[cig-commits] [commit] master: Merge remote-tracking branch 'upstream/master' into Time_dependent_radioactive_heating (7f87f36)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Thu May 22 15:35:33 PDT 2014
Repository : https://github.com/geodynamics/aspect
On branch : master
Link : https://github.com/geodynamics/aspect/compare/4a5e27e5690a0e0c1e13e19100af7398e37f36b8...d31f4e9435a1c12781f5b673b672cbd29c41c2c2
>---------------------------------------------------------------
commit 7f87f3633269f058f0e0bfeaf3dfe0f4e4bf4d6c
Merge: a584315 8a5f6c5
Author: Siqi Zhang <siqi.zhang at mq.edu.au>
Date: Wed May 21 11:54:20 2014 -0500
Merge remote-tracking branch 'upstream/master' into Time_dependent_radioactive_heating
>---------------------------------------------------------------
7f87f3633269f058f0e0bfeaf3dfe0f4e4bf4d6c
.gitignore | 16 +
benchmark/inclusion/CMakeLists.txt | 10 +
benchmark/inclusion/adaptive.prm | 9 +-
benchmark/inclusion/{base.prm => global.prm.base} | 9 +-
benchmark/inclusion/inclusion.cc | 628 +++++++++
benchmark/inclusion/run.sh | 2 +-
cookbooks/free-surface.prm | 140 ++
cookbooks/future/crameri_benchmark_1.prm | 132 ++
cookbooks/future/crameri_benchmark_2.prm | 130 ++
data/initial-temperature/solidus.Mars | 13 +
.../manual/cookbooks/benchmarks}/inclusion.prm | 9 +-
.../cookbooks/free_surface/free_surface_blob.png | Bin 0 -> 8818 bytes
.../free_surface/free_surface_topography.png | Bin 0 -> 5467 bytes
doc/manual/manual.bib | 23 +
doc/manual/manual.tex | 269 ++--
doc/manual/parameters.tex | 826 ++++++++++--
doc/modules/changes.h | 63 +
include/aspect/adiabatic_conditions.h | 1 -
include/aspect/boundary_composition/box.h | 1 -
.../boundary_composition/initial_composition.h | 1 -
include/aspect/boundary_composition/interface.h | 5 +-
.../boundary_composition/spherical_constant.h | 1 -
include/aspect/boundary_temperature/box.h | 1 -
.../boundary_temperature/initial_temperature.h | 1 -
include/aspect/boundary_temperature/interface.h | 5 +-
.../boundary_temperature/spherical_constant.h | 1 -
include/aspect/boundary_temperature/tan_gurnis.h | 1 -
.../compositional_initial_conditions/function.h | 1 -
.../compositional_initial_conditions/interface.h | 6 +-
include/aspect/geometry_model/box.h | 1 -
include/aspect/geometry_model/interface.h | 5 +-
include/aspect/geometry_model/spherical_shell.h | 1 -
include/aspect/global.h | 14 +-
include/aspect/gravity_model/interface.h | 5 +-
include/aspect/gravity_model/radial.h | 1 -
include/aspect/gravity_model/vertical.h | 1 -
include/aspect/heating_model/constant_heating.h | 1 -
include/aspect/heating_model/function.h | 1 -
include/aspect/heating_model/interface.h | 5 +-
include/aspect/initial_conditions/adiabatic.h | 1 -
include/aspect/initial_conditions/box.h | 1 -
include/aspect/initial_conditions/function.h | 1 -
.../initial_conditions/harmonic_perturbation.h | 1 -
include/aspect/initial_conditions/interface.h | 5 +-
.../{harmonic_perturbation.h => solidus.h} | 112 +-
.../aspect/initial_conditions/spherical_shell.h | 1 -
include/aspect/introspection.h | 61 +-
.../aspect/material_model/composition_reaction.h | 1 -
include/aspect/material_model/duretz_et_al.h | 154 ---
include/aspect/material_model/interface.h | 5 +-
include/aspect/material_model/latent_heat.h | 1 -
.../{composition_reaction.h => multicomponent.h} | 138 +-
include/aspect/material_model/simple.h | 1 -
.../{simple.h => simple_compressible.h} | 44 +-
include/aspect/material_model/steinberger.h | 1 -
include/aspect/material_model/table.h | 1 -
include/aspect/material_model/tan_gurnis.h | 1 -
include/aspect/mesh_refinement/composition.h | 1 -
include/aspect/mesh_refinement/density.h | 1 -
include/aspect/mesh_refinement/interface.h | 28 +-
.../minimum_refinement_function.h} | 52 +-
.../mesh_refinement/nonadiabatic_temperature.h | 1 -
