1 |
tim |
1424 |
#include <cstdlib> |
2 |
|
|
#include <cstdio> |
3 |
|
|
#include <cstring> |
4 |
|
|
#include <cmath> |
5 |
|
|
#include <iostream> |
6 |
|
|
#include <string> |
7 |
|
|
#include <map> |
8 |
|
|
#include <fstream> |
9 |
|
|
|
10 |
|
|
#include "Globals.hpp" |
11 |
|
|
#include "SimInfo.hpp" |
12 |
|
|
#include "SimSetup.hpp" |
13 |
tim |
1429 |
#include "simpleBuilderCmd.h" |
14 |
tim |
1424 |
#include "StringUtils.hpp" |
15 |
|
|
#include "LatticeFactory.hpp" |
16 |
tim |
1427 |
#include "Vector3d.hpp" |
17 |
tim |
1429 |
#include "MoLocator.hpp" |
18 |
|
|
#include "Lattice.hpp" |
19 |
tim |
1424 |
|
20 |
|
|
using namespace std; |
21 |
|
|
|
22 |
tim |
1429 |
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol); |
23 |
tim |
1432 |
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF); |
24 |
tim |
1424 |
|
25 |
|
|
int main( int argc, char* argv[]){ |
26 |
|
|
|
27 |
|
|
gengetopt_args_info args_info; |
28 |
|
|
string latticeType; |
29 |
|
|
string inputFileName; |
30 |
|
|
string outPrefix; |
31 |
|
|
string outMdFileName; |
32 |
|
|
SimInfo* oldInfo; |
33 |
|
|
SimSetup* oldSimSetup; |
34 |
|
|
BaseLattice* simpleLat; |
35 |
|
|
int numMol; |
36 |
|
|
double latticeConstant; |
37 |
tim |
1429 |
vector<double> lc; |
38 |
tim |
1424 |
double mass; |
39 |
tim |
1432 |
const double rhoConvertConst = 1.661; |
40 |
tim |
1424 |
double density; |
41 |
|
|
int nx, ny, nz; |
42 |
|
|
double Hmat[3][3]; |
43 |
|
|
MoLocator *locator; |
44 |
tim |
1427 |
vector<Vector3d> latticePos; |
45 |
|
|
vector<Vector3d> latticeOrt; |
46 |
tim |
1424 |
int numMolPerCell; |
47 |
|
|
int curMolIndex; |
48 |
|
|
DumpWriter* writer; |
49 |
tim |
1432 |
|
50 |
tim |
1424 |
// parse command line arguments |
51 |
|
|
if (cmdline_parser (argc, argv, &args_info) != 0) |
52 |
|
|
exit(1) ; |
53 |
|
|
|
54 |
tim |
1432 |
//process density |
55 |
tim |
1424 |
if(!args_info.density_given && !args_info.ndensity_given){ |
56 |
tim |
1432 |
cerr << "SimpleBuilder Error: density or number density must be given" << endl; |
57 |
|
|
cmdline_parser_print_help(); |
58 |
|
|
exit(1); |
59 |
tim |
1424 |
} |
60 |
tim |
1432 |
else if(args_info.density_given){ |
61 |
|
|
if( args_info.ndensity_given) |
62 |
|
|
cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl; |
63 |
|
|
|
64 |
|
|
density = args_info.density_arg; |
65 |
|
|
} |
66 |
|
|
else if(args_info.ndensity_given){ |
67 |
|
|
//convert number density to density |
68 |
|
|
} |
69 |
tim |
1424 |
|
70 |
tim |
1432 |
|
71 |
|
|
//get lattice type |
72 |
tim |
1424 |
latticeType = UpperCase(args_info.latticetype_arg); |
73 |
|
|
if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){ |
74 |
|
|
cerr << latticeType << " is an invalid lattice type" << endl; |
75 |
tim |
1429 |
cerr << LatticeFactory::getInstance()->toString() << endl; |
76 |
tim |
1424 |
exit(1); |
77 |
|
|
} |
78 |
tim |
1432 |
|
79 |
|
|
//get the number of unit cell |
80 |
tim |
1429 |
nx = args_info.nx_arg; |
81 |
tim |
1424 |
if(nx <= 0){ |
82 |
|
|
cerr << "The number of unit cell in h direction must be greater than 0" << endl; |
83 |
|
|
exit(1); |
84 |
|
|
} |
85 |
|
|
|
86 |
tim |
1429 |
ny = args_info.ny_arg; |
87 |
|
|
if(ny <= 0){ |
88 |
tim |
1424 |
cerr << "The number of unit cell in l direction must be greater than 0" << endl; |
89 |
|
|
exit(1); |
90 |
|
|
} |
91 |
|
|
|
92 |
tim |
1429 |
nz = args_info.nz_arg; |
93 |
|
|
if(nz <= 0){ |
94 |
tim |
