Welcome back!
If you were here last week and you have already cloned the github repository,
you can update the phs directory with all of my new updates by navigating to
the phs directory (by changing directories with cd phs), and then
running git pull. This command 'pulls' any updated files from the github
repo into your own personal computer. Now, if you list the files (ls) in this
directory you should see a new week_2 folder. Move into this directory.
Before we get too involved, let's take a moment to recap what we learned last
week. Move up to the parent directory and then into the week_1 in one
command, with cd ../week_1. Be sure to tab complete! In the week_1
directory there are cheatsheets for the shell and for vim. Let's open and read
through the shell cheatsheet with vim shell_cheatsheet.md. Close the file in
vim with :q or :q!. Now open and read through the vim cheatsheet file. Now
move back to the week_2 directory with cd ../week_2.
Now that we're in week_2 (check with pwd), we're going to make a fake
directory that holds our classwork with mkdir classes. Now move into this
directory, using tab complete. Let's make a new empty file for quantum with
touch quantum (check to see that it is empty using cat, head, tail, or
ls -lah). Print text in the shell using echo (try echo "Hello, world").
Make a new file using this text with the redirection command >. Therefore, to
store some text about E&M we can use echo "Maxwell's equations" > em. To
append things to this file we use >>, while using >
overwrites. Therefore we can remind ourselves about more E&M things with echo "everything is a multipole expansion" >> em. Lastly let's make a file in vim
for classical mechanics with vim classical, write your favorite equation in
insert mode (press i in regular mode), escape insert mode with Esc, and write
and quit (= save and close) the file with :wq in regular mode.
% pwd
/home/eric/phs/week_2/classes
% touch quantum
% echo "Maxwell's equations" > em
% echo "everything is a multipole expansion" >> em
% vim classical
% ls
classical em quantum
% ls -lah
total 36K
drwxr-xr-x 2 eric users 4.0K May 10 15:30 .
drwxr-xr-x 3 eric users 4.0K May 10 15:31 ..
-rw-r--r-- 1 eric users 7 May 10 15:30 classical
-rw-r--r-- 1 eric users 56 May 10 15:27 em
-rw-r--r-- 1 eric users 0 May 10 15:20 quantum
What if we want to learn information from all of these files at once? We can
use the wildcard operator *, which returns all matching entries. For example,
ls * will list all of the files, ls e* will only return entries that begin
with e (this will return em), and ls *m will only return entries that end
with m (this will return em and quantum). Try out these commands.
We can use this wildcard operator anywhere in the command line that would
typically except a filename. For example, to list all of the contents of all of
our files, we can use cat * (concatenation). Even further, we can take
all of our class information and turn it into one big file by redirecting
the output of cat * to a new file with >:
% cat * > all_my_classes
% ls
all_my_classes classical em quantum
% cat all_my_classes
F = ma
Maxwell's equations
everything is a multipole expansion
Let's say that classical is a well-made file, and we want to use it as a
template for some other file. Copy it to a new file with cp classical new_classical. Let's additionally say that we want our all_my_classes file
to be more specific, so we can move it to have a new name with mv all_my_classes class_notes_winter_2018.
Let's say that you really didn't like quantum and didn't learn anything (hence
why it is empty!). To remove the file, we use rm quantum. Ensure we
have removed it with ls. WARNING: This is not your childproofed delete from
Windows or Mac-- when you remove something, it is gone for good. There is no
recycle bin (unless you choose to make one). rm can be dangerous, especially
when combined with the wildcard (be very careful before running rm *!).
Now it is springtime, and we need to do some spring cleaning to make our classes directory relevant for this quarter. Let's make a separate directory in the parent directory for classes from winter 2018:
% mkdir ../winter_2018
% ls ..
classes README.md winter_2018
% pwd
/home/eric/phs/week_2/classes
Note that here we executed commands that 'remotely' by using them with the
parent directory variable ... Now, we wish to move all of our files to this
winter_2018 directory, which we can do with mv * ../winter_2018. Here the
wildcard selects all files, and moves them to our recently created directory.
