1 |
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#include <cstdlib> |
2 |
< |
#include <cstdio> |
3 |
< |
#include <cstring> |
4 |
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#include <cmath> |
5 |
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#include <iostream> |
6 |
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#include <string> |
7 |
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#include <map> |
8 |
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#include <fstream> |
9 |
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|
10 |
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#include "io/Globals.hpp" |
11 |
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#include "brains/SimInfo.hpp" |
12 |
< |
#include "brains/SimSetup.hpp" |
13 |
< |
#include "applications/simpleBuilder/simpleBuilderCmd.h" |
14 |
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#include "utils/StringUtils.hpp" |
15 |
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#include "applications/simpleBuilder/LatticeFactory.hpp" |
16 |
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#include "math/Vector3.hpp" |
17 |
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#include "applications/simpleBuilder/MoLocator.hpp" |
18 |
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#include "applications/simpleBuilder/Lattice.hpp" |
19 |
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|
20 |
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using namespace std; |
21 |
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|
22 |
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void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol); |
23 |
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double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF); |
24 |
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|
25 |
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int main( int argc, char* argv[]){ |
26 |
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|
27 |
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gengetopt_args_info args_info; |
28 |
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string latticeType; |
29 |
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string inputFileName; |
30 |
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string outPrefix; |
31 |
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string outMdFileName; |
32 |
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string outInitFileName; |
33 |
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SimInfo* oldInfo; |
34 |
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SimSetup* oldSimSetup; |
35 |
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BaseLattice* simpleLat; |
36 |
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int numMol; |
37 |
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double latticeConstant; |
38 |
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vector<double> lc; |
39 |
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double mass; |
40 |
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const double rhoConvertConst = 1.661; |
41 |
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double density; |
42 |
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int nx, ny, nz; |
43 |
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double Hmat[3][3]; |
44 |
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MoLocator *locator; |
45 |
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vector<Vector3d> latticePos; |
46 |
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vector<Vector3d> latticeOrt; |
47 |
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int numMolPerCell; |
48 |
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int curMolIndex; |
49 |
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DumpWriter* writer; |
50 |
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|
51 |
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// parse command line arguments |
52 |
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if (cmdline_parser (argc, argv, &args_info) != 0) |
53 |
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exit(1) ; |
54 |
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|
55 |
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density = args_info.density_arg; |
