[cig-commits] [commit] master: Add descriptions of data output for non-solenoidal field. Fix overfilled verbatim in document. (4873f5e)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Tue Apr 8 03:04:31 PDT 2014
Repository : ssh://geoshell/calypso
On branch : master
Link : https://github.com/geodynamics/calypso/compare/bf5dcaf71a4089a4c2f22940f4edea71b9abedd1...9730b061d69d156b271dfe841a55ae371b4e1c03
>---------------------------------------------------------------
commit 4873f5e1acc772f43f44f088070984edac31125d
Author: Hiroaki Matsui <h_kemono at mac.com>
Date: Thu Mar 20 12:35:57 2014 -0700
Add descriptions of data output for non-solenoidal field.
Fix overfilled verbatim in document.
>---------------------------------------------------------------
4873f5e1acc772f43f44f088070984edac31125d
doc/tex_src/controls_CALYPSO.tex | 20 ++++++---
doc/tex_src/install_CALYPSO.tex | 6 ++-
doc/tex_src/outlines_CALYPSO.tex | 18 ++++----
doc/tex_src/programs_CALYPSO.tex | 90 ++++++++++++++++++++++++++++++----------
4 files changed, 94 insertions(+), 40 deletions(-)
diff --git a/doc/tex_src/controls_CALYPSO.tex b/doc/tex_src/controls_CALYPSO.tex
index e59673c..6553c4a 100644
--- a/doc/tex_src/controls_CALYPSO.tex
+++ b/doc/tex_src/controls_CALYPSO.tex
@@ -99,14 +99,22 @@ Supported field in the present version is listed in Table \ref{table:fields}
\hline
\verb|viscous_diffusion| & Viscous diffusion
& $-\nu \nabla \times \nabla \times \bvec{u}$ \\
-\verb|thermal_diffusion| & Termal diffusion & $ \kappa \nabla^{2} T $ \\
-\verb|magnetic_diffusion| & Magnetic diffusion
-& $-\eta \nabla \times \nabla \times \bvec{B}$ \\
-\verb poynting_flux & Poynting flux & $ \bvec{E} \times \bvec{B} $ \\
-\verb Lorentz_force & Lorentz force & $ \bvec{J} \times \bvec{B} $ \\
-\verb Coriolis_force & Coriolis force & $ -2 \Omega \hat{z} \times \bvec{u} $ \\
\verb buoyancy & Thermal buoyancy & $ -\alpha_{T} T \bvec{g} $ \\
\verb composite_buoyancy & Compositional buoyancy & $ -\alpha_{C} C\bvec{g} $\\
+\verb Lorentz_force & Lorentz force & $ \bvec{J} \times \bvec{B} $ \\
+\verb Coriolis_force & Coriolis force & $ -2 \Omega \hat{z} \times \bvec{u} $ \\
+\hline
+\verb|thermal_diffusion| & Termal diffusion & $ \kappa_{T} \nabla^{2} T $ \\
+\verb grad_temp & Temperature gradient & $ \nabla T$ \\
+\verb heat_flux & Advective heat flux & $ \bvec{u} T$ \\
+\hline
+\verb composition_diffusion & Compositional diffusion & $ \kappa_{C} \nabla^{2} C $ \\
+\verb grad_composition & Composition gradient & $ \nabla C$ \\
+\verb composite_flux & Advective composition flux & $ \bvec{u} C$ \\
+\hline
+\verb magnetic_diffusion & Magnetic diffusion
+& $-\eta \nabla \times \nabla \times \bvec{B}$ \\
+\verb poynting_flux & Poynting flux & $ \bvec{E} \times \bvec{B} $ \\
\hline
\verb rot_Lorentz_force & Curl of Lorentz force & $ \nabla \times \left(\bvec{J} \times \bvec{B}\right) $ \\
\verb rot_Coriolis_force & Curl of Coriolis force & $ -2 \Omega \nabla \times \left(\hat{z} \times \bvec{u} \right) $ \\
diff --git a/doc/tex_src/install_CALYPSO.tex b/doc/tex_src/install_CALYPSO.tex
index 3606374..c652018 100644
--- a/doc/tex_src/install_CALYPSO.tex
+++ b/doc/tex_src/install_CALYPSO.tex
@@ -90,8 +90,8 @@ After the installation, object modules can be deleted by the following command;
{./configure} generates a Makefile in the current directory. Available options for {\tt configure} can be checked using the {\tt ./configure --help} command. The following options are available in the {\tt configure} command.
%
+{\small
\begin{verbatim}
-
Optional Features:
--disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
@@ -121,6 +121,7 @@ Some influential environment variables:
FFTW3_LIBS linker flags for FFTW3, overriding pkg-config
\end{verbatim}
+}
%
An example of usage of the configure command is the following;
\begin{verbatim}
@@ -208,7 +209,8 @@ CMake is a cross-platform, open-source build system. CMake can be downloaded fro
\end{enumerate}
%
In this section, \verb|[CALYPSO\_HOME]/work| is used as the working directory.
-Options for CMake can be checked by \verb|cmake -i [CALYPSO\_HOME]| command at \verb|[CALYPSO\_HOME]/work|. There are a number of options can be found, but the following valuables are important settings for installation:
+Options for CMake can be checked by \verb|cmake -i [CALYPSO_HOME]| command at \verb|[CALYPSO_HOME]| \\
+\verb|/work|. There are a number of options can be found, but the following valuables are important settings for installation:
%
\begin{description}
\item{\verb|CMAKE_INSTALL_PREFIX|} Install directory
diff --git a/doc/tex_src/outlines_CALYPSO.tex b/doc/tex_src/outlines_CALYPSO.tex
index d08b6f4..d801106 100644
--- a/doc/tex_src/outlines_CALYPSO.tex
+++ b/doc/tex_src/outlines_CALYPSO.tex
@@ -146,34 +146,34 @@ The process of the simulation is as following:
%
\begin{enumerate}
\item Change to the directory for Benchmark Case 1 (for example) \\
+{\small
\begin{verbatim}
[username]$ cd [CALYPSO_DIR]/examples/dynamo_benchmark/dynamobench_case1
\end{verbatim}
+}
\item Create the grid files for the simulation \\
+{\small
\begin{verbatim}
[dynamobench_case_1]$ [CALYPSO_DIR]/bin/gen_sph_grids
\end{verbatim}
+}
\item Run simulation program
+{\small
\begin{verbatim}
[dynamobench_case_1]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_mhd
\end{verbatim}
+}
-\item To continue the simulation change \verb|rst_ctl| in \verb|control_MHD| from \\
-\begin{verbatim}
- rst_ctl dynamo_benchmark_1
-\end{verbatim}
- to
-\begin{verbatim}
- rst_ctl start_from_rst_file
-\end{verbatim}
- Continue simulation by repeating step 2.
+\item To continue the simulation, change the parameter \verb|rst_ctl| in \verb|control_MHD| from \verb|dynamo_benchmark_1| to \verb|start_from_rst_file| and continue simulation by repeating step 2.
\item To check the results for dynamo benchmark, run
+{\small
\begin{verbatim}
[dynamobench_case_1]$ mpirun -np 4 [CALYPSO_DIR]/bin/sph_dynamobench
\end{verbatim}
+}
\end{enumerate}
%
diff --git a/doc/tex_src/programs_CALYPSO.tex b/doc/tex_src/programs_CALYPSO.tex
index e6052b7..ba22d57 100644
--- a/doc/tex_src/programs_CALYPSO.tex
+++ b/doc/tex_src/programs_CALYPSO.tex
@@ -706,17 +706,19 @@ For vector field, spectrum for the poloidal and toroidal components are written
B_{Ssq}(l) &=& \frac{1}{V} \sum_{m=-l}^{m=l} \int \left(\bvec{B}_{Sl}^{\ m} \right)^{2} dV,
\nonumber \\
B_{Tsq}(l) &=& \frac{1}{V} \sum_{m=-l}^{m=l} \int \left(\bvec{B}_{Tl}^{\ m} \right)^{2} dV.
+\nonumber
\end{eqnarray}
-%
-If the vector field $\bvec{F}$ is not solenoidal (i.e. $\nabla \times \bvec{F} \neq 0$), The poloidal component of mean square data are included mean square field of the potential components as
+
+If the vector field $\bvec{F}$ is not solenoidal (i.e. $\nabla \cdot \bvec{F} \neq 0$), The poloidal component of mean square data are included mean square field of the potential components as
%
\begin{eqnarray}
F_{Ssq}(l) &=& \frac{1}{V} \sum_{m=-l}^{m=l} \int \left[\left(\bvec{B}_{Sl}^{\ m} \right)^{2}
+ \left(-\nabla \phi_{Fl}^{\ m} \right)^{2} \right] dV.
-\nonumber \\
+\nonumber
\end{eqnarray}
%
+%
\item{\tt [vol\_pwr\_prefix]\_m.dat} Volume average of mean square amplitude of the fields as a function of spherical harmonic order $m$. The zonal wave number is referred in this spectrum data. For scalar field, the spectrum is
\begin{eqnarray}
f_{sq}(m) &=& \frac{1}{V} \sum_{l=0}^{l=m} \int \left[ \left(f_{l}^{m} \right)^{2}
@@ -749,6 +751,7 @@ B_{Tsq}(n) &=& \frac{1}{V} \sum_{l=n}^{l=l-n} \int \left[\left(\bvec{B}_{Tl}^{\
\end{eqnarray}
\end{description}
+
%
\subsubsection{layered spectrum data}
@@ -822,11 +825,47 @@ The data file has the following headers in the first three lines,
The data consists of time step, time, and Gauss coefficients for each step in one line. If the Gauss coefficients data file exist before starting the simulation, programs append Gauss coefficients at the end of files without checking constancy of the number of data and order of the field. If you change the configuration of data output structure, please move the old Gauss coefficients file to another directory before starting the programs.
\subsection{Spectrum monitor data {\tt [picked\_sph\_prefix].dat}}
-This program output spectrum data at specified spherical harmonics modes and radial points in single text file. Spectrum data marked \verb|[Monitor_On]| are written in our line for each spherical harmonics mode and radial point every \verb|[increment_monitor]| steps. If the spectrum monitor data file exist before starting the simulation, programs append spectrum data at the end of files without checking constancy of the number of data and order of the field. If you change the configuration of data output structure, please move the old spectrum monitor file to another directory before starting the programs.
+This program outputs spherical harmonics coefficients at specified spherical harmonics modes and radial points in single text file. Spectrum data marked \verb|[Monitor_On]| are written in our line for each spherical harmonics mode and radial point every \\
+\verb|[increment_monitor]| steps. If the spectrum monitor data file exist before starting the simulation, programs append spectrum data at the end of files without checking constancy of the number of data and order of the field. If you change the configuration of data output structure, please move the old spectrum monitor file to another directory before starting the programs.
+
+If a vector field $\bvec{F}$ is not a solenoidal field, $\bvec{F}$ is described by the spherical harmonics coefficients of the poloidal $F_{Sl}^{\ m}$, toroidal $F_{Tl}^{\ m}$, and potential $\varphi_{l}^{m}$ components as
+\begin{eqnarray}
+\bvec{F}(r, \theta, \phi) & = & - \frac{1}{r^{2}}\frac{\partial \varphi_{0}^{0}}{\partial r} \hat{r}
+ + \sum_{l=1}^{L} \sum_{m=-l}^{l}
+\left[\nabla \times \nabla \times \left( F_{Sl}^{\ m} \hat{r} \right) + \nabla \times \left(F_{Tl}^{\ m}\right)
+ - \nabla \left(\varphi_{l}^{m} Y_{l}^{m} \right)\right].
+\nonumber
+\end{eqnarray}
+In Calypso, the following coefficients are written for the non-solenoidal vector.
+\begin{description}
+\item{\tt $\verb|[field_name]_pol|$ : }
+ $\left\{\begin{array}{ccr}
+\displaystyle{
+F_{Sl}^{\ m} - \frac{r^{2}}{l \left(l+1\right)} \frac{\partial \varphi_{l}^{m}}{\partial r} }
+& \mbox{for} & \left (l \ne 0 \right)\\
+\displaystyle{
+ -r^{2} \frac{\partial \varphi_{0}^{0}}{\partial r}
+} & \mbox{for} & \left (l = 0 \right)
+\end{array}
+\right.$
+\item{\tt $\verb|[field_name]_dpdr|$ : }
+$
+\left\{
+\begin{array}{ccr}
+\displaystyle{
+\frac{\partial F_{Sl}^{\ m}}{\partial r} - \varphi_{l}^{m}}
+ & \mbox{for} & \left (l \ne 0 \right)\\
+ 0 & \mbox{for} & \left (l = 0 \right)
+\end{array}
+\right. $
+\item{\tt $\verb|[field_name]_tor|$ : } $F_{Tl}^{\ m}$
+\end{description}
+
\newpage
-\section{Data transform program ({\tt sph\_snapshot} and {\tt sph\_zm\_snapshot})}
+\section{Data transform program \\
+({\tt sph\_snapshot} and {\tt sph\_zm\_snapshot})}
\label{section:assemble_sph}
%
\begin{figure}[htbp]
@@ -886,7 +925,9 @@ The same files as the simulation program are read in this program, and field dat
\label{fig:flow_ini}
\end{figure}
%
- The initial fields for dynamo benchmark can set in the simulation program by setting \verb|[INITIAL_TYPE]| flag. This program is used to generate initial field by user. The heat source $q_{T}$ and light element source $q_{C}$ are also defined by this program because $q_{T}$ and $q_{C}$ are defined as scalar fields. The module to define initial field \verb|const_sph_initial_spectr.f90| is saved in \verb|src/programs/data_utilities/INITIAL_FIELD/| directory, and please compile again after modifying this module. This program also needs the files listed in Table \ref{table:inital_fld}.
+ The initial fields for dynamo benchmark can set in the simulation program by setting \verb|[INITIAL_TYPE]| flag. This program is used to generate initial field by user. The heat source $q_{T}$ and light element source $q_{C}$ are also defined by this program because $q_{T}$ and $q_{C}$ are defined as scalar fields. The Fortran source file to define initial field \\
+ \verb|const_sph_initial_spectr.f90| is saved in \verb|src/programs/data_utilities| \\
+ \verb|/INITIAL_FIELD/| directory, and please compile again after modifying this module. This program also needs the files listed in Table \ref{table:inital_fld}.
%
\begin{table}[htdp]
\caption{List of files for simulation {\tt sph\_initial\_field} }
@@ -908,7 +949,6 @@ The same files as the simulation program are read in this program, and field dat
This program generates the spectrum data files \verb|[rst_prefix].0.[domain#].fst|. To use generated initial data file, please set
\hyperref[href_t:i_step_init_ctl]{{\tt [ISTEP\_START]}} to be 0 and \hyperref[href_t:restart_file_ctl]{{\tt [INITIAL\_TYPE]}} to be \hyperref[href_t:restart_file_ctl]{{\tt start\_from\_rst\_file}}.
-\newpage
\section{Initial field modification program \\
({\tt sph\_add\_initial\_field})}
\label{sec:ad_initial_field}
@@ -923,7 +963,7 @@ This program generates the spectrum data files \verb|[rst_prefix].0.[domain#].fs
%
{\bf Caution: This program overwrites existing initial field data. Please run it after taking a backup.} \\
- This program modifies or adds new data to an initial field file. It could be used to start a new geodynamo simulation by adding seed magnetic field or source terms to a non-magnetic convection simulation. The initial fields to be added are also defined in \verb|const_sph_initial_spectr.f90|. \verb|data_utilities/INITIAL_FIELD/| directory. This program also needs the files listed in Table \ref{table:inital_fld}.
+ This program modifies or adds new data to an initial field file. It could be used to start a new geodynamo simulation by adding seed magnetic field or source terms to a non-magnetic convection simulation. The initial fields to be added are also defined in \verb|const_sph_initial_spectr.f90|. \verb|data_utilities/INITIAL_FIELD/| directory. This program also needs the files listed in Table \ref{table:add_inital_fld}.
%
\begin{table}[htdp]
\caption{List of files for simulation {\tt sph\_add\_initial\_field} }
@@ -939,7 +979,7 @@ This program generates the spectrum data files \verb|[rst_prefix].0.[domain#].fs
\verb|[rst_prefix].[step #].[domain#].fst| & Distributed & Input/Output \\ \hline
\end{tabular}
\end{center}
-\label{table:inital_fld}
+\label{table:add_inital_fld}
\end{table}
%
This program generates the spectrum data files \verb|[rst_prefix].[step#].[domain#].fst|. To use generated initial data file, set
@@ -970,8 +1010,11 @@ This program is only used to check solution for dynamo benchmark by Christensen
\end{table}
\subsection{Dynamo benchmark data {\tt dynamobench.dat}}
- In benchmark test by Christensen {\it et. al.}, both global values and local values are checked. As global results, Kinetic energy $1/V \int \frac{1}{2} u^{2} dV$ in the fluid shell, magnetic energy in the fluid shell $1/V 1/(E Pm) \int \frac{1}{2} B^{2} dV$ (for case 1 and 2), and magnetic energy in the solid inner sphere $1/V_{i} 1/(E Pm) \int \frac{1}{2} B^{2} dV_{i}$ (for case 2 only). Benchmark also requests
- By increasing number of grid point at mid-dpeth of the fluid shell in the equatorial plane by \hyperref[href_t:nphi_mid_eq_ctl]{{\tt nphi\_mid\_eq\_ctl}}, program can find accurate solution for the point where $u_{r} = 0$ and $\partial u_{r} / \partial \phi > 0$. Angular frequency of the field pattern with respect to the $\phi$ direction is also required. The benchmark test also requires temperature and $\theta$ component of velocity. In the text file {\tt dynamobench.dat}, the following data are written in one line for every {\tt i\_step\_check\_ctl} step.
+ In benchmark test by Christensen {\it et. al.}, both global values and local values are checked. As global results, Kinetic energy
+ $\displaystyle{ \frac{1}{V} \int \frac{1}{2} u^{2} dV}$ in the fluid shell, magnetic energy in the fluid shell
+ $\displaystyle{ \frac{1}{V} \frac{1}{E Pm} \int \frac{1}{2} B^{2} dV}$ (for case 1 and 2), and magnetic energy in the solid inner sphere
+ $\displaystyle{ \frac{1}{V_{i}} \frac{1}{E Pm} \int \frac{1}{2} B^{2} dV_{i}}$ (for case 2 only). Benchmark also requests
+ By increasing number of grid point at mid-dpeth of the fluid shell in the equatorial plane by \hyperref[href_t:nphi_mid_eq_ctl]{{\tt nphi\_mid\_eq\_ctl}}, program can find accurate solution for the point where $u_{r} = 0$ and $\partial u_{r} / \partial \phi > 0$. Angular frequency of the field pattern with respect to the $\phi$ direction is also required. The benchmark test also requires temperature and $\theta$ component of velocity. In the text file {\tt dynamobench.dat}, the following data are written in one line for every \verb|[i_step_rst_ctl]| step.
%
\begin{description}
\item{\tt t\_step: } Time step number
@@ -999,18 +1042,19 @@ This program is only used to check solution for dynamo benchmark by Christensen
{\small
\begin{verbatim}
-
-t_step time KE_pol KE_tor KE_total ME_pol ME_tor ME_total
- ME_pol_icore ME_tor_icore ME_total_icore omega_ic_z MAG_torque_ic_
-z phi_1 phi_2 phi_3 phi_4 omega_vp44 omega_vt54 B_theta
-v_phi temp
- 20000 9.999999999998981E-001 1.534059732073072E+001 2.431439471284618
-E+001 3.965499203357688E+001 2.405694011955009E+000 1.648662987055900E+000
- 4.054356999010911E+000 3.908687924452961E+001 4.812865754441352E-001 3.
-956816581997376E+001 5.220517005592486E+000 -2.321885847438682E+002 3.59417
-5626663308E-001 1.930213889461227E+000 3.501010216256124E+000 5.0718065430
-51021E+000 7.808553595635292E-001 -1.649583441437563E-001 -5.136522824340612
-E+000 -8.047915942925034E+000 3.752181234262930E-001
+t_step time KE_pol KE_tor KE_total ME_pol ME_t
+or ME_total ME_pol_icore ME_tor_icore ME_total_icore
+ omega_ic_z MAG_torque_ic_z phi_1 phi_2 phi_3
+phi_4 omega_vp44 omega_vt54 B_theta v_phi temp
+ 20000 9.999999999998981E-001 1.534059732073072E+001 2
+.431439471284618E+001 3.965499203357688E+001 2.4056940119550
+09E+000 1.648662987055900E+000 4.054356999010911E+000 3.90
+8687924452961E+001 4.812865754441352E-001 3.956816581997376E
++001 5.220517005592486E+000 -2.321885847438682E+002 3.59417
+5626663308E-001 1.930213889461227E+000 3.501010216256124E+00
+0 5.071806543051021E+000 7.808553595635292E-001 -1.64958344
+1437563E-001 -5.136522824340612E+000 -8.047915942925034E+000
+ 3.752181234262930E-001
...
\end{verbatim}
}
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