CaNPAN_projects

Introduction

https://github.com/dpa1983/canpan_projects.git is a github public repository with tutorials, Python 3 Jupyter notebooks and other files that are being developed for CaNPAN projects in computational nuclear astrophysics. These projects may require doing both MESA stellar evolution simulations and NuGrid one- or multi-zone post-processing nucleosynthesis computations. For some projects conducting Monte Carlo sensitivity and uncertainty studies for selected reaction rates may also be necessary.

Here are basic instructions on how to get started using canpan_projects tools on Astrohub web servers:

1. Preferably, use the Google Chrome internet browser.
2. If you have not done this before, go to the site github.com and register there for free, e.g. as a student or a teacher.
3. Go to Astrohub Gateway that offers an access to NuGrid WENDI hub (click on the red hub there). It can be used only by NuGrid members (all others can access TINA hub that makes it possible to use canpan_projects tools for beginners). Spawn (by clicking on the orange bar) the Jupyter Lab Application: MESAHub: Run and analyse MESA/NuGrid simulations. Then, in the Jupyter Lab Launcher window click Terminal.
4. In an opened linux terminal window, go to the directory /user/scratch14_outreach, make there a directory with your name and go to it.
5. Inside the new directory your_name execute the following command: git clone https://github.com/dpa1983/canpan_projects.git. It will clone the github repository canpan_projects in your directory.

Running MESA and NuGrid codes on astrohub

Running MESA and NuGrid codes on NuGrid WENDI (wendi2) hub server

To run stellar evolution simulations with the MESA code revision 5329 on astrohub/wendi2, go to a mesa work directory, e.g. to /user/scratch14_outreach/your_name/canpan_projects/nova/nova_framework_canpan/ne_nova, and execute the following commands:

• export MESA_DIR=/user/mesa/mesa_5329
• export OMP_NUM_THREADS=4

Note that these commands must be executed in every MESA work directory where you are going to run stellar evolution simulations.

After that, try to first execute the command ./mk to see that everything is set up correctly, otherwise there will be some error messages. Make sure that the mesa work directory has the sub-directories LOGS, photos, co_nova_hdf (in co-nova) or ne_nova_hdf (in ne_nova), and co_nova_plots (in co-nova) or ne_nova_plots (in ne_nova), and if it does not, make them. For MESA custom stellar evolution simulations, run the code with the command nice -n 19 ./rn. For MESA nova simulations, use the special script with desired nova model parameters, e.g. for an ONe nova case try to use ./run_mesa 1.3 30 X 2010, where 1.3 is the ONe WD mass, 30 is its central temperature in MK, X is the symbol coding the mass accretion rate $$2\times 10^{-10}\ M_\odot\mathrm{yr}^{-1}$$, and 2010 is the number of models to compute (for more details on MESA nova simulations, see README_nova.md file in the nova directory).

To simulate nova nucleosynthesis with a larger nuclear reaction network than in MESA, run the NuGrid multi-zone post-processing nucleosynthesis code mppnp from your copy of the directory run_nova_canpan. To do this on the wendi2 hub server first change, unless it has already been done, the default path PCD=../CODE to PCD=/user/scratch14_wendi3/dpa/nuppn_nova/frames/mppnp/CODE in the file Makefile in the directory run_nova_canpan. Then execute the commands

• make distclean, and
• make

They should not report any errors. For further details, see the README_nova.md file in the nova directory. For NuGrid one-zone post-processing nucleosynthesis computations, the same things have to be done in the directory ppn_nova_canpan.

For NuGrid one-zone post-processing computations of nucleosynthesis in the rp-process during Type-I X-ray bursts on an accreting neutron star use the path PCD=/user/scratch14_wendi3/dpa/nuppn_xrb/frames/mppnp/CODE in the file Makefile in the directory ppn_xrb_canpan.

Running MESA on PPMstar hub server

To run MESA on astrohub/PPMstar load MESA latest lab. Then, in a terminal window go to a mesa work directory, e.g. to /user/scratch14_ppmstar/Pavel/work_mesa_5329, and execute the following commands:

• export MESA_DIR=/user/mesa/mesa_5329
• export OMP_NUM_THREADS=4
• export MESASDK_ROOT=/home/user/mesasdk

The last command is needed only for MESA code installation. If it is necessary, the MESA revision 5329 can be replaced with the revision 7624, in which case a different mesasdk package will probably be required for the MESA code installation.

Running MESA on CSA hub server

To run MESA simulations on astrohub/CSA choose MESA latest lab, go to a mesa work directory, e.g. to /user/scratch14_wendi3/dpa/my_mesa_5329/work, and execute the following commands:

• export MESA_DIR=/user/scratch14_ppmstar/mesa/mesa_5329
• export OMP_NUM_THREADS=4