25 |
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26 |
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#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 |
+ |
#include "UseTheForce/ForceFieldFactory.hpp" |
32 |
+ |
#include "io/DirectionalAtomTypesSectionParser.hpp" |
33 |
+ |
#include "io/AtomTypesSectionParser.hpp" |
34 |
+ |
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
35 |
+ |
#include "io/ElectrostaticAtomTypesSectionParser.hpp" |
36 |
+ |
#include "io/EAMAtomTypesSectionParser.hpp" |
37 |
+ |
#include "io/StickyAtomTypesSectionParser.hpp" |
38 |
+ |
#include "io/BondTypesSectionParser.hpp" |
39 |
+ |
#include "io/BendTypesSectionParser.hpp" |
40 |
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#include "io/TorsionTypesSectionParser.hpp" |
41 |
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|
42 |
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namespace oopse { |
43 |
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|
46 |
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return new DUFF(); |
47 |
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} |
48 |
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|
49 |
< |
//register createDUFF to ForceFieldCreator |
50 |
< |
ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
49 |
> |
//register createDUFF to ForceFieldFactory |
50 |
> |
bool registerDUFFStatus = ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
51 |
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|
52 |
+ |
DUFF::DUFF(){ |
53 |
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|
54 |
+ |
//the order of adding section parsers are important |
55 |
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//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
56 |
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//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
57 |
+ |
//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
58 |
+ |
//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
59 |
+ |
//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
60 |
+ |
//important. AtomTypesSectionParser should be added before other atom type section parsers. |
61 |
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//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
62 |
+ |
//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
63 |
+ |
//not important. |
64 |
+ |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
65 |
+ |
spMan_.push_back(new AtomTypesSectionParser()); |
66 |
+ |
spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
67 |
+ |
spMan_.push_back(new ElectrostaticAtomTypesSectionParser()); |
68 |
+ |
spMan_.push_back(new EAMAtomTypesSectionParser()); |
69 |
+ |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
70 |
+ |
spMan_.push_back(new BondTypesSectionParser()); |
71 |
+ |
spMan_.push_back(new BendTypesSectionParser()); |
72 |
+ |
spMan_.push_back(new TorsionTypesSectionParser()); |
