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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 "lattice/LatticeFactory.hpp" |
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> |
#include "utils/MoLocator.hpp" |
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> |
#include "lattice/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 "applications/simpleBuilder/MoLocator.hpp" |
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#include "applications/simpleBuilder/Lattice.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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|
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< |
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol); |
| 67 |
< |
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF); |
| 66 |
> |
void createMdFile(const std::string&oldMdFileName, |
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> |
const std::string&newMdFileName, |
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int nMol); |
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|
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< |
int main( int argc, char* argv[]){ |
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int main(int argc, char *argv []) { |
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|
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// register force fields |
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registerForceFields(); |
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registerLattice(); |
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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; |
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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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> |
std::string latticeType; |
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> |
std::string inputFileName; |
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> |
std::string outputFileName; |
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Lattice *simpleLat; |
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RealType latticeConstant; |
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std::vector<RealType> lc; |
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const RealType rhoConvertConst = 1.661; |
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RealType density; |
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int nx, ny, nz; |
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double Hmat[3][3]; |
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> |
Mat3x3d hmat; |
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MoLocator *locator; |
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< |
vector<Vector3d> latticePos; |
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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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> |
std::vector<Vector3d> latticePos; |
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> |
std::vector<Vector3d> latticeOrt; |
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int nMolPerCell; |
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> |
DumpWriter *writer; |
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|
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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) ; |
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|
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> |
if (cmdline_parser(argc, argv, &args_info) != 0) |
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exit(1); |
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|
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density = args_info.density_arg; |
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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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< |
if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){ |
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cerr << latticeType << " is an invalid lattice type" << endl; |
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cerr << LatticeFactory::getInstance()->toString() << endl; |
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exit(1); |
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latticeType = "FCC"; |
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|
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
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if (simpleLat == NULL) { |
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sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n", |
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latticeType.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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nMolPerCell = simpleLat->getNumSitesPerCell(); |
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|
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//get the number of unit cell |
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//get the number of unit cells in each direction: |
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|
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nx = args_info.nx_arg; |
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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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> |
if (nx <= 0) { |
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> |
sprintf(painCave.errMsg, "The number of unit cells in the x direction " |
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> |
"must be greater than 0."); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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} |
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|
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ny = args_info.ny_arg; |
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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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> |
|
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> |
if (ny <= 0) { |
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> |
sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
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> |
"must be greater than 0."); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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} |
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|
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nz = args_info.nz_arg; |
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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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if (nz <= 0) { |
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> |
sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
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> |
"must be greater than 0."); |
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> |
painCave.isFatal = 1; |
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simError(); |
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} |
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|
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> |
|
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int nSites = nMolPerCell * nx * ny * nz; |
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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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> |
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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else { |
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sprintf(painCave.errMsg, "No input .md file name was specified " |
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"on the command line"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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|
