def convert_numeric(self):
for name,attr in self._attributes.iteritems():
self[name] = string2val(attr)
#end for
if 'text' in self:
self.value = string2val(self.text)
del self.text
#end if
texts = []
for name,elem in self._elements.iteritems():
if isinstance(elem,XMLelement):
if 'text' in elem and len(elem._attributes)==0 and len(elem._elements)==0:
self[name] = string2val(elem.text)
texts.append(name)
else:
elem.convert_numeric()
#end if
#end if
#end if
for name in texts:
self._elements[name] = self[name]
def test_string2val():
import numpy as np
from testing import value_eq
from superstring import string2val
v = string2val('False')
assert(isinstance(v,bool))
assert(v==False)
v = string2val('True')
assert(isinstance(v,bool))
assert(v==True)
v = string2val('43')
assert(isinstance(v,int))
assert(v==43)
v = string2val('3.14')
assert(isinstance(v,float))
assert(np.abs(v-3.14)<1e-6)
v = string2val('1 2 3 4',delim=' ')
assert(isinstance(v,np.ndarray))
assert(value_eq(v,np.array([1,2,3,4],dtype=int)))
v = string2val('1, 2, 3, 4',delim=',')
assert(isinstance(v,np.ndarray))
assert(value_eq(v,np.array([1,2,3,4],dtype=int)))
v = string2val('1. 2 3 4',delim=' ')
assert(isinstance(v,np.ndarray))
assert(value_eq(v,np.array([1,2,3,4],dtype=float)))
v = string2val('1., 2, 3, 4',delim=',')
assert(isinstance(v,np.ndarray))
assert(value_eq(v,np.array([1,2,3,4],dtype=float)))
def readfile(self, filepath):
text = open(filepath, 'r').read()
if '<UPF' not in text:
upf_format = 'old'
lines = text.split('\n')
xml = '<upf>\n'
for l in lines:
if l.find('/>') != -1:
ln = l.replace('/>', '>').replace('<', '</')
else:
ln = l
#end if
xml += ln + '\n'
#end for
xml += '</upf>\n'
tmppath = filepath + '_tmp'
open(tmppath, 'w').write(xml)
x = readxml(tmppath, contract_names=True, strip_prefix='pp_')
os.system('rm ' + tmppath)
x.convert_numeric()
x.condense()
x.remove_hidden()
pp = x.upf
else:
upf_format = 'new'
#x = readxml(filepath,contract_names=True,strip_prefix='pp_')
#x.convert_numeric()
#x.condense()
#x.remove_hidden()
#pp = x.upf
pp = obj()
pp_contents = open(filepath, 'r').read()
#end if
if upf_format == 'old':
lines = pp.header.split('\n')
h = obj()
i = 0
h.version = string2val(lines[i].split()[0])
i += 1
h.element = string2val(lines[i].split()[0])
i += 1
h.type = string2val(lines[i].split()[0])
i += 1
ncc = string2val(lines[i].split()[0])
i += 1
h.nonlinear_cc = dict(T=True, F=False)[ncc]
h.functional = lines[i].split()[0:4]
i += 1
h.Z = string2val(lines[i].split()[0])
i += 1
h.total_energy = string2val(lines[i].split()[0])
i += 1
h.wfc_cutoff, h.rho_cutoff = array(lines[i].split()[0:2],
dtype=float)
i += 1
h.lmax = string2val(lines[i].split()[0])
i += 1
h.npts = string2val(lines[i].split()[0])
i += 1
h.nwfc = string2val(lines[i].split()[0])
i += 1
pp.header = h
if 'beta' in pp. nonlocal:
beta = pp. nonlocal .beta
if isinstance(beta, str):
beta = [beta]
#end if
b = obj()
for i in range(len(beta)):
sections = beta[i].split('\n', 2)
p = string2val(sections[0].split()[0])
v = string2val(sections[2])
b[p] = v
#end for
pp. nonlocal .beta = b
#end if
dij = pp. nonlocal .dij
d = obj()
lines = dij.split('\n')[1:]
for l in lines:
t = l.split()
d[int(t[0]), int(t[1])] = string2val(t[2])
#end for
pp. nonlocal .dij = d
pswfc = pp.pswfc
tokens = pswfc.split()
nwfc = pp.header.nwfc
npts = pp.header.npts
wf = []
for n in range(nwfc):
i = n * (4 + npts)
label = tokens[i]
l = int(tokens[i + 1])
ws = []
for v in tokens[i + 4:i + 4 + npts]:
ws.append(float(v))
#end for
orb = obj()
orb.label = label
orb.l = l
orb.wfc = array(ws)
wf.append(orb)
#end for
pp.pswfc = wf
#fill in standard fields
self.pp = pp
