Detailed Description
TrajectoryReader for CHARMM ".dcd" data files.
It is assumed that the atoms belonging to all species and molecules of a species occur in the file consecutively. Currently it has only been tested with Hoomd generated trajectory files.
Definition at line 32 of file DCDTrajectoryReader.h.
#include <DCDTrajectoryReader.h>
Public Member Functions | |
| DCDTrajectoryReader (System &system) | |
| Constructor. More... | |
| virtual | ~DCDTrajectoryReader () |
| Destructor. More... | |
| void | open (std::string filename) |
| Read trajectory file header and initialize simulation parameters. 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::DCDTrajectoryReader::DCDTrajectoryReader | ( | System & | system | ) |
Constructor.
Definition at line 35 of file DCDTrajectoryReader.cpp.
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virtual |
Destructor.
Definition at line 45 of file DCDTrajectoryReader.cpp.
Member Function Documentation
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virtual |
Read trajectory file header and initialize simulation parameters.
- Parameters
-
filename name of trajectory file
Implements McMd::TrajectoryReader.
Definition at line 55 of file DCDTrajectoryReader.cpp.
References McMd::TrajectoryReader::addMolecules(), Util::DArray< Data >::allocate(), McMd::TrajectoryReader::nAtomTotal_, and UTIL_THROW.
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virtual |
Read a single frame.
Frames are assumed to be read consecutively.
- Returns
- true if this frame exists, false if at end
Implements McMd::TrajectoryReader.
Definition at line 91 of file DCDTrajectoryReader.cpp.
References McMd::Molecule::begin(), McMd::TrajectoryReader::boundary(), Simp::Species::capacity(), Util::Array< Data >::cArray(), McMd::System::molecule(), 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 trajectory file.
Implements McMd::TrajectoryReader.
Definition at line 205 of file DCDTrajectoryReader.cpp.
The documentation for this class was generated from the following files:
