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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <map> |
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#include <fstream> |
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|
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#include "io/Globals.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "brains/SimSetup.hpp" |
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#include "applications/simpleBuilder/simpleBuilderCmd.h" |
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#include "utils/StringUtils.hpp" |
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#include "applications/simpleBuilder/LatticeFactory.hpp" |
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#include "math/Vector3.hpp" |
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#include "applications/simpleBuilder/MoLocator.hpp" |
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#include "applications/simpleBuilder/Lattice.hpp" |
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#include "brains/Register.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "io/DumpWriter.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/StringUtils.hpp" |
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|
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using namespace std; |
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using namespace oopse; |
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void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
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int numMol); |
67 |
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|
68 |
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void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol); |
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double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF); |
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int main(int argc, char *argv []) { |
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|
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int main( int argc, char* argv[]){ |
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//register force fields |
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registerForceFields(); |
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|
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gengetopt_args_info args_info; |
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std::string latticeType; |
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std::string inputFileName; |
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std::string outPrefix; |
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std::string outMdFileName; |
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std::string outInitFileName; |
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BaseLattice *simpleLat; |
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int numMol; |
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double latticeConstant; |
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std::vector<double> lc; |
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double mass; |
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const double rhoConvertConst = 1.661; |
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double density; |
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int nx, |
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ny, |
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nz; |
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Mat3x3d hmat; |
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MoLocator *locator; |
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std::vector<Vector3d> latticePos; |
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std::vector<Vector3d> latticeOrt; |
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int numMolPerCell; |
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int curMolIndex; |
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DumpWriter *writer; |
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|
|
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gengetopt_args_info args_info; |
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string latticeType; |
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string inputFileName; |
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< |
string outPrefix; |
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string outMdFileName; |
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string outInitFileName; |
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< |
SimInfo* oldInfo; |
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< |
SimSetup* oldSimSetup; |
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BaseLattice* simpleLat; |
36 |
< |
int numMol; |
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< |
double latticeConstant; |
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vector<double> lc; |
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< |
double mass; |
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const double rhoConvertConst = 1.661; |
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< |
double density; |
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< |
int nx, ny, nz; |
43 |
< |
double Hmat[3][3]; |
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< |
MoLocator *locator; |
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< |
vector<Vector3d> latticePos; |
46 |
< |
vector<Vector3d> latticeOrt; |
