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Merge branch 'array_pml'

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Jan Petykiewicz 2017-03-28 22:08:11 -07:00
commit 4633ababa5
9 changed files with 508 additions and 407 deletions
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73
fdtd.py
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@ -8,12 +8,17 @@ import sys
import time
import numpy
import h5py
import lzma
import dill
from fdtd.simulation import Simulation
from masque import Pattern, shapes
import gridlock
import pcgen
import fdfd_tools
__author__ = 'Jan Petykiewicz'
def perturbed_l3(a: float, radius: float, **kwargs) -> Pattern:
@ -75,7 +80,7 @@ def perturbed_l3(a: float, radius: float, **kwargs) -> Pattern:
def main():
max_t = 8000 # number of timesteps
dx = 15 # discretization (nm/cell)
dx = 25 # discretization (nm/cell)
pml_thickness = 8 # (number of cells)
wl = 1550 # Excitation wavelength and fwhm
@ -109,28 +114,15 @@ def main():
eps=n_slab**2)
mask = perturbed_l3(a, r)
for i in range(5000):
print(i)
grid.draw_polygons(surface_normal=gridlock.Direction.z,
grid.draw_polygons(surface_normal=gridlock.Direction.z,
center=[0, 0, 0],
thickness=2 * th,
eps=n_air**2,
polygons=mask.as_polygons())
return
print(grid.shape, numpy.prod(grid.shape))
print('grid shape: {}'.format(grid.shape))
# #### Create the simulation grid ####
sim = Simulation(grid.grids)
# Conducting boundaries and pmls in every direction
c_args = []
pml_args = []
for d in (0, 1, 2):
for p in (-1, 1):
c_args += [{'direction': d, 'polarity': p}]
pml_args += [{'direction': d, 'polarity': p, 'epsilon_eff': n_slab**2}]
sim.init_conductors(c_args)
sim.init_cpml(pml_args)
sim = Simulation(grid.grids, do_poynting=True, pml_thickness=8)
# Source parameters and function
w = 2 * numpy.pi * dx / wl
@ -141,31 +133,44 @@ def main():
def field_source(i):
t0 = i * sim.dt - delay
return numpy.sin(w * t0) * numpy.exp(-alpha * t0**2)
with open('sources.c', 'w') as f:
f.write(sim.sources['E'])
f.write('\n==========================================\n')
f.write(sim.sources['H'])
if sim.update_S:
f.write('\n==========================================\n')
f.write(sim.sources['S'])
# #### Run a bunch of iterations ####
# event = sim.whatever([prev_event]) indicates that sim.whatever should be queued
# immediately and run once prev_event is finished.
output_file = h5py.File('simulation_output.h5', 'w')
start = time.perf_counter()
for t in range(max_t):
event = sim.cpml_E([])
sim.update_E([event]).wait()
sim.update_E([]).wait()
sim.E[1][tuple(grid.shape//2)] += field_source(t)
event = sim.conductor_E([])
event = sim.cpml_H([event])
event = sim.update_H([event])
sim.conductor_H([event]).wait()
ind = numpy.ravel_multi_index(tuple(grid.shape//2), dims=grid.shape, order='C') + numpy.prod(grid.shape)
sim.E[ind] += field_source(t)
e = sim.update_H([])
if sim.update_S:
e = sim.update_S([e])
e.wait()
print('iteration {}: average {} iterations per sec'.format(t, (t+1)/(time.perf_counter()-start)))
sys.stdout.flush()
if t % 100 == 0:
print('iteration {}: average {} iterations per sec'.format(t, (t+1)/(time.perf_counter()-start)))
sys.stdout.flush()
# Save field slices
if (t % 20 == 0 and (max_t - t < 1000 or t < 1000)) or t == max_t-1:
print('saving E-field')
for j, f in enumerate(sim.E):
a = f.get()
output_file['/E{}_t{}'.format('xyz'[j], t)] = a[:, :, round(a.shape[2]/2)]
with lzma.open('saved_simulation', 'wb') as f:
def unvec(f):
return fdfd_tools.unvec(f, grid.shape)
d = {
'grid': grid,
'E': unvec(sim.E.get()),
'H': unvec(sim.H.get()),
}
if sim.S is not None:
d['S'] = unvec(sim.S.get())
dill.dump(d, f)
if __name__ == '__main__':
main()

73
fdtd/base.py
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@ -1,73 +0,0 @@
"""
Basic code snippets for opencl FDTD
"""
from typing import List
import numpy
def shape_source(shape: List[int] or numpy.ndarray) -> str:
"""
Defines sx, sy, sz C constants specifying the shape of the grid in each of the 3 dimensions.
:param shape: [sx, sy, sz] values.
:return: String containing C source.
