input_schmiddu.txt

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!             Input file for DOUAR-WSMP version 0.3 - 07/08/2013               |
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This file is read by two subroutines in the code:
- read_controlling_parameters
- read_input_file
The indications between [] indicate the type of the read parameter. It can be
an integer [int], a real*8 [dp], a character chain [char] or a boolean [bool].


CONTROLLING PARAMETERS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]debug is a parameter that switches on/off various prints and outputs
(the level of printing for error, warning and messages of the solver id%cntl(4)
is set to the debug value).
if debug is zero, no debugging 
if debug is equal to one, this triggers the terminal display of some key
parameters 
if debug is equal to two, same as debug equal to one, and the code produces
various vtk files in the DEBUG subdirectories (surfaces, olsf, ...), as well as
cross sections for all nonlinear iterations. Careful, memory consuming!

      debug = 1

[bool]doDoRuRe is a flag that triggers the production of output files needed to
produce the DoRuRes. DoRuRe stands for 'Douar Run Report'. 

      doDoRuRe = F

[bool]compute_qp_gram triggers the production of qpgrams for every grid.

      compute_qpgram = F


SAVING
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-
The current output file is always kept temporarily and deleted after the next
output file was written. When time equals n*savstep + savoffset the files are
kept permanently.

[int] savoffset is the timestep from which on output will be saved

      savoffset = 1

[int] every savstep'th value after savoffset will be saved

      savstep = 2

RESTART
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]irestart is a restart flag; if irestart is not 0, the run will restart from
an output file given by [char]restartfile and at step.

      irestart = 2

      restartfile = OUT/time_0002.bin


SPINUP PHASE
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-
The spinup phase values will be used during the initial nstep_spinup steps of a
DOUAR run. These values will overrule the values given in later sections as long
as the current DOUAR step is less than or equal to nstep_spinup. Note that if
nstep_spinup is less than 1, these values will not be used. The values that are
currently supported for the general spinup phase are: dt_spinup,
griditer_spinup, nonlinear_iterations_spinup, and tol_spinup. Also note that
spinup phase variables that apply to the material, surface or cloud definitions
are given in their respective definition sections.

[int]nstep_spinup is the number of steps used for the spinup phase

      nstep_spinup = 4

[dp]dt is the time step length (if dt is negative, courant conidition is used
and automatic time stepping is turned on)

      dt_spinup = 1.03125d-05

[int]griditer is a flag that allows for nonlinear iterations; when positive, a
fixed number (griditer) of iterations is permitted; when negative, the number of
nonlinear iterations is determined by a convergence criterion.

      griditer_spinup = -10

[int]nonlinear_iterations is the maximum number of nonlinear iterations (i.e.
the iterations on a given constant grid)
if nonlinear_iterations is positive, it simply is the number of nonlinear
iterations performed for each grid. When negative it indicates an upper bound
of nonlinear iterations, but the actual number of nonlinear iterations is
determined by a convergence criterion (see the 'tol' parameter)

      nonlinear_iterations_spinup = -100

[dp]tol_spinup is the tolerance used to estimate convergence on the computed
velocity field during the spinup phase. Note that an adaptive tolerance cannot
be used during the spinup phase.

      tol_spinup = 0.01d0

[bool]sstemp_spinup is a flag for whether a steady-state thermal calculation
should be performed during the spinup phase iterations. If true, a uniform
viscosity value should be provided for the first time step using the option
sstemp_viscosity_spinup below.

      sstemp_spinup = T

[dp]sstemp_viscosity_spinup is a reference linear viscosity value to be used for
all materials during the first time step of the spinup phase when calculating a
steady-state thermal field.  This is done to ensure the first calculation
using temperature-dependent material properties considers thermal advection and
diffusion with an approximation of the velocity field in the nonlinear case. If
negative, this value will be ignored and the normal material properties will be
used.

      sstemp_viscosity_spinup = 3.82368d-04

[dp]sstemp_penalty_spinup is the penalty factor that corresponds to use of the
sstemp_viscosity_spinup above. A value of 1.d8 is recommended.

      sstemp_penalty_spinup = 1.d8

[bool]all_surf_fixed_spinup is a flag to fix all surface positions during the
spinup phase. Individual surface positions can be fixed in the section below for
surface definitions. If true, this option will override the option to fix
individual surfaces.

      all_surf_fixed_spinup = T

[bool]fixed_cloud_spinup is a flag to skip the update of the cloud particle
positions during the spinup phase. If true, cloud particles positions will not
be updated.

      fixed_cloud_spinup = F


TIMESTEPPING
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[dp]dt is the time step length (if dt is negative, courant conidition is used
and automatic time stepping is turned on)

      dt = 1.03125d-03

[int]nstep is the number of time steps

      nstep = 205

[dp]courant is only used when dt is negative; it determines the size of the time
step from the maximum value of the velocity field amplitude. The time step s
the product of courant by the ratio of the smallest leaf size by the maximum
velocity.

