[FLASH-USERS] Helmhotlz EOS question

[Robert Fisher]

Hi Malia :

  Ok, good -- without nuclear burning, there are a few major checks to
focus on. I'd be certain to read in your zeroeth checkpoint file and
inspect the composition very closely in a tool like yt to ensure everything
is initialized properly. Once you have confirmed the t = 0 data is valid,
 I would be concerned about the hydrodynamic stability, which you can test
by lowering the CFL number.

  Best wishes,

  Bob

On Thu, May 4, 2017 at 2:24 PM, Malia Jenks <rikku.hotaru at gmail.com> wrote:

> I am not using nuclear burning for the simulation. I do call
> physics/sourceTerms/Burn/BurnMain/nuclearBurn and Simulation/SimulationComposition
> in my Config file to get the species information from the burn unit but I
> have useBurn set to false. I use the same mass fractions for all points on
> my initial grid, so all the abar and zbar values should be the same. I am
> not sure that the error isn't appearing in the t=0 data. I know it is after
> successfully reading in my data file and then I get the following outputs
> before the error message:
>
>   iteration, no. not moved =            0           9
>   iteration, no. not moved =            1           2
>   iteration, no. not moved =            2           0
>  refined: total leaf blocks =           64
>  refined: total blocks =           80
>  [amr_morton_process]: Initializing surr_blks using standard orrery
> implementati
>  on
>
> Thanks
>
> Malia
>
> On Thu, May 4, 2017 at 5:04 AM, Robert Fisher <rfisher1 at umassd.edu> wrote:
>
>> Hi Malia :
>>
>>   When you say the initial EOS data, I presume you mean that you've
>> verified the t = 0 data to be good. Helmholtz is fairly robust on good
>> data, so I suspect if you inspected the data passed to Helmholtz during
>> this call, you will find it to be already corrupted.
>>
>>   To add to Dean's comment, in my experience as well, when the code dies
>> in Helmholtz, it is usually the symptom and not the underlying disease. The
>> 'bad' data which manifests itself in this way is usually symptomatic of a
>> more fundamental problem elsewhere in the code. For instance, you may be
>> encountering a numerical instability in the hydrodynamics, or the nuclear
>> burning, but because these modules do not trap NaNs or Infs, they will
>> happily propagate to Helmholtz, where an exception is thrown.   You will
>> need to root out the underlying cause, because the NaNs and Infs will
>> progressively corrupt the simulation.
>>
>>   Are you using nuclear burning in this simulation?
>>
>>   Best wishes,
>>
>>   Bob
>>
>> On Wed, May 3, 2017 at 5:02 PM, Jenks, Malia T. <mjenks at ou.edu> wrote:
>>
>>> I am getting the following error from the helmholtz eos about negative
>>> pressure:
>>>
>>>  [eos_helm] Negative total pressure.
>>>    values: dens,temp:   2.321442471007820E-004
>>> 1549.01220000000
>>>
>>>    values: abar,zbar:                 Infinity
>>> NaN
>>>
>>>    coulomb coupling parameter Gamma:
>>> NaN
>>>
>>>   Prad   1.45198E-02 Pion  0.00000E+00 Pele           NaN Pcoul
>>> 0.00000E+00
>>>
>>>   Ptot            NaN df_d    8.31451E+21
>>>
>>>
>>>
>>> I know that the initial mass fraction supplied to the eos is correct.
>>> The initial call of the eos sets abar and zbar correctly. I am not sure
>>> what is causing them to error. I also don't know why I am getting a NaN for
>>> the electron Pressure. Could anyone help point me to what is going wrong
>>> and how I can solve it?
>>>
>>> Thanks,
>>>
>>> Malia Jenks
>>>
>>>
>>
>>
>> --
>> Dr. Robert Fisher
>> Associate Professor / Graduate Program Director
>> University of Massachusetts/Dartmouth
>> Department of Physics
>> 285 Old Westport Road
>> North Dartmouth, Massachusetts 02747
>> robert.fisher at umassd.edu
>> http://www.novastella.org
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.novastella.org&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=nUT1oi3cRbKdsMTgT8_PUA&m=IsU8-Q_7pskVm8mOGqAylHzx3sb3Wi_WleaKUvuYnhg&s=n3YrwE4TWfK7mKn_s3nlTXXvpfQUJIOx-9P9XNvgwN0&e=>
>>
>
>


-- 
Dr. Robert Fisher
Associate Professor / Graduate Program Director
University of Massachusetts/Dartmouth
Department of Physics
285 Old Westport Road
North Dartmouth, Massachusetts 02747
robert.fisher at umassd.edu
http://www.novastella.org
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