From e87f5c586a9d7552333bb9dbcb0d3b2616b4c653 Mon Sep 17 00:00:00 2001
From: kkleiner1 <kevingk2@illinois.edu>
Date: Tue, 11 May 2021 21:32:20 -0500
Subject: [PATCH] avg function can now perform reblocking

---
 gather.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/gather.py b/gather.py
index 7e9e507..30c408f 100644
--- a/gather.py
+++ b/gather.py
@@ -46,9 +46,14 @@ def extract_from_fname(fname):
             }
 
 
-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, correlated=True):
+    if (correlated == False):
+        mean=np.mean(data,axis=0)
+        error=np.std(data,axis=0)/np.sqrt(len(data)-1)
+    else:
+        vals = pyqmc.reblock.reblock(data, reblock)
+        mean=np.mean(data,axis=0)
+        error=scipy.stats.sem(vals,axis=0)
     return mean,error
 
 def calculate_entropy(dm):
@@ -71,7 +76,7 @@ def read_vmc(fname):
         #print(list(f.keys()))
         warmup=2
         energy=f['energytotal'][warmup:,...]
-        e_tot,error=avg(energy)
+        e_tot,error=avg(energy, correlated=True)
     
         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)
@@ -134,4 +139,4 @@ def create(fname):
 
     #df2=pd.DataFrame([create(name) for name in fhci])
     #df2.to_csv("hci.csv", index=False)
-    
\ No newline at end of file
+