_DesmondFrame contains simulation data at a particular time.
Each raw frame may contain position and velocity of pseudo atoms. Data
for pseudo atoms can appear behind component ct or solvent ct. We don't
want to expose them in most cases.
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rawframe,
natom=None,
frame_id=None,
cst=None) |
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getStructure(self)
Get a Structure associated with this frame. |
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getMinimalDifference(self,
pos1,
pos2)
Calculate the smallest difference between two sets of points in the
frame, paying attention to periodic boundary conditions. |
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__len__(self)
Return the number of atoms in the frame. |
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numpy array with shape (self._natom, 3)
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position
Position of the real atoms in the frame.
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numpy array with shape (self._natom,3)
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pseudo_position
Position of pseudo particles in the frame.
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numpy array with shape (self._natom, 3)
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velocity
Velocity of the real atoms in the frame.
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numpy array with shape (self._nparticles, 3)
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particle_position
Position for all particles in the frame, including pseudo atoms.
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numpy array with shape (self._nparticles, 3)
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particle_velocity
Velocity for all particles in the frame, including pseudo atoms.
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atom_total
Number of real atoms in this frame.
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particle_total
Number of particles in this frame, including atoms and pseudo atoms.
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a numpy array with shape (9,).
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box
The simulation box for the frame.
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a BoundaryCondition instance
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boundary_condition
The periodic boundary condition for this frame.
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time
Chemical time (ps) for this frame.
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charge
Numpy array of atom charges with shape (self._nparticles, 1).
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mass
Numpy array of atom masses with shape (self._nparticles, 1).
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total_mass
Total mass of all atoms in the frame.
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set_pseudo_position
Update positions on the pseudo particles Only works when all pseudo
particles are in a single CT
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