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

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python3ified things, replaced mixed whitespace and xrange calls
1
2 ##############################################################################
3 #
4 # Copyright (c) 2009-2013 by University of Queensland
5 # http://www.uq.edu.au
6 #
7 # Primary Business: Queensland, Australia
8 # Licensed under the Open Software License version 3.0
9 # http://www.opensource.org/licenses/osl-3.0.php
10 #
11 # Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 # Development since 2012 by School of Earth Sciences
13 #
14 ##############################################################################
15
16 __copyright__="""Copyright (c) 2009-2013 by University of Queensland
17 http://www.uq.edu.au
18 Primary Business: Queensland, Australia"""
19 __license__="""Licensed under the Open Software License version 3.0
20 http://www.opensource.org/licenses/osl-3.0.php"""
21 __url__="https://launchpad.net/escript-finley"
22
23 """
24 Author: Antony Hallam antony.hallam@uqconnect.edu.au
25 """
26
27 ############################################################FILE HEADER
28 # example08c.py
29 # Create either a 2D syncline or anticline model using pycad meshing
30 # tools. Wave equation solution.
31
32 #######################################################EXTERNAL MODULES
33 import matplotlib
34 matplotlib.use('agg') #It's just here for automated testing
35 from esys.pycad import * #domain constructor
36 from esys.pycad.gmsh import Design #Finite Element meshing package
37 from esys.finley import MakeDomain #Converter for escript
38 import os #file path tool
39 from math import * # math package
40 from esys.escript import *
41 from esys.escript.unitsSI import *
42 from esys.escript.linearPDEs import LinearPDE
43 from esys.escript.pdetools import Projector
44 from esys.weipa import saveVTK
45 from cblib import toRegGrid, subsample
46 import matplotlib
47 matplotlib.use('agg') #It's just here for automated testing
48
49 import pylab as pl #Plotting package
50 import numpy as np
51
52 ########################################################MPI WORLD CHECK
53 if getMPISizeWorld() > 1:
54 import sys
55 print("This example will not run in an MPI world.")
56 sys.exit(0)
57
58 #################################################ESTABLISHING VARIABLES
59 #set modal to 1 for a syncline or -1 for an anticline structural
60 #configuration
61 modal=-1
62
63 # the folder to put our outputs in, leave blank "" for script path -
64 # note this folder path must exist to work
65 save_path= os.path.join("data","example08c")
66 mkDir(save_path)
67
68 ################################################ESTABLISHING PARAMETERS
69 #Model Parameters
70 width=1000.0*m #width of model
71 depth=1000.0*m #depth of model
72 dx=5
73 xstep=dx # calculate the size of delta x
74 ystep=dx # calculate the size of delta y
75
76 sspl=51 #number of discrete points in spline
77 dsp=width/(sspl-1) #dx of spline steps for width
78 dep_sp=500.0*m #avg depth of spline
79 h_sp=250.*m #heigh of spline
80 orit=-1.0 #orientation of spline 1.0=>up -1.0=>down
81
82 vel2=1800.; vel1=3000.
83 rho2=2300.; rho1=3100. #density
84 mu2=(vel2**2.)*rho2/8.; mu1=(vel1**2.)*rho1/8. #bulk modulus
85 lam2=mu2*6.; lam1=mu1*6. #lames constant
86
87
88 # Time related variables.
89 testing=True
90 if testing:
91 print('The testing end time is currently selected. This severely limits the number of time iterations.')
92 print("Try changing testing to False for more iterations.")
93 tend=0.001
94 else:
95 tend=0.5 # end time
96
97 h=0.0001 # time step
98 # data recording times
99 rtime=0.0 # first time to record
100 rtime_inc=tend/50.0 # time increment to record
101 # will introduce a spherical source at middle left of bottom face
102 xc=[width/2,0]
103 #Check to make sure number of time steps is not too large.