Ensure this is the case with ls and ls ../winter_2018. Finally move to the
week_2 directory with cd ... If you want, you can delete the two
directories you created with rm -r winter_2018 classes, but you can also keep
them if you want. Again, be careful! rm -r will delete without asking for
your approval, and there is no 'undo'.
Next we will work through more shell exercises that were originally located in
phs/shell/exercise_1.
Files in your home directory that start with a . (they are 'hidden') and end
in rc are configuration files for given program. Today we will modify a
.bashrc, which gives options for bash (which is probably the shell you are
using). You can ensure this with echo $0 (every line you enter into the shell
is literally passed to the bash function (or whatever this command returned),
and the shell organizes the input and output in a user-friendly command line).
Your .bashrc file is executed line by line in bash every time you start up
bash or open a terminal, which effectively personalizes your shell.
Ensure you are in the week_2 directory with pwd. A sample bashrc is already
in this week_2 directory as my_bashrc. Investigate it with
head/tail/cat. See if you have a .bashrc already located in your home
directory. Since it is a dotfile, you need to specify the -a (all) command to
ls: ls -a ~. Whether or not you already have one, open one in vim with vim ~/.bashrc. Once open in vim, open my sample file in the same vim screen with
:vsplit my_bashrc.
Now we will use vim to copy and paste select lines from one bashrc to the
other. You can tell which file is which on the bottom, where it will say
my_bashrc or ~/.bashrc. Switch between the two sides of your screen with
Ctrl-W Ctrl-W in normal mode. Select some text in my_bashrc with visual
block mode V, then sweeping text with j or k, and they yanking (=copying)
with y. Change screens with Ctrl-W Ctrl-W, navigate to where you want it
with j and k, and paste it with p or P.
We will work through the lines in the bashrc together. Briefly, an alias is a
keybinding, so alias v='vim' means that anytime I type v, it literally gets
turned into the command vim. Think of these as 'keyboard shortcuts'.
Functions in bash execute a series of commands that act on the function
parameters. $@ means 'all of the parameters you pass', $1 means 'the first
parameter you pass', and so on. PS1 is what your shell prompt says (for me it says
eric@eric-arch ~). If you wanted, you could put echo "Hi there" in your
.bashrc, and every time bash opened it would greet you with "Hi there".
If you want more examples of what experienced users put in their .bashrc, try
this
thread
for some ideas
Ensure you are in the week_2 directory with pwd. Now we're going to examine
the contents of the file othello.txt with command-line tools. Spoiler alert
for anyone who hasn't read Othello... We will:
- Estimate how many lines Othello has, and how many Lodovico has
- Print out the first sentence of each of Othello's lines
- See how many times Othello's name is called in the play
First, print out the file (using cat or head) to get an idea of the structure:
% cat othello.txt
Othello, the Moore of Venice
[1]Shakespeare homepage | [2]Othello | Entire play
#### Many more lines here ####
LODOVICO
[To IAGO] O Spartan dog,
More fell than anguish, hunger, or the sea!
Look on the tragic loading of this bed;
This is thy work: the object poisons sight;
Let it be hid. Gratiano, keep the house,
And seize upon the fortunes of the Moor,
For they succeed on you. To you, lord governor,
Remains the censure of this hellish villain;
The time, the place, the torture: O, enforce it!
Myself will straight aboard: and to the state
This heavy act with heavy heart relate.
ExeuntNow use less to view the document with less othello.txt. In less you can
navigate using the same key bindings as in vim, so 'j' and 'k' scroll up or
down, and 'f' and 'b' page through forwards and back. Notice that everytime
Othello speaks, the document first prints OTHELLO. Based on this pattern, we
can find Othello's lines using grep (the syntax for grep is grep PATTERN FILE, where PATTERN is what you are searching for, and FILE is the file you're
searching; for details check out man grep):
% grep 'OTHELLO' othello.txt
OTHELLO
OTHELLO
#### Many more lines here ####
OTHELLOTo count the number of entries that grep found, we can use the '-c' option. We apply this to count Othello's lines:
% grep -c 'OTHELLO' othello.txt
296Another alternative is to PASS all of the lines of grep's output into another
command line program. This is called 'piping', and uses the character |. This
is similar to redirection (< or <<), but it pipes the output from one
program into the input of another. Here we use the 'word count' program wc,
with the option -l which counts the number of lines. Notice that there are
usually many ways to solve a problem, and there are lots of powerful and small
command line programs that can be combined with pipes.
