|
| def | __init__ (self) |
| |
| def | setPositionsAndVelocities (self, positions, velocities) |
| |
| def | setUniformMass (self, mass) |
| |
| def | isEmpty (self) |
| |
| def | getParticleCount (self) |
| |
| def | getPositions (self) |
| |
| def | getPosition (self, index) |
| |
| def | getVelocities (self) |
| |
| def | getVelocity (self, index) |
| |
| def | getMass (self, index) |
| |
| def | getMomentum (self, index) |
| |
| def | getCenterOfMass (self) |
| |
| def | getCenterOfPositions (self) |
| |
| def | getCenterOfMassVelocity (self) |
| |
| def | rotateAroundNormalizedAxis (self, axis, angle) |
| |
| def | shiftToCenterOfMassFrame (self) |
| |
| def | getGyrationTensor (self) |
| |
|
def | getMomentOfInertiaTensor (self) |
| |
|
def | getTotalAngularMomentumVector (self) |
| |
|
def | getRotationFrequencyVector (self) |
| |
| def | getGyrationTensorPrincipalMoments (self) |
| |
| def | getGyrationTensorEigensystem (self) |
| |
| def | getRadiusOfGyrationSquared (self) |
| |
| def | getRadiusOfGyration (self) |
| |
| def | getAsphericity (self) |
| |
| def | getAcylindricity (self) |
| |
| def | getRelativeShapeAnisotropy (self) |
| |
| def | getOrientationAngle (self, axis) |
| |
| def | getOrientationAngles (self, axis) |
| |
| def | __eq__ (self, rhs) |
| |
| def | __ne__ (self, rhs) |
| |
|
|
| positions |
| |
|
| velocities |
| |
|
| uniformMass |
| |
|
| gyrationTensor |
| |
Represents the state of a collection of particles.
Definition at line 11 of file ParticleCollection.py.
◆ __init__()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.__init__ |
( |
|
self | ) |
|
◆ __eq__()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.__eq__ |
( |
|
self, |
|
|
|
rhs |
|
) |
| |
The equality operator.
Returns whether this instance stores the same particles (i.e. their
count, positions, velocities, and masses) as the given `rhs` instance.
Having set a different uniform mass in two instances makes them not
equal, even if there are no particles.
@param[in] rhs The right-hand-side instance to compare to.
@return Returns whether the two instances are equal, or `NotImplemented`
if the two instances are not of the same type.
Definition at line 668 of file ParticleCollection.py.
◆ __ne__()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.__ne__ |
( |
|
self, |
|
|
|
rhs |
|
) |
| |
The inequality operator.
@param[in] rhs The right-hand-side instance to compare to.
@return Returns `NotImplemented` if the two instances are not of the
same type, and `not self == rhs` otherwise.
Definition at line 697 of file ParticleCollection.py.
◆ getAcylindricity()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getAcylindricity |
( |
|
self | ) |
|
Returns the acylindricity \f$ c \f$, i.e.
\f[
\lambda_y^2 - \lambda_x^2
\f]
where \f$ \lambda_x^2 \f$ is the smallest eigenvalue of the gyration
tensor, \f$ \lambda_z^2 \f$ is the largest eigenvalue, and
\f$ \lambda_y^2 \f$ is the one in between.
Definition at line 573 of file ParticleCollection.py.
◆ getAsphericity()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getAsphericity |
( |
|
self | ) |
|
Returns the asphericity \f$ b \f$, i.e.
\f[
\lambda_z^2 - \frac{1}{2} \left( \lambda_x^2 + \lambda_y^2 \right)
\f]
where \f$ \lambda_z^2 \f$ is the largest eigenvalue of the gyration
tensor, and \f$ \lambda_x^2 \f$ and \f$ \lambda_y^2 \f$ are the two
smallest eigenvalues.
Definition at line 557 of file ParticleCollection.py.
◆ getCenterOfMass()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getCenterOfMass |
( |
|
self | ) |
|
Returns the center of mass of the particles, as an instance of
`Vector3DReal`.
@throw RuntimeError
Throws if `isEmpty()`.
@throw RuntimeError
Throws if the mass has not been specified for all particles.
Definition at line 251 of file ParticleCollection.py.
◆ getCenterOfMassVelocity()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getCenterOfMassVelocity |
( |
|
self | ) |
|
Returns the velocity of the center of mass, as an instance of
`Vector3DReal`.
@throw RuntimeError
Throws if `isEmpty()`.
@throw RuntimeError
Throws if the mass has not been specified for all particles.