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< |
int numMolPerCell; |
48 |
< |
int curMolIndex; |
49 |
< |
DumpWriter* writer; |
50 |
< |
|
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// parse command line arguments |
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if (cmdline_parser (argc, argv, &args_info) != 0) |
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exit(1) ; |
54 |
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|
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density = args_info.density_arg; |
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// parse command line arguments |
98 |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
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exit(1); |
100 |
|
|
101 |
< |
//get lattice type |
58 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
59 |
< |
if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){ |
60 |
< |
cerr << latticeType << " is an invalid lattice type" << endl; |
61 |
< |
cerr << LatticeFactory::getInstance()->toString() << endl; |
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< |
exit(1); |
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} |
101 |
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density = args_info.density_arg; |
102 |
|
|
103 |
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//get the number of unit cell |
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nx = args_info.nx_arg; |
67 |
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if(nx <= 0){ |
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cerr << "The number of unit cell in h direction must be greater than 0" << endl; |
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exit(1); |
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} |
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//get lattice type |
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latticeType = UpperCase(args_info.latticetype_arg); |
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|
|
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< |
ny = args_info.ny_arg; |
107 |
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if(ny <= 0){ |
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< |
cerr << "The number of unit cell in l direction must be greater than 0" << endl; |
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< |
exit(1); |
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} |
106 |
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if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
107 |
> |
std::cerr << latticeType << " is an invalid lattice type" << std::endl; |
108 |
> |
std::cerr << LatticeFactory::getInstance()->toString() << std::endl; |
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exit(1); |
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} |
111 |
|
|
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< |
nz = args_info.nz_arg; |
113 |
< |
if(nz <= 0){ |
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cerr << "The number of unit cell in k direction must be greater than 0" << endl; |
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< |
exit(1); |
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} |
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|
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//get input file name |
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< |
if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
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else { |
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< |
cerr <<"You must specify a input file name.\n" << endl; |
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< |
cmdline_parser_print_help(); |
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< |
exit(1); |
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} |
112 |
> |
//get the number of unit cell |
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nx = args_info.nx_arg; |
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|
|
115 |
< |
|
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< |
//parse md file and set up the system |
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< |
oldInfo = new SimInfo; |
118 |
< |
if(oldInfo == NULL){ |
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< |
cerr << "error in creating SimInfo" << endl; |
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< |
exit(1); |
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} |
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> |
if (nx <= 0) { |
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> |
std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl; |
117 |
> |
exit(1); |
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> |
} |
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|
|
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< |
oldSimSetup = new SimSetup(); |
102 |
< |
if(oldSimSetup == NULL){ |
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cerr << "error in creating SimSetup" << endl; |
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exit(1); |
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} |
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ny = args_info.ny_arg; |
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|
|
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< |
oldSimSetup->suspendInit(); |
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< |
oldSimSetup->setSimInfo(oldInfo ); |
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< |
oldSimSetup->parseFile(&inputFileName[0] ); |
