@bhourahine I have a couple of questions regarding the format

I'm storing the helical z-axis like in DFTB+ in the first lattice vector (shape(lattice) == [3, 1]), is this the best representation?
formats not supporting helical boundary conditions will drop the helical axis on write (similar behavior as with lattice vectors in molecular formats)
helical boundary conditions only round-trip in gen format at the moment
Turbomole coord also supports 1D periodic boundary conditions, however the periodic dimension is always given along the x-axis (shape(lattice) == [3, 3]), probably requires rotation of the coordinate system to write this in gen format
FHI-aims geometry.in can define 1D periodicity as well, have to check in detail how this is supposed to work for the atom_frac keywords, but same issues as with the Turbomole coord format

Currently tested error conditions for gen format:

  Starting invalid1-gen ... (7/15)
       ... invalid1-gen [EXPECTED FAIL]
  Message: Error: Could not read number of atoms
 --> (input):1:1-2
  |
1 | -2  F
  | ^^ expected integer value
  |
  Starting invalid2-gen ... (8/15)
       ... invalid2-gen [EXPECTED FAIL]
  Message: Error: Invalid input version found
 --> (input):1:4
  |
1 | 2  X
  |    ^ unknown identifier
  |
  Starting invalid3-gen ... (9/15)
       ... invalid3-gen [EXPECTED FAIL]
  Message: Error: Cannot map symbol to atomic number
 --> (input):2:4-7
  |
2 | Ga ***As
  |    ^^^^ unknown element
  |
  Starting invalid4-gen ... (10/15)
       ... invalid4-gen [EXPECTED FAIL]
  Message: Error: Cannot read coordinates
 --> (input):2
  |
2 | 
  |^ unexpected value
  |
  Starting invalid5-gen ... (11/15)
       ... invalid5-gen [EXPECTED FAIL]
  Message: Error: Unexpected end of file
 --> (input):4
  |
4 | 
  |^ missing lattice information
  |
  Starting invalid6-gen ... (12/15)
       ... invalid6-gen [EXPECTED FAIL]
  Message: Error: Cannot read lattice vector
 --> (input):6:1-13
  |
6 | ************* ************* 0.0000000E+00
  | ^^^^^^^^^^^^^ expected real value
  |
  Starting invalid7-gen ... (13/15)
       ... invalid7-gen [EXPECTED FAIL]
  Message: Error: Cannot read lattice vector
  --> (input):16:5-9
   |
16 | 3.0 ***** 1
   |     ^^^^^ expected real value
   |
  Starting invalid8-gen ... (14/15)
       ... invalid8-gen [EXPECTED FAIL]
  Message: Error: Invalid helical axis rotation order
 --> (input):6:23-25
  |
6 | 0.2140932670E+01 18.0 -10
  |                       ^^^ expected positive value
  |
  Starting invalid9-gen ... (15/15)
       ... invalid9-gen [EXPECTED FAIL]
  Message: Error: Cannot read origin
 --> (input):5:37
  |
5 | 0.0000000000E+00    0.0000000000E+00
  |                                     ^ expected real value
  |

Codecov Report

Merging #30 (01aa78b) into main (9e2ebec) will increase coverage by 0.35%. The diff coverage is 75.00%.

@@            Coverage Diff             @@
##             main      #30      +/-   ##
==========================================
+ Coverage   67.47%   67.82%   +0.35%     
==========================================
  Files          56       56              
  Lines        6020     6313     +293     
  Branches     1867     1951      +84     
==========================================
+ Hits         4062     4282     +220     
- Misses        670      671       +1     
- Partials     1288     1360      +72

Impacted Files	Coverage Δ
src/mctc/io/write/vasp.f90	`76.74% <33.33%> (-4.21%)`	:arrow_down:
src/mctc/io/write/aims.f90	`41.66% <50.00%> (-12.88%)`	:arrow_down:
src/mctc/io/write/genformat.f90	`72.41% <50.00%> (-14.55%)`	:arrow_down:
src/mctc/io/write/turbomole.f90	`78.57% <60.00%> (-12.34%)`	:arrow_down:
src/mctc/io/read/genformat.f90	`71.18% <63.88%> (-3.53%)`	:arrow_down:
test/test_read_turbomole.f90	`80.58% <75.00%> (-0.70%)`	:arrow_down:
test/test_read_genformat.f90	`76.70% <77.98%> (+3.40%)`	:arrow_up:
test/test_read_aims.f90	`76.78% <78.37%> (+0.57%)`	:arrow_up:
src/mctc/io/read/aims.f90	`64.00% <100.00%> (+5.09%)`	:arrow_up:
src/mctc/io/read/turbomole.f90	`76.38% <100.00%> (-0.33%)`	:arrow_down:
... and 4 more

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grimme-lab / mctc-lib

Implement support for helical boundary conditions in gen format #30

Codecov Report