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polish for inclusion into thesis

master
Stephen McQuay 9 years ago
parent
commit
c682b12bea
10 changed files with 43 additions and 76 deletions
  1. +3
    -3
      bin/iqmgr.py
  2. +5
    -7
      bin/master.py
  3. +0
    -1
      bin/minion.py
  4. +2
    -2
      bin/resolution.2D.py
  5. +0
    -2
      bin/shepherd.py
  6. +25
    -27
      interp/baker/__init__.py
  7. +8
    -11
      interp/grid/__init__.py
  8. +0
    -3
      interp/grid/delaunay.py
  9. +0
    -14
      interp/grid/qhull.py
  10. +0
    -6
      interp/tools.py

+ 3
- 3
bin/iqmgr.py View File

@@ -2,9 +2,9 @@

import sys
import time
import interp.bootstrap
from interp.cluster import QueueManager, get_qs
from optparse import OptionParser
from interp.cluster import QueueManager, get_qs
from optparse import OptionParser

if __name__ == '__main__':
parser = OptionParser(usage = "usage: %s [options] <status|watch|add|fresult #|slay|clear|clearall|clearresults>")


+ 5
- 7
bin/master.py View File

@@ -4,20 +4,18 @@ import sys
import os

import time

import shelve
from progressbar import *
from collections import defaultdict
from optparse import OptionParser

import numpy as np

import interp.bootstrap

import logging
log = logging.getLogger("interp")

from interp.cluster import QueueManager, get_qs
import numpy as np

from interp.cluster import QueueManager, get_qs

from progressbar import *

if __name__ == '__main__':
parser = OptionParser(usage = "usage: %s [options] <server> <interp count>")


+ 0
- 1
bin/minion.py View File

@@ -11,7 +11,6 @@ import datetime

import numpy as np

import interp.bootstrap
from interp.grid.gmsh import ggrid
from interp.tools import baker_exact_3D as exact



+ 2
- 2
bin/resolution.2D.py View File

@@ -6,8 +6,8 @@ import time
from progressbar import *

from interp.grid.DD import *
from interp.tools import *
from interp import bootstrap
from interp.tools import *
from interp import bootstrap

EXTRA_POINTS = 64



+ 0
- 2
bin/shepherd.py View File

@@ -10,8 +10,6 @@ import pickle

import numpy as np

import interp.bootstrap

from interp.cluster import QueueManager, get_qs

if __name__ == '__main__':


+ 25
- 27
interp/baker/__init__.py View File

@@ -11,37 +11,35 @@ log = logging.getLogger('interp')

def get_phis(X, R):
"""
The get_phis function is used to get barycentric coordonites for a point on
a triangle or tetrahedron:

The get_phis function is used to get barycentric coordonites for a
point on a triangle or tetrahedron. This is equation (*\ref{eq:qlinarea}*)

in 2D:

X -- the destination point (2D)
X = [0,0]
r -- the three points that make up the containing triangular simplex (2D)
r = [[-1, -1], [0, 2], [1, -1]]
X - the destination point (2D)
X = [0,0]
R - the three points that make up the 2-D triangular simplex
R = [[-1, -1], [0, 2], [1, -1]]

this will return [0.333, 0.333, 0.333]


in 3D:

X -- the destination point (3D)
X = [0,0,0]
R -- the four points that make up the containing simplex, tetrahedron (3D)
R = [
[0.0, 0.0, 1.0],
[0.94280904333606508, 0.0, -0.3333333283722672],
[-0.47140452166803232, 0.81649658244673617, -0.3333333283722672],
[-0.47140452166803298, -0.81649658244673584, -0.3333333283722672],
]
X - the destination point (3D)
X = [0,0,0]
R - the four points that make up the 3-D simplex (tetrahedron)
R = [
[ 0.0000, 0.0000, 1.0000],
[ 0.9428, 0.0000, -0.3333],
[-0.4714, 0.8165, -0.3333],
[-0.4714, -0.8165, -0.3333],
]

this will return [0.25, 0.25, 0.25, 0.25]
"""

# baker: eq 7
# TODO: perhaps also test len(R[0]) .. ?
# equations (*\ref{eq:lin3d}*) and (*\ref{eq:lin2d}*)
if len(X) == 2:
log.debug("running 2D")
A = np.array([
@@ -85,7 +83,7 @@ def qlinear(X, R):
"""
this calculates the linear portion of q from R to X

also, this is baker eq 3
This is equation (*\ref{eq:qlinbasis}*)

