write output from C tests to temporary directory (NanoComp#1126)

* write output from C tests to temporary directory

* fix

* replace rmdir with POSIX ntfw

* put am_master before nftw rather than delete_directory

doc/docs/Python_Tutorials/Eigenmode_Source.md

@@ -17,7 +17,7 @@ The first structure, shown in the schematic below, is a 2d ridge waveguide with
 
 The simulation script is in [examples/oblique-source.py](https://github.com/NanoComp/meep/blob/master/python/examples/oblique-source.py). The notebook is [examples/oblique-source.ipynb](https://nbviewer.jupyter.org/github/NanoComp/meep/blob/master/python/examples/oblique-source.ipynb).
 
-The simulation consists of two separate parts: (1) computing the Poynting flux and (2) plotting the field profile. The field profile is generated by setting the flag `compute_flux=False`. For the single-mode case, a constant-amplitude current source (`eig_src=False`) excites both the waveguide mode and radiating fields in *both* directions (i.e., forwards and backwards). This is shown in the main inset of the first of two figures above. The `EigenModeSource` excites only the *forward-going* waveguide mode **A** as shown in the smaller inset. Exciting this mode requires setting `eig_src=True`, `fsrc=0.15`, `kx=0.4`, and `bnum=1`. Note that `EigenModeSource` is a line centered at the origin extending the length of the entire cell. The constant-amplitude source is a line that is slightly larger than the waveguide width. The parameter `rot_angle` specifies the rotation angle of the waveguide axis and is initially 0° (i.e., straight or horizontal orientation). This enables `eig_parity` to include `EVEN_Y` in addition to `ODD_Z` and the simulation to include an overall mirror symmetry plane in the y-direction.
+The simulation consists of two separate parts: (1) computing the Poynting flux and (2) plotting the field profile. The field profile is generated by setting the flag `compute_flux=False`. For the single-mode case, a constant-amplitude current source (`eig_src=False`) excites both the waveguide mode and radiating fields in *both* directions (i.e., forwards and backwards). This is shown in the main inset of the first of two figures above. The `EigenModeSource` excites only the *forward-going* waveguide mode **A** as shown in the smaller inset. Launching this mode requires setting `eig_src=True`, `fsrc=0.15`, `kx=0.4`, and `bnum=1`. Note that the length of the `EigenModeSource` must be large enough that it captures the entire guided mode (i.e., the fields should decay to roughly zero at the edges). The line source does *not* need to span the entire length of the cell but should be slightly larger than the waveguide width. The parameter `rot_angle` specifies the rotation angle of the waveguide axis and is initially 0° (i.e., straight or horizontal orientation). This enables `eig_parity` to include `EVEN_Y` in addition to `ODD_Z` and the simulation to include an overall mirror symmetry plane in the y-direction.
 
 For the multi-mode case, a constant-amplitude current source excites a superposition of the two waveguide modes in addition to the radiating field. This is shown in the main inset of the second figure above. The `EigenModeSource` excites only a given mode: **A** (`fsrc=0.35`, `kx=0.4`, `bnum=2`) or **B** (`fsrc=0.35`, `kx=1.2`, `bnum=1`) as shown in the smaller insets.
 
@@ -35,8 +35,10 @@ pml_layers = [mp.PML(thickness=2)]
 # rotation angle (in degrees) of waveguide, counter clockwise (CCW) around z-axis
 rot_angle = np.radians(20)
 
+w = 1.0 # width of waveguide
+
 geometry = [mp.Block(center=mp.Vector3(),
-                     size=mp.Vector3(mp.inf,1,mp.inf),
+                     size=mp.Vector3(mp.inf,w,mp.inf),
                      e1=mp.Vector3(1).rotate(mp.Vector3(z=1), rot_angle),
                      e2=mp.Vector3(y=1).rotate(mp.Vector3(z=1), rot_angle),
                      material=mp.Medium(epsilon=12))]
@@ -54,7 +56,7 @@ eig_src = True # eigenmode (True) or constant-amplitude (False) source
 if eig_src:
     sources = [mp.EigenModeSource(src=mp.GaussianSource(fsrc,fwidth=0.2*fsrc) if compute_flux else mp.ContinuousSource(fsrc),
                                   center=mp.Vector3(),
-                                  size=mp.Vector3(y=14),
+                                  size=mp.Vector3(y=3*w),
                                   direction=mp.NO_DIRECTION,
                                   eig_kpoint=kpoint,
                                   eig_band=bnum,
@@ -63,7 +65,7 @@ if eig_src:
 else:
     sources = [mp.Source(src=mp.GaussianSource(fsrc,fwidth=0.2*fsrc) if compute_flux else mp.ContinuousSource(fsrc),
                          center=mp.Vector3(),
-                         size=mp.Vector3(y=2),
+                         size=mp.Vector3(y=3*w),
                          component=mp.Ez)]
 
