XYZ issue

[NathandB94]

Hi Both,

I have a set of xyz's that are a bit weird, some of the crystals are just long chains of two molecules. I have uploaded the simulation files to dropbox in the link below. Under that is the printed error statement. The link might not contain all the files yet, give it until the end of the day before the download. There are a total of 3125 simulations.

https://www.dropbox.com/scl/fo/ntzqdjpw2elc7qoktgjxj/h?rlkey=ltnhsovvhoulvtwevxjvo0y6p&dl=0

CA:A-Ratios-INFO: Options:: AR: True CDA: False Checked: None Selected: [] Auto Plot: False CA:GUI-INFO: Started Calculations... Traceback (most recent call last): File "/Users/Nathan/Documents/GitHub/crystalaspects/src/crystalaspects/analysis/gui_threads.py", line 98, in run xyz_df = ar.collect_all( ^^^^^^^^^^^^^^^ File "/Users/Nathan/Documents/GitHub/crystalaspects/src/crystalaspects/analysis/ar_dataframes.py", line 218, in collect_all crystal_info = shape.get_zingg_analysis() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/Nathan/Documents/GitHub/crystalaspects/src/crystalaspects/analysis/shape_analysis.py", line 175, in get_zingg_analysis sa_vol_vals = self.get_sa_vol_ratio() ^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/Nathan/Documents/GitHub/crystalaspects/src/crystalaspects/analysis/shape_analysis.py", line 117, in get_sa_vol_ratio hull = ConvexHull(self.xyz) ^^^^^^^^^^^^^^^^^^^^ File "_qhull.pyx", line 2431, in scipy.spatial._qhull.ConvexHull.init File "_qhull.pyx", line 353, in scipy.spatial._qhull._Qhull.init scipy.spatial._qhull.QhullError: QH6154 Qhull precision error: Initial simplex is flat (facet 1 is coplanar with the interior point)

While executing: | qhull i Qt Options selected for Qhull 2019.1.r 2019/06/21: run-id 203115330 incidence Qtriangulate _pre-merge _zero-centrum _max-width 1.5e+02 Error-roundoff 6.6e-14 _one-merge 4.6e-13 _near-inside 2.3e-12 Visible-distance 1.3e-13 U-max-coplanar 1.3e-13 Width-outside 2.6e-13 _wide-facet 7.9e-13 _maxoutside 5.3e-13

The input to qhull appears to be less than 3 dimensional, or a computation has overflowed.

Qhull could not construct a clearly convex simplex from points:

• p1381(v4): -0.28 -72 0
• p2763(v3): -0.25 73 0
• p0(v2): -0.22 0.1 0
• p1(v1): -0.28 0.21 0

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 6.6e-14. The center point, facets and distances to the center point are as follows:

center point -0.258 0.4343 0

facet p2763 p0 p1 distance= 0 facet p1381 p0 p1 distance= 0 facet p1381 p2763 p1 distance= 0 facet p1381 p2763 p0 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: -0.282 -2.225e-308 difference= 0.282 1: -72.02 73.44 difference= 145.5 2: 0 0 difference= 0

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 6.6e-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.

[NathandB94]

Alvin and I have sorted this issue. This requires removing the convex hull due to there being sometimes up to three crystals in a single simulation.