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##############################################################################
#
# Copyright (c) 2015-2018 by The University of Queensland
# http://www.uq.edu.au
#
# Primary Business: Queensland, Australia
# Licensed under the Apache License, version 2.0
# http://www.apache.org/licenses/LICENSE-2.0
#
# Development until 2012 by Earth Systems Science Computational Center (ESSCC)
# Development 2012-2013 by School of Earth Sciences
# Development from 2014 by Centre for Geoscience Computing (GeoComp)
#
##############################################################################
"""
Test script to run test model COMMEMI-4
"""
from __future__ import print_function, division
import matplotlib
# The following line is here to allow automated testing. Remove or comment if
# you would like to display the final plot in a window instead.
matplotlib.use('agg')
import datetime
import numpy
import esys.downunder.magtel2d as mt2d
import esys.escript as escript
import esys.escript.pdetools as pdetools
try:
import esys.finley as finley
HAVE_FINLEY = True
except ImportError:
HAVE_FINLEY = False
HAVE_DIRECT = escript.hasFeature("PASO_DIRECT") or escript.hasFeature('trilinos')
def setupMesh(mode, coord, elem_sizes):
#---------------------------------------------------------------------------
# DESCRIPTION:
# -----------
# This is a utility function which setups the COMMEMI-4 mesh.
#
#
# ARGUMENTS:
# ----------
# mode :: TE or TM mode.
# coord :: dictionary with coordinate tuples.
# elem_sizes :: mesh element sizes, large, normal, small.
#
# RETURNS:
# --------
# <Nothing> A mesh file is written to the output folder.
#
#
# AUTHOR:
# -------
# Ralf Schaa,
# University of Queensland
#
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
# Imports.
#---------------------------------------------------------------------------
import esys.pycad as pycad # @UnresolvedImport
import esys.finley as finley # @UnresolvedImport
import esys.escript as escript # @UnresolvedImport
import esys.weipa as weipa # @UnresolvedImport
# <Note>: "@UnresolvedImport" ignores any warnings in Eclipse/PyDev (PyDev has trouble with external libraries).
model = "COMMEMI-4"
print("Preparing the mesh " + model + " ...")
print("")
# Warn about magnetotelluric TM mode:
if mode.lower() == 'tm':
print("TM mode not yet supported")
return
# Path to write the mesh:
outpath = "../out/commemi4"
# --------------------------------------------------------------------------
# Initialisations.
# --------------------------------------------------------------------------
# Get coordinates from dictionary as list of tuples
a0 = coord["air"]
l1 = coord["lyr1"]
s1 = coord["slab"]
b1 = coord["basin"]
l2 = coord["lyr2"]
l3 = coord["lyr3"]
# Mesh length from top-boundary.
x_extent = abs(a0[3][0]-a0[0][0])
# --------------------------------------------------------------------------
# Point definitions.
# --------------------------------------------------------------------------
#<Note>: define all points spanning the mesh, anomalies and layers;
# note also shared domain points must be defined only once.
# Mesh top boundary.
air = []
air.append( pycad.Point( *a0[0] ) ) # 0: left , top (@ boundary)
air.append( pycad.Point( *a0[3] ) ) # 3: right , top (@ boundary)
# First-layer.
ly1 = []
ly1.append( pycad.Point( *l1[0] ) ) # 0: left , top (@ air/earth interface)
ly1.append( pycad.Point( *l1[1] ) ) # 1: left , bottom (@ boundary)
ly1.append( pycad.Point( *l1[2] ) ) # 2: right , bottom (@ slab/basin)
ly1.append( pycad.Point( *l1[3] ) ) # 3: right , bottom (@ boundary)
ly1.append( pycad.Point( *l1[4] ) ) # 4: right , top (@ air/earth interface)
# Slab.
sl1 = []
sl1.append( ly1[1] ) # 0: left , top (@ boundary)
sl1.append( pycad.Point( *s1[1] ) ) # 1: left , bottom (@ boundary)
sl1.append( pycad.Point( *s1[2] ) ) # 2: right , bottom (@ slab/basin)
sl1.append( ly1[2] ) # 3: right , top (@ slab/basin)