 sim = mp.Simulation(cell_size=cell_size,
@@ -109,7 +111,7 @@ Finally, we demonstrate that the total power in a waveguide with *arbitrary* ori
 Planewaves in Homogeneous Media
 -------------------------------
 
-The eigenmode source can also be used to launch [planewaves](https://en.wikipedia.org/wiki/Plane_wave) in homogeneous media. The dispersion relation for a planewave is ω=|$\vec{k}$|/$n$ where ω is the angular frequency of the planewave and $\vec{k}$ its wavevector; $n$ is the refractive index of the homogeneous medium. This example demonstrates launching planewaves in a uniform medium with $n$ of 1.5 at three rotation angles: 0°, 20°, and 40°. Bloch-periodic boundaries via the `k_point` are used and specified by the wavevector $\vec{k}$. PML boundaries are used only along the x-direction.
+The eigenmode source can also be used to launch [planewaves](https://en.wikipedia.org/wiki/Plane_wave) in homogeneous media. The dispersion relation for a planewave is ω=|$\vec{k}$|/$n$ where ω is the angular frequency of the planewave and $\vec{k}$ its wavevector; $n$ is the refractive index of the homogeneous medium. This example demonstrates launching planewaves in a uniform medium with $n$ of 1.5 at three rotation angles: 0°, 20°, and 40°. Bloch-periodic boundaries via the `k_point` are used and specified by the wavevector $\vec{k}$. PML boundaries are used only along the $x$-direction.
 
 The simulation script is in [examples/oblique-planewave.py](https://github.com/NanoComp/meep/blob/master/python/examples/oblique-planewave.py). The notebook is in [examples/oblique-planewave.ipynb](https://nbviewer.jupyter.org/github/NanoComp/meep/blob/master/python/examples/oblique-planewave.ipynb).
 
