_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.
|
__init__(self,
rawframe,
natom=None,
frame_id=None,
cst=None) |
|
|
|
|
|
getStructure(self)
Get a Structure associated with this frame. |
|
|
|
getMinimalDifference(self,
pos1,
pos2)
Calculate the smallest difference between two sets of points in the
frame, paying attention to periodic boundary conditions. |
|
|
|
|
|
position(self)
Position of the real atoms in the frame. |
|
|
|
|
|
velocity(self)
Velocity of the real atoms in the frame. |
|
|
|
particle_position(self)
Position for all particles in the frame, including pseudo atoms. |
|
|
|
particle_velocity(self)
Velocity for all particles in the frame, including pseudo atoms. |
|
|
|
atom_total(self)
Number of real atoms in this frame. |
|
|
|
particle_total(self)
Number of particles in this frame, including atoms and pseudo atoms. |
|
|
|
|
|
|
|
__len__(self)
Return the number of atoms in the frame. |
|
|
a numpy array with shape (9,).
|
box(self)
The simulation box for the frame. |
|
|
a BoundaryCondition instance
|
|
|
time(self)
Chemical time (ps) for this frame. |
|
|
|
charge(self)
Numpy array of atom charges with shape (self._nparticles, 1). |
|
|
|
mass(self)
Numpy array of atom masses with shape (self._nparticles, 1). |
|
|
|
total_mass(self)
Total mass of all atoms in the frame. |
|
|
|
set_pseudo_position(self)
Update positions on the pseudo particles Only works when all pseudo
particles are in a single CT |
|
|