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Hi Axel,
I hope I didn't make that mistake. Using openPMD viewer for each frame I took a slice in 'x' direction and then capture the charge density at the maximum y position.
Please find all files considered attached to this email. Let me know if you need more information...
Best regards,
Danila.
________________________________________
From: picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of Axel Huebl [a.huebl@hzdr.de]
Sent: Sunday, January 22, 2017 11:04 PM
To: picongpu-users@hzdr.de
Subject: Re: [PIConGPU-Users] Gas profile
Hi Danila,
are you sure that in your script your
"sim_x"
is actually "dy" of our cells?
Looks to me that you mismatched that your profile and laser propagation
is "y".
Cheers,
Axel
On 18.01.2017 15:36, Khikhlukha Danila wrote:
> Hi Axel,
> indeed, you are right, the longitudinal gas profile is still super gaussian, however the parameters of that distribution is somehow different from my input.
> I attach the updated density plot and my gasConfig.param file for your convenient.
>
> Regards,
> Danila.
> ________________________________________
> From: picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of Khikhlukha Danila
> Sent: Wednesday, January 18, 2017 11:48 AM
> To: picongpu-users@hzdr.de
> Subject: Re: [PIConGPU-Users] [PIConGPU-Users] [PIConGPU-Users] Gas profile
>
> Hi Axel,
> please ind the plotting script attached to this email.
>
> Cheers,
> D.
> ________________________________________
> From: picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of Axel Huebl [a.huebl@hzdr.de]
> Sent: Wednesday, January 18, 2017 11:40 AM
> To: picongpu-users@hzdr.de
> Subject: Re: [PIConGPU-Users] [PIConGPU-Users] Gas profile
>
> Hi Danila,
>
>
> actually it looks to me like your analytical formula is not the same as
> your input.
>
> In your initial mail, you said you kept the gasPower of
> `GaussianParameter` as it was, which is a slight super-Gauss profile as
> your red dots show.
>
> Your power in your analytical formula looks way steeper to me.
>
> Can you show us how you plot the blue line?
>
>
> Cheers,
> Axel
>
> On 17.01.2017 09:18, Khikhlukha Danila wrote:
>> Dear all,
>> as I didn't stop my simulation I have a further update on the strange
>> gas profile. On the attached picture it is seen that the gas density is
>> finally changing, but following some different formula...
>>
>> Regards,
>> Danila.
>> ------------------------------------------------------------------------
>> *From:* picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of
>> Khikhlukha Danila
>> *Sent:* Monday, January 16, 2017 1:26 PM
>> *To:* picongpu-users@hzdr.de
>> *Subject:* Re: [PIConGPU-Users] [PIConGPU-Users] [PIConGPU-Users] Gas
>> profile
>>
>> Sure, here it is:
>> danila@GPU: simOutput$ grep -ni -A 3 -B 3 PIC_ELECTRONS
>> ../picongpu/include/simulation_defines/param/speciesInitialization.param
>> <...>
>> --
>> 85-typedef mpl::vector<
>> 86-#if (PARAM_IONIZATION == 0)
>> 87-
>> 88: CreateGas<gasProfiles::Gaussian, startPosition::Random,
>> PIC_Electrons>
>> 89- #if (ENABLE_IONS == 1)
>> 90: ,DeriveSpecies<PIC_Electrons,PIC_Ions>
>> 91- #endif
>> 92-
>> 93-#else
>>
>> Best,
>> Danila.
>> ------------------------------------------------------------------------
>> *From:* picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of
>> Richard Pausch [r.pausch@hzdr.de]
>> *Sent:* Monday, January 16, 2017 1:08 PM
>> *To:* picongpu-users@hzdr.de
>> *Subject:* Re: [PIConGPU-Users] [PIConGPU-Users] Gas profile
>>
>> Hi Danila,
>>
>> just to make sure you are using the right init pipeline (because this
>> looks like a homogeneous gas/density profile): Could you send us the
>> |InitPipline| definition in your |speciesInitialization.param| file?
