Return-Path: Received: from [149.220.60.110] (account huebl@hzdr.de [149.220.60.110] verified) by hzdr.de (CommuniGate Pro SMTP 6.1.12) with ESMTPSA id 15526854 for picongpu-users@hzdr.de; Mon, 23 Jan 2017 15:45:50 +0100 Subject: Re: Gas profile To: picongpu-users@hzdr.de References: From: Axel Huebl Organization: HZDR Message-ID: Date: Mon, 23 Jan 2017 15:45:50 +0100 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit 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>> PIC_Electrons> >>> 89- #if (ENABLE_IONS == 1) >>> 90: ,DeriveSpecies >>> 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>> 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 >>>> 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 >>>>> >>>>> ############################################################# >>>>> This message is sent to you because you are subscribed to >>>>> the mailing list . >>>>> To unsubscribe, E-mail to: >>>>> To switch to the DIGEST mode, E-mail to >>>>> To switch to the INDEX mode, E-mail to >>>>> Send administrative queries to >>>>> >>>>> >>>>> >>>>> ############################################################# >>>>> This message is sent to you because you are subscribed to >>>>> the mailing list . >>>>> To unsubscribe, E-mail to: >>>>> To switch to the DIGEST mode, E-mail to >>>>> To switch to the INDEX mode, E-mail to >>>>> Send administrative queries to >>>>> >>>> >>>> >>>> >>>> ############################################################# >>>> This message is sent to you because you are subscribed to >>>> the mailing list . >>>> To unsubscribe, E-mail to: >>>> To switch to the DIGEST mode, E-mail to >>>> To switch to the INDEX mode, E-mail to >>>> Send administrative queries to >>>> >>> ​ >>> >>> -- >>> 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 >>> >>> >>> >>> ############################################################# >>> This message is sent to you because you are subscribed to >>> the mailing list . >>> To unsubscribe, E-mail to: >>> To switch to the DIGEST mode, E-mail to >>> To switch to the INDEX mode, E-mail to >>> Send administrative queries to >>> >> >> -- >> >> 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 >> the mailing list . >> To unsubscribe, E-mail to: >> To switch to the DIGEST mode, E-mail to >> To switch to the INDEX mode, E-mail to >> Send administrative queries to >> >> >> >> ############################################################# >> This message is sent to you because you are subscribed to >> the mailing list . >> To unsubscribe, E-mail to: >> To switch to the DIGEST mode, E-mail to >> To switch to the INDEX mode, E-mail to >> Send administrative queries to >> > > -- > > 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 > the mailing list . > To unsubscribe, E-mail to: > To switch to the DIGEST mode, E-mail to > To switch to the INDEX mode, E-mail to > Send administrative queries to > > > > ############################################################# > This message is sent to you because you are subscribed to > the mailing list . > To unsubscribe, E-mail to: > To switch to the DIGEST mode, E-mail to > To switch to the INDEX mode, E-mail to > Send administrative queries to > -- 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