"""
sxyz = """
// Field sizes
const int sx = {shape[0]};
const int sy = {shape[1]};
const int sz = {shape[2]};
""".format(shape=shape)
return sxyz
# Defines dix, diy, diz constants used for stepping in the x, y, z directions in a linear array
# (ie, given Ex[i] referring to position (x, y, z), Ex[i+diy] will refer to position (x, y+1, z))
dixyz_source = """
// Convert offset in field xyz to linear index offset
const int dix = sz * sy;
const int diy = sz;
const int diz = 1;
"""
# Given a linear index i and shape sx, sy, sz, defines x, y, and z
# as the 3D indices of the current element (i).
xyz_source = """
// Convert linear index to field index (xyz)
const int x = i / (sz * sy);
const int y = (i - x * sz * sy) / sz;
const int z = (i - y * sz - x * sz * sy);
"""
# Source code for updating the E field; maxes use of dixyz_source.
maxwell_E_source = """
// E update equations
Ex[i] += dt / epsx[i] * ((Hz[i] - Hz[i-diy]) - (Hy[i] - Hy[i-diz]));
Ey[i] += dt / epsy[i] * ((Hx[i] - Hx[i-diz]) - (Hz[i] - Hz[i-dix]));
Ez[i] += dt / epsz[i] * ((Hy[i] - Hy[i-dix]) - (Hx[i] - Hx[i-diy]));
"""
# Source code for updating the H field; maxes use of dixyz_source and assumes mu=0
maxwell_H_source = """
// H update equations
Hx[i] -= dt * ((Ez[i+diy] - Ez[i]) - (Ey[i+diz] - Ey[i]));
Hy[i] -= dt * ((Ex[i+diz] - Ex[i]) - (Ez[i+dix] - Ez[i]));
Hz[i] -= dt * ((Ey[i+dix] - Ey[i]) - (Ex[i+diy] - Ex[i]));
"""
def type_to_C(float_type: numpy.float32 or numpy.float64) -> str:
"""
Returns a string corresponding to the C equivalent of a numpy type.
Only works for float32 and float64.
:param float_type: numpy.float32 or numpy.float64
:return: string containing the corresponding C type (eg. 'double')
"""
if float_type == numpy.float32:
arg_type = 'float'
elif float_type == numpy.float64:
arg_type = 'double'
else:
raise Exception('Unsupported type')
return arg_type

185
fdtd/boundary.py
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@ -1,185 +0,0 @@
from typing import List, Dict
import numpy
def conductor(direction: int,
polarity: int,
) -> List[str]:
"""
Create source code for conducting boundary conditions.
:param direction: integer in range(3), corresponding to x,y,z.
:param polarity: -1 or 1, specifying eg. a -x or +x boundary.
:return: [E_source, H_source] source code for E and H boundary update steps.
"""
if direction not in range(3):
raise Exception('Invalid direction: {}'.format(direction))
if polarity not in (-1, 1):
raise Exception('Invalid polarity: {}'.format(polarity))
r = 'xyz'[direction]
uv = 'xyz'.replace(r, '')
if polarity < 0:
bc_e = """
if ({r} == 0) {{
E{r}[i] = 0;
E{u}[i] = E{u}[i+di{r}];
E{v}[i] = E{v}[i+di{r}];
}}
"""
bc_h = """
if ({r} == 0) {{
H{r}[i] = H{r}[i+di{r}];
H{u}[i] = 0;
H{v}[i] = 0;
}}
"""
elif polarity > 0:
bc_e = """
if ({r} == s{r} - 1) {{
E{r}[i] = -E{r}[i-2*di{r}];
E{u}[i] = +E{u}[i-di{r}];
E{v}[i] = +E{v}[i-di{r}];
}} else if ({r} == s{r} - 2) {{
E{r}[i] = 0;
}}
"""
bc_h = """
if ({r} == s{r} - 1) {{
H{r}[i] = +H{r}[i-di{r}];
H{u}[i] = -H{u}[i-2*di{r}];
H{v}[i] = -H{v}[i-2*di{r}];
}} else if ({r} == s{r} - 2) {{
H{u}[i] = 0;
H{v}[i] = 0;
}}
"""
else:
raise Exception()
replacements = {'r': r, 'u': uv[0], 'v': uv[1]}
return [s.format(**replacements) for s in (bc_e, bc_h)]
def cpml(direction: int,
polarity: int,
dt: float,
thickness: int=8,
epsilon_eff: float=1,
) -> Dict:
"""
Generate source code for complex phase matched layer (cpml) absorbing boundaries.
These are not full boundary conditions and require a conducting boundary to be added
in the same direction as the pml.
:param direction: integer in range(3), corresponding to x, y, z directions.
:param polarity: -1 or 1, corresponding to eg. -x or +x direction.
:param dt: timestep used by the simulation
:param thickness: Number of cells used by the pml (the grid is NOT expanded to add these cells). Default 8.
:param epsilon_eff: Effective epsilon_r of the pml layer. Default 1.
:return: Dict with entries 'E', 'H' (update equations for E and H) and 'psi_E', 'psi_H' (lists of str,
specifying the field names of the cpml fields used in the E and H update steps. Eg.,
Psi_xn_Ex for the complex Ex component for the x- pml.)