# Basin.
bs1 = []
bs1.append( ly1[2] ) # 0: left , top (@ slab/basin)
bs1.append( sl1[2] ) # 1: left , centre (@ slab/basin)
bs1.append( pycad.Point( *b1[2] ) ) # 2: left , bottom (@ lyr1/basin)
bs1.append( pycad.Point( *b1[3] ) ) # 3: centre, bottom (@ lyr1/basin)
bs1.append( pycad.Point( *b1[4] ) ) # 4: edge , bottom (@ lyr1/basin)
bs1.append( pycad.Point( *b1[5] ) ) # 5: right , bottom (@ boundary)
bs1.append( ly1[3] ) # 6: right , top
# Second-Layer.
ly2 = []
ly2.append( sl1[1] ) # 0: left , top (@ lyr2/slab)
ly2.append( pycad.Point( *l2[1] ) ) # 1: left , bottom (@ boundary)
ly2.append( pycad.Point( *l2[2] ) ) # 2: right , bottom (@ boundary)
ly2.append( bs1[5] ) # 3: right , top (@ basin/boundary)
ly2.append( bs1[4] ) # 4: edge , top (@ lyr2/basin)
ly2.append( bs1[3] ) # 5: centre, top (@ lyr2/basin)
ly2.append( bs1[2] ) # 6: left , top (@ lyr2/basin)
ly2.append( sl1[2] ) # 7: left , centre (@ slab/basin)
# Basement layer.
ly3 = []
ly3.append( ly2[1] ) # 0: left , top (@ boundary)
ly3.append( pycad.Point( *l3[1] ) ) # 1: left , bottom (@ boundary)
ly3.append( pycad.Point( *l3[2] ) ) # 2: right , bottom (@ boundary)
ly3.append( ly2[2] ) # 3: right , top (@ boundary)
#___________________________________________________________________________
# --------------------------------------------------------------------------
# Line definitions.
# --------------------------------------------------------------------------
#<Note>: connects the points to define lines counterclockwise;
# shared lines are re-used to ensure that all domains
# are recognised as parts of the same mesh.
# Air.
ln0 = []
ln0.append( pycad.Line(air[0], ly1[0]) ) # 0 left-top to left-bottom.
ln0.append( pycad.Line(ly1[0], ly1[4]) ) # 1 left-bottom to right-bottom (air-earth interface).
ln0.append( pycad.Line(ly1[4], air[1]) ) # 2 right-bottom to right-top.
ln0.append( pycad.Line(air[1], air[0]) ) # 3 right-top to left-top.
# Top Layer.
ln1 = []
ln1.append( pycad.Line(ly1[0], ly1[1]) ) # 0 left-top to left-bottom.
ln1.append( pycad.Line(ly1[1], ly1[2]) ) # 1 left-bottom to start-slab/basin.
ln1.append( pycad.Line(ly1[2], ly1[3]) ) # 2 start-slab/basin to basin-boundary
ln1.append( pycad.Line(ly1[3], ly1[4]) ) # 3 basin-boundary to right-top.
ln1.append( -ln0[1] ) # 4 right-top to left-top.
# Slab.
ln2 = []
ln2.append( pycad.Line(sl1[0], sl1[1]) ) # 0 left-top to left-bottom.
ln2.append( pycad.Line(sl1[1], sl1[2]) ) # 1 left-bottom to right-bottom.
ln2.append( pycad.Line(sl1[2], sl1[3]) ) # 2 right-bottom to right-top.
ln2.append( -ln1[1] ) # 3 right-top to left-top
# Basin.
ln3 = []
ln3.append( -ln2[2] ) # 0 left-top to left-centre.
ln3.append( pycad.Line(bs1[1], bs1[2]) ) # 1 left-centre to left-bottom.
ln3.append( pycad.Line(bs1[2], bs1[3]) ) # 2 left-bottom to mid-bottom.
ln3.append( pycad.Line(bs1[3], bs1[4]) ) # 3 mid-bottom to right-mid-top.
ln3.append( pycad.Line(bs1[4], bs1[5]) ) # 4 right-mid-top to right-bottom.
ln3.append( pycad.Line(bs1[5], bs1[6]) ) # 5 right-bottom to right-top.
ln3.append( -ln1[2] ) # 6 right-top to right-slab/basin.
