|
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Right, but are you using the right cell_size in
sim_x, sim_ne = np.loadtxt('check_data', unpack=True)
?
this "sim_x" should be an array of spatial "dy" steps.
Maybe you can print it and compare to your dx, dy, dz in your
gridConfig.param
Axel
On 23.01.2017 09:53, Khikhlukha Danila wrote:
> 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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>>>>>
>>>>
>>>>
>>>>
>>>> #############################################################
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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
>>
>> #############################################################
>> This message is sent to you because you are subscribed to
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>> To unsubscribe, E-mail to: <picongpu-users-off@hzdr.de>
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>>
>>
>>
>> #############################################################
>> This message is sent to you because you are subscribed to
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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
>
> #############################################################
> This message is sent to you because you are subscribed to
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> To unsubscribe, E-mail to: <picongpu-users-off@hzdr.de>
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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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