[Users] Open numbered CarpetHDF5 with visit

[Jens Mahlmann]

Dear all,

I have made some use of hdf5_merger and hdf5_slicer to convert my 3D 
simulation output into hdf5 files which only contain the data of one 
iteration - for example in the format var.iteration.h5 (i.e. var.*.h5).

Visit recognizes this as a database, however, I am not able to use the 
time slider to jump between the numbered files. Is there any further 
conversion which I have to undertake? I would be glad to hear some best 
practices.

Thank you very much and my best!

Jens

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[Users] Spacetime evolution with hydro refluxing

[Jens Mahlmann]

Dear all,


I have recently changed my hydro simulations to the Refluxing strategy 
implemented by Erik Schnetter. For this I have changed the standard 
configuration to a *cell centred refinement, staggered boundaries and 
low order spatial prolongation for the hydro variables*. Since then I 
experience problems with BSSN or, more specifically, the 
QuasilocalMeasures thorn (a=0.9 black hole). After an initially fine 
behaviour, *no Eigenvector with value one is found and the spacetime 
gradually crashes*.


I am still puzzled where this is coming from. Does anybody have some 
experience with the combination spacetime evolution + hydro refluxing, 
i.e. the somewhat different grid setup? I would be glad for any input to 
see where I start to fix my work.


Thank you very much and my best from Valencia

Jens
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[Users] hdf5 output generation for Mathematica and VisIt

[Jens Mahlmann]

Dear all,

I hope I may approach you with a rather general question on output 
generation. For visualization, I find it convenient to use both 
SimulationTools for Mathematica as well as VisIt. Both are fine with 
reading hdf5 files and the interface to Carpet data is in general very nice.

However, I find that depending on if I activate 
CarpetIOHDF5::one_file_per_group or not, I have difficulties of opening 
the files in one or the other (with yes I am great for visit but not for 
SimulationTools and vice versa).

Especially, I would like to have the 3D output in one file per group, 
and the 2D output not. Is there an option to do so? Or does anybody have 
a best practice for a student of how to overcome this in post process? I 
want to avoid running all simulations twice...

Thank you and my best!

Jens


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[Users] `tl >= 0 and tl < timelevels' failure in recovering with ML_BSSN

[Jens Mahlmann]

Dear all,

I have encountered an `tl >= 0 and tl < timelevels' error when 
recovering checkpoints while using ML_BSSN and helpers.


I am currently running a minimal example in which I merely activate

ML_BSSN ML_BSSN_Helper ML_ADMConstraints

without giving any further options (nor using them for spacetime 
evolution). The errors occur after I want to to the recovering.


I am sure there is something very basic I am missing in my parameter 
file. I have included the example in the following.


Thank you for your help and input!

My best from Tel Aviv

Jens

#
# Parameter file for the testing of a force-free evolver
# Author: Jens Mahlmann
#

#
# Thorn specification
#
# Kerr setup thorns
#
ActiveThorns= " Carpet CarpetLib  CarpetInterp 
CarpetReduce "
ActiveThorns= " CartGrid3D CoordBase CarpetRegrid2 
SymBase Boundary ReflectionSymmetry  "
ActiveThorns= " ADMBase ADMCoupling ADMMacros 
InitBase MoL Time "
ActiveThorns= " ML_BSSN ML_BSSN_Helper 
ML_ADMConstraints NewRad"
ActiveThorns= " CoordGauge StaticConformal 
LoopControl AEILocalInterp Formaline  "
ActiveThorns= " TmunuBase "
ActiveThorns= "  SphericalSurface NaNChecker 
SpaceMask "
ActiveThorns= " SummationByParts "
ActiveThorns= " IOUtil CarpetIOBasic CarpetIOASCII 
CarpetIOScalar CarpetIOHDF5 "
ActiveThorns= " CarpetTracker CarpetMask "
ActiveThorns= " LocalInterp Slab CarpetSlab Exact  
Fortran "
ActiveThorns= "  Dissipation "

###
# Simulation management
###

Cactus::terminate   = time
Cactus::cctk_final_time = 1000.0

Carpet::output_timers_every = 512
Carpet::print_timestats_every   = 512

CarpetLib::interleave_communications= yes
CarpetLib::combine_sends= yes
CarpetLib::print_memstats_every = 1024
CarpetLib::print_timestats_every= 1024

#
# Grid specifications
#


driver::ghost_size = 4

CartGrid3D::type= "CoordBase"
CartGrid3D::domain  = "full"


