Index: ../trunk-jpl/test/NightlyRun/test2005.m
===================================================================
--- ../trunk-jpl/test/NightlyRun/test2005.m	(revision 25687)
+++ ../trunk-jpl/test/NightlyRun/test2005.m	(revision 25688)
@@ -39,7 +39,7 @@
 md.mask.ocean_levelset(md.mesh.elements(pos,:))=1;
 
 %make sure wherever there is an ice load, that the mask is set to ice:
-pos=find(md.solidearth.surfaceload.icethicknesschange);
+%pos=find(md.solidearth.surfaceload.icethicknesschange); % TODO: Do we need to do this twice?
 md.mask.ice_levelset(md.mesh.elements(pos,:))=-1;
 % }}}
 
@@ -51,7 +51,6 @@
 %Materials: 
 md.materials=materials('hydro');
 
-
 %Miscellaneous
 md.miscellaneous.name='test2005';
 
@@ -85,7 +84,6 @@
 end
 deltathickness(end,:)=0:1:9;
 md.solidearth.surfaceload.icethicknesschange=deltathickness;
-
 %hack: 
 md.geometry.surface=zeros(md.mesh.numberofvertices,1);
 md.geometry.thickness=ones(md.mesh.numberofvertices,1);
@@ -102,6 +100,6 @@
 
 %Fields and tolerances to track changes
 field_names={'Sealevel1','Sealevel5','Sealevel10','Seustatic10'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
+field_tolerances={1e-13,1e-13,1e-13,1e-13};
 field_values={S1,S5,S10,Seus10};
 
Index: ../trunk-jpl/test/NightlyRun/runme.py
===================================================================
--- ../trunk-jpl/test/NightlyRun/runme.py	(revision 25687)
+++ ../trunk-jpl/test/NightlyRun/runme.py	(revision 25688)
@@ -113,7 +113,7 @@
     # }}}
     #Process Ids according to benchmarks {{{
     if benchmark == 'nightly':
-        test_ids = test_ids.intersection(set(range(1, 1000)))
+        test_ids = test_ids.intersection(set(range(1, 1000)).union(set(range(2001, 2500))))
     elif benchmark == 'validation':
         test_ids = test_ids.intersection(set(range(1001, 2000)))
     elif benchmark == 'ismip':
Index: ../trunk-jpl/test/NightlyRun/test2005.py
===================================================================
--- ../trunk-jpl/test/NightlyRun/test2005.py	(nonexistent)
+++ ../trunk-jpl/test/NightlyRun/test2005.py	(revision 25688)
@@ -0,0 +1,116 @@
+#Test Name: EarthSlr
+import numpy as np
+
+from gmshplanet import *
+from gmtmask import *
+from lovenumbers import *
+from materials import *
+from model import *
+from parameterize import *
+from paterson import *
+from solve import *
+
+
+# Mesh earth
+md = model()
+md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) #700 km resolution mesh
+
+# Parameterize solidearth solution
+# Solidearth loading #{{{
+md.solidearth.surfaceload.icethicknesschange = np.zeros((md.mesh.numberofelements, 1))
+md.solidearth.sealevel = np.zeros((md.mesh.numberofvertices, 1))
+md.dsl.global_average_thermosteric_sea_level_change = np.zeros((2, 1))
+md.dsl.sea_surface_height_change_above_geoid = np.zeros((md.mesh.numberofvertices + 1, 1))
+md.dsl.sea_water_pressure_change_at_sea_floor = np.zeros((md.mesh.numberofvertices + 1, 1))
+
+# Antarctica
+late = md.mesh.lat[md.mesh.elements - 1].sum(axis=1) / 3
+longe = md.mesh.long[md.mesh.elements - 1].sum(axis=1) / 3
+pos = np.where(late < -80)[0]
+md.solidearth.surfaceload.icethicknesschange[pos] = -100
+# Greenland
+pos = np.where(np.logical_and.reduce((late > 70, late < 80, longe > -60, longe < -30)))[0]
+md.solidearth.surfaceload.icethicknesschange[pos] = -100
+
+# Elastic loading from love numbers
+md.solidearth.lovenumbers = lovenumbers('maxdeg', 100)
+#}}}
+
+# Mask #{{{
+mask = gmtmask(md.mesh.lat, md.mesh.long)
+icemask = np.ones((md.mesh.numberofvertices, 1))
+pos = np.where(mask == 0)[0]
+icemask[pos] = -1
+pos = np.where(mask[md.mesh.elements - 1].sum(axis=1) < 3)[0]
+icemask[md.mesh.elements[pos, :] - 1] = -1
+md.mask.ice_levelset = icemask
+md.mask.ocean_levelset = -icemask
+
+# Make sure that the elements that have loads are fully grounded
+pos = np.nonzero(md.solidearth.surfaceload.icethicknesschange)[0]
+md.mask.ocean_levelset[md.mesh.elements[pos, :] - 1] = 1
+
+# Make sure wherever there is an ice load, that the mask is set to ice:
+#pos = np.nonzero(md.solidearth.surfaceload.icethicknesschange)[0] # TODO: Do we need to do this twice?
+md.mask.ice_levelset[md.mesh.elements[pos, :] - 1] = -1
+# }}}
+
+md.solidearth.settings.ocean_area_scaling = 0
+
+# Geometry for the bed; arbitrary
+md.geometry.bed = -np.ones((md.mesh.numberofvertices, 1))
+
+# Materials
+md.materials = materials('hydro')
+
+# Miscellaneous
+md.miscellaneous.name = 'test2005'
+
+# Solution parameters
+md.solidearth.settings.reltol = np.nan
+md.solidearth.settings.abstol = 1e-3
+md.solidearth.settings.computesealevelchange = 1
+
+# Max number of iterations reverted back to 10 (i.e. the original default value)
+md.solidearth.settings.maxiter = 10
+
+# Eustatic + rigid + elastic + rotation run
+md.solidearth.settings.rigid = 1
+md.solidearth.settings.elastic = 1
+md.solidearth.settings.rotation = 1
+
+# Transient settings
+md.timestepping.start_time = 0
+md.timestepping.final_time = 10
+md.timestepping.time_step = 1
+md.transient.isslr = 1
+md.transient.issmb = 0
+md.transient.isgia = 1
+md.transient.ismasstransport = 0
+md.transient.isstressbalance = 0
+md.transient.isthermal = 0
+dh = np.asarray(md.solidearth.surfaceload.icethicknesschange).T
+deltathickness = np.zeros((md.mesh.numberofelements + 1, 10))
+for i in range(10):
+    deltathickness[0:-1, i] = dh * (i + 1)
+deltathickness[-1, :] = np.arange(0, 10, 1)
+md.solidearth.surfaceload.icethicknesschange = deltathickness
+
+# Hack
+md.geometry.surface = np.zeros((md.mesh.numberofvertices, 1))
+md.geometry.thickness = np.ones((md.mesh.numberofvertices, 1))
+md.geometry.base = -np.ones((md.mesh.numberofvertices, 1))
+md.geometry.bed = md.geometry.base
+
+# Run transient solution
+md = solve(md, 'Transient')
+
+S1 = md.results.TransientSolution[1 - 1].Sealevel
+S5 = md.results.TransientSolution[5 - 1].Sealevel
+S10 = md.results.TransientSolution[10 - 1].Sealevel
+Seus10 = md.results.TransientSolution[10 - 1].Bslr
+
+#Fields and tolerances to track changes
+field_names = ['Sealevel1', 'Sealevel5', 'Sealevel10', 'Seustatic10']
+field_tolerances = [1e-13, 1e-13, 1e-13, 1e-13]
+field_values = [S1, S5, S10, Seus10]
Index: ../trunk-jpl/test/NightlyRun/test2002.py
===================================================================
--- ../trunk-jpl/test/NightlyRun/test2002.py	(revision 25687)
+++ ../trunk-jpl/test/NightlyRun/test2002.py	(revision 25688)
@@ -51,7 +51,7 @@
 md.mask.ocean_levelset[md.mesh.elements[pos, :] - 1] = 1
 
 #make sure wherever there is an ice load, that the mask is set to ice:
-#pos = np.nonzero(md.solidearth.surfaceload.icethicknesschange)[0] # Do we need to do this twice?
+#pos = np.nonzero(md.solidearth.surfaceload.icethicknesschange)[0] # TODO: Do we need to do this twice?
 md.mask.ice_levelset[md.mesh.elements[pos, :] - 1] = -1
 # }}}
 
@@ -71,7 +71,7 @@
 md.solidearth.settings.abstol = 1e-3
 md.solidearth.settings.computesealevelchange = 1
 
-#max number of iteration reverted back to 10 (i.e., the original default value)
+#max number of iterations reverted back to 10 (i.e., the original default value)
 md.solidearth.settings.maxiter = 10
 
 #eustatic run:
Index: ../trunk-jpl/src/m/classes/SMBpddSicopolis.py
===================================================================
--- ../trunk-jpl/src/m/classes/SMBpddSicopolis.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/SMBpddSicopolis.py	(revision 25688)
@@ -1,29 +1,29 @@
 import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
-from checkfield import checkfield
+from helpers import *
+from MatlabFuncs import *
+from project3d import project3d
 from WriteData import WriteData
-from project3d import project3d
-from MatlabFuncs import *
-from helpers import *
 
 
 class SMBpddSicopolis(object):
-    """
-    SMBpddSicopolis Class definition
+    """SMBPDDSICOPOLIS class definition
 
     Usage:
         SMBpddSicopolis = SMBpddSicopolis()
-"""
+    """
 
-    def __init__(self):  # {{{
-        self.precipitation = float('NaN')
-        self.monthlytemperatures = float('NaN')
-        self.temperature_anomaly = float('NaN')
-        self.precipitation_anomaly = float('NaN')
-        self.smb_corr = float('NaN')
+    def __init__(self, *args):  # {{{
+        self.precipitation = np.nan
+        self.monthlytemperatures = np.nan
+        self.temperature_anomaly = np.nan
+        self.precipitation_anomaly = np.nan
+        self.smb_corr = np.nan
         self.desfac = 0
-        self.s0p = float('NaN')
-        self.s0t = float('NaN')
+        self.s0p = np.nan
+        self.s0t = np.nan
         self.rlaps = 0
         self.isfirnwarming = 0
         self.steps_per_step = 1
@@ -30,42 +30,35 @@
         self.averaging = 0
         self.requested_outputs = []
 
-        self.setdefaultparameters()
+        nargs = len(args)
+        if nargs == 0:
+            self.setdefaultparameters()
+        else:
+            raise Exception('constructor not supported')
     # }}}
 
     def __repr__(self):  # {{{
-        string = '   surface forcings parameters:'
-        string += '\n   SICOPOLIS PDD scheme (Calov & Greve, 2005) :'
-
-        string = "%s\n%s" % (string, fielddisplay(self, 'monthlytemperatures', 'monthly surface temperatures [K]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'precipitation', 'monthly surface precipitation [m/yr water eq]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'temperature_anomaly', 'anomaly to monthly reference temperature (additive [K])'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'precipitation_anomaly', 'anomaly to monthly precipitation (multiplicative, e.g. q = q0*exp(0.070458*DeltaT) after Huybrechts (2002)) [no unit])'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'smb_corr', 'correction of smb after PDD call [m/a]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 's0p', 'should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 's0t', 'should be set to elevation from temperature source (between 0 and a few 1000s m, default is 0) [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'rlaps', 'present day lapse rate (default is 7.4 degree/km)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'desfac', 'desertification elevation factor (default is -log(2.0)/1000)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isfirnwarming', 'is firnwarming (Reeh 1991) activated (0 or 1, default is 1)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'averaging', 'averaging methods from short to long steps'))
-        string = "%s\n\t\t%s" % (string, '0: Arithmetic (default)')
-        string = "%s\n\t\t%s" % (string, '1: Geometric')
-        string = "%s\n\t\t%s" % (string, '2: Harmonic')
-
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested (TemperaturePDD, SmbAccumulation, SmbMelt)'))
+        s = '   surface forcings parameters:\n'
+        s += '   SICOPOLIS PDD scheme (Calov & Greve, 2005):\n'
+        s += '{}\n'.format(fielddisplay(self, 'monthlytemperatures', 'monthly surface temperatures [K]'))
+        s += '{}\n'.format(fielddisplay(self, 'precipitation', 'monthly surface precipitation [m/yr water eq]'))
+        s += '{}\n'.format(fielddisplay(self, 'temperature_anomaly', 'anomaly to monthly reference temperature (additive [K])'))
+        s += '{}\n'.format(fielddisplay(self, 'precipitation_anomaly', 'anomaly to monthly precipitation (multiplicative, e.g. q = q0*exp(0.070458*DeltaT) after Huybrechts (2002)) [no unit])'))
+        s += '{}\n'.format(fielddisplay(self, 'smb_corr', 'correction of smb after PDD call [m/a]'))
+        s += '{}\n'.format(fielddisplay(self, 's0p', 'should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]'))
+        s += '{}\n'.format(fielddisplay(self, 's0t', 'should be set to elevation from temperature source (between 0 and a few 1000s m, default is 0) [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'rlaps', 'present day lapse rate (default is 7.4 degree/km)'))
+        s += '{}\n'.format(fielddisplay(self, 'desfac', 'desertification elevation factor (default is -log(2.0)/1000)'))
+        s += '{}\n'.format(fielddisplay(self, 'isfirnwarming', 'is firnwarming (Reeh 1991) activated (0 or 1, default is 1)'))
+        s += '{}\n'.format(fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'))
+        s += '{}\n'.format(fielddisplay(self, 'averaging', 'averaging methods from short to long steps'))
+        s += '\t\t{}\n'.format('0: Arithmetic (default)')
+        s += '\t\t{}\n'.format('1: Geometric')
+        s += '\t\t{}\n'.format('2: Harmonic')
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested (TemperaturePDD, SmbAccumulation, SmbMelt)'))
+        return s
     # }}}
 
-    @staticmethod
-    def SMBpddSicopolis(*args):  # {{{
-        nargin = len(args)
-
-        if nargin == 0:
-            return SMBpddSicopolis()
-        else:
-            raise RuntimeError('SMBpddSicopolis: constructor not supported')
-    # }}}
-
     def extrude(self, md):  # {{{
         self.precipitation = project3d(md, 'vector', self.precipitation, 'type', 'node')
         self.monthlytemperatures = project3d(md, 'vector', self.monthlytemperatures, 'type', 'node')
@@ -82,7 +75,6 @@
     # }}}
 
     def initialize(self, md):  # {{{
-
         if np.isnan(self.s0p):
             self.s0p = np.zeros((md.mesh.numberofvertices, ))
             print('      no SMBpddSicopolis.s0p specified: values set as zero')
@@ -102,6 +94,7 @@
         if np.isnan(self.smb_corr):
             self.smb_corr = np.zeros((md.mesh.numberofvertices, ))
             print('      no SMBpddSicopolis.smb_corr specified: values set as zero')
+        return self
     # }}}
 
     def setdefaultparameters(self):  # {{{
@@ -108,13 +101,12 @@
         self.isfirnwarming = 1
         self.desfac = -np.log(2.0) / 1000
         self.rlaps = 7.4
-
+        return self
     # }}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        if (strcmp(solution, 'TransientSolution') and md.transient.issmb == 0):
+        if solution == 'TransientSolution' and not md.transient.issmb:
             return
-
         if 'MasstransportAnalysis' in analyses:
             md = checkfield(md, 'fieldname', 'smb.desfac', '<=', 1, 'numel', 1)
             md = checkfield(md, 'fieldname', 'smb.s0p', '>=', 0, 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices, 1])
@@ -122,26 +114,20 @@
             md = checkfield(md, 'fieldname', 'smb.rlaps', '>=', 0, 'numel', 1)
             md = checkfield(md, 'fieldname', 'smb.monthlytemperatures', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices, 12])
             md = checkfield(md, 'fieldname', 'smb.precipitation', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices, 12])
-
         md = checkfield(md, 'fieldname', 'smb.steps_per_step', '>=', 1, 'numel', [1])
         md = checkfield(md, 'fieldname', 'smb.averaging', 'numel', [1], 'values', [0, 1, 2])
         md = checkfield(md, 'fieldname', 'smb.requested_outputs', 'stringrow', 1)
-
         return md
     # }}}
 
     def marshall(self, prefix, md, fid):  # {{{
-
         yts = md.constants.yts
-
         WriteData(fid, prefix, 'name', 'md.smb.model', 'data', 10, 'format', 'Integer')
-
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'isfirnwarming', 'format', 'Boolean')
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'desfac', 'format', 'Double')
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 's0p', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 's0t', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'rlaps', 'format', 'Double')
-
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'monthlytemperatures', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts)
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'precipitation', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts)
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'temperature_anomaly', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts)
@@ -158,5 +144,4 @@
             outputs = [outputs, defaultoutputs(self, md)]  #add defaults
 
         WriteData(fid, prefix, 'data', outputs, 'name', 'md.smb.requested_outputs', 'format', 'StringArray')
-
     # }}}
Index: ../trunk-jpl/src/m/classes/giaivins.py
===================================================================
--- ../trunk-jpl/src/m/classes/giaivins.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/giaivins.py	(revision 25688)
@@ -7,11 +7,10 @@
 
 
 class giaivins(object):
-    """
-    GIA class definition for Ivins and James model
+    """GIA class definition for Ivins and James model
 
-       Usage:
-          giaivins = giaivins()
+    Usage:
+        giaivins = giaivins()
     """
 
     def __init__(self, *args): #{{{
@@ -20,7 +19,6 @@
         self.cross_section_shape    = 0
 
         nargin = len(args)
-
         if nargin == 0:
             self.setdefaultparameters()
         else:
@@ -29,15 +27,15 @@
 
     def __repr__(self): #{{{
         s = '   giaivins parameters:\n'
-        s += "{}\n".format(fielddisplay(self, 'mantle_viscosity', 'mantle viscosity [Pa s]'))
-        s += "{}\n".format(fielddisplay(self, 'lithosphere_thickness', 'lithosphere thickness (km)'))
-        s += "{}\n".format(fielddisplay(self, 'cross_section_shape', "1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore"))
-
+        s += '{}\n'.format(fielddisplay(self, 'mantle_viscosity', 'mantle viscosity [Pa s]'))
+        s += '{}\n'.format(fielddisplay(self, 'lithosphere_thickness', 'lithosphere thickness (km)'))
+        s += '{}\n'.format(fielddisplay(self, 'cross_section_shape', "1: square-edged (default). 2: elliptical. See iedge in GiaDeflectionCore"))
         return s
     #}}}
 
     def setdefaultparameters(self): #{{{
         self.cross_section_shape = 1
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): #{{{
@@ -48,9 +46,15 @@
         md = checkfield(md, 'fieldname', 'gia.lithosphere_thickness', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices], '>', 0)
         md = checkfield(md, 'fieldname', 'gia.cross_section_shape', 'numel', [1], 'values', [1, 2])
 
-        #be sure that if we are running a masstransport ice flow model coupled with giaivins, that thickness forcings
-        #are not provided into the future.
-
+        # Be sure that if we are running a masstransport ice flow model coupled 
+        # with giaivins, that thickness forcings are not provided into the 
+        # future.
+        if solution == 'TransientSolution' and md.transient.ismasstransport and md.transient.isgia:
+            # Figure out if thickness is a transient forcing
+            if md.geometry.thickness.shape[0] == md.mesh.numberofvertices + 1:
+                # Recover the furthest time "in time"
+                if md.geometry.thickness[-1, -1] != md.timestepping.start_time:
+                    md.checkmessage('if masstransport is on, transient thickness forcing for the giaivins model should not be provided in the future. Synchronize your start_time to correspond to the most recent transient thickness forcing timestep')
         return md
     #}}}
 
Index: ../trunk-jpl/src/m/classes/rotational.py
===================================================================
--- ../trunk-jpl/src/m/classes/rotational.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/rotational.py	(revision 25688)
@@ -6,12 +6,11 @@
 
 
 class rotational(object):
-    '''
-    ROTATIONAL class definition
+    """ROTATIONAL class definition
 
-        Usage:
-            rotational = rotational()
-    '''
+    Usage:
+        rotational = rotational()
+    """
 
     def __init__(self, *args): #{{{
         self.equatorialmoi      = 0
@@ -19,7 +18,6 @@
         self.langularvelocity   = 0
 
         nargin = len(args)
-
         if nargin == 0:
             self.setdefaultparameters()
         else:
@@ -31,27 +29,25 @@
         s += '{}\n'.format(fielddisplay(self, 'equatorialmoi', 'mean equatorial moment of inertia [kg m^2]'))
         s += '{}\n'.format(fielddisplay(self, 'polarmoi', 'polar moment of inertia [kg m^2]'))
         s += '{}\n'.format(fielddisplay(self, 'angularvelocity', 'mean rotational velocity of earth [per second]'))
-
         return s
     #}}}
 
     def setdefaultparameters(self): # {{{
-        #moment of inertia
+        # Moment of inertia
         self.equatorialmoi  = 8.0077e37 # [kg m^2]
         self.polarmoi       = 8.0345e37 # [kg m^2]
 
-        #mean rotational velocity of earth
+        # Mean rotational velocity of earth
         self.angularvelocity = 7.2921e-5 # [s^-1]
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): # {{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslr):
             return md
-
         md = checkfield(md, 'fieldname', 'solidearth.rotational.equatorialmoi', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'solidearth.rotational.polarmoi', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'solidearth.rotational.angularvelocity', 'NaN', 1, 'Inf', 1)
-
         return md
     #}}}
 
Index: ../trunk-jpl/src/m/classes/SMBforcing.m
===================================================================
--- ../trunk-jpl/src/m/classes/SMBforcing.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/SMBforcing.m	(revision 25688)
@@ -31,14 +31,10 @@
 			end
 		end % }}}
 		function list = defaultoutputs(self,md) % {{{
-
 			list = {''};
-
 		end % }}}
 		function self = extrude(self,md) % {{{
-
 			self.mass_balance=project3d(md,'vector',self.mass_balance,'type','node');
-
 		end % }}}
 		function self = initialize(self,md) % {{{
 
@@ -49,9 +45,7 @@
 
 		end % }}}
 		function md = checkconsistency(self,md,solution,analyses) % {{{
-
 			if (strcmp(solution,'TransientSolution') & md.transient.issmb == 0), return; end
-
 			if ismember('MasstransportAnalysis',analyses),
 				md = checkfield(md,'fieldname','smb.mass_balance','timeseries',1,'NaN',1,'Inf',1);
 			end
Index: ../trunk-jpl/src/m/classes/nodalvalue.m
===================================================================
--- ../trunk-jpl/src/m/classes/nodalvalue.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/nodalvalue.m	(revision 25688)
@@ -59,10 +59,10 @@
 		end % }}}
 		function md = marshall(self,prefix,md,fid) % {{{
 
-		WriteData(fid,prefix,'data',self.name,'name','md.nodalvalue.name','format','String');
-		WriteData(fid,prefix,'data',self.definitionstring,'name','md.nodalvalue.definitionenum','format','String');
-		WriteData(fid,prefix,'data',self.model_string,'name','md.nodalvalue.model_enum','format','String');
-		WriteData(fid,prefix,'data',self.node,'name','md.nodalvalue.node','format','Integer');
+			WriteData(fid,prefix,'data',self.name,'name','md.nodalvalue.name','format','String');
+			WriteData(fid,prefix,'data',self.definitionstring,'name','md.nodalvalue.definitionenum','format','String');
+			WriteData(fid,prefix,'data',self.model_string,'name','md.nodalvalue.model_enum','format','String');
+			WriteData(fid,prefix,'data',self.node,'name','md.nodalvalue.node','format','Integer');
 
 		end % }}}
 	end
Index: ../trunk-jpl/src/m/classes/dsl.py
===================================================================
--- ../trunk-jpl/src/m/classes/dsl.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/dsl.py	(revision 25688)
@@ -7,12 +7,11 @@
 
 
 class dsl(object):
-    '''
-    DSL - slass definition
+    """DSL - slass definition
 
-        Usage:
-            dsl = dsl()
-    '''
+    Usage:
+        dsl = dsl()
+    """
 
     def __init__(self): #{{{
         self.global_average_thermosteric_sea_level_change = 0 #corresponds to zostoga field in CMIP5 archives. Specified as a temporally variable global rate (mm/yr)
@@ -22,12 +21,11 @@
     #}}}
 
     def __repr__(self): #{{{
-        s = "   dsl parameters:"
-        s = "%s\n%s" % (s, fielddisplay(self, 'global_average_thermosteric_sea_level_change', 'corresponds to zostoga field in CMIP5 archives. Specified as a temporally variable global rate (mm/yr)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'sea_surface_height_change_above_geoid', 'corresponds to zos field in CMIP5 archives. Spatial average is 0. Specified as a spatio-temporally variable rate (mm/yr)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'sea_water_pressure_change_at_sea_floor', 'corresponds to bpo field in CMIP5 archives. Specified as a spatio-temporally variable rate (in Pa/yr)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'compute_fingerprints', 'do we use the sea water pressure change to compute fingerprints and correct sea_surface_height_change_above_geoid'))
-
+        s = '   dsl parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'global_average_thermosteric_sea_level_change', 'corresponds to zostoga field in CMIP5 archives. Specified as a temporally variable global rate (mm/yr)'))
+        s += '{}\n'.format(fielddisplay(self, 'sea_surface_height_change_above_geoid', 'corresponds to zos field in CMIP5 archives. Spatial average is 0. Specified as a spatio-temporally variable rate (mm/yr)'))
+        s += '{}\n'.format(fielddisplay(self, 'sea_water_pressure_change_at_sea_floor', 'corresponds to bpo field in CMIP5 archives. Specified as a spatio-temporally variable rate (in Pa/yr)'))
+        s += '{}\n'.format(fielddisplay(self, 'compute_fingerprints', 'do we use the sea water pressure change to compute fingerprints and correct sea_surface_height_change_above_geoid'))
         return s
     #}}}
 
@@ -42,21 +40,18 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses): #{{{
-        # Early retun
+        # Early return
         if 'SealevelriseAnalysis' not in analyses:
             return md
-
         if solution == 'TransientSolution' and md.transient.isslr == 0:
             return md
-
         md = checkfield(md, 'fieldname', 'dsl.global_average_thermosteric_sea_level_change', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'dsl.sea_surface_height_change_above_geoid', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
         md = checkfield(md, 'fieldname', 'dsl.sea_water_pressure_change_at_sea_floor', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
         md = checkfield(md, 'fieldname', 'dsl.compute_fingerprints', 'NaN', 1, 'Inf', 1, 'values', [0, 1])
-
         if self.compute_fingerprints:
-            #check geodetic flag of slr is on:
-            if md.slr.geodetic == 0:
+            # Check if geodetic flag of slr is on
+            if not md.slr.geodetic:
                 raise RuntimeError('DSL checkconsistency error message: if bottom pressure fingerprints computations are requested, slr class should have geodetic flag on')
         return md
     # }}}
Index: ../trunk-jpl/src/m/classes/stressbalance.py
===================================================================
--- ../trunk-jpl/src/m/classes/stressbalance.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/stressbalance.py	(revision 25688)
@@ -1,18 +1,19 @@
+import sys
+
 import numpy as np
-import sys
+
+from checkfield import checkfield
+from fielddisplay import fielddisplay
+import MatlabFuncs as m
 from project3d import project3d
-from fielddisplay import fielddisplay
-from checkfield import checkfield
 from WriteData import WriteData
-import MatlabFuncs as m
 
 
 class stressbalance(object):
-    """
-    STRESSBALANCE class definition
+    """STRESSBALANCE class definition
 
-       Usage:
-          stressbalance = stressbalance()
+    Usage:
+        stressbalance = stressbalance()
     """
 
     def __init__(self):  # {{{
@@ -40,37 +41,31 @@
 
     #}}}
     def __repr__(self):  # {{{
-
-        string = '   StressBalance solution parameters:'
-        string = "%s\n%s" % (string, '      Convergence criteria:')
-        string = "%s\n%s" % (string, fielddisplay(self, 'restol', 'mechanical equilibrium residual convergence criterion'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'reltol', 'velocity relative convergence criterion, NaN: not applied'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'abstol', 'velocity absolute convergence criterion, NaN: not applied'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isnewton', "0: Picard's fixed point, 1: Newton's method, 2: hybrid"))
-        string = "%s\n%s" % (string, fielddisplay(self, 'maxiter', 'maximum number of nonlinear iterations'))
-
-        string = "%s\n%s" % (string, '\n      boundary conditions:')
-        string = "%s\n%s" % (string, fielddisplay(self, 'spcvx', 'x - axis velocity constraint (NaN means no constraint) [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'spcvy', 'y - axis velocity constraint (NaN means no constraint) [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'spcvz', 'z - axis velocity constraint (NaN means no constraint) [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'icefront', 'segments on ice front list (last column 0: Air, 1: Water, 2: Ice'))
-
-        string = "%s\n%s" % (string, '\n      Rift options:')
-        string = "%s\n%s" % (string, fielddisplay(self, 'rift_penalty_threshold', 'threshold for instability of mechanical constraints'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'rift_penalty_lock', 'number of iterations before rift penalties are locked'))
-
-        string = "%s\n%s" % (string, '\n      Penalty options:')
-        string = "%s\n%s" % (string, fielddisplay(self, 'penalty_factor', 'offset used by penalties: penalty = Kmax * 1.0**offset'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vertex_pairing', 'pairs of vertices that are penalized'))
-
-        string = "%s\n%s" % (string, '\n      Other:')
-        string = "%s\n%s" % (string, fielddisplay(self, 'shelf_dampening', 'use dampening for floating ice ? Only for FS model'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'FSreconditioning', 'multiplier for incompressibility equation. Only for FS model'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'referential', 'local referential'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'loadingforce', 'loading force applied on each point [N / m^3]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-
-        return string
+        s = '   StressBalance solution parameters:\n'
+        s += '      Convergence criteria:\n'
+        s += '{}\n'.format(fielddisplay(self, 'restol', 'mechanical equilibrium residual convergence criterion'))
+        s += '{}\n'.format(fielddisplay(self, 'reltol', 'velocity relative convergence criterion, NaN: not applied'))
+        s += '{}\n'.format(fielddisplay(self, 'abstol', 'velocity absolute convergence criterion, NaN: not applied'))
+        s += '{}\n'.format(fielddisplay(self, 'isnewton', "0: Picard's fixed point, 1: Newton's method, 2: hybrid"))
+        s += '{}\n'.format(fielddisplay(self, 'maxiter', 'maximum number of nonlinear iterations'))
+        s += '      boundary conditions:\n'
+        s += '{}\n'.format(fielddisplay(self, 'spcvx', 'x - axis velocity constraint (NaN means no constraint) [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'spcvy', 'y - axis velocity constraint (NaN means no constraint) [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'spcvz', 'z - axis velocity constraint (NaN means no constraint) [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'icefront', 'segments on ice front list (last column 0: Air, 1: Water, 2: Ice'))
+        s = "%s\n%s" % (s, '\n      Rift options:')
+        s += '{}\n'.format(fielddisplay(self, 'rift_penalty_threshold', 'threshold for instability of mechanical constraints'))
+        s += '{}\n'.format(fielddisplay(self, 'rift_penalty_lock', 'number of iterations before rift penalties are locked'))
+        s += '      Penalty options:\n'
+        s += '{}\n'.format(fielddisplay(self, 'penalty_factor', 'offset used by penalties: penalty = Kmax * 1.0**offset'))
+        s += '{}\n'.format(fielddisplay(self, 'vertex_pairing', 'pairs of vertices that are penalized'))
+        s += '      Other:\n'
+        s += '{}\n'.format(fielddisplay(self, 'shelf_dampening', 'use dampening for floating ice ? Only for FS model'))
+        s += '{}\n'.format(fielddisplay(self, 'FSreconditioning', 'multiplier for incompressibility equation. Only for FS model'))
+        s += '{}\n'.format(fielddisplay(self, 'referential', 'local referential'))
+        s += '{}\n'.format(fielddisplay(self, 'loadingforce', 'loading force applied on each point [N / m^3]'))
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
@@ -102,7 +97,6 @@
         self.rift_penalty_lock = 10
         #output default:
         self.requested_outputs = ['default']
-
         return self
     #}}}
 
@@ -112,13 +106,14 @@
         else:
             list = ['Vx', 'Vy', 'Vel', 'Pressure']
         return list
-
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if 'StressbalanceAnalysis' not in analyses:
             return md
+        if solution == 'TransientSolution' and not md.transient.isstressbalance:
+            return md
 
         md = checkfield(md, 'fieldname', 'stressbalance.spcvx', 'Inf', 1, 'timeseries', 1)
         md = checkfield(md, 'fieldname', 'stressbalance.spcvy', 'Inf', 1, 'timeseries', 1)
@@ -158,7 +153,6 @@
             pos = np.nonzero(np.logical_and(md.mask.ocean_levelset, md.mesh.vertexonbase))
             if np.any(np.logical_not(np.isnan(md.stressbalance.referential[pos, :]))):
                 md.checkmessage("no referential should be specified for basal vertices of grounded ice")
-
         return md
     # }}}
 
@@ -182,13 +176,11 @@
         WriteData(fid, prefix, 'object', self, 'class', 'stressbalance', 'fieldname', 'rift_penalty_lock', 'format', 'Integer')
         WriteData(fid, prefix, 'object', self, 'class', 'stressbalance', 'fieldname', 'rift_penalty_threshold', 'format', 'Integer')
         WriteData(fid, prefix, 'object', self, 'class', 'stressbalance', 'fieldname', 'referential', 'format', 'DoubleMat', 'mattype', 1)
-
         if isinstance(self.loadingforce, (list, tuple, np.ndarray)) and np.size(self.loadingforce, 1) == 3:
             WriteData(fid, prefix, 'data', self.loadingforce[:, 0], 'format', 'DoubleMat', 'mattype', 1, 'name', 'md.stressbalance.loadingforcex')
             WriteData(fid, prefix, 'data', self.loadingforce[:, 1], 'format', 'DoubleMat', 'mattype', 1, 'name', 'md.stressbalance.loadingforcey')
             WriteData(fid, prefix, 'data', self.loadingforce[:, 2], 'format', 'DoubleMat', 'mattype', 1, 'name', 'md.stressbalance.loadingforcez')
-
-    #process requested outputs
+        # Process requested outputs
         outputs = self.requested_outputs
         indices = [i for i, x in enumerate(outputs) if x == 'default']
         if len(indices) > 0:
Index: ../trunk-jpl/src/m/classes/frictionshakti.py
===================================================================
--- ../trunk-jpl/src/m/classes/frictionshakti.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/frictionshakti.py	(revision 25688)
@@ -25,9 +25,9 @@
     #}}}
 
     def __repr__(self):  # {{{
-        s = "Basal shear stress parameters: Sigma_b = coefficient^2 * Neff * u_b\n(effective stress Neff = rho_ice * g * thickness + rho_water * g * (head - b))\n"
+        s = 'Basal shear stress parameters: Sigma_b = coefficient^2 * Neff * u_b\n'
+        s += '(effective stress Neff = rho_ice * g * thickness + rho_water * g * (head - b))\n'
         s += "{}\n".format(fielddisplay(self, "coefficient", "friction coefficient [SI]"))
-
         return s
     #}}}
 
