| 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 |
+ |
#include "io/TorsionTypesSectionParser.hpp" |
| 41 |
+ |
#include "UseTheForce/ForceFieldCreator.hpp" |
| 42 |
|
|
| 43 |
|
namespace oopse { |
| 44 |
|
|
| 45 |
< |
//definition of createDUFF |
| 35 |
< |
ForceField* createDUFF() { |
| 36 |
< |
return new DUFF(); |
| 37 |
< |
} |
| 38 |
< |
|
| 39 |
< |
//register createDUFF to ForceFieldFactory |
| 40 |
< |
ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
| 41 |
< |
|
| 42 |
< |
|
| 43 |
< |
ParseState DUFF::getSection(const std::string& section) { |
| 44 |
< |
ParseState result; |
| 45 |
> |
//static ForceFieldBuilder<DUFF>* DUFFCreator = new ForceFieldBuilder<DUFF>("DUFF"); |
| 46 |
|
|
| 47 |
< |
switch(section) { |
| 47 |
< |
case "AtomTypes" : |
| 48 |
< |
result = DUFF::AtomTypeSection; |
| 49 |
< |
break; |
| 50 |
< |
case "DirectionalAtomTypes" : |
| 51 |
< |
result = DUFF::DirectionalAtomTypeSection; |
| 52 |
< |
break; |
| 47 |
> |
DUFF::DUFF(){ |
| 48 |
|
|
| 49 |
< |
case "BondTypes" : |
| 50 |
< |
result = DUFF::BondTypeSection; |
| 56 |
< |
break; |
| 49 |
> |
//set default force field filename |
| 50 |
> |
setForceFieldFileName("DUFF.frc"); |
| 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; |
| 52 |
> |
//the order of adding section parsers are important |
| 53 |
> |
//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
| 54 |
> |
//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
| 55 |
> |
//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
| 56 |
> |
//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
| 57 |
> |
//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
| 58 |
> |
//important. AtomTypesSectionParser should be added before other atom type section parsers. |
| 59 |
> |
//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
| 60 |
> |
//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
| 61 |
> |
//not important. |
| 62 |
> |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
| 63 |
> |
spMan_.push_back(new AtomTypesSectionParser()); |
| 64 |
> |
spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
| 65 |
> |
spMan_.push_back(new ElectrostaticAtomTypesSectionParser()); |
| 66 |
> |
spMan_.push_back(new EAMAtomTypesSectionParser()); |
| 67 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
| 68 |
> |
spMan_.push_back(new BondTypesSectionParser()); |
| 69 |
> |
spMan_.push_back(new BendTypesSectionParser()); |
| 70 |
> |
spMan_.push_back(new TorsionTypesSectionParser()); |
| 71 |
> |
|
| 72 |
|
} |
| 73 |
|
|
| 74 |
|
void DUFF::parse(const std::string& filename) { |
| 75 |
|
ifstrstream* ffStream; |
| 76 |
< |
ffStream = openForceFiledFile(filename); |
| 75 |
< |
const int bufferSize = 65535; |
| 76 |
< |
std::string line; |
| 77 |
< |
char buffer[bufferSize]; |
| 78 |
< |
int lineNo = 0; |
| 79 |
< |
ParseState currentSection = DUFF::UnknownSection; |
