Bradley S. Meyer Blog

Previous posts have assumed users have installed the necessary linux/os or Cygwin libraries on the user's own computer. While this procedure has generally worked, some users may find it too complicated or may run into trouble because of installed library conflicts.... read more

Calculations shown in this blog have, to date, used as default the network file my_net.xml. This file is by now somewhat out of date, so in this post I will show how I updated the data from JINA. I will then describe how to download the various available files.

To begin, I installed the Nucnet-Project jina_to_webnucleo. Once I successfully compiled the project with project_make, I then download the default Reaclib library. My download was called results12011649. I also downloaded the file winvne_v2.0.dat. I moved these files to the jina_to_webnucleo directory. Next, I converted the JINA nuclear data to an appropriate webnucleo XML file by typing... read more

In my previous post, I added fission cycling to an r-process calculation. For the given initial conditions and no fission, the nuclear flow to higher charge caused the abundance distribution to pile up at the top of the network. When fission was included, however, nuclei could fragment into smaller pieces and start capturing neutrons and working their way up to higher charge again. This is called fission cycling during the r-process of nucleosynthesis. In this post I explore fission cycling in some more detail.... read more

I have previously shown how to run an r-process calculation. This calculation, however, did not include fission cycling. In this post, I show how I can do this. To illustrate, I will allow two of the heaviest nuclei in the network to fission, and since I will limit the nuclei to Z <= 90, I will have the Z = 89 and Z = 90 with N = 184 isotopes fission. This requires creating some fission reaction data and adding it to the input for the network calculation.... read more

The most convenient way to input data into our reaction network codes is with XML input. If you have your own reaction rate data and would like to put it in the appropriate XML format, there are libnucnet example codes available to do that. We have also written a Python routine create_reaction_xml.py that you can use to convert reaction rate text data to our XML. I describe how to do that in this post.... read more

In my previous blog posts, I have used compiled codes to read output from calculations with NucNet Tools. To make graphs, I have output data into columnar format and then used other programs (mainly IDL in my case) to make graphs. In this post, I describe our package wnutils, which allows a user to read and plot output data from NucNet Tools with Python.... read more

I previously showed the packages to install to run NucNet Tools codes on Cygwin. In this post, I show how to install the necessary packages by typing in a single command. To do so, open in Windows a Command Prompt. The easiest thing to do is to type cmd into the command search window near the Windows start icon. That opens the Command Prompt, which will show something like:... read more

In my last post, I listed the packages necessary to install to run NucNet Tools codes on Cygwin. These packages allow you to run nearly all calculations described in this blow. To make flow diagrams in Cygwin, however, you will need to install dot2tex separately. Note that linux users should already have installed this if they typed the explicit commands to install packages needed for NucNet Tools.... read more

In my last post, I showed the explicit commands for installing the linux libraries needed for NucNet Tools and related codes. The libraries to install are drawn from a list that I will update as needed. Users should refer to that post to keep their library installations up-to-date.

In this post, I similarly list the packages one needs to install for Cygwin. Those packages are here. Like the linux/MacOs list, I will keep this list up-to-date, so Cygwin users should refer to this list as frequently as needed.

I have previously shown how to install libraries needed for NucNet Tools and related codes for linux and MacOs. I now maintain an updatable list of packages (libraries) for various flavors of linux, and in this post, I show the explicit commands one would type to install the needed packages.... read more

In previous posts, I have plotted mass fractions versus properties from output xml by printing properties to one file and mass fractions to another. In this post, I will show how to use the code analysis/print_output to print the desired data to a single file.

I begin by rerunning the first calculation presented in this blog, namely, simple hydrogen burning. I carry out the steps in that post again by typing... read more

In my recent posts, I have been running calculations with the network/run_entropy.cpp examples code. These calculations have had the parameter τ set to infinity, so the density has remained fixed. In this post, I will show how to use the code to run network calculations with simple one-zone hydrodynamics.