@@ -44,9 +44,7 @@
         # Early return
         if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses:
             return md
-
         md = checkfield(md, 'fieldname', 'friction.coefficient', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
-
         return md
     # }}}
 
Index: ../trunk-jpl/src/m/classes/flowequation.m
===================================================================
--- ../trunk-jpl/src/m/classes/flowequation.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/flowequation.m	(revision 25688)
@@ -12,7 +12,7 @@
 		isHO                           = 0;
 		isFS                           = 0;
 		isNitscheBC                    = 0;
-      FSNitscheGamma                 = 1e6;
+		FSNitscheGamma                 = 1e6;
 		fe_SSA                         = '';
 		fe_HO                          = '';
 		fe_FS                          = '';
Index: ../trunk-jpl/src/m/classes/slr.py
===================================================================
--- ../trunk-jpl/src/m/classes/slr.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/slr.py	(revision 25688)
@@ -49,79 +49,77 @@
     #}}}
 
     def __repr__(self):  # {{{
-        s = '   slr parameters:'
-        s = "%s\n%s" % (s, fielddisplay(self, 'deltathickness', 'thickness change: ice height equivalent [m]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'sealevel', 'current sea level (prior to computation) [m]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'spcthickness', 'thickness constraints (NaN means no constraint) [m]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'reltol', 'sea level rise relative convergence criterion, (NaN: not applied)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'abstol', 'sea level rise absolute convergence criterion, (default, NaN: not applied)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'maxiter', 'maximum number of nonlinear iterations'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'love_h', 'load Love number for radial displacement'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'love_k', 'load Love number for gravitational potential perturbation'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'love_l', 'load Love number for horizontal displaements'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'tide_love_k', 'tidal load Love number (degree 2)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'tide_love_h', 'tidal load Love number (degree 2)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'fluid_love', 'secular fluid Love number'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'equatorial_moi', 'mean equatorial moment of inertia [kg m^2]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'polar_moi', 'polar moment of inertia [kg m^2]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'angular_velocity', 'mean rotational velocity of earth [per second]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'ocean_area_scaling', 'correction for model representation of ocean area [default: No correction]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'hydro_rate', 'rate of hydrological expansion [mm / yr]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'geodetic', 'compute geodetic SLR? (in addition to steric?) default 0'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'geodetic_run_frequency', 'how many time steps we skip before we run SLR solver during transient (default: 1)'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'rigid', 'rigid earth graviational potential perturbation'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'elastic', 'elastic earth graviational potential perturbation'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'rotation', 'earth rotational potential perturbation'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'degacc', 'accuracy (default .01 deg) for numerical discretization of the Green''s functions'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'transitions', 'indices into parts of the mesh that will be icecaps'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-
+        s = '   slr parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'deltathickness', 'thickness change: ice height equivalent [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'sealevel', 'current sea level (prior to computation) [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'spcthickness', 'thickness constraints (NaN means no constraint) [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'reltol', 'sea level rise relative convergence criterion, (NaN: not applied)'))
+        s += '{}\n'.format(fielddisplay(self, 'abstol', 'sea level rise absolute convergence criterion, (default, NaN: not applied)'))
+        s += '{}\n'.format(fielddisplay(self, 'maxiter', 'maximum number of nonlinear iterations'))
+        s += '{}\n'.format(fielddisplay(self, 'love_h', 'load Love number for radial displacement'))
+        s += '{}\n'.format(fielddisplay(self, 'love_k', 'load Love number for gravitational potential perturbation'))
+        s += '{}\n'.format(fielddisplay(self, 'love_l', 'load Love number for horizontal displaements'))
+        s += '{}\n'.format(fielddisplay(self, 'tide_love_k', 'tidal load Love number (degree 2)'))
+        s += '{}\n'.format(fielddisplay(self, 'tide_love_h', 'tidal load Love number (degree 2)'))
+        s += '{}\n'.format(fielddisplay(self, 'fluid_love', 'secular fluid Love number'))
+        s += '{}\n'.format(fielddisplay(self, 'equatorial_moi', 'mean equatorial moment of inertia [kg m^2]'))
+        s += '{}\n'.format(fielddisplay(self, 'polar_moi', 'polar moment of inertia [kg m^2]'))
+        s += '{}\n'.format(fielddisplay(self, 'angular_velocity', 'mean rotational velocity of earth [per second]'))
+        s += '{}\n'.format(fielddisplay(self, 'ocean_area_scaling', 'correction for model representation of ocean area [default: No correction]'))
+        s += '{}\n'.format(fielddisplay(self, 'hydro_rate', 'rate of hydrological expansion [mm / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'geodetic', 'compute geodetic SLR? (in addition to steric?) default 0'))
+        s += '{}\n'.format(fielddisplay(self, 'geodetic_run_frequency', 'how many time steps we skip before we run SLR solver during transient (default: 1)'))
+        s += '{}\n'.format(fielddisplay(self, 'rigid', 'rigid earth graviational potential perturbation'))
+        s += '{}\n'.format(fielddisplay(self, 'elastic', 'elastic earth graviational potential perturbation'))
+        s += '{}\n'.format(fielddisplay(self, 'rotation', 'earth rotational potential perturbation'))
+        s += '{}\n'.format(fielddisplay(self, 'degacc', 'accuracy (default .01 deg) for numerical discretization of the Green''s functions'))
+        s += '{}\n'.format(fielddisplay(self, 'transitions', 'indices into parts of the mesh that will be icecaps'))
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
         return s
     # }}}
 
     def setdefaultparameters(self):  # {{{
-        #Convergence criterion: absolute, relative and residual
-        self.reltol = 0.01 #default
-        self.abstol = np.nan #1 mm of sea level rise
-        #maximum of non - linear iterations.
+        # Convergence criterion: absolute, relative and residual
+        self.reltol = 0.01 # default
+        self.abstol = np.nan # 1 mm of sea level rise
+        # Maximum number of non-linear iterations
         self.maxiter = 5
-        #computational flags:
+        # Computational flags
         self.geodetic = 0
         self.rigid = 1
         self.elastic = 1
         self.ocean_area_scaling = 0
         self.rotation = 1
-        #tidal love numbers:
-        self.tide_love_h = 0.6149  #degree 2
-        self.tide_love_k = 0.3055  #degree 2
-        #secular fluid love number:
+        # Tidal love numbers
+        self.tide_love_h = 0.6149 # degree 2
+        self.tide_love_k = 0.3055 # degree 2
+        # Secular fluid love number
         self.fluid_love = 0.942
-        #moment of inertia:
+        # Moment of inertia
         self.equatorial_moi = 8.0077e37  # [kg m^2]
         self.polar_moi = 8.0345e37  # [kg m^2]
-        #mean rotational velocity of earth
-        self.angular_velocity = 7.2921e-5  # [s^ - 1]
-        #numerical discretization accuracy
+        # Mean rotational velocity of earth
+        self.angular_velocity = 7.2921e-5  # [s^-1]
+        # Numerical discretization accuracy
         self.degacc = 0.01
-        #hydro
+        # Hydro
         self.hydro_rate = 0
-        #how many time steps we skip before we run SLR solver during transient
+        # How many time steps we skip before we run SLR solver during transient
         self.geodetic_run_frequency = 1
-        #output default:
+        # Output default
         self.requested_outputs = ['default']
-        #transitions should be a cell array of vectors:
+        # Transitions should be a list of vectors
         self.transitions = []
-        #horizontal displacement?  (not by default)
+        # Horizontal displacement? (not on by default)
         self.horiz = 0
-        #earth area
+        # Earth area
         self.planetradius = planetradius('earth')
-
         return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
-        if (solution != 'SealevelriseAnalysis') or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        # Early return
+        if 'SealevelriseAnalysis' not in analyses or (solution == 'TransientSolution' and not md.transient.isslr):
             return md
 
         md = checkfield(md, 'fieldname', 'slr.deltathickness', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofelements])
@@ -145,11 +143,11 @@
         md = checkfield(md, 'fieldname', 'slr.requested_outputs', 'stringrow', 1)
         md = checkfield(md, 'fieldname', 'slr.horiz', 'NaN', 1, 'Inf', 1, 'values', [0, 1])
 
-        #check that love numbers are provided at the same level of accuracy:
+        # Check that love numbers are provided at the same level of accuracy:
         if (size(self.love_h, 0) != size(self.love_k, 0)) or (size(self.love_h, 0) != size(self.love_l, 0)):
             raise Exception('slr error message: love numbers should be provided at the same level of accuracy')
 
-        #cross check that whereever we have an ice load, the mask is < 0 on each vertex:
+        # Cross check that whereever we have an ice load, the mask is < 0 on each vertex:
         pos = np.where(self.deltathickness)
         maskpos = md.mask.ice_levelset[md.mesh.elements[pos, :]]
         els = np.where(maskpos > 0)
@@ -156,10 +154,17 @@
         if len(els[0]) > 0:
             warnings.warn('slr checkconsistency fail: there are elements with ice loads where some vertices are not on the ice!')
 
-        #check that  if geodetic is requested, we are a mesh3dsurface model (planet), or if we are not,
-        #a coupler to a planet model is provided.
-        if self.geodetic and not md.transient.iscoupler and domaintype(md.mesh) != 'mesh3dsurface':
-            raise Exception('model is requesting geodetic computations without being a mesh3dsurface, or being coupled to one!')
+        # Check that if geodetic is requested, we are a mesh3dsurface model (planet), or if we are not, a coupler to a planet model is provided
+        if self.geodetic:
+            if md.transient.iscoupler:
+                # We are good
+                pass
+            else:
+                if md.mesh.__class__.__name__ == 'mesh3dsurface':
+                    # We are good
+                    pass
+                else:
+                    raise Exception('model is requesting geodetic computations without being a mesh3dsurface, or being coupled to one!')
         return md
     # }}}
 
@@ -195,7 +200,7 @@
         WriteData(fid, prefix, 'object', self, 'fieldname', 'geodetic', 'format', 'Integer')
         WriteData(fid, prefix, 'object', self, 'fieldname', 'planetradius', 'format', 'Double')
 
-    #process requested outputs
+        # Process requested outputs
         outputs = self.requested_outputs
         indices = [i for i, x in enumerate(outputs) if x == 'default']
         if len(indices) > 0:
Index: ../trunk-jpl/src/m/classes/linearbasalforcings.py
===================================================================
--- ../trunk-jpl/src/m/classes/linearbasalforcings.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/linearbasalforcings.py	(revision 25688)
@@ -2,20 +2,20 @@
 
 from checkfield import checkfield
 from fielddisplay import fielddisplay
+from project3d import project3d
 from WriteData import WriteData
 
 
 class linearbasalforcings(object):
-    """
-    LINEAR BASAL FORCINGS class definition
+    """LINEAR BASAL FORCINGS class definition
 
-       Usage:
-          basalforcings = linearbasalforcings()
+    Usage:
+        basalforcings = linearbasalforcings()
     """
 
-    def __init__(self, *args):  # {{{
-
-        if not len(args):
+    def __init__(self, *args): #{{{
+        nargs = len(args)
+        if nargs == 0:
             print('empty init')
             self.deepwater_melting_rate = 0.
             self.deepwater_elevation = 0.
@@ -25,9 +25,9 @@
             self.perturbation_melting_rate = float('NaN')
             self.geothermalflux = float('NaN')
 
-    #set defaults
+            # set defaults
             self.setdefaultparameters()
-        elif len(args) == 1 and args[0].__module__ == 'basalforcings':
+        elif nargs == 1 and args[0].__module__ == 'basalforcings':
             print('converting basalforings to linearbasalforcings')
             inv = args[0]
             self.groundedice_melting_rate = inv.groundedice_melting_rate
@@ -38,46 +38,55 @@
             self.upperwater_melting_rate = 0.
             self.upperwater_elevation = 0.
 
-    #set defaults
+            # Set defaults
             self.setdefaultparameters()
         else:
             raise Exception('constructor not supported')
     #}}}
-    def __repr__(self):  # {{{
-        string = "   linear basal forcings parameters:"
-        string = "%s\n%s" % (string, fielddisplay(self, "deepwater_melting_rate", "basal melting rate (positive if melting applied for floating ice whith base < deepwater_elevation) [m/yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "deepwater_elevation", "elevation of ocean deepwater [m]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "upperwater_melting_rate", "upper melting rate (positive if melting applied for floating ice whith base >= upperwater_elevation) [m/yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "upperwater_elevation", "elevation of ocean upper water [m]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "groundedice_melting_rate", "basal melting rate (positive if melting) [m/yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "perturbation_melting_rate", "perturbation applied to computed melting rate (positive if melting) [m/yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "geothermalflux", "geothermal heat flux [W/m^2]"))
-        return string
+
+    def __repr__(self): #{{{
+        s = '   linear basal forcings parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, "deepwater_melting_rate", "basal melting rate (positive if melting applied for floating ice whith base < deepwater_elevation) [m/yr]"))
+        s += '{}\n'.format(fielddisplay(self, "deepwater_elevation", "elevation of ocean deepwater [m]"))
+        s += '{}\n'.format(fielddisplay(self, "upperwater_melting_rate", "upper melting rate (positive if melting applied for floating ice whith base >= upperwater_elevation) [m/yr]"))
+        s += '{}\n'.format(fielddisplay(self, "upperwater_elevation", "elevation of ocean upper water [m]"))
+        s += '{}\n'.format(fielddisplay(self, "groundedice_melting_rate", "basal melting rate (positive if melting) [m/yr]"))
+        s += '{}\n'.format(fielddisplay(self, "perturbation_melting_rate", "perturbation applied to computed melting rate (positive if melting) [m/yr]"))
+        s += '{}\n'.format(fielddisplay(self, "geothermalflux", "geothermal heat flux [W/m^2]"))
+        return s
     #}}}
-    def initialize(self, md):  # {{{
+
+    def extrude(self, md): #{{{
+        self.perturbation_melting_rate = project3d(md, 'vector', self.perturbation_melting_rate, 'type', 'node', 'layer', 1)
+        self.groundedice_melting_rate = project3d(md, 'vector', self.groundedice_melting_rate, 'type', 'node', 'layer', 1)
+        self.geothermalflux = project3d(md, 'vector', self.geothermalflux, 'type', 'node', 'layer', 1) # Bedrock only gets geothermal flux
+        return self
+    #}}}
+
+    def initialize(self, md): #{{{
         if np.all(np.isnan(self.groundedice_melting_rate)):
             self.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices))
             print("      no basalforcings.groundedice_melting_rate specified: values set as zero")
         return self
     #}}}
+
     def setdefaultparameters(self):  # {{{
         self.deepwater_melting_rate = 50.0
         self.deepwater_elevation = -800.0
         self.upperwater_melting_rate = 0.0
         self.upperwater_elevation = -400.0
+        return self
     #}}}
-    def checkconsistency(self, md, solution, analyses):  # {{{
 
+    def checkconsistency(self, md, solution, analyses): #{{{
         if not np.all(np.isnan(self.perturbation_melting_rate)):
             md = checkfield(md, 'fieldname', 'basalforcings.perturbation_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
-
-        if 'MasstransportAnalysis' in analyses and not (solution == 'TransientSolution' and not md.transient.ismasstransport):
+        if 'MasstransportAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.ismasstransport:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'singletimeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.upperwater_melting_rate', '>=', 0, 'singletimeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'singletimeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<=', 0, 'singletimeseries', 1)
-
         if 'BalancethicknessAnalysis' in analyses:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'singletimeseries', 1)
@@ -84,8 +93,7 @@
             md = checkfield(md, 'fieldname', 'basalforcings.upperwater_melting_rate', '>=', 0, 'singletimeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'singletimeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<=', 0, 'singletimeseries', 1)
-
-        if 'ThermalAnalysis' in analyses and not (solution == 'TransientSolution' and not md.transient.isthermal):
+        if 'ThermalAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isthermal:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'singletimeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.upperwater_melting_rate', '>=', 0, 'singletimeseries', 1)
@@ -94,8 +102,9 @@
             md = checkfield(md, 'fieldname', 'basalforcings.geothermalflux', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0)
 
         return md
-    # }}}
-    def marshall(self, prefix, md, fid):  # {{{
+    #}}}
+
+    def marshall(self, prefix, md, fid): #{{{
         yts = md.constants.yts
 
         WriteData(fid, prefix, 'name', 'md.basalforcings.model', 'data', 2, 'format', 'Integer')
@@ -106,4 +115,4 @@
         WriteData(fid, prefix, 'object', self, 'fieldname', 'deepwater_elevation', 'format', 'DoubleMat', 'mattype', 3, 'name', 'md.basalforcings.deepwater_elevation', 'yts', yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_melting_rate', 'format', 'DoubleMat', 'mattype', 3, 'timeserieslength', 2, 'name', 'md.basalforcings.upperwater_melting_rate', 'scale', 1. / yts, 'yts', yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_elevation', 'format', 'DoubleMat', 'mattype', 3, 'name', 'md.basalforcings.upperwater_elevation', 'yts', yts)
-    # }}}
+    #}}}
Index: ../trunk-jpl/src/m/classes/solidearthsettings.py
===================================================================
--- ../trunk-jpl/src/m/classes/solidearthsettings.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/solidearthsettings.py	(revision 25688)
@@ -6,12 +6,11 @@
 
 
 class solidearthsettings(object):
-    '''
-    SOLIDEARTHSETTINGS class definition
+    """SOLIDEARTHSETTINGS class definition
 
-        Usage:
-            solidearthsettings = solidearthsettings()
-    '''
+    Usage:
+        solidearthsettings = solidearthsettings()
+    """
 
     def __init__(self, *args): #{{{
         nargin = len(args)
@@ -33,19 +32,18 @@
         s += '{}\n'.format(fielddisplay(self, 'rigid', 'rigid earth graviational potential perturbation'))
         s += '{}\n'.format(fielddisplay(self, 'elastic', 'elastic earth graviational potential perturbation'))
         s += '{}\n'.format(fielddisplay(self, 'degacc', 'accuracy (default .01 deg) for numerical discretization of the Green\'s functions'))
-
         return s
     #}}}
 
     def setdefaultparameters(self): # {{{
-        #Convergence criterion: absolute, relative, and residual
+        # Convergence criterion: absolute, relative, and residual
         self.reltol = 0.01 # 1 percent
         self.abstol = np.nan # default
 
-        #maximum of non-linear iterations
+        # Maximum of non-linear iterations
         self.maxiter = 5
 
-        #computational flags
+        # Computational flags
         self.rigid = 1
         self.elastic = 1
         self.rotation = 1
@@ -52,20 +50,20 @@
         self.ocean_area_scaling = 0
         self.computesealevelchange = 0
 
-        #numerical discetization accuracy
+        # Numerical discretization accuracy
         self.degacc = .01
 
-        #how many time steps we skip before we run solidearthsettings solver during transient
+        # How many time steps we skip before we run solidearthsettings solver during transient
         self.runfrequency = 1
 
-        #horizontal displacemnet? (not by default)
+        # Horizontal displacement? (not on by default)
         self.horiz = 0
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): # {{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslr):
             return md
-
         md = checkfield(md, 'fieldname', 'solidearth.settings.reltol', 'size', [1])
         md = checkfield(md, 'fieldname', 'solidearth.settings.abstol', 'size', [1])
         md = checkfield(md, 'fieldname', 'solidearth.settings.maxiter', 'size', [1], '>=', 1)
@@ -73,18 +71,17 @@
         md = checkfield(md, 'fieldname', 'solidearth.settings.degacc', 'size', [1], '>=', 1e-10)
         md = checkfield(md, 'fieldname', 'solidearth.settings.horiz', 'NaN', 1, 'Inf', 1, 'values', [0, 1])
 
-        #a coupler to planet model is provided
+        # A coupler to planet model is provided
         if self.computesealevelchange:
             if md.transient.iscoupler:
-                #we are good
+                # We are good
                 pass
             else:
                 if md.mesh.__class__.__name__ == 'mesh3dsurface':
-                    #we are good
+                    # We are good
                     pass
                 else:
                     raise Exception('model is requesting sealevel computations without being a mesh3dsurface, or being coupled to one!')
-
         return md
     #}}}
 
Index: ../trunk-jpl/src/m/classes/sealevelmodel.py
===================================================================
--- ../trunk-jpl/src/m/classes/sealevelmodel.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/sealevelmodel.py	(revision 25688)
@@ -1,6 +1,8 @@
 from copy import deepcopy
 import warnings
+
 import numpy as np
+
 from fielddisplay import fielddisplay
 from generic import generic
 from getsubattr import getsubattr
@@ -46,11 +48,9 @@
         self.eltransitions = []
         self.planet = ''
 
-        # Create a default object
         self.setdefaultparameters()
 
         if len(args):
-            # Use provided options to set fields
             options = pairoptions(*args)
 
             # Recover all the icecap models
@@ -89,27 +89,27 @@
     def checkconsistency(slm, solutiontype):  # {{{
         # Is the coupler turned on?
         for i in range(len(slm.icecaps)):
-            if slm.icecaps[i].transient.iscoupler == 0:
+            if not slm.icecaps[i].transient.iscoupler:
                 warnings.warn('sealevelmodel checkconsistency error: icecap model {} should have the transient coupler option turned on!'.format(slm.icecaps[i].miscellaneous.name))
 
-        if slm.earth.transient.iscoupler == 0:
+        if not slm.earth.transient.iscoupler:
             warnings.warn('sealevelmodel checkconsistency error: earth model should have the transient coupler option turned on!')
 
         # Check that the transition vectors have the right size
         for i in range(len(slm.icecaps)):
             if slm.icecaps[i].mesh.numberofvertices != len(slm.earth.slr.transitions[i]):
-                raise RuntimeError('sealevelmodel checkconsistency issue with size of transition vector for ice cap: {} name: {}'.format(i, slm.icecaps[i].miscellaneous.name))
+                raise Exception('sealevelmodel checkconsistency issue with size of transition vector for ice cap: {} name: {}'.format(i, slm.icecaps[i].miscellaneous.name))
 
         # Check that run frequency is the same everywhere
         for i in range(len(slm.icecaps)):
             if slm.icecaps[i].slr.geodetic_run_frequency != slm.earth.geodetic_run_frequency:
-                raise RuntimeError('sealevelmodel checkconsistency error: icecap model {} should have the same run frequency as earth!'.format(slm.icecaps[i].miscellaneous.name))
+                raise Exception('sealevelmodel checkconsistency error: icecap model {} should have the same run frequency as earth!'.format(slm.icecaps[i].miscellaneous.name))
 
         # Make sure steric_rate is the same everywhere
         for i in range(len(slm.icecaps)):
             md = slm.icecaps[i]
             if np.nonzero(md.slr.steric_rate - slm.earth.slr.steric_rate[slm.earth.slr.transitions[i]]) != []:
-                raise RuntimeError('steric rate on ice cap {} is not the same as for the earth'.format(md.miscellaneous.name))
+                raise Exception('steric rate on ice cap {} is not the same as for the earth'.format(md.miscellaneous.name))
     #}}}
 
     def mergeresults(self):  # {{{
@@ -167,7 +167,7 @@
 
     def addbasin(self, bas):  # {{{
         if bas.__class__.__name__ != 'basin':
-            raise RuntimeError('addbasin method only takes a \'basin\' class object as input')
+            raise Exception('addbasin method only takes a \'basin\' class object as input')
         self.basins.append(bas)
     #}}}
 
@@ -386,7 +386,7 @@
     def viscousiterations(self):  #{{{
         for i in range(len(self.icecaps)):
             ic = self.icecaps[i]
-            mvi = ic.resutls.TransientSolution[0].StressbalanceConvergenceNumSteps
+            mvi = ic.results.TransientSolution[0].StressbalanceConvergenceNumSteps
             for j in range(1, len(ic.results.TransientSolution) - 1):
                 mvi = np.max(mvi, ic.results.TransientSolution[j].StressbalanceConvergenceNumSteps)
             print("{}, {}: {}".format(i, self.icecaps[i].miscellaneous.name, mvi))
@@ -464,7 +464,7 @@
         ic = self.earth
 
         if not noearth:
-            ic.results.TransientSolution = ic.resutls.TransientSolution[:mintimestep]
+            ic.results.TransientSolution = ic.results.TransientSolution[:mintimestep]
 
         self.earth = ic
 
Index: ../trunk-jpl/src/m/classes/surfaceload.py
===================================================================
--- ../trunk-jpl/src/m/classes/surfaceload.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/surfaceload.py	(revision 25688)
@@ -30,27 +30,22 @@
         s += '{}\n'.format(fielddisplay(self, 'icethicknesschange', 'thickness change: ice height equivalent [mIce/yr]'))
         s += '{}\n'.format(fielddisplay(self, 'waterheightchange', 'water height change: water height equivalent [mWater/yr]'))
         s += '{}\n'.format(fielddisplay(self, 'other', 'other loads (sediments) [kg/m^2/yr]'))
-
         return s
     #}}}
 
     def setdefaultparameters(self): # {{{
-        return
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): # {{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslr):
             return md
-
         if len(self.icethicknesschange):
             md  = checkfield(md,'fieldname', 'solidearth.surfaceload.icethicknesschange', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
-
         if len(self.waterheightchange):
             md  = checkfield(md,'fieldname', 'solidearth.surfaceload.waterheightchange', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
-
         if len(self.other):
             md  = checkfield(md,'fieldname', 'solidearth.surfaceload.other', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
-
         return md
     #}}}
 
@@ -57,13 +52,10 @@
     def marshall(self, prefix, md, fid): #{{{
         if len(self.icethicknesschange) == 0:
             self.icethicknesschange = np.zeros((md.mesh.numberofelements + 1, ))
-
         if len(self.waterheightchange) == 0:
             self.waterheightchange = np.zeros((md.mesh.numberofelements + 1, ))
-
         if len(self.other) == 0:
             self.other = np.zeros((md.mesh.numberofelements + 1, ))
-
         WriteData(fid, prefix, 'object', self, 'fieldname', 'icethicknesschange', 'name', 'md.solidearth.surfaceload.icethicknesschange', 'format', 'DoubleMat', 'mattype', 2, 'timeserieslength', md.mesh.numberofelements + 1, 'yts', md.constants.yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'waterheightchange', 'name', 'md.solidearth.surfaceload.waterheightchange', 'format', 'DoubleMat', 'mattype', 2, 'timeserieslength', md.mesh.numberofelements + 1, 'yts', md.constants.yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'other', 'name', 'md.solidearth.surfaceload.other', 'format', 'DoubleMat', 'mattype', 2, 'timeserieslength', md.mesh.numberofelements + 1, 'yts', md.constants.yts)
Index: ../trunk-jpl/src/m/classes/lovenumbers.py
===================================================================
--- ../trunk-jpl/src/m/classes/lovenumbers.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/lovenumbers.py	(revision 25688)
@@ -8,25 +8,24 @@
 
 
 class lovenumbers(object): #{{{
-    '''
-    LOVENUMBERS numbers class definition
+    """LOVENUMBERS class definition
 
-        Usage:
-            lovenumbers = lovenumbers() #will setup love numbers deg 1001 by default
-            lovenumbers = lovenumbers('maxdeg', 10001);  #supply numbers of degrees required (here, 10001)
-    '''
+    Usage:
+        lovenumbers = lovenumbers() #will setup love numbers deg 1001 by default
+        lovenumbers = lovenumbers('maxdeg', 10001);  #supply numbers of degrees required (here, 10001)
+    """
 
     def __init__(self, *args): #{{{
-        #regular love numbers:
-        self.h = []  #provided by PREM model
-        self.k = []  #idem
-        self.l = []  #idem
+        # Regular love numbers
+        self.h = []  # Provided by PREM model
+        self.k = []  # idem
+        self.l = []  # idem
 
-        #tidal love numbers for computing rotational feedback:
+        # Tidal love numbers for computing rotational feedback
         self.th = []
         self.tk = []
         self.tl = []
-        self.tk2secular = 0 #deg 2 secular number.
+        self.tk2secular = 0 # deg 2 secular number
 
         options = pairoptions(*args)
         maxdeg = options.getfieldvalue('maxdeg', 1000)
@@ -35,7 +34,7 @@
     #}}}
 
     def setdefaultparameters(self, maxdeg, referenceframe): #{{{
-        #initialize love numbers:
+        # Initialize love numbers
         self.h = getlovenumbers('type', 'loadingverticaldisplacement', 'referenceframe', referenceframe, 'maxdeg', maxdeg)
         self.k = getlovenumbers('type', 'loadinggravitationalpotential', 'referenceframe', referenceframe, 'maxdeg', maxdeg)
         self.l = getlovenumbers('type', 'loadinghorizontaldisplacement', 'referenceframe', referenceframe, 'maxdeg', maxdeg)
@@ -43,14 +42,14 @@
         self.tk = getlovenumbers('type', 'tidalgravitationalpotential', 'referenceframe', referenceframe, 'maxdeg', maxdeg)
         self.tl = getlovenumbers('type', 'tidalhorizontaldisplacement', 'referenceframe', referenceframe, 'maxdeg', maxdeg)
 
-        #secular fluid love number:
+        # Secular fluid love number
         self.tk2secular = 0.942
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): #{{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslr):
             return
-
         md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.h', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.k', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.l', 'NaN', 1, 'Inf', 1)
@@ -58,10 +57,10 @@
         md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.th', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.tk', 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'solidearth.lovenumbers.tk2secular', 'NaN', 1, 'Inf', 1)
-
-        #check that love numbers are provided at the same level of accuracy:
+        # Check that love numbers are provided at the same level of accuracy
         if (self.h.shape[0] != self.k.shape[0]) or (self.h.shape[0] != self.l.shape[0]):
             raise ValueError('lovenumbers error message: love numbers should be provided at the same level of accuracy')
+        return md
     #}}}
 
     def defaultoutputs(self, md): #{{{
@@ -69,8 +68,7 @@
     #}}}
 
     def __repr__(self): #{{{
-        s = '   lovenumbers parameters:'
-
+        s = '   lovenumbers parameters:\n'
         s += '{}\n'.format(fielddisplay(self, 'h', 'load Love number for radial displacement'))
         s += '{}\n'.format(fielddisplay(self, 'k', 'load Love number for gravitational potential perturbation'))
         s += '{}\n'.format(fielddisplay(self, 'l', 'load Love number for horizontal displacements'))
@@ -77,7 +75,6 @@
         s += '{}\n'.format(fielddisplay(self, 'th', 'tidal load Love number (deg 2)'))
         s += '{}\n'.format(fielddisplay(self, 'tk', 'tidal load Love number (deg 2)'))
         s += '{}\n'.format(fielddisplay(self, 'tk2secular', 'secular fluid Love number'))
-
         return s
     #}}}
 
Index: ../trunk-jpl/src/m/classes/frictionpism.py
===================================================================
--- ../trunk-jpl/src/m/classes/frictionpism.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/frictionpism.py	(revision 25688)
@@ -1,17 +1,18 @@
 import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
 from project3d import project3d
-from checkfield import checkfield
 from WriteData import WriteData
 
 
 class frictionpism(object):
-    """
-    frictionpism class definition
+    """FRICTIONPISM class definition
 
