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b4c1ead
Remove unused files
nedtaylor Jul 22, 2024
26695c4
Add FORD documentation
nedtaylor Jul 22, 2024
c73403b
Handle random seed
nedtaylor Jul 22, 2024
557e2f2
Add fpm support
nedtaylor Jul 23, 2024
86277cc
Remove old files
nedtaylor Jul 23, 2024
cc37fb8
Remove superfluous bash scripts
nedtaylor Jul 23, 2024
3d3c320
Move element charge and mass procedure
nedtaylor Jul 23, 2024
0216bb5
Remove need for elements file
nedtaylor Jul 23, 2024
c10f4f7
Add f90wrap remake option
nedtaylor Jul 24, 2024
085adeb
Add get_element_energies python procedure
nedtaylor Jul 24, 2024
46dffe1
Remove duplicate POSCAR_host
nedtaylor Jul 24, 2024
f3656cc
Remove backup files
nedtaylor Jul 24, 2024
694d87c
Add cmake dependency
nedtaylor Jul 25, 2024
da30c43
Remove use of chem.in
nedtaylor Jul 25, 2024
a8521e4
Handle bond radii in input file
nedtaylor Jul 25, 2024
e287d43
Fix bond_info update
nedtaylor Jul 25, 2024
c147440
Fix bond database
nedtaylor Jul 25, 2024
49ebef3
Add bond test
nedtaylor Jul 25, 2024
bc19294
Remove printing
nedtaylor Jul 25, 2024
bd17e86
Fix bond database initialisation
nedtaylor Jul 25, 2024
bc3bd59
Remove redundant print
nedtaylor Jul 25, 2024
142dbec
Fix method probability ratio
nedtaylor Jul 25, 2024
cb4176a
Add perovskite example data
nedtaylor Jul 25, 2024
ddfa474
Fix host species element names
nedtaylor Jul 25, 2024
7054277
Add default ASE calculator
nedtaylor Jul 25, 2024
0e419c6
Fix distributions write procedure
nedtaylor Jul 25, 2024
784b4b6
Add new booleans to wrapper
nedtaylor Jul 25, 2024
0621c94
Remove blank line
nedtaylor Jul 25, 2024
db6b8e8
Fix element database radius initialisation
nedtaylor Jul 25, 2024
352d170
Fix gridpoint update
nedtaylor Jul 25, 2024
7876d3f
Fix dimension reduction of placement
nedtaylor Jul 25, 2024
53da432
Remove printing
nedtaylor Jul 25, 2024
9c2605f
Update example
nedtaylor Jul 25, 2024
87515e3
Add energy
nedtaylor Jul 26, 2024
53c2251
Add calculator warning
nedtaylor Jul 26, 2024
5c05c7d
Add automatic add to bond database
nedtaylor Jul 26, 2024
7b88e28
Fix lowtol and uptol
nedtaylor Jul 26, 2024
39e247a
Improve global min placement method
nedtaylor Jul 27, 2024
f91f6f2
Fix error printing unit
nedtaylor Jul 27, 2024
a3af54b
Add example host file
nedtaylor Jul 27, 2024
770d5de
Rename buildmap to evaluator
nedtaylor Jul 27, 2024
acc9563
Rename buildmap to evaluator
nedtaylor Jul 27, 2024
6bb8cf7
Fix bond_info set procedure
nedtaylor Jul 27, 2024
2919780
Remove file
nedtaylor Jul 29, 2024
269de23
Improve edit_geom documentation and remove unused procedures
nedtaylor Jul 29, 2024
73f0a0a
Fix library path
nedtaylor Jul 29, 2024
e7b06d5
Add unit test
nedtaylor Jul 29, 2024
e1d8716
Add coverage build files
nedtaylor Jul 30, 2024
a4e16cd
Add error handling
nedtaylor Jul 30, 2024
5134acb
Fix write format
nedtaylor Jul 30, 2024
29839e4
Add extXYZ read write test
nedtaylor Jul 30, 2024
26df5a1
Fix element property setting
nedtaylor Jul 30, 2024
a8d217a
Add clone basis and element properties tests
nedtaylor Jul 30, 2024
cbc976f
Add missing elements and fix charge
nedtaylor Jul 30, 2024
d7c8cd1
Add properties test
nedtaylor Jul 30, 2024
2867c07
Improve rw_geom documentation and tidy code
nedtaylor Jul 30, 2024
bc4794d
Fix initialisation
nedtaylor Jul 30, 2024
3e26436
Fix tests
nedtaylor Jul 30, 2024
7886899
Remove unused procedures
nedtaylor Jul 31, 2024
4c89618
Change basis and species type names
nedtaylor Jul 31, 2024
2096de0