"""
if direction not in range(3):
raise Exception('Invalid direction: {}'.format(direction))
if polarity not in (-1, 1):
raise Exception('Invalid polarity: {}'.format(polarity))
if thickness <= 2:
raise Exception('It would be wise to have a pml with 4+ cells of thickness')
if epsilon_eff <= 0:
raise Exception('epsilon_eff must be positive')
m = (3.5, 1)
sigma_max = 0.8 * (m[0] + 1) / numpy.sqrt(epsilon_eff)
alpha_max = 0 # TODO: Decide what to do about non-zero alpha
transverse = numpy.delete(range(3), direction)
r = 'xyz'[direction]
np = 'nVp'[numpy.sign(polarity)+1]
uv = ['xyz'[i] for i in transverse]
xe = numpy.arange(1, thickness+1, dtype=float)[::-1]
xh = numpy.arange(1, thickness+1, dtype=float)[::-1]
if polarity > 0:
xe -= 0.5
elif polarity < 0:
xh -= 0.5
def par(x):
sigma = ((x / thickness) ** m[0]) * sigma_max
alpha = ((1 - x / thickness) ** m[1]) * alpha_max
p0 = numpy.exp(-(sigma + alpha) * dt)
p1 = sigma / (sigma + alpha) * (p0 - 1)
return p0, p1
p0e, p1e = par(xe)
p0h, p1h = par(xh)
vals = {'r': r,
'u': uv[0],
'v': uv[1],
'np': np,
'th': thickness,
'p0e': ', '.join((str(x) for x in p0e)),
'p1e': ', '.join((str(x) for x in p1e)),
'p0h': ', '.join((str(x) for x in p0h)),
'p1h': ', '.join((str(x) for x in p1h)),
'se': '-+'[direction % 2],
'sh': '+-'[direction % 2]}
if polarity < 0:
bounds_if = """
if ( 0 < {r} && {r} < {th} + 1 ) {{
const int ir = {r} - 1; // index into pml parameters
const int ip = {v} + {u} * s{v} + ir * s{v} * s{u}; // linear index into Psi
"""
elif polarity > 0:
bounds_if = """
if ( (s{r} - 1) > {r} && {r} > (s{r} - 1) - ({th} + 1) ) {{
const int ir = (s{r} - 1) - ({r} + 1); // index into pml parameters
const int ip = {v} + {u} * s{v} + ir * s{v} * s{u}; // linear index into Psi
"""
else:
raise Exception('Bad polarity (=0)')
code_e = """
// pml parameters:
const float p0[{th}] = {{ {p0e} }};
const float p1[{th}] = {{ {p1e} }};
Psi_{r}{np}_E{u}[ip] = p0[ir] * Psi_{r}{np}_E{u}[ip] + p1[ir] * (H{v}[i] - H{v}[i-di{r}]);
Psi_{r}{np}_E{v}[ip] = p0[ir] * Psi_{r}{np}_E{v}[ip] + p1[ir] * (H{u}[i] - H{u}[i-di{r}]);
E{u}[i] {se}= dt / eps{u}[i] * Psi_{r}{np}_E{u}[ip];
E{v}[i] {sh}= dt / eps{v}[i] * Psi_{r}{np}_E{v}[ip];
}}
"""
code_h = """
// pml parameters:
const float p0[{th}] = {{ {p0h} }};
const float p1[{th}] = {{ {p1h} }};
Psi_{r}{np}_H{u}[ip] = p0[ir] * Psi_{r}{np}_H{u}[ip] + p1[ir] * (E{v}[i+di{r}] - E{v}[i]);
Psi_{r}{np}_H{v}[ip] = p0[ir] * Psi_{r}{np}_H{v}[ip] + p1[ir] * (E{u}[i+di{r}] - E{u}[i]);
H{u}[i] {sh}= dt * Psi_{r}{np}_H{u}[ip];
H{v}[i] {se}= dt * Psi_{r}{np}_H{v}[ip];
}}
"""
pml_data = {
'E': (bounds_if + code_e).format(**vals),
'H': (bounds_if + code_h).format(**vals),
'psi_E': ['Psi_{r}{np}_E{u}'.format(**vals),
'Psi_{r}{np}_E{v}'.format(**vals)],
'psi_H': ['Psi_{r}{np}_H{u}'.format(**vals),
'Psi_{r}{np}_H{v}'.format(**vals)],
}
return pml_data

84
fdtd/kernels/common.cl Normal file
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@ -0,0 +1,84 @@
{#
/* Common code for E, H updates
*
* Template parameters:
* ftype type name (e.g. float or double)
* shape list of 3 ints specifying shape of fields
*/
#}
typedef {{ftype}} ftype;
/*
* Field size info
*/
const size_t sx = {{shape[0]}};
const size_t sy = {{shape[1]}};
const size_t sz = {{shape[2]}};
const size_t field_size = sx * sy * sz;
//Since we use i to index into Ex[], Ey[], ... rather than E[], do nothing if
// i is outside the bounds of Ex[].
if (i >= field_size) {
PYOPENCL_ELWISE_CONTINUE;
}
/*
* Array indexing
*/
// Given a linear index i and shape (sx, sy, sz), defines x, y, and z
// as the 3D indices of the current element (i).
