| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include <cstring> |
| 44 |
|
#include "primitives/DirectionalAtom.hpp" |
| 45 |
|
#include "primitives/RigidBody.hpp" |
| 46 |
|
|
| 47 |
< |
namespace oopse { |
| 47 |
> |
namespace OpenMD { |
| 48 |
|
void BaseAtomVisitor::visit(RigidBody *rb) { |
| 49 |
|
//vector<Atom*> myAtoms; |
| 50 |
|
//vector<Atom*>::iterator atomIter; |
| 73 |
|
return data == NULL ? false : true; |
| 74 |
|
} |
| 75 |
|
|
| 76 |
< |
bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
| 77 |
< |
std::set<std::string>::iterator strIter; |
| 78 |
< |
strIter = ssdAtomType.find(atomType); |
| 79 |
< |
return strIter != ssdAtomType.end() ? true : false; |
| 80 |
< |
} |
| 81 |
< |
|
| 82 |
< |
void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
| 83 |
< |
std::vector<AtomInfo*>atoms; |
| 84 |
< |
|
| 85 |
< |
//we need to convert SSD into 4 different atoms |
| 86 |
< |
//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of |
| 87 |
< |
//the mass of the water with a dipole moment |
| 88 |
< |
Vector3d h1(0.0, -0.75695, 0.5206); |
| 89 |
< |
Vector3d h2(0.0, 0.75695, 0.5206); |
| 90 |
< |
Vector3d ox(0.0, 0.0, -0.0654); |
| 91 |
< |
Vector3d u(0, 0, 1); |
| 92 |
< |
RotMat3x3d rotMatrix; |
| 93 |
< |
RotMat3x3d rotTrans; |
| 94 |
< |
AtomInfo * atomInfo; |
| 95 |
< |
Vector3d pos; |
| 96 |
< |
Vector3d newVec; |
| 97 |
< |
Quat4d q; |
| 98 |
< |
AtomData * atomData; |
| 99 |
< |
GenericData *data; |
| 100 |
< |
bool haveAtomData; |
| 101 |
< |
|
| 102 |
< |
//if atom is not SSD atom, just skip it |
| 103 |
< |
if (!isSSDAtom(datom->getType())) |
| 104 |
< |
return; |
| 105 |
< |
|
| 106 |
< |
data = datom->getPropertyByName("ATOMDATA"); |
| 107 |
< |
|
| 108 |
< |
if (data != NULL) { |
| 109 |
< |
atomData = dynamic_cast<AtomData *>(data); |
| 110 |
< |
|
| 111 |
< |
if (atomData == NULL) { |
| 112 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 113 |
< |
atomData = new AtomData; |
| 114 |
< |
haveAtomData = false; |
| 115 |
< |
} else |
| 116 |
< |
haveAtomData = true; |
| 117 |
< |
} else { |
| 118 |
< |
atomData = new AtomData; |
| 119 |
< |
haveAtomData = false; |
| 120 |
< |
} |
| 121 |
< |
|
| 122 |
< |
pos = datom->getPos(); |
| 123 |
< |
q = datom->getQ(); |
| 124 |
< |
rotMatrix = datom->getA(); |
| 125 |
< |
|
| 126 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
| 127 |
< |
//transposeMat3(rotMatrix, rotTrans); |
| 128 |
< |
rotTrans = rotMatrix.transpose(); |
| 129 |
< |
|
| 130 |
< |
//center of mass of the water molecule |
| 131 |
< |
//matVecMul3(rotTrans, u, newVec); |
| 132 |
< |
newVec = rotTrans * u; |
| 133 |
< |
|
| 134 |
< |
atomInfo = new AtomInfo; |
| 135 |
< |
atomInfo->atomTypeName = "X"; |
| 136 |
< |
atomInfo->pos[0] = pos[0]; |
| 137 |
< |
atomInfo->pos[1] = pos[1]; |
| 138 |
< |
atomInfo->pos[2] = pos[2]; |
| 139 |
< |
atomInfo->dipole[0] = newVec[0]; |
| 140 |
< |
atomInfo->dipole[1] = newVec[1]; |
| 141 |
< |
atomInfo->dipole[2] = newVec[2]; |
| 142 |
< |
|
| 143 |
< |
atomData->addAtomInfo(atomInfo); |
| 144 |
< |
|
| 145 |
< |
//oxygen |
| 146 |
< |
//matVecMul3(rotTrans, ox, newVec); |
| 147 |
< |
newVec = rotTrans * ox; |
| 148 |
< |
|
| 149 |
< |
atomInfo = new AtomInfo; |
| 150 |
< |
atomInfo->atomTypeName = "O"; |
| 151 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 152 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 153 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 154 |
< |
atomInfo->dipole[0] = 0.0; |
| 155 |
< |
atomInfo->dipole[1] = 0.0; |
| 156 |
< |
atomInfo->dipole[2] = 0.0; |
| 157 |
< |
atomData->addAtomInfo(atomInfo); |
| 158 |
< |
|
| 159 |
< |
//hydrogen1 |
| 160 |
< |
//matVecMul3(rotTrans, h1, newVec); |
| 161 |
< |
newVec = rotTrans * h1; |
| 162 |
< |
atomInfo = new AtomInfo; |