     Usage:
-      frictionpism = frictionpism()
+        frictionpism = frictionpism()
     """
+
     def __init__(self):
         self.pseudoplasticity_exponent = 0.
         self.threshold_speed = 0.
@@ -28,7 +29,7 @@
         self.till_friction_angle = project3d(md, 'vector', self.till_friction_angle, 'type', 'node', 'layer', 1)
         self.sediment_compressibility_coefficient = project3d(md, 'vector', self.sediment_compressibility_coefficient, 'type', 'node', 'layer', 1)
         return self
-        # }}}
+    # }}}
 
     def setdefaultparameters(self):  # {{{
         self.pseudoplasticity_exponent = 0.6
@@ -39,13 +40,11 @@
     # }}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-
-        #Early return
+        # Early return
         if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses:
             return md
-        if solution == 'TransientSolution' and md.transient.isstressbalance == 0 and md.transient.isthermal == 0:
+        if solution == 'TransientSolution' and not md.transient.isstressbalance and not md.transient.isthermal:
             return md
-
         md = checkfield(md, 'fieldname', 'friction.pseudoplasticity_exponent', 'numel', [1], '>', 0, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.threshold_speed', 'numel', [1], '>', 0, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.delta', 'numel', [1], '>', 0, '<', 1, 'NaN', 1, 'Inf', 1)
@@ -52,21 +51,21 @@
         md = checkfield(md, 'fieldname', 'friction.void_ratio', 'numel', [1], '>', 0, '<', 1, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.till_friction_angle', 'NaN', 1, 'Inf', 1, '<', 360., '>', 0., 'size', [md.mesh.numberofvertices])  #User should give angle in degrees, Matlab calculates in rad
         md = checkfield(md, 'fieldname', 'friction.sediment_compressibility_coefficient', 'NaN', 1, 'Inf', 1, '<', 1., '>', 0., 'size', [md.mesh.numberofvertices])
+        return md
     # }}}
 
     def __repr__(self):  # {{{
-        string = 'Basal shear stress parameters for the PISM friction law (See Aschwanden et al. 2016 for more details)'
-        string = "%s\n%s" % (string, fielddisplay(self, 'pseudoplasticity_exponent', 'pseudoplasticity exponent [dimensionless]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'threshold_speed', 'threshold speed [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'delta', 'lower limit of the effective pressure, expressed as a fraction of overburden pressure [dimensionless]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'void_ratio', 'void ratio at a reference effective pressure [dimensionless]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'till_friction_angle', 'till friction angle [deg], recommended default: 30 deg'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'sediment_compressibility_coefficient', 'coefficient of compressibility of the sediment [dimensionless], recommended default: 0.12'))
-        # }}}
+        s = 'Basal shear stress parameters for the PISM friction law (See Aschwanden et al. 2016 for more details)\n'
+        s += "{}\n".format(fielddisplay(self, 'pseudoplasticity_exponent', 'pseudoplasticity exponent [dimensionless]'))
+        s += "{}\n".format(fielddisplay(self, 'threshold_speed', 'threshold speed [m / yr]'))
+        s += "{}\n".format(fielddisplay(self, 'delta', 'lower limit of the effective pressure, expressed as a fraction of overburden pressure [dimensionless]'))
+        s += "{}\n".format(fielddisplay(self, 'void_ratio', 'void ratio at a reference effective pressure [dimensionless]'))
+        s += "{}\n".format(fielddisplay(self, 'till_friction_angle', 'till friction angle [deg], recommended default: 30 deg'))
+        s += "{}\n".format(fielddisplay(self, 'sediment_compressibility_coefficient', 'coefficient of compressibility of the sediment [dimensionless], recommended default: 0.12'))
+    # }}}
 
     def marshall(self, prefix, md, fid):  # {{{
         yts = md.constants.yts
-
         WriteData(fid, prefix, 'name', 'md.friction.law', 'data', 10, 'format', 'Integer')
         WriteData(fid, prefix, 'class', 'friction', 'object', self, 'fieldname', 'pseudoplasticity_exponent', 'format', 'Double')
         WriteData(fid, prefix, 'class', 'friction', 'object', self, 'fieldname', 'threshold_speed', 'format', 'Double', 'scale', 1. / yts)
@@ -74,4 +73,4 @@
         WriteData(fid, prefix, 'class', 'friction', 'object', self, 'fieldname', 'void_ratio', 'format', 'Double')
         WriteData(fid, prefix, 'class', 'friction', 'object', self, 'fieldname', 'till_friction_angle', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'class', 'friction', 'object', self, 'fieldname', 'sediment_compressibility_coefficient', 'format', 'DoubleMat', 'mattype', 1)
-        # }}}
+    # }}}
Index: ../trunk-jpl/src/m/classes/m1qn3inversion.py
===================================================================
--- ../trunk-jpl/src/m/classes/m1qn3inversion.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/m1qn3inversion.py	(revision 25688)
@@ -1,44 +1,42 @@
 import numpy as np
+
+from checkfield import checkfield
+from fielddisplay import fielddisplay
+from marshallcostfunctions import marshallcostfunctions
 from project3d import project3d
-from fielddisplay import fielddisplay
-from checkfield import checkfield
-from WriteData import WriteData
 from supportedcontrols import supportedcontrols
 from supportedcostfunctions import supportedcostfunctions
-from marshallcostfunctions import marshallcostfunctions
+from WriteData import WriteData
 
 
 class m1qn3inversion(object):
-    '''
-    M1QN3 class definition
+    """M1QN3 class definition
 
-   Usage:
-      m1qn3inversion = m1qn3inversion()
-    '''
+    Usage:
+        m1qn3inversion = m1qn3inversion()
+    """
 
     def __init__(self, *args):  # {{{
-
         if not len(args):
             print('empty init')
             self.iscontrol = 0
             self.incomplete_adjoint = 0
-            self.control_parameters = float('NaN')
-            self.control_scaling_factors = float('NaN')
+            self.control_parameters = np.nan
+            self.control_scaling_factors = np.nan
             self.maxsteps = 0
             self.maxiter = 0
             self.dxmin = 0.
             self.gttol = 0.
-            self.cost_functions = float('NaN')
-            self.cost_functions_coefficients = float('NaN')
-            self.min_parameters = float('NaN')
-            self.max_parameters = float('NaN')
-            self.vx_obs = float('NaN')
-            self.vy_obs = float('NaN')
-            self.vz_obs = float('NaN')
-            self.vel_obs = float('NaN')
-            self.thickness_obs = float('NaN')
+            self.cost_functions = np.nan
+            self.cost_functions_coefficients = np.nan
+            self.min_parameters = np.nan
+            self.max_parameters = np.nan
+            self.vx_obs = np.nan
+            self.vy_obs = np.nan
+            self.vz_obs = np.nan
+            self.vel_obs = np.nan
+            self.thickness_obs = np.nan
 
-            #set defaults
             self.setdefaultparameters()
         elif len(args) == 1 and args[0].__module__ == 'inversion':
             print('converting inversion to m1qn3inversion')
@@ -65,50 +63,36 @@
     #}}}
 
     def __repr__(self):  # {{{
-        string = '   m1qn3inversion parameters:'
-        string = "%s\n%s" % (string, fielddisplay(self, 'iscontrol', 'is inversion activated?'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'control_parameters', 'ex: [''FrictionCoefficient''], or [''MaterialsRheologyBbar'']'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'control_scaling_factors', 'order of magnitude of each control (useful for multi - parameter optimization)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'maxsteps', 'maximum number of iterations (gradient computation)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'maxiter', 'maximum number of Function evaluation (forward run)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'dxmin', 'convergence criterion: two points less than dxmin from eachother (sup - norm) are considered identical'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'gttol', '||g(X)||/||g(X0)|| (g(X0): gradient at initial guess X0)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'cost_functions', 'indicate the type of response for each optimization step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vx_obs', 'observed velocity x component [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vy_obs', 'observed velocity y component [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vel_obs', 'observed velocity magnitude [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'thickness_obs', 'observed thickness [m]'))
-        string = "%s\n%s" % (string, 'Available cost functions:')
-        string = "%s\n%s" % (string, '   101: SurfaceAbsVelMisfit')
-        string = "%s\n%s" % (string, '   102: SurfaceRelVelMisfit')
-        string = "%s\n%s" % (string, '   103: SurfaceLogVelMisfit')
-        string = "%s\n%s" % (string, '   104: SurfaceLogVxVyMisfit')
-        string = "%s\n%s" % (string, '   105: SurfaceAverageVelMisfit')
-        string = "%s\n%s" % (string, '   201: ThicknessAbsMisfit')
-        string = "%s\n%s" % (string, '   501: DragCoefficientAbsGradient')
-        string = "%s\n%s" % (string, '   502: RheologyBbarAbsGradient')
-        string = "%s\n%s" % (string, '   503: ThicknessAbsGradient')
-        return string
+        s = '   m1qn3inversion parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'iscontrol', 'is inversion activated?'))
+        s += '{}\n'.format(fielddisplay(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity'))
+        s += '{}\n'.format(fielddisplay(self, 'control_parameters', 'ex: [''FrictionCoefficient''], or [''MaterialsRheologyBbar'']'))
+        s += '{}\n'.format(fielddisplay(self, 'control_scaling_factors', 'order of magnitude of each control (useful for multi - parameter optimization)'))
+        s += '{}\n'.format(fielddisplay(self, 'maxsteps', 'maximum number of iterations (gradient computation)'))
+        s += '{}\n'.format(fielddisplay(self, 'maxiter', 'maximum number of Function evaluation (forward run)'))
+        s += '{}\n'.format(fielddisplay(self, 'dxmin', 'convergence criterion: two points less than dxmin from eachother (sup - norm) are considered identical'))
+        s += '{}\n'.format(fielddisplay(self, 'gttol', '||g(X)||/||g(X0)|| (g(X0): gradient at initial guess X0)'))
+        s += '{}\n'.format(fielddisplay(self, 'cost_functions', 'indicate the type of response for each optimization step'))
+        s += '{}\n'.format(fielddisplay(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'))
+        s += '{}\n'.format(fielddisplay(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex'))
+        s += '{}\n'.format(fielddisplay(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex'))
+        s += '{}\n'.format(fielddisplay(self, 'vx_obs', 'observed velocity x component [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vy_obs', 'observed velocity y component [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vel_obs', 'observed velocity magnitude [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'thickness_obs', 'observed thickness [m]'))
+        s += '{}\n'.format('Available cost functions:')
+        s += '{}\n'.format('   101: SurfaceAbsVelMisfit')
+        s += '{}\n'.format('   102: SurfaceRelVelMisfit')
+        s += '{}\n'.format('   103: SurfaceLogVelMisfit')
+        s += '{}\n'.format('   104: SurfaceLogVxVyMisfit')
+        s += '{}\n'.format('   105: SurfaceAverageVelMisfit')
+        s += '{}\n'.format('   201: ThicknessAbsMisfit')
+        s += '{}\n'.format('   501: DragCoefficientAbsGradient')
+        s += '{}\n'.format('   502: RheologyBbarAbsGradient')
+        s += '{}\n'.format('   503: ThicknessAbsGradient')
+        return s
     #}}}
 
-    def extrude(self, md):  # {{{
-        self.vx_obs = project3d(md, 'vector', self.vx_obs, 'type', 'node')
-        self.vy_obs = project3d(md, 'vector', self.vy_obs, 'type', 'node')
-        self.vel_obs = project3d(md, 'vector', self.vel_obs, 'type', 'node')
-        self.thickness_obs = project3d(md, 'vector', self.thickness_obs, 'type', 'node')
-        if not np.any(np.isnan(self.cost_functions_coefficients)):
-            self.cost_functions_coefficients = project3d(md, 'vector', self.cost_functions_coefficients, 'type', 'node')
-        if not np.any(np.isnan(self.min_parameters)):
-            self.min_parameters = project3d(md, 'vector', self.min_parameters, 'type', 'node')
-        if not np.any(np.isnan(self.max_parameters)):
-            self.max_parameters = project3d(md, 'vector', self.max_parameters, 'type', 'node')
-        return self
-    #}}}
-
     def setdefaultparameters(self):  # {{{
         #default is incomplete adjoint for now
         self.incomplete_adjoint = 1
@@ -129,8 +113,22 @@
         return self
     #}}}
 
+    def extrude(self, md):  # {{{
+        self.vx_obs = project3d(md, 'vector', self.vx_obs, 'type', 'node')
+        self.vy_obs = project3d(md, 'vector', self.vy_obs, 'type', 'node')
+        self.vel_obs = project3d(md, 'vector', self.vel_obs, 'type', 'node')
+        self.thickness_obs = project3d(md, 'vector', self.thickness_obs, 'type', 'node')
+        if not np.any(np.isnan(self.cost_functions_coefficients)):
+            self.cost_functions_coefficients = project3d(md, 'vector', self.cost_functions_coefficients, 'type', 'node')
+        if not np.any(np.isnan(self.min_parameters)):
+            self.min_parameters = project3d(md, 'vector', self.min_parameters, 'type', 'node')
+        if not np.any(np.isnan(self.max_parameters)):
+            self.max_parameters = project3d(md, 'vector', self.max_parameters, 'type', 'node')
+        return self
+    #}}}
+
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if not self.iscontrol:
             return md
 
@@ -152,10 +150,11 @@
 
         if solution == 'BalancethicknessSolution':
             md = checkfield(md, 'fieldname', 'inversion.thickness_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
+        elif solution == 'BalancethicknessSoftSolution':
+            md = checkfield(md, 'fieldname', 'inversion.thickness_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
         else:
             md = checkfield(md, 'fieldname', 'inversion.vx_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
             md = checkfield(md, 'fieldname', 'inversion.vy_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
-
         return md
     # }}}
 
@@ -179,12 +178,12 @@
         WriteData(fid, prefix, 'object', self, 'class', 'inversion', 'fieldname', 'vz_obs', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts)
         WriteData(fid, prefix, 'object', self, 'class', 'inversion', 'fieldname', 'thickness_obs', 'format', 'DoubleMat', 'mattype', 1)
 
-    #process control parameters
+        # Process control parameters
         num_control_parameters = len(self.control_parameters)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'control_parameters', 'format', 'StringArray')
         WriteData(fid, prefix, 'data', num_control_parameters, 'name', 'md.inversion.num_control_parameters', 'format', 'Integer')
 
-    #process cost functions
+        # Process cost functions
         num_cost_functions = np.size(self.cost_functions)
         data = marshallcostfunctions(self.cost_functions)
         WriteData(fid, prefix, 'data', data, 'name', 'md.inversion.cost_functions', 'format', 'StringArray')
Index: ../trunk-jpl/src/m/classes/inversion.m
===================================================================
--- ../trunk-jpl/src/m/classes/inversion.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/inversion.m	(revision 25688)
@@ -107,7 +107,6 @@
 					md = checkmessage(md,['inversion can only be performed for SSA, HO or FS ice flow models']);
 				end
 			end
-
 			if strcmp(solution,'BalancethicknessSolution')
 				md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1);
 			elseif strcmp(solution,'BalancethicknessSoftSolution')
Index: ../trunk-jpl/src/m/classes/qmustatistics.m
===================================================================
--- ../trunk-jpl/src/m/classes/qmustatistics.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/qmustatistics.m	(revision 25688)
@@ -116,7 +116,7 @@
 				WriteData(fid,prefix,'name','md.qmu.statistics.numstatistics','data',length(self.method),'format','Integer');
 				for i=1:length(self.method),
 					m=self.method(i); 
-					WriteData(fid,prefix,'name',sprintf('md.qmu.statistics.method(%i).name',i),'data',m.name,'Format','String');
+					WriteData(fid,prefix,'name',sprintf('md.qmu.statistics.method(%i).name',i),'data',m.name,'format','String');
 					WriteData(fid,prefix,'data',m.fields,'name',sprintf('md.qmu.statistics.method(%i).fields',i),'format','StringArray');
 					WriteData(fid,prefix,'data',m.steps,'name',sprintf('md.qmu.statistics.method(%i).steps',i),'format','IntMat','mattype',3);
 
Index: ../trunk-jpl/src/m/classes/sealevelmodel.m
===================================================================
--- ../trunk-jpl/src/m/classes/sealevelmodel.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/sealevelmodel.m	(revision 25688)
@@ -26,14 +26,12 @@
 	end
 	methods
 		function slm = sealevelmodel(varargin) % {{{
+			slm=setdefaultparameters(slm);
 
-			if nargin==0, 
-				slm=setdefaultparameters(slm);
-			else 
-				slm=setdefaultparameters(slm);
+			if nargin==1,
 
-				options=pairoptions(varargin{:}); 
-			
+				options=pairoptions(varargin{:});
+
 				%recover all the icecap models: 
 				slm.icecaps=getfieldvalues(options,'ice_cap',{}); 
 				
@@ -418,19 +416,19 @@
 			self.earth=md;
 
 		end % }}}
-function viscousiterations(self) % {{{
-	for  i=1:length(self.icecaps),
-		ic=self.icecaps{i}; 
-		mvi=ic.results.TransientSolution(1).StressbalanceConvergenceNumSteps;
-		for j=2:length(ic.results.TransientSolution)-1,
-			mvi=max(mvi,ic.results.TransientSolution(j).StressbalanceConvergenceNumSteps);
-		end
-		disp(sprintf('%i, %s: %i',i,self.icecaps{i}.miscellaneous.name,mvi));
-	end
-end % }}}
+		function viscousiterations(self) % {{{
+			for  i=1:length(self.icecaps),
+				ic=self.icecaps{i};
+				mvi=ic.results.TransientSolution(1).StressbalanceConvergenceNumSteps;
+				for j=2:length(ic.results.TransientSolution)-1,
+					mvi=max(mvi,ic.results.TransientSolution(j).StressbalanceConvergenceNumSteps);
+				end
+				disp(sprintf('%i, %s: %i',i,self.icecaps{i}.miscellaneous.name,mvi));
+			end
+		end % }}}
 		function maxtimestep(self) % {{{
 			for  i=1:length(self.icecaps),
-				ic=self.icecaps{i}; 
+				ic=self.icecaps{i};
 				mvi=length(ic.results.TransientSolution);
 				timei=ic.results.TransientSolution(end).time;
 				disp(sprintf('%i, %s: %i/%g',i,self.icecaps{i}.miscellaneous.name,mvi,timei));
Index: ../trunk-jpl/src/m/classes/giamme.py
===================================================================
--- ../trunk-jpl/src/m/classes/giamme.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/giamme.py	(revision 25688)
@@ -7,12 +7,11 @@
 
 
 class giamme(object):
-    '''
-    GIAMME class definition
+    """GIAMME class definition
 
-        Usage:
-            gia = giamme() #gia class based on a multi-model ensemble (ex: Caron et al 2017 statistics)
-    '''
+    Usage:
+        gia = giamme() #gia class based on a multi-model ensemble (ex: Caron et al 2017 statistics)
+    """
 
     def __init__(self, *args): #{{{
         self.modelid    = 0 #index into the multi-model ensemble
@@ -32,22 +31,21 @@
         s += '{}\n'.format(fielddisplay(self, 'modelid', 'index into the multi-model ensemble, determines which field will be used.'))
         s += '{}\n'.format(fielddisplay(self, 'Ngia', 'geoid (mm/yr).'))
         s += '{}\n'.format(fielddisplay(self, 'Ugia', 'uplift (mm/yr).'))
-
         return s
     #}}}
 
     def setdefaultparameters(self): # {{{
-        return
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): # {{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if 'SealevelriseAnalysis' not in analyses:
             return md
-
+        if solution == 'TransientSolution' and not md.transient.isslr:
+            return md
         md = checkfield(md, 'field', self.Ngia, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'field', self.Ugia, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'field', self.modelid, 'NaN', 1, 'Inf', 1, '>=', 0, '<=', len(self.Ngia))
-
         return md
     #}}}
 
@@ -70,6 +68,5 @@
         for i in range(len(self.Ngia)):
             self.Ngia[i] = project3d(md, 'vector', self.Ngia[i], 'type', 'node', 'layer', 1)
             self.Ugia[i] = project3d(md, 'vector', self.Ugia[i], 'type', 'node', 'layer', 1)
-
         return self
     #}}}
Index: ../trunk-jpl/src/m/classes/qmu.py
===================================================================
--- ../trunk-jpl/src/m/classes/qmu.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/qmu.py	(revision 25688)
@@ -11,11 +11,10 @@
 
 
 class qmu(object):
-    """
-    QMU class definition
+    """QMU class definition
 
-       Usage:
-          qmu = qmu()
+    Usage:
+        qmu = qmu()
     """
 
     def __init__(self):  # {{{
@@ -43,17 +42,14 @@
         self.adjacency = float('NaN')
         self.vertex_weight = float('NaN')
 
-    #set defaults
         self.setdefaultparameters()
-
     #}}}
     def __repr__(self):  # {{{
         s = '   qmu parameters:\n'
-
-        s += "%s\n" % fielddisplay(self, 'isdakota', 'is qmu analysis activated?')
-        s += "%s\n" % fielddisplay(self, 'output', 'are we outputting ISSM results, default is 0')
+        s += '{}\n'.format(fielddisplay(self, 'isdakota', 'is QMU analysis activated?'))
+        s += '{}\n'.format(fielddisplay(self, 'output', 'are we outputting ISSM results, default is 0'))
         maxlen = 0
-        s += "         variables:  (arrays of each variable class)\n"
+        s += '         variables:  (arrays of each variable class)\n'
 
     # OrderedStruct's iterator returns individual name / array - of - functions pairs
         for variable in self.variables:
@@ -73,7 +69,7 @@
             b = 1 if len(size) < 2 else size[1]
             s += "            %-*s:    [%ix%i]    '%s'\n" % (maxlen + 1, fname, a, b, type(response[1][0]))
 
-        s += "%s\n" % fielddisplay(self, 'numberofresponses', 'number of responses')
+        s += '{}\n'.format(fielddisplay(self, 'numberofresponses', 'number of responses'))
 
         if type(self.method) != OrderedDict:
             self.method = [self.method]
@@ -90,7 +86,7 @@
         for param in params:
             print(type(param))
             print(param)
-            s += "         params:  (array of method - independent parameters)\n"
+            s += "         params:  (array of method-independent parameters)\n"
             fnames = vars(param)
             maxlen = 0
             for fname in fnames:
@@ -115,18 +111,17 @@
                 size = np.shape(getattr(result, fname))
                 s += "            %-*s:    [%ix%i]    '%s'\n" % (maxlen + 1, fname, a, b, type(getattr(result, fname)))
 
-        s += "%s\n" % fielddisplay(self, 'variablepartitions', '')
-        s += "%s\n" % fielddisplay(self, 'variablepartitions_npart', '')
-        s += "%s\n" % fielddisplay(self, 'variablepartitions_nt', '')
-        s += "%s\n" % fielddisplay(self, 'variabledescriptors', '')
-        s += "%s\n" % fielddisplay(self, 'responsedescriptors', '')
-        s += "%s\n" % fielddisplay(self, 'method', 'array of dakota_method class')
-        s += "%s\n" % fielddisplay(self, 'mass_flux_profile_directory', 'directory for mass flux profiles')
-        s += "%s\n" % fielddisplay(self, 'mass_flux_profiles', 'list of mass_flux profiles')
-        s += "%s\n" % fielddisplay(self, 'mass_flux_segments', '')
-        s += "%s\n" % fielddisplay(self, 'adjacency', '')
-        s += "%s\n" % fielddisplay(self, 'vertex_weight', 'weight applied to each mesh vertex')
-
+        s += '{}\n'.format(fielddisplay(self, 'variablepartitions', ''))
+        s += '{}\n'.format(fielddisplay(self, 'variablepartitions_npart', ''))
+        s += '{}\n'.format(fielddisplay(self, 'variablepartitions_nt', ''))
+        s += '{}\n'.format(fielddisplay(self, 'variabledescriptors', ''))
+        s += '{}\n'.format(fielddisplay(self, 'responsedescriptors', ''))
+        s += '{}\n'.format(fielddisplay(self, 'method', 'array of dakota_method class'))
+        s += '{}\n'.format(fielddisplay(self, 'mass_flux_profile_directory', 'directory for mass flux profiles'))
+        s += '{}\n'.format(fielddisplay(self, 'mass_flux_profiles', 'list of mass_flux profiles'))
+        s += '{}\n'.format(fielddisplay(self, 'mass_flux_segments', ''))
+        s += '{}\n'.format(fielddisplay(self, 'adjacency', ''))
+        s += '{}\n'.format(fielddisplay(self, 'vertex_weight', 'weight applied to each mesh vertex'))
         return s
     # }}}
 
Index: ../trunk-jpl/src/m/classes/slr.m
===================================================================
--- ../trunk-jpl/src/m/classes/slr.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/slr.m	(revision 25688)
@@ -135,7 +135,7 @@
 			%	warning('slr checkconsistency fail: there are elements with ice loads where some vertices are not on the ice!');
 			%end
 
-			%check that  if geodetic is requested, we are a mesh3dsurface model (planet), or if we are not, 
+			%check that if geodetic is requested, we are a mesh3dsurface model (planet), or if we are not, 
 			%a coupler to a planet model is provided. 
 			if self.geodetic,
 				if md.transient.iscoupler, 
Index: ../trunk-jpl/src/m/classes/friction.py
===================================================================
--- ../trunk-jpl/src/m/classes/friction.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/friction.py	(revision 25688)
@@ -20,26 +20,23 @@
         self.coupling = 0
         self.effective_pressure = np.nan
         self.effective_pressure_limit = 0
-
-        #set defaults
         self.setdefaultparameters()
     #}}}
 
     def __repr__(self):  # {{{
-        s = "Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s - 1) * u_b, \n(effective stress Neff = rho_ice * g * thickness + rho_water * g * base, r = q / p and s = 1 / p)\n"
-        s = "{}\n".format(fielddisplay(self, "coefficient", "friction coefficient [SI]"))
-        s = "{}\n".format(fielddisplay(self, "p", "p exponent"))
-        s = "{}\n".format(fielddisplay(self, "q", "q exponent"))
-        s = "{}\n".format(fielddisplay(self, 'coupling', 'Coupling flag 0: uniform sheet (negative pressure ok, default), 1: ice pressure only, 2: water pressure assuming uniform sheet (no negative pressure), 3: use provided effective_pressure, 4: used coupled model (not implemented yet)'))
-        s = "{}\n".format(fielddisplay(self, 'effective_pressure', 'Effective Pressure for the forcing if not coupled [Pa]'))
-        s = "{}\n".format(fielddisplay(self, 'effective_pressure_limit', 'Neff do not allow to fall below a certain limit: effective_pressure_limit * rho_ice * g * thickness (default 0)'))
-        
+        s = 'Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s - 1) * u_b,\n'
+        s += '(effective stress Neff = rho_ice * g * thickness + rho_water * g * base, r = q / p and s = 1 / p)\n'
+        s += '{}\n'.format(fielddisplay(self, "coefficient", "friction coefficient [SI]"))
+        s += '{}\n'.format(fielddisplay(self, "p", "p exponent"))
+        s += '{}\n'.format(fielddisplay(self, "q", "q exponent"))
+        s += '{}\n'.format(fielddisplay(self, 'coupling', 'Coupling flag 0: uniform sheet (negative pressure ok, default), 1: ice pressure only, 2: water pressure assuming uniform sheet (no negative pressure), 3: use provided effective_pressure, 4: used coupled model (not implemented yet)'))
+        s += '{}\n'.format(fielddisplay(self, 'effective_pressure', 'Effective Pressure for the forcing if not coupled [Pa]'))
+        s += '{}\n'.format(fielddisplay(self, 'effective_pressure_limit', 'Neff do not allow to fall below a certain limit: effective_pressure_limit * rho_ice * g * thickness (default 0)'))
         return s
     #}}}
 
     def setdefaultparameters(self):  # {{{
         self.effective_pressure_limit = 0
-
         return self
     #}}}
 
@@ -47,7 +44,7 @@
         self.coefficient = project3d(md, 'vector', self.coefficient, 'type', 'node', 'layer', 1)
         self.p = project3d(md, 'vector', self.p, 'type', 'element')
         self.q = project3d(md, 'vector', self.q, 'type', 'element')
-    #if self.coupling == 0:  #doesnt work with empty loop, so just skip it?
+        # If self.coupling == 0:  #doesnt work with empty loop, so just skip it?
         if self.coupling in[3, 4]:
             self.effective_pressure = project3d(md, 'vector', self.effective_pressure, 'type', 'node', 'layer', 1)
         elif self.coupling > 4:
@@ -61,12 +58,11 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses:
             return md
-        if solution == 'TransientSoluition' and not md.transient.isstressbalance and not md.transient.isthermal:
+        if solution == 'TransientSolution' and not md.transient.isstressbalance and not md.transient.isthermal:
             return md
-
         md = checkfield(md, 'fieldname', 'friction.coefficient', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.q', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofelements])
         md = checkfield(md, 'fieldname', 'friction.p', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofelements])
@@ -76,13 +72,11 @@
             md = checkfield(md, 'fieldname', 'friction.effective_pressure', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
         elif self.coupling > 4:
             raise ValueError('not supported yet')
-
         return md
     # }}}
 
     def marshall(self, prefix, md, fid):  # {{{
         WriteData(fid, prefix, 'name', 'md.friction.law', 'data', 1, 'format', 'Integer')
-
         if type(self.coefficient) in [np.ndarray] and (self.coefficient.shape[0] == md.mesh.numberofvertices or self.coefficient.shape[0] == (md.mesh.numberofvertices + 1)):
             mattype = 1
             tsl = md.mesh.numberofvertices
@@ -89,7 +83,6 @@
         else:
             mattype = 2
             tsl = md.mesh.numberofelements
-
         WriteData(fid, prefix, 'object', self, 'fieldname', 'coefficient', 'format', 'DoubleMat', 'mattype', mattype, 'timeserieslength', tsl + 1, 'yts', md.constants.yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'p', 'format', 'DoubleMat', 'mattype', 2)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'q', 'format', 'DoubleMat', 'mattype', 2)
Index: ../trunk-jpl/src/m/classes/dslmme.py
===================================================================
--- ../trunk-jpl/src/m/classes/dslmme.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/dslmme.py	(revision 25688)
@@ -7,12 +7,11 @@
 
 
 class dslmme(object):
-    '''
-    DSLMME class definition
+    """DSLMME class definition
 
-        Usage:
-            dsl = dslmme() #dynamic sea level class based on a multi-model ensemble of CMIP5 outputs
-    '''
+    Usage:
+        dsl = dslmme() #dynamic sea level class based on a multi-model ensemble of CMIP5 outputs
+    """
 
     def __init__(self, *args): #{{{
         self.modelid                                        = 0 #index into the multi-model ensemble
@@ -36,30 +35,25 @@
         s += '{}\n'.format(fielddisplay(self, 'sea_surface_height_change_above_geoid', 'corresponds to zos fields in CMIP5 archives. Spatial average is 0. Specified as a spatio-temporally variable rate (mm/yr) for each ensemble.'))
         s += '{}\n'.format(fielddisplay(self, 'sea_water_pressure_change_at_sea_floor', 'corresponds to bpo fields in CMIP5 archives. Specified as a spatio-temporally variable rate (in mm/yr) for each ensemble.'))
         s += '{}\n'.format(fielddisplay(self, 'compute_fingerprints', 'do we use the sea water pressure change to compute fingerprints and correct sea_surface_height_change_above_geoid'))
-
         return s
     #}}}
 
-    def setdefaultparameters(self): # {{{
-        return
+    def setdefaultparameters(self): #{{{
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): # {{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslr):
             return md
-
         for i in range(len(self.global_average_thermosteric_sea_level_change)):
             md = checkfield(md, 'field', self.global_average_thermosteric_sea_level_change[i], 'NaN', 1, 'Inf', 1)
             md = checkfield(md, 'field', self.sea_surface_height_change_above_geoid[i], 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'field', self.sea_water_pressure_change_at_sea_floor[i], 'NaN', 1, 'Inf', 1, 'timeseries', 1)
-
         md = checkfield(md, 'field', self.modelid, 'NaN', 1, 'Inf', 1, '>=', 1, '<=',len(self.global_average_thermosteric_sea_level_change))
-        
         if self.compute_fingerprints:
             #check geodetic flag of slr is on
-            if md.solidearth.settings.computesealevelchange == 0,
+            if not md.solidearth.settings.computesealevelchange:
                 raise Exception('DSL checkconsistency error message: if bottom pressure fingerprints computations are requested, slr class should have geodetic flag on')
-
         return md
     #}}}
 
Index: ../trunk-jpl/src/m/classes/initialization.py
===================================================================
--- ../trunk-jpl/src/m/classes/initialization.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/initialization.py	(revision 25688)
@@ -1,13 +1,13 @@
 import numpy as np
+
+from checkfield import checkfield
+from fielddisplay import fielddisplay
 from project3d import project3d
-from fielddisplay import fielddisplay
-from checkfield import checkfield
 from WriteData import WriteData
 
 
 class initialization(object):
-    """
-    INITIALIZATION class definition
+    """INITIALIZATION class definition
 
     Usage:
     initialization = initialization()
@@ -14,45 +14,42 @@
     """
 
     def __init__(self):  # {{{
+        self.vx = np.nan
+        self.vy = np.nan
+        self.vz = np.nan
+        self.vel = np.nan
+        self.enthalpy = np.nan
+        self.pressure = np.nan
+        self.temperature = np.nan
+        self.waterfraction = np.nan
+        self.watercolumn = np.nan
+        self.sediment_head = np.nan
+        self.epl_head = np.nan
+        self.epl_thickness = np.nan
+        self.hydraulic_potential = np.nan
+        self.channelarea = np.nan
 
-        self.vx = float('NaN')
-        self.vy = float('NaN')
-        self.vz = float('NaN')
-        self.vel = float('NaN')
-        self.enthalpy = float('NaN')
-        self.pressure = float('NaN')
-        self.temperature = float('NaN')
-        self.waterfraction = float('NaN')
-        self.watercolumn = float('NaN')
-        self.sediment_head = float('NaN')
-        self.epl_head = float('NaN')
-        self.epl_thickness = float('NaN')
-        self.hydraulic_potential = float('NaN')
-        self.channelarea = float('NaN')
-
-    #set defaults
+        #set defaults
         self.setdefaultparameters()
-
     #}}}
 
     def __repr__(self):  # {{{
-        string = '   initial field values:'
-        string = "%s\n%s" % (string, fielddisplay(self, 'vx', 'x component of velocity [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vy', 'y component of velocity [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vz', 'z component of velocity [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vel', 'velocity norm [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'pressure', 'pressure [Pa]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'temperature', 'temperature [K]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'enthalpy', 'enthalpy [J]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'waterfraction', 'fraction of water in the ice'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'watercolumn', 'thickness of subglacial water [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'sediment_head', 'sediment water head of subglacial system [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'epl_head', 'epl water head of subglacial system [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'epl_thickness', 'thickness of the epl [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'hydraulic_potential', 'Hydraulic potential (for GlaDS) [Pa]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'channelarea', 'subglaciale water channel area (for GlaDS) [m2]'))
-
-        return string
+        s = '   initial field values:\n'
+        s += '{}\n'.format(fielddisplay(self, 'vx', 'x component of velocity [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vy', 'y component of velocity [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vz', 'z component of velocity [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vel', 'velocity norm [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'pressure', 'pressure [Pa]'))
+        s += '{}\n'.format(fielddisplay(self, 'temperature', 'temperature [K]'))
+        s += '{}\n'.format(fielddisplay(self, 'enthalpy', 'enthalpy [J]'))
+        s += '{}\n'.format(fielddisplay(self, 'waterfraction', 'fraction of water in the ice'))
+        s += '{}\n'.format(fielddisplay(self, 'watercolumn', 'thickness of subglacial water [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'sediment_head', 'sediment water head of subglacial system [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'epl_head', 'epl water head of subglacial system [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'epl_thickness', 'thickness of the epl [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'hydraulic_potential', 'Hydraulic potential (for GlaDS) [Pa]'))
+        s += '{}\n'.format(fielddisplay(self, 'channelarea', 'subglaciale water channel area (for GlaDS) [m2]'))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
@@ -69,11 +66,8 @@
         self.epl_thickness = project3d(md, 'vector', self.epl_thickness, 'type', 'node', 'layer', 1)
 