73 |
+ |
|
74 |
+ |
} |
75 |
+ |
|
76 |
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void DUFF::parse(const std::string& filename) { |
77 |
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ifstrstream* ffStream; |
78 |
< |
ffStream = openForceFiledFile(filename); |
78 |
> |
ffStream = openForceFieldFile(filename); |
79 |
> |
|
80 |
> |
spMan_.parse(*ffStream, *this); |
81 |
> |
|
82 |
> |
ForceField::AtomTypeContainer::MapTypeIterator i; |
83 |
> |
AtomType* at; |
84 |
> |
|
85 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
86 |
> |
at->makeFortranAtomType(); |
87 |
> |
} |
88 |
> |
|
89 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
90 |
> |
at->complete(); |
91 |
> |
} |
92 |
> |
|
93 |
> |
} |
94 |
> |
|
95 |
> |
/* |
96 |
> |
ParseState DUFF::getSection(const std::string& section) { |
97 |
> |
ParseState result; |
98 |
> |
|
99 |
> |
switch(section) { |
100 |
> |
case "AtomTypes" : |
101 |
> |
result = DUFF::AtomTypeSection; |
102 |
> |
break; |
103 |
> |
case "DirectionalAtomTypes" : |
104 |
> |
result = DUFF::DirectionalAtomTypeSection; |
105 |
> |
break; |
106 |
> |
|
107 |
> |
case "BondTypes" : |
108 |
> |
result = DUFF::BondTypeSection; |
109 |
> |
break; |
110 |
> |
|
111 |
> |
case "BendTypes" : |
112 |
> |
result = DUFF::BendTypeSection; |
113 |
> |
break; |
114 |
> |
|
115 |
> |
case "TorsionTypes" : |
116 |
> |
result = DUFF::TorsionTypeSection; |
117 |
> |
break; |
118 |
> |
default: |
119 |
> |
result = DUFF::UnknownSection; |
120 |
> |
} |
121 |
> |
|
122 |
> |
return result; |
123 |
> |
} |
124 |
> |
|
125 |
> |
void DUFF::parse(const std::string& filename) { |
126 |
> |
ifstrstream* ffStream; |
127 |
> |
ffStream = openForceFieldFile(filename); |
128 |
|
const int bufferSize = 65535; |
129 |
< |
char line[bufferSize]; |
130 |
< |
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) |
129 |
> |
std::string line; |
130 |
> |
char buffer[bufferSize]; |
131 |
|
int lineNo = 0; |
132 |
< |
|
133 |
< |
while(ffStream.getline(line, bufferSize)){ |
132 |
> |
int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
133 |
> |
ParseState currentSection = DUFF::UnknownSection; |
134 |
> |
|
135 |
> |
while(ffStream.getline(buffer, bufferSize)){ |
136 |
|
++lineNo; |
137 |
|
|
138 |
< |
//a line begins with '#' or '!' is comment which is skipped |
139 |
< |
if (line[0] != '#' ||line[0] != '!') { |
140 |
< |
StringTokenizer tokenizer(line); |
141 |
< |
|
142 |
< |
if (tokenizer.countTokens() >= 4) { |
61 |
< |
atomTypeName = tokenizer.nextToken(); |
62 |
< |
mass = tokenizer.nextTokenAsFloat(); |
63 |
< |
epsilon = tokenizer.nextTokenAsFloat(); |
64 |
< |
sigma = tokenizer.nextTokenAsFloat(); |
138 |
> |
line = trimSpaces(buffer); |
139 |
> |
//a line begins with "//" is comment |
140 |
> |
if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
141 |
> |
continue; |
142 |
> |
} else { |
143 |
|
|
144 |
< |
atomType = new AtomType(); |
145 |
