| 47 |
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#include <string> |
| 48 |
|
#include <map> |
| 49 |
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#include <fstream> |
| 50 |
+ |
#include <algorithm> |
| 51 |
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|
| 52 |
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#include "config.h" |
| 53 |
< |
|
| 53 |
> |
#include "shapedLatticeSpherical.hpp" |
| 54 |
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#include "nanoparticleBuilderCmd.h" |
| 54 |
– |
#include "sphericalNanoparticle.hpp" |
| 55 |
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#include "lattice/LatticeFactory.hpp" |
| 56 |
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#include "utils/MoLocator.hpp" |
| 57 |
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#include "lattice/Lattice.hpp" |
| 67 |
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using namespace oopse; |
| 68 |
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void createMdFile(const std::string&oldMdFileName, |
| 69 |
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const std::string&newMdFileName, |
| 70 |
< |
int numMol); |
| 70 |
> |
std::vector<int> numMol); |
| 71 |
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|
| 72 |
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int main(int argc, char *argv []) { |
| 73 |
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|
| 78 |
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gengetopt_args_info args_info; |
| 79 |
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std::string latticeType; |
| 80 |
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std::string inputFileName; |
| 81 |
< |
std::string outPrefix; |
| 82 |
< |
std::string outMdFileName; |
| 83 |
< |
std::string outInitFileName; |
| 81 |
> |
std::string outputFileName; |
| 82 |
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|
| 85 |
– |
|
| 86 |
– |
|
| 83 |
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Lattice *simpleLat; |
| 84 |
< |
int numMol; |
| 84 |
> |
MoLocator* locator; |
| 85 |
> |
int* numMol; |
| 86 |
> |
int nComponents; |
| 87 |
|
double latticeConstant; |
| 88 |
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std::vector<double> lc; |
| 89 |
< |
double mass; |
| 89 |
> |
double mass; |
| 90 |
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const double rhoConvertConst = 1.661; |
| 91 |
|
double density; |
| 92 |
< |
|
| 95 |
< |
|
| 92 |
> |
double particleRadius; |
| 93 |
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|
| 94 |
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Mat3x3d hmat; |
| 98 |
– |
MoLocator *locator; |
| 99 |
– |
sphericalNanoparticle *nanoparticle; |
| 95 |
|
std::vector<Vector3d> latticePos; |
| 96 |
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std::vector<Vector3d> latticeOrt; |
| 97 |
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int numMolPerCell; |
| 98 |
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int nShells; /* Number of shells in nanoparticle*/ |
| 99 |
< |
int numSites; |
| 105 |
< |
|
| 99 |
> |
|
| 100 |
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DumpWriter *writer; |
| 101 |
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|
| 102 |
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// Parse Command Line Arguments |
| 103 |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
| 104 |
|
exit(1); |
| 105 |
< |
|
| 112 |
< |
|
| 113 |
< |
|
| 105 |
> |
|
| 106 |
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/* get lattice type */ |
| 107 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