         #Lithostatic pressure by default
-        #        self.pressure = md.constants.g * md.materials.rho_ice * (md.geometry.surface[:, 0] - md.mesh.z)
-        #self.pressure = md.constants.g * md.materials.rho_ice * (md.geometry.surface-md.mesh.z.reshape(-1, ))
-
         if np.ndim(md.geometry.surface) == 2:
-            print('Reshaping md.geometry.surface for you convenience but you should fix it in you files')
+            print('Reshaping md.geometry.surface for your convenience but you should fix it in your model set up')
             self.pressure = md.constants.g * md.materials.rho_ice * (md.geometry.surface.reshape(-1, ) - md.mesh.z)
         else:
             self.pressure = md.constants.g * md.materials.rho_ice * (md.geometry.surface - md.mesh.z)
@@ -86,21 +80,21 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        if 'StressbalanceAnalysis' in analyses:
+        if 'StressbalanceAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isstressbalance:
             if not np.any(np.logical_or(np.isnan(md.initialization.vx), np.isnan(md.initialization.vy))):
                 md = checkfield(md, 'fieldname', 'initialization.vx', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
                 md = checkfield(md, 'fieldname', 'initialization.vy', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
-        if 'MasstransportAnalysis' in analyses:
+        if 'MasstransportAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.ismasstransport:
             md = checkfield(md, 'fieldname', 'initialization.vx', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'initialization.vy', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
-        if 'BalancethicknessAnalysis' in analyses:
+        if 'BalancethicknessAnalysis' in analyses and solution == 'BalancethicknessSolution':
             md = checkfield(md, 'fieldname', 'initialization.vx', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'initialization.vy', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
-            #Triangle with zero velocity
+            # Triangle with zero velocity
             if np.any(np.logical_and(np.sum(np.abs(md.initialization.vx[md.mesh.elements - 1]), axis=1) == 0,
                                      np.sum(np.abs(md.initialization.vy[md.mesh.elements - 1]), axis=1) == 0)):
                 md.checkmessage("at least one triangle has all its vertices with a zero velocity")
-        if 'ThermalAnalysis' in analyses and not (solution == 'TransientSolution' and md.transient.isthermal == 0):
+        if 'ThermalAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isthermal:
             md = checkfield(md, 'fieldname', 'initialization.vx', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'initialization.vy', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'initialization.temperature', 'NaN', 1, 'Inf', 1, 'size', 'universal')
@@ -107,12 +101,12 @@
             if md.mesh.dimension() == 3:
                 md = checkfield(md, 'fieldname', 'initialization.vz', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'initialization.pressure', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
-            if ('EnthalpyAnalysis' in analyses and md.thermal.isenthalpy):
-                md = checkfield(md, 'fieldname', 'initialization.waterfraction', '>=', 0, 'size', [md.mesh.numberofvertices])
-                md = checkfield(md, 'fieldname', 'initialization.watercolumn', '>=', 0, 'size', [md.mesh.numberofvertices])
-                pos = np.nonzero(md.initialization.waterfraction > 0.)[0]
-                if(pos.size):
-                    md = checkfield(md, 'fieldname', 'delta Tpmp', 'field', np.absolute(md.initialization.temperature[pos] - (md.materials.meltingpoint - md.materials.beta * md.initialization.pressure[pos])), '<', 1e-11, 'message', 'set temperature to pressure melting point at locations with waterfraction > 0')
+        if 'EnthalpyAnalysis' in analyses and md.thermal.isenthalpy:
+            md = checkfield(md, 'fieldname', 'initialization.waterfraction', '>=', 0, 'size', [md.mesh.numberofvertices])
+            md = checkfield(md, 'fieldname', 'initialization.watercolumn', '>=', 0, 'size', [md.mesh.numberofvertices])
+            pos = np.nonzero(md.initialization.waterfraction > 0.)[0]
+            if(pos.size):
+                md = checkfield(md, 'fieldname', 'delta Tpmp', 'field', np.absolute(md.initialization.temperature[pos] - (md.materials.meltingpoint - md.materials.beta * md.initialization.pressure[pos])), '<', 1e-11, 'message', 'set temperature to pressure melting point at locations with waterfraction > 0')
         if 'HydrologyShreveAnalysis' in analyses:
             if hasattr(md.hydrology, 'hydrologyshreve'):
                 md = checkfield(md, 'fieldname', 'initialization.watercolumn', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
@@ -133,9 +127,7 @@
     # }}}
 
     def marshall(self, prefix, md, fid):  # {{{
-
         yts = md.constants.yts
-
         WriteData(fid, prefix, 'object', self, 'fieldname', 'vx', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'vy', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'vz', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts)
Index: ../trunk-jpl/src/m/classes/SMBforcing.py
===================================================================
--- ../trunk-jpl/src/m/classes/SMBforcing.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/SMBforcing.py	(revision 25688)
@@ -1,41 +1,46 @@
 import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
-from checkfield import checkfield
+from project3d import project3d
 from WriteData import WriteData
-from project3d import project3d
 
 
 class SMBforcing(object):
-    """
-    SMBforcing Class definition
+    """SMBFORCING class definition
 
-       Usage:
-          SMB = SMBforcing()
+    Usage:
+        SMB = SMBforcing()
     """
 
-    def __init__(self):  # {{{
-        self.mass_balance = float('NaN')
-        self.requested_outputs = []
+    def __init__(self, *args):  # {{{
         self.isclimatology = 0
+        self.mass_balance = np.nan
         self.steps_per_step = 1
+        self.requested_outputs = []
         self.averaging = 0
+
+        nargs = len(args)
+        if nargs == 0:
+            pass
+        else:
+            raise Exception('constructor not supported')
     #}}}
 
     def __repr__(self):  # {{{
-        string = "   surface forcings parameters:"
-        string = "%s\n%s" % (string, fielddisplay(self, 'mass_balance', 'surface mass balance [m/yr ice eq]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isclimatology', 'repeat all forcings when past last forcing time (default false)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'averaging', 'averaging methods from short to long steps'))
-        string = "%s\n\t\t%s" % (string, '0: Arithmetic (default)')
-        string = "%s\n\t\t%s" % (string, '1: Geometric')
-        string = "%s\n\t\t%s" % (string, '2: Harmonic')
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-        return string
+        s = '   surface forcings parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'mass_balance', 'surface mass balance [m/yr ice eq]'))
+        s += '{}\n'.format(fielddisplay(self, 'isclimatology', 'repeat all forcings when past last forcing time (default false)'))
+        s += '{}\n'.format(fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'))
+        s += '{}\n'.format(fielddisplay(self, 'averaging', 'averaging methods from short to long steps'))
+        s += '\t\t{}\n'.format('0: Arithmetic (default)')
+        s += '\t\t{}\n'.format('1: Geometric')
+        s += '\t\t{}\n'.format('2: Harmonic')
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
-
         self.mass_balance = project3d(md, 'vector', self.mass_balance, 'type', 'node')
         return self
     #}}}
@@ -48,24 +53,22 @@
         if np.all(np.isnan(self.mass_balance)):
             self.mass_balance = np.zeros((md.mesh.numberofvertices))
             print("      no SMBforcing.mass_balance specified: values set as zero")
-
         return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
+        if solution == 'TransientSolution' and not md.transient.issmb:
+            return
         if 'MasstransportAnalysis' in analyses:
             md = checkfield(md, 'fieldname', 'smb.mass_balance', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
-
         if 'BalancethicknessAnalysis' in analyses:
             md = checkfield(md, 'fieldname', 'smb.mass_balance', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
-
         md = checkfield(md, 'fieldname', 'smb.steps_per_step', '>=', 1, 'numel', [1])
         md = checkfield(md, 'fieldname', 'smb.averaging', 'numel', [1], 'values', [0, 1, 2])
         md = checkfield(md, 'fieldname', 'masstransport.requested_outputs', 'stringrow', 1)
         md = checkfield(md, 'fieldname', 'smb.isclimatology', 'values', [0, 1])
-        if (self.isclimatology > 0):
+        if self.isclimatology:
             md = checkfield(md, 'fieldname', 'smb.mass_balance', 'size', [md.mesh.numberofvertices + 1], 'message', 'mass_balance must have md.mesh.numberofvertices + 1 rows in order to force a climatology')
-
         return md
     # }}}
 
@@ -84,5 +87,4 @@
             outputs = outputscopy
         WriteData(fid, prefix, 'data', outputs, 'name', 'md.smb.requested_outputs', 'format', 'StringArray')
         WriteData(fid, prefix, 'object', self, 'class', 'smb', 'fieldname', 'isclimatology', 'format', 'Boolean')
-
     # }}}
Index: ../trunk-jpl/src/m/classes/spatiallinearbasalforcings.m
===================================================================
--- ../trunk-jpl/src/m/classes/spatiallinearbasalforcings.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/spatiallinearbasalforcings.m	(revision 25688)
@@ -80,7 +80,7 @@
 			end
 		end % }}}
 		function disp(self) % {{{
-			disp(sprintf('   basal forcings parameters:'));
+			disp(sprintf('   spatial linear basal forcings parameters:'));
 
 			fielddisplay(self,'groundedice_melting_rate','basal melting rate (positive if melting) [m/yr]');
 			fielddisplay(self,'deepwater_melting_rate','basal melting rate (positive if melting applied for floating ice whith base < deepwater_elevation) [m/yr]');
@@ -99,12 +99,12 @@
 			pos=find(md.geometry.base>md.basalforcings.deepwater_elevation & md.geometry.base<md.basalforcings.upperwater_elevation);
 			floatingice_melting_rate(pos)=md.basalforcings.deepwater_melting_rate(pos).*(md.geometry.base(pos)-md.basalforcings.upperwater_elevation(pos))./(md.basalforcings.deepwater_elevation(pos)-md.basalforcings.upperwater_elevation(pos));
 			WriteData(fid,prefix,'name','md.basalforcings.model','data',6,'format','Integer');
-			WriteData(fid,prefix,'data',floatingice_melting_rate,'format','DoubleMat','name','md.basalforcings.floatingice_melting_rate','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts)
-			WriteData(fid,prefix,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','name','md.basalforcings.groundedice_melting_rate','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts)
+			WriteData(fid,prefix,'data',floatingice_melting_rate,'format','DoubleMat','name','md.basalforcings.floatingice_melting_rate','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
+			WriteData(fid,prefix,'object',self,'fieldname','groundedice_melting_rate','format','DoubleMat','name','md.basalforcings.groundedice_melting_rate','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
 			WriteData(fid,prefix,'object',self,'fieldname','geothermalflux','name','md.basalforcings.geothermalflux','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts);
-			WriteData(fid,prefix,'object',self,'fieldname','deepwater_melting_rate','format','DoubleMat','name','md.basalforcings.deepwater_melting_rate','scale',1./yts,'mattype',1)
-			WriteData(fid,prefix,'object',self,'fieldname','deepwater_elevation','format','DoubleMat','name','md.basalforcings.deepwater_elevation','mattype',1)
-			WriteData(fid,prefix,'object',self,'fieldname','upperwater_elevation','format','DoubleMat','name','md.basalforcings.upperwater_elevation','mattype',1)
+			WriteData(fid,prefix,'object',self,'fieldname','deepwater_melting_rate','format','DoubleMat','name','md.basalforcings.deepwater_melting_rate','scale',1./yts,'mattype',1);
+			WriteData(fid,prefix,'object',self,'fieldname','deepwater_elevation','format','DoubleMat','name','md.basalforcings.deepwater_elevation','mattype',1);
+			WriteData(fid,prefix,'object',self,'fieldname','upperwater_elevation','format','DoubleMat','name','md.basalforcings.upperwater_elevation','mattype',1);
 		end % }}}
 	end
 end
Index: ../trunk-jpl/src/m/classes/nodalvalue.py
===================================================================
--- ../trunk-jpl/src/m/classes/nodalvalue.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/nodalvalue.py	(revision 25688)
@@ -2,37 +2,37 @@
 
 from checkfield import checkfield
 from fielddisplay import fielddisplay
+from pairoptions import pairoptions
 from WriteData import WriteData
 
 
-class dslmme(object):
-    '''
-    NODALVALUE class definition
+class nodalvalue(object):
+    """NODALVALUE class definition
 
-        Usage:
-            nodalvalue=nodalvalue()
-            nodalvalue=nodalvalue(
-                'name', 'SealevelriseSNodalValue',
-                'definitionstring', 'Outputdefinition1',
-                'model_string', 'SealevelriseS',
-                'node', 1
-                )
-    ''' 
+    Usage:
+        nodalvalue=nodalvalue()
+        nodalvalue=nodalvalue(
+            'name', 'SealevelriseSNodalValue',
+            'definitionstring', 'Outputdefinition1',
+            'model_string', 'SealevelriseS',
+            'node', 1
+        )
+    """
 
     def __init__(self, *args): #{{{
         self.name               = ''
-        self.definitionstring   = '' #string that identifies this output definition uniquely, from 'Outputdefinition[1-10]'
-        self.model_string       = '' #string for field that is being retrieved
+        self.definitionstring   = '' # string that identifies this output definition uniquely, from 'Outputdefinition[1-10]'
+        self.model_string       = '' # string for field that is being retrieved
         self.node               = np.nan #for which node are we retrieving the value?
         
         #use provided options to change fields
         options = pairoptions(*args)
 
-        #get name
-        self.name               = options.getfieldvalue(options, 'name', '')
-        self.definitionstring   = options.getfieldvalue(options, 'definitionstring', '')
-        self.model_string       = options.getfieldvalue(options, 'model_string', '')
-        self.node               = options.getfieldvalue(options, 'node', '')
+        # Get name
+        self.name               = options.getfieldvalue('name', '')
+        self.definitionstring   = options.getfieldvalue('definitionstring', '')
+        self.model_string       = options.getfieldvalue('model_string', '')
+        self.node               = options.getfieldvalue('node', '')
     #}}}
 
     def __repr__(self): # {{{
@@ -41,12 +41,11 @@
         s += '{}\n'.format(fielddisplay(self, 'definitionstring', 'string that identifies this output definition uniquely, from \'Outputdefinition[1-10]\''))
         s += '{}\n'.format(fielddisplay(self, 'model_string', 'string for field that is being retrieved'))
         s += '{}\n'.format(fielddisplay(self, 'node', 'vertex index at which we retrieve the value'))
-
         return s
     #}}}
 
     def setdefaultparameters(self): # {{{
-        return
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses): # {{{
@@ -54,10 +53,9 @@
             raise Exception('nodalvalue error message: \'name\' field should be a string!')
         OutputdefinitionStringArray = []
         for i in range(100):
-            OutputdefinitionStringArray[i] = 'Outputdefinition{}'.format(i)
+            OutputdefinitionStringArray.append('Outputdefinition{}'.format(i))
         md = checkfield(md, 'fieldname', 'self.definitionstring', 'field', self.definitionstring, 'values', OutputdefinitionStringArray)
         md = checkfield(md, 'fieldname', 'self.node', 'field', self.node, 'values', range(md.mesh.numberofvertices))
-
         return md
     #}}}
 
Index: ../trunk-jpl/src/m/classes/solidearth.py
===================================================================
--- ../trunk-jpl/src/m/classes/solidearth.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/solidearth.py	(revision 25688)
@@ -11,12 +11,11 @@
 
 
 class solidearth(object):
-    '''
-    SOLIDEARTH class definition
+    """SOLIDEARTH class definition
 
-        Usage:
-            solidearth = solidearth()
-    '''
+    Usage:
+        solidearth = solidearth()
+    """
 
     def __init__(self, *args):  #{{{
         self.sealevel = np.nan
@@ -50,21 +49,18 @@
     #}}}
 
     def setdefaultparameters(self):  # {{{
-        return
+        return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and md.transient.isslr == 0):
+        if ('SealevelriseAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isslr):
             return md
-
         md = checkfield(md, 'fieldname', 'solidearth.sealevel', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
         md = checkfield(md, 'fieldname', 'solidearth.requested_outputs', 'stringrow', 1)
-
         self.settings.checkconsistency(md, solution, analyses)
         self.surfaceload.checkconsistency(md, solution, analyses)
         self.lovenumbers.checkconsistency(md, solution, analyses)
         self.rotational.checkconsistency(md, solution, analyses)
-
         return md
     #}}}
 
@@ -91,8 +87,7 @@
         WriteData(fid, prefix, 'data', outputs, 'name', 'md.solidearth.requested_outputs', 'format', 'StringArray')
     #}}}
 
-    def extrude(self, md):  #{{{
+    def extrude(self, md): #{{{
         self.sealevel = project3d(md, 'vector', self.sealevel, 'type', 'node')
-
         return self
     #}}}
Index: ../trunk-jpl/src/m/classes/frictioncoulomb.py
===================================================================
--- ../trunk-jpl/src/m/classes/frictioncoulomb.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/frictioncoulomb.py	(revision 25688)
@@ -22,26 +22,24 @@
         self.effective_pressure = np.nan
         self.effective_pressure_limit = 0
 
-        #set defaults
         self.setdefaultparameters()
     #}}}
 
     def __repr__(self):  # {{{
-        s = "Basal shear stress parameters: Sigma_b = min(coefficient^2 * Neff ^r * |u_b|^(s - 1) * u_b, \n coefficientcoulomb^2 * rho_i * g * (h - h_f)), (effective stress Neff = rho_ice * g * thickness + rho_water * g * bed, r = q / p and s = 1 / p).\n"
-        s = "{}\n".format(fielddisplay(self, "coefficient", "power law (Weertman) friction coefficient [SI]"))
-        s = "{}\n".format(fielddisplay(self, "coefficientcoulomb", "Coulomb friction coefficient [SI]"))
-        s = "{}\n".format(fielddisplay(self, "p", "p exponent"))
-        s = "{}\n".format(fielddisplay(self, "q", "q exponent"))
-        s = "{}\n".format(fielddisplay(self, 'coupling', 'Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure)  and 2 for coupled(not implemented yet)'))
-        s = "{}\n".format(fielddisplay(self, 'effective_pressure', 'Effective Pressure for the forcing if not coupled [Pa]'))
-        s = "{}\n".format(fielddisplay(self, 'effective_pressure_limit', 'Neff do not allow to fall below a certain limit: effective_pressure_limit * rho_ice * g * thickness (default 0)'))
-        
+        s = 'Basal shear stress parameters: Sigma_b = min(coefficient^2 * Neff ^r * |u_b|^(s - 1) * u_b,\n'
+        s += 'coefficientcoulomb^2 * rho_i * g * (h - h_f)), (effective stress Neff = rho_ice * g * thickness + rho_water * g * bed, r = q / p and s = 1 / p).\n'
+        s += '{}\n'.format(fielddisplay(self, "coefficient", "power law (Weertman) friction coefficient [SI]"))
+        s += '{}\n'.format(fielddisplay(self, "coefficientcoulomb", "Coulomb friction coefficient [SI]"))
+        s += '{}\n'.format(fielddisplay(self, "p", "p exponent"))
+        s += '{}\n'.format(fielddisplay(self, "q", "q exponent"))
+        s += '{}\n'.format(fielddisplay(self, 'coupling', 'Coupling flag: 0 for default, 1 for forcing(provide md.friction.effective_pressure)  and 2 for coupled(not implemented yet)'))
+        s += '{}\n'.format(fielddisplay(self, 'effective_pressure', 'Effective Pressure for the forcing if not coupled [Pa]'))
+        s += '{}\n'.format(fielddisplay(self, 'effective_pressure_limit', 'Neff do not allow to fall below a certain limit: effective_pressure_limit * rho_ice * g * thickness (default 0)'))
         return s
     #}}}
 
     def setdefaultparameters(self):  # {{{
         self.effective_pressure_limit = 0
-
         return self
     #}}}
 
@@ -56,14 +54,12 @@
             raise ValueError('not implemented yet')
         elif self.coupling > 2:
             raise ValueError('not supported yet')
-
         return self
     #}}}
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses:
             return md
-
         md = checkfield(md, 'fieldname', 'friction.coefficient', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.coefficientcoulomb', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.q', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofelements])
@@ -76,7 +72,6 @@
             raise ValueError('not implemented yet')
         elif self.coupling > 2:
             raise ValueError('not supported yet')
-
         return md
     # }}}
 
Index: ../trunk-jpl/src/m/classes/spatiallinearbasalforcings.py
===================================================================
--- ../trunk-jpl/src/m/classes/spatiallinearbasalforcings.py	(nonexistent)
+++ ../trunk-jpl/src/m/classes/spatiallinearbasalforcings.py	(revision 25688)
@@ -0,0 +1,110 @@
+import numpy as np
+
+from checkfield import checkfield
+from fielddisplay import fielddisplay
+from project3d import project3d
+from structtoobj import structtoobj
+from WriteData import WriteData
+
+
+class spatiallinearbasalforcings(object):
+    """SPATIAL LINEAR BASAL FORCINGS class definition
+
+    Usage:
+        spatiallinearbasalforcings = spatiallinearbasalforcings()
+    """
+
+    def __init__(self, *args): #{{{
+        nargs = len(args):
+        if nargs == 0:
+            self.groundedice_melting_rate   = np.nan
+            self.deepwater_melting_rate     = np.nan
+            self.deepwater_elevation        = np.nan
+            self.upperwater_elevation       = np.nan
+            self.geothermalflux             = np.nan
+
+            self.setdefaultparameters()
+        elif nargs == 1:
+            lb = args[0]
+            if lb.__module__ == 'linearbasalforcings':
+                nvertices = len(lb.groundedice_melting_rate)
+                self.groundedice_melting_rate   = lb.groundedice_melting_rate
+                self.deepwater_melting_rate     = lb.geothermalflux
+                self.deepwater_elevation        = lb.deepwater_elevation * np.ones((nvertices, ))
+                self.upperwater_elevation       = lb.deepwater_melting_rate * np.ones((nvertices, ))
+                self.geothermalflux             = lb.upperwater_elevation * np.ones((nvertices, ))
+            else:
+                # TODO: This has not been tested
+                self = structtoobj(self, lb)
+        else:
+            raise Exception('constructor not supported')
+    #}}}
+
+    def __repr__(self): #{{{
+        s = '   spatial linear basal forcings parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'groundedice_melting_rate', 'basal melting rate (positive if melting) [m/yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'deepwater_melting_rate', 'basal melting rate (positive if melting applied for floating ice whith base < deepwater_elevation) [m/yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'deepwater_elevation', 'elevation of ocean deepwater [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'upperwater_elevation', 'elevation of ocean upperwater [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'geothermalflux', 'geothermal heat flux [W/m^2]'))
+        return s
+    #}}}
+
+    def extrude(self, md): #{{{
+        self.groundedice_melting_rate = project3d(md, 'vector', self.groundedice_melting_rate, 'type', 'node', 'layer', 1) 
+        self.deepwater_melting_rate = project3d(md, 'vector', self.deepwater_melting_rate, 'type', 'node', 'layer', 1) 
+        self.deepwater_elevation = project3d(md, 'vector', self.deepwater_elevation, 'type', 'node', 'layer', 1)
+        self.upperwater_elevation = project3d(md, 'vector', self.upperwater_elevation, 'type', 'node', 'layer', 1) 
+        self.geothermalflux = project3d(md, 'vector', self.geothermalflux, 'type', 'node', 'layer', 1) # Bedrock only gets geothermal flux
+        return self
+    #}}}
+
+    def initialize(self, md): #{{{
+        if np.all(np.isnan(self.groundedice_melting_rate)):
+            self.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices))
+            print('      no basalforcings.groundedice_melting_rate specified: values set as zero')
+        return self
+    #}}}
+
+    def setdefaultparameters(self): #{{{
+        return self
+    #}}}
+
+    def checkconsistency(self, md, solution, analyses): #{{{
+        if 'MasstransportAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.ismasstransport:
+            md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0)
+            md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '<', 0)
+        if 'BalancethicknessAnalysis' in analyses:
+            raise Exception('not implemented yet!')
+            md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
+            md = checkfield(md, x'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'numel', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'numel', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<=', 0, 'numel', 1)
+        if 'ThermalAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isthermal:
+            raise Exception('not implemented yet!')
+            md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.deepwater_melting_rate', '>=', 0, 'numel', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.deepwater_elevation', '<', 'basalforcings.upperwater_elevation', 'numel', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.upperwater_elevation', '<', 0, 'numel', 1)
+            md = checkfield(md, 'fieldname', 'basalforcings.geothermalflux', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0)
+        return md
+    # }}}
+
+    def marshall(self, prefix, md, fid): #{{{
+        yts = md.constants.yts
+
+        floatingice_melting_rate = np.zeros((md.mesh.numberofvertices, ))
+        pos = np.where(md.geometry.base <= md.basalforcings.deepwater_elevation)[0]
+        floatingice_melting_rate[pos] = md.basalforcings.deepwater_melting_rate[pos]
+        pos = np.where(np.logical_and.reduce(md.geometry.base > md.basalforcings.deepwater_elevation, md.geometry.base < md.basalforcings.upperwater_elevation))
+        floatingice_melting_rate[pos] = md.basalforcings.deepwater_melting_rate[pos] * (md.geometry.base[pos] - md.basalforcings.upperwater_elevation[pos]) / (md.basalforcings.deepwater_elevation[pos] - md.basalforcings.upperwater_elevation[pos])
+        WriteData(fid, prefix, 'name', 'md.basalforcings.model', 'data', 6, 'format', 'Integer')
+        WriteData(fid, prefix, 'data', floatingice_melting_rate, 'format', 'DoubleMat', 'name', 'md.basalforcings.floatingice_melting_rate', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts)
+        WriteData(fid, prefix, 'object', self, 'fieldname', 'groundedice_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.groundedice_melting_rate', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1,'yts', md.constants.yts)
+        WriteData(fid, prefix,'object', self, 'fieldname', 'geothermalflux', 'name', 'md.basalforcings.geothermalflux', 'format', 'DoubleMat', 'mattype', 1,'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts)
+        WriteData(fid, prefix, 'object', self, 'fieldname', 'deepwater_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.deepwater_melting_rate', 'scale', 1. / yts, 'mattype', 1)
+        WriteData(fid, prefix, 'object', self, 'fieldname', 'deepwater_elevation', 'format', 'DoubleMat', 'name', 'md.basalforcings.deepwater_elevation', 'mattype', 1)
+        WriteData(fid, prefix, 'object', self, 'fieldname', 'upperwater_elevation', 'format', 'DoubleMat', 'name', 'md.basalforcings.upperwater_elevation', 'mattype', 1)
+    #}}}
Index: ../trunk-jpl/src/m/classes/qmu/normal_uncertain.m
===================================================================
--- ../trunk-jpl/src/m/classes/qmu/normal_uncertain.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/qmu/normal_uncertain.m	(revision 25688)
@@ -160,7 +160,7 @@
 			scale=[];
 		end % }}}
 		%new methods:
-			function distributed=isdistributed(self) % {{{
+		function distributed=isdistributed(self) % {{{
 			if strncmp(self.descriptor,'distributed_',12),
 				distributed=1;
 			else
@@ -167,7 +167,7 @@
 				distributed=0;
 			end
 		end % }}}
-	function scaled=isscaled(self) % {{{
+		function scaled=isscaled(self) % {{{
 			if strncmp(self.descriptor,'scaled_',7),
 				scaled=1;
 			else
Index: ../trunk-jpl/src/m/classes/qmu/response_function.m
===================================================================
--- ../trunk-jpl/src/m/classes/qmu/response_function.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/qmu/response_function.m	(revision 25688)
@@ -115,13 +115,13 @@
             grell=allempty(grell);
         end % }}}
 		%new methods: 
-	function scaled =isscaled(self) % {{{
-		if strncmp(self.descriptor,'scaled_',7),
-			scaled=1;
-		else
-			scaled=0;
-		end
-	end % }}}
+    	function scaled =isscaled(self) % {{{
+    		if strncmp(self.descriptor,'scaled_',7),
+    			scaled=1;
+    		else
+    			scaled=0;
+    		end
+    	end % }}}
     end
     methods (Static)
         function [rdesc]=dakota_write(fidi,dresp,rdesc) % {{{
Index: ../trunk-jpl/src/m/classes/qmu/normal_uncertain.py
===================================================================
--- ../trunk-jpl/src/m/classes/qmu/normal_uncertain.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/qmu/normal_uncertain.py	(revision 25688)
@@ -9,8 +9,7 @@
 
 
 class normal_uncertain(object):
-    '''
-    NORMAL_UNCERTAIN class definition
+    """NORMAL_UNCERTAIN class definition
 
     Usage:
         [nuv] = normal_uncertain(
@@ -37,7 +36,8 @@
             'stddev',.05,
             'partition',vpartition
             )
-    '''
+    """
+
     def __init__(self): #{{{
         self.descriptor = ''
         self.mean       = np.nan
@@ -230,6 +230,13 @@
     #}}}
 
     #new methods:
+    def isdistributed(self): #{{{
+        if strncmp(self.descriptor, 'distributed_', 12):
+            return True
+        else:
+            return False
+    #}}}
+    
     def isscaled(self): #{{{
         if strncmp(self.descriptor, 'scaled_', 7):
             return True
Index: ../trunk-jpl/src/m/classes/giaivins.m
===================================================================
--- ../trunk-jpl/src/m/classes/giaivins.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/giaivins.m	(revision 25688)
@@ -34,7 +34,7 @@
 				%figure out if thickness is a transient forcing: 
 				if size(md.geometry.thickness,1)==md.mesh.numberofvertices+1,
 					%recover the furthest time "in time": 
-					if(thickness(end,end)~=md.timestepping.start_time),
+					if(md.geometry.thickness(end,end)~=md.timestepping.start_time),
 						md = checkmessage(md,['if ismasstransport is on, transient thickness forcing'...
 							' for the giaivins model should not be provided in the future.'...
 							' Synchronize your start_time to correspond to the most recent transient'...
@@ -50,7 +50,7 @@
 			fielddisplay(self,'mantle_viscosity','mantle viscosity[Pa s]');
 			fielddisplay(self,'lithosphere_thickness','lithosphere thickness (km)');
 			fielddisplay(self,'cross_section_shape','1: square-edged (default). 2: elliptical.  See iedge in GiaDeflectionCore');
-
+True
 		end % }}}
 		function marshall(self,prefix,md,fid) % {{{
 			WriteData(fid,prefix,'name','md.gia.model','data',1,'format','Integer');
Index: ../trunk-jpl/src/m/classes/geometry.py
===================================================================
--- ../trunk-jpl/src/m/classes/geometry.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/geometry.py	(revision 25688)
@@ -7,14 +7,13 @@
 
 
 class geometry(object):
-    '''
-    GEOMETRY class definition
+    """GEOMETRY class definition
 
-        Usage:
-            geometry = geometry()
-    '''
+    Usage:
+        geometry = geometry()
+    """
 
-    def __init__(self): #{{{
+    def __init__(self, *args): #{{{
         self.surface = np.nan
         self.thickness = np.nan
         self.base = np.nan
@@ -21,17 +20,19 @@
         self.bed = np.nan
         self.hydrostatic_ratio = np.nan
 
-        #set defaults
-        self.setdefaultparameters()
+        nargs = len(args)
+        if nargs == 0:
+            self.setdefaultparameters()
+        else:
+            raise Exception('constructor not supported')
     #}}}
 
     def __repr__(self): #{{{
-        s = "   geometry parameters:"
-        s = "%s\n%s" % (s, fielddisplay(self, 'surface', 'ice upper surface elevation [m]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'thickness', 'ice thickness [m]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'base', 'ice base elevation [m]'))
-        s = "%s\n%s" % (s, fielddisplay(self, 'bed', 'bed elevation [m]'))
-        
+        s = '   geometry parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'surface', 'ice upper surface elevation [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'thickness', 'ice thickness [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'base', 'ice base elevation [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'bed', 'bed elevation [m]'))
         return s
     #}}}
 
Index: ../trunk-jpl/src/m/classes/flowequation.py
===================================================================
--- ../trunk-jpl/src/m/classes/flowequation.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/flowequation.py	(revision 25688)
@@ -22,7 +22,7 @@
         self.isHO = 0
         self.isFS = 0
         self.isNitscheBC = 0
-        self.FSNitscheGamma = 1e-6
+        self.FSNitscheGamma = 1e6
         self.fe_SSA = ''
         self.fe_HO = ''
         self.fe_FS = ''
@@ -31,67 +31,61 @@
         self.augmented_lagrangian_rlambda = 1.
         self.augmented_lagrangian_rholambda = 1.
         self.XTH_theta = 0.
-        self.vertex_equation = float('NaN')
-        self.element_equation = float('NaN')
-        self.borderSSA = float('NaN')
-        self.borderHO = float('NaN')
-        self.borderFS = float('NaN')
-
-    #set defaults
+        self.vertex_equation = np.nan
+        self.element_equation = np.nan
+        self.borderSSA = np.nan
+        self.borderHO = np.nan
+        self.borderFS = np.nan
+        
         self.setdefaultparameters()
-
     #}}}
 
     def __repr__(self):  # {{{
         s = '   flow equation parameters:\n'
-        s += "{}\n".format(fielddisplay(self, 'isSIA', "is the Shallow Ice Approximation (SIA) used?"))
-        s += "{}\n".format(fielddisplay(self, 'isSSA', "is the Shelfy-Stream Approximation (SSA) used?"))
-        s += "{}\n".format(fielddisplay(self, 'isL1L2', "are L1L2 equations used?"))
-        s += "{}\n".format(fielddisplay(self, 'isMLHO', "are Mono-layer Higher-Order equations used?"))
-        s += "{}\n".format(fielddisplay(self, 'isHO', "is the Higher-Order (HO) approximation used?"))
-        s += "{}\n".format(fielddisplay(self, 'isFS', "are the Full-FS (FS) equations used?"))
-        s += "{}\n".format(fielddisplay(self, 'isNitscheBC', "is weakly imposed condition used?"))
-        s += "{}\n".format(fielddisplay(self, 'FSNitscheGamma', "Gamma value for the Nitsche term (default: 1e6)"))
-        s += "{}\n".format(fielddisplay(self, 'fe_SSA', "Finite Element for SSA: 'P1', 'P1bubble' 'P1bubblecondensed' 'P2'"))
-        s += "{}\n".format(fielddisplay(self, 'fe_HO', "Finite Element for HO:  'P1', 'P1bubble', 'P1bubblecondensed', 'P1xP2', 'P2xP1', 'P2', 'P2bubble', 'P1xP3', 'P2xP4'"))
-        s += "{}\n".format(fielddisplay(self, 'fe_FS', "Finite Element for FS:  'P1P1' (debugging only) 'P1P1GLS' 'MINIcondensed' 'MINI' 'TaylorHood' 'LATaylorHood' 'XTaylorHood'"))
-        s += "{}\n".format(fielddisplay(self, 'vertex_equation', "flow equation for each vertex"))
-        s += "{}\n".format(fielddisplay(self, 'element_equation', "flow equation for each element"))
-        s += "{}\n".format(fielddisplay(self, 'borderSSA', "vertices on SSA's border (for tiling)"))
-        s += "{}\n".format(fielddisplay(self, 'borderHO', "vertices on HO's border (for tiling)"))
-        s += "{}".format(fielddisplay(self, 'borderFS', "vertices on FS' border (for tiling)"))
-
+        s += '{}\n'.format(fielddisplay(self, 'isSIA', "is the Shallow Ice Approximation (SIA) used?"))
+        s += '{}\n'.format(fielddisplay(self, 'isSSA', "is the Shelfy-Stream Approximation (SSA) used?"))
+        s += '{}\n'.format(fielddisplay(self, 'isL1L2', "are L1L2 equations used?"))
+        s += '{}\n'.format(fielddisplay(self, 'isMLHO', "are Mono-layer Higher-Order equations used?"))
+        s += '{}\n'.format(fielddisplay(self, 'isHO', "is the Higher-Order (HO) approximation used?"))
+        s += '{}\n'.format(fielddisplay(self, 'isFS', "are the Full-FS (FS) equations used?"))
+        s += '{}\n'.format(fielddisplay(self, 'isNitscheBC', "is weakly imposed condition used?"))
+        s += '{}\n'.format(fielddisplay(self, 'FSNitscheGamma', "Gamma value for the Nitsche term (default: 1e6)"))
+        s += '{}\n'.format(fielddisplay(self, 'fe_SSA', "Finite Element for SSA: 'P1', 'P1bubble' 'P1bubblecondensed' 'P2'"))
+        s += '{}\n'.format(fielddisplay(self, 'fe_HO', "Finite Element for HO:  'P1', 'P1bubble', 'P1bubblecondensed', 'P1xP2', 'P2xP1', 'P2', 'P2bubble', 'P1xP3', 'P2xP4'"))
+        s += '{}\n'.format(fielddisplay(self, 'fe_FS', "Finite Element for FS:  'P1P1' (debugging only) 'P1P1GLS' 'MINIcondensed' 'MINI' 'TaylorHood' 'LATaylorHood' 'XTaylorHood'"))
+        s += '{}\n'.format(fielddisplay(self, 'vertex_equation', "flow equation for each vertex"))
+        s += '{}\n'.format(fielddisplay(self, 'element_equation', "flow equation for each element"))
+        s += '{}\n'.format(fielddisplay(self, 'borderSSA', "vertices on SSA's border (for tiling)"))
+        s += '{}\n'.format(fielddisplay(self, 'borderHO', "vertices on HO's border (for tiling)"))
+        s += '{}\n'.format(fielddisplay(self, 'borderFS', "vertices on FS' border (for tiling)"))
         return s
     #}}}
 
