Index: wflow-py/_version.py
===================================================================
diff -u -r0b41e43f37d232133cd4d014e63c39941525df35 -re59169d4b535e077a267eba3d2ba75f73803fbc8
--- wflow-py/_version.py	(.../_version.py)	(revision 0b41e43f37d232133cd4d014e63c39941525df35)
+++ wflow-py/_version.py	(.../_version.py)	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -2,4 +2,4 @@
 VERSION='1.0.master.1'
 MVERSION='1.0.master'
 NVERSION='1.0.1'
-BUILD='2017-09-05 08:53:12.915000'
+BUILD='2017-09-05 09:18:23.637000'
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/ET.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Index: wflow-py/wflow/__init__.py
===================================================================
diff -u -r0b41e43f37d232133cd4d014e63c39941525df35 -re59169d4b535e077a267eba3d2ba75f73803fbc8
--- wflow-py/wflow/__init__.py	(.../__init__.py)	(revision 0b41e43f37d232133cd4d014e63c39941525df35)
+++ wflow-py/wflow/__init__.py	(.../__init__.py)	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -2,7 +2,7 @@
 __version__='1.0.master'
 __release__='1.0.master.1'
 __versionnr__='1.0.1'
-__build__='2017-09-05 08:53:12.915000'
+__build__='2017-09-05 09:18:23.637000'
 
 import os, sys
 import osgeo.gdal as gdal
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/glacier.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/groundwater.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/hargreaves.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/reporting.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/rootzone.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/routing.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/snow.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Index: wflow-py/wflow/sphy/ET.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/ET.py	(revision 0)
+++ wflow-py/wflow/sphy/ET.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,15 @@
+#-Function to calculate the potential evapotranspiration
+def ETpot(etr, kc):
+    etpot = etr * kc
+    return etpot
+
+#-Function to calculate the actual evapotranspiration
+def ETact(pcr, etpot, rootwater, rootsat, etreddry, rainfrac):
+    etredwet = pcr.ifthenelse(rootwater >= rootsat, pcr.scalar(0), 1)
+    etact = pcr.ifthenelse(rainfrac > 0, pcr.min(etpot * etreddry * etredwet, rootwater), 0)
+    return etact
+    
+    
+    
+    
+    
Index: wflow-py/wflow/sphy/__init__.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/__init__.py	(revision 0)
+++ wflow-py/wflow/sphy/__init__.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1 @@

\ No newline at end of file
Index: wflow-py/wflow/sphy/glacier.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/glacier.py	(revision 0)
+++ wflow-py/wflow/sphy/glacier.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,21 @@
+print 'glacier module imported'
+
+#-Function to calculate melt from clean ice or debris covered glaciers
+def GlacCDMelt(pcr, temp, ddf, glacfrac):
+    glacdmelt = pcr.max(0, temp) * ddf * glacfrac
+    return glacdmelt
+
+#-Total glacier melt
+def GMelt(glaccimelt, glacdcmelt):
+    glacmelt = glaccimelt + glacdcmelt
+    return glacmelt
+
+#-Function to calculate runoff from glaciers
+def GlacR(glacf, gmelt, glacfrac):
+    glacr = glacf * gmelt * glacfrac
+    return glacr
+
+#-Function to calculate glacier percolation to groundwater
+def GPerc(glacf, gmelt, glacfrac):
+    gperc = (1 - glacf) * gmelt * glacfrac
+    return gperc
