| 1 |
/* |
| 2 |
* Copyright (c) 2013 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 "config.h" |
| 44 |
#include "icosahedralBuilderCmd.h" |
| 45 |
#include "utils/MoLocator.hpp" |
| 46 |
#include "utils/Tuple.hpp" |
| 47 |
#include "brains/SimInfo.hpp" |
| 48 |
#include "brains/SimCreator.hpp" |
| 49 |
#include "io/DumpWriter.hpp" |
| 50 |
#include "math/SquareMatrix3.hpp" |
| 51 |
|
| 52 |
using namespace OpenMD; |
| 53 |
using namespace std; |
| 54 |
|
| 55 |
// |
| 56 |
// Create Mackay icosaheron structure. |
| 57 |
// |
| 58 |
// Heavily modified from a code created by: Yanting Wang 07/21/2003 |
| 59 |
// |
| 60 |
|
| 61 |
vector<Vector3d> Points; |
| 62 |
vector<pair<int, int> > Edges; |
| 63 |
vector<tuple3<int, int, int> > Facets; |
| 64 |
vector<Vector3d> Basis; // Basis vectors of the edges |
| 65 |
|
| 66 |
// |
| 67 |
// function np |
| 68 |
// |
| 69 |
// Calculate number of particles on the nth layer. |
| 70 |
// |
| 71 |
|
| 72 |
int np( int n ) { |
| 73 |
if( n<0 ) return -1; |
| 74 |
else if( n==0 ) return 1; |
| 75 |
else if( n==1 ) return 12; |
| 76 |
else if( n==2 ) return 42; |
| 77 |
else { |
| 78 |
int count = 0; |
| 79 |
count += 12; // edge particles |
| 80 |
count += (n-1)*30; // side particles |
| 81 |
for( int i = 1; i <= n-2; i++ ) count += i*20; // body particles |
| 82 |
return count; |
| 83 |
} |
| 84 |
} |
| 85 |
|
| 86 |
// |
| 87 |
// function init |
| 88 |
// |
| 89 |
// Initialize some constants. |
| 90 |
// |
| 91 |
|
| 92 |
void init() { |
| 93 |
|
| 94 |
Basis.clear(); |
| 95 |
Edges.clear(); |
| 96 |
Facets.clear(); |
| 97 |
Points.clear(); |
| 98 |
|
| 99 |
// |
| 100 |
// Initialize Basis vectors. |
| 101 |
// |
| 102 |
const RealType HGR = ( sqrt(5.0) + 1.0 ) / 4.0; // half of the golden ratio |
| 103 |
|
| 104 |
Basis.push_back( Vector3d( HGR, 0.0, 0.5 )); |
| 105 |
Basis.push_back( Vector3d( HGR, 0.0, -0.5 )); |
| 106 |
Basis.push_back( Vector3d( 0.5, HGR, 0.0 )); |
| 107 |
Basis.push_back( Vector3d( -0.5, HGR, 0.0 )); |
| 108 |
Basis.push_back( Vector3d( 0.0, 0.5, HGR )); |
| 109 |
Basis.push_back( Vector3d( 0.0, -0.5, HGR )); |
| 110 |
Basis.push_back( Vector3d( 0.5, -HGR, 0.0 )); |
| 111 |
Basis.push_back( Vector3d( 0.0, 0.5, -HGR )); |
| 112 |
Basis.push_back( Vector3d( -HGR, 0.0, 0.5 )); |
| 113 |
Basis.push_back( Vector3d( 0.0, -0.5, -HGR )); |
| 114 |
Basis.push_back( Vector3d( -HGR, 0.0, -0.5 )); |
| 115 |
Basis.push_back( Vector3d( -0.5, -HGR, 0.0 )); |
| 116 |
|
| 117 |
// |
| 118 |
// Initialize 30 edges |
| 119 |
// |
| 120 |
|
| 121 |
Edges.push_back(std::make_pair(0, 1)); |
| 122 |
Edges.push_back(std::make_pair(0, 2)); |
| 123 |
Edges.push_back(std::make_pair(0, 4)); |
| 124 |
Edges.push_back(std::make_pair(0, 5)); |
| 125 |
Edges.push_back(std::make_pair(0, 6)); |
| 126 |
|
| 127 |
Edges.push_back(std::make_pair(10, 3)); |
| 128 |
Edges.push_back(std::make_pair(10, 7)); |
| 129 |
Edges.push_back(std::make_pair(10, 8)); |
| 130 |
Edges.push_back(std::make_pair(10, 9)); |
| 131 |
Edges.push_back(std::make_pair(10, 11)); |
| 132 |
|
| 133 |
Edges.push_back(std::make_pair(1, 2)); |
| 134 |
Edges.push_back(std::make_pair(1, 6)); |
| 135 |
Edges.push_back(std::make_pair(1, 7)); |
| 136 |
Edges.push_back(std::make_pair(1, 9)); |
| 137 |
