[Meep-discuss] Multiple field components in plot2D and animate2D

[Nikolaos Matthaiakakis]

Hello all,

this is probably something relatively simple but I am having trouble including 
multiple field components in the plot2D method and animate2D class (for example 
including both mp.Ex and mp.Ey). Is there a simple way to set this up through 
the user interface?

Thank you very much

Best wishes
Nikolaos

p.s I also tried using mp.to_appeneded and mp.output_efield_  but h5utils gives 
the following error when trying to convert h5 files:

“h5topng error: invalid colormap file”

This error persists in new environments and freshly installed h5utils as well.

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Re: [Meep-discuss] Multiple field components in plot2D and animate2D

[Nikolaos Matthaiakakis]

Thank you for the reply. So currently plot2D and animate2D don’t support this. 
I will use get_array() instead when I need to play with combinations of fields 
then.

One more question I have is if mp.output_efield_x() can be used for a certain 
volume or it always includes the entire simulation region.

Best wishes
Nikolaos

p.s the colormap error might have been due to a problem with a sub process call 
instead of with h5utils itself.

From: Alec Hammond<mailto:alec.m.hamm...@gmail.com>
Sent: 29 December 2020 18:14
To: Nikolaos Matthaiakakis<mailto:nikolao...@outlook.com>; 
meep-discuss@ab-initio.mit.edu<mailto:meep-discuss@ab-initio.mit.edu>
Subject: Re: Multiple field components in plot2D and animate2D

Why not just plot Hz in that case?

As of now, you can’t do multiple components using plot2D.
You can of course do it manually using get_array().


From: meep-discuss  on behalf of 
Nikolaos Matthaiakakis
Sent: Tuesday, December 29, 2020 8:19:13 AM
To: meep-discuss@ab-initio.mit.edu 
Subject: [Meep-discuss] Multiple field components in plot2D and animate2D


Hello all,



this is probably something relatively simple but I am having trouble including 
multiple field components in the plot2D method and animate2D class (for example 
including both mp.Ex and mp.Ey). Is there a simple way to set this up through 
the user interface?



Thank you very much



Best wishes

Nikolaos



p.s I also tried using mp.to_appeneded and mp.output_efield_  but h5utils gives 
the following error when trying to convert h5 files:



“h5topng error: invalid colormap file”



This error persists in new environments and freshly installed h5utils as well.



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[Meep-discuss] non-uniform gridding

[Nikolaos Matthaiakakis]

Dear Danny,

I am also very interested in using a non-uniform grid in my code. If I manage 
to do this I will provide further information. Please let me know if you have 
made any progress with your own code as well.

I am trying to simulate graphene plasmons for a nano-rectangle pattern 70nm x 
65nm which I typically do with a BEM code but this time I need to include 
materials with anisotropic and possibly nonlinear properties which the BEM code 
cant handle. Hence I started using Meep which is overall an amazing simulation 
tool.

Sadly since graphene plasmons are in the infrared range I am having troubles 
with the very high resolution due to the nanoscale dimensions of my structure 
combined with the large simulation region required due to the several 
micrometer scale wavelengths.

I feel like if a non-uniform grid was included in Meep by default I would never 
look back towards commercial solutions. Saying that, I will try my best to get 
the scaling transformation running.

Best wishes
Nikolaos Matthaiakakis

P.s

I am not sure what you are working on but depending on your structure maybe an 
FEM solver would be more suitable (could be true for my case too). Sadly I am 
not familiar with any good quality free FEM tools that are suitable for lossy 
dispersive materials/anisotropic/nonlinear materials.


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[Meep-discuss] non-uniform gridding

[Nikolaos Matthaiakakis]

I apologize this was meant to be sent as a response to 
https://www.mail-archive.com/meep-discuss@ab-initio.mit.edu/msg06628.html by I 
ended up opening a new thread by mistake.