| 108 |
< |
|
| 107 |
> |
latticeType = "FCC"; |
| 108 |
> |
|
| 109 |
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/* get input file name */ |
| 110 |
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if (args_info.inputs_num) |
| 111 |
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inputFileName = args_info.inputs[0]; |
| 112 |
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else { |
| 113 |
< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
| 113 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified" |
| 114 |
> |
"on the command line"); |
| 115 |
> |
painCave.isFatal = 1; |
| 116 |
|
cmdline_parser_print_help(); |
| 117 |
< |
exit(1); |
| 117 |
> |
simError(); |
| 118 |
|
} |
| 119 |
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|
| 120 |
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/* parse md file and set up the system */ |
| 121 |
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SimCreator oldCreator; |
| 122 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 123 |
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|
| 130 |
– |
nShells = 0; |
| 131 |
– |
if (args_info.coreShellRadius_given){ |
| 132 |
– |
nShells = args_info.coreShellRadius_given; |
| 133 |
– |
} |
| 134 |
– |
|
| 135 |
– |
nComponents = oldInfo->getNMoleculeStamp(); |
| 136 |
– |
|
| 137 |
– |
/* Check to see if we have enough components to build that many shells. */ |
| 138 |
– |
if (nShells){ |
| 139 |
– |
if (oldInfo->getNMoleculeStamp() != nShells) { |
| 140 |
– |
std::cerr << "Not enough components present in MD file to build specified number of shells" |
| 141 |
– |
<< std::endl; |
| 142 |
– |
exit(1); |
| 143 |
– |
} |
| 144 |
– |
} |
| 145 |
– |
|
| 146 |
– |
|
| 147 |
– |
//creat lattice |
| 148 |
– |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 149 |
– |
|
| 150 |
– |
if (simpleLat == NULL) { |
| 151 |
– |
std::cerr << "Error in creating lattice" << std::endl; |
| 152 |
– |
exit(1); |
| 153 |
– |
} |
| 154 |
– |
|
| 155 |
– |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 156 |
– |
|
| 157 |
– |
/*calculate lattice constant (in Angstrom) |
| 158 |
– |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 159 |
– |
1.0 / 3.0);*/ |
| 160 |
– |
|
| 124 |
|
latticeConstant = args_info.latticeCnst_arg; |
| 125 |
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particleRadius = args_info.radius_arg; |
| 126 |
< |
particleDiameter = 2.0 * particleRadius; |
| 126 |
> |
Globals* simParams = oldInfo->getSimParams(); |
| 127 |
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|
| 128 |
< |
/* set lattice constant */ |
| 129 |
< |
lc.push_back(latticeConstant); |
| 130 |
< |
simpleLat->setLatticeConstant(lc); |
| 128 |
> |
/* Create nanoparticle */ |
| 129 |
> |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
| 130 |
> |
particleRadius); |
| 131 |
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|
| 132 |
< |
|
| 133 |
< |
/*determine the output file names*/ |
| 134 |
< |
if (args_info.output_given){ |
| 135 |
< |
outInitFileName = args_info.output_arg; |
| 136 |
< |
}else{ |
| 137 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 132 |
> |
/* Build a lattice and get lattice points for this lattice constant */ |
| 133 |
> |
vector<Vector3d> sites = nanoParticle.getSites(); |
| 134 |
> |
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
| 135 |
> |
|
| 136 |
> |
std::cout <<"nSites: " << sites.size() << std::endl; |
| 137 |
> |
|
| 138 |
> |
/* Get number of lattice sites */ |
| 139 |
> |
int nSites = sites.size(); |
| 140 |
> |
|
| 141 |
> |
std::vector<Component*> components = simParams->getComponents(); |