|
| 138 |
Edges.push_back(std::make_pair(8, 3)); |
| 139 |
Edges.push_back(std::make_pair(8, 4)); |
| 140 |
Edges.push_back(std::make_pair(8, 5)); |
| 141 |
Edges.push_back(std::make_pair(8, 11)); |
| 142 |
|
| 143 |
Edges.push_back(std::make_pair(2, 3)); |
| 144 |
Edges.push_back(std::make_pair(2, 4)); |
| 145 |
Edges.push_back(std::make_pair(2, 7)); |
| 146 |
|
| 147 |
Edges.push_back(std::make_pair(11, 5)); |
| 148 |
Edges.push_back(std::make_pair(11, 6)); |
| 149 |
Edges.push_back(std::make_pair(11, 9)); |
| 150 |
|
| 151 |
Edges.push_back(std::make_pair(6, 5)); |
| 152 |
Edges.push_back(std::make_pair(6, 9)); |
| 153 |
|
| 154 |
Edges.push_back(std::make_pair(3, 4)); |
| 155 |
Edges.push_back(std::make_pair(3, 7)); |
| 156 |
|
| 157 |
Edges.push_back(std::make_pair(7, 9)); |
| 158 |
|
| 159 |
Edges.push_back(std::make_pair(5, 4)); |
| 160 |
|
| 161 |
// |
| 162 |
// Initialize 20 facets |
| 163 |
// |
| 164 |
|
| 165 |
Facets.push_back(make_tuple3(0, 1, 2)); |
| 166 |
Facets.push_back(make_tuple3(0, 2, 4)); |
| 167 |
Facets.push_back(make_tuple3(0, 4, 5)); |
| 168 |
Facets.push_back(make_tuple3(0, 5, 6)); |
| 169 |
Facets.push_back(make_tuple3(0, 1, 6)); |
| 170 |
|
| 171 |
Facets.push_back(make_tuple3(10, 3, 7)); |
| 172 |
Facets.push_back(make_tuple3(10, 3, 8)); |
| 173 |
Facets.push_back(make_tuple3(10, 8, 11)); |
| 174 |
Facets.push_back(make_tuple3(10, 9, 11)); |
| 175 |
Facets.push_back(make_tuple3(10, 7, 9)); |
| 176 |
|
| 177 |
Facets.push_back(make_tuple3(1, 2, 7)); |
| 178 |
Facets.push_back(make_tuple3(1, 7, 9)); |
| 179 |
Facets.push_back(make_tuple3(1, 6, 9)); |
| 180 |
|
| 181 |
Facets.push_back(make_tuple3(8, 5, 11)); |
| 182 |
Facets.push_back(make_tuple3(8, 4, 5)); |
| 183 |
Facets.push_back(make_tuple3(8, 3, 4)); |
| 184 |
|
| 185 |
Facets.push_back(make_tuple3(2, 3, 7)); |
| 186 |
Facets.push_back(make_tuple3(2, 3, 4)); |
| 187 |
|
| 188 |
Facets.push_back(make_tuple3(11, 5, 6)); |
| 189 |
Facets.push_back(make_tuple3(11, 6, 9)); |
| 190 |
} |
| 191 |
|
| 192 |
// |
| 193 |
// function ih |
| 194 |
// |
| 195 |
// Create nth layer particles. |
| 196 |
// The distance between nearest neighbors has the unit length of 1. |
| 197 |
|
| 198 |
vector<Vector3d> ih( int n ) { |
| 199 |
|
| 200 |
if( n < 0 ) return Points; |
| 201 |
|
| 202 |
if( n==0 ) { |
| 203 |
// center particle only |
| 204 |
Points.push_back(Vector3d( 0.0, 0.0, 0.0 )); |
| 205 |
return Points; |
| 206 |
} |
| 207 |
|
| 208 |
// |
| 209 |
// Generate edge particles |
| 210 |
// |
| 211 |
for( vector<Vector3d>::iterator i = Basis.begin(); i != Basis.end(); ++i ) { |
| 212 |
|
| 213 |
Points.push_back( (*i) * RealType(n) ); |
| 214 |
} |
| 215 |
|
| 216 |
// |
| 217 |
// Generate side particles |
| 218 |
// |
| 219 |
|
| 220 |
if( n<2 ) return Points; |
| 221 |
|
| 222 |
for( vector<pair<int,int> >::iterator i=Edges.begin(); |
| 223 |
i != Edges.end(); ++i ) { |
| 224 |
|
| 225 |
Vector3d e1 = Basis[ (*i).first ] * RealType(n); |
| 226 |
Vector3d e2 = Basis[ (*i).second ] * RealType(n); |
| 227 |
|
| 228 |
for( int j = 1; j <= n-1; j++ ) { |
| 229 |
Points.push_back( e1 + (e2-e1) * RealType(j) / RealType(n)); |
| 230 |
} |
| 231 |
} |
| 232 |
|
| 233 |
// |
| 234 |
// Generate body particles |
| 235 |
// |
