scnc
/
qmcpack
mirror of https://github.com/QMCPACK/qmcpack.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

nexus: lib fixes identified via 2to3

This commit is contained in:
Jaron Krogel 2019-11-21 17:13:17 -05:00
parent 9b1250b9e8
commit e4bc753483
8 changed files with 27 additions and 27 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
nexus/lib/basisset.py
View File

@ -975,7 +975,7 @@ class GaussianBasisSet(DevBase):
else:
plotter = plot
#end if
plotter(range(len(lwidths)),lwidths,lstyle,label=l)
plotter(list(range(len(lwidths))),lwidths,lstyle,label=l)
#end if
#end for
if label:

4
nexus/lib/fileio.py
View File

@ -933,7 +933,7 @@ class XsfFile(StandardFile):
ndim = 3
permute = dim!=0
if permute:
r = range(0,ndim)
r = list(range(0,ndim))
r.pop(dim)
permutation = tuple([dim]+r)
data = data.transpose(permutation)
@ -948,7 +948,7 @@ class XsfFile(StandardFile):
def line_plot(self,dim,filepath):
r,d = self.line_data(dim)
savetxt(filepath,array(zip(r,d)))
savetxt(filepath,array(list(zip(r,d))))
#end def line_plot
#end class XsfFile

2
nexus/lib/nexus.py
View File

@ -224,7 +224,7 @@ class Settings(NexusCore):
self.process_noncore_settings(kw)
# transfer select core data to the global namespace
nexus_core_noncore.transfer_from(nexus_core,nexus_core_noncore.keys())
nexus_core_noncore.transfer_from(nexus_core,list(nexus_core_noncore.keys()))
nexus_noncore.set(**nexus_core_noncore.copy()) # prevent write to core namespace
# copy final core and noncore settings

4
nexus/lib/numerics.py
View File

@ -797,11 +797,11 @@ def simstats(x,dim=None):
reshape = ndim>2
nblocks = shape[dim]
if permute:
r = range(ndim)
r = list(range(ndim))
r.pop(dim)
r.append(dim)
permutation = tuple(r)
r = range(ndim)
r = list(range(ndim))
r.pop(ndim-1)
r.insert(dim,ndim-1)
invperm = tuple(r)

6
nexus/lib/qmcpack.py
View File

@ -120,7 +120,7 @@ class Qmcpack(Simulation):
if self.system is None:
self.should_twist_average = False
elif nexus_core.generate_only:
twistnums = range(len(self.system.structure.kpoints))
twistnums = list(range(len(self.system.structure.kpoints)))
if self.should_twist_average:
self.twist_average(twistnums)
#end if
@ -222,7 +222,7 @@ class Qmcpack(Simulation):
self.error('wavefunction file not found:\n'+h5file)
#end if
twistnums = range(len(structure.kpoints))
twistnums = list(range(len(structure.kpoints)))
if self.should_twist_average:
self.twist_average(twistnums)
elif not has_twist and orb_elem.twistnum is None:
@ -446,7 +446,7 @@ class Qmcpack(Simulation):
output_files = []
else:
if self.should_twist_average and not isinstance(self.input,TracedQmcpackInput):
self.twist_average(range(len(self.system.structure.kpoints)))
self.twist_average(list(range(len(self.system.structure.kpoints))))
br = self.bundle_request
input = self.input.trace(br.quantity,br.values)
input.generate_filenames(self.infile)

2
nexus/lib/qmcpack_quantity_analyzers.py
View File

@ -3104,7 +3104,7 @@ class RectilinearGrid(SpaceGridBase):
self.error('ndu is different than len(gmap)')
#end if
du = 1./self.odu[d]
fine_interval_centers[d] = self.umin + .5*du + du*array(range(ndu))
fine_interval_centers[d] = self.umin + .5*du + du*array(list(range(ndu)))
find_interval_domains[d] = zeros((ndu,))
#end for
#checks are done on each source spacegrid to determine interpolation compatibility

2
nexus/lib/qmcpack_result_analyzers.py
View File

@ -294,7 +294,7 @@ class OptimizationAnalyzer(ResultAnalyzer):
#plot energy and variance
figure()
r = range(nopt)
r = list(range(nopt))
subplot(3,1,1)
errorbar(r,en,enerr,fmt='b')
ylabel('Energy (Ha)')