Definition at line 299 of file ParticleCollection.py.
◆ getCenterOfPositions()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getCenterOfPositions |
( |
|
self | ) |
|
Returns the unweighted average of all particle positions, as an instance
of `Vector3DReal`.
@throw RuntimeError
Throws if `isEmpty()`.
Definition at line 276 of file ParticleCollection.py.
◆ getGyrationTensor()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getGyrationTensor |
( |
|
self | ) |
|
Returns the gyration tensor \f$ S \f$.
The returned object is a \f$ 3 \times 3 \f$ symmetric matrix of type
`numpy.ndarray`.
Given \f$ N \f$ particles with positions \f$ \vec{r}^{(i)} \f$ (in any
Cartesian coordinate frame), the \f$ \left( m, n \right) \f$-component
of the gyration tensor is defined by
\f[
S_{mn}
=
\frac{ 1 }{ 2 N^2 }
\sum_{i = 1}^N
\sum_{j = 1}^N
\left( \vec{r}^{(i)}_m - \vec{r}^{(j)}_m \right)
\left( \vec{r}^{(i)}_n - \vec{r}^{(j)}_n \right)
\f]
@throw ValueError
Throws if there are no particles in this instance.
Definition at line 392 of file ParticleCollection.py.
◆ getGyrationTensorEigensystem()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getGyrationTensorEigensystem |
( |
|
self | ) |
|
Returns the eigenvalues and eigenvectors of the gyration tensor (as
returned by `getGyrationTensor`).
The returned object is a list, with each element being a list of first
the eigenvalue, and second the associated eigenvector. The tuples are
sorted by the value of the eigenvalue, smallest first.
The eigenvalues are real and of type `numpy.float64`, and the
eigenvectors are of type `numpy.ndarray` with three entries of type
`numpy.float64`.
Definition at line 509 of file ParticleCollection.py.
◆ getGyrationTensorPrincipalMoments()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getGyrationTensorPrincipalMoments |
( |
|
self | ) |
|
Returns the eigenvalues \f$ \lambda_x^2 \f$, \f$ \lambda_y^2 \f$, and
\f$ \lambda_z^2 \f$ of the gyration tensor (as returned by
`getGyrationTensor`). The eigenvalues are arranged such that
\f$ \lambda_x^2 \le \lambda_y^2 \le \lambda_y^z \f$.
The eigenvalues are real and of type `numpy.float64`, and returned as
the elements of a list.
Definition at line 483 of file ParticleCollection.py.
◆ getMass()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getMass |
( |
|
self, |
|
|
|
index |
|
) |
| |
Returns the mass of the particle with the given `index` as a `float`.
@throw IndexError
Throws if `index` is negative or `index >= getParticleCount()`.
@throw RuntimeError
Throws if no mass has been specified for the given particle.
@throw TypeError
Throws if `index` is not an `int`.
@param[in] index
The index of the particle to query, in the range of
`[0, getParticleCount() - 1]`.
Definition at line 206 of file ParticleCollection.py.
◆ getMomentum()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getMomentum |
( |
|
self, |
|
|
|
index |
|
) |
| |
Returns the momentum of the particle with the given `index`, as an
instance of `Vector3DReal`
@throw IndexError
Throws if `index` is negative or `index >= getParticleCount()`.
@throw RuntimeError
Throws if no mass has been specified for the given particle.
@throw TypeError
Throws if `index` is not an `int`.
@param[in] index
The index of the particle to query, in the range of
`[0, getParticleCount() - 1]`.
Definition at line 236 of file ParticleCollection.py.
◆ getOrientationAngle()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getOrientationAngle |
( |
|
self, |
|
|
|
axis |
|
) |
| |
Returns the angle between the given `axis` and the eigenvector of the
gyration tensor that corresponds to the largest eigenvalue.
Definition at line 601 of file ParticleCollection.py.
◆ getOrientationAngles()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getOrientationAngles |
( |
|
self, |
|
|
|
axis |
|
) |
| |
Returns the angle between the given `axis` and the eigenvectors of the
gyration tensor. The returned value is a list, sorted by increasing
eigenvalues, of pairs of eigenvalue and corresponding angle.
Definition at line 616 of file ParticleCollection.py.
◆ getParticleCount()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getParticleCount |
( |
|
self | ) |
|
◆ getPosition()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getPosition |
( |
|
self, |
|
|
|
index |
|
) |
| |
Returns the position of the particle with the given `index`, as an
instance of `Vector3DReal`.
