diff --git a/nbody6_quick_guide.md b/nbody6_quick_guide.md
index cb2132bef84449399ba31f5cbce985522d3e8933..a170cc3994113ec3cca5aeed313334bb11137f0d 100644
--- a/nbody6_quick_guide.md
+++ b/nbody6_quick_guide.md
@@ -3,47 +3,44 @@
## prerequisites/documents/scripts:
* This doc
* nbody6++\_manual.pdf
-* nbody6++ itself:
-* readout script:
-* config generator script: `python_scripts_for_nbody6/nbody6_config_generator.py`
+* nbody6++ itself: todo
+* readout scripts: todo
+* Mcluster
+* python, pip, a virtualenvironment and having the content of requirements.txt installed
## Tutorial
-### Set up config
+### General
We will go through the configuration file, and what all the variables mean, but they are also described in nbody6++\_manual.pdf.
-The formatting for the config file is very plain, but I have created a script to generate the config files called `python_scripts_for_nbody6/nbody6_config_generator.py`
-Better idea: the software package `mcluster` does this job for us. it will generate a file that nbody6 can read in, plus some initialisation summaries.
-With the `-h` option you can see the variables that can be customized, and in the `McLusterManual.pdf` most of the options are explained.
+The formatting for the config file is very plain, but we utilise a handy software package called mcluster (@Mcluster) to generate initial settings for nbody6++ simulations. It accepts command line arguments to construct these config files, which saves us a headache in arranging the numbers correctly. We will use a script made by David that does some extra things for you. The usage is explained below (@custom script and usage). After the configuration has been generated, we can start an nbody6 simulation with this configuration. The steps are explained bellow (@feeding config to nbody6))
-# Official
+#### Mcluster
To run mcluster:
```
./vol/ph/astro/dhendriks/mcluster/mcluster [OPTIONS]
```
-
It will generate (at least) 2 files, one of which should be used as an input for nbody6
+With `mcluster -h` you can see the options that are customizable.
-# Custom script and usage:
+#### Custom script and usage:
To generate a set up:
-* Run `mcluster_script.sh <name of setup>` in the directory you want nbody6 to store your data.
-* run `<path to nbody6> < <name of setup>.input
- * Optionally, you can do the following command: `screen -S <session name>' and then run '<path to nbody6> < <name of setup>.input` (type `man screen` for some explanation, or look it up on google)
-* Let the code run.
-
+* Run `<path to mclusterscript dir>/mcluster_script.sh <name of setup>` in the directory you want nbody6 to store your data.
+You want to run the above command in the directory you want the data of nbody6 to be outputted.
+#### feeding config to nbody6
+IMPORTANT: execute the below commands in a directory designed to store the output. Nbody6++ automatically outputs the files to the directory it has been called from.
-### To run the code:
-To run a simulation we must pass the config file to the executable of nbody6++.
-
-```
-./vol/ph/astro_code/dhendriks/nbody6 < "full path to configuration file."
-```
+To run a simulation we must pass the config file to the executable of nbody6++. Like this:
+`<path to nbody6> < <name of setup>.input`
+An example would be:
+`/vol/ph/astro_code/dhendriks/nbody6 < /vol/ph/astro_code/dhendriks/work_dir/nbody6/default.input`
Based on the input configuration this file will run until it gets terminated (by the code or by you).
-### Reading out the data:
-As Nbody6 outputs the data as fortran binaries, we first need to
-
+Optionally, you can do the following command: `screen -S <session name>' and then run '<path to nbody6> < <name of setup>.input` (type `man screen` for some explanation, or look it up on google)
+Now, the code runs, and you should leave it alone (or detach the terminal) until it is done.
+### Reading out the data:
+Nbody6 outputs in a couple of data formats: ascii/plain text, binary, and optionally hdf5. We have configured it to output the main file to hdf5, so that we dont have to manually read out the binaries. Some other files are plaintext so we can access them quite easily. We created 2 example scripts: `python_scripts_for_nbody6/hdf5_readout_nbody6pp_example.py` for reading out hdf5 files, and `python_scripts_for_nbody6/ascii_readout_nbody6pp_example.py` for reading out normal files with pandas.
\ No newline at end of file
diff --git a/python_scripts_for_nbody6/ascii_readout_nbody6pp_example.py b/python_scripts_for_nbody6/ascii_readout_nbody6pp_example.py
index a8f8eba9124abc6e83fedce9efad6bca20ebb37a..f108eeb7567ce4932daa6f5d443adab17cbaeb65 100644
--- a/python_scripts_for_nbody6/ascii_readout_nbody6pp_example.py
+++ b/python_scripts_for_nbody6/ascii_readout_nbody6pp_example.py
@@ -8,17 +8,19 @@ import pandas as pd
# Point to the source directory.
source_dir = '/vol/ph/astro_code/dhendriks/work_dir/nbody6'
+filename = 'sev.83_0'
+
# Create the header line labels and data line labels
header_line_labels = ['NS', 'TIME[Myr]']
N_LABEL = ['TIME[NB]', 'I', 'NAME', 'K*', 'RI[RC]', 'M[M*]', 'Log10(L[L*])', 'LOG10(RS[R*])' , 'LOG10(Teff[K]']
# Go through file
-with open(os.path.join(source_dir, 'sev.83_0'), 'r') as f:
+with open(os.path.join(source_dir, filename), 'r') as f:
header_1_data = f.readline().split()
data = []
for line in f:
data.append(line.split())
-df = pd.DataFrame(data, columns=N_LABEL)
\ No newline at end of file
+df = pd.DataFrame(data, columns=N_LABEL)
diff --git a/python_scripts_for_nbody6/extra_functions.py b/python_scripts_for_nbody6/extra_functions.py
new file mode 100644
index 0000000000000000000000000000000000000000..effc1d95fb7f8a6fb5d0a29c27ce651f9c73d3e2
--- /dev/null
+++ b/python_scripts_for_nbody6/extra_functions.py
@@ -0,0 +1,10 @@
+import h5py
+
+def hdf_recursive(hdf_obj, prefix=''):
+ for key in list(hdf_obj.keys()):
+ item = hdf_obj[key]
+ path = '{}/{}'.format(prefix, key)
+ if isinstance(item, h5py.Dataset):
+ yield (path, item)
+ elif isinstance(item, h5py.Group):
+ yield from hdf_recursive(item, path)
\ No newline at end of file
diff --git a/python_scripts_for_nbody6/hdf5_readout_nbody6pp_example.py b/python_scripts_for_nbody6/hdf5_readout_nbody6pp_example.py
new file mode 100644
index 0000000000000000000000000000000000000000..2f6556b4286cd31a92be4ddc4a3c4fa7d782c716
--- /dev/null
+++ b/python_scripts_for_nbody6/hdf5_readout_nbody6pp_example.py
@@ -0,0 +1,32 @@
+import h5py
+import os
+from extra_functions import *
+
+source_dir = '/vol/ph/astro_code/dhendriks/work_dir/nbody6'
+filename = 'snap.40_0.h5part'
+
+f = h5py.File(os.path.join(source_dir, filename), 'r')
+
+# For a tree view of the file
+for (path, dset) in hdf_recursive(f):
+ print(path, dset)
+
+# # List all groups
+print("Keys: %s" % f.keys())
+
+a_group_key = list(f.keys())[0]
+
+# Get the data of e.g. step 0
+data_step0 = list(f['Step#0'])
+print(data_step0)
+
+# get the data of e.g. binaries in step 0
+data_step0_binaries = list(f['Step#0']['Binaries'])
+print(data_step0_binaries)
+
+# get the data of e.g. the eccentricity of binaries in step 0
+data_step0_binaries_ecc = list(f['Step#0']['Binaries']['ECC'])
+print(data_step0_binaries_ecc)
+
+
+
diff --git a/python_scripts_for_nbody6/config_defaults.py b/python_scripts_for_nbody6/old_or_unfinished_scripts/config_defaults.py
similarity index 100%
rename from python_scripts_for_nbody6/config_defaults.py
rename to python_scripts_for_nbody6/old_or_unfinished_scripts/config_defaults.py
diff --git a/python_scripts_for_nbody6/nbody6_config_generator.py b/python_scripts_for_nbody6/old_or_unfinished_scripts/nbody6_config_generator.py
similarity index 100%
rename from python_scripts_for_nbody6/nbody6_config_generator.py
rename to python_scripts_for_nbody6/old_or_unfinished_scripts/nbody6_config_generator.py
diff --git a/python_scripts_for_nbody6/readout_script.py b/python_scripts_for_nbody6/old_or_unfinished_scripts/readout_script.py
similarity index 100%
rename from python_scripts_for_nbody6/readout_script.py
rename to python_scripts_for_nbody6/old_or_unfinished_scripts/readout_script.py
diff --git a/python_scripts_for_nbody6/readout_script_nbody6pp_binaries.py b/python_scripts_for_nbody6/old_or_unfinished_scripts/readout_script_nbody6pp_binaries.py
similarity index 100%
rename from python_scripts_for_nbody6/readout_script_nbody6pp_binaries.py
rename to python_scripts_for_nbody6/old_or_unfinished_scripts/readout_script_nbody6pp_binaries.py
diff --git a/python_scripts_for_nbody6/test_input.py b/python_scripts_for_nbody6/old_or_unfinished_scripts/test_input.py
similarity index 100%
rename from python_scripts_for_nbody6/test_input.py
rename to python_scripts_for_nbody6/old_or_unfinished_scripts/test_input.py
diff --git a/python_scripts_for_nbody6/out.hdf5 b/python_scripts_for_nbody6/out.hdf5
deleted file mode 100644
index 82daee09f5d9bab4d4ef6cf1c24d6067e7457f8a..0000000000000000000000000000000000000000
Binary files a/python_scripts_for_nbody6/out.hdf5 and /dev/null differ