104 print("Time step size= ",h, "Expected number of outputs= ",tend/h)
105
106 U0=0.1 # amplitude of point source
107 ls=500 # length of the source
108 source=np.zeros(ls,'float') # source array
109 decay1=np.zeros(ls,'float') # decay curve one
110 decay2=np.zeros(ls,'float') # decay curve two
111 time=np.zeros(ls,'float') # time values
112 g=np.log(0.01)/ls
113
114 dfeq=50 #Dominant Frequency
115 a = 2.0 * (np.pi * dfeq)**2.0
116 t0 = 5.0 / (2.0 * np.pi * dfeq)
117 srclength = 5. * t0
118 ls = int(srclength/h)
119 print('source length',ls)
120 source=np.zeros(ls,'float') # source array
121 ampmax=0
122 for it in range(0,ls):
123 t = it*h
124 tt = t-t0
125 dum1 = np.exp(-a * tt * tt)
126 source[it] = -2. * a * tt * dum1
127 if (abs(source[it]) > ampmax):
128 ampmax = abs(source[it])
129 time[t]=t*h
130
131 ####################################################DOMAIN CONSTRUCTION
132 # Domain Corners
133 p0=Point(0.0, 0.0, 0.0)
134 p1=Point(0.0, depth, 0.0)
135 p2=Point(width, depth, 0.0)
136 p3=Point(width, 0.0, 0.0)
137
138 # Generate Material Boundary
139 x=[ Point(i*dsp\
140 ,dep_sp+modal*orit*h_sp*cos(pi*i*dsp/dep_sp+pi))\
141 for i in range(0,sspl)\
142 ]
143 mysp = Spline(*tuple(x))
144 # Start and end of material boundary.
145 x1=mysp.getStartPoint()
146 x2=mysp.getEndPoint()
147
148 # Create TOP BLOCK
149 # lines
150 tbl1=Line(p0,x1)
151 tbl2=mysp
152 tbl3=Line(x2,p3)
153 l30=Line(p3, p0)
154 # curve
155 tblockloop = CurveLoop(tbl1,tbl2,tbl3,l30)
156 # surface
157 tblock = PlaneSurface(tblockloop)
158 # Create BOTTOM BLOCK
159 # lines
160 bbl1=Line(x1,p1)
161 bbl3=Line(p2,x2)
162 bbl4=-mysp
163 l12=Line(p1, p2)
164 # curve
165 bblockloop = CurveLoop(bbl1,l12,bbl3,bbl4)
166
167 # surface
168 bblock = PlaneSurface(bblockloop)
169
170 #clockwise check as splines must be set as polygons in the point order
171 #they were created. Otherwise get a line across plot.
172 bblockloop2=CurveLoop(mysp,Line(x2,p2),Line(p2,p1),Line(p1,x1))
173
174 ################################################CREATE MESH FOR ESCRIPT
175 # Create a Design which can make the mesh
176 d=Design(dim=2, element_size=dx, order=2)
177 # Add the subdomains and flux boundaries.
178 d.addItems(PropertySet("top",tblock),PropertySet("bottom",bblock),\
179 PropertySet("linetop",l30))
180 # Create the geometry, mesh and Escript domain
181 d.setScriptFileName(os.path.join(save_path,"example08c.geo"))
182 d.setMeshFileName(os.path.join(save_path,"example08c.msh"))
183 domain=MakeDomain(d, optimizeLabeling=True)
184 x=domain.getX()
185 print("Domain has been generated ...")
186
187 lam=Scalar(0,Function(domain))
188 lam.setTaggedValue("top",lam1)
189 lam.setTaggedValue("bottom",lam2)
190 mu=Scalar(0,Function(domain))
191 mu.setTaggedValue("top",mu1)
192 mu.setTaggedValue("bottom",mu2)
193 rho=Scalar(0,Function(domain))
194 rho.setTaggedValue("top",rho1)
195 rho.setTaggedValue("bottom",rho2)
196
197 ##########################################################ESTABLISH PDE
198 mypde=LinearPDE(domain) # create pde
199 mypde.setSymmetryOn() # turn symmetry on
200 # turn lumping on for more efficient solving
201 #mypde.getSolverOptions().setSolverMethod(mypde.getSolverOptions().LUMPING)
202 kmat = kronecker(domain) # create the kronecker delta function of the domain
203 mypde.setValue(D=rho*kmat) #set the general form value D
204
205 ##########################################################ESTABLISH ABC
206 # Define where the boundary decay will be applied.