Index: wflow-py/wflow/sphy/groundwater.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/groundwater.py	(revision 0)
+++ wflow-py/wflow/sphy/groundwater.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,19 @@
+print 'groundwater module imported'
+
+#-Function to calculate groundwater recharge
+def GroundWaterRecharge(pcr, deltagw, gwrecharge, subperc, glacperc):
+    gwseep = (1 - pcr.exp(-1 / deltagw)) * (subperc + glacperc)
+    gwrecharge = (pcr.exp(-1 / deltagw) * gwrecharge) + gwseep
+    return gwrecharge
+
+#-Function to calculate baseflow
+def BaseFlow(pcr, gw, baser, gwrecharge, basethresh, alphagw):
+    baser = pcr.ifthenelse(gw <= basethresh, 0, (baser * pcr.exp(-alphagw) + gwrecharge * (1 - pcr.exp(-alphagw))))
+    return baser
+
+#-Function to calculate the groundwater height, taken from the bottom of the gw layer (zero reference)
+def HLevel(pcr, Hgw, alphagw, gwrecharge, yield_gw):
+    Hgw = (Hgw * pcr.exp(-alphagw)) + ((gwrecharge * (1 - pcr.exp(-alphagw))) / (800 * yield_gw * alphagw))
+    return Hgw
+
+
Index: wflow-py/wflow/sphy/hargreaves.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/hargreaves.py	(revision 0)
+++ wflow-py/wflow/sphy/hargreaves.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,15 @@
+#-Extraterrestrial radiation    
+def extrarad(self, pcr):
+    DayNo = self.wf_supplyJulianDOY() # timecalc.julian(self)[0]
+    LatRad = self.Lat * (self.pi / 180)
+    dr = 1 + 0.033 * pcr.cos((2 * self.pi * DayNo) /  365)
+    delta = 0.409 * pcr.sin(((2 * self.pi * DayNo) / 365) - 1.39)
+    omegas = pcr.acos(-1 * pcr.tan(LatRad) * pcr.tan(delta))
+    Ra = ((24 * 60) / self.pi) * self.Gsc * dr * (pcr.scalar(omegas) * pcr.sin(LatRad) * pcr.sin(delta) +\
+        pcr.cos(LatRad) * pcr.cos(delta) * pcr.sin(omegas))
+    return Ra    
+
+#-Modified Hargreaves for calculation of ETref
+def Hargreaves(pcr, ra, temp, tempmax, tempmin):
+    ETref = pcr.max(0.0023 * 0.408 * ra * (temp + 17.8) * (pcr.max(tempmax - tempmin, 0))**0.5, 0)
+    return ETref
\ No newline at end of file
Index: wflow-py/wflow/sphy/reporting.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/reporting.py	(revision 0)
+++ wflow-py/wflow/sphy/reporting.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,57 @@
+#-Function to report the output
+def REPM(self, pcr, tot, var, fname, outops, TSS=False, MAP=False):
+    if outops == 'Day':
+        if TSS:
+            TSS.sample(var)
+        if MAP:
+            self.report(var, self.outpath + fname)
+        tot = 0
+    elif outops == 'Month':
+        dim = [31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31]
+        if self.calendar.isleap(self.curdate.year):
+            dim[1] = 29
+        else:
+            dim[1] = 28
+        tot = tot + var
+        if self.curdate.day == dim[self.curdate.month-1]:
+            if TSS:
+                TSS.sample(tot)
+            if MAP:
+                self.report(tot, self.outpath + fname + 'M')
+            tot = 0
+    elif outops == 'Year':
+        if self.calendar.isleap(self.curdate.year):
+            ydays = 366
+        else:
+            ydays = 365
+        tot = tot + var
+        if self.timecalc.julian(self)[0] == ydays:
+            if TSS:
+                TSS.sample(tot)
+            if MAP:
+                self.report(tot, self.outpath + fname + 'Y')
+            tot = 0
+    else:
+        tot = tot + var
+        if self.curdate == self.enddate:
+            pcr.report(tot, self.outpath + fname + '.map')
+            tot = 0
+    return tot
+ 
