fotran a StickyType is created |
324 |
+ |
int setStickyStatus; |
325 |
+ |
if (isSticky) { |
326 |
+ |
makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
327 |
+ |
} |
328 |
+ |
|
329 |
+ |
|
330 |
+ |
if (!setDipoleStatus || !setStickyStatus) { |
331 |
+ |
|
332 |
+ |
} |
333 |
+ |
|
334 |
+ |
} |
335 |
|
} |
336 |
|
|
337 |
|
void DUFF::parseBondType(const std::string& line, int lineNo){ |
358 |
|
|
359 |
|
//switch is a maintain nightmare |
360 |
|
switch(bt) { |
361 |
< |
case "FixedBondType" : |
361 |
> |
case "Fixed" : |
362 |
|
bondType = new FixedBondType(); |
363 |
|
break; |
364 |
|
|
365 |
< |
case "HarmonicBondType" : |
365 |
> |
case "Harmonic" : |
366 |
|
if (nTokens < 1) { |
367 |
|
|
368 |
|
} else { |
373 |
|
|
374 |
|
break; |
375 |
|
|
376 |
< |
case "CubicBondType" : |
376 |
> |
case "Cubic" : |
377 |
|
if (nTokens < 4) { |
378 |
|
|
379 |
|
} else { |
387 |
|
} |
388 |
|
break; |
389 |
|
|
390 |
< |
case "QuadraticBondType" : |
390 |
> |
case "Quartic" : |
391 |
|
if (nTokens < 5) { |
392 |
|
|
393 |
|
} else { |
403 |
|
} |
404 |
|
break; |
405 |
|
|
406 |
< |
case "PolynomialBondType " : |
406 |
> |
case "Polynomial" : |
407 |
|
if (nTokens < 2 || nTokens % 2 != 0) { |
408 |
|
|
409 |
|
} else { |
415 |
|
for (int i = 0; i < nPairs; ++i) { |
416 |
|
power = tokenizer.nextTokenAsInt(); |
417 |
|
coefficient = tokenizer.nextTokenAsDouble(); |
418 |
< |
|
260 |
< |
if (power < 0) { |
261 |
< |
|
262 |
< |
} else { |
263 |
< |
pbt->setCoefficient(power, coefficient); |
264 |
< |
} |
418 |
> |
pbt->setCoefficient(power, coefficient); |
419 |
|
} |
420 |
|
} |
421 |
|
|
456 |
|
//switch is a maintain nightmare |
457 |
|
switch(bt) { |
458 |
|
|
459 |
< |
case "HarmonicBendType" : |
459 |
> |
case "Harmonic" : |
460 |
|
|
461 |
|
if (nTokens < 1) { |
462 |
|
|
466 |
|
bendType = new HarmonicBendType(theta0, ktheta); |
467 |
|
} |
468 |
|
break; |
469 |
< |
case "GhostBendType" : |
469 |
> |
case "GhostBend" : |
470 |
|
if (nTokens < 1) { |
471 |
|
|
472 |
|
} else { |
475 |
|
} |
476 |
|
break; |
477 |
|
|
478 |
< |
case "UreyBradleyBendType" : |
478 |
> |
case "UreyBradley" : |
479 |
|
if (nTokens < 3) { |
480 |
|
|
481 |
|
} else { |
486 |
|
} |
487 |
|
break; |
488 |
|
|
489 |
< |
case "CubicBendType" : |
489 |
> |
case "Cubic" : |
490 |
|
if (nTokens < 4) { |
491 |
|
|
492 |
|
} else { |
500 |
|
} |
501 |
|
break; |
502 |
|
|
503 |
< |
case "QuadraticBendType" : |
503 |
> |
case "Quartic" : |
504 |
|
if (nTokens < 5) { |
505 |
|
|
506 |
|
} else { |
516 |
|
} |
517 |
|
break; |
518 |
|
|
519 |
< |
case "PolynomialBendType " : |
519 |
> |
case "Polynomial" : |
520 |
|
if (nTokens < 2 || nTokens % 2 != 0) { |
521 |
|
|
522 |
|
} else { |
528 |
|
for (int i = 0; i < nPairs; ++i) { |
