[cig-commits] commit 2503 by heister to /var/svn/dealii/aspect
dealii.demon at gmail.com
dealii.demon at gmail.com
Sun Apr 13 07:33:40 PDT 2014
Revision 2503
apply astyle formatting
U trunk/aspect/include/aspect/boundary_composition/box.h
U trunk/aspect/include/aspect/boundary_composition/initial_composition.h
U trunk/aspect/include/aspect/boundary_composition/spherical_constant.h
U trunk/aspect/include/aspect/boundary_temperature/initial_temperature.h
U trunk/aspect/include/aspect/geometry_model/interface.h
U trunk/aspect/include/aspect/initial_conditions/harmonic_perturbation.h
U trunk/aspect/include/aspect/material_model/interface.h
U trunk/aspect/include/aspect/material_model/latent_heat.h
U trunk/aspect/include/aspect/mesh_refinement/composition.h
U trunk/aspect/include/aspect/plugins.h
U trunk/aspect/include/aspect/simulator.h
U trunk/aspect/include/aspect/simulator_access.h
U trunk/aspect/include/aspect/termination_criteria/end_time.h
U trunk/aspect/include/aspect/termination_criteria/interface.h
U trunk/aspect/include/aspect/velocity_boundary_conditions/gplates.h
U trunk/aspect/source/boundary_composition/initial_composition.cc
U trunk/aspect/source/boundary_composition/interface.cc
U trunk/aspect/source/boundary_composition/spherical_constant.cc
U trunk/aspect/source/boundary_temperature/constant.cc
U trunk/aspect/source/boundary_temperature/initial_temperature.cc
U trunk/aspect/source/boundary_temperature/interface.cc
U trunk/aspect/source/geometry_model/box.cc
U trunk/aspect/source/geometry_model/interface.cc
U trunk/aspect/source/geometry_model/sphere.cc
U trunk/aspect/source/gravity_model/interface.cc
U trunk/aspect/source/initial_conditions/adiabatic.cc
U trunk/aspect/source/initial_conditions/harmonic_perturbation.cc
U trunk/aspect/source/initial_conditions/interface.cc
U trunk/aspect/source/main.cc
U trunk/aspect/source/material_model/interface.cc
U trunk/aspect/source/material_model/latent_heat.cc
U trunk/aspect/source/material_model/simple.cc
U trunk/aspect/source/material_model/steinberger.cc
U trunk/aspect/source/mesh_refinement/composition.cc
U trunk/aspect/source/mesh_refinement/density.cc
U trunk/aspect/source/mesh_refinement/nonadiabatic_temperature.cc
U trunk/aspect/source/mesh_refinement/topography.cc
U trunk/aspect/source/mesh_refinement/viscosity.cc
U trunk/aspect/source/postprocess/composition_statistics.cc
U trunk/aspect/source/postprocess/depth_average.cc
U trunk/aspect/source/postprocess/heat_flux_statistics.cc
U trunk/aspect/source/postprocess/table_heat_flux_statistics.cc
U trunk/aspect/source/postprocess/temperature_statistics.cc
U trunk/aspect/source/postprocess/visualization/density.cc
U trunk/aspect/source/postprocess/visualization/dynamic_topography.cc
U trunk/aspect/source/postprocess/visualization/friction_heating.cc
U trunk/aspect/source/postprocess/visualization/melt_fraction.cc
U trunk/aspect/source/postprocess/visualization/nonadiabatic_pressure.cc
U trunk/aspect/source/postprocess/visualization/nonadiabatic_temperature.cc
U trunk/aspect/source/postprocess/visualization/partition.cc
U trunk/aspect/source/postprocess/visualization/seismic_vp.cc
U trunk/aspect/source/postprocess/visualization/seismic_vs.cc
U trunk/aspect/source/postprocess/visualization/specific_heat.cc
U trunk/aspect/source/postprocess/visualization/strain_rate.cc
U trunk/aspect/source/postprocess/visualization/thermal_expansivity.cc
U trunk/aspect/source/postprocess/visualization/thermodynamic_phase.cc
U trunk/aspect/source/postprocess/visualization/viscosity.cc
U trunk/aspect/source/postprocess/visualization/viscosity_ratio.cc
U trunk/aspect/source/postprocess/visualization.cc
U trunk/aspect/source/simulator/assembly.cc
U trunk/aspect/source/simulator/checkpoint_restart.cc
U trunk/aspect/source/simulator/core.cc
U trunk/aspect/source/simulator/helper_functions.cc
U trunk/aspect/source/simulator/initial_conditions.cc
U trunk/aspect/source/simulator/nullspace.cc
U trunk/aspect/source/simulator/parameters.cc
U trunk/aspect/source/simulator/solver.cc
U trunk/aspect/source/termination_criteria/end_time.cc
U trunk/aspect/source/termination_criteria/interface.cc
U trunk/aspect/source/velocity_boundary_conditions/gplates.cc
http://www.dealii.org/websvn/revision.php?repname=Aspect+Repository&path=%2F&rev=2503&peg=2503
Diff:
Modified: trunk/aspect/include/aspect/boundary_composition/box.h
===================================================================
--- trunk/aspect/include/aspect/boundary_composition/box.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/boundary_composition/box.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -39,7 +39,7 @@
*/
template <int dim>
class Box : public Interface<dim>,
- public SimulatorAccess<dim>
+ public SimulatorAccess<dim>
{
public:
/**
Modified: trunk/aspect/include/aspect/boundary_composition/initial_composition.h
===================================================================
--- trunk/aspect/include/aspect/boundary_composition/initial_composition.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/boundary_composition/initial_composition.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -70,7 +70,7 @@
* Nusselt number indicating heat flux.