// (ie, converts linear index [i] to field indices (x, y, z)
const size_t x = i / (sz * sy);
const size_t y = (i - x * sz * sy) / sz;
const size_t z = (i - y * sz - x * sz * sy);
// Calculate linear index offsets corresponding to offsets in 3D
// (ie, if E[i] <-> E(x, y, z), then E[i + diy] <-> E(x, y + 1, z)
const size_t dix = sz * sy;
const size_t diy = sz;
const size_t diz = 1;
/*
* Pointer math
*/
//Pointer offsets into the components of a linearized vector-field
// (eg. Hx = H + XX, where H and Hx are pointers)
const size_t XX = 0;
const size_t YY = field_size;
const size_t ZZ = field_size * 2;
//Define pointers to vector components of each field (eg. Hx = H + XX)
__global ftype *Ex = E + XX;
__global ftype *Ey = E + YY;
__global ftype *Ez = E + ZZ;
__global ftype *Hx = H + XX;
__global ftype *Hy = H + YY;
__global ftype *Hz = H + ZZ;
/*
* Implement periodic boundary conditions
*
* mx ([m]inus [x]) gives the index offset of the adjacent cell in the minus-x direction.
* In the event that we start at x == 0, we actually want to wrap around and grab the cell
* x_{-1} == (sx - 1) instead, ie. mx = (sx - 1) * dix .
*
* px ([p]lus [x]) gives the index offset of the adjacent cell in the plus-x direction.
* In the event that we start at x == (sx - 1), we actually want to wrap around and grab
* the cell x_{+1} == 0 instead, ie. px = -(sx - 1) * dix .
*/
{% for r in 'xyz' %}
int m{{r}} = -di{{r}};
int p{{r}} = +di{{r}};
int wrap_{{r}} = (s{{r}} - 1) * di{{r}};
if ( {{r}} == 0 ) {
m{{r}} = wrap_{{r}};
} else if ( {{r}} == s{{r}} - 1 ) {
p{{r}} = -wrap_{{r}};
}
{% endfor %}

78
fdtd/kernels/update_e.cl Normal file
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@ -0,0 +1,78 @@
/*
* Update E-field, including any PMLs.
*
* Template parameters:
* common_header: Rendered contents of common.cl
* pmls: [('x', 'n'), ('z', 'p'),...] list of pml axes and polarities
* pml_thickness: Number of cells (integer)
*
* OpenCL args:
* E, H, dt, eps, [p{01}e{np}, Psi_{xyz}{np}_E]
*/
{{common_header}}
////////////////////////////////////////////////////////////////////////////
__global ftype *epsx = eps + XX;
__global ftype *epsy = eps + YY;
__global ftype *epsz = eps + ZZ;
{% if pmls -%}
const int pml_thickness = {{pml_thickness}};
{%- endif %}
/*
* Precalclate derivatives
*/
ftype dHxy = Hx[i] - Hx[i + my];
ftype dHxz = Hx[i] - Hx[i + mz];
ftype dHyx = Hy[i] - Hy[i + mx];
ftype dHyz = Hy[i] - Hy[i + mz];
ftype dHzx = Hz[i] - Hz[i + mx];
ftype dHzy = Hz[i] - Hz[i + my];
/*
* PML Update
*/
// PML effects on E
ftype pExi = 0;
ftype pEyi = 0;
ftype pEzi = 0;
{% for r, p in pmls -%}
{%- set u, v = ['x', 'y', 'z'] | reject('equalto', r) -%}
{%- set psi = 'Psi_' ~ r ~ p ~ '_E' -%}
{%- if r != 'y' -%}
{%- set se, sh = '-', '+' -%}
{%- else -%}
{%- set se, sh = '+', '-' -%}
{%- endif -%}
{%- if p == 'n' %}
if ( {{r}} < pml_thickness ) {
const size_t ir = {{r}}; // index into pml parameters
{%- elif p == 'p' %}
if ( s{{r}} > {{r}} && {{r}} >= s{{r}} - pml_thickness ) {
const size_t ir = (s{{r}} - 1) - {{r}}; // index into pml parameters
{%- endif %}
const size_t ip = {{v}} + {{u}} * s{{v}} + ir * s{{v}} * s{{u}}; // linear index into Psi
{{psi ~ u}}[ip] = p0e{{p}}[ir] * {{psi ~ u}}[ip] + p1e{{p}}[ir] * dH{{v ~ r}};
{{psi ~ v}}[ip] = p0e{{p}}[ir] * {{psi ~ v}}[ip] + p1e{{p}}[ir] * dH{{u ~ r}};
pE{{u}}i {{se}}= {{psi ~ u}}[ip];
pE{{v}}i {{sh}}= {{psi ~ v}}[ip];
}
{%- endfor %}
/*
* Update E
*/
Ex[i] += dt / epsx[i] * (dHzy - dHyz + pExi);
Ey[i] += dt / epsy[i] * (dHxz - dHzx + pEyi);
Ez[i] += dt / epsz[i] * (dHyx - dHxy + pEzi);

125
fdtd/kernels/update_h.cl Normal file
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@ -0,0 +1,125 @@
/*
* Update H-field, including any PMLs.