529 |
|
power = tokenizer.nextTokenAsInt(); |
530 |
|
coefficient = tokenizer.nextTokenAsDouble(); |
531 |
< |
|
378 |
< |
if (power < 0) { |
379 |
< |
|
380 |
< |
} else { |
381 |
< |
pbt->setCoefficient(power, coefficient); |
382 |
< |
} |
531 |
> |
pbt->setCoefficient(power, coefficient); |
532 |
|
} |
533 |
|
} |
534 |
|
|
551 |
|
std::string at3; |
552 |
|
std::string at4; |
553 |
|
std::string tt; |
554 |
< |
TorsionType* bendType = NULL; |
554 |
> |
TorsionType* torsionType = NULL; |
555 |
|
|
556 |
|
int nTokens = tokenizer.countTokens(); |
557 |
|
|
570 |
|
|
571 |
|
switch(tt) { |
572 |
|
|
573 |
< |
case "CubicTorsionType" : |
573 |
> |
case "Cubic" : |
574 |
|
if (nTokens < 4) { |
575 |
|
|
576 |
|
} else { |
584 |
|
} |
585 |
|
break; |
586 |
|
|
587 |
< |
case "QuadraticTorsionType" : |
587 |
> |
case "Quartic" : |
588 |
|
if (nTokens < 5) { |
589 |
|
|
590 |
|
} else { |
600 |
|
} |
601 |
|
break; |
602 |
|
|
603 |
< |
case "PolynomialTorsionType " : |
603 |
> |
case "Polynomial" : |
604 |
|
if (nTokens < 2 || nTokens % 2 != 0) { |
605 |
|
|
606 |
|
} else { |
612 |
|
for (int i = 0; i < nPairs; ++i) { |
613 |
|
power = tokenizer.nextTokenAsInt(); |
614 |
|
coefficient = tokenizer.nextTokenAsDouble(); |
615 |
< |
|
467 |
< |
if (power < 0) { |
468 |
< |
|
469 |
< |
} else { |
470 |
< |
pbt->setCoefficient(power, coefficient); |
471 |
< |
} |
615 |
> |
pbt->setCoefficient(power, coefficient); |
616 |
|
} |
617 |
|
} |
618 |
|
|
619 |
|
break; |
620 |
< |
case "CharmmTorsionType" : |
620 |
> |
case "Charmm" : |
621 |
|
|
622 |
|
if (nTokens < 3 || nTokens % 3 != 0) { |
623 |
|
|
624 |
|
} else { |
625 |
|
int nSets = nTokens / 3; |
626 |
|
|
483 |
– |
double kchi; |
484 |
– |
int n; |
485 |
– |
double delta; |
627 |
|
CharmmTorsionType* ctt = new CharmmTorsionType(); |
628 |
|
|
629 |
|
for (int i = 0; i < nSets; ++i) { |
630 |
< |
kchi = tokenizer.nextTokenAsDouble(); |
631 |
< |
n = tokenizer.nextTokenAsInt(); |
632 |
< |
delta = tokenizer.nextTokenAsDouble(); |
630 |
> |
double kchi = tokenizer.nextTokenAsDouble(); |
631 |
> |
int n = tokenizer.nextTokenAsInt(); |
632 |
> |
double delta = tokenizer.nextTokenAsDouble(); |
633 |
|
|
634 |
< |
if (n < 0 || n > 6) { |
494 |
< |
|
495 |
< |
} else { |
496 |
< |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
497 |
< |
} |
634 |
> |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
635 |
|
} |
636 |
|
} |
637 |
|
default: |
638 |
|
|
639 |
|
} |
640 |
|
|
641 |
< |
if (bendType != NULL) { |
642 |
< |
addTorsionType(at1, at2, at3, bendType); |
641 |
> |
if (torsionType != NULL) { |
642 |
> |
addTorsionType(at1, at2, at3, at4, torsionType); |
643 |
|
} |
644 |
|
} |
645 |
|
|
646 |
|
} //end namespace oopse |
510 |
– |
|