From 796be57be270047810ad6fa36f9c8c51ecf091d0 Mon Sep 17 00:00:00 2001
From: Mathieu Deiber <z3509544@ad.unsw.edu.au>
Date: Tue, 19 Nov 2019 16:53:57 +1100
Subject: [PATCH] correct mid side node and layer number bug

---
 RMA2SERAPHIN_3DRMA11_20191118.py | 29 +++++++++++++++++++++--------
 py_rmatools_v03.py               |  1 +
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/RMA2SERAPHIN_3DRMA11_20191118.py b/RMA2SERAPHIN_3DRMA11_20191118.py
index 36d61be..9dbf1a4 100644
--- a/RMA2SERAPHIN_3DRMA11_20191118.py
+++ b/RMA2SERAPHIN_3DRMA11_20191118.py
@@ -13,12 +13,11 @@ import pandas as pd
 import numpy as np
 plt.rcParams.update({'figure.max_open_warning': 0})
 
-
 # In[65]:
 
-meshFilename = 'pok005.rm1'
+meshFilename = 'KMA003.rm1'
 channelWidth = 100
-RMAfilenames = ['POA034']
+RMAfilenames = ['KMA008']
 
 #If RMA11
 constNum = [1]
@@ -26,10 +25,10 @@ constNum = [1]
 #If RMA11 3D
 
 #Options = [4,8,1,'Max']  #Option available 'Max' , an integer correspond to the layer number to extract the results, if 2D use options = [1] - 'Percentile' (percentile only work for RMA11 FOR now)
-Options = [8]
+Options = [9] #if we specified 8 layers in RMA10 then the bed layer is layer #9
 percentiles = [0.5,0.8,0.9,0.95,1]
-NodeLayersFile = 'NodeLayers005.txt' #the node layer file was created by getting the nodes number from the RMA Outfile (just run RMA11 for a few steps)
-Nnodes = 6674 #Number of nodes (including mid side node) - thisn umber also correspond to the last node number in the nodelayers file
+NodeLayersFile = 'NodeLayers003.txt' #the node layer file was created by getting the nodes number from the RMA Outfile (just run RMA11 for a few steps)
+Nnodes = 6127 #Number of nodes (including mid side node) - thisn umber also correspond to the last node number in the nodelayers file
 # In[66]:
 
 def isElementOneD(nodelist1):
@@ -480,7 +479,10 @@ def writeConst(param,key):
             tempArr.append(tempR[n])
         tempVal1 = max(tempArr)                    
     elif isinstance(option, int):
-       temppos = (option - 1 ) * 2
+       if key in  cornerNodes:
+           temppos = (option - 1 ) * 2
+       else:
+            temppos = option
        temppos2 = min([temppos,len(nodelayer[key])-1])
        tempVal1 = tempR[nodelayer[key][temppos2]]
     else:
@@ -626,6 +628,8 @@ def readNodeLayers(fname,Nnodes):
 
 #Read mesh file and extract node (except mid node) and elements - plus convert 1D element to 2D for vizualisation
 nodelayer = {}
+midSideNodes = []
+cornerNodes = []
 NodeList = [] 
 ElementList = []
 ElementDict = {}
@@ -649,6 +653,13 @@ with open(meshFilename) as f:
         
         temp = re.findall('.....',line)
         ElementDict[int(temp[0])] = [int(temp[i]) for i in range(1,9) if int(temp[i]) != 0 and int(temp[9]) < 100]
+        
+        for idx, n in enumerate(ElementDict[int(temp[0])]):
+            if idx%2 == 0:
+                cornerNodes.append(n)
+            else:
+                midSideNodes.append(n)
+            
         ElementList.append(int(temp[0]))
         line = f.readline()
           
@@ -656,6 +667,8 @@ with open(meshFilename) as f:
         NodeList.extend(value)
     
     NodeList = list(set(NodeList))
+    cornerNodes = list(set(cornerNodes))
+    midSideNodes = list(set(midSideNodes))
 
     line = f.readline()
     while line and line != '      9999\n':
@@ -699,7 +712,7 @@ for key, value in nodeDict.items():
 # In[72]:
 for run in RMAfilenames:
     for option in Options:
-        RMAfilename = '{}'.format(run)
+        RMAfilename = '{}/{}'.format(run,run)
         R=rma()
         R.open(RMAfilename)
         R.next()
diff --git a/py_rmatools_v03.py b/py_rmatools_v03.py
index 7e2af6e..4f136b0 100644
--- a/py_rmatools_v03.py
+++ b/py_rmatools_v03.py
@@ -4,6 +4,7 @@ import sys
 from array import array
 
 
+
 # Updated 10/11/15 BMM : Added mesh.
 # Updated 10/11/15 MD : Added dictionnary initialisation in mesh.
 # Update 8/11/2019 MD : Improve performance (used array instead of unpack)