36 |
|
//register createDUFF to ForceFieldCreator |
37 |
|
ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
38 |
|
|
39 |
+ |
|
40 |
+ |
ParseState DUFF::getSection(const std::string& section) { |
41 |
+ |
ParseState result; |
42 |
+ |
|
43 |
+ |
switch(section) { |
44 |
+ |
case "AtomTypes" : |
45 |
+ |
result = DUFF::AtomTypeSection; |
46 |
+ |
break; |
47 |
+ |
|
48 |
+ |
case "BondTypes" : |
49 |
+ |
result = DUFF::BondTypeSection; |
50 |
+ |
break; |
51 |
+ |
|
52 |
+ |
case "BendTypes" : |
53 |
+ |
result = DUFF::BendTypeSection; |
54 |
+ |
break; |
55 |
+ |
|
56 |
+ |
case "TorsionTypes" : |
57 |
+ |
result = DUFF::TorsionTypeSection; |
58 |
+ |
break; |
59 |
+ |
default: |
60 |
+ |
result = DUFF::UnknownSection; |
61 |
+ |
} |
62 |
+ |
|
63 |
+ |
return result; |
64 |
+ |
} |
65 |
+ |
|
66 |
|
void DUFF::parse(const std::string& filename) { |
67 |
|
ifstrstream* ffStream; |
68 |
|
ffStream = openForceFiledFile(filename); |
69 |
|
const int bufferSize = 65535; |
70 |
< |
char line[bufferSize]; |
71 |
< |
AtomType* atomType; |
45 |
< |
std::string atomTypeName; |
46 |
< |
double mass; |
47 |
< |
double epsilon; |
48 |
< |
double sigma; |
49 |
< |
int status; |
50 |
< |
int ident = 1; //ident begins from 1 (fortran's index begins from 1) |
70 |
> |
std::string line; |
71 |
> |
char buffer[bufferSize]; |
72 |
|
int lineNo = 0; |
73 |
< |
|
74 |
< |
while(ffStream.getline(line, bufferSize)){ |
73 |
> |
ParseState currentSection = DUFF::UnknownSection; |
74 |
> |
|
75 |
> |
while(ffStream.getline(buffer, bufferSize)){ |
76 |
|
++lineNo; |
77 |
|
|
78 |
< |
//a line begins with '#' or '!' is comment which is skipped |
79 |
< |
if (line[0] != '#' ||line[0] != '!') { |
80 |
< |
StringTokenizer tokenizer(line); |
81 |
< |
|
82 |
< |
if (tokenizer.countTokens() >= 4) { |
61 |
< |
atomTypeName = tokenizer.nextToken(); |
62 |
< |
mass = tokenizer.nextTokenAsFloat(); |
63 |
< |
epsilon = tokenizer.nextTokenAsFloat(); |
64 |
< |
sigma = tokenizer.nextTokenAsFloat(); |
78 |
> |
line = trimSpaces(buffer); |
79 |
> |
//a line begins with "//" is comment |
80 |
> |
if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
81 |
> |
continue; |
82 |
> |
} else { |
83 |
|
|
84 |
< |
atomType = new AtomType(); |
85 |
< |
atomType->setName(atomTypeName); |
86 |
< |
atomType->setMass(mass); |
87 |
< |
|
70 |
< |
//by default, all of the properties in AtomTypeProperties is set to 0 |
71 |
< |
//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
72 |
< |
atomType->setLennardJones(); |
84 |
> |
switch(currentSection) { |
85 |
> |
case DUFF::AtomTypeSection : |
86 |
> |
parseAtomType(line, lineNo); |
87 |
> |
break; |
88 |
|
|
89 |
< |
atomType->setIdent(ident); |
90 |
< |
atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
91 |
< |
atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
77 |
< |
atomType->complete(); |
78 |
< |
//notify a new LJtype atom type is created |
79 |
< |
newLJtype(&ident, &sigma, &epsilon, &status); |
89 |
> |
case DUFF::BondTypeSection : |
90 |
> |
parseBondType(line, lineNo); |
91 |
> |
break; |
92 |
|
|
93 |
< |
//add atom type to AtomTypeContainer |
94 |
< |
addAtomType(atomTypeName, atomType); |
95 |
< |
++ident; |
93 |
> |
case DUFF::BendTypeSection : |
94 |
> |
parseBendType(line, lineNo); |