| 163 |
< |
atomInfo->atomTypeName = "H"; |
| 164 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 165 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 166 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 167 |
< |
atomInfo->dipole[0] = 0.0; |
| 168 |
< |
atomInfo->dipole[1] = 0.0; |
| 169 |
< |
atomInfo->dipole[2] = 0.0; |
| 170 |
< |
atomData->addAtomInfo(atomInfo); |
| 171 |
< |
|
| 172 |
< |
//hydrogen2 |
| 173 |
< |
//matVecMul3(rotTrans, h2, newVec); |
| 174 |
< |
newVec = rotTrans * h2; |
| 175 |
< |
atomInfo = new AtomInfo; |
| 176 |
< |
atomInfo->atomTypeName = "H"; |
| 177 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 178 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 179 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 180 |
< |
atomInfo->dipole[0] = 0.0; |
| 181 |
< |
atomInfo->dipole[1] = 0.0; |
| 182 |
< |
atomInfo->dipole[2] = 0.0; |
| 183 |
< |
atomData->addAtomInfo(atomInfo); |
| 184 |
< |
|
| 185 |
< |
//add atom data into atom's property |
| 186 |
< |
|
| 187 |
< |
if (!haveAtomData) { |
| 188 |
< |
atomData->setID("ATOMDATA"); |
| 189 |
< |
datom->addProperty(atomData); |
| 190 |
< |
} |
| 191 |
< |
|
| 192 |
< |
setVisited(datom); |
| 193 |
< |
} |
| 194 |
< |
|
| 195 |
< |
const std::string SSDAtomVisitor::toString() { |
| 196 |
< |
char buffer[65535]; |
| 197 |
< |
std::string result; |
| 198 |
< |
|
| 199 |
< |
sprintf(buffer, |
| 200 |
< |
"------------------------------------------------------------------\n"); |
| 201 |
< |
result += buffer; |
| 202 |
< |
|
| 203 |
< |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 204 |
< |
result += buffer; |
| 205 |
< |
|
| 206 |
< |
sprintf(buffer, |
| 207 |
< |
"Visitor Description: Convert SSD into 4 different atoms\n"); |
| 208 |
< |
result += buffer; |
| 209 |
< |
|
| 210 |
< |
sprintf(buffer, |
| 211 |
< |
"------------------------------------------------------------------\n"); |
| 212 |
< |
result += buffer; |
| 213 |
< |
|
| 214 |
< |
return result; |
| 215 |
< |
} |
| 216 |
< |
|
| 217 |
< |
|
| 218 |
< |
bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) { |
| 219 |
< |
std::set<std::string>::iterator strIter; |
| 220 |
< |
strIter = tredAtomType.find(atomType); |
| 221 |
< |
return strIter != tredAtomType.end() ? true : false; |
| 222 |
< |
} |
| 223 |
< |
|
| 224 |
< |
void TREDAtomVisitor::visit(DirectionalAtom *datom) { |
| 225 |
< |
std::vector<AtomInfo*>atoms; |
| 226 |
< |
|
| 227 |
< |
// we need to convert a TRED into 4 different atoms: |
| 228 |
< |
// one oxygen atom, two hydrogen atoms, and one atom which is the center of |
| 229 |
< |
// the mass of the water with a dipole moment |
| 230 |
< |
Vector3d h1(0.0, -0.75695, 0.5206); |
| 231 |
< |
Vector3d h2(0.0, 0.75695, 0.5206); |
| 232 |
< |
Vector3d ox(0.0, 0.0, -0.0654); |
| 233 |
< |
Vector3d u(0, 0, 1); |
| 234 |
< |
RotMat3x3d rotMatrix; |
| 235 |
< |
RotMat3x3d rotTrans; |
| 236 |
< |
AtomInfo * atomInfo; |
| 237 |
< |
Vector3d pos; |
| 238 |
< |
Vector3d newVec; |
| 239 |
< |
Quat4d q; |
| 240 |
< |
AtomData * atomData; |
| 241 |
< |
GenericData *data; |
| 242 |
< |
bool haveAtomData; |
| 243 |
< |
|
| 244 |
< |
// if the atom is not a TRED atom, skip it |
| 245 |
< |
if (!isTREDAtom(datom->getType())) |
| 246 |
< |
return; |
| 247 |
< |
|
| 248 |
< |
data = datom->getPropertyByName("ATOMDATA"); |
| 249 |
< |
|
| 250 |
< |
if (data != NULL) { |
| 251 |
< |
atomData = dynamic_cast<AtomData *>(data); |
| 252 |
< |
|
| 253 |
< |
if (atomData == NULL) { |
| 254 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 255 |
< |
atomData = new AtomData; |
| 256 |
< |
haveAtomData = false; |
| 257 |
< |
} else |
| 258 |
< |
haveAtomData = true; |
| 259 |
< |
} else { |
| 260 |
< |
atomData = new AtomData; |
| 261 |
< |
