[FLASH-USERS] Two questions from a newbie, thanks!

Majid Masnavi majidmasnavi at creol.ucf.edu
Fri Feb 6 13:29:32 EST 2015 

Thanks Chang

Actually I am looking for 2d simulation. So, it's great. From where should I start!?
Best
M

Sent from my iPhone

On Feb 6, 2015, at 13:23, pchang <pchang at lle.rochester.edu<mailto:pchang at lle.rochester.edu>> wrote:

Hi,
I believe so. But I am working on laser and cylindrical target. So I specified a cylindrical target in cylindrical coordinate. There shouldn't be a problem to specify a spherical target. The problem is, the ray tracing is only good for Cartesian (2D and maybe 3D) and 2D cylindrical (r-z) coordinate if I remember correctly. Therefore, you may not be able to do the full 3D simulation. I may try using cylindrical coordinate so that you can have at least 2D spherical simulation with azimuthal symmetric.
I know a guy who is also doing similar problem. He may have experience on it.

Po-Yu



--
Po-Yu Chang

Postdoctoral Associate
Department of Mechanical Engineering,
Fusion Science Center for Extreme States of Matter,
Laboratory for Laser Energetics
University of Rochester
250 East River Road
Rochester, New York 14623
Phone: (585) 273-5179
FAX: (585) 275-5960
pchang at lle.rochester.edu<mailto:pchang at lle.rochester.edu>


On 2/6/2015 12:53 PM, Majid Masnavi wrote:
Hello,

I would like to use the code to solve interaction of laser and spherical target. Is there any way to define spherical target?

Cheers
M

Sent from my iPhone

On Feb 6, 2015, at 11:38, Di Sheng <disheng222 at gmail.com<mailto:disheng222 at gmail.com>> wrote:

Hi Po-Yu,
Many thanks!
It's very helpful.

Best
Sheng

2015-02-06 10:27 GMT-06:00 pchang <pchang at lle.rochester.edu<mailto:pchang at lle.rochester.edu>>:
Hi Sheng,
For your first question, since I never got the error "Assertion `dataset >= 0' failed", I can't say too much about it.

About the group frequency, you may try the example "LaserSlab" (section 25.7.5 in the flash user's guide) or look at the flash.par in that example. Following are the section in my flash.par . The group bounds (rt_mgdBounds) needs to match what is given in the table. You can find the format of the table in section 21.4.3 in the flash user's guide.

Cheers,

Po-Yu

########################################
#                                      #
#     RADIATION/OPACITY PARAMETERS     #
#                                      #
########################################
rt_useMGD       = .true.
rt_mgdNumGroups = 12
rt_mgdBounds_1  = 1.0e-02
rt_mgdBounds_2  = 3.831e-02
rt_mgdBounds_3  = 1.468e-01
rt_mgdBounds_4  = 5.623e-01
rt_mgdBounds_5  = 2.154e+00
rt_mgdBounds_6  = 8.254e+00
rt_mgdBounds_7  = 3.162e+01
rt_mgdBounds_8  = 1.212e+02
rt_mgdBounds_9  = 4.642e+02
rt_mgdBounds_10  = 1.778e+03
rt_mgdBounds_11  = 6.813e+03
rt_mgdBounds_12  = 2.610e+04
rt_mgdBounds_13  = 1.0e+05
rt_mgdFlMode    = "fl_harmonic"
rt_mgdFlCoef    = 1.0

rt_mgdXlBoundaryType = "reflecting"
rt_mgdXrBoundaryType = "vacuum"
rt_mgdYlBoundaryType = "vacuum"
rt_mgdYrBoundaryType = "vacuum"
rt_mgdZlBoundaryType = "reflecting"
rt_mgdZrBoundaryType = "reflecting"

useOpacity     = .true.