The starting point is to consider a ball of radius R. We consider the ball to have uniform properties, such as the density, which can change as the ball's radius expands or contracts with time. The run_entropy.cpp code solves a set of three similtaneous first order differential equations for the three quantities x[0], x[1], and x[2]. Together these quantities form a state vector x. The three components of x are, first, the scaled radius... read more

In a previous post, I showed how one can modify reaction rates during a network calculation. This was done with the default rate modifier, which uses views to select out reactions and then multiply them by a constant factor. In this post, I will show how you can modify rates with your own rate modification routine.... read more

In my last post, I included NSE (Coulomb) corrections to the chemical potentials of the nuclear species in a constant entropy calculation. These NSE corrections affect the relationship between the forward and reverse nuclear reaction rates in detailed balance and, consequently, the final NSE abundances to which the system evolved. The calculation did not, however, include corrections to the entropy. This is a slight inconsistency that I will address in this post.... read more

In my last post, I studied the default NSE corrections in NucNet Tools (specifically, the Coulomb corrections in Bravo and Garcia-Senz). In this post, I will apply these corrections to a network calculation.

I will use the constant entropy calculation I previously made. I will in fact make two calculations--one with screening but no NSE corrections and one with both screening and NSE corrections. I begin by editing my nucnet-tools-code/data_pub/zone.xml file from the previous calculation. I first run the calculation with screening but no NSE correction. I change the use screening property from no to yes:... read more

In a previous post, I included electron screening in a network calculation. Because electrons surround nuclei, they "screen" the positive charge of the nuclei, thereby making it easier for interacting nuclei to overcome their mutual Coulomb repulsion. The Coulomb interaction of nuclei and electrons also alters the energy of the nuclei away from the simple ideal gas form usually used in network calculations. This changes the chemical potential of species and, therefore, their abundance in nuclear statistical equilibrium (NSE).... read more

In a previous post, I demonstrated how to compile NucNet Tools with clang and gcc. Since then, we have made NucNet Tools dependent on Boost program options, which are compiled libraries. This adds some difficulty in that the libraries compiled for gcc are not compatible with clang. In this post, I will show how I switch between gcc and clang to compile NucNet Tools.... read more

In my last post, I ran a calculation at fixed density with no charge-changing reactions but with entropy generation. The calculation began with pure ⁴He at a mass density of 3 x 10⁹ g/cc and a temperature of 2 billion Kelvins. The system evolved into nuclear statistical equilibrium (NSE) in about a nanosecond with a temperature of 10.318 billion Kelvins.... read more

In a previous post, I ran a network calculation at constant entropy. In a subsequent post, I computed the entropy generation rate for that network calculation. The modeled system generated entropy during its expansion; thus, holding the entropy constant is not a consistent treatment. In this calculation, I will include entropy generation in my network calculation.... read more

In my last post, I showed how to compute electron screening and include it in a network calculation. In this post, I will how a user could change the screening to his or her own parameterization.

The parameterization I will use here is that of DeWitt, Graboske, and Cooper. I first write files my_screen.cpp and my_screen.h, based on screen.cpp and screen.h in the nucnet-tools-code/user directory. The file my_screen.cpp, like the parent screen.cpp, has five key functions:... read more

In this post, I will demonstrate how to include the default screening in a network calculation. Electron screening arises from the fact that the Coulomb potential of a nucleus can be altered by the surrounding charges. In the case of an astrophysical plasma, the nucleus can attract an electron cloud which screens the positive nuclear charge from other charges. The effect is to make it easier for a charged projectile nucleus to penetrate the Coulomb barrier of a charged target nucleus thereby enhancing the reaction rate.... read more

In a previous post, I mentioned that NucNet Tools examples now depend on the Boost program options library, which is a compiled library. This should present no problem to users who install Boost through the normal instructions. Neverthless, there may be users who wish to work with their own installation of Boost. In this post I will show how to do this.... read more

In my previous post, I explored the entropy generation rate during a network calculation by computing that rate for a particular reaction, namely, ⁴⁶Ar + ⁴He → ⁴⁹Ca + n. I was able to confirm the value of the rate at a particular time step with available data. That rate did not change the electron-to-nucleon ratio. In this post I will repeat the exercise of confirming the entropy generation rate for a reaction, but this time I will do it for a weak decay since this is a more complex calculation.... read more

In my previous post, I computed the entropy generation rate during my constant-entropy r-process calculation. The calculation showed substantial entropy generation at certain points during the calculation. In this post, I will seek to understand that entropy generation.... read more

In my previous post, I ran an r-process calculation at constant entropy. In this post, I will begin to consider to what extent the entropy would really be constant in such an expansion by computing the entropy generation rate (in units of Boltzmann's constant) during the calculation.... read more