32
nexus/lib/structure.py
View File

@ -379,7 +379,7 @@ def reduce_tilematrix(tiling):
tilematrix = T.copy()
del t
tbar = identity(dim) #basis for shearing
dr = range(dim)
dr = list(range(dim))
#dr = [1,0,2]
other = dim*[0] # other[d] = dimensions other than d
for d in dr:
@ -1967,7 +1967,7 @@ class Structure(Sobj):
return
elif magnetization=='':
magnetization = identifiers
indices = range(len(self.elem))
indices = list(range(len(self.elem)))
else:
indices = self.locate(identifiers)
#end if
@ -2040,14 +2040,14 @@ class Structure(Sobj):
nrem = len(indices)
nadd = len(pos)
if nadd<nrem:
ar = array(range(0,nadd))
rr = array(range(nadd,nrem))
ar = array(list(range(0,nadd)))
rr = array(list(range(nadd,nrem)))
self.elem[indices[ar]] = elem[:]
self.pos[indices[ar]] = pos[:]
self.remove(indices[rr])
elif nadd>nrem:
ar = array(range(0,nrem))
er = array(range(nrem,nadd))
ar = array(list(range(0,nrem)))
er = array(list(range(nrem,nadd)))
self.elem[indices[ar]] = elem[ar]
self.pos[indices[ar]] = pos[ar]
ii = indices[ar[-1]]
@ -2072,7 +2072,7 @@ class Structure(Sobj):
np = len(pos)
nps= len(self.pos)
d = empty((np,))
ip = array(range(np))
ip = array(list(range(np)))
ips= nn.ravel()
for i in ip:
j = ips[i]
@ -2951,7 +2951,7 @@ class Structure(Sobj):
# get nearest neighbor index pairs in the large cell
neigh_pairs = voronoi_neighbors(ss.pos)
# create a mapping from large to small indices
large_to_small = 3**d*range(len(self.pos))
large_to_small = 3**d*list(range(len(self.pos)))
# find the neighbor pairs in the small cell
neighbors = obj()
small_inds = set(ss.locate(sn.pos))
@ -3262,7 +3262,7 @@ class Structure(Sobj):
#end if
#end for
npos,dim = pos.shape
drange = range(dim)
drange = list(range(dim))
n = len(surface)
i=0
while i<n:
@ -3600,7 +3600,7 @@ class Structure(Sobj):
kindices = []
kpoints = []
shift = empty((ndim,))
kr = range(nkpoints)
kr = list(range(nkpoints))
for k in range(imin[2],imax[2]+1):
for j in range(imin[1],imax[1]+1):
for i in range(imin[0],imax[0]+1):
@ -4164,7 +4164,7 @@ class Structure(Sobj):
#end if
ref = reference.tile((3,3,3))
ref.recenter(reference.center)
rmap = array(3**3*range(len(reference.pos)),dtype=int)
rmap = array(3**3*list(range(len(reference.pos)),dtype=int))
nn = nearest_neighbors(1,ref.pos,self.pos).ravel()
displacement = self.pos - ref.pos[nn]
if not map:
@ -4203,8 +4203,8 @@ class Structure(Sobj):
rbonds = rbv[ir]
ib = empty((neighbors,),dtype=int)
ibr = empty((neighbors,),dtype=int)
r = range(neighbors)
rr = range(neighbors)
r = list(range(neighbors))
rr = list(range(neighbors))
for n in range(neighbors):
mindist = 1e99
ibmin = -1
@ -4322,7 +4322,7 @@ class Structure(Sobj):
ntile = ncells*natoms
pos = empty((ntile,dim))
ind = empty((ntile,),dtype=int)
oind = range(natoms)
oind = list(range(natoms))
for nt in range(ncells):
n=nt*natoms
ind[n:n+natoms]=oind[:]
@ -4695,7 +4695,7 @@ class Structure(Sobj):
self.pos = pos
if selective_dynamics or spos.shape[1]>3:
move = array(spos[:,3:6],dtype=str)
self.freeze(range(self.size()),directions=move=='F')
self.freeze(list(range(self.size())),directions=move=='F')
#end if
#end def read_poscar
@ -5631,7 +5631,7 @@ class DefectStructure(Structure):
nn = nearest_neighbors(1,dlarge,dsmall)
dist = dsmall.distances(dlarge[nn.ravel()])
dmatch = dist<dist_cutoff
ismall = array(range(len(dsmall.pos)))
ismall = array(list(range(len(dsmall.pos))))
ismall = ismall[dmatch]
ilarge = nn[ismall]
if natoms1<natoms2: