| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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, 24107 (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> |
| 65 |
|
#include "utils/StringUtils.hpp" |
| 66 |
|
|
| 67 |
|
using namespace std; |
| 68 |
< |
using namespace oopse; |
| 68 |
> |
using namespace OpenMD; |
| 69 |
|
void createMdFile(const std::string&oldMdFileName, |
| 70 |
|
const std::string&newMdFileName, |
| 71 |
|
std::vector<int> numMol); |
| 79 |
|
gengetopt_args_info args_info; |
| 80 |
|
std::string latticeType; |
| 81 |
|
std::string inputFileName; |
| 81 |
– |
std::string outPrefix; |
| 82 |
|
std::string outputFileName; |
| 83 |
– |
std::string outInitFileName; |
| 83 |
|
|
| 85 |
– |
|
| 86 |
– |
|
| 87 |
– |
Lattice *simpleLat; |
| 84 |
|
MoLocator* locator; |
| 89 |
– |
int* numMol; |
| 85 |
|
int nComponents; |
| 86 |
|
double latticeConstant; |
| 87 |
|
std::vector<double> lc; |
| 93 |
– |
double mass; |
| 88 |
|
|
| 89 |
< |
const double rhoConvertConst = 1.661; |
| 96 |
< |
double density; |
| 97 |
< |
double particleRadius; |
| 98 |
< |
|
| 99 |
< |
|
| 89 |
> |
RealType particleRadius; |
| 90 |
|
|
| 91 |
|
Mat3x3d hmat; |
| 92 |
|
std::vector<Vector3d> latticePos; |
| 93 |
|
std::vector<Vector3d> latticeOrt; |
| 104 |
– |
int numMolPerCell; |
| 105 |
– |
int nShells; /* Number of shells in nanoparticle*/ |
| 94 |
|
|
| 107 |
– |
|
| 95 |
|
DumpWriter *writer; |
| 96 |
|
|
| 97 |
|
// Parse Command Line Arguments |
| 98 |
|
if (cmdline_parser(argc, argv, &args_info) != 0) |
| 99 |
|
exit(1); |
| 100 |
< |
|
| 114 |
< |
|
| 115 |
< |
|
| 100 |
> |
|
| 101 |
|
/* get lattice type */ |
| 102 |
|
latticeType = "FCC"; |
| 103 |
|
|
| 105 |
|
if (args_info.inputs_num) |
| 106 |
|
inputFileName = args_info.inputs[0]; |
| 107 |
|
else { |
| 108 |
< |
sprintf(painCave.errMsg, "No input .md file name was specified" |
| 109 |
< |
"on the command line"); |
| 108 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified " |
| 109 |
> |
"on the command line"); |
| 110 |
|
painCave.isFatal = 1; |
| 111 |
|
cmdline_parser_print_help(); |
| 112 |
|
simError(); |
| 116 |
|
SimCreator oldCreator; |
| 117 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 118 |
|
|
| 119 |
< |
|
| 135 |
< |
latticeConstant = args_info.latticeCnst_arg; |
| 119 |
> |
latticeConstant = args_info.latticeConstant_arg; |
| 120 |
|
particleRadius = args_info.radius_arg; |
| 121 |
|
Globals* simParams = oldInfo->getSimParams(); |
| 122 |
|
|
| 139 |
– |
|
| 140 |
– |
/* create Molocators */ |
| 141 |
– |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 142 |
– |
|
| 123 |
|
/* Create nanoparticle */ |
| 124 |
< |
shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
| 124 |
> |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
| 125 |
> |
particleRadius); |
| 126 |
|
|
| 127 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
| 128 |
< |
vector<Vector3d> sites = nanoParticle.getPoints(); |
| 129 |
< |
vector<Vector3d> orientations = nanoParticle.getPointsOrt(); |
| 128 |
> |
vector<Vector3d> sites = nanoParticle.getSites(); |
| 129 |
> |
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
| 130 |
|
|
| 150 |
– |
std::cout <<"nSites: " << sites.size() << std::endl; |
| 131 |
|
|
| 132 |
< |
/* Get number of lattice sites */ |
| 133 |
< |
int nSites = sites.size(); |
