Scripts and Programming

Collects for useful shell, gnuplot and python scripts & codes

Find all xml files in source and run saxon to transform and save the object files to output files with same directory structures	​XML transform script;​testing cases	The java files folder and stylesheets folder are all located under the same folder as the script
Get Max and Min of one column of all ASCII data files using gnuplot	​shell script;​gnuplot script	data files example Rho000.data and Vy000.data. All located under test/
Python function with multiple returns	​multiple return function	test. one return is a list
Python script to read csv file	​read csv file; ​example csv file	the example csv file comes from DDiMAP
Python scripts to read, write and parse fasta files	​read;​write; ​parse; ​fasta file to a List; ​example fasta file	biopython needed. The example fasta file comes from DDiMAP
Python Script to rotate and save Window in VisIt	​Save to curve	Save line plot to curve/text file
Python Script to rotate and save Window in VisIt	​Rotate&Save	Tested with VisIt 2.6.2
Relink all executable files in all the subdirectories	​Relink astrobear for all subfolders	For Bruce, on alfalfa
Convert gif files to movie files on Mac	​Movie Convert	Using ffmpeg; For Mac
Interpolate from fine grids to coarse grids with AstroBEAR	blog:bliu08282014	Set Info%ErrFlag to be 1; Read in data and set as level 1 AMR grid instead of 0
cherry pick the values for specific time steps	​transfer gravity;	pick up gravity values around ts
hdf5 data to txt	​HDF5 to ASCII; ​ASCII to TXT;	The hdf5 files need to be from single-core runs
Read in chombo files with multi-processors and reWrite the same frame using single-core. Useful when transferring hdf5 files to txt files.	​scrambler.f90; ​subst for run-directory; ​script;	Replace the scrambler.f90 file with the new one. The frame number in script need to be updated. 8.19.2014
bash and gnuplot script: plot Multiple Data files to Multiple eps	​plot.sh ​gnuplot template	bash arithmetic expressions; use gnuplot to generate multiple figures; special symbols in gnuplot; use gnuplot variables in title; string parse in bash script; multiplots; multipanels; convert eps to png file…
Scripts to transfer the hdf4 file to text on BH2	​hdf4_to_ascii; ​combine_pos_var; ​combine_pos_var; ​combine_pos_var_v2	hdf4 module needed
Extended 2D data to 3D (Set Precisions!)	​SI along y;​SI along z; ​cgs along z;	Generate 3D initial data to testing the Ablative RT 3D module code. The initial profile is along y/z direction. Everything along z is same. 2D data in 2Ddata/ and 3D data generated in 3Ddata/