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//parse md file and set up the system |
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oldInfo = new SimInfo; |
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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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|
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< |
oldSimSetup = new SimSetup(); |
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< |
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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> |
SimCreator oldCreator; |
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> |
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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> |
Globals* simParams = oldInfo->getSimParams(); |
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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){ |
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< |
cerr << "Error in creating lattice" << endl; |
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< |
exit(1); |
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< |
} |
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> |
// Calculate lattice constant (in Angstroms) |
| 160 |
|
|
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< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 161 |
> |
RealType avgMass = getMolMass(oldInfo->getMoleculeStamp(0), |
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> |
oldInfo->getForceField()); |
| 163 |
> |
|
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> |
latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density, |
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> |
(RealType)(1.0 / 3.0)); |
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|
|
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< |
//calculate lattice constant (in Angstrom) |
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< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0); |
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> |
// Set the lattice constant |
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|
|
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– |
//set lattice constant |
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|
lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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|
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//calculate the total number of molecules |
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numMol = nx * ny * nz * numMolPerCell; |
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|
|
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< |
if (oldInfo->n_mol != numMol){ |
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> |
// Calculate the lattice sites and fill the lattice vector. |
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|
|
| 174 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 143 |
< |
outMdFileName = outPrefix + ".md"; |
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> |
// Get the standard orientations of the cell sites |
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|
|
| 176 |
< |
//creat new .md file on fly which corrects the number of molecule |
| 177 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
| 178 |
< |
cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl; |
| 179 |
< |
cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl; |
| 180 |
< |
exit(1); |
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> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 177 |
> |
|
| 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 |
> |
// 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 |
< |
//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"; |
| 197 |
> |
outputFileName = args_info.output_arg; |
| 198 |
|
|
| 199 |
< |
|
| 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(); |
| 199 |
> |
// create a new .md file on the fly which corrects the number of molecules |
| 200 |
|
|
| 201 |
< |
//creat Molocator |
| 165 |
< |
locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
| 201 |
> |
createMdFile(inputFileName, outputFileName, nSites); |
| 202 |
|
|
| 203 |
< |
//fill Hmat |
| 204 |
< |
Hmat[0][0] = nx * latticeConstant; |
| 169 |
< |
Hmat[0][1] = 0.0; |
| 170 |
< |
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; |
| 174 |
< |
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; |
| 178 |
< |
Hmat[2][2] = nz * latticeConstant ; |
| 209 |
> |
SimCreator newCreator; |
| 210 |
> |
SimInfo* newInfo = newCreator.createSim(outputFileName, false); |
| 211 |
|
|
| 212 |
< |
//set Hmat |
| 181 |
< |
oldInfo->setBoxM(Hmat); |
| 182 |
< |
|
| 183 |
< |
//place the molecules |
| 212 |
> |
// fill Hmat |
| 213 |
|
|
| 214 |
< |
curMolIndex = 0; |
| 214 |
> |
hmat(0, 0) = nx * latticeConstant; |
| 215 |
> |
hmat(0, 1) = 0.0; |
| 216 |
> |
hmat(0, 2) = 0.0; |
| 217 |
|
|
| 218 |
< |
//get the orientation of the cell sites |
| 219 |
< |
//for the same type of molecule in same lattice, it will not change |
| 220 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 218 |
> |
hmat(1, 0) = 0.0; |
| 219 |
> |
hmat(1, 1) = ny * latticeConstant; |
| 220 |
> |
hmat(1, 2) = 0.0; |
| 221 |
|
|
| 222 |
< |
for(int i =0; i < nx; i++){ |
| 223 |
< |
for(int j=0; j < ny; j++){ |
| 224 |
< |
for(int k = 0; k < nz; k++){ |
| 222 |
> |
hmat(2, 0) = 0.0; |
| 223 |
> |
hmat(2, 1) = 0.0; |
| 224 |
> |
hmat(2, 2) = nz * latticeConstant; |
| 225 |
|
|
| 226 |
< |
//get the position of the cell sites |
| 196 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 226 |
> |
// Set Hmat |
| 227 |
|
|
| 228 |
< |
for(int l = 0; l < numMolPerCell; l++) |
| 199 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); |
| 200 |
< |
} |
| 201 |
< |
} |
| 202 |
< |
} |
| 228 |
> |
newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 229 |
|
|
| 230 |
< |
//create dumpwriter and write out the coordinates |
| 231 |
< |
oldInfo->finalName = outInitFileName; |
| 232 |
< |
writer = new DumpWriter( oldInfo ); |
| 233 |
< |
if(writer == NULL){ |
| 234 |
< |
cerr << "error in creating DumpWriter" << endl; |
| 235 |
< |
exit(1); |
| 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 |
< |
writer->writeFinal(0); |
| 240 |
< |
cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl; |
| 213 |
< |
//delete objects |
| 239 |
> |
|
| 240 |
> |
// Create DumpWriter and write out the coordinates |
| 241 |
|
|
| 242 |
< |
//delete oldInfo and oldSimSetup |
| 216 |
< |
if(oldInfo != NULL) |
| 217 |
< |
delete oldInfo; |
| 242 |
> |
writer = new DumpWriter(newInfo, outputFileName); |
| 243 |
|
|
| 244 |
< |
if(oldSimSetup != NULL) |
| 245 |
< |
delete oldSimSetup; |
| 246 |
< |
|
| 247 |
< |
if (writer != NULL) |
| 248 |
< |
delete writer; |
| 244 |
> |
if (writer == NULL) { |
| 245 |
> |
sprintf(painCave.errMsg, "error in creating DumpWriter"); |
| 246 |
> |
painCave.isFatal = 1; |
| 247 |
> |
simError(); |
| 248 |
> |
} |
| 249 |
> |
|
| 250 |
> |
writer->writeDump(); |
| 251 |
> |
|
| 252 |
> |
// deleting the writer will put the closing at the end of the dump file. |
| 253 |
> |
|
| 254 |
> |
delete writer; |
| 255 |
> |
|
| 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 string& oldMdFileName, const string& newMdFileName, int numMol){ |
| 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; |
| 273 |
|
newMdFile.open(newMdFileName.c_str()); |
| 274 |
|
|
| 275 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 238 |
– |
while(!oldMdFile.eof()){ |
| 276 |
|
|
| 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 << endl; |
| 283 |
< |
} |
| 284 |
< |
else |
| 246 |
< |
newMdFile << buffer << endl; |
| 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 |
|
} |
| 288 |
|
|
| 289 |
|
oldMdFile.close(); |
| 290 |
|
newMdFile.close(); |
| 253 |
– |
|
| 291 |
|
} |
| 292 |
|
|
| 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 |
– |
} |