% grep -c 'LODOVICO' othello.txt
39
% grep 'LODOVICO' othello.txt | wc -l
39Print out the first line of each of Othello's lines using the '-A' option
for grep. Unsure what -A does? Use man grep, then search (/) for -A with
/-A + Enter. Use q to quit the man page. In this case, grep -A 2 'OTHELLO' othello.txt will print the line containing 'OTHELLO' as well as
the following two lines (-A for After).
% grep -A 2 'OTHELLO' othello.txt
OTHELLO
#### Many more lines here ###
OTHELLO
O fool! fool! fool!
--
OTHELLO
Soft you; a word or two before you go.
--
OTHELLO
I kiss'd thee ere I kill'd thee: no way but this;If we wanted to navigate this in an easier way, we can pipe the output of this
command into less with grep -A 2 'OTHELLO' othello.txt | less, in which you
can use vim-style navigation key bindings.
Next we are going to extract information with the a toy data file containing random
data, data_file.csv. Using command line tools, we will:
- Display the 'Reduced Chai Values' and 'Final Energy Values'
- Show only the last two 'Reduced Chai Values'
- Find out how many data lines are in the file
- Find out how many data points are in the file
First get an idea of what the file looks like with less. Use the search
function of less (press '/' followed by your search string, for example
'Values') to probe the file's contents. Use the 'n' key to jump to the next
match, 'N' to go to previous. Use the keys 'k' and 'j' to scroll.
% less data_file.csv
Reduced Chai Values:
6575839, 7151022, 7334710, 4978808
#### Many more lines ####
Final Energy Values:
3880766, 14001684, 13718481, 8132653
#### Many more lines ####Find the 'Reduced Chai Values' and 'Final Energy Values' by calling grep with
the '-A' option. Pipe the second into less to be able to scroll through and
search the output.
% grep -A 1 'Reduced Chai Values' data_file.csv
Reduced Chai Values:
6575839, 7151022, 7334710, 4978808
--
#### More lines here ####
Reduced Chai Values:
9074041, 6222272, 14989142, 5701998
% grep -A 1 'Final Energy Values' data_file.csv | less
Final Energy Values:
3880766, 14001684, 13718481, 8132653
--
#### More lines here ####
--
Final Energy Values:
10340226, 8981179, 12774173, 8236417
lines 1-65To show only the last two 'Reduced Chai Values', pipe the output of grep into
tail, and tell tail to only output the last 6 lines with the '-n' option.
% grep -A 1 'Reduced Chai Values' data_file.csv | tail -n 6
--
Reduced Chai Values:
1056171, 5042308, 4669985, 10144310
--
Reduced Chai Values:
9074041, 6222272, 14989142, 5701998
Use the '-c' option for grep to count the data lines, coupled with the '-v'
option to invert the selection (only showing lines that DO NOT match the
search; in the following case we show any line not containing a colon). As
before, you can also use the wc (word count) command to count the number of lines grep
outputs.
% grep -c -v ':' data_file.csv
5000
% grep -v ':' data_file.csv | wc -l
5000To verify there are four data entries on each line, we will count the total
number of data points using the word (-w) option of wc instead of the line
(-l) option.
Again, we grep for all of the lines containing data with the '-v' option for
grep, and then pipe the output into wc.
% grep -c -v ':' data_file.csv | wc -w
20000Therefore, since there are 5000 lines and 20000 'words', there are four data entries per line (unless the file isn't uniform).
