Description
In this assignment you will write a code to read in the data file you symbolically linked
to your home directory in the first homework, MW 000.txt using Python. We are also going
to get used to keeping track of units using AstroPy.
1 Storing Data Locally
If you wish to download a file from nimoy to your laptop you can do this by:
1. navigate from the command line to the desired place on your computer that you want
to store the file.
2. in command line, type: sftp username@nimoy.as.arizona.edu
3. this will prompt you for your password, then you will be connected to your nimoy
home directory (like with ssh)
4. navigate to wherever the file is on nimoy
5. type: get filename (where filename is the file you want. like MW 000.txt)
The file will show up on your computer in the directory you listed the sftp command.
2 Organization of Data File
Each files is organized as follows:
• First Row is the time in units of Myr (equivalent to SnapNumber*10/0.7)
• Second Row is the total number of particles
• Third Row describes the units of the columns that follows the fourth row
• Fourth Row describes the header name for each column that follows
The remaining rows contain the particle data:
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1. First Column type: Particle Type. Type 1 = Dark Matter, Type 2 = Disk Stars, Type
3 = Bulge Stars
2. Second Column m : Mass of the particle in units of 1010M
3. Third-Fifth Columns x, y, z : Position (x,y,z) in kpc measured from the center of mass
position of the Milky Way
4. Sixth-Eighth Columns vx, vy, vz: Velocity (vx,vy,vz) in km/s measured in a cartesian
coordinate system centered on the location of the Milky Way
Each column is delimited by tabs (spaces)
3 Create a ReadFile Program
Create a new python script, or Jupyter notebook, entitled ReadFile. We will use this code
throughout the course, so if you start with a Jupyter notebook, you will need to download
the final product as a python script (open the File tab, select Download as Python ) so that
you can import it in later programs (like in Part 4).
In ReadFile, create a function called Read that will :
1. open and read the MW 000.txt data file.
2. returns: the time, and total number of particles as variables (first two lines of the file).
3. returns: particle type, mass, x,y,z, vx,vy,vz columns as a data array
To do this, follow these steps in Python (watch your indentation! ):
• the first lines of the code import relevant modules: NumPy and AstroPy
import numpy as np
import astropy.units as u
• Define the function Read that takes the name of the file as input.
def Read(filename):
• open the file
file = open(filename,‘r’ )
• Read the first line and store the time in units of Myr. For example:
line1 = file.readline()
label, value = line1.split()
time = float(value)*u.Myr
Do the same for the 2nd line for the total number of particles.
• close the file
file.close()
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• store the remainder of the file using the NumPy function np.genfromtxt. This allows
you to use the column header information (4th line of the file, starting with #)
data = np.genfromtxt(filename,dtype=None,names=True,skip header=3)
parameters: “dtype=None” means line is split using white spaces
“skip header=3” skipping the first 3 lines .
the flag “names=True” creates arrays to store the data with the right labels
the labels are : ”type, m, x, y,z, vx, vy, vz”
• return the time, total number of particles and the full data array
• test your code!! make sure it returns the right properties. For example, if you
wanted to know the particle type of the 2nd particle in the file you would write
print(data[’type’][1]) and then check this against the real value in MW 000.txt. Make
sure to test the other data labels too.
• If you are in a Jupyter Notebook, download the file as a .py file. This way you can
import it into the next code you need to write. Note, don’t forget to delete the tests
from the actual .py script so that the function can be imported in Part 3.
4 Create a new program, ParticleProperties, that uses
ReadFile
Create a new python script or Jupyter notebook, entitled ParticleProperties. In that code,
create a new function called ParticleInfo, which takes as inputs: filename, particle type and
particle number. The function should return the following properties for any given particle of any given type (Disk, Halo, etc):
1) Magnitude of the distance in kpc;
2) Magnitude of the velocity in km/s;
3) Mass in units of M .
Round the distance and velocity values to 3 decimal places using np.around(value,3).
Since you need to read in the file again, call Read from ReadFile by adding the following to
the list of modules: from ReadFile import Read
Hints:
• To read in, say, the x position of all particles: x = data[‘x’] . Don’t forget to assign
kpc as the unit using AstroPy (or km/s for velocity).
• To create an index for all particles with a given property, use the NumPy function
np.where. For example, if I wanted to store all x components of particles that are more
than 2 kpc away in the x component, I would write:
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index = np.where(data[‘x’] > 2)
xnew = data[‘x’][index]
5 Prove Your Codes Work!
Use ParticleProperties to determine the following properties of 100th disk particle of the
Milky Way at SnapNumber 0 (be careful of indexing to get the right particle!):
1. 3D Distance,
2. 3D Velocity
3. mass
4. Convert the 3D Distance of the particle to LIGHTYEARS (3 decimal places) using
AstroPy (hint: use the “to” function – google it if you’re not sure ! ).
6 Homework Submission
• You must DOCUMENT your code . Explain EACH step. I’m not joking.
• Clone your class repository (or go to your cloned version).
• Create a directory called Homeworks/Homework2. Save your code and answers to
question 5 in that directory. Your answer to question 5 should be saved EITHER:
1. As part of your Jupyter notebook solution.
2. Take a screen shot of your python output (with the relevant print statements for
each quantity) from the command line.
• Push your Homework2 directory to your public 400B yourlastname repository on GitHub
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