Detailed Description
TrajectoryReader for Lammps dump trajectory files.
This class assumes that atom ids are ordered by molecule and species, with consecutive ids for atoms in the same molecule and consecutive blocks for molecules in the same species. It does not require that the atoms be ordered consecutively by id within the dump file.
Definition at line 30 of file mcMd/trajectory/LammpsDumpReader.h.
#include <LammpsDumpReader.h>
Public Member Functions | |
| LammpsDumpReader (System &system) | |
| Constructor. More... | |
| virtual | ~LammpsDumpReader () |
| Destructor. More... | |
| void | open (std::string filename) |
| Open file. More... | |
| bool | readFrame () |
| Read a single frame. More... | |
| void | close () |
| Close file. More... | |
 Public Member Functions inherited from McMd::TrajectoryReader | |
| TrajectoryReader (System &system) | |
| Constructor. More... | |
| virtual | ~TrajectoryReader () |
| Destructor. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from McMd::TrajectoryReader | |
| System & | system () const |
| Get a reference to the parent System. More... | |
| Simulation & | simulation () const |
| Get a reference to the parent Simulation. More... | |
| Boundary & | boundary () const |
| Get the Boundary. More... | |
| virtual void | addMolecules () |
| Add all molecules to system. More... | |
| Protected Attributes inherited from McMd::TrajectoryReader | |
| int | nAtomTotal_ |
| Total number of atoms (all species) More... | |
Constructor & Destructor Documentation
| McMd::LammpsDumpReader::LammpsDumpReader | ( | System & | system | ) |
Constructor.
Definition at line 28 of file mcMd/trajectory/LammpsDumpReader.cpp.
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virtual |
Destructor.
Definition at line 35 of file mcMd/trajectory/LammpsDumpReader.cpp.
Member Function Documentation
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virtual |
Open file.
- Parameters
-
filename input file name.
Implements McMd::TrajectoryReader.
Definition at line 41 of file mcMd/trajectory/LammpsDumpReader.cpp.
References McMd::TrajectoryReader::addMolecules(), McMd::Simulation::fileMaster(), McMd::TrajectoryReader::nAtomTotal_, Util::FileMaster::openInputFile(), McMd::TrajectoryReader::simulation(), and UTIL_THROW.
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virtual |
Read a single frame.
Frames are assumed to be read consecutively.
- Returns
- true if this frame is available, false if end of file
Implements McMd::TrajectoryReader.
Definition at line 62 of file mcMd/trajectory/LammpsDumpReader.cpp.
References McMd::Molecule::begin(), McMd::TrajectoryReader::boundary(), Simp::Species::capacity(), Util::checkString(), Util::Dimension, Util::getNextLine(), McMd::System::molecule(), McMd::TrajectoryReader::nAtomTotal_, Util::ArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), Simp::OrthorhombicBoundary::setOrthorhombic(), Simp::OrthorhombicBoundary::shift(), McMd::TrajectoryReader::simulation(), McMd::Simulation::species(), McMd::TrajectoryReader::system(), and UTIL_THROW.
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virtual |
Close file.
Implements McMd::TrajectoryReader.
Definition at line 164 of file mcMd/trajectory/LammpsDumpReader.cpp.
The documentation for this class was generated from the following files:
