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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/Olivine_fabrics.svg b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/Olivine_fabrics.svg new file mode 100644 index 00000000000..980fc4c9cc9 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/Olivine_fabrics.svg @@ -0,0 +1,25590 @@ + + + +A[001][010][001]BCDE diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/cpo.part.prm b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/cpo.part.prm new file mode 100644 index 00000000000..4ebeb984000 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/cpo.part.prm @@ -0,0 +1,87 @@ +#specify posstprocessor objects that will be run at the end of each time step +#The statistics is important for cpo plotter for reading the data +#The particles and crystal preferred orientation are required for CPO calculations +subsection Postprocess + set List of postprocessors = velocity statistics, visualization, particles, crystal preferred orientation + + #specify data output for visualizing in paraview or visit + subsection Visualization + set Time between graphical output = 1e5 + set List of output variables = stress, viscosity, strain rate + end + + #specify CPO data output + subsection Crystal Preferred Orientation + set Time between data output = 1e5 + set Write in background thread = true + set Compress cpo data files = false # so results are human readable + set Write out raw cpo data = mineral 0: volume fraction, mineral 0: Euler angles #, mineral 1: volume fraction, mineral 1: Euler angles #specify what to output, here will only output volume fraction and Euler angles for mineral 0 (olivine) + set Write out draw volume weighted cpo data = mineral 0: volume fraction, mineral 0: Euler angles, mineral 1: volume fraction, mineral 1: Euler angles + + #specify output parameters for draw volume weighted cpo, the pole figures are plotted with these data + end + + # Here is for data results read by paraview and visit + # Exclude output properties so as to allow fast reading by paraview + # because if number of particles is large, paraview will crash + subsection Particles + set Time between data output = 1e4 + set Data output format = vtu + set Exclude output properties = volume fraction, rotation_matrix + end +end + +# subsection Particles was part of subsection Postprocess but from V3.0 it standalone +subsection Particles + set List of particle properties = integrated strain, crystal preferred orientation, cpo elastic tensor, cpo bingham average, integrated strain invariant, velocity, pT path #what particle properties are calculated + + # When specifying locations for particles using subsection Generator below, below 3 lines are commented + #set Load balancing strategy = add particles + #set Minimum particles per cell = 128 + #set Maximum particles per cell = 512 + # use a ascii file particle_one.dat to specify initial locations of particles + set Particle generator name = ascii file + + # + subsection Generator + subsection Ascii file + # you may need to change the below path to the absolute path in your local computer + # the particle_one.dat is located in the cookbook folder + set Data directory = /aspect/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/ + set Data file name = particle_one.dat + end + end + + # parameters for DRex + subsection Crystal Preferred Orientation + # a random seed to 'randomize' initial Euler angles for the grains + set Random number seed = 301 + set Number of grains per particle = 500 ## Annotation grain count + set Property advection method = Backward Euler ## Annotation Property advection method + set Property advection tolerance = 1e-15 + set CPO derivatives algorithm = D-Rex 2004 + + subsection Initial grains + # prescribe types of mineral + # The A,B,C,D,E types of olivine fabric can be set here by changing + # A-fabric to B-fabric for example + set Minerals = Olivine: A-fabric, Enstatite ## Annotation Minerals + + # The two minerals are not interacting with each other. + set Volume fractions minerals = 0.7,0.3 ## Annotation Volume fractions minerals + end + + # DRex parameters following Kaminski et al., 2004 + subsection D-Rex 2004 + set Mobility = 125 ## 125+-75 Annotation LPO Mobility + set Stress exponents = 3.5 + set Exponents p = 1.5 + set Nucleation efficiency = 5 ## Annotation Nucleation efficiency + set Threshold GBS = 0.3 ## Annotation TGBS + end + end + + subsection CPO Bingham Average + set Random number seed = 200 + end +end diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/cpo_pole_figure_config.toml b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/cpo_pole_figure_config.toml new file mode 100644 index 00000000000..771ad1b1210 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/cpo_pole_figure_config.toml @@ -0,0 +1,15 @@ +base_dir = "/Users/tian_bc/Documents/postdoc/postdoc_meetings_workshops/2024-ASPECT-hack/aspect-output/drex_olivine_branch_CPO_based_on_yijun/main240613/" +experiment_dirs = ["out_drex_olivineE/"] +compressed = false + +[pole_figures] + elastisity_header = false #not yet implemented + small_figure = true + no_description_text = false #false + color_scale = "Gray" + times = [1.0,1e5,3e5] + particle_ids = [0] + axes = ["AAxis","BAxis","CAxis"] + minerals = ["Olivine","Enstatite"] + grain_data_file_prefix = "weighted_CPO" + particle_data_dir = "particles_cpo" \ No newline at end of file diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/crystal_preferred_orientation_olivine_fraters_billen_2021.md b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/crystal_preferred_orientation_olivine_fraters_billen_2021.md new file mode 100644 index 00000000000..8bb203a3162 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/crystal_preferred_orientation_olivine_fraters_billen_2021.md @@ -0,0 +1,129 @@ +# [WIP] Olivine Fabric Developments Under Simple Shear + +*This section was contributed by Xiaochuan Tian, with helps from Yijun Wang and Menno Fraters. It is +based on a section in {cite:t}`fraters_billen_2021_cpo` +by Menno Fraters and Magali Billen published in 2021.* + +This cookbook explains how to set up a numerical experiment for fabric +developments of a single olivine particle under simple shear macroscopic strain. +It uses ASPECT's +crystal preferred orientation (CPO) implementation, which is described in detail in +{cite:t}`fraters_billen_2021_cpo` and the paper is open accessed at +[here](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021GC009846). +The fabric calculation is based on DRex (Kaminski et al., 2004) at +[here](https://academic.oup.com/gji/article/158/2/744/2013756). +This notebook describe how to use ASPECT CPO implementation to calculate the major +olivine fabrics observed in the lab experiments. It focuses on reproducing Fig. 3 +of {cite}`fraters_billen_2021_cpo`. + +## Motivation +The Earth's plates can move relative to each other because the underlying mantle +can flow/(be deformed) to accommodate such motions. +This flowing motion reflects dynamics inside the planet but cannot be observed directly +as the depth of interest is beyond human's drilling ability. However, indirect observation +from seismic anisotropy provides information about directionality of the speed of seismic +waves that propagate inside the Earth. If such directionality is controlled by +the mantle's motion/deformation, we can then use seismic anisotropy observations +to infer mantle's deformation. + +Olivine is a major mineral of the Earth's upper mantle where continuous deformation +takes place. People care about olivine fabric developments under simple shear as it may +provide a bridge that links seismic anisotropy observations to the +flows in the upper mantle that accommodate plate motions. Indeed, high temperature and +pressure lab experiments using Griggs apparatus to investigate olivine fabrics developments +under simple shear do find systematic types of fabrics based on the stress and water content conditions +(see Karato et al., 2008 for details). Here is a +[link](https://doi.org/10.1146/annurev.earth.36.031207.124120) to the paper. + +## Model setup + +Following {cite:t}`fraters_billen_2021_cpo`, we prescribe simple shear in a 3d Cartesian box/cube +with dimensions of $1 \times 1 \times 1 $ $[m^3]$. The shear strain rate +$\dot{\epsilon}_{xz} = -5\times 10^{-6} [s^{-1}]$. The olivine particle is placed +right at the center of the cubic box so it stays stationary. The DRex implementation +keep tracks of rotations of crystal grains within the particle under macroscopic deformation. + +```{figure-md} fig:model_setup_3D_box + + +3D shear box with velocity vectors. The grey ball is the central olivine particle. +``` + +The model shows how crystal grains rotate and align under simple shear with pole figures. + +## The input file + +:::{tip} +Update the input file with update_prm_files.sh inside +/aspect/contrib/utilities if the model doesn't run. +See Pull Request #5873 +[conversations](https://github.com/geodynamics/aspect/pull/5873#issuecomment-2167145176) for detail. +::: + +Instead of solving Stokes equation with initial and boundary conditions, we instead prescribe +a constant simple shear strain rate field by setting Nonlinear solver scheme to +"single Advecgion, no Stokes" and +prescribing the Stokes solution with a function. In this case, what we only care is the +prescribed strain rate that is exerted onto the olivine particle. Parameters useful for the Stokes +equation is not important in this case. + +```{literalinclude} prescribe_stokes.part.prm +``` + +The second part of the input file specify what to output and what minerals to keep track of +CPO development. It also specifies the parameters for the DRex algorithm. + +```{literalinclude} cpo.part.prm +``` + +The complete input file is located at +[/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/olivineA.prm](https://www.github.com/geodynamics/aspect/blob/main/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/olivineA.prm). + +## Plotting