haveAtomData = false; |
| 262 |
< |
} |
| 263 |
< |
|
| 264 |
< |
pos = datom->getPos(); |
| 265 |
< |
q = datom->getQ(); |
| 266 |
< |
rotMatrix = datom->getA(); |
| 267 |
< |
|
| 268 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
| 269 |
< |
// transposeMat3(rotMatrix, rotTrans); |
| 270 |
< |
rotTrans = rotMatrix.transpose(); |
| 271 |
< |
|
| 272 |
< |
// center of mass of the water molecule |
| 273 |
< |
// matVecMul3(rotTrans, u, newVec); |
| 274 |
< |
newVec = rotTrans * u; |
| 275 |
< |
|
| 276 |
< |
atomInfo = new AtomInfo; |
| 277 |
< |
atomInfo->atomTypeName = "TRED"; |
| 278 |
< |
atomInfo->pos[0] = pos[0]; |
| 279 |
< |
atomInfo->pos[1] = pos[1]; |
| 280 |
< |
atomInfo->pos[2] = pos[2]; |
| 281 |
< |
atomInfo->dipole[0] = newVec[0]; |
| 282 |
< |
atomInfo->dipole[1] = newVec[1]; |
| 283 |
< |
atomInfo->dipole[2] = newVec[2]; |
| 284 |
< |
|
| 285 |
< |
atomData->addAtomInfo(atomInfo); |
| 286 |
< |
|
| 287 |
< |
// oxygen |
| 288 |
< |
// matVecMul3(rotTrans, ox, newVec); |
| 289 |
< |
newVec = rotTrans * ox; |
| 290 |
< |
|
| 291 |
< |
atomInfo = new AtomInfo; |
| 292 |
< |
atomInfo->atomTypeName = "O"; |
| 293 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 294 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 295 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 296 |
< |
atomInfo->dipole[0] = 0.0; |
| 297 |
< |
atomInfo->dipole[1] = 0.0; |
| 298 |
< |
atomInfo->dipole[2] = 0.0; |
| 299 |
< |
atomData->addAtomInfo(atomInfo); |
| 300 |
< |
|
| 301 |
< |
// hydrogen1 |
| 302 |
< |
// matVecMul3(rotTrans, h1, newVec); |
| 303 |
< |
newVec = rotTrans * h1; |
| 304 |
< |
atomInfo = new AtomInfo; |
| 305 |
< |
atomInfo->atomTypeName = "H"; |
| 306 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 307 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 308 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 309 |
< |
atomInfo->dipole[0] = 0.0; |
| 310 |
< |
atomInfo->dipole[1] = 0.0; |
| 311 |
< |
atomInfo->dipole[2] = 0.0; |
| 312 |
< |
atomData->addAtomInfo(atomInfo); |
| 313 |
< |
|
| 314 |
< |
// hydrogen2 |
| 315 |
< |
// matVecMul3(rotTrans, h2, newVec); |
| 316 |
< |
newVec = rotTrans * h2; |
| 317 |
< |
atomInfo = new AtomInfo; |
| 318 |
< |
atomInfo->atomTypeName = "H"; |
| 319 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 320 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 321 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 322 |
< |
atomInfo->dipole[0] = 0.0; |
| 323 |
< |
atomInfo->dipole[1] = 0.0; |
| 324 |
< |
atomInfo->dipole[2] = 0.0; |
| 325 |
< |
atomData->addAtomInfo(atomInfo); |
| 326 |
< |
|
| 327 |
< |
// add atom data into atom's property |
| 328 |
< |
|
| 329 |
< |
if (!haveAtomData) { |
| 330 |
< |
atomData->setID("ATOMDATA"); |
| 331 |
< |
datom->addProperty(atomData); |
| 332 |
< |
} |
| 333 |
< |
|
| 334 |
< |
setVisited(datom); |
| 335 |
< |
} |
| 336 |
< |
|
| 337 |
< |
const std::string TREDAtomVisitor::toString() { |
| 338 |
< |
char buffer[65535]; |
| 339 |
< |
std::string result; |
| 340 |
< |
|
| 341 |
< |
sprintf(buffer, |
| 342 |
< |
"------------------------------------------------------------------\n"); |
| 343 |
< |
result += buffer; |
| 344 |
< |
|
| 345 |
< |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 346 |
< |
result += buffer; |
| 347 |
< |
|
| 348 |
< |
sprintf(buffer, |
| 349 |
< |
"Visitor Description: Convert the TRED atom into 4 different atoms\n"); |
| 350 |
< |
result += buffer; |
| 351 |
< |
|
| 352 |
< |
sprintf(buffer, |
| 353 |
< |
"------------------------------------------------------------------\n"); |
| 354 |
< |
result += buffer; |
| 355 |
< |
|
| 356 |
< |
return result; |
| 357 |
< |
} |
| 358 |
< |
|
| 359 |
< |
|
| 360 |
< |
bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
| 361 |