< |
atomType->setName(atomTypeName); |
146 |
< |
atomType->setMass(mass); |
147 |
< |
|
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(); |
144 |
> |
switch(currentSection) { |
145 |
> |
case DUFF::AtomTypeSection : |
146 |
> |
parseAtomType(line, lineNo, atomIdent); |
147 |
> |
break; |
148 |
|
|
149 |
< |
atomType->setIdent(ident); |
150 |
< |
atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
151 |
< |
atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
152 |
< |
atomType->complete(); |
153 |
< |
//notify a new LJtype atom type is created |
154 |
< |
newLJtype(&ident, &sigma, &epsilon, &status); |
149 |
> |
case DUFF::DirectionalAtomTypeSection : |
150 |
> |
parseDirectionalAtomType(line, lineNo); |
151 |
> |
break; |
152 |
> |
|
153 |
> |
case DUFF::BondTypeSection : |
154 |
> |
parseBondType(line, lineNo); |
155 |
> |
break; |
156 |
|
|
157 |
< |
//add atom type to AtomTypeContainer |
158 |
< |
addAtomType(atomTypeName, atomType); |
159 |
< |
++ident; |
157 |
> |
case DUFF::BendTypeSection : |
158 |
> |
parseBendType(line, lineNo); |
159 |
> |
break; |
160 |
> |
|
161 |
> |
case DUFF::TorsionTypeSection : |
162 |
> |
parseTorsionType(line, lineNo); |
163 |
> |
break; |
164 |
> |
|
165 |
> |
case DUFF::UnknownSection: |
166 |
> |
StringTokenizer tokenizer(line); |
167 |
> |
|
168 |
> |
std::string keyword = tokenizer.nextToken(); |
169 |
> |
std::string section = tokenizer.nextToken(); |
170 |
> |
|
171 |
> |
ParseState newSection = getSection(section); |
172 |
> |
if (keyword != "begin" || keyword != "end") { |
173 |
> |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
174 |
> |
} else if (keyword == "begin") { |
175 |
> |
if (newSection == DUFF::UnknownSection) { |
176 |
> |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
177 |
> |
} else { |
178 |
> |
//enter a new section |
179 |
> |
currentSection = newSection; |
180 |
> |
} |
181 |
> |
|
182 |
> |
} else if (keyword == "end"){ |
183 |
> |
if (currentSection == newSection) ) { |
184 |
> |
//leave a section |
185 |
> |
currentSection = DUFF::UnknownSection; |
186 |
> |
} else { |
187 |
> |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
188 |
> |
} |
189 |
> |
|
190 |
> |
} |
191 |
> |
break; |
192 |
> |
default : |
193 |
|
|
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(); |
194 |
|
} |
195 |
|
|
196 |
|
} |
199 |
|
delete ffStream; |
200 |
|
} |
201 |
|
|
202 |
+ |
void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
203 |
+ |
StringTokenizer tokenizer(line); |
204 |
+ |
int nTokens = tokenizer.countTokens(); |
205 |
|
|
206 |
< |
void DUFF::parseAtomType(){ |
206 |
> |
//in AtomTypeSection, a line at least contains 5 tokens |
207 |
> |
//atomTypeName, is Directional, isLJ, isCharge and mass |
208 |
> |
if (nTokens < 5) { |
209 |
> |
|
210 |
> |
} else { |
211 |
> |
|
212 |
> |
std::string atomTypeName = tokenizer.nextToken(); |
213 |
> |
bool isDirectional = tokenizer.nextTokenAsBool(); |
