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fixed twist averaged energy density 

git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6266 e5b18d87-469d-4833-9cc0-8cdfa06e9491
This commit is contained in:
Jaron Krogel 2014-03-13 20:46:03 +00:00
parent 69a8b77541
commit 43935b5fc5
8 changed files with 105 additions and 40 deletions
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36
project_suite/library/hdfreader.py
View File

@ -12,6 +12,8 @@ try:
except ImportError:
h5py = unavailable('h5py')
#end try
from debug import *
class HDFgroup(DevBase):
@ -84,15 +86,17 @@ class HDFgroup(DevBase):
#end def __init__
def _remove_hidden(self):
def _remove_hidden(self,deep=True):
if '_parent' in self:
del self._parent
#end if
for name,value in self.iteritems():
if isinstance(value,HDFgroup):
value._remove_hidden()
#end if
#end for
if deep:
for name,value in self.iteritems():
if isinstance(value,HDFgroup):
value._remove_hidden()
#end if
#end for
#end if
for name in list(self.keys()):
if name[0]=='_':
del self[name]
@ -109,9 +113,13 @@ class HDFgroup(DevBase):
self[name][:] = 0
#end if
#end for
for value in self._groups:
for name,value in self._groups.iteritems():
if isinstance(value,str):
ci(ls(),gs())
#end if
value.zero(*names)
#end for
#self.sum(*names)
#end def zero
@ -142,6 +150,7 @@ class HDFgroup(DevBase):
self.error(name+' not found in minsize partner')
#end if
#end for
#self.sum(*names)
#end def minsize
@ -180,6 +189,7 @@ class HDFgroup(DevBase):
self.error(name+' not found in accumulate partner')
#end if
#end for
#self.sum(*names)
#end def accumulate
@ -189,11 +199,21 @@ class HDFgroup(DevBase):
self[name] /= normalization
#end if
#end for
for value in self._groups:
for name,value in self._groups.iteritems():
value.normalize(normalization,*names)
#end for
#self.sum(*names)
#end def normalize
def sum(self,*names):
for name in names:
if name in self and isinstance(self[name],ndarray) and name=='value':
s = self[name].mean(0).sum()
print ' sum = {0}'.format(s)
#end if
#end for
#end def sum
#end class HDFgroup

2
project_suite/library/plotting.py
View File

@ -9,3 +9,5 @@ except (ImportError,RuntimeError):
figure,plot,xlabel,ylabel,title,show,ylim,legend,xlim,rcParams,savefig,bar,xticks,subplot,grid,setp,errorbar,loglog,semilogx,semilogy,text = unavailable('matplotlib.pyplot','figure','plot','xlabel','ylabel','title','show','ylim','legend','xlim','rcParams','savefig','bar','xticks','subplot','grid','setp','errorbar','loglog','semilogx','semilogy','text')
#end try
# savefig(savefile,format='png',bbox_inches ='tight',pad_inches=.3)

5
project_suite/library/pwscf.py
View File

@ -23,14 +23,15 @@ class Pwscf(Simulation):
def __init__(self,**sim_args):
has_group_atoms = 'group_atoms' in sim_args
group_atoms = True
group_atoms = False
if has_group_atoms:
group_atoms = sim_args['group_atoms']
del sim_args['group_atoms']
#end if
Simulation.__init__(self,**sim_args)
if group_atoms and isinstance(self.system,PhysicalSystem):
self.system.structure.group_atoms()
self.warn('requested grouping by atomic species, but pwscf does not group atoms anymore!')
#self.system.structure.group_atoms()
#end if
#end def post_init