| 80 |
< |
|
| 81 |
< |
while(ffStream.getline(buffer, bufferSize)){ |
| 82 |
< |
++lineNo; |
| 76 |
> |
ffStream = openForceFieldFile(filename); |
| 77 |
|
|
| 78 |
< |
line = trimSpaces(buffer); |
| 85 |
< |
//a line begins with "//" is comment |
| 86 |
< |
if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
| 87 |
< |
continue; |
| 88 |
< |
} else { |
| 78 |
> |
spMan_.parse(*ffStream, *this); |
| 79 |
|
|
| 80 |
< |
switch(currentSection) { |
| 81 |
< |
case DUFF::AtomTypeSection : |
| 92 |
< |
parseAtomType(line, lineNo); |
| 93 |
< |
break; |
| 80 |
> |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 81 |
> |
AtomType* at; |
| 82 |
|
|
| 83 |
< |
case DUFF::BondTypeSection : |
| 84 |
< |
parseBondType(line, lineNo); |
| 97 |
< |
break; |
| 98 |
< |
|
| 99 |
< |
case DUFF::BendTypeSection : |
| 100 |
< |
parseBendType(line, lineNo); |
| 101 |
< |
break; |
| 102 |
< |
|
| 103 |
< |
case DUFF::TorsionTypeSection : |
| 104 |
< |
parseTorsionType(line, lineNo); |
| 105 |
< |
break; |
| 106 |
< |
|
| 107 |
< |
case DUFF::UnknownSection: |
| 108 |
< |
StringTokenizer tokenizer(line); |
| 109 |
< |
|
| 110 |
< |
std::string keyword = tokenizer.nextToken(); |
| 111 |
< |
std::string section = tokenizer.nextToken(); |
| 112 |
< |
|
| 113 |
< |
ParseState newSection = getSection(section); |
| 114 |
< |
if (keyword != "begin" || keyword != "end") { |
| 115 |
< |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
| 116 |
< |
} else if (keyword == "begin") { |
| 117 |
< |
if (newSection == DUFF::UnknownSection) { |
| 118 |
< |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
| 119 |
< |
} else { |
| 120 |
< |
//enter a new section |
| 121 |
< |
currentSection = newSection; |
| 122 |
< |
} |
| 123 |
< |
|
| 124 |
< |
} else if (keyword == "end"){ |
| 125 |
< |
if (currentSection == newSection) ) { |
| 126 |
< |
//leave a section |
| 127 |
< |
currentSection = DUFF::UnknownSection; |
| 128 |
< |
} else { |
| 129 |
< |
std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
| 130 |
< |
} |
| 131 |
< |
|
| 132 |
< |
} |
| 133 |
< |
break; |
| 134 |
< |
default : |
| 135 |
< |
|
| 136 |
< |
} |
| 137 |
< |
|
| 138 |
< |
} |
| 139 |
< |
} |
| 140 |
< |
|
| 141 |
< |
delete ffStream; |
| 142 |
< |
} |
| 143 |
< |
|
| 144 |
< |
|
| 145 |
< |
void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
| 146 |
< |
StringTokenizer tokenizer(line); |
| 147 |
< |
int nTokens = tokenizer.countTokens(); |
| 148 |
< |
|
| 149 |
< |
//in AtomTypeSection, a line at least contains 5 tokens |
| 150 |
< |
//atomTypeName, is Directional, isLJ, isCharge and mass |
| 151 |
< |
if (nTokens < 5) { |
| 152 |
< |
sprintf( painCave.errMsg, |
| 153 |
< |
"Not enough tokens when parsing DUFF Force Field : %s\n" |
| 154 |
< |
"in line %d : %s\n", |
| 155 |
< |
filename.c_str(), lineNo, line); |
| 156 |
< |
painCave.severity = OOPSE_ERROR; |