# Layer below.
ln4 = []
ln4.append( pycad.Line(ly2[0], ly2[1]) ) # 0 left-top to left-bottom.
ln4.append( pycad.Line(ly2[1], ly2[2]) ) # 1 left-bottom to right-bottom.
ln4.append( pycad.Line(ly2[2], ly2[3]) ) # 2 right-bottom to right-top.
ln4.append( -ln3[4] ) # 3 right-top to right-mid-top.
ln4.append( -ln3[3] ) # 4 right-mid-top to mid-bottom.
ln4.append( -ln3[2] ) # 5 mid-bottom to left-bottom.
ln4.append( -ln3[1] ) # 6 left-bottom to left-centre.
ln4.append( -ln2[1] ) # 7 left-centre to left-top.
# Basement layer.
ln5 = []
ln5.append( pycad.Line(ly3[0], ly3[1]) ) # 0 left-top to left-bottom.
ln5.append( pycad.Line(ly3[1], ly3[2]) ) # 1 left-bottom to right-bottom.
ln5.append( pycad.Line(ly3[2], ly3[3]) ) # 2 right-bottom to right-top.
ln5.append( -ln4[1] ) # 3 right-top to left-top.
#___________________________________________________________________________
# --------------------------------------------------------------------------
# Domain definitions.
# --------------------------------------------------------------------------
# First define all borders.
borders = []
borders.append( pycad.CurveLoop(*ln0) )
borders.append( pycad.CurveLoop(*ln1) )
borders.append( pycad.CurveLoop(*ln2) )
borders.append( pycad.CurveLoop(*ln3) )
borders.append( pycad.CurveLoop(*ln4) )
borders.append( pycad.CurveLoop(*ln5) )
# And next the domains.
domains = []
for i in range( len(borders) ):
domains.append( pycad.PlaneSurface(borders[i]) )
#___________________________________________________________________________
# --------------------------------------------------------------------------
# Set element sizes in domains.
# --------------------------------------------------------------------------
# Horizontal extents of segments along slab and basin:
x_extents = []
x_extents.append( l1[2][0] - l1[0][0] ) # 0
x_extents.append( l1[3][0] - l1[2][0] ) # 1
# Number of elements in the air-domain, first-layer as well as slab- and basin-domain.
domains[0].setElementDistribution( x_extent / elem_sizes["large"] )
domains[1].setElementDistribution( x_extent / (elem_sizes["small"]) )
domains[2].setElementDistribution( 0.4*x_extent / (elem_sizes["small"]) )
domains[3].setElementDistribution( 0.5*x_extent / (elem_sizes["small"]) )
#<Note> slab and basin multiplied by approximate ratio of their x_extent.
#___________________________________________________________________________
#---------------------------------------------------------------------------
# Now define the gmsh 'design' object.
#---------------------------------------------------------------------------
design2D = pycad.gmsh.Design(dim=2, element_size=elem_sizes['large'], keep_files=False)
# Also specify the domains for tagging with property values later on:
design2D.addItems(
pycad.PropertySet( "air" , domains[0]) ,
pycad.PropertySet( "lyr1" , domains[1]) ,
pycad.PropertySet( "slab" , domains[2]) ,
pycad.PropertySet( "basin" , domains[3]) ,
pycad.PropertySet( "lyr2" , domains[4]) ,
pycad.PropertySet( "lyr3" , domains[5]) )
# Now define the unstructured finley-mesh..
model2D = finley.MakeDomain(design2D)
#___________________________________________________________________________
return model2D
def generateCommemi4Mesh():
#---------------------------------------------------------------------------
# DESCRIPTION:
# ------------
# Script for preparing the COMMEMI-2 2D model.
#
# The COMMEMI-4 2D model consist of a 3-layered halfspace,
# hosting an anomalous horizontal slab and a basin-structure
# in the first layer.
#
# References:
# -----------
# See Franke A., p.89, 2003 (MSc. Thesis).
#
# Antje Franke, "Zweidimensionale Finite-Elemente-Modellierung
# niederfrequenter elektromagnetischer Felder in der Fernzone",
# Diplomarbeit (MSc.), 2003, Technische Universtitaet Freiberg.
#
# --------------------------------------------------------------------------
#---------------------------------------------------------------------------
# Geometric mesh parameters.
# --------------------------------------------------------------------------
# Horizontal extent and start point of mesh.
a_extent = 50000 # 50km - Vertical extent of air-layer in (m).
z_extent = 50000 # 50km - Vertical extent of subsurface in (m).
x_extent = 60000 # 60km - Horizontal extent of model in (m).