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< |
oldSimSetup->createSim(); |
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|
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< |
if(oldInfo->nComponents >=2){ |
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cerr << "can not build the system with more than two components" << endl; |
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< |
exit(1); |
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} |
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|
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//get mass of molecule. |
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//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
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mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
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|
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//creat lattice |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
123 |
< |
if(simpleLat == NULL){ |
124 |
< |
cerr << "Error in creating lattice" << endl; |
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< |
exit(1); |
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} |
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> |
if (ny <= 0) { |
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> |
std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
124 |
> |
exit(1); |
125 |
> |
} |
126 |
|
|
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< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
129 |
< |
|
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< |
//calculate lattice constant (in Angstrom) |
131 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0); |
132 |
< |
|
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//set lattice constant |
134 |
< |
lc.push_back(latticeConstant); |
135 |
< |
simpleLat->setLatticeConstant(lc); |
136 |
< |
|
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< |
//calculate the total number of molecules |
138 |
< |
numMol = nx * ny * nz * numMolPerCell; |
127 |
> |
nz = args_info.nz_arg; |
128 |
|
|
129 |
< |
if (oldInfo->n_mol != numMol){ |
129 |
> |
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 |
> |
} |
133 |
|
|
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< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
135 |
< |
outMdFileName = outPrefix + ".md"; |
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 |
> |
} |
142 |
|
|
143 |
< |
//creat new .md file on fly which corrects the number of molecule |
144 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
145 |
< |
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 |
< |
|
152 |
< |
//determine the output file names |
153 |
< |
if (args_info.output_given) |
154 |
< |
outInitFileName = args_info.output_arg; |
155 |
< |
else |
156 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
157 |
< |
|
158 |
< |
|
159 |
< |
//allocat memory for storing pos, vel and etc |
160 |
< |
oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
161 |
< |
for (int i = 0; i < oldInfo->n_atoms; i++) |
162 |
< |
oldInfo->atoms[i]->setCoords(); |
143 |
> |
//parse md file and set up the system |
144 |
> |
SimCreator oldCreator; |
145 |
> |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
146 |
|
|
147 |
< |
//creat Molocator |
148 |
< |
locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
147 |
> |
if (oldInfo->getNMoleculeStamp()>= 2) { |
148 |
> |
std::cerr << "can not build the system with more than two components" |
149 |
> |
<< std::endl; |
150 |
> |
exit(1); |
151 |
> |
} |
152 |
|
|
153 |
< |
//fill Hmat |
168 |
< |
Hmat[0][0] = nx * latticeConstant; |
169 |
< |
Hmat[0][1] = 0.0; |
170 |
< |
Hmat[0][2] = 0.0; |
153 |
> |
//get mass of molecule. |
154 |
|
|
155 |
< |
Hmat[1][0] = 0.0; |
173 |
< |
Hmat[1][1] = ny * latticeConstant; |
174 |
< |
Hmat[1][2] = 0.0; |
155 |
> |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
156 |
|
|
157 |
< |
Hmat[2][0] = 0.0; |
158 |
< |
Hmat[2][1] = 0.0; |
178 |
< |
Hmat[2][2] = nz * latticeConstant ; |
157 |
> |
//creat lattice |
158 |
> |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
159 |
|
|
160 |
< |
//set Hmat |
161 |
< |
oldInfo->setBoxM(Hmat); |
162 |
< |
|
163 |
< |
//place the molecules |
160 |
> |
if (simpleLat == NULL) { |
161 |
> |
std::cerr << "Error in creating lattice" << std::endl; |
162 |
> |
exit(1); |
163 |
> |
} |
164 |
|
|
165 |
< |
curMolIndex = 0; |
165 |
> |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
166 |
|
|
167 |
< |
//get the orientation of the cell sites |
168 |
< |
//for the same type of molecule in same lattice, it will not change |
169 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
167 |
> |
//calculate lattice constant (in Angstrom) |
168 |
> |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
169 |
> |
1.0 / 3.0); |
170 |
|
|
171 |
< |
for(int i =0; i < nx; i++){ |
172 |
< |
for(int j=0; j < ny; j++){ |
173 |
< |
for(int k = 0; k < nz; k++){ |
171 |
> |
//set lattice constant |
172 |
> |
lc.push_back(latticeConstant); |
173 |
> |
simpleLat->setLatticeConstant(lc); |
174 |
|
|
175 |
< |
//get the position of the cell sites |
176 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
175 |
> |
//calculate the total number of molecules |
176 |
> |
numMol = nx * ny * nz * numMolPerCell; |
177 |
|
|
178 |
< |
for(int l = 0; l < numMolPerCell; l++) |
179 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); |
180 |
< |
} |
178 |
> |
if (oldInfo->getNGlobalMolecules() != numMol) { |
179 |
> |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