95 |
> |
break; |
96 |
> |
|
97 |
> |
case DUFF::TorsionTypeSection : |
98 |
> |
parseTorsionType(line, lineNo); |
99 |
> |
break; |
100 |
> |
|
101 |
> |
case DUFF::UnknownSection: |
102 |
> |
StringTokenizer tokenizer(line); |
103 |
> |
|
104 |
> |
std::string keyword = tokenizer.nextToken(); |
105 |
> |
std::string section = tokenizer.nextToken(); |
106 |
> |
|
107 |
> |
ParseState newSection = getSection(section); |
108 |
> |
if (keyword != "begin" || keyword != "end") { |
109 |
> |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
110 |
> |
} else if (keyword == "begin") { |
111 |
> |
if (newSection == DUFF::UnknownSection) { |
112 |
> |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
113 |
> |
} else { |
114 |
> |
//enter a new section |
115 |
> |
currentSection = newSection; |
116 |
> |
} |
117 |
> |
|
118 |
> |
} else if (keyword == "end"){ |
119 |
> |
if (currentSection == newSection) ) { |
120 |
> |
//leave a section |
121 |
> |
currentSection = DUFF::UnknownSection; |
122 |
> |
} else { |
123 |
> |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
124 |
> |
} |
125 |
> |
|
126 |
> |
} |
127 |
> |
break; |
128 |
> |
default : |
129 |
|
|
85 |
– |
} else { |
86 |
– |
sprintf( painCave.errMsg, |
87 |
– |
"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
88 |
– |
"in line %d : %s\n", |
89 |
– |
filename.c_str(), lineNo, line); |
90 |
– |
painCave.severity = OOPSE_ERROR; |
91 |
– |
painCave.isFatal = 1; |
92 |
– |
simError(); |
130 |
|
} |
131 |
|
|
132 |
|
} |
136 |
|
} |
137 |
|
|
138 |
|
|
139 |
< |
void DUFF::parseAtomType(){ |
139 |
> |
void DUFF::parseAtomType(const std::string& line, int lineNo){ |
140 |
> |
StringTokenizer tokenizer(line); |
141 |
> |
|
142 |
> |
if (tokenizer.countTokens() >= 4) { |
143 |
> |
atomTypeName = tokenizer.nextToken(); |
144 |
> |
mass = tokenizer.nextTokenAsFloat(); |
145 |
> |
epsilon = tokenizer.nextTokenAsFloat(); |
146 |
> |
sigma = tokenizer.nextTokenAsFloat(); |
147 |
> |
|
148 |
> |
atomType = new AtomType(); |
149 |
> |
atomType->setName(atomTypeName); |
150 |
> |
atomType->setMass(mass); |
151 |
> |
|
152 |
> |
//by default, all of the properties in AtomTypeProperties is set to 0 |
153 |
> |
//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
154 |
> |
atomType->setLennardJones(); |
155 |
> |
|
156 |
> |
atomType->setIdent(ident); |
157 |
> |
atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
158 |
> |
atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
159 |
> |
atomType->complete(); |
160 |
> |
//notify a new LJtype atom type is created |
161 |
> |
newLJtype(&ident, &sigma, &epsilon, &status); |
162 |
> |
|
163 |
> |
//add atom type to AtomTypeContainer |
164 |
> |
addAtomType(atomTypeName, atomType); |
165 |
> |
++ident; |
166 |
> |
|
167 |
> |
} else { |
168 |
> |
sprintf( painCave.errMsg, |
169 |
> |
"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
170 |
> |
"in line %d : %s\n", |
171 |
> |
filename.c_str(), lineNo, line); |
172 |
> |
painCave.severity = OOPSE_ERROR; |
173 |
> |
painCave.isFatal = 1; |
174 |
> |
simError(); |
175 |
> |
} |
176 |
|
} |
177 |
|
|
178 |
< |
void DUFF::parseBondType(){ |
178 |
> |
void DUFF::parseBondType(const std::string& line, int lineNo){ |
179 |
> |
|
180 |
> |
StringTokenizer tokenizer(line); |
