fixes

docs/source/conf.py

@@ -36,7 +36,7 @@
 author = 'Marco Musy'
 
 # The short X.Y version
-version = '2019.1.1'
+version = '2019.1.2'
 
 
 # -- General configuration ---------------------------------------------------

examples/advanced/fitplanes.py

@@ -9,7 +9,7 @@
 """
 from vtkplotter import *
 
-vp = Plotter(verbose=0, axes=0)
+vp = Plotter(verbose=0, axes=0, bg='w')
 
 s = vp.load(datadir+"shapes/cow.vtk").alpha(0.3).subdivide()  # remesh
 

examples/basic/annotations.py

@@ -7,6 +7,6 @@
 with open("basic/align1.py") as fname:
     t = fname.read()
 
-actor2d = Text(t, pos=3, s=1.2, bg="lb", font="courier")
+actor2d = Text(t, pos=3, s=1.2, c='k', bg="lb", font="courier")
 
 show(actor2d, verbose=0, axes=0)

examples/basic/carcrash.py

@@ -4,7 +4,7 @@
 rate=10 limits the speed of the loop to maximum 10 fps
 """
 from __future__ import division, print_function
-from vtkplotter import Plotter, Plane, Text
+from vtkplotter import Plotter, Plane, Text, datadir
 
 vp = Plotter(interactive=0, axes=0)
 

examples/basic/rotateImage.py

@@ -2,7 +2,7 @@
 Normal jpg/png images can be 
 loaded and rendered as any vtkImageActor
 """
-from vtkplotter import Plotter, Text
+from vtkplotter import Plotter, Text, datadir
 
 vp = Plotter(axes=3, verbose=0)
 

examples/basic/texturecubes.py

@@ -3,7 +3,7 @@
 any jpg file can be used as texture.
 """
 from vtkplotter import Plotter, Cube, Text
-from vtkplotter.utils import textures, textures_path
+from vtkplotter.settings import textures, textures_path
 
 print(__doc__)
 print(textures_path)

examples/basic/trail.py

@@ -1,5 +1,6 @@
 """
-Example usage of addTrail(). Add a triling line to a moving object.
+Example usage of addTrail(). 
+Add a trailing line to a moving object.
 """
 print(__doc__)
 from vtkplotter import Plotter, sin, Sphere, Point

examples/other/dolfin/README.md

@@ -32,3 +32,7 @@ python example.py  # on mac OSX try 'pythonw' instead
 | [![stokes](https://user-images.githubusercontent.com/32848391/53044917-95838100-348c-11e9-9a94-aa10b8f1658c.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/ex07_stokes-iterative.py)<br/> `ex07_stokes-iterative.py`  | Stokes equations with an iterative solver. |
 |    |    |
 | [![elastodyn](https://user-images.githubusercontent.com/32848391/54932788-bd4a8680-4f1b-11e9-9326-33645171a45e.gif)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/elastodynamics.py)<br/> `elastodynamics.py`             | Perform time integration of transient elastodynamics using the generalized-alpha method. |
+|    |    |
+| [![stokes](https://user-images.githubusercontent.com/32848391/55098209-aba0e480-50bd-11e9-8842-42d3f0b2d9c8.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin/stokes.py)<br/> `stokes.py`                                | Solve 2D navier-stokes equations with boundary conditions. |
+
+

examples/other/dolfin/ascalarbar.py

@@ -19,11 +19,5 @@
 ################################## vtkplotter
 from vtkplotter.dolfin import plot
 
-plot(u, mode='color', vmin=-6, vmax=6, style=1, text=__doc__)
+plot(u, mode='color', vmin=-3, vmax=3, style=1, text=__doc__)
 
-
-################################# pylab
-#import pylab as plt
-#c = plot(u, mode='color', vmin=-3, vmax=3)
-#plt.colorbar(c)
-#plt.show()

examples/other/dolfin/calc_surface_area.py

@@ -0,0 +1,43 @@
+from dolfin import *
+import sympy as sp
+# Credits:
+# https://github.com/pf4d/fenics_scripts/calc_surface_area.py
+
+x, y = sp.symbols('x, y')
+
+# surface :
+def s(x,y):        return sp.exp(x)
+
+# x-derivative of surface
+def dsdx(x,y):     return s(x,y).diff(x, 1)
+
+# y-derivative of surface
+def dsdy(x,y):     return s(x,y).diff(y, 1)
+
+# outward-pointing-normal-vector magnitude at surface :
+def n_mag_s(x,y):  return sp.sqrt(1 + dsdx(x,y)**2 + dsdy(x,y)**2)
+
+# surface area of surface :
+def area(x,y):     return sp.integrate(n_mag_s(x,y), (x,0,1), (y,0,1))
+
+A_exact = area(x,y)
+
+for n in [5,10,100,500]:
+	mesh  = UnitSquareMesh(n,n)
+	Q     = FunctionSpace(mesh, "CG", 1)
+	e     = Expression('exp(x[0])', degree=2)
+	f     = interpolate(e, Q)
+	A_num = assemble( sqrt(f.dx(0)**2 + f.dx(1)**2 + 1) *  dx)
+	print('for n = %i -- error = %.2e' % (n, abs(A_exact.evalf()-A_num)))
+
+n        = 10
+mesh     = UnitSquareMesh(n,n)
+Q        = FunctionSpace(mesh, "CG", 1)
+e        = Expression('exp(x[0])', degree=2)
+f        = interpolate(e, Q)
+A_vector = project( sqrt(f.dx(0)**2 + f.dx(1)**2 + 1), Q)
+
+
+from vtkplotter.dolfin import plot
+plot(A_vector)
+

