Return-Path: Received: from [178.24.5.94] (account huebl@hzdr.de HELO [192.168.178.22]) by hzdr.de (CommuniGate Pro SMTP 6.1.12) with ESMTPSA id 15519524 for picongpu-users@hzdr.de; Sun, 22 Jan 2017 23:04:50 +0100 Subject: Re: Gas profile To: picongpu-users@hzdr.de References: From: Axel Huebl Organization: HZDR Message-ID: <7ce941d5-3178-cd8b-6dec-c1aa601cc4f4@hzdr.de> Date: Sun, 22 Jan 2017 23:04:49 +0100 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit 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