[cig-commits] r4423 -
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats
sue at geodynamics.org
sue at geodynamics.org
Thu Aug 24 15:22:48 PDT 2006
Author: sue
Date: 2006-08-24 15:22:48 -0700 (Thu, 24 Aug 2006)
New Revision: 4423
Added:
short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx
Log:
added lyx file
Added: short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx
===================================================================
--- short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx 2006-08-24 22:10:03 UTC (rev 4422)
+++ short/3D/PyLith/branches/pylith-0.8/doc/userguide/fileformats/fileformats.lyx 2006-08-24 22:22:48 UTC (rev 4423)
@@ -0,0 +1,2037 @@
+#LyX 1.4.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 245
+\begin_document
+\begin_header
+\textclass book
+\begin_preamble
+
+\end_preamble
+\language english
+\inputencoding latin1
+\fontscheme default
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry true
+\use_amsmath 1
+\cite_engine basic
+\use_bibtopic false
+\paperorientation portrait
+\leftmargin 1in
+\topmargin 1in
+\rightmargin 1in
+\bottommargin 1in
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 2
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\end_header
+
+\begin_body
+
+\begin_layout Chapter
+File Formats
+\end_layout
+
+\begin_layout Section
+Input Files
+\end_layout
+
+\begin_layout Standard
+PyLith gathers its input from several different types of files.
+ All of these area ASCII files and can include comment lines that begin
+ with '#'.
+ Note that the placement of comments is restricted to certain locations
+ in some files (see the discussion of each file format for more information).
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.coord
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+\color black
+xx.coord
+\family default
+\color default
+ file contains the coordinates of all of the vertices in the finite-element
+ mesh.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing vertices of the finite-element mesh.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# First, specify units of coordinates.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+coord_unit = km
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Now specify the coordinates of each vertex.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Vertex number
+\end_layout
+
+\begin_layout LyX-Code
+# (2) X coordinate
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Y coordinate
+\end_layout
+
+\begin_layout LyX-Code
+# (4) Z coordinate
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Note: No comments are allowed within the list of vertex coordinates
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+1 0.000000e+00 0.000000e+00 0.000000e+00
+\end_layout
+
+\begin_layout LyX-Code
+2 1.000000e+00 0.000000e+00 0.000000e+00
+\end_layout
+
+\begin_layout LyX-Code
+3 0.000000e+00 2.000000e+00 0.000000e+00
+\end_layout
+
+\begin_layout LyX-Code
+4 1.000000e+00 2.000000e+00 3.000000e+00
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+\color black
+xx.coord
+\family default
+\color default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.connect
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+\color black
+xx.connect
+\family default
+\color default
+ file contains the finite-element mesh topology and material type information,
+ including the element type, material type, and the lists of vertices for
+ each element.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing finite-element mesh topology and material type
+\end_layout
+
+\begin_layout LyX-Code
+# information.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Element number
+\end_layout
+
+\begin_layout LyX-Code
+# (2) Element type
+\end_layout
+
+\begin_layout LyX-Code
+# 1 = Linear hexahedron (8 vertices)
+\end_layout
+
+\begin_layout LyX-Code
+# 2 = Linear hexahedron with 1 set of collapsed vertices
+\end_layout
+
+\begin_layout LyX-Code
+# (7 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 3 = Linear hexahedron with 2 sets of collapsed vertices
+\end_layout
+
+\begin_layout LyX-Code
+# (6 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 4 = Linear hexahedron with 4 vertices collapsed to a point
+\end_layout
+
+\begin_layout LyX-Code
+# (5 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 5 = Linear tetrahedron (4 vertices)
+\end_layout
+
+\begin_layout LyX-Code
+# 6 = Quadratix hexahedron (20 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 7 = Quadratic hexahedron with 3 vertices along one edge
+\end_layout
+
+\begin_layout LyX-Code
+# collapsed to a point (18 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 8 = Quadratic hexahedron with 3 sets of collapsed vertices