*/
virtual
- double minimal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const;
+ double minimal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const;
/**
* Return the maximal composition on that part of the boundary
@@ -80,7 +80,7 @@
* Nusselt number indicating heat flux.
*/
virtual
- double maximal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const;
+ double maximal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const;
/**
* Declare the parameters this class takes through input files.
Modified: trunk/aspect/include/aspect/boundary_composition/spherical_constant.h
===================================================================
--- trunk/aspect/include/aspect/boundary_composition/spherical_constant.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/boundary_composition/spherical_constant.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -69,7 +69,7 @@
* Nusselt number indicating heat flux.
*/
virtual
- double minimal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const;
+ double minimal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const;
/**
* Return the maximal composition on that part of the boundary
@@ -79,7 +79,7 @@
* Nusselt number indicating heat flux.
*/
virtual
- double maximal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const;
+ double maximal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const;
/**
* Declare the parameters this class takes through input files.
Modified: trunk/aspect/include/aspect/boundary_temperature/initial_temperature.h
===================================================================
--- trunk/aspect/include/aspect/boundary_temperature/initial_temperature.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/boundary_temperature/initial_temperature.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -67,7 +67,7 @@
* Nusselt number indicating heat flux.
*/
virtual
- double minimal_temperature (const std::set<types::boundary_id>& fixed_boundary_ids) const;
+ double minimal_temperature (const std::set<types::boundary_id> &fixed_boundary_ids) const;
/**
* Return the maximal the temperature on that part of the boundary
@@ -77,7 +77,7 @@
* Nusselt number indicating heat flux.
*/
virtual
- double maximal_temperature (const std::set<types::boundary_id>& fixed_boundary_ids) const;
+ double maximal_temperature (const std::set<types::boundary_id> &fixed_boundary_ids) const;
/**
* Declare the parameters this class takes through input files.
Modified: trunk/aspect/include/aspect/geometry_model/interface.h
===================================================================
--- trunk/aspect/include/aspect/geometry_model/interface.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/geometry_model/interface.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -128,7 +128,7 @@
/**
* Returns a set of periodic boundary pairs. The elements of the set are
a pair of boundary ids and a cartesian unit direction each. The base class
- returns an empty set, so this does nothing unless you specifically use a
+ returns an empty set, so this does nothing unless you specifically use a
geometry model with periodic boundary conditions
**/
virtual
Modified: trunk/aspect/include/aspect/initial_conditions/harmonic_perturbation.h
===================================================================
--- trunk/aspect/include/aspect/initial_conditions/harmonic_perturbation.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/initial_conditions/harmonic_perturbation.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -44,71 +44,71 @@
template <int dim>
class HarmonicPerturbation : public Interface<dim>, public ::aspect::SimulatorAccess<dim>
{
- public:
- /**
- * Return the initial temperature as a function of position.
- */
- virtual
- double initial_temperature (const Point<dim> &position) const;
+ public:
+ /**
+ * Return the initial temperature as a function of position.
+ */
+ virtual
+ double initial_temperature (const Point<dim> &position) const;
- /**
- * Declare the parameters this class takes through input files.
- */
- static
- void
- declare_parameters (ParameterHandler &prm);
+ /**
+ * Declare the parameters this class takes through input files.
+ */
+ static
+ void
+ declare_parameters (ParameterHandler &prm);
- /**
- * Read the parameters this class declares from the parameter
- * file.
- */
- virtual
- void
- parse_parameters (ParameterHandler &prm);
+ /**
+ * Read the parameters this class declares from the parameter
+ * file.
+ */
+ virtual
+ void
+ parse_parameters (ParameterHandler &prm);
- private:
+ private:
- /**
- * Returns spherical coordinates of a cartesian position.
- */
- const Tensor<1,dim>
- spherical_surface_coordinates(const Tensor<1,dim> &position) const;
+ /**
+ * Returns spherical coordinates of a cartesian position.
+ */
+ const Tensor<1,dim>
+ spherical_surface_coordinates(const Tensor<1,dim> &position) const;
- /**
- * The radial/depth wave number of the harmonic perturbation.
- * All wave number variables are in fact twice the wave number in a
- * mathematical sense. This allows the user to prescribe
- * a single up- / downswing or half periods.
- */
- int vertical_wave_number;
+ /**
+ * The radial/depth wave number of the harmonic perturbation.
