| 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 <cstdlib> |
| 43 |
#include <cstdio> |
| 44 |
#include <cstring> |
| 45 |
#include <cmath> |
| 46 |
#include <iostream> |
| 47 |
#include <string> |
| 48 |
#include <map> |
| 49 |
#include <fstream> |
| 50 |
|
| 51 |
#include "config.h" |
| 52 |
|
| 53 |
#include "nanorodBuilderCmd.h" |
| 54 |
#ifdef HAVE_CGAL |
| 55 |
#include "GeometryBuilder.hpp" |
| 56 |
#endif |
| 57 |
#include "lattice/LatticeFactory.hpp" |
| 58 |
#include "utils/MoLocator.hpp" |
| 59 |
#include "lattice/Lattice.hpp" |
| 60 |
#include "brains/Register.hpp" |
| 61 |
#include "brains/SimInfo.hpp" |
| 62 |
#include "brains/SimCreator.hpp" |
| 63 |
#include "io/DumpWriter.hpp" |
| 64 |
#include "math/Vector3.hpp" |
| 65 |
#include "math/SquareMatrix3.hpp" |
| 66 |
#include "utils/StringUtils.hpp" |
| 67 |
|
| 68 |
using namespace std; |
| 69 |
using namespace oopse; |
| 70 |
void createMdFile(const std::string&oldMdFileName, |
| 71 |
const std::string&newMdFileName, |
| 72 |
int numMol); |
| 73 |
|
| 74 |
int main(int argc, char *argv []) { |
| 75 |
|
| 76 |
//register force fields |
| 77 |
registerForceFields(); |
| 78 |
registerLattice(); |
| 79 |
|
| 80 |
gengetopt_args_info args_info; |
| 81 |
std::string latticeType; |
| 82 |
std::string inputFileName; |
| 83 |
std::string outPrefix; |
| 84 |
std::string outMdFileName; |
| 85 |
std::string outInitFileName; |
| 86 |
std::string outGeomFileName; |
| 87 |
|
| 88 |
|
| 89 |
Lattice *simpleLat; |
| 90 |
int numMol; |
| 91 |
double latticeConstant; |
| 92 |
std::vector<double> lc; |
| 93 |
double mass; |
| 94 |
const double rhoConvertConst = 1.661; |
| 95 |
double density; |
| 96 |
double rodLength; |
| 97 |
double rodDiameter; |
| 98 |
|
| 99 |
|
| 100 |
int nx, ny, nz; |
| 101 |
Mat3x3d hmat; |
| 102 |
MoLocator *locator; |
| 103 |
std::vector<Vector3d> latticePos; |
| 104 |
std::vector<Vector3d> latticeOrt; |
| 105 |
int numMolPerCell; |
| 106 |
int curMolIndex; |
| 107 |
DumpWriter *writer; |
| 108 |
|
| 109 |
// parse command line arguments |
| 110 |
if (cmdline_parser(argc, argv, &args_info) != 0) |
| 111 |
exit(1); |
| 112 |
|
| 113 |
|
| 114 |
// Check for lib CGAL, if we don't have it, we should exit.... |
| 115 |
|
| 116 |
#ifndef HAVE_CGAL |
| 117 |
std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL." |
| 118 |
<< std::endl; |
| 119 |
exit(1); |
| 120 |
#endif |
| 121 |
|
| 122 |
|
| 123 |
|
| 124 |
//get lattice type |
| 125 |
latticeType = UpperCase(args_info.latticetype_arg); |
| 126 |
|
| 127 |
|
| 128 |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 129 |
if (simpleLat == NULL) { |
| 130 |
sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n", |
| 131 |
latticeType.c_str()); |
| 132 |
painCave.isFatal = 1; |
| 133 |
simError(); |
| 134 |
} |
| 135 |
|
| 136 |
//get input file name |
| 137 |
if (args_info.inputs_num) |
| 138 |
inputFileName = args_info.inputs[0]; |
| 139 |
else { |
| 140 |
std::cerr << "You must specify a input file name.\n" << std::endl; |
| 141 |
cmdline_parser_print_help(); |
| 142 |
exit(1); |
| 143 |
} |
| 144 |
|
| 145 |
//parse md file and set up the system |
| 146 |
SimCreator oldCreator; |
| 147 |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 148 |
|
| 149 |
if (oldInfo->getNMoleculeStamp()> 1) { |
| 150 |
std::cerr << "can not build nanorod with more than one components" |
| 151 |
<< std::endl; |
| 152 |
exit(1); |
| 153 |
} |
| 154 |
|
| 155 |
//get mass of molecule. |
| 156 |
|
| 157 |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 158 |
|
| 159 |
//creat lattice |
| 160 |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 161 |
|
| 162 |
if (simpleLat == NULL) { |
| 163 |
