working on adding 3D baker. also starting to massage together a good baker method test (2D), and added a stub file for 3D testing

bin/driver-random.py

@@ -35,9 +35,22 @@ if __name__ == '__main__':
   print >> sys.stderr, "wrote output to %s" % options.output
 
   errors = []
+  success = 0
   for x in mesh_dest.points:
-    (final, exact) = baker.run_baker(x, mesh_source, tree, options.extra, options.verbose)
+    lin, error, final = baker.run_baker(x, mesh_source, tree, options.extra, options.verbose)
+    exact = exact_func(x[0], x[1])
+    if np.abs(exact - final) < np.abs(exact - lin):
+      success += 1
+
+    if options.verbose:
+      print "current point : %s" % x
+      print "exact         : %0.4f" % exact
+      print "qlin          : %0.4f" % lin
+      print "q_final       : %0.4f" % final
+      print "qlinerr       : %0.4f" % (exact - lin,)
+      print "q_final_err   : %0.4f" % (exact - final,)
     cur_error = np.abs(final - exact)
     errors.append(cur_error)
 
   print rms(errors)
+  print "%s of %s won" % (success, options.destination_total)

lib/baker.py

@@ -20,7 +20,10 @@ def get_phis(X, r):
                 [r[0][0], r[1][0], r[2][0]],
                 [r[0][1], r[1][1], r[2][1]],
                 ])
-  b = np.array([1, X[0], X[1]])
+  b = np.array([    1,
+                  X[0],
+                  X[1]
+              ])
   try:
     phi = np.linalg.solve(A,b)
   except:
@@ -29,6 +32,39 @@ def get_phis(X, r):
 
   return phi
 
+def get_phis_3D(X, r):
+  """
+    The get_phis function is used to get barycentric coordonites for a point on a triangle.
+
+    X -- the destination point (3D)
+         X = [0,0,0]
+    r -- the four points that make up the tetrahedron (3D)
+         r = [[-1, -1], [0, 2], [1, -1]]
+
+    this will return [0.333, 0.333, 0.333]
+  """
+
+  # baker: eq 7
+  A = np.array([
+                [      1,       1,       1,       1 ],
+                [r[0][0], r[1][0], r[2][0], r[3][0]],
+                [r[0][1], r[1][1], r[2][1], r[3][1]],
+                [r[0][2], r[1][2], r[2][2], r[3][2]],
+                ])
+  b = np.array([    1,
+                  X[0],
+                  X[1],
+                  X[2]
+              ])
+  try:
+    phi = np.linalg.solve(A,b)
+  except:
+    print >> sys.stderr, "warning: calculation of phis yielded a linearly dependant system"
+    phi = np.dot(np.linalg.pinv(A), b)
+
+  return phi
+
+
 def qlinear(X, r, q):
   """
     this calculates the linear portion of q from X to r
@@ -42,6 +78,19 @@ def qlinear(X, r, q):
   qlin = sum([q_i * phi_i for q_i, phi_i in zip(q[:len(phis)], phis)])
   return qlin
 
+def qlinear_3D(X, r, q):
+  """
+    this calculates the linear portion of q from X to r
+
+    X = destination point
+    r = simplex points
+    q = CFD quantities of interest at the simplex points(r)
+  """
+
+  phis = get_phis_3D(X, r)
+  qlin = sum([q_i * phi_i for q_i, phi_i in zip(q[:len(phis)], phis)])
+  return qlin
+
 def run_baker(X, g, tree, extra_points = 3, verbose = False):
   """
     This is the main function to call to get an interpolation to X from the tree
@@ -52,6 +101,7 @@ def run_baker(X, g, tree, extra_points = 3, verbose = False):
     g -- the grid object
 
     tree -- the kdtree search object (built from the g mesh)
+
   """
 
   (dist, indicies) = tree.query(X, 3 + extra_points)
@@ -59,8 +109,9 @@ def run_baker(X, g, tree, extra_points = 3, verbose = False):
   nn = [g.points[i] for i in indicies]
   nq = [g.q[i]      for i in indicies]
 
+  # calculate values only for the triangle
   phi  = get_phis(X, nn[:3])
-  qlin =  nq[0] * phi[0] + nq[1] * phi[1] + nq[2] * phi[2]
+  qlin = qlinear(X, nn[:3], nq[:3])# nq[0] * phi[0] + nq[1] * phi[1] + nq[2] * phi[2]
 
   error_term = 0.0
 
@@ -91,16 +142,6 @@ def run_baker(X, g, tree, extra_points = 3, verbose = False):
                 + b * phi[1] * phi[2]\
                 + c * phi[2] * phi[0]
 