180 |
> |
outMdFileName = outPrefix + ".md"; |
181 |
> |
|
182 |
> |
//creat new .md file on fly which corrects the number of molecule |
183 |
> |
createMdFile(inputFileName, outMdFileName, numMol); |
184 |
> |
std::cerr |
185 |
> |
<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
186 |
> |
<< std::endl; |
187 |
> |
std::cerr << "A new .md file: " << outMdFileName |
188 |
> |
<< " is generated, use it to rerun the simpleBuilder" << std::endl; |
189 |
> |
exit(1); |
190 |
|
} |
202 |
– |
} |
191 |
|
|
192 |
< |
//create dumpwriter and write out the coordinates |
193 |
< |
oldInfo->finalName = outInitFileName; |
194 |
< |
writer = new DumpWriter( oldInfo ); |
195 |
< |
if(writer == NULL){ |
196 |
< |
cerr << "error in creating DumpWriter" << endl; |
197 |
< |
exit(1); |
198 |
< |
} |
199 |
< |
writer->writeFinal(0); |
212 |
< |
cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl; |
213 |
< |
//delete objects |
192 |
> |
//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()); |
200 |
|
|
201 |
< |
//delete oldInfo and oldSimSetup |
202 |
< |
if(oldInfo != NULL) |
203 |
< |
delete oldInfo; |
204 |
< |
|
219 |
< |
if(oldSimSetup != NULL) |
220 |
< |
delete oldSimSetup; |
221 |
< |
|
222 |
< |
if (writer != NULL) |
223 |
< |
delete writer; |
224 |
< |
return 0; |
225 |
< |
} |
201 |
> |
//fill Hmat |
202 |
> |
hmat(0, 0)= nx * latticeConstant; |
203 |
> |
hmat(0, 1) = 0.0; |
204 |
> |
hmat(0, 2) = 0.0; |
205 |
|
|
206 |
< |
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){ |
207 |
< |
ifstream oldMdFile; |
208 |
< |
ofstream newMdFile; |
230 |
< |
const int MAXLEN = 65535; |
231 |
< |
char buffer[MAXLEN]; |
206 |
> |
hmat(1, 0) = 0.0; |
207 |
> |
hmat(1, 1) = ny * latticeConstant; |
208 |
> |
hmat(1, 2) = 0.0; |
209 |
|
|
210 |
< |
//create new .md file based on old .md file |
211 |
< |
oldMdFile.open(oldMdFileName.c_str()); |
212 |
< |
newMdFile.open(newMdFileName.c_str()); |
210 |
> |
hmat(2, 0) = 0.0; |
211 |
> |
hmat(2, 1) = 0.0; |
212 |
> |
hmat(2, 2) = nz * latticeConstant; |
213 |
|
|
214 |
< |
oldMdFile.getline(buffer, MAXLEN); |
215 |
< |
while(!oldMdFile.eof()){ |
214 |
> |
//set Hmat |
215 |
> |
oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
216 |
|
|
217 |
< |
//correct molecule number |
218 |
< |
if(strstr(buffer, "nMol") !=NULL){ |
219 |
< |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
220 |
< |
newMdFile << buffer << endl; |
217 |
> |
//place the molecules |
218 |
> |
|
219 |
> |
curMolIndex = 0; |
220 |
> |
|
221 |
> |
//get the orientation of the cell sites |
222 |
> |
//for the same type of molecule in same lattice, it will not change |
223 |
> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
224 |
> |
|
225 |
> |
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++) { |
231 |
> |
|
232 |
> |
//get the position of the cell sites |
233 |
> |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
234 |
> |
|
235 |
> |
for(int l = 0; l < numMolPerCell; l++) { |
236 |
> |
if (mol != NULL) { |
237 |
> |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
238 |
> |
} else { |
239 |
> |
std::cerr << std::endl; |
240 |
> |
} |
241 |
> |
mol = oldInfo->nextMolecule(mi); |
242 |
> |
} |
243 |
> |
} |
244 |
> |
} |
245 |
|
} |
245 |
– |
else |
246 |
– |
newMdFile << buffer << endl; |
246 |
|
|
247 |
< |
oldMdFile.getline(buffer, MAXLEN); |
248 |
< |
} |
247 |
> |
//create dumpwriter and write out the coordinates |
248 |
> |
oldInfo->setFinalConfigFileName(outInitFileName); |
249 |
> |
writer = new DumpWriter(oldInfo, oldInfo->getDumpFileName()); |
250 |
|
|
251 |
< |
oldMdFile.close(); |
252 |
< |
newMdFile.close(); |
251 |
> |
if (writer == NULL) { |
252 |
> |
std::cerr << "error in creating DumpWriter" << std::endl; |
253 |
> |
exit(1); |
254 |
> |
} |
255 |
|
|
256 |
+ |
writer->writeDump(); |
257 |
+ |
std::cout << "new initial configuration file: " << outInitFileName |
258 |
+ |
<< " is generated." << std::endl; |
259 |
+ |
|
260 |
+ |
//delete objects |
261 |
+ |
|
262 |
+ |
//delete oldInfo and oldSimSetup |
263 |
+ |
if (oldInfo != NULL) |
264 |
+ |
delete oldInfo; |
265 |
+ |
|
266 |
+ |
if (writer != NULL) |
267 |
+ |
delete writer; |
268 |
+ |
|
269 |
+ |
return 0; |
270 |
|
} |
271 |
|
|
272 |
< |
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){ |
273 |
< |
int nAtoms; |
274 |
< |
AtomStamp* currAtomStamp; |
275 |
< |
double totMass; |
276 |
< |
|
277 |
< |
totMass = 0; |
262 |
< |
nAtoms = molStamp->getNAtoms(); |
272 |
> |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
273 |
> |
int numMol) { |
274 |
> |
ifstream oldMdFile; |
275 |
> |
ofstream newMdFile; |
276 |
> |
const int MAXLEN = 65535; |
277 |
> |
char buffer[MAXLEN]; |
278 |
|
|
279 |
< |
for(size_t i=0; i<nAtoms; i++){ |
280 |
< |
currAtomStamp = molStamp->getAtom(i); |
281 |
< |
totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
267 |
< |
} |
279 |
> |
//create new .md file based on old .md file |
280 |
> |
oldMdFile.open(oldMdFileName.c_str()); |
281 |
> |
newMdFile.open(newMdFileName.c_str()); |
282 |
|
|
283 |
< |
return totMass; |
283 |
> |
oldMdFile.getline(buffer, MAXLEN); |
284 |
> |
|
285 |
> |
while (!oldMdFile.eof()) { |
286 |
> |
|
287 |
> |
//correct molecule number |
288 |
> |
if (strstr(buffer, "nMol") != NULL) { |
289 |
> |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
290 |
> |
newMdFile << buffer << std::endl; |
291 |
> |
} else |
292 |
> |
newMdFile << buffer << std::endl; |
293 |
> |
|
294 |
> |
oldMdFile.getline(buffer, MAXLEN); |
295 |
> |
} |
296 |
> |
|
297 |
> |
oldMdFile.close(); |
298 |
> |
newMdFile.close(); |
299 |
|
} |
300 |
+ |
|