| 132 |
> |
std::vector<int> vacancyTargets; |
| 133 |
> |
vector<bool> isVacancy; |
| 134 |
> |
|
| 135 |
> |
Vector3d myLoc; |
| 136 |
> |
RealType myR; |
| 137 |
|
|
| 138 |
+ |
for (int i = 0; i < sites.size(); i++) |
| 139 |
+ |
isVacancy.push_back(false); |
| 140 |
|
|
| 141 |
+ |
if (args_info.vacancyPercent_given) { |
| 142 |
+ |
if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) { |
| 143 |
+ |
sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value."); |
| 144 |
+ |
painCave.isFatal = 1; |
| 145 |
+ |
simError(); |
| 146 |
+ |
} else { |
| 147 |
+ |
RealType vF = args_info.vacancyPercent_arg / 100.0; |
| 148 |
+ |
RealType vIR; |
| 149 |
+ |
RealType vOR; |
| 150 |
+ |
if (args_info.vacancyInnerRadius_given) { |
| 151 |
+ |
vIR = args_info.vacancyInnerRadius_arg; |
| 152 |
+ |
} else { |
| 153 |
+ |
vIR = 0.0; |
| 154 |
+ |
} |
| 155 |
+ |
if (args_info.vacancyOuterRadius_given) { |
| 156 |
+ |
vOR = args_info.vacancyOuterRadius_arg; |
| 157 |
+ |
} else { |
| 158 |
+ |
vOR = particleRadius; |
| 159 |
+ |
} |
| 160 |
+ |
if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) { |
| 161 |
+ |
|
| 162 |
+ |
for (int i = 0; i < sites.size(); i++) { |
| 163 |
+ |
myLoc = sites[i]; |
| 164 |
+ |
myR = myLoc.length(); |
| 165 |
+ |
if (myR >= vIR && myR <= vOR) { |
| 166 |
+ |
vacancyTargets.push_back(i); |
| 167 |
+ |
} |
| 168 |
+ |
} |
| 169 |
+ |
std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end()); |
| 170 |
+ |
|
| 171 |
+ |
int nTargets = vacancyTargets.size(); |
| 172 |
+ |
vacancyTargets.resize((int)(vF * nTargets)); |
| 173 |
+ |
|
| 174 |
+ |
|
| 175 |
+ |
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
| 176 |
+ |
"\tsites between %lf and %lf.", (int) vacancyTargets.size(), |
| 177 |
+ |
vIR, vOR); |
| 178 |
+ |
painCave.isFatal = 0; |
| 179 |
+ |
simError(); |
| 180 |
|
|
| 181 |
+ |
isVacancy.clear(); |
| 182 |
+ |
for (int i = 0; i < sites.size(); i++) { |
| 183 |
+ |
bool vac = false; |
| 184 |
+ |
for (int j = 0; j < vacancyTargets.size(); j++) { |
| 185 |
+ |
if (i == vacancyTargets[j]) vac = true; |
| 186 |
+ |
} |
| 187 |
+ |
isVacancy.push_back(vac); |
| 188 |
+ |
} |
| 189 |
+ |
|
| 190 |
+ |
} else { |
| 191 |
+ |
sprintf(painCave.errMsg, "Something is strange about the vacancy\n" |
| 192 |
+ |
"\tinner or outer radii. Check their values."); |
| 193 |
+ |
painCave.isFatal = 1; |
| 194 |
+ |
simError(); |
| 195 |
+ |
} |
| 196 |
+ |
} |
| 197 |
+ |
} |
| 198 |
|
|
| 199 |
+ |
/* Get number of lattice sites */ |
| 200 |
+ |
int nSites = sites.size() - vacancyTargets.size(); |
| 201 |
+ |
|
| 202 |
|
std::vector<Component*> components = simParams->getComponents(); |
| 203 |
|
std::vector<RealType> molFractions; |
| 204 |
+ |
std::vector<RealType> shellRadii; |
| 205 |
|
std::vector<RealType> molecularMasses; |
| 206 |
|
std::vector<int> nMol; |
| 207 |
+ |
std::map<int, int> componentFromSite; |
| 208 |
|
nComponents = components.size(); |
| 163 |
– |
|
| 209 |
|
|
| 210 |
< |
|
| 211 |
< |
if (nComponents == 1) { |
| 210 |
> |
if (args_info.molFraction_given && args_info.shellRadius_given) { |
| 211 |
> |
sprintf(painCave.errMsg, "Specify either molFraction or shellRadius " |
| 212 |
> |
"arguments, but not both!"); |
| 213 |
> |
painCave.isFatal = 1; |
| 214 |
> |
simError(); |
| 215 |
> |
} |
| 216 |
> |
|
| 217 |
> |