      courant = .5d0

[bool]normaladvect is a flag used to determine which algorithm to use to
calculate the new geoletry of the normals to the surfaces at the nodes on the
surfaces
if normaladvect is T, the normals are advected using the velocity gradient
if normaladvect is F, the normals are re-computed from the geometry of the
surface

      normaladvect = T


GRID ITERATIONS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]griditer is a flag that allows for nonlinear iterations; when positive, a
fixed number (griditer) of iterations is permitted; when negative, the number of
nonlinear iterations is determined by a convergence criterion.

      griditer = -100

[dp]octree_refine_ratio is the threshold value used to determine whether the
octree has converged or not. the larger the value, the less stringent the test.

      octree_refine_ratio = .025d0


NONLINEAR ITERATIONS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]nonlinear_iterations is the maximum number of nonlinear iterations (i.e.
the iterations on a given constant grid)
if nonlinear_iterations is positive, it simply is the number of nonlinear
iterations performed for each grid. When negative it indicates an upper bound
of nonlinear iterations, but the actual number of nonlinear iterations is
determined by a convergence criterion (see the 'tol' parameter)

      nonlinear_iterations = -100

[int]nb_iter_nl_min is the number of nonlinear iterations required for velocity
convergence when using the convergence criterion tolerance value below. Note
that this is different than simply requiring a given number of nonlinear
iterations as the velocity field must also be converged within the tolerance
below.

      nb_iter_nl_min = 0 

[dp]tol is the relative tolerance used to estimate convergence on the computed
velocity field

      tol = 0.01d0

[bool]adaptive_tol is a flag that toggles on/off the evolution of the tol
parameter with the grid level: when velocity convergence is reached on a grid,
the latest meaure of the velocity difference between the two last obtained
solutions is put in tol, so that on the following generated grid, the solution
reaches at least the same level of convergence. It allows to start with a not
too stringent value of tol at uniform octree level that evolves with every
grid, assuming that increasing the level of refinement of the octree allows to
better capture the solution, hence allowing a tighter convergence. 

      adaptive_tol = F


OCTREES
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]leveluniform_oct is the level of uniform discretization of space; note that
a level is a power of two used to divide the unit cube

      leveluniform_oct = 5

[int]levelmax_oct is maximum level of octree discretization

      levelmax_oct = 6

[double]vex is the vertical exaggeration scaling factor that allows for
variable aspect ratio elements. The value should range between 0-1, which
will be multiplied by the vertical scale of the model domain. For example, a
value of 0.25 would correspond to a model of dimensions 1x1x0.25, where the
elements are 1/4 as tall as they are wide. NOTE: vex MUST be larger than the
highest surface/element in the model at all times.

      vex = 0.25d0

[bool]ismooth is a flag to impose an additional level of smoothing after
refinement for the surfaces and strain rate. It ensures that no leaf is flanked
by other leaves differing by more than 1 level of refinement

      ismooth = F

[int]noctreemax is the maximum size of any octree used in all computations

      noctreemax = 10000000

[dp]refine_ratio is used to determine octree refinement based on a given
criterion. All leaves where the criterion is larger than refine_ratio times the
maximum of this criterion are refined 

      refine_ratio = -5500

[int]refine_criterion determines which refinement algorithm is to be used.
Several criteria exist for the refinement of the osolve octree. 1 is the second 
invariant of the deviatoric strain-rate tensor; 2 is the sum of the squares of
the diagonal terms of the deviatoric strain-rate tensor; 3 is the second
invariant of the deviatoric strain rate tensor timses the leaf size. any other
value sets the criterion to zero and leads to no refinement. 

      refine_criterion = 0

[int]initial_refine_level is the initial level at which the refinement of the
octree will be performed. it has to be smaller than levelmax_oct
this should be used (different from levelmax_oct) in case the flow is very 
localized (nonlinear/plastic analysis)

      initial_refine_level = 5

[bool]renumber_nodes is a flag that can toggle on/off the renumbering of the
nodes by mean of Sloan's algorithm (T/F)

      renumber_nodes = T


NESTED MODEL PARAMETERS (Ignored if nest = F)
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[bool]nest is the flag that determines whether this model should run as a nested
version within a larger scale model

      nest = F

[char]ssoutdir is the directory where the nest output should be written (no more
than 5 characters)

      ssoutdir = SSOUT

[char]lsoutfile is the file that is read to define the velocity B/Cs for the
nest (i.e., the model output in which the nest is embedded, not necessarily the
full scale (L'=1) model).

      lsoutfile = OUT/time_0001.bin

[dp]sselemx, sselemy and sselemz are the ratios of the size of the elements in
the nest in the x, y and z directions, relative to the larger scale model (which
again does not need to be the full scale (L'=1) model).