56 |
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|
57 |
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//get lattice type |
58 |
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latticeType = UpperCase(args_info.latticetype_arg); |
59 |
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if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){ |
60 |
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cerr << latticeType << " is an invalid lattice type" << endl; |
61 |
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cerr << LatticeFactory::getInstance()->toString() << endl; |
62 |
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exit(1); |
63 |
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} |
64 |
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|
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//get the number of unit cell |
66 |
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nx = args_info.nx_arg; |
67 |
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if(nx <= 0){ |
68 |
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cerr << "The number of unit cell in h direction must be greater than 0" << endl; |
69 |
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exit(1); |
70 |
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} |
71 |
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|
72 |
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ny = args_info.ny_arg; |
73 |
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if(ny <= 0){ |
74 |
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cerr << "The number of unit cell in l direction must be greater than 0" << endl; |
75 |
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exit(1); |
76 |
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} |
77 |
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|
78 |
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nz = args_info.nz_arg; |
79 |
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if(nz <= 0){ |
80 |
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cerr << "The number of unit cell in k direction must be greater than 0" << endl; |
81 |
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exit(1); |
82 |
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} |
83 |
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|
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//get input file name |
85 |
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if (args_info.inputs_num) |
86 |
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inputFileName = args_info.inputs[0]; |
87 |
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else { |
88 |
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cerr <<"You must specify a input file name.\n" << endl; |
89 |
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cmdline_parser_print_help(); |
90 |
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exit(1); |
91 |
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} |
92 |
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|
93 |
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|
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//parse md file and set up the system |
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oldInfo = new SimInfo; |
96 |
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if(oldInfo == NULL){ |
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cerr << "error in creating SimInfo" << endl; |
98 |
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exit(1); |
99 |
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} |
100 |
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|
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oldSimSetup = new SimSetup(); |
102 |
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if(oldSimSetup == NULL){ |
103 |
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cerr << "error in creating SimSetup" << endl; |
104 |
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exit(1); |
105 |
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} |
106 |
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|
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oldSimSetup->suspendInit(); |
108 |
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oldSimSetup->setSimInfo(oldInfo ); |
