| 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. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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, 234107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
#include <cstdlib> |
| 44 |
#include <cstdio> |
| 45 |
#include <cstring> |
| 46 |
#include <cmath> |
| 47 |
#include <iostream> |
| 48 |
#include <string> |
| 49 |
#include <map> |
| 50 |
#include <fstream> |
| 51 |
#include <algorithm> |
| 52 |
|
| 53 |
#include "config.h" |
| 54 |
#include "shapedLatticeSpherical.hpp" |
| 55 |
#include "nanoparticleBuilderCmd.h" |
| 56 |
#include "lattice/LatticeFactory.hpp" |
| 57 |
#include "utils/MoLocator.hpp" |
| 58 |
#include "lattice/Lattice.hpp" |
| 59 |
#include "brains/Register.hpp" |
| 60 |
#include "brains/SimInfo.hpp" |
| 61 |
#include "brains/SimCreator.hpp" |
| 62 |
#include "io/DumpWriter.hpp" |
| 63 |
#include "math/Vector3.hpp" |
| 64 |
#include "math/SquareMatrix3.hpp" |
| 65 |
#include "utils/StringUtils.hpp" |
| 66 |
|
| 67 |
using namespace std; |
| 68 |
using namespace OpenMD; |
| 69 |
void createMdFile(const std::string&oldMdFileName, |
| 70 |
const std::string&newMdFileName, |
| 71 |
std::vector<int> numMol); |
| 72 |
|
| 73 |
int main(int argc, char *argv []) { |
| 74 |
|
| 75 |
registerLattice(); |
| 76 |
|
| 77 |
gengetopt_args_info args_info; |
| 78 |
std::string latticeType; |
| 79 |
std::string inputFileName; |
| 80 |
std::string outputFileName; |
| 81 |
MoLocator* locator; |
| 82 |
int nComponents; |
| 83 |
double latticeConstant; |
| 84 |
RealType particleRadius; |
| 85 |
Mat3x3d hmat; |
| 86 |
DumpWriter *writer; |
| 87 |
|
| 88 |
// Parse Command Line Arguments |
| 89 |
if (cmdline_parser(argc, argv, &args_info) != 0) |
| 90 |
exit(1); |
| 91 |
|
| 92 |
/* get lattice type */ |
| 93 |
latticeType = "FCC"; |
| 94 |
|
| 95 |
/* get input file name */ |
| 96 |
if (args_info.inputs_num) |
| 97 |
inputFileName = args_info.inputs[0]; |
| 98 |
else { |
| 99 |
sprintf(painCave.errMsg, "No input .md file name was specified " |
| 100 |
"on the command line"); |
| 101 |
painCave.isFatal = 1; |
| 102 |
cmdline_parser_print_help(); |
| 103 |
simError(); |
| 104 |
} |
| 105 |
|
| 106 |
/* parse md file and set up the system */ |
| 107 |
SimCreator oldCreator; |
| 108 |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 109 |
|
| 110 |
latticeConstant = args_info.latticeConstant_arg; |
| 111 |
particleRadius = args_info.radius_arg; |
| 112 |
Globals* simParams = oldInfo->getSimParams(); |
| 113 |
|
| 114 |
/* Create nanoparticle */ |
| 115 |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
| 116 |
particleRadius); |
| 117 |
|
| 118 |
/* Build a lattice and get lattice points for this lattice constant */ |
| 119 |
vector<Vector3d> sites = nanoParticle.getSites(); |
| 120 |
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
| 121 |
|
| 122 |
|
| 123 |
std::vector<int> vacancyTargets; |
| 124 |
vector<bool> isVacancy; |
| 125 |
|
| 126 |
Vector3d myLoc; |
| 127 |
RealType myR; |
| 128 |
|
| 129 |
for (unsigned int i = 0; i < sites.size(); i++) |
| 130 |
isVacancy.push_back(false); |
| 131 |
|
| 132 |
if (args_info.vacancyPercent_given) { |
| 133 |
if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) { |
| 134 |
sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value."); |
| 135 |
painCave.isFatal = 1; |
| 136 |
simError(); |
| 137 |
} else { |
| 138 |
RealType vF = args_info.vacancyPercent_arg / 100.0; |
| 139 |
RealType vIR; |
| 140 |
RealType vOR; |
| 141 |
if (args_info.vacancyInnerRadius_given) { |
| 142 |
vIR = args_info.vacancyInnerRadius_arg; |
| 143 |
} else { |
| 144 |
vIR = 0.0; |
| 145 |
} |
| 146 |
if (args_info.vacancyOuterRadius_given) { |
| 147 |
vOR = args_info.vacancyOuterRadius_arg; |
