fix(su2): CRLF crashes, FFD/NPERIODIC warning spam, and point column trim

[AhmedMoustafaa]

Fix SU2 reader: CRLF line endings, double-trim bug, NPERIODIC and FFD sections

Summary

This PR fixes four bugs in the SU2 mesh reader that together caused 4 crashes and
134,634 spurious warnings when reading SU2 v7/v8 tutorial meshes. After the patch,
all 50 tutorial meshes load successfully with only 454 expected warnings (string tag
substitutions).

Metric	Before	After	Delta
Failures	4	0	-4
Total warnings	134,634	454	-134,180

---

Fixes

1. CRLF line endings crash the point coordinate reader

Affected files: any SU2 mesh generated on Windows or by certain solvers (e.g.
CIRA, commercial CFD exporters).

np.fromfile(..., sep=' ') uses C-level I/O and bypasses Python's text-mode
\r\n → \n translation. On CRLF files, the \r characters are treated as
non-numeric tokens and stop the read early, producing a reshape error:

ValueError: cannot reshape array of size 259228 into shape (51846,5)

This crashed 4 meshes in the tutorial suite:

compressible_flow/ActuatorDisk_VariableLoad/propeller_variable_load.su2
compressible_flow/Transitional_Flat_Plate/grid.su2
compressible_flow/Transitional_Flat_Plate/Langtry_and_Menter/T3A/grid.su2
multiphysics/unsteady_fsi_python/airfoil.su2

All four have 100% CRLF line endings. The fix replaces np.fromfile with explicit
line-by-line reading, which is handled correctly by Python's text mode:

# Before (broken on CRLF files):
points = np.fromfile(
    f, count=num_verts * (dim + extra_columns), dtype=ftype, sep=" "
).reshape(num_verts, dim + extra_columns)
 
# After (safe on both LF and CRLF):
raw = [f.readline().split()[:dim] for _ in range(num_verts)]
points = np.array(raw, dtype=ftype)

---

2. Double-trimming of extra point columns

This bug was introduced alongside the CRLF fix. After switching to line-by-line
reading with [:dim] slicing, points already has exactly dim columns.
The subsequent points[:, :-extra_columns] then incorrectly trims real coordinate
data. Fix: remove the redundant column trim from points; keep it only on
first_line which is still built from the full-width raw line:

# Before (trims already-clean data):
if extra_columns > 0:
    first_line = first_line[:-extra_columns]
    points = points[:, :-extra_columns]   # ← wrong, points is already [:dim]
 
# After:
if extra_columns > 0:
    first_line = first_line[:-extra_columns]
    # points already sliced to [:dim] during line-by-line read

---

3. NPERIODIC section causes spurious warnings

SU2 turbomachinery meshes (e.g. propeller, compressor cases) append a NPERIODIC
block after the boundary markers. Its data lines contain no = sign, so the main
parser loop emitted a warning for each one:

Warning: meshio could not parse line
 0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
 skipping.....

Fix: explicitly skip the data lines following NPERIODIC and PERIODIC_INDEX:

elif name == "NPERIODIC":
    nperiodic = int(rest_of_line)
    for _ in range(nperiodic):
        f.readline()  # PERIODIC_INDEX= n
        f.readline()  # translation vector
        f.readline()  # rotation center
        f.readline()  # rotation angles

---

4. FFD box sections cause massive warning spam

SU2 shape optimisation meshes embed Free-Form Deformation (FFD) box definitions
between the mesh header and the element data. Three sub-sections —
FFD_CORNER_POINTS, FFD_CONTROL_POINTS, and FFD_SURFACE_POINTS — each have
a count followed by bare data lines with no = sign. The parser emitted a warning
for every single line, producing tens of thousands of spurious warnings per mesh:

Warning: meshio could not parse line
 -0.0403        0       -0.04836
 skipping.....
Warning: meshio could not parse line
  0.8463        0       -0.04836
 skipping.....
... (60,000+ times)

Fix: skip the N data lines following each of the three keywords:

elif name == "FFD_CORNER_POINTS":
    for _ in range(int(rest_of_line)):
        f.readline()
 
elif name == "FFD_CONTROL_POINTS":
    for _ in range(int(rest_of_line)):
        f.readline()
 
elif name == "FFD_SURFACE_POINTS":
    for _ in range(int(rest_of_line)):
        f.readline()

Note: other FFD_* keywords (FFD_TAG, FFD_DEGREE_I/J/K, FFD_LEVEL,
FFD_PARENTS, FFD_CHILDREN) have their value on the keyword line itself and are
already silently handled by the generic split("=") fallthrough — no change needed
for those.

---

Per-file impact

File	Status	Warnings before	Warnings after	Delta
compressible_flow/Inviscid_ONERAM6/mesh_ONERAM6_inv_ffd.su2	pass	60,320	14	-60,306
design/Inviscid_3D_Constrained_ONERAM6/mesh_ONERAM6_inv_FFD.su2	pass	60,320	14	-60,306
design/Inc_Turbulent_Bend_Wallfunctions/sudo_coarse_FFD.su2	pass	8,120	8	-8,112
multiphysics/steady_cht/mesh_cht_3cyl_ffd.su2	pass	2,733	21	-2,712
design/Unsteady_Shape_Opt_NACA0012/unsteady_naca0012_FFD.su2	pass	1,402	4	-1,398
incompressible_flow/Inc_Streamwise_Periodic/fluid_FFD.su2	pass	396	12	-384
design/Multi_Objective_Shape_Design/mesh_wedge_inv_FFD.su2	pass	311	8	-303
incompressible_flow/Inc_Species_Transport/1__FFD-box-writing/mesh_out.su2	pass	172	10	-162
incompressible_flow/Inc_Species_Transport/2__mesh-deform-test/primitiveVenturi.su2	pass	172	10	-162
incompressible_flow/Inc_Species_Transport/3__gradient-validation/primitiveVenturi.su2	pass	172	10	-162
incompressible_flow/Inc_Species_Transport/4__optimization/primitiveVenturi.su2	pass	172	10	-162
compressible_flow/Turbulent_ONERAM6/mesh_ONERAM6_turb_hexa_43008.su2	pass	39	6	-33
compressible_flow/Turbulent_ONERAM6/mesh_ONERAM6_100k.su2	pass	15	6	-9
structural_mechanics/cantilever/mesh_cantilever.su2	pass	11	8	-3
multiphysics/unsteady_fsi_python/airfoil.su2	fail→pass	0	4	+4
compressible_flow/ActuatorDisk_VariableLoad/propeller_variable_load.su2	fail→pass	0	10	+10
compressible_flow/Transitional_Flat_Plate/Langtry_and_Menter/T3A/grid.su2	fail→pass	0	10	+10
compressible_flow/Transitional_Flat_Plate/grid.su2	fail→pass	0	10	+10

Remaining warnings (454 total)

All remaining warnings are expected and pre-existing — meshio does not support
string boundary tags and substitutes integers:

Warning: meshio does not support tags of string type.
    Surface tag  inlet will be replaced by 1
Warning: meshio does not support tags of string type.
    Surface tag  outlet will be replaced by 2

These are a separate issue unrelated to this PR.

---

Test setup

Tested against all 50 .su2 mesh files from the
SU2 v8.0 tutorial repository covering
compressible flow, incompressible flow, multiphysics, structural mechanics, and
shape design cases.