updated readme

README

@@ -1,3 +1,70 @@
+Quick Reference:
+
+Basic work-flow to create a thor run and generate flux tables
+──────────────────────────────────────────────────────────────────────────
+
+    "ssh -X kkorista@thor.cs.wmich.edu" to connect
+
+    "qnodes | grep -B2 researcj|less" to get a list of available nodes
+
+    "qstat" to see current status of torque job queue
+
+    Create directory for a new grid run on Thor
+
+    Copy three files to the directory:
+        - cloudy input file from "cloudy-agn/scripts/cloudy/", rename to "mpi_grid.in"
+        - torque submission script "cloudy.pbs" from "cloudy-agn/scripts/thor"
+        - SED table from "cloudy-agn/sed/"
+
+    Edit "cloudy.pbs" to update the working directory and the name of the run
+
+    Edit "mpi_grid.in" as relevant to this run
+
+    "qsub cloudy.pbs" submits the script to the scheduler
+
+    "qstat" to see status of your run, or "watch qstat" to watch the status (ctrl-c to exit watch)
+
+    Wait for run to complete.
+
+    Copy mpi_grid.out to a directory of your choice on your local machine
+
+    Run "cloudy-agn/scripts/operations/package_tables.sh <directory>" where the command line argument <directory> points at the directory where you stored mpi_grid.out
+
+    This should generate the flux tables in that directory under the subdirectory "fortfiles", with a .tar.gz archive in the main directory.
+
+
+Compiling cloudy on Thor
+──────────────────────────────────────────────────────────────────────────
+    "module avail" to check available modules
+    "module list" to list loaded modules
+    "module load <module>" to load a module
+
+    Load one of the openmpi modules before compiling the mpi version of cloudy
+
+
+Getting the latest version of my software
+──────────────────────────────────────────────────────────────────────────
+
+rsync -aac kkorista@159.203.46.10:~/cloudy.agn <local dir>
+
+    <local dir> command line argument here is where you want to save the project on your local machine, use "." for current directory
+
+use SSH keys
+─────────────
+    This creates a public key and a private key and sends the public key to the remote server, which is sufficient for secure authentication.
+
+    "ssh-keygen" to create and save a key
+    "ssh-copy-id kkorista@thor.cs.wmich.edu" to set up key authentication on the remote server
+
+
+
+
+
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+Detailed Information
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+
 Generally, the software is intended to be run by a single command in while working in a directory that contains several cloudy grid output files in subdirectories. This command is the script "scripts/meta/process_gridoutputs.sh". The output files must be named "mpi_grid.out". For instance, the structure I used looks like this:
 .
 ├── magdziarz
@@ -75,6 +142,7 @@ subdirs
 
 "analysis" give information about emission lines and the continuum, but these are not updated for c17, yet.
 
+"sed" contains various formats of the SEDs we've analyzed, and the .tab files can be used as cloudy input files for the "table sed" command
 
 process_gridoutputs.sh
 ─────────────
@@ -142,6 +210,10 @@ subtract_fortfiles <file1> <file2> <4 char header>
 
 where the difference will be file1 - file2, and the new table's header will start with the 4 characters in the third command line argument.
 
+sed/*
+─────────────
+Routines created to produce spectral energy distributions. 
+
 
 convert_sed_ryd_to_ev.cpp
 ─────────────
@@ -151,50 +223,7 @@ save_table2d_slice.cpp
 ─────────────
 OLD. Used to extract slices along constant hden or phi from a flux table, mostly for examination during debugging. Lots of easy ways to do this in graphing software and what have you. This may not even work anymore and I'll probably remove it soon.
 
-sed/*
-─────────────
-OLD. These were routines created to produce spectral energy distributions. We don't take this approach anymore, since it's not necessary to create the SED more than once. SEDs are stored in tables in the directory "reference", instead, and the "sed" subdirectory will probably be removed soon.
 
 
 
-syntax things
-─────────────
-I will write more about these.
 
-mpirun ~/bin/c17.exe
-
-ssftp korista@159.203.46.
-
-module avail 
-module list
-module load <module>
-
-ssh -X kkorista@thor.cs.wmich.edu
-
-qstat
-qnodes | grep -B2 researcj|less
-
-rsync -aac korista@agn.science:~/cloudy-agn ~/cloudy-agn
-
-
-159.203.46.10
-
-touch <file>
-
-rsync -aac kkorista@159.203.46.10:~/cloudy-agn
-
-module remove
-module avail
-module list
-module load
-
-make directory on thor
-copy cloudy input script into directory
-copy cloudy.pbs torque submission script to directory
-edit cloudy input script as needed
-edit cloudy.pbs to point to the new directory and give it a new name
-qsub clouyd.pbs 
-
-ssh-keygen 
-ssh-copy-id kkorista@thor.cs.wmich.edu
-this creates a public key and a private key and sends the public key to the remote server, which is sufficient for the remote server to