| 148 |
} else { |
| 149 |
vOR = particleRadius; |
| 150 |
} |
| 151 |
if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) { |
| 152 |
|
| 153 |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 154 |
myLoc = sites[i]; |
| 155 |
myR = myLoc.length(); |
| 156 |
if (myR >= vIR && myR <= vOR) { |
| 157 |
vacancyTargets.push_back(i); |
| 158 |
} |
| 159 |
} |
| 160 |
std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end()); |
| 161 |
|
| 162 |
int nTargets = vacancyTargets.size(); |
| 163 |
vacancyTargets.resize((int)(vF * nTargets)); |
| 164 |
|
| 165 |
|
| 166 |
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
| 167 |
"\tsites between %lf and %lf.", (int) vacancyTargets.size(), |
| 168 |
vIR, vOR); |
| 169 |
painCave.isFatal = 0; |
| 170 |
painCave.severity = OPENMD_INFO; |
| 171 |
simError(); |
| 172 |
|
| 173 |
isVacancy.clear(); |
| 174 |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 175 |
bool vac = false; |
| 176 |
for (unsigned int j = 0; j < vacancyTargets.size(); j++) { |
| 177 |
if (i == vacancyTargets[j]) vac = true; |
| 178 |
} |
| 179 |
isVacancy.push_back(vac); |
| 180 |
} |
| 181 |
|
| 182 |
} else { |
| 183 |
sprintf(painCave.errMsg, "Something is strange about the vacancy\n" |
| 184 |
"\tinner or outer radii. Check their values."); |
| 185 |
painCave.isFatal = 1; |
| 186 |
simError(); |
| 187 |
} |
| 188 |
} |
| 189 |
} |
| 190 |
|
| 191 |
/* Get number of lattice sites */ |
| 192 |
int nSites = sites.size() - vacancyTargets.size(); |
| 193 |
|
| 194 |
std::vector<Component*> components = simParams->getComponents(); |
| 195 |
std::vector<RealType> molFractions; |
| 196 |
std::vector<RealType> shellRadii; |
| 197 |
std::vector<int> nMol; |
| 198 |
std::map<int, int> componentFromSite; |
| 199 |
nComponents = components.size(); |
| 200 |
|
| 201 |
if (args_info.molFraction_given && args_info.shellRadius_given) { |
| 202 |
sprintf(painCave.errMsg, "Specify either molFraction or shellRadius " |
| 203 |
"arguments, but not both!"); |
| 204 |
painCave.isFatal = 1; |
| 205 |
simError(); |
| 206 |
} |
| 207 |
|
| 208 |
if (nComponents == 1) { |
| 209 |
molFractions.push_back(1.0); |
| 210 |
shellRadii.push_back(particleRadius); |
| 211 |
} else if (args_info.molFraction_given) { |
| 212 |
if ((int)args_info.molFraction_given == nComponents) { |
| 213 |
for (int i = 0; i < nComponents; i++) { |
| 214 |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 215 |
} |
| 216 |
} else if ((int)args_info.molFraction_given == nComponents-1) { |
| 217 |
RealType remainingFraction = 1.0; |
| 218 |
for (int i = 0; i < nComponents-1; i++) { |
| 219 |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 220 |
remainingFraction -= molFractions[i]; |
| 221 |
} |
| 222 |
molFractions.push_back(remainingFraction); |
| 223 |
} else { |
| 224 |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
| 225 |
"for all of the components in the <MetaData> block."); |
| 226 |
painCave.isFatal = 1; |
| 227 |
simError(); |
| 228 |
} |
| 229 |
} else if ((int)args_info.shellRadius_given) { |
| 230 |
if ((int)args_info.shellRadius_given == nComponents) { |
| 231 |
for (int i = 0; i < nComponents; i++) { |
| 232 |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
| 233 |
} |
| 234 |
} else if ((int)args_info.shellRadius_given == nComponents-1) { |
| 235 |
for (int i = 0; i < nComponents-1; i++) { |
| 236 |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
| 237 |
} |
| 238 |
shellRadii.push_back(particleRadius); |
| 239 |
} else { |
| 240 |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n" |
| 241 |
"\tshell radii for all of the components in the <MetaData> block."); |
| 242 |
painCave.isFatal = 1; |
| 243 |
simError(); |
| 244 |
} |
| 245 |
} else { |