self.r = pp.mesh.r[1:]
self.local = convert(pp.local, 'Ry', self.energy_units)[1:]
nl = obj()
vnl = zeros(self.local.shape)
if 'beta' in pp. nonlocal:
beta = pp. nonlocal .beta
for t, d in pp. nonlocal .dij.iteritems():
bi = beta[t[0]]
bj = beta[t[1]]
if not isinstance(bi, str) and not isinstance(bj, str):
bb = d * bi * bj
else: # the file is being misread, fix later
bb = 0 * pp.mesh.r
#end if
naftcut = len(pp.mesh.r) - len(bb)
if naftcut > 0:
bb = append(bb, zeros((naftcut, )))
#end if
vnl += bb[1:] / self.r**2
#end for
#end if
vnl = convert(vnl, 'Ry', self.energy_units)
nl[0] = vnl
self. nonlocal = nl
h = pp.header
p = obj()
p[0] = self.local
p[1] = self.local + self. nonlocal [0]
self.potentials = p
self.element = h.element
self.type = h.type
self.Z = h.Z
def readfile(self,filepath):
text = open(filepath,'r').read()
if '<UPF' not in text:
upf_format = 'old'
lines = text.split('\n')
xml = '<upf>\n'
for l in lines:
if l.find('/>')!=-1:
ln = l.replace('/>','>').replace('<','</')
else:
ln = l
#end if
xml+=ln+'\n'
#end for
xml += '</upf>\n'
tmppath = filepath+'_tmp'
open(tmppath,'w').write(xml)
x = readxml(tmppath,contract_names=True,strip_prefix='pp_')
os.system('rm '+tmppath)
x.convert_numeric()
x.condense()
x.remove_hidden()
pp = x.upf
else:
upf_format = 'new'
#x = readxml(filepath,contract_names=True,strip_prefix='pp_')
#x.convert_numeric()
#x.condense()
#x.remove_hidden()
#pp = x.upf
pp = obj()
#end if
if upf_format=='old':
lines = pp.header.split('\n')
h = obj()
i=0
h.version = string2val(lines[i].split()[0]); i+=1
h.element = string2val(lines[i].split()[0]); i+=1
h.type = string2val(lines[i].split()[0]); i+=1
ncc = string2val(lines[i].split()[0]); i+=1
h.nonlinear_cc = dict(T=True,F=False)[ncc]
h.functional = lines[i].split()[0:4]; i+=1
h.Z = string2val(lines[i].split()[0]); i+=1
h.total_energy = string2val(lines[i].split()[0]); i+=1
h.wfc_cutoff,h.rho_cutoff = array(lines[i].split()[0:2],dtype=float); i+=1
h.lmax = string2val(lines[i].split()[0]); i+=1
h.npts = string2val(lines[i].split()[0]); i+=1
h.nwfc = string2val(lines[i].split()[0]); i+=1
pp.header = h
if 'beta' in pp.nonlocal:
beta = pp.nonlocal.beta
if isinstance(beta,str):
beta = [beta]
#end if
b = obj()
for i in range(len(beta)):
sections = beta[i].split('\n',2)
p = string2val(sections[0].split()[0])
v = string2val(sections[2])
b[p]=v
#end for
pp.nonlocal.beta = b
#end if
dij = pp.nonlocal.dij
d = obj()
lines = dij.split('\n')[1:]
for l in lines:
t = l.split()
d[int(t[0]),int(t[1])] = string2val(t[2])
#end for
pp.nonlocal.dij = d
pswfc = pp.pswfc
tokens = pswfc.split()
nwfc= pp.header.nwfc
npts= pp.header.npts
wf = []
for n in range(nwfc):
i = n*(4+npts)
label = tokens[i]
l = int(tokens[i+1])
ws = []
for v in tokens[i+4:i+4+npts]:
ws.append(float(v))
#end for
orb = obj()
orb.label = label
orb.l = l
orb.wfc = array(ws)
wf.append(orb)
#end for
pp.pswfc = wf
#fill in standard fields
self.pp = pp
self.r = pp.mesh.r[1:]
self.local = convert(pp.local,'Ry',self.energy_units)[1:]
nl = obj()
vnl = zeros(self.local.shape)
if 'beta' in pp.nonlocal:
beta = pp.nonlocal.beta
for t,d in pp.nonlocal.dij.iteritems():
bi = beta[t[0]]
bj = beta[t[1]]
if not isinstance(bi,str) and not isinstance(bj,str):
bb = d*bi*bj
else: # the file is being misread, fix later
bb = 0*pp.mesh.r
#end if
naftcut = len(pp.mesh.r)-len(bb)
if naftcut>0:
bb=append(bb,zeros((naftcut,)))
#end if
vnl += bb[1:]/self.r**2
#end for
#end if
vnl = convert(vnl,'Ry',self.energy_units)
nl[0] = vnl
self.nonlocal = nl
h = pp.header
p = obj()
p[0] = self.local
p[1] = self.local+self.nonlocal[0]
self.potentials = p
self.element = h.element
self.type = h.type
self.Z = h.Z