214 |
> |
bool isLJ = tokenizer.nextTokenAsBool(); |
215 |
> |
bool isCharge = tokenizer.nextTokenAsBool(); |
216 |
> |
double mass = tokenizer.nextTokenAsDouble(); |
217 |
> |
double epsilon; |
218 |
> |
double sigma; |
219 |
> |
double charge; |
220 |
> |
nTokens -= 5; |
221 |
> |
|
222 |
> |
//parse epsilon and sigma |
223 |
> |
if (isLJ) { |
224 |
> |
if (nTokens >= 2) { |
225 |
> |
epsilon = tokenizer.nextTokenAsDouble(); |
226 |
> |
sigma = tokenizer.nextTokenAsDouble(); |
227 |
> |
nTokens -= 2; |
228 |
> |
} else { |
229 |
> |
|
230 |
> |
} |
231 |
> |
} |
232 |
> |
|
233 |
> |
//parse charge |
234 |
> |
if (isCharge) { |
235 |
> |
if (nTokens >= 1) { |
236 |
> |
charge = tokenizer.nextTokenAsDouble(); |
237 |
> |
nTokens -= 1; |
238 |
> |
} else { |
239 |
> |
|
240 |
> |
} |
241 |
> |
} |
242 |
> |
|
243 |
> |
AtomType* atomType; |
244 |
> |
if (isDirectional) { |
245 |
> |
atomType = new DirectionalAtomType(); |
246 |
> |
} else { |
247 |
> |
atomType = new AtomType(); |
248 |
> |
} |
249 |
> |
|
250 |
> |
atomType->setName(atomTypeName); |
251 |
> |
atomType->setMass(mass); |
252 |
> |
|
253 |
> |
if (isLJ) { |
254 |
> |
atomType->setLennardJones(); |
255 |
> |
} |
256 |
> |
|
257 |
> |
if (isCharge) { |
258 |
> |
atomType->setCharge(); |
259 |
> |
} |
260 |
> |
|
261 |
> |
atomType->setIdent(ident); |
262 |
> |
|
263 |
> |
atomType->complete(); |
264 |
> |
|
265 |
> |
int setLJStatus; |
266 |
> |
|
267 |
> |
//notify a new LJtype atom type is created |
268 |
> |
if (isLJ) { |
269 |
> |
newLJtype(&ident, &sigma, &epsilon, &setLJStatus); |
270 |
> |
} |
271 |
> |
|
272 |
> |
int setChargeStatus; |
273 |
> |
if (isCharge) { |
274 |
> |
newChargeType(&ident, &charge, &setChargeStatus) |
275 |
> |
} |
276 |
> |
|
277 |
> |
if (setLJStatus && setChargeStatus) { |
278 |
> |
//add atom type to AtomTypeContainer |
279 |
> |
addAtomType(atomTypeName, atomType); |
280 |
> |
++ident; |
281 |
> |
} else { |
282 |
> |
//error in notifying fortran |
283 |
> |
delete atomType; |
284 |
> |
} |
285 |
> |
} |
286 |
> |
|
287 |
|
} |
288 |
|
|
289 |
< |
void DUFF::parseBondType(){ |
289 |
> |
|
290 |
> |
void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) { |
291 |
> |
StringTokenizer tokenizer(line); |
292 |
> |
int nTokens = tokenizer.countTokens(); |
293 |
> |
|
294 |
> |
//in DirectionalAtomTypeSection, a line at least contains 6 tokens |
295 |
> |
//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
296 |
> |
if (nTokens < 6) { |
297 |
> |
std::cerr << "Not enought tokens" << std::endl; |
298 |
> |
} else { |
299 |
> |
|
300 |
> |
|
301 |
> |
std::string atomTypeName = tokenizer.nextToken(); |
302 |
> |
bool isDipole = tokenizer.nextTokenAsBool(); |
303 |
> |
bool isSticky = tokenizer.nextTokenAsBool(); |
304 |
> |
double Ixx = tokenizer.nextTokenAsDouble(); |
305 |
> |
double Iyy = tokenizer.nextTokenAsDouble(); |
306 |
> |
double Izz = tokenizer.nextTokenAsDouble(); |
