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Marissa Adams (madams@pas.rochester.edu)
Graduated from the University of Rochester with a Physics B.S., and Mathematics B.A. From May 2014 to August 2015 I have been employed as a technical assistant in the group. In the Fall of 2015 I will be continuing my education at the University of Rochester Department of Physics & Astronomy as a PhD student (plasma physics). Here, on my page, I am documenting, as well as describing projects I have worked on/assisted with during my stay! Hopefully you find it useful.
Projects
CollidingFlows
Image 1. Temporal evolution of the column density map of two colliding flows over approximately 27 Myr. Left panes are the projection of the mass down the x-axis, down the barrel of the two flows. The right panes illustrate the collision region, looking down the y-axis. Units of distance are in parsecs. Pink points are the sinks that form. The flows collide at a shear angle of 15 degrees from the normal.
With E. Kaminski, A. Frank, F. Heitsch, C. Hiag, and J. Carroll-Nellenback.
- See the CollidingFlows Figures for our paper.
- My page on the particular E vs. t Plots featured on our figures page, mentioned above.
- Erica's High Resolution CollidingFlows Page.
For this project I was tasked with managing and running the supercomputer jobs, which spit out over 30 TB of output! I also visualized all the output, and did the post processing.
Visualizing PN/PPN Data with SHAPE
With B. Balick, M. Huarte-Espinosa, A. Frank.
Under Construction
- Shape Wiki User Guide that I have crafted.
Turbulence Studies
With J. Carroll-Nellenback, A. Frank.
Scripts
Image Compressor (bash)
- Utilizes ghost script.
- Takes an image and compresses it. Good for larger vector images.
- Wrote a blog post on it for shits and giggles.
#!/bin/bash
#Script compressor.sh
files=$@
if [ "$files" == "" ];
then
echo "Error: No files specified, dude."
exit
fi
for i in $files;
do
echo \"$i\"
gs \
-o "${i%.pdf}-comp.pdf" \
-sDEVICE=pdfwrite \
-dColorConversionStrategy=/LeaveColorUnchanged \
-dColorsampleMonoImages=false \
-dColorsampleGrayImages=false \
-dColorsampleColorImages=false \
-dAutoFilterColorImages=false \
-dAutoFilterGrayImages=false \
-dColorImageFilter=/FlateEncode \
-dGrayImageFilter=/FlateEncode \
"${i}"
done
Name Changer (python)
- For post processing elements (in particular column density maps).
- Changes the name of the file easily so you don't have to do funky visualization stuff in visit.
import os
import sys
start = int(sys.argv[1])
end = int(sys.argv[2])
for i in range(start,end+1):
inpfig="Mass_along_1_00"+str(i)+".bov"
outfig="mass1_along_1_00"+str(i)+".bov"
sfig = "mv %s %s" %(inpfig,outfig)
os.system(sfig)
.okc to .csv Converter (python)
- Reads in .okc files, converts the data in the .okc to proper units, spits out a .csv so you can import the data into excel.
#!/usr/bin/env python
# ^ program.py not python program.py
import glob
import numpy
time_scaler = 0.00825*3.81360279481384188E+14*3.16888E-8*1E-6
mass_scaler = 0.619591607894786331E+32*5.03E-34
# cd into the out directory
out_dir = "./out/"
# Accessing the *.okc files and sorts them
lst = glob.glob(out_dir + "*.okc")
lst.sort()
with open("./s15_rawsink_data_scaled.csv", "w") as sink_f:
sink_f.write("Time" + "," + "Core 1 Mass" + "," + "Core 2 Mass" + "," + "Core 3 Mass" + ","+ "Core 4 Mass" + "," + "Core 5 Ma\
ss\n")
for i in range(0,len(lst)):
with open(lst[i]) as f:
okc_lines = f.readlines()
noparams, nosinks, noparams_mm = [int(x) for x in okc_lines[0].split()]
sinkdata =[float(y[3]) for y in [x.split() for x in okc_lines[-nosinks:]]]
sink_f.write(str(i*time_scaler) + ",")
for j in sinkdata:
sink_f.write(str(j*mass_scaler) + ",")
for j in range(0,5-len(sinkdata)):
sink_f.write("0.0" + ",")
sink_f.write("\n")
Post Processing Submissions (bash)
- Creates post processing directories in your out directory.
- Edits and submits the jobs for your executable.
- You do have to manually move the simulation into the directory once the job has completed.
#!/bin/bash
## INITIALIZING INVARIANTS ##
#Put the name of your executable here!
EXECUTABLE="astrobear_Bvn"
#Put the name of your bash script here!
SUBMISSION_SCRIPT="job.sh"
## FINDING RUN DIRECTORIES ##
#/scratch/[USERNAME]/[REST OF PATH]/ Make sure script is here <--
cd /scratch/[USERNAME]/[REST OF PATH]/
PP_PATH="Directory1, Directory2"
## MAKING A LOOP ##
for d in ${PP_PATH}; do
cd ${d}
## MAKING UNIQUE DIRECTORIES ##
#Name of the directory we're going to create in...
DIRECTORY_NAME="${EXECUTABLE}_`echo ${d} | tr -d '/'`_`date +%s`"
#your out directory.
OUTPUT_DIR="out/"
#Checker to see if you have an out directory.
if [ \! -e ${OUTPUT_DIR} ] || [ \! -d ${OUTPUT_DIR} ]; then
echo "There is a problem with your ${OUTPUT_DIR} directory, please check. Exiting."
exit
fi
#Makes a new directory in your out directory for post processing with the executable, run, and date in the name.
mkdir out/${DIRECTORY_NAME}
## EDITTING BATCH SCRIPT ##
#Note this change is universal for all PP_PATH
sed -i 's/--reservation .*//' job.sh
sed -i 's/-N .*/-N 32/' job.sh
sed -i 's/--ntasks-per-node .*/--ntasks-per-node 16/' job.sh
sed -i 's/-c .*/-c 1/' job.sh
sed -i 's/-p .*/-p debug/' job.sh
sed -i 's/--time .*/--time 00-00:30:00/' job.sh
sed -i 's/#SBATCH --mail-user email1@pas.rochester.edu/##SBATCH --mail-user email1@pas.rochester.edu/' job.sh
# sed -i 's/#SBATCH --mail-user email2@pas.rochester.edu/##SBATCH --mail-user email2@pas.rochester.edu/' job.sh
sed -i "s/astrobear.* > astrobear.*.log/${EXECUTABLE} > ${EXECUTABLE}.log/" job.sh
## SUBMIT BATCH SCRIPT ##
sbatch ${SUBMISSION_SCRIPT}
cd ../../
done
Recent Blog Entries
Page last updated at 06-02-2015.
Attachments (2)
- pview1b_Martin.pdf (16.9 MB ) - added by 10 years ago.
- s15cdm.png (8.1 MB ) - added by 10 years ago.