if (nComponents == 1) { |
| 218 |
|
molFractions.push_back(1.0); |
| 219 |
< |
} else { |
| 220 |
< |
if (args_info.molFraction_given == nComponents) { |
| 219 |
> |
shellRadii.push_back(particleRadius); |
| 220 |
> |
} else if (args_info.molFraction_given) { |
| 221 |
> |
if ((int)args_info.molFraction_given == nComponents) { |
| 222 |
|
for (int i = 0; i < nComponents; i++) { |
| 223 |
|
molFractions.push_back(args_info.molFraction_arg[i]); |
| 224 |
|
} |
| 225 |
< |
} else if (args_info.molFraction_given == nComponents-1) { |
| 225 |
> |
} else if ((int)args_info.molFraction_given == nComponents-1) { |
| 226 |
|
RealType remainingFraction = 1.0; |
| 227 |
|
for (int i = 0; i < nComponents-1; i++) { |
| 228 |
|
molFractions.push_back(args_info.molFraction_arg[i]); |
| 235 |
|
painCave.isFatal = 1; |
| 236 |
|
simError(); |
| 237 |
|
} |
| 238 |
< |
} |
| 239 |
< |
|
| 240 |
< |
RealType totalFraction = 0.0; |
| 241 |
< |
|
| 242 |
< |
/* Do some simple sanity checking*/ |
| 243 |
< |
|
| 244 |
< |
|
| 245 |
< |
|
| 246 |
< |
for (int i = 0; i < nComponents; i++) { |
| 247 |
< |
if (molFractions.at(i) < 0.0) { |
| 248 |
< |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 249 |
< |
" less than zero!"); |
| 238 |
> |
} else if ((int)args_info.shellRadius_given) { |
| 239 |
> |
if ((int)args_info.shellRadius_given == nComponents) { |
| 240 |
> |
for (int i = 0; i < nComponents; i++) { |
| 241 |
> |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
| 242 |
> |
} |
| 243 |
> |
} else if ((int)args_info.shellRadius_given == nComponents-1) { |
| 244 |
> |
for (int i = 0; i < nComponents-1; i++) { |
| 245 |
> |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
| 246 |
> |
} |
| 247 |
> |
shellRadii.push_back(particleRadius); |
| 248 |
> |
} else { |
| 249 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n" |
| 250 |
> |
"\tshell radii for all of the components in the <MetaData> block."); |
| 251 |
|
painCave.isFatal = 1; |
| 252 |
|
simError(); |
| 253 |
|
} |
| 254 |
< |
if (molFractions.at(i) > 1.0) { |
| 255 |
< |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 256 |
< |
" greater than one!"); |
| 204 |
< |
painCave.isFatal = 1; |
| 205 |
< |
simError(); |
| 206 |
< |
} |
| 207 |
< |
totalFraction += molFractions.at(i); |
| 208 |
< |
} |
| 209 |
< |
if (abs(totalFraction - 1.0) > 1e-6) { |
| 210 |
< |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 254 |
> |
} else { |
| 255 |
> |
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n" |
| 256 |
> |
"\tbut have not specified either molFraction or shellRadius arguments."); |
| 257 |
|
painCave.isFatal = 1; |
| 258 |
|
simError(); |
| 259 |
|
} |
| 260 |
< |
|
| 261 |
< |
int remaining = nSites; |
| 262 |
< |
for (int i=0; i < nComponents-1; i++) { |
| 263 |
< |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 264 |
< |
remaining -= nMol.at(i); |
| 265 |
< |
} |
| 266 |
< |
nMol.push_back(remaining); |
| 260 |
> |
|
| 261 |
> |
if (args_info.molFraction_given) { |
| 262 |
> |
RealType totalFraction = 0.0; |
| 263 |
> |
|
| 264 |
> |
/* Do some simple sanity checking*/ |
| 265 |
> |
|
| 266 |
> |
for (int i = 0; i < nComponents; i++) { |
| 267 |
> |
if (molFractions.at(i) < 0.0) { |
| 268 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 269 |
> |
" less than zero!"); |
| 270 |
> |
painCave.isFatal = 1; |
| 271 |
> |