* Also precalculate values for poynting vector if necessary.
*
* Template parameters:
* common_header: Rendered contents of common.cl
* pmls: [('x', 'n'), ('z', 'p'),...] list of pml axes and polarities
* pml_thickness: Number of cells (integer)
* do_poynting: Whether to precalculate poynting vector components (boolean)
*
* OpenCL args:
* E, H, dt, [p{01}h{np}, Psi_{xyz}{np}_H], [oS]
*/
{{common_header}}
////////////////////////////////////////////////////////////////////////////
{% if pmls -%}
const int pml_thickness = {{pml_thickness}};
{%- endif %}
/*
* Precalculate derivatives
*/
ftype dExy = Ex[i + py] - Ex[i];
ftype dExz = Ex[i + pz] - Ex[i];
ftype dEyx = Ey[i + px] - Ey[i];
ftype dEyz = Ey[i + pz] - Ey[i];
ftype dEzx = Ez[i + px] - Ez[i];
ftype dEzy = Ez[i + py] - Ez[i];
{%- if do_poynting %}
/*
* Precalculate averaged E
*/
ftype aExy = Ex[i + py] + Ex[i];
ftype aExz = Ex[i + pz] + Ex[i];
ftype aEyx = Ey[i + px] + Ey[i];
ftype aEyz = Ey[i + pz] + Ey[i];
ftype aEzx = Ez[i + px] + Ez[i];
ftype aEzy = Ez[i + py] + Ez[i];
{%- endif %}
/*
* PML Update
*/
// PML contributions to H
ftype pHxi = 0;
ftype pHyi = 0;
ftype pHzi = 0;
{%- for r, p in pmls -%}
{%- set u, v = ['x', 'y', 'z'] | reject('equalto', r) -%}
{%- set psi = 'Psi_' ~ r ~ p ~ '_H' -%}
{%- if r != 'y' -%}
{%- set se, sh = '-', '+' -%}
{%- else -%}
{%- set se, sh = '+', '-' -%}
{%- endif -%}
{%- if p == 'n' %}
if ( {{r}} < pml_thickness ) {
const size_t ir = {{r}}; // index into pml parameters
{%- elif p == 'p' %}
if ( s{{r}} > {{r}} && {{r}} >= s{{r}} - pml_thickness ) {
const size_t ir = (s{{r}} - 1) - {{r}}; // index into pml parameters
{%- endif %}
const size_t ip = {{v}} + {{u}} * s{{v}} + ir * s{{v}} * s{{u}}; // linear index into Psi
{{psi ~ u}}[ip] = p0h{{p}}[ir] * {{psi ~ u}}[ip] + p1h{{p}}[ir] * dE{{v ~ r}};
{{psi ~ v}}[ip] = p0h{{p}}[ir] * {{psi ~ v}}[ip] + p1h{{p}}[ir] * dE{{u ~ r}};
pH{{u}}i {{sh}}= {{psi ~ u}}[ip];
pH{{v}}i {{se}}= {{psi ~ v}}[ip];
}
{%- endfor %}
/*
* Update H
*/
{% if do_poynting -%}
// Save old H for averaging
ftype Hx_old = Hx[i];
ftype Hy_old = Hy[i];
ftype Hz_old = Hz[i];
{%- endif %}
// H update equations
Hx[i] -= dt * (dEzy - dEyz + pHxi);
Hy[i] -= dt * (dExz - dEzx + pHyi);
Hz[i] -= dt * (dEyx - dExy + pHzi);
{% if do_poynting -%}
// Average H across timesteps
ftype aHxt = Hx[i] + Hx_old;
ftype aHyt = Hy[i] + Hy_old;
ftype aHzt = Hz[i] + Hz_old;
/*
* Calculate unscaled S components at H locations
*/
__global ftype *oSxy = oS + 0 * field_size;
__global ftype *oSyz = oS + 1 * field_size;
__global ftype *oSzx = oS + 2 * field_size;
__global ftype *oSxz = oS + 3 * field_size;
__global ftype *oSyx = oS + 4 * field_size;
__global ftype *oSzy = oS + 5 * field_size;
oSxy[i] = aEyx * aHzt;
oSxz[i] = -aEzx * aHyt;
oSyz[i] = aEzy * aHxt;
oSyx[i] = -aExy * aHzt;
oSzx[i] = aExz * aHyt;
oSzy[i] = -aEyz * aHxt;
{%- endif -%}

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fdtd/kernels/update_s.cl Normal file
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/*
* Update E-field, including any PMLs.