+\end_layout
+
+\begin_layout LyX-Code
+# (15 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 9 = Quadratic hexahedron with 9 vertices collapsed to a point
+\end_layout
+
+\begin_layout LyX-Code
+# (13 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# 10 = Quadratic tetrahedron (10 vertices) [NOT IMPLEMENTED]
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Material type, numbered consecutively beginning with '1'
+\end_layout
+
+\begin_layout LyX-Code
+# (4) Infinite element flag, required but not currently implemented
+\end_layout
+
+\begin_layout LyX-Code
+# 0 = only valid value
+\end_layout
+
+\begin_layout LyX-Code
+# (5)+ Vertices in the element, identified by vertex number
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Note: No comments are allowed within the mesh information.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+1 5 1 0 2911 2865 2886 2864
+\end_layout
+
+\begin_layout LyX-Code
+2 5 2 0 843 3999 4029 3926
+\end_layout
+
+\begin_layout LyX-Code
+3 5 1 0 684 8975 2346 6219
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+\color black
+xx.connect
+\family default
+\color default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.bc
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+\color black
+xx.bc
+\family default
+\color default
+ file specifies the displacements, velocity, and/or forces applied to vertices
+ on the boundaries.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing boundary conditions at vertices.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# First, specify units of coordinates for each type of boundary
+\end_layout
+
+\begin_layout LyX-Code
+# conditon.
+ All three are required even if they are not all used.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+displacement_units = m
+\end_layout
+
+\begin_layout LyX-Code
+velocity_units = m/s
+\end_layout
+
+\begin_layout LyX-Code
+force_units = newton
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Boundary conditions applied to vertices.
+ You must specify a flag and
+\end_layout
+
+\begin_layout LyX-Code
+# value for each degree of freedom, even if some are free.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Vertex number
+\end_layout
+
+\begin_layout LyX-Code
+# (2) Boundary condition flag for x DOF
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Boundary condition flag for y DOF
+\end_layout
+
+\begin_layout LyX-Code
+# (4) Boundary condition flag for z DOF
+\end_layout
+
+\begin_layout LyX-Code
+# 0 = Free
+\end_layout
+
+\begin_layout LyX-Code
+# 1 = Fixed displacement
+\end_layout
+
+\begin_layout LyX-Code
+# 2 = Constant velocity
+\end_layout
+
+\begin_layout LyX-Code
+# 3 = Constant force
+\end_layout
+
+\begin_layout LyX-Code
+# A 2 or more digit code may be used for the boundary condition
+\end_layout
+
+\begin_layout LyX-Code
+# flag.
+ If used, the the final digit refers to the condition
+\end_layout
+
+\begin_layout LyX-Code
+# type as defined above, while the beginning digit(s) refer to
+\end_layout
+
+\begin_layout LyX-Code
+# the time history to be used.
+\end_layout
+
+\begin_layout LyX-Code
+# (5) Boundary condition value for x DOF
+\end_layout
+
+\begin_layout LyX-Code
+# (6) Boundary condition value for y DOF
+\end_layout
+
+\begin_layout LyX-Code
+# (7) Boundary condition value for z DOF
+\end_layout
+
+\begin_layout LyX-Code
+1 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
+\end_layout
+
+\begin_layout LyX-Code
+3 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
+\end_layout
+
+\begin_layout LyX-Code
+12 0 1 0 0.0000e+00 0.0000e+00 0.0000e+00
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+\color black
+xx.bc
+\family default
+\color default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.time
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+\color black
+xx.time
+\family default
+\color default
+ file specifies the time stepping parameters for the simulation.
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+\color red
+Warning:
+\series default
+\color default
+The convergence criteria depend on the type of solution and material models.
+ The time step for a linear elastic problem is much different than that
+ for a nonlinear or time-dependent problem.
+
+\end_layout
+
+\begin_layout LyX-Code
+# File containing time stepping parameters.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# First, specify units used in values with dimensions of time.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+time_units = year
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Time stepping parameters are given in groups.