      sselemx = 0.5d0
      sselemy = 0.5d0
      sselemz = 0.5d0

[dp]xminls, yminls and zminls denote the location of the origin of the nested
model within the large scale reference model

      xminls = 0.25d0
      yminls = 0.25d0
      zminls = 0.109375d0

[dp]sselemx0, sselemy0 and sselemz0 are the ratios of the size of the elements
in the nest in the x, y and z directions, relative to the FULL scale model (that
for which L'=1). This is only used for rescaling the output values for VTK
visualization.

      sselemx0 = 0.5d0
      sselemy0 = 0.5d0
      sselemz0 = 0.5d0


BOUNDARY CONDITIONS AND VELOCITY CONSTRAINTS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[bool]2d_invariants forces the calculation of the strain rate tensor invariants
to two dimensions. This assumes no strain in the y direction, and sets eyy, exy
and eyz to zero.

      invariants_2d = F

[bool]damp_surface suppresses oscillations of interfaces with a density
contrast using the method described in Kaus et al., 2010 (PEPI). When enabled,
this allows the user to use a time step (dt) that is 20-100x longer.

      damp_surface = T

[dp]damp_factor is a scaling factor applied to the surface damping. A factor of
0 will disable surface damping, while a factor of 1 will use full damping.
Intermediate values will provide partial damping.

      damp_factor = 0.5d0

[char]bctype is a parameter that selects the type of boundary condition that
will be applied in the simulation. The names of the types are listed below and
described in detail in the user's guide. The current available bctypes are:
basic, 2Dpunch, 2D_punch_vert, 3D_punch,folding, jgr, model1, nest,
parallipipede, pipo, riedel, ritske, ritske_isurf, segmented_s-line, sphere,
subduction

Types requiring additional input values are listed below.

- basic            -> Basic velocity boundary conditions specified for each face
                   -> [char]bcorder is the order in which to apply the boundary
                      conditions to the faces ('xyz', 'xzy', 'yxz', 'yzx',
                      'zxy', or 'zyx'). For example, 'xyz' would corresponding
                      to applying the velocity B/Cs on the faces at x=0 and x=1
                      first, then at y=0 and y=1, then at z=0 and z=1.
                   -> [bool]fix(u,v,w)(x,y,z)(0,1) are the flags for whether the
                      given velocity component should be fixed (T) or free (F)
                      along the given face. For example, fixux0 = T would apply
                      the specified velocity constraint for the x-component (u)
                      at x=0.
                   -> [dp](u,v,w)(x,y,z)(0,1) are the component velocities to be
                      applied along the faces. For example, ux0 = 1.d0 would
                      apply a velocity of 1.0 in the x-direction (u) on the face
                      at x=0.
                   -> [dp](u,v)trans are translation velocities that can be
                      applied to all boundary conditions in either the x- (u) or
                      y- (v) directions. For example, utrans = -1.d0 would
                      subtract 1.0 from all u component velocities along all
                      faces.

- segmented_s_line -> S-line geometry split into 3 segments
                   -> [dp]bc_param1 is l, the height of the Moho above the model
                      base
                   -> [dp]bc_param2 is phi, the subduction angle
                   -> [dp]bc_param3 is theta, the angle of the oblique segment
                      relative to the normal segments
                   -> [dp]bc_param4 is xsym, the middle of oblique segment along
                      the x-axis
                   -> [dp]bc_param5 is ystart, the width of 'padding' along
                      the y-axis
                   -> [dp]bc_param6 is yend, the end of the oblique segment
                      along the y-axis
                   -> [dp]bc_param7 is ymax, the x-width of the applied BCs
                   -> [dp]bc_param8 vin, the scaling factor for all velocity BCs
                   -> [dp]bc_param9 is nelemx the number of elements across
                      which to spread the velocity BCs on the x=0 face
                   -> [dp]bc_param10 is nelemz the number of elements across
                      which to spread the velocity BCs on the z=0 face
                   -> [dp]bc_param11 is uextra, an additional velocity in the x
                      direction, added to influx velocity, vin
                   -> [dp]bc_param12 is vextra, an additional velocity in the y
                      direction, currently not implemented
                   -> [dp](u,v)trans are translation velocities that can be
                      applied to all boundary conditions in either the x- (u) or
                      y- (v) directions. For example, utrans = -1.d0 would
                      subtract 1.0 from all u component velocities along all
                      faces.

- segmented_s_line_round
                   -> S-line geometry split into 3 segments with one rounded end
                   -> [dp]bc_param1 is l, the height of the Moho above the model
                      base
                   -> [dp]bc_param2 is phi, the subduction angle
                   -> [dp]bc_param3 is theta, the angle of the oblique segment
                      relative to the normal segments
                   -> [dp]bc_param4 is xsym, the middle of oblique segment along
                      the x-axis
                   -> [dp]bc_param5 is ystart, the width of 'padding' along
                      the y-axis
                   -> [dp]bc_param6 is yend, the end of the oblique segment
                      along the y-axis
                   -> [dp]bc_param7 is ymax, the x-width of the applied BCs
                   -> [dp]bc_param8 vin, the scaling factor for all velocity BCs
                   -> [dp]bc_param9 is nelemx the number of elements across
                      which to spread the velocity BCs on the x=0 face
                   -> [dp]bc_param10 is nelemz the number of elements across
                      which to spread the velocity BCs on the z=0 face
                   -> [dp]bc_param11 is uextra, an additional velocity in the x
                      direction, added to influx velocity, vin
                   -> [dp]bc_param12 is vextra, an additional velocity in the y
                      direction, currently not implemented
                   -> [dp]bc_param13 is arcradius, the radius of the arcuate end
                      of the rounded boundary velocities
                   -> [dp](u,v)trans are translation velocities that can be
                      applied to all boundary conditions in either the x- (u) or
                      y- (v) directions. For example, utrans = -1.d0 would
                      subtract 1.0 from all u component velocities along all
                      faces.

- rot_subduction   
    -> upper section of a downwards rotating squashed sphere or cylinder 
        (rotation around the -y-axis) 
    -> [dp]bc_param1 is y0 the center of the rotating element 
    -> [dp]bc_param2 is h, the maximum height of the rotating element influx 
        within element will be mass-balanced by bottom outflux 
    -> [dp]bc_param3 is rx, the x-width of the rotating element 
    -> [dp]bc_param4 is wy, the y-width of the rotating element.  wy>0 will 
        produce a squashed sphere, wy<0 a cylinder 
    -> [dp]bc_param5 is vin, velocity of the rotating element at (0,y0,h) 
    -> [dp]bc_param6 is vtop, the velocity of influx above the rotating 
        element (ususally vin)
    -> [dp]bc_param7 is vback, the velocity at the rights side and along the
        other parts of bottom and left side NOTE: measured in -y direction 
    -> [dp]bc_param8 is nelemx the number of elements across which to spread 
        the velocity BCs in x- or y-direction 
    -> [dp]bc_param9 is nelemz the number of elements across which to spread 
        the velocity BCs on the z-direction 
    -> [dp]bc_param10 is tempcase, the selection for temperature boundary 
           conditions at the base 
            0: uniform temperature 
            1: overall gradient from temp2 at x=0 to tepmscale at x=1
            2: uniform temp2 for indenter footprint, tempscale elsewhere
            3: gradient from tempscale at x=0 to temp2 at x=rx within the 
               indenter footprint, tempscale elsewhere
            4: gradient from tempscale at x=0 to temp2 at the edge of the 
               rotating element, tempscale elsewhere
            5: radial gradient from tempscale at (x=0,y=y0) to temp 2 at the 
               edge of the indenter, tempscale elsewhere
    -> [dp]bc_param11 is temp2 in Celsius and should be less than tempscale
    -> [dp]bc_param12 is strictflow, set to 1 for strictly horizontal flow 
        at x=1, y=0 and y=1 faces.
    -> [dp]bc_param13 is indomain, for setting temperature and velocity inside
        the indenter directly:
            0: no restriction
            1: Velocity set to rotation with vin at ridge
            2: Temperature set to temp2 for entire indenter
            3: 1&2 combined: both temperature and velocity prescribed

- rot_sub_init   
    -> temperature initialisation for rot_subduction boundary conditions
    -> [dp]bc_param1 to 5: As in rot_subduction
    -> [dp]bc_param6 is shellwidth, the width of unconstrained velocity and
	   temperature above the indenter
    -> [dp]bc_param7 is tempcase, for selecting the geotherm at x=0
           0: linear temperature gradient
           1: "typical" geotherm after R. Bendick simulations
    -> [dp]bc_param8 is nl_heat, the nonlinear geotherm component in Kelvin.
           Compute by hr^2*Q/k_T with Q the heat source at the surface
           and k_T the average thermal conductivity.
    -> [dp]bc_param9 is hr, the exponential decay length of heat source
           concentration.

- iso_only         -> Applies zero displacement boundary conditions to all faces
                      and dynamically calculates an initial optimal time step
                      for isostatic compensation of the model geometry. NOTE:
                      This option modifies params%dt and params%nstep, and uses
                      the spinup parameters/materials.
                   -> [dp]bc_param1 is the maximum allowable velocity for
                      isostatic compensation. The recommended value is 1.0.


      bctype = rot_subduction 

      bc_param1 = 5.00000d-01
      bc_param2 = 7.50000d-02
      bc_param3 = 5.00000d-01
      bc_param4 = 3.75000d-01
      bc_param5 = 0.00000d+00
      bc_param6 = 0.00000d+00
      bc_param7 = 0.00000d+00
      bc_param8 = 3d+00
      bc_param9 = 5d+00
      bc_param10 = 2
      bc_param11 = 8.00000d+02
      bc_param12 = 0
 