+ * All wave number variables are in fact twice the wave number in a
+ * mathematical sense. This allows the user to prescribe
+ * a single up- / downswing or half periods.
+ */
+ int vertical_wave_number;
- /**
- * The lateral wave number of the harmonic perturbation in the first dimension.
- * This is the only lateral wave number in 2D and equals the degree of
- * the spherical harmonics in a 3D spherical shell.
- */
- int lateral_wave_number_1;
+ /**
+ * The lateral wave number of the harmonic perturbation in the first dimension.
+ * This is the only lateral wave number in 2D and equals the degree of
+ * the spherical harmonics in a 3D spherical shell.
+ */
+ int lateral_wave_number_1;
- /**
- * The lateral wave number of the harmonic perturbation in the second dimension.
- * This is not used in 2D and equals the order of
- * the spherical harmonics in a 3D spherical shell.
- */
- int lateral_wave_number_2;
+ /**
+ * The lateral wave number of the harmonic perturbation in the second dimension.
+ * This is not used in 2D and equals the order of
+ * the spherical harmonics in a 3D spherical shell.
+ */
+ int lateral_wave_number_2;
- /**
- * The maximal magnitude of the harmonic perturbation.
- */
- double magnitude;
+ /**
+ * The maximal magnitude of the harmonic perturbation.
+ */
+ double magnitude;
- /**
- * The background temperature the harmonic perturbation is applied on in
- * an incompressible material model. In case of a compressible material model
- * the perturbation is applied on top of an adiabatic profile and this variable
- * is not used at all.
- */
- double reference_temperature;
+ /**
+ * The background temperature the harmonic perturbation is applied on in
+ * an incompressible material model. In case of a compressible material model
+ * the perturbation is applied on top of an adiabatic profile and this variable
+ * is not used at all.
+ */
+ double reference_temperature;
};
}
}
Modified: trunk/aspect/include/aspect/material_model/interface.h
===================================================================
--- trunk/aspect/include/aspect/material_model/interface.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/material_model/interface.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -322,7 +322,7 @@
const NonlinearDependence::Dependence dependence) const;
/**
- * Return the partial derivative of the compressibility function on the
+ * Return the partial derivative of the compressibility function on the
* variable indicates as last argument.
*
* The default implementation of this function returns zero
@@ -564,7 +564,7 @@
* The product of (minus) the change of entropy $-\Delta S$ at a
* phase transition and the derivative of the phase function
* $X=X(p,T,\mathfrak c,\mathbf x)$ with regard to temperature
- * at the given positions.
+ * at the given positions.
*/
std::vector<double> entropy_derivative_temperature;
/**
@@ -658,10 +658,10 @@
* Return the compressibility coefficient
* $ rac 1
ho rac{\partial
ho}{\partial p}$ of the model as a
* function of temperature, pressure and position.
- *
- * The compressibility can equivalently be computed as
- * $- rac 1V rac{\partial V}{\partial p}$. Note the difference
- * in sign.
+ *
+ * The compressibility can equivalently be computed as
+ * $- rac 1V rac{\partial V}{\partial p}$. Note the difference
+ * in sign.
*/
virtual double compressibility (const double temperature,
const double pressure,
@@ -684,89 +684,92 @@
* $lpha=- rac{1}{
ho} rac{d
ho}{dT}$. Since the density
* <i>decreases</i> with temperature for almost all models,
* $lpha$ is usually positive.
- *
- * The thermal expansion coefficient can equivalently be computed as
- * $ rac 1V rac{\partial V}{\partial T}$. Note the difference
- * in sign.
*
+ * The thermal expansion coefficient can equivalently be computed as
+ * $ rac 1V rac{\partial V}{\partial T}$. Note the difference
+ * in sign.
+ *
* This function has a default implementation that computes $lpha$
- * through its definition above, using the density() and density_derivative()
- * functions.
+ * through its definition above, using the density() and
+ * density_derivative() functions.
*/
virtual double thermal_expansion_coefficient (const double temperature,
const double pressure,
const std::vector<double> &compositional_fields,
const Point<dim> &position) const=0;
- /**
- * Return the product of the change in entropy across phase
- * transitions, the pressure derivative of the phase function
- * (if this is the pressure derivative) or the product of the
- * former two and the Clapeyron slope (if this is the
- * temperature derivative).
- * The entropy change across a phase transition can be calculated
- * as $ rac{\gamma \Delta
ho}{
ho_ ext{light}
ho_ ext{heavy}}$.
- * $\gamma$ is the Clapeyron slope of the phase transition,
- * $\Delta
ho$ is the density jump across the phase transition,
- * $
ho_ ext{light}$ is the density of the light material
- * (above the phase transition) and $
ho_ ext{heavy}$ the
- * density of the heavy material (below the phase transition).
- * The phase function hat values ranging from 0 to 1 indicating
- * which percentage of the material has already undergone the phase
- * transition. Its argument is usually the excess pressure
- * $\pi = p - p_0 - \gamma T$, where $p_0$ is the zero-degree
- * transition pressure.
