diff --git a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Calib.csv b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Calib.csv
index 253d576d39c0b716e48a59acfbd6eaebd167d9e8..8dd88633eb892b585e36ad94ae1a7728edfb01a5 100644
--- a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Calib.csv
+++ b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Calib.csv
@@ -1,11 +1,11 @@
Point ID,velocity [m/s],p
-213477,-3.1501339538783E-09,-0.000612563931219
-213877,-5.0478701346619E-09,-0.00052175300792
-289534,-7.29459298244234E-09,-0.000646024643905
-291183,-6.32200936129086E-09,
-368496,-5.74124368559349E-09,
-369920,-8.73382761515364E-09,
-411549,-3.57727344378565E-05,
-412975,-0.000247944606447,
-456893,-1.11110602070443E-05,
-464705,-1.04339793793533E-06,
+213477,-6.01293315609868E-09,-0.000512048602104
+213877,-9.44190762000011E-09,-0.000435009598732
+289534,-1.31847397575032E-08,-0.000550001859667
+291183,-1.151378512169E-08,
+368496,3.02552559150763E-11,
+369920,5.7598867000074E-08,
+411549,-2.02172697999999E-05,
+412975,-2.02968881739993E-05,
+456893,-9.61987414000148E-06,
+464705,-8.75040560000082E-07,
diff --git a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Valid.csv b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Valid.csv
index 9cf167512c7259eb5525dc06b2986c02127864db..6538bdc38da913ee8359f95ca0fac4a3b76126c3 100644
--- a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Valid.csv
+++ b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_BJ_Valid.csv
@@ -1,11 +1,11 @@
Point ID,velocity [m/s],p
-211000,-4.63595719896294E-09,-0.000612018819243
-213679,-4.69661368654853E-09,-0.00273427145921
-288307,-6.71000338911042E-09,
-290985,-4.266393146494E-09,
-369720,-9.3872564187562E-09,
-371144,-1.07399803228038E-08,
-409300,3.87015337562542E-06,
-412777,-0.000409375032883,
-456693,-1.20544981530828E-05,
-458121,-1.15012743378166E-05,
+211000,-8.65610483529437E-09,-0.000508442521096
+213679,-8.57212409182632E-09,-0.000791501253845
+288307,-1.22924430986942E-08,
+290985,-8.06463456348974E-09,
+369720,5.24445349999619E-08,
+371144,5.46578840001895E-08,
+409300,-4.01861310100006E-06,
+412777,-1.9790045576E-05,
+456693,-1.03115168010007E-05,
+458121,-9.96050132499871E-06,
diff --git a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Calib.csv b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Calib.csv
index 10a1ffd3d4e675cd4a013ffaccf8f61d2d4e1093..46c85f103b6b232f235318754514db254a47c365 100644
--- a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Calib.csv
+++ b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Calib.csv
@@ -1,11 +1,11 @@
Point ID,velocity [m/s],p
-213477,-3.29954507543466E-09,-0.000611728467187
-213877,-5.15226592197707E-09,-0.00052175300792
-289534,-7.33745823275519E-09,-0.000646011841667
-291183,-6.39771692597621E-09,
-368496,-5.73688444726558E-09,
-369920,-8.72457032603235E-09,
-411549,-3.58838172823732E-05,
-412975,-0.000251905487028,
-456893,-1.10910011504393E-05,
-464705,-1.03665328767649E-06,
+213477,-6.02462467659551E-09,-0.000512063503266
+213877,-9.46295344351773E-09,-0.000435009598732
+289534,-1.32122605742106E-08,-0.000550001859667
+291183,-1.15416136193072E-08,
+368496,1.26442105009427E-11,
+369920,5.78530839999013E-08,
+411549,-2.0257182678E-05,
+412975,-2.03267960270006E-05,
+456893,-9.61009527300103E-06,
+464705,-8.72376472000019E-07,
diff --git a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Valid.csv b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Valid.csv
index 4153ea73564ba2610d62480e5720258dd3fdccad..184e70c172b2882e32abfd01474cdf44bd362a44 100644
--- a/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Valid.csv
+++ b/BayesValidRox/tests/PA-A/data/NumError_stokesdarcy_ER_Valid.csv
@@ -1,11 +1,11 @@
Point ID,velocity [m/s],p
-211000,-4.62438370345676E-09,-0.000612018819243
-213679,-4.64937847402262E-09,-0.002732613482024
-288307,-6.80251947782237E-09,
-290985,-4.36051020295682E-09,
-369720,-9.42074916669028E-09,
-371144,-1.07789688407079E-08,
-409300,3.88806918309453E-06,
-412777,-0.000415127149622,
-456693,-1.20557327912903E-05,
-458121,-1.14803534740239E-05,
+211000,-8.67756668010791E-09,-0.000508517026903
+213679,-8.58945858378855E-09,-0.000791400671007
+288307,-1.23216701652891E-08,
+290985,-8.07960608889262E-09,
+369720,5.27448629998985E-08,
+371144,5.49417799999971E-08,
+409300,-4.01708482300012E-06,
+412777,-1.98200807899999E-05,
+456693,-1.0312153187001E-05,
+458121,-9.95049160000018E-06,
diff --git a/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Calib.csv b/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Calib.csv
index ed6a9002134c05e73f6751fad89f6b225023d46c..c2216c198b983bb424de305c5541c3b3186efd4b 100644
--- a/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Calib.csv
+++ b/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Calib.csv
@@ -1,11 +1,11 @@
Point ID,velocity [m/s],p
-213477,-8.25945944599614E-08,-0.003600040357142
-213877,-9.27615132110407E-08,-0.004825463284485
-289534,-3.23718851769298E-08,-0.004093205707939
-291183,-1.31586469663849E-08,
-368496,-2.76182543234E-07,
-369920,-1.98371460263E-07,
-411549,-0.000141252689569,
-412975,-0.000154191808643,
-456893,7.5119555009017E-05,
-464705,-3.50022387393E-07,
+213477,-2.05048428542796E-10,-0.000547164534404
+213877,-1.88688732714874E-07,-0.000527086965905
+289534,1.65905593993196E-07,-0.00052233572499
+291183,-2.05932868278287E-07,
+368496,5.75873337846173E-09,
+369920,1.84901928544619E-08,
+411549,-2.78997602956534E-05,
+412975,-3.21319480434872E-05,
+456893,2.39792778179269E-06,
+464705,9.81350544200461E-08,
diff --git a/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Valid.csv b/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Valid.csv
index d075aa831ac564697ec9a268ef369a687034f7ec..f17c5209ec1846a16544c795f686ab4c3cd1d082 100644
--- a/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Valid.csv
+++ b/BayesValidRox/tests/PA-A/data/NumError_stokespnm_Valid.csv
@@ -1,11 +1,11 @@
Point ID,velocity [m/s],p
-211000,-7.83141306435595E-08,-0.003711665822599
-213679,-2.41707629757772E-08,-0.003191870910599
-288307,-1.57369968407E-07,
-290985,-1.46897863081E-07,
-369720,4.08649885196E-07,
-371144,-2.42593923987E-07,
-409300,-4.17272636542E-07,
-412777,-0.000172950583848,
-456693,6.5008158150108E-05,
-458121,-5.6165820183915E-05,
+211000,1.31663704311795E-07,-0.000553128920495
+213679,-4.32279322692355E-08,-0.00068042732929
+288307,-1.09598214889512E-07,
+290985,-1.69287655826011E-09,
+369720,2.17679052132274E-08,
+371144,2.23218831593861E-08,
+409300,-1.13037871290271E-06,
+412777,-3.04337959277623E-05,
+456693,4.2120703707464E-06,
+458121,4.08303844164112E-07,
diff --git a/BayesValidRox/tests/PA-A/models/numError/ER_Interface.py b/BayesValidRox/tests/PA-A/models/numError/ER_Interface.py
new file mode 100644
index 0000000000000000000000000000000000000000..b8f3ceb56404cc1b3e2c9f7a391c6f7489935185
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/ER_Interface.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Feb 23 2021
+
+This script updates the interface parameters N and M in the inputfile for the
+stokes-darcy model with general coupling condition (ER).
+
+@author: Farid Mohammadi, M.Sc.
+Department of Hydromechanics and Modelling of Hydrosystems (LH2)
+Institute for Modelling Hydraulic and Environmental Systems (IWS),
+University of Stuttgart
+www.iws.uni-stuttgart.de/lh2/
+Pfaffenwaldring 61
+70569 Stuttgart
+Room: 1.009
+"""
+
+import numpy as np
+from scipy.interpolate import interp1d
+
+
+def interpol_1D(path_to_csv, newintLoc):
+ data = np.genfromtxt(path_to_csv, dtype=float, delimiter=',', names=True)
+ intLoc = data['S']/1e3 # mm to m
+ N = data['N']
+ M = data['M']
+
+ f_N = interp1d(intLoc, N)
+ f_M = interp1d(intLoc, M)
+
+ return np.hstack((f_N(newintLoc),f_M(newintLoc)))
+
+def update_InputFile(inputFile, newParams):
+ """
+ Finds this pattern with <IC1> and replace it with the new value from
+ the newParams array.
