[FLASH-USERS] Proton Imaging on existing checkpoint files

[Ryan Farber]

Hi Wang,

Good to hear everything is working! Best of luck with your research.

Best,
--------
Ryan


On Sun, Jul 12, 2020 at 11:47 PM Wang <astrowjz at mail.bnu.edu.cn> wrote:

> Hi Ryan,
>
> Thanks for your help!
>
> I checked again, maybe some commands conflict with the file I generated, I
> use other commands to put the detector, and it works.
>
> Thank you very much!
>
> Best,
> Wang
>
>
> On Jul 13, 2020, at 02:49, Ryan Farber <rjfarber at umich.edu> wrote:
>
> Hi Wang,
>
> I don't have experience using Laserslab simulations, so I don't quite
> understand the workflow.
>
> I recommended including a logfile for the case restart = .false. to
> confirm your initial run was successful. That may help others chime in
> for you to get the help you need.
>
> Are you saying that the checkpoint file is corrupted? Or is the "empty
> image" from looking at modu3d_forced_hdf5_plt_cnt_0000?
>
> If you're concerned the plt_cnt file is empty, note this warning message:
>  WARNING you have called IO_writePlotfile but no plot_vars are defined.
>  put the vars you want in the plotfile in your flash.par (plot_var_1 =
> "dens")
>
> You also have some runs end with:
>  [ 07-12-2020  16:42:22.879 ] [DRIVER_ABORT]: Driver_abort() called by PE
>         0
>  [ 07-12-2020  16:42:22.879 ] abort_message: pi_createProtons3DRec:
> proton does not hit domain boundary!
>
> There were 19 runs in the logfile that you sent. What are the differences
> between the runs?
>
> Best,
> --------
> Ryan
>
>
> On Sun, Jul 12, 2020 at 2:05 PM Wang <astrowjz at mail.bnu.edu.cn> wrote:
>
>> Hi Ryan,
>>
>> Thanks for your advice!
>>
>> I run with restart = .false. before, it will produce a new checkpoint
>> file, but I want to use the checkpoint file that I have obtained from
>> Laserslab simulation, so that I can get magnetic information from proton
>> image.
>>
>> If I run with restart = .false., I can get an image of uniform proton
>> distribution, otherwise, if I run with restart = .true. to load data, I can
>> only get an empty image.
>>
>> Do you mean I should run first time with restart = .false. to rewrite
>> the checkpoint file and run second time with restart = .true. to obtain
>> proton image?
>>
>> Best,
>> Wang
>>
>> On Jul 13, 2020, at 00:30, Ryan Farber <rjfarber at umich.edu> wrote:
>>
>> Hi Wang,
>>
>> It looks like you accidentally left restart = .true. in flash.par. If
>> that was intentional, it would be helpful to see the logfile of the run
>> with restart = .false. that produces the checkpoint file you're trying to
>> restart from.
>>
>> Best,
>> --------
>> Ryan
>>
>>
>> On Sun, Jul 12, 2020 at 6:22 AM Wang <astrowjz at mail.bnu.edu.cn> wrote:
>>
>>> Hi all,
>>>
>>> Recently I am using FLASH to simulate proton images. I have already run
>>> a simulation and generated a 3D check point file. And I tended to use
>>> proton imaging unit and let a proton beam pass through the simulation
>>> region of the check point files. If everything’s ok, I can obtain a txt
>>> file which records proton’s position.
>>>
>>> But now, I can only obtain an empty file, I don’t know how to fix it.
>>> Thank you for your help, and any suggestions would be greatly
>>> appreciated.
>>>
>>> This is the setup of protonimaging:
>>> ./setup ProtonImaging -auto -3d -geometry=cartesian -parfile=flash.par
>>> -nxb=32 -nyb=32 -nzb=32 +protonImaging --without-unit=physics/Hydro
>>> --without-unit=physics/Eos -objdir=astrowjz/protonimaging pi_maxBeams=1
>>> pi_maxDetectors=1 threadProtonTrace=True
>>>
>>>
>>> Best,
>>> Wang
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
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