PRESSURE
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]smoothing_type is a parameter allows to choose which type of smoothing is
to be applied to the pressure field: 0 is none, 1 is center->nodes->center, 2 is
the same, but weighted by neighbouring elemental volumes, 3 is regular grid+SPH,
and 4 is SPH.  

      smoothing_type = 1

[dp]pressure0 is the pressure value used to initialize the pressure field
prior to any dynamic pressure calculations. The suggested value is the
lithostatic pressure at half the thickness of the model. NOTE: This value
should be given as a postive number, which will be converted to a negative
value to be consistent with the engineering pressure sign convention used in
DOUAR (where compression is negative).

      pressure0 = 4.89697d-02
      
[dp]plastic_stress_min is the minimum allowable yield stress used in the
pressure-dependent plasticity calculations. If plastic_stress_min is positive,
this value will be used. If negative, the code will operate as it did in v0.1
and earlier.

      plastic_stress_min = 3.86124d-05


CLOUD
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]npmin and [int]npmax are used to update the 3D volumetric cloud. npmin
corresponds to the minimum number of particles in any leaf; npmax is the maximum
allowable number in any leaf

      npmin = 1
      npmax = 4

[bool]gridcloud is a flag for whether particle injection to form the cloud
should occur randomly (F) or on a regularly spaced grid (T). The default is for
random injection, as was previously done in DOUAR.

      gridcloud = F

[bool]centerptcloud is a flag for whether a particle should be placed at the
center of each element when using gridcloud.

      centerptcloud = T

[int]clnpx, clnpy, clnpz are the numbers of particles to be injected in each
element in the x, y and z directions when using gridcloud.

      clnpx = 2
      clnpy = 2
      clnpz = 2

[bool]fixed_cloud is a flag to skip the update of the cloud particle positions
during the simulation. If true, cloud particles positions will not be updated.

      fixed_cloud = F


FEM + DIVFEM + MUMPS/WSMP
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]matrule determines the rule used to assign material properties to
elements that are cut by a surface. The default value (0) will use divFEM to
determine the element properties. A value of 1 will assign the properties of
the material that occupies the majority of the element, whereas a value of 2
will assign the properties of the volumetric minority of the element. NOTE:
divFEM is always used for any element containing void material.

      matrule = 0

[int]levelcut is the number of levels used to estimate the volume integrals in
the divFEM algorithm for cut cells; by testing, it has been estimated that a
value of 2 is very accurate

      levelcut = 2

[int]levelapprox is the number of levels used to estimate the remaining
integrals using an improved version of Marthijn's clever algorithm, usually 3 is
plenty

      levelapprox = 3

[dp]penalty is a global penalty parameter used to impose the bad faces or
incompatible faces linear constraints

      penalty = 1.d8

[bool]excl_vol is a parameter that toggles off the assumption that lsf's are
built on top of one another

      excl_vol = F 


TEMPERATURE
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[dp] tempscale is the temperature at the base of the model in Celsius.
[bool] sstemp_on_restart is a flag allowing the user to utilize a steady-state
thermal calculation for the first time step following a restart. This option is
useful, for instance, for calculating the thermal field with a previous velocity
solution.  ztemp is the elevation where temperature = 0. In scaled units.

      calculate_temp = T

      ztemp = 1.2750d-01

      tempscale = 1100.d0

      sstemp_on_restart = F


ISOSTASY
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-
[bool]isostasy enables calculation of local isostasy with the equilibrium state
based on the initial geometry. Local isostasy will be used if this is true and
flexure is false.

      isostasy = F

[bool]flexure enables calculation of flexural isostasy using the parameters
below. Note that either local or flexural isostasy will be used, based on this
value. Both must be true for flexure to be used.

      flexure = F

[dp]elastic_plate_thickness is the thickness of the elastic plate used in the
flexural isostasy calculation, in meters (?)

      elastic_plate_thickness = 20.d3

[dp]density_difference is the difference in density between the crust and mantle
in ??? I believe this is abs(rhoc-rhom)*g. (kg/m^3 * m/s^2)

      density_difference = 3.d3

[bool]isobc enables modification of the velocity boundary conditions for certain
boundary condition types to account for changes in the Moho depth

      isobc = F


MATERIALS
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[int]nmat is number of materials

      nmat = 3

[int]material0 determines what is the material above the 1st surface (the free
surface) if material0 is 0 then it is the void and the properties "0" are used
for that part of the model; otherwise the material is one of the material,
comprised between 1 and nmat

      material0 = 0

[bool]materials_on_cloud is a flag to determine whether material property
assignment should be done using the surfaces and level set functions (false) or
using the material numbers assigned to the cloud particles in each element
(true)

      materials_on_cloud = F

[bool]bulkvisc determines whether the user will input a material penalty value
that scales with the shear viscosity or whether an independent bulk viscosity
will be listed. If true, the values listed for [dp]penaltyi below should be
bulk viscosity values for each material. Otherwise, the listed penalty value
will be multiplied by the shear viscosity to enforce the incompressibility
condition.