| 142 |
> |
std::vector<RealType> molFractions; |
| 143 |
> |
std::vector<RealType> molecularMasses; |
| 144 |
> |
std::vector<int> nMol; |
| 145 |
> |
nComponents = components.size(); |
| 146 |
> |
|
| 147 |
> |
if (nComponents == 1) { |
| 148 |
> |
molFractions.push_back(1.0); |
| 149 |
> |
} else { |
| 150 |
> |
if (args_info.molFraction_given == nComponents) { |
| 151 |
> |
for (int i = 0; i < nComponents; i++) { |
| 152 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 153 |
> |
} |
| 154 |
> |
} else if (args_info.molFraction_given == nComponents-1) { |
| 155 |
> |
RealType remainingFraction = 1.0; |
| 156 |
> |
for (int i = 0; i < nComponents-1; i++) { |
| 157 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 158 |
> |
remainingFraction -= molFractions[i]; |
| 159 |
> |
} |
| 160 |
> |
molFractions.push_back(remainingFraction); |
| 161 |
> |
} else { |
| 162 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
| 163 |
> |
"for all of the components in the <MetaData> block."); |
| 164 |
> |
painCave.isFatal = 1; |
| 165 |
> |
simError(); |
| 166 |
> |
} |
| 167 |
> |
} |
| 168 |
> |
|
| 169 |
> |
RealType totalFraction = 0.0; |
| 170 |
> |
|
| 171 |
> |
/* Do some simple sanity checking*/ |
| 172 |
> |
|
| 173 |
> |
for (int i = 0; i < nComponents; i++) { |
| 174 |
> |
if (molFractions.at(i) < 0.0) { |
| 175 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 176 |
> |
" less than zero!"); |
| 177 |
> |
painCave.isFatal = 1; |
| 178 |
> |
simError(); |
| 179 |
> |
} |
| 180 |
> |
if (molFractions.at(i) > 1.0) { |
| 181 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 182 |
> |
" greater than one!"); |
| 183 |
> |
painCave.isFatal = 1; |
| 184 |
> |
simError(); |
| 185 |
> |
} |
| 186 |
> |
totalFraction += molFractions.at(i); |
| 187 |
|
} |
| 188 |
< |
|
| 189 |
< |
|
| 190 |
< |
|
| 191 |
< |
|
| 192 |
< |
|
| 181 |
< |
/* create Molocators */ |
| 182 |
< |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 183 |
< |
|
| 184 |
< |
/* create a new spherical nanoparticle */ |
| 185 |
< |
nanoparticle = new sphericalNanoparticle(particleRadius,latticeConstant); |
| 186 |
< |
/* Build a nanoparticle to see how many sites are there */ |
| 187 |
< |
numSites = new int[nComponents] |
| 188 |
< |
int numSites = nanoparticle.getNMol(simpleLat); |
| 189 |
< |
|
| 188 |
> |
if (abs(totalFraction - 1.0) > 1e-6) { |
| 189 |
> |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 190 |
> |
painCave.isFatal = 1; |
| 191 |
> |
simError(); |
| 192 |
> |
} |
| 193 |
|
|
| 194 |
+ |
int remaining = nSites; |
| 195 |
+ |
for (int i=0; i < nComponents-1; i++) { |
| 196 |
+ |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 197 |
+ |
remaining -= nMol.at(i); |
| 198 |
+ |
} |
| 199 |
+ |
nMol.push_back(remaining); |
| 200 |
+ |
|
| 201 |
+ |
|
| 202 |
+ |
|
| 203 |
+ |
// recompute actual mol fractions and perform final sanity check: |
| 204 |
+ |
|
| 205 |
+ |
int totalMolecules = 0; |
| 206 |
+ |
RealType totalMass = 0.0; |
| 207 |
+ |
for (int i=0; i < nComponents; i++) { |
| 208 |
+ |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 209 |
+ |
totalMolecules += nMol.at(i); |
| 210 |
+ |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
| 211 |
+ |
oldInfo->getForceField())); |
| 212 |
+ |
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
| 213 |
+ |
} |
| 214 |
+ |
RealType avgMass = totalMass / (RealType) totalMolecules; |
| 215 |
+ |
|
| 216 |
+ |
if (totalMolecules != nSites) { |
| 217 |
+ |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 218 |
+ |
"to the number of lattice sites!"); |
| 219 |
+ |
painCave.isFatal = 1; |
| 220 |
+ |
simError(); |