207 bn=20.
208 bleft=xstep*bn; bright=width-(xstep*bn); bbot=depth-(ystep*bn)
209 # btop=ystep*bn # don't apply to force boundary!!!
210
211 # locate these points in the domain
212 left=x[0]-bleft; right=x[0]-bright; bottom=x[1]-bbot
213
214 tgamma=0.85 # decay value for exponential function
215 def calc_gamma(G,npts):
216 func=np.sqrt(abs(-1.*np.log(G)/(npts**2.)))
217 return func
218
219 gleft = calc_gamma(tgamma,bleft)
220 gright = calc_gamma(tgamma,bleft)
221 gbottom= calc_gamma(tgamma,ystep*bn)
222
223 print('gamma', gleft,gright,gbottom)
224
225 # calculate decay functions
226 def abc_bfunc(gamma,loc,x,G):
227 func=exp(-1.*(gamma*abs(loc-x))**2.)
228 return func
229
230 fleft=abc_bfunc(gleft,bleft,x[0],tgamma)
231 fright=abc_bfunc(gright,bright,x[0],tgamma)
232 fbottom=abc_bfunc(gbottom,bbot,x[1],tgamma)
233 # apply these functions only where relevant
234 abcleft=fleft*whereNegative(left)
235 abcright=fright*wherePositive(right)
236 abcbottom=fbottom*wherePositive(bottom)
237 # make sure the inside of the abc is value 1
238 abcleft=abcleft+whereZero(abcleft)
239 abcright=abcright+whereZero(abcright)
240 abcbottom=abcbottom+whereZero(abcbottom)
241 # multiply the conditions together to get a smooth result
242 abc=abcleft*abcright*abcbottom
243
244 ############################################FIRST TIME STEPS AND SOURCE
245 # define small radius around point xc
246 src_length = 40; print("src_length = ",src_length)
247 # set initial values for first two time steps with source terms
248 xb=FunctionOnBoundary(domain).getX()
249 y=source[0]*(cos(length(x-xc)*3.1415/src_length)+1)*whereNegative(length(xb-src_length))
250 src_dir=numpy.array([0.,1.]) # defines direction of point source as down
251 y=y*src_dir
252 mypde.setValue(y=y) #set the source as a function on the boundary
253 # initial value of displacement at point source is constant (U0=0.01)
254 # for first two time steps
255 u=[0.0,0.0]*wherePositive(x)
256 u_m1=u
257
258 ####################################################ITERATION VARIABLES
259 n=0 # iteration counter
260 t=0 # time counter
261 ##############################################################ITERATION
262 while t<tend:
263 # get current stress
264 g=grad(u); stress=lam*trace(g)*kmat+mu*(g+transpose(g))
265 mypde.setValue(X=-stress*abc) # set PDE values
266 accel = mypde.getSolution() #get PDE solution for accelleration
267 u_p1=(2.*u-u_m1)+h*h*accel #calculate displacement
268 u_p1=u_p1*abc # apply boundary conditions
269 u_m1=u; u=u_p1 # shift values by 1
270 # save current displacement, acceleration and pressure
271 if (t >= rtime):
272 saveVTK(os.path.join(save_path,"ex08c.%05d.vtu"%n),\
273 vector_displacement=u,displacement=length(u),\
274 vector_acceleration=accel,acceleration=length(accel),\
275 tensor=stress)
276 rtime=rtime+rtime_inc #increment data save time
277 # increment loop values
278 t=t+h; n=n+1
279 if (n < ls):
280 y=source[n]*(cos(length(x-xc)*3.1415/src_length)+1)*whereNegative(length(x-xc)-src_length)
281 y=y*src_dir; mypde.setValue(y=y) #set the source as a function on the boundary
282 print("time step %d, t=%s"%(n,t))

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