181 |
> |
std::string at1; |
182 |
> |
std::string at2; |
183 |
> |
std::string bt; |
184 |
> |
BondType* bondType = NULL; |
185 |
> |
double b0; |
186 |
> |
|
187 |
> |
int nTokens = tokenizer.countTokens(); |
188 |
> |
|
189 |
> |
if (nTokens < 4) { |
190 |
> |
|
191 |
> |
return; |
192 |
> |
} |
193 |
> |
|
194 |
> |
at1 = tokenizer.nextToken(); |
195 |
> |
at2 = tokenizer.nextToken(); |
196 |
> |
bt = tokenizer.nextToken(); |
197 |
> |
b0 = tokenizer.nextTokenAsDouble(); |
198 |
> |
nTokens -= 4; |
199 |
> |
|
200 |
> |
//switch is a maintain nightmare |
201 |
> |
switch(bt) { |
202 |
> |
case "FixedBondType" : |
203 |
> |
bondType = new FixedBondType(); |
204 |
> |
break; |
205 |
> |
|
206 |
> |
case "HarmonicBondType" : |
207 |
> |
if (nTokens < 1) { |
208 |
> |
|
209 |
> |
} else { |
210 |
> |
|
211 |
> |
double kb = tokenizer.nextTokenAsDouble(); |
212 |
> |
bondType = new HarmonicBondType(b0, kb); |
213 |
> |
} |
214 |
> |
|
215 |
> |
break; |
216 |
> |
|
217 |
> |
case "CubicBondType" : |
218 |
> |
if (nTokens < 4) { |
219 |
> |
|
220 |
> |
} else { |
221 |
> |
|
222 |
> |
double k3 = tokenizer.nextTokenAsDouble(); |
223 |
> |
double k2 = tokenizer.nextTokenAsDouble(); |
224 |
> |
double k1 = tokenizer.nextTokenAsDouble(); |
225 |
> |
double k0 = tokenizer.nextTokenAsDouble(); |
226 |
> |
|
227 |
> |
bondType = new CubicBondType(b0, k3, k2, k1, k0); |
228 |
> |
} |
229 |
> |
break; |
230 |
> |
|
231 |
> |
case "QuadraticBondType" : |
232 |
> |
if (nTokens < 5) { |
233 |
> |
|
234 |
> |
} else { |
235 |
> |
|
236 |
> |
b0 = tokenizer.nextTokenAsDouble(); |
237 |
> |
double k4 = tokenizer.nextTokenAsDouble(); |
238 |
> |
double k3 = tokenizer.nextTokenAsDouble(); |
239 |
> |
double k2 = tokenizer.nextTokenAsDouble(); |
240 |
> |
double k1 = tokenizer.nextTokenAsDouble(); |
241 |
> |
double k0 = tokenizer.nextTokenAsDouble(); |
242 |
> |
|
243 |
> |
bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
244 |
> |
} |
245 |
> |
break; |
246 |
> |
|
247 |
> |
case "PolynomialBondType " : |
248 |
> |
if (nTokens < 2 || nTokens % 2 != 0) { |
249 |
> |
|
250 |
> |
} else { |
251 |
> |
int nPairs = nTokens / 2; |
252 |
> |
int power; |
253 |
> |
double coefficient; |
254 |
> |
PolynomialBondType pbt = new PolynomialBondType(); |
255 |
> |
|
256 |
> |
for (int i = 0; i < nPairs; ++i) { |
257 |
> |
power = tokenizer.nextTokenAsInt(); |
258 |
> |
coefficient = tokenizer.nextTokenAsDouble(); |
259 |
> |
|
260 |
> |
if (power < 0) { |
261 |
> |
|
262 |
> |
} else { |
263 |
> |
pbt->setCoefficient(power, coefficient); |
264 |
> |
} |
265 |
> |
} |
266 |
> |
} |
267 |
> |
|
268 |
> |
break; |
269 |
> |
|
270 |
> |
default: |
271 |
> |
|
272 |
> |
} |
273 |
> |
|
274 |
> |
if (bondType != NULL) { |
275 |
> |
addBondType(at1, at2, bondType); |
276 |
> |
} |
277 |
|
} |
278 |
|
|
279 |
< |
void DUFF::parseBendType(){ |
279 |
> |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
280 |
> |
StringTokenizer tokenizer(line); |
281 |
> |
std::string at1; |
282 |
> |
std::string at2; |
283 |
> |
std::string at3; |
284 |
> |
std::string bt; |
285 |
> |
double theta0; |
286 |
> |
BendType* bendType = NULL; |
287 |
> |
|
288 |
> |
int nTokens = tokenizer.countTokens(); |
289 |
> |
|
290 |
> |
if (nTokens < 5) { |
291 |
> |
|