+ """
+ NofPa = newParams.shape[0]
+ text_to_search_list = ['<IC%s>'%(i+1) for i in range(NofPa)]
+
+ # Read in the file
+ with open(inputFile, 'r') as file :
+ filedata = file.read()
+
+ # Replace the target string
+ for text_to_search, param in zip(text_to_search_list, newParams):
+ filedata = filedata.replace(text_to_search, '{:0.2e}'.format(param))
+
+ # Write the file out again
+ with open(inputFile, 'w') as file:
+ file.write(filedata)
+
+ return
+
+def replace_ER_Interface_Params(inputFile):
+ path_to_csv = '/home/farid/scientific/bayesian-validation/BayesValidRox/tests/PA-A/data/BLvalues.csv'
+ keyword = 'CavityHeight' # [4.975,5.125]
+
+ # Find the interface location
+ filedata = open(inputFile).readlines()
+ for line in filedata:
+ if keyword in line:
+ newintLoc = float(line.split('= ')[1].split(' ')[0])
+
+ # Compute the interface params
+ newParams = interpol_1D(path_to_csv,newintLoc)
+
+ # Replace the values in the input file
+ update_InputFile(inputFile,newParams)
diff --git a/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_BJ.csv b/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_BJ.csv
index 7644cfc166b3106b2524fa4a54d83c47dd0b4a82..2435ea586cde3dbb0a7e0f1cabe4aa1b4d334755 100644
--- a/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_BJ.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_BJ.csv
@@ -1,21 +1,21 @@
Point ID,velocity [m/s],p
-1,-4.635957198962943e-09,-0.000612563931218983
-1,-3.1501339538782977e-09,-0.0006120188192431436
-2,-4.696613686548533e-09,-0.0005217530079198776
-2,-5.0478701346619025e-09,-0.0027342714592095015
-3,-6.710003389110418e-09,-0.0006460246439045675
-3,-7.2945929824423415e-09,
-4,-4.266393146494001e-09,
-4,-6.322009361290864e-09,
-5,-5.741243685593492e-09,
-5,-9.387256418756197e-09,
-6,-8.73382761515364e-09,
-6,-1.0739980322803792e-08,
-7,3.870153375625422e-06,
-7,-3.5772734437856494e-05,
-8,-0.0004093750328827004,
-8,-0.0002479446064472412,
-9,-1.2054498153082773e-05,
-9,-1.1111060207044309e-05,
-10,-1.1501274337816634e-05,
-10,-1.043397937935333e-06,
+1,-8.656104835294368e-09,-0.0005120486021040482
+1,-6.01293315609868e-09,-0.0005084425210959975
+2,-8.572124091826318e-09,-0.00043500959873199463
+2,-9.441907620000105e-09,-0.0007915012538450005
+3,-1.2292443098694248e-08,-0.0005500018596670542
+3,-1.3184739757503206e-08,
+4,-8.064634563489736e-09,
+4,-1.1513785121689985e-08,
+5,3.025525591507632e-11,
+5,5.2444534999961855e-08,
+6,5.7598867000073976e-08,
+6,5.465788400018951e-08,
+7,-4.018613101000064e-06,
+7,-2.021726979999994e-05,
+8,-1.9790045576000004e-05,
+8,-2.029688817399935e-05,
+9,-1.0311516801000694e-05,
+9,-9.619874140001476e-06,
+10,-9.960501324998707e-06,
+10,-8.750405600000819e-07,
diff --git a/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_ER.csv b/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_ER.csv
index fbd0289d54bb6080824ad9cb7ffb923818ce8524..d15a4dc2af36dfbfd4c0a0f30361aee091ccfda3 100644
--- a/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_ER.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/NumError_stokesdarcy_ER.csv
@@ -1,21 +1,21 @@
Point ID,velocity [m/s],p
-1,-4.624383703456755e-09,-0.0006117284671869651
-1,-3.299545075434659e-09,-0.0006120188192431436
-2,-4.649378474022618e-09,-0.0005217530079198776
-2,-5.152265921977067e-09,-0.0027326134820242357
-3,-6.802519477822373e-09,-0.0006460118416665501
-3,-7.337458232755185e-09,
-4,-4.360510202956816e-09,
-4,-6.397716925976213e-09,
-5,-5.736884447265578e-09,
-5,-9.420749166690277e-09,
-6,-8.724570326032349e-09,
-6,-1.0778968840707886e-08,
-7,3.888069183094529e-06,
-7,-3.588381728237324e-05,
-8,-0.0004151271496216548,
-8,-0.0002519054870275775,
-9,-1.205573279129026e-05,
-9,-1.1091001150439257e-05,
-10,-1.1480353474023879e-05,
-10,-1.0366532876764875e-06,
+1,-8.677566680107909e-09,-0.0005120635032659915
+1,-6.024624676595507e-09,-0.0005085170269029382
+2,-8.589458583788546e-09,-0.00043500959873199463
+2,-9.462953443517727e-09,-0.0007914006710069976
+3,-1.2321670165289075e-08,-0.0005500018596669433
+3,-1.321226057421056e-08,
+4,-8.079606088892616e-09,
+4,-1.1541613619307172e-08,
+5,1.2644210500942652e-11,
+5,5.2744862999898475e-08,
+6,5.785308399990128e-08,
+6,5.4941779999997074e-08,
+7,-4.0170848230001175e-06,
+7,-2.0257182677999985e-05,
+8,-1.9820080789999944e-05,
+8,-2.0326796027000594e-05,
+9,-1.0312153187001015e-05,
+9,-9.610095273001034e-06,
+10,-9.95049160000018e-06,
+10,-8.723764720000192e-07,
diff --git a/BayesValidRox/tests/PA-A/models/numError/NumError_stokespnm.csv b/BayesValidRox/tests/PA-A/models/numError/NumError_stokespnm.csv
index 35d4ac928045ac617d280acf783f89ec8f3b89ed..745a054e6e9bc99c2a00a62cf5dc58a723fbccc4 100644
--- a/BayesValidRox/tests/PA-A/models/numError/NumError_stokespnm.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/NumError_stokespnm.csv
@@ -1,21 +1,21 @@
Point ID,velocity [m/s],p
-211000,-7.831413064355946e-08,-0.003600040357141886
-213477,-8.259459445996139e-08,-0.003711665822598567
-213679,-2.4170762975777242e-08,-0.004825463284485418
-213877,-9.276151321104066e-08,-0.0031918709105993284
-288307,-1.573699684066507e-07,-0.004093205707938767
-289534,-3.237188517692983e-08,
-290985,-1.468978630810244e-07,
-291183,-1.3158646966384932e-08,
-368496,-2.7618254323371014e-07,
-369720,4.086498851960051e-07,
-369920,-1.983714602633198e-07,
-371144,-2.4259392398748106e-07,
-409300,-4.1727263654195297e-07,
-411549,-0.00014125268956858785,
-412777,-0.00017295058384770673,
-412975,-0.0001541918086431468,
-456693,6.500815815010763e-05,
-456893,7.511955500901723e-05,
-458121,-5.616582018391508e-05,
-464705,-3.500223873926791e-07,
+1,1.3166370431179518e-07,-0.0005471645344037714
+1,-2.0504842854279618e-10,-0.0005531289204946397
+2,-4.322793226923553e-08,-0.0005270869659048803
+2,-1.886887327148743e-07,-0.0006804273292899199
+3,-1.0959821488951213e-07,-0.0005223357249895438
+3,1.6590559399319614e-07,
+4,-1.692876558260112e-09,
+4,-2.0593286827828721e-07,
+5,5.7587333784617305e-09,
+5,2.1767905213227352e-08,
+6,1.84901928544619e-08,
+6,2.2321883159386102e-08,
+7,-1.1303787129027083e-06,
+7,-2.789976029565343e-05,
+8,-3.0433795927762254e-05,
+8,-3.2131948043487174e-05,
+9,4.2120703707464e-06,
+9,2.3979277817926867e-06,
+10,4.083038441641115e-07,
+10,9.813505442004612e-08,
diff --git a/BayesValidRox/tests/PA-A/models/numError/NumericalError.py b/BayesValidRox/tests/PA-A/models/numError/NumericalError.py
index 637ba311004060eaca3893f96cfb2db39bf40159..2b118d796f45688f292c2303145ff9d6f585fb23 100755
--- a/BayesValidRox/tests/PA-A/models/numError/NumericalError.py
+++ b/BayesValidRox/tests/PA-A/models/numError/NumericalError.py
@@ -20,7 +20,8 @@ import pandas as pd
from scipy import stats
from scipy import optimize
from sklearn.metrics import mean_squared_error
-
+import matplotlib
+matplotlib.use('agg')
import matplotlib.pyplot as plt
plt.rcParams.update({'font.size': 20})
plt.rc('figure', figsize = (24, 16))
@@ -83,7 +84,7 @@ def plotFits(h_k, S_k, params, method, Case):
plt.xlabel('Mesh size $h$ [m]')
plt.ylabel('Velocity [m/s]') if case=='velocity' else plt.ylabel('Pressure [bar]')
- fig.savefig('./'+OutputDir+'/fit_'+str(idx+1)+'.svg',bbox_inches='tight')
+ # fig.savefig('./'+OutputDir+'/fit_'+str(idx+1)+'.pdf',bbox_inches='tight')
plt.close()
def plotSRQs(h, S_k, params, method, case):
@@ -420,16 +421,17 @@ if __name__ == "__main__":
labels = ['1312x768','656x384','328x192']
Items = ['Calib']
- modelName = 'stokesdarcy_ER' #'stokesdarcy_ER' & 'stokesdarcy_BJ' & 'stokespnm'
+ modelName = 'stokespnm' #'stokesdarcy_ER' & 'stokesdarcy_BJ' & 'stokespnm'
list_of_files = ['./'+modelName+'/'+'ffpm_'+modelName+'_'+key+'.csv' for key in Case]
if 'darcy' in modelName:
- h = 1e-5 # actual normal mesh spacing
+ h = 1.5625e-05 # actual normal mesh spacing
h_k = np.array([7.8125e-06, 1.5625e-05, 3.125e-05])
elif 'pnm' in modelName:
- h = 2.5e-09 # actual normal mesh spacing
- h_k = np.array([6.25e-10, 2.5e-09, 1.0e-08]) #1.25e-08
+ h = 6.103515625e-11 # actual normal mesh spacing
+ # h_k = np.array([6.25e-10, 2.5e-09, 1.0e-08]) #1.25e-08
+ h_k = np.array([1.52587890625e-11, 6.103515625e-11, 2.44140625e-10])
S_k_calib = read_data(list_of_files, Case)
diff --git a/BayesValidRox/tests/PA-A/models/numError/Plots_stokesdarcy_ER_p/fit_1.svg b/BayesValidRox/tests/PA-A/models/numError/Plots_stokesdarcy_ER_p/fit_1.svg
deleted file mode 100644
index 94f9e529cfc0ebafc390358c4659bfe75deca9bc..0000000000000000000000000000000000000000
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diff --git a/BayesValidRox/tests/PA-A/models/numError/__pycache__/ER_Interface.cpython-36.pyc b/BayesValidRox/tests/PA-A/models/numError/__pycache__/ER_Interface.cpython-36.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..36dfada93de52a365c738247a675b25b93ff7f79
Binary files /dev/null and b/BayesValidRox/tests/PA-A/models/numError/__pycache__/ER_Interface.cpython-36.pyc differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/model_exe.py b/BayesValidRox/tests/PA-A/models/numError/model_exe.py
new file mode 100755
index 0000000000000000000000000000000000000000..e71547047524fe096ab029e37e8319a292ec6131
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/model_exe.py
@@ -0,0 +1,123 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jul 19 16:48:59 2019
+
+@author: farid
+"""
+import numpy as np
+import os, sys
+import zipfile
+import argparse
+from ER_Interface import replace_ER_Interface_Params
+
+# parse arguments
+parser = argparse.ArgumentParser(
+ prog='\033[1m\033[94m' + 'python3.7' + '\033[0m' + ' ' + sys.argv[0],
+ description='Run Stokes-Darcy model and extract outputs.'
+)
+parser.add_argument('model', help="model name")
+parser.add_argument('file', help="input file")
+parser.add_argument('-a', '--averaging', default=True, help='Uses averaging scripts to average quantities in the porous medium. True = averaging. False = no averaging')
+args = vars(parser.parse_args())
+
+# Specification
+model = args['model']
+inputFile = args['file']
+averaging = args['averaging']
+
+velocity_points = "../../../velocity_points.csv"
+pressure_points = "../../../pressure_points.csv"
+
+# Run the model
+if model == 'stokesdarcy':
+ model_exe = 'stokes_darcybox_regular_2d'
+ model_dir = 'stokesdarcy'
+ pvdfile1 = 'regular_2D_stokesdarcy_250_micron_stokes'
+ pvdfile2 = 'regular_2D_stokesdarcy_250_micron_darcy'
+ darcyfile = 'regular_2D_stokesdarcy_250_micron_darcy-00001.vtu'
+ stokesfile = 'regular_2D_stokesdarcy_250_micron_stokes-00001.vtu'
+
+elif model == 'stokespnm':
+ model_exe = 'stokes_pnm_regular_2d'
+ model_dir = 'stokespnm'
+ pvdfile1 = 'regular_2D_stokespnm_250_micron_stokes'
+ pvdfile2 = 'regular_2D_stokespnm_250_micron_pnm'
+ darcyfile = 'regular_2D_stokespnm_250_micron_pnm-00001.vtp'
+ stokesfile = 'regular_2D_stokespnm_250_micron_stokes-00001.vtu'
+ if not averaging:
+ velocity_points = "../velocity_points_pnm.csv"
+ pressure_points = "../pressure_points_pnm.csv"
+
+
+else:
+ raise Exception('This model does not exist. \
+ Please verify the model name.')
