Fix issue 73

fixed the documentation for all of the chemistry software (minus molpro), machine-learning/tensorflow and introduction, lang/python, numlang/matlab and octave

found issues added as comments in the markdown source code

docs.it4i/software/chemistry/phonopy.md

@@ -14,7 +14,7 @@ $ ml av phonopy
 
 ## Example of the Calculation of Phonon Density of States and Thermal Properties of Aluminum Using the VASP Code
 
-# Generating Displacements
+### Generating Displacements
 
 All of the Phonopy calculations generally require a [POSCAR][1] with well relaxed forces in order for the resulting values to carry any physical meaning.
 
@@ -57,7 +57,7 @@ $ phonopy -d mesh.conf -c POSCAR
 
 For the list of all the possible phonopy tags, see [official documentation][d].
 
-# Running the Jobs
+### Running the Jobs
 
 Each unique displacement is named `POSCAR-XXX`, in our case we have only one, which is named `POSCAR-001`. If you are calculating plus and minus displacements, the minus displacement immediately follows the plus displacement.
 Each unique displacement should then be moved to a separate folder, with every displacement file renamed to POSCAR, and POTCAR, [KPOINTS][3] and [INCAR][4] should be added.
@@ -65,7 +65,7 @@ If one doesn't use the automatic settings for the KPOINTS generation, it is impo
 During the calculation, we need to move one of the atoms specified in POSCAR and calculate the forces (`ISIF = 0`, `ISMEAR` according to the type of the material at question).
 After this, we can submit the VASP calculation using the `qsub` command.
 
-# Calculating the Force Constants
+### Calculating the Force Constants
 
 After the calculations finish, we can generate the FORCE_SETS file using the following command:
 
@@ -73,7 +73,7 @@ After the calculations finish, we can generate the FORCE_SETS file using the fol
 $ phonopy -f POSCAR-???.dir/vasprun.xml
 ```
 
-# Calculating the DOS and Thermal Properties
+### Calculating the DOS and Thermal Properties
 
 Assuming we wrote all of our required parameters (such as the q-point mesh) to the mesh.conf file, we can then derive the phonon density of states (DOS)