include/aspect/mesh_refinement/temperature.h | 1 -
.../mesh_refinement/thermal_energy_density.h | 1 -
include/aspect/mesh_refinement/topography.h | 1 -
include/aspect/mesh_refinement/velocity.h | 1 -
include/aspect/mesh_refinement/viscosity.h | 1 -
include/aspect/particle/generator.h | 1 -
include/aspect/particle/integrator.h | 1 -
include/aspect/particle/output.h | 1 -
include/aspect/particle/particle.h | 1 -
include/aspect/particle/world.h | 1 -
include/aspect/plugins.h | 1 -
.../aspect/postprocess/composition_statistics.h | 1 -
include/aspect/postprocess/depth_average.h | 1 -
include/aspect/postprocess/duretz_et_al.h | 1 -
include/aspect/postprocess/dynamic_topography.h | 23 +-
include/aspect/postprocess/heat_flux_statistics.h | 1 -
include/aspect/postprocess/interface.h | 5 +-
...tatistics.h => spherical_velocity_statistics.h} | 13 +-
.../postprocess/table_heat_flux_statistics.h | 1 -
.../aspect/postprocess/table_velocity_statistics.h | 1 -
include/aspect/postprocess/tan_gurnis.h | 1 -
.../aspect/postprocess/temperature_statistics.h | 1 -
.../{dynamic_topography.h => topography.h} | 21 +-
include/aspect/postprocess/tracer.h | 1 -
...statistics.h => velocity_boundary_statistics.h} | 17 +-
include/aspect/postprocess/velocity_statistics.h | 1 -
include/aspect/postprocess/visualization.h | 5 +-
.../visualization/artificial_viscosity.h | 1 -
include/aspect/postprocess/visualization/density.h | 1 -
.../postprocess/visualization/dynamic_topography.h | 61 +-
.../postprocess/visualization/error_indicator.h | 1 -
.../postprocess/visualization/friction_heating.h | 1 -
.../postprocess/visualization/melt_fraction.h | 1 -
.../visualization/nonadiabatic_pressure.h | 1 -
.../visualization/nonadiabatic_temperature.h | 1 -
.../aspect/postprocess/visualization/partition.h | 1 -
.../postprocess/visualization/seismic_anomalies.h | 1 -
.../aspect/postprocess/visualization/seismic_vp.h | 1 -
.../aspect/postprocess/visualization/seismic_vs.h | 1 -
.../postprocess/visualization/specific_heat.h | 1 -
.../aspect/postprocess/visualization/strain_rate.h | 1 -
.../visualization/thermal_expansivity.h | 1 -
.../visualization/thermodynamic_phase.h | 1 -
.../aspect/postprocess/visualization/viscosity.h | 1 -
.../postprocess/visualization/viscosity_ratio.h | 1 -
include/aspect/simulator.h | 217 ++-
include/aspect/simulator_access.h | 7 +-
include/aspect/termination_criteria/end_time.h | 1 -
include/aspect/termination_criteria/interface.h | 5 +-
.../termination_criteria/steady_rms_velocity.h | 1 -
include/aspect/termination_criteria/user_request.h | 1 -
.../velocity_boundary_conditions/duretz_et_al.h | 1 -
.../aspect/velocity_boundary_conditions/function.h | 1 -
.../aspect/velocity_boundary_conditions/gplates.h | 1 -
.../velocity_boundary_conditions/interface.h | 5 +-
.../velocity_boundary_conditions/zero_velocity.h | 1 -
source/adiabatic_conditions.cc | 1 -
source/boundary_composition/box.cc | 1 -
source/boundary_composition/initial_composition.cc | 1 -
source/boundary_composition/interface.cc | 1 -
source/boundary_composition/spherical_constant.cc | 1 -
source/boundary_temperature/box.cc | 1 -
source/boundary_temperature/initial_temperature.cc | 1 -
source/boundary_temperature/interface.cc | 1 -
source/boundary_temperature/spherical_constant.cc | 1 -
source/boundary_temperature/tan_gurnis.cc | 1 -
.../compositional_initial_conditions/function.cc | 11 +-
.../compositional_initial_conditions/interface.cc | 1 -
source/geometry_model/box.cc | 1 -
source/geometry_model/interface.cc | 1 -
source/geometry_model/spherical_shell.cc | 1 -
source/global.cc | 1 -
source/gravity_model/interface.cc | 1 -
source/gravity_model/vertical.cc | 1 -
source/heating_model/constant_heating.cc | 1 -
source/heating_model/function.cc | 14 +-
source/heating_model/interface.cc | 1 -
source/initial_conditions/adiabatic.cc | 11 +-
