| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 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 |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include <cstring> |
| 43 |
#include "visitors/AtomVisitor.hpp" |
| 44 |
#include "primitives/DirectionalAtom.hpp" |
| 45 |
#include "math/MatVec3.h" |
| 46 |
#include "primitives/RigidBody.hpp" |
| 47 |
|
| 48 |
namespace oopse { |
| 49 |
void BaseAtomVisitor::visit(RigidBody *rb) { |
| 50 |
//vector<Atom*> myAtoms; |
| 51 |
//vector<Atom*>::iterator atomIter; |
| 52 |
|
| 53 |
//myAtoms = rb->getAtoms(); |
| 54 |
|
| 55 |
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
| 56 |
// (*atomIter)->accept(this); |
| 57 |
} |
| 58 |
|
| 59 |
void BaseAtomVisitor::setVisited(Atom *atom) { |
| 60 |
GenericData *data; |
| 61 |
data = atom->getPropertyByName("VISITED"); |
| 62 |
|
| 63 |
//if visited property is not existed, add it as new property |
| 64 |
if (data == NULL) { |
| 65 |
data = new GenericData(); |
| 66 |
data->setID("VISITED"); |
| 67 |
atom->addProperty(data); |
| 68 |
} |
| 69 |
} |
| 70 |
|
| 71 |
bool BaseAtomVisitor::isVisited(Atom *atom) { |
| 72 |
GenericData *data; |
| 73 |
data = atom->getPropertyByName("VISITED"); |
| 74 |
return data == NULL ? false : true; |
| 75 |
} |
| 76 |
|
| 77 |
bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
| 78 |
std::set<std::string>::iterator strIter; |
| 79 |
strIter = ssdAtomType.find(atomType); |
| 80 |
return strIter != ssdAtomType.end() ? true : false; |
| 81 |
} |
| 82 |
|
| 83 |
void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
| 84 |
std::vector<AtomInfo*>atoms; |
| 85 |
|
| 86 |
//we need to convert SSD into 4 differnet atoms |
| 87 |
//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass |
| 88 |
//of the water with a dipole moment |
| 89 |
Vector3d h1(0.0, -0.75695, 0.5206); |
| 90 |
Vector3d h2(0.0, 0.75695, 0.5206); |
| 91 |
Vector3d ox(0.0, 0.0, -0.0654); |
| 92 |
Vector3d u(0, 0, 1); |
| 93 |
RotMat3x3d rotMatrix; |
| 94 |
RotMat3x3d rotTrans; |
| 95 |
AtomInfo * atomInfo; |
| 96 |
Vector3d pos; |
| 97 |
Vector3d newVec; |
| 98 |
Quat4d q; |
| 99 |
AtomData * atomData; |
| 100 |
GenericData *data; |
| 101 |
bool haveAtomData; |
| 102 |
|
| 103 |
//if atom is not SSD atom, just skip it |
| 104 |
if (!isSSDAtom(datom->getType())) |
| 105 |
return; |
| 106 |
|
| 107 |
data = datom->getPropertyByName("ATOMDATA"); |
| 108 |
|
| 109 |
if (data != NULL) { |
| 110 |
atomData = dynamic_cast<AtomData *>(data); |
| 111 |
|
| 112 |
if (atomData == NULL) { |
| 113 |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 114 |
atomData = new AtomData; |
| 115 |
haveAtomData = false; |
| 116 |
} else |
| 117 |
haveAtomData = true; |
| 118 |
} else { |
| 119 |
atomData = new AtomData; |
| 120 |
haveAtomData = false; |
| 121 |
} |
| 122 |
|
| 123 |
pos = datom->getPos(); |
| 124 |
q = datom->getQ(); |
| 125 |
rotMatrix = datom->getA(); |
| 126 |
|
| 127 |
// We need A^T to convert from body-fixed to space-fixed: |
| 128 |
//transposeMat3(rotMatrix, rotTrans); |
| 129 |
rotTrans = rotMatrix.transpose(); |
| 130 |
|
| 131 |
//center of mass of the water molecule |
| 132 |
//matVecMul3(rotTrans, u, newVec); |
| 133 |
newVec = rotTrans * u; |
