Development#85

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srichers wants to merge 287 commits intoreleasefrom development

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Commits on Apr 4, 2023

Fix bug in initial conditions that causes density matrix to have trace 0 if particle weight is zero, causing crash in Emu
Sherwood Richers
committed
some tweaks to plotting scripts to make the compatible with current output formats
Sherwood Richers
committed

Commits on Apr 5, 2023

clarify condition for outputting files and prevent divide by zero
Sherwood Richers
committed
added ability to create set of particles - one particle for each species in the direction of the specified flux
Sherwood Richers
committed

Commits on Jul 5, 2023

update version of cuda base image, since docker seems unable to find the old one
Sherwood Richers
committed

Commits on Jul 27, 2023

move install to same line as update or update has no effect
Sherwood Richers
committed
going back to cuda 11.4, but a version that is actually availabel on dockerhub
Sherwood Richers
committed
some more plotting tweaks. Fixed error with dataset name - I don't know why it was changed in the first place...
Sherwood Richers
committed

Commits on Sep 14, 2023

reduce scalar output over MPI
Sherwood Richers
committed
reduce scalar output over MPI (#86 )

srichers
and
Sherwood Richers
authored
remove print line
Sherwood Richers
committed

Commits on Sep 19, 2023

reduce offdiag mag properly by only taking sqrt after mpi reduction
Sherwood Richers
committed
Merge branch 'elnConservativePerturbations' into development
Sherwood Richers
committed
remove print line...again?
Sherwood Richers
committed

Commits on Sep 20, 2023

make perturbations only on the diagonal elements, let vacuum potential do off-diagonal perturbations. This is a more physically palettable way of doing perturbations
Sherwood Richers
committed
update amrex
Sherwood Richers
committed

Commits on Sep 25, 2023

Revert "make perturbations only on the diagonal elements, let vacuum potential do off-diagonal perturbations. This is a more physically palettable way of doing perturbations"
Sherwood Richers
committed

Commits on Oct 19, 2023

Specify the modules used in Emu in README (#87 )
javierigm
authored

Commits on Dec 7, 2023

Readmechanges (#89 )

authored
Pressure tensor output (#88 )

srichers
and
Sherwood Richers
authored

Commits on Jan 18, 2024

Particles store the phase space volume they occupy
Sherwood Richers
committed
set evolution equations for N and L to be zero in code generation script in anticipation of changing them based on opacities. Set Vphase to not evolve in time.
Sherwood Richers
committed
whitespace
Sherwood Richers
committed
infrastructure to set IMFPs and chemical potentials in the parameter file
Sherwood Richers
committed

Commits on Jan 26, 2024

redefining f --> Nrho (before was f ---> Nrho)
erickurquilla1999
committed

Commits on Feb 1, 2024

do not divide by cell volume, since this is already done in the code itself.
Sherwood Richers
committed

Commits on Feb 2, 2024

computing volume of phase space
erickurquilla1999
committed
deleting lines that convert twice mu to erg
erickurquilla1999
committed
adding delta E as an input parameter to compute phase space volume
erickurquilla1999
committed
adding new input parameters to input files to run collitions
erickurquilla1999
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adding collition term in QKE
erickurquilla1999
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moving line that compute derivates, now it set the phase volume to zero meaning its time derivative its zero after it is used in collision term
erickurquilla1999
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considering the particle that carry antineutrinos in the fast flavor test
erickurquilla1999
committed

Commits on Feb 14, 2024

Fixing an error in the collision term
erickurquilla1999
committed

Commits on Feb 28, 2024

including adaptative time step for absortion and emission
erickurquilla1999
committed

Commits on Mar 7, 2024

creating vacuum paticles initial condition script
erickurquilla1999
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adding attenuation parameter to the time derivative of N_Ab due to the hamiltonians
erickurquilla1999
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Commits on Mar 8, 2024

solving mistake to compute time step due to collisions
erickurquilla1999
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adding collision test input file
erickurquilla1999
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testing if the particles converge to the expected equilibrium distribution
erickurquilla1999
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solving issue to copy GNUmakefile_jenkins to Exec directory
erickurquilla1999
committed