+
+# If stockesdarcyER, update the interface params
+if 'ER' in inputFile:
+ replace_ER_Interface_Params(inputFile)
+
+NewCommand = model_exe + ' ' + inputFile
+
+Process1 = os.system('./../../../'+model_dir+'/%s > log.out 2>&1' %NewCommand)
+
+if Process1 != 0:
+ print('\nMessage 1:')
+ print('\tIf value of \'%d\' is a non-zero value, then compilation problems \n' % Process1)
+
+# Extract velocity and pressure values
+Command = "pvpython ../../../../extractpointdataovertime.py \
+ -f "+pvdfile1+".pvd "+pvdfile2+".pvd\
+ -p "
+
+
+Process2 = os.system(Command + velocity_points)
+if Process2 != 0:
+ print('\nMessage 2:')
+ print('\tIf value of \'%d\' is a non-zero value, then compilation problems \n' % Process2)
+
+Process3 = os.system(Command + pressure_points + ' -var p')
+if Process3 != 0:
+ print('\nMessage 3:')
+ print('\tIf value of \'%d\' is a non-zero value, then compilation problems \n' % Process3)
+
+# Averaging
+if averaging:
+ if model == 'stokesdarcy':
+ Command_avg = "./../../../"+model_dir+"/averaging_stokesdarcy.py "+ "-fd "+darcyfile+" -fs "+stokesfile+ " -p "
+ elif model == 'stokespnm':
+ Command_avg = "./../../../"+model_dir+"/averaging_stokespnm.py "+ "-fd "+darcyfile+" -fs "+stokesfile+ " -p "
+
+ Process4 = os.system(Command_avg + velocity_points + ' ' + pressure_points)
+ if Process4 != 0:
+ print('\nMessage 4:')
+ print('\tIf value of \'%d\' is a non-zero value, then compilation problems \n' % Process4)
+
+# Combine csv files and remove them
+pointVel = np.genfromtxt('ffpm_{}_velocity.csv'.format(model), delimiter=',')
+pointP = np.genfromtxt('ffpm_{}_p.csv'.format(model), delimiter=',')
+if averaging:
+ averagedVel = np.genfromtxt('averagedVelocityValues.csv', delimiter=',')
+ averagedP = np.genfromtxt('averagedPressureValues.csv', delimiter=',')
+ pointVel[:12] = averagedVel[:12] # 12: number of the points in pm
+ pointP[:2] = averagedP[:2] # 2: number of the points in pm
+# Save to csv files
+np.savetxt('ffpm_{}_velocity_final.csv'.format(model), pointVel, delimiter=',')
+np.savetxt('ffpm_{}_p_final.csv'.format(model), pointP, delimiter=',')
+
+
+# Zip auxillary files
+keys = ['vtu', 'vtp', 'pvd', '.csv']
+filePaths = [path for path in os.listdir(os.getcwd()) for key in keys if key in path]
+
+zip_file = zipfile.ZipFile('outFiles.zip', 'w')
+with zip_file:
+ # writing each file one by one
+ for path in filePaths:
+ if 'final' not in path:
+ zip_file.write(path)
+
+for path in filePaths:
+ if 'final' not in path:
+ os.remove(path)
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_p.csv
deleted file mode 100644
index ad0426641cbeb423726f1415bfe38d9d8230a958..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_p.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-1.409779936075210571e-01
-1.280300021171569824e-01
-1.241889968514442444e-01
-3.966639935970306396e-02
-1.696210056543350220e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_p_final.csv
similarity index 60%
rename from BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_p.csv
rename to BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_p_final.csv
index 4efd63fd63edf41e0dd60fda3fc71031e7a3d68e..51dcbbd848a878c9a999ad72cb135e93529a0a8c 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_p_final.csv
@@ -1,5 +1,5 @@
-1.420460045337677002e-01
-1.290850043296813965e-01
+1.420461684465408325e-01
+1.290845423936843872e-01
1.250949949026107788e-01
4.071079939603805542e-02
1.707819998264312744e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_velocity.csv
deleted file mode 100644
index 3debca4da4e2fa5229213362b1ff92a0029195be..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-2.848069925676099956e-05,2.020320062001701444e-05,0.000000000000000000e+00
-1.349250032944837585e-05,-1.856900053098797798e-05,0.000000000000000000e+00
-3.026460035471245646e-05,-1.283520032302476466e-05,0.000000000000000000e+00
-3.635949906310997903e-05,2.537580030548269860e-06,0.000000000000000000e+00
-4.626809823093935847e-05,2.773919959508930333e-06,0.000000000000000000e+00
-4.048800110467709601e-05,2.811779995681717992e-05,0.000000000000000000e+00
-1.161399995908141136e-05,-2.800830043270252645e-05,0.000000000000000000e+00
-3.875040056300349534e-05,-2.110639979946427047e-05,0.000000000000000000e+00
-7.651610189896018710e-07,-4.119340155739337206e-05,0.000000000000000000e+00
-5.705569856218062341e-05,-3.393389852135442197e-05,0.000000000000000000e+00
-5.830169902765192091e-05,2.832380005202139728e-06,0.000000000000000000e+00
-5.850649904459714890e-05,3.198319973307661712e-05,0.000000000000000000e+00
-9.610199776943773031e-05,-1.124269983847625554e-04,0.000000000000000000e+00
-1.787799992598593235e-03,-1.113210018957033753e-04,0.000000000000000000e+00
-1.936689950525760651e-03,2.314599896635627374e-06,0.000000000000000000e+00
-1.971930032595992088e-03,2.610199953778646886e-05,0.000000000000000000e+00
-2.236580010503530502e-03,-3.924210031982511282e-04,0.000000000000000000e+00
-2.414179965853691101e-03,9.541430472381762229e-07,0.000000000000000000e+00
-2.456140005961060524e-03,8.359449566341936588e-06,0.000000000000000000e+00
-1.105769988498650491e-04,-3.748100134544074535e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..e4e16f1973b37ba4e14bdcb92acfe4ca379416b7
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/ffpm_stokesdarcy_velocity_final.csv
@@ -0,0 +1,20 @@
+2.850944005849953555e-05,2.022558201097979236e-05,0.000000000000000000e+00
+1.350654755327695966e-05,-1.858842417590267360e-05,0.000000000000000000e+00
+3.029674551591199361e-05,-1.284843263960055992e-05,0.000000000000000000e+00
+3.639810284994382528e-05,2.540879547846541797e-06,0.000000000000000000e+00
+4.631782223540881205e-05,2.777586454888263633e-06,0.000000000000000000e+00
+4.053034709627922894e-05,2.815173673198501092e-05,0.000000000000000000e+00
+1.162640863316966033e-05,-2.803774872361941561e-05,0.000000000000000000e+00
+3.879129756612087476e-05,-2.112816746091539244e-05,0.000000000000000000e+00
+1.542961680963284704e-05,-4.468019681169721480e-05,0.000000000000000000e+00
+2.851222695561261844e-04,-3.746420108541315130e-05,0.000000000000000000e+00
+3.056353254677901532e-04,2.821594478993015576e-06,0.000000000000000000e+00
+3.103969673610151858e-04,3.174190650234720579e-05,0.000000000000000000e+00
+9.741890244185924530e-05,-1.095979969250038266e-04,0.000000000000000000e+00
+1.756850047968327999e-03,-1.057740009855479002e-04,0.000000000000000000e+00
+1.898049958981573582e-03,2.412690037090214901e-06,0.000000000000000000e+00
+1.932939980179071426e-03,2.654379932209849358e-05,0.000000000000000000e+00
+2.260510111227631569e-03,-3.821149875875562429e-04,0.000000000000000000e+00
+2.434710040688514709e-03,1.005200033432629425e-06,0.000000000000000000e+00
+2.477400004863739014e-03,8.666390385769773275e-06,0.000000000000000000e+00
+1.174179997178725898e-04,-3.746410075109452009e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..1663af6dacd45ffa7c807444354b15ecb8970ef0
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/log.out
@@ -0,0 +1,110 @@
+
+### # # # #
+# # # # ## ## # # #
+# # # # # # # # # # #
+### ## # # ##
+
+Dune for Multi-{ Phase,
+ Component,
+ Scale,
+ Physics,
+ ...} flow and transport in porous media
+
+Reading parameters from file stokesdarcy_BJ_params.input.
+Computed bounding box tree with 83967 nodes for 41984 grid entites in 0.0183629 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 0.27209 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 1.90878 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-08
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 18
+ -- Newton.TargetSteps = 10
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 419839 nodes for 209920 grid entites in 0.0776521 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.722e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 7.882e-13
+Assemble/solve/update time: 2.58056(18.3446%)/11.4272(81.2333%)/0.0593731(0.42207%)
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 0.270618 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 2.44871 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-6"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ Darcy ]
+[ Darcy.Problem ]
+Name = "darcy"
+[ Darcy.SpatialParams ]
+AlphaBeaversJoseph = "1.0"
+Permeability = "3.25e-9"
+[ Grid ]
+Cells0 = "656"
+Cells1 = "384"
+Positions0 = "-125e-6 0.010125"
+Positions1 = "0 0.6e-2"
+[ Problem ]
+EnableGravity = "false"
+EnableInertiaTerms = "false"
+Name = "regular_2D_stokesdarcy_250_micron"
+SlipCondition = "BJ"
+[ Stokes ]
+[ Stokes.FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForIC = "true"
+[ Stokes.Grid ]
+CavityHeight = "0.005"
+CavityLength = "1.025e-2"
+InletLength = "0.0"
+[ Stokes.Problem ]
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Newton ]
+EnableAbsoluteResidualCriterion = "false"
+EnableChop = "false"
+EnablePartialReassembly = "false"
+EnableResidualCriterion = "false"
+EnableShiftCriterion = "true"
+MaxAbsoluteResidual = "1e-5"
+MaxRelativeShift = "1e-8"
+MaxSteps = "18"
+MinSteps = "2"
+ResidualReduction = "1e-5"
+SatisfyResidualAndShiftCriterion = "false"
+TargetSteps = "10"
+UseLineSearch = "false"
+[ Vtk ]
+AddProcessRank = "true"
+
+# Unused parameters:
+Darcy.Problem.Pressure = "0.0"
+
+### # # # #
+# # # # ## ## # # #
+# # # # # # # # # # #
+### ## # # ##
+
+Dune for Multi-{ Phase,
+ Component,
+ Scale,
+ Physics,
+ ...} flow and transport in porous media
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/outFiles.zip
index 74e1166b427923a23db4777f7eaffa548cd82971..1516ba62832680452a1462021b8d7622f252dff5 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/stokesdarcy_BJ_params.input b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/stokesdarcy_BJ_params.input
index 06e24289fa7117879e689708f8362a3a86c4b445..41698aaf3cac5bb6a1c1e279d27fb0c27c0332b6 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/stokesdarcy_BJ_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/coarse_grid/stokesdarcy_BJ_params.input
@@ -1,8 +1,8 @@
[Grid]
Positions0 = -125e-6 0.010125
Positions1 = 0 0.6e-2
-Cells0 = 328 #1025
-Cells1 = 192 #600
+Cells0 = 656 #656
+Cells1 = 384 #384
[Stokes.Grid]
InletLength = 0.0
@@ -31,7 +31,7 @@ AlphaBeaversJoseph = 1.0
[Problem]
EnableGravity = false
EnableInertiaTerms = false
-Name = regular_2D_stokesdarcy_250_micron_BJ
+Name = regular_2D_stokesdarcy_250_micron
SlipCondition = BJ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_p.csv
index a6198ef8f04c711abc04d01d491b10c7f64b7838..2e0a34d0feee9ca1665e0d8983dfdd71249e3322 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_p.csv
@@ -1,6 +1,6 @@
fine,normal,coarse
-0.142557993531227,0.142046004533768,0.140977993607521
-0.129592999815941,0.129085004329681,0.128030002117157
-0.125530004501343,0.125094994902611,0.124188996851444
-0.041502300649881,0.040710799396038,0.039666399359703
-0.171332001686096,0.170781999826431,0.169621005654335
+0.142814241349697,0.142558217048645,0.142046168446541
+0.129847206175328,0.12959298491478,0.129084542393684
+0.125747509300709,0.125530004501343,0.125094994902611
+0.041898051276803,0.041502300649881,0.040710799396038
+0.171607002615929,0.171332001686096,0.170781999826431
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_velocity.csv
index ee7810e78207cc39c3038ebcef54fc8fce79e8f8..dd4a3e7556268357aebcff7d5738a1d98e986b5a 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_velocity.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/ffpm_stokesdarcy_BJ_velocity.csv
@@ -1,21 +1,21 @@
fine,normal,coarse
-3.49637490045459E-05,3.49549850084728E-05,3.49187563559575E-05
-2.2983215935109E-05,2.29773341147484E-05,2.29533297336137E-05
-3.29173157825504E-05,3.29086621631283E-05,3.28738254841544E-05
-3.64960258292536E-05,3.64865798677938E-05,3.64479421165548E-05
-4.6413153607739E-05,4.6400807412686E-05,4.63511763157055E-05
-4.93606102336552E-05,4.93472619181997E-05,4.92939033539029E-05
-3.03605762213224E-05,3.03526840624708E-05,3.03207831062799E-05
-4.41840307571021E-05,4.41724006882772E-05,4.41256575734351E-05
-4.12539378871417E-05,4.12433303926591E-05,4.12005073179159E-05
-6.64705740372145E-05,6.64533382812882E-05,6.63842014885771E-05
-5.8449888509476E-05,5.84339549173172E-05,5.83704590182806E-05
-6.67722171617282E-05,6.67529925466937E-05,6.66778486127238E-05
-0.000150654773315,0.000147903427753,0.000146636160216
-0.001780248584956,0.001760031315156,0.001791262453969
-0.001917841537992,0.001898051492416,0.001936691333651
-0.001953419114071,0.001933122225897,0.001972102778213
-0.002302890376228,0.002292578859429,0.002270745337358
-0.002444330122333,0.002434710248193,0.002414180154404
-0.002487375664436,0.002477415163113,0.002456154231574
-0.000393485370488,0.000392610329928,0.000390781036976
+3.49681317056766E-05,3.49638036532589E-05,3.49551475484234E-05
+2.29863199407513E-05,2.29833134741732E-05,2.29773005410169E-05
+3.29214438462703E-05,3.29171577842244E-05,3.29085856601326E-05
+3.65008448145996E-05,3.64961238607896E-05,3.64866819531696E-05
+4.64194692905435E-05,4.64133230689942E-05,4.64010306258957E-05
+4.93678197939397E-05,4.9361227424061E-05,4.93480426843037E-05
+3.0364835398224E-05,3.03608030809422E-05,3.03527384463785E-05
+4.41892553186266E-05,4.41834984260658E-05,4.41719846409443E-05
+4.72693216746951E-05,4.7269336802323E-05,4.72693670575787E-05
+0.000287494410794,0.000287520633062,0.000287573077599
+0.000305561951225,0.000305590750659,0.000305648349528
+0.000311933759532,0.000311961088474,0.000312015746358
+0.000152664079865,0.000150654773315,0.000146636160216
+0.001790357219856,0.001780248584956,0.001760031315156
+0.00192773656078,0.001917841537992,0.001898051492416
+0.001963567558158,0.001953419114071,0.001933122225897
+0.002308046134628,0.002302890376228,0.002292578859429
+0.002449140059403,0.002444330122333,0.002434710248193
+0.002492355915098,0.002487375664436,0.002477415163113
+0.000393922890768,0.000393485370488,0.000392610329928
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/ffpm_stokesdarcy_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/ffpm_stokesdarcy_velocity.csv
deleted file mode 100644
index 916ba5c6b806b38d90359a63044fc1bcb35571ca..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/ffpm_stokesdarcy_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-2.851600038411561400e-05,2.023120032390579581e-05,0.000000000000000000e+00
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/outFiles.zip
deleted file mode 100644
index 065781fd40deb7619a6e50056fbc7f422845ccbe..0000000000000000000000000000000000000000
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/outFiles.zip and /dev/null differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/stokesdarcy_BJ_params.input b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/stokesdarcy_BJ_params.input
index f9a8c6cf49dd1779301419db40f9ac52366de95f..ea7f3076c800efc1e08f4067f9f8ca9b1c67255c 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/stokesdarcy_BJ_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/stokesdarcy_BJ_params.input
@@ -1,8 +1,8 @@
[Grid]
Positions0 = -125e-6 0.010125
Positions1 = 0 0.6e-2
-Cells0 = 1312 #1025
-Cells1 = 768 #600
+Cells0 = 2624 #656
+Cells1 = 1536 #384
[Stokes.Grid]
InletLength = 0.0
@@ -31,7 +31,7 @@ AlphaBeaversJoseph = 1.0
[Problem]
EnableGravity = false
EnableInertiaTerms = false
-Name = regular_2D_stokesdarcy_250_micron_BJ
+Name = regular_2D_stokesdarcy_250_micron
SlipCondition = BJ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/ffpm_stokesdarcy_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_p_final.csv
similarity index 60%
rename from BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/ffpm_stokesdarcy_p.csv
rename to BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_p_final.csv
index c6a1ca1c28f204b3a4009188e0e8fb1a51963b91..0dcea5e9cb981ff51982cf62b2a81fb4466188b1 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/fine_grid/ffpm_stokesdarcy_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_p_final.csv
@@ -1,5 +1,5 @@
-1.425579935312271118e-01
-1.295929998159408569e-01
+1.425582170486450195e-01
+1.295929849147796631e-01
1.255300045013427734e-01
4.150230064988136292e-02
1.713320016860961914e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_velocity.csv
deleted file mode 100644
index 03b5c4b875b8c70a6a33a69a79239f83c116aeb4..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..add51111f00bf9c00200a683b6aa7d1abccd1eee
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/ffpm_stokesdarcy_velocity_final.csv
@@ -0,0 +1,20 @@
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..fc51562b87b7b296333eef86bc8ab25e17c47d2c
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/log.out
@@ -0,0 +1,96 @@
+
+You idiot! You signed the order to destroy Earth!