@@ -162,7 +164,7 @@ plt.axis('off')
 plt.show()
 ```
 
-Note that this example involves a `ContinuousSource` for the time profile. For a pulsed source, the oblique planewave is incident at a given angle for only a *single* frequency component of the source; see [Tutorial/Basics/Angular Reflectance Spectrum of a Planar Interface](../Python_Tutorials/Basics.md#angular-reflectance-spectrum-of-a-planar-interface). This is a fundamental feature of FDTD simulations and not of Meep per se. To simulate an incident planewave at multiple angles for a given frequency ω, you will need to do separate simulations involving different values of $\vec{k}$ (`k_point`) since each set of ($\vec{k}$,ω) specifying the Bloch-periodic boundaries and the frequency of the source will produce a different angle of the planewave. For more details, refer to Section 4.5 ("Efficient Frequency-Angle Coverage") in [Chapter 4](https://arxiv.org/abs/1301.5366) ("Electromagnetic Wave Source Conditions") of [Advances in FDTD Computational Electrodynamics: Photonics and Nanotechnology](https://www.amazon.com/Advances-FDTD-Computational-Electrodynamics-Nanotechnology/dp/1608071707).
+Note that the line source spans the *entire* length of the cell. (Planewave sources extending into the PML region must include `is_integrated=True`.) This example involves a continuous-wave (CW) time profile. For a pulse profile, the oblique planewave is incident at a given angle for only a *single* frequency component of the source; see [Tutorial/Basics/Angular Reflectance Spectrum of a Planar Interface](../Python_Tutorials/Basics.md#angular-reflectance-spectrum-of-a-planar-interface). This is a fundamental feature of FDTD simulations and not of Meep per se. To simulate an incident planewave at multiple angles for a given frequency ω, you will need to do separate simulations involving different values of $\vec{k}$ (`k_point`) since each set of ($\vec{k}$,ω) specifying the Bloch-periodic boundaries and the frequency of the source will produce a different angle of the planewave. For more details, refer to Section 4.5 ("Efficient Frequency-Angle Coverage") in [Chapter 4](https://arxiv.org/abs/1301.5366) ("Electromagnetic Wave Source Conditions") of [Advances in FDTD Computational Electrodynamics: Photonics and Nanotechnology](https://www.amazon.com/Advances-FDTD-Computational-Electrodynamics-Nanotechnology/dp/1608071707).
 
 Shown below are the steady-state field profiles generated by the planewave for the three rotation angles. Residues of the backward-propagating waves due to the discretization are slightly visible.
 

doc/docs/Scheme_Tutorials/Eigenmode_Source.md

@@ -17,7 +17,7 @@ The first structure, shown in the schematic below, is a 2d ridge waveguide with
 
 The simulation script is in [examples/oblique-source.ctl](https://github.com/NanoComp/meep/blob/master/scheme/examples/oblique-source.ctl).
 
-The simulation consists of two parts: (1) computing the Poynting flux and (2) plotting the field profile. The field profile is generated by setting the flag `compute-flux=false`. For the single-mode case, a constant-amplitude current source (`eig-src=false`) excites both the waveguide mode and radiating fields in *both* directions (i.e., forwards and backwards). This is shown in the main inset of the first of two figures above. The `eigenmode-source` excites only the *forward-going* waveguide mode **A** as shown in the smaller inset. Exciting this mode requires setting `eig-src=true`, `fsrc=0.15`, `kx=0.4`, and `bnum=1`. Note that `eigenmode-source` is a line centered at the origin extending the length of the entire cell. The constant-amplitude source is a line that is slightly larger than the waveguide width. The parameter `rot-angle` specifies the rotation angle of the waveguide axis and is initially 0° (i.e., straight or horizontal orientation). This enables `eig-parity` to include `EVEN-Y` in addition to `ODD-Z` and the cell to include an overall mirror symmetry plane in the y-direction.
+The simulation consists of two parts: (1) computing the Poynting flux and (2) plotting the field profile. The field profile is generated by setting the flag `compute-flux=false`. For the single-mode case, a constant-amplitude current source (`eig-src=false`) excites both the waveguide mode and radiating fields in *both* directions (i.e., forwards and backwards). This is shown in the main inset of the first of two figures above. The `eigenmode-source` excites only the *forward-going* waveguide mode **A** as shown in the smaller inset. Launching this mode requires setting `eig-src=true`, `fsrc=0.15`, `kx=0.4`, and `bnum=1`. Note that the length of the `EigenModeSource` must be large enough that it captures the entire guided mode (i.e., the fields should decay to roughly zero at the edges). The line source does *not* need to span the entire length of the cell but should be slightly larger than the waveguide width. The parameter `rot-angle` specifies the rotation angle of the waveguide axis and is initially 0° (i.e., straight or horizontal orientation). This enables `eig-parity` to include `EVEN-Y` in addition to `ODD-Z` and the cell to include an overall mirror symmetry plane in the y-direction.
 
 For the multi-mode case, a constant-amplitude current source excites a superposition of the two waveguide modes in addition to the radiating field. This is shown in the main inset of the second figure above. The `eigenmode-source` excites only a given mode: **A** (`fsrc=0.35`, `kx=0.4`, `bnum=2`) or **B** (`fsrc=0.35`, `kx=1.2`, `bnum=1`) as shown in the smaller insets.
 
@@ -32,9 +32,12 @@ For the multi-mode case, a constant-amplitude current source excites a superposi
 (define-param rot-angle 20)
 (set! rot-angle (deg->rad rot-angle))
 
+; width of waveguide
+(define-param w 1.0)
+
 (set! geometry (list (make block
                        (center 0 0 0)
-                       (size infinity 1 infinity)
+                       (size infinity w infinity)
                        (e1 (rotate-vector3 (vector3 0 0 1) rot-angle (vector3 1 0 0)))
                        (e2 (rotate-vector3 (vector3 0 0 1) rot-angle (vector3 0 1 0)))
                        (material (make medium (epsilon 12))))))
@@ -54,7 +57,7 @@ For the multi-mode case, a constant-amplitude current source excites a superposi
                    (make eigenmode-source
                      (src (if compute-flux? (make gaussian-src (frequency fsrc) (fwidth (* 0.2 fsrc))) (make continuous-src (frequency fsrc))))
                      (center 0 0 0)
-                     (size 0 14 0)
+                     (size 0 (* 3 w) 0)
                      (direction (if (= rot-angle 0) AUTOMATIC NO-DIRECTION))
                      (eig-kpoint kpoint)
                      (eig-band bnum)
@@ -63,7 +66,7 @@ For the multi-mode case, a constant-amplitude current source excites a superposi
                    (make source
                      (src (if compute-flux? (make gaussian-src (frequency fsrc) (fwidth (* 0.2 fsrc))) (make continuous-src (frequency fsrc))))
                      (center 0 0 0)
-                     (size 0 2 0)
+                     (size 0 (* 3 w) 0)
                      (component Ez)))))
 
 (if (= rot-angle 0)
@@ -103,7 +106,7 @@ Finally, we demonstrate that the total power in a waveguide with *arbitrary* ori
 Planewaves in Homogeneous Media
 -------------------------------
 
-The eigenmode source can also be used to launch [planewaves](https://en.wikipedia.org/wiki/Plane_wave) in homogeneous media. The dispersion relation for a planewave is ω=|$\vec{k}$|/$n$ where ω is the angular frequency of the planewave and $\vec{k}$ its wavevector; $n$ is the refractive index of the homogeneous medium. This example demonstrates launching planewaves in a uniform medium with $n$ of 1.5 at three rotation angles: 0°, 20°, and 40°. Bloch-periodic boundaries via the `k-point` are used and specified by the wavevector $\vec{k}$. PML boundaries are used only along the x-direction.
+The eigenmode source can also be used to launch [planewaves](https://en.wikipedia.org/wiki/Plane_wave) in homogeneous media. The dispersion relation for a planewave is ω=|$\vec{k}$|/$n$ where ω is the angular frequency of the planewave and $\vec{k}$ its wavevector; $n$ is the refractive index of the homogeneous medium. This example demonstrates launching planewaves in a uniform medium with $n$ of 1.5 at three rotation angles: 0°, 20°, and 40°. Bloch-periodic boundaries via the `k-point` are used and specified by the wavevector $\vec{k}$. PML boundaries are used only along the $x$-direction.
 
 The simulation script is in [examples/oblique-planewave.ctl](https://github.com/NanoComp/meep/blob/master/scheme/examples/oblique-planewave.ctl).
 
@@ -144,7 +147,7 @@ The simulation script is in [examples/oblique-planewave.ctl](https://github.com/
                           (at-end output-efield-z)))
 ```
 