16
project_suite/library/pwscf_input.py
View File

@ -957,8 +957,8 @@ class PwscfInput(SimulationInput):
self.k_points.nkpoints = nkpoints
self.k_points.kpoints = kpoints
self.k_points.weights = s.kweights.copy()
self.k_points.change_specifier('crystal',self) #added to make debugging easier
#end if
self.k_points.change_specifier('crystal',self) #added to make debugging easier
atoms = p.get_ions()
masses = obj()
@ -1126,7 +1126,7 @@ def generate_scf_input(prefix = 'pwscf',
pseudos = None,
system = None,
use_folded = True,
group_atoms = True):
group_atoms = False):
if pseudos is None:
pseudos = []
#end if
@ -1255,8 +1255,11 @@ def generate_scf_input(prefix = 'pwscf',
if system is not None:
structure = system.structure
if group_atoms:
structure.group_atoms()
self.warn('requested grouping by atomic species, but pwscf does not group atoms anymore!')
#end if
#if group_atoms: # disabled, hopefully not needed for qmcpack
# structure.group_atoms()
##end if
if structure.at_Gpoint():
pw.k_points.clear()
pw.k_points.set(
@ -1331,7 +1334,7 @@ def generate_relax_input(prefix = 'pwscf',
pseudos = None,
system = None,
use_folded = False,
group_atoms = True):
group_atoms = False):
if pseudos is None:
pseudos = []
#end if
@ -1419,8 +1422,11 @@ def generate_relax_input(prefix = 'pwscf',
if system is not None:
structure = system.structure
if group_atoms:
structure.group_atoms()
self.warn('requested grouping by atomic species, but pwscf does not group atoms anymore!')
#end if
#if group_atoms: #don't group atoms for pwscf, any downstream consequences?
# structure.group_atoms()
##end if
if structure.at_Gpoint():
pw.k_points.clear()
pw.k_points.set(

16
project_suite/library/qmcpack_analyzer_base.py
View File

@ -3,6 +3,7 @@ from numpy import minimum,resize
from generic import obj
from hdfreader import HDFgroup
from qaobject import QAobject
from debug import *
class QAinformation(obj):
@ -16,6 +17,7 @@ class QAdata(QAobject):
for value in self:
value[:] = 0
#end for
#self.sum()
#end def zero
def minsize(self,other):
@ -26,6 +28,7 @@ class QAdata(QAobject):
self.error(name+' not found in minsize partner')
#end if
#end for
#self.sum()
#end def minsize
def accumulate(self,other):
@ -36,20 +39,31 @@ class QAdata(QAobject):
self.error(name+' not found in accumulate partner')
#end if
#end for
#self.sum()
#end def accumulate
def normalize(self,normalization):
for value in self:
value/=normalization
#end for
#self.sum()
#end def normalize
def sum(self):
s = 0
for value in self:
s+=value.sum()
#end for
print ' sum = {0}'.format(s)
#end def sum
#end class QAdata
class QAHDFdata(QAdata):
def zero(self):
for value in self:
for name,value in self.iteritems():
if isinstance(value,HDFgroup):
value.zero('value','value_squared')
#end if

21
project_suite/library/qmcpack_input.py
View File

@ -2573,6 +2573,7 @@ class QmcpackInput(SimulationInput,Names):
def incorporate_system(self,system):
self.warn('incorporate_system may or may not work\n please check the qmcpack input produced\n if it is wrong, please contact the developer')
system = system.copy()
system.check_folded_system()
system.change_units('B')
system.structure.group_atoms()
@ -2664,7 +2665,7 @@ class QmcpackInput(SimulationInput,Names):
)
particlesets.append(eps)
if len(ions)>0:
eps.randomsrc = 'ion0'
#eps.randomsrc = 'ion0' # don't do randomsrc by default
ips = particleset(
name='ion0',
)
@ -2717,7 +2718,12 @@ class QmcpackInput(SimulationInput,Names):
if abs(net_spin) > 1e-1:
if ddet!=None:
ddet.occupation.spindataset = 1 #jtk mark check
if 'occupation' in ddet:
ddet.occupation.spindataset = 1
else:
ss = self.get('sposets')
ss[ddet.sposet].spindataset = 1
#end if
#end if
#end if
#end def incorporate_system
@ -3175,7 +3181,8 @@ def generate_particlesets(electrons = 'e',
ions = 'ion0',
up = 'u',
down = 'd',
system = None
system = None,
randomsrc = False
):
if system is None:
QmcpackInput.class_error('generate_particlesets argument system must not be None')
@ -3219,7 +3226,9 @@ def generate_particlesets(electrons = 'e',
)
particlesets.append(eps)
if len(ions)>0:
eps.randomsrc = iname
if randomsrc:
eps.randomsrc = iname
#end if
ips = particleset(name=iname)
groups = []
for ion in ions:
@ -4203,6 +4212,7 @@ def generate_basic_input(id = 'qmc',
buffer = None,
lr_dim_cutoff = 15,
remove_cell = False,
randomsrc = False,
meshfactor = 1.0,
precision = 'float',
twistnum = None,
@ -4258,7 +4268,8 @@ def generate_basic_input(id = 'qmc',
if system!=None:
particlesets = generate_particlesets(
system = system
system = system,
randomsrc = randomsrc or tuple(bconds)!=('p','p','p')
)
#end if