# Start point of mesh.
x_start = 0 #-x_extent/2.0
# Mesh elements sizes.
elem_sizes = {
'large' : 4.00 * x_extent/100.0, #
'normal': 2.00 * x_extent/100.0, #
'small' : 0.25 * x_extent/100.0 #
}
#____________________________________________________________________________
#---------------------------------------------------------------------------
# Coordinate definitions.
# --------------------------------------------------------------------------
# X-coordinates of all domain corners (in order of appearance, left to right).
x0 = x_start # left (@ boundary)
x1 = x_start + 24000 # centre (@ slab/basin)
x2 = x_start + 24000 + 8000 # edge-bottom (@ slab/lyr1)
x3 = x_start + 24000 + 8000 + 3000 # edge-top (@ slab/lyr1)
x4 = x_start + x_extent # right (@ boundary)
# Y-coordinates of all domain corners (in order of appearance, top to bottom).
y0 = a_extent # top
y1 = 0 # centre (@ air/earth)
y2 =-500 # lyr1-bottom (@ boundary-left)
y3 =-1000 # basin-bottom (@ boundary-right)
y4 =-2000 # slab-bottom (@ boundary-left)
y5 =-4000 # basin-bottom (@ centre)
y6 =-25000 # lyr1-bottom
y7 =-z_extent # bottom
# Save in dictionary as a list of tuples for each domain, from left-top corner, counterclockwise.
coord = {
'air' : ([x0, y0, 0], # 0: left , top
[x0, y1, 0], # 1: left , bottom (@ air/earth)
[x4, y1, 0], # 2: right , bottom (@ air/earth)
[x4, y0, 0]), # 3: right , top
'lyr1' : ([x0, y1, 0], # 0: left , top
[x0, y2, 0], # 1: left , bottom
[x1, y2, 0], # 2: right , bottom (@ slab/basin)
[x4, y2, 0], # 3: right , bottom (@ boundary)
[x4, y1, 0]), # 4: right , top
'slab' : ([x0, y2, 0], # 0: left , top
[x0, y4, 0], # 1: left , bottom
[x1, y4, 0], # 2: right , bottom (@ slab/basin)
[x1, y2, 0]), # 3: right , top (@ slab/basin)
'basin': ([x1, y2, 0], # 0: left , top (@ slab/basin)
[x1, y4, 0], # 1: left , centre (@ slab/basin)
[x1, y5, 0], # 2: left , bottom (@ lyr1/basin)
[x2, y5, 0], # 3: centre, bottom (@ lyr1/basin)
[x3, y3, 0], # 4: edge , bottom (@ lyr1/basin)
[x4, y3, 0], # 5: right , bottom (@ boundary)
[x4, y2, 0]), # 6: right , top
'lyr2' : ([x0, y4, 0], # 0: left , top
[x0, y6, 0], # 1: left , bottom
[x4, y6, 0], # 2: right , bottom
[x4, y3, 0], # 3: right , top (@ basin/boundary)
[x3, y3, 0], # 4: edge , top (@ lyr2/basin)
[x2, y5, 0], # 5: centre, top (@ lyr2/basin)
[x1, y5, 0], # 6: left , top (@ lyr2/basin)
[x1, y4, 0]), # 7: left , centre (@ slab/basin)
