47 |
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#include <string> |
48 |
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#include <map> |
49 |
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#include <fstream> |
50 |
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#include <algorithm> |
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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 |
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#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 |
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|
86 |
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|
83 |
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Lattice *simpleLat; |
84 |
< |
int numMol; |
84 |
> |
MoLocator* locator; |
85 |
> |
int* numMol; |
86 |
> |
int nComponents; |
87 |
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double latticeConstant; |
88 |
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std::vector<double> lc; |
89 |
< |
double mass; |
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> |
double mass; |
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const double rhoConvertConst = 1.661; |
91 |
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double density; |
92 |
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|
95 |
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|
92 |
> |
double particleRadius; |
93 |
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|
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Mat3x3d hmat; |
98 |
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MoLocator *locator; |
99 |
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sphericalNanoparticle *nanoparticle; |
95 |
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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 |
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int numSites; |
105 |
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|
99 |
> |
|
100 |
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DumpWriter *writer; |
101 |
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|
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// Parse Command Line Arguments |
103 |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
104 |
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exit(1); |
105 |
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112 |
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|
113 |
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|
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|
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/* get lattice type */ |
107 |
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latticeType = UpperCase(args_info.latticetype_arg); |
108 |
< |
|
107 |
> |
latticeType = "FCC"; |
108 |
> |
|
109 |
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/* get input file name */ |
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if (args_info.inputs_num) |
111 |
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inputFileName = args_info.inputs[0]; |
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else { |
113 |
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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; |
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cmdline_parser_print_help(); |
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exit(1); |
117 |
> |
simError(); |
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} |
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|
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/* parse md file and set up the system */ |
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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|
130 |
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nShells = 0; |
131 |
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if (args_info.coreShellRadius_given){ |
132 |
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nShells = args_info.coreShellRadius_given; |
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} |
134 |
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|
135 |
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nComponents = oldInfo->getNMoleculeStamp(); |
136 |
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|
137 |
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/* Check to see if we have enough components to build that many shells. */ |
138 |
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if (nShells){ |
139 |
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if (oldInfo->getNMoleculeStamp() != nShells) { |
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std::cerr << "Not enough components present in MD file to build specified number of shells" |
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<< std::endl; |
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exit(1); |
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} |
144 |
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} |
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|
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|
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//creat lattice |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
150 |
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if (simpleLat == NULL) { |
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std::cerr << "Error in creating lattice" << std::endl; |
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exit(1); |
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} |
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|
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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|
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/*calculate lattice constant (in Angstrom) |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
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1.0 / 3.0);*/ |
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|
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latticeConstant = args_info.latticeCnst_arg; |
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particleRadius = args_info.radius_arg; |
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particleDiameter = 2.0 * particleRadius; |
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Globals* simParams = oldInfo->getSimParams(); |
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|
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/* set lattice constant */ |
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lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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/* Create nanoparticle */ |
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shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
130 |
> |
particleRadius); |
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|
132 |
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|
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/*determine the output file names*/ |
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if (args_info.output_given){ |
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outInitFileName = args_info.output_arg; |
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}else{ |
137 |
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outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
132 |
> |
/* Build a lattice and get lattice points for this lattice constant */ |
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> |
vector<Vector3d> sites = nanoParticle.getSites(); |
134 |
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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 |
> |
|
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> |
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 |
|
|