307 |
> |
nTokens -= 6; |
308 |
> |
|
309 |
> |
AtomType* atomType = getAtomType(atomTypeName); |
310 |
> |
if (atomType == NULL) { |
311 |
> |
|
312 |
> |
} |
313 |
> |
|
314 |
> |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
315 |
> |
if (dAtomType == NULL) { |
316 |
> |
|
317 |
> |
|
318 |
> |
} |
319 |
> |
|
320 |
> |
if (isDipole) { |
321 |
> |
dAtomType->setDipole(); |
322 |
> |
} |
323 |
> |
|
324 |
> |
if (isSticky) { |
325 |
> |
dAtomType->setSticky(); |
326 |
> |
} |
327 |
> |
|
328 |
> |
Mat3x3d inertialMat; |
329 |
> |
inertialMat(0, 0) = Ixx; |
330 |
> |
inertialMat(1, 1) = Iyy; |
331 |
> |
inertialMat(2, 2) = Izz; |
332 |
> |
dAtomType->setI(inertialMat); |
333 |
> |
|
334 |
> |
//read dipole moment |
335 |
> |
double dipole; |
336 |
> |
if (isDipole) { |
337 |
> |
if (nTokens >= 1) { |
338 |
> |
dipole = tokenizer.nextTokenAsDouble(); |
339 |
> |
nTokens -= 1; |
340 |
> |
} else { |
341 |
> |
|
342 |
> |
} |
343 |
> |
} |
344 |
> |
|
345 |
> |
//read sticky parameters |
346 |
> |
double w0; |
347 |
> |
double v0; |
348 |
> |
double v0p; |
349 |
> |
double rl; |
350 |
> |
double ru; |
351 |
> |
double rlp; |
352 |
> |
double rup; |
353 |
> |
if (isSticky) { |
354 |
> |
if (nTokens >= 7) { |
355 |
> |
w0 = tokenizer.nextTokenAsDouble(); |
356 |
> |
v0 = tokenizer.nextTokenAsDouble(); |
357 |
> |
v0p = tokenizer.nextTokenAsDouble(); |
358 |
> |
rl = tokenizer.nextTokenAsDouble(); |
359 |
> |
ru = tokenizer.nextTokenAsDouble(); |
360 |
> |
rlp = tokenizer.nextTokenAsDouble(); |
361 |
> |
rup = tokenizer.nextTokenAsDouble(); |
362 |
> |
nTokens -= 7; |
363 |
> |
} else { |
364 |
> |
|
365 |
> |
} |
366 |
> |
} |
367 |
> |
|
368 |
> |
|
369 |
> |
//notify fotran a newDipoleType is created |
370 |
> |
int ident = dAtomType->getIdent(); |
371 |
> |
int setDipoleStatus; |
372 |
> |
if (isDipole) { |
373 |
> |
newDipoleType(&ident, &dipole, &setDipoleStatus); |
374 |
> |
} |
375 |
> |
|
376 |
> |
//notify fotran a StickyType is created |
377 |
> |
int setStickyStatus; |
378 |
> |
if (isSticky) { |
379 |
> |
makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
380 |
> |
} |
381 |
> |
|
382 |
> |
|
383 |
> |
if (!setDipoleStatus || !setStickyStatus) { |
384 |
> |
|
385 |
> |
} |
386 |
> |
|
387 |
> |
} |
388 |
|
} |
389 |
|
|
390 |
< |
void DUFF::parseBendType(){ |
390 |
> |
void DUFF::parseBondType(const std::string& line, int lineNo){ |
391 |
> |
|
392 |
> |
StringTokenizer tokenizer(line); |
393 |
> |
std::string at1; |
394 |
> |
std::string at2; |
395 |
> |
std::string bt; |
396 |
> |
BondType* bondType = NULL; |
397 |
> |
double b0; |
398 |
> |
|
399 |
> |
int nTokens = tokenizer.countTokens(); |
400 |
> |
|
401 |
> |
if (nTokens < 4) { |
402 |
> |
|
403 |
> |
return; |
404 |
> |
} |
405 |
> |
|
406 |
> |
at1 = tokenizer.nextToken(); |
407 |
> |
at2 = tokenizer.nextToken(); |
408 |
> |
bt = tokenizer.nextToken(); |
409 |
> |
b0 = tokenizer.nextTokenAsDouble(); |
410 |