Improve documentation
nedtaylor Jul 31, 2024
fb3df24
Improve documentation
nedtaylor Jul 31, 2024
6df8791
Add wrapper for new procedures
nedtaylor Jul 31, 2024
fb01bd8
Improve documentation and names
nedtaylor Jul 31, 2024
52bd4b5
Improve documentation and names
nedtaylor Jul 31, 2024
2dbd677
Move basis to graph procedure
nedtaylor Jul 31, 2024
6db0acf
Move read_structures module to app
nedtaylor Jul 31, 2024
cc26900
Move files to app
nedtaylor Jul 31, 2024
1dd6b4a
Improve documentation
nedtaylor Jul 31, 2024
bba308a
Improve documentation
nedtaylor Jul 31, 2024
8d91e69
Fix errors
nedtaylor Jul 31, 2024
602d51a
Fix documentation
nedtaylor Jul 31, 2024
1988a23
Fix FORD file
nedtaylor Jul 31, 2024
8ee57ae
Create LICENSE
nedtaylor Aug 1, 2024
15ecc63
Add extended basis type
nedtaylor Aug 2, 2024
ba141ca
Change evaulation to use image atoms
nedtaylor Aug 2, 2024
016d19a
Change 4body to improper dihedral angle
nedtaylor Aug 3, 2024
6da95f5
Fix basis conversion
nedtaylor Aug 3, 2024
9d6a9cf
Fix image atom placement
nedtaylor Aug 3, 2024
a2d1461
Fix memory reference
nedtaylor Aug 3, 2024
a3eaf38
Change handling of atom ignore list
nedtaylor Aug 3, 2024
02aa4bd
Add update_images procedure
nedtaylor Aug 3, 2024
43ca158
Handle ignore list
nedtaylor Aug 3, 2024
e30934e
Handle ignore list
nedtaylor Aug 3, 2024
9c8d66e
Fix allocation
nedtaylor Aug 3, 2024
d283065
Fix image cell distance procedure
nedtaylor Aug 4, 2024
6e06352
Remove debug printing
nedtaylor Aug 4, 2024
3e6e672
Remove old warning printing
nedtaylor Aug 4, 2024
8de23d1
Add min fail handler
nedtaylor Aug 4, 2024
6db1c62
Fix bondlength tolerance handler
nedtaylor Aug 4, 2024
a06c61a
Comment out 4-body
nedtaylor Aug 5, 2024
fdf9f8e
Change testing parameters
nedtaylor Aug 7, 2024
8806bce
Add script version of notebook
nedtaylor Aug 7, 2024
df64f1f
Fix unit test printing
nedtaylor Aug 8, 2024
3e2d0c2
Fix type conversion issues
nedtaylor Aug 13, 2024
adc7b65
Fix image_species dimension
nedtaylor Aug 13, 2024
2dde7dd
Improve comments
nedtaylor Aug 13, 2024
c8e94be
Change initialisation to zero
nedtaylor Aug 13, 2024
da13823
Add distance scaling to distribution functions
nedtaylor Aug 13, 2024
47419ae
Convert from multiplication to addition
nedtaylor Aug 13, 2024
9d9b9b9
Optimise evaluation
nedtaylor Aug 13, 2024
59e1411
Fix indentation
nedtaylor Aug 13, 2024
3189a49
Add angle maps
nedtaylor Aug 13, 2024
1631f91
Add distributions update wrapper
nedtaylor Aug 14, 2024
56276ec
Fix update evolver handling
nedtaylor Aug 14, 2024
d4f2cad
Add carbon example
nedtaylor Aug 14, 2024
e0f5b1e
Add chgnet example
nedtaylor Aug 14, 2024
0fbb8c9
Change version requirements
nedtaylor Aug 14, 2024
254d524
Add normalisation
nedtaylor Aug 14, 2024
d195242
Fix typos
nedtaylor Aug 14, 2024
482e6bb
Fix loop limits
nedtaylor Aug 14, 2024
16d4f01
4-body angle range from 0 to pi
nedtaylor Aug 14, 2024
566dc8e
Add multiplier method
nedtaylor Aug 15, 2024
621d9eb
Add explicit type and limits
nedtaylor Aug 15, 2024
4215098
Remove associate
nedtaylor Aug 15, 2024
942f148
Fix associate
nedtaylor Aug 15, 2024
6779f7f
Set up multipler evaluator method
nedtaylor Aug 16, 2024
f56a090
Make lowtol and uptol variables
nedtaylor Aug 16, 2024
bdd89f7
Add property getter to allocate_species
nedtaylor Aug 16, 2024
389be9c
Fix example rangle
nedtaylor Aug 16, 2024
525015e
Allocate pair_index
nedtaylor Aug 16, 2024
bf6fbfd
Fix default bond radius
nedtaylor Aug 16, 2024
bb925b3
Fix defaults
nedtaylor Aug 16, 2024
d067219
Add graphite
