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Big documentation and structure updates

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- Split math into fdmath package
- Rename waveguide into _2d _3d and _cyl variants
- pdoc-based documentation
This commit is contained in:
Jan Petykiewicz 2019-11-24 23:47:31 -08:00
parent f0ef31c25d
commit d6e7e3dee1
25 changed files with 2579 additions and 1338 deletions
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3
make_docs.sh Executable file
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@ -0,0 +1,3 @@
#!/bin/bash
cd ~/projects/meanas
pdoc3 --html --force --template-dir pdoc_templates -o doc .

24
meanas/eigensolvers.py
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@ -15,10 +15,13 @@ def power_iteration(operator: sparse.spmatrix,
"""
Use power iteration to estimate the dominant eigenvector of a matrix.
:param operator: Matrix to analyze.
:param guess_vector: Starting point for the eigenvector. Default is a randomly chosen vector.
:param iterations: Number of iterations to perform. Default 20.
:return: (Largest-magnitude eigenvalue, Corresponding eigenvector estimate)
Args:
operator: Matrix to analyze.
guess_vector: Starting point for the eigenvector. Default is a randomly chosen vector.
iterations: Number of iterations to perform. Default 20.
Returns:
(Largest-magnitude eigenvalue, Corresponding eigenvector estimate)
"""
if numpy.any(numpy.equal(guess_vector, None)):
v = numpy.random.rand(operator.shape[0])
@ -91,12 +94,15 @@ def signed_eigensolve(operator: sparse.spmatrix or spalg.LinearOperator,
Find the largest-magnitude positive-only (or negative-only) eigenvalues and
eigenvectors of the provided matrix.
:param operator: Matrix to analyze.
:param how_many: How many eigenvalues to find.
:param negative: Whether to find negative-only eigenvalues.
Args:
operator: Matrix to analyze.
how_many: How many eigenvalues to find.
negative: Whether to find negative-only eigenvalues.
Default False (positive only).
:return: (sorted list of eigenvalues, 2D ndarray of corresponding eigenvectors)
eigenvectors[:, k] corresponds to the k-th eigenvalue
Returns:
(sorted list of eigenvalues, 2D ndarray of corresponding eigenvectors)
`eigenvectors[:, k]` corresponds to the k-th eigenvalue
"""
# Use power iteration to estimate the dominant eigenvector
lm_eigval, _ = power_iteration(operator)

17
meanas/fdfd/__init__.py
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@ -1,2 +1,17 @@
from . import solvers, operators, functional, scpml, waveguide, waveguide_mode
"""
Tools for finite difference frequency-domain (FDFD) simulations and calculations.
These mostly involve picking a single frequency, then setting up and solving a
matrix equation (Ax=b) or eigenvalue problem.
Submodules:
- `operators`, `functional`: General FDFD problem setup.
- `solvers`: Solver interface and reference implementation.
- `scpml`: Stretched-coordinate perfectly matched layer (scpml) boundary conditions
- `waveguide_2d`: Operators and mode-solver for waveguides with constant cross-section.
- `waveguide_3d`: Functions for transforming `waveguide_2d` results into 3D.
"""
from . import solvers, operators, functional, scpml, waveguide_2d, waveguide_3d
# from . import farfield, bloch TODO

2
meanas/fdfd/bloch.py
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@ -83,7 +83,7 @@ import scipy.optimize
from scipy.linalg import norm
import scipy.sparse.linalg as spalg
from . import field_t
from .. import field_t
logger = logging.getLogger(__name__)

6
meanas/fdfd/farfield.py
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@ -1,7 +1,7 @@
"""
Functions for performing near-to-farfield transformation (and the reverse).
"""
from typing import Dict, List
from typing import Dict, List, Any
import numpy
from numpy.fft import fft2, fftshift, fftfreq, ifft2, ifftshift
from numpy import pi
@ -14,7 +14,7 @@ def near_to_farfield(E_near: field_t,
dx: float,
dy: float,
padded_size: List[int] = None
) -> Dict[str]:
) -> Dict[str, Any]:
"""
Compute the farfield, i.e. the distribution of the fields after propagation
through several wavelengths of uniform medium.
@ -122,7 +122,7 @@ def far_to_nearfield(E_far: field_t,
dkx: float,
dky: float,
padded_size: List[int] = None
) -> Dict[str]:
) -> Dict[str, Any]:
"""
Compute the farfield, i.e. the distribution of the fields after propagation
through several wavelengths of uniform medium.

188
meanas/fdfd/functional.py
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@ -2,88 +2,41 @@
Functional versions of many FDFD operators. These can be useful for performing
FDFD calculations without needing to construct large matrices in memory.
The functions generated here expect field inputs with shape (3, X, Y, Z),
The functions generated here expect `field_t` inputs with shape (3, X, Y, Z),
e.g. E = [E_x, E_y, E_z] where each component has shape (X, Y, Z)
"""
from typing import List, Callable
from typing import List, Callable, Tuple
import numpy
from .. import dx_lists_t, field_t
from ..fdmath.functional import curl_forward, curl_back
__author__ = 'Jan Petykiewicz'
functional_matrix = Callable[[field_t], field_t]
def curl_h(dxes: dx_lists_t) -> functional_matrix:
"""
Curl operator for use with the H field.
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Function for taking the discretized curl of the H-field, F(H) -> curlH
"""
dxyz_b = numpy.meshgrid(*dxes[1], indexing='ij')
def dh(f, ax):
return (f - numpy.roll(f, 1, axis=ax)) / dxyz_b[ax]
def ch_fun(h: field_t) -> field_t:
e = numpy.empty_like(h)
e[0] = dh(h[2], 1)
e[0] -= dh(h[1], 2)
e[1] = dh(h[0], 2)
e[1] -= dh(h[2], 0)
e[2] = dh(h[1], 0)
e[2] -= dh(h[0], 1)
return e
return ch_fun
def curl_e(dxes: dx_lists_t) -> functional_matrix:
"""
Curl operator for use with the E field.
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Function for taking the discretized curl of the E-field, F(E) -> curlE
"""
dxyz_a = numpy.meshgrid(*dxes[0], indexing='ij')
def de(f, ax):
return (numpy.roll(f, -1, axis=ax) - f) / dxyz_a[ax]
def ce_fun(e: field_t) -> field_t:
h = numpy.empty_like(e)
h[0] = de(e[2], 1)
h[0] -= de(e[1], 2)
h[1] = de(e[0], 2)
h[1] -= de(e[2], 0)
h[2] = de(e[1], 0)
h[2] -= de(e[0], 1)
return h
return ce_fun
field_transform_t = Callable[[field_t], field_t]
def e_full(omega: complex,
dxes: dx_lists_t,
epsilon: field_t,
mu: field_t = None
) -> functional_matrix:
) -> field_transform_t:
"""
Wave operator del x (1/mu * del x) - omega**2 * epsilon, for use with E-field,
with wave equation
(del x (1/mu * del x) - omega**2 * epsilon) E = -i * omega * J
Wave operator for use with E-field. See `operators.e_full` for details.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param epsilon: Dielectric constant
:param mu: Magnetic permeability (default 1 everywhere)
:return: Function implementing the wave operator A(E) -> E
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
epsilon: Dielectric constant
mu: Magnetic permeability (default 1 everywhere)
Return:
Function `f` implementing the wave operator
`f(E)` -> `-i * omega * J`
"""
ch = curl_h(dxes)
ce = curl_e(dxes)
ch = curl_back(dxes[1])
ce = curl_forward(dxes[0])
def op_1(e):
curls = ch(ce(e))
@ -103,18 +56,23 @@ def eh_full(omega: complex,
dxes: dx_lists_t,
epsilon: field_t,
mu: field_t = None
) -> functional_matrix:
) -> Callable[[field_t, field_t], Tuple[field_t, field_t]]:
"""
Wave operator for full (both E and H) field representation.
See `operators.eh_full`.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param epsilon: Dielectric constant
:param mu: Magnetic permeability (default 1 everywhere)
:return: Function implementing the wave operator A(E, H) -> (E, H)
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
epsilon: Dielectric constant
mu: Magnetic permeability (default 1 everywhere)
Returns:
Function `f` implementing the wave operator
`f(E, H)` -> `(J, -M)`
"""
ch = curl_h(dxes)
ce = curl_e(dxes)
ch = curl_back(dxes[1])
ce = curl_forward(dxes[0])
def op_1(e, h):
return (ch(h) - 1j * omega * epsilon * e,
@ -133,23 +91,27 @@ def eh_full(omega: complex,
def e2h(omega: complex,
dxes: dx_lists_t,
mu: field_t = None,
) -> functional_matrix:
) -> field_transform_t:
"""
Utility operator for converting the E field into the H field.
For use with e_full -- assumes that there is no magnetic current M.
Utility operator for converting the `E` field into the `H` field.
For use with `e_full` -- assumes that there is no magnetic current `M`.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param mu: Magnetic permeability (default 1 everywhere)
:return: Function for converting E to H
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
mu: Magnetic permeability (default 1 everywhere)
Return:
Function `f` for converting `E` to `H`,
`f(E)` -> `H`
"""
A2 = curl_e(dxes)
ce = curl_forward(dxes[0])
def e2h_1_1(e):
return A2(e) / (-1j * omega)
return ce(e) / (-1j * omega)
def e2h_mu(e):
return A2(e) / (-1j * omega * mu)
return ce(e) / (-1j * omega * mu)
if numpy.any(numpy.equal(mu, None)):
return e2h_1_1
@ -160,18 +122,22 @@ def e2h(omega: complex,
def m2j(omega: complex,
dxes: dx_lists_t,
mu: field_t = None,
) -> functional_matrix:
) -> field_transform_t:
"""
Utility operator for converting magnetic current (M) distribution
into equivalent electric current distribution (J).
For use with e.g. e_full().
Utility operator for converting magnetic current `M` distribution
into equivalent electric current distribution `J`.
For use with e.g. `e_full`.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param mu: Magnetic permeability (default 1 everywhere)
:return: Function for converting M to J
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
mu: Magnetic permeability (default 1 everywhere)
Returns:
Function `f` for converting `M` to `J`,
`f(M)` -> `J`
"""
ch = curl_h(dxes)
ch = curl_back(dxes[1])
def m2j_mu(m):
J = ch(m / mu) / (-1j * omega)
@ -192,10 +158,23 @@ def e_tfsf_source(TF_region: field_t,
dxes: dx_lists_t,
epsilon: field_t,
mu: field_t = None,
) -> functional_matrix:
) -> field_transform_t:
"""
Operator that turuns an E-field distribution into a total-field/scattered-field
Operator that turns an E-field distribution into a total-field/scattered-field
(TFSF) source.
Args:
TF_region: mask which is set to 1 in the total-field region, and 0 elsewhere
(i.e. in the scattered-field region).
Should have the same shape as the simulation grid, e.g. `epsilon[0].shape`.
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Dielectric constant distribution
mu: Magnetic permeability (default 1 everywhere)
Returns:
Function `f` which takes an E field and returns a current distribution,
`f(E)` -> `J`
"""
# TODO documentation
A = e_full(omega, dxes, epsilon, mu)
@ -205,7 +184,28 @@ def e_tfsf_source(TF_region: field_t,
return neg_iwj / (-1j * omega)
def poynting_e_cross_h(dxes: dx_lists_t):
def poynting_e_cross_h(dxes: dx_lists_t) -> Callable[[field_t, field_t], field_t]:
"""
Generates a function that takes the single-frequency `E` and `H` fields
and calculates the cross product `E` x `H` = \\( E \\times H \\) as required
for the Poynting vector, \\( S = E \\times H \\)
Note:
This function also shifts the input `E` field by one cell as required
for computing the Poynting cross product (see `meanas.fdfd` module docs).
Note:
If `E` and `H` are peak amplitudes as assumed elsewhere in this code,
the time-average of the poynting vector is `<S> = Re(S)/2 = Re(E x H) / 2`.
The factor of `1/2` can be omitted if root-mean-square quantities are used
instead.
Args:
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
Returns:
Function `f` that returns E x H as required for the poynting vector.
"""
def exh(e: field_t, h: field_t):
s = numpy.empty_like(e)
ex = e[0] * dxes[0][0][:, None, None]