- *
- * This function has a default implementation that sets
- * the entropy gradient to zero (assuming no phase changes).
- */
- virtual double entropy_derivative (const double temperature,
- const double pressure,
- const std::vector<double> &compositional_fields,
- const Point<dim> &position,
- const NonlinearDependence::Dependence dependence) const;
+ /**
+ * Return the product of the change in entropy across phase
+ * transitions, the pressure derivative of the phase function
+ * (if this is the pressure derivative) or the product of the
+ * former two and the Clapeyron slope (if this is the
+ * temperature derivative).
+ * The entropy change across a phase transition can be calculated
+ * as $ rac{\gamma \Delta
ho}{
ho_ ext{light}
ho_ ext{heavy}}$.
+ * $\gamma$ is the Clapeyron slope of the phase transition,
+ * $\Delta
ho$ is the density jump across the phase transition,
+ * $
ho_ ext{light}$ is the density of the light material
+ * (above the phase transition) and $
ho_ ext{heavy}$ the
+ * density of the heavy material (below the phase transition).
+ * The phase function hat values ranging from 0 to 1 indicating
+ * which percentage of the material has already undergone the phase
+ * transition. Its argument is usually the excess pressure
+ * $\pi = p - p_0 - \gamma T$, where $p_0$ is the zero-degree
+ * transition pressure.
+ *
+ * This function has a default implementation that sets
+ * the entropy gradient to zero (assuming no phase changes).
+ */
+ virtual double entropy_derivative (const double temperature,
+ const double pressure,
+ const std::vector<double> &compositional_fields,
+ const Point<dim> &position,
+ const NonlinearDependence::Dependence dependence) const;
- /**
- * Return the change in the compositional field compositional_variable
- * due to reactions between different compositional fields.
- * It is assumed that there is always an equilibrium between the
- * compositional fields (because the time scale of reactions is
- * normally much shorter than that of convection), so this is an actual
- * amount of material, which is added to or substracted from the current
- * value of the compositional field, and NOT a reaction rate.
- * The idea is, that in dependence of temperature, pressure, position and
- * the compositional fields themselves an equilibrium can be calculated,
- * and the difference between the current value and the equilibrium can
- * be added to the respective compositional field.
- *
- * For mass conservation it should ALWAYS be checked that what is subtracted
- * from one field is added to another field (and the other way round) and
- * that it is never more substracted than the actual value of a field (so
- * it does not get negative).
- *
- * This function has a default implementation that sets
- * the reaction term to zero (assuming no reactions).
- */
- virtual double reaction_term (const double temperature,
- const double pressure,
- const std::vector<double> &compositional_fields,
- const Point<dim> &position,
- const unsigned int compositional_variable) const;
+ /**
+ * Return the change in the compositional field compositional_variable
+ * due to reactions between different compositional fields.
+ * It is assumed that there is always an equilibrium between the
+ * compositional fields (because the time scale of reactions is
+ * normally much shorter than that of convection), so this is an actual
+ * amount of material, which is added to or substracted from the current
+ * value of the compositional field, and NOT a reaction rate.
+ * The idea is, that in dependence of temperature, pressure, position and
+ * the compositional fields themselves an equilibrium can be calculated,
+ * and the difference between the current value and the equilibrium can
+ * be added to the respective compositional field.
+ *
+ * For mass conservation it should ALWAYS be checked that what is subtracted
+ * from one field is added to another field (and the other way round) and
+ * that it is never more substracted than the actual value of a field (so
+ * it does not get negative).
+ *
+ * This function has a default implementation that sets
+ * the reaction term to zero (assuming no reactions).
+ */
+ virtual double reaction_term (const double temperature,
+ const double pressure,
+ const std::vector<double> &compositional_fields,
+ const Point<dim> &position,
+ const unsigned int compositional_variable) const;
- /**
- * Return the thermal conductivity $k$ of the model as a function of temperature,
- * pressure and position. The units of $k$ are $ extrm{W} / extrm{m} / extrm{K}$
- * in 3d, and $ extrm{W} / extrm{K}$ in 2d. This is easily see by considering that
- * $k$ is the heat flux density (i.e., Watts per unit area perpendicular to the heat
- * flux direction) per unit temperature gradient (i.e., Kelvin per meter). The unit
- * area has units $m^2$ in 3d, but only $m$ in 2d, yielding the stated units for $k$.
- *
- * Note that the thermal <i>conductivity</i> $k$ is related to the thermal
- * <i>diffusivity</i> $\kappa$ as $k = \kappa
ho c_p$. In essence, the conductivity
- * relates to the question of how thermal energy diffuses whereas the diffusivity
- * relates to the question of how the temperature diffuses. $\kappa$ has units
- * $ extrm{m}^2/ extrm{s}$.