pole figure +To plot pole figures from + +## Model results +```{figure-md} fig:initCPO + + +Initial randomized CPO at time zero. +``` + +```{figure-md} fig:olivine_fabrics + + +Olivine A-E type fabrics under simple shear with a shear strain of 1.5 +at 3e5 seconds of model time under constant shear strain rate: + $\dot{\epsilon}_{xz} = -5\times 10^{-6} [s^{-1}]$. +Note that the color scales range from 0 to 5 but actual results may be larger. +``` + +When we look at the visualization output of this model (see also +{numref}`fig:olivine_fabrics`), we can see + + + +## Extending the model + +This simple 1 $m^{3}$ cube simple shear model for tracking olivine fabric development using +the crystal preferred orientation implementation can be extended for various settings. +Some ideas for adapting the model setup: + +- Setup high pressure and temperature lab experiments for olivine CPO. + After benchmarking against the lab experiment results, it could then be + extended beyond parameter space limited by lab experiment. + +- Add CPO calculations in large scale geodynamic models like mantle plume, + lower crust delamination and mid-ocean ridges. + +- Include anisotropic viscosity to feed this CPO back to influence the stokes solution. + +## References: +- Fraters, M. R. T., & Billen, M. I. (2021). +On the implementation and usability of crystal preferred orientation evolution in geodynamic modeling. Geochemistry, Geophysics, Geosystems, 22(10), e2021GC009846. + +- Kaminski, E., Ribe, N. M., & Browaeys, J. T. (2004). +D-Rex, a program for calculation of seismic anisotropy due to crystal lattice preferred orientation in the convective upper mantle. Geophysical Journal International, 158(2), 744–752. + +- Karato, S., Jung, H., Katayama, I., & Skemer, P. (2008). +Geodynamic significance of seismic anisotropy of the upper mantle: New insights from laboratory studies. Annu. Rev. Earth Planet. Sci., 36, 59–95. diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/initial_random_cpo.png b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/initial_random_cpo.png new file mode 100644 index 00000000000..76861c61dcd Binary files /dev/null and b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/initial_random_cpo.png differ diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/model_setup_3D_box.png b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/model_setup_3D_box.png new file mode 100644 index 00000000000..980c4506fa1 Binary files /dev/null and b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/model_setup_3D_box.png differ diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/prescribe_stokes.part.prm b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/prescribe_stokes.part.prm new file mode 100644 index 00000000000..649975b3511 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/doc/prescribe_stokes.part.prm @@ -0,0 +1,53 @@ +# we prescribe the simple shear strain rate by setting solver scheme +# as "single Advection, no Stokes" +# see below "subsection Prescribed Stokes solution " +set Nonlinear solver scheme = single Advection, no Stokes +# The model run to 3e5 seconds, at which the total strain will +# be 1.5 with strain rate of 5e-6 1/s. +set End time = 3e5 +set Use years in output instead of seconds = false + +# Set zero gravity +subsection Gravity model + set Model name = vertical + + subsection Vertical + set Magnitude = 0 + end +end + +# 1m by 1m by 1m cube +# center is at (0,0,0) +subsection Geometry model + set Model name = box + + subsection Box + set X extent = 1 + set Y extent = 1 + set Z extent = 1 + set Box origin X coordinate = -0.5 + set Box origin Y coordinate = -0.5 + set Box origin Z coordinate = -0.5 + end +end + +# Here prescribing velocity field so that it results in +# simple shear strain rate epsilon_xz = -5e6 1/s +# as z ranges from -0.5 to 0.5 meter. +subsection Prescribed Stokes solution + set Model name = function + + subsection Velocity function + set Variable names = x,y,z,t + set Function expression = z/1e5;0;0 ## Annotation set velocity condition + end +end + +# The default X,Y,Z repetitions is 1, so will be 2 by 2 by 2 grids without refinement +# Here with setting "Initial global refinement" to be 1, it becomes +4 by 4 by 4 grids. +subsection Mesh refinement + set Initial global refinement = 1 + set Initial adaptive refinement = 0 + set Time steps between mesh refinement = 10000 +end diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/olivineA.prm b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/olivineA.prm new file mode 100644 index 00000000000..d79c8699d86 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/olivineA.prm @@ -0,0 +1,170 @@ +set CFL number = 0.01 ##Annotation CFL number +set Timing output frequency = 1000 +set Dimension = 3 +set Pressure normalization = surface +set Surface pressure = 0 +set Nonlinear solver scheme = single