Commits on Mar 15, 2024

doing fast compilation in collision test
erickurquilla1999
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clarifying better the collision time steps, now delta t collision is collision_CFL / ( c * max_IMFP )
erickurquilla1999
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deletting renomarlization function. It will not be used anymore
erickurquilla1999
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solving mistake in compilation comand to compile the code for 3 flavors
erickurquilla1999
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Commits on Mar 16, 2024

Setting default collision time step to infinite. It will change if the code do collisions.
erickurquilla1999
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Commits on Mar 17, 2024

setting right indentation
erickurquilla1999
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including attenuation parameter to compute the time steps due to potentials
erickurquilla1999
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computing minimum between time steps due to potentials and collision even if max_adaptive_speedup>1 is not satisfy
erickurquilla1999
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solve mistake in chemical potential units in coment
erickurquilla1999
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add coment on the energy units
erickurquilla1999
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delete the individual parms arguments
erickurquilla1999
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Commits on Mar 24, 2024

creating collisional flavor instability test
erickurquilla1999
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Commits on Mar 27, 2024

delete print line
erickurquilla1999
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now reads plt* files for time steps of more than 5 digits
erickurquilla1999
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now reads plt files for time steps with more than 5 digits
erickurquilla1999
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Commits on Apr 17, 2024

print useful info for bipolar test
Sherwood Richers
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make a better babysitting plot
Sherwood Richers
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improve babysitting plots
Sherwood Richers
committed

Commits on Apr 19, 2024

improve babysitting script to also plot the ELN
Sherwood Richers
committed

Commits on Apr 30, 2024

upgraded cassowary to a V100 GPU
Sherwood Richers
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installed P100 GPU in jenkins server. Corrected cuda version on cassowary
Sherwood Richers
committed

Commits on May 1, 2024

add function to initialize the background enviroment Ye, rho and T
erickurquilla1999
committed

Commits on May 6, 2024

K plot (#91 )

javierigm
and
Sherwood Richers
authored

Commits on May 22, 2024

insert chemical potential for neutrinos and antineutrino independently
erickurquilla1999
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set python script that generate initial condition for collisional instability test
erickurquilla1999
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set input file for collisional instability test
erickurquilla1999
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Create a Jenkins test for collisional flavor instability
erickurquilla1999
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change cuda version to 7.0
Sherwood Richers
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delete std cout line
erickurquilla1999
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correct cuda version for jenkins
Sherwood Richers
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change order of commands first reduce_data_fft.py then reduce_data.py
erickurquilla1999
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delete function to initialize background quantities on this branch
erickurquilla1999
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Merge branch 'collisions' of https://github.com/AMReX-Astro/Emu into collisions
erickurquilla1999
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Solve mistake on collisional instability test. Now it read the right input file
erickurquilla1999
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Solve mistake on collisional instability test. Now it read the right python script
erickurquilla1999
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add python script for collision instability test
erickurquilla1999
committed

Commits on May 23, 2024

solve problem of defining chemical potentials for antineutrinos in the input parameter file
erickurquilla1999
committed

Commits on May 24, 2024

Kmax t hdf5 (#93 )

srichers
and
Sherwood Richers
authored

Commits on May 29, 2024

Merge remote-tracking branch 'origin/development' into collisions
erickurquilla1999
committed
rename f -> N for particles
erickurquilla1999
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finish renaming f -> N everywhere
erickurquilla1999
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Commits on Jun 3, 2024

comment lines that assert if N and Nbar are negatives, this lines will be deleted since now N and Nbar will no longer be used
erickurquilla1999
committed

