/[escript]/trunk/doc/examples/cookbook/example08c.py
ViewVC logotype

Annotation of /trunk/doc/examples/cookbook/example08c.py

Parent Directory Parent Directory | Revision Log Revision Log


Revision 3075 - (hide annotations)
Wed Jul 28 02:51:20 2010 UTC (8 years, 6 months ago) by ahallam
File MIME type: text/x-python
File size: 9431 byte(s)
Updates to cookbook example. Lumping turned off for order 2 models until bug resolves.
1 ahallam 3075
2     ########################################################
3     #
4     # Copyright (c) 2009-2010 by University of Queensland
5     # Earth Systems Science Computational Center (ESSCC)
6     # http://www.uq.edu.au/esscc
7     #
8     # Primary Business: Queensland, Australia
9     # Licensed under the Open Software License version 3.0
10     # http://www.opensource.org/licenses/osl-3.0.php
11     #
12     ########################################################
13    
14     __copyright__="""Copyright (c) 2009-2010 by University of Queensland
15     Earth Systems Science Computational Center (ESSCC)
16     http://www.uq.edu.au/esscc
17     Primary Business: Queensland, Australia"""
18     __license__="""Licensed under the Open Software License version 3.0
19     http://www.opensource.org/licenses/osl-3.0.php"""
20     __url__="https://launchpad.net/escript-finley"
21    
22     """
23     Author: Antony Hallam antony.hallam@uqconnect.edu.au
24     """
25    
26     ############################################################FILE HEADER
27     # example08c.py
28     # Create either a 2D syncline or anticline model using pycad meshing
29     # tools. Wave equation solution.
30    
31     #######################################################EXTERNAL MODULES
32     import matplotlib
33     matplotlib.use('agg') #It's just here for automated testing
34     from esys.pycad import * #domain constructor
35     from esys.pycad.gmsh import Design #Finite Element meshing package
36     from esys.finley import MakeDomain #Converter for escript
37     import os #file path tool
38     from math import * # math package
39     from esys.escript import *
40     from esys.escript.unitsSI import *
41     from esys.escript.linearPDEs import LinearPDE
42     from esys.escript.pdetools import Projector
43     from cblib import toRegGrid, subsample
44     import pylab as pl #Plotting package
45     import numpy as np
46    
47     ########################################################MPI WORLD CHECK
48     if getMPISizeWorld() > 1:
49     import sys
50     print "This example will not run in an MPI world."
51     sys.exit(0)
52    
53     #################################################ESTABLISHING VARIABLES
54     #set modal to 1 for a syncline or -1 for an anticline structural
55     #configuration
56     modal=-1
57    
58     # the folder to put our outputs in, leave blank "" for script path -
59     # note this folder path must exist to work
60     save_path= os.path.join("data","example08c")
61     mkDir(save_path)
62    
63     ################################################ESTABLISHING PARAMETERS
64     #Model Parameters
65     width=1000.0*m #width of model
66     depth=1000.0*m #depth of model
67     dx=5
68     xstep=dx # calculate the size of delta x
69     ystep=dx # calculate the size of delta y
70    
71     sspl=51 #number of discrete points in spline
72     dsp=width/(sspl-1) #dx of spline steps for width
73     dep_sp=500.0*m #avg depth of spline
74     h_sp=250.*m #heigh of spline
75     orit=-1.0 #orientation of spline 1.0=>up -1.0=>down
76    
77     vel2=1800.; vel1=3000.
78     rho2=2300.; rho1=3100. #density
79     mu2=(vel2**2.)*rho2/8.; mu1=(vel1**2.)*rho1/8. #bulk modulus
80     lam2=mu2*6.; lam1=mu1*6. #lames constant
81    
82    
83     # Time related variables.
84     tend=0.5 # end time
85     h=0.0001 # time step
86     # data recording times
87     rtime=0.0 # first time to record
88     rtime_inc=tend/50.0 # time increment to record
89     # will introduce a spherical source at middle left of bottom face
90     xc=[width/2,0]
91     #Check to make sure number of time steps is not too large.