CoordBase::domainsize   = "minmax"
CoordBase::xmax = 128.0 #16.0 #32.0 #40.0 #332.8 
#40.0 #96.0
CoordBase::ymax = 128.0 #16.0 #32.0 #40.0 #332.8 
#40.0 #96.0
CoordBase::zmax = 128.0 #16.0 #32.0 #40.0 #332.8 
#40.0 #96.0
CoordBase::xmin = -128.0 # 0.0 #-32.0 #-40.0 
#-332.8 #-40.0 #-24.0 #-24.0
CoordBase::ymin = -128.0 #0.0 #-32.0 #-40.0 #-332.8 
#-40.0 #-24.0 #-24.0
CoordBase::zmin = -128.0 # -16.0 #-32.0 #-40.0 
#-332.8 #-40.0 #-24.0 #-24.0
CoordBase::dx   = 4.0 #1.6 #5.12 #1.6 #2.0 #62.5 
#3.2 #0.8
CoordBase::dy   = 4.0 #1.6 #5.12 #1.6 #2.0 #62.5 
#3.2 #0.8
CoordBase::dz   = 4.0 #1.6 #5.12 #1.6 #2.0 #62.5 
#3.2 #0.8
CoordBase::boundary_size_x_lower= 4
CoordBase::boundary_size_y_lower= 4
CoordBase::boundary_size_z_lower= 4
CoordBase::boundary_size_x_upper= 4
CoordBase::boundary_size_y_upper= 4
CoordBase::boundary_size_z_upper= 4
CoordBase::boundary_shiftout_x_lower= 0
CoordBase::boundary_shiftout_y_lower= 0
CoordBase::boundary_shiftout_z_lower= 0
CoordBase::boundary_shiftout_x_upper= 0
CoordBase::boundary_shiftout_y_upper= 0
CoordBase::boundary_shiftout_z_upper= 0
ReflectionSymmetry::reflection_x= "no"
ReflectionSymmetry::reflection_y= "no"
ReflectionSymmetry::reflection_z= "no"
ReflectionSymmetry::avoid_origin_x  = "no"
ReflectionSymmetry::avoid_origin_y  = "no"
ReflectionSymmetry::avoid_origin_z  = "no"

#
# Grid management
#

Carpet::domain_from_coordbase   = "yes"
Carpet::enable_all_storage  = "yes"
Carpet::use_buffer_zones= "yes"
Carpet::schedule_barriers   = "n

[Users] Grid function timelevels

[Jens Mahlmann]

Dear all,

I am currently optimizing some code in the Einstein Toolkit and have a 
general question on time levels and declarations.

Throughout my evolution, I use some quantities (initialized as grid 
functions with various time levels) which are not changed throughout the 
evolution or only changed explicitly in some moments. At the moment, I 
make sure in every time step via

variable[i3D] = variable_p[i3D]

that I have the correct values at the respective time.

Is there a better way to do this? I.e. is there a way to declare a grid 
function or to register it such that it stays untouched throughout the 
time evolution except when I change it explicitly?

Thank you very much and my best from Valencia

Jens Mahlmann

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[Users] Reduction operations during runtime

[Jens Mahlmann]

Dear all,

I am currently trying to use the results of a global reduction operation 
(average) during runtime for the derivation of source terms.


Especially, I run

* if (CCTK_Reduce(cctkGH, -1, CCTK_ReductionHandle("average"), 1,
          CCTK_VARIABLE_REAL,
          magvaravg, 1,
          CCTK_VarIndex("FFEvolve::magvar")))
    CCTK_WARN(0, "Error while reducing FFEvolve::magvaravg");*

with OPTION:GLOBAL prior to my source term derivation (especially not in 
the Analysis schedule block). However, this basically gives me NaNs 
during runtime. Still, when I produce output of the respective 
quantities, everything works fine - it seems that only the quantity 
storing the average value is not available for all processes during runtime.


Maybe you have a hint for me - I am sure I am missing something basic.

Thank you very much for your input and my best from Valencia

Jens

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[Users] Robin Boundary Conditions

[Jens Mahlmann]

Dear all,

I am currently experimenting with the setup of Robin boundary conditions 
(I need a decay to the power of 3 in my physical field variables). 
However, I am finding myself a bit troubled with the correct 
understanding and implementation of the corresponding table handles.

Does anybody have a minimal example for the implementation of Robin 
boundary conditions with a non default decay power? Or a hint where I 
could improve my understanding of the implementation?

Thank you very much and my best from Valencia

Jens

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Re: [Users] outreach and visibility of the toolkit

[Jens Mahlmann]

Dear all,

regarding the outreach and visibility topic I have one suggestion 
concerning the hurdles of getting started with the Einstein Toolkit. 
Already two times this year I met people who were rather interested in 
the ET but did not know how to get started.


The initial hurdle of starting with the ET could be lowered, if one 
offered for example the contact to a "starting buddy" who agrees to 
Skype for example 2 times 30 minutes with somebody who wants to get 
started and provides appropriate slides/scripts/examples/tasks to kick 
off - also, this might take away the fear to contact the community with 
further questions. Alternatively, in a lighter and more standardized 
version of this, one could offer a monthly Hangout giving a "How to get 
started" presentation and leaving room for Q In any case, I would be 
on board for any of these points.