simError(); |
| 272 |
> |
} |
| 273 |
> |
if (molFractions.at(i) > 1.0) { |
| 274 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 275 |
> |
" greater than one!"); |
| 276 |
> |
painCave.isFatal = 1; |
| 277 |
> |
simError(); |
| 278 |
> |
} |
| 279 |
> |
totalFraction += molFractions.at(i); |
| 280 |
> |
} |
| 281 |
> |
if (abs(totalFraction - 1.0) > 1e-6) { |
| 282 |
> |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 283 |
> |
painCave.isFatal = 1; |
| 284 |
> |
simError(); |
| 285 |
> |
} |
| 286 |
> |
|
| 287 |
> |
int remaining = nSites; |
| 288 |
> |
for (int i=0; i < nComponents-1; i++) { |
| 289 |
> |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 290 |
> |
remaining -= nMol.at(i); |
| 291 |
> |
} |
| 292 |
> |
nMol.push_back(remaining); |
| 293 |
> |
|
| 294 |
> |
// recompute actual mol fractions and perform final sanity check: |
| 295 |
> |
|
| 296 |
> |
int totalMolecules = 0; |
| 297 |
> |
for (int i=0; i < nComponents; i++) { |
| 298 |
> |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 299 |
> |
totalMolecules += nMol.at(i); |
| 300 |
> |
} |
| 301 |
> |
|
| 302 |
> |
if (totalMolecules != nSites) { |
| 303 |
> |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 304 |
> |
"to the number of lattice sites!"); |
| 305 |
> |
painCave.isFatal = 1; |
| 306 |
> |
simError(); |
| 307 |
> |
} |
| 308 |
> |
} else { |
| 309 |
|
|
| 310 |
< |
|
| 311 |
< |
|
| 312 |
< |
// recompute actual mol fractions and perform final sanity check: |
| 313 |
< |
|
| 314 |
< |
int totalMolecules = 0; |
| 315 |
< |
RealType totalMass = 0.0; |
| 316 |
< |
for (int i=0; i < nComponents; i++) { |
| 317 |
< |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 318 |
< |
totalMolecules += nMol.at(i); |
| 319 |
< |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
| 320 |
< |
oldInfo->getForceField())); |
| 321 |
< |
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
| 310 |
> |
for (int i = 0; i < shellRadii.size(); i++) { |
| 311 |
> |
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
| 312 |
> |
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
| 313 |
> |
painCave.isFatal = 1; |
| 314 |
> |
simError(); |
| 315 |
> |
} |
| 316 |
> |
if (shellRadii.at(i) <= 0.0 ) { |
| 317 |
> |
sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
| 318 |
> |
painCave.isFatal = 1; |
| 319 |
> |
simError(); |
| 320 |
> |
} |
| 321 |
> |
} |
| 322 |
|
} |
| 235 |
– |
RealType avgMass = totalMass / (RealType) totalMolecules; |
| 323 |
|
|
| 324 |
< |
if (totalMolecules != nSites) { |
| 325 |
< |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 326 |
< |
"to the number of lattice sites!"); |
| 327 |
< |
painCave.isFatal = 1; |
| 324 |
> |
vector<int> ids; |
| 325 |
> |
if ((int)args_info.molFraction_given){ |
| 326 |
> |
sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle."); |
| 327 |
> |
painCave.isFatal = 0; |
| 328 |
|
simError(); |
| 329 |
< |
} |
| 243 |
< |
|
| 329 |
> |
/* Random particle is the default case*/ |
| 330 |
|
|
| 331 |
< |
|
| 332 |
< |
|
| 333 |
< |
vector<int> ids; |
| 248 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 249 |
< |
/* Random particle is the default case*/ |
| 250 |
< |
if (!args_info.ShellRadius_given){ |
| 251 |
< |
/* do the iPod thing, Shuffle da vector */ |
| 331 |
> |
for (int i = 0; i < sites.size(); i++) |
| 332 |
> |
if (!isVacancy[i]) ids.push_back(i); |
| 333 |
> |
|
| 334 |
|
std::random_shuffle(ids.begin(), ids.end()); |
| 253 |
– |
} else{ /*Handle core-shell with multiple components.*/ |
| 254 |
– |
std::cout << "Creating a core-shell nanoparticle." << std::endl; |
| 255 |
– |
if (nComponents != args_info.ShellRadius_given + 1){ |
| 256 |
– |
sprintf(painCave.errMsg, "Number of .md components " |
| 257 |
– |
"does not match the number of shell radius specifications"); |
| 258 |
– |
painCave.isFatal = 1; |
| 259 |
– |
simError(); |
| 260 |
– |
} |
| 335 |
|
|
| 336 |
< |
} |
| 336 |
> |
} else{ |
| 337 |
> |
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
| 338 |
> |
painCave.isFatal = 0; |
| 339 |
> |
simError(); |
| 340 |
|
|
| 341 |
+ |
RealType smallestSoFar; |
| 342 |
+ |
int myComponent = -1; |
| 343 |
+ |
nMol.clear(); |
| 344 |
+ |
nMol.resize(nComponents); |
| 345 |
+ |
|
| 346 |
+ |
for (int i = 0; i < sites.size(); i++) { |
| 347 |
+ |
myLoc = sites[i]; |
| 348 |
+ |
myR = myLoc.length(); |
| 349 |
+ |
smallestSoFar = particleRadius; |
| 350 |
+ |
if (!isVacancy[i]) { |
| 351 |
+ |
for (int j = 0; j < nComponents; j++) { |
| 352 |
+ |
if (myR <= shellRadii[j]) { |
| 353 |
+ |
if (shellRadii[j] <= smallestSoFar) { |
| 354 |
+ |
smallestSoFar = shellRadii[j]; |
| 355 |
+ |
myComponent = j; |
| 356 |
+ |
} |
| 357 |
+ |
} |
| 358 |
+ |
} |
| 359 |
+ |
componentFromSite[i] = myComponent; |
| 360 |
+ |
nMol[myComponent]++; |
| 361 |
+ |
} |
| 362 |
+ |
} |
| 363 |
+ |
} |
| 364 |
|
|
| 265 |
– |
|
| 266 |
– |
|
| 365 |
|
outputFileName = args_info.output_arg; |
| 366 |
< |
|
| 367 |
< |
|
| 270 |
< |
//creat new .md file on fly which corrects the number of molecule |
| 366 |
> |
|
| 367 |
> |
//creat new .md file on fly which corrects the number of molecule |
| 368 |
|
createMdFile(inputFileName, outputFileName, nMol); |
| 369 |
|
|
| 370 |
|
if (oldInfo != NULL) |
| 371 |
|
delete oldInfo; |
| 372 |
|
|
| 276 |
– |
|
| 277 |
– |
// We need to read in new siminfo object. |
| 278 |
– |
//parse md file and set up the system |
| 279 |
– |
//SimCreator NewCreator; |
| 373 |
|
SimCreator newCreator; |
| 374 |
|
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 375 |
< |
|
| 283 |
< |
|
| 375 |
> |
|
| 376 |
|
// Place molecules |
| 377 |
|
Molecule* mol; |
| 378 |
|
SimInfo::MoleculeIterator mi; |
| 379 |
|
mol = NewInfo->beginMolecule(mi); |
| 380 |
+ |
|
| 381 |
|
int l = 0; |
| 382 |
+ |
int whichSite = 0; |
| 383 |
|
|
| 384 |
|
for (int i = 0; i < nComponents; i++){ |
| 385 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 386 |
|
NewInfo->getForceField()); |
| 387 |
< |
for (int n = 0; n < nMol.at(i); n++) { |
| 388 |
< |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 389 |
< |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 390 |
< |
l++; |
| 387 |
> |
|
| 388 |
> |
if (!args_info.molFraction_given) { |
| 389 |
> |
for (int n = 0; n < sites.size(); n++) { |
| 390 |
> |
if (!isVacancy[n]) { |
| 391 |
> |
if (componentFromSite[n] == i) { |
| 392 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 393 |
> |
locator->placeMol(sites[n], orientations[n], mol); |
| 394 |
> |
l++; |
| 395 |
> |
} |
| 396 |
> |
} |
| 397 |
> |
} |
| 398 |
> |
} else { |
| 399 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
| 400 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 401 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 402 |
> |
l++; |
| 403 |
> |
} |
| 404 |
|
} |
| 405 |
|
} |
| 406 |
|
|
| 300 |
– |
|
| 301 |
– |
|
| 407 |
|
//fill Hmat |
| 408 |
< |
hmat(0, 0)= 2.0*particleRadius; |
| 408 |
> |
hmat(0, 0)= 10.0*particleRadius; |
| 409 |
|
hmat(0, 1) = 0.0; |
| 410 |
|
hmat(0, 2) = 0.0; |
| 411 |
|
|
| 412 |
|
hmat(1, 0) = 0.0; |
| 413 |
< |
hmat(1, 1) = 2.0*particleRadius; |
| 413 |
> |
hmat(1, 1) = 10.0*particleRadius; |
| 414 |
|
hmat(1, 2) = 0.0; |
| 415 |
|
|
| 416 |
|
hmat(2, 0) = 0.0; |
| 417 |
|
hmat(2, 1) = 0.0; |
| 418 |
< |
hmat(2, 2) = 2.0*particleRadius; |
| 418 |
> |
hmat(2, 2) = 10.0*particleRadius; |
| 419 |
|
|
| 420 |
|
//set Hmat |
| 421 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 422 |
|
|
| 423 |
|
|
| 424 |
|
//create dumpwriter and write out the coordinates |
| 425 |
< |
writer = new DumpWriter(NewInfo,outputFileName); |
| 425 |
> |
writer = new DumpWriter(NewInfo, outputFileName); |
| 426 |
|
|
| 427 |
|
if (writer == NULL) { |
| 428 |
< |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
| 429 |
< |
painCave.isFatal = 1; |
| 430 |
< |
simError(); |
| 428 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
| 429 |
> |
painCave.isFatal = 1; |
| 430 |
> |
simError(); |
| 431 |
|
} |
| 432 |
|
|
| 433 |
|
writer->writeDump(); |
| 329 |
– |
std::cout << "new initial configuration file: " << outInitFileName |
| 330 |
– |
<< " is generated." << std::endl; |
| 331 |
– |
|
| 434 |
|
|
| 435 |
|
// deleting the writer will put the closing at the end of the dump file |
| 436 |
+ |
|
| 437 |
|
delete writer; |
| 438 |
|
|
| 439 |
|
// cleanup a by calling sim error..... |
| 440 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 440 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 441 |
|
"generated.\n", outputFileName.c_str()); |
| 442 |
|
painCave.isFatal = 0; |
| 443 |
|
simError(); |
| 444 |
|
return 0; |
| 445 |
|
} |
| 446 |
|
|
| 447 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 447 |
> |
void createMdFile(const std::string&oldMdFileName, |
| 448 |
> |
const std::string&newMdFileName, |
| 449 |
|
std::vector<int> nMol) { |
| 450 |
|
ifstream oldMdFile; |
| 451 |
|
ofstream newMdFile; |
| 455 |
|
//create new .md file based on old .md file |
| 456 |
|
oldMdFile.open(oldMdFileName.c_str()); |
| 457 |
|
newMdFile.open(newMdFileName.c_str()); |
| 354 |
– |
|
| 458 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 459 |
< |
|
| 459 |
> |
|
| 460 |
|
int i = 0; |
| 461 |
|
while (!oldMdFile.eof()) { |
| 462 |
< |
|
| 462 |
> |
|
| 463 |
|
//correct molecule number |
| 464 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 465 |
|
if(i<nMol.size()){ |
| 466 |
< |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 466 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 467 |
|
newMdFile << buffer << std::endl; |
| 468 |
|
i++; |
| 469 |
|
} |
| 475 |
|
|
| 476 |
|
oldMdFile.close(); |
| 477 |
|
newMdFile.close(); |
| 478 |
+ |
|
| 479 |
+ |
if (i != nMol.size()) { |
| 480 |
+ |
sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n" |
| 481 |
+ |
"\tstatements in component blocks. Make sure that all\n" |
| 482 |
+ |
"\tcomponents in the template file have nMol=1"); |
| 483 |
+ |
painCave.isFatal = 1; |
| 484 |
+ |
simError(); |
| 485 |
+ |
} |
| 486 |
+ |
|
| 487 |
|
} |
| 488 |
|
|