examples/other/dolfin/elastodynamics.py

@@ -2,6 +2,7 @@
 Time-integration of the 
 elastodynamics equation
 '''
+from __future__ import division, print_function
 from dolfin import *
 import numpy as np
 

examples/other/dolfin/ex04_mixed-poisson.py

@@ -2,6 +2,7 @@
 Solving Poisson equation using 
 a mixed (two-field) formulation.
 """
+# needs python3
 # https://fenicsproject.org/docs/dolfin/2018.1.0/python/demos/mixed-poisson
 from dolfin import *
 

examples/other/dolfin/pi_estimate.py

@@ -0,0 +1,15 @@
+from dolfin import *
+from mshr   import Circle, generate_mesh
+from vtkplotter.dolfin import plot, printc
+# Credits:
+# https://github.com/pf4d/fenics_scripts/pi_estimate.py
+
+domain = Circle(Point(0.0,0.0), 1.0)
+
+for res in [2**k for k in range(8)]:
+	mesh = generate_mesh(domain, res)
+	A    = assemble(Constant(1) * dx(domain=mesh))
+	printc("resolution = %i, \t |A - pi| = %.5e" % (res, abs(A-pi)))
+printc('~pi is about', A, c='yellow')
+
+plot(mesh, style=1, axes=3)

examples/other/dolfin/run_all.sh

@@ -37,12 +37,20 @@ python ascalarbar.py
 echo Running collisions.py
 python collisions.py
 
+echo Running calc_surface_area.py
+python calc_surface_area.py
+
 echo Running markmesh.py
 python markmesh.py
 
 echo Running elastodynamics.py
 python elastodynamics.py
 
+echo Running pi_estimate.py
+python pi_estimate.py
+
+echo Running stokes.py
+python stokes.py
 
 
 

examples/other/dolfin/stokes.py

@@ -0,0 +1,52 @@
+"""
+This demo solves the Stokes equations, using quadratic elements for
+the velocity and first degree elements for the pressure (Taylor-Hood elements).
+"""
+# Credits:
+# https://github.com/pf4d/fenics_scripts/blob/master/cbc_block/stokes.py
+from dolfin import *
+from time import time
+from vtkplotter.dolfin import plot, datadir
+
+t0 = time()
+print("calculating... please wait...")
+
+# Load mesh and subdomains
+mesh = Mesh(datadir+"dolfin_fine.xml")
+sub_domains = MeshFunction("size_t", mesh,
+                           datadir+"dolfin_fine_subdomains.xml.gz")
+
+# Define function spaces
+P2 = VectorElement("Lagrange", mesh.ufl_cell(), 2)
+P1 = FiniteElement("Lagrange", mesh.ufl_cell(), 1)
+TH = P2 * P1
+W = FunctionSpace(mesh, TH)
+
+# No-slip boundary condition for velocity
+noslip = Constant((0, 0))
+bc0 = DirichletBC(W.sub(0), noslip, sub_domains, 0)
+
+# Inflow boundary condition for velocity
+inflow = Expression(("-sin(x[1]*pi)", "0.0"), degree=2)
+bc1 = DirichletBC(W.sub(0), inflow, sub_domains, 1)
+bcs = [bc0, bc1]
+
+# Define variational problem
+(u, p) = TrialFunctions(W)
+(v, q) = TestFunctions(W)
+f = Constant((0, 0))
+a = (inner(grad(u), grad(v)) - div(v)*p + q*div(u))*dx
+L = inner(f, v)*dx
+w = Function(W)
+
+solve(a == L, w, bcs, solver_parameters={'linear_solver' : 'mumps'})
+tf = time()
+print("time to solve:", tf-t0)
+
+# Split the mixed solution using a shallow copy
+(u, p) = w.split()
+
+##################################
+plot(u, at=0, N=2, text="velocity", mode='mesh and arrows', 
+	 scale=.03, wire=1, scalarbar=False, style=1)
+plot(p, at=1, text="pressure", cmap='jet')

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='vtkplotter',
-    version='2019.1.1', # change also in vtkplotter/__init__.py and docs/source/conf.py
+    version='2019.1.2', # change also in vtkplotter/__init__.py and docs/source/conf.py
     packages=['vtkplotter'],
     scripts=['bin/vtkplotter', 'bin/vtkconvert'],
     install_requires=['vtk'],
@@ -78,8 +78,7 @@
 #  open build/html/index.html
 #
 # mount_staging
-# cp to ~/Projects/StagingServer/var/www/html/vtkplotter.embl.es
-#
+# cp -r build/html/* ~/Projects/StagingServer/var/www/html/vtkplotter.embl.es/