      bulkvisc = F

[bool]init_e2d determines whether an initial e2d value will be used to put
plastic materials on yield in the first time step, or whether the standard
initial material viscosity will be used. If true, an initial e2d value will be
used to ensure plastic materials behave as desired.

      init_e2d = T

[dp]e2d0 is the initial strain rate value to use if init_e2d is true. This
value will be used in only the first nonlinear iteration of the first time
step and should be in scaled DOUAR units.

      init_e2d = 2.08276d-05

[int]dommat is the number of the dominant material type. If negative, dommat is
ignored. Otherwise, if the volume of the material corresponding to the given
dommat number is greater than zero, the element material properties will be set
to the dominant material properties. When using dommat, the value should be
between 1 and nmat.

      dommat = -1

[dp]domvol is the volume of an element that must be occupied by the material
listed above (dommat) before the entire element is converted to that material.

      domvol = 0.125d0

[dp]densityi, [dp]viscosityi and [dp]penaltyi are the density, viscosity and
incompressibility used for material i; there should be nmat sets of material
properties; there should also be a nil material if material0 has been set to 0
[dp]expon is the nonlinear viscosity exponent
[dp]diffusivity is the heat diffusivity
[dp]expansion is the coefficient of thermal expansion
[dp]heat is the heat production
[char]plasticity_type is the type of plasticity
(No, vM, DPI, DPII, DPIII, DPIV, DPV, DPVI, DPVII, MC, Tresca), defined below
[char]plasticity_ss_type_coh is the type of strain softening applied to the
cohesion/yield strength
[char]plasticity_ss_type_phi is the type of strain softening applied to phi
Plasticity_ss_types:
- tot_strain       -> The accumulated incremental strain will be used (default
                      prior to adding the plasticity_ss_type option)
- strain_rate      -> The square root of the second invariant of the strain rate
                      (e2d) will be used
- step_strain_rate -> The square root of the second invariant of the strain rate
                      from the previous time step (e2dp) will be used. Note that
                      in contrast to the 'strain_rate' case, this value will NOT
                      change during iterations
- log_step_s_rate  -> The base 10 log of the square root of the second invariant
                      of the strain rate from the previous time step (e2dp) will
                      be used. As above, this value will not change during
                      iterations.
- step_srs+srh     -> The square root of the second invariant of the strain rate
                      from the previous time step (e2dp) will be used. This is
                      similar to the step_strain_rate case above, but with the
                      option for strain rate hardening/strengthening in addition
                      to strain rate softening/weakening
[dp]plasticity_XXX_params are the plasticity parameters
For the various plastic materials defined below, the associated plasticity
parameters correspond to the following, unless otherwise noted.
- [dp]plasticity_1st_param is the angle of internal friction, phi
- [dp]plasticity_2nd_param is the cohesion or yield strength
- [dp]plasticity_3rd_param is the onset value for strain softening of phi (A
  negative value for this parameter will disable strain softening of phi)
- [dp]plasticity_4th_param is the terminal value for strain softening of phi
- [dp]plasticity_5th_param is the fully strain-softened phi value
- [dp]plasticity_6th_param is the onset value for strain weakening of the
  cohesion (A negative value for this parameter will disable strain weakening of
  the cohesion)
- [dp]plasticity_7th_param is the terminal value for strain weakening of the
  cohesion/yield strength (A negative value for this parameter will disable
  strain weakening of the cohesion/yield strength)
- [dp]plasticity_7th_param is the terminal value for strain weakening of the
  cohesion/yield strength
- [dp]plasticity_8th_param is the fully strain-weakened cohesion/yield strength
- [dp]plasticity_9th_param is the onset value for strain hardening of phi (A
  negative value for this parameter will disable strain hardening of phi)
- [dp]plasticity_10th_param is the terminal value for strain hardening of phi
- [dp]plasticity_11th_param is the fully strain-hardened phi value
- [dp]plasticity_12th_param is the onset value for strain strengthening of the
  cohesion/yield strength (A negative value for this parameter will disable
  strain strengthening of the cohesion/yield strength)
- [dp]plasticity_13th_param is the terminal value for strain strengthening of
  the cohesion/yield strength
- [dp]plasticity_14th_param is the fully strain-strengthened cohesion/yield
  strength
Plasticity types:
- No    -> no plasticity, purely (nonlinear) viscous material
- vM    -> von Mises yield criterion
        -> [dp]plasticity_1st_param is the yield strength
        -> [dp]plasticity_2nd_param-plasticity_5th_param and
           plasticity_9th_param-plasticity_11th_param are NOT used
- DPI-VII-> Drucker-Prager type of yield criterion
- DPI   -> the yield locus passes through the outer apices of the Mohr-Coulomb
           hexagonal cone
- DPII  -> the yield locus passes through the inner apices of the Mohr-Coulomb
           hexagonal cone
- DPIII -> The average case, intermediate to DPI and DPII (USE ONLY FOR TESTING;
           this case can not easily be derived as a simplification of the
           Mohr-Coulomb criterion)
- DPIV  -> Plane strain Drucker-Prager formulation for associative materials
           (USE ONLY FOR TESTING)
- DPV   -> Drucker-Prager type of yield criterion that does not calculate the
           values of alpha and k from phi and c. They are specified here. Note
           that strain softening cannot be used for this DP type.
        -> [dp]plasticity_1st_param is alpha
        -> [dp]plasticity_2nd_param is k
        -> [dp]plasticity_3rd_param-plasticity_14th_param are NOT used
- DPVI  -> Drucker-Prager type of yield criterion that uses the equation below
           sigma_y = pressure * tan(phi) + c
           (USE ONLY FOR TESTING)
- DPVII -> Drucker-Prager type of yield criterion that uses the same 2D
           formulation that is used in Sopale
           sigma_y = pressure*sin(phi) + c*cos(phi)
- MC    -> Mohr-Coulomb type of yield criterion
- Tresca-> Tresca type of yield criterion
        -> [dp]plasticity_1st_param is the yield strength
        -> [dp]plasticity_2nd_param-plasticity_5th_param and
           plasticity_9th_param-plasticity_11th_param are NOT used
[dp]mattrans_[xmin,xmax,ymin,ymax,zmin,zmax] are the min/max spatial coordinates
where the material transition from the given material to material transnum,
listed below. A negative value will disable a given mattrans.
[int]transnum is the material number used when one of the above mattrans
criteria is met.

