updated quickstart guide and added option to install polaristools onl…

…y (compile script)

QUICKSTART.md

@@ -83,7 +83,13 @@ These files can be opened with, for example, [SAOImageDS9](https://sites.google.
 Simulations are performed similarly for thermal emission (`dust`) and stellar scattered radiation (`dust_mc`).
 Please refer to the [command list](projects/CommandList.cmd) in the `projects` folder or the [manual](manual.pdf) (Table 2.4 - 2.10) for available options of the command file.
 
-**HINT**: For thermal emission simulations, a temperature simulation has to be performed first.
+**HINT**: For thermal emission simulations, a temperature simulation (`temp`) has to be performed first.
+
+**HINT**: To include self-scattering, `<source_dust nr_photons = "Nph">` (`Nph` is the number of photon packages) and `<path_grid>` with the path to the grid file of the temperature simulation (e.g. "projects/disk/example/temp/grid_temp.dat") have to be provided in the command file (`dust_mc`).
+
+**HINT**: `dust` simulations only include directly emitted radiation of the dust.
+`dust_mc` simulations include directly emitted and scattered stellar radiation, scattered radiation thermally emitted by dust, but **not** directly emitted radiation of the dust.
+Thus, the user has to combine the results of `dust` and `dust_mc` simulations to obtain a complete spectrum.
 
 **HINT**: The previous results will be overwritten, if the same command file is used. Please change `<path_out>` in the command file to use a new directory for the new results.
 
@@ -165,9 +171,13 @@ $$
 
 Additional parameter values to modify the model can be defined in the function `update_parameter` in the file `tools/polaris_tools_modules/model.py`.
 
-**Hint**: For any changes in the files, the user has to recompile with:
+**Hint**: For any changes in the files, the user has to recompile PolarisTools with:
 ```bash
-./compile.sh -u
+./compile.sh -t
+```
+or if compiled without the script:
+```
+python3 tools/setup.py install --user &>/dev/null
 ```
 
 
@@ -181,9 +191,13 @@ polaris-gen model_name grid_filename.dat
 ```
 where `model_name` is the name of the model in the dictionary of `model.py`.
 
-**Hint**: For any changes in the files, the user has to recompile with:
+**Hint**: For any changes in the files, the user has to recompile PolarisTools with:
 ```bash
-./compile.sh -u
+./compile.sh -t
+```
+or if compiled without the script:
+```
+python3 tools/setup.py install --user &>/dev/null
 ```
 
 

compile.sh

@@ -288,19 +288,26 @@ function update_installation()
     fi
     cd ".."
 
+    install_polaristools
+
+    source ${HOME}/.bashrc
+
+    exit
+}
+
+
+function install_polaristools()
+{
     # compile and install PolarisTools if available
-    # PolarisTools is no longer maintained and is not shipped with POLARIS anymore
     if [[ -d "tools" ]]; then
         cd "tools/"
         python3 setup.py install --user &>/dev/null \
             && { echo -e "Compile and installing PolarisTools [${GREEN}done${NC}]"; echo ""; } \
             || { echo -e "Compile and installing PolarisTools [${RED}Error${NC}]"; exit 1; }
         cd ".."
+    else
+        echo -e "Compile and installing PolarisTools [${RED}Error${NC}]"; exit 1;
     fi
-
-    source ${HOME}/.bashrc
-
-    exit
 }
 
 
@@ -313,15 +320,16 @@ function usage() {
     echo ""
     echo "usage: compile.sh [-h] [-frdu] [-c CXX_COMPILER] [-g CMAKE_GENERATOR]"
     echo ""
-    echo "Install and compile POLARIS"
+    echo "Install POLARIS, PolarisTools, and optionally the cfitsio and CCfits libraries"
     echo -e "${YELLOW}HINT:${NC} For first installation, use option -f"
     echo ""
     echo "optional arguments:"
     echo "-h      show this help message and exit"
-    echo "-f      first installation (compile POLARIS and install the cfitsio and CCfits libraries)"
-    echo "-r      clear and compile POLARIS (release mode) (default)"
-    echo "-d      clear and compile POLARIS (debug mode)"
-    echo "-u      re-compile POLARIS if necessary with last configuration (update)"
+    echo "-f      first installation (compile POLARIS, PolarisTools, and the cfitsio and CCfits libraries)"
+    echo "-r      clear and compile POLARIS and PolarisTools (release mode) (default)"
+    echo "-d      clear and compile POLARIS and PolarisTools (debug mode)"
+    echo "-u      re-compile POLARIS and PolarisTools if necessary with last configuration (update)"
+    echo "-t      (re-)compile PolarisTools only"
     echo "-c CXX_compiler"
     echo "        choose the c++ compiler you want to use:"
     echo "          - gcc (default)"
@@ -338,7 +346,7 @@ function usage() {
 release=false
 debug=false
 
-while getopts "hfrduc:g:D" opt; do
+while getopts "hfrdutc:g:D" opt; do
     case $opt in
     h)
         usage
@@ -360,6 +368,11 @@ while getopts "hfrduc:g:D" opt; do
     f)
         DO_FITS=true
         ;;
+    t)
+        install_polaristools
+        source ${HOME}/.bashrc
+        exit
+        ;;
     c)
         if [[ ${OPTARG,,} = "gcc" ]]; then
             CXX="g++"
@@ -626,13 +639,7 @@ install_polaris
 
 # compile and install PolarisTools if available
 if [[ -d "tools" ]]; then
-    # go to PolarisTools dir
-    cd "tools/"
-
-    # compile and install PolarisTools
-    python3 setup.py install --user &>/dev/null \
-        && { echo -e "Compile and installing PolarisTools [${GREEN}done${NC}]"; echo ""; } \
-        || { echo -e "Compile and installing PolarisTools [${RED}Error${NC}]"; exit 1; }
+    install_polaristools
 
     # set POLARISTOOLS_PATH as environment variable
     set_envvar_TOOLS_str="export POLARISTOOLS_PATH=\"$HOME/.local/bin\""