+#-Function to initialise the reporting
+def reporting(self, pcr, tot, var):
+    for outops in ['Day','Month','Year','Final']:
+        try:
+            TSS = eval('self.' + tot + '_' + outops + 'TS')
+            try:
+                MAP = eval('self.' + tot + '_' + outops + '_map')
+                setattr(self, tot + '_'+outops, REPM(self, pcr, eval('self.'+tot+'_'+outops), var, eval('self.'+tot+'_fname'), outops, TSS, MAP))
+            except:
+                setattr(self, tot + '_'+outops, REPM(self, pcr, eval('self.'+tot+'_'+outops), var, eval('self.'+tot+'_fname'), outops, TSS))
+        except:
+            try:
+                MAP = eval('self.' + tot + '_' + outops + '_map')
+                setattr(self, tot + '_'+outops, REPM(self, pcr, eval('self.'+tot+'_'+outops), var, eval('self.'+tot+'_fname'), outops, False, MAP))
+            except:
+                pass    
+    
Index: wflow-py/wflow/sphy/rootzone.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/rootzone.py	(revision 0)
+++ wflow-py/wflow/sphy/rootzone.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,20 @@
+#-Function to calculate rootzone runoff
+def RootRunoff(pcr, rainfrac, rootwater, rootsat):
+    rootrunoff = pcr.ifthenelse(rainfrac > 0, pcr.max(rootwater - rootsat, 0), 0)
+    return rootrunoff
+
+#-Function to calculate rootzone drainage
+def RootDrainage(pcr, rootwater, rootdrain, rootfield, rootsat, drainvel, rootTT):
+    rootexcess = pcr.max(rootwater - rootfield, 0)
+    rootexcessfrac = rootexcess / (rootsat - rootfield)
+    rootlat = rootexcessfrac * drainvel
+    rootdrainage = pcr.max(pcr.min(rootwater, rootlat * (1-pcr.exp(-1/rootTT)) + rootdrain * pcr.exp(-1/rootTT)), 0)
+    return rootdrainage
+
+#-Function to calculate rootzone percolation
+def RootPercolation(pcr, rootwater, subwater, rootfield, rootTT, subsat):
+    rootexcess = pcr.max(rootwater - rootfield, 0)
+    rootperc = rootexcess * (1 - pcr.exp(-1 / rootTT))
+    rootperc = pcr.ifthenelse(subwater >= subsat, 0, pcr.min(subsat - subwater, rootperc))
+    rootperc = pcr.max(pcr.min(rootperc, rootwater), 0)
+    return rootperc
Index: wflow-py/wflow/sphy/routing.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/routing.py	(revision 0)
+++ wflow-py/wflow/sphy/routing.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,7 @@
+print 'routing module imported'
+
+def ROUT(pcr, q, oldq, flowdir, kx):
+    rr = (q * 0.001 * pcr.cellarea()) / (24*3600)
+    ra = pcr.accuflux(flowdir, rr)
+    ra = (1 - kx) * ra + kx * oldq
+    return ra
Index: wflow-py/wflow/sphy/snow.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/snow.py	(revision 0)
+++ wflow-py/wflow/sphy/snow.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,35 @@
+print 'snow module imported'
+
+#-Function to calculate the potential snow melt
+def PotSnowMelt(pcr, temp, ddfs):
+    melt = pcr.max(0, temp) * ddfs
+    return melt
+#-Function to calculate the actual snow melt
+def ActSnowMelt(pcr, snowstore, potmelt):
+    melt = pcr.min(snowstore, potmelt)
+    return melt
+
+#-Function that updates the snow storage
+def SnowStoreUpdate(pcr, snowstore, snow, actmelt, temp, snowwatstore):
+    snowstore = snowstore + snow - actmelt + pcr.ifthenelse(temp < 0, pcr.scalar(snowwatstore), 0)
+    return snowstore
+
+#-Function that determines the maximum amount of water that can be stored in the snowpack
+def MaxSnowWatStorage(snowsc, snowstore):
+    maxsnowwatstore = snowsc * snowstore
+    return maxsnowwatstore
+