X = destination point
R = a inter.grid object; must have R.points and R.q
@@ -100,9 +98,12 @@ def qlinear(X, R):
return phis, qlin

def get_error(phi, R, S, order = 2):
#TODO: change the equation names in the comments
B = [] # baker eq 9
w = [] # baker eq 11
"""
Calculate the error approximation terms, returning the unknowns
a,b, and c in equation (*\ref{eq:quadratic2d}*).
"""
B = [] # equation ((*\ref{eq:B2d}*)
w = [] # equation ((*\ref{eq:w}*)

cur_pattern = pattern(len(phi), order)
log.info("pattern: %s" % cur_pattern)
@@ -150,8 +151,7 @@ def run_baker(X, R, S, order=2):
This is the main function to call to get an interpolation to X from the
input meshes

X -- the destination point (2D)
X = [0,0]
X -- the destination point

R = Simplex
S = extra points
@@ -190,9 +190,7 @@ def run_baker(X, R, S, order=2):

def memoize(f):
"""
for more information on what I'm doing here,
please read:

for more information on what I'm doing here, please read:
http://en.wikipedia.org/wiki/Memoize
"""
cache = {}


+ 8
- 11
interp/grid/__init__.py View File

@@ -20,8 +20,9 @@ class grid(object):
"""
verts = array of arrays (if passed in, will convert to numpy.array)
[
[x0,y0],
[x1,y1], ...
[x0,y0 <, z0>],
[x1,y1 <, z1>],
...
]

q = array (1D) of physical values
@@ -97,10 +98,9 @@ class grid(object):
"""
this returns two grid objects: R and S.

R is a grid object that is supposedly a containing simplex around point X
R is a grid object that is a containing simplex around point X

S is S_j from baker's paper : some verts from all point that are not the
simplex
S : some verts from all points that are not the simplex
"""
simplex_size = self.dim + 1
log.debug("extra verts: %d" % extra_points)
@@ -228,8 +228,9 @@ class cell(object):
X = point of interest
G = corrensponding grid object (G.verts)

because of the way i'm storing things, a cell simply stores indicies, and
so one must pass in a reference to the grid object containing real verts.
because of the way i'm storing things, a cell simply stores indicies,
and so one must pass in a reference to the grid object containing real
verts.

this simply calls grid.simplex.contains
"""
@@ -255,10 +256,6 @@ def contains(X, R):
tests if X (point) is in R

R is a simplex, represented by a list of n-degree coordinates

it now correctly checks for 2/3-D verts

TODO: write unit test ...
"""
phis = get_phis(X, R)



+ 0
- 3
interp/grid/delaunay.py View File

@@ -51,9 +51,6 @@ class dgrid(basegrid):
def construct_connectivity(self):
"""
a call to this method prepares the internal connectivity structure.

this is part of the __init__ for a interp.grid.delaunay.grid, but can be
called from any grid object
"""
log.info('start')
qdelaunay_string = get_qdelaunay_dump_str(self)


+ 0
- 14
interp/grid/qhull.py View File

@@ -1,14 +0,0 @@
def parse_qhull_file(filename, verbose=False):
f = open(filename, 'r')

if verbose:
print 'filename: ', filename
degree = int(f.readline().strip())
print "degree:", degree
print "number of points", f.readline().strip()

verts = []
for p in f:
v = [float(i) for i in p.strip().split()]
verts.append(v)
return verts

+ 0
- 6
interp/tools.py View File

@@ -1,6 +1,5 @@
import os

import inspect
import numpy as np

import logging
@@ -27,8 +26,6 @@ def baker_exact_2D(X):
"""
x ,y = X

# TODO: this is not baker's function!! this is:
# np.power(np.sin(x*np.pi/2.0) * np.sin(y*np.pi/2.0),2)
answer = np.power((np.sin(x * np.pi) * np.cos(y * np.pi)), 2)
log.debug(answer)
return answer
@@ -83,6 +80,3 @@ def improved(qlin, err, final, exact):
return True
else:
return False

def percent_improvement(answer, exact):
return np.abs(answer['error']) / exact

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