Next we will perform similar exercises, but this time use the supercomputer
output file dextran_qm_dft.out. We will:
- See the steps and energies for each relaxation of the dextran molecule
- Save the energies for each relaxation step
- Save the geometries along each relaxation step
- Combine the energies and geometries into one file
As always, first get a feel for the file by displaying it with less (or
vim). Knowing that NWChem outputs a @ at the beginning of a line with
energy information on it, search for ^@. The ^ is a regular expression that
matches the beginning of a line, so this search only returns lines that begin
with a @. If we wanted to only search for @, we need to use /\@, where
the \ is an escape character-- these are needed when the character we are
searching for has other uses in the program. Also search for 'Geometry' to get
an idea of what those parts of the file look like.
% less dextran_qm_dft.outPlease copy the file /lrz/sys/applications/nwchem/6.3/impi/.nwchemrc to your
home directory.
This file is necessary for NWChem to find the standard libraries.
argument 1 = optimize.nw
#### More lines here ####
Northwest Computational Chemistry Package (NWChem) 6.3
------------------------------------------------------
Environmental Molecular Sciences Laboratory
dextran_qm_dft.out lines 1-65/24471 0%
Now that we are familiar with the output format, let's use grep to grab only
the lines we need from the file. Once again, the '^' tells grep to only match
'@' symbols at the beginning of a line. Note that the syntax of regular
experessions (e.g. how we are using ^) is preserved across programs. We can
save these energies and deltas by redirecting the stdout of grep to another
file, 'dextran_energies.out'.
% grep '^@' dextran_qm_dft.out@ Step Energy Delta E Gmax Grms Xrms Xmax Walltime
@ ---- ---------------- -------- -------- -------- -------- -------- --------
@ 0 -686.92664205 0.0D+00 0.02562 0.00530 0.00000 0.00000 124.6
@ 1 -686.93572937 -9.1D-03 0.00495 0.00123 0.05800 0.21419 230.6
@ 2 -686.93688173 -1.2D-03 0.00371 0.00079 0.03159 0.12217 377.7
@ 3 -686.93728094 -4.0D-04 0.00183 0.00045 0.02043 0.06471 536.9
@ 4 -686.93765371 -3.7D-04 0.00231 0.00055 0.02664 0.09902 685.2
@ 5 -686.93795400 -3.0D-04 0.00218 0.00046 0.02601 0.08722 834.3
@ 6 -686.93815263 -2.0D-04 0.00214 0.00036 0.02147 0.06602 982.6
@ 7 -686.93820464 -5.2D-05 0.00078 0.00014 0.00714 0.01937 1114.2
@ 8 -686.93823383 -2.9D-05 0.00089 0.00015 0.00618 0.01997 1236.3
@ 9 -686.93825965 -2.6D-05 0.00063 0.00014 0.00684 0.02057 1365.8
@ 10 -686.93828289 -2.3D-05 0.00065 0.00012 0.00676 0.02784 1504.9
@ 11 -686.93829701 -1.4D-05 0.00049 0.00010 0.00514 0.02142 1618.2
@ 12 -686.93830468 -7.7D-06 0.00046 0.00008 0.00443 0.01556 1748.7
@ 13 -686.93830745 -2.8D-06 0.00013 0.00003 0.00102 0.00292 1827.3
@ 14 -686.93830891 -1.5D-06 0.00006 0.00001 0.00100 0.00300 1906.5
@ 15 -686.93830931 -4.1D-07 0.00005 0.00001 0.00041 0.00128 1978.5
@ 15 -686.93830931 -4.1D-07 0.00005 0.00001 0.00041 0.00128 1978.5
% grep '^@' dextran_qm_dft.out > dextran_energies.out
% cat dextran_energies.out@ Step Energy Delta E Gmax Grms Xrms Xmax Walltime
@ ---- ---------------- -------- -------- -------- -------- -------- --------
@ 0 -686.92664205 0.0D+00 0.02562 0.00530 0.00000 0.00000 124.6
@ 1 -686.93572937 -9.1D-03 0.00495 0.00123 0.05800 0.21419 230.6