For tonight my very best from Valencia

Jens Mahlmann


On 10/18/2017 07:37 PM, David Radice wrote:

Hi Hevli,

let me add, as an example of NS merger simulations done with the ET, our 
(Princeton/Parma/Frankfurt groups) simulations with the WhiskyTHC code, which 
includes microphysical nuclear EOS and neutrinos:

https://www.youtube.com/watch?v=dhS77N0tyEA

Ref. https://arxiv.org/abs/1601.02426

Cheers,

David


On Oct 18, 2017, at 6:38 AM, helvi witek <hwi...@icc.ub.edu> wrote:

Dear all,

let me pick up on our discussion on the visibility of the Einstein Toolkit 
within the LIGO/VIRGO Scientific collaboration, our scientific community in 
general and the public that we had during the workshop last week.

In the end of the week we are opening our traveling exhibition "Unraveling the dark 
universe" and, as probably many of you these days, we will have a number of outreach 
talks about gravitational waves. In this context I was looking for animations produced 
with the toolkit, in addition to the BBH material that I already had from the SXS 
collaboration, to give more credit to it.

I noticed a few things that we could improve
- update the gallery on the website. At the moment the only animation of an 
event is that by Barry for GW150914. It would be nice to have more of a 
collection for the other events, and in particular for GW170817. As first step 
we could collect links to the youtube channels of different groups.
- that brings me to a second suggestion: should we bundle those animations, 
e.g., in a ET youtube channel? At the moment, a quick search leads to filmed 
talks and lectures (which is important, too, of course), but try the same for 
SXS and you'll get a list of animations by the collaboration. A first step to 
give more visibility to the toolkit could be to add the logo to the credits.

This is essentially to spark some discussion, and if there is interest, we can 
follow up on it in one of the next calls.

cheers,
Helvi

===
Dr. Helvi Witek
Marie-Curie Research Fellow
Dep. Fisica Quantica i Astrofisica & ICCUB
Universitat de Barcelona
===

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Re: [Users] ADMMacros: Identidier is undefined

[Jens Mahlmann]

Hi Ian!

in the following, I assembled an exemplary code reproducing the problem 
when compiling. I figured that making use of TRRICCI and UPPERMET in 
different files does not yield any problems. So for now I split up my 
routines to avoid this double declaration.


My best!

Jens

#include "cctk.h"
#include "cctk_Arguments.h"
#include "cctk_Parameters.h"
#include "cctk_Functions.h"

#include 
#include "loopcontrol.h"


void FFEvolve_Test1 (CCTK_ARGUMENTS)
{
  DECLARE_CCTK_ARGUMENTS;
  DECLARE_CCTK_PARAMETERS;

  int const ni = cctk_lsh[0];
  int const nj = cctk_lsh[1];
  int const nk = cctk_lsh[2];
  int const np = cctk_ash[0] * cctk_ash[1] * cctk_ash[2];

const int di = 1;
const int dj = cctk_lsh[0];
const int dk = cctk_lsh[0]*cctk_lsh[1];
#include "EinsteinBase/ADMMacros/src/macro/DA_declare.h"
#include "EinsteinBase/ADMMacros/src/macro/UPPERMET_declare.h"

#pragma omp parallel
  {
  CCTK_LOOP3(test1, i, j, k, 0, 0, 0, ni , nj , nk , ni , nj , 
nk  )

  {
CCTK_INT ijk;

ijk = CCTK_GFINDEX3D(cctkGH, i,j,k);
#include "EinsteinBase/ADMMacros/src/macro/DA_guts.h"
#include "EinsteinBase/ADMMacros/src/macro/UPPERMET_guts.h"

}CCTK_ENDLOOP3(test1);
}

#include "EinsteinBase/ADMMacros/src/macro/UPPERMET_undefine.h"
#include "EinsteinBase/ADMMacros/src/macro/DA_undefine.h"

}

void FFEvolve_Test2 (CCTK_ARGUMENTS)
{
  DECLARE_CCTK_ARGUMENTS;
  DECLARE_CCTK_PARAMETERS;

  int const ni = cctk_lsh[0];
  int const nj = cctk_lsh[1];
  int const nk = cctk_lsh[2];
  int const np = cctk_ash[0] * cctk_ash[1] * cctk_ash[2];

const int di = 1;
const int dj = cctk_lsh[0];
const int dk = cctk_lsh[0]*cctk_lsh[1];
#include "EinsteinBase/ADMMacros/src/macro/TRRICCI_declare.h"

#pragma omp parallel
  {
  CCTK_LOOP3(test2, i, j, k, 0, 0, 0, ni , nj , nk , ni , nj , 
nk  )