| 246 |
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n" |
| 247 |
"\tbut have not specified either molFraction or shellRadius arguments."); |
| 248 |
painCave.isFatal = 1; |
| 249 |
simError(); |
| 250 |
} |
| 251 |
|
| 252 |
if (args_info.molFraction_given) { |
| 253 |
RealType totalFraction = 0.0; |
| 254 |
|
| 255 |
/* Do some simple sanity checking*/ |
| 256 |
|
| 257 |
for (int i = 0; i < nComponents; i++) { |
| 258 |
if (molFractions.at(i) < 0.0) { |
| 259 |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 260 |
" less than zero!"); |
| 261 |
painCave.isFatal = 1; |
| 262 |
simError(); |
| 263 |
} |
| 264 |
if (molFractions.at(i) > 1.0) { |
| 265 |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 266 |
" greater than one!"); |
| 267 |
painCave.isFatal = 1; |
| 268 |
simError(); |
| 269 |
} |
| 270 |
totalFraction += molFractions.at(i); |
| 271 |
} |
| 272 |
if (abs(totalFraction - 1.0) > 1e-6) { |
| 273 |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 274 |
painCave.isFatal = 1; |
| 275 |
simError(); |
| 276 |
} |
| 277 |
|
| 278 |
int remaining = nSites; |
| 279 |
for (int i=0; i < nComponents-1; i++) { |
| 280 |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 281 |
remaining -= nMol.at(i); |
| 282 |
} |
| 283 |
nMol.push_back(remaining); |
| 284 |
|
| 285 |
// recompute actual mol fractions and perform final sanity check: |
| 286 |
|
| 287 |
int totalMolecules = 0; |
| 288 |
for (int i=0; i < nComponents; i++) { |
| 289 |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 290 |
totalMolecules += nMol.at(i); |
| 291 |
} |
| 292 |
|
| 293 |
if (totalMolecules != nSites) { |
| 294 |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 295 |
"to the number of lattice sites!"); |
| 296 |
painCave.isFatal = 1; |
| 297 |
simError(); |
| 298 |
} |
| 299 |
} else { |
| 300 |
|
| 301 |
for (unsigned int i = 0; i < shellRadii.size(); i++) { |
| 302 |
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
| 303 |
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
| 304 |
painCave.isFatal = 1; |
| 305 |
simError(); |
| 306 |
} |
| 307 |
if (shellRadii.at(i) <= 0.0 ) { |
| 308 |
sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
| 309 |
painCave.isFatal = 1; |
| 310 |
simError(); |
| 311 |
} |
| 312 |
} |
| 313 |
} |
| 314 |
|
| 315 |
vector<int> ids; |
| 316 |
if ((int)args_info.molFraction_given){ |
| 317 |
sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle."); |
| 318 |
painCave.isFatal = 0; |
| 319 |
painCave.severity = OPENMD_INFO; |
| 320 |
simError(); |
| 321 |
/* Random particle is the default case*/ |
| 322 |
|
| 323 |
for (unsigned int i = 0; i < sites.size(); i++) |
| 324 |
if (!isVacancy[i]) ids.push_back(i); |
| 325 |
|
| 326 |
std::random_shuffle(ids.begin(), ids.end()); |
| 327 |
|
| 328 |
} else{ |
| 329 |
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
| 330 |
painCave.isFatal = 0; |
| 331 |
painCave.severity = OPENMD_INFO; |
| 332 |
simError(); |
| 333 |
|
| 334 |
RealType smallestSoFar; |
| 335 |
int myComponent = -1; |
| 336 |
nMol.clear(); |
| 337 |
nMol.resize(nComponents); |
| 338 |
|
| 339 |
for (unsigned int i = 0; i < sites.size(); i++) { |
| 340 |
myLoc = sites[i]; |
| 341 |
myR = myLoc.length(); |
| 342 |
smallestSoFar = particleRadius; |
| 343 |
if (!isVacancy[i]) { |
| 344 |
for (int j = 0; j < nComponents; j++) { |
| 345 |
if (myR <= shellRadii[j]) { |
| 346 |
if (shellRadii[j] <= smallestSoFar) { |
| 347 |
smallestSoFar = shellRadii[j]; |
| 348 |
myComponent = j; |
| 349 |
} |
| 350 |
} |
| 351 |
} |
| 352 |
componentFromSite[i] = myComponent; |
| 353 |
nMol[myComponent]++; |
| 354 |
} |
| 355 |
} |
| 356 |
} |
| 357 |
|
| 358 |
outputFileName = args_info.output_arg; |
| 359 |
|
| 360 |
