Atomistic file extension

[MSallermann]

Implements the format suggested in #15.

Includes a partial refactor of the parsing of the segment header keywords:

• keyword/value pairs are now specified as their own pegtl rules, see keywords.hpp and atomistic_keywords.hpp
  • This allows one to be flexible regarding the shapes etc., which is useful for e.g for multiline keywords like the new 'basis'
  • Also makes it possible to transparently select, which keyword value pairs are allowed for which file format
• Validation of keywords with regards to the mesh has been moved to a single pass, once the header is read.
• Overall the refactor ended up quite verbose ... suggestions welcome.

Then the fileformat discussed in the issue has been implemented with some minor changes.

• For the basis I chose the format:

  # basis:
  # 0 0 0
  # 0.5 0 0

• In compatibility mode, the version string reads:

  # OOMMF OVF 2.0
  ##% AOVF_COMP 1.0

• The lattice meshtype needs to be selected with an additional: #%% meshtype lattice, which overwrites any other meshtype
• Extensive unit tests for the new format have been added.
• On reading in a file, the fileformat is automatically detected and saved in a new member of ovf_file : ovf_extension_format.

  /* OVF file formats */
  #define OVF_EXTENSION_FORMAT_OVF                0 // Standard OVF 2 format
  #define OVF_EXTENSION_FORMAT_AOVF              1 // Atomistic extension, with new keywords
  #define OVF_EXTENSION_FORMAT_AOVF_COMP  2 // Atomistic extension in compatibility format, (##% prefix for new keywords)

• On writing a file, having set meshtype lattice will lead to an error if OVF_EXTENSION_FORMAT_OVF is used.

TODO

• [ ] Fortran bindings
• [ ] Maybe squash some commits to remove noise from the log
• [ ] Formatting
• [ ] General pass to clean up some rough edges
• [ ] Check if performance has suffered
• [ ] Check all edge cases, where unexpected behaviour may occur
• [ ] Naming of some files variables should probably be improved
• [ ] Bravais and basis vectors should probably be saved as doubles not floats
• [x] When using the plain OVF format ##% lines are not ignored

[coveralls]

Coverage increased (+1.4%) to 94.286% when pulling 32da6aa6708063b275da9f76fe2b1cb3fe399088 on MSallermann:atomistic_v2 into 6e3383eea0a71f78aa1e11dcb5680da980979b1b on spirit-code:master.

[codecov[bot]]

Codecov Report

Merging #16 (32da6aa) into master (6e3383e) will increase coverage by 0.15%. The diff coverage is 77.58%.

@@            Coverage Diff             @@
##           master      #16      +/-   ##
==========================================
+ Coverage   52.22%   52.37%   +0.15%     
==========================================
  Files           8       10       +2     
  Lines        1779     1814      +35     
==========================================
+ Hits          929      950      +21     
- Misses        850      864      +14