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Development - #11

Merged

nedtaylor merged 456 commits into

mainfrom

development

Sep 24, 2024

Merged

Development#11
nedtaylor merged 456 commits into
mainfrom
development

This pull request is big! We're only showing the most recent 250 commits

Commits on Jul 22, 2024
- Remove unused files
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- Add FORD documentation
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- Handle random seed
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Commits on Jul 23, 2024
- Add fpm support
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- Remove old files
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- Remove superfluous bash scripts
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- Move element charge and mass procedure
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- Remove need for elements file
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Commits on Jul 24, 2024
- Add f90wrap remake option
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- Add get_element_energies python procedure
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- Remove duplicate POSCAR_host
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- Remove backup files
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Commits on Jul 25, 2024
- Add cmake dependency
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- Remove use of chem.in
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  da30c43
- Handle bond radii in input file
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- Fix bond_info update
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  e287d43
- Fix bond database
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  c147440
- Add bond test
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  49ebef3
- Remove printing
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  bc19294
- Fix bond database initialisation
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- Remove redundant print
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  bc3bd59
- Fix method probability ratio
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- Add perovskite example data
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- Fix host species element names
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- Add default ASE calculator
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- Fix distributions write procedure
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- Add new booleans to wrapper
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- Remove blank line
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  0621c94
- Fix element database radius initialisation
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- Fix gridpoint update
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  352d170
- Fix dimension reduction of placement
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- Remove printing
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- Update example
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Commits on Jul 26, 2024
- Add energy
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- Add calculator warning
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- Add automatic add to bond database
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- Fix lowtol and uptol
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Commits on Jul 27, 2024
- Improve global min placement method
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  39e247a
- Fix error printing unit
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- Add example host file
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  a3af54b
- Rename buildmap to evaluator
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  770d5de
- Rename buildmap to evaluator
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- Fix bond_info set procedure
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Commits on Jul 29, 2024
- Remove file
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  2919780
- Improve edit_geom documentation and remove unused procedures
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- Fix library path
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- Add unit test
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Commits on Jul 30, 2024
- Add coverage build files
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- Add error handling
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- Fix write format
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- Add extXYZ read write test
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  29839e4
- Fix element property setting
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  26df5a1
- Add clone basis and element properties tests
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  a8d217a
- Add missing elements and fix charge
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- Add properties test
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- Improve rw_geom documentation and tidy code
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- Fix initialisation
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- Fix tests
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Commits on Jul 31, 2024
- Remove unused procedures
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  7886899
- Change basis and species type names
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  4c89618
- Improve documentation
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  2096de0
- Improve documentation
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- Add wrapper for new procedures
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  6df8791
- Improve documentation and names
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  fb01bd8
- Improve documentation and names
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  52bd4b5
- Move basis to graph procedure
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  2dbd677
- Move read_structures module to app
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  6db0acf
- Move files to app
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  cc26900
- Improve documentation
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  1dd6b4a
- Improve documentation
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  bba308a
- Fix errors
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  8d91e69
- Fix documentation
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- Fix FORD file
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Commits on Aug 1, 2024
- Create LICENSE
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Commits on Aug 2, 2024
- Add extended basis type
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  15ecc63
- Change evaulation to use image atoms
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Commits on Aug 3, 2024
- Change 4body to improper dihedral angle
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  016d19a
- Fix basis conversion
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  6da95f5
- Fix image atom placement
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  9d6a9cf
- Fix memory reference
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  a2d1461
- Change handling of atom ignore list
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  a3eaf38
- Add update_images procedure
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  02aa4bd
- Handle ignore list
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- Handle ignore list
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- Fix allocation
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Commits on Aug 4, 2024
- Fix image cell distance procedure
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  d283065
- Remove debug printing
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  6e06352
- Remove old warning printing
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  3e6e672
- Add min fail handler
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- Fix bondlength tolerance handler
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Commits on Aug 5, 2024
- Comment out 4-body
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Commits on Aug 7, 2024
- Change testing parameters
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- Add script version of notebook
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Commits on Aug 8, 2024
- Fix unit test printing
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Commits on Aug 13, 2024
- Fix type conversion issues
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  3e2d0c2
- Fix image_species dimension
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- Improve comments
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  2dde7dd
- Change initialisation to zero
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  c8e94be
- Add distance scaling to distribution functions
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  da13823
- Convert from multiplication to addition
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  47419ae
- Optimise evaluation
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- Fix indentation
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- Add angle maps
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Commits on Aug 14, 2024
- Add distributions update wrapper
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  1631f91
- Fix update evolver handling
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- Add carbon example
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- Add chgnet example
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- Change version requirements
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- Add normalisation
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  254d524
- Fix typos
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  d195242
- Fix loop limits
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  482e6bb
- 4-body angle range from 0 to pi
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Commits on Aug 15, 2024
- Add multiplier method
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- Add explicit type and limits
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  621d9eb
- Remove associate
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- Fix associate
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Commits on Aug 16, 2024
- Set up multipler evaluator method
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- Make lowtol and uptol variables
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  f56a090
- Add property getter to allocate_species
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  bdd89f7
- Fix example rangle
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- Allocate pair_index
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  525015e
- Fix default bond radius
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- Fix defaults
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  bb925b3
- Add graphite
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  d067219
- Allow handling of basis_type extended types