>>
>> It should look similar to:
>>
>> |typedef mpl::vector< CreateGas<gasProfiles::Gaussian,
>> startPosition::Random, PIC_Electrons> > InitPipeline; |
>>
>> Best regards,
>> Richard
>>
>> Am 16.01.17 um 12:54 schrieb Khikhlukha Danila:
>>
>>> Hi Richard,
>>>
>>> 1. Thanks for a hint. The average for the last column gives a values
>>> closer to the analytical one -- see the plot attached. However, it
>>> looks like the problem is still there...
>>>
>>> 2. I have checked my version of PoG (0.2.1), and it looks like the fix
>>> is there...
>>> danila@GPU: picongpu$ git log --grep 1625
>>> commit aa4f203104bf04b0aceb6e00d92312f2706bc514
>>> Author: Axel Huebl <axel.huebl@plasma.ninja>
>>> Date: Thu Nov 3 18:36:38 2016 +0100
>>>
>>> Fix #1625: HDF5 openPMD positionOffset
>>>
>>> Fix the offset in particlePatches and the positionOffset
>>> to use the totalCellIdx of a particle instead of the globalCellIdx.
>>>
>>> I also checked my version of openPMD viewer. It is quite old, however
>>> I didn't find any significant changes in the core of if recently...
>>>
>>> Regards,
>>> Danila.
>>> ------------------------------------------------------------------------
>>> *From:* picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of
>>> Richard Pausch [r.pausch@hzdr.de]
>>> *Sent:* Monday, January 16, 2017 11:04 AM
>>> *To:* picongpu-users@hzdr.de
>>> *Subject:* Re: [PIConGPU-Users] [PIConGPU-Users] Gas profile
>>>
>>> Hi Danila,
>>>
>>> the gas setup you are using looks correct to me. You should get the
>>> gas profile you are expecting.
>>>
>>> 1): However, your python code only uses one density value from the zy
>>> slice. Thus, due to the random particle initialization, or an
>>> ionization method, or the used particle shape, ... the resulting
>>> density value varies statically as you can see in your
>>> `sim_gas_profile.png`. If you use `print '%.4g\t%.4g' % (ex[1],
>>> np.mean(ne[:,-1]))` instead, you should get an average value of the
>>> `-1` slice which should more closely resemble your analytical gas
>>> profile.
>>>
>>> 2): A am not an expert in openPMD, but your code looks correct. Your
>>> position ex[1] is for your setup your maximum y position as intended.
>>> Are the following bug fixes already included in your PIConGPU version?
>>> (https://github.com/ComputationalRadiationPhysics/picongpu/pull/1626,
>>> https://github.com/ComputationalRadiationPhysics/picongpu/pull/1627)
>>>
>>> Best regard,
>>> Richard
>>>
>>> Am 16.01.2017 um 10:00 schrieb Khikhlukha Danila:
>>>> Hi Axel,
>>>> thanks for you replay. If this is correct, then I observe some strange behavior which I can't explain. Most likely I did some mistake in the settings, however at the moment I can't find it...Maybe you can advice me, what settings should I check...
>>>>
>>>> 1. So I'm trying to calculate a LWFA in a 4mm plasma channel. To specify it I modified gasConfig.param as follows:
>>>> (PMACC_C_VALUE(float_64, gasCenterLeft_SI, 1.0e-4))
>>>> (PMACC_C_VALUE(float_64, gasCenterRight_SI, 3.9e-3))
>>>> (PMACC_C_VALUE(float_64, gasSigmaLeft_SI, 0.5e-4))
>>>> (PMACC_C_VALUE(float_64, gasSigmaRight_SI, 0.5e-4))
>>>> I left gasFactor and gasPower unchanged. Please find a plot to verify my settings of the initial gas distribution attached.
>>>>
>>>> 2. Fro a given time step
>>>> danila@GPU: run_0021$ grep -ni DELTA_T_SI picongpu/include/simulation_defines/param/gridConfig.param
>>>> 32: BOOST_CONSTEXPR_OR_CONST float_64 DELTA_T_SI = 1.7639e-16;
>>>> I expect my simulation to finish after 4e-3/2.99792458e8/1.7639e-16 ~ 76000 steps. In fact I specified 100k steps.
>>>>
>>>> 3. To verify the gas density which was used during the simulation I did the following. For every simulation dump I took YZ cross section of my computational domain. I used openPMD viewer do it. My idea was to get a density of undisturbed plasma just before the laser pulse. So I took a middle value in the last column of the electron density matrix. I also record a position of the right edge of a moving box. I hope attached python script makes it a bit more clear :)
>>>>
>>>> 4. I plot collected data against the expected gas profile and found them to be very different...
