1 |
< |
/* |
1 |
> |
/* |
2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
|
* |
4 |
|
* The University of Notre Dame grants you ("Licensee") a |
49 |
|
#include <fstream> |
50 |
|
|
51 |
|
#include "applications/simpleBuilder/simpleBuilderCmd.h" |
52 |
< |
#include "applications/simpleBuilder/LatticeFactory.hpp" |
53 |
< |
#include "applications/simpleBuilder/MoLocator.hpp" |
54 |
< |
#include "applications/simpleBuilder/Lattice.hpp" |
52 |
> |
#include "lattice/LatticeFactory.hpp" |
53 |
> |
#include "utils/MoLocator.hpp" |
54 |
> |
#include "lattice/Lattice.hpp" |
55 |
|
#include "brains/Register.hpp" |
56 |
|
#include "brains/SimInfo.hpp" |
57 |
|
#include "brains/SimCreator.hpp" |
62 |
|
|
63 |
|
using namespace std; |
64 |
|
using namespace oopse; |
65 |
– |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
66 |
– |
int numMol); |
65 |
|
|
66 |
+ |
void createMdFile(const std::string&oldMdFileName, |
67 |
+ |
const std::string&newMdFileName, |
68 |
+ |
int nMol); |
69 |
+ |
|
70 |
|
int main(int argc, char *argv []) { |
71 |
|
|
72 |
< |
//register force fields |
73 |
< |
registerForceFields(); |
72 |
> |
// register force fields |
73 |
> |
registerForceFields(); |
74 |
> |
registerLattice(); |
75 |
|
|
76 |
< |
gengetopt_args_info args_info; |
77 |
< |
std::string latticeType; |
78 |
< |
std::string inputFileName; |
79 |
< |
std::string outPrefix; |
80 |
< |
std::string outMdFileName; |
81 |
< |
std::string outInitFileName; |
82 |
< |
BaseLattice *simpleLat; |
83 |
< |
int numMol; |
84 |
< |
double latticeConstant; |
85 |
< |
std::vector<double> lc; |
86 |
< |
double mass; |
87 |
< |
const double rhoConvertConst = 1.661; |
88 |
< |
double density; |
89 |
< |
int nx, |
90 |
< |
ny, |
91 |
< |
nz; |
89 |
< |
Mat3x3d hmat; |
90 |
< |
MoLocator *locator; |
91 |
< |
std::vector<Vector3d> latticePos; |
92 |
< |
std::vector<Vector3d> latticeOrt; |
93 |
< |
int numMolPerCell; |
94 |
< |
int curMolIndex; |
95 |
< |
DumpWriter *writer; |
76 |
> |
gengetopt_args_info args_info; |
77 |
> |
std::string latticeType; |
78 |
> |
std::string inputFileName; |
79 |
> |
std::string outputFileName; |
80 |
> |
Lattice *simpleLat; |
81 |
> |
RealType latticeConstant; |
82 |
> |
std::vector<RealType> lc; |
83 |
> |
const RealType rhoConvertConst = 1.661; |
84 |
> |
RealType density; |
85 |
> |
int nx, ny, nz; |
86 |
> |
Mat3x3d hmat; |
87 |
> |
MoLocator *locator; |
88 |
> |
std::vector<Vector3d> latticePos; |
89 |
> |
std::vector<Vector3d> latticeOrt; |
90 |
> |
int nMolPerCell; |
91 |
> |
DumpWriter *writer; |
92 |
|
|
93 |
< |
// parse command line arguments |
94 |
< |
if (cmdline_parser(argc, argv, &args_info) != 0) |
95 |
< |
exit(1); |
93 |
> |
// parse command line arguments |
94 |
> |
if (cmdline_parser(argc, argv, &args_info) != 0) |
95 |
> |
exit(1); |
96 |
|
|
97 |
< |
density = args_info.density_arg; |
97 |
> |
density = args_info.density_arg; |
98 |
|
|
99 |
< |
//get lattice type |
100 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
99 |
> |
//get lattice type |
100 |
> |
latticeType = "FCC"; |
101 |
|
|
102 |
< |
if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
103 |
< |
std::cerr << latticeType << " is an invalid lattice type" << std::endl; |
104 |
< |
std::cerr << LatticeFactory::getInstance()->toString() << std::endl; |
105 |
< |
exit(1); |
106 |
< |
} |
102 |
> |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
103 |
> |
|
104 |
> |
if (simpleLat == NULL) { |
105 |
> |
sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n", |
106 |
> |
latticeType.c_str()); |
107 |
> |
painCave.isFatal = 1; |
108 |
> |
simError(); |
109 |
> |
} |
110 |
> |
nMolPerCell = simpleLat->getNumSitesPerCell(); |
111 |
|
|
112 |
< |
//get the number of unit cell |
113 |
< |
nx = args_info.nx_arg; |
112 |
> |
//get the number of unit cells in each direction: |