< |
std::set<std::string>::iterator strIter; |
| 362 |
< |
strIter = linearAtomType.find(atomType); |
| 363 |
< |
|
| 364 |
< |
return strIter != linearAtomType.end() ? true : false; |
| 365 |
< |
} |
| 366 |
< |
|
| 367 |
< |
void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){ |
| 368 |
< |
linearAtomType.insert(atomType); |
| 369 |
< |
} |
| 370 |
< |
|
| 371 |
< |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
| 372 |
< |
std::vector<AtomInfo*> atoms; |
| 373 |
< |
//we need to convert linear into 4 different atoms |
| 374 |
< |
Vector3d c1(0.0, 0.0, -1.8); |
| 375 |
< |
Vector3d c2(0.0, 0.0, -0.6); |
| 376 |
< |
Vector3d c3(0.0, 0.0, 0.6); |
| 377 |
< |
Vector3d c4(0.0, 0.0, 1.8); |
| 378 |
< |
RotMat3x3d rotMatrix; |
| 379 |
< |
RotMat3x3d rotTrans; |
| 380 |
< |
AtomInfo* atomInfo; |
| 381 |
< |
Vector3d pos; |
| 382 |
< |
Vector3d newVec; |
| 383 |
< |
Quat4d q; |
| 384 |
< |
AtomData* atomData; |
| 385 |
< |
GenericData* data; |
| 386 |
< |
bool haveAtomData; |
| 387 |
< |
AtomType* atomType; |
| 388 |
< |
//if atom is not linear atom, just skip it |
| 389 |
< |
if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne()) |
| 390 |
< |
return; |
| 391 |
< |
|
| 392 |
< |
//setup GayBerne type in fortran side |
| 393 |
< |
data = datom->getAtomType()->getPropertyByName("GayBerne"); |
| 394 |
< |
if (data != NULL) { |
| 395 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 396 |
< |
|
| 397 |
< |
if (gayBerneData != NULL) { |
| 398 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 399 |
< |
|
| 400 |
< |
// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0; |
| 401 |
< |
double halfLen = gayBerneParam.GB_l/2.0; |
| 402 |
< |
c1[2] = -halfLen; |
| 403 |
< |
c2[2] = -halfLen /2; |
| 404 |
< |
c3[2] = halfLen/2; |
| 405 |
< |
c4[2] = halfLen; |
| 406 |
< |
|
| 407 |
< |
} |
| 408 |
< |
|
| 409 |
< |
else { |
| 410 |
< |
sprintf( painCave.errMsg, |
| 411 |
< |
"Can not cast GenericData to GayBerneParam\n"); |
| 412 |
< |
painCave.severity = OOPSE_ERROR; |
| 413 |
< |
painCave.isFatal = 1; |
| 414 |
< |
simError(); |
| 415 |
< |
} |
| 416 |
< |
} |
| 417 |
< |
|
| 418 |
< |
|
| 419 |
< |
data = datom->getPropertyByName("ATOMDATA"); |
| 420 |
< |
if(data != NULL){ |
| 421 |
< |
atomData = dynamic_cast<AtomData*>(data); |
| 422 |
< |
if(atomData == NULL){ |
| 423 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 424 |
< |
atomData = new AtomData; |
| 425 |
< |
haveAtomData = false; |
| 426 |
< |
} else { |
| 427 |
< |
haveAtomData = true; |
| 428 |
< |
} |
| 429 |
< |
} else { |
| 430 |
< |
atomData = new AtomData; |
| 431 |
< |
haveAtomData = false; |
| 432 |
< |
} |
| 433 |
< |
|
| 434 |
< |
|
| 435 |
< |
pos = datom->getPos(); |
| 436 |
< |
q = datom->getQ(); |
| 437 |
< |
rotMatrix = datom->getA(); |
| 438 |
< |
|
| 439 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
| 440 |
< |
rotTrans = rotMatrix.transpose(); |
| 441 |
< |
|
| 442 |
< |
newVec = rotTrans * c1; |
| 443 |
< |
atomInfo = new AtomInfo; |
| 444 |
< |
atomInfo->atomTypeName = "C"; |
| 445 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 446 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 447 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 448 |
< |
atomInfo->dipole[0] = 0.0; |
| 449 |
< |
atomInfo->dipole[1] = 0.0; |
| 450 |
< |
atomInfo->dipole[2] = 0.0; |
| 451 |
< |
atomData->addAtomInfo(atomInfo); |
| 452 |
< |
|
| 453 |
< |
newVec = rotTrans * c2; |
| 454 |
< |
atomInfo = new AtomInfo; |
| 455 |
< |
atomInfo->atomTypeName = "C"; |
| 456 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 457 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 458 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 459 |
< |
atomInfo->dipole[0] = 0.0; |
| 460 |
< |
atomInfo->dipole[1] = 0.0; |