| 134 |
|
| 135 |
atomInfo = new AtomInfo; |
| 136 |
atomInfo->AtomType = "X"; |
| 137 |
atomInfo->pos[0] = pos[0]; |
| 138 |
atomInfo->pos[1] = pos[1]; |
| 139 |
atomInfo->pos[2] = pos[2]; |
| 140 |
atomInfo->dipole[0] = newVec[0]; |
| 141 |
atomInfo->dipole[1] = newVec[1]; |
| 142 |
atomInfo->dipole[2] = newVec[2]; |
| 143 |
|
| 144 |
atomData->addAtomInfo(atomInfo); |
| 145 |
|
| 146 |
//oxygen |
| 147 |
//matVecMul3(rotTrans, ox, newVec); |
| 148 |
newVec = rotTrans * ox; |
| 149 |
|
| 150 |
atomInfo = new AtomInfo; |
| 151 |
atomInfo->AtomType = "O"; |
| 152 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 153 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 154 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 155 |
atomInfo->dipole[0] = 0.0; |
| 156 |
atomInfo->dipole[1] = 0.0; |
| 157 |
atomInfo->dipole[2] = 0.0; |
| 158 |
atomData->addAtomInfo(atomInfo); |
| 159 |
|
| 160 |
//hydrogen1 |
| 161 |
//matVecMul3(rotTrans, h1, newVec); |
| 162 |
newVec = rotTrans * h1; |
| 163 |
atomInfo = new AtomInfo; |
| 164 |
atomInfo->AtomType = "H"; |
| 165 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 166 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 167 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 168 |
atomInfo->dipole[0] = 0.0; |
| 169 |
atomInfo->dipole[1] = 0.0; |
| 170 |
atomInfo->dipole[2] = 0.0; |
| 171 |
atomData->addAtomInfo(atomInfo); |
| 172 |
|
| 173 |
//hydrogen2 |
| 174 |
//matVecMul3(rotTrans, h2, newVec); |
| 175 |
newVec = rotTrans * h2; |
| 176 |
atomInfo = new AtomInfo; |
| 177 |
atomInfo->AtomType = "H"; |
| 178 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 179 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 180 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 181 |
atomInfo->dipole[0] = 0.0; |
| 182 |
atomInfo->dipole[1] = 0.0; |
| 183 |
atomInfo->dipole[2] = 0.0; |
| 184 |
atomData->addAtomInfo(atomInfo); |
| 185 |
|
| 186 |
//add atom data into atom's property |
| 187 |
|
| 188 |
if (!haveAtomData) { |
| 189 |
atomData->setID("ATOMDATA"); |
| 190 |
datom->addProperty(atomData); |
| 191 |
} |
| 192 |
|
| 193 |
setVisited(datom); |
| 194 |
} |
| 195 |
|
| 196 |
const std::string SSDAtomVisitor::toString() { |
| 197 |
char buffer[65535]; |
| 198 |
std::string result; |
| 199 |
|
| 200 |
sprintf(buffer, |
| 201 |
"------------------------------------------------------------------\n"); |
| 202 |
result += buffer; |
| 203 |
|
| 204 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 205 |
result += buffer; |
| 206 |
|
| 207 |
sprintf(buffer, |
| 208 |
"Visitor Description: Convert SSD into 4 different atoms\n"); |
| 209 |
result += buffer; |
| 210 |
|
| 211 |
sprintf(buffer, |
| 212 |
"------------------------------------------------------------------\n"); |
| 213 |
result += buffer; |
| 214 |
|
| 215 |
return result; |
| 216 |
} |
| 217 |
|
| 218 |
bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
| 219 |
std::set<std::string>::iterator strIter; |
| 220 |
strIter = linearAtomType.find(atomType); |
| 221 |
|
| 222 |
return strIter != linearAtomType.end() ? true : false; |
| 223 |
} |
| 224 |
|
| 225 |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
| 226 |
