input.090710.txt

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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

[bool]compute_reaction_forces toggles on/off the reaction forces computations.

     compute_reaction_forces = F


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=0

     restartfile=OUT/time_0170.bin


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.d-4

[int]nstep is the number of time steps

     nstep = 500

[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 = -10

[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 = -10

[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

[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=100000

[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 = 6

[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


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 = 0


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


FEM + DIVFEM + MUMPS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]levelcut is the number of levels used to estimate the volume integrals in
the divFEM algorithmi 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] ztemp is the height interval between which a linear temperature gradient is
set: the temperature is 1 at the bottom, and 0 at ztemp.
[dp] tempscale

     calculate_temp = F

     ztemp = .357d0

     tempscale=1350.d0


ISOSTASY
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

     isostasy = T

     flexure = T


MATERIALS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[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

[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]heat is the heat production

[char]plasticity_type is the type of plasticity
- No    -> no plasticity, purely (nonlinear) viscous material
- vM    -> von Mises yield criterion
       -> [dp]plasticity_1st_param is the yield value
- DPI   -> Drucker-Prager type of yield criterion
       -> the yield locus passes through the outer apices of the Mohr-Coulomb
          hexagon
       -> [dp]plasticity_1st_param is the angle phi
       -> [dp]plasticity_2nd_param is the cohesion c
- DPII  -> Drucker-Prager type of yield criterion
       -> the yield locus passes through the inner apices of the Mohr-Coulomb
          hexagon
       -> [dp]plasticity_1st_param is the angle phi
       -> [dp]plasticity_2nd_param is the cohesion c
- DPIII -> Drucker-Prager type of yield criterion
       -> [dp]plasticity_1st_param is alpha
       -> [dp]plasticity_2nd_param is k
- MC    -> Mohr-Coulomb type of yield criterion
       -> [dp]plasticity_1st_param is the angle phi
       -> [dp]plasticity_2nd_param is the cohesion c

     density0              = 0.d0
     viscosity0            = 1.d-5
     penalty0              = 1.d8
     expon0                = 1.d0
     diffusivity0          = 1.d0
     heat0                 = 0.d0
     activationenergy0     = 0.d0
     plasticity_type0      = No

     density1              = -.83d0
     viscosity1            = 1.d0
     penalty1              = 1.d8
     expon1                = 1.d0
     diffusivity1          = 0.59d0
     heat1                 = 0.d0
     activationenergy1     = 0.d0
     plasticity_type1      = MC
     plasticity_1st_param1 = 15.d0
     plasticity_2nd_param1 = 1.72d-3
     plasticity_3rd_param1 = 0.5d0
     plasticity_4th_param1 = 1.5d0
     plasticity_5th_param1 = 5.d0

     density2              = -.83d0
     viscosity2            = 1.d-3
     penalty2              = 1.d8
     expon2                = 1.d0
     diffusivity2          = 0.59d0
     heat2                 = 0.d0
     activationenergy2     = 0.d0
     plasticity_type2      = MC
     plasticity_1st_param2 = 15.d0
     plasticity_2nd_param2 = 1.72d-3
     plasticity_3rd_param2 = 0.5d0
     plasticity_4th_param2 = 1.5d0
     plasticity_5th_param2 = 5.d0

     density3              = -1.d0
     viscosity3            = 1.d1
     penalty3              = 1.d8
     expon3                = 1.d0
     diffusivity3          = 0.59d0
     heat3                 = 0.d0
     activationenergy3     = 0.d0
     plasticity_type3      = MC
     plasticity_1st_param3 = 15.d0
     plasticity_2nd_param3 = 1.72d-3 
     plasticity_3rd_param3 = 0.5d0
     plasticity_4th_param3 = 1.5d0
     plasticity_5th_param3 = 5.d0

[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=1.d-5
     viscositymax=1.d5


SURFACES
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[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]material is the material type refering to the table of material available
 (max nmat);
- [dp]activation_time is the time the surface becomes active (before that time,
 it is glued to the 0th surface). this parameter is useful when defining
 stratigraphic horizons; default is -1, ie the surface is not glued to the free
 surface
- [int]surface_type is comprised between 1 and 8. 
 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 
- [int]leveloct is the level at which the octree will be refined in the vicinity
 of the surface.