| 157 |
< |
painCave.isFatal = 1; |
| 158 |
< |
simError(); |
| 159 |
< |
|
| 160 |
< |
|
| 161 |
< |
} else { |
| 162 |
< |
|
| 163 |
< |
std::string atomTypeName = tokenizer.nextToken(); |
| 164 |
< |
bool isDirectional = tokenizer.nextTokenAsBool(); |
| 165 |
< |
bool isLJ = tokenizer.nextTokenAsBool(); |
| 166 |
< |
bool isCharge = tokenizer.nextTokenAsBool(); |
| 167 |
< |
double mass = tokenizer.nextTokenAsDouble(); |
| 168 |
< |
double epsilon; |
| 169 |
< |
double sigma; |
| 170 |
< |
double charge; |
| 171 |
< |
nTokens -= 5; |
| 172 |
< |
|
| 173 |
< |
//parse epsilon and sigma |
| 174 |
< |
if (isLJ) { |
| 175 |
< |
if (nTokens >= 2) { |
| 176 |
< |
epsilon = tokenizer.nextTokenAsDouble(); |
| 177 |
< |
sigma = tokenizer.nextTokenAsDouble(); |
| 178 |
< |
nTokens -= 2; |
| 179 |
< |
} else { |
| 180 |
< |
|
| 181 |
< |
} |
| 182 |
< |
} |
| 183 |
< |
|
| 184 |
< |
//parse charge |
| 185 |
< |
if (isCharge) { |
| 186 |
< |
if (nTokens >= 1) { |
| 187 |
< |
charge = tokenizer.nextTokenAsDouble(); |
| 188 |
< |
nTokens -= 1; |
| 189 |
< |
} else { |
| 190 |
< |
|
| 191 |
< |
} |
| 192 |
< |
} |
| 193 |
< |
|
| 194 |
< |
AtomType* atomType; |
| 195 |
< |
if (isDirectional) { |
| 196 |
< |
atomType = new DirectionalAtomType(); |
| 197 |
< |
} else { |
| 198 |
< |
atomType = new AtomType(); |
| 199 |
< |
} |
| 200 |
< |
|
| 201 |
< |
atomType->setName(atomTypeName); |
| 202 |
< |
atomType->setMass(mass); |
| 203 |
< |
|
| 204 |
< |
//by default, all of the properties in AtomTypeProperties is set to 0 |
| 205 |
< |
//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
| 206 |
< |
atomType->setLennardJones(); |
| 207 |
< |
|
| 208 |
< |
atomType->setIdent(ident); |
| 209 |
< |
|
| 210 |
< |
atomType->complete(); |
| 211 |
< |
|
| 212 |
< |
int setLJStatus; |
| 213 |
< |
|
| 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 irectionalAtomTypeSection, a line at least contains 6 tokens |
| 242 |
< |
//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
| 243 |
< |
if (nTokens < 6) { |
| 244 |
< |
|
| 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 |
< |
dAtomType->setDipole(isDipole); |
| 268 |
< |
dAtomType->setSticky(isSticky); |
| 269 |
< |
|
| 270 |
< |
Mat3x3d inertialMat; |
| 271 |
< |
inertialMat(0, 0) = Ixx; |
| 272 |
< |
inertialMat(1, 1) = Ixx; |
| 273 |
< |
inertialMat(2, 2) = Ixx; |
| 274 |
< |
dAtomType->setI(inertialMat); |
| 275 |
< |
|
| 276 |
< |
//read dipole moment |
| 277 |
< |
double dipole; |
| 278 |
< |
if (isDipole) { |
| 279 |
< |
if (nTokens >= 1) { |
| 280 |
< |
dipole = tokenizer.nextTokenAsDouble(); |
| 281 |
< |
nTokens -= 1; |
| 282 |
< |
} else { |
| 283 |
< |
|
| 284 |
< |
} |
| 285 |
< |
} |
| 286 |
< |
|
| 287 |
< |
//read sticky parameters |
| 288 |
< |
double w0; |
| 289 |
< |
double v0; |
| 290 |
< |
double v0p; |
| 291 |
< |
double rl; |
| 292 |
< |
double ru; |
| 293 |