*
* Template parameters:
* common_header: Rendered contents of common.cl
* pmls: [('x', 'n'), ('z', 'p'),...] list of pml axes and polarities
* pml_thickness: Number of cells (integer)
*
* OpenCL args:
* E, H, dt, S, oS
*/
{{common_header}}
//////////////////////////////////////////////////////////////////////
/*
* Calculate S from oS (pre-calculated components)
*/
__global ftype *Sx = S + XX;
__global ftype *Sy = S + YY;
__global ftype *Sz = S + ZZ;
// Use unscaled S components from H locations
__global ftype *oSxy = oS + 0 * field_size;
__global ftype *oSyz = oS + 1 * field_size;
__global ftype *oSzx = oS + 2 * field_size;
__global ftype *oSxz = oS + 3 * field_size;
__global ftype *oSyx = oS + 4 * field_size;
__global ftype *oSzy = oS + 5 * field_size;
ftype s_factor = dt * 0.125;
Sx[i] = (oSxy[i] + oSxz[i] + oSxy[i + my] + oSxz[i + mz]) * s_factor;
Sy[i] = (oSyz[i] + oSyx[i] + oSyz[i + mz] + oSyx[i + mx]) * s_factor;
Sz[i] = (oSzx[i] + oSzy[i] + oSzx[i + mx] + oSzy[i + my]) * s_factor;

259
fdtd/simulation.py
View File

@ -3,15 +3,23 @@ Class for constructing and holding the basic FDTD operations and fields
"""
from typing import List, Dict, Callable
from collections import OrderedDict
import numpy
import jinja2
import warnings
import pyopencl
import pyopencl.array
from pyopencl.elementwise import ElementwiseKernel
from . import boundary, base
from .base import type_to_C
from fdfd_tools import vec
__author__ = 'Jan Petykiewicz'
# Create jinja2 env on module load
jinja_env = jinja2.Environment(loader=jinja2.PackageLoader(__name__, 'kernels'))
class Simulation(object):
@ -20,6 +28,7 @@ class Simulation(object):
"""
E = None # type: List[pyopencl.array.Array]
H = None # type: List[pyopencl.array.Array]
S = None # type: List[pyopencl.array.Array]
eps = None # type: List[pyopencl.array.Array]
dt = None # type: float
@ -30,24 +39,20 @@ class Simulation(object):
update_E = None # type: Callable[[],pyopencl.Event]
update_H = None # type: Callable[[],pyopencl.Event]
conductor_E = None # type: Callable[[],pyopencl.Event]
conductor_H = None # type: Callable[[],pyopencl.Event]
cpml_E = None # type: Callable[[],pyopencl.Event]
cpml_H = None # type: Callable[[],pyopencl.Event]
cpml_psi_E = None # type: Dict[str, pyopencl.array.Array]
cpml_psi_H = None # type: Dict[str, pyopencl.array.Array]
update_S = None # type: Callable[[],pyopencl.Event]
sources = None # type: Dict[str, str]
def __init__(self,
epsilon: List[numpy.ndarray],
dt: float=.99/numpy.sqrt(3),
initial_E: List[numpy.ndarray]=None,
initial_H: List[numpy.ndarray]=None,
context: pyopencl.Context=None,
queue: pyopencl.CommandQueue=None,
float_type: numpy.float32 or numpy.float64=numpy.float32):
dt: float = .99/numpy.sqrt(3),
initial_E: List[numpy.ndarray] = None,
initial_H: List[numpy.ndarray] = None,
context: pyopencl.Context = None,
queue: pyopencl.CommandQueue = None,
float_type: numpy.float32 or numpy.float64 = numpy.float32,
pml_thickness: int = 10,
pmls: List[List[str]] = None,
do_poynting: bool = True):
"""
Initialize the simulation.
@ -67,7 +72,7 @@ class Simulation(object):
Exception('All epsilon grids must have the same shape. Shapes are {}', [e.shape for e in epsilon])
if context is None:
self.context = pyopencl.create_some_context(False)
self.context = pyopencl.create_some_context()
else:
self.context = context
@ -84,126 +89,150 @@ class Simulation(object):
self.dt = dt
self.arg_type = float_type
self.eps = [pyopencl.array.to_device(self.queue, e.astype(float_type)) for e in epsilon]
self.sources = {}
self.eps = pyopencl.array.to_device(self.queue, vec(epsilon).astype(float_type))
if initial_E is None:
self.E = [pyopencl.array.zeros_like(self.eps[0]) for _ in range(3)]
self.E = pyopencl.array.zeros_like(self.eps)
else:
if len(initial_E) != 3:
Exception('Initial_E must be a list of length 3')
if not all((E.shape == epsilon[0].shape for E in initial_E)):
Exception('Initial_E list elements must have same shape as epsilon elements')
self.E = [pyopencl.array.to_device(self.queue, E.astype(float_type)) for E in initial_E]
self.E = pyopencl.array.to_device(self.queue, vec(E).astype(float_type))
if initial_H is None:
self.H = [pyopencl.array.zeros_like(self.eps[0]) for _ in range(3)]
self.H = pyopencl.array.zeros_like(self.eps)
else:
if len(initial_H) != 3:
Exception('Initial_H must be a list of length 3')