std::vector<AtomInfo*> atoms; |
| 227 |
//we need to convert linear into 4 different atoms |
| 228 |
Vector3d c1(0.0, 0.0, -1.8); |
| 229 |
Vector3d c2(0.0, 0.0, -0.6); |
| 230 |
Vector3d c3(0.0, 0.0, 0.6); |
| 231 |
Vector3d c4(0.0, 0.0, 1.8); |
| 232 |
RotMat3x3d rotMatrix; |
| 233 |
RotMat3x3d rotTrans; |
| 234 |
AtomInfo* atomInfo; |
| 235 |
Vector3d pos; |
| 236 |
Vector3d newVec; |
| 237 |
Quat4d q; |
| 238 |
AtomData* atomData; |
| 239 |
GenericData* data; |
| 240 |
bool haveAtomData; |
| 241 |
|
| 242 |
//if atom is not SSD atom, just skip it |
| 243 |
if(!isLinearAtom(datom->getType())) |
| 244 |
return; |
| 245 |
|
| 246 |
data = datom->getPropertyByName("ATOMDATA"); |
| 247 |
if(data != NULL){ |
| 248 |
atomData = dynamic_cast<AtomData*>(data); |
| 249 |
if(atomData == NULL){ |
| 250 |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 251 |
atomData = new AtomData; |
| 252 |
haveAtomData = false; |
| 253 |
} else { |
| 254 |
haveAtomData = true; |
| 255 |
} |
| 256 |
} else { |
| 257 |
atomData = new AtomData; |
| 258 |
haveAtomData = false; |
| 259 |
} |
| 260 |
|
| 261 |
|
| 262 |
pos = datom->getPos(); |
| 263 |
q = datom->getQ(); |
| 264 |
rotMatrix = datom->getA(); |
| 265 |
|
| 266 |
// We need A^T to convert from body-fixed to space-fixed: |
| 267 |
rotTrans = rotMatrix.transpose(); |
| 268 |
|
| 269 |
newVec = rotTrans * c1; |
| 270 |
atomInfo = new AtomInfo; |
| 271 |
atomInfo->AtomType = "C"; |
| 272 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 273 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 274 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 275 |
atomInfo->dipole[0] = 0.0; |
| 276 |
atomInfo->dipole[1] = 0.0; |
| 277 |
atomInfo->dipole[2] = 0.0; |
| 278 |
atomData->addAtomInfo(atomInfo); |
| 279 |
|
| 280 |
newVec = rotTrans * c2; |
| 281 |
atomInfo = new AtomInfo; |
| 282 |
atomInfo->AtomType = "C"; |
| 283 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 284 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 285 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 286 |
atomInfo->dipole[0] = 0.0; |
| 287 |
atomInfo->dipole[1] = 0.0; |
| 288 |
atomInfo->dipole[2] = 0.0; |
| 289 |
atomData->addAtomInfo(atomInfo); |
| 290 |
|
| 291 |
newVec = rotTrans * c3; |
| 292 |
atomInfo = new AtomInfo; |
| 293 |
atomInfo->AtomType = "C"; |
| 294 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 295 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 296 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 297 |
atomInfo->dipole[0] = 0.0; |
| 298 |
atomInfo->dipole[1] = 0.0; |
| 299 |
atomInfo->dipole[2] = 0.0; |
| 300 |
atomData->addAtomInfo(atomInfo); |
| 301 |
|
| 302 |
newVec = rotTrans * c4; |
| 303 |
atomInfo = new AtomInfo; |
| 304 |
atomInfo->AtomType = "C"; |
| 305 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 306 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 307 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 308 |
atomInfo->dipole[0] = 0.0; |
| 309 |
atomInfo->dipole[1] = 0.0; |
| 310 |
atomInfo->dipole[2] = 0.0; |
| 311 |
atomData->addAtomInfo(atomInfo); |
| 312 |
|
| 313 |
//add atom data into atom's property |
| 314 |
|
| 315 |
if(!haveAtomData){ |
| 316 |
atomData->setID("ATOMDATA"); |