+ - Douglas Adams, HGttG
+
+Reading parameters from file stokesdarcy_BJ_params.input.
+Computed bounding box tree with 335871 nodes for 167936 grid entites in 0.0780246 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 0.937992 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 7.7293 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-08
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 18
+ -- Newton.TargetSteps = 10
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 1679359 nodes for 839680 grid entites in 0.295529 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.727e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 2.051e-12
+Assemble/solve/update time: 10.4777(14.0783%)/63.7232(85.6216%)/0.223354(0.300109%)
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 1.19781 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 9.52434 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-6"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ Darcy ]
+[ Darcy.Problem ]
+Name = "darcy"
+[ Darcy.SpatialParams ]
+AlphaBeaversJoseph = "1.0"
+Permeability = "3.25e-9"
+[ Grid ]
+Cells0 = "1312"
+Cells1 = "768"
+Positions0 = "-125e-6 0.010125"
+Positions1 = "0 0.6e-2"
+[ Problem ]
+EnableGravity = "false"
+EnableInertiaTerms = "false"
+Name = "regular_2D_stokesdarcy_250_micron"
+SlipCondition = "BJ"
+[ Stokes ]
+[ Stokes.FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForIC = "true"
+[ Stokes.Grid ]
+CavityHeight = "0.005"
+CavityLength = "1.025e-2"
+InletLength = "0.0"
+[ Stokes.Problem ]
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Newton ]
+EnableAbsoluteResidualCriterion = "false"
+EnableChop = "false"
+EnablePartialReassembly = "false"
+EnableResidualCriterion = "false"
+EnableShiftCriterion = "true"
+MaxAbsoluteResidual = "1e-5"
+MaxRelativeShift = "1e-8"
+MaxSteps = "18"
+MinSteps = "2"
+ResidualReduction = "1e-5"
+SatisfyResidualAndShiftCriterion = "false"
+TargetSteps = "10"
+UseLineSearch = "false"
+[ Vtk ]
+AddProcessRank = "true"
+
+# Unused parameters:
+Darcy.Problem.Pressure = "0.0"
+
+Marvin: I've been talking to the main computer.
+Arthur: And?
+Marvin: It hates me.
+ - Douglas Adams, HGttG
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/outFiles.zip
index ac6793399a7f6fcb069620af1ee5ef0143c9c31e..fbf2d7ef4988fd3316bfc1f811238484436d2cb6 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/stokesdarcy_BJ_params.input b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/stokesdarcy_BJ_params.input
index 894205a273a1a15c6722f5649a6b9bdff728c3bc..541a00bfd1bd7df740f33b30484002ce03f31c21 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/stokesdarcy_BJ_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_BJ/normal_grid/stokesdarcy_BJ_params.input
@@ -1,8 +1,8 @@
[Grid]
Positions0 = -125e-6 0.010125
Positions1 = 0 0.6e-2
-Cells0 = 656 #1025
-Cells1 = 384 #600
+Cells0 = 1312 #656
+Cells1 = 768 #384
[Stokes.Grid]
InletLength = 0.0
@@ -31,7 +31,7 @@ AlphaBeaversJoseph = 1.0
[Problem]
EnableGravity = false
EnableInertiaTerms = false
-Name = regular_2D_stokesdarcy_250_micron_BJ
+Name = regular_2D_stokesdarcy_250_micron
SlipCondition = BJ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_p.csv
deleted file mode 100644
index a3af68c7e673a558fa9f8b3dbbb4aaa366eafd79..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_p.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-1.410750001668930054e-01
-1.281139999628067017e-01
-1.242699995636940002e-01
-3.966569900512695312e-02
-1.697469949722290039e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_p_final.csv
similarity index 60%
rename from BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_p.csv
rename to BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_p_final.csv
index a98b20751294d27cbcc4d6299b68d00c9b93e9ac..c60a5f2639e97c68fe8ab5cb5d71a3b785dbdfa1 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_p_final.csv
@@ -1,5 +1,5 @@
-1.421439945697784424e-01
-1.291690021753311157e-01
+1.421436071395874023e-01
+1.291688382625579834e-01
1.251759976148605347e-01
4.071009904146194458e-02
1.709080040454864502e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_velocity.csv
deleted file mode 100644
index bbd5f44faa8506e80bd505fd9d721a71e1d041d6..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..b4d674f209e273d564ba9f610ffc88f102de7fe7
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/ffpm_stokesdarcy_velocity_final.csv
@@ -0,0 +1,20 @@
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+1.896669971756637096e-03,2.414250047877430916e-06,0.000000000000000000e+00
+1.931570004671812057e-03,2.658209996297955513e-05,0.000000000000000000e+00
+2.261319896206259727e-03,-3.820359997916966677e-04,0.000000000000000000e+00
+2.435589907690882683e-03,1.005670014819770586e-06,0.000000000000000000e+00
+2.478349953889846802e-03,8.685139619046822190e-06,0.000000000000000000e+00
+1.174179997178725898e-04,-3.745690046343952417e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..4979bcb6c2416275ef24eec3c7737cf2a6fb198b
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/log.out
@@ -0,0 +1,115 @@
+
+### # # # #
+# # # # ## ## # # #
+# # # # # # # # # # #
+### ## # # ##
+
+Dune for Multi-{ Phase,
+ Component,
+ Scale,
+ Physics,
+ ...} flow and transport in porous media
+
+Reading parameters from file stokesdarcy_ER_params.input.
+Computed bounding box tree with 83967 nodes for 41984 grid entites in 0.017889 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 0.240291 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 1.91234 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-08
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 18
+ -- Newton.TargetSteps = 10
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 419839 nodes for 209920 grid entites in 0.0702125 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.723e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 7.785e-13
+Assemble/solve/update time: 3.01705(13.7473%)/18.8459(85.8718%)/0.0835903(0.380881%)
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 0.288557 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 2.49798 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-6"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ Darcy ]
+[ Darcy.InterfaceParams ]
+EpsInterface = "5.0e-4"
+N_1_bl = "-1.13e-1"
+[ Darcy.Problem ]
+Name = "darcy"
+[ Darcy.SpatialParams ]
+AlphaBeaversJoseph = "1.0"
+Permeability = "3.25e-9"
+[ Grid ]
+Cells0 = "656"
+Cells1 = "384"
+Positions0 = "-125e-6 0.010125"
+Positions1 = "0 0.6e-2"
+[ Problem ]
+EnableGravity = "false"
+EnableInertiaTerms = "false"
+Name = "regular_2D_stokesdarcy_250_micron"
+SlipCondition = "ER"
+[ Stokes ]
+[ Stokes.FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForIC = "true"
+[ Stokes.Grid ]
+CavityHeight = "0.005"
+CavityLength = "1.025e-2"
+InletLength = "0.0"
+[ Stokes.Problem ]
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Newton ]
+EnableAbsoluteResidualCriterion = "false"
+EnableChop = "false"
+EnablePartialReassembly = "false"
+EnableResidualCriterion = "false"
+EnableShiftCriterion = "true"
+MaxAbsoluteResidual = "1e-5"
+MaxRelativeShift = "1e-8"
+MaxSteps = "18"
+MinSteps = "2"
+ResidualReduction = "1e-5"
+SatisfyResidualAndShiftCriterion = "false"
+TargetSteps = "10"
+UseLineSearch = "false"
+[ Vtk ]
+AddProcessRank = "true"
+
+# Unused parameters:
+Darcy.Problem.Pressure = "0.0"
+Darcy.InterfaceParams.N_s_bl = "0.0"
+Darcy.InterfaceParams.M_bl = "(-7.16e-3,0.0)"
+
+### # # # #
+# # # # ## ## # # #
+# # # # # # # # # # #
+### ## # # ##
+
+Dune for Multi-{ Phase,
+ Component,
+ Scale,
+ Physics,
+ ...} flow and transport in porous media
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/outFiles.zip
index 91b8e91c71cff321f40bf363cb4037a5ca790785..07d4a022233a9e1383d7a3161018e0ab39aac493 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/stokesdarcy_ER_params.input b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/stokesdarcy_ER_params.input
index 88c4fe633b48c5bd0ebead1768362450aaadcd82..86dd065d6cceafa25f57cdf16bfacdc0cb012f3d 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/stokesdarcy_ER_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/coarse_grid/stokesdarcy_ER_params.input
@@ -1,8 +1,8 @@
[Grid]
Positions0 = -125e-6 0.010125
Positions1 = 0 0.6e-2
-Cells0 = 328 #1025
-Cells1 = 192 #600
+Cells0 = 656 #656
+Cells1 = 384 #384
[Stokes.Grid]
InletLength = 0.0
@@ -26,7 +26,7 @@ Pressure = 0.0
[Darcy.SpatialParams]
Permeability = 3.25e-9 # m^2
-AlphaBeaversJoseph = 2.0
+AlphaBeaversJoseph = 1.0
[Darcy.InterfaceParams]
EpsInterface = 5.0e-4
@@ -37,7 +37,7 @@ M_bl = (-7.16e-3,0.0)
[Problem]
EnableGravity = false
EnableInertiaTerms = false
-Name = regular_2D_stokesdarcy_250_micron_ER
+Name = regular_2D_stokesdarcy_250_micron
SlipCondition = ER
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_p.csv
index 26165e6a6766f0b33a755192853edfcf44fc5e98..4aad414ae9adb87620622ddd186450c977da6e6e 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_p.csv
@@ -1,6 +1,6 @@
fine,normal,coarse
-0.142655998468399,0.142143994569778,0.141075000166893
-0.129676997661591,0.129169002175331,0.128113999962807
-0.125611007213593,0.125175997614861,0.124269999563694
-0.041501499712467,0.040710099041462,0.039665699005127
-0.171458005905151,0.170908004045486,0.169746994972229
+0.142911702394486,0.142655670642853,0.142143607139587
+0.12993161380291,0.129677355289459,0.129168838262558
+0.125828512012959,0.125611007213593,0.125175997614861
+0.04189720004797,0.041501499712467,0.040710099041462
+0.171733006834984,0.171458005905151,0.170908004045486
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_velocity.csv
index e46659d1f31edf20e07e8462ba978fade5eba938..dcb7d2b8e1687a0f58edc3081a6915f76f559846 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_velocity.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/ffpm_stokesdarcy_ER_velocity.csv
@@ -1,21 +1,21 @@
fine,normal,coarse
-3.50006355677893E-05,3.49918730672919E-05,3.49555628404179E-05
-2.3007176062106E-05,2.30011544988886E-05,2.29771501184719E-05
-3.29512704814655E-05,3.29426562783574E-05,3.29077801850107E-05
-3.65340861728407E-05,3.65245415316628E-05,3.6485903787985E-05
-4.6461589798775E-05,4.64491455616033E-05,4.63994158286674E-05
-4.9412521551951E-05,4.93991161994017E-05,4.93456169836317E-05
-3.03920601979792E-05,3.03840756253955E-05,3.03521363528739E-05
-4.42293297414147E-05,4.42176125441076E-05,4.41707329955579E-05
-4.12962838132002E-05,4.12856799623822E-05,4.12428532908459E-05
-6.65371798279557E-05,6.65198920091474E-05,6.64505851218752E-05
-5.85109002858775E-05,5.84949630675774E-05,5.84313690669815E-05
-6.6842257979955E-05,6.68229813235231E-05,6.67477041339391E-05
-0.000150489063694,0.000147743594626,0.000146471978873
-0.001779055388143,0.001758798205465,0.001790099016214
-0.001916491589082,0.001896671508292,0.001935381431061
-0.001952079702322,0.001931752906297,0.001970813279026
-0.002303676314873,0.002293364161688,0.002271529869666
-0.002445200210586,0.002435590115315,0.002415070266038
-0.002488315663562,0.002478365171962,0.002457114248238
