Detailed Description
TrajectoryReader for a DdMd trajectory file.
This class assumes that atom tags are ordered by molecule and species, with consecutive ids for atoms in the same molecule and consecutive blocks for molecules in the same species.
Definition at line 31 of file mcMd/trajectory/DdMdTrajectoryReader.h.
#include <DdMdTrajectoryReader.h>
Public Member Functions | |
| DdMdTrajectoryReader (System &system) | |
| Constructor. More... | |
| virtual | ~DdMdTrajectoryReader () |
| Destructor. More... | |
| void | open (std::string filename) |
| Open trajectory file, read header, and allocate memory. More... | |
| bool | readFrame () |
| Read a single frame. More... | |
| void | close () |
| Close trajectory 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::DdMdTrajectoryReader::DdMdTrajectoryReader | ( | System & | system | ) |
Constructor.
Definition at line 29 of file mcMd/trajectory/DdMdTrajectoryReader.cpp.
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virtual |
Destructor.
Definition at line 36 of file mcMd/trajectory/DdMdTrajectoryReader.cpp.
Member Function Documentation
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virtual |
Open trajectory file, read header, and allocate memory.
- Parameters
-
filename trajectory file name
Implements McMd::TrajectoryReader.
Definition at line 42 of file mcMd/trajectory/DdMdTrajectoryReader.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 71 of file mcMd/trajectory/DdMdTrajectoryReader.cpp.
References McMd::Molecule::begin(), McMd::TrajectoryReader::boundary(), Simp::Species::capacity(), Util::Dimension, McMd::System::molecule(), McMd::TrajectoryReader::nAtomTotal_, Util::ArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), McMd::TrajectoryReader::simulation(), McMd::Simulation::species(), McMd::TrajectoryReader::system(), Simp::OrthorhombicBoundary::transformGenToCart(), and UTIL_THROW.
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virtual |
Close trajectory file.
Implements McMd::TrajectoryReader.
Definition at line 129 of file mcMd/trajectory/DdMdTrajectoryReader.cpp.
The documentation for this class was generated from the following files:
