def readfile(self,filepath):
x = readxml(filepath,contract_names=True)
x.convert_numeric()
x.condense()
x.remove_hidden()
pp = x.pseudo
self.pp = pp
h = pp.header
self.element = h.symbol
self.type = h.flavor
self.Z = h.zval
vps = self.pp.semilocal.vps
if not isinstance(vps,list):
vps = [vps]
#end if
g = vps[0].radfunc.grid
if g.type=='linear':
r = linspace(g.ri,g.rf,g.npts)
self.r = r[1:]
else:
self.error('functionality for '+g.type+' grids has not yet been implemented')
#end if
p = obj()
r = self.r
ldict = dict(s=0,p=1,d=2,f=3)
for vp in vps:
l = vp.l
v = 1./r*vp.radfunc.data[1:]
p[ldict[l]]= convert(v,'Ha',self.energy_units)
#end for
self.potentials = p
def readfile(self, filepath):
x = readxml(filepath, contract_names=True)
x.convert_numeric()
x.condense()
x.remove_hidden()
pp = x.pseudo
self.pp = pp
h = pp.header
self.element = h.symbol
self.type = h.flavor
self.Z = h.zval
vps = self.pp.semilocal.vps
if not isinstance(vps, list):
vps = [vps]
#end if
g = vps[0].radfunc.grid
if g.type == 'linear':
r = linspace(g.ri, g.rf, g.npts)
self.r = r[1:]
else:
self.error('functionality for ' + g.type +
' grids has not yet been implemented')
#end if
p = obj()
r = self.r
ldict = dict(s=0, p=1, d=2, f=3)
for vp in vps:
l = vp.l
v = 1. / r * vp.radfunc.data[1:]
p[ldict[l]] = convert(v, 'Ha', self.energy_units)
#end for
self.potentials = p
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
def test_read():
from generic import obj
from xmlreader import readxml, XMLelement
ref = obj(
simulation = obj(
project = obj(
id = 'vmc',
series = '0',
application = obj(
class_ = 'serial',
name = 'qmcpack',
role = 'molecu',
version = '1.0',
)
),
qmc = obj(
method = 'vmc',
move = 'pbyp',
parameter1 = obj(
name = 'walkers',
text = '1',
),
parameter2 = obj(
name = 'warmupSteps',
text = '20',
),
parameter3 = obj(
name = 'blocks',
text = '200',
),
parameter4 = obj(
name = 'steps',
text = '10',
),
parameter5 = obj(
name = 'subSteps',
text = '2',
),
parameter6 = obj(
name = 'timestep',
text = '0.4',
),
),
qmcsystem = obj(
hamiltonian = obj(
name = 'h0',
target = 'e',
type = 'generic',
estimator = obj(
name = 'KEcorr',
psi = 'psi0',
source = 'e',
type = 'chiesa',
),
pairpot1 = obj(
name = 'ElecElec',
source = 'e',
target = 'e',
type = 'coulomb',
),
pairpot2 = obj(
name = 'IonIon',
source = 'ion0',
target = 'ion0',
type = 'coulomb',
),
pairpot3 = obj(
format = 'xml',
name = 'PseudoPot',
source = 'ion0',
type = 'pseudo',
wavefunction = 'psi0',
pseudo = obj(
elementType = 'C',
href = 'C.BFD.xml',
),
),
pairpot4 = obj(
ecut = '60.0',
name = 'MPC',
physical = 'no',
source = 'e',
target = 'e',
type = 'MPC',
),
),
particleset1 = obj(
name = 'e',
random = 'yes',
group1 = obj(
mass = '1.0',
name = 'u',
size = '32',
parameter1 = obj(
name = 'charge',
text = '-1',
),
parameter2 = obj(
name = 'mass',
text = '1.0',
),
),
group2 = obj(
mass = '1.0',
name = 'd',
size = '32',
parameter1 = obj(
name = 'charge',
text = '-1',
),
parameter2 = obj(
name = 'mass',
text = '1.0',
),
),
),
particleset2 = obj(
name = 'ion0',
group = obj(
mass = '21894.7135906',
name = 'C',
size = '16',
attrib = obj(
condition = '0',
datatype = 'posArray',
name = 'position',
text = \
'''6.74632230 6.74632230 0.00000000
1.68658057 1.68658057 1.68658058
3.37316115 3.37316115 0.00000000
5.05974173 5.05974172 1.68658058
0.00000000 3.37316115 3.37316115
1.68658058 5.05974172 5.05974173
3.37316115 6.74632230 3.37316115
5.05974173 8.43290287 5.05974173
3.37316115 0.00000000 3.37316115
5.05974172 1.68658057 5.05974173
6.74632230 3.37316115 3.37316115
8.43290287 5.05974172 5.05974173
10.11948345 10.11948345 6.74632230
5.05974173 5.05974172 8.43290287
6.74632230 6.74632230 6.74632230
8.43290287 8.43290287 8.43290287''',
),
parameter1 = obj(
name = 'charge',
text = '4',
),
parameter2 = obj(
name = 'valence',
text = '4',
),
parameter3 = obj(
name = 'atomicnumber',
text = '6',
),
parameter4 = obj(
name = 'mass',
text = '21894.7135906',
),
),
),
simulationcell = obj(
parameter1 = obj(
name = 'lattice',
text = \
'''6.74632230 6.74632230 0.00000000
0.00000000 6.74632230 6.74632230
6.74632230 0.00000000 6.74632230''',
units = 'bohr',
),
parameter2 = obj(
name = 'bconds',
text = 'p p p',
),
parameter3 = obj(
name = 'LR_dim_cutoff',
text = '15',
),
),
wavefunction = obj(
name = 'psi0',
target = 'e',
determinantset = obj(
slaterdeterminant = obj(
determinant1 = obj(
group = 'u',
id = 'updet',
size = '32',
sposet = 'spo_ud',
),
determinant2 = obj(
group = 'd',
id = 'downdet',
size = '32',
sposet = 'spo_ud',
),
),
),
sposet_builder = obj(
href = 'MISSING.h5',
meshfactor = '1.0',
precision = 'float',
source = 'ion0',
tilematrix = '2 0 0 0 2 0 0 0 2',
truncate = 'no',
twistnum = '0',
type = 'bspline',
version = '0.10',
sposet = obj(
name = 'spo_ud',
size = '32',
spindataset = '0',
type = 'bspline',
),
),
),
),
),
)
files = get_files()
x = readxml(files['vmc.in.xml'])
assert (isinstance(x, XMLelement))
x.remove_hidden()
o = x.to_obj()
assert (object_eq(o, ref))