-0.000393413999603,0.000392541623131,0.000390713875501
+3.50050103426432E-05,3.50006715593031E-05,3.49919939926228E-05
+2.30101726616574E-05,2.30071603493191E-05,2.30011357246425E-05
+3.29554579022419E-05,3.295116317295E-05,3.29425737143662E-05
+3.65389185177527E-05,3.6534187041031E-05,3.65247240875877E-05
+4.64678553544109E-05,4.64616945193283E-05,4.64493728491632E-05
+4.94197003164667E-05,4.94130941861796E-05,4.93998819256054E-05
+3.03963020629109E-05,3.03922622598664E-05,3.03841826537773E-05
+4.42345023958708E-05,4.42287315890611E-05,4.42171899754416E-05
+4.72803054213093E-05,4.72803117434146E-05,4.72803243876253E-05
+0.000286899990256,0.000286926362688,0.000286979107553
+0.000304900586459,0.000304929513001,0.000304987366085
+0.000311270782598,0.000311298253488,0.000311353195268
+0.000152497606105,0.000150489063694,0.000146471978873
+0.001789183979482,0.001779055388143,0.001758798205465
+0.001926401629477,0.001916491589082,0.001896671508292
+0.001962243100335,0.001952079702322,0.001931752906297
+0.002308832391466,0.002303676314873,0.002293364161688
+0.002450005258222,0.002445200210586,0.002435590115315
+0.002493290909362,0.002488315663562,0.002478365171962
+0.000393850187839,0.000393413999603,0.000392541623131
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/ffpm_stokesdarcy_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/ffpm_stokesdarcy_velocity.csv
deleted file mode 100644
index 75c3efce3b450be5e8ebdf3a89e15fd9993ce384..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/ffpm_stokesdarcy_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-2.854639933502767235e-05,2.025210051215253770e-05,0.000000000000000000e+00
-1.352409981336677447e-05,-1.861259988800156862e-05,0.000000000000000000e+00
-3.033599932678043842e-05,-1.286520000576274469e-05,0.000000000000000000e+00
-3.644539901870302856e-05,2.544079961808165535e-06,0.000000000000000000e+00
-4.637829988496378064e-05,2.780760041787289083e-06,0.000000000000000000e+00
-4.058290141983889043e-05,2.818910070345737040e-05,0.000000000000000000e+00
-1.164140030596172437e-05,-2.807410055538639426e-05,0.000000000000000000e+00
-3.884160105371847749e-05,-2.115569986926857382e-05,0.000000000000000000e+00
-7.703209803366917185e-07,-4.128909858991391957e-05,0.000000000000000000e+00
-5.718700049328617752e-05,-3.401239882805384696e-05,0.000000000000000000e+00
-5.844200131832621992e-05,2.838650061676162295e-06,0.000000000000000000e+00
-5.864970080438069999e-05,3.206399924238212407e-05,0.000000000000000000e+00
-1.004410005407407880e-04,-1.120649976655840874e-04,0.000000000000000000e+00
-1.775830052793025970e-03,-1.070779981091618538e-04,0.000000000000000000e+00
-1.916490029543638229e-03,2.444930032652337104e-06,0.000000000000000000e+00
-1.951899961568415165e-03,2.648970075824763626e-05,0.000000000000000000e+00
-2.272639889270067215e-03,-3.768719907384365797e-04,0.000000000000000000e+00
-2.445199992507696152e-03,1.032709974424506072e-06,0.000000000000000000e+00
-2.488299971446394920e-03,8.837059795041568577e-06,0.000000000000000000e+00
-1.209170004585757852e-04,-3.743710112757980824e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/outFiles.zip
deleted file mode 100644
index 8ab50c2d0777f42b9148f40cef287d07deb7e245..0000000000000000000000000000000000000000
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/outFiles.zip and /dev/null differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/stokesdarcy_ER_params.input b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/stokesdarcy_ER_params.input
index a53c9789610e1634de61f938578cb1b90adc3f16..57154d6af87d560355a3a4c182eb2ed463b92972 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/stokesdarcy_ER_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/stokesdarcy_ER_params.input
@@ -1,8 +1,8 @@
[Grid]
Positions0 = -125e-6 0.010125
Positions1 = 0 0.6e-2
-Cells0 = 1312 #1025
-Cells1 = 768 #600
+Cells0 = 2624 #656
+Cells1 = 1536 #384
[Stokes.Grid]
InletLength = 0.0
@@ -26,7 +26,7 @@ Pressure = 0.0
[Darcy.SpatialParams]
Permeability = 3.25e-9 # m^2
-AlphaBeaversJoseph = 2.0
+AlphaBeaversJoseph = 1.0
[Darcy.InterfaceParams]
EpsInterface = 5.0e-4
@@ -37,7 +37,7 @@ M_bl = (-7.16e-3,0.0)
[Problem]
EnableGravity = false
EnableInertiaTerms = false
-Name = regular_2D_stokesdarcy_250_micron_ER
+Name = regular_2D_stokesdarcy_250_micron
SlipCondition = ER
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/ffpm_stokesdarcy_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_p_final.csv
similarity index 60%
rename from BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/ffpm_stokesdarcy_p.csv
rename to BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_p_final.csv
index 11bc7bee780fcb031d4257d23ce62ffe58894eaf..eee6f67139c0d9aadfd372a388fc742a23349a52 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/fine_grid/ffpm_stokesdarcy_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_p_final.csv
@@ -1,5 +1,5 @@
-1.426559984683990479e-01
-1.296769976615905762e-01
+1.426556706428527832e-01
+1.296773552894592285e-01
1.256110072135925293e-01
4.150149971246719360e-02
1.714580059051513672e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_velocity.csv
deleted file mode 100644
index 81794286a2dc2f177f73120c7523b0de722ff8be..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-2.853969999705441296e-05,2.024639979936182499e-05,0.000000000000000000e+00
-1.352060007775435224e-05,-1.860769953054841608e-05,0.000000000000000000e+00
-3.032799941138364375e-05,-1.286200040340190753e-05,0.000000000000000000e+00
-3.643590025603771210e-05,2.543089976825285703e-06,0.000000000000000000e+00
-4.636590165318921208e-05,2.779619990178616717e-06,0.000000000000000000e+00
-4.057290061609819531e-05,2.818000029947143048e-05,0.000000000000000000e+00
-1.163839988294057548e-05,-2.806670090649276972e-05,0.000000000000000000e+00
-3.883120007230900228e-05,-2.115029928972944617e-05,0.000000000000000000e+00
-7.698779995735094417e-07,-4.127850115764886141e-05,0.000000000000000000e+00
-5.717200110666453838e-05,-3.400379864615388215e-05,0.000000000000000000e+00
-5.842609971296042204e-05,2.837530018950928934e-06,0.000000000000000000e+00
-5.863319893251173198e-05,3.205399843864142895e-05,0.000000000000000000e+00
-9.725950076244771481e-05,-1.095199986593797803e-04,0.000000000000000000e+00
-1.755620003677904606e-03,-1.056859982782043517e-04,0.000000000000000000e+00
-1.896669971756637096e-03,2.414250047877430916e-06,0.000000000000000000e+00
-1.931570004671812057e-03,2.658209996297955513e-05,0.000000000000000000e+00
-2.261319896206259727e-03,-3.820359997916966677e-04,0.000000000000000000e+00
-2.435589907690882683e-03,1.005670014819770586e-06,0.000000000000000000e+00
-2.478349953889846802e-03,8.685139619046822190e-06,0.000000000000000000e+00
-1.174179997178725898e-04,-3.745690046343952417e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..53f79e4a211c96dafd370b2405eb184509f02e43
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/ffpm_stokesdarcy_velocity_final.csv
@@ -0,0 +1,20 @@
+2.854635842242103649e-05,2.025222038248841727e-05,0.000000000000000000e+00
+1.352417863920152286e-05,-1.861252318935413541e-05,0.000000000000000000e+00
+3.033589707923667333e-05,-1.286516625809142056e-05,0.000000000000000000e+00
+3.644550150561087776e-05,2.544060288899030464e-06,0.000000000000000000e+00
+4.637840336396692464e-05,2.780783885267213915e-06,0.000000000000000000e+00
+4.058338320334087257e-05,2.818941086335513546e-05,0.000000000000000000e+00
+1.164204695269788203e-05,-2.807405115090588765e-05,0.000000000000000000e+00
+3.884094267014859270e-05,-2.115565811955377740e-05,0.000000000000000000e+00
+1.537254404670047305e-05,-4.471143889528406135e-05,0.000000000000000000e+00
+2.844671019532896139e-04,-3.748607089892885824e-05,0.000000000000000000e+00
+3.049164319932629041e-04,2.824429073090454985e-06,0.000000000000000000e+00
+3.096712555548108980e-04,3.178547007687271275e-05,0.000000000000000000e+00
+1.004410005407407880e-04,-1.120649976655840874e-04,0.000000000000000000e+00
+1.775830052793025970e-03,-1.070779981091618538e-04,0.000000000000000000e+00
+1.916490029543638229e-03,2.444930032652337104e-06,0.000000000000000000e+00
+1.951899961568415165e-03,2.648970075824763626e-05,0.000000000000000000e+00
+2.272639889270067215e-03,-3.768719907384365797e-04,0.000000000000000000e+00
+2.445199992507696152e-03,1.032709974424506072e-06,0.000000000000000000e+00
+2.488299971446394920e-03,8.837059795041568577e-06,0.000000000000000000e+00
+1.209170004585757852e-04,-3.743710112757980824e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..8d92744ba7d463487f8d770d4a7e32aa9585bf04
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/log.out
@@ -0,0 +1,101 @@
+
+You idiot! You signed the order to destroy Earth!
+ - Douglas Adams, HGttG
+
+Reading parameters from file stokesdarcy_ER_params.input.
+Computed bounding box tree with 335871 nodes for 167936 grid entites in 0.077307 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 0.964968 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 7.78451 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-08
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 18
+ -- Newton.TargetSteps = 10
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 1679359 nodes for 839680 grid entites in 0.301194 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.728e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 2.044e-12
+Assemble/solve/update time: 10.5535(13.3912%)/68.0152(86.304%)/0.240166(0.304745%)
+Writing output for problem "regular_2D_stokesdarcy_250_micron_stokes". Took 1.80153 seconds.
+Writing output for problem "regular_2D_stokesdarcy_250_micron_darcy". Took 11.4025 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-6"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ Darcy ]
+[ Darcy.InterfaceParams ]
+EpsInterface = "5.0e-4"
+N_1_bl = "-1.13e-1"
+[ Darcy.Problem ]
+Name = "darcy"
+[ Darcy.SpatialParams ]
+AlphaBeaversJoseph = "1.0"
+Permeability = "3.25e-9"
+[ Grid ]
+Cells0 = "1312"
+Cells1 = "768"
+Positions0 = "-125e-6 0.010125"
+Positions1 = "0 0.6e-2"
+[ Problem ]
+EnableGravity = "false"
+EnableInertiaTerms = "false"
+Name = "regular_2D_stokesdarcy_250_micron"
+SlipCondition = "ER"
+[ Stokes ]
+[ Stokes.FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForIC = "true"
+[ Stokes.Grid ]
+CavityHeight = "0.005"
+CavityLength = "1.025e-2"
+InletLength = "0.0"
+[ Stokes.Problem ]
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Newton ]
+EnableAbsoluteResidualCriterion = "false"
+EnableChop = "false"
+EnablePartialReassembly = "false"
+EnableResidualCriterion = "false"
+EnableShiftCriterion = "true"
+MaxAbsoluteResidual = "1e-5"
+MaxRelativeShift = "1e-8"
+MaxSteps = "18"
+MinSteps = "2"
+ResidualReduction = "1e-5"
+SatisfyResidualAndShiftCriterion = "false"
+TargetSteps = "10"
+UseLineSearch = "false"
+[ Vtk ]
+AddProcessRank = "true"
+
+# Unused parameters:
+Darcy.Problem.Pressure = "0.0"
+Darcy.InterfaceParams.N_s_bl = "0.0"
+Darcy.InterfaceParams.M_bl = "(-7.16e-3,0.0)"
+
+Marvin: I've been talking to the main computer.