-    def extrude(self, md):  # {{{
-        self.element_equation = project3d(md, 'vector', self.element_equation, 'type', 'element')
-        self.vertex_equation = project3d(md, 'vector', self.vertex_equation, 'type', 'node')
-        self.borderSSA = project3d(md, 'vector', self.borderSSA, 'type', 'node')
-        self.borderHO = project3d(md, 'vector', self.borderHO, 'type', 'node')
-        self.borderFS = project3d(md, 'vector', self.borderFS, 'type', 'node')
-        return self
-    #}}}
-
     def setdefaultparameters(self):  # {{{
-        #P1 for SSA
+        # P1 for SSA
         self.fe_SSA = 'P1'
 
-        #P1 for HO
+        # P1 for HO
         self.fe_HO = 'P1'
 
-        #MINI condensed element for FS by default
+        # MINI condensed element for FS by default
         self.fe_FS = 'MINIcondensed'
+        return self
+    #}}}
 
+    def extrude(self, md):  # {{{
+        self.element_equation = project3d(md, 'vector', self.element_equation, 'type', 'element')
+        self.vertex_equation = project3d(md, 'vector', self.vertex_equation, 'type', 'node')
+        self.borderSSA = project3d(md, 'vector', self.borderSSA, 'type', 'node')
+        self.borderHO = project3d(md, 'vector', self.borderHO, 'type', 'node')
+        self.borderFS = project3d(md, 'vector', self.borderFS, 'type', 'node')
         return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-
-        #Early return
+        # Early return
         if ('StressbalanceAnalysis' not in analyses and 'StressbalanceSIAAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isstressbalance):
             return md
-
         md = checkfield(md, 'fieldname', 'flowequation.isSIA', 'numel', [1], 'values', [0, 1])
         md = checkfield(md, 'fieldname', 'flowequation.isSSA', 'numel', [1], 'values', [0, 1])
         md = checkfield(md, 'fieldname', 'flowequation.isL1L2', 'numel', [1], 'values', [0, 1])
@@ -121,15 +115,13 @@
             md = checkfield(md, 'fieldname', 'flowequation.vertex_equation', 'size', [md.mesh.numberofvertices], 'values', np.arange(0, 9 + 1))
             md = checkfield(md, 'fieldname', 'flowequation.element_equation', 'size', [md.mesh.numberofelements], 'values', np.arange(0, 9 + 1))
         else:
-            raise RuntimeError('mesh type not supported yet')
+            raise RuntimeError('Case not supported yet')
         if not (self.isSIA or self.isSSA or self.isL1L2 or self.isMLHO or self.isHO or self.isFS):
             md.checkmessage("no element types set for this model")
-
         if 'StressbalanceSIAAnalysis' in analyses:
             if any(self.element_equation == 1):
                 if np.any(np.logical_and(self.vertex_equation, md.mask.ocean_levelset)):
                     print("\n !!! Warning: SIA's model is not consistent on ice shelves !!!\n")
-
         return md
     # }}}
 
@@ -153,8 +145,7 @@
         WriteData(fid, prefix, 'object', self, 'fieldname', 'borderSSA', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'borderHO', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'borderFS', 'format', 'DoubleMat', 'mattype', 1)
-        #convert approximations to enums
+        # Convert approximations to enums
         WriteData(fid, prefix, 'data', self.vertex_equation, 'name', 'md.flowequation.vertex_equation', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'data', self.element_equation, 'name', 'md.flowequation.element_equation', 'format', 'DoubleMat', 'mattype', 2)
-
     # }}}
Index: ../trunk-jpl/src/m/classes/plumebasalforcings.py
===================================================================
--- ../trunk-jpl/src/m/classes/plumebasalforcings.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/plumebasalforcings.py	(revision 25688)
@@ -1,56 +1,62 @@
 import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
-from checkfield import checkfield
+from project3d import project3d
+from structtoobj import structtoobj
 from WriteData import WriteData
-from project3d import project3d
 
 
 class plumebasalforcings(object):
-    '''
-    PLUME BASAL FORCINGS class definition
+    """PLUME BASAL FORCINGS class definition
 
-        Usage:
-            plumebasalforcings = plumebasalforcings()
-    '''
+    Usage:
+        plumebasalforcings = plumebasalforcings()
+    """
 
-    def __init__(self):  # {{{
-        self.floatingice_melting_rate = float('NaN')
-        self.groundedice_melting_rate = float('NaN')
-        self.mantleconductivity = float('NaN')
-        self.nusselt = float('NaN')
-        self.dtbg = float('NaN')
-        self.plumeradius = float('NaN')
-        self.topplumedepth = float('NaN')
-        self.bottomplumedepth = float('NaN')
-        self.plumex = float('NaN')
-        self.plumey = float('NaN')
-        self.crustthickness = float('NaN')
-        self.uppercrustthickness = float('NaN')
-        self.uppercrustheat = float('NaN')
-        self.lowercrustheat = float('NaN')
+    def __init__(self, *args):  # {{{
+        self.floatingice_melting_rate   = np.nan
+        self.groundedice_melting_rate   = np.nan
+        self.mantleconductivity         = np.nan
+        self.nusselt                    = np.nan
+        self.dtbg                       = np.nan
+        self.plumeradius                = np.nan
+        self.topplumedepth              = np.nan
+        self.bottomplumedepth           = np.nan
+        self.plumex                     = np.nan
+        self.plumey                     = np.nan
+        self.crustthickness             = np.nan
+        self.uppercrustthickness        = np.nan
+        self.uppercrustheat             = np.nan
+        self.lowercrustheat             = np.nan
 
-        self.setdefaultparameters()
+        nargs = len(args)
+        if nargs == 0:
+            self.setdefaultparameters()
+        elif nargs == 1:
+            # TODO: This has not been tested
+            self = structtoobj(self, args[0])
+        else:
+            error('constuctor not supported')
     #}}}
 
     def __repr__(self):  # {{{
-        string = '   mantle plume basal melt parameterization:'
-
-        string = "%s\n%s" % (string, fielddisplay(self, 'groundedice_melting_rate', 'basal melting rate (positive if melting) [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'floatingice_melting_rate', 'basal melting rate (positive if melting) [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'mantleconductivity', 'mantle heat conductivity [W / m^3]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'nusselt', 'nusselt number, ratio of mantle to plume [1]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'dtbg', 'background temperature gradient [degree / m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'plumeradius', 'radius of the mantle plume [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'topplumedepth', 'depth of the mantle plume top below the crust [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'bottomplumedepth', 'depth of the mantle plume base below the crust [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'plumex', 'x coordinate of the center of the plume [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'plumey', 'y coordinate of the center of the plume [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'crustthickness', 'thickness of the crust [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'uppercrustthickness', 'thickness of the upper crust [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'uppercrustheat', 'volumic heat of the upper crust [w / m^3]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'lowercrustheat', 'volumic heat of the lowercrust [w / m^3]'))
-
-        return string
+        s = '   mantle plume basal melt parameterization:\n'
+        s += '{}\n'.format(fielddisplay(self, 'groundedice_melting_rate', 'basal melting rate (positive if melting) [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'floatingice_melting_rate', 'basal melting rate (positive if melting) [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'mantleconductivity', 'mantle heat conductivity [W / m^3]'))
+        s += '{}\n'.format(fielddisplay(self, 'nusselt', 'nusselt number, ratio of mantle to plume [1]'))
+        s += '{}\n'.format(fielddisplay(self, 'dtbg', 'background temperature gradient [degree / m]'))
+        s += '{}\n'.format(fielddisplay(self, 'plumeradius', 'radius of the mantle plume [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'topplumedepth', 'depth of the mantle plume top below the crust [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'bottomplumedepth', 'depth of the mantle plume base below the crust [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'plumex', 'x coordinate of the center of the plume [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'plumey', 'y coordinate of the center of the plume [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'crustthickness', 'thickness of the crust [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'uppercrustthickness', 'thickness of the upper crust [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'uppercrustheat', 'volumic heat of the upper crust [w / m^3]'))
+        s += '{}\n'.format(fielddisplay(self, 'lowercrustheat', 'volumic heat of the lowercrust [w / m^3]'))
+        return s
     #}}}
 
     def initialize(self, md):  #{{{
@@ -60,7 +66,7 @@
         if np.all(np.isnan(self.floatingice_melting_rate)):
             self.floatingice_melting_rate = np.zeros((md.mesh.numberofvertices, ))
             print('      no basalforcings.floatingice_melting_rate specified: values set as zero')
-        return
+        return self
     #}}}
 
     def extrude(self, md):  # {{{
@@ -70,7 +76,7 @@
     #}}}
 
     def setdefaultparameters(self):  # {{{
-        #default values for melting parameterization
+        # Default values for melting parameterization
         self.mantleconductivity = 2.2
         self.nusselt = 300
         self.dtbg = 11 / 1000.
Index: ../trunk-jpl/src/m/classes/friction.m
===================================================================
--- ../trunk-jpl/src/m/classes/friction.m	(revision 25687)
+++ ../trunk-jpl/src/m/classes/friction.m	(revision 25688)
@@ -65,7 +65,7 @@
 				case 4
 				
 				otherwise
-					error('not supported yet');		
+					error('not supported yet');
 			end
 		end % }}}
 		function disp(self) % {{{
Index: ../trunk-jpl/src/m/classes/frictionwaterlayer.py
===================================================================
--- ../trunk-jpl/src/m/classes/frictionwaterlayer.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/frictionwaterlayer.py	(revision 25688)
@@ -35,7 +35,6 @@
         s = "{}\n".format(fielddisplay(self, 'p', 'p exponent'))
         s = "{}\n".format(fielddisplay(self, 'q', 'q exponent'))
         s = "{}\n".format(fielddisplay(self, 'water_layer', 'water thickness at the base of the ice (m)'))
-
         return s
     #}}}
 
@@ -44,15 +43,15 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  #{{{
-        #Early return
-        if ('StressbalanceAnalysis' not in analyses) and ('ThermalAnalysis' not in analyses):
+        # Early return
+        if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses:
             return
-
         md = checkfield(md, 'fieldname', 'friction.coefficient', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.f', 'size', [1], 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.q', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofelements])
         md = checkfield(md, 'fieldname', 'friction.p', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofelements])
         md = checkfield(md, 'fieldname', 'thermal.spctemperature', 'Inf', 1, 'timeseries', 1, '>=', 0.)
+        return md
     # }}}
 
     def extrude(self, md):  # {{{
@@ -60,7 +59,6 @@
         self.p = project3d(md, 'vector', self.p, 'type', 'element')
         self.q = project3d(md, 'vector', self.q, 'type', 'element')
         self.water_layer = project3d(md, 'vector', self.water_layer, 'type', 'node', 'layer', 1)
-
         return self
     # }}}
 
Index: ../trunk-jpl/src/m/classes/masstransport.py
===================================================================
--- ../trunk-jpl/src/m/classes/masstransport.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/masstransport.py	(revision 25688)
@@ -1,16 +1,16 @@
 import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
 from project3d import project3d
-from checkfield import checkfield
 from WriteData import WriteData
 
 
 class masstransport(object):
-    """
-    MASSTRANSPORT class definition
+    """MASSTRANSPORT class definition
 
-       Usage:
-          masstransport = masstransport()
+    Usage:
+        masstransport = masstransport()
     """
 
     def __init__(self):  # {{{
@@ -23,21 +23,20 @@
         self.penalty_factor = 0
         self.requested_outputs = []
 
-    #set defaults
+        # Set defaults
         self.setdefaultparameters()
 
     #}}}
 
     def __repr__(self):  # {{{
-        string = '   Masstransport solution parameters:'
-        string = "%s\n%s" % (string, fielddisplay(self, 'spcthickness', 'thickness constraints (NaN means no constraint) [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isfreesurface', 'do we use free surfaces (FS only) or mass conservation'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'min_thickness', 'minimum ice thickness allowed [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'hydrostatic_adjustment', 'adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' '))
-        string = "%s\n%s" % (string, fielddisplay(self, 'stabilization', '0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin, 4: Flux Correction Transport'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-
-        return string
+        s = '   Masstransport solution parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'spcthickness', 'thickness constraints (NaN means no constraint) [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'isfreesurface', 'do we use free surfaces (FS only) or mass conservation'))
+        s += '{}\n'.format(fielddisplay(self, 'min_thickness', 'minimum ice thickness allowed [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'hydrostatic_adjustment', 'adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' '))
+        s += '{}\n'.format(fielddisplay(self, 'stabilization', '0: no, 1: artificial_diffusivity, 2: streamline upwinding, 3: discontinuous Galerkin, 4: Flux Correction Transport'))
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
@@ -50,21 +49,21 @@
 
     #}}}
     def setdefaultparameters(self):  # {{{
-        #Type of stabilization to use 0:nothing 1:artificial_diffusivity 3:Discontinuous Galerkin
+        # Type of stabilization to use 0:nothing 1:artificial_diffusivity 3:Discontinuous Galerkin
         self.stabilization = 1
-        #Factor applied to compute the penalties kappa = max(stiffness matrix) * 1.0**penalty_factor
+        # Factor applied to compute the penalties kappa = max(stiffness matrix) * 1.0**penalty_factor
         self.penalty_factor = 3
-        #Minimum ice thickness that can be used
+        # Minimum ice thickness that can be used
         self.min_thickness = 1
-        #Hydrostatic adjustment
+        # Hydrostatic adjustment
         self.hydrostatic_adjustment = 'Absolute'
-        #default output
+        # Default output
         self.requested_outputs = ['default']
         return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if ('MasstransportAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.ismasstransport):
             return md
 
@@ -89,7 +88,7 @@
         WriteData(fid, prefix, 'object', self, 'fieldname', 'vertex_pairing', 'format', 'DoubleMat', 'mattype', 3)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'penalty_factor', 'format', 'Double')
 
-    #process requested outputs
+        # Process requested outputs
         outputs = self.requested_outputs
         indices = [i for i, x in enumerate(outputs) if x == 'default']
         if len(indices) > 0:
Index: ../trunk-jpl/src/m/classes/inversion.py
===================================================================
--- ../trunk-jpl/src/m/classes/inversion.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/inversion.py	(revision 25688)
@@ -1,94 +1,77 @@
 import numpy as np
+
+from checkfield import checkfield
+from fielddisplay import fielddisplay
+from marshallcostfunctions import marshallcostfunctions
 from project3d import project3d
-from fielddisplay import fielddisplay
-from checkfield import checkfield
-from WriteData import WriteData
 from supportedcontrols import supportedcontrols
 from supportedcostfunctions import supportedcostfunctions
-from marshallcostfunctions import marshallcostfunctions
+from WriteData import WriteData
 
 
 class inversion(object):
-    """
-    INVERSION class definition
+    """INVERSION class definition
 
-       Usage:
-          inversion = inversion()
+    Usage:
+        inversion = inversion()
     """
 
     def __init__(self):  # {{{
         self.iscontrol = 0
         self.incomplete_adjoint = 0
-        self.control_parameters = float('NaN')
+        self.control_parameters = np.nan
         self.nsteps = 0
-        self.maxiter_per_step = float('NaN')
+        self.maxiter_per_step = np.nan
         self.cost_functions = ''
-        self.cost_functions_coefficients = float('NaN')
-        self.gradient_scaling = float('NaN')
+        self.cost_functions_coefficients = np.nan
+        self.gradient_scaling = np.nan
         self.cost_function_threshold = 0
-        self.min_parameters = float('NaN')
-        self.max_parameters = float('NaN')
-        self.step_threshold = float('NaN')
-        self.vx_obs = float('NaN')
-        self.vy_obs = float('NaN')
-        self.vz_obs = float('NaN')
-        self.vel_obs = float('NaN')
-        self.thickness_obs = float('NaN')
-        self.surface_obs = float('NaN')
+        self.min_parameters = np.nan
+        self.max_parameters = np.nan
+        self.step_threshold = np.nan
+        self.vx_obs = np.nan
+        self.vy_obs = np.nan
+        self.vz_obs = np.nan
+        self.vel_obs = np.nan
+        self.thickness_obs = np.nan
+        self.surface_obs = np.nan
 
-    #set defaults
         self.setdefaultparameters()
-
     #}}}
 
     def __repr__(self):  # {{{
-        string = '   inversion parameters:'
-        string = "%s\n%s" % (string, fielddisplay(self, 'iscontrol', 'is inversion activated?'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'control_parameters', 'ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'nsteps', 'number of optimization searches'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'cost_functions', 'indicate the type of response for each optimization step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'cost_function_threshold', 'misfit convergence criterion. Default is 1%, NaN if not applied'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'maxiter_per_step', 'maximum iterations during each optimization step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'gradient_scaling', 'scaling factor on gradient direction during optimization, for each optimization step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'step_threshold', 'decrease threshold for misfit, default is 30%'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vx_obs', 'observed velocity x component [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vy_obs', 'observed velocity y component [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'vel_obs', 'observed velocity magnitude [m / yr]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'thickness_obs', 'observed thickness [m]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'surface_obs', 'observed surface elevation [m]'))
-        string = "%s\n%s" % (string, 'Available cost functions:')
-        string = "%s\n%s" % (string, '   101: SurfaceAbsVelMisfit')
-        string = "%s\n%s" % (string, '   102: SurfaceRelVelMisfit')
-        string = "%s\n%s" % (string, '   103: SurfaceLogVelMisfit')
-        string = "%s\n%s" % (string, '   104: SurfaceLogVxVyMisfit')
-        string = "%s\n%s" % (string, '   105: SurfaceAverageVelMisfit')
-        string = "%s\n%s" % (string, '   201: ThicknessAbsMisfit')
-        string = "%s\n%s" % (string, '   501: DragCoefficientAbsGradient')
-        string = "%s\n%s" % (string, '   502: RheologyBbarAbsGradient')
-        string = "%s\n%s" % (string, '   503: ThicknessAbsGradient')
-        return string
+        s = '   inversion parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'iscontrol', 'is inversion activated?'))
+        s += '{}\n'.format(fielddisplay(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity'))
+        s += '{}\n'.format(fielddisplay(self, 'control_parameters', 'ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'))
+        s += '{}\n'.format(fielddisplay(self, 'nsteps', 'number of optimization searches'))
+        s += '{}\n'.format(fielddisplay(self, 'cost_functions', 'indicate the type of response for each optimization step'))
+        s += '{}\n'.format(fielddisplay(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'))
+        s += '{}\n'.format(fielddisplay(self, 'cost_function_threshold', 'misfit convergence criterion. Default is 1%, NaN if not applied'))
+        s += '{}\n'.format(fielddisplay(self, 'maxiter_per_step', 'maximum iterations during each optimization step'))
+        s += '{}\n'.format(fielddisplay(self, 'gradient_scaling', 'scaling factor on gradient direction during optimization, for each optimization step'))
+        s += '{}\n'.format(fielddisplay(self, 'step_threshold', 'decrease threshold for misfit, default is 30%'))
+        s += '{}\n'.format(fielddisplay(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex'))
+        s += '{}\n'.format(fielddisplay(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex'))
+        s += '{}\n'.format(fielddisplay(self, 'vx_obs', 'observed velocity x component [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vy_obs', 'observed velocity y component [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'vel_obs', 'observed velocity magnitude [m / yr]'))
+        s += '{}\n'.format(fielddisplay(self, 'thickness_obs', 'observed thickness [m]'))
+        s += '{}\n'.format(fielddisplay(self, 'surface_obs', 'observed surface elevation [m]'))
+        s += '{}\n'.format('Available cost functions:')
+        s += '{}\n'.format('   101: SurfaceAbsVelMisfit')
+        s += '{}\n'.format('   102: SurfaceRelVelMisfit')
+        s += '{}\n'.format('   103: SurfaceLogVelMisfit')
+        s += '{}\n'.format('   104: SurfaceLogVxVyMisfit')
+        s += '{}\n'.format('   105: SurfaceAverageVelMisfit')
+        s += '{}\n'.format('   201: ThicknessAbsMisfit')
+        s += '{}\n'.format('   501: DragCoefficientAbsGradient')
+        s += '{}\n'.format('   502: RheologyBbarAbsGradient')
+        s += '{}\n'.format('   503: ThicknessAbsGradient')
+        return s
     #}}}
 
-    def extrude(self, md):  # {{{
-        self.vx_obs = project3d(md, 'vector', self.vx_obs, 'type', 'node')
-        self.vy_obs = project3d(md, 'vector', self.vy_obs, 'type', 'node')
-        self.vel_obs = project3d(md, 'vector', self.vel_obs, 'type', 'node')
-        self.thickness_obs = project3d(md, 'vector', self.thickness_obs, 'type', 'node')
-        if not np.any(np.isnan(self.cost_functions_coefficients)):
-            self.cost_functions_coefficients = project3d(md, 'vector', self.cost_functions_coefficients, 'type', 'node')
-        if not np.any(np.isnan(self.min_parameters)):
-            self.min_parameters = project3d(md, 'vector', self.min_parameters, 'type', 'node')
-        if not np.any(np.isnan(self.max_parameters)):
-            self.max_parameters = project3d(md, 'vector', self.max_parameters, 'type', 'node')
-        return self
-    #}}}
-
     def setdefaultparameters(self):  # {{{
-
         #default is incomplete adjoint for now
         self.incomplete_adjoint = 1
         #parameter to be inferred by control methods (only
@@ -114,13 +97,26 @@
         #cost_function_threshold is a criteria to stop the control methods.
         #if J[n] - J[n - 1] / J[n] < criteria, the control run stops
         #NaN if not applied
-        self.cost_function_threshold = float('NaN')  #not activated
+        self.cost_function_threshold = np.nan  #not activated
+        return self
+    #}}}
 
+    def extrude(self, md):  # {{{
+        self.vx_obs = project3d(md, 'vector', self.vx_obs, 'type', 'node')
+        self.vy_obs = project3d(md, 'vector', self.vy_obs, 'type', 'node')
+        self.vel_obs = project3d(md, 'vector', self.vel_obs, 'type', 'node')
+        self.thickness_obs = project3d(md, 'vector', self.thickness_obs, 'type', 'node')
+        if not np.any(np.isnan(self.cost_functions_coefficients)):
+            self.cost_functions_coefficients = project3d(md, 'vector', self.cost_functions_coefficients, 'type', 'node')
+        if not np.any(np.isnan(self.min_parameters)):
+            self.min_parameters = project3d(md, 'vector', self.min_parameters, 'type', 'node')
+        if not np.any(np.isnan(self.max_parameters)):
+            self.max_parameters = project3d(md, 'vector', self.max_parameters, 'type', 'node')
         return self
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if not self.iscontrol:
             return md
 
@@ -139,17 +135,17 @@
         md = checkfield(md, 'fieldname', 'inversion.min_parameters', 'size', [md.mesh.numberofvertices, num_controls])
         md = checkfield(md, 'fieldname', 'inversion.max_parameters', 'size', [md.mesh.numberofvertices, num_controls])
 
-    #Only SSA, HO and FS are supported right now
+        # Only SSA, HO and FS are supported right now
         if solution == 'StressbalanceSolution':
             if not (md.flowequation.isSSA or md.flowequation.isHO or md.flowequation.isFS or md.flowequation.isL1L2):
                 md.checkmessage("'inversion can only be performed for SSA, HO or FS ice flow models")
-
         if solution == 'BalancethicknessSolution':
             md = checkfield(md, 'fieldname', 'inversion.thickness_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
+        elif solution == 'BalancethicknessSoftSolution':
+            md = checkfield(md, 'fieldname', 'inversion.thickness_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
         else:
             md = checkfield(md, 'fieldname', 'inversion.vx_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
             md = checkfield(md, 'fieldname', 'inversion.vy_obs', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
-
         return md
     # }}}
 
@@ -176,12 +172,12 @@
         WriteData(fid, prefix, 'object', self, 'fieldname', 'thickness_obs', 'format', 'DoubleMat', 'mattype', 1)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'surface_obs', 'format', 'DoubleMat', 'mattype', 1)
 
-    #process control parameters
+        # Process control parameters
         num_control_parameters = len(self.control_parameters)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'control_parameters', 'format', 'StringArray')
         WriteData(fid, prefix, 'data', num_control_parameters, 'name', 'md.inversion.num_control_parameters', 'format', 'Integer')
 
-    #process cost functions
+        # Process cost functions
         num_cost_functions = np.size(self.cost_functions)
         data = marshallcostfunctions(self.cost_functions)
         WriteData(fid, prefix, 'data', data, 'name', 'md.inversion.cost_functions', 'format', 'StringArray')
Index: ../trunk-jpl/src/m/classes/basalforcings.py
===================================================================
--- ../trunk-jpl/src/m/classes/basalforcings.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/basalforcings.py	(revision 25688)
@@ -1,56 +1,48 @@
+import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
 from project3d import project3d
-from checkfield import checkfield
 from WriteData import WriteData
-import numpy as np
 
 
 class basalforcings(object):
-    """
-    BASAL FORCINGS class definition
+    """BASAL FORCINGS class definition
 
-       Usage:
-          basalforcings = basalforcings()
+    Usage:
+        basalforcings = basalforcings()
     """
 
     def __init__(self):  # {{{
-        self.groundedice_melting_rate = float('NaN')
-        self.floatingice_melting_rate = float('NaN')
-        self.geothermalflux = float('NaN')
+        self.groundedice_melting_rate = np.nan
+        self.floatingice_melting_rate = np.nan
+        self.geothermalflux = np.nan
 
-    #set defaults
         self.setdefaultparameters()
-
     #}}}
 
     def __repr__(self):  # {{{
-        string = "   basal forcings parameters:"
-
-        string = "%s\n%s" % (string, fielddisplay(self, "groundedice_melting_rate", "basal melting rate (positive if melting) [m / yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "floatingice_melting_rate", "basal melting rate (positive if melting) [m / yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "geothermalflux", "geothermal heat flux [W / m^2]"))
-        return string
+        s = '   basal forcings parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, "groundedice_melting_rate", "basal melting rate (positive if melting) [m / yr]"))
+        s += '{}\n'.format(fielddisplay(self, "floatingice_melting_rate", "basal melting rate (positive if melting) [m / yr]"))
+        s += '{}\n'.format(fielddisplay(self, "geothermalflux", "geothermal heat flux [W / m^2]"))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
         self.groundedice_melting_rate = project3d(md, 'vector', self.groundedice_melting_rate, 'type', 'node', 'layer', 1)
         self.floatingice_melting_rate = project3d(md, 'vector', self.floatingice_melting_rate, 'type', 'node', 'layer', 1)
-        self.geothermalflux = project3d(md, 'vector', self.geothermalflux, 'type', 'node', 'layer', 1)  #bedrock only gets geothermal flux
+        self.geothermalflux = project3d(md, 'vector', self.geothermalflux, 'type', 'node', 'layer', 1) # Bedrock only gets geothermal flux
         return self
     #}}}
 
     def initialize(self, md):  # {{{
         if np.all(np.isnan(self.groundedice_melting_rate)):
-            self.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices))
+            self.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices, ))
             print("      no basalforcings.groundedice_melting_rate specified: values set as zero")
-
         if np.all(np.isnan(self.floatingice_melting_rate)):
-            self.floatingice_melting_rate = np.zeros((md.mesh.numberofvertices))
+            self.floatingice_melting_rate = np.zeros((md.mesh.numberofvertices, ))
             print("      no basalforcings.floatingice_melting_rate specified: values set as zero")
-    #if np.all(np.isnan(self.geothermalflux)):
-    #self.geothermalflux = np.zeros((md.mesh.numberofvertices))
-    #print "      no basalforcings.geothermalflux specified: values set as zero"
-
         return self
     #}}}
 
@@ -59,27 +51,21 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-
-        if 'MasstransportAnalysis' in analyses and not (solution == 'TransientSolution' and not md.transient.ismasstransport):
+        if 'MasstransportAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.ismasstransport:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.floatingice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
-
         if 'BalancethicknessAnalysis' in analyses:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'basalforcings.floatingice_melting_rate', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
-
-        if 'ThermalAnalysis' in analyses and not (solution == 'TransientSolution' and not md.transient.isthermal):
+        if 'ThermalAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.isthermal:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.floatingice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.geothermalflux', 'NaN', 1, 'Inf', 1, 'timeseries', 1, '>=', 0)
-
         return md
     # }}}
 
     def marshall(self, prefix, md, fid):  # {{{
-
         yts = md.constants.yts
-
         WriteData(fid, prefix, 'name', 'md.basalforcings.model', 'data', 1, 'format', 'Integer')
         WriteData(fid, prefix, 'object', self, 'fieldname', 'groundedice_melting_rate', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'floatingice_melting_rate', 'format', 'DoubleMat', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', md.constants.yts)
Index: ../trunk-jpl/src/m/classes/thermal.py
===================================================================
--- ../trunk-jpl/src/m/classes/thermal.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/thermal.py	(revision 25688)
@@ -1,13 +1,13 @@
 import numpy as np
+
+from checkfield import checkfield
+from fielddisplay import fielddisplay
 from project3d import project3d
-from fielddisplay import fielddisplay
-from checkfield import checkfield
 from WriteData import WriteData
 
 
 class thermal(object):
-    """
-    THERMAL class definition
+    """THERMAL class definition
 
        Usage:
           thermal = thermal()
@@ -27,26 +27,23 @@
         self.watercolumn_upperlimit = 0
         self.fe = 'P1'
         self.requested_outputs = []
-
-    #set defaults
         self.setdefaultparameters()
-
     #}}}
 
     def __repr__(self):  # {{{
-        string = '   Thermal solution parameters:'
-        string = "%s\n%s" % (string, fielddisplay(self, 'spctemperature', 'temperature constraints (NaN means no constraint) [K]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'stabilization', '0: no, 1: artificial_diffusivity, 2: SUPG'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'maxiter', 'maximum number of non linear iterations'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'reltol', 'relative tolerance criterion'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'penalty_lock', 'stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'penalty_threshold', 'threshold to declare convergence of thermal solution (default is 0)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isenthalpy', 'use an enthalpy formulation to include temperate ice (default is 0)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isdynamicbasalspc', 'enable dynamic setting of basal forcing. required for enthalpy formulation (default is 0)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isdrainicecolumn', 'wether waterfraction drainage is enabled for enthalpy formulation (default is 1)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'watercolumn_upperlimit', 'upper limit of basal watercolumn for enthalpy formulation (default is 1000m)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-        return string
+        s = '   Thermal solution parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'spctemperature', 'temperature constraints (NaN means no constraint) [K]'))
+        s += '{}\n'.format(fielddisplay(self, 'stabilization', '0: no, 1: artificial_diffusivity, 2: SUPG'))
+        s += '{}\n'.format(fielddisplay(self, 'maxiter', 'maximum number of non linear iterations'))
+        s += '{}\n'.format(fielddisplay(self, 'reltol', 'relative tolerance criterion'))
+        s += '{}\n'.format(fielddisplay(self, 'penalty_lock', 'stabilize unstable thermal constraints that keep zigzagging after n iteration (default is 0, no stabilization)'))
+        s += '{}\n'.format(fielddisplay(self, 'penalty_threshold', 'threshold to declare convergence of thermal solution (default is 0)'))
+        s += '{}\n'.format(fielddisplay(self, 'isenthalpy', 'use an enthalpy formulation to include temperate ice (default is 0)'))
+        s += '{}\n'.format(fielddisplay(self, 'isdynamicbasalspc', 'enable dynamic setting of basal forcing. required for enthalpy formulation (default is 0)'))
+        s += '{}\n'.format(fielddisplay(self, 'isdrainicecolumn', 'wether waterfraction drainage is enabled for enthalpy formulation (default is 1)'))
+        s += '{}\n'.format(fielddisplay(self, 'watercolumn_upperlimit', 'upper limit of basal watercolumn for enthalpy formulation (default is 1000m)'))
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
@@ -63,7 +60,6 @@
             return ['Enthalpy', 'Temperature', 'Waterfraction', 'Watercolumn', 'BasalforcingsGroundediceMeltingRate']
         else:
             return ['Temperature', 'BasalforcingsGroundediceMeltingRate']
-
     #}}}
 
     def setdefaultparameters(self):  # {{{
@@ -90,18 +86,15 @@
         #default output
         self.requested_outputs = ['default']
         return self
-
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if ('ThermalAnalysis' not in analyses and 'EnthalpyAnalysis' not in analyses) or (solution == 'TransientSolution' and not md.transient.isthermal):
             return md
-
         md = checkfield(md, 'fieldname', 'thermal.stabilization', 'numel', [1], 'values', [0, 1, 2])
         md = checkfield(md, 'fieldname', 'thermal.spctemperature', 'Inf', 1, 'timeseries', 1)
         md = checkfield(md, 'fieldname', 'thermal.requested_outputs', 'stringrow', 1)
-
         if 'EnthalpyAnalysis' in analyses and md.thermal.isenthalpy and md.mesh.dimension() == 3:
             md = checkfield(md, 'fieldname', 'thermal.isdrainicecolumn', 'numel', [1], 'values', [0, 1])
             md = checkfield(md, 'fieldname', 'thermal.watercolumn_upperlimit', '>=', 0)
@@ -122,7 +115,6 @@
                 if np.isnan(md.stressbalance.reltol):
                     md.checkmessage("for a steadystate computation, thermal.reltol (relative convergence criterion) must be defined!")
                 md = checkfield(md, 'fieldname', 'thermal.reltol', '>', 0., 'message', "reltol must be larger than zero")
-
         return md
     # }}}
 