113 |
|
|
114 |
< |
if (nx <= 0) { |
116 |
< |
std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl; |
117 |
< |
exit(1); |
118 |
< |
} |
114 |
> |
nx = args_info.nx_arg; |
115 |
|
|
116 |
< |
ny = args_info.ny_arg; |
116 |
> |
if (nx <= 0) { |
117 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the x direction " |
118 |
> |
"must be greater than 0."); |
119 |
> |
painCave.isFatal = 1; |
120 |
> |
simError(); |
121 |
> |
} |
122 |
|
|
123 |
< |
if (ny <= 0) { |
123 |
< |
std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
124 |
< |
exit(1); |
125 |
< |
} |
123 |
> |
ny = args_info.ny_arg; |
124 |
|
|
125 |
< |
nz = args_info.nz_arg; |
125 |
> |
if (ny <= 0) { |
126 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
127 |
> |
"must be greater than 0."); |
128 |
> |
painCave.isFatal = 1; |
129 |
> |
simError(); |
130 |
> |
} |
131 |
|
|
132 |
< |
if (nz <= 0) { |
130 |
< |
std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl; |
131 |
< |
exit(1); |
132 |
< |
} |
132 |
> |
nz = args_info.nz_arg; |
133 |
|
|
134 |
< |
//get input file name |
135 |
< |
if (args_info.inputs_num) |
136 |
< |
inputFileName = args_info.inputs[0]; |
137 |
< |
else { |
138 |
< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
139 |
< |
cmdline_parser_print_help(); |
140 |
< |
exit(1); |
141 |
< |
} |
134 |
> |
if (nz <= 0) { |
135 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
136 |
> |
"must be greater than 0."); |
137 |
> |
painCave.isFatal = 1; |
138 |
> |
simError(); |
139 |
> |
} |
140 |
|
|
141 |
< |
//parse md file and set up the system |
144 |
< |
SimCreator oldCreator; |
145 |
< |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
141 |
> |
int nSites = nMolPerCell * nx * ny * nz; |
142 |
|
|
143 |
< |
if (oldInfo->getNMoleculeStamp()>= 2) { |
144 |
< |
std::cerr << "can not build the system with more than two components" |
145 |
< |
<< std::endl; |
146 |
< |
exit(1); |
147 |
< |
} |
143 |
> |
//get input file name |
144 |
> |
if (args_info.inputs_num) |
145 |
> |
inputFileName = args_info.inputs[0]; |
146 |
> |
else { |
147 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified " |
148 |
> |
"on the command line"); |
149 |
> |
painCave.isFatal = 1; |
150 |
> |
simError(); |
151 |
> |
} |
152 |
|
|
153 |
< |
//get mass of molecule. |
153 |
> |
//parse md file and set up the system |
154 |
|
|
155 |
< |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
155 |
> |
SimCreator oldCreator; |
156 |
> |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
157 |
> |
Globals* simParams = oldInfo->getSimParams(); |
158 |
|
|
159 |
< |
//creat lattice |
158 |
< |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
159 |
> |
// Calculate lattice constant (in Angstroms) |
160 |
|
|
161 |
< |
if (simpleLat == NULL) { |
162 |
< |
std::cerr << "Error in creating lattice" << std::endl; |
162 |
< |
exit(1); |
163 |
< |
} |
161 |
> |
RealType avgMass = getMolMass(oldInfo->getMoleculeStamp(0), |
162 |
> |
oldInfo->getForceField()); |
163 |
|
|
164 |
< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
164 |
> |
latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density, |
165 |
> |
(RealType)(1.0 / 3.0)); |
166 |
> |
|
167 |
> |
// Set the lattice constant |
168 |
> |
|
169 |
> |
lc.push_back(latticeConstant); |
170 |
> |
simpleLat->setLatticeConstant(lc); |
171 |
|
|
172 |
< |
//calculate lattice constant (in Angstrom) |
168 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
169 |
< |
1.0 / 3.0); |
172 |
> |
// Calculate the lattice sites and fill the lattice vector. |
173 |
|
|
174 |
< |
//set lattice constant |
172 |
< |
lc.push_back(latticeConstant); |
173 |
< |
simpleLat->setLatticeConstant(lc); |
174 |
> |
// Get the standard orientations of the cell sites |
175 |
|
|
176 |
< |
//calculate the total number of molecules |