> |
nTokens -= 4; |
411 |
> |
|
412 |
> |
//switch is a maintain nightmare |
413 |
> |
switch(bt) { |
414 |
> |
case "Fixed" : |
415 |
> |
bondType = new FixedBondType(); |
416 |
> |
break; |
417 |
> |
|
418 |
> |
case "Harmonic" : |
419 |
> |
if (nTokens < 1) { |
420 |
> |
|
421 |
> |
} else { |
422 |
> |
|
423 |
> |
double kb = tokenizer.nextTokenAsDouble(); |
424 |
> |
bondType = new HarmonicBondType(b0, kb); |
425 |
> |
} |
426 |
> |
|
427 |
> |
break; |
428 |
> |
|
429 |
> |
case "Cubic" : |
430 |
> |
if (nTokens < 4) { |
431 |
> |
|
432 |
> |
} else { |
433 |
> |
|
434 |
> |
double k3 = tokenizer.nextTokenAsDouble(); |
435 |
> |
double k2 = tokenizer.nextTokenAsDouble(); |
436 |
> |
double k1 = tokenizer.nextTokenAsDouble(); |
437 |
> |
double k0 = tokenizer.nextTokenAsDouble(); |
438 |
> |
|
439 |
> |
bondType = new CubicBondType(b0, k3, k2, k1, k0); |
440 |
> |
} |
441 |
> |
break; |
442 |
> |
|
443 |
> |
case "Quartic" : |
444 |
> |
if (nTokens < 5) { |
445 |
> |
|
446 |
> |
} else { |
447 |
> |
|
448 |
> |
b0 = tokenizer.nextTokenAsDouble(); |
449 |
> |
double k4 = tokenizer.nextTokenAsDouble(); |
450 |
> |
double k3 = tokenizer.nextTokenAsDouble(); |
451 |
> |
double k2 = tokenizer.nextTokenAsDouble(); |
452 |
> |
double k1 = tokenizer.nextTokenAsDouble(); |
453 |
> |
double k0 = tokenizer.nextTokenAsDouble(); |
454 |
> |
|
455 |
> |
bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
456 |
> |
} |
457 |
> |
break; |
458 |
> |
|
459 |
> |
case "Polynomial" : |
460 |
> |
if (nTokens < 2 || nTokens % 2 != 0) { |
461 |
> |
|
462 |
> |
} else { |
463 |
> |
int nPairs = nTokens / 2; |
464 |
> |
int power; |
465 |
> |
double coefficient; |
466 |
> |
PolynomialBondType pbt = new PolynomialBondType(); |
467 |
> |
|
468 |
> |
for (int i = 0; i < nPairs; ++i) { |
469 |
> |
power = tokenizer.nextTokenAsInt(); |
470 |
> |
coefficient = tokenizer.nextTokenAsDouble(); |
471 |
> |
pbt->setCoefficient(power, coefficient); |
472 |
> |
} |
473 |
> |
} |
474 |
> |
|
475 |
> |
break; |
476 |
> |
|
477 |
> |
default: |
478 |
> |
|
479 |
> |
} |
480 |
> |
|
481 |
> |
if (bondType != NULL) { |
482 |
> |
addBondType(at1, at2, bondType); |
483 |
> |
} |
484 |
|
} |
485 |
|
|
486 |
< |
void DUFF::parseTorsionType(){ |
486 |
> |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
487 |
> |
StringTokenizer tokenizer(line); |
488 |
> |
std::string at1; |
489 |
> |
std::string at2; |
490 |
> |
std::string at3; |
491 |
> |
std::string bt; |
492 |
> |
double theta0; |
493 |
> |
BendType* bendType = NULL; |
494 |
|
|
495 |
+ |
int nTokens = tokenizer.countTokens(); |
496 |
+ |
|
497 |
+ |
if (nTokens < 5) { |
498 |
+ |
|
499 |
+ |
return; |
500 |
+ |
} |
501 |
+ |
|
502 |
+ |
at1 = tokenizer.nextToken(); |
503 |
+ |
at2 = tokenizer.nextToken(); |
504 |
+ |
at3 = tokenizer.nextToken(); |
505 |
+ |
bt = tokenizer.nextToken(); |
506 |
+ |
theta0 = tokenizer.nextTokenAsDouble(); |
507 |
+ |
nTokens -= 5; |
