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Erick/production 1.0#106

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erickurquilla1999 wants to merge 83 commits intodevelopmentAMReX-Astro/Emu:developmentfrom erick/production_1.0AMReX-Astro/Emu:erick/production_1.0Copy head branch name to clipboard

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Commits on Nov 4, 2024

• Make IMFP calculation energy dependent

  shankar-1729

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• Ensure that rho, temp and Ye are uniformally spaced.

  shankar-1729

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Commits on Nov 7, 2024

• Implement function to calculate maximum of IMFP over the grid (UNTESTED)

  

  shankar-1729

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  erickurquilla1999

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• Move multifab for IMFB inside compute_max_IMFP function, correct temperature units

  

  shankar-1729

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  erickurquilla1999

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• do not input ba, dm and ngrow inside compute_max_IMFP function

  

  shankar-1729

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  erickurquilla1999

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• calculate max_IMFP_abs inside function compute_dt

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  shankar-1729

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  erickurquilla1999

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• Remove dt calculation from compute_dt function

  

  shankar-1729

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  erickurquilla1999

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• Adding basics comments and documentation to new functions

  erickurquilla1999

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• Change the position of the calculation of the maximum IMFP

  erickurquilla1999

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• Compute maximum of IMFP when IMFP method is 1 too

  erickurquilla1999

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• Compute the maximum IMFP and pass it as a parameter to the compute_dt function.

  erickurquilla1999

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• Cleaning up the compute_dt function and adding documentation.

  erickurquilla1999

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• Include a generated file to compute the trace of the neutrino number density for mesh quantities

  erickurquilla1999

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• Solving issue in generated file to compute trace of mesh neutrino and antineutrino number densities

  erickurquilla1999

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• Compute maximum trace of the neutrino and antineutrino from mesh quantities to compute the correct time step

  erickurquilla1999

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• Create a function that computes the minimum value in a MultiFab in parallel.

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  erickurquilla1999

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• Set some if statements to handle simulations with empty periodic boundary conditions and black holes.

  erickurquilla1999

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• Generate a new file to compute the trace on mesh quantities

  erickurquilla1999

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• Solve syntaxis mistakes and compute the minumin time step rather than the minimum potential

  erickurquilla1999

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• Make function compute_max_IMFP return a multifab with the maximum inverse mean free paths in the grid center

  erickurquilla1999

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• Compute the minimum combination of TrN/Opacity*c. This quantity provides a better representation of the time derivative of N than the previous 1/Opacity*c.

  erickurquilla1999

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• Delete commented lines and handle periodic empty boundary conditions and black holes in the function that computes the time step.

  erickurquilla1999

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• Cleaning up and addiing comments to the compute_dt function

  erickurquilla1999

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• Add documentation for header file of Evolve.cpp file

  erickurquilla1999

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• Delete unnecessary generation of two files that compute the trace.

  erickurquilla1999

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• Setting the min(TrN, TrNbar) to one in case it is zero

  erickurquilla1999

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• Cleaning space

  erickurquilla1999

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• Cleaning up compute_max_IMFP function

  erickurquilla1999

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• Creating documentation for compute_max_IMFP function

  erickurquilla1999

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• Set the new time step to agree with the new function that computes the time step.

  erickurquilla1999

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• Solving issue when looping over the MultiFabs. Now it does not loop over ghost cells since the MultiFab containing the maximum IMFP for every cell does not have ghost cells.

  erickurquilla1999

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• Delete unnecessary lines

  erickurquilla1999

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• Update empty periodic boundary condition test

  erickurquilla1999

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• Setting the right cfl factors for particles to equilibrium test

  erickurquilla1999

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• Set up the Fermi-Dirac test for multi-energy particles with the following time step CFL factors.

  erickurquilla1999

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• Delete unnecessary functions

  erickurquilla1999

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• Solving possible issue with zero inverse mean free path

  erickurquilla1999

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• Improve documentation

  erickurquilla1999

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• Solve syntax issue

  erickurquilla1999

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• Solving issue with fermi dirac test