-Note that this example involves a `continuous-source` for the time profile. For a pulsed source, the oblique planewave is incident at a given angle for only a *single* frequency component of the source; see [Tutorial/Basics/Angular Reflectance Spectrum of a Planar Interface](../Scheme_Tutorials/Basics.md#angular-reflectance-spectrum-of-a-planar-interface). This is a fundamental feature of FDTD simulations and not of Meep per se. To simulate an incident planewave at multiple angles for a given frequency ω, you will need to do separate simulations involving different values of $\vec{k}$ (`k-point`) since each set of ($\vec{k}$,ω) specifying the Bloch-periodic boundaries and the frequency of the source will produce a different angle of the planewave. For more details, refer to Section 4.5 ("Efficient Frequency-Angle Coverage") in [Chapter 4](https://arxiv.org/abs/1301.5366) ("Electromagnetic Wave Source Conditions") of [Advances in FDTD Computational Electrodynamics: Photonics and Nanotechnology](https://www.amazon.com/Advances-FDTD-Computational-Electrodynamics-Nanotechnology/dp/1608071707).
+Note that the line source spans the *entire* length of the cell. (Planewave sources extending into the PML region must include `(is-integrated true)`.) This example involves a continuous-wave (CW) time profile. For a pulse profile, the oblique planewave is incident at a given angle for only a *single* frequency component of the source; see [Tutorial/Basics/Angular Reflectance Spectrum of a Planar Interface](../Scheme_Tutorials/Basics.md#angular-reflectance-spectrum-of-a-planar-interface). This is a fundamental feature of FDTD simulations and not of Meep per se. To simulate an incident planewave at multiple angles for a given frequency ω, you will need to do separate simulations involving different values of $\vec{k}$ (`k-point`) since each set of ($\vec{k}$,ω) specifying the Bloch-periodic boundaries and the frequency of the source will produce a different angle of the planewave. For more details, refer to Section 4.5 ("Efficient Frequency-Angle Coverage") in [Chapter 4](https://arxiv.org/abs/1301.5366) ("Electromagnetic Wave Source Conditions") of [Advances in FDTD Computational Electrodynamics: Photonics and Nanotechnology](https://www.amazon.com/Advances-FDTD-Computational-Electrodynamics-Nanotechnology/dp/1608071707).
 