424
meanas/fdfd/operators.py
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@ -1,18 +1,19 @@
"""
Sparse matrix operators for use with electromagnetic wave equations.
These functions return sparse-matrix (scipy.sparse.spmatrix) representations of
These functions return sparse-matrix (`scipy.sparse.spmatrix`) representations of
a variety of operators, intended for use with E and H fields vectorized using the
meanas.vec() and .unvec() functions (column-major/Fortran ordering).
`meanas.vec()` and `meanas.unvec()` functions.
E- and H-field values are defined on a Yee cell; epsilon values should be calculated for
cells centered at each E component (mu at each H component).
E- and H-field values are defined on a Yee cell; `epsilon` values should be calculated for
cells centered at each E component (`mu` at each H component).
Many of these functions require a 'dxes' parameter, of type meanas.dx_lists_type; see
the meanas.types submodule for details.
Many of these functions require a `dxes` parameter, of type `dx_lists_t`; see
the `meanas.types` submodule for details.
The following operators are included:
- E-only wave operator
- H-only wave operator
- EH wave operator
@ -20,8 +21,6 @@ The following operators are included:
- E to H conversion
- M to J conversion
- Poynting cross products
Also available:
- Circular shifts
- Discrete derivatives
- Averaging operators
@ -33,6 +32,7 @@ import numpy
import scipy.sparse as sparse
from .. import vec, dx_lists_t, vfield_t
from ..fdmath.operators import shift_with_mirror, rotation, curl_forward, curl_back
__author__ = 'Jan Petykiewicz'
@ -46,26 +46,35 @@ def e_full(omega: complex,
pmc: vfield_t = None,
) -> sparse.spmatrix:
"""
Wave operator del x (1/mu * del x) - omega**2 * epsilon, for use with E-field,
with wave equation
Wave operator
$$ \\nabla \\times (\\frac{1}{\\mu} \\nabla \\times) - \\omega^2 \\epsilon $$
del x (1/mu * del x) - omega**2 * epsilon
for use with the E-field, with wave equation
$$ (\\nabla \\times (\\frac{1}{\\mu} \\nabla \\times) - \\omega^2 \\epsilon) E = -\\imath \\omega J $$
(del x (1/mu * del x) - omega**2 * epsilon) E = -i * omega * J
To make this matrix symmetric, use the preconditions from e_full_preconditioners().
To make this matrix symmetric, use the preconditioners from `e_full_preconditioners()`.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param epsilon: Vectorized dielectric constant
:param mu: Vectorized magnetic permeability (default 1 everywhere).
:param pec: Vectorized mask specifying PEC cells. Any cells where pec != 0 are interpreted
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Vectorized dielectric constant
mu: Vectorized magnetic permeability (default 1 everywhere).
pec: Vectorized mask specifying PEC cells. Any cells where `pec != 0` are interpreted
as containing a perfect electrical conductor (PEC).
The PEC is applied per-field-component (ie, pec.size == epsilon.size)
:param pmc: Vectorized mask specifying PMC cells. Any cells where pmc != 0 are interpreted
The PEC is applied per-field-component (i.e. `pec.size == epsilon.size`)
pmc: Vectorized mask specifying PMC cells. Any cells where `pmc != 0` are interpreted
as containing a perfect magnetic conductor (PMC).
The PMC is applied per-field-component (ie, pmc.size == epsilon.size)
:return: Sparse matrix containing the wave operator
The PMC is applied per-field-component (i.e. `pmc.size == epsilon.size`)
Returns:
Sparse matrix containing the wave operator.
"""
ce = curl_e(dxes)
ch = curl_h(dxes)
ch = curl_back(dxes[1])
ce = curl_forward(dxes[0])
if numpy.any(numpy.equal(pec, None)):
pe = sparse.eye(epsilon.size)
@ -90,15 +99,18 @@ def e_full(omega: complex,
def e_full_preconditioners(dxes: dx_lists_t
) -> Tuple[sparse.spmatrix, sparse.spmatrix]:
"""
Left and right preconditioners (Pl, Pr) for symmetrizing the e_full wave operator.
Left and right preconditioners `(Pl, Pr)` for symmetrizing the `e_full` wave operator.
The preconditioned matrix A_symm = (Pl @ A @ Pr) is complex-symmetric
The preconditioned matrix `A_symm = (Pl @ A @ Pr)` is complex-symmetric
(non-Hermitian unless there is no loss or PMLs).
The preconditioner matrices are diagonal and complex, with Pr = 1 / Pl
The preconditioner matrices are diagonal and complex, with `Pr = 1 / Pl`
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Preconditioner matrices (Pl, Pr)
Args:
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
Returns:
Preconditioner matrices `(Pl, Pr)`.
"""
p_squared = [dxes[0][0][:, None, None] * dxes[1][1][None, :, None] * dxes[1][2][None, None, :],
dxes[1][0][:, None, None] * dxes[0][1][None, :, None] * dxes[1][2][None, None, :],
@ -118,24 +130,33 @@ def h_full(omega: complex,
pmc: vfield_t = None,
) -> sparse.spmatrix:
"""
Wave operator del x (1/epsilon * del x) - omega**2 * mu, for use with H-field,
with wave equation
(del x (1/epsilon * del x) - omega**2 * mu) H = i * omega * M
Wave operator
$$ \\nabla \\times (\\frac{1}{\\epsilon} \\nabla \\times) - \\omega^2 \\mu $$
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param epsilon: Vectorized dielectric constant
:param mu: Vectorized magnetic permeability (default 1 everywhere)
:param pec: Vectorized mask specifying PEC cells. Any cells where pec != 0 are interpreted
del x (1/epsilon * del x) - omega**2 * mu
for use with the H-field, with wave equation
$$ (\\nabla \\times (\\frac{1}{\\epsilon} \\nabla \\times) - \\omega^2 \\mu) E = \\imath \\omega M $$
(del x (1/epsilon * del x) - omega**2 * mu) E = i * omega * M
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Vectorized dielectric constant
mu: Vectorized magnetic permeability (default 1 everywhere)
pec: Vectorized mask specifying PEC cells. Any cells where `pec != 0` are interpreted
as containing a perfect electrical conductor (PEC).
The PEC is applied per-field-component (ie, pec.size == epsilon.size)
:param pmc: Vectorized mask specifying PMC cells. Any cells where pmc != 0 are interpreted
The PEC is applied per-field-component (i.e. `pec.size == epsilon.size`)
pmc: Vectorized mask specifying PMC cells. Any cells where `pmc != 0` are interpreted
as containing a perfect magnetic conductor (PMC).
The PMC is applied per-field-component (ie, pmc.size == epsilon.size)
:return: Sparse matrix containing the wave operator
The PMC is applied per-field-component (i.e. `pmc.size == epsilon.size`)
Returns:
Sparse matrix containing the wave operator.
"""
ec = curl_e(dxes)
hc = curl_h(dxes)
ch = curl_back(dxes[1])
ce = curl_forward(dxes[0])
if numpy.any(numpy.equal(pec, None)):
pe = sparse.eye(epsilon.size)
@ -153,7 +174,7 @@ def h_full(omega: complex,
else:
m = sparse.diags(mu)
A = pm @ (ec @ pe @ e_div @ hc - omega**2 * m) @ pm
A = pm @ (ce @ pe @ e_div @ ch - omega**2 * m) @ pm
return A
@ -165,24 +186,42 @@ def eh_full(omega: complex,
pmc: vfield_t = None
) -> sparse.spmatrix:
"""
Wave operator for [E, H] field representation. This operator implements Maxwell's
Wave operator for `[E, H]` field representation. This operator implements Maxwell's
equations without cancelling out either E or H. The operator is
$$ \\begin{bmatrix}
-\\imath \\omega \\epsilon & \\nabla \\times \\\\
\\nabla \\times & \\imath \\omega \\mu
\\end{bmatrix} $$
[[-i * omega * epsilon, del x ],
[del x, i * omega * mu]]
for use with a field vector of the form hstack(vec(E), vec(H)).
for use with a field vector of the form `cat(vec(E), vec(H))`:
$$ \\begin{bmatrix}
-\\imath \\omega \\epsilon & \\nabla \\times \\\\
\\nabla \\times & \\imath \\omega \\mu
\\end{bmatrix}
\\begin{bmatrix} E \\\\
H
\\end{bmatrix}
= \\begin{bmatrix} J \\\\
-M
\\end{bmatrix} $$
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param epsilon: Vectorized dielectric constant
:param mu: Vectorized magnetic permeability (default 1 everywhere)
:param pec: Vectorized mask specifying PEC cells. Any cells where pec != 0 are interpreted
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Vectorized dielectric constant
mu: Vectorized magnetic permeability (default 1 everywhere)
pec: Vectorized mask specifying PEC cells. Any cells where `pec != 0` are interpreted
as containing a perfect electrical conductor (PEC).
The PEC is applied per-field-component (i.e., pec.size == epsilon.size)
:param pmc: Vectorized mask specifying PMC cells. Any cells where pmc != 0 are interpreted
The PEC is applied per-field-component (i.e. `pec.size == epsilon.size`)
pmc: Vectorized mask specifying PMC cells. Any cells where `pmc != 0` are interpreted
as containing a perfect magnetic conductor (PMC).
The PMC is applied per-field-component (i.e., pmc.size == epsilon.size)
:return: Sparse matrix containing the wave operator
The PMC is applied per-field-component (i.e. `pmc.size == epsilon.size`)
Returns:
Sparse matrix containing the wave operator.
"""
if numpy.any(numpy.equal(pec, None)):
pe = sparse.eye(epsilon.size)
@ -200,34 +239,14 @@ def eh_full(omega: complex,
iwm *= sparse.diags(mu)
iwm = pm @ iwm @ pm
A1 = pe @ curl_h(dxes) @ pm
A2 = pm @ curl_e(dxes) @ pe
A1 = pe @ curl_back(dxes[1]) @ pm
A2 = pm @ curl_forward(dxes[0]) @ pe
A = sparse.bmat([[-iwe, A1],
[A2, iwm]])
return A
def curl_h(dxes: dx_lists_t) -> sparse.spmatrix:
"""
Curl operator for use with the H field.
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Sparse matrix for taking the discretized curl of the H-field
"""
return cross(deriv_back(dxes[1]))
def curl_e(dxes: dx_lists_t) -> sparse.spmatrix:
"""
Curl operator for use with the E field.
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Sparse matrix for taking the discretized curl of the E-field
"""
return cross(deriv_forward(dxes[0]))
def e2h(omega: complex,
dxes: dx_lists_t,
mu: vfield_t = None,
@ -235,17 +254,20 @@ def e2h(omega: complex,
) -> sparse.spmatrix:
"""
Utility operator for converting the E field into the H field.
For use with e_full -- assumes that there is no magnetic current M.
For use with `e_full()` -- assumes that there is no magnetic current M.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param mu: Vectorized magnetic permeability (default 1 everywhere)
:param pmc: Vectorized mask specifying PMC cells. Any cells where pmc != 0 are interpreted
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
mu: Vectorized magnetic permeability (default 1 everywhere)
pmc: Vectorized mask specifying PMC cells. Any cells where `pmc != 0` are interpreted
as containing a perfect magnetic conductor (PMC).
The PMC is applied per-field-component (ie, pmc.size == epsilon.size)
:return: Sparse matrix for converting E to H
The PMC is applied per-field-component (i.e. `pmc.size == epsilon.size`)
Returns:
Sparse matrix for converting E to H.
"""
op = curl_e(dxes) / (-1j * omega)
op = curl_forward(dxes[0]) / (-1j * omega)
if not numpy.any(numpy.equal(mu, None)):
op = sparse.diags(1 / mu) @ op
@ -261,16 +283,18 @@ def m2j(omega: complex,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Utility operator for converting M field into J.
Converts a magnetic current M into an electric current J.
For use with eg. e_full.
Operator for converting a magnetic current M into an electric current J.
For use with eg. `e_full()`.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param mu: Vectorized magnetic permeability (default 1 everywhere)
:return: Sparse matrix for converting E to H
Args:
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
mu: Vectorized magnetic permeability (default 1 everywhere)
Returns:
Sparse matrix for converting M to J.
"""
op = curl_h(dxes) / (1j * omega)
op = curl_back(dxes[1]) / (1j * omega)
if not numpy.any(numpy.equal(mu, None)):
op = op @ sparse.diags(1 / mu)
@ -278,178 +302,17 @@ def m2j(omega: complex,
return op
def rotation(axis: int, shape: List[int], shift_distance: int=1) -> sparse.spmatrix:
"""
Utility operator for performing a circular shift along a specified axis by a
specified number of elements.
:param axis: Axis to shift along. x=0, y=1, z=2
:param shape: Shape of the grid being shifted
:param shift_distance: Number of cells to shift by. May be negative. Default 1.
:return: Sparse matrix for performing the circular shift
"""
if len(shape) not in (2, 3):
raise Exception('Invalid shape: {}'.format(shape))
if axis not in range(len(shape)):
raise Exception('Invalid direction: {}, shape is {}'.format(axis, shape))
shifts = [abs(shift_distance) if a == axis else 0 for a in range(3)]
shifted_diags = [(numpy.arange(n) + s) % n for n, s in zip(shape, shifts)]
ijk = numpy.meshgrid(*shifted_diags, indexing='ij')
n = numpy.prod(shape)
i_ind = numpy.arange(n)
j_ind = numpy.ravel_multi_index(ijk, shape, order='C')
vij = (numpy.ones(n), (i_ind, j_ind.ravel(order='C')))
d = sparse.csr_matrix(vij, shape=(n, n))
if shift_distance < 0:
d = d.T
return d
def shift_with_mirror(axis: int, shape: List[int], shift_distance: int=1) -> sparse.spmatrix:
"""
Utility operator for performing an n-element shift along a specified axis, with mirror
boundary conditions applied to the cells beyond the receding edge.
:param axis: Axis to shift along. x=0, y=1, z=2
:param shape: Shape of the grid being shifted
:param shift_distance: Number of cells to shift by. May be negative. Default 1.
:return: Sparse matrix for performing the circular shift
"""
if len(shape) not in (2, 3):
raise Exception('Invalid shape: {}'.format(shape))
if axis not in range(len(shape)):
raise Exception('Invalid direction: {}, shape is {}'.format(axis, shape))
if shift_distance >= shape[axis]:
raise Exception('Shift ({}) is too large for axis {} of size {}'.format(
shift_distance, axis, shape[axis]))
def mirrored_range(n, s):
v = numpy.arange(n) + s
v = numpy.where(v >= n, 2 * n - v - 1, v)
v = numpy.where(v < 0, - 1 - v, v)
return v
shifts = [shift_distance if a == axis else 0 for a in range(3)]
shifted_diags = [mirrored_range(n, s) for n, s in zip(shape, shifts)]
ijk = numpy.meshgrid(*shifted_diags, indexing='ij')
n = numpy.prod(shape)
i_ind = numpy.arange(n)
j_ind = numpy.ravel_multi_index(ijk, shape, order='C')
vij = (numpy.ones(n), (i_ind, j_ind.ravel(order='C')))
d = sparse.csr_matrix(vij, shape=(n, n))
return d
def deriv_forward(dx_e: List[numpy.ndarray]) -> List[sparse.spmatrix]:
"""
Utility operators for taking discretized derivatives (forward variant).
:param dx_e: Lists of cell sizes for all axes [[dx_0, dx_1, ...], ...].
:return: List of operators for taking forward derivatives along each axis.
"""
shape = [s.size for s in dx_e]
n = numpy.prod(shape)
dx_e_expanded = numpy.meshgrid(*dx_e, indexing='ij')
def deriv(axis):
return rotation(axis, shape, 1) - sparse.eye(n)
Ds = [sparse.diags(+1 / dx.ravel(order='C')) @ deriv(a)
for a, dx in enumerate(dx_e_expanded)]
return Ds
def deriv_back(dx_h: List[numpy.ndarray]) -> List[sparse.spmatrix]:
"""
Utility operators for taking discretized derivatives (backward variant).
:param dx_h: Lists of cell sizes for all axes [[dx_0, dx_1, ...], ...].
:return: List of operators for taking forward derivatives along each axis.
"""
shape = [s.size for s in dx_h]
n = numpy.prod(shape)
dx_h_expanded = numpy.meshgrid(*dx_h, indexing='ij')
def deriv(axis):
return rotation(axis, shape, -1) - sparse.eye(n)
Ds = [sparse.diags(-1 / dx.ravel(order='C')) @ deriv(a)
for a, dx in enumerate(dx_h_expanded)]
return Ds
def cross(B: List[sparse.spmatrix]) -> sparse.spmatrix:
"""
Cross product operator
:param B: List [Bx, By, Bz] of sparse matrices corresponding to the x, y, z
portions of the operator on the left side of the cross product.
:return: Sparse matrix corresponding to (B x), where x is the cross product
"""
n = B[0].shape[0]
zero = sparse.csr_matrix((n, n))
return sparse.bmat([[zero, -B[2], B[1]],
[B[2], zero, -B[0]],
[-B[1], B[0], zero]])
def vec_cross(b: vfield_t) -> sparse.spmatrix:
"""
Vector cross product operator
:param b: Vector on the left side of the cross product
:return: Sparse matrix corresponding to (b x), where x is the cross product
"""
B = [sparse.diags(c) for c in numpy.split(b, 3)]
return cross(B)
def avgf(axis: int, shape: List[int]) -> sparse.spmatrix:
"""
Forward average operator (x4 = (x4 + x5) / 2)
:param axis: Axis to average along (x=0, y=1, z=2)
:param shape: Shape of the grid to average
:return: Sparse matrix for forward average operation
"""
if len(shape) not in (2, 3):
raise Exception('Invalid shape: {}'.format(shape))
n = numpy.prod(shape)
return 0.5 * (sparse.eye(n) + rotation(axis, shape))
def avgb(axis: int, shape: List[int]) -> sparse.spmatrix:
"""
Backward average operator (x4 = (x4 + x3) / 2)
:param axis: Axis to average along (x=0, y=1, z=2)
:param shape: Shape of the grid to average
:return: Sparse matrix for backward average operation
"""
return avgf(axis, shape).T
def poynting_e_cross(e: vfield_t, dxes: dx_lists_t) -> sparse.spmatrix:
"""
Operator for computing the Poynting vector, containing the (E x) portion of the Poynting vector.
Operator for computing the Poynting vector, containing the
(E x) portion of the Poynting vector.
:param e: Vectorized E-field for the ExH cross product
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Sparse matrix containing (E x) portion of Poynting cross product
Args:
e: Vectorized E-field for the ExH cross product
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
Returns:
Sparse matrix containing (E x) portion of Poynting cross product.
"""
shape = [len(dx) for dx in dxes[0]]
@ -472,9 +335,12 @@ def poynting_h_cross(h: vfield_t, dxes: dx_lists_t) -> sparse.spmatrix:
"""
Operator for computing the Poynting vector, containing the (H x) portion of the Poynting vector.
:param h: Vectorized H-field for the HxE cross product
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Sparse matrix containing (H x) portion of Poynting cross product
Args:
h: Vectorized H-field for the HxE cross product
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
Returns:
Sparse matrix containing (H x) portion of Poynting cross product.
"""
shape = [len(dx) for dx in dxes[0]]
@ -499,8 +365,22 @@ def e_tfsf_source(TF_region: vfield_t,
mu: vfield_t = None,
) -> sparse.spmatrix:
"""
Operator that turns an E-field distribution into a total-field/scattered-field
(TFSF) source.
Operator that turns a desired E-field distribution into a
total-field/scattered-field (TFSF) source.
TODO: Reference Rumpf paper
Args:
TF_region: Mask, which is set to 1 inside the total-field region and 0 in the
scattered-field region
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Vectorized dielectric constant
mu: Vectorized magnetic permeability (default 1 everywhere).
Returns:
Sparse matrix that turns an E-field into a current (J) distribution.
"""
# TODO documentation
A = e_full(omega, dxes, epsilon, mu)
@ -518,7 +398,19 @@ def e_boundary_source(mask: vfield_t,
"""
Operator that turns an E-field distrubtion into a current (J) distribution
along the edges (external and internal) of the provided mask. This is just an
e_tfsf_source with an additional masking step.
`e_tfsf_source()` with an additional masking step.
Args:
mask: The current distribution is generated at the edges of the mask,
i.e. any points where shifting the mask by one cell in any direction
would change its value.
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Vectorized dielectric constant
mu: Vectorized magnetic permeability (default 1 everywhere).
Returns:
Sparse matrix that turns an E-field into a current (J) distribution.
"""
full = e_tfsf_source(TF_region=mask, omega=omega, dxes=dxes, epsilon=epsilon, mu=mu)