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[Meep-discuss] Coordinate transform and nonlinear materials

[Nikolaos Matthaiakakis]

Dear all,

I was wondering if anyone has experience with using the coordinate transform 
with nonlinear materials (materials with chi3 etc).

https://meep.readthedocs.io/en/latest/Python_User_Interface/#medium

https://meep.readthedocs.io/en/latest/Units_and_Nonlinearity/

Would the transform(self, m) function work in this case (for example for third 
harmonic generation)?

Thank you

Best wishes
Nikolaos

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Re: [Meep-discuss] Coordinate transform and nonlinear materials

[Nikolaos Matthaiakakis]

Thank you very much for the reply. I will try to implement it this way and will 
provide updates if successful.


Sent: 15 December 2020 23:43

Subject: Re: [Meep-discuss] Coordinate transform and nonlinear materials

You have to modify the math to handle nonlinear materials in transformation 
optics; there was a recent paper on this:

https://www.nature.com/articles/s41598-018-22215-x



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Re: [Meep-discuss] Coordinate transform and nonlinear materials

[Nikolaos Matthaiakakis]

Thank you for the reply, I see that in the code now. So it would not work with 
simple diagonal chi3 tensors? I am pretty new to nonlinear optics (and meep to 
be honest). Wouldn’t it be ok with the non-diagonal values as zero?

I guess that means that I cannot use the coordinate transform when trying to 
simulate 3rd harmonic generation in graphene for example.

This is going to make things a bit challenging.

From: Andrew Stone<mailto:andrewston...@gmail.com>
Sent: 15 December 2020 21:39
To: Nikolaos Matthaiakakis<mailto:nikolao...@outlook.com>
Cc: meep-discuss@ab-initio.mit.edu<mailto:meep-discuss@ab-initio.mit.edu>
Subject: Re: [Meep-discuss] Coordinate transform and nonlinear materials

No. Using the transform function would transform all other properties of the 
material, but leave the nonlinearities unchanged. While I do not have 
experience, an examination of the code 
(https://github.com/NanoComp/meep/blob/8ac118ae57161a365bec36acdab776048030a089/python/geom.py#L443)
 shows that the "transform" function operates only on Susceptibilities, 
permittivities, permeabilities, and conductivities, consistent with the 
documentation. Fully implementing the "transform" function for nonlinear 
materials is also not possible at present since only diagonal chi tensors are 
supported.

On Tue, Dec 15, 2020 at 9:56 AM Nikolaos Matthaiakakis 
mailto:nikolao...@outlook.com>> wrote:
Dear all,

I was wondering if anyone has experience with using the coordinate transform 
with nonlinear materials (materials with chi3 etc).

https://meep.readthedocs.io/en/latest/Python_User_Interface/#medium

https://meep.readthedocs.io/en/latest/Units_and_Nonlinearity/

Would the transform(self, m) function work in this case (for example for third 
harmonic generation)?

Thank you

Best wishes
Nikolaos

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Re: [Meep-discuss] Dispersive conductivity for 2D materials

[Nikolaos Matthaiakakis]

Thank you very much for the reply. So I should, for example, use the Drude 
model to fit the graphene conductivity over the desired frequency range and 
follow the tip from FAQ and assign it in the form of an anisotropic volumetric 
conductivity (or permittivity) to a block with a 1/resolution thickness and 
conductivity(permittivity)*resolution?

“How do I model graphene or other 2d materials with single-atom thickness?

Typically, graphene and similar "2d" materials are mathematically represented 
as a delta function 
conductivity in Maxwell's equations because their thickness is negligible 
compared to the wavelength, where the conductivity is furthermore usually 
anisotropic (producing surface-parallel currents in response to the 
surface-parallel components of the electric field). In a discretized computer 
model like Meep, this is approximated by an anisotropic volume conductivity (or 
other polarizable dispersive material) whose thickness is proportional to 
(1/resolution) and whose amplitude is proportional resolution. For example, 
this could be represented by a one-pixel-thick 
conductor
 can be represented by e.g. a 
Block with 
size=meep.Vector3(x,y,1/resolution) in a 3d cell, with the value of the 
conductivity explicitly multiplied by resolution. “

I suppose a surface conductivity model (found in some commercial FDTD solvers) 
is not currently available and there is only a volumetric approach. I will try 
to implement it the volumetric conductivity approach then.