@ 2 -686.93688173 -1.2D-03 0.00371 0.00079 0.03159 0.12217 377.7
@ 3 -686.93728094 -4.0D-04 0.00183 0.00045 0.02043 0.06471 536.9
@ 4 -686.93765371 -3.7D-04 0.00231 0.00055 0.02664 0.09902 685.2
@ 5 -686.93795400 -3.0D-04 0.00218 0.00046 0.02601 0.08722 834.3
@ 6 -686.93815263 -2.0D-04 0.00214 0.00036 0.02147 0.06602 982.6
@ 7 -686.93820464 -5.2D-05 0.00078 0.00014 0.00714 0.01937 1114.2
@ 8 -686.93823383 -2.9D-05 0.00089 0.00015 0.00618 0.01997 1236.3
@ 9 -686.93825965 -2.6D-05 0.00063 0.00014 0.00684 0.02057 1365.8
@ 10 -686.93828289 -2.3D-05 0.00065 0.00012 0.00676 0.02784 1504.9
@ 11 -686.93829701 -1.4D-05 0.00049 0.00010 0.00514 0.02142 1618.2
@ 12 -686.93830468 -7.7D-06 0.00046 0.00008 0.00443 0.01556 1748.7
@ 13 -686.93830745 -2.8D-06 0.00013 0.00003 0.00102 0.00292 1827.3
@ 14 -686.93830891 -1.5D-06 0.00006 0.00001 0.00100 0.00300 1906.5
@ 15 -686.93830931 -4.1D-07 0.00005 0.00001 0.00041 0.00128 1978.5
@ 15 -686.93830931 -4.1D-07 0.00005 0.00001 0.00041 0.00128 1978.5
Now we have the electronic energies at each relaxation step (as well as position deltas between steps) saved to a file.
Now we need to get the geometry at each relaxation step. Here, we'll use the
'-A' option for grep to print out the lines following our matches. At first,
we may not know how many lines to print out, so we'll try something excessive,
perhaps 40? Then narrow it down (or expand it) to make sure you get all the
atoms. Once we're satisfied that we're getting the results we want, we can
redirect the output to a file for saving.
% grep -A 40 'Geometry "geometry"' dextran_qm_dft.out Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 C 6.0000 -1.46614374 1.14413858 0.20689570
2 C 6.0000 -0.06510930 1.71491488 0.52712986
3 C 6.0000 1.01933089 0.89126609 -0.19986268
#### More lines here ####
20 H 1.0000 -0.60963072 -2.48793956 1.59468758
21 H 1.0000 -1.82931112 -2.81641725 0.34650697
22 H 1.0000 1.71835792 -2.27555426 -0.39890742
23 H 1.0000 2.96714682 0.88238211 -0.22383765
24 H 1.0000 -0.14249451 -3.77623236 -0.91338242
Atomic Mass
-----------
C 12.000000
O 15.994910
H 1.007825
Effective nuclear repulsion energy (a.u.) 827.3774954752
Looks like we overshot by 10 lines
% grep -A 30 'Geometry "geometry"' dextran_qm_dft.out Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 C 6.0000 -1.46614374 1.14413858 0.20689570
2 C 6.0000 -0.06510930 1.71491488 0.52712986
3 C 6.0000 1.01933089 0.89126609 -0.19986268
#### More lines here ####
20 H 1.0000 -0.60963072 -2.48793956 1.59468758
21 H 1.0000 -1.82931112 -2.81641725 0.34650697
22 H 1.0000 1.71835792 -2.27555426 -0.39890742
23 H 1.0000 2.96714682 0.88238211 -0.22383765
24 H 1.0000 -0.14249451 -3.77623236 -0.91338242
% grep -A 30 'Geometry "geometry"' dextran_qm_dft.out > dextran_geometries.outFinally, let's combine our energies and geometries files into one total file with by
redirecting the output of cat into a new file dextran_full_output:
% cat dextran_energies.out dextran_geometries.out > dextran_full_output
If we wanted to, we could define
a bash function which runs all these commands on the file automatically, but we
will save this for another time. If you're curious, check out the relevant
sections of index.md in phs/shell/exercise_1. HERE
Next we will practice using the wildcard operator * to select and move
consistently named files. We will be using the the files in directory 'plots'.
