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Nexus: extend structure plotting capabilities #3220

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merged 3 commits into from
Jun 4, 2021
Merged

Nexus: extend structure plotting capabilities #3220

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4974f24
nexus: update structure plotting capabilities
jtkrogel Jun 3, 2021
14b90a1
Merge branch 'develop' of https://github.com/QMCPACK/qmcpack into nx_…
jtkrogel Jun 3, 2021
6513a9e
Merge branch 'develop' into nx_structure_plots
ye-luo Jun 3, 2021
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20 changes: 17 additions & 3 deletions nexus/lib/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3072,7 +3072,7 @@ def voronoi_species_radii(self):


# test needed
# get nearest neighbors according to constrants (voronoi, max distance, coord. number)
# get nearest neighbors according to constraints (voronoi, max distance, coord. number)
def nearest_neighbors(self,indices=None,rmax=None,nmax=None,restrict=False,voronoi=False,distances=False,**spec_max):
if indices is None:
indices = arange(len(self.pos))
Expand Down Expand Up @@ -5032,7 +5032,7 @@ def write_fhi_aims(self,filepath=None):
#end def write_fhi_aims


def plot2d_ax(self,ix,iy,*args,**kwargs):
def plot2d_ax(self,ix=0,iy=1,*args,**kwargs):
if self.dim!=3:
self.error('plot2d_ax is currently only implemented for 3 dimensions')
#end if
Expand All @@ -5049,7 +5049,7 @@ def plot2d_ax(self,ix,iy,*args,**kwargs):
#end def plot2d_ax


def plot2d_pos(self,ix,iy,*args,**kwargs):
def plot2d_pos(self,ix=0,iy=1,*args,**kwargs):
if self.dim!=3:
self.error('plot2d_pos is currently only implemented for 3 dimensions')
#end if
Expand All @@ -5063,6 +5063,20 @@ def plot2d_pos(self,ix,iy,*args,**kwargs):
#end def plot2d_pos


def plot2d_points(self,points,ix=0,iy=1,*args,**kwargs):
if self.dim!=3:
self.error('plot2d_points is currently only implemented for 3 dimensions')
#end if
iz = list(set([0,1,2])-set([ix,iy]))[0]
pp = np.array(points,dtype=float)
a = self.axes[iz]
for i in range(len(pp)):
pp[i] -= dot(a,pp[i])/dot(a,a)*a
#end for
plot(pp[:,ix],pp[:,iy],*args,**kwargs)
#end def plot2d_points


def plot2d(self,pos_style='b.',ax_style='k-'):
if self.dim!=3:
self.error('plot2d is currently only implemented for 3 dimensions')
Expand Down