readme file

README

@@ -1,28 +1,20 @@
 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
-│   ├── grids
+│   └── grids
-│   │   ├── halfsolar
+│       ├── halfsolar
-│   │   │   └── 4thdex
+│       │   └── 4thdex
-│   │   │       ├── cldn_22.00
+│       │       ├── cldn_22.00
-│   │   │       ├── cldn_23.00
+│       │       ├── cldn_23.00
-│   │   │       ├── cldn_24.00
+│       │       ├── cldn_24.00
-│   │   │       └── nonitrogen
+│       │       └── nonitrogen
-│   │   └── solar
+│       └── solar
-│   │       └── 4thdex
+│           └── 4thdex
-│   │           ├── cldn_22.00
+│               ├── cldn_22.00
-│   │           ├── cldn_22.50
+│               ├── cldn_22.50
-│   │           ├── cldn_23.00
+│               ├── cldn_23.00
-│   │           ├── cldn_23.50
+│               ├── cldn_23.50
-│   │           └── cldn_24.00
+│               └── cldn_24.00
-│   └── points
-│       ├── collapsed_default
-│       ├── collapsed_doubled
-│       ├── coll_def
-│       ├── coll_doub
-│       ├── conv_test_1
-│       ├── conv_test_2
-│       └── test
 └── mehdipour
     ├── grids
     │   └── solar
@@ -163,3 +155,46 @@ 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 

scripts/cloudy/magdziarz.mpi_grid.in

@@ -4,10 +4,12 @@ title magdziarz 1997 hden_vs_phi .25 dex
 //
 //////  Output continua and included lines
 //
-save last incident continuum "incident_continuum"
+save 
-save line labels "line_labels"
+//save last incident continuum "incident_continuum"
+//save line labels "line_labels"
 save continuum bins "continuum_bins"
-save diffuse continuum "diffuse_continuum"
+//save diffuse continuum "diffuse_continuum"
+save emitted continuum "emitted_continuum"
 //
 //////  Report almost everything
 //
@@ -23,12 +25,12 @@ Database print
 //
 // Defaults: 10, 10, 6
 //
-database H-like element hydrogen resolved levels 18
+//database H-like element hydrogen resolved levels 18
-database H-like element helium resolved levels 15
+//database H-like element helium resolved levels 15
-database He-like element helium resolved levels 15
+//database He-like element helium resolved levels 15
-//database H-like element hydrogen collapsed levels 30
+database H-like element hydrogen resolved levels 18 collapsed levels 30
-//database H-like element helium collapsed levels 30
+database H-like element helium resolved levels 15 collapsed levels 30
-//database He-like element helium collapsed levels 40
+database He-like element helium resolved levels 15 collapsed levels 40
 //
 //////  low-metal abundance for AGN testing ~2017
 // metals 0.5
@@ -48,7 +50,7 @@ set nend 5000
 //  InwT = Inward Diffuse + Reflected Inward
 //  InwC = Reflected Inward
 //
-//      derived quantities added in Otho's program ~2017
+//     possible derived quantities added in Otho's program ~2017
 //  InwD = InwT - InwC = Inward Diffuse
 //  nFnD = nFnu - InwC = Total Diffuse
 //

scripts/cloudy/mehdipour.mpi_grid.in

@@ -4,8 +4,12 @@ title mehdipour ngc5548 4thdex grid
 //
 //////	Output continua and included lines
 //
-save last incident continuum "incident_continuum"
+save 
-save line labels "line_labels"
+//save last incident continuum "incident_continuum"
+//save line labels "line_labels"
+save continuum bins "continuum_bins"
+//save diffuse continuum "diffuse_continuum"
+save emitted continuum "emitted_continuum"
 //
 //////  Report almost everything
 //
@@ -21,12 +25,12 @@ Database print
 //
 // Defaults: 10, 10, 6
 //
-database H-like element hydrogen resolved levels 18
+//database H-like element hydrogen resolved levels 18
-database H-like element helium resolved levels 15
+//database H-like element helium resolved levels 15
-database He-like element helium resolved levels 15
+//database He-like element helium resolved levels 15
-//database H-like element hydrogen collapsed levels 30
+database H-like element hydrogen resolved levels 18 collapsed levels 30
-//database H-like element helium collapsed levels 30
+database H-like element helium resolved levels 15 collapsed levels 30
-//database He-like element helium collapsed levels 40
+database He-like element helium resolved levels 15 collapsed levels 40
 //
 //////  low-metal abundance for AGN testing ~2017
 // metals 0.5
@@ -46,7 +50,7 @@ set nend 5000
 //  InwT = Inward Diffuse + Reflected Inward
 //  InwC = Reflected Inward
 //
-//      derived quantities added in Otho's program ~2017
+//     possible derived quantities added in Otho's program ~2017
 //  InwD = InwT - InwC = Inward Diffuse
 //  nFnD = nFnu - InwC = Total Diffuse
 //

src/spectral_lines.hpp

@@ -2,8 +2,8 @@
 #define spectral_lines_hpp
 
 #include "agn.hpp"
-#include "png++-0.2.5/gray_pixel.hpp"
+//#include "png++-0.2.5/gray_pixel.hpp"
-#include "png++-0.2.5/image.hpp"
+//#include "png++-0.2.5/image.hpp"
 
 
 namespace agn {