+ The elastic solution
+\end_layout
+
+\begin_layout LyX-Code
+# corresponds to group 0 and must always be defined.
+ Although some of
+\end_layout
+
+\begin_layout LyX-Code
+# the parameters do not have any meaning for the elastic solution,
+\end_layout
+
+\begin_layout LyX-Code
+# they must be present anyway.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Time step group number (=0 for elastic solution).
+\end_layout
+
+\begin_layout LyX-Code
+# (2) The number of time steps in the group (=1 for elastic solution).
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Time step size (given in units of time_units).
+\end_layout
+
+\begin_layout LyX-Code
+# (4) Amount of implicitness.
+ Real dimensionless parameter that
+\end_layout
+
+\begin_layout LyX-Code
+# ranges from 0.0 (fully explicit) to 1.0 (fully implicit).
+ The
+\end_layout
+
+\begin_layout LyX-Code
+# value is generally set to 0.5.
+\end_layout
+
+\begin_layout LyX-Code
+# (5) Maximum number of equilibrium iterations before stiffness
+\end_layout
+
+\begin_layout LyX-Code
+# matrix is reformed.
+\end_layout
+
+\begin_layout LyX-Code
+# (6) Number of time steps between initial reformation of stiffness
+\end_layout
+
+\begin_layout LyX-Code
+# matrix.
+\end_layout
+
+\begin_layout LyX-Code
+# <0 Indicates that reformation should occur only for the first
+\end_layout
+
+\begin_layout LyX-Code
+# step in each time step group.
+\end_layout
+
+\begin_layout LyX-Code
+# =0 Indicates that reformation should never occur.
+\end_layout
+
+\begin_layout LyX-Code
+# (7) Large deformation solution flag (only Linear strain is
+\end_layout
+
+\begin_layout LyX-Code
+# presently available).
+\end_layout
+
+\begin_layout LyX-Code
+# 0 = Linear strain
+\end_layout
+
+\begin_layout LyX-Code
+# 1 = Large strain but use only linear contribution to the
+\end_layout
+
+\begin_layout LyX-Code
+# stiffness matrix (sometimes results in better convergence)
+\end_layout
+
+\begin_layout LyX-Code
+# 2 = Large strain and use nonlinear contribution to the
+\end_layout
+
+\begin_layout LyX-Code
+# stiffness matrix
+\end_layout
+
+\begin_layout LyX-Code
+# (8) Convergence tolerance for displacements (dimensionless value)
+\end_layout
+
+\begin_layout LyX-Code
+# (9) Convergence tolerance for forces (dimensionless value)
+\end_layout
+
+\begin_layout LyX-Code
+# (10) Convergence tolerance for energy (dimensionless value)
+\end_layout
+
+\begin_layout LyX-Code
+# (11) Maximum number of equilibrium iterations
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+ 0 1 0.0 5.0e-01 1001 4 0 1.0e+00 1.0e+0 1.0e+00 1
+\end_layout
+
+\begin_layout LyX-Code
+ 1 100 0.1 5.0e-01 1001 -1 0 1.0e+00 1.0e+0 1.0e+00 1
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+\color black
+xx.time
+\family default
+\color default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+xx.prop
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.prop
+\family default
+ file specifies the properties for each material model in the problem.
+\end_layout
+
+\begin_layout Quote
+
+\series bold
+\color red
+Warning:
+\series default
+\color default
+ The materials must be listed in order according to the material number
+ assigned to the elements in
+\family typewriter
+xx.connect.
+
+\family default
+
+\end_layout
+
+\begin_layout LyX-Code
+# File containing material properties.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# The material type and material property values are specified using a
+\end_layout
+
+\begin_layout LyX-Code
+# "keyword = value" syntax.
+ The keywords for the different material
+\end_layout
+
+\begin_layout LyX-Code
+# types are given below.