nedtaylor Aug 16, 2024
94e0562
Allow handling of basis_type extended types
nedtaylor Aug 16, 2024
4c3b26e
Fix association
nedtaylor Aug 16, 2024
07d119d
Update test cases
nedtaylor Aug 16, 2024
8ad1e43
Fix counting of bonds
nedtaylor Aug 17, 2024
a2b4f7c
Fix unit cell inclusion
nedtaylor Aug 17, 2024
87ffdaa
Add value checks
nedtaylor Aug 17, 2024
c474c98
Centre grid
nedtaylor Aug 17, 2024
565c06e
Convert to using get_viable_gridpoints procedure
nedtaylor Aug 17, 2024
fb4e748
Add grid shift
nedtaylor Aug 17, 2024
a15c452
Fix array temporary
nedtaylor Aug 17, 2024
5508d35
Increase default width and sigma
nedtaylor Aug 17, 2024
5a8e25a
Get seed if not provided
nedtaylor Aug 17, 2024
bc1a2e6
Use cartesian coordinates
nedtaylor Aug 17, 2024
b220f38
Fix angle point order
nedtaylor Aug 17, 2024
76e64c0
Set 3-body upper distance tolerance to 2.5
nedtaylor Aug 18, 2024
089f3eb
Remove commented line
nedtaylor Aug 18, 2024
5bc64c2
Improve error printing
nedtaylor Aug 18, 2024
1135d2f
Add new example
nedtaylor Aug 18, 2024
01eb343
Add function width setting
nedtaylor Aug 18, 2024
a0510cc
Update size
nedtaylor Aug 18, 2024
2ac1e86
Fix lattice order
nedtaylor Aug 19, 2024
d71b755
Add more test cases
nedtaylor Aug 19, 2024
39568ab
Update grid handling
nedtaylor Aug 20, 2024
e414098
Add new host
nedtaylor Aug 20, 2024
e07ebca
Shift host basis
nedtaylor Aug 20, 2024
e06cc7e
Handle grid offset
nedtaylor Aug 20, 2024
4c37a7e
Set default basis name
nedtaylor Aug 20, 2024
12600d2
Fix missing grid_offset handling
nedtaylor Aug 20, 2024
cc18e57
Make ignore_list optional
nedtaylor Aug 23, 2024
3295779
Optimise distribution function calculator
nedtaylor Aug 23, 2024
20dbd66
Add comments
nedtaylor Aug 23, 2024
5e4c458
Add comments
nedtaylor Aug 23, 2024
a8dd280
Fix 4-body do concurrent
nedtaylor Aug 23, 2024
d86449e
Fix basis extension cutoff
nedtaylor Aug 23, 2024
ee2b29c
Add comments
nedtaylor Aug 23, 2024
af066f1
Add comments
nedtaylor Aug 23, 2024
db27653
Improve comments
nedtaylor Aug 23, 2024
dbe9ff6
Improve comments
nedtaylor Aug 23, 2024
80e3392
Update README
nedtaylor Aug 23, 2024
b53e14f
Fix indentation
nedtaylor Aug 23, 2024
e1e6a6c
Add comments
nedtaylor Aug 23, 2024
77caed9
Add comments
nedtaylor Aug 23, 2024
6c082d8
Add set difference procedure
nedtaylor Sep 5, 2024
5b1f3d0
Add kbT scaling
nedtaylor Sep 5, 2024
0690457
Handle normalisation zero division
nedtaylor Sep 5, 2024
a18581d
Handle normalisation zero division
nedtaylor Sep 5, 2024
778eb6a
Combine distributino functions using set difference
nedtaylor Sep 5, 2024
5bd4222
Move weight scale to inside set difference
nedtaylor Sep 5, 2024
a7f1199
Handle kbT in wrapper
nedtaylor Sep 6, 2024
f8a1510
Remove incorrect renormalisation
nedtaylor Sep 6, 2024
b0a9c82
Change kbT name for python
nedtaylor Sep 6, 2024
b4f1abc
Fix array temporaries
nedtaylor Sep 6, 2024
2535bf3
Add local power law
nedtaylor Sep 6, 2024
07b8482
Update test
nedtaylor Sep 6, 2024
0187d36
Remove unnecessary comments
nedtaylor Sep 6, 2024
3ccad73
Update examples
nedtaylor Sep 6, 2024
ae656e1
Improve atom handling
nedtaylor Sep 6, 2024
97ed277
Fix update_images procedure
nedtaylor Sep 6, 2024
cf3d845
Add viability default
nedtaylor Sep 6, 2024
ed7d9e2
Add image testing
nedtaylor Sep 6, 2024
bbedfbf
Use offset
nedtaylor Sep 6, 2024
4a253a3
Change kbT default
nedtaylor Sep 6, 2024
28ea6b9
Add unit test
nedtaylor Sep 7, 2024
4ad677d
Add error handling
nedtaylor Sep 7, 2024
c91482f
Fix indentation
nedtaylor Sep 7, 2024
cfd1d70
Add normalisation deallocation
nedtaylor Sep 7, 2024
06ebce4
Remove unused files
nedtaylor Sep 7, 2024
0ce2c16
Fix allocated check
nedtaylor Sep 7, 2024
ffa9847
Change host
nedtaylor Sep 7, 2024
1092ac3
Add brew gcov installation handling
nedtaylor Sep 7, 2024
1ace634
Update ignore list
nedtaylor Sep 7, 2024
01ce153
Add uniform error handling
nedtaylor Sep 7, 2024
c3f8f73
Add evolver test
nedtaylor Sep 7, 2024
1c7e332
Update evolver to use uniform error handling
nedtaylor Sep 7, 2024
d8d782c
Add unit test
nedtaylor Sep 7, 2024
6c61e1b
Add implicit none
nedtaylor Sep 7, 2024
290049b
Add default handling
nedtaylor Sep 7, 2024
a13a0e2
Add unit tests
nedtaylor Sep 7, 2024
2f2e0f9
Add unit tests
nedtaylor Sep 7, 2024
5be4a98
Add unit test
nedtaylor Sep 7, 2024
41a7a48
Fix printing
nedtaylor Sep 7, 2024
21eb85c
Remove blank line
nedtaylor Sep 7, 2024
622ecfc
Add unit tests
nedtaylor Sep 7, 2024
2104252
Fix printing
nedtaylor Sep 7, 2024
5c93ad0
Add unit tests
nedtaylor Sep 7, 2024
03d1c43
Fix quicksort duplicate catching
nedtaylor Sep 7, 2024
0c3c2c2
Improve optional argument handling
nedtaylor Sep 7, 2024
20630d2
Add unit tests
nedtaylor Sep 7, 2024
dd63bb0
Add unit tests
nedtaylor Sep 7, 2024
8fed760
Add unit tests
nedtaylor Sep 8, 2024
0770854
Fix plane projection cycling
nedtaylor Sep 8, 2024
a4e6ddb
Add unit tests
nedtaylor Sep 8, 2024
a504338
Fix grid offset in void method
nedtaylor Sep 8, 2024
44f17fe
Fix comments
nedtaylor Sep 8, 2024
579b4b6
Add grid offset
nedtaylor Sep 8, 2024
506f78d
Remove commented sections
nedtaylor Sep 8, 2024
ee31ca3
Add unit tests
nedtaylor Sep 8, 2024
c718448
Remove unused variables
nedtaylor Sep 8, 2024
093b274
Add unit tests
nedtaylor Sep 8, 2024
a742ae5
Reformat variables
nedtaylor Sep 8, 2024
5eb0163
Use custom error handling
nedtaylor Sep 8, 2024
6a414cb
Remove debug printing
nedtaylor Sep 8, 2024
6b05106
Replace unused host example files
nedtaylor Sep 9, 2024
2715b05
Rename example
nedtaylor Sep 9, 2024
6626796
Add separate graphite example
nedtaylor Sep 9, 2024
93143cc
Use custom error handling
nedtaylor Sep 9, 2024
cd1a15c
Merge pull request #7 from nedtaylor/fix_viability
nedtaylor Sep 9, 2024
54339ea
Merge pull request #8 from nedtaylor/library
nedtaylor Sep 9, 2024
322f16d
Remove default DFs rom calculate
nedtaylor Sep 9, 2024
986b505
Update example
nedtaylor Sep 9, 2024
0978ead
Improve handling of ase Atoms objects
nedtaylor Sep 10, 2024
76366bb
Update module import names
nedtaylor Sep 10, 2024
430b875
Update version number
nedtaylor Sep 10, 2024
6cedee3
Update version number
nedtaylor Sep 10, 2024
c7a7cd1
Convert to local procedures
nedtaylor Sep 10, 2024
8bad038
Add paper reference to README
nedtaylor Sep 11, 2024
524b559
Fix blank line
nedtaylor Sep 11, 2024
3f19999
Fix defaults to double radius
nedtaylor Sep 12, 2024
12b02de
Fix test errors
nedtaylor Sep 20, 2024
f2a4a86
Fix inverse procedure
nedtaylor Sep 20, 2024
e7a97d2
Fix inverse procedure
nedtaylor Sep 20, 2024
953c474
Fix incorrect energy analyser placement
nedtaylor Sep 22, 2024
c6496f6
Handle missing elements in database
nedtaylor Sep 22, 2024
f229bb9
Fix missing variables
nedtaylor Sep 22, 2024
497387d
9 precalculate viability (#10)
nedtaylor Sep 24, 2024
d5f7cab
Add badges and coverage workflow
nedtaylor Sep 24, 2024
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92 changes: 92 additions & 0 deletions .github/coverage.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,92 @@
name: run-code-coverage