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  94e0562
- Fix association
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- Update test cases
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Commits on Aug 17, 2024
- Fix counting of bonds
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  8ad1e43
- Fix unit cell inclusion
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  a2b4f7c
- Add value checks
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  87ffdaa
- Centre grid
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  c474c98
- Convert to using get_viable_gridpoints procedure
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  565c06e
- Add grid shift
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  fb4e748
- Fix array temporary
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  a15c452
- Increase default width and sigma
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  5508d35
- Get seed if not provided
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  5a8e25a
- Use cartesian coordinates
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- Fix angle point order
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Commits on Aug 18, 2024
- Set 3-body upper distance tolerance to 2.5
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  76e64c0
- Remove commented line
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  089f3eb
- Improve error printing
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  5bc64c2
- Add new example
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  1135d2f
- Add function width setting
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- Update size
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Commits on Aug 19, 2024
- Fix lattice order
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- Add more test cases
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Commits on Aug 20, 2024
- Update grid handling
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- Add new host
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  e414098
- Shift host basis
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- Handle grid offset
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  e06cc7e
- Set default basis name
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- Fix missing grid_offset handling
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Commits on Aug 23, 2024
- Make ignore_list optional
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  cc18e57
- Optimise distribution function calculator
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- Add comments
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- Add comments
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  5e4c458
- Fix 4-body do concurrent
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  a8dd280
- Fix basis extension cutoff
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- Add comments
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- Add comments
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  af066f1
- Improve comments
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  db27653
- Improve comments
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  dbe9ff6
- Update README
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  80e3392
- Fix indentation
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- Add comments
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- Add comments
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Commits on Sep 5, 2024
- Add set difference procedure
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  6c082d8
- Add kbT scaling
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  5b1f3d0
- Handle normalisation zero division
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  0690457
- Handle normalisation zero division
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  a18581d
- Combine distributino functions using set difference
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  778eb6a
- Move weight scale to inside set difference
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Commits on Sep 6, 2024
- Handle kbT in wrapper
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  a7f1199
- Remove incorrect renormalisation
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  f8a1510
- Change kbT name for python
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  b0a9c82
- Fix array temporaries
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  b4f1abc
- Add local power law
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  2535bf3
- Update test
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  07b8482
- Remove unnecessary comments
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  0187d36
- Update examples
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  3ccad73
- Improve atom handling
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  ae656e1
- Fix update_images procedure
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- Add viability default
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- Add image testing
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- Use offset
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  bbedfbf
- Change kbT default
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Commits on Sep 7, 2024
- Add unit test
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  28ea6b9
- Add error handling
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  4ad677d
- Fix indentation
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  c91482f
- Add normalisation deallocation
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  cfd1d70
- Remove unused files
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  06ebce4
- Fix allocated check
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  0ce2c16
- Change host
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  ffa9847
- Add brew gcov installation handling
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  1092ac3
- Update ignore list
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  1ace634
- Add uniform error handling
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  01ce153
- Add evolver test
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  c3f8f73
- Update evolver to use uniform error handling
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  1c7e332
- Add unit test
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  d8d782c
- Add implicit none
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  6c61e1b
- Add default handling
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- Add unit tests
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  a13a0e2
- Add unit tests
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  2f2e0f9
- Add unit test
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  5be4a98
- Fix printing
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  41a7a48
- Remove blank line
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  21eb85c
- Add unit tests
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  622ecfc
- Fix printing
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  2104252
- Add unit tests
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  5c93ad0
- Fix quicksort duplicate catching
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  03d1c43
- Improve optional argument handling
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- Add unit tests
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- Add unit tests
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Commits on Sep 8, 2024
- Add unit tests
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  8fed760
- Fix plane projection cycling
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  0770854
- Add unit tests
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  a4e6ddb
- Fix grid offset in void method
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  a504338
- Fix comments
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  committed
  44f17fe
- Add grid offset
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  579b4b6
- Remove commented sections
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  506f78d
- Add unit tests
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  ee31ca3
- Remove unused variables
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  c718448
- Add unit tests
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  093b274
- Reformat variables
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  a742ae5
- Use custom error handling
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  5eb0163
- Remove debug printing
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Commits on Sep 9, 2024
- Replace unused host example files
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  6b05106
- Rename example
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  2715b05
- Add separate graphite example
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  6626796
- Use custom error handling
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  93143cc
- Merge pull request #7 from nedtaylor/fix_viability
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  cd1a15c
- Merge pull request #8 from nedtaylor/library
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  54339ea
- Remove default DFs rom calculate
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  322f16d
- Update example
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Commits on Sep 10, 2024
- Improve handling of ase Atoms objects
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  0978ead
- Update module import names
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  76366bb
- Update version number
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  430b875
- Update version number
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  6cedee3
- Convert to local procedures
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  c7a7cd1
Commits on Sep 11, 2024
- Add paper reference to README
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  8bad038
- Fix blank line
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Commits on Sep 12, 2024
- Fix defaults to double radius
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  3f19999
Commits on Sep 20, 2024
- Fix test errors
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  12b02de
- Fix inverse procedure
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  f2a4a86
- Fix inverse procedure
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Commits on Sep 22, 2024
- Fix incorrect energy analyser placement
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  953c474
- Handle missing elements in database
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  c6496f6
- Fix missing variables
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  f229bb9
Commits on Sep 24, 2024
- 9 precalculate viability (#10)
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  authored
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- Add badges and coverage workflow
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  committed
  d5f7cab

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Commits on Aug 16, 2024