From gforjan at gmu.edu  Fri Jan  2 04:22:11 2009
From: gforjan at gmu.edu (Gary F Forjan)
Date: Fri, 02 Jan 2009 05:22:11 -0500
Subject: [FLASH-USERS] XFlash Velocity Options with Windows Vista
Message-ID: <f61dd8cb66282.495da483@gmu.edu>

Hello All

I have been having a problem trying to use the velocity options feature in xflash under MS Windows Vista.  When I try to plot the velocity vectors, the entire plot is obscured with black lines.  This happens no matter how I set the xskip and yskip parameters or the size of the vectors.  I tried plotting the velocity vectors using the same settings on my Windows XP computer and it worked fine so the problem seems to be with Vista.  Would anyone know how to get this option to work under Vista?

Thank you for any assistance,

Gary Forjan
Computational Sciences Department
College of Science
George Mason University 


From gforjan at gmu.edu  Fri Jan  2 08:32:13 2009
From: gforjan at gmu.edu (Gary F Forjan)
Date: Fri, 02 Jan 2009 09:32:13 -0500
Subject: [FLASH-USERS] Fwd:  XFlash Velocity Options with Windows Vista
Message-ID: <f710a42966f63.495ddf1d@gmu.edu>

Hello all again,

I should have perhaps mentioned I am using FLASH 2.5 and the fidlr3 version of the FLASH IDL routines.  Thanks,

Gary Forjan
Computational Sciences Department
College of Science
George Mason University
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From nhearn at uchicago.edu  Sat Jan  3 00:30:52 2009
From: nhearn at uchicago.edu (Nathan Hearn)
Date: Fri, 2 Jan 2009 23:30:52 -0700
Subject: [FLASH-USERS] QuickFlash Analysis Library for Flash 2.5 and 3
Message-ID: <2467fdc0901022230i76fb92f2v1f8d45c671d96a36@mail.gmail.com>

Hello everyone,

    I want to announce the initial public release of the QuickFlash
analysis library for Flash 2.5 and 3.0 data files.  (Pre-release
versions of this library were distributed under the PreFlash name.)

    QuickFlash is an object-oriented, C++-based library for
high-performance access to and analysis of datasets in Flash plot and
checkpoint files.  (For Flash 3, particle data is also accessible.)
This library is particularly well-suited for memory-limited
environments, making use of on-demand loading of block data with
transparent read-ahead buffering and caching.  QuickFlash uses a
representation of the Flash AMR tree to allow fast identification of
blocks and cells from spatial coordinates, and provides iterators for
efficient traversal of the tree.

    A number of example programs are provided with the distribution,
including a slicer, an isosurface extractor, and various utilities for
querying Flash data files.  The only requirements for QuickFlash are a
C++ compiler, a recent version of Python, and the HDF5 library (with a
version 1.6.x-compatible API); image output is provided via the
optional ImageMagick C++ bindings.  A Python interface to many of the
QuickFlash classes and routines is also available.

    QuickFlash is distributed under the GNU General Public License,
version 2, and is available at SourceForge:

http://quickflash.sourceforge.net

If you have any questions about the library, please feel free to ask
via the flash-users mailing list or through the QuickFlash help forum
at

http://sourceforge.net/forum/?group_id=244184

You can also contact me via email at nhearn at users.sourceforge.net.

    Happy New Year!


- Nathan


-- 
Nathan C. Hearn
nhearn at ucar.edu

Project Scientist
Computational & Information Systems Laboratory
National Center for Atmospheric Research


From brockp at umich.edu  Wed Jan  7 18:43:07 2009
From: brockp at umich.edu (Brock Palen)
Date: Wed, 7 Jan 2009 19:43:07 -0500
Subject: [FLASH-USERS] Flash to be covered on RCE?
Message-ID: <775E3FF7-3BE4-481D-A402-8656A5AB3727@umich.edu>

Hello,
I am putting together a new Podcast, on HPC and Research Computing.
Would one or two core people who can speak on flash be available for  
a 30-60 minute interview?

Website is:  www.rce-cast.com

I hope we can work something out.


Brock Palen
www.umich.edu/~brockp
Center for Advanced Computing
brockp at umich.edu
(734)936-1985





From dubey at flash.uchicago.edu  Thu Jan 15 10:06:38 2009
From: dubey at flash.uchicago.edu (Anshu Dubey)
Date: Thu, 15 Jan 2009 10:06:38 -0600
Subject: [FLASH-USERS] FLASH3.1.1 Release
Message-ID: <5b942a610901150806s14af5140q8df0edbcbaeb29d3@mail.gmail.com>

The Flash Center is pleased to announce the release of the
next minor version of the FLASH code, version 3.1.1. FLASH 3.1.1
primarily resolves bugs found in the 3.1 release.

The most important bug resolutions in this release pertain to the
mapping of active particles to the mesh, where mapping routines used some
data from Paramesh which wasn't yet updated, resulting in potentially undefined
behavior.  There was an additional bug in the same section of the code when
calculating the block/processor/corner IDs of neighboring blocks where
a block face touches 4 neighbors at a higher refinement level (3D
simulations only).

More minor improvements and bug fixes include -

1. fidlr can read PnetCDF output files without failing

2. Bugs in implementations of Balsara's algorithm for prolonging
  divergence-free face-centered magnetic fields have been fixed.

3. A redundancy for keeping both magnetic resistivity and magnetic
  viscosity has been removed in materialProperties/MagneticResistivity
  unit. Only magnetic resistivity is being used with proper scalings
  in this release.

4. MPI tag values overflowed in PARAMESH when
  using certain MPI implementations.  This has now been resolved in pm40
  and pm4dev.  The old behavior of assigning each MPI message a unique
  tag ID can be restored by defining PM_UNIQUE_MPI_TAGS pre-processor
  definition in setup script call.

5. There was extremely poor performance when reading particle data
  from a checkpoint file on BG/P.  We revert to the old contiguous
  particle attribute read of FLASH 3.0 when particle fields are the same
  in the checkpoint file and flash3 binary to improve performance.

New additions to the code include

1. An alternative implementation of PFFT routines which map FLASH grid
data to a
   uniform Pencil grid.  This implemetation uses less memory than the
FLASH 3.1 implementation.
  Additionally there is a new file containing subroutines that operate
on a list
  datatype which may be included in any module to construct a linked
list  object
  of user-specified node types.

2. A routine to find all neighboring block/proc IDs to a particular
local block in the
    Paramesh implementation of the Grid unit.

The release is available at:

http://flash.uchicago.edu/website/download/

A stripped down version of FLASH3 that may be downloaded without a
license is also available at the same location. This version is
essentially the FLASH framework without any implementations.
Flash Center is also providing support for "add-ons" to the
code. Please see the section on "What's new in this release" in the
first chapter of the user's guide for details.


From polandart at gmail.com  Sat Jan 24 20:34:05 2009
From: polandart at gmail.com (Arthur Poland)
Date: Sat, 24 Jan 2009 21:34:05 -0500
Subject: [FLASH-USERS] Flash2.5 question MHD Wave Energy
In-Reply-To: <5b942a610901150806s14af5140q8df0edbcbaeb29d3@mail.gmail.com>
References: <5b942a610901150806s14af5140q8df0edbcbaeb29d3@mail.gmail.com>
Message-ID: <497BCF9D.3000809@gmu.edu>

We are using the MHD modules in flash2.5. We set off an explosion
(energy input) which distorts the magnetic field as expected. This
distortion should carry magnetic wave energy from the explosion point.
 From what I can see this energy transport is not included in flash. Has
anyone worked to include it?

  On another note, conduction is almost exclusively along the magnetic
field. In flash it is handled isotropically. We have developed a module
that limits conduction to being only along the magnetic field. If
someone wants it, please let me know.
Thanks
Art Poland

-- 
Dr. Art Poland
George Mason University
Mail Stop 6A2
4400 University Dr.
Fairfax VA 22030
Research Building I Rm. 346
Dept. of Computational and Data Sciences
Dept. of Physics and Astronomy
Office 703-993-8404
Home 540-347-5003
Cell 540-222-1940
Fax 540-347-5526



From mateuszr at umich.edu  Sun Jan 25 16:46:08 2009
From: mateuszr at umich.edu (Mateusz Ruszkowski)
Date: Sun, 25 Jan 2009 17:46:08 -0500 (EST)
Subject: [FLASH-USERS] Temperature calculation using cosmology Module
In-Reply-To: <49396F66.20409@astro.rug.nl>
References: <49396F66.20409@astro.rug.nl>
Message-ID: <Pine.LNX.4.64.0901251739030.27978@lem.astro.lsa.umich.edu>


  Hi all,

I was wondering if there is any follow up on the question that Latif asked 
(enclosed below). I would also be interested to know what the anser is.
More speciically the question is: what kind of temperature is stored in 
the plot files whan the cosmology module is on?

   thanks,
     Mateusz

> I am including cosmology module in my simulation. I want to ask how  FLASH 
> calculates temperature after applying redshift to hydro quantities.Does it 
> calculate physical temperature or  calculates Temperature/(scale)^2 and i 
> have to convert it back to physical temperature as  all calculations are made 
> in comoving coordinates. How it works?


From dubey at flash.uchicago.edu  Sun Jan 25 17:32:59 2009
From: dubey at flash.uchicago.edu (Anshu Dubey)
Date: Sun, 25 Jan 2009 17:32:59 -0600
Subject: [FLASH-USERS] Flash2.5 question MHD Wave Energy
In-Reply-To: <497BCF9D.3000809@gmu.edu>
References: <5b942a610901150806s14af5140q8df0edbcbaeb29d3@mail.gmail.com>
	<497BCF9D.3000809@gmu.edu>
Message-ID: <5b942a610901251532y7fda9770sf984956079e3c99d@mail.gmail.com>

To the best of my knowledge this isn't something anyone has worked on, but
Dongwook (copied on this mail) can give a more definitive answer.

We are always interested in any modules contributed by the users. If you
don't mind making it available to the community, we'll be happy to translate it
to FLASH3 and include it in the next release with appropriate acknowledgements.

Anshu


On Sat, Jan 24, 2009 at 8:34 PM, Arthur Poland <polandart at gmail.com> wrote:
> We are using the MHD modules in flash2.5. We set off an explosion
> (energy input) which distorts the magnetic field as expected. This
> distortion should carry magnetic wave energy from the explosion point.
> From what I can see this energy transport is not included in flash. Has
> anyone worked to include it?
>
>  On another note, conduction is almost exclusively along the magnetic
> field. In flash it is handled isotropically. We have developed a module
> that limits conduction to being only along the magnetic field. If
> someone wants it, please let me know.
> Thanks
> Art Poland
>
> --
> Dr. Art Poland
> George Mason University
> Mail Stop 6A2
> 4400 University Dr.
> Fairfax VA 22030
> Research Building I Rm. 346
> Dept. of Computational and Data Sciences
> Dept. of Physics and Astronomy
> Office 703-993-8404
> Home 540-347-5003
> Cell 540-222-1940
> Fax 540-347-5526
>
>


From Alejandro.Bolanos at physik.uni-wuerzburg.de  Wed Jan 28 03:58:19 2009
From: Alejandro.Bolanos at physik.uni-wuerzburg.de (Alejandro.Bolanos at physik.uni-wuerzburg.de)
Date: Wed, 28 Jan 2009 10:58:19 +0100
Subject: [FLASH-USERS] Stuck with fidlr2 - wrong ELF class: ELFCLASS64
Message-ID: <OFE2A125ED.8D478B4A-ONC125754C.0036C735-C125754C.0036C738@physik.uni-wuerzburg.de>

Dear flash-users,


I am new to flash and am using flash 2.5, hdf5 1.6.5 and idl
5.6.? I have successfully run the sedov test problem and a problem set
by myself. I have the datasets, but can't visualize them with fidlr2.


I have also compiled the shared-object library h5_wrappers.so,
but there appears to be problem involving the 64-bit architecture
(wrong ELF class: ELFCLASS64). The error output is as follows:


IDL> xflash

% Compiled module: XFLASH.

initializing xflash????? ?

... IDL version = 5.6

... PNG graphics will be used

... xflash directory is/home/abolanos/FLASH2.5/tools/fidlr2/

% Compiled module: XFLASH_DEFAULTS.

% Compiled module: VAR_INDEX.

% Compiled module: COLOR_INDEX.

% Compiled module: CW_FIELD.

% Compiled module: CW_BGROUP.

% Compiled module: XMANAGER.

% Compiled module: DETERMINE_FILE_TYPE.

% Compiled module: GET_XFLASH_PATH.

% Loaded DLM: HDF.

% XMANAGER: Caught unexpected error from client application. Message follows...

% CALL_EXTERNAL: Error loading sharable executable.

???????????????? Symbol: hdf5_check_file_exist, File = /home/abolanos/FLASH2.5/tools/fidlr2/h5_wrappers.so

???????????????? /home/abolanos/FLASH2.5/tools/fidlr2/h5_wrappers.so: wrong ELF class: ELFCLASS64

% Execution halted at:? DETERMINE_FILE_TYPE?? 29 /home/abolanos/FLASH2.5/tools/fidlr2/determine_file_type.pro

%?????????????????????? XFLASH_EVENT?????? 77 /home/abolanos/FLASH2.5/tools/fidlr2/xflash.pro

%?????????????????????? XMANAGER_EVLOOP_STANDARD? 478 /opt2/rsi/idl_5.6/lib/xmanager.pro

%?????????????????????? XMANAGER????????? 708 /opt2/rsi/idl_5.6/lib/xmanager.pro

%?????????????????????? XFLASH?????????? 1782 /home/abolanos/FLASH2.5/tools/fidlr2/xflash.pro

%?????????????????????? $MAIN$


What can I do to fix this?