Once again thank you for your time.

Best wishes

Nikolaos
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[Meep-discuss] Obtaining polarization dependent Poynting flux

[Nikolaos Matthaiakakis]

Dear all,

Since mp.get_fluxes() gives the Poynting flux due to all field components, I 
was wondering if there is a smart way to obtain the Poynting flux through a 
monitor region separately for Ex and Ey, as well as the phase associated with 
them.

Thank you for your time.

Best wishes
Nikolaos

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Re: [Meep-discuss] Obtaining polarization dependent Poynting flux

[Nikolaos Matthaiakakis]

Thank you very much, I see it is well documented in the user interface page.

From: Steven G. Johnson<mailto:stevenj@gmail.com>
Sent: 11 November 2020 22:45
To: Nikolaos Matthaiakakis<mailto:nikolao...@outlook.com>
Cc: meep-discuss@ab-initio.mit.edu<mailto:meep-discuss@ab-initio.mit.edu>
Subject: Re: [Meep-discuss] Obtaining polarization dependent Poynting flux

You get use the dft_fields feature to get whatever Fourier transformed fields 
you want and do whatever calculation you want.


On Nov 11, 2020, at 11:02 AM, Nikolaos Matthaiakakis 
mailto:nikolao...@outlook.com>> wrote:

Dear all,

Since mp.get_fluxes() gives the Poynting flux due to all field components, I 
was wondering if there is a smart way to obtain the Poynting flux through a 
monitor region separately for Ex and Ey, as well as the phase associated with 
them.

Thank you for your time.

Best wishes
Nikolaos

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Re: [Meep-discuss] Obtaining polarization dependent Poynting flux

[Nikolaos Matthaiakakis]

Issue was resolved by removing the reference source field components instead of 
intensity from the second simulation including the geometry


From: Nikolaos Matthaiakakis<mailto:nikolao...@outlook.com>
Sent: 12 November 2020 23:27
To: meep-discuss@ab-initio.mit.edu<mailto:meep-discuss@ab-initio.mit.edu>
Cc: stevenj@gmail.com<mailto:stevenj@gmail.com>
Subject: Re: [Meep-discuss] Obtaining polarization dependent Poynting flux

I am trying to obtain Px and Py for back-scattered light from a gold 
nanorectangle (under mp.Ex source illumination) by defining some dft monitors 
as follows


  1.  set reference simulation dft monitor

## Reflexion DFT monitor
box_DFT_re_ref = sim.add_dft_fields([mp.Ex,mp.Ey,mp.Hx,mp.Hy],
frq_cen,dfrq,nfrq,
center=mp.Vector3(z=-s/2+dpml+0.05),
size=mp.Vector3(s-2*dpml,s-2*dpml),
yee_grid=False)


  1.  run simulation


sim.run(…)


  1.  obtain reference flux

# DFT reflected fields ref
flux_ref=[]
flux_x_ref=[]
flux_y_ref=[]
for n in np.arange(0,nfrq,1):
nfrq_in=int(n)
(Ex,Ey,Hx,Hy)  = [sim.get_dft_array(box_DFT_re_ref,nfrq,nfrq_in) for nfrq 
in [mp.Ex, mp.Ey, mp.Hx, mp.Hy]]
(x,y,z,w)  = sim.get_array_metadata(dft_cell=box_DFT_re_ref)
dxy = 1/resolution**2

flux_density   = np.real( Ex*np.conj(Hy) -Ey*np.conj(Hx) )# array
flux_ref=0.5*np.append(flux_ref, np.sum(flux_density*dxy)) # Total

flux_density   = np.real( Ex*np.conj(Hy) )# array
flux_x_ref=0.5*np.append(flux_x_ref, np.sum(flux_density*dxy)) # Px

flux_density   = np.real( Ey*np.conj(Hx) )# array
flux_y_ref=0.5*np.append(flux_y_ref, np.sum(flux_density*dxy)) # Py