Commits on Jun 4, 2024

change f for N in utility script to generate initial particles conditions
erickurquilla1999
committed
modify initial condition script for msw test. now it gives N_ab instead of N and f_ab as input
erickurquilla1999
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add comments to the function that read the initial conditions of the particles
erickurquilla1999
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change msw test to include the change f_ab ---> N_ab
erickurquilla1999
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reading N_ab for the particle initial condition file instead of N and f_ab independenly
erickurquilla1999
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removing f_ab variables for N_ab when setting perturbation
erickurquilla1999
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delete no needed lines
erickurquilla1999
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repare coll_equi_test.py test to consider N_ab instead of f_ab
erickurquilla1999
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making bypolar test work with the changes f_ab ---> N_ab
erickurquilla1999
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making fast flavor test work for f_ab ---> N_ab
erickurquilla1999
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making fast_flavor_k_test works for f_ab ---> N_ab
erickurquilla1999
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delete print line
erickurquilla1999
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delete print lines
erickurquilla1999
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make attenuation parameter symbolic in code generation scripts
Sherwood Richers
committed
move f-->N in a few more places
Sherwood Richers
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change f to N in test scripts
Sherwood Richers
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change Trf to TrN
Sherwood Richers
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remove unused line
Sherwood Richers
committed

Commits on Jun 7, 2024

Disable AMREX_USE_HDF5
shankar-1729
committed

Commits on Jun 11, 2024

give Jenkins access to the tables stored on the workstation
Sherwood Richers
committed

Commits on Jun 24, 2024

Add support routine set_rho_T_Ye that reads values from HDF5 table GPU-arrays and sets them to corresponding MultiFabs
shankar-1729
committed

Commits on Jun 25, 2024

Commits on Jul 2, 2024

Improve k plot (#95 )

javierigm
and
Sherwood Richers
authored
script to check for an ELN crossing in a particle input file (#92 )

srichers
and
Sherwood Richers
authored
add option to perturb diagonals instead of off-diagonals (#94 )

srichers
and
Sherwood Richers
authored

Commits on Jul 27, 2024

Commits on Jul 31, 2024

Reimplement particle creation at outer boundary
shankar-1729
committed

Commits on Aug 22, 2024

Commits on Aug 23, 2024

Commits on Aug 26, 2024

Resolving conflict between development and Swapnil's EOS branch.
erickurquilla1999
committed

Commits on Aug 27, 2024

Commits on Sep 11, 2024

Commits on Sep 12, 2024

Commits on Sep 16, 2024

Use actual pup* and dt for Vphase calculation
shankar-1729
committed

Commits on Sep 24, 2024

Fix particle creation at boundary and calculate total Vphase
shankar-1729
committed

Commits on Sep 26, 2024

Set correct BC_type (should be moved to parameter file)
shankar-1729
committed

Commits on Sep 27, 2024

Merge pull request #99 from AMReX-Astro/swapnil/eos_table
erickurquilla1999
authored

Commits on Oct 2, 2024

Swapnil/cleanup development (#102 )
shankar-1729
authored

Commits on Oct 8, 2024

Create a file that contains the function which will read background quantities, rho, Ye, and T, from an HDF5 file to an EMU grid
erickurquilla1999
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Call the function that reads the HDF5 file containing rho, Ye, and T from the function that sets these quantities in the EMU multifab mesh.
erickurquilla1999
committed
Solving missing semicolon

erickurquilla1999
authored and
erickurquilla1999
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Update the Make.package file to compile the file that contains the function that reads rho, Ye, and T.

erickurquilla1999
authored and
erickurquilla1999
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Send input parameters to the function that sets rho, Y, and T to the EMU mesh.
erickurquilla1999
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Reading the input number of cells and domain size from the background quantities HDF5 file.
erickurquilla1999
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Resolve the issue when using the pointer that contains the number of cells in the x, y, and z directions

erickurquilla1999
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erickurquilla1999
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Setting rho, Ye, and T in the AMReX mesh MultiFab.

erickurquilla1999
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erickurquilla1999
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Assigning the correct values of densities, temperature, and electron fraction to the mesh MultiFab.

erickurquilla1999
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erickurquilla1999
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Stop the code if the number of cells and domain size in the HDF5 background file do not agree with the number of cells and domain size in the parameter file.

erickurquilla1999
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erickurquilla1999
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Creating a new parameter to control when the code reads the background quantities from an HDF5 file.
erickurquilla1999
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Adding the new parameter to control when the code reads the background quantities rho, Ye and T to the input files.
erickurquilla1999
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Create a Python script to generate vacuum particles with different energy bins centers.
erickurquilla1999
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Now create empty particles at the energy bin center of the Nulib table.
erickurquilla1999
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Deleting unnecessary printing files.