| 317 |
datom->addProperty(atomData); |
| 318 |
} |
| 319 |
|
| 320 |
setVisited(datom); |
| 321 |
|
| 322 |
} |
| 323 |
|
| 324 |
const std::string LinearAtomVisitor::toString(){ |
| 325 |
char buffer[65535]; |
| 326 |
std::string result; |
| 327 |
|
| 328 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 329 |
result += buffer; |
| 330 |
|
| 331 |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 332 |
result += buffer; |
| 333 |
|
| 334 |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
| 335 |
result += buffer; |
| 336 |
|
| 337 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 338 |
result += buffer; |
| 339 |
|
| 340 |
return result; |
| 341 |
} |
| 342 |
|
| 343 |
//----------------------------------------------------------------------------// |
| 344 |
|
| 345 |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 346 |
AtomData *atomData; |
| 347 |
AtomInfo *atomInfo; |
| 348 |
Vector3d pos; |
| 349 |
|
| 350 |
if (isVisited(atom)) |
| 351 |
return; |
| 352 |
|
| 353 |
atomInfo = new AtomInfo; |
| 354 |
|
| 355 |
atomData = new AtomData; |
| 356 |
atomData->setID("ATOMDATA"); |
| 357 |
|
| 358 |
pos = atom->getPos(); |
| 359 |
atomInfo->AtomType = atom->getType(); |
| 360 |
atomInfo->pos[0] = pos[0]; |
| 361 |
atomInfo->pos[1] = pos[1]; |
| 362 |
atomInfo->pos[2] = pos[2]; |
| 363 |
atomInfo->dipole[0] = 0.0; |
| 364 |
atomInfo->dipole[1] = 0.0; |
| 365 |
atomInfo->dipole[2] = 0.0; |
| 366 |
|
| 367 |
atomData->addAtomInfo(atomInfo); |
| 368 |
|
| 369 |
atom->addProperty(atomData); |
| 370 |
|
| 371 |
setVisited(atom); |
| 372 |
} |
| 373 |
|
| 374 |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 375 |
AtomData *atomData; |
| 376 |
AtomInfo *atomInfo; |
| 377 |
Vector3d pos; |
| 378 |
Vector3d u; |
| 379 |
|
| 380 |
if (isVisited(datom)) |
| 381 |
return; |
| 382 |
|
| 383 |
pos = datom->getPos(); |
| 384 |
u = datom->getElectroFrame().getColumn(2); |
| 385 |
|
| 386 |
atomData = new AtomData; |
| 387 |
atomData->setID("ATOMDATA"); |
| 388 |
atomInfo = new AtomInfo; |
| 389 |
|
| 390 |
atomInfo->AtomType = datom->getType(); |
| 391 |
atomInfo->pos[0] = pos[0]; |
| 392 |
atomInfo->pos[1] = pos[1]; |
| 393 |
atomInfo->pos[2] = pos[2]; |
| 394 |
atomInfo->dipole[0] = u[0]; |
| 395 |
atomInfo->dipole[1] = u[1]; |
| 396 |
atomInfo->dipole[2] = u[2]; |
| 397 |
|
| 398 |
atomData->addAtomInfo(atomInfo); |
| 399 |
|
| 400 |
datom->addProperty(atomData); |
| 401 |
|
| 402 |
setVisited(datom); |
| 403 |
} |
| 404 |
|
| 405 |
const std::string DefaultAtomVisitor::toString() { |
| 406 |
char buffer[65535]; |
| 407 |
std::string result; |
| 408 |
|
| 409 |
sprintf(buffer, |
| 410 |
"------------------------------------------------------------------\n"); |
| 411 |
result += buffer; |
| 412 |
|
| 413 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 414 |
result += buffer; |
| 415 |
|
| 416 |
sprintf(buffer, |
| 417 |
"Visitor Description: copy atom infomation into atom data\n"); |
| 418 |
result += buffer; |
| 419 |
|
| 420 |
sprintf(buffer, |
| 421 |
"------------------------------------------------------------------\n"); |
| 422 |
result += buffer; |
| 423 |
|
| 424 |
return result; |
| 425 |
} |
| 426 |
} //namespace oopse |