+Arthur: And?
+Marvin: It hates me.
+ - Douglas Adams, HGttG
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/outFiles.zip
index d16e862ee75eb79e3ae045a7b291d954d1c0184f..7ea4b71d32e3382b7ebb705b0e419edcf612ee8c 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/stokesdarcy_ER_params.input b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/stokesdarcy_ER_params.input
index 8ae0a048acc1224c325a71d82fda408bc6a99873..a1ebfffc5b9763ac135f5925c8044f323fae0fc8 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/stokesdarcy_ER_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokesdarcy_ER/normal_grid/stokesdarcy_ER_params.input
@@ -1,8 +1,8 @@
[Grid]
Positions0 = -125e-6 0.010125
Positions1 = 0 0.6e-2
-Cells0 = 656 #1025
-Cells1 = 384 #600
+Cells0 = 1312 #656
+Cells1 = 768 #384
[Stokes.Grid]
InletLength = 0.0
@@ -26,7 +26,7 @@ Pressure = 0.0
[Darcy.SpatialParams]
Permeability = 3.25e-9 # m^2
-AlphaBeaversJoseph = 2.0
+AlphaBeaversJoseph = 1.0
[Darcy.InterfaceParams]
EpsInterface = 5.0e-4
@@ -37,7 +37,7 @@ M_bl = (-7.16e-3,0.0)
[Problem]
EnableGravity = false
EnableInertiaTerms = false
-Name = regular_2D_stokesdarcy_250_micron_ER
+Name = regular_2D_stokesdarcy_250_micron
SlipCondition = ER
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_p.csv
deleted file mode 100644
index 0d08bba7047ccf677886a0e6a971c7d1010dae54..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_p.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-1.446429938077926636e-01
-1.313609927892684937e-01
-1.276240050792694092e-01
-3.610349819064140320e-02
-1.773239970207214355e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_p_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_p_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..b93ba6da248292b611702c22141647ae09ba9d38
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_p_final.csv
@@ -0,0 +1,5 @@
+1.541270017623901367e-01
+1.398350000381469727e-01
+1.356389969587326050e-01
+4.578920081257820129e-02
+1.871549934148788452e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_velocity.csv
deleted file mode 100644
index 188a3c4c18be9dc4b6ab2eb516ec5dd9194c5b62..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-0.000000000000000000e+00,6.546550139319151640e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-6.129939720267429948e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-4.215590161038562655e-05,0.000000000000000000e+00
-0.000000000000000000e+00,8.056330443650949746e-06,0.000000000000000000e+00
-0.000000000000000000e+00,8.473710295220371336e-06,0.000000000000000000e+00
-0.000000000000000000e+00,9.167750249616801739e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-9.160419722320511937e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-6.857769767520949244e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-1.338680012850090861e-04,0.000000000000000000e+00
--0.000000000000000000e+00,-1.094789986382238567e-04,0.000000000000000000e+00
-0.000000000000000000e+00,8.158520358847454190e-06,0.000000000000000000e+00
-0.000000000000000000e+00,1.093469982151873410e-04,0.000000000000000000e+00
-3.334469874971546233e-05,-1.382420014124363661e-04,0.000000000000000000e+00
-1.212259987369179726e-03,-1.196829980472102761e-04,0.000000000000000000e+00
-1.292680040933191776e-03,6.227829999261302873e-06,0.000000000000000000e+00
-1.335390028543770313e-03,8.288389653898775578e-05,0.000000000000000000e+00
-2.340730046853423119e-03,-3.324029967188835144e-04,0.000000000000000000e+00
-2.506210003048181534e-03,1.913180085466592573e-06,0.000000000000000000e+00
-2.586789894849061966e-03,2.316619975317735225e-05,0.000000000000000000e+00
-7.468419789802283049e-05,-3.378209949005395174e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..3ef6294f919e0b3a4a4d3bd1e37c6ddc73a4b672
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/ffpm_stokespnm_velocity_final.csv
@@ -0,0 +1,20 @@
+3.213385373762589481e-05,2.221720203643418046e-05,0.000000000000000000e+00
+1.554156412938989540e-05,-2.087275317863568347e-05,0.000000000000000000e+00
+3.387460451031998332e-05,-1.435865228799348969e-05,0.000000000000000000e+00
+4.062720472541858641e-05,2.741325395849703028e-06,0.000000000000000000e+00
+5.172404258374507791e-05,2.915390368354864314e-06,0.000000000000000000e+00
+4.497143022558214298e-05,3.097900408421949692e-05,0.000000000000000000e+00
+1.383480114323931698e-05,-3.120060459993467816e-05,0.000000000000000000e+00
+4.306956701005670851e-05,-2.335680260312500423e-05,0.000000000000000000e+00
+1.205656023642397479e-05,-4.756068299022722559e-05,0.000000000000000000e+00
+1.899503519970160981e-04,-3.926292062260923802e-05,0.000000000000000000e+00
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+2.078236394418122093e-04,3.641233154696642499e-05,0.000000000000000000e+00
+3.297060175100341439e-05,-1.028729966492392123e-04,0.000000000000000000e+00
+7.476410246454179287e-04,-8.897160296328365803e-05,0.000000000000000000e+00
+7.981359958648681641e-04,3.282119905634317547e-06,0.000000000000000000e+00
+8.132469956763088703e-04,7.295350224012508988e-05,0.000000000000000000e+00
+2.475240034982562065e-03,-2.765280078165233135e-04,0.000000000000000000e+00
+2.672340022400021553e-03,1.454739958717254922e-06,0.000000000000000000e+00
+2.726929960772395134e-03,1.879269984783604741e-05,0.000000000000000000e+00
+1.229320041602477431e-04,-2.740450145211070776e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..a638a5bac1cb0eaf504d3e56d461a81e7e47f374
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/log.out
@@ -0,0 +1,206 @@
+
+You idiot! You signed the order to destroy Earth!
+ - Douglas Adams, HGttG
+
+Reading parameters from file stokespnm_params.input.
+PoreInscribedRadius is vertex parameter 0
+PoreVolume is vertex parameter 1
+PoreLabel is vertex parameter 2
+ThroatInscribedRadius is element parameter 0
+ThroatLength is element parameter 1
+ThroatLabel is element parameter 2
+
+Found 1 unconnected clusters.
+Creating generic grid from structured lattice with 410 elements and 231 vertices took 0.00544781 seconds.
+plane:
+-0.000125 0.005125
+0.010125 0.005125
+point 0
+0
+0.0005
+0.001
+0.0015
+0.002
+0.0025
+0.003
+0.0035
+0.004
+0.0045
+0.005
+0.0055
+0.006
+0.0065
+0.007
+0.0075
+0.008
+0.0085
+0.009
+0.0095
+0.01
+Using 'TwoPlates' as cross-sectional shape for all throats.
+Using 'Cube' as geometry for all pores.
+Computed bounding box tree with 83967 nodes for 41984 grid entites in 0.0124368 seconds.
+Computing coupling maps and stencils toook 0.0147961 seconds.
+-0.000125
+0.000125
+0.000375
+0.000625
+0.000875
+0.001125
+0.001375
+0.001625
+0.001875
+0.002125
+0.002375
+0.002625
+0.002875
+0.003125
+0.003375
+0.003625
+0.003875
+0.004125
+0.004375
+0.004625
+0.004875
+0.005125
+0.005375
+0.005625
+0.005875
+0.006125
+0.006375
+0.006625
+0.006875
+0.007125
+0.007375
+0.007625
+0.007875
+0.008125
+0.008375
+0.008625
+0.008875
+0.009125
+0.009375
+0.009625
+0.009875
+0.010125
+Writing output for problem "regular_2D_stokespnm_250_micron_stokes". Took 0.22 seconds.
+Writing output for problem "regular_2D_stokespnm_250_micron_pnm". Took 0.0021 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-10
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 20
+ -- Newton.TargetSteps = 4
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 819 nodes for 410 grid entites in 8.4662e-05 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.9121e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 1.9429e-16
+Assemble/solve/update time: 0.86(18.44%)/3.7(80.75%)/0.038(0.82%)
+Assembly and solve took 4.63952 seconds
+numFaceDofs: 84688, numCellCenterDofs: 41984, total FF: 126672, numPNMDofs: 231, total: 126903
+mass flux at outlet is: 0.00200003
+throat 0 : 0
+throat 1 : 0
+throat 2 : 0
+throat 3 : 0
+throat 4 : 0
+throat 5 : 0
+throat 6 : 0
+throat 7 : 0
+throat 8 : 0
+throat 9 : 0
+throat 10 : 0
+throat 11 : 0
+throat 12 : 0
+throat 13 : 0
+throat 14 : 0
+throat 15 : 0
+throat 16 : 0
+throat 17 : 0
+throat 18 : 0
+throat 19 : 0
+throat 20 : 0
+
+vertical net flux (should be zero): 0
+
+##################################
+
+Writing output for problem "regular_2D_stokespnm_250_micron_stokes". Took 0.24 seconds.
+Writing output for problem "regular_2D_stokespnm_250_micron_pnm". Took 0.0076 seconds.
+Simulation took 7.09485 seconds on 1 processes.
+The cumulative CPU time was 7.09486 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-4"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ FluxOverSurface ]
+HorizontalPlaneY = "0.005"
+Verbose = "false"
+[ FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForBeaversJoseph = "true"
+[ Newton ]
+MaxRelativeShift = "1e-10"
+MaxSteps = "20"
+TargetSteps = "4"
+[ PNM ]
+[ PNM.Grid ]
+BoundaryFaceMarker = "1 1 1 2"
+DeletionProbability = "0 0 1 1"
+LowerLeft = "0 125e-6"
+NumPores = "21 11"
+PoreGeometry = "Cube"
+PoreInscribedRadius = "125e-6"
+PriorityList = "2 3 0 1"
+RemoveThroatsOnBoundary = "3"
+ThroatCrossSectionShape = "TwoPlates"
+ThroatInscribedRadius = "125e-6"
+UpperRight = "0.010 0.005125"
+[ PNM.Problem ]
+Name = "pnm"
+TransmissibilityHalfPore = "1.7642875191945115e-05"
+TransmissibilityThroat = "5.26480244078e-06"
+[ Problem ]
+EnableGravity = "false"
+Name = "regular_2D_stokespnm_250_micron"
+[ Stokes ]
+[ Stokes.Grid ]
+Cells1 = "64"
+CellsPerThroat = "16"
+FixedCellsBetweenThroats = "16"
+LowerLeft = "-0.000125000 0.005125"
+Refinement = "0"
+UpperRight = "0.010125 0.006125"
+[ Stokes.Problem ]
+Beta = "35237.668793254459160"
+EnableInertiaTerms = "false"
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+WriteFaceData = "false"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Vtk ]
+AddProcessRank = "true"
+
+Marvin: I've been talking to the main computer.
+Arthur: And?
+Marvin: It hates me.