+ Units for each of the values with dimensions
+\end_layout
+
+\begin_layout LyX-Code
+# must follow the value as illustrated in the examples below.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Materials and keywords:
+\end_layout
+
+\begin_layout LyX-Code
+# Isotropic linear elastic
+\end_layout
+
+\begin_layout LyX-Code
+# materialType ='IsotropicLinearElastic'
+\end_layout
+
+\begin_layout LyX-Code
+# density
+\end_layout
+
+\begin_layout LyX-Code
+# youngsModulus
+\end_layout
+
+\begin_layout LyX-Code
+# poissonsRatio
+\end_layout
+
+\begin_layout LyX-Code
+# endMaterial ='True' (flag indicating end of material)
+\end_layout
+
+\begin_layout LyX-Code
+# Isotropic linear maxwell viscoelastic
+\end_layout
+
+\begin_layout LyX-Code
+# materialType ='IsotropicLinearMaxwellViscoelastic'
+\end_layout
+
+\begin_layout LyX-Code
+# density
+\end_layout
+
+\begin_layout LyX-Code
+# youngsModulus
+\end_layout
+
+\begin_layout LyX-Code
+# poissonsRatio
+\end_layout
+
+\begin_layout LyX-Code
+# viscosity
+\end_layout
+
+\begin_layout LyX-Code
+# endMaterial ='True' (flag indicating end of material)
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Material number 1
+\end_layout
+
+\begin_layout LyX-Code
+materialType = 'IsotropicLinearMaxwellViscoelastic'
+\end_layout
+
+\begin_layout LyX-Code
+density = 3000.0*kg/m**3
+\end_layout
+
+\begin_layout LyX-Code
+youngsModulus = 7.5e10*Pa
+\end_layout
+
+\begin_layout LyX-Code
+poissonsRatio = 0.25
+\end_layout
+
+\begin_layout LyX-Code
+viscosity = 1.0e+18*Pa*s
+\end_layout
+
+\begin_layout LyX-Code
+endMaterial = True
+\end_layout
+
+\begin_layout LyX-Code
+# Material number 2
+\end_layout
+
+\begin_layout LyX-Code
+materialType = 'IsotropicLinearElastic'
+\end_layout
+
+\begin_layout LyX-Code
+density = 3000.0*kg/m**3
+\end_layout
+
+\begin_layout LyX-Code
+youngsModulus = 7.5e10*Pa
+\end_layout
+
+\begin_layout LyX-Code
+poissonsRatio = 0.25
+\end_layout
+
+\begin_layout LyX-Code
+endMaterial = True
+\end_layout
+
+\begin_layout LyX-Code
+# Material number 3
+\end_layout
+
+\begin_layout LyX-Code
+materialType = 'IsotropicLinearMaxwellViscoelastic'
+\end_layout
+
+\begin_layout LyX-Code
+density = 3000.0*kg/m**3
+\end_layout
+
+\begin_layout LyX-Code
+youngsModulus = 7.5e10*Pa
+\end_layout
+
+\begin_layout LyX-Code
+poissonsRatio = 0.25
+\end_layout
+
+\begin_layout LyX-Code
+viscosity = 1.0e+18*Pa*s
+\end_layout
+
+\begin_layout LyX-Code
+endMaterial = True
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement htbp
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.prop
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+xx.statevar
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.statevar
+\family default
+ file specifies which state variables are to be included in the output of
+ the elastic and time dependent solutions.
+\end_layout
+
+\begin_layout LyX-Code
+# File specifying which state variables to output.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# State variables occur in groups of 6, corresponding to the number of
+\end_layout
+
+\begin_layout LyX-Code
+# stress/strain components.