33
project_suite/library/qmcpack_quantity_analyzers.py
View File

@ -346,9 +346,11 @@ class EnergyDensityAnalyzer(HDFAnalyzer):
self.error('attempted load without data')
#end if
name = self.info.name
self.data = QAdata()
self.data = QAHDFdata()
if name in data:
self.data = data[name]
hdfg = data[name]
hdfg._remove_hidden(deep=False)
self.data.transfer_from(hdfg)
del data[name]
else:
self.info.should_remove = True
@ -364,7 +366,7 @@ class EnergyDensityAnalyzer(HDFAnalyzer):
data = self.data
#why is this called 3 times?
print nbe
#print nbe
#transfer hdf data
sg_pattern = re.compile(r'spacegrid\d*')
@ -449,7 +451,7 @@ class EnergyDensityAnalyzer(HDFAnalyzer):
input = self.run_info.input
xml = self.run_info.ordered_input
ps = input.get('particlesets')
if 'ion0' in ps and len(ps.ion0.groups)>1:
if 'ion0' in ps and len(ps.ion0.groups)>1 and 'size' in ps.ion0:
qsx = xml.simulation.qmcsystem
if len(ps)==1:
psx = qsx.particleset
@ -488,11 +490,6 @@ class EnergyDensityAnalyzer(HDFAnalyzer):
#reorder the atomic data
for sg in self.spacegrids:
#print 'qqa'
#import code
#code.interact(local=locals())
sg.reorder_atomic_data(imap)
#end for
#end if
@ -1095,6 +1092,9 @@ class TracesAnalyzer(QAanalyzer):
class DensityMatricesAnalyzer(HDFAnalyzer):
allowed_settings = ['save_data','jackknife','diagonal','occ_tol','coup_tol','stat_tol']
def __init__(self,name,nindent=0):
HDFAnalyzer.__init__(self)
self.info.name = name
@ -1134,19 +1134,18 @@ class DensityMatricesAnalyzer(HDFAnalyzer):
def analyze_local(self):
save_data = False
jackknife = False
diagonal = True
# 1) exclude states that do not contribute to the number trace
# 2) exclude elements that are not statistically significant (1 sigma?)
# 3) use remaining states to form filtered number and energy matrices
# 4) perform jackknife sampling to get eigenvalue error bars
# 5) consider using cross-correlations w/ excluded elements to reduce variance
occ_tol = 1e-3
coup_tol = 1e-4
stat_tol = 2.0
save_data = False
jackknife = False
diagonal = True
occ_tol = 1e-3
coup_tol = 1e-4
stat_tol = 2.0
nbe = QAanalyzer.method_info.nblocks_exclude
self.info.nblocks_exclude = nbe

16
project_suite/library/structure.py
View File

@ -310,8 +310,10 @@ class Structure(Sobj):
def group_atoms(self,folded=True):
if len(self.elem)>0:
order = self.elem.argsort()
self.elem = self.elem[order]
self.pos = self.pos[order]
if (self.elem!=self.elem[order]).any():
self.elem = self.elem[order]
self.pos = self.pos[order]
#end if
#end if
if self.folded_structure!=None and folded:
self.folded_structure.group_atoms(folded)
@ -2375,6 +2377,16 @@ class Crystal(Structure):
basis = [[0,0,0],[.5,0,0]],
basis_vectors = 'conventional'
),
('rocksalt','prim'):obj(
lattice = 'cubic',
cell = 'primitive',
centering = 'F',
constants = 5.64,
units = 'A',
atoms = ('Na','Cl'),
basis = [[0,0,0],[.5,0,0]],
basis_vectors = 'conventional'
),
('copper','prim'):obj(
lattice = 'cubic',
cell = 'primitive',