109 |
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oldSimSetup->parseFile(&inputFileName[0] ); |
110 |
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oldSimSetup->createSim(); |
111 |
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|
112 |
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if(oldInfo->nComponents >=2){ |
113 |
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cerr << "can not build the system with more than two components" << endl; |
114 |
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exit(1); |
115 |
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} |
116 |
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|
117 |
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//get mass of molecule. |
118 |
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//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
119 |
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mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
120 |
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|
121 |
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//creat lattice |
122 |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
123 |
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if(simpleLat == NULL){ |
124 |
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cerr << "Error in creating lattice" << endl; |
125 |
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exit(1); |
126 |
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} |
127 |
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|
128 |
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
129 |
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|
130 |
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//calculate lattice constant (in Angstrom) |
131 |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0); |
132 |
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|
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//set lattice constant |
134 |
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lc.push_back(latticeConstant); |
135 |
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simpleLat->setLatticeConstant(lc); |
136 |
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|
137 |
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//calculate the total number of molecules |
138 |
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numMol = nx * ny * nz * numMolPerCell; |
139 |
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|
140 |
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if (oldInfo->n_mol != numMol){ |
141 |
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|
142 |
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outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
143 |
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outMdFileName = outPrefix + ".md"; |
144 |
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|
145 |
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//creat new .md file on fly which corrects the number of molecule |
146 |
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createMdFile(inputFileName, outMdFileName, numMol); |
147 |
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cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl; |
148 |
< |
cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl; |
149 |
< |
exit(1); |
150 |
< |
} |
151 |
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|
152 |
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//determine the output file names |
153 |
< |
if (args_info.output_given) |
154 |
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outInitFileName = args_info.output_arg; |
155 |
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else |
156 |
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outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
157 |
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|
158 |
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|
159 |
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//allocat memory for storing pos, vel and etc |
160 |
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oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
161 |
< |
for (int i = 0; i < oldInfo->n_atoms; i++) |
162 |
< |
oldInfo->atoms[i]->setCoords(); |
163 |
< |
|
164 |