90
meanas/fdfd/scpml.py
View File

@ -1,5 +1,5 @@
"""
Functions for creating stretched coordinate PMLs.
Functions for creating stretched coordinate perfectly matched layer (PML) absorbers.
"""
from typing import List, Callable
@ -7,23 +7,28 @@ import numpy
from .. import dx_lists_t
__author__ = 'Jan Petykiewicz'
s_function_type = Callable[[float], float]
s_function_t = Callable[[float], float]
"""Typedef for s-functions"""
def prepare_s_function(ln_R: float = -16,
m: float = 4
) -> s_function_type:
) -> s_function_t:
"""
Create an s_function to pass to the SCPML functions. This is used when you would like to
customize the PML parameters.
:param ln_R: Natural logarithm of the desired reflectance
:param m: Polynomial order for the PML (imaginary part increases as distance ** m)
:return: An s_function, which takes an ndarray (distances) and returns an ndarray (complex part
of the cell width; needs to be divided by sqrt(epilon_effective) * real(omega))
Args:
ln_R: Natural logarithm of the desired reflectance
m: Polynomial order for the PML (imaginary part increases as distance ** m)
Returns:
An s_function, which takes an ndarray (distances) and returns an ndarray (complex part
of the cell width; needs to be divided by `sqrt(epilon_effective) * real(omega))`
before use.
"""
def s_factor(distance: numpy.ndarray) -> numpy.ndarray:
@ -36,26 +41,29 @@ def uniform_grid_scpml(shape: numpy.ndarray or List[int],
thicknesses: numpy.ndarray or List[int],
omega: float,
epsilon_effective: float = 1.0,
s_function: s_function_type = None,
s_function: s_function_t = None,
) -> dx_lists_t:
"""
Create dx arrays for a uniform grid with a cell width of 1 and a pml.
If you want something more fine-grained, check out stretch_with_scpml(...).
If you want something more fine-grained, check out `stretch_with_scpml(...)`.
:param shape: Shape of the grid, including the PMLs (which are 2*thicknesses thick)
:param thicknesses: [th_x, th_y, th_z] Thickness of the PML in each direction.
Args:
shape: Shape of the grid, including the PMLs (which are 2*thicknesses thick)
thicknesses: `[th_x, th_y, th_z]`
Thickness of the PML in each direction.
Both polarities are added.
Each th_ of pml is applied twice, once on each edge of the grid along the given axis.
th_* may be zero, in which case no pml is added.
:param omega: Angular frequency for the simulation
:param epsilon_effective: Effective epsilon of the PML. Match this to the material
`th_*` may be zero, in which case no pml is added.
omega: Angular frequency for the simulation
epsilon_effective: Effective epsilon of the PML. Match this to the material
at the edge of your grid.
Default 1.
:param s_function: s_function created by prepare_s_function(...), allowing
customization of pml parameters.
Default uses prepare_s_function() with no parameters.
:return: Complex cell widths (dx_lists)
s_function: created by `prepare_s_function(...)`, allowing customization of pml parameters.
Default uses `prepare_s_function()` with no parameters.
Returns:
Complex cell widths (dx_lists_t) as discussed in `meanas.types`.
"""
if s_function is None:
s_function = prepare_s_function()
@ -88,21 +96,25 @@ def stretch_with_scpml(dxes: dx_lists_t,
omega: float,
epsilon_effective: float = 1.0,
thickness: int = 10,
s_function: s_function_type = None,
s_function: s_function_t = None,
) -> dx_lists_t:
"""
Stretch dxes to contain a stretched-coordinate PML (SCPML) in one direction along one axis.
:param dxes: dx_tuple with coordinates to stretch
:param axis: axis to stretch (0=x, 1=y, 2=z)
:param polarity: direction to stretch (-1 for -ve, +1 for +ve)
:param omega: Angular frequency for the simulation
:param epsilon_effective: Effective epsilon of the PML. Match this to the material at the
Args:
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
axis: axis to stretch (0=x, 1=y, 2=z)
polarity: direction to stretch (-1 for -ve, +1 for +ve)
omega: Angular frequency for the simulation
epsilon_effective: Effective epsilon of the PML. Match this to the material at the
edge of your grid. Default 1.
:param thickness: number of cells to use for pml (default 10)
:param s_function: s_function created by prepare_s_function(...), allowing customization
of pml parameters. Default uses prepare_s_function() with no parameters.
:return: Complex cell widths
thickness: number of cells to use for pml (default 10)
s_function: Created by `prepare_s_function(...)`, allowing customization
of pml parameters. Default uses `prepare_s_function()` with no parameters.
Returns:
Complex cell widths (dx_lists_t) as discussed in `meanas.types`.
Multiple calls to this function may be necessary if multiple absorpbing boundaries are needed.
"""
if s_function is None:
s_function = prepare_s_function()
@ -147,25 +159,3 @@ def stretch_with_scpml(dxes: dx_lists_t,
dxes[1][axis] = dx_bi
return dxes
def generate_periodic_dx(pos: List[numpy.ndarray]) -> dx_lists_t:
"""
Given a list of 3 ndarrays cell centers, creates the cell width parameters for a periodic grid.
:param pos: List of 3 ndarrays of cell centers
:return: (dx_a, dx_b) cell widths (no pml)
"""
if len(pos) != 3:
raise Exception('Must have len(pos) == 3')
dx_a = [numpy.array(numpy.inf)] * 3
dx_b = [numpy.array(numpy.inf)] * 3
for i, p_orig in enumerate(pos):
p = numpy.array(p_orig, dtype=float)
if p.size != 1:
p_shifted = numpy.hstack((p[1:], p[-1] + (p[1] - p[0])))
dx_a[i] = numpy.diff(p)
dx_b[i] = numpy.diff((p + p_shifted) / 2)
return dx_a, dx_b

49
meanas/fdfd/solvers.py
View File

@ -1,5 +1,5 @@
"""
Solvers for FDFD problems.
Solvers and solver interface for FDFD problems.
"""
from typing import List, Callable, Dict, Any
@ -22,10 +22,13 @@ def _scipy_qmr(A: scipy.sparse.csr_matrix,
"""
Wrapper for scipy.sparse.linalg.qmr
:param A: Sparse matrix
:param b: Right-hand-side vector
:param kwargs: Passed as **kwargs to the wrapped function
:return: Guess for solution (returned even if didn't converge)
Args:
A: Sparse matrix
b: Right-hand-side vector
kwargs: Passed as **kwargs to the wrapped function
Returns:
Guess for solution (returned even if didn't converge)
"""
'''
@ -70,27 +73,31 @@ def generic(omega: complex,
"""
Conjugate gradient FDFD solver using CSR sparse matrices.
All ndarray arguments should be 1D array, as returned by meanas.vec().
All ndarray arguments should be 1D arrays, as returned by `meanas.vec()`.
:param omega: Complex frequency to solve at.
:param dxes: [[dx_e, dy_e, dz_e], [dx_h, dy_h, dz_h]] (complex cell sizes)
:param J: Electric current distribution (at E-field locations)
:param epsilon: Dielectric constant distribution (at E-field locations)
:param mu: Magnetic permeability distribution (at H-field locations)
:param pec: Perfect electric conductor distribution
Args:
omega: Complex frequency to solve at.
dxes: `[[dx_e, dy_e, dz_e], [dx_h, dy_h, dz_h]]` (complex cell sizes) as
discussed in `meanas.types`
J: Electric current distribution (at E-field locations)
epsilon: Dielectric constant distribution (at E-field locations)
mu: Magnetic permeability distribution (at H-field locations)
pec: Perfect electric conductor distribution
(at E-field locations; non-zero value indicates PEC is present)
:param pmc: Perfect magnetic conductor distribution
pmc: Perfect magnetic conductor distribution
(at H-field locations; non-zero value indicates PMC is present)
:param adjoint: If true, solves the adjoint problem.
:param matrix_solver: Called as matrix_solver(A, b, **matrix_solver_opts) -> x
Where A: scipy.sparse.csr_matrix
b: numpy.ndarray
x: numpy.ndarray
Default is a wrapped version of scipy.sparse.linalg.qmr()
adjoint: If true, solves the adjoint problem.
matrix_solver: Called as `matrix_solver(A, b, **matrix_solver_opts) -> x`,
where `A`: `scipy.sparse.csr_matrix`;
`b`: `numpy.ndarray`;
`x`: `numpy.ndarray`;
Default is a wrapped version of `scipy.sparse.linalg.qmr()`
which doesn't return convergence info and logs the residual
every 100 iterations.
:param matrix_solver_opts: Passed as kwargs to matrix_solver(...)
:return: E-field which solves the system.
matrix_solver_opts: Passed as kwargs to `matrix_solver(...)`
Returns:
E-field which solves the system.
"""
if matrix_solver_opts is None:

492
meanas/fdfd/waveguide.py
View File

@ -1,492 +0,0 @@
"""
Various operators and helper functions for solving for waveguide modes.
Assuming a z-dependence of the from exp(-i * wavenumber * z), we can simplify Maxwell's
equations in the absence of sources to the form
A @ [H_x, H_y] = wavenumber**2 * [H_x, H_y]
with A =
omega**2 * epsilon * mu +
epsilon * [[-Dy], [Dx]] / epsilon * [-Dy, Dx] +
[[Dx], [Dy]] / mu * [Dx, Dy] * mu
which is the form used in this file.
As the z-dependence is known, all the functions in this file assume a 2D grid
(ie. dxes = [[[dx_e_0, dx_e_1, ...], [dy_e_0, ...]], [[dx_h_0, ...], [dy_h_0, ...]]])
with propagation along the z axis.
"""
# TODO update module docs
from typing import List, Tuple
import numpy
from numpy.linalg import norm
import scipy.sparse as sparse
from .. import vec, unvec, dx_lists_t, field_t, vfield_t
from . import operators
__author__ = 'Jan Petykiewicz'
def operator_e(omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
) -> sparse.spmatrix:
if numpy.any(numpy.equal(mu, None)):
mu = numpy.ones_like(epsilon)
Dfx, Dfy = operators.deriv_forward(dxes[0])
Dbx, Dby = operators.deriv_back(dxes[1])
eps_parts = numpy.split(epsilon, 3)
eps_xy = sparse.diags(numpy.hstack((eps_parts[0], eps_parts[1])))
eps_z_inv = sparse.diags(1 / eps_parts[2])
mu_parts = numpy.split(mu, 3)
mu_yx = sparse.diags(numpy.hstack((mu_parts[1], mu_parts[0])))
mu_z_inv = sparse.diags(1 / mu_parts[2])
op = omega * omega * mu_yx @ eps_xy + \
mu_yx @ sparse.vstack((-Dby, Dbx)) @ mu_z_inv @ sparse.hstack((-Dfy, Dfx)) + \
sparse.vstack((Dfx, Dfy)) @ eps_z_inv @ sparse.hstack((Dbx, Dby)) @ eps_xy
return op
def operator_h(omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
) -> sparse.spmatrix:
"""
Waveguide operator of the form
omega**2 * epsilon * mu +
epsilon * [[-Dy], [Dx]] / epsilon * [-Dy, Dx] +
[[Dx], [Dy]] / mu * [Dx, Dy] * mu
for use with a field vector of the form [H_x, H_y].
This operator can be used to form an eigenvalue problem of the form
A @ [H_x, H_y] = wavenumber**2 * [H_x, H_y]
which can then be solved for the eigenmodes of the system (an exp(-i * wavenumber * z)
z-dependence is assumed for the fields).
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Sparse matrix representation of the operator
"""
if numpy.any(numpy.equal(mu, None)):
mu = numpy.ones_like(epsilon)
Dfx, Dfy = operators.deriv_forward(dxes[0])
Dbx, Dby = operators.deriv_back(dxes[1])
eps_parts = numpy.split(epsilon, 3)
eps_yx = sparse.diags(numpy.hstack((eps_parts[1], eps_parts[0])))
eps_z_inv = sparse.diags(1 / eps_parts[2])
mu_parts = numpy.split(mu, 3)
mu_xy = sparse.diags(numpy.hstack((mu_parts[0], mu_parts[1])))
mu_z_inv = sparse.diags(1 / mu_parts[2])
op = omega * omega * eps_yx @ mu_xy + \
eps_yx @ sparse.vstack((-Dfy, Dfx)) @ eps_z_inv @ sparse.hstack((-Dby, Dbx)) + \
sparse.vstack((Dbx, Dby)) @ mu_z_inv @ sparse.hstack((Dfx, Dfy)) @ mu_xy
return op
def normalized_fields_e(e_xy: numpy.ndarray,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
prop_phase: float = 0,
) -> Tuple[vfield_t, vfield_t]:
"""
Given a vector e_xy containing the vectorized E_x and E_y fields,
returns normalized, vectorized E and H fields for the system.
:param e_xy: Vector containing E_x and E_y fields
:param wavenumber: Wavenumber satisfying `operator_e(...) @ e_xy == wavenumber**2 * e_xy`
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:param prop_phase: Phase shift (dz * corrected_wavenumber) over 1 cell in propagation direction.
Default 0 (continuous propagation direction, i.e. dz->0).
:return: Normalized, vectorized (e, h) containing all vector components.
"""
e = exy2e(wavenumber=wavenumber, dxes=dxes, epsilon=epsilon) @ e_xy
h = exy2h(wavenumber=wavenumber, omega=omega, dxes=dxes, epsilon=epsilon, mu=mu) @ e_xy
e_norm, h_norm = _normalized_fields(e=e, h=h, omega=omega, dxes=dxes, epsilon=epsilon,
mu=mu, prop_phase=prop_phase)
return e_norm, h_norm
def normalized_fields_h(h_xy: numpy.ndarray,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
prop_phase: float = 0,
) -> Tuple[vfield_t, vfield_t]:
"""
Given a vector e_xy containing the vectorized E_x and E_y fields,
returns normalized, vectorized E and H fields for the system.
:param e_xy: Vector containing E_x and E_y fields
:param wavenumber: Wavenumber satisfying `operator_e(...) @ e_xy == wavenumber**2 * e_xy`
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:param dxes_prop: Grid cell width in the propagation direction. Default 0 (continuous).
:return: Normalized, vectorized (e, h) containing all vector components.
"""
e = hxy2e(wavenumber=wavenumber, omega=omega, dxes=dxes, epsilon=epsilon, mu=mu) @ h_xy
h = hxy2h(wavenumber=wavenumber, dxes=dxes, mu=mu) @ h_xy
e_norm, h_norm = _normalized_fields(e=e, h=h, omega=omega, dxes=dxes, epsilon=epsilon,
mu=mu, prop_phase=prop_phase)
return e_norm, h_norm
def _normalized_fields(e: numpy.ndarray,
h: numpy.ndarray,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
prop_phase: float = 0,
) -> Tuple[vfield_t, vfield_t]:
# TODO documentation
shape = [s.size for s in dxes[0]]
dxes_real = [[numpy.real(d) for d in numpy.meshgrid(*dxes[v], indexing='ij')] for v in (0, 1)]
E = unvec(e, shape)
H = unvec(h, shape)
# Find time-averaged Sz and normalize to it
# H phase is adjusted by a half-cell forward shift for Yee cell, and 1-cell reverse shift for Poynting
phase = numpy.exp(-1j * -prop_phase / 2)
Sz_a = E[0] * numpy.conj(H[1] * phase) * dxes_real[0][1] * dxes_real[1][0]
Sz_b = E[1] * numpy.conj(H[0] * phase) * dxes_real[0][0] * dxes_real[1][1]
Sz_tavg = numpy.real(Sz_a.sum() - Sz_b.sum()) * 0.5 # 0.5 since E, H are assumed to be peak (not RMS) amplitudes
assert Sz_tavg > 0, 'Found a mode propagating in the wrong direction! Sz_tavg={}'.format(Sz_tavg)
energy = epsilon * e.conj() * e
norm_amplitude = 1 / numpy.sqrt(Sz_tavg)
norm_angle = -numpy.angle(e[energy.argmax()]) # Will randomly add a negative sign when mode is symmetric
# Try to break symmetry to assign a consistent sign [experimental TODO]
E_weighted = unvec(e * energy * numpy.exp(1j * norm_angle), shape)
sign = numpy.sign(E_weighted[:, :max(shape[0]//2, 1), :max(shape[1]//2, 1)].real.sum())
norm_factor = sign * norm_amplitude * numpy.exp(1j * norm_angle)
e *= norm_factor
h *= norm_factor
return e, h
def exy2h(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Operator which transforms the vector e_xy containing the vectorized E_x and E_y fields,
into a vectorized H containing all three H components
:param wavenumber: Wavenumber satisfying `operator_e(...) @ e_xy == wavenumber**2 * e_xy`
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Sparse matrix representing the operator
"""
e2hop = e2h(wavenumber=wavenumber, omega=omega, dxes=dxes, mu=mu)
return e2hop @ exy2e(wavenumber=wavenumber, dxes=dxes, epsilon=epsilon)
def hxy2e(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Operator which transforms the vector h_xy containing the vectorized H_x and H_y fields,
into a vectorized E containing all three E components
:param wavenumber: Wavenumber satisfying `operator_h(...) @ h_xy == wavenumber**2 * h_xy`
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Sparse matrix representing the operator
"""
h2eop = h2e(wavenumber=wavenumber, omega=omega, dxes=dxes, epsilon=epsilon)
return h2eop @ hxy2h(wavenumber=wavenumber, dxes=dxes, mu=mu)
def hxy2h(wavenumber: complex,
dxes: dx_lists_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Operator which transforms the vector h_xy containing the vectorized H_x and H_y fields,
into a vectorized H containing all three H components
:param wavenumber: Wavenumber satisfying `operator_h(...) @ h_xy == wavenumber**2 * h_xy`
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Sparse matrix representing the operator
"""
Dfx, Dfy = operators.deriv_forward(dxes[0])
hxy2hz = sparse.hstack((Dfx, Dfy)) / (1j * wavenumber)
if not numpy.any(numpy.equal(mu, None)):
mu_parts = numpy.split(mu, 3)
mu_xy = sparse.diags(numpy.hstack((mu_parts[0], mu_parts[1])))
mu_z_inv = sparse.diags(1 / mu_parts[2])
hxy2hz = mu_z_inv @ hxy2hz @ mu_xy
n_pts = dxes[1][0].size * dxes[1][1].size
op = sparse.vstack((sparse.eye(2 * n_pts),
hxy2hz))
return op
def exy2e(wavenumber: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
) -> sparse.spmatrix:
"""
Operator which transforms the vector e_xy containing the vectorized E_x and E_y fields,
into a vectorized E containing all three E components
:param wavenumber: Wavenumber satisfying `operator_e(...) @ e_xy == wavenumber**2 * e_xy`
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:return: Sparse matrix representing the operator
"""
Dbx, Dby = operators.deriv_back(dxes[1])
exy2ez = sparse.hstack((Dbx, Dby)) / (1j * wavenumber)
if not numpy.any(numpy.equal(epsilon, None)):
epsilon_parts = numpy.split(epsilon, 3)
epsilon_xy = sparse.diags(numpy.hstack((epsilon_parts[0], epsilon_parts[1])))
epsilon_z_inv = sparse.diags(1 / epsilon_parts[2])
exy2ez = epsilon_z_inv @ exy2ez @ epsilon_xy
n_pts = dxes[0][0].size * dxes[0][1].size
op = sparse.vstack((sparse.eye(2 * n_pts),
exy2ez))
return op
def e2h(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Returns an operator which, when applied to a vectorized E eigenfield, produces
the vectorized H eigenfield.
:param wavenumber: Wavenumber satisfying A @ v == wavenumber**2 * v
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Sparse matrix representation of the operator
"""
op = curl_e(wavenumber, dxes) / (-1j * omega)
if not numpy.any(numpy.equal(mu, None)):
op = sparse.diags(1 / mu) @ op
return op
def h2e(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t
) -> sparse.spmatrix:
"""
Returns an operator which, when applied to a vectorized H eigenfield, produces
the vectorized E eigenfield.
:param wavenumber: Wavenumber satisfying A @ v == wavenumber**2 * v
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:return: Sparse matrix representation of the operator
"""
op = sparse.diags(1 / (1j * omega * epsilon)) @ curl_h(wavenumber, dxes)
return op
def curl_e(wavenumber: complex, dxes: dx_lists_t) -> sparse.spmatrix:
"""
Discretized curl operator for use with the waveguide E field.
:param wavenumber: Wavenumber satisfying A @ v == wavenumber**2 * v
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:return: Sparse matrix representation of the operator
"""
n = 1
for d in dxes[0]:
n *= len(d)
Bz = -1j * wavenumber * sparse.eye(n)
Dfx, Dfy = operators.deriv_forward(dxes[0])
return operators.cross([Dfx, Dfy, Bz])
def curl_h(wavenumber: complex, dxes: dx_lists_t) -> sparse.spmatrix:
"""
Discretized curl operator for use with the waveguide H field.
:param wavenumber: Wavenumber satisfying A @ v == wavenumber**2 * v
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:return: Sparse matrix representation of the operator
"""
n = 1
for d in dxes[1]:
n *= len(d)
Bz = -1j * wavenumber * sparse.eye(n)
Dbx, Dby = operators.deriv_back(dxes[1])
return operators.cross([Dbx, Dby, Bz])
def h_err(h: vfield_t,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> float:
"""
Calculates the relative error in the H field
:param h: Vectorized H field
:param wavenumber: Wavenumber satisfying A @ v == wavenumber**2 * v
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Relative error norm(OP @ h) / norm(h)
"""
ce = curl_e(wavenumber, dxes)
ch = curl_h(wavenumber, dxes)
eps_inv = sparse.diags(1 / epsilon)
if numpy.any(numpy.equal(mu, None)):
op = ce @ eps_inv @ ch @ h - omega ** 2 * h
else:
op = ce @ eps_inv @ ch @ h - omega ** 2 * (mu * h)
return norm(op) / norm(h)
def e_err(e: vfield_t,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> float:
"""
Calculates the relative error in the E field
:param e: Vectorized E field
:param wavenumber: Wavenumber satisfying A @ v == wavenumber**2 * v
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param mu: Vectorized magnetic permeability grid (default 1 everywhere)
:return: Relative error norm(OP @ e) / norm(e)
"""
ce = curl_e(wavenumber, dxes)
ch = curl_h(wavenumber, dxes)
if numpy.any(numpy.equal(mu, None)):
op = ch @ ce @ e - omega ** 2 * (epsilon * e)
else:
mu_inv = sparse.diags(1 / mu)
op = ch @ mu_inv @ ce @ e - omega ** 2 * (epsilon * e)
return norm(op) / norm(e)
def cylindrical_operator(omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
r0: float,
) -> sparse.spmatrix:
"""
Cylindrical coordinate waveguide operator of the form
TODO
for use with a field vector of the form [E_r, E_y].
This operator can be used to form an eigenvalue problem of the form
A @ [E_r, E_y] = wavenumber**2 * [E_r, E_y]
which can then be solved for the eigenmodes of the system (an exp(-i * wavenumber * theta)
theta-dependence is assumed for the fields).
:param omega: The angular frequency of the system
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types (2D)
:param epsilon: Vectorized dielectric constant grid
:param r0: Radius of curvature for the simulation. This should be the minimum value of
r within the simulation domain.
:return: Sparse matrix representation of the operator
"""
Dfx, Dfy = operators.deriv_forward(dxes[0])
Dbx, Dby = operators.deriv_back(dxes[1])
rx = r0 + numpy.cumsum(dxes[0][0])
ry = r0 + dxes[0][0]/2.0 + numpy.cumsum(dxes[1][0])
tx = rx/r0
ty = ry/r0
Tx = sparse.diags(vec(tx[:, None].repeat(dxes[0][1].size, axis=1)))
Ty = sparse.diags(vec(ty[:, None].repeat(dxes[1][1].size, axis=1)))
eps_parts = numpy.split(epsilon, 3)
eps_x = sparse.diags(eps_parts[0])
eps_y = sparse.diags(eps_parts[1])
eps_z_inv = sparse.diags(1 / eps_parts[2])
pa = sparse.vstack((Dfx, Dfy)) @ Tx @ eps_z_inv @ sparse.hstack((Dbx, Dby))
pb = sparse.vstack((Dfx, Dfy)) @ Tx @ eps_z_inv @ sparse.hstack((Dby, Dbx))
a0 = Ty @ eps_x + omega**-2 * Dby @ Ty @ Dfy
a1 = Tx @ eps_y + omega**-2 * Dbx @ Ty @ Dfx
b0 = Dbx @ Ty @ Dfy
b1 = Dby @ Ty @ Dfx
diag = sparse.block_diag
op = (omega**2 * diag((Tx, Ty)) + pa) @ diag((a0, a1)) + \
- (sparse.bmat(((None, Ty), (Tx, None))) + omega**-2 * pb) @ diag((b0, b1))
return op