Index: ../trunk-jpl/src/m/classes/frictionjosh.py
===================================================================
--- ../trunk-jpl/src/m/classes/frictionjosh.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/frictionjosh.py	(revision 25688)
@@ -1,3 +1,5 @@
+import numpy as np
+
 from checkfield import checkfield
 from fielddisplay import fielddisplay
 from project3d import project3d
@@ -5,32 +7,31 @@
 
 
 class frictionjosh(object):
-    '''
-    FRICTION class definition
+    """FRICTIONJOSH class definition
 
-        Usage:
-            frictionjosh = frictionjosh()
-    '''
+    Usage:
+        frictionjosh = frictionjosh()
+    """
 
     def __init__(self):  # {{{
-        self.coefficient = float('NaN')
-        self.pressure_adjusted_temperature = float('NaN')
+        self.coefficient = np.nan
+        self.pressure_adjusted_temperature = np.nan
         self.gamma = 0
         self.effective_pressure_limit = 0
-        #set defaults
+
         self.setdefaultparameters()
         #self.requested_outputs = []
     #}}}
 
     def __repr__(self):  # {{{
-        string = "Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s - 1) * u_b, \n(effective stress Neff = rho_ice * g * thickness + rho_water * g * base, r = q / p and s = 1 / p)"
-
-        string = "%s\n%s" % (string, fielddisplay(self, "coefficient", "friction coefficient [SI]"))
-        string = "%s\n%s" % (string, fielddisplay(self, 'pressure_adjusted_temperature', 'friction pressure_adjusted_temperature (T - Tpmp) [K]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'gamma', '(T - Tpmp)/gamma [K]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'effective_pressure_limit', 'Neff do not allow to fall below a certain limit: effective_pressure_limit * rho_ice * g * thickness (default 0)'))
-        #string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-        return string
+        s = 'Basal shear stress parameters: Sigma_b = coefficient^2 * Neff ^r * |u_b|^(s - 1) * u_b,\n'
+        s += '(effective stress Neff = rho_ice * g * thickness + rho_water * g * base, r = q / p and s = 1 / p)\n'
+        s += '{}\n'.format(fielddisplay(self, "coefficient", "friction coefficient [SI]"))
+        s += '{}\n'.format(fielddisplay(self, 'pressure_adjusted_temperature', 'friction pressure_adjusted_temperature (T - Tpmp) [K]'))
+        s += '{}\n'.format(fielddisplay(self, 'gamma', '(T - Tpmp)/gamma [K]'))
+        s += '{}\n'.format(fielddisplay(self, 'effective_pressure_limit', 'Neff do not allow to fall below a certain limit: effective_pressure_limit * rho_ice * g * thickness (default 0)'))
+        #s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
@@ -52,16 +53,14 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
+        # Early return
         if 'StressbalanceAnalysis' not in analyses and 'ThermalAnalysis' not in analyses:
             return md
-
         md = checkfield(md, 'fieldname', 'friction.coefficient', 'timeseries', 1, 'NaN', 1, 'Inf', 1)
         md = checkfield(md, 'fieldname', 'friction.pressure_adjusted_temperature','NaN',1,'Inf',1)
         md = checkfield(md, 'fieldname', 'friction.gamma','numel',1,'NaN',1,'Inf',1,'>',0.)
         md = checkfield(md, 'fieldname', 'friction.effective_pressure_limit', 'numel', [1], '>=', 0)
-
-        #Check that temperature is provided
+        # Check that temperature is provided
         md = checkfield(md,'fieldname','initialization.temperature','NaN',1,'Inf',1,'size','universal')
         return md
     # }}}
@@ -72,5 +71,4 @@
         WriteData(fid,prefix,'class','friction','object',self,'fieldname','pressure_adjusted_temperature','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts)
         WriteData(fid,prefix,'class','friction','object',self,'fieldname','gamma','format','Double')
         WriteData(fid,prefix,'object',self,'class','friction','fieldname','effective_pressure_limit','format','Double')
-
     # }}}
Index: ../trunk-jpl/src/m/classes/transient.py
===================================================================
--- ../trunk-jpl/src/m/classes/transient.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/transient.py	(revision 25688)
@@ -1,83 +1,79 @@
+from checkfield import checkfield
 from fielddisplay import fielddisplay
-from checkfield import checkfield
 from WriteData import WriteData
 
 
 class transient(object):
-    """
-    TRANSIENT class definition
+    """TRANSIENT class definition
 
-       Usage:
-          transient = transient()
+    Usage:
+        transient = transient()
     """
 
     def __init__(self):  # {{{
-        self.issmb = False
-        self.ismasstransport = False
-        self.isstressbalance = False
-        self.isthermal = False
-        self.isgroundingline = False
-        self.isgia = False
-        self.isesa = False
-        self.isdamageevolution = False
-        self.ismovingfront = False
-        self.ishydrology = False
-        self.isslr = False
-        self.iscoupler = False
+        self.issmb = 0
+        self.ismasstransport = 0
+        self.isstressbalance = 0
+        self.isthermal = 0
+        self.isgroundingline = 0
+        self.isgia = 0
+        self.isesa = 0
+        self.isdamageevolution = 0
+        self.ismovingfront = 0
+        self.ishydrology = 0
+        self.isslr = 0
+        self.iscoupler = 0
         self.amr_frequency = 0
-        self.isoceancoupling = False
+        self.isoceancoupling = 0
         self.requested_outputs = []
 
-    #set defaults
         self.setdefaultparameters()
+    #}}}
 
-    #}}}
     def __repr__(self):  # {{{
-        string = '   transient solution parameters:'
-        string = "%s\n%s" % (string, fielddisplay(self, 'issmb', 'indicates if a surface mass balance solution is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'ismasstransport', 'indicates if a masstransport solution is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isstressbalance', 'indicates if a stressbalance solution is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isthermal', 'indicates if a thermal solution is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isgroundingline', 'indicates if a groundingline migration is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isgia', 'indicates if a postglacial rebound is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isesa', 'indicates whether an elastic adjustment model is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isdamageevolution', 'indicates whether damage evolution is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'ismovingfront', 'indicates whether a moving front capability is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'ishydrology', 'indicates whether an hydrology model is used'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isslr', 'indicates if a sea level rise solution is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isoceancoupling', 'indicates whether coupling with an ocean model is used in the transient'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'iscoupler', 'indicates whether different models are being run with need for coupling'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'amr_frequency', 'frequency at which mesh is refined in simulations with multiple time_steps'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'list of additional outputs requested'))
-        return string
+        s = '   transient solution parameters:\n'
+        s += '{}\n'.format(fielddisplay(self, 'issmb', 'indicates if a surface mass balance solution is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'ismasstransport', 'indicates if a masstransport solution is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isstressbalance', 'indicates if a stressbalance solution is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isthermal', 'indicates if a thermal solution is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isgroundingline', 'indicates if a groundingline migration is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isgia', 'indicates if a postglacial rebound is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isesa', 'indicates whether an elastic adjustment model is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isdamageevolution', 'indicates whether damage evolution is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'ismovingfront', 'indicates whether a moving front capability is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'ishydrology', 'indicates whether an hydrology model is used'))
+        s += '{}\n'.format(fielddisplay(self, 'isslr', 'indicates if a sea level rise solution is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'isoceancoupling', 'indicates whether coupling with an ocean model is used in the transient'))
+        s += '{}\n'.format(fielddisplay(self, 'iscoupler', 'indicates whether different models are being run with need for coupling'))
+        s += '{}\n'.format(fielddisplay(self, 'amr_frequency', 'frequency at which mesh is refined in simulations with multiple time_steps'))
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'list of additional outputs requested'))
+        return s
     #}}}
 
     def defaultoutputs(self, md):  # {{{
-
         if self.issmb:
             return ['SmbMassBalance']
         else:
             return []
-
     #}}}
 
     def deactivateall(self):  #{{{
-        self.issmb = False
-        self.ismasstransport = False
-        self.isstressbalance = False
-        self.isthermal = False
-        self.isgroundingline = False
-        self.isgia = False
-        self.isesa = False
-        self.isdamageevolution = False
-        self.ismovingfront = False
-        self.ishydrology = False
-        self.isslr = False
-        self.isoceancoupling = False
-        self.iscoupler = False
+        self.issmb = 0
+        self.ismasstransport = 0
+        self.isstressbalance = 0
+        self.isthermal = 0
+        self.isgroundingline = 0
+        self.isgia = 0
+        self.isesa = 0
+        self.isdamageevolution = 0
+        self.ismovingfront = 0
+        self.ishydrology = 0
+        self.isslr = 0
+        self.isoceancoupling = 0
+        self.iscoupler = 0
         self.amr_frequency = 0
 
-    #default output
+        # Default output
         self.requested_outputs = []
         return self
     #}}}
@@ -84,22 +80,22 @@
 
     def setdefaultparameters(self):  # {{{
         #full analysis: Stressbalance, Masstransport and Thermal but no groundingline migration for now
-        self.issmb = True
-        self.ismasstransport = True
-        self.isstressbalance = True
-        self.isthermal = True
-        self.isgroundingline = False
-        self.isgia = False
-        self.isesa = False
-        self.isdamageevolution = False
-        self.ismovingfront = False
-        self.ishydrology = False
-        self.isslr = False
-        self.isoceancoupling = False
-        self.iscoupler = False
+        self.issmb = 1
+        self.ismasstransport = 1
+        self.isstressbalance = 1
+        self.isthermal = 1
+        self.isgroundingline = 0
+        self.isgia = 0
+        self.isesa = 0
+        self.isdamageevolution = 0
+        self.ismovingfront = 0
+        self.ishydrology = 0
+        self.isslr = 0
+        self.isoceancoupling = 0
+        self.iscoupler = 0
         self.amr_frequency = 0
 
-    #default output
+        # Default output
         self.requested_outputs = ['default']
         return self
     #}}}
@@ -123,13 +119,11 @@
         md = checkfield(md, 'fieldname', 'transient.isoceancoupling', 'numel', [1], 'values', [0, 1])
         md = checkfield(md, 'fieldname', 'transient.iscoupler', 'numel', [1], 'values', [0, 1])
         md = checkfield(md, 'fieldname', 'transient.amr_frequency', 'numel', [1], '>=', 0, 'NaN', 1, 'Inf', 1)
-        md = checkfield(md, 'fieldname', 'transient.requested_outputs', 'stringrow', 1)
 
-        if (solution != 'TransientSolution') and (md.transient.iscoupling):
+        if solution != 'TransientSolution' and md.transient.iscoupling:
             md.checkmessage("Coupling with ocean can only be done in transient simulations!")
-        if (md.transient.isdamageevolution and not hasattr(md.materials, 'matdamageice')):
+        if md.transient.isdamageevolution and not hasattr(md.materials, 'matdamageice'):
             md.checkmessage("requesting damage evolution but md.materials is not of class matdamageice")
-
         return md
     # }}}
 
@@ -149,7 +143,7 @@
         WriteData(fid, prefix, 'object', self, 'fieldname', 'iscoupler', 'format', 'Boolean')
         WriteData(fid, prefix, 'object', self, 'fieldname', 'amr_frequency', 'format', 'Integer')
 
-    #process requested outputs
+        # Process requested outputs
         outputs = self.requested_outputs
         indices = [i for i, x in enumerate(outputs) if x == 'default']
         if len(indices) > 0:
Index: ../trunk-jpl/src/m/classes/taoinversion.py
===================================================================
--- ../trunk-jpl/src/m/classes/taoinversion.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/taoinversion.py	(revision 25688)
@@ -1,18 +1,25 @@
 import numpy as np
-from project3d import project3d
-from WriteData import WriteData
+
 from checkfield import checkfield
 from IssmConfig import IssmConfig
 from marshallcostfunctions import marshallcostfunctions
+from project3d import project3d
 from supportedcontrols import *
 from supportedcostfunctions import *
+from WriteData import WriteData
 
 
-class taoinversion(object):
+class taoinversion(object): #{{{
+    """TAOINVERSION class definition
+
+    Usage:
+        inversion = taoinversion()
+    """
+
     def __init__(self):
         self.iscontrol = 0
         self.incomplete_adjoint = 0
-        self.control_parameters = float('NaN')
+        self.control_parameters = np.nan
         self.maxsteps = 0
         self.maxiter = 0
         self.fatol = 0
@@ -21,54 +28,56 @@
         self.grtol = 0
         self.gttol = 0
         self.algorithm = ''
-        self.cost_functions = float('NaN')
-        self.cost_functions_coefficients = float('NaN')
-        self.min_parameters = float('NaN')
-        self.max_parameters = float('NaN')
-        self.vx_obs = float('NaN')
-        self.vy_obs = float('NaN')
-        self.vz_obs = float('NaN')
-        self.vel_obs = float('NaN')
-        self.thickness_obs = float('NaN')
-        self.surface_obs = float('NaN')
+        self.cost_functions = np.nan
+        self.cost_functions_coefficients = np.nan
+        self.min_parameters = np.nan
+        self.max_parameters = np.nan
+        self.vx_obs = np.nan
+        self.vy_obs = np.nan
+        self.vz_obs = np.nan
+        self.vel_obs = np.nan
+        self.thickness_obs = np.nan
+        self.surface_obs = np.nan
+
         self.setdefaultparameters()
+    #}}}
 
     def __repr__(self):
-        string = '   taoinversion parameters:'
-        string = "%s\n%s" % (string, fieldstring(self, 'iscontrol', 'is inversion activated?'))
-        string = "%s\n%s" % (string, fieldstring(self, 'mantle_viscosity', 'mantle viscosity constraints (NaN means no constraint) (Pa s)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'lithosphere_thickness', 'lithosphere thickness constraints (NaN means no constraint) (m)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'cross_section_shape', "1: square-edged, 2: elliptical - edged surface"))
-        string = "%s\n%s" % (string, fieldstring(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity'))
-        string = "%s\n%s" % (string, fieldstring(self, 'control_parameters', 'ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'))
-        string = "%s\n%s" % (string, fieldstring(self, 'maxsteps', 'maximum number of iterations (gradient computation)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'maxiter', 'maximum number of Function evaluation (forward run)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'fatol', 'convergence criterion: f(X) - f(X * ) (X: current iteration, X * : "true" solution, f: cost function)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'frtol', 'convergence criterion: |f(X) - f(X * )| / |f(X * )|'))
-        string = "%s\n%s" % (string, fieldstring(self, 'gatol', 'convergence criterion: ||g(X)|| (g: gradient of the cost function)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'grtol', 'convergence criterion: ||g(X)|| / |f(X)|'))
-        string = "%s\n%s" % (string, fieldstring(self, 'gttol', 'convergence criterion: ||g(X)|| / ||g(X0)|| (g(X0): gradient at initial guess X0)'))
-        string = "%s\n%s" % (string, fieldstring(self, 'algorithm', 'minimization algorithm: ''tao_blmvm'', ''tao_cg'', ''tao_lmvm'''))
-        string = "%s\n%s" % (string, fieldstring(self, 'cost_functions', 'indicate the type of response for each optimization step'))
-        string = "%s\n%s" % (string, fieldstring(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'))
-        string = "%s\n%s" % (string, fieldstring(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex'))
-        string = "%s\n%s" % (string, fieldstring(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex'))
-        string = "%s\n%s" % (string, fieldstring(self, 'vx_obs', 'observed velocity x component [m / yr]'))
-        string = "%s\n%s" % (string, fieldstring(self, 'vy_obs', 'observed velocity y component [m / yr]'))
-        string = "%s\n%s" % (string, fieldstring(self, 'vel_obs', 'observed velocity magnitude [m / yr]'))
-        string = "%s\n%s" % (string, fieldstring(self, 'thickness_obs', 'observed thickness [m]'))
-        string = "%s\n%s" % (string, fieldstring(self, 'surface_obs', 'observed surface elevation [m]'))
-        string = "%s\n%s" % (string, 'Available cost functions:')
-        string = "%s\n%s" % (string, '   101: SurfaceAbsVelMisfit')
-        string = "%s\n%s" % (string, '   102: SurfaceRelVelMisfit')
-        string = "%s\n%s" % (string, '   103: SurfaceLogVelMisfit')
-        string = "%s\n%s" % (string, '   104: SurfaceLogVxVyMisfit')
-        string = "%s\n%s" % (string, '   105: SurfaceAverageVelMisfit')
-        string = "%s\n%s" % (string, '   201: ThicknessAbsMisfit')
-        string = "%s\n%s" % (string, '   501: DragCoefficientAbsGradient')
-        string = "%s\n%s" % (string, '   502: RheologyBbarAbsGradient')
-        string = "%s\n%s" % (string, '   503: ThicknessAbsGradient')
-        return string
+        s = '   taoinversion parameters:\n'
+        s += '{}'.format(fieldstring(self, 'iscontrol', 'is inversion activated?'))
+        s += '{}'.format(fieldstring(self, 'mantle_viscosity', 'mantle viscosity constraints (NaN means no constraint) (Pa s)'))
+        s += '{}'.format(fieldstring(self, 'lithosphere_thickness', 'lithosphere thickness constraints (NaN means no constraint) (m)'))
+        s += '{}'.format(fieldstring(self, 'cross_section_shape', "1: square-edged, 2: elliptical - edged surface"))
+        s += '{}'.format(fieldstring(self, 'incomplete_adjoint', '1: linear viscosity, 0: non - linear viscosity'))
+        s += '{}'.format(fieldstring(self, 'control_parameters', 'ex: {''FrictionCoefficient''}, or {''MaterialsRheologyBbar''}'))
+        s += '{}'.format(fieldstring(self, 'maxsteps', 'maximum number of iterations (gradient computation)'))
+        s += '{}'.format(fieldstring(self, 'maxiter', 'maximum number of Function evaluation (forward run)'))
+        s += '{}'.format(fieldstring(self, 'fatol', 'convergence criterion: f(X) - f(X * ) (X: current iteration, X * : "true" solution, f: cost function)'))
+        s += '{}'.format(fieldstring(self, 'frtol', 'convergence criterion: |f(X) - f(X * )| / |f(X * )|'))
+        s += '{}'.format(fieldstring(self, 'gatol', 'convergence criterion: ||g(X)|| (g: gradient of the cost function)'))
+        s += '{}'.format(fieldstring(self, 'grtol', 'convergence criterion: ||g(X)|| / |f(X)|'))
+        s += '{}'.format(fieldstring(self, 'gttol', 'convergence criterion: ||g(X)|| / ||g(X0)|| (g(X0): gradient at initial guess X0)'))
+        s += '{}'.format(fieldstring(self, 'algorithm', 'minimization algorithm: ''tao_blmvm'', ''tao_cg'', ''tao_lmvm'''))
+        s += '{}'.format(fieldstring(self, 'cost_functions', 'indicate the type of response for each optimization step'))
+        s += '{}'.format(fieldstring(self, 'cost_functions_coefficients', 'cost_functions_coefficients applied to the misfit of each vertex and for each control_parameter'))
+        s += '{}'.format(fieldstring(self, 'min_parameters', 'absolute minimum acceptable value of the inversed parameter on each vertex'))
+        s += '{}'.format(fieldstring(self, 'max_parameters', 'absolute maximum acceptable value of the inversed parameter on each vertex'))
+        s += '{}'.format(fieldstring(self, 'vx_obs', 'observed velocity x component [m / yr]'))
+        s += '{}'.format(fieldstring(self, 'vy_obs', 'observed velocity y component [m / yr]'))
+        s += '{}'.format(fieldstring(self, 'vel_obs', 'observed velocity magnitude [m / yr]'))
+        s += '{}'.format(fieldstring(self, 'thickness_obs', 'observed thickness [m]'))
+        s += '{}'.format(fieldstring(self, 'surface_obs', 'observed surface elevation [m]'))
+        s += '{}'.format('Available cost functions:')
+        s += '{}'.format('   101: SurfaceAbsVelMisfit')
+        s += '{}'.format('   102: SurfaceRelVelMisfit')
+        s += '{}'.format('   103: SurfaceLogVelMisfit')
+        s += '{}'.format('   104: SurfaceLogVxVyMisfit')
+        s += '{}'.format('   105: SurfaceAverageVelMisfit')
+        s += '{}'.format('   201: ThicknessAbsMisfit')
+        s += '{}'.format('   501: DragCoefficientAbsGradient')
+        s += '{}'.format('   502: RheologyBbarAbsGradient')
+        s += '{}'.format('   503: ThicknessAbsGradient')
+        return s
 
     def setdefaultparameters(self):
         #default is incomplete adjoint for now
Index: ../trunk-jpl/src/m/classes/SMBcomponents.py
===================================================================
--- ../trunk-jpl/src/m/classes/SMBcomponents.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/SMBcomponents.py	(revision 25688)
@@ -1,40 +1,47 @@
+import numpy as np
+
+from checkfield import *
 from fielddisplay import fielddisplay
-from checkfield import *
 from project3d import *
 from WriteData import *
 
 
 class SMBcomponents(object):
-    """
-    SMBcomponents Class definition
+    """SMBCOMPONENTS class definition
 
-       Usage:
-          SMBcomponents = SMBcomponents()
+    Usage:
+        SMBcomponents = SMBcomponents()
     """
 
-    def __init__(self):  # {{{
-        self.accumulation = float('NaN')
-        self.runoff = float('NaN')
-        self.evaporation = float('NaN')
+    def __init__(self, *args):  # {{{
         self.isclimatology = 0
+        self.accumulation = np.nan
+        self.runoff = np.nan
+        self.evaporation = np.nan
         self.steps_per_step = 1
         self.averaging = 0
         self.requested_outputs = []
+
+        nargs = len(args)
+        if nargs == 0:
+            pass
+        else:
+            raise Exception('constructor not supported')
     # }}}
 
     def __repr__(self):  # {{{
-        string = "   surface forcings parameters (SMB = accumulation-runoff-evaporation) :"
-        string = "%s\n%s" % (string, fielddisplay(self, 'accumulation', 'accumulated snow [m/yr ice eq]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'runoff', 'amount of ice melt lost from the ice column [m/yr ice eq]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'evaporation', 'mount of ice lost to evaporative processes [m/yr ice eq]'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'isclimatology', 'repeat all forcings when past last forcing time (default false)'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'))
-        string = "%s\n%s" % (string, fielddisplay(self, 'averaging', 'averaging methods from short to long steps'))
-        string = "%s\n\t\t%s" % (string, '0: Arithmetic (default)')
-        string = "%s\n\t\t%s" % (string, '1: Geometric')
-        string = "%s\n\t\t%s" % (string, '2: Harmonic')
-        string = "%s\n%s" % (string, fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
-        return string
+        s = '   surface forcings parameters (SMB = accumulation-runoff-evaporation):\n'
+        s += '{}\n'.format(fielddisplay(self, 'accumulation', 'accumulated snow [m/yr ice eq]'))
+        s += '{}\n'.format(fielddisplay(self, 'runoff', 'amount of ice melt lost from the ice column [m/yr ice eq]'))
+        s += '{}\n'.format(fielddisplay(self, 'evaporation', 'mount of ice lost to evaporative processes [m/yr ice eq]'))
+        s += '{}\n'.format(fielddisplay(self, 'isclimatology', 'repeat all forcings when past last forcing time (default false)'))
+        s += '{}\n'.format(fielddisplay(self, 'steps_per_step', 'number of smb steps per time step'))
+        s += '{}\n'.format(fielddisplay(self, 'averaging', 'averaging methods from short to long steps'))
+        s += '\t\t{}\n'.format('0: Arithmetic (default)')
+        s += '\t\t{}\n'.format('1: Geometric')
+        s += '\t\t{}\n'.format('2: Harmonic')
+        s += '{}\n'.format(fielddisplay(self, 'requested_outputs', 'additional outputs requested'))
+        return s
     # }}}
 
     def extrude(self, md):  # {{{
@@ -52,7 +59,6 @@
         if np.all(np.isnan(self.accumulation)):
             self.accumulation = np.zeros((md.mesh.numberofvertices))
             print("      no SMB.accumulation specified: values set as zero")
-
         if np.all(np.isnan(self.runoff)):
             self.runoff = np.zeros((md.mesh.numberofvertices))
             print("      no SMB.runoff specified: values set as zero")
@@ -60,7 +66,6 @@
         if np.all(np.isnan(self.evaporation)):
             self.evaporation = np.zeros((md.mesh.numberofvertices))
             print("      no SMB.evaporation specified: values set as zero")
-
         return self
     # }}}
 
@@ -73,12 +78,15 @@
             md = checkfield(md, 'fieldname', 'smb.accumulation', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
             md = checkfield(md, 'fieldname', 'smb.runoff', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
             md = checkfield(md, 'fieldname', 'smb.evaporation', 'size', [md.mesh.numberofvertices], 'NaN', 1, 'Inf', 1)
-
         md = checkfield(md, 'fieldname', 'smb.steps_per_step', '>=', 1, 'numel', [1])
         md = checkfield(md, 'fieldname', 'smb.averaging', 'numel', [1], 'values', [0, 1, 2])
         md = checkfield(md, 'fieldname', 'masstransport.requested_outputs', 'stringrow', 1)
         md = checkfield(md, 'fieldname', 'smb.isclimatology', 'values', [0, 1])
-
+        if self.isclimatology:
+            md = checkfield(md, 'fieldname', 'smb.accumulation', 'size', [md.mesh.numberofvertices + 1],
+                'message', 'accumulation must have md.mesh.numberofvertices+1 rows in order to force a climatology')
+            md = checkfield(md, 'fieldname', 'smb.runoff', 'size', [md.mesh.numberofvertices + 1], 'message', 'runoff must have md.mesh.numberofvertices+1 rows in order to force a climatology')
+            md = checkfield(md, 'fieldname', 'smb.evaporation', 'size', [md.mesh.numberofvertices + 1], 'message', 'evaporation must have md.mesh.numberofvertices+1 rows in order to force a climatology')
         return md
     # }}}
 
Index: ../trunk-jpl/src/m/classes/mismipbasalforcings.py
===================================================================
--- ../trunk-jpl/src/m/classes/mismipbasalforcings.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/mismipbasalforcings.py	(revision 25688)
@@ -1,36 +1,35 @@
+import numpy as np
+
+from checkfield import checkfield
 from fielddisplay import fielddisplay
 from project3d import project3d
-from checkfield import checkfield
 from WriteData import WriteData
-import numpy as np
 
 
 class mismipbasalforcings(object):
-    """
-    MISMIP Basal Forcings class definition
+    """MISMIP Basal Forcings class definition
 
     Usage:
-    mismipbasalforcings = mismipbasalforcings()
+        mismipbasalforcings = mismipbasalforcings()
     """
 
     def __init__(self):  # {{{
-        self.groundedice_melting_rate = float('NaN')
-        self.meltrate_factor = float('NaN')
-        self.threshold_thickness = float('NaN')
-        self.upperdepth_melt = float('NaN')
-        self.geothermalflux = float('NaN')
+        self.groundedice_melting_rate = np.nan
+        self.meltrate_factor = np.nan
+        self.threshold_thickness = np.nan
+        self.upperdepth_melt = np.nan
+        self.geothermalflux = np.nan
         self.setdefaultparameters()
-
     #}}}
 
     def __repr__(self):  # {{{
-        string = " MISMIP + basal melt parameterization\n"
-        string = "%s\n%s" % (string, fielddisplay(self, "groundedice_melting_rate", "basal melting rate (positive if melting) [m / yr]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "meltrate_factor", "Melt - rate rate factor [1 / yr] (sign is opposite to MISMIP + benchmark to remain consistent with ISSM convention of positive values for melting)"))
-        string = "%s\n%s" % (string, fielddisplay(self, "threshold_thickness", "Threshold thickness for saturation of basal melting [m]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "upperdepth_melt", "Depth above which melt rate is zero [m]"))
-        string = "%s\n%s" % (string, fielddisplay(self, "geothermalflux", "Geothermal heat flux [W / m^2]"))
-        return string
+        s = '   MISMIP + basal melt parameterization\n'
+        s += '{}\n'.format(fielddisplay(self, "groundedice_melting_rate", "basal melting rate (positive if melting) [m / yr]"))
+        s += '{}\n'.format(fielddisplay(self, "meltrate_factor", "Melt - rate rate factor [1 / yr] (sign is opposite to MISMIP + benchmark to remain consistent with ISSM convention of positive values for melting)"))
+        s += '{}\n'.format(fielddisplay(self, "threshold_thickness", "Threshold thickness for saturation of basal melting [m]"))
+        s += '{}\n'.format(fielddisplay(self, "upperdepth_melt", "Depth above which melt rate is zero [m]"))
+        s += '{}\n'.format(fielddisplay(self, "geothermalflux", "Geothermal heat flux [W / m^2]"))
+        return s
     #}}}
 
     def extrude(self, md):  # {{{
@@ -42,7 +41,7 @@
     def initialize(self, md):  # {{{
         if np.all(np.isnan(self.groundedice_melting_rate)):
             self.groundedice_melting_rate = np.zeros((md.mesh.numberofvertices))
-            print(' no basalforcings.groundedice_melting_rate specified: values set as zero')
+            print('no basalforcings.groundedice_melting_rate specified: values set as zero')
         if np.all(np.isnan(self.geothermalflux)):
             self.geothermalflux = np.zeros((md.mesh.numberofvertices))
             print("      no basalforcings.geothermalflux specified: values set as zero")
@@ -58,20 +57,18 @@
     #}}}
 
     def checkconsistency(self, md, solution, analyses):  # {{{
-        #Early return
-        if 'MasstransportAnalysis' in analyses and not (solution == 'TransientSolution' and md.transient.ismasstransport == 0):
+        # Early return
+        if 'MasstransportAnalysis' in analyses and not solution == 'TransientSolution' and not md.transient.ismasstransport:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.meltrate_factor', '>=', 0, 'numel', [1])
             md = checkfield(md, 'fieldname', 'basalforcings.threshold_thickness', '>=', 0, 'numel', [1])
             md = checkfield(md, 'fieldname', 'basalforcings.upperdepth_melt', '<=', 0, 'numel', [1])
-
         if 'BalancethicknessAnalysis' in analyses:
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'size', [md.mesh.numberofvertices])
             md = checkfield(md, 'fieldname', 'basalforcings.meltrate_factor', '>=', 0, 'numel', [1])
             md = checkfield(md, 'fieldname', 'basalforcings.threshold_thickness', '>=', 0, 'numel', [1])
             md = checkfield(md, 'fieldname', 'basalforcings.upperdepth_melt', '<=', 0, 'numel', [1])
-
-        if 'ThermalAnalysis' in analyses and not (solution == 'TransientSolution' and md.transient.isthermal == 0):
+        if 'ThermalAnalysis' in analyses and not (solution == 'TransientSolution' and not md.transient.isthermal):
             md = checkfield(md, 'fieldname', 'basalforcings.groundedice_melting_rate', 'NaN', 1, 'Inf', 1, 'timeseries', 1)
             md = checkfield(md, 'fieldname', 'basalforcings.meltrate_factor', '>=', 0, 'numel', [1])
             md = checkfield(md, 'fieldname', 'basalforcings.threshold_thickness', '>=', 0, 'numel', [1])
@@ -84,7 +81,6 @@
         yts = md.constants.yts
         if yts != 365.2422 * 24. * 3600.:
             print('WARNING: value of yts for MISMIP + runs different from ISSM default!')
-
         WriteData(fid, prefix, 'name', 'md.basalforcings.model', 'data', 3, 'format', 'Integer')
         WriteData(fid, prefix, 'object', self, 'fieldname', 'groundedice_melting_rate', 'format', 'DoubleMat', 'name', 'md.basalforcings.groundedice_melting_rate', 'mattype', 1, 'scale', 1. / yts, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts)
         WriteData(fid, prefix, 'object', self, 'fieldname', 'geothermalflux', 'name', 'md.basalforcings.geothermalflux', 'format', 'DoubleMat', 'mattype', 1, 'timeserieslength', md.mesh.numberofvertices + 1, 'yts', yts)
Index: ../trunk-jpl/src/m/qmu/qmupart2npart.py
===================================================================
--- ../trunk-jpl/src/m/qmu/qmupart2npart.py	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/qmupart2npart.py	(revision 25688)
@@ -1,10 +1,6 @@
-import numpy as np
-
-
 def qmupart2npart(vector):
     # Vector is full of -1 (no partition) and 0 to npart. We need to identify 
     # npart.
+    npart = int(vector.max() + 1) # cast to int as we may have a NumPy floating point type, which cannot be used as an argument to function range (see src/m/qmu/setupdesign/QmuSetupVariables.py)
 
-    npart = vector.max() + 1
-
     return npart
Index: ../trunk-jpl/src/m/qmu/dakota_out_parse.m
===================================================================
--- ../trunk-jpl/src/m/qmu/dakota_out_parse.m	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/dakota_out_parse.m	(revision 25688)
@@ -89,12 +89,12 @@
 			fline=fgetl(fidi);
 			[ntokens,tokens]=fltokens(fline);
 			method=tokens{1}{1};
-			display(sprintf('Dakota method =''%s''.',method));
+			display(sprintf('Dakota method = ''%s''.',method));
 		elseif strcmp(tokens{1}{1}(7),'N')
 			[fline]=findline(fidi,'methodName = ');
 			[ntokens,tokens]=fltokens(fline);
 			method=tokens{1}{3};
-			display(sprintf('Dakota methodName=''%s''.',method));
+			display(sprintf('Dakota methodName = ''%s''.',method));
 		end
 	end
 
Index: ../trunk-jpl/src/m/qmu/postqmu.py
===================================================================
--- ../trunk-jpl/src/m/qmu/postqmu.py	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/postqmu.py	(revision 25688)
@@ -1,3 +1,4 @@
+from copy import deepcopy
 from os import getpid, stat
 from os.path import isfile
 from subprocess import call
@@ -4,7 +5,7 @@
 
 from dakota_out_parse import *
 from helpers import *
-from loadresultsfromdisk import *
+import loadresultsfromdisk as loadresults
 
 
 def postqmu(md):
@@ -47,16 +48,17 @@
     if md.qmu.output and md.qmu.statistics.method[0]['name'] == 'None':
         if md.qmu.method.method == 'nond_sampling':
             dakotaresults.modelresults = []
-            md2 = copy.deepcopy(md)
+            md2 = deepcopy(md)
             md2.qmu.isdakota = 0
             for i in range(md2.qmu.method.params.samples):
-                print('reading qmu file {}.outbin.{}'.format(md2.miscellaneous.name, i))
-                md2 = loadresultsfromdisk(md2, '{}.outbin.{}'.format(md2.miscellaneous.name, i))
+                outbin_name = '{}.outbin.{}'.format(md2.miscellaneous.name, (i + 1))
+                print('reading qmu file {}'.format(outbin_name))
+                md2 = loadresults.loadresultsfromdisk(md2, outbin_name)
                 dakotaresults.modelresults.append(md2.results)
 
     if md.qmu.statistics.method[0]['name'] != 'None':
         md.qmu.isdakota = 0
-        md = loadresultsfromdisk(md, [md.miscellaneous.name,'.stats'])
+        md = loadresults.loadresultsfromdisk(md, '{}.stats'.format(md.miscellaneous.name))
         md.qmu.isdakota = 1
 
     # put dakotaresults in their right location.
Index: ../trunk-jpl/src/m/qmu/qmupart2npart.m
===================================================================
--- ../trunk-jpl/src/m/qmu/qmupart2npart.m	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/qmupart2npart.m	(revision 25688)
@@ -1,8 +1,3 @@
 function npart=qmupart2npart(vector)
-
-	%vector is full of -1 (no partition) and 0 to npart.  We need to 
-	%identify npart
-
+	%vector is full of -1 (no partition) and 0 to npart. We need to identify npart=
 	npart=max(vector)+1;
-
-
Index: ../trunk-jpl/src/m/qmu/dakota_out_parse.py
===================================================================
--- ../trunk-jpl/src/m/qmu/dakota_out_parse.py	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/dakota_out_parse.py	(revision 25688)
@@ -86,12 +86,12 @@
                 fline = fidi.readline()
                 [ntokens, tokens] = fltokens(fline)
                 method = tokens[0].strip()
-                print('Dakota method =\'' + method + '\'.')
+                print('Dakota method = \'' + method + '\'.')
             elif fline[6] in ['N', 'n']:
                 fline = findline(fidi, 'methodName = ')
                 [ntokens, tokens] = fltokens(fline)
                 method = tokens[2].strip()
-                print('Dakota methodName = "' + method + '".')
+                print('Dakota methodName = \'' + method + '\'.')
 