92     print "Time step size= ",h, "Expected number of outputs= ",tend/h
93    
94     U0=0.1 # amplitude of point source
95     ls=500 # length of the source
96     source=np.zeros(ls,'float') # source array
97     decay1=np.zeros(ls,'float') # decay curve one
98     decay2=np.zeros(ls,'float') # decay curve two
99     time=np.zeros(ls,'float') # time values
100     g=np.log(0.01)/ls
101    
102     dfeq=50 #Dominant Frequency
103     a = 2.0 * (np.pi * dfeq)**2.0
104     t0 = 5.0 / (2.0 * np.pi * dfeq)
105     srclength = 5. * t0
106     ls = int(srclength/h)
107     print 'source length',ls
108     source=np.zeros(ls,'float') # source array
109     ampmax=0
110     for it in range(0,ls):
111     t = it*h
112     tt = t-t0
113     dum1 = np.exp(-a * tt * tt)
114     source[it] = -2. * a * tt * dum1
115     # source[it] = exp(-a * tt * tt) !gaussian
116     if (abs(source[it]) > ampmax):
117     ampmax = abs(source[it])
118     #source[t]=np.exp(g*t)*U0*np.sin(2.*np.pi*t/(0.75*ls))*(np.exp(-.1*g*t)-1)
119     #decay1[t]=np.exp(g*t)
120     #decay2[t]=(np.exp(-.1*g*t)-1)
121     time[t]=t*h
122    
123     ####################################################DOMAIN CONSTRUCTION
124     # Domain Corners
125     p0=Point(0.0, 0.0, 0.0)
126     p1=Point(0.0, depth, 0.0)
127     p2=Point(width, depth, 0.0)
128     p3=Point(width, 0.0, 0.0)
129    
130     # Generate Material Boundary
131     x=[ Point(i*dsp\
132     ,dep_sp+modal*orit*h_sp*cos(pi*i*dsp/dep_sp+pi))\
133     for i in range(0,sspl)\
134     ]
135     mysp = Spline(*tuple(x))
136     # Start and end of material boundary.
137     x1=mysp.getStartPoint()
138     x2=mysp.getEndPoint()
139    
140     # Create TOP BLOCK
141     # lines
142     tbl1=Line(p0,x1)
143     tbl2=mysp
144     tbl3=Line(x2,p3)
145     l30=Line(p3, p0)
146     # curve
147     tblockloop = CurveLoop(tbl1,tbl2,tbl3,l30)
148     # surface
149     tblock = PlaneSurface(tblockloop)
150     # Create BOTTOM BLOCK
151     # lines
152     bbl1=Line(x1,p1)
153     bbl3=Line(p2,x2)
154     bbl4=-mysp
155     l12=Line(p1, p2)
156     # curve
157     bblockloop = CurveLoop(bbl1,l12,bbl3,bbl4)
158    
159     # surface
160     bblock = PlaneSurface(bblockloop)
161    
162     #clockwise check as splines must be set as polygons in the point order
163     #they were created. Otherwise get a line across plot.
164     bblockloop2=CurveLoop(mysp,Line(x2,p2),Line(p2,p1),Line(p1,x1))
165    
166     ################################################CREATE MESH FOR ESCRIPT
167     # Create a Design which can make the mesh
168     d=Design(dim=2, element_size=dx, order=2)
169     # Add the subdomains and flux boundaries.
170     d.addItems(PropertySet("top",tblock),PropertySet("bottom",bblock),\
171     PropertySet("linetop",l30))
172     # Create the geometry, mesh and Escript domain
173     d.setScriptFileName(os.path.join(save_path,"example08c.geo"))
174     d.setMeshFileName(os.path.join(save_path,"example08c.msh"))
175     domain=MakeDomain(d, optimizeLabeling=True)
176     x=domain.getX()
177     print "Domain has been generated ..."
178    
179     lam=Scalar(0,Function(domain))
180     lam.setTaggedValue("top",lam1)
181     lam.setTaggedValue("bottom",lam2)
182     mu=Scalar(0,Function(domain))
183     mu.setTaggedValue("top",mu1)
184     mu.setTaggedValue("bottom",mu2)
185     rho=Scalar(0,Function(domain))
186     rho.setTaggedValue("top",rho1)
187     rho.setTaggedValue("bottom",rho2)
188    
189     ##########################################################ESTABLISH PDE
190     mypde=LinearPDE(domain) # create pde
191     mypde.setSymmetryOn() # turn symmetry on
192     # turn lumping on for more efficient solving
193     #mypde.getSolverOptions().setSolverMethod(mypde.getSolverOptions().LUMPING)
194     kmat = kronecker(domain) # create the kronecker delta function of the domain
195     mypde.setValue(D=rho*kmat) #set the general form value D
196    
197     ##########################################################ESTABLISH ABC
198     # Define where the boundary decay will be applied.