     levelt1             = 7
     itype1              = 0
     surface_type_1      = 1
     rand1               = T
     surface_param_01_1  = 0.357d0
     material1           = 1
     activation_time_1   = -1. 
     leveloct1           = 6
     stretch1            = 1.5d0
     anglemax1           = 180.d0
     criterion1          = 1
     anglemaxoctree1     = 180.d0
     spread_surface_points1 = 1

     levelt2             = 7
     itype2              = 0
     surface_type_2      = 1
     rand2               = T
     surface_param_01_2  = 0.32575d0
     material2           = 2
     activation_time_2   = -1.
     leveloct2           = 6
     stretch2            = 1.5d0
     anglemax2           = 180.d0
     criterion2          = 1
     anglemaxoctree2     = 180.d0
     spread_surface_points2 = 0

     levelt3             = 7
     itype3              = 0
     surface_type_3      = 1
     rand3               = T
     surface_param_01_3  = 0.2945d0
     material3           = 3
     activation_time_3   = -1.
     leveloct3           = 6
     stretch3            = 1.5d0
     anglemax3           = 180.d0
     criterion3          = 1
     anglemaxoctree3     = 180.d0
     spread_surface_points3 = 0

[int]niter_move is the number of iterations used to update particle positions
using an implicit, mid-point algorithm (default is 10)

     niter_move = 10

[dp]stretch is the maximum allowed increase in linear length between two
initially adjacent particles on any surface; when this stretch is achieved, a
new particle is inserted on the surface, half-way along the stretched edge

     stretch = 1.5d0

[dp]anglemax is the maximum allowed angle between two adjacent normals
when the angle is reached a new point is inserted beteen the two points to
reduce the angle between the two normals

     anglemax=180.d0

[int]criterion is criterion used to define the octree in the vicinity of the
sufaces; criterion 1 corresponds to imposing that all leaves that are cut by any
of the surfaces must be at level levelmax_oct; criterion 2 corresponds to
imposing that discretization is proportional to the curvature of the surface;
curvature is calculated from the local divergence of the normals. criterion 3
corresponds to imposing that all leaves that contain at least one particle of
any surface is at levelmax_oct; 

     criterion = 2

[dp]anglemaxoctree is only defined for criterion 2; t is the maximum allowable
angle between two adjacent normals; if the angle is greater than anglemaxoctree,
the local octree leaves are forced to be at level levelmax_oct; otherwise they
are proportionally larger (smaller levels) (default is 10)

    anglemaxoctree = 10.d0


REFINEMENT IN BOXES
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]nboxes is the number of boxes in which the user imposes a set level of
discretization

     nboxes = 2

for each box we need to specify the two end corners and the level
the syntax is [dp]boxnx0, [dp]boxnx1, [dp]boxny0, [dp]boxny1, [dp]boxnz0,
[dp]boxnz1 and boxnlevel where n is the box number

     box1x0=.25d0
     box1x1=.75d0
     box1y0=.0d0
     box1y1=.6d0
     box1z0=.2d0
     box1z1=.4d0
     box1level=6

     box2x0=0.d0
     box2x1=.75d0
     box2y0=.4d0 
     box2y1=.6d0
     box2z0=.2d0
     box2z1=.4d0
     box2level=6

     box3x0=0.d0
     box3x1=1.d0
     box3y0=0.d0
     box3y1=1.d0
     box3z0=0.d0
     box3z1=.001d0
     box3level=6

     box4x0=.4875d0
     box4x1=.5125d0
     box4y0=.4875d0
     box4y1=.5125d0
     box4z0=.0d0
     box4z1=1.d0
     box4level=9


REFINEMENT ON CUBE FACES
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-
[bool]ref_on_faces toggles on/off the user imposed refinement on faces.
For each of the six faces of the cube, on defines the level at which the
desired area is to be refined. this area is given by bottom, top, left and
right coordinates that are comprised between 0 and 1
faces 1,2,3,4,5,6 respectively correspond to x=0,x=1,y=0,y=1,z=0,z=1

     ref_on_faces = F

     level_face1=5
     b1=.02
     t1=.51
     l1=.11
     r1=.81
     level_face2=5
     b2=.45
     t2=.55
     l2=.46
     r2=.56
     level_face3=5
     b3=.0
     t3=.2
     l3=.3
     r3=.7
     level_face4=5
     b4=.4
     t4=.5
     l4=.14
     r4=.4
     level_face5=6
     b5=0.
     t5=1.
     l5=0.
     r5=0.75
     level_face6=5
     b6=.26
     t6=.56
     l6=.16
     r6=.86


