Skip to content

gather.py now includes weighted reblocking in the avg function #12

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
kkleiner1 wants to merge 1 commit into
base: main
Choose a base branch
from
Open

gather.py now includes weighted reblocking in the avg function #12

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
37 changes: 17 additions & 20 deletions gather.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,10 +45,12 @@ def extract_from_fname(fname):
"nconfig":nconfig
}


def avg(data):
mean=np.mean(data,axis=0)
error=np.std(data,axis=0)/np.sqrt(len(data)-1)
def avg(data, reblock=16, weights=None):
if (weights is None):
weights = np.ones(data.shape)
vals = pyqmc.reblock.reblock(data, reblock, weights=weights)
mean=np.mean(vals,axis=0)
error=scipy.stats.sem(vals,axis=0)
return mean,error

def calculate_entropy(dm):
Expand All @@ -65,33 +67,28 @@ def normalize_rdm(rdm1_value,rdm1_norm,warmup):
rdm1=pyqmc.obdm.normalize_obdm(rdm1,rdm1_norm)
rdm1_err=pyqmc.obdm.normalize_obdm(rdm1_err,rdm1_norm)
return rdm1,rdm1_err
def read_vmc(fname):

def read_mc_output(fname, warmup=5, reblock=16):
with h5py.File(fname,'r') as f:
#print(list(f.keys()))
warmup=2
energy=f['energytotal'][warmup:,...]
e_tot,error=avg(energy)

if 'weight' in f.keys():
wt = f['weight'][warmup:]
else:
wt = None
e_tot,error = avg(f['energytotal'][warmup:,...], reblock, weights=wt)
rdm1_up,rdm1_up_err=normalize_rdm(f['rdm1_upvalue'],f['rdm1_upnorm'],warmup)
rdm1_down,rdm1_down_err=normalize_rdm(f['rdm1_downvalue'],f['rdm1_downnorm'],warmup)
rdm1=np.array([rdm1_up,rdm1_down])
entropy=calculate_entropy(rdm1)
return e_tot,error,entropy

def read_dmc(fname):
return read_vmc(fname)
return e_tot,error,entropy

def read(fname):
with h5py.File(fname,'r') as f:
e_tot,error,entropy=0.0,0.0,0.0
method=extract_from_fname(fname)["method"]
if 'cc' in method:
e_tot=f['ccsd']['energy'][()]
elif 'vmc' in method:
e_tot,error,entropy=read_vmc(fname)
elif 'dmc' in method:
e_tot,error,entropy=read_dmc(fname)
elif ('vmc' in method) or ('dmc' in method):
e_tot,error,entropy=read_mc_output(fname)
elif 'hf' in method:
e_tot = f['scf']['e_tot'][()]
elif 'fci' in method:
Expand Down Expand Up @@ -134,4 +131,4 @@ def create(fname):

#df2=pd.DataFrame([create(name) for name in fhci])
#df2.to_csv("hci.csv", index=False)