199     bn=50.
200     bleft=xstep*bn; bright=width-(xstep*bn); bbot=depth-(ystep*bn)
201     # btop=ystep*bn # don't apply to force boundary!!!
202    
203     # locate these points in the domain
204     left=x[0]-bleft; right=x[0]-bright; bottom=x[1]-bbot
205    
206     tgamma=0.85 # decay value for exponential function
207     def calc_gamma(G,npts):
208     func=np.sqrt(abs(-1.*np.log(G)/(npts**2.)))
209     return func
210    
211     gleft = calc_gamma(tgamma,bleft)
212     gright = calc_gamma(tgamma,bleft)
213     gbottom= calc_gamma(tgamma,ystep*bn)
214    
215     print 'gamma', gleft,gright,gbottom
216    
217     # calculate decay functions
218     def abc_bfunc(gamma,loc,x,G):
219     func=exp(-1.*(gamma*abs(loc-x))**2.)
220     return func
221    
222     fleft=abc_bfunc(gleft,bleft,x[0],tgamma)
223     fright=abc_bfunc(gright,bright,x[0],tgamma)
224     fbottom=abc_bfunc(gbottom,bbot,x[1],tgamma)
225     # apply these functions only where relevant
226     abcleft=fleft*whereNegative(left)
227     abcright=fright*wherePositive(right)
228     abcbottom=fbottom*wherePositive(bottom)
229     # make sure the inside of the abc is value 1
230     abcleft=abcleft+whereZero(abcleft)
231     abcright=abcright+whereZero(abcright)
232     abcbottom=abcbottom+whereZero(abcbottom)
233     # multiply the conditions together to get a smooth result
234     abc=abcleft*abcright*abcbottom
235    
236     ############################################FIRST TIME STEPS AND SOURCE
237     # define small radius around point xc
238     src_length = 40; print "src_length = ",src_length
239     # set initial values for first two time steps with source terms
240     xb=FunctionOnBoundary(domain).getX()
241     y=source[0]*(cos(length(x-xc)*3.1415/src_length)+1)*whereNegative(length(xb-src_length))
242     src_dir=numpy.array([0.,1.]) # defines direction of point source as down
243     y=y*src_dir
244     mypde.setValue(y=y) #set the source as a function on the boundary
245     # initial value of displacement at point source is constant (U0=0.01)
246     # for first two time steps
247     u=[0.0,0.0]*wherePositive(x)
248     u_m1=u
249    
250     ####################################################ITERATION VARIABLES
251     n=0 # iteration counter
252     t=0 # time counter
253     ##############################################################ITERATION
254     while t<tend:
255     # get current stress
256     g=grad(u); stress=lam*trace(g)*kmat+mu*(g+transpose(g))
257     mypde.setValue(X=-stress*abc) # set PDE values
258     accel = mypde.getSolution() #get PDE solution for accelleration
259     u_p1=(2.*u-u_m1)+h*h*accel #calculate displacement
260     u_p1=u_p1*abc # apply boundary conditions
261     u_m1=u; u=u_p1 # shift values by 1
262     # save current displacement, acceleration and pressure
263     if (t >= rtime):
264     saveVTK(os.path.join(save_path,"ex08c.%05d.vtu"%n),\
265     vector_displacement=u,displacement=length(u),\
266     vector_acceleration=accel,acceleration=length(accel),\
267     tensor=stress)
268     rtime=rtime+rtime_inc #increment data save time
269     # increment loop values
270     t=t+h; n=n+1
271     if (n < ls):
272     y=source[n]*(cos(length(x-xc)*3.1415/src_length)+1)*whereNegative(length(x-xc)-src_length)
273     y=y*src_dir; mypde.setValue(y=y) #set the source as a function on the boundary
274     print n,"-th time step t ",t

  ViewVC Help
Powered by ViewVC 1.1.26