176 |
< |
numMol = nx * ny * nz * numMolPerCell; |
176 |
> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
177 |
|
|
178 |
< |
if (oldInfo->getNGlobalMolecules() != numMol) { |
179 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
180 |
< |
outMdFileName = outPrefix + ".md"; |
178 |
> |
vector<Vector3d> sites; |
179 |
> |
vector<Vector3d> orientations; |
180 |
> |
|
181 |
> |
for(int i = 0; i < nx; i++) { |
182 |
> |
for(int j = 0; j < ny; j++) { |
183 |
> |
for(int k = 0; k < nz; k++) { |
184 |
|
|
185 |
< |
//creat new .md file on fly which corrects the number of molecule |
186 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
187 |
< |
std::cerr |
188 |
< |
<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
189 |
< |
<< std::endl; |
190 |
< |
std::cerr << "A new .md file: " << outMdFileName |
191 |
< |
<< " is generated, use it to rerun the simpleBuilder" << std::endl; |
192 |
< |
exit(1); |
185 |
> |
// Get the position of the cell sites |
186 |
> |
|
187 |
> |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
188 |
> |
|
189 |
> |
for(int l = 0; l < nMolPerCell; l++) { |
190 |
> |
sites.push_back(latticePos[l]); |
191 |
> |
orientations.push_back(latticeOrt[l]); |
192 |
> |
} |
193 |
> |
} |
194 |
|
} |
195 |
+ |
} |
196 |
+ |
|
197 |
+ |
outputFileName = args_info.output_arg; |
198 |
+ |
|
199 |
+ |
// create a new .md file on the fly which corrects the number of molecules |
200 |
|
|
201 |
< |
//determine the output file names |
193 |
< |
if (args_info.output_given) |
194 |
< |
outInitFileName = args_info.output_arg; |
195 |
< |
else |
196 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
197 |
< |
|
198 |
< |
//creat Molocator |
199 |
< |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
201 |
> |
createMdFile(inputFileName, outputFileName, nSites); |
202 |
|
|
203 |
< |
//fill Hmat |
204 |
< |
hmat(0, 0)= nx * latticeConstant; |
203 |
< |
hmat(0, 1) = 0.0; |
204 |
< |
hmat(0, 2) = 0.0; |
203 |
> |
if (oldInfo != NULL) |
204 |
> |
delete oldInfo; |
205 |
|
|
206 |
< |
hmat(1, 0) = 0.0; |
207 |
< |
hmat(1, 1) = ny * latticeConstant; |
208 |
< |
hmat(1, 2) = 0.0; |
206 |
> |
// We need to read in the new SimInfo object, then Parse the |
207 |
> |
// md file and set up the system |
208 |
|
|
209 |
< |
hmat(2, 0) = 0.0; |
210 |
< |
hmat(2, 1) = 0.0; |
212 |
< |
hmat(2, 2) = nz * latticeConstant; |
209 |
> |
SimCreator newCreator; |
210 |
> |
SimInfo* newInfo = newCreator.createSim(outputFileName, false); |
211 |
|
|
212 |
< |
//set Hmat |
215 |
< |
oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
212 |
> |
// fill Hmat |
213 |
|
|
214 |
< |
//place the molecules |
214 |
> |
hmat(0, 0) = nx * latticeConstant; |
215 |
> |
hmat(0, 1) = 0.0; |
216 |
> |
hmat(0, 2) = 0.0; |
217 |
|
|
218 |
< |
curMolIndex = 0; |
218 |
> |
hmat(1, 0) = 0.0; |
219 |
> |
hmat(1, 1) = ny * latticeConstant; |
220 |
> |
hmat(1, 2) = 0.0; |
221 |
|
|
222 |
< |
//get the orientation of the cell sites |
223 |
< |
//for the same type of molecule in same lattice, it will not change |
224 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
222 |
> |
hmat(2, 0) = 0.0; |
223 |
> |
hmat(2, 1) = 0.0; |
224 |
> |
hmat(2, 2) = nz * latticeConstant; |
225 |
|
|
226 |
< |
Molecule* mol; |
226 |
< |
SimInfo::MoleculeIterator mi; |
227 |
< |
mol = oldInfo->beginMolecule(mi); |
228 |
< |
for(int i = 0; i < nx; i++) { |
229 |
< |
for(int j = 0; j < ny; j++) { |
230 |
< |
for(int k = 0; k < nz; k++) { |
226 |
> |
// Set Hmat |
227 |
|
|
228 |
< |
//get the position of the cell sites |
233 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
228 |
> |
newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
229 |
|
|
230 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
231 |
< |
if (mol != NULL) { |
