Skip to content

Commit 236451f

Browse files
nedtaylornedtaylor
authored
Development (#32)
Summary Added: - More examples - Benchmarks Changed: - Improved examples Fixed: - Consideration of image repeat atoms - Fortran executable database reading ------ * Update format * Add files * Add installation guide * Add tutorial templates * Add issue templates * Update README * Tidy up examples * Update ignore list * Handle NaNs in angles and dfs * Add bounds check * Change host setting * Add strip null for species setting * Remove unused variable * Improve gdf printing * Change build name * Fix random placement viable boolean * Update tutorials * Move readthedocs source files * Include docstrings * Update docstrings * Add more structure handling implement evaluate * Add atom division to evaluate * Fix placement methods * Fix element maps * Add learning examples * Add error and warning checks * Add bounding box * Fix bounds default * Add unrelaxed structure print * Remove dev print * Fix theme name * Fix theme * Include requirements * Add file * Update links to ExeQuantCode * Remove duplicate badge * Add bounds unit tests * Fix unit tests * Add file * Update README.md * Add file * Add file exist check * Fix settings printing * Change parallel process * Remove trailing whitespace * Add unit tests * Add file * Handle settings read * Add unit tests * Handle settings read * Add python unit tests * Update ignore list * Fix uninitialised tolerance * Fix missing tolerance * Add missing use statement * Fix viability update * Fix indentation check * Update example * Update version number * Update CITATION * Add RSS script * Add RSS output notebook * Remove print * Add file * Add RAFFLE learning script * Update RSS and RAFFLE scripts * Fix rlxd structure printing * Fix rlxd structure printing * Improve pca analysis * Improve analysis scripts * Add new examples * Improve pca plotting * Fix typos * Fix cell size * Add file * Update examples * Fix distance check across cell edges * Add known structures * Analyse Si|Ge interfaces * Meaningless notebook changes * Move Si slab file * Fix plotting range * Add file * Remove files * Add database files * Add benchmarks * Fix evaluate * Add benchmark * Update Al example * Rename benchmark * Add file * Fix typos * Fix typos * Add file * Add file * Add plotting notebook * Tidy up files * Delete file * Delete file * Add file * Add files * Add graphite diamond example * Move files * Fix indentation * Fix workflows * Add ase installation * Change branch pages * Update python version compatibility * Comment out other branch handling * Update filenames * Revert filename * Add file * Add file * Add energetic calculation * Add insets * Change plotted data * Add files * Change legend * Change legend * Change legend * Fix fortran executable data handling * Update example parameters * Uncomment line * Fix checker
1 parent 2f8e44f commit 236451f

File tree

84 files changed

+110644
-378
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

84 files changed

+110644
-378
lines changed

‎.github/workflows/coverage.yml‎

Lines changed: 10 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -35,6 +35,8 @@ concurrency:
3535

3636
jobs:
3737
run-code-coverage:
38+
# permissions:
39+
# contents: write
3840
environment:
3941
name: github-pages
4042
url: ${{ steps.deployment.outputs.page_url }}
@@ -97,7 +99,7 @@ jobs:
9799
minColorRange: 0
98100

99101
- name: upload artifact
100-
uses: actions/upload-pages-artifact@v1
102+
uses: actions/upload-pages-artifact@v3
101103
with:
102104
path: './build/coverage/'
103105

@@ -106,12 +108,11 @@ jobs:
106108
if: ${{ github.ref == 'refs/heads/main' }}
107109
uses: actions/deploy-pages@v2
108110
id: deployment
109-
with:
110-
path: './build/coverage/' # Use the same coverage directory
111111

112-
- name: deploy to GitHub Pages (non-main branch)
113-
if: ${{ github.ref != 'refs/heads/main' }}
114-
uses: actions/deploy-pages@v2
115-
with:
116-
path: './build/coverage/' # Same local coverage directory
117-
branch: gh-pages-${{ github.head_ref }} # Deploy to a branch-specific GitHub Pages branch
112+
# - name: deploy to Github Pages (development branch)
113+
# if: ${{ github.ref != 'refs/heads/main' }}
114+
# uses: peaceiris/actions-gh-pages@v4
115+
# with:
116+
# publish_dir: ./build/coverage/
117+
# github_token: ${{ secrets.GITHUB_TOKEN }}
118+
# destination_dir: development-branch/