| 236 |
|
| 237 |
if( n<3 ) return Points; |
| 238 |
|
| 239 |
for( vector<tuple3<int,int,int> >::iterator i = Facets.begin(); |
| 240 |
i != Facets.end(); ++i) { |
| 241 |
|
| 242 |
Vector3d e1 = Basis[ (*i).first ] * RealType(n); |
| 243 |
Vector3d e2 = Basis[ (*i).second ] * RealType(n); |
| 244 |
Vector3d e3 = Basis[ (*i).third ] * RealType(n); |
| 245 |
|
| 246 |
for( int j=1; j<=n-2; j++ ) { |
| 247 |
|
| 248 |
Vector3d v1 = e1 + (e2-e1) * RealType(j+1) / RealType(n); |
| 249 |
Vector3d v2 = e1 + (e3-e1) * RealType(j+1) / RealType(n); |
| 250 |
|
| 251 |
for( int k=1; k<=j; k++ ) { |
| 252 |
Points.push_back(v1 + (v2-v1) * RealType(k) / RealType(j+1)); |
| 253 |
} |
| 254 |
} |
| 255 |
} |
| 256 |
return Points; |
| 257 |
} |
| 258 |
|
| 259 |
|
| 260 |
void createMdFile(const std::string&oldMdFileName, |
| 261 |
const std::string&newMdFileName, |
| 262 |
int nMol) { |
| 263 |
ifstream oldMdFile; |
| 264 |
ofstream newMdFile; |
| 265 |
const int MAXLEN = 65535; |
| 266 |
char buffer[MAXLEN]; |
| 267 |
|
| 268 |
//create new .md file based on old .md file |
| 269 |
oldMdFile.open(oldMdFileName.c_str()); |
| 270 |
newMdFile.open(newMdFileName.c_str()); |
| 271 |
oldMdFile.getline(buffer, MAXLEN); |
| 272 |
|
| 273 |
unsigned int i = 0; |
| 274 |
while (!oldMdFile.eof()) { |
| 275 |
|
| 276 |
//correct molecule number |
| 277 |
if (strstr(buffer, "nMol") != NULL) { |
| 278 |
sprintf(buffer, "\tnMol = %i;", nMol); |
| 279 |
newMdFile << buffer << std::endl; |
| 280 |
} else { |
| 281 |
newMdFile << buffer << std::endl; |
| 282 |
} |
| 283 |
|
| 284 |
oldMdFile.getline(buffer, MAXLEN); |
| 285 |
} |
| 286 |
|
| 287 |
oldMdFile.close(); |
| 288 |
newMdFile.close(); |
| 289 |
} |
| 290 |
|
| 291 |
int main(int argc, char *argv []) { |
| 292 |
|
| 293 |
gengetopt_args_info args_info; |
| 294 |
std::string inputFileName; |
| 295 |
std::string outputFileName; |
| 296 |
|
| 297 |
MoLocator* locator; |
| 298 |
RealType latticeConstant; |
| 299 |
int nShells; |
| 300 |
|
| 301 |
DumpWriter *writer; |
| 302 |
|
| 303 |
init(); |
| 304 |
|
| 305 |
// Parse Command Line Arguments |
| 306 |
if (cmdline_parser(argc, argv, &args_info) != 0) |
| 307 |
exit(1); |
| 308 |
|
| 309 |
/* get input file name */ |
| 310 |
if (args_info.inputs_num) |
| 311 |
inputFileName = args_info.inputs[0]; |
| 312 |
else { |
| 313 |
sprintf(painCave.errMsg, "No input .md file name was specified " |
| 314 |
"on the command line"); |
| 315 |
painCave.isFatal = 1; |
| 316 |
cmdline_parser_print_help(); |
| 317 |
simError(); |
| 318 |
} |
| 319 |
|
| 320 |
if (args_info.shells_given) { |
| 321 |
nShells = args_info.shells_arg; |
| 322 |
if( nShells < 0 ) { |
| 323 |
sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n" |
| 324 |
"\tmust be greater than or equal to zero."); |
| 325 |
painCave.isFatal = 1; |
| 326 |
cmdline_parser_print_help(); |
| 327 |
simError(); |
| 328 |
} |
| 329 |
} else { |
| 330 |
sprintf(painCave.errMsg, "icosahedralBuilder: The number of shells\n" |
| 331 |
"\tis required to build a Mackay Icosahedron."); |
| 332 |
painCave.isFatal = 1; |
| 333 |
cmdline_parser_print_help(); |
| 334 |
simError(); |
| 335 |
} |
| 336 |
|
| 337 |
if (args_info.latticeConstant_given) { |
| 338 |
latticeConstant = args_info.latticeConstant_arg; |
