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Nexus: fixing sizing problem in some single atom workflows #3553

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merged 3 commits into from
Oct 22, 2021
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Nexus: fixing sizing problem in some single atom workflows #3553

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a3829a9
nexus: fixing sizing problem in some single atom workflows
jtkrogel Oct 22, 2021
bdb41b5
nexus: add comment
jtkrogel Oct 22, 2021
025a98b
Merge branch 'develop' into nx_ws21_fix1
ye-luo Oct 22, 2021
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8 changes: 8 additions & 0 deletions nexus/lib/qmcpack_input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,7 @@
import os
import inspect
import keyword
import numpy as np
from numpy import fromstring,empty,array,float64,\
loadtxt,ndarray,dtype,sqrt,pi,arange,exp,eye,\
ceil,mod,dot,abs,identity,floor,linalg,where,isclose
Expand Down Expand Up @@ -3987,6 +3988,13 @@ def return_system(self,structure_only=False):
center = axes.sum(0)/2
#end if

# pos must be a 2D array, shape (N,3)
# reshape single atom case, shape (3,) as shape (1,3)
pos = np.asarray(pos)
if len(pos.flatten())==3:
pos.shape = (1,3)
#end if
Comment on lines +3993 to +3996
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Could you add a comment describing the special case being handled here.

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Done


structure = Structure(axes=axes,elem=elem,pos=pos,center=center,units='B')

for name,element in ions.groups.items():
Expand Down