Merge pull request #157 from ICAMS/update_doc

Update doc

docs/source/index.rst

@@ -47,6 +47,7 @@ publication <https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMateri
    Using calphy <running_calphy/running_calphy>
    inputfile
    examples
+   research
    calphy
    faqs
    prologue/extending

docs/source/inputfile.md

@@ -546,6 +546,59 @@ folder_prefix: set1
 
 Prefix string to be added to folder names for calculation. Folders for calculations in calphy are named as `mode-lattice-temperature-pressure`. Therefore, if more than one calculation is run with the same parameters, they will be overwritten. To prevent this, `folder_prefix` can be used. If `folder_prefix` is provided, the folders will be named as `folder_prefix-mode-lattice-temperature-pressure`.
 
+
+---
+
+(script_mode)=
+#### `script_mode`        
+
+_type_: bool \
+_default_: False \
+_example_:
+```
+script_mode: False
+```  
+
+If True, a LAMMPS executable script is written and executed instead of the library interface of LAMMPS.
+Works only with `reference_phase: solid`, and `mode: fe`.
+Needs specification of [`lammps_executable`](lammps_executable) and [`mpi_executable`](mpi_executable).
+
+
+---
+
+(lammps_executable)=
+#### `lammps_executable`        
+
+_type_: string \
+_default_: None \
+_example_:
+```
+lammps_executable: lmp_mpi
+```  
+
+LAMMPS executable to run the calculations with.
+Works only with `reference_phase: solid`, and `mode: fe`.
+Works only if [`script_mode`](script_mode) is `True`.
+
+
+
+---
+
+(mpi_executable)=
+#### `mpi_executable`        
+
+_type_: string \
+_default_: None \
+_example_:
+```
+mpi_executable: mpiexec
+```  
+
+MPI executable to run the LAMMPS with.
+Works only with `reference_phase: solid`, and `mode: fe`.
+Works only if [`script_mode`](script_mode) is `True`.
+
+
 ---
 ---
 

docs/source/research.md

@@ -0,0 +1,16 @@
+# Research using `calphy`
+
+The following research works employed `calphy`:
+
+| Year 	| Material system 	| Calculation 	       | Interatomic Potential 	| Publication 	|
+|------	|-----------------	|--------------------- |-----------------------	|-------------	|
+| 2024  | MgAl, MgCa, AlCa  | phase diagram        | MTP                    | [Poul et. al.](https://www.researchsquare.com/article/rs-4732459/v1)       |
+| 2024  | Mo, Si, Mo$_3$Si, Mo$_5$Si$_3$, MoSi$_2$ | melting temperature        | ACE | [Lenchuk et. al.](https://doi.org/10.1002/adem.202302043)       |
+| 2024  | AlLi | phase diagram | EAM, HDNNP, ACE | [Menon et. al.](https://arxiv.org/abs/2403.05724)       |
+| 2024  | CuZr | phase diagram | ACE | [Leimeroth et. al.](https://doi.org/10.1103/PhysRevMaterials.8.043602)       |
+| 2024  | SiO | phase diagram | ACE | [Erhard et. al.](https://doi.org/10.1038/s41467-024-45840-9)       |
+| 2023  | Mg | phase diagram | ACE | [Ibrahim et. al.](https://doi.org/10.1103/PhysRevMaterials.7.113801)       |
+| 2022  | ZnO | free energies | ML | [Goniakowski et. al.](https://doi.org/10.1021/acs.jpcc.2c06341)       |
+| 2019  | Ti, Si | phase diagram | EAM, SW | [Menon et. al.](https://doi.org/10.1103/PhysRevMaterials.5.103801)       |
+
+Missing works? Reach out to [us](mailto:[email protected]).