Many thanks in advance,


Alejandro
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From Alejandro.Bolanos at physik.uni-wuerzburg.de  Wed Jan 28 07:20:20 2009
From: Alejandro.Bolanos at physik.uni-wuerzburg.de (Alejandro.Bolanos at physik.uni-wuerzburg.de)
Date: Wed, 28 Jan 2009 14:20:20 +0100
Subject: [FLASH-USERS] Stuck with fidlr3,
	too - H5D_OPEN: dataset not found: (67108866, "coordinates")
Message-ID: <OF6B3893AB.1D281E50-ONC125754C.00494602-C125754C.0049460B@physik.uni-wuerzburg.de>

Dear users,

My problem with fidlr2 persists. I have tried switching to fidlr3, but another problem arises at HDF5_OPEN:

IDL> xflash
% Compiled module: XFLASH.
initializing xflash
... IDL version = 5.6
... PNG graphics will be used
% Compiled module: GET_XFLASH_PATH.
... current path is /home/abolanos/FLASH2.5/tools/fidlr3
... XFLASH_DIR is /home/abolanos/FLASH2.5/tools/fidlr3/
% Compiled module: XFLASH_DEFAULTS.
% Compiled module: VAR_INDEX.
% Compiled module: COLOR_INDEX.
% Compiled module: CW_FIELD.
% Compiled module: CW_BGROUP.
% Compiled module: XMANAGER.
IDL>
% Compiled module: DETERMINE_FILE_TYPE.
% Loaded DLM: HDF5.
% Compiled module: GET_DIMENSIONALITY.
% H5D_OPEN: dataset not found: (67108866, "coordinates")
% Execution halted at: GET_DIMENSIONALITY?? 31 /home/abolanos/FLASH2.5/tools/fidlr3/get_dimensionality.pro
%????????????????????? XFLASH_EVENT????? 102 /home/abolanos/FLASH2.5/tools/fidlr3/xflash.pro
%????????????????????? WIDGET_PROCESS_EVENTS
%????????????????????? $MAIN$


I learned from an older post ( http://flash.uchicago.edu/pipermail/flash-users/2004-October/001751.html ) that I should look for nans in the datasets, but I have found none either in the sedov or in my own datasets.

My environment variables (bash) look as follows. When using fidlr2:

?? export XFLASH_DIR=/home/abolanos/FLASH2.5/tools/fidlr3
?? export IDL_DIR=/opt2/rsi/idl_5.6
?? export IDL_PATH=$XFLASH_DIR:$IDL_DIR:$IDL_DIR/lib

And when Using fidlr3 the IDL_PATH variables reads

?? export IDL_PATH=$IDL_DIR:$IDL_DIR/lib:$XFLASH_DIR

as stated in the flash2.5 manual. Should I attach any logfiles for you to diagnose? Any insight would be very much appreciated.


Alejandro Bola?os
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From justin-parsons at uiowa.edu  Fri Jan 30 13:30:22 2009
From: justin-parsons at uiowa.edu (Justin Parsons)
Date: Fri, 30 Jan 2009 13:30:22 -0600
Subject: [FLASH-USERS] I too have trouble with fidlr3.0 and xflash
Message-ID: <db005d60901301130s50c4656fs3f5ed75cc43e2390@mail.gmail.com>

Hello

I'm having trouble running xflash as packaged with FLASH3,3.1 and 3.1.1a.
This is a new problem since upgrading to Ubuntu 8.10.  While running 8.04 I
never came across this problem.  I know what the bone-headed solution is,
but does anyone have any ideas as to what the real problem is?  Below is a
chunk of the error IDL outputs,

>>>>>>>>>>>>>>>

IDL> xflash3

                                          /nonexclusive, $
                                           ^
% Syntax error.
  At: /home/jus-sn/research/bowShock/FLASH3.1.1a/tools/fidlr3.0/xflash3.pro,
Line 216

fstartSuffix = cw_field(suf_base, title = 'suffix: ', value = '1', $
                                         ^
% Syntax error.
  At: /home/jus-sn/research/bowShock/FLASH3.1.1a/tools/fidlr3.0/xflash3.pro,
Line 1770

fendSuffix   = cw_field(suf_base, title = 'to', value = '1', $
                                         ^
% Syntax error.
  At: /home/jus-sn/research/bowShock/FLASH3.1.1a/tools/fidlr3.0/xflash3.pro,
Line 1772

fstep        = cw_field(suf_base, title = '   step', value = '1', $
                                         ^

<<<<<<<<<<<<<<<<<<

And it goes on giving similar errors for other functions with the cw_
prefix.  Any help is appreciated!

Cheers,
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-
Justin Parsons
http://jussn.beevomit.org
:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-
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From flash-users at flash.uchicago.edu  Sat Jan 31 03:44:18 2009
From: flash-users at flash.uchicago.edu (Best Price 2009)
Date: Sat, 31 Jan 2009 03:44:18 -0600 (CST)
Subject: [FLASH-USERS] [SPAM] Dear flash-users@flash.uchicago.edu Sat,
	31 Jan 2009 05:45:07 +0800 85% 0FF
Message-ID: <20090131134507.2532.qmail@amerblind.outbound.ed10.com.com>

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