Merge pull request #130 from lcmd-epfl/io-refactoring

Reorganize i/o modules
Improve ORCA interface
Improve Metatensor interface
Reorder MOs/DMs from Gaussian format
Parce Turbomole MOs files

Author: briling

docs/generate_rst.py

@@ -325,7 +325,7 @@ def render_index_rst(project: str, modules: list[ModuleInfo], out_dir: Path) ->
     out.append(".. toctree::\n   :caption: Modules\n   :hidden:\n\n")
 
 
-    module_order = ['spahm', 'fields', 'qml', 'regression'] + ['compound', 'c2mio', 'equio', 'orcaio']
+    module_order = ['spahm', 'fields', 'qml', 'regression', 'compound']
     def key(m):
         name = m.name.split('.')[1]
         i = module_order.index(name) if name in module_order else len(module_order)

examples/data/AJALIH/AJALIH.xyz

@@ -0,0 +1,54 @@
+52
+0 5
+Fe         0.14005       -0.96028        0.24860
+Br         0.04760       -2.71770       -1.35052
+Br         0.51098       -1.66925        2.48994
+P         -1.67045        0.64630        0.04154
+P          1.49137        1.00407       -0.30691
+N         -0.93908        2.01059       -0.66228
+N          0.40553        2.31997       -0.34154
+H          0.45433        2.85659        0.53275
+C         -2.55204        1.05118        1.62253
+H         -2.90953        0.06097        1.96346
+C         -1.54412        1.56608        2.63497
+H         -2.01575        1.68908        3.62514
+H         -1.15822        2.55927        2.33684
+H         -0.69342        0.87423        2.74906
+C         -3.72734        2.01525        1.48799
+H         -4.18847        2.18853        2.47612
+H         -4.51900        1.63988        0.81933
+H         -3.39664        2.99655        1.10653
+C         -3.00694        0.25147       -1.15704
+H         -3.73205        1.08518       -1.13859
+C         -2.44534        0.09384       -2.58396
+H         -3.26643       -0.15943       -3.27617
+H         -1.70660       -0.72376       -2.61226
+H         -1.95853        1.01106       -2.94640
+C         -3.71205       -1.03192       -0.70123
+H         -4.50441       -1.30055       -1.42033
+H         -4.18484       -0.92853        0.28944
+H         -2.99492       -1.86941       -0.65824
+C         -1.63840        3.16764       -1.22300
+H         -1.09847        3.52187       -2.11776
+H         -1.70279        4.00781       -0.50205
+H         -2.66091        2.88608       -1.51156
+C          2.68323        1.67170        0.94188
+H          2.01024        1.86959        1.79906
+C          3.70079        0.62535        1.40845
+H          4.24437        1.00759        2.28929
+H          4.44836        0.40440        0.63077
+H          3.20072       -0.31373        1.69785
+C          3.36116        2.98145        0.51065
+H          3.92004        3.41133        1.35970
+H          2.64130        3.73739        0.15615
+H          4.08532        2.80049       -0.30140
+C          2.31022        1.03631       -1.96046
+H          2.77156        2.03284       -2.07646
+C          3.35556       -0.07419       -2.02537
+H          3.75174       -0.15693       -3.05216
+H          2.90140       -1.04685       -1.76654
+H          4.21170        0.09757       -1.35527
+C          1.26293        0.80806       -3.03506
+H          1.73652        0.82147       -4.03221
+H          0.47748        1.58087       -3.02229
+H          0.77939       -0.17371       -2.89981

examples/data/AJALIH/AJALIH_5_SPE.densities

@@ -0,0 +1,28 @@
+26
+0 1
+  I     -0.691564    6.065851   10.218679
+  Co    -0.896730    6.291743   12.801124
+  S     -3.111547    5.942715   12.672839
+  C     -0.900957    4.763642   14.175690
+  C     -0.461276    5.983590   14.795995
+  C      0.713137    6.405881   14.113956
+  H      1.264840    7.323863   14.311032
+  C      0.993227    5.481683   13.083596
+  H      1.802106    5.559932   12.358853
+  C      0.015965    4.473016   13.122433
+  H     -0.056529    3.635907   12.428292
+  C     -2.210760    4.059666   14.447381
+  H     -2.673227    4.493474   15.348774
+  H     -2.035736    2.991419   14.671175
+  C     -3.111610    4.202498   13.259335
+  H     -2.727972    3.649740   12.386330
+  H     -4.146425    3.867362   13.435280
+  C     -3.945153    6.793732   14.050514
+  H     -3.869637    7.852090   13.755824
+  H     -3.340371    6.686944   14.965041
+  C     -5.368941    6.350425   14.251741
+  H     -5.442055    5.313038   14.619953
+  H     -5.857396    6.994746   15.002527
+  H     -5.951474    6.421791   13.318039
+  I     -1.173397    8.852094   12.837558
+  H     -0.948251    6.502776   15.620742