 Shown below are the steady-state field profiles generated by the planewave for the three rotation angles. Residues of the backward-propagating waves due to the discretization are slightly visible.
 

python/examples/oblique-source.py

@@ -11,8 +11,10 @@
 # rotation angle (in degrees) of waveguide, counter clockwise (CCW) around z-axis
 rot_angle = np.radians(20)
 
+w = 1.0 # width of waveguide
+
 geometry = [mp.Block(center=mp.Vector3(),
-                     size=mp.Vector3(mp.inf,1,mp.inf),
+                     size=mp.Vector3(mp.inf,w,mp.inf),
                      e1=mp.Vector3(1).rotate(mp.Vector3(z=1), rot_angle),
                      e2=mp.Vector3(y=1).rotate(mp.Vector3(z=1), rot_angle),
                      material=mp.Medium(epsilon=12))]
@@ -30,7 +32,7 @@
 if eig_src:
     sources = [mp.EigenModeSource(src=mp.GaussianSource(fsrc,fwidth=0.2*fsrc) if compute_flux else mp.ContinuousSource(fsrc),
                                   center=mp.Vector3(),
-                                  size=mp.Vector3(y=14),
+                                  size=mp.Vector3(y=3*w),
                                   direction=mp.NO_DIRECTION,
                                   eig_kpoint=kpoint,
                                   eig_band=bnum,
@@ -39,7 +41,7 @@
 else:
     sources = [mp.Source(src=mp.GaussianSource(fsrc,fwidth=0.2*fsrc) if compute_flux else mp.ContinuousSource(fsrc),
                          center=mp.Vector3(),
-                         size=mp.Vector3(y=2),
+                         size=mp.Vector3(y=3*w),
                          component=mp.Ez)]
 
 sim = mp.Simulation(cell_size=cell_size,

scheme/examples/oblique-source.ctl

@@ -8,6 +8,9 @@
 (define-param rot-angle 20)
 (set! rot-angle (deg->rad rot-angle))
 
+; width of waveguide
+(define-param w 1.0)
+
 (set! geometry (list (make block
                        (center 0 0 0)
                        (size infinity 1 infinity)
@@ -30,7 +33,7 @@
                    (make eigenmode-source
                      (src (if compute-flux? (make gaussian-src (frequency fsrc) (fwidth (* 0.2 fsrc))) (make continuous-src (frequency fsrc))))
                      (center 0 0 0)
-                     (size 0 14 0)
+                     (size 0 (* 3 w) 0)
                      (direction (if (= rot-angle 0) AUTOMATIC NO-DIRECTION))
                      (eig-kpoint kpoint)
                      (eig-band bnum)
@@ -39,7 +42,7 @@
                    (make source
                      (src (if compute-flux? (make gaussian-src (frequency fsrc) (fwidth (* 0.2 fsrc))) (make continuous-src (frequency fsrc))))
                      (center 0 0 0)
-                     (size 0 2 0)
+                     (size 0 (* 3 w) 0)
                      (component Ez)))))
 
 (if (= rot-angle 0)