292 |
> |
return; |
293 |
> |
} |
294 |
> |
|
295 |
> |
at1 = tokenizer.nextToken(); |
296 |
> |
at2 = tokenizer.nextToken(); |
297 |
> |
at3 = tokenizer.nextToken(); |
298 |
> |
bt = tokenizer.nextToken(); |
299 |
> |
theta0 = tokenizer.nextTokenAsDouble(); |
300 |
> |
nTokens -= 5; |
301 |
> |
|
302 |
> |
//switch is a maintain nightmare |
303 |
> |
switch(bt) { |
304 |
> |
|
305 |
> |
case "HarmonicBendType" : |
306 |
> |
|
307 |
> |
if (nTokens < 1) { |
308 |
> |
|
309 |
> |
} else { |
310 |
> |
|
311 |
> |
double ktheta = tokenizer.nextTokenAsDouble(); |
312 |
> |
bendType = new HarmonicBendType(theta0, ktheta); |
313 |
> |
} |
314 |
> |
break; |
315 |
> |
case "GhostBendType" : |
316 |
> |
if (nTokens < 1) { |
317 |
> |
|
318 |
> |
} else { |
319 |
> |
double ktheta = tokenizer.nextTokenAsDouble(); |
320 |
> |
bendType = new HarmonicBendType(theta0, ktheta); |
321 |
> |
} |
322 |
> |
break; |
323 |
> |
|
324 |
> |
case "UreyBradleyBendType" : |
325 |
> |
if (nTokens < 3) { |
326 |
> |
|
327 |
> |
} else { |
328 |
> |
double ktheta = tokenizer.nextTokenAsDouble(); |
329 |
> |
double s0 = tokenizer.nextTokenAsDouble(); |
330 |
> |
double kub = tokenizer.nextTokenAsDouble(); |
331 |
> |
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
332 |
> |
} |
333 |
> |
break; |
334 |
> |
|
335 |
> |
case "CubicBendType" : |
336 |
> |
if (nTokens < 4) { |
337 |
> |
|
338 |
> |
} else { |
339 |
> |
|
340 |
> |
double k3 = tokenizer.nextTokenAsDouble(); |
341 |
> |
double k2 = tokenizer.nextTokenAsDouble(); |
342 |
> |
double k1 = tokenizer.nextTokenAsDouble(); |
343 |
> |
double k0 = tokenizer.nextTokenAsDouble(); |
344 |
> |
|
345 |
> |
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
346 |
> |
} |
347 |
> |
break; |
348 |
> |
|
349 |
> |
case "QuadraticBendType" : |
350 |
> |
if (nTokens < 5) { |
351 |
> |
|
352 |
> |
} else { |
353 |
> |
|
354 |
> |
theta0 = tokenizer.nextTokenAsDouble(); |
355 |
> |
double k4 = tokenizer.nextTokenAsDouble(); |
356 |
> |
double k3 = tokenizer.nextTokenAsDouble(); |
357 |
> |
double k2 = tokenizer.nextTokenAsDouble(); |
358 |
> |
double k1 = tokenizer.nextTokenAsDouble(); |
359 |
> |
double k0 = tokenizer.nextTokenAsDouble(); |
360 |
> |
|
361 |
> |
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
362 |
> |
} |
363 |
> |
break; |
364 |
> |
|
365 |
> |
case "PolynomialBendType " : |
366 |
> |
if (nTokens < 2 || nTokens % 2 != 0) { |
367 |
> |
|
368 |
> |
} else { |
369 |
> |
int nPairs = nTokens / 2; |
370 |
> |
int power; |
371 |
> |
double coefficient; |
372 |
> |
PolynomialBendType* pbt = new PolynomialBendType(); |
373 |
> |
|
374 |
> |
for (int i = 0; i < nPairs; ++i) { |
375 |
> |
power = tokenizer.nextTokenAsInt(); |
376 |
> |
coefficient = tokenizer.nextTokenAsDouble(); |
377 |
> |
|
378 |
> |
if (power < 0) { |
379 |
> |
|
380 |
> |
} else { |
381 |
> |
pbt->setCoefficient(power, coefficient); |
382 |
> |
} |
383 |
> |
} |
384 |
> |
} |
385 |
> |
|
386 |
> |
break; |
387 |
> |
|
388 |
> |
default: |
389 |
> |
|
390 |
> |
} |
391 |
> |
|
392 |
> |
if (bendType != NULL) { |
393 |
> |
addBendType(at1, at2, at3, bendType); |
394 |
> |
} |
395 |
> |
|
396 |
|
} |
397 |
|
|
398 |
< |
void DUFF::parseTorsionType(){ |
398 |
> |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