if not all((H.shape == epsilon[0].shape for H in initial_H)):
Exception('Initial_H list elements must have same shape as epsilon elements')
self.H = [pyopencl.array.to_device(self.queue, H.astype(float_type)) for H in initial_H]
self.H = pyopencl.array.to_device(self.queue, vec(H).astype(float_type))
if pmls is None:
pmls = [[d, p] for d in 'xyz' for p in 'np']
ctype = type_to_C(self.arg_type)
E_args = [ctype + ' *E' + c for c in 'xyz']
H_args = [ctype + ' *H' + c for c in 'xyz']
eps_args = [ctype + ' *eps' + c for c in 'xyz']
dt_arg = [ctype + ' dt']
sxyz = base.shape_source(epsilon[0].shape)
E_source = sxyz + base.dixyz_source + base.maxwell_E_source
H_source = sxyz + base.dixyz_source + base.maxwell_H_source
def ptr(arg: str) -> str:
return ctype + ' *' + arg
base_fields = OrderedDict()
base_fields[ptr('E')] = self.E
base_fields[ptr('H')] = self.H
base_fields[ctype + ' dt'] = self.dt
eps_field = OrderedDict()
eps_field[ptr('eps')] = self.eps
common_source = jinja_env.get_template('common.cl').render(
ftype=ctype,
shape=epsilon[0].shape,
)
jinja_args = {
'common_header': common_source,
'pml_thickness': pml_thickness,
'pmls': pmls,
'do_poynting': do_poynting,
}
E_source = jinja_env.get_template('update_e.cl').render(**jinja_args)
H_source = jinja_env.get_template('update_h.cl').render(**jinja_args)
self.sources['E'] = E_source
self.sources['H'] = H_source
if do_poynting:
S_source = jinja_env.get_template('update_s.cl').render(**jinja_args)
self.sources['S'] = S_source
self.oS = pyopencl.array.zeros(self.queue, self.E.shape + (2,), dtype=float_type)
self.S = pyopencl.array.zeros_like(self.E)
S_fields = OrderedDict()
S_fields[ptr('oS')] = self.oS
S_fields[ptr('S')] = self.S
else:
S_fields = OrderedDict()
'''
PML
'''
m = (3.5, 1)
sigma_max = 0.8 * (m[0] + 1) / numpy.sqrt(1.0) # TODO: epsilon_eff (not 1.0)
alpha_max = 0 # TODO: Decide what to do about non-zero alpha
def par(x):
sigma = ((x / pml_thickness) ** m[0]) * sigma_max
alpha = ((1 - x / pml_thickness) ** m[1]) * alpha_max
p0 = numpy.exp(-(sigma + alpha) * dt)
p1 = sigma / (sigma + alpha) * (p0 - 1)
return p0, p1
xen, xep, xhn, xhp = (numpy.arange(1, pml_thickness + 1, dtype=float_type)[::-1] for _ in range(4))
xep -= 0.5
xhn -= 0.5
pml_p_names = [['p' + a + eh + np for np in 'np' for a in '01'] for eh in 'eh']
pml_e_fields = OrderedDict()
pml_h_fields = OrderedDict()
for ne, nh, pe, ph in zip(*pml_p_names, par(xen) + par(xep), par(xhn) + par(xhp)):
pml_e_fields[ptr(ne)] = pyopencl.array.to_device(self.queue, pe)
pml_h_fields[ptr(nh)] = pyopencl.array.to_device(self.queue, ph)
for pml in pmls:
uv = 'xyz'.replace(pml[0], '')
psi_base = 'Psi_' + ''.join(pml) + '_'
psi_names = [[psi_base + eh + c for c in uv] for eh in 'EH']
psi_shape = list(epsilon[0].shape)
psi_shape['xyz'.find(pml[0])] = pml_thickness
for ne, nh in zip(*psi_names):
pml_e_fields[ptr(ne)] = pyopencl.array.zeros(self.queue, tuple(psi_shape), dtype=self.arg_type)
pml_h_fields[ptr(nh)] = pyopencl.array.zeros(self.queue, tuple(psi_shape), dtype=self.arg_type)
self.pml_e_fields = pml_e_fields
self.pml_h_fields = pml_h_fields
'''
Create operations
'''
E_args = OrderedDict()
[E_args.update(d) for d in (base_fields, eps_field, pml_e_fields)]
E_update = ElementwiseKernel(self.context, operation=E_source,
arguments=', '.join(E_args + H_args + dt_arg + eps_args))
arguments=', '.join(E_args.keys()))
H_args = OrderedDict()
[H_args.update(d) for d in (base_fields, pml_h_fields, S_fields)]
H_update = ElementwiseKernel(self.context, operation=H_source,
arguments=', '.join(E_args + H_args + dt_arg))
arguments=', '.join(H_args.keys()))
self.update_E = lambda e: E_update(*E_args.values(), wait_for=e)
self.update_H = lambda e: H_update(*H_args.values(), wait_for=e)
self.update_E = lambda e: E_update(*self.E, *self.H, self.dt, *self.eps, wait_for=e)
self.update_H = lambda e: H_update(*self.E, *self.H, self.dt, wait_for=e)
if do_poynting:
S_args = OrderedDict()
[S_args.update(d) for d in (base_fields, S_fields)]
S_update = ElementwiseKernel(self.context, operation=S_source,
arguments=', '.join(S_args.keys()))
def init_cpml(self, pml_args: List[Dict]):
"""
Initialize absorbing layers (cpml: complex phase matched layer). PMLs are not actual
boundary conditions, so you should add a conducting boundary (.init_conductors()) for
all directions in which you add PMLs.
