| 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 <iostream> |
| 43 |
#include <fstream> |
| 44 |
#include <string> |
| 45 |
|
| 46 |
#include "applications/dump2Xyz/Dump2XYZCmd.h" |
| 47 |
#include "brains/Register.hpp" |
| 48 |
#include "brains/SimCreator.hpp" |
| 49 |
#include "brains/SimInfo.hpp" |
| 50 |
#include "io/DumpReader.hpp" |
| 51 |
#include "utils/simError.h" |
| 52 |
#include "visitors/AtomVisitor.hpp" |
| 53 |
#include "visitors/CompositeVisitor.hpp" |
| 54 |
#include "visitors/RigidBodyVisitor.hpp" |
| 55 |
#include "visitors/OtherVisitor.hpp" |
| 56 |
#include "visitors/ZconsVisitor.hpp" |
| 57 |
#include "selection/SelectionEvaluator.hpp" |
| 58 |
using namespace oopse; |
| 59 |
|
| 60 |
int main(int argc, char* argv[]){ |
| 61 |
|
| 62 |
//register force fields |
| 63 |
registerForceFields(); |
| 64 |
|
| 65 |
gengetopt_args_info args_info; |
| 66 |
std::string dumpFileName; |
| 67 |
std::string mdFileName; |
| 68 |
std::string xyzFileName; |
| 69 |
|
| 70 |
//parse the command line option |
| 71 |
if (cmdline_parser (argc, argv, &args_info) != 0) { |
| 72 |
exit(1) ; |
| 73 |
} |
| 74 |
|
| 75 |
//get the dumpfile name and meta-data file name |
| 76 |
if (args_info.input_given){ |
| 77 |
dumpFileName = args_info.input_arg; |
| 78 |
} else { |
| 79 |
std::cerr << "Does not have input file name" << std::endl; |
| 80 |
exit(1); |
| 81 |
} |
| 82 |
|
| 83 |
mdFileName = dumpFileName; |
| 84 |
mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
| 85 |
|
| 86 |
if (args_info.output_given){ |
| 87 |
xyzFileName = args_info.output_arg; |
| 88 |
} else { |
| 89 |
xyzFileName = dumpFileName; |
| 90 |
xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz"; |
| 91 |
} |
| 92 |
|
| 93 |
//parse md file and set up the system |
| 94 |
SimCreator creator; |
| 95 |
SimInfo* info = creator.createSim(mdFileName, false); |
| 96 |
|
| 97 |
|
| 98 |
|
| 99 |
//creat visitor list |
| 100 |
CompositeVisitor* compositeVisitor = new CompositeVisitor(); |
| 101 |
|
| 102 |
//creat ignore visitor |
| 103 |
if(args_info.ignore_given ||args_info.water_flag){ |
| 104 |
|
| 105 |
IgnoreVisitor* ignoreVisitor = new IgnoreVisitor(info); |
| 106 |
|
| 107 |
for(int i = 0; i < args_info.ignore_given; i++) |
| 108 |
ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]); |
| 109 |
|
| 110 |
//ignore water |
| 111 |
if(args_info.water_flag){ |
| 112 |
ignoreVisitor->addIgnoreType("SSD"); |
| 113 |
ignoreVisitor->addIgnoreType("SSD1"); |
| 114 |
ignoreVisitor->addIgnoreType("SSD_E"); |
| 115 |
ignoreVisitor->addIgnoreType("SSD_RF"); |
| 116 |
ignoreVisitor->addIgnoreType("TIP3P_RB_0"); |
| 117 |
ignoreVisitor->addIgnoreType("TIP4P_RB_0"); |
| 118 |
ignoreVisitor->addIgnoreType("TIP5P_RB_0"); |
| 119 |
ignoreVisitor->addIgnoreType("SPCE_RB_0"); |
| 120 |
ignoreVisitor->addIgnoreType("DPD_RB_0"); |
| 121 |
} |
| 122 |
|
| 123 |
compositeVisitor->addVisitor(ignoreVisitor, 1000); |
| 124 |
} |
| 125 |
|
| 126 |
//creat RigidBody Visitor |
| 127 |
if(args_info.rigidbody_flag){ |
| 128 |
RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info); |
| 129 |
compositeVisitor->addVisitor(rbCOMVisitor, 900); |
| 130 |
} |
| 131 |
|
| 132 |
//create selection visitor |
| 133 |
//if (args_info.selection_given){ |
| 134 |
// SelectionVisitor* selectionVisitor = new SelectionVisitor(info, args_info.selection_arg); |
| 135 |
// compositeVisitor->addVisitor(selectionVisitor, 850); |
| 136 |
//} |
| 137 |
|
| 138 |
SelectionEvaluator* evaluator = NULL; |
| 139 |
if (args_info.selection_given) { |
| 140 |
evaluator = new SelectionEvaluator(info); |
| 141 |
assert(evaluator); |
| 142 |
evaluator->loadScriptString( args_info.selection_arg); |
| 143 |
|
| 144 |
} |
| 145 |
|
| 146 |
//creat SSD atom visitor |
| 147 |
SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info); |
| 148 |
compositeVisitor->addVisitor(ssdVisitor, 800); |
| 149 |
|
| 150 |
LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info); |
| 151 |