### SET Gas (DD) OPACITY OPTIONS ###
op_gasAbsorb   = "op_tabpa"
op_gasEmiss    = "op_tabpe"
op_gasTrans    = "op_tabro"
op_gasFileType = "ionmix4"
op_gasFileName = "DD_0p01Ar_T0p01-1e5_Rho1e16-1e26_vu12_0p01-1e5_Zmin0p01.cn4"

### SET CHAMBER (DD) OPACITY OPTIONS ###
op_chamAbsorb   = "op_tabpa"
op_chamEmiss    = "op_tabpe"
op_chamTrans    = "op_tabro"
op_chamFileType = "ionmix4"
op_chamFileName = "DD_T0p01-1e5_Rho1e16-1e26_vu12_0p01-1e5.cn4"

### SET TARGET (CH) OPACITY OPTIONS ###
op_targAbsorb   = "op_tabpa"
op_targEmiss    = "op_tabpe"
op_targTrans    = "op_tabro"
op_targFileType = "ionmix4"
op_targFileName = "CH_T0p01-1e5_Rho1e16-1e26_vu12_0p01-1e5.cn4"




--
Po-Yu Chang

Postdoctoral Associate
Department of Mechanical Engineering,
Fusion Science Center for Extreme States of Matter,
Laboratory for Laser Energetics
University of Rochester
250 East River Road
Rochester, New York 14623
Phone: (585) 273-5179
FAX: (585) 275-5960
pchang at lle.rochester.edu<mailto:pchang at lle.rochester.edu>


On 2/6/2015 11:04 AM, Di Sheng wrote:
Hi Po-Yu,
Thanks a lot for your help!
As for the first question, after adding "+hdf5typeio" (i.e., ./setup -auto Cellular +hdf5typeio parallelIO=False), I still got the same errors (Assertion `dataset >= 0' failed). In fact, when I use "./setup -auto Cellular +ug", the errors will disappear and the execution goes well. There must be some reason for it. I mean, should I adopt some "-with-unit=...." for Cellular or some more settings for setup ?

As for the second question, I didn't set the group in the flash.par. Could you tell me how to specify the group frequency?
Did I miss any other parameters?

ps. My objective is just to run this application normally, so as to evaluate my own MPI middleware. That's it. I'll be happy as long as it can be run, no matter what kind of settings/parameters are used.

Many thanks again!

Best
Sheng
http://www.mcs.anl.gov/~shdi<http://www.mcs.anl.gov/%7Eshdi>

2015-02-06 9:45 GMT-06:00 pchang <pchang at lle.rochester.edu<mailto:pchang at lle.rochester.edu>>:
Hi Sheng,
For your first question, you may try adding "+hdf5typeio" in your setup.
For your second question, did you specify the radiation/opacity group frequency in the flash.par and xe-100grp-lte.imx? Are the specified the same?

Po-Yu


--
Po-Yu Chang

Postdoctoral Associate
Department of Mechanical Engineering,
Fusion Science Center for Extreme States of Matter,
Laboratory for Laser Energetics
University of Rochester
250 East River Road
Rochester, New York 14623
Phone: (585) 273-5179
FAX: (585) 275-5960
pchang at lle.rochester.edu<mailto:pchang at lle.rochester.edu>




On 2/5/2015 6:08 PM, Di Sheng wrote:
Hi everyone,
I am a newbie of FLASH. I ran into the following problems which already bothered me for a long while. Could any one answer any one of them? many thanks!

1. How to deal with "Assertion `dataset >= 0' failed"?

"./setup -auto Cellular" success, and "make" is also successful. However, when I run "mpirun -np 1 flash4", it shows the following errors:

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
  #000: H5Ddeprec.c line 178 in H5Dcreate1(): not a location ID
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
    major: Invalid arguments to routine
    minor: Bad value
flash4: io_h5create_dataset.c:57: io_h5create_dataset: Assertion `dataset >= 0' failed.

Program received signal SIGABRT: Process abort signal.
 .......

The same situation goes to the "Jeans" application (SimulationMain/Jeans).

2. As for MGDInfinite, I setup it as follows:
./setup -auto MGDInfinite -1d +hdf5typeio +mtmmmt +mgd +uhd3t -with-unit=physics/materialProperties/Opacity/OpacityMain/Constant species=xe mgd_meshgroups=4 parallelIO=FALSE

Then, I add the following lines to the flash.par:
sim_xeMassFrac = 1

eos_xeEosType = "eos_tab"
eos_xeSubType = "ionmix4"
eos_xeTableFile = "xe-100grp-lte.imx"
However, when I run "mpirun -np 1 flash4", I got errors as follows:

 [eos_tabBrowseIonmix4Tables] IONMIX4 file found: xe-100grp-lte.imx
 in eos_inittabulated, tableName = xe-100grp-lte.imx
 in eos_inittabulated, groupName = -none-
At line 158 of file eos_tabReadIonmix4Tables.F90 (unit = 7, file = 'xe-100grp-lte.imx')
Fortran runtime error: Bad value during integer read

------------
Best
Sheng








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