  1.  reset simulation, include geometry, set DFT monitor

# DFT field reflection monitor
box_DFT_re= sim.add_dft_fields([mp.Ex,mp.Ey,mp.Hx,mp.Hy],
frq_cen,dfrq,nfrq,
center=mp.Vector3(z=-s/2+dpml+0.05),
size=mp.Vector3(s-2*dpml,s-2*dpml),
yee_grid=False)


  1.  run simulation
  2.  obtain flux

## Px and Py calculation
flux=[]
flux_x=[]
flux_y=[]
for n in np.arange(0,nfrq,1):
nfrq_in=int(n)
(Ex,Ey,Hx,Hy)  = [sim.get_dft_array(box_DFT_re,nfrq,nfrq_in) for nfrq in 
[mp.Ex, mp.Ey, mp.Hx, mp.Hy]]
(x,y,z,w)  = sim.get_array_metadata(dft_cell=box_DFT_re)
dxy = 1/resolution**2

flux_density   = np.real( Ex*np.conj(Hy) -Ey*np.conj(Hx) )
flux=0.5*np.append(flux,np.sum(flux_density*dxy)) # Total

flux_density   = np.real( Ex*np.conj(Hy) )
flux_x=0.5*np.append(flux_x,np.sum(flux_density*dxy)) # Px

flux_density   = np.real( Ey*np.conj(Hx) )
flux_y=0.5*np.append(flux_y,np.sum(flux_density*dxy)) # Py


  1.  plot results removing source flux and normalize to source

## Plot Px and Py
if mp.am_master():
plt.figure(dpi=150)

plt.plot(1/np.asarray(freqs),-(flux-flux_ref)/flux_ref 
,'r-',label='P_total')
plt.plot(1/np.asarray(freqs),-(flux_x-flux_x_ref)/flux_ref ,'go',label='Px')
plt.plot(1/np.asarray(freqs),(flux_y-flux_y_ref)/flux_ref ,'c*',label='Py')
plt.plot(wl,Rs,'bo-',label='Back-scatter') #results obtained from get_flux 
monitor of identical dimensions

plt.grid(True,which="both",ls="-")
plt.xlabel('wavelength, um')
plt.ylabel(Scattering')
plt.legend(loc='upper left')
plt.title('Px and Py')
   plt.tight_layout()
plt.savefig("media/PxPy.png")

Yet my results are not identical to when I use get_flux (also having removed 
the source flux) as seen in this link. What could be the origin of this 
difference?

Image link: 
https://cdn.discordapp.com/attachments/765260434419875931/776558260483391528/PxPy.png

Thank you

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[Meep-discuss] Scattering flux due to cathodoluminescence (moving charge source)

[Nikolaos Matthaiakakis]

Dear Prof. Johnson and MEEP users,

I have been playing around with the Cherenkov radiation example with the goal 
of monitoring the fields generated due to the interaction of the moving charge 
with a geometry (cathodoluminescence, transition radiation, scattered fields). 
I also aim to obtain the frequency dependent scattering flux due to the 
interaction of the moving charge and the geometry (similar to 
https://meep.readthedocs.io/en/latest/Python_Tutorials/Basics/#mie-scattering-of-a-lossless-dielectric-sphere
 but for a moving charge source and more likely for a conductive dispersive 
material).