Allows use of self.cpml_E(events) and self.cpml_H(events).
All necessary additional fields are created on the opencl device.
self.update_S = lambda e: S_update(*S_args.values(), wait_for=e)
:param pml_args: A list containing dictionaries which are passed to .boundary.cpml(...).
The dt argument is set automatically, but the others must be passed in each entry
of pml_args.
"""
sxyz = base.shape_source(self.eps[0].shape)
# Prepare per-iteration constants for later use
pml_E_source = sxyz + base.dixyz_source + base.xyz_source
pml_H_source = sxyz + base.dixyz_source + base.xyz_source
def type_to_C(float_type) -> str:
"""
Returns a string corresponding to the C equivalent of a numpy type.
Only works for float16, float32, float64.
psi_E = []
psi_H = []
psi_E_names = []
psi_H_names = []
for arg_set in pml_args:
pml_data = boundary.cpml(dt=self.dt, **arg_set)
pml_E_source += pml_data['E']
pml_H_source += pml_data['H']
ti = numpy.delete(range(3), arg_set['direction'])
trans = [self.eps[0].shape[i] for i in ti]
psi_shape = (8, trans[0], trans[1])
psi_E += [pyopencl.array.zeros(self.queue, psi_shape, dtype=self.arg_type)
for _ in pml_data['psi_E']]
psi_H += [pyopencl.array.zeros(self.queue, psi_shape, dtype=self.arg_type)
for _ in pml_data['psi_H']]
psi_E_names += pml_data['psi_E']
psi_H_names += pml_data['psi_H']
ctype = type_to_C(self.arg_type)
E_args = [ctype + ' *E' + c for c in 'xyz']
H_args = [ctype + ' *H' + c for c in 'xyz']
eps_args = [ctype + ' *eps' + c for c in 'xyz']
dt_arg = [ctype + ' dt']
arglist_E = [ctype + ' *' + psi for psi in psi_E_names]
arglist_H = [ctype + ' *' + psi for psi in psi_H_names]
pml_E_args = ', '.join(E_args + H_args + dt_arg + eps_args + arglist_E)
pml_H_args = ', '.join(E_args + H_args + dt_arg + arglist_H)
pml_E = ElementwiseKernel(self.context, arguments=pml_E_args, operation=pml_E_source)
pml_H = ElementwiseKernel(self.context, arguments=pml_H_args, operation=pml_H_source)
self.cpml_E = lambda e: pml_E(*self.E, *self.H, self.dt, *self.eps, *psi_E, wait_for=e)
self.cpml_H = lambda e: pml_H(*self.E, *self.H, self.dt, *psi_H, wait_for=e)
self.cmpl_psi_E = {k: v for k, v in zip(psi_E_names, psi_E)}
self.cmpl_psi_H = {k: v for k, v in zip(psi_H_names, psi_H)}
def init_conductors(self, conductor_args: List[Dict]):
"""
Initialize reflecting boundary conditions.
Allows use of self.conductor_E(events) and self.conductor_H(events).
:param conductor_args: List of dictionaries with which to call .boundary.conductor(...).
"""
sxyz = base.shape_source(self.eps[0].shape)
# Prepare per-iteration constants
bc_E_source = sxyz + base.dixyz_source + base.xyz_source
bc_H_source = sxyz + base.dixyz_source + base.xyz_source
for arg_set in conductor_args:
[e, h] = boundary.conductor(**arg_set)
bc_E_source += e
bc_H_source += h
E_args = [type_to_C(self.arg_type) + ' *E' + c for c in 'xyz']
H_args = [type_to_C(self.arg_type) + ' *H' + c for c in 'xyz']
bc_E = ElementwiseKernel(self.context, arguments=E_args, operation=bc_E_source)
bc_H = ElementwiseKernel(self.context, arguments=H_args, operation=bc_H_source)
self.conductor_E = lambda e: bc_E(*self.E, wait_for=e)
self.conductor_H = lambda e: bc_H(*self.H, wait_for=e)
:param float_type: e.g. numpy.float32
:return: string containing the corresponding C type (eg. 'double')
"""
if float_type == numpy.float16:
arg_type = 'half'
elif float_type == numpy.float32:
arg_type = 'float'
elif float_type == numpy.float64:
arg_type = 'double'
else:
raise Exception('Unsupported type')
return arg_type

2
requirements.txt
View File

@ -1,6 +1,8 @@
numpy
h5py
pyopencl
jinja2
-e git+https://mpxd.net/gogs/jan/float_raster.git@release#egg=float_raster
-e git+https://mpxd.net/gogs/jan/gridlock.git@release#egg=gridlock
-e git+https://mpxd.net/gogs/jan/masque.git@release#egg=masque
-e git+https://mpxd.net/gogs/jan/fdfd_tools.git@master#egg=fdfd_tools