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"""
Operators and helper functions for waveguides with unchanging cross-section.
The propagation direction is chosen to be along the z axis, and all fields
are given an implicit z-dependence of the form `exp(-1 * wavenumber * z)`.
As the z-dependence is known, all the functions in this file assume a 2D grid
(i.e. `dxes = [[[dx_e_0, dx_e_1, ...], [dy_e_0, ...]], [[dx_h_0, ...], [dy_h_0, ...]]]`).
"""
# TODO update module docs
from typing import List, Tuple
import numpy
from numpy.linalg import norm
import scipy.sparse as sparse
from .. import vec, unvec, dx_lists_t, field_t, vfield_t
from ..eigensolvers import signed_eigensolve, rayleigh_quotient_iteration
from . import operators
__author__ = 'Jan Petykiewicz'
def operator_e(omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
) -> sparse.spmatrix:
"""
Waveguide operator of the form
omega**2 * mu * epsilon +
mu * [[-Dy], [Dx]] / mu * [-Dy, Dx] +
[[Dx], [Dy]] / epsilon * [Dx, Dy] * epsilon
for use with a field vector of the form `cat([E_x, E_y])`.
More precisely, the operator is
$$ \\omega^2 \\mu_{yx} \\epsilon_{xy} +
\\mu_{yx} \\begin{bmatrix} -D_{by} \\\\
D_{bx} \\end{bmatrix} \\mu_z^{-1}
\\begin{bmatrix} -D_{fy} & D_{fx} \\end{bmatrix} +
\\begin{bmatrix} D_{fx} \\\\
D_{fy} \\end{bmatrix} \\epsilon_z^{-1}
\\begin{bmatrix} D_{bx} & D_{by} \\end{bmatrix} \\epsilon_{xy} $$
where
\\( \\epsilon_{xy} = \\begin{bmatrix}
\\epsilon_x & 0 \\\\
0 & \\epsilon_y
\\end{bmatrix} \\),
\\( \\mu_{yx} = \\begin{bmatrix}
\\mu_y & 0 \\\\
0 & \\mu_x
\\end{bmatrix} \\),
\\( D_{fx} \\) and \\( D_{bx} \\) are the forward and backward derivatives along x,
and each \\( \\epsilon_x, \\mu_y, \\) etc. is a diagonal matrix representing
This operator can be used to form an eigenvalue problem of the form
`operator_e(...) @ [E_x, E_y] = wavenumber**2 * [E_x, E_y]`
which can then be solved for the eigenmodes of the system (an `exp(-i * wavenumber * z)`
z-dependence is assumed for the fields).
Args:
omega: The angular frequency of the system.
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Sparse matrix representation of the operator.
"""
if numpy.any(numpy.equal(mu, None)):
mu = numpy.ones_like(epsilon)
Dfx, Dfy = operators.deriv_forward(dxes[0])
Dbx, Dby = operators.deriv_back(dxes[1])
eps_parts = numpy.split(epsilon, 3)
eps_xy = sparse.diags(numpy.hstack((eps_parts[0], eps_parts[1])))
eps_z_inv = sparse.diags(1 / eps_parts[2])
mu_parts = numpy.split(mu, 3)
mu_yx = sparse.diags(numpy.hstack((mu_parts[1], mu_parts[0])))
mu_z_inv = sparse.diags(1 / mu_parts[2])
op = omega * omega * mu_yx @ eps_xy + \
mu_yx @ sparse.vstack((-Dby, Dbx)) @ mu_z_inv @ sparse.hstack((-Dfy, Dfx)) + \
sparse.vstack((Dfx, Dfy)) @ eps_z_inv @ sparse.hstack((Dbx, Dby)) @ eps_xy
return op
def operator_h(omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
) -> sparse.spmatrix:
"""
Waveguide operator of the form
omega**2 * epsilon * mu +
epsilon * [[-Dy], [Dx]] / epsilon * [-Dy, Dx] +
[[Dx], [Dy]] / mu * [Dx, Dy] * mu
for use with a field vector of the form `cat([H_x, H_y])`.
More precisely, the operator is
$$ \\omega^2 \\epsilon_{yx} \\mu_{xy} +
\\epsilon_{yx} \\begin{bmatrix} -D_{fy} \\\\
D_{fx} \\end{bmatrix} \\epsilon_z^{-1}
\\begin{bmatrix} -D_{by} & D_{bx} \\end{bmatrix} +
\\begin{bmatrix} D_{bx} \\\\
D_{by} \\end{bmatrix} \\mu_z^{-1}
\\begin{bmatrix} D_{fx} & D_{fy} \\end{bmatrix} \\mu_{xy} $$
where
\\( \\epsilon_{yx} = \\begin{bmatrix}
\\epsilon_y & 0 \\\\
0 & \\epsilon_x
\\end{bmatrix} \\),
\\( \\mu_{xy} = \\begin{bmatrix}
\\mu_x & 0 \\\\
0 & \\mu_y
\\end{bmatrix} \\),
\\( D_{fx} \\) and \\( D_{bx} \\) are the forward and backward derivatives along x,
and each \\( \\epsilon_x, \\mu_y, \\) etc. is a diagonal matrix.
This operator can be used to form an eigenvalue problem of the form
`operator_h(...) @ [H_x, H_y] = wavenumber**2 * [H_x, H_y]`
which can then be solved for the eigenmodes of the system (an `exp(-i * wavenumber * z)`
z-dependence is assumed for the fields).
Args:
omega: The angular frequency of the system.
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Sparse matrix representation of the operator.
"""
if numpy.any(numpy.equal(mu, None)):
mu = numpy.ones_like(epsilon)
Dfx, Dfy = operators.deriv_forward(dxes[0])
Dbx, Dby = operators.deriv_back(dxes[1])
eps_parts = numpy.split(epsilon, 3)
eps_yx = sparse.diags(numpy.hstack((eps_parts[1], eps_parts[0])))
eps_z_inv = sparse.diags(1 / eps_parts[2])
mu_parts = numpy.split(mu, 3)
mu_xy = sparse.diags(numpy.hstack((mu_parts[0], mu_parts[1])))
mu_z_inv = sparse.diags(1 / mu_parts[2])
op = omega * omega * eps_yx @ mu_xy + \
eps_yx @ sparse.vstack((-Dfy, Dfx)) @ eps_z_inv @ sparse.hstack((-Dby, Dbx)) + \
sparse.vstack((Dbx, Dby)) @ mu_z_inv @ sparse.hstack((Dfx, Dfy)) @ mu_xy
return op
def normalized_fields_e(e_xy: numpy.ndarray,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
prop_phase: float = 0,
) -> Tuple[vfield_t, vfield_t]:
"""
Given a vector `e_xy` containing the vectorized E_x and E_y fields,
returns normalized, vectorized E and H fields for the system.
Args:
e_xy: Vector containing E_x and E_y fields
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`.
It should satisfy `operator_e() @ e_xy == wavenumber**2 * e_xy`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
prop_phase: Phase shift `(dz * corrected_wavenumber)` over 1 cell in propagation direction.
Default 0 (continuous propagation direction, i.e. dz->0).
Returns:
`(e, h)`, where each field is vectorized, normalized,
and contains all three vector components.
"""
e = exy2e(wavenumber=wavenumber, dxes=dxes, epsilon=epsilon) @ e_xy
h = exy2h(wavenumber=wavenumber, omega=omega, dxes=dxes, epsilon=epsilon, mu=mu) @ e_xy
e_norm, h_norm = _normalized_fields(e=e, h=h, omega=omega, dxes=dxes, epsilon=epsilon,
mu=mu, prop_phase=prop_phase)
return e_norm, h_norm
def normalized_fields_h(h_xy: numpy.ndarray,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
prop_phase: float = 0,
) -> Tuple[vfield_t, vfield_t]:
"""
Given a vector `h_xy` containing the vectorized H_x and H_y fields,
returns normalized, vectorized E and H fields for the system.
Args:
h_xy: Vector containing H_x and H_y fields
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`.
It should satisfy `operator_h() @ h_xy == wavenumber**2 * h_xy`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
prop_phase: Phase shift `(dz * corrected_wavenumber)` over 1 cell in propagation direction.
Default 0 (continuous propagation direction, i.e. dz->0).
Returns:
`(e, h)`, where each field is vectorized, normalized,
and contains all three vector components.
"""
e = hxy2e(wavenumber=wavenumber, omega=omega, dxes=dxes, epsilon=epsilon, mu=mu) @ h_xy
h = hxy2h(wavenumber=wavenumber, dxes=dxes, mu=mu) @ h_xy
e_norm, h_norm = _normalized_fields(e=e, h=h, omega=omega, dxes=dxes, epsilon=epsilon,
mu=mu, prop_phase=prop_phase)
return e_norm, h_norm
def _normalized_fields(e: numpy.ndarray,
h: numpy.ndarray,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
prop_phase: float = 0,
) -> Tuple[vfield_t, vfield_t]:
# TODO documentation
shape = [s.size for s in dxes[0]]
dxes_real = [[numpy.real(d) for d in numpy.meshgrid(*dxes[v], indexing='ij')] for v in (0, 1)]
E = unvec(e, shape)
H = unvec(h, shape)
# Find time-averaged Sz and normalize to it
# H phase is adjusted by a half-cell forward shift for Yee cell, and 1-cell reverse shift for Poynting
phase = numpy.exp(-1j * -prop_phase / 2)
Sz_a = E[0] * numpy.conj(H[1] * phase) * dxes_real[0][1] * dxes_real[1][0]
Sz_b = E[1] * numpy.conj(H[0] * phase) * dxes_real[0][0] * dxes_real[1][1]
Sz_tavg = numpy.real(Sz_a.sum() - Sz_b.sum()) * 0.5 # 0.5 since E, H are assumed to be peak (not RMS) amplitudes
assert Sz_tavg > 0, 'Found a mode propagating in the wrong direction! Sz_tavg={}'.format(Sz_tavg)
energy = epsilon * e.conj() * e
norm_amplitude = 1 / numpy.sqrt(Sz_tavg)
norm_angle = -numpy.angle(e[energy.argmax()]) # Will randomly add a negative sign when mode is symmetric
# Try to break symmetry to assign a consistent sign [experimental TODO]
E_weighted = unvec(e * energy * numpy.exp(1j * norm_angle), shape)
sign = numpy.sign(E_weighted[:, :max(shape[0]//2, 1), :max(shape[1]//2, 1)].real.sum())
norm_factor = sign * norm_amplitude * numpy.exp(1j * norm_angle)
e *= norm_factor
h *= norm_factor
return e, h
def exy2h(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Operator which transforms the vector `e_xy` containing the vectorized E_x and E_y fields,
into a vectorized H containing all three H components
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`.
It should satisfy `operator_e() @ e_xy == wavenumber**2 * e_xy`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Sparse matrix representing the operator.
"""
e2hop = e2h(wavenumber=wavenumber, omega=omega, dxes=dxes, mu=mu)
return e2hop @ exy2e(wavenumber=wavenumber, dxes=dxes, epsilon=epsilon)
def hxy2e(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Operator which transforms the vector `h_xy` containing the vectorized H_x and H_y fields,
into a vectorized E containing all three E components
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`.
It should satisfy `operator_h() @ h_xy == wavenumber**2 * h_xy`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Sparse matrix representing the operator.
"""
h2eop = h2e(wavenumber=wavenumber, omega=omega, dxes=dxes, epsilon=epsilon)
return h2eop @ hxy2h(wavenumber=wavenumber, dxes=dxes, mu=mu)
def hxy2h(wavenumber: complex,
dxes: dx_lists_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Operator which transforms the vector `h_xy` containing the vectorized H_x and H_y fields,
into a vectorized H containing all three H components
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`.
It should satisfy `operator_h() @ h_xy == wavenumber**2 * h_xy`
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Sparse matrix representing the operator.
"""
Dfx, Dfy = operators.deriv_forward(dxes[0])
hxy2hz = sparse.hstack((Dfx, Dfy)) / (1j * wavenumber)
if not numpy.any(numpy.equal(mu, None)):
mu_parts = numpy.split(mu, 3)
mu_xy = sparse.diags(numpy.hstack((mu_parts[0], mu_parts[1])))
mu_z_inv = sparse.diags(1 / mu_parts[2])
hxy2hz = mu_z_inv @ hxy2hz @ mu_xy
n_pts = dxes[1][0].size * dxes[1][1].size
op = sparse.vstack((sparse.eye(2 * n_pts),
hxy2hz))
return op
def exy2e(wavenumber: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
) -> sparse.spmatrix:
"""
Operator which transforms the vector `e_xy` containing the vectorized E_x and E_y fields,
into a vectorized E containing all three E components
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
It should satisfy `operator_e() @ e_xy == wavenumber**2 * e_xy`
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
Returns:
Sparse matrix representing the operator.
"""
Dbx, Dby = operators.deriv_back(dxes[1])
exy2ez = sparse.hstack((Dbx, Dby)) / (1j * wavenumber)
if not numpy.any(numpy.equal(epsilon, None)):
epsilon_parts = numpy.split(epsilon, 3)
epsilon_xy = sparse.diags(numpy.hstack((epsilon_parts[0], epsilon_parts[1])))
epsilon_z_inv = sparse.diags(1 / epsilon_parts[2])
exy2ez = epsilon_z_inv @ exy2ez @ epsilon_xy
n_pts = dxes[0][0].size * dxes[0][1].size
op = sparse.vstack((sparse.eye(2 * n_pts),
exy2ez))
return op
def e2h(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
mu: vfield_t = None
) -> sparse.spmatrix:
"""
Returns an operator which, when applied to a vectorized E eigenfield, produces
the vectorized H eigenfield.
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Sparse matrix representation of the operator.
"""
op = curl_e(wavenumber, dxes) / (-1j * omega)
if not numpy.any(numpy.equal(mu, None)):
op = sparse.diags(1 / mu) @ op
return op
def h2e(wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t
) -> sparse.spmatrix:
"""
Returns an operator which, when applied to a vectorized H eigenfield, produces
the vectorized E eigenfield.
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
Returns:
Sparse matrix representation of the operator.
"""
op = sparse.diags(1 / (1j * omega * epsilon)) @ curl_h(wavenumber, dxes)
return op
def curl_e(wavenumber: complex, dxes: dx_lists_t) -> sparse.spmatrix:
"""
Discretized curl operator for use with the waveguide E field.
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
Return:
Sparse matrix representation of the operator.
"""
n = 1
for d in dxes[0]:
n *= len(d)
Bz = -1j * wavenumber * sparse.eye(n)
Dfx, Dfy = operators.deriv_forward(dxes[0])
return operators.cross([Dfx, Dfy, Bz])
def curl_h(wavenumber: complex, dxes: dx_lists_t) -> sparse.spmatrix:
"""
Discretized curl operator for use with the waveguide H field.
Args:
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
Return:
Sparse matrix representation of the operator.
"""
n = 1
for d in dxes[1]:
n *= len(d)
Bz = -1j * wavenumber * sparse.eye(n)
Dbx, Dby = operators.deriv_back(dxes[1])
return operators.cross([Dbx, Dby, Bz])
def h_err(h: vfield_t,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> float:
"""
Calculates the relative error in the H field
Args:
h: Vectorized H field
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Relative error `norm(A_h @ h) / norm(h)`.
"""
ce = curl_e(wavenumber, dxes)
ch = curl_h(wavenumber, dxes)
eps_inv = sparse.diags(1 / epsilon)
if numpy.any(numpy.equal(mu, None)):
op = ce @ eps_inv @ ch @ h - omega ** 2 * h
else:
op = ce @ eps_inv @ ch @ h - omega ** 2 * (mu * h)
return norm(op) / norm(h)
def e_err(e: vfield_t,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None
) -> float:
"""
Calculates the relative error in the E field
Args:
e: Vectorized E field
wavenumber: Wavenumber assuming fields have z-dependence of `exp(-i * wavenumber * z)`
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
mu: Vectorized magnetic permeability grid (default 1 everywhere)
Returns:
Relative error `norm(A_e @ e) / norm(e)`.
"""
ce = curl_e(wavenumber, dxes)
ch = curl_h(wavenumber, dxes)
if numpy.any(numpy.equal(mu, None)):
op = ch @ ce @ e - omega ** 2 * (epsilon * e)
else:
mu_inv = sparse.diags(1 / mu)
op = ch @ mu_inv @ ce @ e - omega ** 2 * (epsilon * e)
return norm(op) / norm(e)
def solve_modes(mode_numbers: List[int],
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
mode_margin: int = 2,
) -> Tuple[List[vfield_t], List[complex]]:
"""
Given a 2D region, attempts to solve for the eigenmode with the specified mode numbers.
Args:
mode_numbers: List of 0-indexed mode numbers to solve for
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
epsilon: Dielectric constant
mu: Magnetic permeability (default 1 everywhere)
mode_margin: The eigensolver will actually solve for `(max(mode_number) + mode_margin)`
modes, but only return the target mode. Increasing this value can improve the solver's
ability to find the correct mode. Default 2.
Returns:
(e_xys, wavenumbers)
"""
'''
Solve for the largest-magnitude eigenvalue of the real operator
'''
dxes_real = [[numpy.real(dx) for dx in dxi] for dxi in dxes]
A_r = waveguide.operator_e(numpy.real(omega), dxes_real, numpy.real(epsilon), numpy.real(mu))
eigvals, eigvecs = signed_eigensolve(A_r, max(mode_number) + mode_margin)
e_xys = eigvecs[:, -(numpy.array(mode_number) + 1)]
'''
Now solve for the eigenvector of the full operator, using the real operator's
eigenvector as an initial guess for Rayleigh quotient iteration.
'''
A = waveguide.operator_e(omega, dxes, epsilon, mu)
eigvals, e_xys = rayleigh_quotient_iteration(A, e_xys)
# Calculate the wave-vector (force the real part to be positive)
wavenumbers = numpy.sqrt(eigvals)
wavenumbers *= numpy.sign(numpy.real(wavenumbers))
return e_xys, wavenumbers
def solve_mode(mode_number: int,
*args,
**kwargs
) -> Tuple[vfield_t, complex]:
"""
Wrapper around `solve_modes()` that solves for a single mode.
Args:
mode_number: 0-indexed mode number to solve for
*args: passed to `solve_modes()`
**kwargs: passed to `solve_modes()`
Returns:
(e_xy, wavenumber)
"""
return solve_modes(mode_numbers=[mode_number], *args, **kwargs)