1424 |
cerr << "The number of unit cell in k direction must be greater than 0" << endl; |
95 |
|
|
exit(1); |
96 |
|
|
} |
97 |
|
|
|
98 |
|
|
//get input file name |
99 |
tim |
1429 |
if (args_info.inputs_num) |
100 |
tim |
1424 |
inputFileName = args_info.inputs[0]; |
101 |
|
|
else { |
102 |
|
|
cerr <<"You must specify a input file name.\n" << endl; |
103 |
|
|
cmdline_parser_print_help(); |
104 |
|
|
exit(1); |
105 |
|
|
} |
106 |
|
|
|
107 |
|
|
//determine the output file names |
108 |
|
|
|
109 |
|
|
if (args_info.output_given){ |
110 |
|
|
outPrefix = args_info.output_arg; |
111 |
|
|
} |
112 |
|
|
else |
113 |
|
|
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
114 |
|
|
|
115 |
|
|
outMdFileName = outPrefix + ".md"; |
116 |
|
|
|
117 |
|
|
//parse md file and set up the system |
118 |
|
|
oldInfo = new SimInfo; |
119 |
|
|
if(oldInfo == NULL){ |
120 |
|
|
cerr << "error in creating SimInfo" << endl; |
121 |
|
|
exit(1); |
122 |
|
|
} |
123 |
|
|
|
124 |
tim |
1429 |
oldSimSetup = new SimSetup(); |
125 |
tim |
1424 |
if(oldSimSetup == NULL){ |
126 |
|
|
cerr << "error in creating SimSetup" << endl; |
127 |
|
|
exit(1); |
128 |
|
|
} |
129 |
tim |
1435 |
|
130 |
|
|
oldSimSetup->suspendInit(); |
131 |
tim |
1424 |
oldSimSetup->setSimInfo(oldInfo ); |
132 |
|
|
oldSimSetup->parseFile(&inputFileName[0] ); |
133 |
tim |
1432 |
oldSimSetup->createSim(); |
134 |
tim |
1435 |
|
135 |
tim |
1429 |
if(oldInfo->nComponents >=2){ |
136 |
tim |
1424 |
cerr << "can not build the system with more than two components" << endl; |
137 |
|
|
exit(1); |
138 |
|
|
} |
139 |
tim |
1432 |
|
140 |
|
|
//get mass of molecule. |
141 |
|
|
//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
142 |
|
|
mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
143 |
|
|
|
144 |
tim |
1424 |
//creat lattice |
145 |
tim |
1427 |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
146 |
tim |
1424 |
if(simpleLat == NULL){ |
147 |
|
|
cerr << "Error in creating lattice" << endl; |
148 |
|
|
exit(1); |
149 |
|
|
} |
150 |
|
|
|
151 |
tim |
1429 |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
152 |
tim |
1424 |
|
153 |
tim |
1432 |
//calculate lattice constant (in Angstrom) |
154 |
|
|
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0); |
155 |
|
|
|
156 |
tim |
1424 |
//set lattice constant |
157 |
tim |
1427 |
lc.push_back(latticeConstant); |
158 |
|
|
simpleLat->setLatticeConstant(lc); |
159 |
tim |
1424 |
|
160 |
tim |
1432 |
//calculate the total number of molecules |
161 |
tim |
1435 |
numMol = nx * ny * nz * numMolPerCell; |
162 |
tim |
1424 |
|
163 |
tim |
1435 |
if (oldInfo->n_mol != numMol){ |
164 |
|
|
//creat new .md file on fly which corrects the number of molecule |
165 |
|
|
createMdFile(inputFileName, outMdFileName, numMol); |
166 |
|
|
cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl; |
167 |
|
|
cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl; |
168 |
|
|
exit(1); |
169 |
tim |
1424 |
} |
170 |
|
|
|
171 |
|
|
//allocat memory for storing pos, vel and etc |
172 |
tim |
1435 |
oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
173 |
|
|
for (int i = 0; i < oldInfo->n_atoms; i++) |
174 |
|
|
oldInfo->atoms[i]->setCoords(); |
175 |
tim |
1424 |
|
176 |
|
|
//creat Molocator |
177 |
tim |
1435 |
locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
178 |
tim |
1424 |
|
179 |
tim |
1432 |
//fill Hmat |
180 |
|
|
Hmat[0][0] = nx * latticeConstant; |