| 461 |
< |
atomInfo->dipole[2] = 0.0; |
| 462 |
< |
atomData->addAtomInfo(atomInfo); |
| 463 |
< |
|
| 464 |
< |
newVec = rotTrans * c3; |
| 465 |
< |
atomInfo = new AtomInfo; |
| 466 |
< |
atomInfo->atomTypeName = "C"; |
| 467 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 468 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 469 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 470 |
< |
atomInfo->dipole[0] = 0.0; |
| 471 |
< |
atomInfo->dipole[1] = 0.0; |
| 472 |
< |
atomInfo->dipole[2] = 0.0; |
| 473 |
< |
atomData->addAtomInfo(atomInfo); |
| 474 |
< |
|
| 475 |
< |
newVec = rotTrans * c4; |
| 476 |
< |
atomInfo = new AtomInfo; |
| 477 |
< |
atomInfo->atomTypeName = "C"; |
| 478 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 479 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 480 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 481 |
< |
atomInfo->dipole[0] = 0.0; |
| 482 |
< |
atomInfo->dipole[1] = 0.0; |
| 483 |
< |
atomInfo->dipole[2] = 0.0; |
| 484 |
< |
atomData->addAtomInfo(atomInfo); |
| 485 |
< |
|
| 486 |
< |
//add atom data into atom's property |
| 487 |
< |
|
| 488 |
< |
if(!haveAtomData){ |
| 489 |
< |
atomData->setID("ATOMDATA"); |
| 490 |
< |
datom->addProperty(atomData); |
| 491 |
< |
} |
| 492 |
< |
|
| 493 |
< |
setVisited(datom); |
| 494 |
< |
|
| 495 |
< |
} |
| 496 |
< |
|
| 497 |
< |
const std::string LinearAtomVisitor::toString(){ |
| 498 |
< |
char buffer[65535]; |
| 499 |
< |
std::string result; |
| 500 |
< |
|
| 501 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 502 |
< |
result += buffer; |
| 503 |
< |
|
| 504 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 505 |
< |
result += buffer; |
| 506 |
< |
|
| 507 |
< |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
| 508 |
< |
result += buffer; |
| 509 |
< |
|
| 510 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 511 |
< |
result += buffer; |
| 512 |
< |
|
| 513 |
< |
return result; |
| 514 |
< |
} |
| 515 |
< |
|
| 516 |
< |
bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
| 517 |
< |
std::set<std::string>::iterator strIter; |
| 518 |
< |
strIter = GBLipidAtomType.find(atomType); |
| 519 |
< |
|
| 520 |
< |
return strIter != GBLipidAtomType.end() ? true : false; |
| 521 |
< |
} |
| 522 |
< |
|
| 523 |
< |
void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
| 524 |
< |
std::vector<AtomInfo*> atoms; |
| 525 |
< |
Vector3d c1(0.0, 0.0, 0.0); |
| 526 |
< |
Vector3d c2(0.0, 0.0, 1.0); |
| 527 |
< |
RotMat3x3d rotMatrix; |
| 528 |
< |
RotMat3x3d rotTrans; |
| 529 |
< |
AtomInfo* atomInfo; |
| 530 |
< |
Vector3d pos; |
| 531 |
< |
Vector3d newVec; |
| 532 |
< |
Vector3d dVec; |
| 533 |
< |
Quat4d q; |
| 534 |
< |
AtomData* atomData; |
| 535 |
< |
GenericData* data; |
| 536 |
< |
bool haveAtomData; |
| 537 |
< |
|
| 538 |
< |
//if atom is not GBlipid atom, just skip it |
| 539 |
< |
if(!isGBLipidAtom(datom->getType())) |
| 540 |
< |
return; |
| 541 |
< |
|
| 542 |
< |
data = datom->getPropertyByName("ATOMDATA"); |
| 543 |
< |
if(data != NULL){ |
| 544 |
< |
atomData = dynamic_cast<AtomData*>(data); |
| 545 |
< |
if(atomData == NULL){ |
| 546 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 547 |
< |
atomData = new AtomData; |
| 548 |
< |
haveAtomData = false; |
| 549 |
< |
} else { |
| 550 |
< |
haveAtomData = true; |
| 551 |
< |
} |
| 552 |
< |
} else { |
| 553 |
< |
atomData = new AtomData; |
| 554 |
< |
haveAtomData = false; |
| 555 |
< |
} |
| 556 |
< |
|
| 557 |
< |
|
| 558 |
< |
pos = datom->getPos(); |
| 559 |
< |
q = datom->getQ(); |
| 560 |
< |
rotMatrix = datom->getA(); |
| 561 |
< |
|
| 562 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
| 563 |
< |
rotTrans = rotMatrix.transpose(); |
| 564 |
< |
|
| 565 |
< |
newVec = rotTrans * c1; |
| 566 |
< |