     #  loop through the file to find the function evaluation summary
         counter = 0
Index: ../trunk-jpl/src/m/qmu/setupdesign/QmuSetupVariables.py
===================================================================
--- ../trunk-jpl/src/m/qmu/setupdesign/QmuSetupVariables.py	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/setupdesign/QmuSetupVariables.py	(revision 25688)
@@ -1,4 +1,5 @@
 from copy import deepcopy
+
 from helpers import *
 from MatlabFuncs import *
 from normal_uncertain import *
@@ -7,21 +8,23 @@
 
 
 def QmuSetupVariables(md, variables):
-    #get descriptor
+    """QMUSETUPVARIABLES function
+    """
+
+    # Get descriptor
     descriptor = variables.descriptor
 
-    #decide whether this is a distributed variable, which will drive whether we expand it into npart values,
-    #or if we just carry it forward as is.
+    # Decide whether this is a distributed variable, which will drive whether we expand it into npart values, or if we just carry it forward as is
 
+    # Ok, key off according to type of descriptor
     dvar = []
-
-    #ok, key off according to type of descriptor:
     if strncmp(descriptor, 'scaled_', 7):
-        #we have a scaled variable, expand it over the partition. First recover the partition.
+        # We have a scaled variable, expand it over the partition. First recover the partition.
         partition = variables.partition
-        #figure out number of partitions
+        # Figure out number of partitions
         npart = qmupart2npart(partition)
-        #figure out number of time steps
+
+        # Figure out number of time steps
         nt = variables.nsteps
 
         if isinstance(variables, uniform_uncertain):
@@ -43,13 +46,12 @@
             if nstddev != nt or nmean != nt:
                 raise RuntimeError('QmuSetupVariables error message: stddev and mean fields should have the same number of cols as the number of time steps')
 
-        #ok, dealing with semi-discrete distributed variable. Distribute according to how many
-        #partitions we want, and number of time steps
+        # Ok, dealing with semi-discrete distributed variable. Distribute according to how many partitions we want, and number of time steps
         if nt == 1:
             for j in range(npart):
                 dvar.append(deepcopy(variables))
 
-                # text parsing in dakota requires literal "'identifier'" not just "identifier"
+                # Text parsing in Dakota requires literal "'identifier'" not just "identifier"
                 dvar[-1].descriptor = "'" + str(variables.descriptor) + '_' + str(j + 1) + "'"
 
                 if isinstance(variables, uniform_uncertain):
@@ -63,7 +65,7 @@
                 for k in range(nt):
                     dvar.append(deepcopy(variables))
 
-                    # text parsing in dakota requires literal "'identifier'" not just "identifier"
+                    # Text parsing in Dakota requires literal "'identifier'" not just "identifier"
                     dvar[-1].descriptor = "'" + str(variables.descriptor) + '_' + str(j + 1) + '_' + str(k + 1) + "'"
 
                     if isinstance(variables, uniform_uncertain):
@@ -75,7 +77,7 @@
     else:
         dvar.append(deepcopy(variables))
 
-        # text parsing in dakota requires literal "'identifier'" not just "identifier"
+        # text parsing in Dakota requires literal "'identifier'" not just "identifier"
         dvar[-1].descriptor = "'" + str(variables.descriptor) + "'"
 
     return dvar
Index: ../trunk-jpl/src/m/qmu/preqmu.py
===================================================================
--- ../trunk-jpl/src/m/qmu/preqmu.py	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/preqmu.py	(revision 25688)
@@ -10,7 +10,7 @@
 
 
 def preqmu(md, options):
-    """QMU - apply Quantification of Margins and Uncertainties techniques
+    """PREQMU - apply Quantification of Margins and Uncertainties techniques
     to a solution sequence (like stressbalance.py, progonstic.py, etc ...),
     using the Dakota software from Sandia.
 
@@ -35,24 +35,25 @@
     options.addfielddefault('imethod', 0)
     options.addfielddefault('iparams', 0)
 
-    # when running in library mode, the in file needs to be called md.miscellaneous.name.qmu.in
+    # When running in library mode, the in file needs to be called md.miscellaneous.name.qmu.in
     qmufile = md.miscellaneous.name
 
-    # retrieve variables and resposnes for this particular analysis.
+    # Retrieve variables and resposnes for this particular analysis.
     #print type(md.qmu.variables)
     #print md.qmu.variables.__dict__
-    #print ivar
+    # Print ivar
     variables = md.qmu.variables  #[ivar]
     responses = md.qmu.responses  #[iresp]
 
-    # expand variables and responses
+    # Expand variables and responses
     #print variables.__dict__
     #print responses.__dict__
     variables = expandvariables(md, variables)
     responses = expandresponses(md, responses)
 
-    # go through variables and responses, and check they don't have more than
-    #   md.qmu.numberofpartitions values. Also determine numvariables and numresponses
+    # Go through variables and responses, and check they don't have more than
+    # md.qmu.numberofpartitions values. Also determine numvariables and 
+    # numresponses
     #{{{
     numvariables = 0
     variable_fieldnames = fieldnames(variables)
@@ -81,11 +82,11 @@
         numresponses = numresponses + np.size(vars(responses)[field_name])
     #}}}
 
-    # create in file for dakota
+    # Create in file for Dakota
     #dakota_in_data(md.qmu.method[imethod], variables, responses, md.qmu.params[iparams], qmufile)
     dakota_in_data(md.qmu.method, variables, responses, md.qmu.params, qmufile)
 
-    # build a list of variables and responses descriptors. the list is not expanded.
+    # Build a list of variables and responses descriptors. the list is not expanded.
     #{{{
     variabledescriptors = []
     # variable_fieldnames = fieldnames(md.qmu.variables[ivar])
@@ -114,7 +115,7 @@
             responsedescriptors.append(fieldresponses.descriptor)
     #}}}
 
-    #build a list of variable partitions
+    # Build a list of variable partitions
     variablepartitions = []
     variablepartitions_npart = []
     variablepartitions_nt = []
@@ -124,10 +125,13 @@
         fieldvariable = vars(md.qmu.variables)[field_name]
         if type(fieldvariable) in [list, np.ndarray]:
             for j in range(np.size(fieldvariable)):
-                if fieldvariable[j].isscaled():
+                if fieldvariable[j].isscaled() or fieldvariable[j].isdistributed():
                     variablepartitions.append(fieldvariable[j].partition)
                     variablepartitions_npart.append(qmupart2npart(fieldvariable[j].partition))
-                    variablepartitions_nt.append(fieldvariable[j].nsteps)
+                    if hasattr(fieldvariable[j], 'nsteps'):
+                        variablepartitions_nt.append(fieldvariable[j].nsteps)
+                    else:
+                        variablepartitions_nt.append(1)
                 else:
                     variablepartitions.append([])
                     variablepartitions_npart.append(0)
@@ -136,15 +140,18 @@
             if fieldvariable.isscaled():
                 variablepartitions.append(fieldvariable.partition)
                 variablepartitions_npart.append(qmupart2npart(fieldvariable.partition))
-                variablepartitions_nt.append(fieldvariable.nsteps)
+                if hasattr(fieldvariable, 'nsteps'):
+                    variablepartitions_nt.append(fieldvariable.nsteps)
+                else:
+                    variablepartitions_nt.append(1)
             else:
                 variablepartitions.append([])
                 variablepartitions_npart.append(0)
                 variablepartitions_nt.append(1)
 
-    #build a list of response partitions
+    # Build a list of response partitions
     responsepartitions = []
-    responsepartitions_npart = []
+    responsepartitions_npart = np.array([])
     response_fieldnames = fieldnames(md.qmu.responses)
     for i in range(len(response_fieldnames)):
         field_name = response_fieldnames[i]
@@ -153,19 +160,22 @@
             for j in range(np.size(fieldresponses)):
                 if fieldresponse[j].isscaled():
                     responsepartitions.append(fieldresponse[j].partition)
-                    responsepartitions_npart.append(qmupart2npart(fieldresponse[j].partition))
+                    responsepartitions_npart = np.append(responsepartitions_npart, qmupart2npart(fieldresponse[j].partition))
                 else:
                     responsepartitions.append([])
-                    responsepartitions_npart.append(0)
+                    responsepartitions_npart = np.append(responsepartitions_npart, 0)
         else:
             if fieldresponse.isscaled():
                 responsepartitions.append(fieldresponse.partition)
-                responsepartitions_npart.append(qmupart2npart(fieldresponse.partition))
+                responsepartitions_npart = np.append(responsepartitions_npart, qmupart2npart(fieldresponse.partition))
             else:
                 responsepartitions.append([])
-                responsepartitions_npart.append(0)
+                responsepartitions_npart = np.append(responsepartitions_npart, 0)
 
-    # register the fields that will be needed by the Qmu model.
+    if responsepartitions_npart.shape[0] != 1:
+        responsepartitions_npart = responsepartitions_npart.reshape(1, -1)
+
+    # Register the fields that will be needed by the Qmu model.
     md.qmu.numberofresponses = numresponses
     md.qmu.variabledescriptors = variabledescriptors
     md.qmu.variablepartitions = variablepartitions
@@ -175,9 +185,9 @@
     md.qmu.responsepartitions = responsepartitions
     md.qmu.responsepartitions_npart = responsepartitions_npart
 
-    # now, we have to provide all the info necessary for the solutions to compute the
-    # responses. For ex, if mass_flux is a response, we need a profile of points.
-    # For a misfit, we need the observed velocity, etc ...
+    # Now, we have to provide all the info necessary for the solutions to 
+    # compute the responses. For example, if mass_flux is a response, we need a 
+    # profile of points. For a misfit, we need the observed velocity, etc.
     md = process_qmu_response_data(md)
 
     return md
Index: ../trunk-jpl/src/m/qmu/preqmu.m
===================================================================
--- ../trunk-jpl/src/m/qmu/preqmu.m	(revision 25687)
+++ ../trunk-jpl/src/m/qmu/preqmu.m	(revision 25688)
@@ -100,7 +100,7 @@
 	if fieldvariable.isscaled() | fieldvariable.isdistributed();
 		variablepartitions{end+1}=fieldvariable.partition;
 		variablepartitions_npart(end+1)=qmupart2npart(fieldvariable.partition);
-		if isfield(struct(fieldvariable),'nsteps'),
+		if isprop(fieldvariable,'nsteps'),
 			variablepartitions_nt(end+1)=fieldvariable.nsteps;
 		else
 			variablepartitions_nt(end+1)=1;
Index: ../trunk-jpl/src/m/solve/marshall.py
===================================================================
--- ../trunk-jpl/src/m/solve/marshall.py	(revision 25687)
+++ ../trunk-jpl/src/m/solve/marshall.py	(revision 25688)
@@ -4,15 +4,15 @@
 
 
 def marshall(md):
-    '''
-    MARSHALL - outputs a compatible binary file from @model md, for certain solution type.
+    """MARSHALL - outputs a compatible binary file from @model md, for certain solution type.
 
-        The routine creates a compatible binary file from @model md
-        This binary file will be used for parallel runs in JPL-package
+    The routine creates a compatible binary file from @model md
+    his binary file will be used for parallel runs in JPL-package
 
-        Usage:
-            marshall(md)
-    '''
+    Usage:
+        marshall(md)
+    """
+
     if md.verbose.solution:
         print("marshalling file {}.bin".format(md.miscellaneous.name))
 
@@ -22,7 +22,9 @@
     except IOError as e:
         raise IOError("marshall error message: could not open '%s.bin' file for binary writing. Due to: ".format(md.miscellaneous.name), e)
 
-    for field in md.properties():
+    fields = md.properties()
+    fields.sort() # sort fields so that comparison of binary files is easier
+    for field in fields:
         #Some properties do not need to be marshalled
         if field in ['results', 'radaroverlay', 'toolkits', 'cluster', 'private']:
             continue
@@ -41,9 +43,11 @@
     #close file
     try:
         fid.close()
-        # # Uncomment the following to make a copy of the binary input file for 
-        # # debugging purposes (can be fed into scripts/ReadBin.py).
-        copy_cmd = "cp {}.bin {}.py.bin".format(md.miscellaneous.name, md.miscellaneous.name)
-        subprocess.call(copy_cmd, shell=True)
+
+        # Uncomment the following to make a copy of the binary input file for 
+        # debugging purposes (can be fed into scripts/ReadBin.py).
+        # copy_cmd = "cp {}.bin {}.py.bin".format(md.miscellaneous.name, md.miscellaneous.name)
+        # subprocess.call(copy_cmd, shell=True)
+
     except IOError as e:
         print("marshall error message: could not close file '{}.bin' due to:".format(md.miscellaneous.name), e)
Index: ../trunk-jpl/src/m/solve/marshall.m
===================================================================
--- ../trunk-jpl/src/m/solve/marshall.m	(revision 25687)
+++ ../trunk-jpl/src/m/solve/marshall.m	(revision 25688)
@@ -17,8 +17,8 @@
 	error(['marshall error message: could not open ' [md.miscellaneous.name '.bin'],' file for binary writing']);
 end
 
-%Go through all model fields: check that it is a class and call checkconsistency
-fields=properties('model');
+% Go through all model fields: check that it is a class and call checkconsistency
+fields=sort(properties('model')); %sort fields so that comparison of binary files is easier
 for i=1:length(fields),
 	field=fields{i};
 
@@ -42,9 +42,11 @@
 
 %close file
 st=fclose(fid);
-% % Uncomment the following to make a copy of the binary input file for debugging 
-% % purposes (can be fed into scripts/ReadBin.py).
-copyfile([md.miscellaneous.name '.bin'], [md.miscellaneous.name '.m.bin'])
+
+% Uncomment the following to make a copy of the binary input file for debugging 
+% purposes (can be fed into scripts/ReadBin.py).
+% copyfile([md.miscellaneous.name '.bin'], [md.miscellaneous.name '.m.bin'])
+
 if st==-1,
 	error(['marshall error message: could not close file ' [md.miscellaneous.name '.bin']]);
 end
Index: ../trunk-jpl/src/m/solve/WriteData.py
===================================================================
--- ../trunk-jpl/src/m/solve/WriteData.py	(revision 25687)
+++ ../trunk-jpl/src/m/solve/WriteData.py	(revision 25688)
@@ -163,10 +163,10 @@
             fid.write(pack('i', 1))
         for i in range(s[0]):
             if np.ndim(data) == 1:
-                fid.write(pack('d', float(data[i])))  #get to the "c" convention, hence the transpose
+                fid.write(pack('d', float(data[i])))
             else:
                 for j in range(s[1]):
-                    fid.write(pack('d', float(data[i][j])))  #get to the "c" convention, hence the transpose
+                    fid.write(pack('d', float(data[i][j])))
     # }}}
 
     elif datatype == 'DoubleMat':  # {{{
@@ -351,11 +351,10 @@
 
 
 def FormatToCode(datatype):  # {{{
+    """ FORMATTOCODE - This routine takes the datatype string, and hardcodes it 
+    into an integer, which is passed along the record, in order to identify the 
+    nature of the dataset being sent.
     """
-    This routine takes the datatype string, and hardcodes it into an integer, which
-    is passed along the record, in order to identify the nature of the dataset being
-    sent.
-    """
     if datatype == 'Boolean':
         code = 1
     elif datatype == 'Integer':
Index: ../trunk-jpl/src/m/solve/loadresultsfromcluster.py
===================================================================
--- ../trunk-jpl/src/m/solve/loadresultsfromcluster.py	(revision 25687)
+++ ../trunk-jpl/src/m/solve/loadresultsfromcluster.py	(revision 25688)
@@ -42,8 +42,8 @@
                 filelist.append('dakota_tabular.dat')
         if md.qmu.output and md.qmu.statistics.method[0]['name'] == 'None':
             if md.qmu.method.method == 'nond_sampling':
-                for i in range(len(md.qmu.method.params.samples)):
-                    filelist.append(md.miscellaneous.name + '.outbin' + str(i))
+                for i in range(md.qmu.method.params.samples):
+                    filelist.append(md.miscellaneous.name + '.outbin.' + str(i + 1))
         if md.qmu.statistics.method[0]['name'] != 'None':
             filelist.append(md.miscellaneous.name + '.stats')
     else:
Index: ../trunk-jpl/src/m/miscellaneous/pretty_print.m
===================================================================
--- ../trunk-jpl/src/m/miscellaneous/pretty_print.m	(revision 25687)
+++ ../trunk-jpl/src/m/miscellaneous/pretty_print.m	(revision 25688)
@@ -14,64 +14,57 @@
 %   large data structure (default is length of 6).
 %   - Add an argument that allows the user to specify the number of values that 
 %   they would like to display from the head and tail of each dimension of 
-%   'data'.
+%   'data' (default is 3 from each end).
+%   - Add an argument that allows the user to designate the number of 
+%   significant figures to print for each floating point value (default is 8).
 
 if ndims(data)==1
 	if length(data)>6
-		disp(sprintf('[%d %d %d ... %d %d %d]',data(1),data(2),data(3),data(end-2),data(end-1),data(end)));
+		output=sprintf('[%.8f %.8f %.8f ... %.8f %.8f %.8f]',data(1),data(2),data(3),data(end-2),data(end-1),data(end));
 	else
-		disp(data);
+		output=sprintf('%.8f',data);
 	end
 elseif ndims(data)==2
 	shape=size(data);
 	if shape(1)>6
-		% if shape(2)==1
-		% 	disp('NOTE: Single column printed as row!');
-		% 	disp(sprintf('[%d %d %d ... %d %d %d]',data(1,1),data(2,1),data(3,1),data(end-2,1),data(end-1,1),data(end,1)));
-		% else
 		if shape(2)>6
-			disp('[');
-			disp(sprintf('[%d %d %d ... %d %d %d]',data(1,1),data(1,2),data(1,3),data(1,end-2),data(1,end-1),data(1,end)));
-			disp(sprintf('[%d %d %d ... %d %d %d]',data(2,1),data(2,2),data(2,3),data(2,end-2),data(2,end-1),data(2,end)));
-			disp(sprintf('[%d %d %d ... %d %d %d]',data(3,1),data(3,2),data(3,3),data(3,end-2),data(3,end-1),data(3,end)));
-			disp('...');
-			disp(sprintf('[%d %d %d ... %d %d %d]',data(end-2,1),data(end-2,2),data(end-2,3),data(end-2,end-2),data(end-2,end-1),data(end-2,end)));
-			disp(sprintf('[%d %d %d ... %d %d %d]',data(end-1,1),data(end-1,2),data(end-1,3),data(end-1,end-2),data(end-1,end-1),data(end-1,end)));
-			disp(sprintf('[%d %d %d ... %d %d %d]',data(end,1),data(end,2),data(end,3),data(end,end-2),data(end,end-1),data(end,end)));
-			disp(sprintf(']\n'));
+			output=sprintf('[[%.8f %.8f %.8f ... %.8f %.8f %.8f]\n',data(1,1),data(1,2),data(1,3),data(1,end-2),data(1,end-1),data(1,end));
+			output=sprintf('%s [%.8f %.8f %.8f ... %.8f %.8f %.8f]\n',data(2,1),data(2,2),data(2,3),data(2,end-2),data(2,end-1),data(2,end));
+			output=sprintf('%s [%.8f %.8f %.8f ... %.8f %.8f %.8f]\n',data(3,1),data(3,2),data(3,3),data(3,end-2),data(3,end-1),data(3,end));
+			output=sprintf('%s ...\n',output);
+			output=sprintf('%s [%.8f %.8f %.8f ... %.8f %.8f %.8f]\n',data(end-2,1),data(end-2,2),data(end-2,3),data(end-2,end-2),data(end-2,end-1),data(end-2,end));
+			output=sprintf('%s [%.8f %.8f %.8f ... %.8f %.8f %.8f]\n',data(end-1,1),data(end-1,2),data(end-1,3),data(end-1,end-2),data(end-1,end-1),data(end-1,end));
+			output=sprintf('%s [%.8f %.8f %.8f ... %.8f %.8f %.8f]]',data(end,1),data(end,2),data(end,3),data(end,end-2),data(end,end-1),data(end,end));
 		else
-			disp('[');
-			disp(data(1,:));
-			disp(data(2,:));
-			disp(data(3,:));
-			disp('...');
-			disp(data(end-2,:));
-			disp(data(end-1,:));
-			disp(data(end,:));
-			disp(sprintf(']\n'));
+			output=sprintf('[[%.8f]\n',data(1,:));
+			output=sprintf('%s [%.8f]\n',output,data(2,:));
+			output=sprintf('%s [%.8f]\n',output,data(3,:));
+			output=sprintf('%s ...\n',output);
+			output=sprintf('%s [%.8f]\n',output,data(end-2,:));
+			output=sprintf('%s [%.8f]\n',output,data(end-1,:));
+			output=sprintf('%s [%.8f]]',output,data(end,:));
 		end
 	else
-		% if shape(2)==1
-		% 	data=transpose(data)
-		% 	sprintf('% NOTE: Single column printed as row!');
-		% 	% Get shape of transposed structure
-		% 	shape=size(data);
-		% 	if shape(2)>6
-		% 		disp(sprintf('[%d %d %d ... %d %d %d]',data(1,1),data(2,1),data(3,1),data(end-2,1),data(end-1,1),data(end,1)));
-		% 	else
-		% 		disp(data);
-		% 	end
-		% else
 		if shape(2)>6
-			disp('[');
 			for i=1:shape(1)
-				disp(sprintf('[%d %d %d ... %d %d %d]',data(i,1),data(i,2),data(i,3),data(i,end-2),data(i,end-1),data(i,end)));
+				if i==1
+					output='[';
+				else
+					output=sprintf('%s ',output);
+				end
+
+				output=sprintf('%s[%.8f %.8f %.8f ... %.8f %.8f %.8f]',output,data(i,1),data(i,2),data(i,3),data(i,end-2),data(i,end-1),data(i,end));
+
+				if i==shape(1)
+					output=sprintf('%s]',output);
+				end
 			end
-			disp(sprintf(']\n'));
 		else
-			disp(data);
+			output=sprintf('%.8f',data);
 		end
 	end
 else
-	disp(data);
+	output=sprintf('%.8f',data);
 end
+
+disp(output);
Index: ../trunk-jpl/src/c/modules/FrontalForcingsx
===================================================================
--- ../trunk-jpl/src/c/modules/FrontalForcingsx	(revision 25687)
+++ ../trunk-jpl/src/c/modules/FrontalForcingsx	(revision 25688)

Property changes on: ../trunk-jpl/src/c/modules/FrontalForcingsx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,2 ##
+.deps
+.dirstamp
Index: ../trunk-jpl/src/c/modules/OceanExchangeDatax
===================================================================
--- ../trunk-jpl/src/c/modules/OceanExchangeDatax	(revision 25687)
+++ ../trunk-jpl/src/c/modules/OceanExchangeDatax	(revision 25688)

Property changes on: ../trunk-jpl/src/c/modules/OceanExchangeDatax
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+.deps
Index: ../trunk-jpl/src/c/modules/QmuStatisticsx/QmuStatisticsx.cpp
===================================================================
--- ../trunk-jpl/src/c/modules/QmuStatisticsx/QmuStatisticsx.cpp	(revision 25687)
+++ ../trunk-jpl/src/c/modules/QmuStatisticsx/QmuStatisticsx.cpp	(revision 25688)
@@ -1000,7 +1000,7 @@
 		} /*}}}*/
 	}
 
-	_printf0_("Done with MeanVariance :\n");
+	_printf0_("Done with MeanVariance:\n");
 	IssmComm::SetComm(ISSM_MPI_COMM_WORLD);
 
 } /*}}}*/
@@ -1160,7 +1160,7 @@
 			}
 		}
 	}
-	_printf0_("Done with SampleSeries :\n");
+	_printf0_("Done with SampleSeries:\n");
 	IssmComm::SetComm(ISSM_MPI_COMM_WORLD);
 
 } /*}}}*/
Index: ../trunk-jpl/src/c/modules/QmuStatisticsx
===================================================================
--- ../trunk-jpl/src/c/modules/QmuStatisticsx	(revision 25687)
+++ ../trunk-jpl/src/c/modules/QmuStatisticsx	(revision 25688)

Property changes on: ../trunk-jpl/src/c/modules/QmuStatisticsx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,2 ##
+.deps
+.dirstamp
Index: ../trunk-jpl/src/c/modules/KillIcebergsx
===================================================================
--- ../trunk-jpl/src/c/modules/KillIcebergsx	(revision 25687)
+++ ../trunk-jpl/src/c/modules/KillIcebergsx	(revision 25688)

Property changes on: ../trunk-jpl/src/c/modules/KillIcebergsx
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,2 ##
+.dirstamp
+.deps
Index: ../trunk-jpl/src/c/toolkits/codipack
===================================================================
--- ../trunk-jpl/src/c/toolkits/codipack	(revision 25687)
+++ ../trunk-jpl/src/c/toolkits/codipack	(revision 25688)

Property changes on: ../trunk-jpl/src/c/toolkits/codipack
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+.deps
Index: ../trunk-jpl/src/c/classes/Inputs
===================================================================
--- ../trunk-jpl/src/c/classes/Inputs	(revision 25687)
+++ ../trunk-jpl/src/c/classes/Inputs	(revision 25688)

Property changes on: ../trunk-jpl/src/c/classes/Inputs
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,2 ##
+.deps
+.dirstamp
Index: ../trunk-jpl/src/c/classes/Dakota
===================================================================
--- ../trunk-jpl/src/c/classes/Dakota	(revision 25687)
+++ ../trunk-jpl/src/c/classes/Dakota	(revision 25688)

Property changes on: ../trunk-jpl/src/c/classes/Dakota
___________________________________________________________________
Modified: svn:ignore
## -1 +1,2 ##
 .deps
+.dirstamp
Index: ../trunk-jpl/src/c
===================================================================
--- ../trunk-jpl/src/c	(revision 25687)
+++ ../trunk-jpl/src/c	(revision 25688)

Property changes on: ../trunk-jpl/src/c
___________________________________________________________________
Modified: svn:ignore
## -22,3 +22,4 ##
 issm_slr
 issm_ocean
 issm_dakota
+issm_post
Index: ../trunk-jpl/src/wrappers/CoordTransform
===================================================================
--- ../trunk-jpl/src/wrappers/CoordTransform	(revision 25687)
+++ ../trunk-jpl/src/wrappers/CoordTransform	(revision 25688)

Property changes on: ../trunk-jpl/src/wrappers/CoordTransform
___________________________________________________________________
Added: svn:ignore
## -0,0 +1 ##
+.deps
Index: ../trunk-jpl/test/NightlyRun/test2006.m
===================================================================
--- ../trunk-jpl/test/NightlyRun/test2006.m	(revision 25687)
+++ ../trunk-jpl/test/NightlyRun/test2006.m	(revision 25688)
@@ -52,7 +52,6 @@
 %Materials: 
 md.materials=materials('hydro');
 
-
 %Miscellaneous
 md.miscellaneous.name='test2006';
 
@@ -137,43 +136,44 @@
 	end
 end 
 % }}}
-	%algorithm:  % {{{
-	md.qmu.method     =dakota_method('nond_samp');
-	md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),...
-	'seed',1234,...
-	'samples',10,...
-	'sample_type','random');
-	md.qmu.output=1; 
-	%}}}
-	%parameters % {{{
-	md.qmu.params.direct=true;
-	md.qmu.params.interval_type='forward';
-	md.qmu.params.analysis_driver='matlab';
-	md.qmu.params.evaluation_scheduling='master';
-	md.qmu.params.processors_per_evaluation=2;
-	md.qmu.params.tabular_graphics_data=true; 
-	md.qmu.isdakota=1;
-	md.verbose=verbose(0); md.verbose.qmu=1;
-	% }}}
-	%qmu statistics %{{{
-	md.qmu.statistics.nfiles_per_directory=2;
-	md.qmu.statistics.ndirectories=5;
-	
-	md.qmu.statistics.method(1).name='Histogram';
-	md.qmu.statistics.method(1).fields={'Sealevel','BslrIce'};
-	md.qmu.statistics.method(1).steps=1:10;
-	md.qmu.statistics.method(1).nbins=20;
 
-	md.qmu.statistics.method(2).name='MeanVariance';
-	md.qmu.statistics.method(2).fields={'Sealevel','BslrIce'};
-	md.qmu.statistics.method(2).steps=[1:10];
+%algorithm:  % {{{
+md.qmu.method     =dakota_method('nond_samp');
+md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),...
+'seed',1234,...
+'samples',10,...
+'sample_type','random');
+md.qmu.output=1; 
+%}}}
+%parameters % {{{
+md.qmu.params.direct=true;
+md.qmu.params.interval_type='forward';
+md.qmu.params.analysis_driver='matlab';
+md.qmu.params.evaluation_scheduling='master';
+md.qmu.params.processors_per_evaluation=2;
+md.qmu.params.tabular_graphics_data=true; 
+md.qmu.isdakota=1;
+md.verbose=verbose(0); md.verbose.qmu=1;
+% }}}
+%qmu statistics %{{{
+md.qmu.statistics.nfiles_per_directory=2;
+md.qmu.statistics.ndirectories=5;
 
-	md.qmu.statistics.method(3).name='SampleSeries';
-	md.qmu.statistics.method(3).fields={'Sealevel','BslrIce'};
-	md.qmu.statistics.method(3).steps=[1:10];
-	md.qmu.statistics.method(3).indices=locations;
-	%}}}
+md.qmu.statistics.method(1).name='Histogram';
+md.qmu.statistics.method(1).fields={'Sealevel','BslrIce'};
+md.qmu.statistics.method(1).steps=[1:10];
+md.qmu.statistics.method(1).nbins=20;
 
+md.qmu.statistics.method(2).name='MeanVariance';
+md.qmu.statistics.method(2).fields={'Sealevel','BslrIce'};
+md.qmu.statistics.method(2).steps=[1:10];
+
+md.qmu.statistics.method(3).name='SampleSeries';
+md.qmu.statistics.method(3).fields={'Sealevel','BslrIce'};
+md.qmu.statistics.method(3).steps=[1:10];
+md.qmu.statistics.method(3).indices=locations;
+%}}}
+
 %run transient dakota solution: 
 mds=solve(md,'Transient');
 
@@ -181,7 +181,9 @@
 md.qmu.statistics.method(1).name='None';
 md=solve(md,'Transient');
 
-%compare statistics with our own here: 
+disp(mds.results.StatisticsSolution)
+
+%compare statistics with our own here:
 svalues=mds.results.StatisticsSolution(end).SealevelSamples; %all values at locations. 
 
 dvalues=zeros(md.qmu.method.params.samples,length(locations));
@@ -189,6 +191,9 @@
 	dvalues(i,:)=md.results.dakota.modelresults{i}.TransientSolution(end).Sealevel(locations);
 end
 
+disp(dvalues)
+disp(size(dvalues))
+
 samplesnorm=norm(dvalues-svalues,'fro');
 
