Minor updates on stale calls.

fdata.py

@@ -24,7 +24,7 @@
 import numpy as np
 from copy import copy, deepcopy
 import os,time,platform,shutil,sys
-from subprocess import Popen, PIPE, CREATE_NEW_CONSOLE
+from subprocess import Popen, PIPE
 from time import sleep
 from collections import Counter
 from matplotlib.patches import Rectangle
@@ -544,7 +544,7 @@ def plot(self,save='',angle=[45,45],color='k',connections=False,equal_axes=True,
         plt.clf()
         fig = plt.figure(figsize=[8.275,11.7])
         ax = plt.axes(projection='3d')
-        ax.set_aspect('equal', 'datalim')
+        ax.set_aspect('auto', 'datalim')
 
         ax.set_xlabel(xlabel,size=font_size)
         ax.set_ylabel(ylabel,size=font_size)
@@ -707,7 +707,7 @@ def topo(self,save='',cbar=True,equal_axes=True, method = 'nearest', divisions=[
         ax = plt.axes([0.15,0.15,0.7,0.7])
         if xlims: ax.set_xlim(xlims)
         if ylims: ax.set_ylim(ylims)
-        if equal_axes: ax.set_aspect('equal', 'datalim')
+        if equal_axes: ax.set_aspect('auto', 'datalim')
         CS = plt.contourf(X,Y,vals,levels)
         if clims: CS.vmin=clims[0]; CS.vmax=clims[1]
         if xlabel: plt.xlabel(xlabel,size=font_size)		
@@ -722,7 +722,7 @@ def topo(self,save='',cbar=True,equal_axes=True, method = 'nearest', divisions=[
         for t in ax.get_yticklabels():
             t.set_fontsize(font_size)
 
-        ax.set_aspect('equal', 'datalim')
+        ax.set_aspect('auto', 'datalim')
         extension, save_fname, pdf = save_name(save,variable='zone_topo'+str(self.index),time=1)
         plt.savefig(save_fname, dpi=200, facecolor='w', edgecolor='w',orientation='portrait', 
         format=extension,transparent=True, bbox_inches=None, pad_inches=0.1)
@@ -2936,7 +2936,7 @@ def __setstate__(self, data_dict):
     def read(self,filename='',gridfilename='',inconfilename='',full_connectivity=dflt.full_connectivity,skip=[]):			#Reads data from file.
         '''Read FEHM input file and construct fdata object.
 
-        :param filename: Name of FEHM input file. Alternatively, supplying 'fehmn.files' will cause PyFEHM to query this file for input, grid and restart file names if they are available.
+        :param filename: Name of FEHM input *.dat file. 
         :type filename: str
         :param gridfilename: Name of FEHM grid file.
         :type gridfilename: str
@@ -2949,8 +2949,8 @@ def read(self,filename='',gridfilename='',inconfilename='',full_connectivity=dfl
 
         # set up paths
         if filename: self._path.filename = filename
-        if gridfilename: self.grid._path.filename = filename
-        if inconfilename: self.incon._path.filename = filename
+        if gridfilename: self.grid._path.filename = gridfilename
+        if inconfilename: self.incon._path.filename = inconfilename
 
         # THERE WILL ALWAYS BE A GRID PATH TO READ - INPUT FILES CANNOT BE READ WITHOUT A GRID
         self.grid.read(self.grid._path.full_path,full_connectivity=full_connectivity)
@@ -2976,7 +2976,7 @@ def read(self,filename='',gridfilename='',inconfilename='',full_connectivity=dfl
                         [self._read_cont,self._read_macro,self._read_zonn,self._read_zonn,self._read_macro,
                          self._read_time,self._read_ctrl,self._read_iter,self._read_macro,self._read_macro,
                          self._read_boun,self._read_macro,self._read_strs,self._read_text,self._read_sol,
-                        self._read_nfinv,self._read_hist,self._read_histnode,self._read_carb,self._read_model,
+                         self._read_nfinv,self._read_hist,self._read_histnode,self._read_carb,self._read_model,
                          self._read_macro,self._read_nobr,self._read_flxz,self._read_rlpm,self._read_macro,
                          self._read_trac,self._read_model,self._read_model,self._read_vapl,self._read_adif,
                          self._read_ngas,self._read_flxo,self._read_head,self._read_flxn, self._read_air, self._read_air])))

