Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Optimize bulk structure before thermal expansion calculation #71

Merged
merged 3 commits into from
Nov 20, 2023
Merged

Optimize bulk structure before thermal expansion calculation #71

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c8491f0
Optimize bulk structure before thermal expansion calculation
jan-janssen Nov 20, 2023
fc50161
Update thermal_expansion_with_lammps.ipynb
jan-janssen Nov 20, 2023
a460b07
Update thermal_expansion_with_lammps.ipynb
jan-janssen Nov 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 29 additions & 4 deletions docs/source/materialproperties.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -293,16 +293,41 @@ the `pair_style` and `pair_coeff` commands, this extended format enables referen
potentials `"Filename": [[]],` as well as the atomic species `"Species": [["Al"]],` to enable consistency checks if the
interatomic potential implements all the interactions to simulate a given atomic structure.

Finally, the last step of the preparation before starting the actual calculation is optimizing the interatomic structure.
While for the Morse potential used in this example this is not necessary, it is essential for extending this example to
other interactomic potentials. For the structure optimization the `optimize_positions_and_volume()` function is imported
and applied on the `ase.atoms.Atoms` bulk structure for Aluminium:
```
from atomistics.workflows import optimize_positions_and_volume

task_dict = optimize_positions_and_volume(structure=structure)
task_dict
>>> {'optimize_positions_and_volume': Atoms(symbols='Al4', pbc=True, cell=[4.05, 4.05, 4.05])}
```
It returns a `task_dict` with a single task, the optimization of the positions and the volume of the Aluminium structure.
This task is executed with the [LAMMPS](https://www.lammps.org/) molecular dynamics simulation code using the
`evaluate_with_lammps()` function:
```
from atomistics.calculators import evaluate_with_lammps

result_dict = evaluate_with_lammps(
task_dict=task_dict,
potential_dataframe=potential_dataframe,
)
structure_opt = result_dict["structure_with_optimized_positions_and_volume"]
```
The `result_dict` just contains a single element, the `ase.atoms.Atoms` structure object with optimized positions and
volume. After this step the preparation is completed and the three different approximations can be compared in the following.

### Equation of State
The first approximation to calculate the thermal expansion is based on the Equation of State derived by [Moruzzi, V. L. et al.](https://link.aps.org/doi/10.1103/PhysRevB.37.790).
So in analogy to the previous example of calculating the elastic properties from the Equation of State, the `EnergyVolumeCurveWorkflow`
is initialized with the default parameters:
```
from atomistics.calculators import evaluate_with_lammps, get_potential_dataframe
from atomistics.workflows import EnergyVolumeCurveWorkflow

workflow = EnergyVolumeCurveWorkflow(
structure=structure,
structure=structure_opt,
num_points=11,
fit_type='polynomial',
fit_order=3,
Expand Down Expand Up @@ -382,7 +407,7 @@ from atomistics.workflows import QuasiHarmonicWorkflow
from phonopy.units import VaspToTHz

calculator = QuasiHarmonicWorkflow(
structure=structure,
structure=structure_opt,
num_points=11,
vol_range=0.05,
interaction_range=10,
Expand Down Expand Up @@ -525,7 +550,7 @@ is on the one hand related to the large number of force and energy calls and on
structure, as these simulations are typically executed with >5000 atoms rather than the 4 or 108 atoms in the other
approximations.
```
structure_md = structure.repeat(11)
structure_md = structure_opt.repeat(11)
temperature_md_lst = np.linspace(15, 1400, 278)
volume_md_lst = calc_thermal_expansion_md(
structure=structure_md,
Expand Down
Loading
Loading