| 339 |
} else { |
| 340 |
|
| 341 |
int count=0; |
| 342 |
for( int i = 0; i <= nShells; i++ ) count += np( i ); |
| 343 |
sprintf(painCave.errMsg, "icosahedralBuilder: No lattice constant\n" |
| 344 |
"\tgiven. Total number of atoms in a Mackay Icosahedron with\n" |
| 345 |
"\t%d shells is %d.", nShells, count); |
| 346 |
painCave.isFatal = 1; |
| 347 |
painCave.severity = OPENMD_INFO; |
| 348 |
cmdline_parser_print_help(); |
| 349 |
simError(); |
| 350 |
} |
| 351 |
|
| 352 |
/* parse md file and set up the system */ |
| 353 |
SimCreator oldCreator; |
| 354 |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 355 |
|
| 356 |
Globals* simParams = oldInfo->getSimParams(); |
| 357 |
|
| 358 |
//generate the coordinates |
| 359 |
for( int i = 0; i <= nShells; i++ ) ih( i ); |
| 360 |
|
| 361 |
outputFileName = args_info.output_arg; |
| 362 |
|
| 363 |
//creat new .md file on fly which corrects the number of molecule |
| 364 |
|
| 365 |
createMdFile(inputFileName, outputFileName, Points.size()); |
| 366 |
|
| 367 |
if (oldInfo != NULL) |
| 368 |
delete oldInfo; |
| 369 |
|
| 370 |
SimCreator newCreator; |
| 371 |
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 372 |
|
| 373 |
// Place molecules |
| 374 |
Molecule* mol; |
| 375 |
SimInfo::MoleculeIterator mi; |
| 376 |
mol = NewInfo->beginMolecule(mi); |
| 377 |
|
| 378 |
int l = 0; |
| 379 |
|
| 380 |
locator = new MoLocator(NewInfo->getMoleculeStamp(0), |
| 381 |
NewInfo->getForceField()); |
| 382 |
|
| 383 |
Vector3d boxMax; |
| 384 |
Vector3d boxMin; |
| 385 |
|
| 386 |
for (int n = 0; n < Points.size(); n++) { |
| 387 |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 388 |
Vector3d location = Points[n] * latticeConstant; |
| 389 |
Vector3d orientation = Vector3d(0, 0, 1.0); |
| 390 |
|
| 391 |
if (n == 0) { |
| 392 |
boxMax = location; |
| 393 |
boxMin = location; |
| 394 |
} else { |
| 395 |
for (int i = 0; i < 3; i++) { |
| 396 |
boxMax[i] = max(boxMax[i], location[i]); |
| 397 |
boxMin[i] = min(boxMin[i], location[i]); |
| 398 |
} |
| 399 |
} |
| 400 |
|
| 401 |
locator->placeMol(location, orientation, mol); |
| 402 |
l++; |
| 403 |
} |
| 404 |
|
| 405 |
Mat3x3d boundingBox; |
| 406 |
boundingBox(0,0) = 10.0*(boxMax[0] - boxMin[0]); |
| 407 |
boundingBox(1,1) = 10.0*(boxMax[1] - boxMin[1]); |
| 408 |
boundingBox(2,2) = 10.0*(boxMax[2] - boxMin[2]); |
| 409 |
|
| 410 |
//set Hmat |
| 411 |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat( boundingBox ); |
| 412 |
|
| 413 |
//create dumpwriter and write out the coordinates |
| 414 |
writer = new DumpWriter(NewInfo, outputFileName); |
| 415 |
|
| 416 |
if (writer == NULL) { |
| 417 |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
| 418 |
painCave.isFatal = 1; |
| 419 |
simError(); |
| 420 |
} |
| 421 |
|
| 422 |
writer->writeDump(); |
| 423 |
|
| 424 |
// deleting the writer will put the closing at the end of the dump file |
| 425 |
|
| 426 |
delete writer; |
| 427 |
|
| 428 |
// cleanup a by calling sim error..... |
| 429 |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 430 |
"generated.\n", outputFileName.c_str()); |
| 431 |
painCave.isFatal = 0; |
| 432 |
painCave.severity = OPENMD_INFO; |
| 433 |
simError(); |
| 434 |
return 0; |
| 435 |
} |