- */
+ /**
+ * Return the thermal conductivity $k$ of the model as a function of
+ * temperature, pressure and position. The units of $k$ are
+ * $ extrm{W} / extrm{m} / extrm{K}$ in 3d, and $ extrm{W} /
+ * extrm{K}$ in 2d. This is easily see by considering that $k$ is
+ * the heat flux density (i.e., Watts per unit area perpendicular to
+ * the heat flux direction) per unit temperature gradient (i.e.,
+ * Kelvin per meter). The unit area has units $m^2$ in 3d, but only
+ * $m$ in 2d, yielding the stated units for $k$.
+ *
+ * Note that the thermal <i>conductivity</i> $k$ is related to the
+ * thermal <i>diffusivity</i> $\kappa$ as $k = \kappa
ho c_p$. In
+ * essence, the conductivity relates to the question of how thermal
+ * energy diffuses whereas the diffusivity relates to the question of
+ * how the temperature diffuses. $\kappa$ has units
+ * $ extrm{m}^2/ extrm{s}$.
+ */
virtual double thermal_conductivity (const double temperature,
const double pressure,
const std::vector<double> &compositional_fields,
@@ -781,7 +784,7 @@
* @param out
*/
void evaluate(const typename Interface<dim>::MaterialModelInputs &in,
- typename Interface<dim>::MaterialModelOutputs &out) const;
+ typename Interface<dim>::MaterialModelOutputs &out) const;
};
Modified: trunk/aspect/include/aspect/material_model/latent_heat.h
===================================================================
--- trunk/aspect/include/aspect/material_model/latent_heat.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/material_model/latent_heat.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -32,21 +32,21 @@
{
using namespace dealii;
- /**
- * A material model that implements a standard approximation
- * of the latent heat terms following Christensen \& Yuen, 1986.
- * The change of entropy is calculated as
- * $Delta S = \gamma rac{\Delta
ho}{
ho^2}$ with the
- * Clapeyron slope $\gamma$ and the density change $\Delta
ho$
- * of the phase transition being input parameters.
- * This model employs an analytic phase function in the form
- * $X=0.5 \left( 1 + anh \left( rac{\Delta p}{\Delta p_0}
ight)
ight)$
- * with $\Delta p = p - p_transition - \gamma \left( T - T_transition
ight)$
- * and $\Delta p_0$ being the pressure difference over the width
- * of the phase transition (specified as input parameter).
- *
- * @ingroup MaterialModels
- */
+ /**
+ * A material model that implements a standard approximation
+ * of the latent heat terms following Christensen \& Yuen, 1986.
+ * The change of entropy is calculated as
+ * $Delta S = \gamma rac{\Delta
ho}{
ho^2}$ with the
+ * Clapeyron slope $\gamma$ and the density change $\Delta
ho$
+ * of the phase transition being input parameters.
+ * This model employs an analytic phase function in the form
+ * $X=0.5 \left( 1 + anh \left( rac{\Delta p}{\Delta p_0}
ight)
ight)$
+ * with $\Delta p = p - p_transition - \gamma \left( T - T_transition
ight)$
+ * and $\Delta p_0$ being the pressure difference over the width
+ * of the phase transition (specified as input parameter).
+ *
+ * @ingroup MaterialModels
+ */
template <int dim>
class LatentHeat : public MaterialModel::InterfaceCompatibility<dim>, public ::aspect::SimulatorAccess<dim>
{
@@ -213,9 +213,9 @@
virtual
double
phase_function (const Point<dim> &position,
- const double temperature,
- const double pressure,
- const int phase) const;
+ const double temperature,
+ const double pressure,
+ const int phase) const;
/**
* Derivative of the phase function (argument is the
@@ -224,9 +224,9 @@
virtual
double
phase_function_derivative (const Point<dim> &position,
- const double temperature,
- const double pressure,
- const int phase) const;
+ const double temperature,
+ const double pressure,
+ const int phase) const;
// list of depth, width and Clapeyron slopes for the different phase
// transitions
Modified: trunk/aspect/include/aspect/mesh_refinement/composition.h
===================================================================
--- trunk/aspect/include/aspect/mesh_refinement/composition.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/mesh_refinement/composition.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -42,16 +42,16 @@
public SimulatorAccess<dim>
{
public:
- /**
- * Initialize this class for a given simulator. This function calls
- * the corresponding object in the SimulatorAccess class and then
- * initializes the current object by looking up the correct number
- * of compositional fields through the now initialized SimulatorAccess
- * class.
- *
- * @param simulator A reference to the main simulator object.
- */
- virtual void initialize (const Simulator<dim> &simulator);
+ /**
+ * Initialize this class for a given simulator. This function calls
+ * the corresponding object in the SimulatorAccess class and then
+ * initializes the current object by looking up the correct number
+ * of compositional fields through the now initialized SimulatorAccess
+ * class.
+ *
+ * @param simulator A reference to the main simulator object.
+ */
+ virtual void initialize (const Simulator<dim> &simulator);
/**
* Execute this mesh refinement criterion.
Modified: trunk/aspect/include/aspect/plugins.h
===================================================================
--- trunk/aspect/include/aspect/plugins.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/plugins.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -55,7 +55,7 @@
* otherwise unused namespace.
*/
template <typename InterfaceClass,
- typename ModelClass>
+ typename ModelClass>
struct RegisterHelper
{
/**
Modified: trunk/aspect/include/aspect/simulator.h
===================================================================
--- trunk/aspect/include/aspect/simulator.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/simulator.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -109,14 +109,14 @@
struct NullspaceRemoval
{
- enum Kind
- {
- none = 0,
- net_rotation = 0x1,
- net_translation = 0x2,
- angular_momentum = 0x4,
- translational_momentum = 0x8
- };
+ enum Kind
+ {
+ none = 0,
+ net_rotation = 0x1,
+ net_translation = 0x2,
+ angular_momentum = 0x4,
+ translational_momentum = 0x8
+ };
};
public:
@@ -926,7 +926,7 @@
* <code>source/simulator/helper_functions.cc</code>.
*/
void interpolate_onto_velocity_system(const TensorFunction<1,dim> &func,
- LinearAlgebra::Vector &vec);
+ LinearAlgebra::Vector &vec);
/**
* Set up data structures for null space removal. Called after every mesh refinement.
@@ -947,7 +947,7 @@
* <code>source/simulator/nullspace.cc</code>.
*/
void remove_nullspace(LinearAlgebra::BlockVector &relevant_dst,
- LinearAlgebra::BlockVector &tmp_distributed_stokes);
+ LinearAlgebra::BlockVector &tmp_distributed_stokes);
/**
* Remove the angular momentum of the given vector
Modified: trunk/aspect/include/aspect/simulator_access.h
===================================================================
--- trunk/aspect/include/aspect/simulator_access.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/simulator_access.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -293,7 +293,7 @@
*/
void
get_depth_average_composition(const unsigned int composition_index,
- std::vector<double> &values) const;
+ std::vector<double> &values) const;
/**
* Compute a depth average of the current viscosity
Modified: trunk/aspect/include/aspect/termination_criteria/end_time.h
===================================================================
--- trunk/aspect/include/aspect/termination_criteria/end_time.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/termination_criteria/end_time.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -41,7 +41,7 @@
class EndTime : public Interface<dim>, public SimulatorAccess<dim>
{
public:
-
+
/**
* Check this termination criterion and possibly reduce time step size
*/
Modified: trunk/aspect/include/aspect/termination_criteria/interface.h
===================================================================
--- trunk/aspect/include/aspect/termination_criteria/interface.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/termination_criteria/interface.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -91,18 +91,18 @@
bool
execute () = 0;
- /**
- * Check for last time step and if so reduce the time step to user
- * specified end time
- *
- * @return Reduced or current time step size
- *
- * @note A reduced time step size may be returned for the
- * last time step. For all other time steps, the current time step size
- * (provided as argument) will be returned. The returned time step size
- * will be greater than zero, and less than or equal to the given argument
- * put into this function.
- */
+ /**
+ * Check for last time step and if so reduce the time step to user
+ * specified end time
+ *
+ * @return Reduced or current time step size
+ *
+ * @note A reduced time step size may be returned for the
+ * last time step. For all other time steps, the current time step size
+ * (provided as argument) will be returned. The returned time step size
+ * will be greater than zero, and less than or equal to the given argument
+ * put into this function.
+ */
virtual double check_for_last_time_step (const double time_step) const;
/**
@@ -176,19 +176,19 @@
std::pair<bool,bool>
execute () const;
- /**
- * Check all of the termination criteria objects that have
- * been requested in the input file for criteria regarding
- * last time step and if so get the minimum of these values.
- *
- * @return Reduced or current time step size
- *
- * @note A reduced time step size may be returned for the
- * last time step. For all other time steps, the current time step size
- * (provided as argument) will be returned. The returned time step size
- * will be greater than zero, and less than or equal to the given argument
- * put into this function.
- */
+ /**
+ * Check all of the termination criteria objects that have
+ * been requested in the input file for criteria regarding
+ * last time step and if so get the minimum of these values.
+ *
+ * @return Reduced or current time step size
+ *
+ * @note A reduced time step size may be returned for the
+ * last time step. For all other time steps, the current time step size
+ * (provided as argument) will be returned. The returned time step size
+ * will be greater than zero, and less than or equal to the given argument
+ * put into this function.
+ */
double check_for_last_time_step (const double time_step) const;
/**
Modified: trunk/aspect/include/aspect/velocity_boundary_conditions/gplates.h
===================================================================
--- trunk/aspect/include/aspect/velocity_boundary_conditions/gplates.h 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/include/aspect/velocity_boundary_conditions/gplates.h 2014-04-13 14:33:38 UTC (rev 2503)
@@ -160,7 +160,7 @@
* @param s_position Position in spherical coordinates (theta,phi,radius)
*/
Tensor<1,3> sphere_to_cart_velocity(const Tensor<1,2> &s_velocities,
- const Tensor<1,3> &s_position) const;
+ const Tensor<1,3> &s_position) const;
/**
* calculates the index given a certain position
@@ -169,7 +169,7 @@
* @param position Input position, which is converted to spatial index
*/
void
- calculate_spatial_index(int* index, const Tensor<1,3> position) const;
+ calculate_spatial_index(int *index, const Tensor<1,3> position) const;
/**
* This function adds a certain data point to the interpolated
@@ -179,7 +179,7 @@
* need to be tangential to the surface).