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  erickurquilla1999

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Commits on Nov 25, 2024

• Fix time step function: now calculates the time step based on a basic equation. A more advanced time step calculation will be implemented later

  erickurquilla1999

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• Adding comments on the definitions of V_stupid and V_adaptive

  erickurquilla1999

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• Delete unnecessary line that computes the trace of matrices.

  erickurquilla1999

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• Add input parameter for the minimum allowed time step in the simulation

  erickurquilla1999

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• Including the minimum time step barrier in the function that computes time steps.

  erickurquilla1999

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• Including a new neutrino container to store the minimum dt for every particle variable

  erickurquilla1999

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• Delete documentation in Evolve.H header file and input the time step neutrino container in the function that compute the time step

  erickurquilla1999

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• Add a flag to choose between two different methods for computing the time step.

  erickurquilla1999

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• Add a new method to compute the time step based on the time derivative of N and Nbar for all particles.

  erickurquilla1999

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• Delete unnecessary variables and comments.

  erickurquilla1999

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• Add time_step_method flag to input parameters.

  erickurquilla1999

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• Update input parameters.

  erickurquilla1999

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• Improve script that compute dE and antineutrino chemical potential for collisional flavor instability test

  erickurquilla1999

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• Setting asserts at the end of the collisional flavor instability test. In this way the test will always produce a plot that can be convinient for visualization of error

  erickurquilla1999

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• Fix issue with Method 1 for computing the time step

  erickurquilla1999

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• Set collisional flavor instability test to use Method 1 for computing the time step

  erickurquilla1999

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• Fix issue in method 0 to compute time step

  erickurquilla1999

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• Adding comments in st9 initial condition to avoid future confusion

  erickurquilla1999

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• Adding comments to avoid future confusion in fermi-dirac test

  erickurquilla1999

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• Remove 'FIXME' comments.

  erickurquilla1999

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• Return mf_IMFP at the end of the function instead of in every if statement.

  erickurquilla1999

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• Delete print line in main

  erickurquilla1999

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• Create a script to plot the polarization vector components for single particles

  erickurquilla1999

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• Add an if statement to compute the IMFP MultiFab only when the time step method is zero

  erickurquilla1999

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• Set the maximum grid size for every direction in the domain.

  erickurquilla1999

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• Update input file to define max grid size in every direction in the domain.

  erickurquilla1999

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Commits on Nov 27, 2024

• Making convertToHDF5.py script works in 3D simulations

  erickurquilla1999

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Commits on Nov 29, 2024

• Adding a line to stop execution when a NaN appears in N and N bar

  erickurquilla1999

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• Improve section the leave the code is N or Nbar is NaN

  erickurquilla1999

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Commits on Dec 2, 2024

• Plotting best figures in collisional instability test

  erickurquilla1999

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• Adding units to labels and legends

  erickurquilla1999

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• Updating plots and legens in CFI test

  erickurquilla1999

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Commits on Dec 4, 2024

• Delete lines that import unused packages in the collisional instability test.

  erickurquilla1999

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• Setting optimal max_grid_size in tests input file

  erickurquilla1999

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Commits on Jan 4, 2025

• Add a script to save particle information from binary to HDF5, organized per cell

  erickurquilla1999

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• Optimizing script that write particles data per cell. Now it only does the clasification if the file does not exist.

  erickurquilla1999

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• Create a new script for parallel optimization of the write_partices_per_cell script for gpu

  erickurquilla1999

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• Adding an script that write particle information parallelized over grids

  erickurquilla1999

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  773a933

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• Solving issue creating particles file

  erickurquilla1999

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  2d5a3c6

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• Delete thread parallelization

  erickurquilla1999

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• Update write particles per cell script to recive the grid index as input parameter

  erickurquilla1999

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• Delete file

  erickurquilla1999

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• Fix issue with number of amrex grid subdivision

  erickurquilla1999

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