‎.github/workflows/python.yml‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -71,6 +71,7 @@ jobs:
7171
python --version
7272
python -m pip install pip-tools
7373
python -m pip install pytest
74+
python -m pip install parameterized
7475
python -m piptools compile -o requirements.txt pyproject.toml --all-build-deps
7576
python -m pip install -r requirements.txt
7677
@@ -79,7 +80,7 @@ jobs:
7980
cmake --version
8081
python --version
8182
${{ env.FC }} --version
82-
python -m pip install .
83+
python -m pip install '.[ase]'
8384
8485
- name: Test
8586
run: |

‎.gitignore‎

Lines changed: 16 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,4 +33,19 @@ fort.*
3333
*.eps
3434
*.pyc
3535
*.xyz
36-
.coverage
36+
.coverage
37+
*CAR
38+
*.pckl
39+
.DS_Store
40+
fortranobject.c*
41+
*.db
42+
CHG
43+
EIGENVAL
44+
IBZKPT
45+
KPOINTS
46+
PCDAT
47+
REPORT
48+
vasprun.xml
49+
DVASP_MACE_comparison/
50+
pca_model*.pkl
51+
.benchmarks/

‎app/main.f90‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ program raffle_program
1111
use inputs
1212
use read_structures, only: get_gdfs_from_data
1313
use raffle, only: raffle_generator_type, distribs_container_type
14-
use raffle__geom_rw, only: geom_read, geom_write
14+
use raffle__geom_rw, only: geom_read, geom_write, basis_type
1515
implicit none
1616

1717
! Local variables
@@ -21,6 +21,7 @@ program raffle_program
2121
!! Buffer for strings
2222
character(:), allocatable :: next_dir
2323
!! Next directory name
24+
type(basis_type) :: host
2425

2526
real(real32), dimension(:), allocatable :: tmp_energies
2627
!! Temporary array for element energies
@@ -107,7 +108,8 @@ program raffle_program
107108
! set the host structure
108109
!-----------------------------------------------------------------------------
109110
open(newunit=unit, file=filename_host, status='old')
110-
call geom_read(unit, generator%host)
111+
call geom_read(unit, host)
112+
call generator%set_host(host)
111113
close(unit)
112114
if(grid_spacing.gt.1.E-6.and.all(grid.ne.0))then
113115
call stop_program('Cannot specify grid spacing and grid at the same time')

‎app/mod_read_structures.f90‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -132,6 +132,7 @@ function get_gdfs_from_data(input_dir, &
132132
! read the structures from the list of files
133133
!---------------------------------------------------------------------------
134134
num_structures = 0
135+
allocate(basis_list(0))
135136
do i = 1, size(structure_list)
136137
write(*,*) "Reading structure: ", trim(adjustl(structure_list(i)))
137138
select case(ifile_format)
@@ -184,7 +185,7 @@ function get_gdfs_from_data(input_dir, &
184185
trim(basis%spec(j)%name), basis%spec(j)%num, &
185186
j=1, basis%nspec &
186187
)
187-
call distribs_container%add(basis)
188+
basis_list = [ basis_list, basis ]
188189
end do
189190
cycle
190191
end select

‎docs/requirements.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
sphinx==7.1.2
22
sphinx-rtd-theme==1.3.0rc1
3-
f90wrap==0.2.16
3+
f90wrap==0.2.16

‎docs/source/install.rst‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -251,4 +251,4 @@ To test the installation of the Python library, navigate to the repository root
251251
252252
pytest
253253
254-
This will run the unit tests for the Python wrapper, as well as compile and run the Fortran unit tests.
254+
This will run the unit tests for the Python wrapper, as well as compile and run the Fortran unit tests.

‎docs/source/raffle.distributions.rst‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
raffle.distributions module
2+
===========================
3+
4+
.. .. automodule:: raffle.Raffle__Distribs_Container
5+
.. :members:
6+
.. :undoc-members:
7+
.. :show-inheritance:
8+
9+
.. autoclass:: raffle.Raffle__Distribs_Container
10+
:members:
11+
:undoc-members:
12+
:show-inheritance:

‎docs/source/raffle.generator.rst‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
raffle.generator module
2+
=======================
3+
4+
.. .. automodule:: raffle.Generator
5+
.. :members:
6+
.. :undoc-members:
7+
.. :show-inheritance:
8+
9+
10+
.. autoclass:: raffle.Generator
11+
:members:
12+
:undoc-members:
13+
:show-inheritance:

‎docs/source/raffle.geom.rst‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
raffle.geom_rw module
2+
=======================
3+
4+
.. .. automodule:: raffle.Geom_Rw
5+
.. :members:
6+
.. :undoc-members:
7+
.. :show-inheritance:
8+
9+
.. autoclass:: raffle.Geom_Rw
10+
:members:
11+
:undoc-members:
12+
:show-inheritance:

0 commit comments

Comments
 (0)