dVec = rotTrans * c2; |
| 567 |
< |
atomInfo = new AtomInfo; |
| 568 |
< |
atomInfo->atomTypeName = "GB"; |
| 569 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 570 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 571 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 572 |
< |
atomInfo->dipole[0] = dVec[0]; |
| 573 |
< |
atomInfo->dipole[1] = dVec[1]; |
| 574 |
< |
atomInfo->dipole[2] = dVec[2]; |
| 575 |
< |
atomInfo->hasVector = true; |
| 576 |
< |
atomInfo->charge = 3.0; |
| 577 |
< |
atomInfo->hasCharge = true; |
| 578 |
< |
atomData->addAtomInfo(atomInfo); |
| 579 |
< |
|
| 580 |
< |
//add atom data into atom's property |
| 581 |
< |
|
| 582 |
< |
if(!haveAtomData){ |
| 583 |
< |
atomData->setID("ATOMDATA"); |
| 584 |
< |
datom->addProperty(atomData); |
| 585 |
< |
} |
| 586 |
< |
|
| 587 |
< |
setVisited(datom); |
| 588 |
< |
|
| 589 |
< |
} |
| 590 |
< |
|
| 591 |
< |
const std::string GBLipidAtomVisitor::toString(){ |
| 592 |
< |
char buffer[65535]; |
| 593 |
< |
std::string result; |
| 594 |
< |
|
| 595 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 596 |
< |
result += buffer; |
| 597 |
< |
|
| 598 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 599 |
< |
result += buffer; |
| 600 |
< |
|
| 601 |
< |
sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n"); |
| 602 |
< |
result += buffer; |
| 603 |
< |
|
| 604 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 605 |
< |
result += buffer; |
| 606 |
< |
|
| 607 |
< |
return result; |
| 608 |
< |
} |
| 609 |
< |
|
| 610 |
< |
bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){ |
| 611 |
< |
std::set<std::string>::iterator strIter; |
| 612 |
< |
strIter = Ring5gbAtomType.find(atomType); |
| 613 |
< |
|
| 614 |
< |
return strIter != Ring5gbAtomType.end() ? true : false; |
| 615 |
< |
} |
| 616 |
< |
|
| 617 |
< |
void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){ |
| 618 |
< |
std::vector<AtomInfo*> atoms; |
| 619 |
< |
//we need to convert linear into 4 different atoms |
| 620 |
< |
Vector3d c1(0.0, 0.0, -5.5); |
| 621 |
< |
Vector3d c2(0.0, 0.0, -1.8); |
| 622 |
< |
Vector3d c3(0.0, 0.0, 1.8); |
| 623 |
< |
Vector3d c4(0.0, 0.0, 5.5); |
| 624 |
< |
RotMat3x3d rotMatrix; |
| 625 |
< |
RotMat3x3d rotTrans; |
| 626 |
< |
AtomInfo* atomInfo; |
| 627 |
< |
Vector3d pos; |
| 628 |
< |
Vector3d newVec; |
| 629 |
< |
Vector3d dVec; |
| 630 |
< |
Quat4d q; |
| 631 |
< |
AtomData* atomData; |
| 632 |
< |
GenericData* data; |
| 633 |
< |
bool haveAtomData; |
| 634 |
< |
|
| 635 |
< |
//if atom is not Ring5GB atom, just skip it |
| 636 |
< |
if(!isRing5gbAtom(datom->getType())) |
| 637 |
< |
return; |
| 638 |
< |
|
| 639 |
< |
data = datom->getPropertyByName("ATOMDATA"); |
| 640 |
< |
if(data != NULL){ |
| 641 |
< |
atomData = dynamic_cast<AtomData*>(data); |
| 642 |
< |
if(atomData == NULL){ |
| 643 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 644 |
< |
atomData = new AtomData; |
| 645 |
< |
haveAtomData = false; |
| 646 |
< |
} else { |
| 647 |
< |
haveAtomData = true; |
| 648 |
< |
} |
| 649 |
< |
} else { |
| 650 |
< |
atomData = new AtomData; |
| 651 |
< |
haveAtomData = false; |
| 652 |
< |
} |
| 653 |
< |
|
| 654 |
< |
|
| 655 |
< |
pos = datom->getPos(); |
| 656 |
< |
q = datom->getQ(); |
| 657 |
< |
rotMatrix = datom->getA(); |
| 658 |
< |
|
| 659 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
| 660 |
< |
rotTrans = rotMatrix.transpose(); |
| 661 |
< |
|
| 662 |
< |
newVec = rotTrans * c1; |
| 663 |
< |
atomInfo = new AtomInfo; |
| 664 |
< |
atomInfo->atomTypeName = "K"; |
| 665 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 666 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 667 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 668 |
< |
atomInfo->dipole[0] = 0.0; |
| 669 |
