Author Commit Message Labels Comments Date
Devin Silvia avatarDevin Silvia
actually fixed the running script now.
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demo
Devin Silvia avatarDevin Silvia
correction to run_oxygen_network.out
Devin Silvia avatarDevin Silvia
minor README correction
Devin Silvia avatarDevin Silvia
added information about the CHIANTI dependency in the README
Devin Silvia avatarDevin Silvia
created a run_oxygen_network.py script to run the compile and run the solver and then plot the results
Devin Silvia avatarDevin Silvia
made modification to the plotting script to produce an initial vs. final plot
Devin Silvia avatarDevin Silvia
added the plotting script
Devin Silvia avatarDevin Silvia
this version doesn't not include electrons in the temperature calculations. this is done to make the problem strictly isothermal, but we need to determine how to correctly handle electrons. this version also outputs intermediate solutions for successful solver iterations.
Matthew Turk avatarMatthew Turk
Adding plotting script
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dev
Devin Silvia avatarDevin Silvia
added time and timestep attributes to the solution outputs.
Devin Silvia avatarDevin Silvia
Trying to make sure that 'ge' is being evolved in the right way, conversion factors added to convert from specific energy density to energy density.
Devin Silvia avatarDevin Silvia
added code to output intermediate and final solutions. also removed electrons from the number density calculations so that they wouldn't effect temperature. To put this back in, need to change the initial conditions generation and chemical_network.py (put 1/weight back in gamma_factor function). Can run O species to CIE in 1e9 years with n_O = 1. (128 cells)
Matthew Turk avatarMatthew Turk
Many fixes.
Matthew Turk avatarMatthew Turk
Merge
Matthew Turk avatarMatthew Turk
Primordial network now only outputs 8 cells, and just the
Matthew Turk avatarMatthew Turk
We don't want to include electrons in the mass density, either.
Devin Silvia avatarDevin Silvia
Work through the creation of ICs and the computation of temperature and gas energy to make sure things were being done correctly. Things now appear to work correctly for the oxygen network. The IC temperatures are returned by the C code in a matching fashion. Additional, the values of the RHS for the oxygen species seem to be calculated correctly. The current issue is that the solver doesn't actually evolve the species and things are "solved" This appears to stem from issues with atol and rtol, which may related to the fact that some things are positive definite.
Matthew Turk avatarMatthew Turk
This crazy, bloated contraption is able to solve with a mere 10 iterations the
Devin Silvia avatarDevin Silvia
added a write_oxygen_network.py to test the solver with oxygen. It seems to be suffering for the same issues as the primordial network. rhs_total is always equal to rhs[de]. Things explode into unrealistic values. This may still have something to do with how electrons are being handled.
Matthew Turk avatarMatthew Turk
Fixing up some issues with cooling terms and setting time to something
Devin Silvia avatarDevin Silvia
multiplied by a factor of 'mh' in the equation to calculate temperature. this also changes the output of dT/dge. Still produces a non-convergent result.
Devin Silvia avatarDevin Silvia
printing logT info as well.
Matthew Turk avatarMatthew Turk
Fixing rtol/atol sizes
Devin Silvia avatarDevin Silvia
changed some print commands to get more information at runtime
Matthew Turk avatarMatthew Turk
This adds a few debugging outputs and fixes a few offsets and issues.
Matthew Turk avatarMatthew Turk
* Adding BE_chem_solve from Dan Reynolds' Enzo repository. Note that this
Devin Silvia avatarDevin Silvia
Re-wrote the header comment at in the C++ template code.
Matthew Turk avatarMatthew Turk
A few minor compilation errors fixed.
Devin Silvia avatarDevin Silvia
Added some template code for reading in initial conditions data. Right now it's just in 'main', but it could potentially be put into a separate function if desired. the 'ics' array should be able to be passed into the calculate_temperature function.
Devin Silvia avatarDevin Silvia
First pass on adding initial conditions generation to write_primordial_network.py and added a function to write_rate_reader.py to dump the initial conditions into an HDF5 file. Still need to added code to the template to set up an initial condition reader.
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