//creat new .md file on fly which corrects the number of molecule |
| 361 |
createMdFile(inputFileName, outputFileName, nMol); |
| 362 |
|
| 363 |
delete oldInfo; |
| 364 |
|
| 365 |
SimCreator newCreator; |
| 366 |
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 367 |
|
| 368 |
// Place molecules |
| 369 |
Molecule* mol; |
| 370 |
SimInfo::MoleculeIterator mi; |
| 371 |
mol = NewInfo->beginMolecule(mi); |
| 372 |
|
| 373 |
int l = 0; |
| 374 |
|
| 375 |
for (int i = 0; i < nComponents; i++){ |
| 376 |
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 377 |
NewInfo->getForceField()); |
| 378 |
|
| 379 |
if (!args_info.molFraction_given) { |
| 380 |
for (unsigned int n = 0; n < sites.size(); n++) { |
| 381 |
if (!isVacancy[n]) { |
| 382 |
if (componentFromSite[n] == i) { |
| 383 |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 384 |
locator->placeMol(sites[n], orientations[n], mol); |
| 385 |
l++; |
| 386 |
} |
| 387 |
} |
| 388 |
} |
| 389 |
} else { |
| 390 |
for (int n = 0; n < nMol.at(i); n++) { |
| 391 |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 392 |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 393 |
l++; |
| 394 |
} |
| 395 |
} |
| 396 |
} |
| 397 |
|
| 398 |
//fill Hmat |
| 399 |
hmat(0, 0)= 10.0*particleRadius; |
| 400 |
hmat(0, 1) = 0.0; |
| 401 |
hmat(0, 2) = 0.0; |
| 402 |
|
| 403 |
hmat(1, 0) = 0.0; |
| 404 |
hmat(1, 1) = 10.0*particleRadius; |
| 405 |
hmat(1, 2) = 0.0; |
| 406 |
|
| 407 |
hmat(2, 0) = 0.0; |
| 408 |
hmat(2, 1) = 0.0; |
| 409 |
hmat(2, 2) = 10.0*particleRadius; |
| 410 |
|
| 411 |
//set Hmat |
| 412 |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 413 |
|
| 414 |
|
| 415 |
//create dumpwriter and write out the coordinates |
| 416 |
writer = new DumpWriter(NewInfo, outputFileName); |
| 417 |
|
| 418 |
if (writer == NULL) { |
| 419 |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
| 420 |
painCave.isFatal = 1; |
| 421 |
simError(); |
| 422 |
} |
| 423 |
|
| 424 |
writer->writeDump(); |
| 425 |
|
| 426 |
// deleting the writer will put the closing at the end of the dump file |
| 427 |
|
| 428 |
delete writer; |
| 429 |
|
| 430 |
// cleanup a by calling sim error..... |
| 431 |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 432 |
"generated.\n", outputFileName.c_str()); |
| 433 |
painCave.isFatal = 0; |
| 434 |
painCave.severity = OPENMD_INFO; |
| 435 |
simError(); |
| 436 |
return 0; |
| 437 |
} |
| 438 |
|
| 439 |
void createMdFile(const std::string&oldMdFileName, |
| 440 |
const std::string&newMdFileName, |
| 441 |
std::vector<int> nMol) { |
| 442 |
ifstream oldMdFile; |
| 443 |
ofstream newMdFile; |
| 444 |
const int MAXLEN = 65535; |
| 445 |
char buffer[MAXLEN]; |
| 446 |
|
| 447 |
//create new .md file based on old .md file |
| 448 |
oldMdFile.open(oldMdFileName.c_str()); |
| 449 |
newMdFile.open(newMdFileName.c_str()); |
| 450 |
oldMdFile.getline(buffer, MAXLEN); |
| 451 |
|
| 452 |
unsigned int i = 0; |
| 453 |
while (!oldMdFile.eof()) { |
| 454 |
|
| 455 |
//correct molecule number |
| 456 |
if (strstr(buffer, "nMol") != NULL) { |
| 457 |
if(i<nMol.size()){ |
| 458 |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 459 |
newMdFile << buffer << std::endl; |
| 460 |
i++; |
| 461 |
} |
| 462 |
} else |
| 463 |
newMdFile << buffer << std::endl; |
| 464 |
|
| 465 |
oldMdFile.getline(buffer, MAXLEN); |
| 466 |
} |
| 467 |
|
| 468 |
oldMdFile.close(); |
| 469 |
newMdFile.close(); |
| 470 |
|
| 471 |
if (i != nMol.size()) { |
| 472 |
sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n" |
| 473 |
"\tstatements in component blocks. Make sure that all\n" |
| 474 |
"\tcomponents in the template file have nMol=1"); |
| 475 |
painCave.isFatal = 1; |
| 476 |
simError(); |
| 477 |
} |
| 478 |
|
| 479 |
} |
| 480 |
|
