Finished initial draft of 1.0 documentation

coreyjcochrane · Nov 25, 2023 · 760d31b · 760d31b
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diff --git a/docs/functions.rst b/docs/functions.rst
@@ -17,11 +17,6 @@ Main calculation functions
 
 .. mat:autofunction:: MagFldParent
 
-:mat:func:`KSMagFldJupiter`
-+++++++++++++++++++++++++++
-
-.. mat:autofunction:: KSMagFldJupiter
-
 :mat:func:`MpauseFld`
 +++++++++++++++++++++
 
@@ -48,36 +43,81 @@ Main calculation functions
 .. mat:autofunction:: dLegendreS
 
 
-Magnetopause functions
-----------------------
+Coordinate transformation functions
+-----------------------------------
 
-.. mat:module:: functions.magnetopauseModels
+.. mat:module:: functions.coordinates
    :noindex:
 
-:mat:func:`GetMPsurfAB2005`
-+++++++++++++++++++++++++++
+:mat:func:`Bcyl2Bxyz`
++++++++++++++++++++++
 
-.. mat:autofunction:: GetMPsurfAB2005
+.. mat:autofunction:: Bcyl2Bxyz
 
-:mat:func:`GetMPsurfS1997`
-++++++++++++++++++++++++++
+:mat:func:`Bsph2Bxyz`
++++++++++++++++++++++
 
-.. mat:autofunction:: GetMPsurfS1997
+.. mat:autofunction:: Bsph2Bxyz
 
-:mat:func:`GetMPsurfSM1996`
-+++++++++++++++++++++++++++
+:mat:func:`Bxyz2Bcyl`
++++++++++++++++++++++
 
-.. mat:autofunction:: GetMPsurfSM1996
+.. mat:autofunction:: Bxyz2Bcyl
 
-:mat:func:`MPboxHarmonic`
+:mat:func:`Bxyz2Bsph`
++++++++++++++++++++++
+
+.. mat:autofunction:: Bxyz2Bsph
+
+:mat:func:`cyl2xyz`
++++++++++++++++++++
+
+.. mat:autofunction:: cyl2xyz
+
+:mat:func:`KS_BJSMtoBS3C`
 +++++++++++++++++++++++++
 
-.. mat:autofunction:: MPboxHarmonic
+.. mat:autofunction:: KS_BJSMtoBS3C
 
-:mat:func:`MPsphericalHarmonic`
-+++++++++++++++++++++++++++++++
+:mat:func:`KS_BpJSOtoBxyz`
+++++++++++++++++++++++++++
 
-.. mat:autofunction:: MPsphericalHarmonic
+.. mat:autofunction:: KS_BpJSOtoBxyz
+
+:mat:func:`KS_S3CtoJSM`
++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_S3CtoJSM
+
+:mat:func:`KS_S3CtoJSO`
++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_S3CtoJSO
+
+:mat:func:`KS_xyz2pJSO`
++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_xyz2pJSO
+
+:mat:func:`RotateVecSpice`
+++++++++++++++++++++++++++
+
+.. mat:autofunction:: RotateVecSpice
+
+:mat:func:`sph2xyz`
++++++++++++++++++++
+
+.. mat:autofunction:: sph2xyz
+
+:mat:func:`xyz2cyl`
++++++++++++++++++++
+
+.. mat:autofunction:: xyz2cyl
+
+:mat:func:`xyz2sph`
++++++++++++++++++++
+
+.. mat:autofunction:: xyz2sph
 
 
 Khurana and Schwarzl (2005) Jupiter model functions
@@ -86,32 +126,112 @@ Khurana and Schwarzl (2005) Jupiter model functions
 .. mat:module:: functions.KS2005functions
    :noindex:
 
-:mat:func:`VIP4noDipole`
-++++++++++++++++++++++++
+:mat:func:`MagFldJupiterKS2005`
++++++++++++++++++++++++++++++++
 
-.. mat:autofunction:: VIP4noDipole
+.. mat:autofunction:: MagFldJupiterKS2005
 
+:mat:func:`KS_BMPperp`
+++++++++++++++++++++++
 
-Additional supporting functions
--------------------------------
+.. mat:autofunction:: KS_BMPperp
 
-.. mat:module:: functions
-   :noindex:
+:mat:func:`KS_BtailShield`
+++++++++++++++++++++++++++
 
-:mat:func:`Bsph2Bxyz`
+.. mat:autofunction:: KS_BtailShield
+
+:mat:func:`KS_CheckIfInsideMappedMP`
+++++++++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_CheckIfInsideMappedMP
+
+:mat:func:`KS_CheckIfInsideMP`
+++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_CheckIfInsideMP
+
+:mat:func:`KS_CsheetN`
+++++++++++++++++++++++
+
+.. mat:autofunction:: KS_CsheetN
+
+:mat:func:`KS_CsheetStruc`
+++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_CsheetStruc
+
+:mat:func:`KS_ctime2et`
++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_ctime2et
+
+:mat:func:`KS_ctimer`
 +++++++++++++++++++++
 
-.. mat:autofunction:: Bsph2Bxyz
+.. mat:autofunction:: KS_ctimer
 
-:mat:func:`Bxyz2Bsph`
+:mat:func:`KS_DipoleFld`
+++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_DipoleFld
+
+:mat:func:`KS_DipoleShieldCylS3`
+++++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_DipoleShieldCylS3
+
+:mat:func:`KS_DipoleShielded`
++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_DipoleShielded
+
+:mat:func:`KS_etimer`
 +++++++++++++++++++++
 
-.. mat:autofunction:: Bxyz2Bsph
+.. mat:autofunction:: KS_etimer
 
-:mat:func:`ConvertSwarmCDF`
+:mat:func:`KS_GetBIMF`
+++++++++++++++++++++++
+
+.. mat:autofunction:: KS_GetBIMF
+
+:mat:func:`KS_GetMappedSunAngle`
+++++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_GetMappedSunAngle
+
+:mat:func:`KS_JSun`
++++++++++++++++++++
+
+.. mat:autofunction:: KS_JSun
+
+:mat:func:`KS_TailMagNoTilt`
+++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_TailMagNoTilt
+
+:mat:func:`KS_TailMagShieldCylS3`
++++++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_TailMagShieldCylS3
+
+:mat:func:`KS_Upot`
++++++++++++++++++++
+
+.. mat:autofunction:: KS_Upot
+
+:mat:func:`KS_VIP4noDipole`
 +++++++++++++++++++++++++++
 
-.. mat:autofunction:: ConvertSwarmCDF
+.. mat:autofunction:: KS_VIP4noDipole
+
+
+Additional supporting functions
+-------------------------------
+
+.. mat:module:: functions
+   :noindex:
 
 :mat:func:`ExcitationSpectrum`
 ++++++++++++++++++++++++++++++
@@ -148,11 +268,6 @@ Additional supporting functions
 
 .. mat:autofunction:: GetExcitations
 
-:mat:func:`GetGaussCoeffs`
-++++++++++++++++++++++++++
-
-.. mat:autofunction:: GetGaussCoeffs
-
 :mat:func:`GetModelOpts`
 ++++++++++++++++++++++++
 
@@ -188,16 +303,12 @@ Additional supporting functions
 
 .. mat:autofunction:: PlotSpectrum
 
-:mat:func:`RotateVecSpice`
-++++++++++++++++++++++++++
-
-.. mat:autofunction:: RotateVecSpice
-
 :mat:func:`vlines`
 ++++++++++++++++++
 
 .. mat:autofunction:: vlines
 
+
 Model coefficient functions
 ---------------------------
 
@@ -208,7 +319,94 @@ Model coefficient functions
 .. mat:module:: modelCoeffs
    :noindex:
 
-:func:`coeffsBode1994G`
-+++++++++++++++++++++++
+:mat:func:`coeffsBode1994G`
++++++++++++++++++++++++++++
 
 .. mat:autofunction:: coeffsBode1994G
+
+:mat:func:`ConvertSwarmCDF`
++++++++++++++++++++++++++++
+
+.. mat:autofunction:: ConvertSwarmCDF
+
+:mat:func:`GetGaussCoeffs`
+++++++++++++++++++++++++++
+
+.. mat:autofunction:: GetGaussCoeffs
+
+:mat:func:`KS_coeffsBIMF`
++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsBIMF
+
+:mat:func:`KS_coeffsCSdeform`
++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsCSdeform
+
+:mat:func:`KS_coeffsCsheet`
++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsCsheet
+
+:mat:func:`KS_coeffsCsheetStruc`
+++++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsCsheetStruc
+
+:mat:func:`KS_coeffsJSMdipole`
+++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsJSMdipole
+
+:mat:func:`KS_coeffsJSun`
++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsJSun
+
+:mat:func:`KS_coeffsMpause`
++++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsMpause
+
+:mat:func:`KS_coeffsMtail`
+++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsMtail
+
+:mat:func:`KS_coeffsVIP4`
++++++++++++++++++++++++++
+
+.. mat:autofunction:: KS_coeffsVIP4
+
+
+Magnetopause functions
+----------------------
+
+.. mat:module:: functions.magnetopauseModels
+   :noindex:
+
+:mat:func:`GetMPsurfAB2005`
++++++++++++++++++++++++++++
+
+.. mat:autofunction:: GetMPsurfAB2005
+
+:mat:func:`GetMPsurfS1997`
+++++++++++++++++++++++++++
+
+.. mat:autofunction:: GetMPsurfS1997
+
+:mat:func:`GetMPsurfSM1996`
++++++++++++++++++++++++++++
+
+.. mat:autofunction:: GetMPsurfSM1996
+
+:mat:func:`MPboxHarmonic`
++++++++++++++++++++++++++
+
+.. mat:autofunction:: MPboxHarmonic
+
+:mat:func:`MPsphericalHarmonic`
++++++++++++++++++++++++++++++++
+
+.. mat:autofunction:: MPsphericalHarmonic
diff --git a/functions/ExcitationSpectrum.m b/functions/ExcitationSpectrum.m
@@ -112,7 +112,7 @@
 
     disp(['Evaluating ' magModelDescrip ' field model for T = ' num2str(Tinterest_h) ' h.'])
     if contains(magModelDescrip, 'KS2005')
-        [Bvec, Mdip_nT, Odip_km] = KSMagFldJupiter(rM_km, thetaM, phiM, t_h*3600, SPHOUT);
+        [Bvec, Mdip_nT, Odip_km] = MagFldJupiterKS2005(rM_km, thetaM, phiM, t_h*3600, SPHOUT);
     else
         [Bvec, Mdip_nT, Odip_km] = MagFldParent(parentName, rM_km, thetaM, phiM, MagModel, ...
             CsheetModel, magPhase, SPHOUT);

diff --git a/functions/GetBplotAndLsq.m b/functions/GetBplotAndLsq.m
@@ -73,7 +73,7 @@ function GetBplotAndLsq(ets, t_h, r_km, theta, phi, xyz_km, BrSC, BthSC, BphiSC,
     Nmax = 10;
     disp(['Evaluating ' magModelDescrip ' field model with Nmax = ' num2str(Nmax) '.'])
     if any(strcmp(strtrim(strsplit(magModelDescrip, '+')), 'KS2005'))
-        [Bvec, Mdip_nT, Odip_km] = KSMagFldJupiter(r_km, theta, phi, ets, 1);
+        [Bvec, Mdip_nT, Odip_km] = MagFldJupiterKS2005(r_km, theta, phi, ets, 1);
     else
         [Bvec, Mdip_nT, Odip_km] = MagFldParent(parentName, r_km, theta, phi, MagModel, ...
             CsheetModel, magPhase, 1, Nmax);

diff --git a/functions/GetBplotAndLsqMoon.m b/functions/GetBplotAndLsqMoon.m
@@ -81,7 +81,7 @@ function GetBplotAndLsqMoon(ets, t_h, r_km, theta, phi, xyz_km, r_RM, BxSC, BySC
 
     disp(['Evaluating ' magModelDescrip ' for flybys.'])
     if strcmp(magModelDescrip, 'KS2005')
-        [Bvec, Mdip_nT, Odip_km] = KSMagFldJupiter(r_km, theta, phi, ets, 1);
+        [Bvec, Mdip_nT, Odip_km] = MagFldJupiterKS2005(r_km, theta, phi, ets, 1);
     else
         [Bvec, Mdip_nT, Odip_km] = MagFldParent(parentName, r_km, theta, phi, MagModel, ...
             CsheetModel, magPhase, 1);

diff --git a/functions/GetBplotAndLsqNeptune.m b/functions/GetBplotAndLsqNeptune.m
@@ -95,7 +95,7 @@ function GetBplotAndLsqNeptune(ets, t_h, r_km, theta, phi, xyz_km, BrSC, BthSC,
     Nmax = 8;
     disp(['Evaluating ' magModelDescrip ' field model with Nmax = ' num2str(Nmax) '.'])
     if strcmp(magModelDescrip, 'KS2005')
-        [Bvec, Mdip_nT, Odip_km] = KSMagFldJupiter(r_km, theta, phi, ets, 1);
+        [Bvec, Mdip_nT, Odip_km] = MagFldJupiterKS2005(r_km, theta, phi, ets, 1);
     else
         [Bvec, Mdip_nT, Odip_km] = MagFldParent(parentName, r_km, theta, phi, MagModel, ...
             CsheetModel, magPhase, 1, Nmax);