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"""
Tools for working with waveguide modes in 3D domains.
This module relies heavily on `waveguide_2d` and mostly just transforms
its parameters into 2D equivalents and expands the results back into 3D.
"""
from typing import Dict, List, Tuple
import numpy
import scipy.sparse as sparse
from .. import vec, unvec, dx_lists_t, vfield_t, field_t
from . import operators, waveguide_2d, functional
def solve_mode(mode_number: int,
omega: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
epsilon: field_t,
mu: field_t = None,
) -> Dict[str, complex or numpy.ndarray]:
"""
Given a 3D grid, selects a slice from the grid and attempts to
solve for an eigenmode propagating through that slice.
Args:
mode_number: Number of the mode, 0-indexed
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
axis: Propagation axis (0=x, 1=y, 2=z)
polarity: Propagation direction (+1 for +ve, -1 for -ve)
slices: `epsilon[tuple(slices)]` is used to select the portion of the grid to use
as the waveguide cross-section. `slices[axis]` should select only one item.
epsilon: Dielectric constant
mu: Magnetic permeability (default 1 everywhere)
Returns:
`{'E': List[numpy.ndarray], 'H': List[numpy.ndarray], 'wavenumber': complex}`
"""
if mu is None:
mu = numpy.ones_like(epsilon)
slices = tuple(slices)
'''
Solve the 2D problem in the specified plane
'''
# Define rotation to set z as propagation direction
order = numpy.roll(range(3), 2 - axis)
reverse_order = numpy.roll(range(3), axis - 2)
# Find dx in propagation direction
dxab_forward = numpy.array([dx[order[2]][slices[order[2]]] for dx in dxes])
dx_prop = 0.5 * sum(dxab_forward)[0]
# Reduce to 2D and solve the 2D problem
args_2d = {
'omega': omega,
'dxes': [[dx[i][slices[i]] for i in order[:2]] for dx in dxes],
'epsilon': vec([epsilon[i][slices].transpose(order) for i in order]),
'mu': vec([mu[i][slices].transpose(order) for i in order]),
}
e_xy, wavenumber_2d = waveguide_2d.solve_mode(mode_number, **args_2d)
'''
Apply corrections and expand to 3D
'''
# Correct wavenumber to account for numerical dispersion.
wavenumber = 2/dx_prop * numpy.arcsin(wavenumber_2d * dx_prop/2)
shape = [d.size for d in args_2d['dxes'][0]]
ve, vh = waveguide.normalized_fields_e(e_xy, wavenumber=wavenumber_2d, **args_2d, prop_phase=dx_prop * wavenumber)
e = unvec(ve, shape)
h = unvec(vh, shape)
# Adjust for propagation direction
h *= polarity
# Apply phase shift to H-field
h[:2] *= numpy.exp(-1j * polarity * 0.5 * wavenumber * dx_prop)
e[2] *= numpy.exp(-1j * polarity * 0.5 * wavenumber * dx_prop)
# Expand E, H to full epsilon space we were given
E = numpy.zeros_like(epsilon, dtype=complex)
H = numpy.zeros_like(epsilon, dtype=complex)
for a, o in enumerate(reverse_order):
E[(a, *slices)] = e[o][:, :, None].transpose(reverse_order)
H[(a, *slices)] = h[o][:, :, None].transpose(reverse_order)
results = {
'wavenumber': wavenumber,
'wavenumber_2d': wavenumber_2d,
'H': H,
'E': E,
}
return results
def compute_source(E: field_t,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
epsilon: field_t,
mu: field_t = None,
) -> field_t:
"""
Given an eigenmode obtained by `solve_mode`, returns the current source distribution
necessary to position a unidirectional source at the slice location.
Args:
E: E-field of the mode
wavenumber: Wavenumber of the mode
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
axis: Propagation axis (0=x, 1=y, 2=z)
polarity: Propagation direction (+1 for +ve, -1 for -ve)
slices: `epsilon[tuple(slices)]` is used to select the portion of the grid to use
as the waveguide cross-section. `slices[axis]` should select only one item.
mu: Magnetic permeability (default 1 everywhere)
Returns:
J distribution for the unidirectional source
"""
E_expanded = expand_e(E=E, dxes=dxes, wavenumber=wavenumber, axis=axis,
polarity=polarity, slices=slices)
smask = [slice(None)] * 4
if polarity > 0:
smask[axis + 1] = slice(slices[axis].start, None)
else:
smask[axis + 1] = slice(None, slices[axis].stop)
mask = numpy.zeros_like(E_expanded, dtype=int)
mask[tuple(smask)] = 1
masked_e2j = operators.e_boundary_source(mask=vec(mask), omega=omega, dxes=dxes, epsilon=vec(epsilon), mu=vec(mu))
J = unvec(masked_e2j @ vec(E_expanded), E.shape[1:])
return J
def compute_overlap_e(E: field_t,
wavenumber: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
) -> field_t: # TODO DOCS
"""
Given an eigenmode obtained by `solve_mode`, calculates an overlap_e for the
mode orthogonality relation Integrate(((E x H_mode) + (E_mode x H)) dot dn)
[assumes reflection symmetry].
Args:
E: E-field of the mode
H: H-field of the mode (advanced by half of a Yee cell from E)
wavenumber: Wavenumber of the mode
omega: Angular frequency of the simulation
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
axis: Propagation axis (0=x, 1=y, 2=z)
polarity: Propagation direction (+1 for +ve, -1 for -ve)
slices: `epsilon[tuple(slices)]` is used to select the portion of the grid to use
as the waveguide cross-section. slices[axis] should select only one item.
mu: Magnetic permeability (default 1 everywhere)
Returns:
overlap_e such that `numpy.sum(overlap_e * other_e)` computes the overlap integral
"""
slices = tuple(slices)
Ee = expand_e(E=E, wavenumber=wavenumber, dxes=dxes,
axis=axis, polarity=polarity, slices=slices)
start, stop = sorted((slices[axis].start, slices[axis].start - 2 * polarity))
slices2 = list(slices)
slices2[axis] = slice(start, stop)
slices2 = (slice(None), *slices2)
Etgt = numpy.zeros_like(Ee)
Etgt[slices2] = Ee[slices2]
Etgt /= (Etgt.conj() * Etgt).sum()
return Etgt
def expand_e(E: field_t,
wavenumber: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
) -> field_t:
"""
Given an eigenmode obtained by `solve_mode`, expands the E-field from the 2D
slice where the mode was calculated to the entire domain (along the propagation
axis). This assumes the epsilon cross-section remains constant throughout the
entire domain; it is up to the caller to truncate the expansion to any regions
where it is valid.
Args:
E: E-field of the mode
wavenumber: Wavenumber of the mode
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types`
axis: Propagation axis (0=x, 1=y, 2=z)
polarity: Propagation direction (+1 for +ve, -1 for -ve)
slices: `epsilon[tuple(slices)]` is used to select the portion of the grid to use
as the waveguide cross-section. slices[axis] should select only one item.
Returns:
`E`, with the original field expanded along the specified `axis`.
"""
slices = tuple(slices)
# Determine phase factors for parallel slices
a_shape = numpy.roll([1, -1, 1, 1], axis)
a_E = numpy.real(dxes[0][axis]).cumsum()
r_E = a_E - a_E[slices[axis]]
iphi = polarity * -1j * wavenumber
phase_E = numpy.exp(iphi * r_E).reshape(a_shape)
# Expand our slice to the entire grid using the phase factors
E_expanded = numpy.zeros_like(E)
slices_exp = list(slices)
slices_exp[axis] = slice(E.shape[axis + 1])
slices_exp = (slice(None), *slices_exp)
slices_in = (slice(None), *slices)
E_expanded[slices_exp] = phase_E * numpy.array(E)[slices_in]
return E_expanded

