[cig-commits] [commit] master: Merge branch 'master' into compressible_perplex (e552fae)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed May 21 14:03:01 PDT 2014
Repository : https://github.com/geodynamics/aspect
On branch : master
Link : https://github.com/geodynamics/aspect/compare/a7135c1f7697d39efff2f47a79ca1e1395cff504...73a71ba37f203bfed63bb8b602fdbd30ab99b1af
>---------------------------------------------------------------
commit e552fae9538a8e920ab1b85f64ba305082ace67e
Merge: f45252b fa9e02e
Author: Rene Gassmoeller <R.Gassmoeller at mailbox.org>
Date: Wed May 21 09:52:14 2014 -0500
Merge branch 'master' into compressible_perplex
>---------------------------------------------------------------
e552fae9538a8e920ab1b85f64ba305082ace67e
.gitignore | 27 +-
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 +-
benchmark/tangurnis/ba/tan.prm | 3 -
benchmark/tangurnis/tala/tan.prm | 3 -
benchmark/tangurnis/tala_c/tan.prm | 3 -
...elike-boundary.prm => composition-reaction.prm} | 22 +-
cookbooks/convection-box-3d.prm | 1 -
cookbooks/convection-box.prm | 3 +-
cookbooks/future/blankenbach.prm | 1 -
cookbooks/future/nettranslation.prm | 1 -
cookbooks/future/periodic_box.prm | 1 -
.../radiogenic_heating.prm} | 75 +-
.../radiogenic_heating_function.prm} | 77 +-
cookbooks/future/steinberger.prm | 1 -
cookbooks/future/table_model.prm | 1 -
cookbooks/latent-heat.prm | 1 -
data/initial-temperature/solidus.Mars | 13 +
.../manual/cookbooks/benchmarks}/inclusion.prm | 9 +-
doc/manual/cookbooks/composition-reaction/0.png | Bin 0 -> 1893 bytes
doc/manual/cookbooks/composition-reaction/12.png | Bin 0 -> 76562 bytes
doc/manual/cookbooks/composition-reaction/2.png | Bin 0 -> 41622 bytes
doc/manual/cookbooks/composition-reaction/20.png | Bin 0 -> 71281 bytes
doc/manual/cookbooks/composition-reaction/4.png | Bin 0 -> 50452 bytes
doc/manual/cookbooks/composition-reaction/8.png | Bin 0 -> 66259 bytes
doc/manual/manual.tex | 244 ++--
doc/manual/parameters.tex | 826 ++++++++++--
doc/modules/changes.h | 60 +
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 | 1 -
include/aspect/gravity_model/interface.h | 5 +-
include/aspect/gravity_model/radial.h | 1 -
include/aspect/gravity_model/vertical.h | 1 -
.../constant_heating.h} | 41 +-
.../function.h | 48 +-
.../{gravity_model => heating_model}/interface.h | 110 +-
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 +-
.../{simple.h => composition_reaction.h} | 25 +-
include/aspect/material_model/duretz_et_al.h | 154 ---
include/aspect/material_model/interface.h | 5 +-
include/aspect/material_model/latent_heat.h | 1 -
.../material_model/{simple.h => multicomponent.h} | 130 +-
include/aspect/material_model/simple.h | 1 -
.../{simple.h => simple_compressible.h} | 42 +-
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} | 49 +-
.../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 -
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 | 50 +-
include/aspect/simulator_access.h | 1 -
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 | 3 +-
.../aspect/velocity_boundary_conditions/gplates.h | 17 +-
.../velocity_boundary_conditions/interface.h | 20 +-
.../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 | 90 ++
source/heating_model/function.cc | 129 ++
.../{gravity_model => heating_model}/interface.cc | 78 +-
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 +-
.../{simple.cc => composition_reaction.cc} | 166 ++-
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/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 | 142 +-
