78 |
|
gengetopt_args_info args_info; |
79 |
|
std::string latticeType; |
80 |
|
std::string inputFileName; |
81 |
– |
std::string outPrefix; |
81 |
|
std::string outputFileName; |
83 |
– |
std::string outInitFileName; |
82 |
|
|
85 |
– |
|
86 |
– |
|
83 |
|
Lattice *simpleLat; |
84 |
|
MoLocator* locator; |
85 |
|
int* numMol; |
87 |
|
double latticeConstant; |
88 |
|
std::vector<double> lc; |
89 |
|
double mass; |
94 |
– |
|
90 |
|
const double rhoConvertConst = 1.661; |
91 |
|
double density; |
92 |
|
double particleRadius; |
98 |
– |
|
99 |
– |
|
93 |
|
|
94 |
|
Mat3x3d hmat; |
95 |
|
std::vector<Vector3d> latticePos; |
97 |
|
int numMolPerCell; |
98 |
|
int nShells; /* Number of shells in nanoparticle*/ |
99 |
|
|
107 |
– |
|
100 |
|
DumpWriter *writer; |
101 |
|
|
102 |
|
// Parse Command Line Arguments |
103 |
|
if (cmdline_parser(argc, argv, &args_info) != 0) |
104 |
|
exit(1); |
105 |
< |
|
114 |
< |
|
115 |
< |
|
105 |
> |
|
106 |
|
/* get lattice type */ |
107 |
|
latticeType = "FCC"; |
108 |
|
|
121 |
|
SimCreator oldCreator; |
122 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
123 |
|
|
134 |
– |
|
124 |
|
latticeConstant = args_info.latticeCnst_arg; |
125 |
|
particleRadius = args_info.radius_arg; |
126 |
|
Globals* simParams = oldInfo->getSimParams(); |
127 |
|
|
139 |
– |
|
140 |
– |
/* create Molocators */ |
141 |
– |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
142 |
– |
|
128 |
|
/* Create nanoparticle */ |
129 |
< |
shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
129 |
> |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
130 |
> |
particleRadius); |
131 |
|
|
132 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
133 |
< |
vector<Vector3d> sites = nanoParticle.getPoints(); |
134 |
< |
vector<Vector3d> orientations = nanoParticle.getPointsOrt(); |
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(); |
154 |
– |
|
140 |
|
|
156 |
– |
|
157 |
– |
|
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(); |
163 |
– |
|
146 |
|
|
165 |
– |
|
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 |
< |
} |
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 |
< |
|
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 |
< |
|
170 |
> |
|
171 |
|
/* Do some simple sanity checking*/ |
172 |
|
|
192 |
– |
|
193 |
– |
|
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" |
220 |
|
simError(); |
221 |
|
} |
222 |
|
|
244 |
– |
|
245 |
– |
|
246 |
– |
|
223 |
|
vector<int> ids; |
224 |
|
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
225 |
|
/* Random particle is the default case*/ |
293 |
|
|
294 |
|
|
295 |
|
//create dumpwriter and write out the coordinates |
296 |
< |
writer = new DumpWriter(NewInfo,outputFileName); |
296 |
> |
writer = new DumpWriter(NewInfo, outputFileName); |
297 |
|
|
298 |
|
if (writer == NULL) { |
299 |
|
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
302 |
|
} |
303 |
|
|
304 |
|
writer->writeDump(); |
329 |
– |
std::cout << "new initial configuration file: " << outInitFileName |
330 |
– |
<< " is generated." << std::endl; |
331 |
– |
|
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..... |