std::cerr << "Error in creating lattice" << std::endl; |
| 164 |
exit(1); |
| 165 |
} |
| 166 |
|
| 167 |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 168 |
|
| 169 |
//calculate lattice constant (in Angstrom) |
| 170 |
//latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 171 |
// 1.0 / 3.0); |
| 172 |
|
| 173 |
latticeConstant = args_info.latticeCnst_arg; |
| 174 |
rodLength = args_info.length_arg; |
| 175 |
rodDiameter = args_info.width_arg; |
| 176 |
|
| 177 |
//set lattice constant |
| 178 |
lc.push_back(latticeConstant); |
| 179 |
simpleLat->setLatticeConstant(lc); |
| 180 |
|
| 181 |
|
| 182 |
//determine the output file names |
| 183 |
if (args_info.output_given) |
| 184 |
outInitFileName = args_info.output_arg; |
| 185 |
else |
| 186 |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 187 |
|
| 188 |
|
| 189 |
|
| 190 |
|
| 191 |
|
| 192 |
|
| 193 |
//creat Molocator |
| 194 |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 195 |
|
| 196 |
/* |
| 197 |
Assume we are carving nanorod out of a cublic block of material and that |
| 198 |
the shape the material will fit within that block.... |
| 199 |
The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the |
| 200 |
diameter of the particle. |
| 201 |
*/ |
| 202 |
// Number of Unit Cells in Length first |
| 203 |
ny = (int)(rodLength/latticeConstant); |
| 204 |
// Number of unit cells in Width |
| 205 |
nx = (int)(rodDiameter/latticeConstant); |
| 206 |
nz = (int)(rodDiameter/latticeConstant); |
| 207 |
|
| 208 |
|
| 209 |
|
| 210 |
// Create geometry for nanocrystal |
| 211 |
#ifdef HAVE_CGAL |
| 212 |
GeometryBuilder myGeometry(rodLength,rodDiameter); |
| 213 |
if (args_info.genGeomview_given){ |
| 214 |
if (args_info.genGeomview_flag){ |
| 215 |
outGeomFileName = getPrefix(inputFileName.c_str()) + ".off"; |
| 216 |
myGeometry.dumpGeometry(outGeomFileName); |
| 217 |
} |
| 218 |
} |
| 219 |
|
| 220 |
#endif |
| 221 |
|
| 222 |
/* |
| 223 |
We have to build the system first to figure out how many molecules |
| 224 |
there are then create a md file and then actually build the |
| 225 |
system. |
| 226 |
*/ |
| 227 |
|
| 228 |
//place the molecules |
| 229 |
|
| 230 |
curMolIndex = 0; |
| 231 |
|
| 232 |
//get the orientation of the cell sites |
| 233 |
//for the same type of molecule in same lattice, it will not change |
| 234 |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 235 |
|
| 236 |
|
| 237 |
/* |
| 238 |
void BaseLattice::getLatticePointsPos(std::vector<Vector3d>& |
| 239 |
latticePos, int nx, int ny, int nz){ |
| 240 |
|
| 241 |
latticePos.resize(nCellSites); |
| 242 |
|
| 243 |
for( int i=0;i < nCellSites;i++){ |
| 244 |
|
| 245 |
latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5); |
| 246 |
latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5); |
| 247 |
latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5); |
| 248 |
} |
| 249 |
|
| 250 |
*/ |
| 251 |
|
| 252 |
|
| 253 |
|
| 254 |
|
| 255 |
numMol = 0; |
| 256 |
for(int i = -nx; i < nx; i++) { |
| 257 |
for(int j = -ny; j < ny; j++) { |
| 258 |
for(int k = -nz; k < nz; k++) { |
| 259 |
//if (oldInfo->getNGlobalMolecules() != numMol) { |
| 260 |
|
| 261 |
|
| 262 |
|
| 263 |
//get the position of the cell sites |
| 264 |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 265 |
|
| 266 |
for(int l = 0; l < numMolPerCell; l++) { |
| 267 |
|
| 268 |
#ifdef HAVE_CGAL |
| 269 |
if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 270 |
numMol++; |
| 271 |
} |
| 272 |
#endif |
| 273 |
} |
| 274 |
} |
| 275 |
} |
| 276 |
} |
| 277 |
std::cerr << "numMol before is " << numMol << std::endl; |
| 278 |
|
| 279 |
// needed for writing out new md file. |
| 280 |
|