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//creat Molocator |
165 |
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locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
166 |
< |
|
167 |
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//fill Hmat |
168 |
< |
Hmat[0][0] = nx * latticeConstant; |
169 |
< |
Hmat[0][1] = 0.0; |
170 |
< |
Hmat[0][2] = 0.0; |
171 |
< |
|
172 |
< |
Hmat[1][0] = 0.0; |
173 |
< |
Hmat[1][1] = ny * latticeConstant; |
174 |
< |
Hmat[1][2] = 0.0; |
175 |
< |
|
176 |
< |
Hmat[2][0] = 0.0; |
177 |
< |
Hmat[2][1] = 0.0; |
178 |
< |
Hmat[2][2] = nz * latticeConstant ; |
179 |
< |
|
180 |
< |
//set Hmat |
181 |
< |
oldInfo->setBoxM(Hmat); |
182 |
< |
|
183 |
< |
//place the molecules |
184 |
< |
|
185 |
< |
curMolIndex = 0; |
186 |
< |
|
187 |
< |
//get the orientation of the cell sites |
188 |
< |
//for the same type of molecule in same lattice, it will not change |
189 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
190 |
< |
|
191 |
< |
for(int i =0; i < nx; i++){ |
192 |
< |
for(int j=0; j < ny; j++){ |
193 |
< |
for(int k = 0; k < nz; k++){ |
194 |
< |
|
195 |
< |
//get the position of the cell sites |
196 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
197 |
< |
|
198 |
< |
for(int l = 0; l < numMolPerCell; l++) |
199 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); |
200 |
< |
} |
201 |
< |
} |
202 |
< |
} |
203 |
< |
|
204 |
< |
//create dumpwriter and write out the coordinates |
205 |
< |
oldInfo->finalName = outInitFileName; |
206 |
< |
writer = new DumpWriter( oldInfo ); |
207 |
< |
if(writer == NULL){ |
208 |
< |
cerr << "error in creating DumpWriter" << endl; |
209 |
< |
exit(1); |
210 |
< |
} |
211 |
< |
writer->writeFinal(0); |
212 |
< |
cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl; |
213 |
< |
//delete objects |
214 |
< |
|
215 |
< |
//delete oldInfo and oldSimSetup |
216 |
< |
if(oldInfo != NULL) |
217 |
< |
delete oldInfo; |
218 |
< |
|
219 |
< |
if(oldSimSetup != NULL) |
220 |
< |
delete oldSimSetup; |
221 |
< |
|
222 |
< |
if (writer != NULL) |
223 |
< |
delete writer; |
224 |
< |
return 0; |
225 |
< |
} |
226 |
< |
|
227 |
< |
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){ |
228 |
< |
ifstream oldMdFile; |
229 |
< |
ofstream newMdFile; |
230 |
< |
const int MAXLEN = 65535; |
231 |
< |
char buffer[MAXLEN]; |
232 |
< |
|
233 |
< |
//create new .md file based on old .md file |
234 |
< |
oldMdFile.open(oldMdFileName.c_str()); |
235 |
< |
newMdFile.open(newMdFileName.c_str()); |
236 |
< |
|
237 |
< |
oldMdFile.getline(buffer, MAXLEN); |
238 |
< |
while(!oldMdFile.eof()){ |
239 |
< |
|
240 |
< |
//correct molecule number |
241 |
< |
if(strstr(buffer, "nMol") !=NULL){ |
242 |
< |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
243 |
< |
newMdFile << buffer << endl; |
244 |
< |
} |
245 |
< |
else |
246 |
< |
newMdFile << buffer << endl; |
247 |
< |
|
248 |
< |
oldMdFile.getline(buffer, MAXLEN); |
249 |
< |
} |
250 |
< |
|
251 |
< |
oldMdFile.close(); |
252 |
< |
newMdFile.close(); |
253 |
< |
|
254 |
< |
} |
255 |
< |
|
256 |
< |
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){ |
257 |
< |
int nAtoms; |
258 |
< |
AtomStamp* currAtomStamp; |
259 |
< |
double totMass; |
260 |
< |
|
261 |
< |
totMass = 0; |
262 |
< |
nAtoms = molStamp->getNAtoms(); |
263 |
< |
|
264 |
< |
for(size_t i=0; i<nAtoms; i++){ |
265 |
< |
currAtomStamp = molStamp->getAtom(i); |
266 |
< |
totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
267 |
< |
} |
268 |
< |
|
269 |
< |
return totMass; |
270 |
< |
} |
1 |
> |
#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 "io/Globals.hpp" |
11 |
> |
#include "brains/SimInfo.hpp" |
12 |
> |
#include "brains/SimSetup.hpp" |
13 |
> |
#include "applications/simpleBuilder/simpleBuilderCmd.h" |
14 |
> |
#include "utils/StringUtils.hpp" |
15 |
> |
#include "applications/simpleBuilder/LatticeFactory.hpp" |
16 |
> |
#include "math/Vector3.hpp" |
17 |
> |
#include "applications/simpleBuilder/MoLocator.hpp" |
18 |
> |
#include "applications/simpleBuilder/Lattice.hpp" |
19 |
> |
|
20 |
> |
using namespace std; |
21 |
> |
|
22 |
> |
void createMdFile(const string&oldMdFileName, const string&newMdFileName, |
23 |
> |
int numMol); |
24 |
> |
double getMolMass(MoleculeStamp * molStamp, ForceFields * myFF); |
25 |
> |
|
26 |
> |
int main(int argc, char *argv []) { |
27 |
> |
gengetopt_args_info args_info; |