By including a non dispersive material (see the code at the end of this 
message) the following results can be obtained:

Simulation: 
https://cdn.discordapp.com/attachments/767857295517548625/779371382819127336/simulation.png
Ey component: 
https://cdn.discordapp.com/attachments/767857295517548625/779371340486148106/cher_Ey.gif
Hz component: 
https://cdn.discordapp.com/attachments/767857295517548625/779371365673205771/cher_Hz.gif

I have encountered the following issues:


  1.  For the Ey component there seems to remain a strong source like field at 
the origin of the moving charge. I am unsure why this happens. This is also 
true for the Cherenkov radiation example without any changes.
  2.  When flux monitors are included in the simulation, the following error 
pops up “RuntimeError: meep: allocate field components (by adding sources) 
before adding dft objects”. Do the dft/flux objects etc need to be saved and 
reinitialized in every with step functions?
  3.  Less important issue but h5utils gives a colormap error "h5topng error: 
invalid colormap file" which is not resolved even when given a direct path. I 
have overcome this by saving the png files with a different method so I just 
include this here as a possible bug.

These issues do not change when the default material is set to 1 (vacuum) and 
the Cherenkov radiation effect is no longer there. Ey: 
https://cdn.discordapp.com/attachments/767857295517548625/779372550844710952/no_cher_Ey.gif

I imagine the solution to these issues is not that easy but I was wondering if 
there are any pointers as to how this could be resolved. It would be amazing to 
be able to perform cathodoluminescence simulations on MEEP (and maybe even 
calculate the EELS response through the absorbed energy in the geometry).

With dispersive materials high resolution and possibly changes to the Courant 
factor/ PML are required (for metals at least) so I haven’t had the time to 
verify if everything works yet (for now I have been getting the NaN or Inf 
fields error).

Thank you very much for your time.

Best wishes
Nikolaos

CL code:

import meep as mp
import numpy as np
import h5py
import matplotlib.pyplot as plt


sx = 60
sy = 60
cell_size = mp.Vector3(sx,sy,0)

dpml = 1
pml_layers = [mp.PML(thickness=dpml)]

v = 0.7 # velocity of point charge

#symmetries = [mp.Mirror(direction=mp.Y)]

material_set=mp.Medium(epsilon=12)

geometry = [mp.Block(mp.Vector3(0.2,0.5,mp.inf),
 center=mp.Vector3(0,0,0),
 material=material_set)]

sim = mp.Simulation(resolution=25,
cell_size=cell_size,
default_material=mp.Medium(index=1),
#symmetries=symmetries,
boundary_layers=pml_layers,
geometry=geometry
)

def move_source(sim):
sim.change_sources([mp.Source(mp.ContinuousSource(frequency=1e-10),
  component=mp.Ex,
  
center=mp.Vector3(-0.5*sx+dpml+v*sim.meep_time()))])

#box_tr = sim.add_flux(frq_cen, dfrq, nfrq, 
mp.FluxRegion(center=mp.Vector3(x=sx/2-dpml-1),size=mp.Vector3(0,sx-2*dpml)))

sim.use_output_directory("Data")
sim.run(move_source,
mp.at_every(1, mp.output_png(mp.Ey, "-Zc bluered")),
until=sx/v)




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[Meep-discuss] In plane anisotropic conductivity of Black phosphorus

[Nikolaos Matthaiakakis]

Dear all and Prof. Johnson,

I have written a code that studies the polarization dependent scattering 
properties of a plasmonic nanodisks. As a test material I used gold from the 
material library included with Meep and everything works well. For the actual 
simulation that I am interested in I need to include the dispersive in plane 
anisotropic conductivity of single layer Black phosphorus.

As explained here 
https://www.mail-archive.com/meep-discuss@ab-initio.mit.edu/msg06578.html and 
in the meep FAQ the properties of dispersive 2D materials can be fitted with 
the use of the DrudeSusceptibility and LorentzianSusceptibility while defining 
the structure thickness as 1/resolution and multiplying the conductivity by the 
resolution.

Can the same be achieved for materials that have in plane anisotropic 
conductivity? The difficulty I am having is that I am unware of how I can 
define these properties in Meep for a material like Black phosphorus that 
involves in plane anisotropy and requires a tensor to properly describe its 
conductivity.

I was wondering if there is an available example or information that I may have 
missed.