EROSION
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[bool]erosion is a flag that toggles on/off the erosion. 

     erosion = F

if erosion is on, one also needs to set the erosion level/height, [dp]zerosion
Note that this is a first attempt at erosion; in future versions, DOUAR
should be easily linked to a surface processes model like CASCADE

     zerosion=.357d0

If erosion is on, one also needs to define a length scale and a velocity scale
to properly translate the uplift rate produced by DOUAR into something that is
adequate for CASCADE; 
[dp]length_scale is the scale of the unit model in km 
[dp]velocity_scale is the velocity scale in km/Myr. 
if length_scale is negative, erosion is assumed to be perfect (no call to
CASCADE is needed)

     length_scale=350.d0
     velocity_scale=10.d0

One then needs to define the erosion constants in CASCADE
[dp]fluvial_erosion is the fluvial erosion constant in 1/m^2
[dp]diffusion_erosion is the diffusion erosion constant in m^2/yr
(4d-2 32d-2)

     fluvial_erosion=4.d-2
     diffusion_erosion=32.d-2

One finally needs to specify the boundary conditions for CASCADE
if [int]baselevelx0 is set to 1 then the boundary at x=0 is set at baselevel
(water and sediment exit)
if [int]baselevelx1 is set to 1 then the boundary at x=1 is set at baselevel
(water and sediment exit)
if [int]baselevely0 is set to 1 then the boundary at y=0 is set at baselevel
(water and sediment exit)
if [int]baselevely1 is set to 1 then the boundary at y=1 is set at baselevel
(water and sediment exit)

     baselevelx0=1
     baselevelx1=1
     baselevely0=0
     baselevely1=1


MATRIX VISUALISATION
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[bool]visualise_matrix allows the user to turn on the visual representation of
the matrices used in the code. Be careful, the generated postscript files are
huge!

     visualise_matrix = F


CROSS SECTIONS
_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-

[int]nsections is the number of cross-sections to be output. [dp]scale is the
scale used to produce the postscript file.
[int]xyz takes values 1, 2 or 3, and corresponds to planes defined by
x=constant, y=constant, and z=constant resp.
The [bool]flags are self explanatory. [char]colormap is the chosen colormap (jet
or hot). [int]ncolours is the number of colours used to produce the plot. 

nsections = 0

xyz_1          = 1 
slice_1        = 0.5001
flag_press_1   = T
flag_spress_1  = T 
flag_e2d_1     = T
flag_e3d_1     = F
flag_lode_1    = F 
flag_crit_1    = F 
flag_grid_1    = T 
flag_mu_1      = F   
flag_u_1       = F
flag_v_1       = F
flag_w_1       = F
flag_q_1       = F 
flag_uvw_1     = F 
flag_lsf_1     = F 
flag_vfield_1  = F 
flag_colour_1  = T
flag_plastic_1 = F
flag_velvect_1 = T
scale_1        = 500.
colormap_1     = jet
ncolours_1     = 256

xyz_2          = 2
slice_2        = 0.901
flag_press_2   = T
flag_e2d_2     = T
flag_e3d_2     = F 
flag_lode_2    = F 
flag_crit_2    = F 
flag_grid_2    = F 
flag_mu_2      = F   
flag_u_2       = F
flag_v_2       = F
flag_w_2       = F
flag_q_2       = F 
flag_uvw_2     = F 
flag_lsf_2     = F 
flag_vfield_2  = F 
flag_colour_2  = T
flag_plastic_2 = F
flag_velvect_2 = F
scale_2        = 800.
colormap_2     = jet 
ncolours_2     = 256


xyz_3          = 3
slice_3        = 0.0010
flag_press_3   = F 
flag_e2d_3     = F
flag_e3d_3     = F
flag_lode_3    = F 
flag_crit_3    = F 
flag_grid_3    = F 
flag_mu_3      = F   
flag_u_3       = F
flag_v_3       = F
flag_w_3       = F
flag_q_3       = F
flag_uvw_3     = F 
flag_lsf_3     = F 
flag_vfield_3  = F 
flag_colour_3  = T
flag_plastic_3 = F
flag_velvect_3 = F
scale_3        = 400.
colormap_3     = jet
ncolours_3     = 256