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"""
Operators and helper functions for cylindrical waveguides with unchanging cross-section.
WORK IN PROGRESS, CURRENTLY BROKEN
As the z-dependence is known, all the functions in this file assume a 2D grid
(i.e. `dxes = [[[dr_e_0, dx_e_1, ...], [dy_e_0, ...]], [[dr_h_0, ...], [dy_h_0, ...]]]`).
"""
# TODO update module docs
from typing import List, Tuple, Dict
import numpy
from numpy.linalg import norm
import scipy.sparse as sparse
from .. import vec, unvec, dx_lists_t, field_t, vfield_t
from ..eigensolvers import signed_eigensolve, rayleigh_quotient_iteration
from . import operators
__author__ = 'Jan Petykiewicz'
def cylindrical_operator(omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
r0: float,
) -> sparse.spmatrix:
"""
Cylindrical coordinate waveguide operator of the form
TODO
for use with a field vector of the form `[E_r, E_y]`.
This operator can be used to form an eigenvalue problem of the form
A @ [E_r, E_y] = wavenumber**2 * [E_r, E_y]
which can then be solved for the eigenmodes of the system
(an `exp(-i * wavenumber * theta)` theta-dependence is assumed for the fields).
Args:
omega: The angular frequency of the system
dxes: Grid parameters `[dx_e, dx_h]` as described in `meanas.types` (2D)
epsilon: Vectorized dielectric constant grid
r0: Radius of curvature for the simulation. This should be the minimum value of
r within the simulation domain.
Returns:
Sparse matrix representation of the operator
"""
Dfx, Dfy = operators.deriv_forward(dxes[0])
Dbx, Dby = operators.deriv_back(dxes[1])
rx = r0 + numpy.cumsum(dxes[0][0])
ry = r0 + dxes[0][0]/2.0 + numpy.cumsum(dxes[1][0])
tx = rx/r0
ty = ry/r0
Tx = sparse.diags(vec(tx[:, None].repeat(dxes[0][1].size, axis=1)))
Ty = sparse.diags(vec(ty[:, None].repeat(dxes[1][1].size, axis=1)))
eps_parts = numpy.split(epsilon, 3)
eps_x = sparse.diags(eps_parts[0])
eps_y = sparse.diags(eps_parts[1])
eps_z_inv = sparse.diags(1 / eps_parts[2])
pa = sparse.vstack((Dfx, Dfy)) @ Tx @ eps_z_inv @ sparse.hstack((Dbx, Dby))
pb = sparse.vstack((Dfx, Dfy)) @ Tx @ eps_z_inv @ sparse.hstack((Dby, Dbx))
a0 = Ty @ eps_x + omega**-2 * Dby @ Ty @ Dfy
a1 = Tx @ eps_y + omega**-2 * Dbx @ Ty @ Dfx
b0 = Dbx @ Ty @ Dfy
b1 = Dby @ Ty @ Dfx
diag = sparse.block_diag
op = (omega**2 * diag((Tx, Ty)) + pa) @ diag((a0, a1)) + \
- (sparse.bmat(((None, Ty), (Tx, None))) + omega**-2 * pb) @ diag((b0, b1))
return op
def solve_mode(mode_number: int,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
r0: float,
) -> Dict[str, complex or field_t]:
"""
TODO: fixup
Given a 2d (r, y) slice of epsilon, attempts to solve for the eigenmode
of the bent waveguide with the specified mode number.
Args:
mode_number: Number of the mode, 0-indexed
omega: Angular frequency of the simulation
dxes: Grid parameters [dx_e, dx_h] as described in meanas.types.
The first coordinate is assumed to be r, the second is y.
epsilon: Dielectric constant
r0: Radius of curvature for the simulation. This should be the minimum value of
r within the simulation domain.
Returns:
`{'E': List[numpy.ndarray], 'H': List[numpy.ndarray], 'wavenumber': complex}`
"""
'''
Solve for the largest-magnitude eigenvalue of the real operator
'''
dxes_real = [[numpy.real(dx) for dx in dxi] for dxi in dxes]
A_r = waveguide.cylindrical_operator(numpy.real(omega), dxes_real, numpy.real(epsilon), r0)
eigvals, eigvecs = signed_eigensolve(A_r, mode_number + 3)
e_xy = eigvecs[:, -(mode_number+1)]
'''
Now solve for the eigenvector of the full operator, using the real operator's
eigenvector as an initial guess for Rayleigh quotient iteration.
'''
A = waveguide.cylindrical_operator(omega, dxes, epsilon, r0)
eigval, e_xy = rayleigh_quotient_iteration(A, e_xy)
# Calculate the wave-vector (force the real part to be positive)
wavenumber = numpy.sqrt(eigval)
wavenumber *= numpy.sign(numpy.real(wavenumber))
# TODO: Perform correction on wavenumber to account for numerical dispersion.
shape = [d.size for d in dxes[0]]
e_xy = numpy.hstack((e_xy, numpy.zeros(shape[0] * shape[1])))
fields = {
'wavenumber': wavenumber,
'E': unvec(e_xy, shape),
# 'E': unvec(e, shape),
# 'H': unvec(h, shape),
}
return fields

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from typing import Dict, List, Tuple
import numpy
import scipy.sparse as sparse
from .. import vec, unvec, dx_lists_t, vfield_t, field_t
from . import operators, waveguide, functional
from ..eigensolvers import signed_eigensolve, rayleigh_quotient_iteration
def vsolve_waveguide_mode_2d(mode_number: int,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
mu: vfield_t = None,
mode_margin: int = 2,
) -> Tuple[vfield_t, complex]:
"""
Given a 2d region, attempts to solve for the eigenmode with the specified mode number.
:param mode_number: Number of the mode, 0-indexed.
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param epsilon: Dielectric constant
:param mu: Magnetic permeability (default 1 everywhere)
:param mode_margin: The eigensolver will actually solve for (mode_number + mode_margin)
modes, but only return the target mode. Increasing this value can improve the solver's
ability to find the correct mode. Default 2.
:return: (e_xy, wavenumber)
"""
'''
Solve for the largest-magnitude eigenvalue of the real operator
'''
dxes_real = [[numpy.real(dx) for dx in dxi] for dxi in dxes]
A_r = waveguide.operator_e(numpy.real(omega), dxes_real, numpy.real(epsilon), numpy.real(mu))
eigvals, eigvecs = signed_eigensolve(A_r, mode_number + mode_margin)
e_xy = eigvecs[:, -(mode_number + 1)]
'''
Now solve for the eigenvector of the full operator, using the real operator's
eigenvector as an initial guess for Rayleigh quotient iteration.
'''
A = waveguide.operator_e(omega, dxes, epsilon, mu)
eigval, e_xy = rayleigh_quotient_iteration(A, e_xy)
# Calculate the wave-vector (force the real part to be positive)
wavenumber = numpy.sqrt(eigval)
wavenumber *= numpy.sign(numpy.real(wavenumber))
return e_xy, wavenumber
def solve_waveguide_mode(mode_number: int,
omega: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
epsilon: field_t,
mu: field_t = None,
) -> Dict[str, complex or numpy.ndarray]:
"""
Given a 3D grid, selects a slice from the grid and attempts to
solve for an eigenmode propagating through that slice.
:param mode_number: Number of the mode, 0-indexed
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param axis: Propagation axis (0=x, 1=y, 2=z)
:param polarity: Propagation direction (+1 for +ve, -1 for -ve)
:param slices: epsilon[tuple(slices)] is used to select the portion of the grid to use
as the waveguide cross-section. slices[axis] should select only one
:param epsilon: Dielectric constant
:param mu: Magnetic permeability (default 1 everywhere)
:return: {'E': List[numpy.ndarray], 'H': List[numpy.ndarray], 'wavenumber': complex}
"""
if mu is None:
mu = numpy.ones_like(epsilon)
slices = tuple(slices)
'''
Solve the 2D problem in the specified plane
'''
# Define rotation to set z as propagation direction
order = numpy.roll(range(3), 2 - axis)
reverse_order = numpy.roll(range(3), axis - 2)
# Find dx in propagation direction
dxab_forward = numpy.array([dx[order[2]][slices[order[2]]] for dx in dxes])
dx_prop = 0.5 * sum(dxab_forward)[0]
# Reduce to 2D and solve the 2D problem
args_2d = {
'omega': omega,
'dxes': [[dx[i][slices[i]] for i in order[:2]] for dx in dxes],
'epsilon': vec([epsilon[i][slices].transpose(order) for i in order]),
'mu': vec([mu[i][slices].transpose(order) for i in order]),
}
e_xy, wavenumber_2d = vsolve_waveguide_mode_2d(mode_number, **args_2d)
'''
Apply corrections and expand to 3D
'''
# Correct wavenumber to account for numerical dispersion.
wavenumber = 2/dx_prop * numpy.arcsin(wavenumber_2d * dx_prop/2)
print(wavenumber_2d / wavenumber)
shape = [d.size for d in args_2d['dxes'][0]]
ve, vh = waveguide.normalized_fields_e(e_xy, wavenumber=wavenumber_2d, **args_2d, prop_phase=dx_prop * wavenumber)
e = unvec(ve, shape)
h = unvec(vh, shape)
# Adjust for propagation direction
h *= polarity
# Apply phase shift to H-field
h[:2] *= numpy.exp(-1j * polarity * 0.5 * wavenumber * dx_prop)
e[2] *= numpy.exp(-1j * polarity * 0.5 * wavenumber * dx_prop)
# Expand E, H to full epsilon space we were given
E = numpy.zeros_like(epsilon, dtype=complex)
H = numpy.zeros_like(epsilon, dtype=complex)
for a, o in enumerate(reverse_order):
E[(a, *slices)] = e[o][:, :, None].transpose(reverse_order)
H[(a, *slices)] = h[o][:, :, None].transpose(reverse_order)
results = {
'wavenumber': wavenumber,
'wavenumber_2d': wavenumber_2d,
'H': H,
'E': E,
}
return results
def compute_source(E: field_t,
wavenumber: complex,
omega: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
epsilon: field_t,
mu: field_t = None,
) -> field_t:
"""
Given an eigenmode obtained by solve_waveguide_mode, returns the current source distribution
necessary to position a unidirectional source at the slice location.
:param E: E-field of the mode
:param wavenumber: Wavenumber of the mode
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param axis: Propagation axis (0=x, 1=y, 2=z)
:param polarity: Propagation direction (+1 for +ve, -1 for -ve)
:param slices: epsilon[tuple(slices)] is used to select the portion of the grid to use
as the waveguide cross-section. slices[axis] should select only one
:param mu: Magnetic permeability (default 1 everywhere)
:return: J distribution for the unidirectional source
"""
E_expanded = expand_wgmode_e(E=E, dxes=dxes, wavenumber=wavenumber, axis=axis,
polarity=polarity, slices=slices)
smask = [slice(None)] * 4
if polarity > 0:
smask[axis + 1] = slice(slices[axis].start, None)
else:
smask[axis + 1] = slice(None, slices[axis].stop)
mask = numpy.zeros_like(E_expanded, dtype=int)
mask[tuple(smask)] = 1
masked_e2j = operators.e_boundary_source(mask=vec(mask), omega=omega, dxes=dxes, epsilon=vec(epsilon), mu=vec(mu))
J = unvec(masked_e2j @ vec(E_expanded), E.shape[1:])
return J
def compute_overlap_e(E: field_t,
wavenumber: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
) -> field_t: # TODO DOCS
"""
Given an eigenmode obtained by solve_waveguide_mode, calculates overlap_e for the
mode orthogonality relation Integrate(((E x H_mode) + (E_mode x H)) dot dn)
[assumes reflection symmetry].i
overlap_e makes use of the e2h operator to collapse the above expression into
(vec(E) @ vec(overlap_e)), allowing for simple calculation of the mode overlap.
:param E: E-field of the mode
:param H: H-field of the mode (advanced by half of a Yee cell from E)
:param wavenumber: Wavenumber of the mode
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:param axis: Propagation axis (0=x, 1=y, 2=z)
:param polarity: Propagation direction (+1 for +ve, -1 for -ve)
:param slices: epsilon[tuple(slices)] is used to select the portion of the grid to use
as the waveguide cross-section. slices[axis] should select only one
:param mu: Magnetic permeability (default 1 everywhere)
:return: overlap_e for calculating the mode overlap
"""
slices = tuple(slices)
Ee = expand_wgmode_e(E=E, wavenumber=wavenumber, dxes=dxes,
axis=axis, polarity=polarity, slices=slices)
start, stop = sorted((slices[axis].start, slices[axis].start - 2 * polarity))
slices2 = list(slices)
slices2[axis] = slice(start, stop)
slices2 = (slice(None), *slices2)
Etgt = numpy.zeros_like(Ee)
Etgt[slices2] = Ee[slices2]
Etgt /= (Etgt.conj() * Etgt).sum()
return Etgt
def solve_waveguide_mode_cylindrical(mode_number: int,
omega: complex,
dxes: dx_lists_t,
epsilon: vfield_t,
r0: float,
) -> Dict[str, complex or field_t]:
"""
TODO: fixup
Given a 2d (r, y) slice of epsilon, attempts to solve for the eigenmode
of the bent waveguide with the specified mode number.
:param mode_number: Number of the mode, 0-indexed
:param omega: Angular frequency of the simulation
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types.
The first coordinate is assumed to be r, the second is y.
:param epsilon: Dielectric constant
:param r0: Radius of curvature for the simulation. This should be the minimum value of
r within the simulation domain.
:return: {'E': List[numpy.ndarray], 'H': List[numpy.ndarray], 'wavenumber': complex}
"""
'''
Solve for the largest-magnitude eigenvalue of the real operator
'''
dxes_real = [[numpy.real(dx) for dx in dxi] for dxi in dxes]
A_r = waveguide.cylindrical_operator(numpy.real(omega), dxes_real, numpy.real(epsilon), r0)
eigvals, eigvecs = signed_eigensolve(A_r, mode_number + 3)
e_xy = eigvecs[:, -(mode_number+1)]
'''
Now solve for the eigenvector of the full operator, using the real operator's
eigenvector as an initial guess for Rayleigh quotient iteration.
'''
A = waveguide.cylindrical_operator(omega, dxes, epsilon, r0)
eigval, e_xy = rayleigh_quotient_iteration(A, e_xy)
# Calculate the wave-vector (force the real part to be positive)
wavenumber = numpy.sqrt(eigval)
wavenumber *= numpy.sign(numpy.real(wavenumber))
# TODO: Perform correction on wavenumber to account for numerical dispersion.
shape = [d.size for d in dxes[0]]
e_xy = numpy.hstack((e_xy, numpy.zeros(shape[0] * shape[1])))
fields = {
'wavenumber': wavenumber,
'E': unvec(e_xy, shape),
# 'E': unvec(e, shape),
# 'H': unvec(h, shape),
}
return fields
def expand_wgmode_e(E: field_t,
wavenumber: complex,
dxes: dx_lists_t,
axis: int,
polarity: int,
slices: List[slice],
) -> field_t:
slices = tuple(slices)
# Determine phase factors for parallel slices
a_shape = numpy.roll([1, -1, 1, 1], axis)
a_E = numpy.real(dxes[0][axis]).cumsum()
r_E = a_E - a_E[slices[axis]]
iphi = polarity * -1j * wavenumber
phase_E = numpy.exp(iphi * r_E).reshape(a_shape)
# Expand our slice to the entire grid using the phase factors
E_expanded = numpy.zeros_like(E)
slices_exp = list(slices)
slices_exp[axis] = slice(E.shape[axis + 1])
slices_exp = (slice(None), *slices_exp)
slices_in = (slice(None), *slices)
E_expanded[slices_exp] = phase_E * numpy.array(E)[slices_in]
return E_expanded