+ - Douglas Adams, HGttG
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/outFiles.zip
index 9c3daca7cc01651e0a7e3f446024d0a00c880df9..1d1a5567c01fa2233971d59735f214fa4b0235ea 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm-00000.vtp b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm-00000.vtp
deleted file mode 100644
index ee3b2f5a32e59e167f4ec66b725015390a780754..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm-00000.vtp
+++ /dev/null
@@ -1,598 +0,0 @@
-<?xml version="1.0"?>
-<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian">
- <PolyData>
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm-00001.vtp b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm-00001.vtp
deleted file mode 100644
index 6334fe34af2aa1b282f969b9c6117a7f4962c809..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm-00001.vtp
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm.pvd b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_pnm.pvd
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes-00000.vtu b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes-00000.vtu
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes-00001.vtu b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes-00001.vtu
deleted file mode 100644
index 488975a213bca1789e355c7365307b2d3667a26b..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes-00001.vtu
+++ /dev/null
@@ -1,1435 +0,0 @@
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes.pvd b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes.pvd
deleted file mode 100644
index 5ef420d9d7bef526d4da3ebdd2cafc7402304fba..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/regular_2D_stokespnm_250_micron_stokes.pvd
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<VTKFile type="Collection" version="0.1" byte_order="LittleEndian">
-<Collection>
-<DataSet timestep="0" group="" part="0" name="" file="regular_2D_stokespnm_250_micron_stokes-00000.vtu"/>
-<DataSet timestep="1" group="" part="0" name="" file="regular_2D_stokespnm_250_micron_stokes-00001.vtu"/>
-</Collection>
-</VTKFile>
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/stokespnm_params.input b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/stokespnm_params.input
index 9c75e1c3b5c932831a2678d590dd84bf464ce8e6..1ad6f2d71cb4dcc5d4d1306d12fee940e9c40445 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/stokespnm_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/coarse_grid/stokespnm_params.input
@@ -1,17 +1,17 @@
[Stokes.Grid]
LowerLeft = -0.000125000 0.005125 # inlet length: 0.25e-2 m
UpperRight = 0.010125 0.006125 # outlet length: 0.25e-2 m, heigth channel: 1e-3 m
-CellsPerThroat = 3
-Cells1 = 10
-FixedCellsBetweenThroats = 2
+CellsPerThroat = 16
+Cells1 = 64
+FixedCellsBetweenThroats = 16
Refinement = 0
[PNM.Grid]
LowerLeft = 0 125e-6
UpperRight = 0.010 0.005125 # 20 x 10 block, block size 250e-6 m
NumPores = 21 11
-PoreRadius = 125e-6
-ThroatRadius = 125e-6
+PoreInscribedRadius = 125e-6
+ThroatInscribedRadius = 125e-6
PriorityList = 2 3 0 1
BoundaryFaceMarker = 1 1 1 2
DeletionProbability = 0 0 1 1
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_p.csv
index bf6c8b6b2ea54f220e03704762061400439a6c34..db1818e2f450557f0c98690e0679337b87e090a4 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_p.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_p.csv
@@ -1,6 +1,6 @@
fine,normal,coarse
-0.150693997740746,0.14877100288868,0.144642993807793
-0.137317001819611,0.135386005043983,0.131360992789269
-0.133849993348122,0.131653994321823,0.127624005079269
-0.040089998394251,0.038667999207974,0.036103498190641
-0.184107005596161,0.181937992572784,0.177323997020721
+0.154964998364449,0.154688000679016,0.15412700176239
+0.140677005052567,0.140397995710373,0.139835000038147
+0.136442005634308,0.136176005005836,0.135638996958733
+0.04677340015769,0.046440601348877,0.045789200812578
+0.188085004687309,0.187796995043755,0.187154993414879
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_velocity.csv
index 4c549d0b4c415cc853194c61a824743026361ca1..0b062b578f23a0feb8bcadf1fdde8b5f32bd94a0 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_velocity.csv
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/ffpm_stokespnm_velocity.csv
@@ -1,21 +1,21 @@
fine,normal,coarse
-6.5857901063282E-05,6.59185971016996E-05,6.55881012789905E-05
-6.16881006862968E-05,6.17480982327834E-05,6.14688033238053E-05
-4.23740013164002E-05,4.23915007559117E-05,4.23105993831996E-05
-8.23819027573336E-06,8.17720956547419E-06,7.99921963334782E-06
-8.73765020514838E-06,8.63908007886494E-06,8.37527022667928E-06
-9.22870021895506E-05,9.23176994547248E-05,9.16935969144106E-05
-9.21667015063576E-05,9.22679973882623E-05,9.18403966352344E-05
-6.87443025526591E-05,6.8807997290194E-05,6.88189029460773E-05
-0.000134657995659,0.000134828995215,0.000134208996315
-0.000109729997348,0.000110063003376,0.000111861997771
-8.46364036988234E-06,8.34307957120473E-06,8.03572038421407E-06
-0.00011049999739,0.000110298002255,0.000109091000922
-0.000144811990044,0.000144404230623,0.00012651891646
-0.001455336842265,0.001378867864722,0.001212136931764
-0.001551224843844,0.001466151830376,0.001298720854697
-0.001601505396798,0.00151697332281,0.001329861594046
-0.002336998955398,0.002355708308839,0.002322470804904
-0.002476610501769,0.002490980686685,0.002508750120255
-0.002556395996982,0.002571994680837,0.002584202845364
-0.00036233469274,0.000362682536637,0.000306445921445
+3.90664641650466E-05,3.90513552546504E-05,3.90378016696384E-05
+2.60232980393375E-05,2.60231049168079E-05,2.60197844567342E-05
+3.67921150011533E-05,3.67845642115914E-05,3.67754153561901E-05
+4.07195853211572E-05,4.07089293342771E-05,4.06976355430658E-05
+5.18061394257956E-05,5.17941041315599E-05,5.17805841717733E-05
+5.46088658606319E-05,5.45870165794528E-05,5.45677099277932E-05
+3.41303303540186E-05,3.41290626693036E-05,3.41240154564482E-05
+4.89951817046851E-05,4.89816569198559E-05,4.89671814483331E-05
+4.90650508124817E-05,4.90340859307871E-05,4.90292302405883E-05
+0.000193965752543,0.000193589148089,0.000193568569628
+0.000205510127402,0.000205111761685,0.000205094091649
+0.000210989390727,0.000210581953656,0.000210560791182
+0.00010802737625,0.000109184948626,0.000109756855595
+0.0007529163618,0.000781406341346,0.000795502231882
+0.000798142744255,0.000829218777558,0.000844594558431
+0.000816512638889,0.000849174892356,0.000865372357668
+0.002490638667067,0.002492345211649,0.002495214104838
+0.002672340418358,0.00267174048719,0.002673140526436
+0.002726994715163,0.002726687419107,0.002728236898199
+0.000300354703027,0.000300449252378,0.000303036919181
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_p.csv
deleted file mode 100644
index 6d9ec4ecf8c8473c658151e6b23f1edfb687d473..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_p.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-1.506939977407455444e-01
-1.373170018196105957e-01
-1.338499933481216431e-01
-4.008999839425086975e-02
-1.841070055961608887e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_p_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_p_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..2a4347ed612ff07ccc4c3f95d8c72a29a343fe50
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_p_final.csv
@@ -0,0 +1,5 @@
+1.549649983644485474e-01
+1.406770050525665283e-01
+1.364420056343078613e-01
+4.677340015769004822e-02
+1.880850046873092651e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_velocity.csv
deleted file mode 100644
index e76204ef32445d46d9411970202e043848e6c421..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-0.000000000000000000e+00,6.585790106328204274e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-6.168810068629682064e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-4.227400131640024483e-05,0.000000000000000000e+00
-0.000000000000000000e+00,8.238190275733359158e-06,0.000000000000000000e+00
-0.000000000000000000e+00,8.737650205148383975e-06,0.000000000000000000e+00
-0.000000000000000000e+00,9.228700218955054879e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-9.216670150635764003e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-6.874430255265906453e-05,0.000000000000000000e+00
--0.000000000000000000e+00,-1.346579956589266658e-04,0.000000000000000000e+00
--0.000000000000000000e+00,-1.097299973480403423e-04,0.000000000000000000e+00
-0.000000000000000000e+00,8.463640369882341474e-06,0.000000000000000000e+00
-0.000000000000000000e+00,1.104999973904341459e-04,0.000000000000000000e+00
-3.936119901482015848e-05,-1.393599959556013346e-04,0.000000000000000000e+00
-1.449799980036914349e-03,-1.268280029762536287e-04,0.000000000000000000e+00
-1.551219960674643517e-03,3.892269887728616595e-06,0.000000000000000000e+00
-1.599870040081441402e-03,7.235600060084834695e-05,0.000000000000000000e+00
-2.307940041646361351e-03,-3.673920000437647104e-04,0.000000000000000000e+00
-2.476610010489821434e-03,1.559939960316114593e-06,0.000000000000000000e+00
-2.556320047006011009e-03,1.970559969777241349e-05,0.000000000000000000e+00
-5.951790080871433020e-05,-3.574129950720816851e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..55fe262c184ed30abcb9b3b171bf2bf04e46b591
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/ffpm_stokespnm_velocity_final.csv
@@ -0,0 +1,20 @@
+3.210495150979264523e-05,2.220860301216376342e-05,0.000000000000000000e+00
+1.554810186848998299e-05,-2.086350189833829916e-05,0.000000000000000000e+00
+3.386307814018385542e-05,-1.434305105241229228e-05,0.000000000000000000e+00
+4.060472878070209291e-05,2.748370324726079339e-06,0.000000000000000000e+00
+5.169781790159699852e-05,2.926520354176731509e-06,0.000000000000000000e+00
+4.492461784522117085e-05,3.097440359756120642e-05,0.000000000000000000e+00
+1.385517612098596807e-05,-3.118465208284959544e-05,0.000000000000000000e+00
+4.305221804057346446e-05,-2.333005316712544186e-05,0.000000000000000000e+00
+1.205497790245248784e-05,-4.752412993160426126e-05,0.000000000000000000e+00
+1.895562924441943618e-04,-3.920718228578976721e-05,0.000000000000000000e+00
+2.050738527240500962e-04,2.881207803357629672e-06,0.000000000000000000e+00
+2.073819270343642295e-04,3.644973419390282025e-05,0.000000000000000000e+00
+3.427769843256101012e-05,-1.042669973685406148e-04,0.000000000000000000e+00
+7.906379760242998600e-04,-8.783730299910530448e-05,0.000000000000000000e+00
+8.445780258625745773e-04,5.284539838612545282e-06,0.000000000000000000e+00
+8.621159940958023071e-04,7.500220090150833130e-05,0.000000000000000000e+00
+2.480319933965802193e-03,-2.722250064834952354e-04,0.000000000000000000e+00
+2.673140028491616249e-03,1.631609961805224884e-06,0.000000000000000000e+00
+2.728170016780495644e-03,1.910319952003192157e-05,0.000000000000000000e+00
+1.271009969059377909e-04,-2.750940038822591305e-04,0.000000000000000000e+00
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..e04c3f584e6856b4d79218768fdd98f9ff8d7569
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/log.out
@@ -0,0 +1,202 @@
+
+Let's get the cow off the ice.
+
+Reading parameters from file stokespnm_params.input.
+PoreInscribedRadius is vertex parameter 0
+PoreVolume is vertex parameter 1
+PoreLabel is vertex parameter 2
+ThroatInscribedRadius is element parameter 0
+ThroatLength is element parameter 1
+ThroatLabel is element parameter 2
+
+Found 1 unconnected clusters.
+Creating generic grid from structured lattice with 410 elements and 231 vertices took 0.00574464 seconds.
+plane:
+-0.000125 0.005125
+0.010125 0.005125
+point 0
+0
+0.0005
+0.001
+0.0015
+0.002
+0.0025
+0.003
+0.0035
+0.004
+0.0045
+0.005
+0.0055
+0.006
+0.0065
+0.007
+0.0075
+0.008
+0.0085
+0.009
+0.0095
+0.01
+Using 'TwoPlates' as cross-sectional shape for all throats.
+Using 'Cube' as geometry for all pores.
+Computed bounding box tree with 1343487 nodes for 671744 grid entites in 0.234156 seconds.
+Computing coupling maps and stencils toook 0.263177 seconds.
+-0.000125
+0.000125
+0.000375
+0.000625
+0.000875
+0.001125
+0.001375
+0.001625
+0.001875
+0.002125
+0.002375
+0.002625
+0.002875
+0.003125
+0.003375
+0.003625
+0.003875
+0.004125
+0.004375
+0.004625
+0.004875
+0.005125
+0.005375
+0.005625
+0.005875
+0.006125
+0.006375
+0.006625
+0.006875
+0.007125
+0.007375
+0.007625
+0.007875
+0.008125
+0.008375
+0.008625
+0.008875
+0.009125
+0.009375
+0.009625
+0.009875
+0.010125
+Writing output for problem "regular_2D_stokespnm_250_micron_stokes". Took 3.6 seconds.
+Writing output for problem "regular_2D_stokespnm_250_micron_pnm". Took 0.002 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-10
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 20
+ -- Newton.TargetSteps = 4
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 819 nodes for 410 grid entites in 8.5218e-05 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.9831e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 2.7006e-14
+Assemble/solve/update time: 16(8.45%)/1.7e+02(91.18%)/0.7(0.38%)
+Assembly and solve took 187.098 seconds
+numFaceDofs: 1346368, numCellCenterDofs: 671744, total FF: 2018112, numPNMDofs: 231, total: 2018343
+mass flux at outlet is: 0.002
+throat 0 : 0
+throat 1 : 0
+throat 2 : 0
+throat 3 : 0
+throat 4 : 0
+throat 5 : 0
+throat 6 : 0
+throat 7 : 0
+throat 8 : 0
+throat 9 : 0
+throat 10 : 0
+throat 11 : 0
+throat 12 : 0
+throat 13 : 0
+throat 14 : 0
+throat 15 : 0
+throat 16 : 0
+throat 17 : 0
+throat 18 : 0
+throat 19 : 0
+throat 20 : 0
+
+vertical net flux (should be zero): 0
+
+##################################
+
+Writing output for problem "regular_2D_stokespnm_250_micron_stokes". Took 4.9 seconds.
+Writing output for problem "regular_2D_stokespnm_250_micron_pnm". Took 0.004 seconds.
+Simulation took 224.041 seconds on 1 processes.