erickurquilla1999
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erickurquilla1999
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Solve issue with data type when reading doubles from an HDF5 file

erickurquilla1999
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erickurquilla1999
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Create an initial condition input parameter for the Fermi-Dirac test.

erickurquilla1999
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erickurquilla1999
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Compute the delta phase space in the input file of the particles.
erickurquilla1999
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Remove unneeded semicolon.

erickurquilla1999
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erickurquilla1999
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Redefining the phase space volume calculation based on precomputed quantities in the input script.
erickurquilla1999
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Generate comments in Doxygen style for a function that reads the initial conditions of the particles.

erickurquilla1999
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erickurquilla1999
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Using np.zeros when generating the initial condition for multi-energy particles.
erickurquilla1999
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Resolve issue with the colon.
erickurquilla1999
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Cleaning the Python script that generates vacuum multi-energy particles.
erickurquilla1999
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Modify the Python script that generates the initial conditions for the collisional instability test to compute the phase space volume.

erickurquilla1999
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erickurquilla1999
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Simplifying the calculation of the phase space volume.

erickurquilla1999
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erickurquilla1999
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Solve issue with initial condition not reproducing the right neutrino number density in collisional stability test
erickurquilla1999
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Update the initial condition script for monoenergetic vacuum particles in the collision-to-equilibrium test.
erickurquilla1999
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Convert the units of the background data from MeV to ergs when setting it in the MultiFab.

erickurquilla1999
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erickurquilla1999
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Add comments and convert the temperature from ergs to MeV when interpolating the chemical potentials and neutrino opacities.

erickurquilla1999
authored and
erickurquilla1999
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Create a Python script for the Fermi-Dirac test.

erickurquilla1999
authored and
erickurquilla1999
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Update the input parameters for the Fermi-Dirac test.

erickurquilla1999
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erickurquilla1999
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Create a python script to generate a constant background matter field. This hdf5 file is read into the EMU mesh.
erickurquilla1999
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Update the input parameters for the Fermi-Dirac test.

erickurquilla1999
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erickurquilla1999
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Read the background matter HDF5 file path from the input parameters.
erickurquilla1999
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Add a script to write all particle information into HDF5 files.

erickurquilla1999
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erickurquilla1999
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Add Fermi-Dirac test to Jenkinsfile.
erickurquilla1999
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Updating the path in Ganon where the EOS and NuLib tables will be located, and the file names in the input parameters file in the Fermi-Dirac parameter file.
erickurquilla1999
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Solving the issue with the Fermi-Dirac test path to the EOS and NuLib tables.
erickurquilla1999
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Trying to fix Jenkins problem when reading tables
erickurquilla1999
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Do just 2 test in Jenskins
erickurquilla1999
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Trying to fix Jenkins problem when reading tables
erickurquilla1999
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Trying to fix Jenkins problem when reading tables
erickurquilla1999
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Trying to fix Jenkins problem when reading tables
erickurquilla1999
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Trying to fix Jenkins problem when reading tables
erickurquilla1999
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Adding all tests to Jenkins.
erickurquilla1999
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Solving the issue of plots using LaTeX text settings that do not run in Jenkins.
erickurquilla1999
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Creating an input for the boundary condition type.
erickurquilla1999
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use proper variable name

Sherwood Richers
authored and
erickurquilla1999
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Include an exception for Jupyter Notebook files in the ".gitignore" file.

erickurquilla1999
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erickurquilla1999
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Include a GNUmakefile for Perlmutter compilation.

erickurquilla1999
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erickurquilla1999
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Making the ReadHDF5RhoYeT.cpp file compile without MPI and cleaning up some comments.
erickurquilla1999
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Update default makefile to include HDF5 files in the compilation
erickurquilla1999
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Delete comment
erickurquilla1999
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Commits on Oct 9, 2024

Merge pull request #103 from AMReX-Astro/upload_rho_ye_T_tested
shankar-1729
authored

Commits on Oct 14, 2024

Setting rho, Ye, and T in the AMReX mesh MultiFab.
erickurquilla1999
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Assigning the correct values of densities, temperature, and electron fraction to the mesh MultiFab.