 %Fields and tolerances to track changes
Index: ../trunk-jpl/test/NightlyRun/test2006.py
===================================================================
--- ../trunk-jpl/test/NightlyRun/test2006.py	(nonexistent)
+++ ../trunk-jpl/test/NightlyRun/test2006.py	(revision 25688)
@@ -0,0 +1,236 @@
+#Test Name: EarthSlr Dakota Sampling glaciers
+import numpy as np
+
+from dmeth_params_set import *
+from gmshplanet import *
+from gmtmask import *
+from lovenumbers import *
+from materials import *
+from model import *
+from nodalvalue import *
+from normal_uncertain import *
+from response_function import *
+from solve import *
+
+
+# Mesh earth
+md = model()
+md.cluster = generic('name', oshostname(), 'np', 5)
+md.mesh = gmshplanet('radius', 6.371012 * 1e3, 'resolution', 700.) #700 km resolution mesh
+
+# Parameterize solidearth solution
+# Solidearth loading #{{{
+md.solidearth.surfaceload.icethicknesschange = np.zeros((md.mesh.numberofelements, 1))
+md.solidearth.sealevel = np.zeros((md.mesh.numberofvertices, 1))
+md.dsl.global_average_thermosteric_sea_level_change = np.zeros((2, 1))
+md.dsl.sea_surface_height_change_above_geoid = np.zeros((md.mesh.numberofvertices + 1, 1))
+md.dsl.sea_water_pressure_change_at_sea_floor = np.zeros((md.mesh.numberofvertices + 1, 1))
+
+# Antarctica
+late = md.mesh.lat[md.mesh.elements - 1].sum(axis=1) / 3
+longe = md.mesh.long[md.mesh.elements - 1].sum(axis=1) / 3
+pos = np.where(late < -80)[0]
+md.solidearth.surfaceload.icethicknesschange[pos] = -100
+# Greenland
+pos = np.where(np.logical_and.reduce((late > 70, late < 80, longe > -60, longe < -30)))[0]
+md.solidearth.surfaceload.icethicknesschange[pos] = -100
+
+# Elastic loading from love numbers
+md.solidearth.lovenumbers = lovenumbers('maxdeg', 100)
+#}}}
+
+# Mask #{{{
+mask = gmtmask(md.mesh.lat, md.mesh.long)
+icemask = np.ones((md.mesh.numberofvertices, 1))
+pos = np.where(mask == 0)[0]
+icemask[pos] = -1
+pos = np.where(mask[md.mesh.elements - 1].sum(axis=1) < 3)[0]
+icemask[md.mesh.elements[pos, :] - 1] = -1
+md.mask.ice_levelset = icemask
+md.mask.ocean_levelset = -icemask
+
+# Make sure that the elements that have loads are fully grounded
+pos = np.nonzero(md.solidearth.surfaceload.icethicknesschange)[0]
+md.mask.ocean_levelset[md.mesh.elements[pos, :] - 1] = 1
+
+# Make sure wherever there is an ice load, that the mask is set to ice:
+#pos = np.nonzero(md.solidearth.surfaceload.icethicknesschange)[0] # TODO: Do we need to do this twice?
+md.mask.ice_levelset[md.mesh.elements[pos, :] - 1] = -1
+# }}}
+
+md.solidearth.settings.ocean_area_scaling = 0
+
+# Geometry for the bed; arbitrary
+md.geometry.bed = -np.ones((md.mesh.numberofvertices, 1))
+
+# Materials
+md.materials = materials('hydro')
+
+# Miscellaneous
+md.miscellaneous.name = 'test2006'
+
+# Solution parameters
+md.solidearth.settings.reltol = np.nan
+md.solidearth.settings.abstol = 1e-3
+md.solidearth.settings.computesealevelchange = 1
+
+# Max number of iterations reverted back to 10 (i.e. the original default value)
+md.solidearth.settings.maxiter = 10
+
+# Eustatic + rigid + elastic + rotation run
+md.solidearth.settings.rigid = 1
+md.solidearth.settings.elastic = 1
+md.solidearth.settings.rotation = 1
+
+# Transient settings
+md.timestepping.start_time = 0
+md.timestepping.final_time = 10
+md.timestepping.time_step = 1
+md.transient.isslr = 1
+md.transient.issmb = 0
+md.transient.isgia = 1
+md.transient.ismasstransport = 0
+md.transient.isstressbalance = 0
+md.transient.isthermal = 0
+dh = np.asarray(md.solidearth.surfaceload.icethicknesschange).T
+deltathickness = np.zeros((md.mesh.numberofelements + 1, 10))
+for i in range(10):
+    deltathickness[0:-1, i] = dh * (i + 1)
+deltathickness[-1, :] = np.arange(0, 10, 1)
+md.solidearth.surfaceload.icethicknesschange = deltathickness
+
+# Hack
+md.geometry.surface = np.zeros((md.mesh.numberofvertices, 1))
+md.geometry.thickness = np.ones((md.mesh.numberofvertices, 1))
+md.geometry.base = -np.ones((md.mesh.numberofvertices, 1))
+md.geometry.bed = md.geometry.base
+
+# Uncertainty quantification
+# Ice sheets #{{{
+npart = 1
+nt = 1
+partition = -np.ones((md.mesh.numberofelements, 1))
+pos = np.where(late < -80)[0]
+partition[pos] = 0
+pos = np.where(np.logical_and.reduce((late > 70, late < 80, longe > -60, longe < -30)))[0]
+partition[pos] = 0
+
+# Variables
+qmuvar = OrderedStruct()
+qmuvar.surfaceload = normal_uncertain.normal_uncertain(
+    'descriptor',   'scaled_SurfaceloadIceThicknessChange',
+    'mean',         1 * np.ones((npart, nt)),
+    'stddev',       1 * np.ones((npart, nt)), # 10% standard deviation
+    'partition',    partition,
+    'transient',    'on',
+    'nsteps',       nt
+)
+#}}}
+
+# Correlation
+md.qmu.correlation_matrix = []
+
+# Variables final declaration
+md.qmu.variables = OrderedStruct()
+md.qmu.variables.surfaceload = qmuvar.surfaceload
+
+locations = [1, 5, 10, 15, 20]
+
+# Responses #{{{
+md.qmu.responses.sealevel1 = response_function.response_function('descriptor', 'Outputdefinition1')
+md.qmu.responses.sealevel2 = response_function.response_function('descriptor', 'Outputdefinition2')
+md.qmu.responses.sealevel3 = response_function.response_function('descriptor', 'Outputdefinition3')
+md.qmu.responses.sealevel4 = response_function.response_function('descriptor', 'Outputdefinition4')
+md.qmu.responses.sealevel5 = response_function.response_function('descriptor', 'Outputdefinition5')
+
+# Output definitions
+for i in range(len(locations)):
+    if i == 0:
+        md.outputdefinition.definitions = [
+            nodalvalue(
+                'name',             'SNode',
+                'definitionstring', 'Outputdefinition1',
+                'model_string',     'Sealevel',
+                'node',             locations[i]
+            )
+        ]
+    else:
+        md.outputdefinition.definitions.append(
+            nodalvalue(
+                'name',             'SNode',
+                'definitionstring', 'Outputdefinition' + str(i + 1),
+                'model_string',     'Sealevel',
+                'node',             locations[i]
+            )
+        )
+#}}}
+
+# Algorithm #{{{
+md.qmu.method = dakota_method.dakota_method('nond_samp')
+md.qmu.method = dmeth_params_set(
+    md.qmu.method,
+    'seed',             1234,
+    'samples',          10,
+    'sample_type',      'random'
+)
+md.qmu.output = 1
+#}}}
+# Parameters #{{{
+md.qmu.params.direct = True
+md.qmu.params.interval_type = 'forward'
+md.qmu.params.analysis_driver = 'matlab'
+md.qmu.params.evaluation_scheduling = 'master'
+md.qmu.params.processors_per_evaluation = 2
+md.qmu.params.tabular_graphics_data = True
+md.qmu.isdakota = 1
+md.verbose = verbose(0)
+md.verbose.qmu = 1
+#}}}
+# QMU statistics #{{{
+
+# TODO: Abstract reshaping of arrays away to src/m/classes/qmustatistics.py::marshall or src/m/solve/WriteData.py
+#
+md.qmu.statistics.nfiles_per_directory = 2
+md.qmu.statistics.ndirectories = 5
+
+md.qmu.statistics.method[0]['name'] = 'Histogram'
+md.qmu.statistics.method[0]['fields'] = ['Sealevel', 'BslrIce']
+md.qmu.statistics.method[0]['steps'] = np.arange(1, 10 + 1).reshape(1, -1)
+md.qmu.statistics.method[0]['nbins'] = 20
+
+md.qmu.statistics.addmethod()
+md.qmu.statistics.method[1]['name'] = 'MeanVariance'
+md.qmu.statistics.method[1]['fields'] = ['Sealevel', 'BslrIce']
+md.qmu.statistics.method[1]['steps'] = np.arange(1, 10 + 1).reshape(1, -1)
+
+md.qmu.statistics.addmethod()
+md.qmu.statistics.method[2]['name'] = 'SampleSeries'
+md.qmu.statistics.method[2]['fields'] = ['Sealevel', 'BslrIce']
+md.qmu.statistics.method[2]['steps'] = np.arange(1, 10 + 1).reshape(1, -1)
+md.qmu.statistics.method[2]['indices'] = np.asarray(locations).reshape(1, -1)
+#}}}
+
+# Run transient Dakota solution
+mds = solve(md, 'Transient')
+
+# Run without statistics computations
+md.qmu.statistics.method[0]['name'] = 'None'
+md = solve(md, 'Transient')
+
+# Compare statistics with our own here
+#
+# TODO: SealevelSamples should be an attribute of mds.results.StatisticsSolution[-1] (see test2006.m)
+#
+svalues = mds.results.StatisticsSolution[0].SealevelSamples # all values at locations
+
+dvalues = np.zeros((md.qmu.method.params.samples, len(locations)))
+
+for i in range(md.qmu.method.params.samples):
+    dvalues[i, :] = md.results.dakota.modelresults[i].TransientSolution[-1].Sealevel[locations].flatten()
+
+samplesnorm = np.linalg.norm(dvalues - svalues, 'fro')
+
+# Fields and tolerances to track changes
+field_names = ['Samples Norm']
+field_tolerances = [1e-13]
+field_values = [samplesnorm]
Index: ../trunk-jpl/test/NightlyRun/runme.m
===================================================================
--- ../trunk-jpl/test/NightlyRun/runme.m	(revision 25687)
+++ ../trunk-jpl/test/NightlyRun/runme.m	(revision 25688)
@@ -106,7 +106,7 @@
 % }}}
 %Process Ids according to benchmarks{{{
 if strcmpi(benchmark,'nightly'),
-	test_ids=intersect(test_ids,[1:999]);
+	test_ids=intersect(test_ids,union([1:999],[2001:2500]));
 elseif strcmpi(benchmark,'validation'),
 	test_ids=intersect(test_ids,[1001:1999]);
 elseif strcmpi(benchmark,'ismip'),
@@ -218,9 +218,7 @@
 					%our output is in the correct order (n,1) or (1,1), so we do not need to transpose again
 					archive_cell=archread(['../Archives/' archive_name '.arch'],[archive_name '_field' num2str(k)]);
 					archive=archive_cell{1};
-					error_diff=full(max(abs(archive(:)-field(:)))/(max(abs(archive(:)))+eps));
-
-					%disp test result
+					error_diff=full(max(abs(archive(:)-field(:)))/(max(abs(archive(:)))+eps));					%disp test result
 					if (error_diff>tolerance | isnan(error_diff));
 						disp(sprintf(['ERROR   difference: %-7.2g > %7.2g test id: %i test name: %s field: %s'],...
 							error_diff,tolerance,id,id_string,fieldname));
Index: ../trunk-jpl/test/NightlyRun
===================================================================
--- ../trunk-jpl/test/NightlyRun	(revision 25687)
+++ ../trunk-jpl/test/NightlyRun	(revision 25688)

Property changes on: ../trunk-jpl/test/NightlyRun
___________________________________________________________________
Modified: svn:ignore
## -17,3 +17,6 ##
 run
 run.old
 run_matlab
+test218.qmu.in
+test218.qmu.out
+test218.qmu.err
Index: ../trunk-jpl/test
===================================================================
--- ../trunk-jpl/test	(revision 25687)
+++ ../trunk-jpl/test	(revision 25688)

Property changes on: ../trunk-jpl/test
___________________________________________________________________
Modified: svn:mergeinfo
## -0,0 +0,1 ##
   Merged /issm/branches/trunk-larour-SLPS2020/test:r25330-25625
Index: ../trunk-jpl/src/m/classes/results.py
===================================================================
--- ../trunk-jpl/src/m/classes/results.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/results.py	(revision 25688)
@@ -2,19 +2,18 @@
 
 
 class results(object):
-    '''
-    RESULTS class definition
+    """RESULTS class definition
 
-       Usage:
-          results = results()
+    Usage:
+        results = results()
 
-        TODO:
-        - Modify output so that it matches that of 
+    TODO:
+    - Modify output so that it matches that of 
 
-            disp(md.results.<<solutionstring>>)
+        disp(md.results.<<solutionstring>>)
 
-        where <<solutionstring>> is one of the values from solve.m
-    '''
+    where <<solutionstring>> is one of the values from solve.m
+    """
 
     def __init__(self, *args):  # {{{
         pass
Index: ../trunk-jpl/src/m/classes/qmustatistics.py
===================================================================
--- ../trunk-jpl/src/m/classes/qmustatistics.py	(revision 25687)
+++ ../trunk-jpl/src/m/classes/qmustatistics.py	(revision 25688)
@@ -25,16 +25,15 @@
         # name : name of method, one of 'None', 'Histogram', 'SampleSeries', or 'MeanVariance'
         # fields : fields for the statistics being requested, ex: 'Sealevel', 'BslrIce', 'BsrlHydro'
         # steps : time steps at which each field statistic is computed, ex: [1, 2, 5, 20] or [range(1:100)]
-        # nbins : number of bins for 'Histgogram' statistics
+        # nbins : number of bins for 'Histogram' statistics
         # indices : vertex indices at which to retrieve samples
 
         nargs = len(args)
-
         if nargs == 0:
             # Create a default object
             self.setdefaultparameters()
         elif nargs == 1:
-            # NOTE: The following has not been tested. Remove this note when it has.
+            # NOTE: The following has not been tested. Remove this note when it has
             inputstruct = args[0]
             list1 = properties('qmustatistics')
             list2 = fieldnames(inputstruct)
@@ -47,18 +46,14 @@
     #}}}
 
     def __repr__(self):  # {{{
-        s = '{}\n'.format('qmustatistics: post-Dakota run processing of QMU statistics:')
-
+        s = 'qmustatistics: post-Dakota run processing of QMU statistics:\n'
         if self.method[0]['name'] == 'None':
             return s
-
         s += '{}\n'.format(fielddisplay(self, 'nfiles_per_directory', 'number of files per output directory'))
         s += '{}\n'.format(fielddisplay(self, 'ndirectories', 'number of output directories; should be < numcpus'))
-
         for i in range(len(self.method)):
             s += '{}\n'.format('   method # {}'.format(i))
             s += '{}\n'.format(self.method[i])
-
         return s
     #}}}
 
@@ -66,6 +61,7 @@
         self.method[0]['name'] = 'None'
         self.nfiles_per_directory   = 5 # Number of files per output directory
         self.ndirectories           = 50 # Number of output directories; should be < numcpus
+        return self
     #}}}
 
     @staticmethod
@@ -114,18 +110,17 @@
             WriteData(fid, prefix, 'name', 'md.qmu.statistics.nfiles_per_directory', 'data', self.nfiles_per_directory, 'format', 'Integer')
             WriteData(fid, prefix, 'name', 'md.qmu.statistics.ndirectories', 'data', self.ndirectories, 'format', 'Integer')
             WriteData(fid, prefix, 'name', 'md.qmu.statistics.numstatistics', 'data', len(self.method), 'format', 'Integer')
-            for i in range(len(self.method)):
-                m = self.method[i]
-                WriteData(fid, prefix, 'name', 'md.qmu.statistics.method[{}][\'name\']'.format(i), 'data', m['name'], 'Format', 'String')
-                WriteData(fid, prefix, 'data', m['fields'], 'name', 'md.qmu.statistics.method[{}][\'fields\']'.format(i), 'format', 'StringArray')
-                WriteData(fid, prefix, 'data', m['steps'], 'name', 'md.qmu.statistics.method[{}][\'steps\']'.format(i), 'format', 'IntMat', 'mattype', 3)
-
+            for i in range(1, len(self.method) + 1):
+                m = self.method[i - 1]
+                WriteData(fid, prefix, 'name', 'md.qmu.statistics.method({}).name'.format(i), 'data', m['name'], 'format', 'String')
+                WriteData(fid, prefix, 'data', m['fields'], 'name', 'md.qmu.statistics.method({}).fields'.format(i), 'format', 'StringArray')
+                WriteData(fid, prefix, 'data', m['steps'], 'name', 'md.qmu.statistics.method({}).steps'.format(i), 'format', 'IntMat', 'mattype', 3)
                 if m['name'] == 'Histogram':
-                    WriteData(fid, prefix, 'name', 'md.qmu.statistics.method[{}][\'nbins\']'.format(i), 'data', m['nbins'], 'format', 'Integer')
+                    WriteData(fid, prefix, 'name', 'md.qmu.statistics.method({}).nbins'.format(i), 'data', m['nbins'], 'format', 'Integer')
                 elif m['name'] == 'MeanVariance':
                     pass # do nothing
                 elif m['name'] == 'SampleSeries':
-                    WriteData(fid, prefix, 'data', m['indices'], 'name', 'md.qmu.statistics.method[{}][\'indices\']'.format(i), 'format', 'IntMat', 'mattype', 3)
+                    WriteData(fid, prefix, 'data', m['indices'], 'name', 'md.qmu.statistics.method({}).indices'.format(i), 'format', 'IntMat', 'mattype', 3)
                 else:
                     raise Exception('qmustatistics marshall error message: unknown type ''{}'' for qmu.statistics.method[{}]'.format(m['name'], i))
     #}}}
@@ -133,3 +128,15 @@
     def extrude(self, md): #{{{
         return self
     #}}}
+
+    def addmethod(self, *args): #{{{
+        """ADDMETHOD - Add new, empty method or passed dict to self.method
+        """
+        nargs = len(args)
+        if nargs == 0:
+            self.method.append({})
+        elif nargs == 1:
+            self.method.append(args[0])
+        else:
+            raise Exception('Number of args should be 0 (appends empty dict to methods member) or 1 (appends passed dict to methods member)')
+    #}}}
Index: ../trunk-jpl/src/m/solve/parseresultsfromdisk.py
===================================================================
--- ../trunk-jpl/src/m/solve/parseresultsfromdisk.py	(revision 25687)
+++ ../trunk-jpl/src/m/solve/parseresultsfromdisk.py	(revision 25688)
@@ -1,17 +1,81 @@
+from collections import OrderedDict
 import struct
+
 import numpy as np
-from collections import OrderedDict
+
 import results as resultsclass
 
 
-def parseresultsfromdisk(md, filename, iosplit):
+def parseresultsfromdisk(md, filename, iosplit): #{{{
     if iosplit:
         saveres = parseresultsfromdiskiosplit(md, filename)
     else:
         saveres = parseresultsfromdiskioserial(md, filename)
+        #saveres = parseresultsfromdiskioserialsequential(md, filename)
     return saveres
+#}}}
 
+def parseresultsfromdiskiosplit(md, filename):  # {{{
+    #Open file
+    try:
+        fid = open(filename, 'rb')
+    except IOError as e:
+        raise IOError("parseresultsfromdisk error message: could not open '{}' for binary reading.".format(filename))
 
+    saveres = []
+
+    #if we have done split I / O, ie, we have results that are fragmented across patches,
+    #do a first pass, and figure out the structure of results
+    loadres = ReadDataDimensions(fid)
+    while loadres:
+
+        #Get time and step
+        if loadres['step'] > len(saveres):
+            for i in range(len(saveres), loadres['step'] - 1):
+                saveres.append(None)
+            saveres.append(resultsclass.results())
+        setattr(saveres[loadres['step'] - 1], 'step', loadres['step'])
+        setattr(saveres[loadres['step'] - 1], 'time', loadres['time'])
+
+    #Add result
+        setattr(saveres[loadres['step'] - 1], loadres['fieldname'], float('NaN'))
+
+    #read next result
+        loadres = ReadDataDimensions(fid)
+
+    #do a second pass, and figure out the size of the patches
+    fid.seek(0)  #rewind
+    loadres = ReadDataDimensions(fid)
+    while loadres:
+
+        #read next result
+        loadres = ReadDataDimensions(fid)
+
+    #third pass, this time to read the real information
+    fid.seek(0)  #rewind
+    loadres = ReadData(fid, md)
+    while loadres:
+
+        #Get time and step
+        if loadres['step'] > len(saveres):
+            for i in range(len(saveres), loadres['step'] - 1):
+                saveres.append(None)
+            saveres.append(saveresclass.saveres())
+        setattr(saveres[loadres['step'] - 1], 'step', loadres['step'])
+        setattr(saveres[loadres['step'] - 1], 'time', loadres['time'])
+
+    #Add result
+        setattr(saveres[loadres['step'] - 1], loadres['fieldname'], loadres['field'])
+
+    #read next result
+        loadres = ReadData(fid, md)
+
+    #close file
+    fid.close()
+
+    return saveres
+# }}}
+
 def parseresultsfromdiskioserial(md, filename):  # {{{
     #Open file
     try:
@@ -72,78 +136,14 @@
     fid.close()
 
     return saveres
-    # }}}
+# }}}
 
-
-def parseresultsfromdiskiosplit(md, filename):  # {{{
-    #Open file
-    try:
-        fid = open(filename, 'rb')
-    except IOError as e:
-        raise IOError("loadresultsfromdisk error message: could not open '{}' for binary reading.".format(filename))
-
-    saveres = []
-
-    #if we have done split I / O, ie, we have results that are fragmented across patches,
-    #do a first pass, and figure out the structure of results
-    loadres = ReadDataDimensions(fid)
-    while loadres:
-
-        #Get time and step
-        if loadres['step'] > len(saveres):
-            for i in range(len(saveres), loadres['step'] - 1):
-                saveres.append(None)
-            saveres.append(resultsclass.results())
-        setattr(saveres[loadres['step'] - 1], 'step', loadres['step'])
-        setattr(saveres[loadres['step'] - 1], 'time', loadres['time'])
-
-    #Add result
-        setattr(saveres[loadres['step'] - 1], loadres['fieldname'], float('NaN'))
-
-    #read next result
-        loadres = ReadDataDimensions(fid)
-
-    #do a second pass, and figure out the size of the patches
-    fid.seek(0)  #rewind
-    loadres = ReadDataDimensions(fid)
-    while loadres:
-
-        #read next result
-        loadres = ReadDataDimensions(fid)
-
-    #third pass, this time to read the real information
-    fid.seek(0)  #rewind
-    loadres = ReadData(fid, md)
-    while loadres:
-
-        #Get time and step
-        if loadres['step'] > len(saveres):
-            for i in range(len(saveres), loadres['step'] - 1):
-                saveres.append(None)
-            saveres.append(saveresclass.saveres())
-        setattr(saveres[loadres['step'] - 1], 'step', loadres['step'])
-        setattr(saveres[loadres['step'] - 1], 'time', loadres['time'])
-
-    #Add result
-        setattr(saveres[loadres['step'] - 1], loadres['fieldname'], loadres['field'])
-
-    #read next result
-        loadres = ReadData(fid, md)
-
-    #close file
-    fid.close()
-
-    return saveres
-    # }}}
-
-
 def ReadData(fid, md):  # {{{
-    '''
-    READDATA -
+    """READDATA
 
-        Usage:
-           field = ReadData(fid, md)
-    '''
+    Usage:
+        field = ReadData(fid, md)
+    """
 
     #read field
     try:
@@ -290,18 +290,17 @@
         saveres = None
 
     return saveres
-    # }}}
+# }}}
 
 
 def ReadDataDimensions(fid):  # {{{
-    """
-    READDATADIMENSIONS - read data dimensions, step and time, but not the data itself.
+    """READDATADIMENSIONS - read data dimensions, step and time, but not the data itself.
 
-        Usage:
-           field = ReadDataDimensions(fid)
+    Usage:
+        field = ReadDataDimensions(fid)
     """
 
-    #read field
+    # Read field
     try:
         length = struct.unpack('i', fid.read(struct.calcsize('i')))[0]
         fieldname = struct.unpack('{}s'.format(length), fid.read(length))[0][:-1]
@@ -309,7 +308,7 @@
         step = struct.unpack('i', fid.read(struct.calcsize('i')))[0]
         datatype = struct.unpack('i', fid.read(struct.calcsize('i')))[0]
         M = struct.unpack('i', fid.read(struct.calcsize('i')))[0]
-        N = 1  #default
+        N = 1 # default
         if datatype == 1:
             fid.seek(M * 8, 1)
         elif datatype == 2:
@@ -332,4 +331,4 @@
         saveres = None
 
     return saveres
-    # }}}
+# }}}
Index: ../trunk-jpl/src/m/solve/parseresultsfromdisk.m
===================================================================
--- ../trunk-jpl/src/m/solve/parseresultsfromdisk.m	(revision 25687)
+++ ../trunk-jpl/src/m/solve/parseresultsfromdisk.m	(revision 25688)
@@ -1,4 +1,4 @@
-function results=parseresultsfromdisk(md,filename,iosplit)
+function results=parseresultsfromdisk(md,filename,iosplit) % {{{
 
 if iosplit,
 	results=parseresultsfromdiskiosplit(md,filename);
@@ -6,53 +6,67 @@
 	results=parseresultsfromdiskioserial(md,filename);
 	%results=parseresultsfromdiskioserialsequential(md,filename);
 end
+% }}}
+function results=parseresultsfromdiskiosplit(md,filename) % {{{
 
-function results=parseresultsfromdiskioserialsequential(md,filename) % {{{
-
 %Open file
 fid=fopen(filename,'rb');
 if(fid==-1),
 	error(['loadresultsfromdisk error message: could not open ',filename,' for binary reading']);
 end
+results=struct();
 
-%first pass to figure out the steps we have: 
-steps=[];
-while  1, 
-	result  = ReadDataDimensions(fid);
-	if isempty(result),
-		break;
+%if we have done split I/O, ie, we have results that are fragmented across patches,
+%do a first pass, and figure out the structure of results
+result=ReadDataDimensions(fid);
+while ~isempty(result),
+
+	%Get time and step
+	results(result.step).step=result.step;
+	if result.time~=-9999,
+		results(result.step).time=result.time;
 	end
-	if result.step~=-9999,
-		steps=[steps result.step];
-	end
+
+	%Add result
+	results(result.step).(result.fieldname)=NaN;
+
+	%read next result
+	result=ReadDataDimensions(fid);
 end
 
-steps=unique(steps);
+%do a second pass, and figure out the size of the patches
+fseek(fid,0,-1); %rewind
+result=ReadDataDimensions(fid);
+while ~isempty(result),
+	%read next result
+	result=ReadDataDimensions(fid);
+end
 
-%create structure: 
-results=struct('step',num2cell(steps));
+%third pass, this time to read the real information
+fseek(fid,0,-1); %rewind
+result=ReadData(fid,md);
+while ~isempty(result),
 
-%second pass to fill the steps we have: 
-fseek(fid,0,-1); %rewind
-while  1, 
-	result  = ReadData(fid,md);
-	if isempty(result),
-		break;
+	%Get time and step
+	results(result.step).step=result.step;
+	if result.time~=-9999,
+		results(result.step).time=result.time;
 	end
-	if result.step==-9999,
-		result.step=1;
-		result.time=0;
+
+	%Add result
+	results(result.step).(result.fieldname)=result.field;
+
+	%read next result
+	try,
+		result=ReadData(fid,md);
+	catch me,
+		disp('WARNING: file corrupted, results partial recovery');
+		result=[];
 	end
-	%find where we are putting this step: 
-	ind=find(steps==result.step);
-	if isempty(ind),
-		error('could not find a step in our pre-structure! Something is very off!');
-	end
 
-	%plug: 
-	results(ind).time=result.time;
-	results(ind).(result.fieldname)=result.field;
 end
+
+%close file
 fclose(fid);
 % }}}
 function results=parseresultsfromdiskioserial(md,filename) % {{{
@@ -70,7 +84,7 @@
 
 	%read next result
 	try,
-		result  = ReadData(fid,md);
+		result = ReadData(fid,md);
 	catch me,
 		disp('WARNING: file corrupted, trying partial recovery');
 		continue;
@@ -91,7 +105,7 @@
 end
 fclose(fid);
 
-%Now, process all results and find how many steps we have
+%Now, process all results and find out how many steps we have
 numresults = numel(allresults);
 allsteps   = zeros(numresults,1);
 for i=1:numresults
@@ -104,18 +118,18 @@
 results=struct();
 for i=1:numresults
 	result = allresults{i};
-
 	index = 1;
-	if result.step ~= -9999
+	if(result.step ~= -9999)
 		index = find(result.step == allsteps);
+		results(index).step=result.step;
 	end
-
-	if(result.step~=-9999) results(index).step=result.step; end
-	if(result.time~=-9999) results(index).time=result.time; end
+	if(result.time~=-9999)
+		results(index).time=result.time;
+	end
 	results(index).(result.fieldname)=result.field;
 end
 % }}}
-function results=parseresultsfromdiskiosplit(md,filename) % {{{
+function results=parseresultsfromdiskioserialsequential(md,filename) % {{{
 
 %Open file
 fid=fopen(filename,'rb');
@@ -122,61 +136,47 @@
 if(fid==-1),
 	error(['loadresultsfromdisk error message: could not open ',filename,' for binary reading']);
 end
-results=struct();
 
-%if we have done split I/O, ie, we have results that are fragmented across patches,
-%do a first pass, and figure out the structure of results
-result=ReadDataDimensions(fid);
-while ~isempty(result),
-
-	%Get time and step
-	results(result.step).step=result.step;
-	if result.time~=-9999,
-		results(result.step).time=result.time;
+%first pass to figure out the steps we have: 
+steps=[];
+while  1, 
+	result  = ReadDataDimensions(fid);
+	if isempty(result),
+		break;
 	end
+	if result.step~=-9999,
+		steps=[steps result.step];
+	end
+end
 
-	%Add result
-	results(result.step).(result.fieldname)=NaN;
+steps=unique(steps);
 
-	%read next result
-	result=ReadDataDimensions(fid);
-end
+%create structure: 
+results=struct('step',num2cell(steps));
 
-%do a second pass, and figure out the size of the patches
+%second pass to fill the steps we have: 
 fseek(fid,0,-1); %rewind
-result=ReadDataDimensions(fid);
-while ~isempty(result),
-	%read next result
-	result=ReadDataDimensions(fid);
-end
-
-%third pass, this time to read the real information
-fseek(fid,0,-1); %rewind
-result=ReadData(fid,md);
-while ~isempty(result),
-
-	%Get time and step
-	results(result.step).step=result.step;
-	if result.time~=-9999,
-		results(result.step).time=result.time;
+while  1, 
+	result  = ReadData(fid,md);
+	if isempty(result),
+		break;
 	end
-
-	%Add result
-	results(result.step).(result.fieldname)=result.field;
-
-	%read next result
-	try,
-		result=ReadData(fid,md);
-	catch me,
-		disp('WARNING: file corrupted, results partial recovery');
-		result=[];
+	if result.step==-9999,
+		result.step=1;
+		result.time=0;
 	end
+	%find where we are putting this step: 
+	ind=find(steps==result.step);
+	if isempty(ind),
+		error('could not find a step in our pre-structure! Something is very off!');
+	end
 
+	%plug: 
+	results(ind).time=result.time;
+	results(ind).(result.fieldname)=result.field;
 end
-
-%close file
 fclose(fid);
-	% }}}
+%}}}
 function result=ReadData(fid,md) % {{{
 
 %read field
@@ -311,11 +311,12 @@
 		field=temp_field; 
 	end
 
+	if time~=-9999,
+		time=time/yts;
+	end
+
 	result.fieldname=fieldname;
 	result.time=time;
-	if result.time~=-9999,
-		result.time=time/yts;
-	end
 	result.step=step;
 	result.field=field;
 end
Index: ../trunk-jpl/src/m/solve/loadresultsfromdisk.py
===================================================================
--- ../trunk-jpl/src/m/solve/loadresultsfromdisk.py	(revision 25687)
+++ ../trunk-jpl/src/m/solve/loadresultsfromdisk.py	(revision 25688)
@@ -1,5 +1,7 @@
 import os
 
+import numpy as np # Remove: used temporarily for debugging
+
 from helpers import fieldnames
 from parseresultsfromdisk import parseresultsfromdisk
 from postqmu import postqmu
@@ -39,8 +41,8 @@
         structure = parseresultsfromdisk(md, filename, not md.settings.io_gather)
         if not structure:
             raise RuntimeError("No result found in binary file '{}'. Check for solution crash.".format(filename))
-        if not structure[0].SolutionType:
-            if structure[-1].SolutionType:
+        if not hasattr(structure[0], 'SolutionType'):
+            if hasattr(structure[-1], 'SolutionType'):
                 structure[0].SolutionType = structure[-1].SolutionType
             else:
                 print('Cannot find a solution type in the results! Ascribing one: \'NoneSolution\'.')
@@ -64,7 +66,7 @@
             setattr(getattr(md.results, structure[0].SolutionType)[0], 'outlog', '')
 
         if getattr(md.results, structure[0].SolutionType)[0].errlog:
-            print("loadresultsfromcluster info message: error during solution. Check your errlog and outlog model fields.")
+            print("loadresultsfromdisk info message: error during solution. Check your errlog and outlog model fields.")
 
         # If only one solution, extract it from list for user friendliness
         if len(structure) == 1 and structure[0].SolutionType != 'TransientSolution':
Index: ../trunk-jpl/src/m/solve/loadresultsfromdisk.m
===================================================================
--- ../trunk-jpl/src/m/solve/loadresultsfromdisk.m	(revision 25687)
+++ ../trunk-jpl/src/m/solve/loadresultsfromdisk.m	(revision 25688)
@@ -61,7 +61,7 @@
 	end
 
 	if ~isempty(md.results.(structure(1).SolutionType)(1).errlog),
-		disp(['loadresultsfromcluster info message: error during solution. Check your errlog and outlog model fields']);
+		disp(['loadresultsfromdisk info message: error during solution. Check your errlog and outlog model fields']);
 	end
 
 %post processes qmu results if necessary
Index: ../trunk-jpl/src
===================================================================
--- ../trunk-jpl/src	(revision 25687)
+++ ../trunk-jpl/src	(revision 25688)

Property changes on: ../trunk-jpl/src
___________________________________________________________________
Modified: svn:mergeinfo
## -0,0 +0,1 ##
   Merged /issm/branches/trunk-larour-SLPS2020/src:r25330-25625