Parsing IP outputs

tutorial/databases_qepy/iron-metal/flow-iron.py

@@ -7,7 +7,7 @@
 from yambopy.io.factories import PwNscfTasks, PwBandsTasks, PwRelaxTasks
 from yambopy.flow import YambopyFlow, PwTask, E2yTask, YamboTask
 from schedulerpy import Scheduler
-from yambopy import yambopyenv
+from yambopy.env import yambopyenv
 
 #sch = Scheduler.factory(scheduler="slurm",ntasks=8,walltime="10:00:00")
 sch = Scheduler.factory(scheduler="bash")

yamboparser/yambofile.py

@@ -111,7 +111,11 @@ def parse_output(self,**parse_kwargs):
         zip_tags = parse_kwargs.get('zip_tags',False) #flag--default behavior is to do nothing
         #get the tags of the columns
         if self.type in YamboFile._outputs_type.keys():  #== "output_absorption":
-            tags = [tag.strip() for tag in re.findall('([ `0-9a-zA-Z\-\/]+)\[[0-9]\]',''.join(self.lines))]
+            pattern = '([ `0-9a-zA-Z\-\/]+)\[[0-9]\]'
+            tags = [tag.strip() for tag in re.findall(pattern,''.join(self.lines))]
+            if len(tags) < 2 and self.type in ["output_loss", "output_abs", "output_alpha"]: # temporary fix for IP case: E[1] [eV]          Im(eps)            Re(eps)
+                lines_with_matches = [line for line in self.lines if re.search(pattern, line)] 
+                tags = [tag.strip() for tag in lines_with_matches[0].replace("#","").replace("\n","").replace("[eV]","").split()]
         if self.type == "output_gw":
             tags = [line.replace('(meV)','').replace('Sc(Eo)','Sc|Eo') for line in self.lines if all(tag in line for tag in ['K-point','Band','Eo'])][0]
             tags = tags[2:].strip().split()

yambopy/__init__.py

@@ -37,17 +37,6 @@
 """
 import numpy as np
 
-class yambopyenv():
-    YAMBO = "yambo"
-    P2Y = "p2y"
-    E2Y = "e2y"
-    YPP = "ypp"
-    SCHEDULER = "bash"
-    YAMBO_RT = "yambo_rt"
-    YPP_RT = "ypp_rt"
-    YAMBO_NL = "yambo_nl"
-    YPP_NL = "ypp_nl"
-
 #tools and units
 from yambopy.tools.jsonencoder import *
 from yambopy.units import *

yambopy/dbs/bsekerneldb.py

@@ -4,6 +4,7 @@
 #
 import os
 from yambopy import *
+from yambopy.dbs.savedb import YamboSaveDB
 from yambopy.units import *
 from itertools import product
 

yambopy/env/__init__.py

@@ -0,0 +1,10 @@
+class yambopyenv():
+    YAMBO = "yambo"
+    P2Y = "p2y"
+    E2Y = "e2y"
+    YPP = "ypp"
+    SCHEDULER = "bash"
+    YAMBO_RT = "yambo_rt"
+    YPP_RT = "ypp_rt"
+    YAMBO_NL = "yambo_nl"
+    YPP_NL = "ypp_nl"

yambopy/flow/task.py

@@ -34,7 +34,7 @@
 from qepy.ph import PhIn
 from qepy.dynmat import DynmatIn
 from qepy import qepyenv
-from yambopy import yambopyenv
+from yambopy.env import yambopyenv
 from yambopy.tools.string import marquee
 from yambopy.tools.duck import isiter, isstring
 from yambopy.io.inputfile import YamboIn

yambopy/io/inputfile.py

@@ -7,9 +7,10 @@
 import json
 import re
 from subprocess import Popen, PIPE
-from yambopy import yambopyenv
+from yambopy.env import yambopyenv
 from yambopy.tools.duck import isstring
 
+
 def issave(path):
     """ Check if yambo SAVE folder is present either as directory or as symlink """
     if os.path.isdir(path) or os.path.islink(path): return True

yambopy/io/iofile.py

@@ -1,7 +1,7 @@
 import os
 import re
 from subprocess import Popen, PIPE
-from yambopy import yambopyenv
+from yambopy.env import yambopyenv
 from yambopy.tools.duck import isstring
 
 class YamboIO(object):