on:
push:
branches: ["main"]
paths:
- ".github/workflows/coverage.yml"
- "CMakeLists.txt"
- "**.f90"
pull_request:
branches: ["main"]
paths:
- ".github/workflows/coverage.yml"
- "CMakeLists.txt"
- "**.f90"
workflow_dispatch:

permissions:
contents: read
pages: write
id-token: write

concurrency:
group: pages
cancel-in-progress: false

jobs:
run-code-coverage:
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
compiler: [gcc]
version: [13]
steps:
- name: checkout repo
uses: actions/checkout@v4

- name: actions-setup-cmake
uses: jwlawson/actions-setup-cmake@v2.0.1
with:
cmake-version: '3.27.x'

- uses: fortran-lang/setup-fortran@v1
id: setup-fortran
with:
compiler: ${{ matrix.compiler }}
version: ${{ matrix.version }}

- name: Install gcovr
run: |
pip --version
pip install gcovr

- run: |
sudo apt-get update
sudo apt-get install -y cmake make
cmake --version
mkdir -p build
cd build
cmake -DCMAKE_BUILD_TYPE=Debug ..
make
make coverage

- name: Get coverage percentage
run: |
pip install bs4
echo "COVERAGE_PERCENTAGE="$(python ./tools/coverage_badge.py) >> $GITHUB_ENV

- name: Create coverage badge
uses: schneegans/dynamic-badges-action@v1.7.0
with:
auth: ${{ secrets.GIST_SECRET }}
gistID: 48f14ebb5636b54d3813e4b4494903eb
filename: raffle_coverage.json # Use test.svg if you want to use the SVG mode.
label: Coverage
message: ${{ env.COVERAGE_PERCENTAGE }}%
valColorRange: ${{ env.COVERAGE_PERCENTAGE }}
maxColorRange: 100
minColorRange: 0

- name: upload artifact
uses: actions/upload-pages-artifact@v1
with:
path: './build/coverage/'

- name: deploy to Github Pages
uses: actions/deploy-pages@v2
id: deployment
27 changes: 26 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,29 @@
\#
bin/
obj/
*.mod
*.mod
*.smod
*.so
*.txt
DTESTING/
DTEST/
build/
src/*.egg-info
*.egg-info
iteration*
doc/html
settings.json
example/example_files/database*
**/POSCAR*
iteration/
*.traj
*.png
*.param
fort.*
*.o
*.out
*.dat
*.err
*.e
*.log
*.agr
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