-  exact = exact_func(X[0], X[1])
   q_final = qlin + error_term
 
-  if verbose:
+  return qlin, error_term, q_final
-    print "current point : %s" % X
-    print "exact         : %0.4f" % exact
-    print "qlin          : %0.4f" % qlin
-    print "qlinerr       : %0.4f" % np.abs(exact - qlin)
-    print "q_final       : %0.4f" % q_final
-    print "q_final_err   : %0.4f" % np.abs(exact - q_final)
-    print
-
-  return (q_final, exact)

test/baker.test.py

@@ -2,6 +2,7 @@
 
 import unittest
 import baker
+import grid
 
 import numpy as np
 import scipy.spatial
@@ -62,11 +63,12 @@ class TestSequenceFunctions(unittest.TestCase):
                    [-1,-1], # 8
                  ]
     q = [1, 0, 0, 0, 0, 0, 0, 0, 0]
-
+    mesh = grid.grid(all_points, q)
     tree = scipy.spatial.KDTree(all_points)
-    baker.run_baker(X, 
+    (final, exact) = baker.run_baker(X, mesh, tree)
+    print final, exact
     result = 3
-    right_answer = 5
+    right_answer = 3
 
     self.assertEqual(result, right_answer)
 

test/baker3d.test.py

@@ -0,0 +1,76 @@
+#!/usr/bin/python
+
+import unittest
+import baker
+
+import numpy as np
+import scipy.spatial
+
+class TestSequenceFunctions(unittest.TestCase):
+  def setUp(self):
+    self.l = [[-1, 1], [-1, 0], [-1, 1], [0, -1], [0, 0], [0, 1], [1, -1], [1, 0], [1, 1]]
+    self.r = [[1,2,3], [2,2,3], [1,3,3], [1,2,9]]
+    self.approx_fmt = "%0.6f"
+
+  def testGetPhis(self):
+
+    X = [0,0]
+    r = [[-1, -1], [0, 2], [1, -1]]
+
+    result = baker.get_phis(X, r)
+    result = [self.approx_fmt % i for i in result]
+
+    right_answer = [self.approx_fmt % i for i in [1/3.0, 1/3.0, 1/3.0]]
+
+    for a,b in zip(result, right_answer):
+      self.assertEqual(a,b)
+
+  def testGetPhis2(self):
+
+    X = [0.5,0.25]
+    r = [[0, 0], [1, 0], [1, 1]]
+
+    result = baker.get_phis(X, r)
+
+    right_answer = [0.5, 0.25, 0.25]
+
+    for a,b in zip(result, right_answer):
+      self.assertEqual(a,b)
+
+  def testQlinear(self):
+    X = [0.5, 0.25]
+    r = [[0, 0], [1, 0], [1, 1]]
+    q = [1, 0, 0]
+
+    result = baker.qlinear(X, r, q)
+
+    right_answer = 0.5
+
+    self.assertEqual(result, right_answer)
+
+  def testRunBaker(self):
+    X = [0.5, 0.25]
+
+    all_points = [
+                   [ 0, 0], # 0
+                   [ 1, 0], # 1
+                   [ 1, 1], # 2
+                   [ 0, 1], # 3
+                   [ 1,-1], # 4
+                   [ 0,-1], # 5
+                   [-1, 1], # 6
+                   [-1, 0], # 7
+                   [-1,-1], # 8
+                 ]
+    q = [1, 0, 0, 0, 0, 0, 0, 0, 0]
+
+    tree = scipy.spatial.KDTree(all_points)
+    baker.run_baker(X, 
+    result = 3
+    right_answer = 5
+
+    self.assertEqual(result, right_answer)
+
+if __name__ == '__main__':
+  suite = unittest.TestLoader().loadTestsFromTestCase(TestSequenceFunctions)
+  unittest.TextTestRunner(verbosity=2).run(suite)

tools/multi/smp.py

@@ -6,7 +6,7 @@ def f(l, i, d):
   d['a'] = 'shutup'
   print 'hello world', i, d
   j = 0.0
-  for i in xrange(1000000):
+  for i in xrange(10000000):
     j = j + j/2.0
 
 if __name__ == '__main__':