>>>>
>>>> Could you please advise me if there is any setting I need to double check? Please let me know if you need more information about my run...
>>>>
>>>> Best regards,
>>>> Danila.
>>>>
>>>> ________________________________________
>>>> From: picongpu-users@hzdr.de [picongpu-users@hzdr.de] on behalf of Axel Huebl [a.huebl@hzdr.de]
>>>> Sent: Friday, January 13, 2017 4:19 PM
>>>> To: picongpu-users@hzdr.de
>>>> Subject: Re: [PIConGPU-Users] [PIConGPU-Users] Gas profile
>>>>
>>>> Hi,
>>>>
>>>> yes that is exactly the profile you are looking for and the right way to
>>>> init it. It only varies along y (longitudinally) as you described.
>>>>
>>>> Otherwise: just use FreeFormula.
>>>>
>>>> Cheers,
>>>> Axel
>>>>
>>>> On 13.01.2017 16:10, Khikhlukha Danila wrote:
>>>>> Dear all,
>>>>> this question is a bit basic, however I would like to double check if my
>>>>> understanding is correct.
>>>>>
>>>>> Using PoG 0.2.1 I want to simulate LWFA in a plasma channel of let say 3
>>>>> mm long. I want my gas profile to be uniform in transverse direction. In
>>>>> the longitudinal direction I want my gas profile to have a plateau and
>>>>> super-gaussain up/down ramps -- exactly how it is specified in
>>>>> gasConfig.param file. Am I correct that to achieve it the only thing I
>>>>> need to do is to fix numerical values for a length of ramps and plateau
>>>>> to fit my overall plasma length?
>>>>> Please note that in the speciesIntizialation.param file this profile is
>>>>> already pointed a source of particles.
>>>>>
>>>>> Thanks a lot for you support,
>>>>> Danila.
>>>> --
>>>>
>>>> Axel Huebl
>>>> Phone +49 351 260 3582
>>>> https://www.hzdr.de/crp
>>>> Computational Radiation Physics
>>>> Laser Particle Acceleration Division
>>>> Helmholtz-Zentrum Dresden - Rossendorf e.V.
>>>>
>>>> Bautzner Landstrasse 400, 01328 Dresden
>>>> POB 510119, D-01314 Dresden
>>>> Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
>>>> Prof. Dr.Dr.h.c. P. Joehnk
>>>> VR 1693 beim Amtsgericht Dresden
>>>>
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>>>
>>>
>>>
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>>
>>
>> --
>> Laser Particle Acceleration
>> Helmholtz-Zentrum Dresden-Rossendorf e.V.
>>
>> Bautzner Landstraße 400, 01328 Dresden
>> Germany
>> Phone: +49 351 260 3547
>> Email: r.pausch@hzdr.de
>> http://www.hzdr.de
>>
>> Vorstand: Prof. Dr. Dr. h. c. Roland Sauerbrey, Prof. Dr. Dr. h. c. Peter Joehnk
>> Vereinsregister: VR 1693 beim Amtsgericht Dresden
>>
>>
>>
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>
> --
>
> Axel Huebl
> Phone +49 351 260 3582
> https://www.hzdr.de/crp
> Computational Radiation Physics
> Laser Particle Acceleration Division
> Helmholtz-Zentrum Dresden - Rossendorf e.V.
>
> Bautzner Landstrasse 400, 01328 Dresden
> POB 510119, D-01314 Dresden
> Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
> Prof. Dr.Dr.h.c. P. Joehnk
> VR 1693 beim Amtsgericht Dresden
>
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>
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--
Axel Huebl
Phone +49 351 260 3582
https://www.hzdr.de/crp
Computational Radiation Physics
Laser Particle Acceleration Division
Helmholtz-Zentrum Dresden - Rossendorf e.V.
Bautzner Landstrasse 400, 01328 Dresden
POB 510119, D-01314 Dresden
Vorstand: Prof. Dr.Dr.h.c. R. Sauerbrey
Prof. Dr.Dr.h.c. P. Joehnk
VR 1693 beim Amtsgericht Dresden
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