  {
CCTK_INT ijk;

ijk = CCTK_GFINDEX3D(cctkGH, i,j,k);
#include "EinsteinBase/ADMMacros/src/macro/TRRICCI_guts.h"

}CCTK_ENDLOOP3(test1);
}

#include "EinsteinBase/ADMMacros/src/macro/TRRICCI_undefine.h"


}


On 07/11/2017 11:09 AM, Ian Hinder wrote:

On 11 Jul 2017, at 09:42, Jens Mahlmann <jensm...@alumni.uv.es> wrote:


Dear all,

I am currently working on an analysis thorn which makes use of different 
quantities provided by the thorn ADMMacros. In one .cc file I assemble 
different routines. Especialy, one of those uses UPPERMET, and another one uses 
TRRICCI.

Using the declaration and definition from the thorn documentation, I made sure 
to correctly employ the includes of _declare, _guts, and, _undefine.

However, when compiling I keep receiving the following error:
In file included from 
/scratch/je/jensflo/EinsteinTools/Cactus/arrangements/EinsteinBase/ADMMacros/src/macro/UPPERMET_guts.h(14),
  from 
/scratch/je/jensflo/EinsteinTools/Cactus/arrangements/EinsteinBase/ADMMacros/src/macro/TRRICCI_guts.h(15),
  from 
/scratch/je/jensflo/EinsteinTools/Cactus/configs/sim/build/FFEvolve/FFEvolve_Analysis.cc(412):
/scratch/je/jensflo/EinsteinTools/Cactus/arrangements/EinsteinBase/ADMMacros/src/macro/DETG_guts.h(36):
 error: identifier "detg_psi4" is undefined
   DETG_PSI4 = 1;

This error occurs for a variety of other identifiers in the same place. If I 
take out the TRRICCI part from the code, I do not get these error messages. I 
would be so glad about an insight into this.
Thank you so much and my best from Valencia

Hi,

I have never used ADMMacros, but looking at the code, it looks like DETG_PSI4 
is defined in DETG_declare.h, which also declares the variable it names 
(CCTK_REAL DETG_PSI4), and this header is included by UPPERMET_declare.h, which 
is included by TRRICCI_declare.h.  So as far as I can see, if you include 
TRRICCI_declare.h, you should get the declaration of DETG_PSI4, which is 
detg_psi4.

One thing to check is that you have included the header files in your function, 
not at the top of the file with the other includes.  Could you post your code, 
or a small cut down example which we can use to reproduce the problem?



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[Users] ADMMacros: Identidier is undefined

[Jens Mahlmann]

Dear all,

I am currently working on an analysis thorn which makes use of different 
quantities provided by the thorn ADMMacros. In one .cc file I assemble 
different routines. Especialy, one of those uses UPPERMET, and another 
one uses TRRICCI.


Using the declaration and definition from the thorn documentation, I 
made sure to correctly employ the includes of _declare, _guts, and, 
_undefine.


However, when compiling I keep receiving the following error:

In file included from 
/scratch/je/jensflo/EinsteinTools/Cactus/arrangements/EinsteinBase/ADMMacros/src/macro/UPPERMET_guts.h(14),
 from 
/scratch/je/jensflo/EinsteinTools/Cactus/arrangements/EinsteinBase/ADMMacros/src/macro/TRRICCI_guts.h(15),
 from 
/scratch/je/jensflo/EinsteinTools/Cactus/configs/sim/build/FFEvolve/FFEvolve_Analysis.cc(412):
/scratch/je/jensflo/EinsteinTools/Cactus/arrangements/EinsteinBase/ADMMacros/src/macro/DETG_guts.h(36): 
error: identifier "detg_psi4" is undefined

  DETG_PSI4 = 1;

This error occurs for a variety of other identifiers in the same place. 
If I take out the TRRICCI part from the code, I do not get these error 
messages. I would be so glad about an insight into this.


Thank you so much and my best from Valencia

Jens

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[Users] Tracer particles: Processor distribution of array

[Jens Mahlmann]

Dear all,

I am currently working on the implementation of tracer particles into an 
evolution code. As for this, my orientation is the particle 
implementation of GRHydro. The number of particles is, in this case, is 
distributed equally across the processors by the DISTRIB=DEFAULT option. 
Is there any experience out there with distributing arrays according to 
a transfer function (e.g., some sort of density), such that higher 
density regions have more traced particles? In the documentation I only 
found the DISTRIB=CONSTANT option - which would not serve the purpose.


Thank you very much and my best!

Jens

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[Users] Thorn documentation on homepage

[Jens Mahlmann]

Dear all,

I have been trying to access the thorn documentation on the homepage 
this morning. I keep receiving "Not found" prompts. Sorry to use this 
channel - however, I did not find a webmaster on the homepage for direct 
contact.

Thank you so much and my best!

Jens

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