*/
double
- add_interpolation_point(Tensor<1,3>& surf_vel,
+ add_interpolation_point(Tensor<1,3> &surf_vel,
const Tensor<1,3> position,
const int spatial_index[2],
const double time_weight,
@@ -201,8 +201,8 @@
*/
Tensor<1,3>
get_grid_point_position(const unsigned int theta_index,
- const unsigned int phi_index,
- const bool cartesian) const;
+ const unsigned int phi_index,
+ const bool cartesian) const;
/**
* Returns the arc distance of two points on a sphere surface.
@@ -215,7 +215,7 @@
*/
Tensor<1,3>
interpolate ( const Tensor<1,3> position,
- const double time_weight) const;
+ const double time_weight) const;
/**
* Bounds the theta and phi indices to the right sizes.
@@ -369,7 +369,7 @@
*/
void
end_time_dependence (const int timestep,
- const bool first_process);
+ const bool first_process);
/**
* Create a filename out of the name template.
Modified: trunk/aspect/source/boundary_composition/initial_composition.cc
===================================================================
--- trunk/aspect/source/boundary_composition/initial_composition.cc 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/source/boundary_composition/initial_composition.cc 2014-04-13 14:33:38 UTC (rev 2503)
@@ -45,7 +45,7 @@
template <int dim>
double
InitialComposition<dim>::
- minimal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const
+ minimal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const
{
return min_composition;
}
@@ -55,7 +55,7 @@
template <int dim>
double
InitialComposition<dim>::
- maximal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const
+ maximal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const
{
return max_composition;
}
@@ -111,15 +111,15 @@
"A model in which the composition at the boundary"
"is chosen to be the same as given in the initial"
"conditions."
- "
"
- "Because this class simply takes what the initial "
- "composition had described, this class can not "
- "know certain pieces of information such as the "
- "minimal and maximal composition on the boundary. "
- "For operations that require this, for example in "
- "postprocessing, this boundary composition model "
- "must therefore be told what the minimal and "
- "maximal values on the boundary are. This is done "
- "using parameters set in section ``Boundary composition model/Initial composition''.")
+ "
"
+ "Because this class simply takes what the initial "
+ "composition had described, this class can not "
+ "know certain pieces of information such as the "
+ "minimal and maximal composition on the boundary. "
+ "For operations that require this, for example in "
+ "postprocessing, this boundary composition model "
+ "must therefore be told what the minimal and "
+ "maximal values on the boundary are. This is done "
+ "using parameters set in section ``Boundary composition model/Initial composition''.")
}
}
Modified: trunk/aspect/source/boundary_composition/interface.cc
===================================================================
--- trunk/aspect/source/boundary_composition/interface.cc 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/source/boundary_composition/interface.cc 2014-04-13 14:33:38 UTC (rev 2503)
@@ -108,18 +108,18 @@
const std::string pattern_of_names
= std_cxx1x::get<dim>(registered_plugins).get_pattern_of_names ();
try
- {
- prm.declare_entry ("Model name", "",
- Patterns::Selection (pattern_of_names),
- "Select one of the following models:
"
- +
- std_cxx1x::get<dim>(registered_plugins).get_description_string());
- }
+ {
+ prm.declare_entry ("Model name", "",
+ Patterns::Selection (pattern_of_names),
+ "Select one of the following models:
"
+ +
+ std_cxx1x::get<dim>(registered_plugins).get_description_string());
+ }
catch (const ParameterHandler::ExcValueDoesNotMatchPattern &)
- {
+ {
// ignore the fact that the default value for this parameter
// does not match the pattern
- }
+ }
}
prm.leave_subsection ();
Modified: trunk/aspect/source/boundary_composition/spherical_constant.cc
===================================================================
--- trunk/aspect/source/boundary_composition/spherical_constant.cc 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/source/boundary_composition/spherical_constant.cc 2014-04-13 14:33:38 UTC (rev 2503)
@@ -65,7 +65,7 @@
template <int dim>
double
SphericalConstant<dim>::
- minimal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const
+ minimal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const
{
return std::min (inner_composition, outer_composition);
}
@@ -75,7 +75,7 @@
template <int dim>
double
SphericalConstant<dim>::
- maximal_composition (const std::set<types::boundary_id>& fixed_boundary_ids) const
+ maximal_composition (const std::set<types::boundary_id> &fixed_boundary_ids) const
{
return std::max (inner_composition, outer_composition);
}
Modified: trunk/aspect/source/boundary_temperature/constant.cc
===================================================================