source/initial_conditions/box.cc | 1 -
source/initial_conditions/function.cc | 10 +-
source/initial_conditions/harmonic_perturbation.cc | 1 -
source/initial_conditions/interface.cc | 1 -
source/initial_conditions/solidus.cc | 324 +++++
source/initial_conditions/spherical_shell.cc | 1 -
source/main.cc | 61 +-
source/material_model/composition_reaction.cc | 1 -
source/material_model/duretz_et_al.cc | 210 ---
source/material_model/interface.cc | 1 -
source/material_model/latent_heat.cc | 1 -
source/material_model/multicomponent.cc | 471 +++++++
source/material_model/simple.cc | 86 +-
source/material_model/simple_compressible.cc | 289 ++++
source/material_model/steinberger.cc | 1 -
source/material_model/table.cc | 1 -
source/material_model/tan_gurnis.cc | 1 -
source/mesh_refinement/composition.cc | 1 -
source/mesh_refinement/density.cc | 1 -
source/mesh_refinement/interface.cc | 83 +-
.../mesh_refinement/minimum_refinement_function.cc | 128 ++
source/mesh_refinement/nonadiabatic_temperature.cc | 1 -
source/mesh_refinement/temperature.cc | 1 -
source/mesh_refinement/thermal_energy_density.cc | 1 -
source/mesh_refinement/topography.cc | 1 -
source/mesh_refinement/velocity.cc | 1 -
source/mesh_refinement/viscosity.cc | 1 -
source/particle/generator.cc | 1 -
source/particle/integrator.cc | 1 -
source/particle/output.cc | 1 -
source/particle/particle.cc | 1 -
source/postprocess/composition_statistics.cc | 13 +-
source/postprocess/depth_average.cc | 1 -
source/postprocess/duretz_et_al.cc | 64 +-
source/postprocess/dynamic_topography.cc | 114 +-
source/postprocess/heat_flux_statistics.cc | 1 -
source/postprocess/interface.cc | 1 -
.../postprocess/spherical_velocity_statistics.cc | 173 +++
source/postprocess/table_heat_flux_statistics.cc | 1 -
source/postprocess/table_velocity_statistics.cc | 1 -
source/postprocess/tan_gurnis.cc | 1 -
source/postprocess/temperature_statistics.cc | 6 +-
source/postprocess/topography.cc | 140 ++
source/postprocess/tracer.cc | 1 -
source/postprocess/velocity_boundary_statistics.cc | 210 +++
source/postprocess/velocity_statistics.cc | 1 -
source/postprocess/visualization.cc | 4 +-
.../visualization/artificial_viscosity.cc | 1 -
source/postprocess/visualization/density.cc | 9 +-
.../visualization/dynamic_topography.cc | 234 +++-
.../postprocess/visualization/error_indicator.cc | 1 -
.../postprocess/visualization/friction_heating.cc | 1 -
source/postprocess/visualization/melt_fraction.cc | 11 +-
.../visualization/nonadiabatic_pressure.cc | 1 -
.../visualization/nonadiabatic_temperature.cc | 1 -
source/postprocess/visualization/partition.cc | 1 -
.../postprocess/visualization/seismic_anomalies.cc | 1 -
source/postprocess/visualization/seismic_vp.cc | 1 -
source/postprocess/visualization/seismic_vs.cc | 1 -
source/postprocess/visualization/specific_heat.cc | 9 +-
source/postprocess/visualization/strain_rate.cc | 1 -
.../visualization/thermal_expansivity.cc | 1 -
.../visualization/thermodynamic_phase.cc | 1 -
source/postprocess/visualization/viscosity.cc | 1 -
.../postprocess/visualization/viscosity_ratio.cc | 1 -
source/simulator/assembly.cc | 176 +--
source/simulator/checkpoint_restart.cc | 1 -
source/simulator/core.cc | 312 ++++-
source/simulator/freesurface.cc | 650 +++++++++
source/simulator/helper_functions.cc | 118 +-
source/simulator/initial_conditions.cc | 44 +-
source/simulator/introspection.cc | 105 +-
source/simulator/nullspace.cc | 12 +-
source/simulator/parameters.cc | 65 +-
source/simulator/simulator_access.cc | 12 +-
source/simulator/solver.cc | 81 +-
source/termination_criteria/end_time.cc | 1 -
source/termination_criteria/interface.cc | 1 -
source/termination_criteria/steady_rms_velocity.cc | 1 -
source/termination_criteria/user_request.cc | 1 -
.../velocity_boundary_conditions/duretz_et_al.cc | 64 -