We will:
- Select only the 'CCFreq' and 'CCTime' plots
- Select only the 'tmax-140' plots
- Select only the 'CCFreq' and 'tmax-140' plots, then zip them up so that they can be easily emailed
First move into the plots directory. We will select all the 'CCFreq' files or
'CCTime' files using 'globbing', or 'wildcards'. A wildcard is a * on the
command line, which tells Bash to try to match anything there. Let's try it.
Examine the output of these commands:
% ls CCFreq*
% ls CCFreq_*
% ls CCFreq_* CCTime_*Now create a directory and copy the selected files into that directory:
% mkdir final_plots
% cp CCFreq_* CCTime_* final_plots
% ls final_plots/CCFreq_L-8_tmax-10_dt-0.1.png CCFreq_L-8_tmax-30_dt-0.2.png
CCTime_L-8_tmax-140_dt-0.5.png CCFreq_L-8_tmax-10_dt-0.2.png
CCFreq_L-8_tmax-50_dt-1.png CCTime_L-8_tmax-140_dt-1.png
CCFreq_L-8_tmax-120_dt-1.png CCTime_L-8_tmax-10_dt-0.1.png
CCTime_L-8_tmax-30_dt-0.2.png CCFreq_L-8_tmax-140_dt-0.2.png
CCTime_L-8_tmax-10_dt-0.2.png CCTime_L-8_tmax-50_dt-1.png
CCFreq_L-8_tmax-140_dt-0.5.png CCTime_L-8_tmax-120_dt-1.png
CCFreq_L-8_tmax-140_dt-1.png CCTime_L-8_tmax-140_dt-0.2.png
Now, try selecting for only the 'tmax-140' plots, including all three of 'CCFreq', 'CCTime', and 'Board'
% ls *_tmax-140_*Board_L-8_tmax-140_dt-0.2.png CCFreq_L-8_tmax-140_dt-0.2.png
CCTime_L-8_tmax-140_dt-0.2.png Board_L-8_tmax-140_dt-0.5.png
CCFreq_L-8_tmax-140_dt-0.5.png CCTime_L-8_tmax-140_dt-0.5.png
Board_L-8_tmax-140_dt-1.png CCFreq_L-8_tmax-140_dt-1.png
CCTime_L-8_tmax-140_dt-1.png
Now select all files that are both 'CCFreq' and also 'tmax-140' plots, copy
them into a new directory called 'presentation_plots', then zip it up using the
zip command so that you can email it. Make sure to pass the '-r' option
(recursive) to the zip command so that it zips the entire
'presentation_plots' directory.
% mkdir presentation_plots
% cp CCFreq_*_tmax-140* presentation_plots
% zip -r presentation_plots.zip presentation_plots/To examine this newly created zip file we can first learn its filetype with
file, and then list the file contents using unzip, which is the inverse
to zip. Then we will extract the files to a new folder (with the -d flag)
with unzip:
% file presentation_plots.zipA
presentation_plots.zip: Zip archive data, at least v1.0 to extract
% unzip -l presentation_plots.zip
Archive: presentation_plots.zip
Length Date Time Name
--------- ---------- ----- ----
0 2018-05-13 21:54 presentation_plots/
13434 2018-05-13 21:54 presentation_plots/CCFreq_L-8_tmax-140_dt-1.png
21676 2018-05-13 21:54 presentation_plots/CCFreq_L-8_tmax-140_dt-0.2.png
16966 2018-05-13 21:54 presentation_plots/CCFreq_L-8_tmax-140_dt-0.5.png
--------- -------
52076 4 files
% mkdir unzipped_folder
% unzip presentation_plots.zip -d unzipped_folder
Archive: presentation_plots.zip
creating: unzipped_folder/presentation_plots/
inflating: unzipped_folder/presentation_plots/CCFreq_L-8_tmax-140_dt-1.png
inflating: unzipped_folder/presentation_plots/CCFreq_L-8_tmax-140_dt-0.2.png
inflating: unzipped_folder/presentation_plots/CCFreq_L-8_tmax-140_dt-0.5.png
Another common (though oddly confusing to use) file compression tool is tar.