--- trunk/aspect/source/boundary_temperature/constant.cc 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/source/boundary_temperature/constant.cc 2014-04-13 14:33:38 UTC (rev 2503)
@@ -43,8 +43,8 @@
return it->second;
else
{
- Assert (false, ExcMessage ("Unknown boundary indicator."));
- return std::numeric_limits<double>::quiet_NaN();
+ Assert (false, ExcMessage ("Unknown boundary indicator."));
+ return std::numeric_limits<double>::quiet_NaN();
}
}
@@ -58,7 +58,7 @@
double min = it->second;
++it;
- for( ; it != boundary_temperatures.end(); ++it)
+ for ( ; it != boundary_temperatures.end(); ++it)
if ( it->second < min )
min = it->second;
@@ -76,10 +76,10 @@
double max = it->second;
++it;
- for( ; it != boundary_temperatures.end(); ++it)
+ for ( ; it != boundary_temperatures.end(); ++it)
if ( it->second > max )
max = it->second;
-
+
return max;
}
@@ -94,14 +94,14 @@
prm.enter_subsection("Constant");
{
prm.declare_entry ("Boundary indicator to temperature mappings", "",
- Patterns::Map (Patterns::Integer(0, std::numeric_limits<types::boundary_id>::max()),
- Patterns::Double()),
- "A comma separated list of mappings between boundary "
- "indicators and the temperature associated with the "
- "boundary indicators. The format for this list is "
- "``indicator1 : value1, indicator2 : value2, ...'', "
- "where each indicator is a valid boundary indicator "
- "and each value is the temperature of that boundary." );
+ Patterns::Map (Patterns::Integer(0, std::numeric_limits<types::boundary_id>::max()),
+ Patterns::Double()),
+ "A comma separated list of mappings between boundary "
+ "indicators and the temperature associated with the "
+ "boundary indicators. The format for this list is "
+ "``indicator1 : value1, indicator2 : value2, ...'', "
+ "where each indicator is a valid boundary indicator "
+ "and each value is the temperature of that boundary." );
}
prm.leave_subsection ();
}
@@ -139,10 +139,10 @@
while (ss.peek()==' ') ss.get(c); // eat spaces
if (ss.peek() != ':')
- {
+ {
Assert(false, ExcMessage("Cannot parse boundary temperature list, format"
"``boundary_id : value'' appears to be missing"));
- }
+ }
else
ss.get(c); // read the ':'
@@ -150,9 +150,9 @@
std::getline(ss,value); // read until the end of the string
AssertThrow (boundary_temperatures.find(boundary_id) == boundary_temperatures.end(),
- ExcMessage ("Boundary indicator <" + Utilities::int_to_string(boundary_id) +
- "> appears more than once in the list of indicators "
- "for constant temperature boundary conditions."));
+ ExcMessage ("Boundary indicator <" + Utilities::int_to_string(boundary_id) +
+ "> appears more than once in the list of indicators "
+ "for constant temperature boundary conditions."));
boundary_temperatures[boundary_id] = Utilities::string_to_double(value);
}
Modified: trunk/aspect/source/boundary_temperature/initial_temperature.cc
===================================================================
--- trunk/aspect/source/boundary_temperature/initial_temperature.cc 2014-04-13 14:28:54 UTC (rev 2502)
+++ trunk/aspect/source/boundary_temperature/initial_temperature.cc 2014-04-13 14:33:38 UTC (rev 2503)
@@ -44,7 +44,7 @@
template <int dim>
double
InitialTemperature<dim>::
- minimal_temperature (const std::set<types::boundary_id>& fixed_boundary_ids) const
+ minimal_temperature (const std::set<types::boundary_id> &fixed_boundary_ids) const
{
return min_temperature;
}
@@ -54,7 +54,7 @@
template <int dim>
double
InitialTemperature<dim>::
- maximal_temperature (const std::set<types::boundary_id>& fixed_boundary_ids) const
+ maximal_temperature (const std::set<types::boundary_id> &fixed_boundary_ids) const
{
return max_temperature;
}
@@ -110,15 +110,15 @@
"A model in which the temperature at the boundary"
"is chosen to be the same as given in the initial"
"conditions."
- "
"
- "Because this class simply takes what the initial "
- "temperature had described, this class can not "
- "know certain pieces of information such as the "
- "minimal and maximal temperature on the boundary. "
- "For operations that require this, for example in "
- "postprocessing, this boundary temperature model "
- "must therefore be told what the minimal and "
- "maximal values on the boundary are. This is done "
- "using parameters set in section ``Boundary temperature model/Initial temperature''.")
+ "
"
+ "Because this class simply takes what the initial "
+ "temperature had described, this class can not "
+ "know certain pieces of information such as the "
+ "minimal and maximal temperature on the boundary. "
+ "For operations that require this, for example in "
+ "postprocessing, this boundary temperature model "
+ "must therefore be told what the minimal and "
+ "maximal values on the boundary are. This is done "
+ "using parameters set in section ``Boundary temperature model/Initial temperature''.")
}
}
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