+#-Function to calculate the actual snow water storage 
+def SnowWatStorage(pcr, temp, maxsnowwatstore, snowwatstore, actmelt, rain):
+    snowwatstore = pcr.ifthenelse(temp < 0, 0, pcr.min(maxsnowwatstore, snowwatstore + actmelt + rain))
+    return snowwatstore
+
+#-Function to calculate the total snow storage (snowstore + snowwatstore)
+def TotSnowStorage(snowstore, snowwatstore, snowfrac, rainfrac):
+    totalsnowstore = (snowstore + snowwatstore) * (snowfrac + rainfrac)
+    return totalsnowstore
+
+#-Function to calculate runoff from snow
+def SnowR(pcr, snowwatstore, maxsnowwatstore, actmelt, rain, oldsnowwatstore, snowfrac):
+    snowr = pcr.ifthenelse(snowwatstore == maxsnowwatstore, (((actmelt + rain) - (snowwatstore - oldsnowwatstore)) * snowfrac), 0)
+    return snowr
Index: wflow-py/wflow/sphy/subzone.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/subzone.py	(revision 0)
+++ wflow-py/wflow/sphy/subzone.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,21 @@
+#-Function to calculate capillary rise
+def CapilRise(pcr, subfield, subwater, capmax, rootwater, rootsat, rootfield):
+    subrelwat = pcr.max(pcr.min((subwater / subfield), 1), 0)
+    rootrelwat = pcr.max(pcr.min((rootwater / rootfield), 1), 0)
+    caprise = pcr.min(subwater, capmax * (1 - rootrelwat) * subrelwat)
+    caprise = pcr.min(caprise, rootsat - rootwater)  # adding caprise can not exceed saturated rootwater content
+    return caprise
+
+#-Function to calculate percolation from subsoil (only if groundwater module is used)
+def SubPercolation(pcr, subwater, subfield, subTT, gw, gwsat):
+    subperc =  pcr.ifthenelse((gw < gwsat) & ((subwater - subfield) > 0), (subwater - subfield) * (1 - pcr.exp(-1 / subTT)), 0)
+    return subperc
+
+#-Function to calculate drainage from subsoil (only if groundwater module is NOT used)
+def SubDrainage(pcr, subwater, subfield, subsat, drainvel, subdrainage, subTT):
+    subexcess = pcr.max(subwater - subfield, 0)
+    subexcessfrac = subexcess / (subsat - subfield)
+    sublateral = subexcessfrac * drainvel
+    subdrainage = (sublateral + subdrainage) * (1 - pcr.exp(-1 / subTT))
+    subdrainage = pcr.max(pcr.min(subdrainage, subwater), 0)
+    return subdrainage
\ No newline at end of file
Index: wflow-py/wflow/sphy/timecalc.py
===================================================================
diff -u
--- wflow-py/wflow/sphy/timecalc.py	(revision 0)
+++ wflow-py/wflow/sphy/timecalc.py	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -0,0 +1,15 @@
+
+#-Function to return the julian day of the year
+def julian(self):
+    y= self.curdate.year
+    start= self.datetime.datetime(y,1,1).toordinal()
+    current= self.curdate.toordinal()
+    day= current-start+1
+    return day, 1
+
+#-Function to calculate the number of timesteps for the model run
+def timesteps(self):
+    nrTimeSteps = (self.enddate - self.startdate).days + 1
+    print 'Running SPHY for '+str(self.startdate.day)+'-'+str(self.startdate.month)+'-'+str(self.startdate.year)+' through '+str(self.enddate.day)+'-'+str(self.enddate.month)+'-'+str(self.enddate.year)
+    print 'with '+str(nrTimeSteps)+' daily timesteps'
+    return nrTimeSteps
\ No newline at end of file
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/subzone.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Fisheye: Tag e59169d4b535e077a267eba3d2ba75f73803fbc8 refers to a dead (removed) revision in file `wflow-py/wflow/timecalc.py'.
Fisheye: No comparison available.  Pass `N' to diff?
