params/mirrors cleaning + usable test suite (issues #11 and #10)

Context

This pull request solves:

• issue #11 : "The test suite lasts too long".
• issue #10 : "Several tests still display windows even with "nogui" option".

Modifications

root / fwk

• mpirun.py and run.py have been merged. These files were huge copy/paste of each other. The purpose was to be sure that the workspace folder was created by rank#0 process. Now, run.py checks whether MPI is used or not and does what is expected (automatically).
• wutils used setand grep unix command to display environment variables. This code has been rewritten in order to work also on windows.
• Variables such as OMP_NUM_THREADS or MKL_DYNAMIC are now set to predefined and controlled values if (and only if) they are not previously set by the user. For example OMP_NUM_THREADS is set to 1 if OMP_NUM_THREADS does not appear in the list of environment variables.

fdtd

• The tests named fdtd1d_1c and fdtd1d_1d have been modified in order to:
  • compute something even if --nogui is set.
  • completely hide matplotlib commands when --nogui is set (these tests failed if they were run in a ssh terminal without X display)

mirrors

• Some old files have been put in a new mirrors/attic folder: imported_10x10.py, imported_30x30.py, loop_old.py, loop_old2.py
• Some broken tests have been moved to mirrors/broken: NISP_Leg_cond.py (too old matplotlib), mirrors01.py, mirrors03.py, mirrors_test_battery.py (bad mesh with wrong normals)
• A folder named figs has been created for the scripts producing figures for reports: LSP*.py, numpy_matplotlib*
• mirrors/mirror_ss.py: the only working model for mirror! It has been cleaned. An "nogui" option has been added in the parameter list. Its defaut size has been decreased.
• mirror source code:
  • removal of unneeded header
  • basic code formatting
  • removal of unused code
  • additional comments/doc
• Tests:
  • mirrors02.py has been deleted (same as mirrors/mirror_ss.py and mirrors/tests/test1/simple.py )
  • mirrors/tests/test1/simple.py was moved to mirrors/tests
  • all loop*.py have been reduced in size so that they run in a few seconds.
  • all loop*.py can be run either with GUI or not with the desired result.

Test suite

• The test suite now runs in less than a minute (with 6 cores).
• It has been tested on ubuntu and windows

mirrors/models/mirror_ss.py

 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-# Simple 2D wave-propagation test in 1 material
-
+# simplified model of a mirror and a holder 
+# (two rectangular blocks on top of each other)
 
 import mirrors as m
 import tbox
@@ -9,31 +9,46 @@ import tbox.gmsh as gmsh
 
 def model(p={}):
     # configure/build mesh
-    pars={ 'L' : p['L'] , 'L_1' : p['L_1'], 'H' : p['H'], 'H_1' : p['H_1'], 'W' : p['W'], 'nL' : p['nL'], 'nL_1' : p['nL_1'], 'nH' : p['nH'], 'nH_1' : p['nH_1'], 'nW' : p['nW'] }
-    msh = gmsh.MeshLoader("mirror.geo",__file__).execute(**pars)
-    pbl = m.Problem(msh,"thermomechanical",22)
+
+    # [RB] what is the purpose of this dictionnary 
+    # why couldn't we use "p" instead??
+    pars = { 'L' : p['L'] , 
+    'L_1' : p['L_1'], 
+    'H' : p['H'], 
+    'H_1' : p['H_1'], 
+    'W' : p['W'], 
+    'nL' : p['nL'], 
+    'nL_1' : p['nL_1'], 
+    'nH' : p['nH'], 
+    'nH_1' : p['nH_1'], 
+    'nW' : p['nW'] }
+
+    msh = gmsh.MeshLoader("mirror.geo", __file__).execute(**pars)
+    pbl = m.Problem(msh, "thermomechanical", 22)
 
     # configure pbl
-    m.Medium(pbl, "Holder", "TZM",330000,0.36,0.114,0.5E-05)
-    m.Medium(pbl, "Mirror", "ScMo",330000,0.36,0.114,0.4E-05)
+    m.Medium(pbl, "Holder", "TZM", 330000, 0.36, 0.114, 0.5E-05)
+    m.Medium(pbl, "Mirror", "ScMo", 330000, 0.36, 0.114, 0.4E-05)
 
-    clamped = tbox.Pt(1,1,1)
-    values_clamped = tbox.Pt(0,0,0)
+    clamped = tbox.Pt(1, 1, 1)
+    values_clamped = tbox.Pt(0, 0, 0)
 
-    xyclamped = tbox.Pt(1,1,0)
-    xzclamped = tbox.Pt(1,0,1)
+    xyclamped = tbox.Pt(1, 1, 0)
+    xzclamped = tbox.Pt(1, 0, 1)
 
     T = p['T']
-    m.uDirichlet(pbl, "Vertical clamped line", "Vertical clamped line_name",xyclamped,values_clamped)
-    m.uDirichlet(pbl, "Horizontal clamped line", "Horizontal clamped line_name",xzclamped,values_clamped)
-    m.TDirichlet(pbl, "Clamped Side", "Clamped",T)
+    m.uDirichlet(pbl, "Vertical clamped line", 
+                      "Vertical clamped line_name", 
+                      xyclamped, values_clamped)
+    m.uDirichlet(pbl, "Horizontal clamped line", 
+                      "Horizontal clamped line_name", 
+                      xzclamped, values_clamped)
+    m.TDirichlet(pbl, "Clamped Side", "Clamped", T)
 
     return (pbl, msh) # retourner pbl sinon il semble detruit...
 
 
 def runmodel(**d):
-    from fwk.wutils import parseargs
-    args=parseargs()
     
     p={}
     p['L']    = 250.0
@@ -49,18 +64,20 @@ def runmodel(**d):
     p['T']    = 70.
     p.update(d)
     
+    # builds an instance of the model with given parameters
     (pbl, msh) = model(p)
+
+    # retrieves command-line arguments
     from fwk.wutils import parseargs
-    args=parseargs()
+    args = parseargs()
 
-    solver = m.Solver(pbl,args.k)
+    # creates a solver and runs it
+    solver = m.Solver(pbl, args.k)
     solver.start()
 
-
-
     if not args.nogui:
         from mirrors.viewer import GUI
-        GUI().open( 'mirror')
+        GUI().open('mirror')
 
     return pbl.Sol