@throw IndexError
Throws if `index` is negative or `index >= getParticleCount()`.
@throw TypeError
Throws if `index` is not an `int`.
@param[in] index
The index of the particle to query, in the range of
`[0, getParticleCount() - 1]`.
Definition at line 143 of file ParticleCollection.py.
◆ getPositions()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getPositions |
( |
|
self | ) |
|
Returns a reference to the internal list of position vectors.
@warning
It is assumed that the returned reference will not be manipulated!
Definition at line 124 of file ParticleCollection.py.
◆ getRadiusOfGyration()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getRadiusOfGyration |
( |
|
self | ) |
|
Returns the radius of gyration \f$ R_g \f$, i.e. the square root of the
result of `getRadiusOfGyrationSquared`.
Definition at line 543 of file ParticleCollection.py.
◆ getRadiusOfGyrationSquared()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getRadiusOfGyrationSquared |
( |
|
self | ) |
|
Returns the sum of the eigenvalues of the gyration tensor, as returned
by `getGyrationTensorPrincipalMoments`
Definition at line 532 of file ParticleCollection.py.
◆ getRelativeShapeAnisotropy()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getRelativeShapeAnisotropy |
( |
|
self | ) |
|
Returns the relative shape anisotropy \f$ \kappa^2 \f$, i.e.
\f[
\frac{ b^2 + \frac{3}{4} c^2 }{ R_g^4 }
\f]
where \f$ b \f$ is the asphericity, \f$ c \f$ is the acylindricity, and
\f$ R_g \f$ is the radius of gyration.
Definition at line 588 of file ParticleCollection.py.
◆ getVelocities()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getVelocities |
( |
|
self | ) |
|
Returns a reference to the internal list of velocity vectors.
@warning
It is assumed that the returned reference will not be manipulated!
Definition at line 161 of file ParticleCollection.py.
◆ getVelocity()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.getVelocity |
( |
|
self, |
|
|
|
index |
|
) |
| |
Returns the velocity of the particle with the given `index`, as an
instance of `Vector3DReal`
@throw IndexError
Throws if `index` is negative or `index >= getParticleCount()`.
@throw TypeError
Throws if `index` is not an `int`.
@param[in] index
The index of the particle to query, in the range of
`[0, getParticleCount() - 1]`.
Definition at line 180 of file ParticleCollection.py.
◆ isEmpty()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.isEmpty |
( |
|
self | ) |
|
◆ rotateAroundNormalizedAxis()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.rotateAroundNormalizedAxis |
( |
|
self, |
|
|
|
axis, |
|
|
|
angle |
|
) |
| |
Rotates all position and velocity vectors around the given `axis` for
the given `angle`.
@throw TypeError
Throws if one of the arguments is of the wrong type.
@throw ValueError
Throws if `axis` is not a unit-length vector.
@param[in] axis
The axis to rotate around, which must have unit length.
@param[in] angle
The angle to rotate, in radians, as an instance of `float`.
Definition at line 331 of file ParticleCollection.py.
◆ setPositionsAndVelocities()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.setPositionsAndVelocities |
( |
|
self, |
|
|
|
positions, |
|
|
|
velocities |
|
) |
| |
Sets the particle positions and velocities.
The given arguments will be copied into an instance-internal store.
@throw TypeError
Throws if the arguments do not have the types specified in their
documentation.
@throw ValueError
Throws if the `positions` and `velocities` lists do not have
equal length.
@param[in] positions
A list of `Vector3DReal` instances, describing the particle
positions.
@param[in] velocities
A list of `Vector3DReal` instances, describing the particle
velocities.
Definition at line 46 of file ParticleCollection.py.
◆ setUniformMass()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.setUniformMass |
( |
|
self, |
|
|
|
mass |
|
) |
| |
Sets a uniform mass for all particles, including currently stored ones
and ones that may be added or altered later.
@throw TypeError
Throws if `mass` is neither `int` nor `float`.
@throw ValueError
Throws if `mass` is smaller than `0`.
@param[in] mass
The particle mass, which must be a non-negative `int` or
`float`.
Definition at line 88 of file ParticleCollection.py.
◆ shiftToCenterOfMassFrame()
| def MPCDAnalysis.ParticleCollection.ParticleCollection.shiftToCenterOfMassFrame |
( |
|
self | ) |
|
Transforms the positions and velocities into the center of mass frame.
Definition at line 356 of file ParticleCollection.py.
The documentation for this class was generated from the following file:
