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Implement support for helical boundary conditions in gen format#30

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awvwgk merged 1 commit intogrimme-lab:mainfrom
awvwgk:helical
Feb 2, 2022
Merged

Implement support for helical boundary conditions in gen format#30
awvwgk merged 1 commit intogrimme-lab:mainfrom
awvwgk:helical

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@awvwgk awvwgk commented Jan 26, 2022

@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
  |

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codecov bot commented Jan 26, 2022 •
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Codecov Report

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

Impacted file tree graph

@@            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%) ⬇️
src/mctc/io/write/aims.f90 41.66% <50.00%> (-12.88%) ⬇️
src/mctc/io/write/genformat.f90 72.41% <50.00%> (-14.55%) ⬇️
src/mctc/io/write/turbomole.f90 78.57% <60.00%> (-12.34%) ⬇️
src/mctc/io/read/genformat.f90 71.18% <63.88%> (-3.53%) ⬇️
test/test_read_turbomole.f90 80.58% <75.00%> (-0.70%) ⬇️
test/test_read_genformat.f90 76.70% <77.98%> (+3.40%) ⬆️
test/test_read_aims.f90 76.78% <78.37%> (+0.57%) ⬆️
src/mctc/io/read/aims.f90 64.00% <100.00%> (+5.09%) ⬆️
src/mctc/io/read/turbomole.f90 76.38% <100.00%> (-0.33%) ⬇️
... and 4 more

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@awvwgk
Implement support for helical boundary conditions in gen format
01aa78b 
- gen 1D periodicity is along the z-axis stored in the first lattice vector
- the helical angle and the order of the screw axis are stored in the second vector
@awvwgk awvwgk merged commit 5db20f9 into grimme-lab:main Feb 2, 2022
@awvwgk awvwgk deleted the helical branch February 2, 2022 23:27
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