source/simulator/checkpoint_restart.cc | 1 -
source/simulator/core.cc | 236 +++-
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 | 53 +-
source/simulator/simulator_access.cc | 5 +-
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 | 16 +-
source/velocity_boundary_conditions/gplates.cc | 27 +-
source/velocity_boundary_conditions/interface.cc | 7 +-
.../velocity_boundary_conditions/zero_velocity.cc | 1 -
tests/CMakeLists.txt | 41 +-
.../{composition-active.prm => always_refine.prm} | 15 +-
tests/always_refine/screen-output | 124 ++
tests/always_refine/statistics | 28 +
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 +
.../composition_reaction.prm | 41 +-
tests/composition_reaction/screen-output | 142 ++
tests/composition_reaction/statistics | 28 +
tests/conservative_with_mpi.prm | 1 -
tests/depth_average_01.prm | 1 -
tests/depth_average_02.prm | 1 -
tests/depth_average_03.prm | 1 -
tests/depth_average_04.prm | 1 -
tests/diffusion-velocity.prm | 1 -
tests/diffusion.prm | 1 -
.../latent-heat.prm => tests/direct_solver_1.prm | 10 +-
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 +
tests/graphical_output.prm | 1 -
tests/inclusion_2.cc | 634 +++++++++
tests/inclusion_2.prm | 7 +-
tests/inclusion_2/screen-output | 2 +
tests/inclusion_4.cc | 2 +
tests/inclusion_4.prm | 7 +-
tests/inclusion_4/screen-output | 2 +
tests/inclusion_adaptive.cc | 2 +
tests/inclusion_adaptive.prm | 7 +-
tests/inclusion_adaptive/screen-output | 9 +-
cookbooks/latent-heat.prm => tests/latent_heat.prm | 33 +-
tests/latent_heat/screen-output | 45 +
tests/latent_heat/statistics | 13 +
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 | 73 +-
tests/multicomponent_arithmetic/screen-output | 76 ++
tests/multicomponent_arithmetic/statistics | 17 +
.../multicomponent_geometric.prm | 73 +-
tests/multicomponent_geometric/screen-output | 76 ++
tests/multicomponent_geometric/statistics | 17 +
.../multicomponent_harmonic.prm | 73 +-
tests/multicomponent_harmonic/screen-output | 76 ++
tests/multicomponent_harmonic/statistics | 17 +
.../multicomponent_max_composition.prm | 73 +-
tests/multicomponent_max_composition/screen-output | 76 ++
tests/multicomponent_max_composition/statistics | 17 +
tests/no_flow.prm | 3 +-
tests/non_conservative_with_mpi.prm | 1 -
tests/passive_comp.prm | 1 -
tests/passive_comp/statistics | 2 +-
tests/plugin.prm | 1 -
...position-active.prm => postprocess_initial.prm} | 15 +-
tests/postprocess_initial/screen-output | 103 ++
tests/postprocess_initial/statistics | 27 +
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/radiogenic_heating.prm | 111 ++
.../screen-output | 28 +-
tests/radiogenic_heating/statistics | 13 +
tests/refinement_topography.prm | 1 -
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 +-
tests/sol_cx_2.prm | 1 -
tests/sol_cx_2_conservative.prm | 1 -
tests/sol_cx_2_normalized_pressure.prm | 1 -
tests/sol_cx_2_q3.prm | 1 -
tests/sol_cx_4.prm | 1 -
tests/sol_cx_4_conservative.prm | 1 -
tests/sol_cx_4_normalized_pressure.prm | 1 -
...4_normalized_pressure_large_static_pressure.prm | 1 -
..._4_normalized_pressure_low_solver_tolerance.prm | 1 -
tests/sol_cx_tracers.prm | 1 -
tests/sol_kz_2.prm | 1 -
tests/sol_kz_2_cheaper_first_phase_solver.prm | 1 -
tests/sol_kz_2_conservative.prm | 1 -
tests/sol_kz_2_no_first_phase_solver.prm | 1 -
tests/sol_kz_2_q3.prm | 1 -
tests/sol_kz_4.prm | 1 -
tests/sol_kz_4_conservative.prm | 1 -
.../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 +
345 files changed, 11554 insertions(+), 2149 deletions(-)
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