| 281 |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 282 |
outMdFileName = outPrefix + ".md"; |
| 283 |
|
| 284 |
//creat new .md file on fly which corrects the number of molecule |
| 285 |
createMdFile(inputFileName, outMdFileName, numMol); |
| 286 |
|
| 287 |
if (oldInfo != NULL) |
| 288 |
delete oldInfo; |
| 289 |
|
| 290 |
|
| 291 |
// We need to read in new siminfo object. |
| 292 |
//parse md file and set up the system |
| 293 |
//SimCreator NewCreator; |
| 294 |
|
| 295 |
SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false); |
| 296 |
|
| 297 |
// This was so much fun the first time, lets do it again. |
| 298 |
|
| 299 |
Molecule* mol; |
| 300 |
SimInfo::MoleculeIterator mi; |
| 301 |
mol = NewInfo->beginMolecule(mi); |
| 302 |
numMol = 0; |
| 303 |
int countMol = 0; |
| 304 |
for(int i = -nx; i < nx; i++) { |
| 305 |
for(int j = -ny; j < ny; j++) { |
| 306 |
for(int k = -nz; k < nz; k++) { |
| 307 |
|
| 308 |
//get the position of the cell sites |
| 309 |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 310 |
|
| 311 |
for(int l = 0; l < numMolPerCell; l++) { |
| 312 |
if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 313 |
countMol++; |
| 314 |
if (mol != NULL) { |
| 315 |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 316 |
numMol++; |
| 317 |
} else { |
| 318 |
std::cerr<<"Error in placing molecule " << countMol << std::endl; |
| 319 |
} |
| 320 |
mol = NewInfo->nextMolecule(mi); |
| 321 |
} |
| 322 |
|
| 323 |
} |
| 324 |
} |
| 325 |
} |
| 326 |
} |
| 327 |
|
| 328 |
std::cerr << "numMol after is " << numMol << std::endl; |
| 329 |
|
| 330 |
//fill Hmat |
| 331 |
hmat(0, 0)= nx * latticeConstant; |
| 332 |
hmat(0, 1) = 0.0; |
| 333 |
hmat(0, 2) = 0.0; |
| 334 |
|
| 335 |
hmat(1, 0) = 0.0; |
| 336 |
hmat(1, 1) = ny * latticeConstant; |
| 337 |
hmat(1, 2) = 0.0; |
| 338 |
|
| 339 |
hmat(2, 0) = 0.0; |
| 340 |
hmat(2, 1) = 0.0; |
| 341 |
hmat(2, 2) = nz * latticeConstant; |
| 342 |
|
| 343 |
//set Hmat |
| 344 |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 345 |
|
| 346 |
|
| 347 |
//create dumpwriter and write out the coordinates |
| 348 |
NewInfo->setFinalConfigFileName(outInitFileName); |
| 349 |
writer = new DumpWriter(NewInfo); |
| 350 |
|
| 351 |
if (writer == NULL) { |
| 352 |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 353 |
exit(1); |
| 354 |
} |
| 355 |
|
| 356 |
writer->writeDump(); |
| 357 |
std::cout << "new initial configuration file: " << outInitFileName |
| 358 |
<< " is generated." << std::endl; |
| 359 |
|
| 360 |
//delete objects |
| 361 |
|
| 362 |
//delete oldInfo and oldSimSetup |
| 363 |
|
| 364 |
if (NewInfo != NULL) |
| 365 |
delete NewInfo; |
| 366 |
|
| 367 |
if (writer != NULL) |
| 368 |
delete writer; |
| 369 |
delete simpleLat; |
| 370 |
cmdline_parser_free(&args_info); |
| 371 |
return 0; |
| 372 |
} |
| 373 |
|
| 374 |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 375 |
int numMol) { |
| 376 |
ifstream oldMdFile; |
| 377 |
ofstream newMdFile; |
| 378 |
const int MAXLEN = 65535; |
| 379 |
char buffer[MAXLEN]; |
| 380 |
|
| 381 |
//create new .md file based on old .md file |
| 382 |
oldMdFile.open(oldMdFileName.c_str()); |
| 383 |
newMdFile.open(newMdFileName.c_str()); |
| 384 |
|
| 385 |
oldMdFile.getline(buffer, MAXLEN); |
| 386 |
|
| 387 |
while (!oldMdFile.eof()) { |
| 388 |
|
| 389 |
//correct molecule number |
| 390 |
if (strstr(buffer, "nMol") != NULL) { |
| 391 |
sprintf(buffer, "\tnMol = %i;", numMol); |
| 392 |
newMdFile << buffer << std::endl; |
| 393 |
} else |
| 394 |
newMdFile << buffer << std::endl; |
| 395 |
|
| 396 |
oldMdFile.getline(buffer, MAXLEN); |
| 397 |
} |
| 398 |
|
| 399 |
oldMdFile.close(); |
| 400 |
newMdFile.close(); |
| 401 |
} |
| 402 |
|