'lyr3' : ([x0, y6, 0], # 0: left , top
[x0, y7, 0], # 1: left , bottom
[x4, y7, 0], # 2: right , bottom
[x4, y6, 0]), # 3: right , top
}
#___________________________________________________________________________
#---------------------------------------------------------------------------
# Setup the COMMEMI-4 mesh.
#---------------------------------------------------------------------------
# This creates the mesh and saves it to the output folder.
return setupMesh("TE", coord, elem_sizes)
#___________________________________________________________________________
if HAVE_FINLEY:
# ---
# Initialisations
# ---
# Get timing:
startTime = datetime.datetime.now()
# Mode (TE includes air-layer, whereas TM does not):
mode = 'TE'
# Read the mesh file and define the 'finley' domain:
#mesh_file = "commemi4_tm.fly"
#domain = finley.ReadMesh(mesh_file, numDim=2)
if escript.hasFeature('gmsh'):
domain=generateCommemi4Mesh()
# Sounding frequencies (in Hz):
freq_def = {"high":1.0e+0,"low":1.0e-0,"step":1}
# Frequencies will be mapped on a log-scale from
# 'high' to 'low' with 'step' points per decade.
# (also only one frequency must be passed via dict)
# Step sizes for sampling along vertical and horizontal axis (in m):
xstep=300
zstep=250
# ---
# Resistivity model
# ---
# Resistivity values assigned to tagged regions (in Ohm.m):
rho = [
1.0e+14, # 0: air 1.0e-30
25.0 , # 1: lyr1 0.04
10.0 , # 2: slab 0.1
2.5 , # 3: basin 0.4
1000.0 , # 4: lyr2 0.001
5.0 # 5: lyr3 0.2
]
# Tags must match those in the file:
tags = ["air", "lyr1", "slab", "basin", "lyr2", "lyr3"]
# Optional user defined map of resistivity:
def f4(x,z,r): return escript.sqrt(escript.sqrt(x*x+z*z))/r
maps = [None, None, None, None, f4, None]
# ---
# Layer definitions for 1D response at boundaries.
# ---
# List with resistivity values for left and right boundary.
rho_1d_left = [ rho[0], rho[1], rho[2], rho[4], rho[5] ]
rho_1d_rght = [ rho[0], rho[1], rho[3], rho[4], rho[5] ]
# Associated interfaces for 1D response left and right (must match the mesh file).
ifc_1d_left = [ 50000, 0, -500, -2000, -25000, -50000]
ifc_1d_rght = [ 50000, 0, -500, -1000, -25000, -50000]
# Save in dictionary with layer interfaces and resistivities left and right:
ifc_1d = {"left":ifc_1d_left , "right":ifc_1d_rght}
rho_1d = {"left":rho_1d_left , "right":rho_1d_rght}
# ---
# Adjust parameters here for TM mode
# ---
# Simply delete first element from lists:
if mode.upper() == 'TM':
tags.pop(0)
rho.pop(0)
rho_1d['left'].pop(0)
rho_1d['right'].pop(0)
ifc_1d['left'].pop(0)
ifc_1d['right'].pop(0)
if maps is not None:
maps.pop(0)
# ---
# Run MT_2D
# ---
# Class options:
mt2d.MT_2D._solver = "DIRECT"
mt2d.MT_2D._debug = False
if mt2d.MT_2D._solver == "DIRECT" and not escript.hasFeature('paso'):
print("Trilinos direct solvers cannot currently handle PDE systems. Please compile with Paso.")
elif mt2d.MT_2D._solver == "DIRECT" and not HAVE_DIRECT:
if escript.getMPISizeWorld() > 1:
print("Direct solvers and multiple MPI processes are not currently supported.")
else:
print("escript was not built with support for direct solvers, aborting.")
elif not escript.hasFeature('gmsh'):
print("This example requires gmsh, aborting.")
else:
# Instantiate an MT_2D object with required & optional parameters:
obj_mt2d = mt2d.MT_2D(domain, mode, freq_def, tags, rho, rho_1d, ifc_1d,
xstep=xstep ,zstep=zstep, maps=None, plot=True)
# Solve for fields, apparent resistivity and phase:
mt2d_fields, arho_2d, aphi_2d = obj_mt2d.pdeSolve()
#
print("Runtime:", datetime.datetime.now()-startTime)
print("Done!")
else: # no finley
print("Finley module not available.")
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