erickurquilla1999
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erickurquilla1999
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Organizing and structuring the parameter file to avoid reading variables that are not needed in different situations.
erickurquilla1999
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Update Fermi-Dirac test parameter file
erickurquilla1999
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Add an if statement to avoid evolving particles that are inside the black hole when simulating an NSM.
erickurquilla1999
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Solve syntax issue.

erickurquilla1999
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erickurquilla1999
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Writing derivatives of N and Nbar in symbolic Hermitian format.
erickurquilla1999
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"Creating a function to set particles to N=0 and Nbar=0 in the boundary cells."
erickurquilla1999
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Creating a flag for boundary conditions that set particles to N=0 and Nbar=0 in the boundary cells.
erickurquilla1999
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Add function to set particles to N=0 and Nbar=0 in the boundary cells in Evole.cpp file.
erickurquilla1999
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Add the code in main to do periodic boundary conditions but initialize particles with N=0 and Nbar=0 at the boundary
erickurquilla1999
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Solving bracket issue.

erickurquilla1999
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erickurquilla1999
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Adding return when particles are in boundary cells

erickurquilla1999
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erickurquilla1999
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Resolve the issue in the plots in the Fermi-Dirac test script.
erickurquilla1999
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Resolve rebase conflict
erickurquilla1999
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Including the declaration of the number of cells in the x direction in the function to set the background values of rho, Ye, and T
erickurquilla1999
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Delete repeted lines
erickurquilla1999
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cleaning up the code
erickurquilla1999
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Commits on Oct 15, 2024

Add indentation in if statement in parameter file
erickurquilla1999
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Delete repeated comment
erickurquilla1999
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Allowing IMFP method = 1 do periodic boundary initialization
erickurquilla1999
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Allow periodic vacuum initialization of boundary condition without do_nsm flag
erickurquilla1999
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Adding flag to compute do_periodic_empty_bc = 0 to avoid error
erickurquilla1999
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Solve error in if statement that avoids computation of quantities for particles in black hole and boundary cells
erickurquilla1999
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Add boundary condition test for periodic empty functions
erickurquilla1999
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Create initial condition for empty boundary condition test
erickurquilla1999
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Commits on Oct 16, 2024

Add periodic empty boundary conditions to Jenkins
erickurquilla1999
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Cleaning up and writing comments
erickurquilla1999
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Cleaning up and adding comments to BC empty particle test
erickurquilla1999
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Delete if statement to check if IMFP method is one or two and just check if do NSM is activated or empty periodic BC are activated
erickurquilla1999
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Solving possible issue with time step
erickurquilla1999
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Solving issue with time step problem
erickurquilla1999
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Add comments and clean up particles_at_boundary_cells function
erickurquilla1999
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Change name of function particles_at_boundary_cells to empty_particles_at_boundary_cells
erickurquilla1999
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Add if statement to check if IMFP method is equal to 2 before the if statement for do NSM
erickurquilla1999
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Commits on Oct 18, 2024

Solve issue in periodic empty boundary condition test
erickurquilla1999
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Move black hole parameter out of the IMFP method 2 so we can run simulations with a black hole in all methods.
erickurquilla1999
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Adding do_nsm parameter to all input files
erickurquilla1999
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Remove if statement so the empty periodic boundary condition can be run independently of the IMFP method
erickurquilla1999
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Adding comments
erickurquilla1999
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Making the parameter to do empty periodic BC independent of the IMFP method
erickurquilla1999
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Remove unnecessary line
erickurquilla1999
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Make the code able to simulate a black hole independently of the IMFP type.
erickurquilla1999
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Change variable name from do_nsm to do_blackhole.
erickurquilla1999
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Update comments
erickurquilla1999
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Update empty periodic BC test to include a black hole in the domain center and test if the particles inside the black hole are initialized to zero.
erickurquilla1999
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Cleaning up up and adding returns to speed up
erickurquilla1999
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Reorganize the parameter file
erickurquilla1999
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Clean and comment the code
erickurquilla1999
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Update and organize input paramter files
erickurquilla1999
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Delete debbug print line
erickurquilla1999
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Commits on Oct 21, 2024