Checkhull Error

[sjtuzhanglei]

casm-learn -s fit_ga.json --checkhull --indiv 0
Loading fit_ga.json
Loading Hall of Fame: fit_ga_halloffame.pkl

Get problem data...

Reading existing problem specs from: fit_ga_specs.pkl

DONE

-- Check: individual 0 --
Index: Selected #Selected CV RMS wRMS Estimator FeatureSelection Note

0: 1111100101001111111000000010000011000000... 102          0.15444827   0.12728705   0.12728705   LinearRegression         GeneticAlgorithm         

Writing: /pscratch/sd/v/voz5005/casm/cluster_expansions/clex.formation_energy/calctype.default/ref.default/bset.default/eci.__tmp/eci.json

Error in casm.query
proj: /pscratch/sd/v/voz5005/casm
Attempted to execute: 'query -k 'clex_hull_dist(ALL,atom_frac) clex(formation_energy) clex_hull_dist(/pscratch/sd/v/voz5005/casm/.casm/tmp/ALL_dft_hull,atom_frac) ' -c ALL -t config -v -o STDOUT'
---- stdout: ---------------------

---- stderr: ---------------------
Print:

• clex_hull_dist(ALL,atom_frac) clex(formation_energy) clex_hull_dist(/pscratch/sd/v/voz5005/casm/.casm/tmp/ALL_dft_hull,atom_frac)
  to "STDOUT"

ERROR: QH6154 qhull precision error: initial facet 1 is coplanar with the interior point
ERRONEOUS FACET:

• f1
  • flags: bottom simplicial flipped
  • normal: -0 -1 -0 0
  • offset: 0
  • vertices: p16(v3) p0(v2) p19(v1) p4(v0)
  • neighboring facets: f2 f3 f4 f5

While executing: | qhull
Options selected for Qhull 2015.0.6.r 2015/10/20:
run-id 1312832550 _pre-merge _zero-centrum _max-width 17
Error-roundoff 1.4e-14 _one-merge 1.3e-13 _near-inside 6.3e-13
Visible-distance 8.4e-14 U-coplanar-distance 8.4e-14 Width-outside 1.7e-13
_wide-facet 5e-13

  2 flipped facets
818 zero divisors during gaussian elimination

The input to qhull appears to be less than 4 dimensional, or a
computation has overflowed.

Qhull could not construct a clearly convex simplex from points:

• p1(v4): 0.4 0 0.6 -0.0029
• p16(v3): 0 0 1 -11
• p0(v2): 0.33 0 0.67 -0.39
• p19(v1): 1 0 0 6.4
• p4(v0): 0 0 1 3

The center point is coplanar with a facet, or a vertex is coplanar
with a neighboring facet. The maximum round off error for
computing distances is 1.4e-14. The center point, facets and distances
to the center point are as follows:

center point 0.3467 0 0.6533 -0.3806

facet p16 p0 p19 p4 distance= 0
facet p1 p0 p19 p4 distance= 0
facet p1 p16 p19 p4 distance= 0
facet p1 p16 p0 p4 distance= 0
facet p1 p16 p0 p19 distance= 0

These points either have a maximum or minimum x-coordinate, or
they maximize the determinant for k coordinates. Trial points
are first selected from points that maximize a coordinate.

The min and max coordinates for each dimension are:
0: 0 1 difference= 1
1: 0 0 difference= 0
2: 0 1 difference= 1
3: -10.88 6.381 difference= 17.26

If the input should be full dimensional, you have several options that
may determine an initial simplex:

• use 'QJ' to joggle the input and make it full dimensional
• use 'QbB' to scale the points to the unit cube
• use 'QR0' to randomly rotate the input for different maximum points
• use 'Qs' to search all points for the initial simplex
• use 'En' to specify a maximum roundoff error less than 1.4e-14.
• trace execution with 'T3' to see the determinant for each point.

If the input is lower dimensional:

• use 'QJ' to joggle the input and make it full dimensional
• use 'Qbk:0Bk:0' to delete coordinate k from the input. You should
  pick the coordinate with the least range. The hull will have the
  correct topology.
• determine the flat containing the points, rotate the points
  into a coordinate plane, and delete the other coordinates.
• add one or more points to make the input full dimensional.

---

Traceback (most recent call last):
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 402, in _infer_columns
line = self._buffered_line()
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 635, in _buffered_line
return self._next_line()
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 736, in _next_line
orig_line = self._next_iter_line(row_num=self.pos + 1)
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 800, in _next_iter_line
line = next(self.data)
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/global/homes/v/voz5005/.local/conda/envs/casm/bin/casm-learn", line 8, in
sys.exit(main())
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/casm/scripts/casm_learn.py", line 162, in main
casm.learn.fit.checkhull(input,
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/casm/learn/fit.py", line 2147, in checkhull
sel.query([clex_hull_dist_long, clex_Eform, clex_dft_hull_dist_long],
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/casm/project/selection.py", line 272, in query
df = query(self.proj,
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/casm/project/query.py", line 57, in query
return pandas.read_csv(sout, sep=compat.str(' +'), engine='python')
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1448, in init
self._engine = self._make_engine(f, self.engine)
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 131, in init
) = self._infer_columns()
File "/global/homes/v/voz5005/.local/conda/envs/casm/lib/python3.9/site-packages/pandas/io/parsers/python_parser.py", line 430, in _infer_columns
raise EmptyDataError("No columns to parse from file") from err
pandas.errors.EmptyDataError: No columns to parse from file