I apologize for taking your time once again and I am grateful for your help. 
Thank you for providing such an excellent simulation tool free of charge.

Best wishes
Nikolaos
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[Meep-discuss] 45 degrees and circularly polarized source

[Nikolaos Matthaiakakis]

Dear all,
I am new to MEEP and I am trying to simulate a gold plasmonic scatterer.
I am specifically interested in utilizing a 45degrees polarized source (between 
x and y polarization)  or a circularly polarized source in order to excite the 
plasmonic nanoparticle.  What would be the most efficient method to achieve 
this when using a GaussianSource spanning the entire simulation region (with 
k_point=mp.Vector3()) and PML boundaries all around. Would another type of 
source be more suitable?
This is my code for an x-polarized source

## Create source
# is_integrated=True necessary for any planewave source extending into PML
sources = [mp.Source(mp.GaussianSource(frq_cen,fwidth=dfrq,is_integrated=True),
 center=mp.Vector3(0,0,-0.5*s+dpml),
 size=mp.Vector3(s,s,0),
 component=src_cmpt)]

## Create simulation object for empty cell
sim = mp.Simulation(resolution=resolution,
cell_size=cell_size,
boundary_layers=pml_layers,
sources=sources,
k_point=mp.Vector3(),
Courant=courant,
symmetries=symmetries,
split_chunks_evenly=False
)
 Thank you very much for your time.
Best wishes
Nikolaos

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[Meep-discuss] dispersive conductivity input for 2D materials

[Nikolaos Matthaiakakis]

Dear all,
I have seen that it is possible to input a dispersive complex permittivity for 
a material by using for example DrudeSusceptibility or 
LorentzianSusceptibility. Is it possible to do the same for conductivity models 
such as the ones that are commonly used for 2D materials? I am also interested 
in implementing this for anisotropic 2D materials.
Using an effective permittivity to simulate graphene plasmons seems to require 
extremely high discretization given that non-uniform grid is not available. The 
fact that plasmons in graphene are in the IR range make this even more 
difficult. So I was wondering if this can be avoided.
Thank you for your time.
Best wishes
Nikolaos


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[Meep-discuss] Removing source flux from add_near2far box

[Nikolaos Matthaiakakis]

Dear all,

I was wondering if the source related flux can be removed from a nearfield box 
defined as

nearfield_box = sim.add_near2far(frq_cen, dfrq, nfrq,
 
mp.Near2FarRegion(center=mp.Vector3(x=-lxm/2),size=mp.Vector3(0,2*lym/2,2*lzm/2),
 weight=+1),
 
mp.Near2FarRegion(center=mp.Vector3(x=+lxm/2),size=mp.Vector3(0,2*lym/2,2*lzm/2),
 weight=-1),
 
mp.Near2FarRegion(center=mp.Vector3(y=-lym/2),size=mp.Vector3(2*lxm/2,0,2*lzm/2),
 weight=+1),
 
mp.Near2FarRegion(center=mp.Vector3(y=+lym/2),size=mp.Vector3(2*lxm/2,0,2*lzm/2),
 weight=-1))

by using sim.load_minus_flux_data(,) in a similar way as used for flux monitors.

Thank you for your time

Best wishes
Nikolaos

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[Meep-discuss] Dispersive conductivity for 2D materials

[Nikolaos Matthaiakakis]

Dear all I apologize for reposting this but I mistakenly sent it as a reply to 
another topic before,

I have seen that it is possible to input a dispersive complex permittivity for 
a material by using for example DrudeSusceptibility or 
LorentzianSusceptibility. Is it possible to do the same for conductivity models 
such as the ones that are commonly used for 2D materials? I am also interested 
in implementing this for anisotropic 2D materials.
Using an effective permittivity to simulate graphene plasmons seems to require 
extremely high discretization given that non-uniform grid is not available. The 
fact that plasmons in graphene are in the IR range make this even more 
difficult. So I was wondering if this can be avoided.
Thank you for your time.

Best wishes
Nikolaos

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