< |
atomInfo->dipole[1] = 0.0; |
| 670 |
< |
atomInfo->dipole[2] = 0.0; |
| 671 |
< |
atomData->addAtomInfo(atomInfo); |
| 672 |
< |
|
| 673 |
< |
newVec = rotTrans * c2; |
| 674 |
< |
atomInfo = new AtomInfo; |
| 675 |
< |
atomInfo->atomTypeName = "K"; |
| 676 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 677 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 678 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 679 |
< |
atomInfo->dipole[0] = 0.0; |
| 680 |
< |
atomInfo->dipole[1] = 0.0; |
| 681 |
< |
atomInfo->dipole[2] = 0.0; |
| 682 |
< |
atomData->addAtomInfo(atomInfo); |
| 683 |
< |
|
| 684 |
< |
newVec = rotTrans * c3; |
| 685 |
< |
atomInfo = new AtomInfo; |
| 686 |
< |
atomInfo->atomTypeName = "K"; |
| 687 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 688 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 689 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 690 |
< |
atomInfo->dipole[0] = 0.0; |
| 691 |
< |
atomInfo->dipole[1] = 0.0; |
| 692 |
< |
atomInfo->dipole[2] = 0.0; |
| 693 |
< |
atomData->addAtomInfo(atomInfo); |
| 694 |
< |
|
| 695 |
< |
newVec = rotTrans * c4; |
| 696 |
< |
atomInfo = new AtomInfo; |
| 697 |
< |
atomInfo->atomTypeName = "K"; |
| 698 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 699 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 700 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 701 |
< |
atomInfo->dipole[0] = 0.0; |
| 702 |
< |
atomInfo->dipole[1] = 0.0; |
| 703 |
< |
atomInfo->dipole[2] = 0.0; |
| 704 |
< |
atomData->addAtomInfo(atomInfo); |
| 705 |
< |
|
| 706 |
< |
//add atom data into atom's property |
| 707 |
< |
|
| 708 |
< |
if(!haveAtomData){ |
| 709 |
< |
atomData->setID("ATOMDATA"); |
| 710 |
< |
datom->addProperty(atomData); |
| 711 |
< |
} |
| 712 |
< |
|
| 713 |
< |
setVisited(datom); |
| 714 |
< |
|
| 715 |
< |
} |
| 716 |
< |
|
| 717 |
< |
const std::string Ring5gbAtomVisitor::toString(){ |
| 718 |
< |
char buffer[65535]; |
| 719 |
< |
std::string result; |
| 720 |
< |
|
| 721 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 722 |
< |
result += buffer; |
| 723 |
< |
|
| 724 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 725 |
< |
result += buffer; |
| 726 |
< |
|
| 727 |
< |
sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n"); |
| 728 |
< |
result += buffer; |
| 729 |
< |
|
| 730 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 731 |
< |
result += buffer; |
| 732 |
< |
|
| 733 |
< |
return result; |
| 734 |
< |
} |
| 735 |
< |
|
| 736 |
< |
bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){ |
| 737 |
< |
std::set<std::string>::iterator strIter; |
| 738 |
< |
strIter = HeadAtomType.find(atomType); |
| 739 |
< |
|
| 740 |
< |
return strIter != HeadAtomType.end() ? true : false; |
| 741 |
< |
} |
| 742 |
< |
|
| 743 |
< |
void HeadAtomVisitor::visit(DirectionalAtom* datom){ |
| 744 |
< |
std::vector<AtomInfo*> atoms; |
| 745 |
< |
//we need to convert linear into 2 different atoms |
| 746 |
< |
Vector3d c1(0.0, 0.0, -1.5); |
| 747 |
< |
Vector3d c2(0.0, 0.0, 1.5); |
| 748 |
< |
RotMat3x3d rotMatrix; |
| 749 |
< |
RotMat3x3d rotTrans; |
| 750 |
< |
AtomInfo* atomInfo; |
| 751 |
< |
Vector3d pos; |
| 752 |
< |
Vector3d newVec; |
| 753 |
< |
Vector3d dVec; |
| 754 |
< |
Quat4d q; |
| 755 |
< |
AtomData* atomData; |
| 756 |
< |
GenericData* data; |
| 757 |
< |
bool haveAtomData; |
| 758 |
< |
|
| 759 |
< |
//if atom is not Head atom, just skip it |
| 760 |
< |
if(!isHeadAtom(datom->getType())) |
| 761 |
< |
return; |
| 762 |
< |
|
| 763 |
< |
data = datom->getPropertyByName("ATOMDATA"); |
| 764 |
< |
if(data != NULL){ |
| 765 |
< |
atomData = dynamic_cast<AtomData*>(data); |
| 766 |
< |
if(atomData == NULL){ |
| 767 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 768 |