109
meanas/fdmath/functional.py Normal file
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@ -0,0 +1,109 @@
"""
Math functions for finite difference simulations
Basic discrete calculus etc.
"""
from typing import List, Callable, Tuple, Dict
import numpy
from .. import field_t, field_updater
def deriv_forward(dx_e: List[numpy.ndarray] = None) -> field_updater:
"""
Utility operators for taking discretized derivatives (backward variant).
Args:
dx_e: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
List of functions for taking forward derivatives along each axis.
"""
if dx_e:
derivs = [lambda f: (numpy.roll(f, -1, axis=0) - f) / dx_e[0][:, None, None],
lambda f: (numpy.roll(f, -1, axis=1) - f) / dx_e[1][None, :, None],
lambda f: (numpy.roll(f, -1, axis=2) - f) / dx_e[2][None, None, :]]
else:
derivs = [lambda f: numpy.roll(f, -1, axis=0) - f,
lambda f: numpy.roll(f, -1, axis=1) - f,
lambda f: numpy.roll(f, -1, axis=2) - f]
return derivs
def deriv_back(dx_h: List[numpy.ndarray] = None) -> field_updater:
"""
Utility operators for taking discretized derivatives (forward variant).
Args:
dx_h: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
List of functions for taking forward derivatives along each axis.
"""
if dx_h:
derivs = [lambda f: (f - numpy.roll(f, 1, axis=0)) / dx_h[0][:, None, None],
lambda f: (f - numpy.roll(f, 1, axis=1)) / dx_h[1][None, :, None],
lambda f: (f - numpy.roll(f, 1, axis=2)) / dx_h[2][None, None, :]]
else:
derivs = [lambda f: f - numpy.roll(f, 1, axis=0),
lambda f: f - numpy.roll(f, 1, axis=1),
lambda f: f - numpy.roll(f, 1, axis=2)]
return derivs
def curl_forward(dx_e: List[numpy.ndarray] = None) -> field_updater:
"""
Curl operator for use with the E field.
Args:
dx_e: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
Function `f` for taking the discrete forward curl of a field,
`f(E)` -> curlE \\( = \\nabla_f \\times E \\)
"""
Dx, Dy, Dz = deriv_forward(dx_e)
def ce_fun(e: field_t) -> field_t:
output = numpy.empty_like(e)
output[0] = Dy(e[2])
output[1] = Dz(e[0])
output[2] = Dx(e[1])
output[0] -= Dz(e[1])
output[1] -= Dx(e[2])
output[2] -= Dy(e[0])
return output
return ce_fun
def curl_back(dx_h: List[numpy.ndarray] = None) -> field_updater:
"""
Create a function which takes the backward curl of a field.
Args:
dx_h: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
Function `f` for taking the discrete backward curl of a field,
`f(H)` -> curlH \\( = \\nabla_b \\times H \\)
"""
Dx, Dy, Dz = deriv_back(dx_h)
def ch_fun(h: field_t) -> field_t:
output = numpy.empty_like(h)
output[0] = Dy(h[2])
output[1] = Dz(h[0])
output[2] = Dx(h[1])
output[0] -= Dz(h[1])
output[1] -= Dx(h[2])
output[2] -= Dy(h[0])
return output
return ch_fun

231
meanas/fdmath/operators.py Normal file
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@ -0,0 +1,231 @@
"""
Matrix operators for finite difference simulations
Basic discrete calculus etc.
"""
from typing import List, Callable, Tuple, Dict
import numpy
import scipy.sparse as sparse
from .. import field_t, vfield_t
def rotation(axis: int, shape: List[int], shift_distance: int=1) -> sparse.spmatrix:
"""
Utility operator for performing a circular shift along a specified axis by a
specified number of elements.
Args:
axis: Axis to shift along. x=0, y=1, z=2
shape: Shape of the grid being shifted
shift_distance: Number of cells to shift by. May be negative. Default 1.
Returns:
Sparse matrix for performing the circular shift.
"""
if len(shape) not in (2, 3):
raise Exception('Invalid shape: {}'.format(shape))
if axis not in range(len(shape)):
raise Exception('Invalid direction: {}, shape is {}'.format(axis, shape))
shifts = [abs(shift_distance) if a == axis else 0 for a in range(3)]
shifted_diags = [(numpy.arange(n) + s) % n for n, s in zip(shape, shifts)]
ijk = numpy.meshgrid(*shifted_diags, indexing='ij')
n = numpy.prod(shape)
i_ind = numpy.arange(n)
j_ind = numpy.ravel_multi_index(ijk, shape, order='C')
vij = (numpy.ones(n), (i_ind, j_ind.ravel(order='C')))
d = sparse.csr_matrix(vij, shape=(n, n))
if shift_distance < 0:
d = d.T
return d
def shift_with_mirror(axis: int, shape: List[int], shift_distance: int=1) -> sparse.spmatrix:
"""
Utility operator for performing an n-element shift along a specified axis, with mirror
boundary conditions applied to the cells beyond the receding edge.
Args:
axis: Axis to shift along. x=0, y=1, z=2
shape: Shape of the grid being shifted
shift_distance: Number of cells to shift by. May be negative. Default 1.
Returns:
Sparse matrix for performing the shift-with-mirror.
"""
if len(shape) not in (2, 3):
raise Exception('Invalid shape: {}'.format(shape))
if axis not in range(len(shape)):
raise Exception('Invalid direction: {}, shape is {}'.format(axis, shape))
if shift_distance >= shape[axis]:
raise Exception('Shift ({}) is too large for axis {} of size {}'.format(
shift_distance, axis, shape[axis]))
def mirrored_range(n, s):
v = numpy.arange(n) + s
v = numpy.where(v >= n, 2 * n - v - 1, v)
v = numpy.where(v < 0, - 1 - v, v)
return v
shifts = [shift_distance if a == axis else 0 for a in range(3)]
shifted_diags = [mirrored_range(n, s) for n, s in zip(shape, shifts)]
ijk = numpy.meshgrid(*shifted_diags, indexing='ij')
n = numpy.prod(shape)
i_ind = numpy.arange(n)
j_ind = numpy.ravel_multi_index(ijk, shape, order='C')
vij = (numpy.ones(n), (i_ind, j_ind.ravel(order='C')))
d = sparse.csr_matrix(vij, shape=(n, n))
return d
def deriv_forward(dx_e: List[numpy.ndarray]) -> List[sparse.spmatrix]:
"""
Utility operators for taking discretized derivatives (forward variant).
Args:
dx_e: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
List of operators for taking forward derivatives along each axis.
"""
shape = [s.size for s in dx_e]
n = numpy.prod(shape)
dx_e_expanded = numpy.meshgrid(*dx_e, indexing='ij')
def deriv(axis):
return rotation(axis, shape, 1) - sparse.eye(n)
Ds = [sparse.diags(+1 / dx.ravel(order='C')) @ deriv(a)
for a, dx in enumerate(dx_e_expanded)]
return Ds
def deriv_back(dx_h: List[numpy.ndarray]) -> List[sparse.spmatrix]:
"""
Utility operators for taking discretized derivatives (backward variant).
Args:
dx_h: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
List of operators for taking forward derivatives along each axis.
"""
shape = [s.size for s in dx_h]
n = numpy.prod(shape)
dx_h_expanded = numpy.meshgrid(*dx_h, indexing='ij')
def deriv(axis):
return rotation(axis, shape, -1) - sparse.eye(n)
Ds = [sparse.diags(-1 / dx.ravel(order='C')) @ deriv(a)
for a, dx in enumerate(dx_h_expanded)]
return Ds
def cross(B: List[sparse.spmatrix]) -> sparse.spmatrix:
"""
Cross product operator
Args:
B: List `[Bx, By, Bz]` of sparse matrices corresponding to the x, y, z
portions of the operator on the left side of the cross product.
Returns:
Sparse matrix corresponding to (B x), where x is the cross product.
"""
n = B[0].shape[0]
zero = sparse.csr_matrix((n, n))
return sparse.bmat([[zero, -B[2], B[1]],
[B[2], zero, -B[0]],
[-B[1], B[0], zero]])
def vec_cross(b: vfield_t) -> sparse.spmatrix:
"""
Vector cross product operator
Args:
b: Vector on the left side of the cross product.
Returns:
Sparse matrix corresponding to (b x), where x is the cross product.
"""
B = [sparse.diags(c) for c in numpy.split(b, 3)]
return cross(B)
def avg_forward(axis: int, shape: List[int]) -> sparse.spmatrix:
"""
Forward average operator `(x4 = (x4 + x5) / 2)`
Args:
axis: Axis to average along (x=0, y=1, z=2)
shape: Shape of the grid to average
Returns:
Sparse matrix for forward average operation.
"""
if len(shape) not in (2, 3):
raise Exception('Invalid shape: {}'.format(shape))
n = numpy.prod(shape)
return 0.5 * (sparse.eye(n) + rotation(axis, shape))
def avg_back(axis: int, shape: List[int]) -> sparse.spmatrix:
"""
Backward average operator `(x4 = (x4 + x3) / 2)`
Args:
axis: Axis to average along (x=0, y=1, z=2)
shape: Shape of the grid to average
Returns:
Sparse matrix for backward average operation.
"""
return avg_forward(axis, shape).T
def curl_forward(dx_e: List[numpy.ndarray]) -> sparse.spmatrix:
"""
Curl operator for use with the E field.
Args:
dx_e: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
Sparse matrix for taking the discretized curl of the E-field
"""
return cross(deriv_forward(dx_e))
def curl_back(dx_h: List[numpy.ndarray]) -> sparse.spmatrix:
"""
Curl operator for use with the H field.
Args:
dx_h: Lists of cell sizes for all axes
`[[dx_0, dx_1, ...], [dy_0, dy_1, ...], ...]`.
Returns:
Sparse matrix for taking the discretized curl of the H-field
"""
return cross(deriv_back(dx_h))

2
meanas/fdtd/__init__.py
View File

@ -1,5 +1,5 @@
"""
Basic FDTD functionality
Utilities for running finite-difference time-domain (FDTD) simulations
"""
from .base import maxwell_e, maxwell_h

64
meanas/fdtd/base.py
View File

@ -5,70 +5,14 @@ from typing import List, Callable, Tuple, Dict
import numpy
from .. import dx_lists_t, field_t, field_updater
from ..fdmath.functional import curl_forward, curl_back
__author__ = 'Jan Petykiewicz'
def curl_h(dxes: dx_lists_t = None) -> field_updater:
"""
Curl operator for use with the H field.
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Function for taking the discretized curl of the H-field, F(H) -> curlH
"""
if dxes:
dxyz_b = numpy.meshgrid(*dxes[1], indexing='ij')
def dh(f, ax):
return (f - numpy.roll(f, 1, axis=ax)) / dxyz_b[ax]
else:
def dh(f, ax):
return f - numpy.roll(f, 1, axis=ax)
def ch_fun(h: field_t) -> field_t:
output = numpy.empty_like(h)
output[0] = dh(h[2], 1)
output[1] = dh(h[0], 2)
output[2] = dh(h[1], 0)
output[0] -= dh(h[1], 2)
output[1] -= dh(h[2], 0)
output[2] -= dh(h[0], 1)
return output
return ch_fun
def curl_e(dxes: dx_lists_t = None) -> field_updater:
"""
Curl operator for use with the E field.
:param dxes: Grid parameters [dx_e, dx_h] as described in meanas.types
:return: Function for taking the discretized curl of the E-field, F(E) -> curlE
"""
if dxes is not None:
dxyz_a = numpy.meshgrid(*dxes[0], indexing='ij')
def de(f, ax):
return (numpy.roll(f, -1, axis=ax) - f) / dxyz_a[ax]
else:
def de(f, ax):
return numpy.roll(f, -1, axis=ax) - f
def ce_fun(e: field_t) -> field_t:
output = numpy.empty_like(e)
output[0] = de(e[2], 1)
output[1] = de(e[0], 2)
output[2] = de(e[1], 0)
output[0] -= de(e[1], 2)
output[1] -= de(e[2], 0)
output[2] -= de(e[0], 1)
return output
return ce_fun
def maxwell_e(dt: float, dxes: dx_lists_t = None) -> field_updater:
curl_h_fun = curl_h(dxes)
curl_h_fun = curl_back(dxes[1])
def me_fun(e: field_t, h: field_t, epsilon: field_t):
e += dt * curl_h_fun(h) / epsilon
@ -78,7 +22,7 @@ def maxwell_e(dt: float, dxes: dx_lists_t = None) -> field_updater:
def maxwell_h(dt: float, dxes: dx_lists_t = None) -> field_updater:
curl_e_fun = curl_e(dxes)
curl_e_fun = curl_forward(dxes[0])
def mh_fun(e: field_t, h: field_t):
h -= dt * curl_e_fun(e)

1
meanas/fdtd/energy.py
View File

@ -35,6 +35,7 @@ def poynting_divergence(s: field_t = None,
if s is None:
s = poynting(e, h, dxes=dxes)
#TODO use deriv operators
ds = ((s[0] - numpy.roll(s[0], 1, axis=0)) +
(s[1] - numpy.roll(s[1], 1, axis=1)) +
(s[2] - numpy.roll(s[2], 1, axis=2)))

3
meanas/test/__init__.py
View File

@ -0,0 +1,3 @@
"""
Tests (run with `python3 -m pytest -rxPXs | tee results.txt`)
"""

3
meanas/test/test_fdfd_pml.py
View File

@ -101,7 +101,7 @@ def j_distribution(request, shape, epsilon, dxes, omega, src_polarity):
slices[dim] = slice(shape[dim + 1] // 2,
shape[dim + 1] // 2 + 1)
j = fdfd.waveguide_mode.compute_source(E=e, wavenumber=wavenumber_corrected, omega=omega, dxes=dxes,
j = fdfd.waveguide_3d.compute_source(E=e, wavenumber=wavenumber_corrected, omega=omega, dxes=dxes,
axis=dim, polarity=src_polarity, slices=slices, epsilon=epsilon)
yield j
@ -145,4 +145,3 @@ def sim(request, shape, epsilon, dxes, j_distribution, omega, pec, pmc):
)
return sim

17
meanas/types.py
View File

@ -6,17 +6,20 @@ from typing import List, Callable
# Field types
field_t = numpy.ndarray # vector field with shape (3, X, Y, Z) (e.g. [E_x, E_y, E_z])
vfield_t = numpy.ndarray # linearized vector field (vector of length 3*X*Y*Z)
field_t = numpy.ndarray
"""vector field with shape (3, X, Y, Z) (e.g. `[E_x, E_y, E_z]`)"""
vfield_t = numpy.ndarray
"""Linearized vector field (vector of length 3*X*Y*Z)"""
dx_lists_t = List[List[numpy.ndarray]]
'''
'dxes' datastructure which contains grid cell width information in the following format:
[[[dx_e_0, dx_e_1, ...], [dy_e_0, ...], [dz_e_0, ...]],
[[dx_h_0, dx_h_1, ...], [dy_h_0, ...], [dz_h_0, ...]]]
where dx_e_0 is the x-width of the x=0 cells, as used when calculating dE/dx,
and dy_h_0 is the y-width of the y=0 cells, as used when calculating dH/dy, etc.
`[[[dx_e_0, dx_e_1, ...], [dy_e_0, ...], [dz_e_0, ...]],
[[dx_h_0, dx_h_1, ...], [dy_h_0, ...], [dz_h_0, ...]]]`
where `dx_e_0` is the x-width of the `x=0` cells, as used when calculating dE/dx,
and `dy_h_0` is the y-width of the `y=0` cells, as used when calculating dH/dy, etc.
'''
dx_lists_t = List[List[numpy.ndarray]]
field_updater = Callable[[field_t], field_t]

46
pdoc_templates/config.mako Normal file
View File

@ -0,0 +1,46 @@
<%!
# Template configuration. Copy over in your template directory
# (used with --template-dir) and adapt as required.
html_lang = 'en'
show_inherited_members = False
extract_module_toc_into_sidebar = True
list_class_variables_in_index = True
sort_identifiers = True
show_type_annotations = True
# Show collapsed source code block next to each item.
# Disabling this can improve rendering speed of large modules.
show_source_code = True
# If set, format links to objects in online source code repository
# according to this template. Supported keywords for interpolation
# are: commit, path, start_line, end_line.
#git_link_template = 'https://github.com/USER/PROJECT/blob/{commit}/{path}#L{start_line}-L{end_line}'
#git_link_template = 'https://gitlab.com/USER/PROJECT/blob/{commit}/{path}#L{start_line}-L{end_line}'
#git_link_template = 'https://bitbucket.org/USER/PROJECT/src/{commit}/{path}#lines-{start_line}:{end_line}'
#git_link_template = 'https://CGIT_HOSTNAME/PROJECT/tree/{path}?id={commit}#n{start-line}'
git_link_template = None
# A prefix to use for every HTML hyperlink in the generated documentation.
# No prefix results in all links being relative.
link_prefix = ''
# Enable syntax highlighting for code/source blocks by including Highlight.js
syntax_highlighting = True
# Set the style keyword such as 'atom-one-light' or 'github-gist'
# Options: https://github.com/highlightjs/highlight.js/tree/master/src/styles
# Demo: https://highlightjs.org/static/demo/
hljs_style = 'github'
# If set, insert Google Analytics tracking code. Value is GA
# tracking id (UA-XXXXXX-Y).
google_analytics = ''
# If set, render LaTeX math syntax within \(...\) (inline equations),
# or within \[...\] or $$...$$ or `.. math::` (block equations)
# as nicely-formatted math formulas using MathJax.
# Note: in Python docstrings, either all backslashes need to be escaped (\\)
# or you need to use raw r-strings.
latex_math = True
%>