source/velocity_boundary_conditions/function.cc | 10 +-
source/velocity_boundary_conditions/gplates.cc | 3 +-
source/velocity_boundary_conditions/interface.cc | 1 -
.../velocity_boundary_conditions/zero_velocity.cc | 1 -
tests/always_refine/statistics | 26 +-
tests/composition-active/statistics | 144 +-
tests/composition-passive-tracers/statistics | 36 +-
tests/composition_names.prm | 151 +++
tests/composition_names/screen-output | 43 +
tests/composition_names/solution-00000.0000.vtu | 43 +
tests/composition_names/statistics | 19 +
tests/composition_reaction/statistics | 36 +-
.../latent-heat.prm => tests/direct_solver_1.prm | 9 +-
tests/direct_solver_1/screen-output | 98 ++
tests/direct_solver_1/statistics | 18 +
tests/dynamic_topography.prm | 130 ++
tests/dynamic_topography/dynamic_topography.00000 | 64 +
tests/dynamic_topography/screen-output | 71 +
tests/dynamic_topography/solution-00000.0000.vtu | 43 +
.../free_surface_blob.prm | 64 +-
tests/free_surface_blob/screen-output | 208 +++
tests/free_surface_blob/statistics | 24 +
tests/free_surface_relaxation.cc | 178 +++
.../free_surface_relaxation.prm | 75 +-
tests/free_surface_relaxation/screen-output | 194 +++
tests/free_surface_relaxation/statistics | 23 +
tests/inclusion_2.cc | 634 +++++++++
tests/inclusion_2.prm | 6 +-
tests/inclusion_2/screen-output | 2 +
tests/inclusion_4.cc | 2 +
tests/inclusion_4.prm | 6 +-
tests/inclusion_4/screen-output | 2 +
tests/inclusion_adaptive.cc | 2 +
tests/inclusion_adaptive.prm | 6 +-
tests/inclusion_adaptive/screen-output | 9 +-
cookbooks/latent-heat.prm => tests/latent_heat.prm | 32 +-
tests/latent_heat/screen-output | 45 +
.../{radiogenic_heating => latent_heat}/statistics | 4 +-
tests/minimum_refinement_function.prm | 211 +++
tests/minimum_refinement_function/screen-output | 143 ++
.../solution-00003.0000.vtu | 39 +
.../solution-00003.0001.vtu | 39 +
tests/minimum_refinement_function/statistics | 23 +
.../multicomponent_arithmetic.prm | 72 +-
tests/multicomponent_arithmetic/screen-output | 76 ++
tests/multicomponent_arithmetic/statistics | 17 +
.../multicomponent_geometric.prm | 72 +-
tests/multicomponent_geometric/screen-output | 76 ++
tests/multicomponent_geometric/statistics | 17 +
.../multicomponent_harmonic.prm | 72 +-
tests/multicomponent_harmonic/screen-output | 76 ++
tests/multicomponent_harmonic/statistics | 17 +
.../multicomponent_max_composition.prm | 72 +-
tests/multicomponent_max_composition/screen-output | 76 ++
tests/multicomponent_max_composition/statistics | 17 +
tests/passive_comp/statistics | 2 +-
tests/postprocess_initial/statistics | 24 +-
tests/prmbackslash-2.prm | 168 +++
tests/{sol_cx_2 => prmbackslash-2}/screen-output | 0
tests/{sol_cx_2 => prmbackslash-2}/statistics | 0
tests/{maxtimestep.prm => prmbackslash.prm} | 16 +-
tests/{maxtimestep => prmbackslash}/screen-output | 0
tests/{maxtimestep => prmbackslash}/statistics | 0
tests/simple-compressible.prm | 97 ++
tests/simple-compressible/depth_average.gnuplot | 1407 ++++++++++++++++++++
tests/simple-compressible/screen-output | 52 +
.../statistics | 11 +-
tests/simple_compressibility_iterated_stokes.cc | 2 +
... => simple_compressibility_iterated_stokes.prm} | 34 +-
.../screen-output | 2 +-
.../solidus-initial-conditions.prm | 44 +-
.../depth_average.gnuplot | 707 ++++++++++
tests/solidus-initial-conditions/screen-output | 45 +
...e_vel.prm => spherical_velocity_statistics.prm} | 5 +-
tests/spherical_velocity_statistics/screen-output | 206 +++
tests/spherical_velocity_statistics/statistics | 32 +
tests/stokes/statistics | 2 +-
...ne_vel.prm => velocity_boundary_statistics.prm} | 2 +-
tests/velocity_boundary_statistics/screen-output | 206 +++
tests/velocity_boundary_statistics/statistics | 37 +
301 files changed, 12604 insertions(+), 1842 deletions(-)
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