232 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
233 |
< |
} else { |
234 |
< |
std::cerr << std::endl; |
235 |
< |
} |
236 |
< |
mol = oldInfo->nextMolecule(mi); |
237 |
< |
} |
238 |
< |
} |
239 |
< |
} |
240 |
< |
} |
230 |
> |
// place the molecules |
231 |
> |
|
232 |
> |
Molecule* mol; |
233 |
> |
locator = new MoLocator(newInfo->getMoleculeStamp(0), |
234 |
> |
newInfo->getForceField()); |
235 |
> |
for (int n = 0; n < nSites; n++) { |
236 |
> |
mol = newInfo->getMoleculeByGlobalIndex(n); |
237 |
> |
locator->placeMol(sites[n], orientations[n], mol); |
238 |
> |
} |
239 |
> |
|
240 |
> |
// Create DumpWriter and write out the coordinates |
241 |
|
|
242 |
< |
//create dumpwriter and write out the coordinates |
243 |
< |
oldInfo->setFinalConfigFileName(outInitFileName); |
244 |
< |
writer = new DumpWriter(oldInfo, oldInfo->getDumpFileName()); |
242 |
> |
writer = new DumpWriter(newInfo, outputFileName); |
243 |
> |
|
244 |
> |
if (writer == NULL) { |
245 |
> |
sprintf(painCave.errMsg, "error in creating DumpWriter"); |
246 |
> |
painCave.isFatal = 1; |
247 |
> |
simError(); |
248 |
> |
} |
249 |
|
|
250 |
< |
if (writer == NULL) { |
252 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
253 |
< |
exit(1); |
254 |
< |
} |
250 |
> |
writer->writeDump(); |
251 |
|
|
252 |
< |
writer->writeDump(); |
257 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
258 |
< |
<< " is generated." << std::endl; |
252 |
> |
// deleting the writer will put the closing at the end of the dump file. |
253 |
|
|
254 |
< |
//delete objects |
254 |
> |
delete writer; |
255 |
|
|
256 |
< |
//delete oldInfo and oldSimSetup |
257 |
< |
if (oldInfo != NULL) |
258 |
< |
delete oldInfo; |
259 |
< |
|
260 |
< |
if (writer != NULL) |
267 |
< |
delete writer; |
268 |
< |
|
269 |
< |
return 0; |
256 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
257 |
> |
"generated.\n", outputFileName.c_str()); |
258 |
> |
painCave.isFatal = 0; |
259 |
> |
simError(); |
260 |
> |
return 0; |
261 |
|
} |
262 |
|
|
263 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
264 |
< |
int numMol) { |
265 |
< |
ifstream oldMdFile; |
266 |
< |
ofstream newMdFile; |
267 |
< |
const int MAXLEN = 65535; |
268 |
< |
char buffer[MAXLEN]; |
263 |
> |
void createMdFile(const std::string&oldMdFileName, |
264 |
> |
const std::string&newMdFileName, |
265 |
> |
int nMol) { |
266 |
> |
ifstream oldMdFile; |
267 |
> |
ofstream newMdFile; |
268 |
> |
const int MAXLEN = 65535; |
269 |
> |
char buffer[MAXLEN]; |
270 |
|
|
271 |
< |
//create new .md file based on old .md file |
272 |
< |
oldMdFile.open(oldMdFileName.c_str()); |
273 |
< |
newMdFile.open(newMdFileName.c_str()); |
271 |
> |
//create new .md file based on old .md file |
272 |
> |
oldMdFile.open(oldMdFileName.c_str()); |
273 |
> |
newMdFile.open(newMdFileName.c_str()); |
274 |
|
|
275 |
< |
oldMdFile.getline(buffer, MAXLEN); |
275 |
> |
oldMdFile.getline(buffer, MAXLEN); |
276 |
|
|
277 |
< |
while (!oldMdFile.eof()) { |
277 |
> |
while (!oldMdFile.eof()) { |
278 |
|
|
279 |
< |
//correct molecule number |
280 |
< |
if (strstr(buffer, "nMol") != NULL) { |
281 |
< |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
282 |
< |
newMdFile << buffer << std::endl; |
283 |
< |
} else |
284 |
< |
newMdFile << buffer << std::endl; |
279 |
> |
//correct molecule number |
280 |
> |
if (strstr(buffer, "nMol") != NULL) { |
281 |
> |
sprintf(buffer, "\t\tnMol = %d;", nMol); |
282 |
> |
newMdFile << buffer << std::endl; |
283 |
> |
} else |
284 |
> |
newMdFile << buffer << std::endl; |
285 |
|
|
286 |
< |
oldMdFile.getline(buffer, MAXLEN); |
287 |
< |
} |
286 |
> |
oldMdFile.getline(buffer, MAXLEN); |
287 |
> |
} |
288 |
|
|
289 |
< |
oldMdFile.close(); |
290 |
< |
newMdFile.close(); |
289 |
> |
oldMdFile.close(); |
290 |
> |
newMdFile.close(); |
291 |
|
} |
292 |
|
|