181 |
|
|
Hmat[0][1] = 0.0; |
182 |
|
|
Hmat[0][2] = 0.0; |
183 |
|
|
|
184 |
tim |
1435 |
Hmat[1][0] = 0.0; |
185 |
|
|
Hmat[1][1] = ny * latticeConstant; |
186 |
tim |
1432 |
Hmat[1][2] = 0.0; |
187 |
|
|
|
188 |
tim |
1435 |
Hmat[2][0] = 0.0; |
189 |
tim |
1432 |
Hmat[2][1] = 0.0; |
190 |
tim |
1435 |
Hmat[2][2] = nz * latticeConstant ; |
191 |
tim |
1432 |
|
192 |
|
|
//set Hmat |
193 |
tim |
1435 |
oldInfo->setBoxM(Hmat); |
194 |
tim |
1432 |
|
195 |
tim |
1427 |
//place the molecules |
196 |
tim |
1424 |
|
197 |
tim |
1427 |
curMolIndex = 0; |
198 |
tim |
1424 |
|
199 |
tim |
1427 |
//get the orientation of the cell sites |
200 |
|
|
//for the same type of molecule in same lattice, it will not change |
201 |
|
|
latticeOrt = simpleLat->getLatticePointsOrt(); |
202 |
tim |
1424 |
|
203 |
|
|
for(int i =0; i < nx; i++){ |
204 |
|
|
for(int j=0; j < ny; j++){ |
205 |
|
|
for(int k = 0; k < nz; k++){ |
206 |
|
|
|
207 |
tim |
1427 |
//get the position of the cell sites |
208 |
|
|
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
209 |
|
|
|
210 |
tim |
1424 |
for(int l = 0; l < numMolPerCell; l++) |
211 |
tim |
1435 |
locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); |
212 |
tim |
1424 |
} |
213 |
|
|
} |
214 |
|
|
} |
215 |
|
|
|
216 |
|
|
//create dumpwriter and write out the coordinates |
217 |
tim |
1435 |
writer = new DumpWriter( oldInfo ); |
218 |
tim |
1424 |
if(writer == NULL){ |
219 |
|
|
cerr << "error in creating DumpWriter" << endl; |
220 |
|
|
exit(1); |
221 |
|
|
} |
222 |
tim |
1429 |
writer->writeFinal(0); |
223 |
tim |
1424 |
|
224 |
|
|
//delete objects |
225 |
tim |
1435 |
|
226 |
|
|
//delete oldInfo and oldSimSetup |
227 |
|
|
if(oldInfo != NULL) |
228 |
tim |
1424 |
delete oldInfo; |
229 |
|
|
|
230 |
tim |
1435 |
if(oldSimSetup != NULL) |
231 |
|
|
delete oldSimSetup; |
232 |
tim |
1424 |
|
233 |
|
|
if (writer != NULL) |
234 |
|
|
delete writer; |
235 |
|
|
return 0; |
236 |
|
|
} |
237 |
|
|
|
238 |
|
|
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){ |
239 |
|
|
ifstream oldMdFile; |
240 |
|
|
ofstream newMdFile; |
241 |
|
|
const int MAXLEN = 65535; |
242 |
|
|
char buffer[MAXLEN]; |
243 |
|
|
|
244 |
|
|
//create new .md file based on old .md file |
245 |
tim |
1429 |
oldMdFile.open(oldMdFileName.c_str()); |
246 |
|
|
newMdFile.open(newMdFileName.c_str()); |
247 |
tim |
1424 |
|
248 |
|
|
oldMdFile.getline(buffer, MAXLEN); |
249 |
|
|
while(!oldMdFile.eof()){ |
250 |
|
|
|
251 |
tim |
1435 |
//correct molecule number |
252 |
|
|
if(strstr(buffer, "nMol") !=NULL){ |
253 |
tim |
1429 |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
254 |
|
|
newMdFile << buffer << endl; |
255 |
|
|
} |
256 |
tim |
1424 |
else |
257 |
|
|
newMdFile << buffer << endl; |
258 |
|
|
|
259 |
|
|
oldMdFile.getline(buffer, MAXLEN); |
260 |
|
|
} |
261 |
|
|
|
262 |
|
|
oldMdFile.close(); |
263 |
|
|
newMdFile.close(); |
264 |
|
|
|
265 |
|
|
} |
266 |
tim |
1432 |
|
267 |
|
|
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){ |
268 |
|
|
int nAtoms; |
269 |
|
|
AtomStamp* currAtomStamp; |
270 |
|
|
double totMass; |
271 |
|
|
|
272 |
|
|
totMass = 0; |
273 |
|
|
nAtoms = molStamp->getNAtoms(); |
274 |
|
|
|
275 |
|
|
for(size_t i=0; i<nAtoms; i++){ |
276 |
|
|
currAtomStamp = molStamp->getAtom(i); |
277 |
|
|
totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
278 |
|
|
} |
279 |
|
|
|
280 |
|
|
return totMass; |
281 |
|
|
} |