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 "applications/simpleBuilder/simpleBuilderCmd.h" |
11 |
#include "applications/simpleBuilder/LatticeFactory.hpp" |
12 |
#include "applications/simpleBuilder/MoLocator.hpp" |
13 |
#include "applications/simpleBuilder/Lattice.hpp" |
14 |
#include "brains/SimInfo.hpp" |
15 |
#include "brains/SimCreator.hpp" |
16 |
#include "io/DumpWriter.hpp" |
17 |
#include "math/Vector3.hpp" |
18 |
#include "math/SquareMatrix3.hpp" |
19 |
#include "utils/StringUtils.hpp" |
20 |
#include "UseTheForce/DUFF.hpp" |
21 |
#include "UseTheForce/EAM.hpp" |
22 |
#include "UseTheForce/ForceFieldCreator.hpp" |
23 |
|
24 |
using namespace std; |
25 |
using namespace oopse; |
26 |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
27 |
int numMol); |
28 |
|
29 |
int main(int argc, char *argv []) { |
30 |
|
31 |
ForceFieldBuilder<DUFF> DUFFCreator("DUFF"); |
32 |
ForceFieldBuilder<DUFF> WATERCreator("WATER"); |
33 |
ForceFieldBuilder<DUFF> LJCreator("LJ"); |
34 |
//in theory, EAM can also be merged |
35 |
ForceFieldBuilder<EAM> EAMCreator("EAM"); |
36 |
|
37 |
gengetopt_args_info args_info; |
38 |
std::string latticeType; |
39 |
std::string inputFileName; |
40 |
std::string outPrefix; |
41 |
std::string outMdFileName; |
42 |
std::string outInitFileName; |
43 |
BaseLattice *simpleLat; |
44 |
int numMol; |
45 |
double latticeConstant; |
46 |
std::vector<double> lc; |
47 |
double mass; |
48 |
const double rhoConvertConst = 1.661; |
49 |
double density; |
50 |
int nx, |
51 |
ny, |
52 |
nz; |
53 |
Mat3x3d hmat; |
54 |
MoLocator *locator; |
55 |
std::vector<Vector3d> latticePos; |
56 |
std::vector<Vector3d> latticeOrt; |
57 |
int numMolPerCell; |
58 |
int curMolIndex; |
59 |
DumpWriter *writer; |
60 |
|
61 |
// parse command line arguments |
62 |
if (cmdline_parser(argc, argv, &args_info) != 0) |
63 |
exit(1); |
64 |
|
65 |
density = args_info.density_arg; |
66 |
|
67 |
//get lattice type |
68 |
latticeType = UpperCase(args_info.latticetype_arg); |
69 |
|
70 |
if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
71 |
std::cerr << latticeType << " is an invalid lattice type" << std::endl; |
72 |
std::cerr << LatticeFactory::getInstance()->toString() << std::endl; |
73 |
exit(1); |
74 |
} |
75 |
|
76 |
//get the number of unit cell |
77 |
nx = args_info.nx_arg; |
78 |
|
79 |
if (nx <= 0) { |
80 |
std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl; |
81 |
exit(1); |
82 |
} |
83 |
|
84 |
ny = args_info.ny_arg; |
85 |
|
86 |
if (ny <= 0) { |
87 |
std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
88 |
exit(1); |
89 |
} |
90 |
|
91 |
nz = args_info.nz_arg; |
92 |
|
93 |
if (nz <= 0) { |
94 |
std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl; |
95 |
exit(1); |
96 |
} |
97 |
|
98 |
//get input file name |
99 |
if (args_info.inputs_num) |
100 |
inputFileName = args_info.inputs[0]; |
101 |
else { |
102 |
std::cerr << "You must specify a input file name.\n" << std::endl; |
103 |
cmdline_parser_print_help(); |
104 |
exit(1); |
105 |
} |
106 |
|
107 |
//parse md file and set up the system |
108 |
SimCreator oldCreator; |
109 |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
110 |
|
111 |
if (oldInfo->getNMoleculeStamp()>= 2) { |
112 |
std::cerr << "can not build the system with more than two components" |
113 |
<< std::endl; |
114 |
exit(1); |
115 |
} |
116 |
|
117 |
//get mass of molecule. |
118 |
|
119 |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
120 |
|
121 |
//creat lattice |
122 |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
123 |
|
124 |
if (simpleLat == NULL) { |
125 |
std::cerr << "Error in creating lattice" << std::endl; |
126 |
exit(1); |
127 |
} |
128 |
|
129 |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
130 |
|
131 |
//calculate lattice constant (in Angstrom) |
132 |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
133 |
1.0 / 3.0); |
134 |
|
135 |
//set lattice constant |