28 |
> |
string latticeType; |
29 |
> |
string inputFileName; |
30 |
> |
string outPrefix; |
31 |
> |
string outMdFileName; |
32 |
> |
string outInitFileName; |
33 |
> |
SimInfo *oldInfo; |
34 |
> |
SimSetup *oldSimSetup; |
35 |
> |
BaseLattice *simpleLat; |
36 |
> |
int numMol; |
37 |
> |
double latticeConstant; |
38 |
> |
vector < double > lc; |
39 |
> |
double mass; |
40 |
> |
const double rhoConvertConst = 1.661; |
41 |
> |
double density; |
42 |
> |
int nx, |
43 |
> |
ny, |
44 |
> |
nz; |
45 |
> |
double Hmat[3][3]; |
46 |
> |
MoLocator *locator; |
47 |
> |
vector < Vector3d > latticePos; |
48 |
> |
vector < Vector3d > latticeOrt; |
49 |
> |
int numMolPerCell; |
50 |
> |
int curMolIndex; |
51 |
> |
DumpWriter *writer; |
52 |
> |
|
53 |
> |
// parse command line arguments |
54 |
> |
if (cmdline_parser(argc, argv, &args_info) != 0) |
55 |
> |
exit(1); |
56 |
> |
|
57 |
> |
density = args_info.density_arg; |
58 |
> |
|
59 |
> |
//get lattice type |
60 |
> |
latticeType = UpperCase(args_info.latticetype_arg); |
61 |
> |
|
62 |
> |
if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
63 |
> |
cerr << latticeType << " is an invalid lattice type" << endl; |
64 |
> |
cerr << LatticeFactory::getInstance()->toString() << endl; |
65 |
> |
exit(1); |
66 |
> |
} |
67 |
> |
|
68 |
> |
//get the number of unit cell |
69 |
> |
nx = args_info.nx_arg; |
70 |
> |
|
71 |
> |
if (nx <= 0) { |
72 |
> |
cerr << "The number of unit cell in h direction must be greater than 0" |
73 |
> |
<< endl; |
74 |
> |
exit(1); |
75 |
> |
} |
76 |
> |
|
77 |
> |
ny = args_info.ny_arg; |
78 |
> |
|
79 |
> |
if (ny <= 0) { |
80 |
> |
cerr << "The number of unit cell in l direction must be greater than 0" |
81 |
> |
<< endl; |
82 |
> |
exit(1); |
83 |
> |
} |
84 |
> |
|
85 |
> |
nz = args_info.nz_arg; |
86 |
> |
|
87 |
> |
if (nz <= 0) { |
88 |
> |
cerr << "The number of unit cell in k direction must be greater than 0" |
89 |
> |
<< endl; |
90 |
> |
exit(1); |
91 |
> |
} |
92 |
> |
|
93 |
> |
//get input file name |
94 |
> |
if (args_info.inputs_num) |
95 |
> |
inputFileName = args_info.inputs[0]; |
96 |
> |
else { |
97 |
> |
cerr << "You must specify a input file name.\n" << endl; |
98 |
> |
cmdline_parser_print_help(); |
99 |
> |
exit(1); |
100 |
> |
} |
101 |
> |
|
102 |
> |
//parse md file and set up the system |
103 |
> |
oldInfo = new SimInfo; |
104 |
> |
|
105 |
> |
if (oldInfo == NULL) { |
106 |
> |
cerr << "error in creating SimInfo" << endl; |
107 |
> |
exit(1); |
108 |
> |
} |
109 |
> |
|
110 |
> |
oldSimSetup = new SimSetup(); |
111 |
> |
|
112 |
> |
if (oldSimSetup == NULL) { |
113 |
> |
cerr << "error in creating SimSetup" << endl; |
114 |
> |
exit(1); |
115 |
> |
} |
116 |
> |
|
117 |
> |
oldSimSetup->suspendInit(); |
118 |
> |
oldSimSetup->setSimInfo(oldInfo); |
119 |
> |
oldSimSetup->parseFile(&inputFileName[0]); |
120 |
> |
oldSimSetup->createSim(); |
121 |
> |
|
122 |
> |
if (oldInfo->nComponents >= 2) { |
123 |
> |
cerr << "can not build the system with more than two components" |
124 |
> |
<< endl; |
125 |
> |
exit(1); |
126 |
> |
} |
127 |
> |
|
128 |
> |
//get mass of molecule. |
129 |
> |
//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
130 |
> |
mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
131 |
> |
|
132 |
> |
//creat lattice |
133 |
> |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
134 |
> |
|
135 |
> |
if (simpleLat == NULL) { |
136 |
> |
cerr << "Error in creating lattice" << endl; |
137 |
> |
exit(1); |
138 |
> |
} |
139 |
> |
|
140 |
> |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
141 |
> |
|
142 |
> |
//calculate lattice constant (in Angstrom) |
143 |
> |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
144 |
> |
1.0 / 3.0); |
145 |
> |
|
146 |
> |
//set lattice constant |
147 |
> |
lc.push_back(latticeConstant); |
148 |
> |
simpleLat->setLatticeConstant(lc); |
149 |
> |
|
150 |
> |
//calculate the total number of molecules |
151 |
> |
numMol = nx * ny * nz * numMolPerCell; |
152 |
> |
|
153 |
> |
if (oldInfo->n_mol != numMol) { |
154 |
> |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
155 |
> |
outMdFileName = outPrefix + ".md"; |
156 |
> |
|
157 |
> |
//creat new .md file on fly which corrects the number of molecule |
158 |
> |
createMdFile(inputFileName, outMdFileName, numMol); |
159 |
> |
cerr |
160 |
> |