< |
double rlp; |
| 294 |
< |
double rup; |
| 295 |
< |
if (isSticky) { |
| 296 |
< |
if (nTokens >= 7) { |
| 297 |
< |
w0 = tokenizer.nextTokenAsDouble(); |
| 298 |
< |
v0 = tokenizer.nextTokenAsDouble(); |
| 299 |
< |
v0p = tokenizer.nextTokenAsDouble(); |
| 300 |
< |
rl = tokenizer.nextTokenAsDouble(); |
| 301 |
< |
ru = tokenizer.nextTokenAsDouble(); |
| 302 |
< |
rlp = tokenizer.nextTokenAsDouble(); |
| 303 |
< |
rup = tokenizer.nextTokenAsDouble(); |
| 304 |
< |
nTokens -= 7; |
| 305 |
< |
} else { |
| 306 |
< |
|
| 307 |
< |
} |
| 308 |
< |
} |
| 309 |
< |
|
| 310 |
< |
|
| 311 |
< |
//notify fotran a newDipoleType is created |
| 312 |
< |
int ident = dAtomType->getIdent(); |
| 313 |
< |
int setDipoleStatus; |
| 314 |
< |
if (isDipole) { |
| 315 |
< |
newDipoleType(&ident, &dipole, &setDipoleStatus); |
| 316 |
< |
} |
| 317 |
< |
|
| 318 |
< |
//notify fotran a StickyType is created |
| 319 |
< |
int setStickyStatus; |
| 320 |
< |
if (isSticky) { |
| 321 |
< |
makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
| 322 |
< |
} |
| 323 |
< |
|
| 324 |
< |
|
| 325 |
< |
if (!setDipoleStatus || !setStickyStatus) { |
| 326 |
< |
|
| 327 |
< |
} |
| 328 |
< |
|
| 83 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 84 |
> |
at->makeFortranAtomType(); |
| 85 |
|
} |
| 330 |
– |
} |
| 86 |
|
|
| 87 |
< |
void DUFF::parseBondType(const std::string& line, int lineNo){ |
| 88 |
< |
|
| 334 |
< |
StringTokenizer tokenizer(line); |
| 335 |
< |
std::string at1; |
| 336 |
< |
std::string at2; |
| 337 |
< |
std::string bt; |
| 338 |
< |
BondType* bondType = NULL; |
| 339 |
< |
double b0; |
| 340 |
< |
|
| 341 |
< |
int nTokens = tokenizer.countTokens(); |
| 342 |
< |
|
| 343 |
< |
if (nTokens < 4) { |
| 344 |
< |
|
| 345 |
< |
return; |
| 87 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 88 |
> |
at->complete(); |
| 89 |
|
} |
| 90 |
|
|
| 348 |
– |
at1 = tokenizer.nextToken(); |
| 349 |
– |
at2 = tokenizer.nextToken(); |
| 350 |
– |
bt = tokenizer.nextToken(); |
| 351 |
– |
b0 = tokenizer.nextTokenAsDouble(); |
| 352 |
– |
nTokens -= 4; |
| 353 |
– |
|
| 354 |
– |
//switch is a maintain nightmare |
| 355 |
– |
switch(bt) { |
| 356 |
– |
case "FixedBondType" : |
| 357 |
– |
bondType = new FixedBondType(); |
| 358 |
– |
break; |
| 359 |
– |
|
| 360 |
– |
case "HarmonicBondType" : |
| 361 |
– |
if (nTokens < 1) { |
| 362 |
– |
|
| 363 |
– |
} else { |
| 364 |
– |
|
| 365 |
– |
double kb = tokenizer.nextTokenAsDouble(); |
| 366 |
– |
bondType = new HarmonicBondType(b0, kb); |
| 367 |
– |
} |
| 368 |
– |
|
| 369 |
– |
break; |
| 370 |
– |
|
| 371 |
– |
case "CubicBondType" : |
| 372 |
– |
if (nTokens < 4) { |
| 373 |
– |
|
| 374 |
– |
} else { |
| 375 |
– |
|
| 376 |
– |
double k3 = tokenizer.nextTokenAsDouble(); |
| 377 |
– |
double k2 = tokenizer.nextTokenAsDouble(); |
| 378 |
– |
double k1 = tokenizer.nextTokenAsDouble(); |