389
pdoc_templates/css.mako Normal file
View File

@ -0,0 +1,389 @@
<%!
from pdoc.html_helpers import minify_css
%>
<%def name="mobile()" filter="minify_css">
.flex {
display: flex !important;
}
body {
line-height: 1.5em;
background: black;
color: #DDD;
}
#content {
padding: 20px;
}
#sidebar {
padding: 30px;
overflow: hidden;
}
.http-server-breadcrumbs {
font-size: 130%;
margin: 0 0 15px 0;
}
#footer {
font-size: .75em;
padding: 5px 30px;
border-top: 1px solid #ddd;
text-align: right;
}
#footer p {
margin: 0 0 0 1em;
display: inline-block;
}
#footer p:last-child {
margin-right: 30px;
}
h1, h2, h3, h4, h5 {
font-weight: 300;
}
h1 {
font-size: 2.5em;
line-height: 1.1em;
}
h2 {
font-size: 1.75em;
margin: 1em 0 .50em 0;
}
h3 {
font-size: 1.4em;
margin: 25px 0 10px 0;
}
h4 {
margin: 0;
font-size: 105%;
}
a {
color: #999;
text-decoration: none;
transition: color .3s ease-in-out;
}
a:hover {
color: #18d;
}
.title code {
font-weight: bold;
}
h2[id^="header-"] {
margin-top: 2em;
}
.ident {
color: #7ff;
}
pre code {
background: transparent;
font-size: .8em;
line-height: 1.4em;
}
code {
background: #0d0d0e;
padding: 1px 4px;
overflow-wrap: break-word;
}
h1 code { background: transparent }
pre {
background: #111;
border: 0;
border-top: 1px solid #ccc;
border-bottom: 1px solid #ccc;
margin: 1em 0;
padding: 1ex;
}
#http-server-module-list {
display: flex;
flex-flow: column;
}
#http-server-module-list div {
display: flex;
}
#http-server-module-list dt {
min-width: 10%;
}
#http-server-module-list p {
margin-top: 0;
}
.toc ul,
#index {
list-style-type: none;
margin: 0;
padding: 0;
}
#index code {
background: transparent;
}
#index h3 {
border-bottom: 1px solid #ddd;
}
#index ul {
padding: 0;
}
#index h4 {
font-weight: bold;
}
#index h4 + ul {
margin-bottom:.6em;
}
/* Make TOC lists have 2+ columns when viewport is wide enough.
Assuming ~20-character identifiers and ~30% wide sidebar. */
@media (min-width: 200ex) { #index .two-column { column-count: 2 } }
@media (min-width: 300ex) { #index .two-column { column-count: 3 } }
dl {
margin-bottom: 2em;
}
dl dl:last-child {
margin-bottom: 4em;
}
dd {
margin: 0 0 1em 3em;
}
#header-classes + dl > dd {
margin-bottom: 3em;
}
dd dd {
margin-left: 2em;
}
dd p {
margin: 10px 0;
}
.name {
background: #111;
font-weight: bold;
font-size: .85em;
padding: 5px 10px;
display: inline-block;
min-width: 40%;
}
.name:hover {
background: #101010;
}
.name > span:first-child {
white-space: nowrap;
}
.name.class > span:nth-child(2) {
margin-left: .4em;
}
.inherited {
color: #777;
border-left: 5px solid #eee;
padding-left: 1em;
}
.inheritance em {
font-style: normal;
font-weight: bold;
}
/* Docstrings titles, e.g. in numpydoc format */
.desc h2 {
font-weight: 400;
font-size: 1.25em;
}
.desc h3 {
font-size: 1em;
}
.desc dt code {
background: inherit; /* Don't grey-back parameters */
}
.source summary,
.git-link-div {
color: #aaa;
text-align: right;
font-weight: 400;
font-size: .8em;
text-transform: uppercase;
}
.source summary > * {
white-space: nowrap;
cursor: pointer;
}
.git-link {
color: inherit;
margin-left: 1em;
}
.source pre {
max-height: 500px;
overflow: auto;
margin: 0;
}
.source pre code {
font-size: 12px;
overflow: visible;
}
.hlist {
list-style: none;
}
.hlist li {
display: inline;
}
.hlist li:after {
content: ',\2002';
}
.hlist li:last-child:after {
content: none;
}
.hlist .hlist {
display: inline;
padding-left: 1em;
}
img {
max-width: 100%;
}
.admonition {
padding: .1em .5em;
margin-bottom: 1em;
}
.admonition-title {
font-weight: bold;
}
.admonition.note,
.admonition.info,
.admonition.important {
background: #610;
}
.admonition.todo,
.admonition.versionadded,
.admonition.tip,
.admonition.hint {
background: #202;
}
.admonition.warning,
.admonition.versionchanged,
.admonition.deprecated {
background: #02b;
}
.admonition.error,
.admonition.danger,
.admonition.caution {
background: darkpink;
}
</%def>
<%def name="desktop()" filter="minify_css">
@media screen and (min-width: 700px) {
#sidebar {
width: 30%;
}
#content {
width: 70%;
max-width: 100ch;
padding: 3em 4em;
border-left: 1px solid #ddd;
}
pre code {
font-size: 1em;
}
.item .name {
font-size: 1em;
}
main {
display: flex;
flex-direction: row-reverse;
justify-content: flex-end;
}
.toc ul ul,
#index ul {
padding-left: 1.5em;
}
.toc > ul > li {
margin-top: .5em;
}
}
</%def>
<%def name="print()" filter="minify_css">
@media print {
#sidebar h1 {
page-break-before: always;
}
.source {
display: none;
}
}
@media print {
* {
background: transparent !important;
color: #000 !important; /* Black prints faster: h5bp.com/s */
box-shadow: none !important;
text-shadow: none !important;
}
a[href]:after {
content: " (" attr(href) ")";
font-size: 90%;
}
/* Internal, documentation links, recognized by having a title,
don't need the URL explicity stated. */
a[href][title]:after {
content: none;
}
abbr[title]:after {
content: " (" attr(title) ")";
}
/*
* Don't show links for images, or javascript/internal links
*/
.ir a:after,
a[href^="javascript:"]:after,
a[href^="#"]:after {
content: "";
}
pre,
blockquote {
border: 1px solid #999;
page-break-inside: avoid;
}
thead {
display: table-header-group; /* h5bp.com/t */
}
tr,
img {
page-break-inside: avoid;
}
img {
max-width: 100% !important;
}
@page {
margin: 0.5cm;
}
p,
h2,
h3 {
orphans: 3;
widows: 3;
}
h1,
h2,
h3,
h4,
h5,
h6 {
page-break-after: avoid;
}
}
</%def>

421
pdoc_templates/html.mako Normal file
View File

@ -0,0 +1,421 @@
<%
import os
import pdoc
from pdoc.html_helpers import extract_toc, glimpse, to_html as _to_html, format_git_link
def link(d, name=None, fmt='{}'):
name = fmt.format(name or d.qualname + ('()' if isinstance(d, pdoc.Function) else ''))
if not isinstance(d, pdoc.Doc) or isinstance(d, pdoc.External) and not external_links:
return name
url = d.url(relative_to=module, link_prefix=link_prefix,
top_ancestor=not show_inherited_members)
return '<a title="{}" href="{}">{}</a>'.format(d.refname, url, name)
def to_html(text):
return _to_html(text, module=module, link=link, latex_math=latex_math)
%>
<%def name="ident(name)"><span class="ident">${name}</span></%def>
<%def name="show_source(d)">
% if (show_source_code or git_link_template) and d.source and d.obj is not getattr(d.inherits, 'obj', None):
<% git_link = format_git_link(git_link_template, d) %>
% if show_source_code:
<details class="source">
<summary>
<span>Expand source code</span>
% if git_link:
<a href="${git_link}" class="git-link">Browse git</a>
%endif
</summary>
<pre><code class="python">${d.source | h}</code></pre>
</details>
% elif git_link:
<div class="git-link-div"><a href="${git_link}" class="git-link">Browse git</a></div>
%endif
%endif
</%def>
<%def name="show_desc(d, short=False)">
<%
inherits = ' inherited' if d.inherits else ''
docstring = glimpse(d.docstring) if short or inherits else d.docstring
%>
% if d.inherits:
<p class="inheritance">
<em>Inherited from:</em>
% if hasattr(d.inherits, 'cls'):
<code>${link(d.inherits.cls)}</code>.<code>${link(d.inherits, d.name)}</code>
% else:
<code>${link(d.inherits)}</code>
% endif
</p>
% endif
<section class="desc${inherits}">${docstring | to_html}</section>
% if not isinstance(d, pdoc.Module):
${show_source(d)}
% endif
</%def>
<%def name="show_module_list(modules)">
<h1>Python module list</h1>
% if not modules:
<p>No modules found.</p>
% else:
<dl id="http-server-module-list">
% for name, desc in modules:
<div class="flex">
<dt><a href="${link_prefix}${name}">${name}</a></dt>
<dd>${desc | glimpse, to_html}</dd>
</div>
% endfor
</dl>
% endif
</%def>
<%def name="show_column_list(items)">
<%
two_column = len(items) >= 6 and all(len(i.name) < 20 for i in items)
%>
<ul class="${'two-column' if two_column else ''}">
% for item in items:
<li><code>${link(item, item.name)}</code></li>
% endfor
</ul>
</%def>
<%def name="show_module(module)">
<%
variables = module.variables(sort=sort_identifiers)
classes = module.classes(sort=sort_identifiers)
functions = module.functions(sort=sort_identifiers)
submodules = module.submodules()
%>
<%def name="show_func(f)">
<dt id="${f.refname}"><code class="name flex">
<%
params = ', '.join(f.params(annotate=show_type_annotations, link=link))
returns = show_type_annotations and f.return_annotation(link=link) or ''
if returns:
returns = ' ->\N{NBSP}' + returns
%>
<span>${f.funcdef()} ${ident(f.name)}</span>(<span>${params})${returns}</span>
</code></dt>
<dd>${show_desc(f)}</dd>
</%def>
<header>
% if http_server:
<nav class="http-server-breadcrumbs">
<a href="/">All packages</a>
<% parts = module.name.split('.')[:-1] %>
% for i, m in enumerate(parts):
<% parent = '.'.join(parts[:i+1]) %>
:: <a href="/${parent.replace('.', '/')}/">${parent}</a>
% endfor
</nav>
% endif
<h1 class="title">${'Namespace' if module.is_namespace else 'Module'} <code>${module.name}</code></h1>
</header>
<section id="section-intro">
${module.docstring | to_html}
${show_source(module)}
</section>
<section>
% if submodules:
<h2 class="section-title" id="header-submodules">Sub-modules</h2>
<dl>
% for m in submodules:
<dt><code class="name">${link(m)}</code></dt>
<dd>${show_desc(m, short=True)}</dd>
% endfor
</dl>
% endif
</section>
<section>
% if variables:
<h2 class="section-title" id="header-variables">Global variables</h2>
<dl>
% for v in variables:
<dt id="${v.refname}"><code class="name">var ${ident(v.name)}</code></dt>
<dd>${show_desc(v)}</dd>
% endfor
</dl>
% endif
</section>
<section>
% if functions:
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
% for f in functions:
${show_func(f)}
% endfor
</dl>
% endif
</section>
<section>
% if classes:
<h2 class="section-title" id="header-classes">Classes</h2>
<dl>
% for c in classes:
<%
class_vars = c.class_variables(show_inherited_members, sort=sort_identifiers)
smethods = c.functions(show_inherited_members, sort=sort_identifiers)
inst_vars = c.instance_variables(show_inherited_members, sort=sort_identifiers)
methods = c.methods(show_inherited_members, sort=sort_identifiers)
mro = c.mro()
subclasses = c.subclasses()
params = ', '.join(c.params(annotate=show_type_annotations, link=link))
%>
<dt id="${c.refname}"><code class="flex name class">
<span>class ${ident(c.name)}</span>
% if params:
<span>(</span><span>${params})</span>
% endif
</code></dt>
<dd>${show_desc(c)}
% if mro:
<h3>Ancestors</h3>
<ul class="hlist">
% for cls in mro:
<li>${link(cls)}</li>
% endfor
</ul>
%endif
% if subclasses:
<h3>Subclasses</h3>
<ul class="hlist">
% for sub in subclasses:
<li>${link(sub)}</li>
% endfor
</ul>
% endif
% if class_vars:
<h3>Class variables</h3>
<dl>
% for v in class_vars:
<dt id="${v.refname}"><code class="name">var ${ident(v.name)}</code></dt>
<dd>${show_desc(v)}</dd>
% endfor
</dl>
% endif
% if smethods:
<h3>Static methods</h3>
<dl>
% for f in smethods:
${show_func(f)}
% endfor
</dl>
% endif
% if inst_vars:
<h3>Instance variables</h3>
<dl>
% for v in inst_vars:
<dt id="${v.refname}"><code class="name">var ${ident(v.name)}</code></dt>
<dd>${show_desc(v)}</dd>
% endfor
</dl>
% endif
% if methods:
<h3>Methods</h3>
<dl>
% for f in methods:
${show_func(f)}
% endfor
</dl>
% endif
% if not show_inherited_members:
<%
members = c.inherited_members()
%>
% if members:
<h3>Inherited members</h3>
<ul class="hlist">
% for cls, mems in members:
<li><code><b>${link(cls)}</b></code>:
<ul class="hlist">
% for m in mems:
<li><code>${link(m, name=m.name)}</code></li>
% endfor
</ul>
</li>
% endfor
</ul>
% endif
% endif
</dd>
% endfor
</dl>
% endif
</section>
</%def>
<%def name="module_index(module)">
<%
variables = module.variables(sort=sort_identifiers)
classes = module.classes(sort=sort_identifiers)
functions = module.functions(sort=sort_identifiers)
submodules = module.submodules()
supermodule = module.supermodule
%>
<nav id="sidebar">
<%include file="logo.mako"/>
<h1>Index</h1>
${extract_toc(module.docstring) if extract_module_toc_into_sidebar else ''}
<ul id="index">
% if supermodule:
<li><h3>Super-module</h3>
<ul>
<li><code>${link(supermodule)}</code></li>
</ul>
</li>
% endif
% if submodules:
<li><h3><a href="#header-submodules">Sub-modules</a></h3>
<ul>
% for m in submodules:
<li><code>${link(m)}</code></li>
% endfor
</ul>
</li>
% endif
% if variables:
<li><h3><a href="#header-variables">Global variables</a></h3>
${show_column_list(variables)}
</li>
% endif
% if functions:
<li><h3><a href="#header-functions">Functions</a></h3>
${show_column_list(functions)}
</li>
% endif
% if classes:
<li><h3><a href="#header-classes">Classes</a></h3>
<ul>
% for c in classes:
<li>
<h4><code>${link(c)}</code></h4>
<%
members = c.functions(sort=sort_identifiers) + c.methods(sort=sort_identifiers)
if list_class_variables_in_index:
members += (c.instance_variables(sort=sort_identifiers) +
c.class_variables(sort=sort_identifiers))
if not show_inherited_members:
members = [i for i in members if not i.inherits]
if sort_identifiers:
members = sorted(members)
%>
% if members:
${show_column_list(members)}
% endif
</li>
% endfor
</ul>
</li>
% endif
</ul>
</nav>
</%def>
<!doctype html>
<html lang="${html_lang}">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
<meta name="generator" content="pdoc ${pdoc.__version__}" />
<%
module_list = 'modules' in context.keys() # Whether we're showing module list in server mode
%>
% if module_list:
<title>Python module list</title>
<meta name="description" content="A list of documented Python modules." />
% else:
<title>${module.name} API documentation</title>
<meta name="description" content="${module.docstring | glimpse, trim, h}" />
% endif
<link href='https://mpxd.net/scripts/normalize.css/normalize.css' rel='stylesheet'>
<link href='https://mpxd.net/scripts/sanitize.css/sanitize.css' rel='stylesheet'>
% if syntax_highlighting:
<link href="https://mpxd.net/scripts/highlightjs/styles/${hljs_style}.min.css" rel="stylesheet">
%endif
<%namespace name="css" file="css.mako" />
<style>${css.mobile()}</style>
<style media="screen and (min-width: 700px)">${css.desktop()}</style>
<style media="print">${css.print()}</style>
% if google_analytics:
<script>
window.ga=window.ga||function(){(ga.q=ga.q||[]).push(arguments)};ga.l=+new Date;
ga('create', '${google_analytics}', 'auto'); ga('send', 'pageview');
</script><script async src='https://www.google-analytics.com/analytics.js'></script>
% endif
% if latex_math:
<script async src='https://mpxd.net/scripts/MathJax/MathJax.js?config=TeX-AMS_CHTML'></script>
% endif
<%include file="head.mako"/>
</head>
<body>
<main>
% if module_list:
<article id="content">
${show_module_list(modules)}
</article>
% else:
<article id="content">
${show_module(module)}
</article>
${module_index(module)}
% endif
</main>
<footer id="footer">
<%include file="credits.mako"/>
<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> ${pdoc.__version__}</a>.</p>
</footer>
% if syntax_highlighting:
<script src="https://mpxd.net/scripts/highlightjs/highlight.pack.js"></script>
<script>hljs.initHighlightingOnLoad()</script>
% endif
% if http_server and module: ## Auto-reload on file change in dev mode
<script>
setInterval(() =>
fetch(window.location.href, {
method: "HEAD",
cache: "no-store",
headers: {"If-None-Match": "${os.stat(module.obj.__file__).st_mtime}"},
}).then(response => response.ok && window.location.reload()), 700);
</script>
% endif
</body>
</html>