508 |
+ |
|
509 |
+ |
//switch is a maintain nightmare |
510 |
+ |
switch(bt) { |
511 |
+ |
|
512 |
+ |
case "Harmonic" : |
513 |
+ |
|
514 |
+ |
if (nTokens < 1) { |
515 |
+ |
|
516 |
+ |
} else { |
517 |
+ |
|
518 |
+ |
double ktheta = tokenizer.nextTokenAsDouble(); |
519 |
+ |
bendType = new HarmonicBendType(theta0, ktheta); |
520 |
+ |
} |
521 |
+ |
break; |
522 |
+ |
case "GhostBend" : |
523 |
+ |
if (nTokens < 1) { |
524 |
+ |
|
525 |
+ |
} else { |
526 |
+ |
double ktheta = tokenizer.nextTokenAsDouble(); |
527 |
+ |
bendType = new HarmonicBendType(theta0, ktheta); |
528 |
+ |
} |
529 |
+ |
break; |
530 |
+ |
|
531 |
+ |
case "UreyBradley" : |
532 |
+ |
if (nTokens < 3) { |
533 |
+ |
|
534 |
+ |
} else { |
535 |
+ |
double ktheta = tokenizer.nextTokenAsDouble(); |
536 |
+ |
double s0 = tokenizer.nextTokenAsDouble(); |
537 |
+ |
double kub = tokenizer.nextTokenAsDouble(); |
538 |
+ |
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
539 |
+ |
} |
540 |
+ |
break; |
541 |
+ |
|
542 |
+ |
case "Cubic" : |
543 |
+ |
if (nTokens < 4) { |
544 |
+ |
|
545 |
+ |
} else { |
546 |
+ |
|
547 |
+ |
double k3 = tokenizer.nextTokenAsDouble(); |
548 |
+ |
double k2 = tokenizer.nextTokenAsDouble(); |
549 |
+ |
double k1 = tokenizer.nextTokenAsDouble(); |
550 |
+ |
double k0 = tokenizer.nextTokenAsDouble(); |
551 |
+ |
|
552 |
+ |
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
553 |
+ |
} |
554 |
+ |
break; |
555 |
+ |
|
556 |
+ |
case "Quartic" : |
557 |
+ |
if (nTokens < 5) { |
558 |
+ |
|
559 |
+ |
} else { |
560 |
+ |
|
561 |
+ |
theta0 = tokenizer.nextTokenAsDouble(); |
562 |
+ |
double k4 = tokenizer.nextTokenAsDouble(); |
563 |
+ |
double k3 = tokenizer.nextTokenAsDouble(); |
564 |
+ |
double k2 = tokenizer.nextTokenAsDouble(); |
565 |
+ |
double k1 = tokenizer.nextTokenAsDouble(); |
566 |
+ |
double k0 = tokenizer.nextTokenAsDouble(); |
567 |
+ |
|
568 |
+ |
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
569 |
+ |
} |
570 |
+ |
break; |
571 |
+ |
|
572 |
+ |
case "Polynomial" : |
573 |
+ |
if (nTokens < 2 || nTokens % 2 != 0) { |
574 |
+ |
|
575 |
+ |
} else { |
576 |
+ |
int nPairs = nTokens / 2; |
577 |
+ |
int power; |
578 |
+ |
double coefficient; |
579 |
+ |
PolynomialBendType* pbt = new PolynomialBendType(); |
580 |
+ |
|
581 |
+ |
for (int i = 0; i < nPairs; ++i) { |
582 |
+ |
power = tokenizer.nextTokenAsInt(); |
583 |
+ |
coefficient = tokenizer.nextTokenAsDouble(); |
584 |
+ |
pbt->setCoefficient(power, coefficient); |
585 |
+ |
} |
586 |
+ |
} |
587 |
+ |
|
588 |
+ |
break; |
589 |
+ |
|
590 |
+ |
default: |
591 |
+ |
|
592 |
+ |
} |
593 |
+ |
|
594 |
+ |
if (bendType != NULL) { |
595 |
+ |
addBendType(at1, at2, at3, bendType); |
596 |
+ |
} |
597 |
+ |
|
598 |
|
} |
599 |
|
|
600 |
< |
} //end namespace oopse |
600 |
> |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
601 |
> |
StringTokenizer tokenizer(line); |
602 |
> |
std::string at1; |
603 |
> |