+The cumulative CPU time was 224.041 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-4"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ FluxOverSurface ]
+HorizontalPlaneY = "0.005"
+Verbose = "false"
+[ FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForBeaversJoseph = "true"
+[ Newton ]
+MaxRelativeShift = "1e-10"
+MaxSteps = "20"
+TargetSteps = "4"
+[ PNM ]
+[ PNM.Grid ]
+BoundaryFaceMarker = "1 1 1 2"
+DeletionProbability = "0 0 1 1"
+LowerLeft = "0 125e-6"
+NumPores = "21 11"
+PoreGeometry = "Cube"
+PoreInscribedRadius = "125e-6"
+PriorityList = "2 3 0 1"
+RemoveThroatsOnBoundary = "3"
+ThroatCrossSectionShape = "TwoPlates"
+ThroatInscribedRadius = "125e-6"
+UpperRight = "0.010 0.005125"
+[ PNM.Problem ]
+Name = "pnm"
+TransmissibilityHalfPore = "1.7642875191945115e-05"
+TransmissibilityThroat = "5.26480244078e-06"
+[ Problem ]
+EnableGravity = "false"
+Name = "regular_2D_stokespnm_250_micron"
+[ Stokes ]
+[ Stokes.Grid ]
+Cells1 = "256"
+CellsPerThroat = "64"
+FixedCellsBetweenThroats = "64"
+LowerLeft = "-0.000125000 0.005125"
+Refinement = "0"
+UpperRight = "0.010125 0.006125"
+[ Stokes.Problem ]
+Beta = "35237.668793254459160"
+EnableInertiaTerms = "false"
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+WriteFaceData = "false"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Vtk ]
+AddProcessRank = "true"
+
+DuMuX got the cow off the ice.
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/outFiles.zip
index 1e69376a9ef482f041cce136d3b51c4aae3133c1..3393f47b4be81e14f768567f090625fa346e02cf 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/stokespnm_params.input b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/stokespnm_params.input
index 51e5d907f234081c9992111561d10a5e0de5647b..3124d607ae4adf55fff4f19d3f434ff950210d38 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/stokespnm_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/fine_grid/stokespnm_params.input
@@ -1,17 +1,17 @@
[Stokes.Grid]
LowerLeft = -0.000125000 0.005125 # inlet length: 0.25e-2 m
UpperRight = 0.010125 0.006125 # outlet length: 0.25e-2 m, heigth channel: 1e-3 m
-CellsPerThroat = 10
-Cells1 = 40
-FixedCellsBetweenThroats = 10
+CellsPerThroat = 64
+Cells1 = 256
+FixedCellsBetweenThroats = 64
Refinement = 0
[PNM.Grid]
LowerLeft = 0 125e-6
UpperRight = 0.010 0.005125 # 20 x 10 block, block size 250e-6 m
NumPores = 21 11
-PoreRadius = 125e-6
-ThroatRadius = 125e-6
+PoreInscribedRadius = 125e-6
+ThroatInscribedRadius = 125e-6
PriorityList = 2 3 0 1
BoundaryFaceMarker = 1 1 1 2
DeletionProbability = 0 0 1 1
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_p.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_p.csv
deleted file mode 100644
index e764ddc64ac85dcaf3752fb2d3666a95406a14c5..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_p.csv
+++ /dev/null
@@ -1,5 +0,0 @@
-1.487710028886795044e-01
-1.353860050439834595e-01
-1.316539943218231201e-01
-3.866799920797348022e-02
-1.819379925727844238e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_p_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_p_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..1e7ef8b3ba80e48587a64a231df37a1263a683cf
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_p_final.csv
@@ -0,0 +1,5 @@
+1.546880006790161133e-01
+1.403979957103729248e-01
+1.361760050058364868e-01
+4.644060134887695312e-02
+1.877969950437545776e-01
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_velocity.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_velocity.csv
deleted file mode 100644
index 72bf447cdee8efe80808754ea811d83195859aa1..0000000000000000000000000000000000000000
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_velocity.csv
+++ /dev/null
@@ -1,20 +0,0 @@
-0.000000000000000000e+00,6.591859710169956088e-05,0.000000000000000000e+00
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_velocity_final.csv b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_velocity_final.csv
new file mode 100644
index 0000000000000000000000000000000000000000..3bdf800e5fe88dd607d5bc04f75964bca5581132
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/ffpm_stokespnm_velocity_final.csv
@@ -0,0 +1,20 @@
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diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/log.out b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/log.out
new file mode 100644
index 0000000000000000000000000000000000000000..618ede0eb484aa4c3d31c672aca25c2f1b669ca3
--- /dev/null
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/log.out
@@ -0,0 +1,205 @@
+
+Elliot Carver: Mr. Jones, are we ready to release our new software?
+Jones: Yes, sir. As requested, it's full of bugs, which means people will be forced to upgrade for years.
+ - James Bond, Tomorrow Never Dies
+
+Reading parameters from file stokespnm_params.input.
+PoreInscribedRadius is vertex parameter 0
+PoreVolume is vertex parameter 1
+PoreLabel is vertex parameter 2
+ThroatInscribedRadius is element parameter 0
+ThroatLength is element parameter 1
+ThroatLabel is element parameter 2
+
+Found 1 unconnected clusters.
+Creating generic grid from structured lattice with 410 elements and 231 vertices took 0.00545189 seconds.
+plane:
+-0.000125 0.005125
+0.010125 0.005125
+point 0
+0
+0.0005
+0.001
+0.0015
+0.002
+0.0025
+0.003
+0.0035
+0.004
+0.0045
+0.005
+0.0055
+0.006
+0.0065
+0.007
+0.0075
+0.008
+0.0085
+0.009
+0.0095
+0.01
+Using 'TwoPlates' as cross-sectional shape for all throats.
+Using 'Cube' as geometry for all pores.
+Computed bounding box tree with 335871 nodes for 167936 grid entites in 0.0571258 seconds.
+Computing coupling maps and stencils toook 0.0654406 seconds.
+-0.000125
+0.000125
+0.000375
+0.000625
+0.000875
+0.001125
+0.001375
+0.001625
+0.001875
+0.002125
+0.002375
+0.002625
+0.002875
+0.003125
+0.003375
+0.003625
+0.003875
+0.004125
+0.004375
+0.004625
+0.004875
+0.005125
+0.005375
+0.005625
+0.005875
+0.006125
+0.006375
+0.006625
+0.006875
+0.007125
+0.007375
+0.007625
+0.007875
+0.008125
+0.008375
+0.008625
+0.008875
+0.009125
+0.009375
+0.009625
+0.009875
+0.010125
+Writing output for problem "regular_2D_stokespnm_250_micron_stokes". Took 0.89 seconds.
+Writing output for problem "regular_2D_stokespnm_250_micron_pnm". Took 0.0064 seconds.
+Instantiated assembler for a stationary problem.
+
+Newton solver configured with the following options and parameters:
+ -- Newton.EnableShiftCriterion = true (relative shift convergence criterion)
+ -- Newton.MaxRelativeShift = 1e-10
+ -- Newton.MinSteps = 2
+ -- Newton.MaxSteps = 20
+ -- Newton.TargetSteps = 4
+ -- Newton.RetryTimeStepReductionFactor = 0.5
+ -- Newton.MaxTimeStepDivisions = 10
+
+Assemble: r(x^k) = dS/dt + div F - q; M = grad rComputed bounding box tree with 819 nodes for 410 grid entites in 8.5536e-05 seconds.
+
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 1 done, maximum relative shift = 1.9416e-01
+Assemble: r(x^k) = dS/dt + div F - q; M = grad r
Solve: M deltax^k = r[K
Update: x^(k+1) = x^k - deltax^k[K
Newton iteration 2 done, maximum relative shift = 4.7601e-15
+Assemble/solve/update time: 3.4(15.37%)/19(83.97%)/0.15(0.66%)
+Assembly and solve took 22.2409 seconds
+numFaceDofs: 337312, numCellCenterDofs: 167936, total FF: 505248, numPNMDofs: 231, total: 505479
+mass flux at outlet is: 0.00200001
+throat 0 : 0
+throat 1 : 0
+throat 2 : 0
+throat 3 : 0
+throat 4 : 0
+throat 5 : 0
+throat 6 : 0
+throat 7 : 0
+throat 8 : 0
+throat 9 : 0
+throat 10 : 0
+throat 11 : 0
+throat 12 : 0
+throat 13 : 0
+throat 14 : 0
+throat 15 : 0
+throat 16 : 0
+throat 17 : 0
+throat 18 : 0
+throat 19 : 0
+throat 20 : 0
+
+vertical net flux (should be zero): 0
+
+##################################
+
+Writing output for problem "regular_2D_stokespnm_250_micron_stokes". Took 1 seconds.
+Writing output for problem "regular_2D_stokespnm_250_micron_pnm". Took 0.003 seconds.
+Simulation took 31.426 seconds on 1 processes.
+The cumulative CPU time was 31.426 seconds.
+
+# Runtime-specified parameters used:
+[ Assembly ]
+[ Assembly.NumericDifference ]
+BaseEpsilon = "1e-4"
+[ Component ]
+LiquidDensity = "1e3"
+LiquidKinematicViscosity = "1e-6"
+[ FluxOverSurface ]
+HorizontalPlaneY = "0.005"
+Verbose = "false"
+[ FreeFlow ]
+EnableUnsymmetrizedVelocityGradient = "true"
+EnableUnsymmetrizedVelocityGradientForBeaversJoseph = "true"
+[ Newton ]
+MaxRelativeShift = "1e-10"
+MaxSteps = "20"
+TargetSteps = "4"
+[ PNM ]
+[ PNM.Grid ]
+BoundaryFaceMarker = "1 1 1 2"
+DeletionProbability = "0 0 1 1"
+LowerLeft = "0 125e-6"
+NumPores = "21 11"
+PoreGeometry = "Cube"
+PoreInscribedRadius = "125e-6"
+PriorityList = "2 3 0 1"
+RemoveThroatsOnBoundary = "3"
+ThroatCrossSectionShape = "TwoPlates"
+ThroatInscribedRadius = "125e-6"
+UpperRight = "0.010 0.005125"
+[ PNM.Problem ]
+Name = "pnm"
+TransmissibilityHalfPore = "1.7642875191945115e-05"
+TransmissibilityThroat = "5.26480244078e-06"
+[ Problem ]
+EnableGravity = "false"
+Name = "regular_2D_stokespnm_250_micron"
+[ Stokes ]
+[ Stokes.Grid ]
+Cells1 = "128"
+CellsPerThroat = "32"
+FixedCellsBetweenThroats = "32"
+LowerLeft = "-0.000125000 0.005125"
+Refinement = "0"
+UpperRight = "0.010125 0.006125"
+[ Stokes.Problem ]
+Beta = "35237.668793254459160"
+EnableInertiaTerms = "false"
+Name = "stokes"
+OutflowLength = "0.5e-3"
+TopInletLeft = "0.0015"
+TopInletRight = "0.0045"
+VyMaxTop = "-1e-3"
+[ Vtk ]
+AddVelocity = "1"
+WriteFaceData = "false"
+
+# Global default parameters used:
+[ Assembly ]
+NumericDifferenceMethod = "1"
+[ Flux ]
+UpwindWeight = "1.0"
+[ Vtk ]
+AddProcessRank = "true"
+
+Elliot Carver: Outstanding.
+ - James Bond, Tomorrow Never Dies
+
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/outFiles.zip b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/outFiles.zip
index 0cc691f8b6b6d37f2a397f1390e441ed2a237624..73e375567a960c27d0ed1d809d56927539772e5e 100644
Binary files a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/outFiles.zip and b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/outFiles.zip differ
diff --git a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/stokespnm_params.input b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/stokespnm_params.input
index e07ff2a1e96109e0bebc3ee9ad9423deed4b125b..364d36f9f5afd5af4bff71ffc354b6f9cf043169 100644
--- a/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/stokespnm_params.input
+++ b/BayesValidRox/tests/PA-A/models/numError/stokespnm/normal_grid/stokespnm_params.input
@@ -1,17 +1,17 @@
[Stokes.Grid]
LowerLeft = -0.000125000 0.005125 # inlet length: 0.25e-2 m
UpperRight = 0.010125 0.006125 # outlet length: 0.25e-2 m, heigth channel: 1e-3 m
-CellsPerThroat = 5
-Cells1 = 20
-FixedCellsBetweenThroats = 5
+CellsPerThroat = 32
+Cells1 = 128
+FixedCellsBetweenThroats = 32
Refinement = 0
[PNM.Grid]
LowerLeft = 0 125e-6
UpperRight = 0.010 0.005125 # 20 x 10 block, block size 250e-6 m
NumPores = 21 11
-PoreRadius = 125e-6
-ThroatRadius = 125e-6
+PoreInscribedRadius = 125e-6
+ThroatInscribedRadius = 125e-6
PriorityList = 2 3 0 1
BoundaryFaceMarker = 1 1 1 2
DeletionProbability = 0 0 1 1