| 221 |
+ |
} |
| 222 |
+ |
|
| 223 |
+ |
vector<int> ids; |
| 224 |
+ |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 225 |
|
/* Random particle is the default case*/ |
| 226 |
|
if (!args_info.ShellRadius_given){ |
| 227 |
< |
std::cout << "Creating a random nanoparticle" << std::endl; |
| 228 |
< |
/* Check to see if we have enough components */ |
| 195 |
< |
if (nComponents != args_info.molFraction_given + 1){ |
| 196 |
< |
std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
| 197 |
< |
exit 1; |
| 198 |
< |
} |
| 199 |
< |
int totComponents = 0; |
| 200 |
< |
for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */ |
| 201 |
< |
numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
| 202 |
< |
totComponents += numMol[i]; |
| 203 |
< |
} |
| 204 |
< |
numMol[nComponents-1] = numSites - totComponents; |
| 205 |
< |
|
| 227 |
> |
/* do the iPod thing, Shuffle da vector */ |
| 228 |
> |
std::random_shuffle(ids.begin(), ids.end()); |
| 229 |
|
} else{ /*Handle core-shell with multiple components.*/ |
| 230 |
|
std::cout << "Creating a core-shell nanoparticle." << std::endl; |
| 231 |
|
if (nComponents != args_info.ShellRadius_given + 1){ |
| 232 |
< |
std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl; |
| 233 |
< |
exit 1; |
| 234 |
< |
} |
| 232 |
> |
sprintf(painCave.errMsg, "Number of .md components " |
| 233 |
> |
"does not match the number of shell radius specifications"); |
| 234 |
> |
painCave.isFatal = 1; |
| 235 |
> |
simError(); |
| 236 |
> |
} |
| 237 |
|
|
| 213 |
– |
|
| 214 |
– |
|
| 238 |
|
} |
| 239 |
|
|
| 217 |
– |
//get the orientation of the cell sites |
| 218 |
– |
//for the same type of molecule in same lattice, it will not change |
| 219 |
– |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 240 |
|
|
| 241 |
|
|
| 242 |
|
|
| 243 |
< |
// needed for writing out new md file. |
| 243 |
> |
outputFileName = args_info.output_arg; |
| 244 |
> |
|
| 245 |
|
|
| 246 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 247 |
< |
outMdFileName = outPrefix + ".md"; |
| 246 |
> |
//creat new .md file on fly which corrects the number of molecule |
| 247 |
> |
createMdFile(inputFileName, outputFileName, nMol); |
| 248 |
|
|
| 228 |
– |
//creat new .md file on fly which corrects the number of molecule |
| 229 |
– |
createMdFile(inputFileName, outMdFileName, numcomponents,numMol); |
| 230 |
– |
|
| 249 |
|
if (oldInfo != NULL) |
| 250 |
|
delete oldInfo; |
| 251 |
|
|
| 253 |
|
// We need to read in new siminfo object. |
| 254 |
|
//parse md file and set up the system |
| 255 |
|
//SimCreator NewCreator; |
| 256 |
+ |
SimCreator newCreator; |
| 257 |
+ |
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 258 |
|
|
| 239 |
– |
SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false); |
| 259 |
|
|
| 260 |
< |
// This was so much fun the first time, lets do it again. |
| 242 |
< |
|
| 260 |
> |
// Place molecules |
| 261 |
|
Molecule* mol; |
| 262 |
|
SimInfo::MoleculeIterator mi; |
| 263 |
|
mol = NewInfo->beginMolecule(mi); |
| 264 |
+ |
int l = 0; |
| 265 |
|
|
| 266 |
< |
|
| 267 |
< |
for(int i = -nx; i < nx; i++) { |
| 268 |
< |
for(int j = -ny; j < ny; j++) { |
| 269 |
< |
for(int k = -nz; k < nz; k++) { |
| 270 |
< |
|
| 271 |
< |
//get the position of the cell sites |
| 272 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 273 |
< |
|
| 255 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 256 |
< |
#ifdef HAVE_CGAL |
| 257 |
< |
if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 258 |
< |
#endif |
| 259 |
< |
if (mol != NULL) { |
| 260 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 261 |
< |
} else { |