<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
161 |
> |
<< endl; |
162 |
> |
cerr << "A new .md file: " << outMdFileName |
163 |
> |
<< " is generated, use it to rerun the simpleBuilder" << endl; |
164 |
> |
exit(1); |
165 |
> |
} |
166 |
> |
|
167 |
> |
//determine the output file names |
168 |
> |
if (args_info.output_given) |
169 |
> |
outInitFileName = args_info.output_arg; |
170 |
> |
else |
171 |
> |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
172 |
> |
|
173 |
> |
//allocat memory for storing pos, vel and etc |
174 |
> |
oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
175 |
> |
|
176 |
> |
for(int i = 0; i < oldInfo->n_atoms; i++) |
177 |
> |
oldInfo->atoms[i]->setCoords(); |
178 |
> |
|
179 |
> |
//creat Molocator |
180 |
> |
locator = new MoLocator(oldInfo->compStamps[0], |
181 |
> |
oldSimSetup->getForceField()); |
182 |
> |
|
183 |
> |
//fill Hmat |
184 |
> |
Hmat[0][0] = nx * latticeConstant; |
185 |
> |
Hmat[0][1] = 0.0; |
186 |
> |
Hmat[0][2] = 0.0; |
187 |
> |
|
188 |
> |
Hmat[1][0] = 0.0; |
189 |
> |
Hmat[1][1] = ny * latticeConstant; |
190 |
> |
Hmat[1][2] = 0.0; |
191 |
> |
|
192 |
> |
Hmat[2][0] = 0.0; |
193 |
> |
Hmat[2][1] = 0.0; |
194 |
> |
Hmat[2][2] = nz * latticeConstant; |
195 |
> |
|
196 |
> |
//set Hmat |
197 |
> |
oldInfo->setBoxM(Hmat); |
198 |
> |
|
199 |
> |
//place the molecules |
200 |
> |
|
201 |
> |
curMolIndex = 0; |
202 |
> |
|
203 |
> |
//get the orientation of the cell sites |
204 |
> |
//for the same type of molecule in same lattice, it will not change |
205 |
> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
206 |
> |
|
207 |
> |
for(int i = 0; i < nx; i++) { |
208 |
> |
for(int j = 0; j < ny; j++) { |
209 |
> |
for(int k = 0; k < nz; k++) { |
210 |
> |
|
211 |
> |
//get the position of the cell sites |
212 |
> |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
213 |
> |
|
214 |
> |
for(int l = 0; l < numMolPerCell; l++) |
215 |
> |
locator->placeMol(latticePos[l], latticeOrt[l], |
216 |
> |
&(oldInfo->molecules[curMolIndex++])); |
217 |
> |
} |
218 |
> |
} |
219 |
> |
} |
220 |
> |
|
221 |
> |
//create dumpwriter and write out the coordinates |
222 |
> |
oldInfo->finalName = outInitFileName; |
223 |
> |
writer = new DumpWriter(oldInfo); |
224 |
> |
|
225 |
> |
if (writer == NULL) { |
226 |
> |
cerr << "error in creating DumpWriter" << endl; |
227 |
> |
exit(1); |
228 |
> |
} |
229 |
> |
|
230 |
> |
writer->writeFinal(0); |
231 |
> |
cout << "new initial configuration file: " << outInitFileName |
232 |
> |
<< " is generated." << endl; |
233 |
> |
|
234 |
> |
//delete objects |
235 |
> |
|
236 |
> |
//delete oldInfo and oldSimSetup |
237 |
> |
if (oldInfo != NULL) |
238 |
> |
delete oldInfo; |
239 |
> |
|
240 |
> |
if (oldSimSetup != NULL) |
241 |
> |
delete oldSimSetup; |
242 |
> |
|
243 |
> |
if (writer != NULL) |
244 |
> |
delete writer; |
245 |
> |
|
246 |
> |
return 0; |
247 |
> |
} |
248 |
> |
|
249 |
> |
void createMdFile(const string&oldMdFileName, const string&newMdFileName, |
250 |
> |
int numMol) { |
251 |
> |
ifstream oldMdFile; |
252 |
> |
ofstream newMdFile; |
253 |
> |
const int MAXLEN = 65535; |
254 |
> |
char buffer[MAXLEN]; |
255 |
> |
|
256 |
> |
//create new .md file based on old .md file |
257 |
> |
oldMdFile.open(oldMdFileName.c_str()); |
258 |
> |
newMdFile.open(newMdFileName.c_str()); |
259 |
> |
|
260 |
> |
oldMdFile.getline(buffer, MAXLEN); |
261 |
> |
|
262 |
> |
while (!oldMdFile.eof()) { |
263 |
> |
|
264 |
> |
//correct molecule number |
265 |
> |
if (strstr(buffer, "nMol") != NULL) { |
266 |
> |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
267 |
> |
newMdFile << buffer << endl; |
268 |
> |
} else |
269 |
> |
newMdFile << buffer << endl; |
270 |
> |
|
271 |
> |
oldMdFile.getline(buffer, MAXLEN); |
272 |
> |
} |
273 |
> |
|
274 |
> |
oldMdFile.close(); |
275 |
> |
newMdFile.close(); |
276 |
> |
} |
277 |
> |
|
278 |
> |
double getMolMass(MoleculeStamp *molStamp, ForceFields *myFF) { |
279 |
> |
int nAtoms; |
280 |
> |
AtomStamp *currAtomStamp; |
281 |
> |
double totMass; |
282 |
> |
|
283 |
> |
totMass = 0; |
284 |
> |
nAtoms = molStamp->getNAtoms(); |
285 |
> |
|
286 |
> |
for(size_t i = 0; i < nAtoms; i++) { |
287 |
> |
currAtomStamp = molStamp->getAtom(i); |
288 |
> |
totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
289 |
> |
} |
290 |
> |
|
291 |
> |
return totMass; |
292 |
> |
} |