I met this error when I’m trying to use PhaseDiagram(entries), I got this error:
My code worked for other chemsys entries in the for loop, could anyone helped me with this issue？Many thanks.
pd = PhaseDiagram(entries)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/lib/python3.11/site-packages/pymatgen/analysis/phase_diagram.py", line 380, in __init__
computed_data = self._compute()
^^^^^^^^^^^^^^^
File "/home/lib/python3.11/site-packages/pymatgen/analysis/phase_diagram.py", line 474, in _compute
facets = get_facets(qhull_data)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/lib/python3.11/site-packages/pymatgen/analysis/phase_diagram.py", line 2058, in get_facets
return ConvexHull(qhull_data, qhull_options="Qt i").simplices
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "_qhull.pyx", line 2425, in scipy.spatial._qhull.ConvexHull.__init__
File "_qhull.pyx", line 343, in scipy.spatial._qhull._Qhull.__init__
scipy.spatial._qhull.QhullError: QH6271 qhull topology error (qh_check_dupridge): wide merge (15330210.7x wider) due to dupridge between f925 and f924 (vertex dist 0.17), merge dist 0.096, while processing p11
- Allow error with option 'Q12'
ERRONEOUS FACET:
- f925
- flags: top newfacet mergehorizon dupridge mergeridge2
- normal: -0.9864 0 -0 0.1644 -0
- offset: -0
- vertices: p11(v45) p4(v44) p15(v35) p54(v27) p61(v6)
- neighboring facets: f865 f28 f926 f924
- ridges:
- r1342 simplicialtop simplicialbot
vertices: p4(v44) p15(v35) p54(v27) p61(v6)
between f925 and f865
- r1343 simplicialbot
vertices: p11(v45) p15(v35) p54(v27) p61(v6)
between f865 and f925
- r1346 simplicialtop
vertices: p11(v45) p4(v44) p15(v35) p54(v27)
between f925 and f28
- r1344 simplicialtop simplicialbot
vertices: p11(v45) p4(v44) p54(v27) p61(v6)
between f925 and f926
- r1345 simplicialbot
vertices: p11(v45) p4(v44) p15(v35) p61(v6)
between f924 and f925
ERRONEOUS OTHER FACET:
- f924
- flags: top newfacet mergehorizon dupridge mergeridge1
- normal: 0.4789 0.4789 0.4789 0.5587 -0
- offset: -0.4788521
- vertices: p11(v45) p4(v44) p24(v36) p15(v35) p61(v6)
- neighboring facets: f717 f925 f28 f926 f636
- ridges:
- r1329 tested simplicialtop
vertices: p4(v44) p24(v36) p15(v35) p61(v6)
between f924 and f717
- r1345 simplicialbot
vertices: p11(v45) p4(v44) p15(v35) p61(v6)
between f924 and f925
- r1341 simplicialtop
vertices: p11(v45) p4(v44) p24(v36) p15(v35)
between f924 and f28
- r1340 simplicialtop simplicialbot
vertices: p11(v45) p4(v44) p24(v36) p61(v6)
between f926 and f924
- r1339 simplicialtop simplicialbot
vertices: p11(v45) p24(v36) p15(v35) p61(v6)
between f636 and f924
While executing: | qhull i i Qt
Options selected for Qhull 2019.1.r 2019/06/21:
run-id 1522070417 incidence incidence Qtriangulate Qxact-merge
_zero-centrum _max-width 3.6e+05 Error-roundoff 4.8e-10 _one-merge 5.3e-09
_near-inside 2.6e-08 Visible-distance 2.9e-09 U-max-coplanar 2.9e-09
Width-outside 5.8e-09 _wide-facet 1.7e-08 _maxoutside 5.8e-09
Last point added to hull was p11. Last merge was #403.
At error exit:
Convex hull of 86 points in 5-d:
Number of vertices: 45
Number of coplanar points: 24
Number of facets: 159
Number of non-simplicial facets: 28
Statistics for: | qhull i i Qt
Number of points processed: 45
Number of hyperplanes created: 491
Number of distance tests for qhull: 7663
Number of distance tests for merging: 8890
Number of distance tests for checking: 0
Number of merged facets: 442
Maximum distance of point above facet: 6.1e-09 (1.1x)
Maximum distance of vertex below facet: -3.1e-09 (0.5x)
precision problems (corrected unless 'Q0' or an error)
1 flipped facets
152 coplanar horizon facets for new vertices
24 coplanar points during partitioning
16 nearly singular or axis-parallel hyperplanes
14 zero divisors during back substitute
35 zero divisors during gaussian elimination
1 dupridges with multiple neighbors
A wide merge error has occurred. Qhull has produced a wide facet due to facet merges and vertex merges.