      density0 = 0.d0
      viscosity0 = 4.00017d-08
      penalty0 = 1.00000d+08
      expon0 = 4.00000d+00
      diffusivity0 = 1.00000d+00
      heat0 = 0.00000d+00
      activationenergy0 = 2.23000d+05
      fviscosity0 = 1.00000d+00
      plasticity_type0 = MC
      plasticity_ss_type_phi0 = step_strain_rate
      plasticity_ss_type_coh0 = step_strain_rate
      plasticity_1st_param0 = 1.50000d+01
      plasticity_2nd_param0 = 3.86124d-05
      plasticity_3rd_param0 = -1.00000d-01
      plasticity_4th_param0 = 1.00000d+01
      plasticity_5th_param0 = 5.00000d+00

      density1 = -8.33333d-01
      viscosity1 = 4.00017d-08
      penalty1 = 1.00000d+08
      expon1 = 4.00000d+00
      diffusivity1 = 1.79301d-03
      heat1 = 3.33826d-01 
      activationenergy1 = 2.23000d+05
      fviscosity1 = 1.00000d+00
      plasticity_type1 = MC
      plasticity_ss_type_phi1 = step_strain_rate
      plasticity_ss_type_coh1 = step_strain_rate
      plasticity_1st_param1 = 1.50000d+01
      plasticity_2nd_param1 = 3.86124d-05
      plasticity_3rd_param1 = -1.00000d-01
      plasticity_4th_param1 = 1.00000d+01
      plasticity_5th_param1 = 5.00000d+00

      density2 = -1.00000d+00
      viscosity2 = 3.82368d+04
      penalty2 = 1.00000d+08
      expon2 = 1.00000d+00
      diffusivity2 = 1.49417d-03
      heat2 = 0.00000d+00
      activationenergy2 = 0.00000d+00
      fviscosity2 = 1.00000d+00
      plasticity_type2 = MC
      plasticity_ss_type_phi2 = step_strain_rate
      plasticity_ss_type_coh2 = step_strain_rate
      plasticity_1st_param2 = 1.50000d+01
      plasticity_2nd_param2 = 3.86124d-05
      plasticity_3rd_param2 = -1.00000d-01
      plasticity_4th_param2 = 1.00000d+01
      plasticity_5th_param2 = 5.00000d+00
      density3 = -1.00000d+00
      viscosity3 = 3.82368d+09
      penalty3 = 1.00000d+08
      expon3 = 1.00000d+00
      diffusivity3 = 1.49417d-03
      heat3 = 0.00000d+00
      activationenergy3 = 0.00000d+00
      fviscosity3 = 1.00000d+00
      plasticity_type3 = MC
      plasticity_ss_type_phi3 = step_strain_rate
      plasticity_ss_type_coh3 = step_strain_rate
      plasticity_1st_param3 = 1.50000d+01
      plasticity_2nd_param3 = 3.86124d-05
      plasticity_3rd_param3 = -1.00000d-01
      plasticity_4th_param3 = 1.00000d+01
      plasticity_5th_param3 = 5.00000d+00