| 262 |
< |
std::cerr<<"Error in placing molecule " << std::endl; |
| 263 |
< |
} |
| 264 |
< |
mol = NewInfo->nextMolecule(mi); |
| 265 |
< |
#ifdef HAVE_CGAL |
| 266 |
< |
} |
| 267 |
< |
#endif |
| 268 |
< |
} |
| 269 |
< |
} |
| 270 |
< |
} |
| 266 |
> |
for (int i = 0; i < nComponents; i++){ |
| 267 |
> |
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 268 |
> |
NewInfo->getForceField()); |
| 269 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
| 270 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 271 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 272 |
> |
l++; |
| 273 |
> |
} |
| 274 |
|
} |
| 275 |
|
|
| 276 |
|
|
| 277 |
|
|
| 278 |
|
//fill Hmat |
| 279 |
< |
hmat(0, 0)= nx * latticeConstant; |
| 279 |
> |
hmat(0, 0)= 2.0*particleRadius; |
| 280 |
|
hmat(0, 1) = 0.0; |
| 281 |
|
hmat(0, 2) = 0.0; |
| 282 |
|
|
| 283 |
|
hmat(1, 0) = 0.0; |
| 284 |
< |
hmat(1, 1) = ny * latticeConstant; |
| 284 |
> |
hmat(1, 1) = 2.0*particleRadius; |
| 285 |
|
hmat(1, 2) = 0.0; |
| 286 |
|
|
| 287 |
|
hmat(2, 0) = 0.0; |
| 288 |
|
hmat(2, 1) = 0.0; |
| 289 |
< |
hmat(2, 2) = nz * latticeConstant; |
| 289 |
> |
hmat(2, 2) = 2.0*particleRadius; |
| 290 |
|
|
| 291 |
|
//set Hmat |
| 292 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 293 |
|
|
| 294 |
|
|
| 295 |
|
//create dumpwriter and write out the coordinates |
| 296 |
< |
NewInfo->setFinalConfigFileName(outInitFileName); |
| 294 |
< |
writer = new DumpWriter(NewInfo); |
| 296 |
> |
writer = new DumpWriter(NewInfo, outputFileName); |
| 297 |
|
|
| 298 |
|
if (writer == NULL) { |
| 299 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 300 |
< |
exit(1); |
| 299 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
| 300 |
> |
painCave.isFatal = 1; |
| 301 |
> |
simError(); |
| 302 |
|
} |
| 303 |
|
|
| 304 |
|
writer->writeDump(); |
| 305 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
| 306 |
< |
<< " is generated." << std::endl; |
| 307 |
< |
|
| 308 |
< |
//delete objects |
| 309 |
< |
|
| 310 |
< |
//delete oldInfo and oldSimSetup |
| 311 |
< |
|
| 312 |
< |
if (NewInfo != NULL) |
| 313 |
< |
delete NewInfo; |
| 314 |
< |
|
| 312 |
< |
if (writer != NULL) |
| 313 |
< |
delete writer; |
| 314 |
< |
delete simpleLat; |
| 315 |
< |
cmdline_parser_free(&args_info); |
| 305 |
> |
|
| 306 |
> |
// deleting the writer will put the closing at the end of the dump file |
| 307 |
> |
|
| 308 |
> |
delete writer; |
| 309 |
> |
|
| 310 |
> |
// cleanup a by calling sim error..... |
| 311 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 312 |
> |
"generated.\n", outputFileName.c_str()); |
| 313 |
> |
painCave.isFatal = 0; |
| 314 |
> |
simError(); |
| 315 |
|
return 0; |
| 316 |
|
} |
| 317 |
|
|
| 318 |
|
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 319 |
< |
int components,int &nummol) { |
| 319 |
> |
std::vector<int> nMol) { |
| 320 |
|
ifstream oldMdFile; |
| 321 |
|
ofstream newMdFile; |
| 322 |
|
const int MAXLEN = 65535; |
| 327 |
|
newMdFile.open(newMdFileName.c_str()); |
| 328 |
|
|
| 329 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 330 |
< |
|
| 330 |
> |
|
| 331 |
> |
int i = 0; |
| 332 |
|
while (!oldMdFile.eof()) { |
| 333 |
|
|
| 334 |
|
//correct molecule number |
| 335 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 336 |
< |
sprintf(buffer, "\tnMol = %i;", numMol); |
| 337 |
< |
newMdFile << buffer << std::endl; |
| 336 |
> |
if(i<nMol.size()){ |
| 337 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 338 |
> |
newMdFile << buffer << std::endl; |
| 339 |
> |
i++; |
| 340 |
> |
} |
| 341 |
|
} else |
| 342 |
|
newMdFile << buffer << std::endl; |
| 343 |
|
|