399 |
> |
StringTokenizer tokenizer(line); |
400 |
> |
std::string at1; |
401 |
> |
std::string at2; |
402 |
> |
std::string at3; |
403 |
> |
std::string at4; |
404 |
> |
std::string tt; |
405 |
> |
TorsionType* bendType = NULL; |
406 |
|
|
407 |
+ |
int nTokens = tokenizer.countTokens(); |
408 |
+ |
|
409 |
+ |
if (nTokens < 5) { |
410 |
+ |
|
411 |
+ |
return; |
412 |
+ |
} |
413 |
+ |
|
414 |
+ |
at1 = tokenizer.nextToken(); |
415 |
+ |
at2 = tokenizer.nextToken(); |
416 |
+ |
at3 = tokenizer.nextToken(); |
417 |
+ |
at4 = tokenizer.nextToken(); |
418 |
+ |
tt = tokenizer.nextToken(); |
419 |
+ |
|
420 |
+ |
nTokens -= 5; |
421 |
+ |
|
422 |
+ |
switch(tt) { |
423 |
+ |
|
424 |
+ |
case "CubicTorsionType" : |
425 |
+ |
if (nTokens < 4) { |
426 |
+ |
|
427 |
+ |
} else { |
428 |
+ |
|
429 |
+ |
double k3 = tokenizer.nextTokenAsDouble(); |
430 |
+ |
double k2 = tokenizer.nextTokenAsDouble(); |
431 |
+ |
double k1 = tokenizer.nextTokenAsDouble(); |
432 |
+ |
double k0 = tokenizer.nextTokenAsDouble(); |
433 |
+ |
|
434 |
+ |
bendType = new CubicTorsionType(k3, k2, k1, k0); |
435 |
+ |
} |
436 |
+ |
break; |
437 |
+ |
|
438 |
+ |
case "QuadraticTorsionType" : |
439 |
+ |
if (nTokens < 5) { |
440 |
+ |
|
441 |
+ |
} else { |
442 |
+ |
|
443 |
+ |
theta0 = tokenizer.nextTokenAsDouble(); |
444 |
+ |
double k4 = tokenizer.nextTokenAsDouble(); |
445 |
+ |
double k3 = tokenizer.nextTokenAsDouble(); |
446 |
+ |
double k2 = tokenizer.nextTokenAsDouble(); |
447 |
+ |
double k1 = tokenizer.nextTokenAsDouble(); |
448 |
+ |
double k0 = tokenizer.nextTokenAsDouble(); |
449 |
+ |
|
450 |
+ |
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
451 |
+ |
} |
452 |
+ |
break; |
453 |
+ |
|
454 |
+ |
case "PolynomialTorsionType " : |
455 |
+ |
if (nTokens < 2 || nTokens % 2 != 0) { |
456 |
+ |
|
457 |
+ |
} else { |
458 |
+ |
int nPairs = nTokens / 2; |
459 |
+ |
int power; |
460 |
+ |
double coefficient; |
461 |
+ |
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
462 |
+ |
|
463 |
+ |
for (int i = 0; i < nPairs; ++i) { |
464 |
+ |
power = tokenizer.nextTokenAsInt(); |
465 |
+ |
coefficient = tokenizer.nextTokenAsDouble(); |
466 |
+ |
|
467 |
+ |
if (power < 0) { |
468 |
+ |
|
469 |
+ |
} else { |
470 |
+ |
pbt->setCoefficient(power, coefficient); |
471 |
+ |
} |
472 |
+ |
} |
473 |
+ |
} |
474 |
+ |
|
475 |
+ |
break; |
476 |
+ |
case "CharmmTorsionType" : |
477 |
+ |
|
478 |
+ |
if (nTokens < 3 || nTokens % 3 != 0) { |
479 |
+ |
|
480 |
+ |
} else { |
481 |
+ |
int nSets = nTokens / 3; |
482 |
+ |
|
483 |
+ |
double kchi; |
484 |
+ |
int n; |
485 |
+ |
double delta; |
486 |
+ |
CharmmTorsionType* ctt = new CharmmTorsionType(); |
487 |
+ |
|
488 |
+ |
for (int i = 0; i < nSets; ++i) { |
489 |
+ |
kchi = tokenizer.nextTokenAsDouble(); |
490 |
+ |
n = tokenizer.nextTokenAsInt(); |
491 |
+ |
delta = tokenizer.nextTokenAsDouble(); |
492 |
+ |
|
493 |
+ |
if (n < 0 || n > 6) { |
494 |
+ |
|
495 |
+ |
} else { |
496 |
+ |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
497 |
+ |
} |
498 |
+ |
} |
499 |
+ |
} |
500 |
+ |
default: |
501 |
+ |
|
502 |
+ |
} |
503 |
+ |
|
504 |
+ |
if (bendType != NULL) { |
505 |
+ |
addTorsionType(at1, at2, at3, bendType); |
506 |
+ |
} |
507 |
|
} |
508 |
|
|
509 |
|
} //end namespace oopse |