[dp]viscositymin and viscositymax are bounds on the viscosity (if negative bound
is not imposed) These bounds are introduced to prevent the viscosity to reach
unrealistic values, especially when using non-linear (power-law or brittle)
rheologies

      viscositymin = 3.82368d-08
      viscositymax = 3.82368d+09


SURFACES
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[bool]remove_surf_pts is a flag for whether surface nodes should be removed to
decrease their density once the pts are closer together than 4xlevelmax_oct.
Note that surface nodes will always be removed if they are advected outside of
the unit cube. Also, it is probably best to leave this false unless you have a
good reason to change it. Use surface point spreading for each surface instead.

      remove_surf_pts = F

[int]ns is number of surfaces to track

      ns = 3

for each surface, one needs to define a levelt, itype, material, surface_type,
activation_time and surface_params.
- [int]levelt is the inital level for the particles on the surface; to be
  accurate and avoid holes in the surface during definition of the lsf, one
  should use levelt eq to levelmax_oct+1 for all surfaces as a minimum value; 
- [int]itype should be 1 for foldable surfaces or 0 for nonfoldable surfaces;
- [int]closed should be 1 for closed surfaces, or 0 for all others;
- [int]surface_type is comprised between 1 and 13 with the surface parameters
  listed below for each type;
- [bool]rand is T for surfaces with random point distribution, F for surfaces
  with regularly spaced points at levelt;
- [dp]surface_param_01-surface_param_12 are the surface parameters below:
  1 corresponds to a flat surface,
    -> surface_param_01 is the z level
  2 to a rectangular emboss,
    -> surface_param_01 is the z level
    -> surface_param_02 and 03 are x1,x2
    -> surface_param_04 and 05 are y1,y2
    -> surface_param_06 is the thickness
  3 to a convex spherical emboss,
    -> surface_param_01 is the z level
    -> surface_param_02 and 03 are x0,y0
    -> surface_param_04 is the radius
  4 to concave spherical emboss,
    -> surface_param_01 is the z level
    -> surface_param_02 and 03 are x0,y0
    -> surface_param_04 is the radius
  5 to a double rectangular emboss,
    -> surface_param_01 is the z level
    -> surface_param_02 and 03 are x1,x2
    -> surface_param_04 and 05 are x3,x4
    -> surface_param_06 and 07 are y1,y2
    -> surface_param_08 and 09 are y3,y4
    -> surface_param_10 is the thickness
  6 to a sinus,
    -> surface_param_01 is the z level
    -> surface_param_02 is the wavelength
    -> surface_param_03 is the amplitude
  7 to a noisy surface,
    -> surface_param_01 is the z level
    -> surface_param_02 is the noise amplitude
  8 to a double sinus,
    -> surface_param_01 is the z level
    -> surface_param_02 is the x-wavelength
    -> surface_param_03 is the x-amplitude
    -> surface_param_04 is the y-wavelength
    -> surface_param_05 is the y-amplitude
  9 to a cosinus,
    -> surface_param_01 is the z level
    -> surface_param_02 is the wavelength
    -> surface_param_03 is the amplitude
  10 to a 2D embankment,
    -> surface_param_01 is z0
    -> surface_param_02 is y0
    -> surface_param_03 is psi
    -> surface_param_04 is the thickness
  11 to a 2D hill,
    -> surface_param_01 is z level
    -> surface_param_02 is the height
    -> surface_param_03 is y0
    -> surface_param_04 is width
  12 to a rectangular emboss with specified slope, 
    -> surface_param_01 is the z level
    -> surface_param_02 is x1
    -> surface_param_03 is x2
    -> surface_param_04 is y1
    -> surface_param_05 is y2 
    -> surface_param_06 is the thickness
    -> surface_param_07 is the slope
  13 to a 2D embankment of finite length and with 2 kinks
    -> surface_param_01 is the z level
    -> surface_param_02 is the thickness (zthick)
    -> surface_param_03 is slope angle (psi)
    -> surface_param_04 is x value for the center of the slope (x0)
    -> surface_param_05 is the x width of the narrow end of the plateau (y0w)
    -> surface_param_06 is the y position for the start of the slope (y0)
    -> surface_param_07 is the y position of the first kink (y1)
    -> surface_param_08 is the angle of the first kink (theta1)
    -> surface_param_09 is the y position of the second kink (y2)
    -> surface_param_10 is the angle of the second kink (theta2)
    -> surface_param_11 is the reference elevation for the flat region
    -> surface_param_12 is the dip angle of the outer dip panel
  14 to a 3D embankment of finite length and with rounded 2 kinks
    -> sp01 is the z level
    -> sp02 is the z level 2
    -> sp03 is slope angle (psi)
    -> sp04 is x value for the center of the slope (xsym)
    -> sp05 is the x width of the narrow end of the plateau (y0w)
    -> sp06 is the y position for the start of the slope (y0)