compositeVisitor->addVisitor(linearVisitor, 750); |
| 152 |
|
| 153 |
//creat default atom visitor |
| 154 |
DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info); |
| 155 |
compositeVisitor->addVisitor(defaultAtomVisitor, 700); |
| 156 |
|
| 157 |
//creat waterType visitor |
| 158 |
if(args_info.watertype_flag){ |
| 159 |
WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
| 160 |
compositeVisitor->addVisitor(waterTypeVisitor, 600); |
| 161 |
} |
| 162 |
|
| 163 |
//create ZconsVisitor |
| 164 |
if(args_info.zconstraint_flag){ |
| 165 |
|
| 166 |
ZConsVisitor* zconsVisitor = new ZConsVisitor(info); |
| 167 |
|
| 168 |
if(zconsVisitor->haveZconsMol()) { |
| 169 |
compositeVisitor->addVisitor(zconsVisitor, 500); |
| 170 |
} else { |
| 171 |
delete zconsVisitor; |
| 172 |
} |
| 173 |
} |
| 174 |
|
| 175 |
//creat wrapping visitor |
| 176 |
|
| 177 |
if(args_info.periodicBox_flag){ |
| 178 |
WrappingVisitor* wrappingVisitor = new WrappingVisitor(info); |
| 179 |
compositeVisitor->addVisitor(wrappingVisitor, 400); |
| 180 |
} |
| 181 |
|
| 182 |
//creat replicate visitor |
| 183 |
if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){ |
| 184 |
Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg); |
| 185 |
ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt); |
| 186 |
compositeVisitor->addVisitor(replicateVisitor, 300); |
| 187 |
} |
| 188 |
|
| 189 |
//creat xyzVisitor |
| 190 |
XYZVisitor* xyzVisitor = new XYZVisitor(info); |
| 191 |
compositeVisitor->addVisitor(xyzVisitor, 200); |
| 192 |
|
| 193 |
std::cout << compositeVisitor->toString(); |
| 194 |
|
| 195 |
//creat prepareVisitor |
| 196 |
PrepareVisitor* prepareVisitor = new PrepareVisitor(); |
| 197 |
|
| 198 |
//open dump file |
| 199 |
DumpReader* dumpReader = new DumpReader(info, dumpFileName); |
| 200 |
int nframes = dumpReader->getNFrames(); |
| 201 |
|
| 202 |
|
| 203 |
std::ofstream xyzStream; |
| 204 |
xyzStream .open(xyzFileName.c_str()); |
| 205 |
|
| 206 |
|
| 207 |
SimInfo::MoleculeIterator miter; |
| 208 |
Molecule::IntegrableObjectIterator iiter; |
| 209 |
Molecule::RigidBodyIterator rbIter; |
| 210 |
Molecule* mol; |
| 211 |
StuntDouble* integrableObject; |
| 212 |
RigidBody* rb; |
| 213 |
|
| 214 |
if (evaluator && !evaluator->isDynamic()) { |
| 215 |
info->getSelectionManager()->setSelectionSet(evaluator->evaluate()); |
| 216 |
} |
| 217 |
|
| 218 |
for (int i = 0; i < nframes; i += args_info.frame_arg){ |
| 219 |
dumpReader->readFrame(i); |
| 220 |
|
| 221 |
//update atoms of rigidbody |
| 222 |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 223 |
|
| 224 |
//change the positions of atoms which belong to the rigidbodies |
| 225 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 226 |
rb->updateAtoms(); |
| 227 |
} |
| 228 |
} |
| 229 |
|
| 230 |
//prepare visit |
| 231 |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 232 |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 233 |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 234 |
integrableObject->accept(prepareVisitor); |
| 235 |
} |
| 236 |
} |
| 237 |
|
| 238 |
//update visitor |
| 239 |
compositeVisitor->update(); |
| 240 |
|
| 241 |
//if dynamic, we need to re-evaluate the selection |
| 242 |
if (evaluator && evaluator->isDynamic()) { |
| 243 |
info->getSelectionManager()->setSelectionSet(evaluator->evaluate()); |
| 244 |
} |
| 245 |
|
| 246 |
//visit stuntdouble |
| 247 |
for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) { |
| 248 |
for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; |
| 249 |
integrableObject = mol->nextIntegrableObject(iiter)) { |
| 250 |
integrableObject->accept(compositeVisitor); |
| 251 |
} |
| 252 |
} |
| 253 |
|
| 254 |
xyzVisitor->writeFrame(xyzStream); |
| 255 |
xyzVisitor->clear(); |
| 256 |
|
| 257 |
}//end for (int i = 0; i < nframes; i += args_info.frame_arg) |
| 258 |
|
| 259 |
xyzStream.close(); |
| 260 |
|
| 261 |
|
| 262 |
delete compositeVisitor; |
| 263 |
delete info; |
| 264 |
|
| 265 |
} |