+ The present groups are:
+\end_layout
+
+\begin_layout LyX-Code
+# 1-6: Cauchy stress
+\end_layout
+
+\begin_layout LyX-Code
+# 7-12: Total strain
+\end_layout
+
+\begin_layout LyX-Code
+# 13-18: Viscous strain
+\end_layout
+
+\begin_layout LyX-Code
+# 18-24: Plastic strain
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Lines:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Total accumulated values for the current time step
+\end_layout
+
+\begin_layout LyX-Code
+# (2) Incremental values (previous to current)
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Rate values (previous to current)
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns (per line):
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Number of state variables to output (0 ≤ value ≤ 24)
+\end_layout
+
+\begin_layout LyX-Code
+# (2)+ State variable number to output (1 ≤ value ≤ 24)
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+ 12 1 2 3 4 5 6 7 8 9 10 11 12
+\end_layout
+
+\begin_layout LyX-Code
+ 12 1 2 3 4 5 6 7 8 9 10 11 12
+\end_layout
+
+\begin_layout LyX-Code
+ 0
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.statevar
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+xx.split
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.split
+\family default
+ file specifies the split node information for modeling dislocations.
+ Dislocations may be used in simulating slip on faults as well as dike intrusion
+s.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing time stepping parameters.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Displacements are specified for each vertex on the fault for each
+\end_layout
+
+\begin_layout LyX-Code
+# element containing the vertex.
+ The displacements on each side of the
+\end_layout
+
+\begin_layout LyX-Code
+# fault or dike should have opposite signs.
+ The displacements
+\end_layout
+
+\begin_layout LyX-Code
+# associated with a single side of the fault for each vertex should be
+\end_layout
+
+\begin_layout LyX-Code
+# the same.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Element number
+\end_layout
+
+\begin_layout LyX-Code
+# (2) Vertex number
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Time history flag
+\end_layout
+
+\begin_layout LyX-Code
+# 0 = Slip only in elastic solution
+\end_layout
+
+\begin_layout LyX-Code
+# -1 = Slip at constant velocity
+\end_layout
+
+\begin_layout LyX-Code
+# n = Slip according to load history n (requires xx.hist file)
+\end_layout
+
+\begin_layout LyX-Code
+# (4) Displacement in x direction
+\end_layout
+
+\begin_layout LyX-Code
+# (5) Displacement in y direction
+\end_layout
+
+\begin_layout LyX-Code
+# (6) Displacement in z direction
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+ 14886 36 0 0.353500000 0.00000000 -0.353500000
+\end_layout
+
+\begin_layout LyX-Code
+ 14887 36 0 0.353500000 0.00000000 -0.353500000
+\end_layout
+
+\begin_layout LyX-Code
+ 14896 36 0 -0.353500000 0.00000000 0.353500000
+\end_layout
+
+\begin_layout LyX-Code
+ 14981 36 0 -0.353500000 0.00000000 0.353500000
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.split
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+xx.fuldat
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.fuldat
+\family default
+ file lists the time step numbers at which full output is desired.
+ The elastic solution (time step 0) is always included in the output.
+ This file is required for time-dependent problems.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing time steps at which full output is desired.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Note: Time step 0 (elastic solution) is always included in the
+\end_layout
+
+\begin_layout LyX-Code
+# output.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# List the time steps, one per line.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+ 10
+\end_layout
+
+\begin_layout LyX-Code
+ 50
+\end_layout
+
+\begin_layout LyX-Code
+ 100
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.fuldat
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.skew
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.skew
+\family default
+ file specifies local coordinate systems for nodes.
+ The local coordinate system is specified using two Euler angles that rotate
+ the local coordinate system to the global coordinate system.
+\end_layout
+
+\begin_layout Standard
+The applied coordinate rotations apply to all boundary conditions associated
+ with the nodes listed in the file.
+ These are useful, for example, if it is desired to apply boundary conditions
+ in a direction normal or tangential to a side of the mesh when the side
+ does not align with the global coordinate directions.
+ Similarly, skew conditions could be used when specifying slip on a fault
+ that lies at an angle to the global coordinates.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing local nodal coordinates.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# First, specify units for rotations.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+rotation_units = degree
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Node number
+\end_layout
+
+\begin_layout LyX-Code
+# (2) Euler angle for rotation in the x-y plane
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Euler angle for rotation in the x-z plane
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+68 12.3 4.2
+\end_layout
+
+\begin_layout LyX-Code
+132 -12.3 -4.2
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.skew
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.keyval
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.keyval
+\family default
+ file specifies some simple parameter settings.
+\end_layout
+
+\begin_layout Subsubsection
+Winkler forces
+\end_layout
+
+\begin_layout Standard
+Scaling factors can be applied to Winkler forces, permitting a quick and
+ easy way to change the density or gravitational acceleration when Winkler
+ forces are used to simulate gravity.
+\end_layout
+
+\begin_layout Paragraph
+Quadrature order
+\end_layout
+
+\begin_layout Description
+Full Quadrature order that should give the exact element matrices when the
+ elements are geometrically undistorted.
+
+\end_layout
+
+\begin_layout Description
+Reduced Quadrature order that is one order less than full quadrature.
+ Note that for linear tetrahedra full and reduced quadrature are equivalent
+ (single integration point).
+\end_layout
+
+\begin_deeper
+\begin_layout Quote
+
+\series bold
+\color red
+Warning:
+\series default
+\color default
+Use with caution as reduced quadrature can lead to numerical instabilities.
+
+\end_layout
+
+\end_deeper
+\begin_layout Description
+Selective Uses Hughes' b-bar formulation to perform reduced quadrature on
+ the dilatational parts of the strain-displacement matrix.
+ This can be useful in nearly-incompressible problems.
+
+\end_layout
+
+\begin_layout Paragraph
+Prestresses
+\end_layout
+
+\begin_layout Standard
+Gravitational prestresses can be computed automatically.
+ In such cases, the elastic properties in the prestress calculation can
+ be set to uniform values independent of the parameters for any of the material
+ models.
+ When gravity is being used and prestresses are not computed automatically,
+ each prestress component can be scaled independently.
+ Reading prestresses from files is presently disabled.
+\end_layout
+
+\begin_layout LyX-Code
+# Simple parameter values for various PyLith settings.
+ Defaults are
+\end_layout
+
+\begin_layout LyX-Code
+# listed.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Scaling factors applied to Winkler forces.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+winklerScaleX = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+winklerScaleY = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+winklerScaleZ = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Scaling factors applied to differential Winkler forces.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+winklerSlipScaleX = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+winklerSlipScaleY = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+winklerSlipScaleZ = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Stress integration and numerical computation of the tangent
+\end_layout
+
+\begin_layout LyX-Code
+# material matrix.
+ Default values should be reasonable for most cases.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+stressTolerance = 1.0e-12*Pa
+\end_layout
+
+\begin_layout LyX-Code
+minimumStrainPerturbation = 1.0e-7
+\end_layout
+
+\begin_layout LyX-Code
+initialStrainPerturbation = 1.0e-1
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Specify whether to use the solution from the previous time step as
+\end_layout
+
+\begin_layout LyX-Code
+# the starting guess for the elastic solution in the current time step.
+\end_layout
+
+\begin_layout LyX-Code
+# This feature has not been tested.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+usePreviousDisplacementFlag = 0
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Quadrature order for the problem.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+quadratureOrder = "Full"
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Gravitational acceleration in each direction.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+gravityX = 0.0*m/(s*s)
+\end_layout
+
+\begin_layout LyX-Code
+gravityY = 0.0*m/(s*s)
+\end_layout
+
+\begin_layout LyX-Code
+gravityZ = 0.0*m/(s*s)
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Factors controlling computation of prestresses.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+prestressAutoCompute = False
+\end_layout
+
+\begin_layout LyX-Code
+prestressAutoChangeElasticProperties = False
+\end_layout
+
+\begin_layout LyX-Code
+prestressAutoComputePoisson = 0.49
+\end_layout
+
+\begin_layout LyX-Code
+prestressAutoComputeYoungs = 1.0e30*Pa
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+prestressScaleXx = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+prestressScaleYy = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+prestressScaleZz = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+prestressScaleXy = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+prestressScaleXz = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+prestressScaleYz = 1.0
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Unit numbers used in Fortran code.