Index: wflow-py/wflow/wflow_sphy.py
===================================================================
diff -u -r0b41e43f37d232133cd4d014e63c39941525df35 -re59169d4b535e077a267eba3d2ba75f73803fbc8
--- wflow-py/wflow/wflow_sphy.py	(.../wflow_sphy.py)	(revision 0b41e43f37d232133cd4d014e63c39941525df35)
+++ wflow-py/wflow/wflow_sphy.py	(.../wflow_sphy.py)	(revision e59169d4b535e077a267eba3d2ba75f73803fbc8)
@@ -257,11 +257,11 @@
     
     # import the required modules
     import datetime, calendar
-    import wflow.reporting as reporting
-    import wflow.timecalc as timecalc
-    import wflow.ET as ET
-    import wflow.rootzone as rootzone
-    import wflow.subzone as subzone
+    import wflow.sphy.reporting as reporting
+    import wflow.sphy.timecalc as timecalc
+    import wflow.sphy.ET as ET
+    import wflow.sphy.rootzone as rootzone
+    import wflow.sphy.subzone as subzone
 
     #from wflow.wflow_lib import *
     from math import pi
@@ -280,15 +280,15 @@
     if self.GlacFLAG == 1:
     	self.SnowFLAG = 1
     	self.GroundFLAG = 1
-    	import glacier # glacier melting processes
+    	import wflow.sphy.glacier as glacier # glacier melting processes
     	self.glacier = glacier
     	del glacier
     if self.SnowFLAG == 1:
-    	import snow # snow melt processes
+    	import wflow.sphy.snow as snow # snow melt processes
     	self.snow = snow
     	del snow
     if self.RoutFLAG == 1:
-    	import routing # simple routing scheme
+    	import wflow.sphy.routing as routing # simple routing scheme
     	self.routing = routing
     	del routing
     if self.LakeFLAG == 1:
@@ -309,7 +309,7 @@
     	self.dynamic_veg = dynamic_veg
     	del dynamic_veg
     if self.GroundFLAG == 1:
-    	import groundwater # groundwater storage as third storage layer. This is used instead of a fixed bottomflux
+    	import wflow.sphy.groundwater as groundwater # groundwater storage as third storage layer. This is used instead of a fixed bottomflux
     	self.groundwater = groundwater
     	del groundwater
     	
@@ -319,20 +319,20 @@
     # self.inpathforcingP = config.get('DIRS','inputforcingdirP')
     # self.outpath = config.get('DIRS', 'outputdir')
     
-    self.starttime = configget(self.config,"run","starttime","0")
-    ds = dt.datetime.strptime(self.starttime, '%Y-%m-%d %H:%M:%S %Z')
-    self.endtime = configget(self.config,"run","endtime","0")
-    de = dt.datetime.strptime(self.endtime, '%Y-%m-%d %H:%M:%S %Z')
+    # self.starttime = configget(self.config,"run","starttime","0")
+    # ds = dt.datetime.strptime(self.starttime, '%Y-%m-%d %H:%M:%S %Z')
+    # self.endtime = configget(self.config,"run","endtime","0")
+    # de = dt.datetime.strptime(self.endtime, '%Y-%m-%d %H:%M:%S %Z')
 	
     # #-set the timing criteria
-    sy = ds.year
-    sm = ds.month
-    sd = ds.day
-    ey = de.year
-    em = de.month
-    ed = de.day
-    self.startdate = self.datetime.datetime(sy,sm,sd)
-    self.enddate = self.datetime.datetime(ey,em,ed)
+    # sy = ds.year
+    # sm = ds.month
+    # sd = ds.day
+    # ey = de.year
+    # em = de.month
+    # ed = de.day
+    # self.startdate = self.datetime.datetime(sy,sm,sd)
+    # self.enddate = self.datetime.datetime(ey,em,ed)
     
     # #-get start date of first forcing file in forcing directory
     # syF = config.getint('TIMING', 'startyear_F')
@@ -584,7 +584,7 @@
     #-and the start date of the first forcing file in your forcing directory.
     #self.counter = (self.startdate - self.startdateF).days
     # #-initial date
-    self.curdate = self.startdate
+    # self.curdate = self.startdate
     #self.curdate = configget(self.config,"run","starttime","0")
     #print self.curdate
 	#-initial soil properties