| 379 |
– |
double k0 = tokenizer.nextTokenAsDouble(); |
| 380 |
– |
|
| 381 |
– |
bondType = new CubicBondType(b0, k3, k2, k1, k0); |
| 382 |
– |
} |
| 383 |
– |
break; |
| 384 |
– |
|
| 385 |
– |
case "QuadraticBondType" : |
| 386 |
– |
if (nTokens < 5) { |
| 387 |
– |
|
| 388 |
– |
} else { |
| 389 |
– |
|
| 390 |
– |
b0 = tokenizer.nextTokenAsDouble(); |
| 391 |
– |
double k4 = tokenizer.nextTokenAsDouble(); |
| 392 |
– |
double k3 = tokenizer.nextTokenAsDouble(); |
| 393 |
– |
double k2 = tokenizer.nextTokenAsDouble(); |
| 394 |
– |
double k1 = tokenizer.nextTokenAsDouble(); |
| 395 |
– |
double k0 = tokenizer.nextTokenAsDouble(); |
| 396 |
– |
|
| 397 |
– |
bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
| 398 |
– |
} |
| 399 |
– |
break; |
| 400 |
– |
|
| 401 |
– |
case "PolynomialBondType " : |
| 402 |
– |
if (nTokens < 2 || nTokens % 2 != 0) { |
| 403 |
– |
|
| 404 |
– |
} else { |
| 405 |
– |
int nPairs = nTokens / 2; |
| 406 |
– |
int power; |
| 407 |
– |
double coefficient; |
| 408 |
– |
PolynomialBondType pbt = new PolynomialBondType(); |
| 409 |
– |
|
| 410 |
– |
for (int i = 0; i < nPairs; ++i) { |
| 411 |
– |
power = tokenizer.nextTokenAsInt(); |
| 412 |
– |
coefficient = tokenizer.nextTokenAsDouble(); |
| 413 |
– |
pbt->setCoefficient(power, coefficient); |
| 414 |
– |
} |
| 415 |
– |
} |
| 416 |
– |
|
| 417 |
– |
break; |
| 418 |
– |
|
| 419 |
– |
default: |
| 420 |
– |
|
| 421 |
– |
} |
| 422 |
– |
|
| 423 |
– |
if (bondType != NULL) { |
| 424 |
– |
addBondType(at1, at2, bondType); |
| 425 |
– |
} |
| 91 |
|
} |
| 92 |
|
|
| 428 |
– |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
| 429 |
– |
StringTokenizer tokenizer(line); |
| 430 |
– |
std::string at1; |
| 431 |
– |
std::string at2; |
| 432 |
– |
std::string at3; |
| 433 |
– |
std::string bt; |
| 434 |
– |
double theta0; |
| 435 |
– |
BendType* bendType = NULL; |
| 436 |
– |
|
| 437 |
– |
int nTokens = tokenizer.countTokens(); |
| 438 |
– |
|
| 439 |
– |
if (nTokens < 5) { |
| 440 |
– |
|
| 441 |
– |
return; |
| 442 |
– |
} |
| 443 |
– |
|
| 444 |
– |
at1 = tokenizer.nextToken(); |
| 445 |
– |
at2 = tokenizer.nextToken(); |
| 446 |
– |
at3 = tokenizer.nextToken(); |
| 447 |
– |
bt = tokenizer.nextToken(); |
| 448 |
– |
theta0 = tokenizer.nextTokenAsDouble(); |
| 449 |
– |
nTokens -= 5; |
| 450 |
– |
|
| 451 |
– |
//switch is a maintain nightmare |
| 452 |
– |
switch(bt) { |
| 453 |
– |
|
| 454 |
– |
case "HarmonicBendType" : |
| 455 |
– |
|
| 456 |
– |
if (nTokens < 1) { |
| 457 |
– |
|
| 458 |
– |
} else { |
| 459 |
– |
|
| 460 |
– |
double ktheta = tokenizer.nextTokenAsDouble(); |
| 461 |
– |
bendType = new HarmonicBendType(theta0, ktheta); |
| 462 |
– |
} |
| 463 |
– |
break; |
| 464 |
– |
case "GhostBendType" : |
| 465 |
– |
if (nTokens < 1) { |
| 466 |
– |
|
| 467 |
– |
} else { |
| 468 |
– |
double ktheta = tokenizer.nextTokenAsDouble(); |
| 469 |
– |
bendType = new HarmonicBendType(theta0, ktheta); |
| 470 |
– |
} |
| 471 |
– |
break; |
| 472 |
– |
|
| 473 |
– |
case "UreyBradleyBendType" : |
| 474 |
– |
if (nTokens < 3) { |
| 475 |
– |
|
| 476 |
– |
} else { |
| 477 |
– |
double ktheta = tokenizer.nextTokenAsDouble(); |
| 478 |
– |
double s0 = tokenizer.nextTokenAsDouble(); |
| 479 |
– |
double kub = tokenizer.nextTokenAsDouble(); |
| 480 |
– |
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
| 481 |
– |
} |
| 482 |
– |
break; |
| 483 |
– |
|
| 484 |
– |
case "CubicBendType" : |
| 485 |
– |
if (nTokens < 4) { |
| 486 |
– |
|
| 487 |
– |
} else { |
| 488 |
– |
|
| 489 |
– |
double k3 = tokenizer.nextTokenAsDouble(); |
| 490 |
– |
double k2 = tokenizer.nextTokenAsDouble(); |
| 491 |
– |
double k1 = tokenizer.nextTokenAsDouble(); |
| 492 |
– |
double k0 = tokenizer.nextTokenAsDouble(); |
| 493 |
– |
|
| 494 |
– |
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
| 495 |
– |
} |
| 496 |
– |
break; |
| 497 |
– |
|
| 498 |
– |
case "QuadraticBendType" : |
| 499 |
– |
if (nTokens < 5) { |
| 500 |
– |
|
| 501 |
– |
} else { |
| 502 |
– |
|
| 503 |
– |
theta0 = tokenizer.nextTokenAsDouble(); |
| 504 |
– |
double k4 = tokenizer.nextTokenAsDouble(); |
| 505 |
– |
double k3 = tokenizer.nextTokenAsDouble(); |
| 506 |
– |
double k2 = tokenizer.nextTokenAsDouble(); |
| 507 |
– |
double k1 = tokenizer.nextTokenAsDouble(); |
| 508 |
– |
double k0 = tokenizer.nextTokenAsDouble(); |
| 509 |
– |
|
| 510 |
– |
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
| 511 |
– |
} |
| 512 |
– |
break; |
| 513 |
– |
|
| 514 |
– |
case "PolynomialBendType " : |
| 515 |
– |
if (nTokens < 2 || nTokens % 2 != 0) { |
| 516 |
– |
|
| 517 |
– |
} else { |
| 518 |
– |
int nPairs = nTokens / 2; |
| 519 |
– |
int power; |
| 520 |
– |
double coefficient; |
| 521 |
– |
PolynomialBendType* pbt = new PolynomialBendType(); |
| 522 |
– |
|
| 523 |
– |
for (int i = 0; i < nPairs; ++i) { |
| 524 |
– |
power = tokenizer.nextTokenAsInt(); |
| 525 |
– |
coefficient = tokenizer.nextTokenAsDouble(); |
| 526 |
– |
pbt->setCoefficient(power, coefficient); |
| 527 |
– |
} |
| 528 |
– |
} |
| 529 |
– |
|
| 530 |
– |
break; |
| 531 |
– |
|
| 532 |
– |
default: |
| 533 |
– |
|
| 534 |
– |
} |
| 535 |
– |
|
| 536 |
– |
if (bendType != NULL) { |
| 537 |
– |
addBendType(at1, at2, at3, bendType); |
| 538 |
– |
} |
| 539 |
– |
|
| 540 |
– |
} |
| 541 |
– |
|
| 542 |
– |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
| 543 |
– |
StringTokenizer tokenizer(line); |
| 544 |
– |
std::string at1; |
| 545 |
– |
std::string at2; |
| 546 |
– |
std::string at3; |
| 547 |
– |
std::string at4; |
| 548 |
– |
std::string tt; |
| 549 |
– |
TorsionType* bendType = NULL; |
| 550 |
– |
|
| 551 |
– |
int nTokens = tokenizer.countTokens(); |
| 552 |
– |
|
| 553 |
– |
if (nTokens < 5) { |
| 554 |
– |
|
| 555 |
– |
return; |
| 556 |
– |
} |
| 557 |
– |
|
| 558 |
– |
at1 = tokenizer.nextToken(); |
| 559 |
– |
at2 = tokenizer.nextToken(); |
| 560 |
– |
at3 = tokenizer.nextToken(); |
| 561 |
– |
at4 = tokenizer.nextToken(); |
| 562 |
– |
tt = tokenizer.nextToken(); |
| 563 |
– |
|
| 564 |
– |
nTokens -= 5; |
| 565 |
– |
|
| 566 |
– |
switch(tt) { |
| 567 |
– |
|
| 568 |
– |
case "CubicTorsionType" : |
| 569 |
– |
if (nTokens < 4) { |
| 570 |
– |
|
| 571 |
– |
} else { |
| 572 |
– |
|
| 573 |
– |
double k3 = tokenizer.nextTokenAsDouble(); |
| 574 |
– |
double k2 = tokenizer.nextTokenAsDouble(); |
| 575 |
– |
double k1 = tokenizer.nextTokenAsDouble(); |
| 576 |
– |
double k0 = tokenizer.nextTokenAsDouble(); |
| 577 |
– |
|
| 578 |
– |
bendType = new CubicTorsionType(k3, k2, k1, k0); |
| 579 |
– |
} |
| 580 |
– |
break; |
| 581 |
– |
|
| 582 |
– |
case "QuadraticTorsionType" : |
| 583 |
– |
if (nTokens < 5) { |
| 584 |
– |
|
| 585 |
– |
} else { |
| 586 |
– |
|
| 587 |
– |
theta0 = tokenizer.nextTokenAsDouble(); |
| 588 |
– |
double k4 = tokenizer.nextTokenAsDouble(); |
| 589 |
– |
double k3 = tokenizer.nextTokenAsDouble(); |
| 590 |
– |
double k2 = tokenizer.nextTokenAsDouble(); |
| 591 |
– |
double k1 = tokenizer.nextTokenAsDouble(); |
| 592 |
– |
double k0 = tokenizer.nextTokenAsDouble(); |
| 593 |
– |
|
| 594 |
– |
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
| 595 |
– |
} |
| 596 |
– |
break; |
| 597 |
– |
|
| 598 |
– |
case "PolynomialTorsionType " : |
| 599 |
– |
if (nTokens < 2 || nTokens % 2 != 0) { |
| 600 |
– |
|
| 601 |
– |
} else { |
| 602 |
– |
int nPairs = nTokens / 2; |
| 603 |
– |
int power; |
| 604 |
– |
double coefficient; |
| 605 |
– |
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
| 606 |
– |
|
| 607 |
– |
for (int i = 0; i < nPairs; ++i) { |
| 608 |
– |
power = tokenizer.nextTokenAsInt(); |
| 609 |
– |
coefficient = tokenizer.nextTokenAsDouble(); |
| 610 |
– |
pbt->setCoefficient(power, coefficient); |
| 611 |
– |
} |
| 612 |
– |
} |
| 613 |
– |
|
| 614 |
– |
break; |
| 615 |
– |
case "CharmmTorsionType" : |
| 616 |
– |
|
| 617 |
– |
if (nTokens < 3 || nTokens % 3 != 0) { |
| 618 |
– |
|
| 619 |
– |
} else { |
| 620 |
– |
int nSets = nTokens / 3; |
| 621 |
– |
|
| 622 |
– |
CharmmTorsionType* ctt = new CharmmTorsionType(); |
| 623 |
– |
|
| 624 |
– |
for (int i = 0; i < nSets; ++i) { |
| 625 |
– |
double kchi = tokenizer.nextTokenAsDouble(); |
| 626 |
– |
int n = tokenizer.nextTokenAsInt(); |
| 627 |
– |
double delta = tokenizer.nextTokenAsDouble(); |
| 628 |
– |
|
| 629 |
– |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
| 630 |
– |
} |
| 631 |
– |
} |
| 632 |
– |
default: |
| 633 |
– |
|
| 634 |
– |
} |
| 635 |
– |
|
| 636 |
– |
if (bendType != NULL) { |
| 637 |
– |
addTorsionType(at1, at2, at3, bendType); |
| 638 |
– |
} |
| 639 |
– |
} |
| 640 |
– |
|
| 93 |
|
} //end namespace oopse |