+ These defaults should work for
+\end_layout
+
+\begin_layout LyX-Code
+# most Unix systems, but may be altered if necessary.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+f77StandardInput = 5
+\end_layout
+
+\begin_layout LyX-Code
+f77StandardOutput = 6
+\end_layout
+
+\begin_layout LyX-Code
+f77FileInput = 10
+\end_layout
+
+\begin_layout LyX-Code
+f77AsciiOutput = 11
+\end_layout
+
+\begin_layout LyX-Code
+f77PlotOutput = 12
+\end_layout
+
+\begin_layout LyX-Code
+f77UcdOutput = 13
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+\color black
+xx.keyval
+\family default
+\color default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+\color black
+xx.hist
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.hist
+\family default
+ files provide time histories for use in boundary conditions.
+\end_layout
+
+\begin_layout LyX-Code
+# File specifying time variation of boundary conditions.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Each time history consists of two or more lines.
+ The first line
+\end_layout
+
+\begin_layout LyX-Code
+# indicates the number of points in the history and the default load
+\end_layout
+
+\begin_layout LyX-Code
+# value for the history.
+ Subsequent lines define time/load pairs.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Line 1, column 1: The number of points in the time history
+\end_layout
+
+\begin_layout LyX-Code
+# Line 1, column 2: The value assigned to every point by default
+\end_layout
+
+\begin_layout LyX-Code
+# (overridden by values in time history)
+\end_layout
+
+\begin_layout LyX-Code
+# Line 2+, column 1: Time (in seconds) for a given load value
+\end_layout
+
+\begin_layout LyX-Code
+# Line 2+, column 2: Load value at given time
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+ 2 1.0
+\end_layout
+
+\begin_layout LyX-Code
+2.84014e+08 0.1
+\end_layout
+
+\begin_layout LyX-Code
+3.15576e+08 0.5
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.hist
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+
+\family typewriter
+\size normal
+xx.wink
+\end_layout
+
+\begin_layout Standard
+The
+\family typewriter
+xx.wink
+\family default
+ file specifies Winkler elements, which may be used as spring foundations
+ in the simulation of gravity.
+\end_layout
+
+\begin_layout LyX-Code
+# File containing Winkler elements.
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Comment lines begin with '#'
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Flags for the degrees of freedom can have the following values:
+\end_layout
+
+\begin_layout LyX-Code
+# 0 = no Winkler force
+\end_layout
+
+\begin_layout LyX-Code
+# 1 = Winkler force applied at all times
+\end_layout
+
+\begin_layout LyX-Code
+# -n = Winkler force applied according to load history n
+\end_layout
+
+\begin_layout LyX-Code
+# (requires xx.hist file)
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+# Columns:
+\end_layout
+
+\begin_layout LyX-Code
+# (1) Vertex number
+\end_layout
+
+\begin_layout LyX-Code
+# (2) Flag for DOF in x-direction
+\end_layout
+
+\begin_layout LyX-Code
+# (3) Flag for DOF in y-direction
+\end_layout
+
+\begin_layout LyX-Code
+# (4) Flag for DOF in z-direction
+\end_layout
+
+\begin_layout LyX-Code
+# (5) Magnitude of restoring force for x-direction
+\end_layout
+
+\begin_layout LyX-Code
+# (6) Magnitude of restoring force for x-direction
+\end_layout
+
+\begin_layout LyX-Code
+# (7) Magnitude of restoring force for x-direction
+\end_layout
+
+\begin_layout LyX-Code
+#
+\end_layout
+
+\begin_layout LyX-Code
+14 0 -1 0 0.0e+00 1.0e+25 0.0e+00
+\end_layout
+
+\begin_layout LyX-Code
+18 0 1 0 1.0e+20 0.0e+00 0.0e+00
+\end_layout
+
+\begin_layout Standard
+\begin_inset Float figure
+placement H
+wide false
+sideways false
+status open
+
+\begin_layout Caption
+Format of
+\family typewriter
+xx.wink
+\family default
+ files.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document
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