Advection, no Stokes +set End time = 3e5 +set Use years in output instead of seconds = false +set Output directory = out_drex_olivineA + +subsection Compositional fields + set Number of fields = 1 + set Names of fields = water + set Compositional field methods = static +end + +subsection Initial composition model + set Model name = function + + subsection Function + set Variable names = x,y,z + set Function expression = 0 + end +end + +subsection Gravity model + set Model name = vertical + + subsection Vertical + set Magnitude = 0 + end +end + +subsection Geometry model + set Model name = box + + subsection Box + set X extent = 1 + set Y extent = 1 + set Z extent = 1 + set Box origin X coordinate = -0.5 + set Box origin Y coordinate = -0.5 + set Box origin Z coordinate = -0.5 + end +end + +subsection Initial temperature model + set Model name = function + + subsection Function + set Function expression = 1 ## Annotation: Temperature function + end +end + +subsection Boundary temperature model + set List of model names = box + set Fixed temperature boundary indicators = bottom, top, left, right, front, back + + subsection Box + set Bottom temperature = 1 + set Left temperature = 1 + set Right temperature = 1 + set Top temperature = 1 + set Front temperature = 1 + set Back temperature = 1 + end +end + +subsection Boundary velocity model + subsection Function + set Variable names = x,y,z,t + set Function expression = z/1e5;0;0 ## Annotation set velocity condition + end +end + +subsection Prescribed Stokes solution + set Model name = function + + subsection Velocity function + set Variable names = x,y,z,t + set Function expression = z/1e5;0;0 ## Annotation set velocity condition + end +end + +subsection Material model + set Model name = simple + + subsection Simple model + set Reference density = 1 + set Reference specific heat = 1 + set Reference temperature = 1 + set Thermal conductivity = 1 + set Thermal expansion coefficient = 1e-10 + set Viscosity = 1 + end +end + +subsection Mesh refinement + set Initial global refinement = 1 + set Initial adaptive refinement = 0 + set Time steps between mesh refinement = 10000 +end + +subsection Postprocess + set List of postprocessors = velocity statistics, visualization, particles, crystal preferred orientation + + subsection Visualization + set Time between graphical output = 1e5 + set List of output variables = stress, viscosity, strain rate + end + + subsection Crystal Preferred Orientation + set Time between data output = 1e5 + set Write in background thread = true + set Compress cpo data files = false + set Write out raw cpo data = mineral 0: volume fraction, mineral 0: Euler angles #, mineral 1: volume fraction, mineral 1: Euler angles + set Write out draw volume weighted cpo data = mineral 0: volume fraction, mineral 0: Euler angles, mineral 1: volume fraction, mineral 1: Euler angles + end + + subsection Particles + set Time between data output = 1e4 + set Data output format = vtu + set Exclude output properties = volume fraction, rotation_matrix + end +end + +subsection Solver parameters + set Temperature solver tolerance = 1e-10 +end + +subsection Particles + set List of particle properties = integrated strain, crystal preferred orientation, cpo elastic tensor, cpo bingham average, integrated strain invariant, velocity, pT path + + #set Load balancing strategy = add particles + #set Minimum particles per cell = 128 + #set Maximum particles per cell = 512 + set Particle generator name = ascii file + + subsection Generator + subsection Ascii file + set Data directory = /Users/tian_bc/Documents/postdoc/postdoc_meetings_workshops/2024-ASPECT-hack/aspect-output/drex_olivine_branch_CPO_based_on_yijun/main240613/ + set Data file name = particle_one.dat + end + end + + subsection Crystal Preferred Orientation + set Random number seed = 301 + set Number of grains per particle = 500 ## Annotation grain count + set Property advection method = Backward Euler ## Annotation Property advection method + set Property advection tolerance = 1e-15 + set CPO derivatives algorithm = D-Rex 2004 + + subsection Initial grains + set Minerals = Olivine: A-fabric, Enstatite ## Annotation Minerals + set Volume fractions minerals = 0.7,0.3 ## Annotation Volume fractions minerals + end + + subsection D-Rex 2004 + set Mobility = 125 ## 125+-75 Annotation LPO Mobility + set Stress exponents = 3.5 + set Exponents p = 1.5 + set Nucleation efficiency = 5 ## Annotation Nucleation efficiency + set Threshold GBS = 0.3 ## Annotation TGBS + end + end + + subsection CPO Bingham Average + set Random number seed = 200 + end +end diff --git a/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/particle_one.dat b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/particle_one.dat new file mode 100644 index 00000000000..d5e8e721f44 --- /dev/null +++ b/cookbooks/crystal_preferred_orientation_olivine_fraters_billen_2021/particle_one.dat @@ -0,0 +1 @@ +0 0 0 \ No newline at end of file