fgrid.py

@@ -523,7 +523,7 @@ def read(self,gridfilename,full_connectivity=False,octree=False):
 		elif isAvs:
 			self._read_avs()		
 			newgridfilename = self._path.full_path.split('.')[:-1]
-			newgridfilename = string.join(newgridfilename,'.')+'.inp'
+			newgridfilename = ".".join(newgridfilename)+'.inp'
 			if os.path.isfile(newgridfilename):
 				newgridfilename = newgridfilename[:-4] + '_new' + newgridfilename[-4:]
 			self.write(newgridfilename, 'fehm')		# write out equivalent fehm grid
@@ -548,7 +548,6 @@ def _read_fehm(self): 		#Read in fehm meshfile for node,element data .
 			nd = infile.readline().strip().split()
 			new_node = fnode(index=int(nd[0]),position=np.array([float(nd[1]),float(nd[2]),float(nd[3])]))
 			self.add_node(new_node)	
-
 		infile.readline()
 		infile.readline()
 		N = infile.readline()
@@ -612,7 +611,6 @@ def _read_avs(self): 		#Read in avs meshfile for node, element data.
 			nd = infile.readline().strip().split()	# read line
 			new_node = fnode(index=int(nd[0]),position=np.array([float(nd[1]),float(nd[2]),float(nd[3])]))
 			self.add_node(new_node)	 				# add node object
-
 		N = N_el
 		connectivity = None
 		for i in range(N): 						# FOR each element

tutorials/tutorial1.py

@@ -13,7 +13,7 @@
 
 # 7.1.2 Grid generation
 x = np.linspace(0,10,11)
-dat.grid.make(root+'_GRID.inp',x=x,y=x,z=x)
+dat.grid.make(gridfilename=root+'_GRID.inp',x=x,y=x,z=x)
 #dat.grid.plot(root+'_GRID.png',color='r',angle=[45,45])
 
 # 7.1.3 Zone creation
@@ -67,7 +67,7 @@
 #dat.iter['machine_tolerance_TMCH'] = -0.5e-5
 
 dat.files.root = root
-dat.run(root+'_INPUT.dat', verbose=True, diagnostic = True) 		# note, because no executable path is specified, PyFEHM retrieves the executable specified in the default path
+dat.run(root+'_INPUT.dat', verbose=True) 		# note, because no executable path is specified, PyFEHM retrieves the executable specified in the default path
 
 asdf
 # 7.1.7 Visualisation

tutorials/tutorial2.py

@@ -25,7 +25,7 @@
 
 Z = list(np.linspace(Z0,Za_base,5)) + list(np.linspace(Za_base,Za_top,11))[1:] + list(np.linspace(Za_top,Z1,5))[1:]
 
-dat.grid.make('quarterGrid.inp', x= X, y = X, z = Z)
+dat.grid.make(gridfilename='quarterGrid.inp', x= X, y = X, z = Z)
 
 dat.grid.plot('quarterGrid.png', angle = [45,45], color = 'b', cutaway = [proX,proY,-1000])
 

tutorials/tutorial3.py

@@ -43,7 +43,7 @@ def simulation(j,param):
 
 	# 7.1.2 Grid generation
 	x = np.linspace(0,10,11)
-	dat.grid.make(root+'_GRID.inp',x=x,y=x,z=x)
+	dat.grid.make(gridfilename=root+'_GRID.inp',x=x,y=x,z=x)
 	dat.grid.plot(root+'_GRID.png',color='r',angle=[45,45])
 
 	# 7.1.3 Zone creation

tutorials/tutorial4.py

@@ -10,7 +10,7 @@
 
 # 7.1.2 Grid generation
 x = np.linspace(0,10,11)
-dat.grid.make(root+'_GRID.inp',x=x,y=x,z=x)
+dat.grid.make(gridfilename=root+'_GRID.inp',x=x,y=x,z=x)
 dat.grid.plot(root+'_GRID.png',color='r',angle=[45,45])
 
 # 7.1.3 Zone creation