std::string at2; |
604 |
> |
std::string at3; |
605 |
> |
std::string at4; |
606 |
> |
std::string tt; |
607 |
> |
TorsionType* torsionType = NULL; |
608 |
|
|
609 |
+ |
int nTokens = tokenizer.countTokens(); |
610 |
+ |
|
611 |
+ |
if (nTokens < 5) { |
612 |
+ |
|
613 |
+ |
return; |
614 |
+ |
} |
615 |
+ |
|
616 |
+ |
at1 = tokenizer.nextToken(); |
617 |
+ |
at2 = tokenizer.nextToken(); |
618 |
+ |
at3 = tokenizer.nextToken(); |
619 |
+ |
at4 = tokenizer.nextToken(); |
620 |
+ |
tt = tokenizer.nextToken(); |
621 |
+ |
|
622 |
+ |
nTokens -= 5; |
623 |
+ |
|
624 |
+ |
switch(tt) { |
625 |
+ |
|
626 |
+ |
case "Cubic" : |
627 |
+ |
if (nTokens < 4) { |
628 |
+ |
|
629 |
+ |
} else { |
630 |
+ |
|
631 |
+ |
double k3 = tokenizer.nextTokenAsDouble(); |
632 |
+ |
double k2 = tokenizer.nextTokenAsDouble(); |
633 |
+ |
double k1 = tokenizer.nextTokenAsDouble(); |
634 |
+ |
double k0 = tokenizer.nextTokenAsDouble(); |
635 |
+ |
|
636 |
+ |
bendType = new CubicTorsionType(k3, k2, k1, k0); |
637 |
+ |
} |
638 |
+ |
break; |
639 |
+ |
|
640 |
+ |
case "Quartic" : |
641 |
+ |
if (nTokens < 5) { |
642 |
+ |
|
643 |
+ |
} else { |
644 |
+ |
|
645 |
+ |
theta0 = tokenizer.nextTokenAsDouble(); |
646 |
+ |
double k4 = tokenizer.nextTokenAsDouble(); |
647 |
+ |
double k3 = tokenizer.nextTokenAsDouble(); |
648 |
+ |
double k2 = tokenizer.nextTokenAsDouble(); |
649 |
+ |
double k1 = tokenizer.nextTokenAsDouble(); |
650 |
+ |
double k0 = tokenizer.nextTokenAsDouble(); |
651 |
+ |
|
652 |
+ |
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
653 |
+ |
} |
654 |
+ |
break; |
655 |
+ |
|
656 |
+ |
case "Polynomial" : |
657 |
+ |
if (nTokens < 2 || nTokens % 2 != 0) { |
658 |
+ |
|
659 |
+ |
} else { |
660 |
+ |
int nPairs = nTokens / 2; |
661 |
+ |
int power; |
662 |
+ |
double coefficient; |
663 |
+ |
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
664 |
+ |
|
665 |
+ |
for (int i = 0; i < nPairs; ++i) { |
666 |
+ |
power = tokenizer.nextTokenAsInt(); |
667 |
+ |
coefficient = tokenizer.nextTokenAsDouble(); |
668 |
+ |
pbt->setCoefficient(power, coefficient); |
669 |
+ |
} |
670 |
+ |
} |
671 |
+ |
|
672 |
+ |
break; |
673 |
+ |
case "Charmm" : |
674 |
+ |
|
675 |
+ |
if (nTokens < 3 || nTokens % 3 != 0) { |
676 |
+ |
|
677 |
+ |
} else { |
678 |
+ |
int nSets = nTokens / 3; |
679 |
+ |
|
680 |
+ |
CharmmTorsionType* ctt = new CharmmTorsionType(); |
681 |
+ |
|
682 |
+ |
for (int i = 0; i < nSets; ++i) { |
683 |
+ |
double kchi = tokenizer.nextTokenAsDouble(); |
684 |
+ |
int n = tokenizer.nextTokenAsInt(); |
685 |
+ |
double delta = tokenizer.nextTokenAsDouble(); |
686 |
+ |
|
687 |
+ |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
688 |
+ |
} |
689 |
+ |
} |
690 |
+ |
default: |
691 |
+ |
|
692 |
+ |
} |
693 |
+ |
|
694 |
+ |
if (torsionType != NULL) { |
695 |
+ |
addTorsionType(at1, at2, at3, at4, torsionType); |
696 |
+ |
} |
697 |
+ |
} |
698 |
+ |
*/ |
699 |
+ |
} //end namespace oopse |