< |
atomData = new AtomData; |
| 769 |
< |
haveAtomData = false; |
| 770 |
< |
} else { |
| 771 |
< |
haveAtomData = true; |
| 772 |
< |
} |
| 773 |
< |
} else { |
| 774 |
< |
atomData = new AtomData; |
| 775 |
< |
haveAtomData = false; |
| 776 |
< |
} |
| 777 |
< |
|
| 778 |
< |
|
| 779 |
< |
pos = datom->getPos(); |
| 780 |
< |
q = datom->getQ(); |
| 781 |
< |
rotMatrix = datom->getA(); |
| 782 |
< |
|
| 783 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
| 784 |
< |
rotTrans = rotMatrix.transpose(); |
| 785 |
< |
|
| 786 |
< |
newVec = rotTrans * c1; |
| 787 |
< |
atomInfo = new AtomInfo; |
| 788 |
< |
atomInfo->atomTypeName = "C"; |
| 789 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 790 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 791 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 792 |
< |
atomInfo->dipole[0] = 0.0; |
| 793 |
< |
atomInfo->dipole[1] = 0.0; |
| 794 |
< |
atomInfo->dipole[2] = 0.0; |
| 795 |
< |
atomData->addAtomInfo(atomInfo); |
| 796 |
< |
|
| 797 |
< |
newVec = rotTrans * c2; |
| 798 |
< |
atomInfo = new AtomInfo; |
| 799 |
< |
atomInfo->atomTypeName = "O"; |
| 800 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 801 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 802 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 803 |
< |
atomInfo->dipole[0] = 0.0; |
| 804 |
< |
atomInfo->dipole[1] = 0.0; |
| 805 |
< |
atomInfo->dipole[2] = 0.0; |
| 806 |
< |
atomData->addAtomInfo(atomInfo); |
| 807 |
< |
|
| 808 |
< |
//add atom data into atom's property |
| 809 |
< |
|
| 810 |
< |
if(!haveAtomData){ |
| 811 |
< |
atomData->setID("ATOMDATA"); |
| 812 |
< |
datom->addProperty(atomData); |
| 813 |
< |
} |
| 814 |
< |
|
| 815 |
< |
setVisited(datom); |
| 816 |
< |
|
| 817 |
< |
} |
| 818 |
< |
|
| 819 |
< |
const std::string HeadAtomVisitor::toString(){ |
| 820 |
< |
char buffer[65535]; |
| 821 |
< |
std::string result; |
| 822 |
< |
|
| 823 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 824 |
< |
result += buffer; |
| 825 |
< |
|
| 826 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 827 |
< |
result += buffer; |
| 828 |
< |
|
| 829 |
< |
sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n"); |
| 830 |
< |
result += buffer; |
| 831 |
< |
|
| 832 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 833 |
< |
result += buffer; |
| 834 |
< |
|
| 835 |
< |
return result; |
| 836 |
< |
} |
| 837 |
< |
|
| 838 |
< |
|
| 839 |
< |
//----------------------------------------------------------------------------// |
| 840 |
< |
|
| 76 |
> |
//------------------------------------------------------------------------// |
| 77 |
> |
|
| 78 |
|
void DefaultAtomVisitor::visit(Atom *atom) { |
| 79 |
|
AtomData *atomData; |
| 80 |
|
AtomInfo *atomInfo; |
| 81 |
|
Vector3d pos; |
| 82 |
< |
|
| 82 |
> |
|
| 83 |
|
if (isVisited(atom)) |
| 84 |
|
return; |
| 85 |
< |
|
| 85 |
> |
|
| 86 |
|
atomInfo = new AtomInfo; |
| 87 |
< |
|
| 87 |
> |
|
| 88 |
|
atomData = new AtomData; |
| 89 |
|
atomData->setID("ATOMDATA"); |
| 90 |
< |
|
| 90 |
> |
|
| 91 |
|
pos = atom->getPos(); |
| 92 |
|
atomInfo->atomTypeName = atom->getType(); |
| 93 |
|
atomInfo->pos[0] = pos[0]; |
| 96 |
|
atomInfo->dipole[0] = 0.0; |
| 97 |
|
atomInfo->dipole[1] = 0.0; |
| 98 |
|
atomInfo->dipole[2] = 0.0; |
| 99 |
< |
|
| 99 |
> |
|
| 100 |
|
atomData->addAtomInfo(atomInfo); |
| 101 |
< |
|
| 101 |
> |
|
| 102 |
|
atom->addProperty(atomData); |
| 103 |
< |
|
| 103 |
> |
|
| 104 |
|
setVisited(atom); |
| 105 |
|
} |
| 106 |
< |
|
| 106 |
> |
|
| 107 |
|
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 108 |
|
AtomData *atomData; |
| 109 |
|
AtomInfo *atomInfo; |
| 159 |
|
|
| 160 |
|
return result; |
| 161 |
|
} |
| 162 |
< |
} //namespace oopse |
| 162 |
> |
} //namespace OpenMD |