Here the syntax is tar -cvf MY_TARFILE.tar FILES_TO_COMPRESS (-c=create a
tar archive, -v=verbose output, -f=use the files I am about to pass). To extract, use
tar -xvf MY_TARFILE.tar (-x=extract).
% tar -cvf presentation_plots.tar presentation_plots/*
presentation_plots/CCFreq_L-8_tmax-140_dt-0.2.png
presentation_plots/CCFreq_L-8_tmax-140_dt-0.5.png
presentation_plots/CCFreq_L-8_tmax-140_dt-1.png
% file presentation_plots.tar
presentation_plots.tar: POSIX tar archive (GNU)
% file presentation_plots.zip
presentation_plots.zip: Zip archive data, at least v1.0 to extract
% tar -xvf presentation_plots.tar
presentation_plots/CCFreq_L-8_tmax-140_dt-0.2.png
presentation_plots/CCFreq_L-8_tmax-140_dt-0.5.png
presentation_plots/CCFreq_L-8_tmax-140_dt-1.png
See what programs are running (task manager) with top. If you want it to be
fancy and have colorful graphics, use htop (install it if you need). See the
low-level hardware commands your system is running with dmesg. View the
background daemon commands your system is running with journalctl. Examine
your cpu with lspcu. See your filesystem with lsblk and df. See your
wireless/wired connection hardware profiles with ip link. Remember your
wireless name (mine is 'wlp4s0'). Use iftop -i wlp4s0 (replace 'wlp4s0' with
your wireless device name) to see the internet traffic you are uploading and
downloading. Use ps to see currently running processes. Use pkill PROCESS_NAME to force kill a given process (I sometimes need to use pkill chromium when my internet bugs out).
In the same way that we were able to modify our bash user experience with a
.bashrc, we can modify our vim experience with a .vimrc. It is also a
hidden file, stored in the home directory. At the start of every vim session,
every line in your vimrc is executed sequentially. As we did with the
.bashrc, open your vimrc in vim with vim ~/.vimrc, then open my sample
vimrc alongside with vsplit my_vimrc. Switch between sides with Ctrl-W Ctrl-W or with Ctrl-W Ctrl-H or Ctrl-W Ctrl-L (you will notice 'h' and 'l'
are the left and right navigation keys in vim). If you want, copy and paste the
entire file by going to the top of the file with gg, enter visual block mode
with V, go to the end of the file with G, yank all of the text with y,
change to the other window with Ctrl-W Ctrl-W, and paste with P.
If you are looking for more commands to put in your .vimrc, google it (or
this link is pretty good too).
There is a suspiciously simple conjecture in mathematics that has never been proven, called the Collatz conjecture. Start with a positive integer, and if it is even divide by two, and if it is odd multiply by three and add 1. The conjecture states that no matter what number you start with, you will end up with 1. (e.g.: 3 -> 10 -> 5 -> 16 -> 8 -> 4 -> 2 -> 1)
We are going to build these Collatz chains using python. Open a new python file
in vim with vim my_collatz.py, and in the first line enter the sh-bang
#!/bin/python3. In the first couple of lines, place a simple print('hey there'). Open another shell and navigate to the same folder. Make the python
file executable with chmod u+x my_collatz.py, and execute it with
./my_collatz. Ensure that your shell prints the expected statement.
Make sure you have a good workflow here! I like to have two terminal windows side by side, one in the shell ready to execute the python file (use the up arrow to access the last command you used), and the other in vim editing the python file. Switch between these windows with Windows+Tab or Alt+Tab.
We will make the Collatz sequence together in class. One key aspect of python
is that you need your spacing to be correct. If you are indented where you
shouldn't be, or not indented where you should be, python will throw an error
(IndentationError: unexpected indent). When errors occur, read the error
message-- it even says what line the error occured on, and tells you the class
of what was wrong.
To make the Collatz sequence, we will use: function definitions (def),
while loops, list appending, casting numbers as ints, if and else
statements, and eventually accept user input from the command line with
sys.argv. To see a completed version of this file, refer to
my_collatz_solution.py.