136 |
lc.push_back(latticeConstant); |
137 |
simpleLat->setLatticeConstant(lc); |
138 |
|
139 |
//calculate the total number of molecules |
140 |
numMol = nx * ny * nz * numMolPerCell; |
141 |
|
142 |
if (oldInfo->getNGlobalMolecules() != numMol) { |
143 |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
144 |
outMdFileName = outPrefix + ".md"; |
145 |
|
146 |
//creat new .md file on fly which corrects the number of molecule |
147 |
createMdFile(inputFileName, outMdFileName, numMol); |
148 |
std::cerr |
149 |
<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
150 |
<< std::endl; |
151 |
std::cerr << "A new .md file: " << outMdFileName |
152 |
<< " is generated, use it to rerun the simpleBuilder" << std::endl; |
153 |
exit(1); |
154 |
} |
155 |
|
156 |
//determine the output file names |
157 |
if (args_info.output_given) |
158 |
outInitFileName = args_info.output_arg; |
159 |
else |
160 |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
161 |
|
162 |
//creat Molocator |
163 |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
164 |
|
165 |
//fill Hmat |
166 |
hmat(0, 0)= nx * latticeConstant; |
167 |
hmat(0, 1) = 0.0; |
168 |
hmat(0, 2) = 0.0; |
169 |
|
170 |
hmat(1, 0) = 0.0; |
171 |
hmat(1, 1) = ny * latticeConstant; |
172 |
hmat(1, 2) = 0.0; |
173 |
|
174 |
hmat(2, 0) = 0.0; |
175 |
hmat(2, 1) = 0.0; |
176 |
hmat(2, 2) = nz * latticeConstant; |
177 |
|
178 |
//set Hmat |
179 |
oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
180 |
|
181 |
//place the molecules |
182 |
|
183 |
curMolIndex = 0; |
184 |
|
185 |
//get the orientation of the cell sites |
186 |
//for the same type of molecule in same lattice, it will not change |
187 |
latticeOrt = simpleLat->getLatticePointsOrt(); |
188 |
|
189 |
Molecule* mol; |
190 |
SimInfo::MoleculeIterator mi; |
191 |
mol = oldInfo->beginMolecule(mi); |
192 |
for(int i = 0; i < nx; i++) { |
193 |
for(int j = 0; j < ny; j++) { |
194 |
for(int k = 0; k < nz; k++) { |
195 |
|
196 |
//get the position of the cell sites |
197 |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
198 |
|
199 |
for(int l = 0; l < numMolPerCell; l++) { |
200 |
if (mol != NULL) { |
201 |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
202 |
} else { |
203 |
std::cerr << std::endl; |
204 |
} |
205 |
mol = oldInfo->nextMolecule(mi); |
206 |
} |
207 |
} |
208 |
} |
209 |
} |
210 |
|
211 |
//create dumpwriter and write out the coordinates |
212 |
oldInfo->setFinalConfigFileName(outInitFileName); |
213 |
writer = new DumpWriter(oldInfo, oldInfo->getDumpFileName()); |
214 |
|
215 |
if (writer == NULL) { |
216 |
std::cerr << "error in creating DumpWriter" << std::endl; |
217 |
exit(1); |
218 |
} |
219 |
|
220 |
writer->writeDump(); |
221 |
std::cout << "new initial configuration file: " << outInitFileName |
222 |
<< " is generated." << std::endl; |
223 |
|
224 |
//delete objects |
225 |
|
226 |
//delete oldInfo and oldSimSetup |
227 |
if (oldInfo != NULL) |
228 |
delete oldInfo; |
229 |
|
230 |
if (writer != NULL) |
231 |
delete writer; |
232 |
|
233 |
return 0; |
234 |
} |
235 |
|
236 |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
237 |
int numMol) { |
238 |
ifstream oldMdFile; |
239 |
ofstream newMdFile; |
240 |
const int MAXLEN = 65535; |
241 |
char buffer[MAXLEN]; |
242 |
|
243 |
//create new .md file based on old .md file |
244 |
oldMdFile.open(oldMdFileName.c_str()); |
245 |
newMdFile.open(newMdFileName.c_str()); |
246 |
|
247 |
oldMdFile.getline(buffer, MAXLEN); |
248 |
|
249 |
while (!oldMdFile.eof()) { |
250 |
|
251 |
//correct molecule number |
252 |
if (strstr(buffer, "nMol") != NULL) { |
253 |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
254 |
newMdFile << buffer << std::endl; |
255 |
} else |
256 |
newMdFile << buffer << std::endl; |
257 |
|
258 |
oldMdFile.getline(buffer, MAXLEN); |
259 |
} |
260 |
|
261 |
oldMdFile.close(); |
262 |
newMdFile.close(); |
263 |
} |
264 |
|