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Formatting equations
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6 files changed

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Diff for: ‎doc/Doxyfile.in

+1-1
Original file line numberDiff line numberDiff line change
@@ -793,7 +793,7 @@ WARNINGS = YES
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# will automatically be disabled.
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# The default value is: YES.
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796-
WARN_IF_UNDOCUMENTED = YES
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WARN_IF_UNDOCUMENTED = NO
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# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
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# potential errors in the documentation, such as not documenting some parameters

Diff for: ‎src/coordinates/gr_user.cpp

+1
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
66
//! \file gr_user.cpp
77
//! \brief Used for arbitrary stationary coordinates in general relativity, with all
88
//! functions evaluated numerically based on the metric.
9+
//!
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//! Original implementation by CJ White.
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1112
// C headers

Diff for: ‎src/coordinates/kerr-schild.cpp

+47-18
Original file line numberDiff line numberDiff line change
@@ -10,22 +10,28 @@
1010
//! Original implementation by CJ White.
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//!
1212
//! Notes:
13-
//! coordinates: t, r, \theta, \phi
14-
//! parameters: M (mass), M > 0
13+
//! - coordinates: t, r, \f$\theta\f$, \f$\phi\f$
14+
//! - parameters: M (mass), M > 0
1515
//! a (spin), -M < a < M
16-
//! metric:
17-
//! ds^2 = -(1 - 2 M r/\Sigma) dt^2
18-
//! + 4 M r/\Sigma dt dr
19-
//! - 4 M a r/\Sigma dt d\phi
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//! + (1 + 2 M r/\Sigma) dr^2
21-
//! - 2 a (1 + 2 M r/\Sigma) \sin^2\theta dr d\phi
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//! + \Sigma d\theta^2
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//! + (r^2 + a^2 + (2 M a^2 r/\Sigma) \sin^2\theta) \sin^2\theta d\phi^2
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//! where \Delta = r^2 - 2 M r + a^2
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//! \Sigma = r^2 + a^2 cos^2\theta
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//! \Xi = r^2 - a^2 cos^2\theta
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//! - metric:
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//! \f{eqnarray*}{
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//! ds^2 &=& -(1 - 2 M r/\Sigma) dt^2 \\
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//! & & + 4 M r/\Sigma dt dr \\
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//! & & - 4 M a r/\Sigma dt d\phi \\
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//! & & + (1 + 2 M r/\Sigma) dr^2 \\
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//! & & - 2 a (1 + 2 M r/\Sigma) \sin^2\theta dr d\phi \\
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//! & & + \Sigma d\theta^2 \\
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//! & & + (r^2 + a^2 + (2 M a^2 r/\Sigma) \sin^2\theta) \sin^2\theta d\phi^2
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//! \f}
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//! where
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//! \f{eqnarray*}{
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//! \Delta &=& r^2 - 2 M r + a^2 \\
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//! \Sigma &=& r^2 + a^2 cos^2\theta \\
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//! \Xi &=& r^2 - a^2 cos^2\theta
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//! \f}
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//! other "Kerr-Schild" coordinates exist
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// C headers
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// C++ headers
@@ -40,11 +46,34 @@
4046
#include "coordinates.hpp"
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//----------------------------------------------------------------------------------------
43-
// KerrSchild Constructor
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// Inputs:
45-
// pmb: pointer to MeshBlock containing this grid
46-
// pin: pointer to runtime inputs
47-
// flag: true if object is for coarse grid only in an AMR calculation
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//! \brief KerrSchild Constructor
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//!
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//! Inputs:
52+
//! - pmb: pointer to MeshBlock containing this grid
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//! - pin: pointer to runtime inputs
54+
//! - flag: true if object is for coarse grid only in an AMR calculation
55+
//!
56+
//! Notes:
57+
//! - coordinates: t, r, \f$\theta\f$, \f$\phi\f$
58+
//! - parameters: M (mass), M > 0
59+
//! a (spin), -M < a < M
60+
//! - metric:
61+
//! \f{eqnarray*}{
62+
//! ds^2 &=& -(1 - 2 M r/\Sigma) dt^2 \\
63+
//! & & + 4 M r/\Sigma dt dr \\
64+
//! & & - 4 M a r/\Sigma dt d\phi \\
65+
//! & & + (1 + 2 M r/\Sigma) dr^2 \\
66+
//! & & - 2 a (1 + 2 M r/\Sigma) \sin^2\theta dr d\phi \\
67+
//! & & + \Sigma d\theta^2 \\
68+
//! & & + (r^2 + a^2 + (2 M a^2 r/\Sigma) \sin^2\theta) \sin^2\theta d\phi^2
69+
//! \f}
70+
//! where
71+
//! \f{eqnarray*}{
72+
//! \Delta &=& r^2 - 2 M r + a^2 \\
73+
//! \Sigma &=& r^2 + a^2 cos^2\theta \\
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//! \Xi &=& r^2 - a^2 cos^2\theta
75+
//! \f}
76+
//! other "Kerr-Schild" coordinates exist
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KerrSchild::KerrSchild(MeshBlock *pmb, ParameterInput *pin, bool flag)
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: Coordinates(pmb, pin, flag) {

Diff for: ‎src/coordinates/minkowski.cpp

+19-9
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@@ -4,12 +4,15 @@
44
// Licensed under the 3-clause BSD License, see LICENSE file for details
55
//========================================================================================
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//! \file minkowski.cpp
7-
//! \brief implements functions for Minkowski (flat) spacetime and Cartesian (t,x,y,z)
8-
//! coordinates in a derived class of the Coordinates abstract base class.
7+
//! \brief implements functions for Minkowski (flat) spacetime and Cartesian (t,x,y,z)
8+
//! coordinates in a derived class of the Coordinates abstract base class.
99
//!
1010
//! Notes:
11-
//! coordinates: t, x, y, z
12-
//! metric: ds^2 = -dt^2 + dx^2 + dy^2 + dz^2
11+
//! - coordinates: t, x, y, z
12+
//! - metric:
13+
//! \f[
14+
//! ds^2 = -dt^2 + dx^2 + dy^2 + dz^2
15+
//! \f]
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1417
// C headers
1518

@@ -24,11 +27,18 @@
2427
#include "coordinates.hpp"
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2629
//----------------------------------------------------------------------------------------
27-
// Minkowski constructor
28-
// Inputs:
29-
// pmb: pointer to block containing this grid
30-
// pin: pointer to runtime inputs (not used)
31-
// flag: true if object is for coarse grid only in an AMR calculation
30+
//! \brief Minkowski constructor
31+
//!
32+
//! Inputs:
33+
//! - pmb: pointer to block containing this grid
34+
//! - pin: pointer to runtime inputs (not used)
35+
//! - flag: true if object is for coarse grid only in an AMR calculation
36+
//! Notes:
37+
//! - coordinates: t, x, y, z
38+
//! - metric:
39+
//! \f[
40+
//! ds^2 = -dt^2 + dx^2 + dy^2 + dz^2
41+
//! \f]
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3343
Minkowski::Minkowski(MeshBlock *pmb, ParameterInput *pin, bool flag)
3444
: Coordinates(pmb, pin, flag) {

Diff for: ‎src/coordinates/schwarzschild.cpp

+25-10
Original file line numberDiff line numberDiff line change
@@ -10,11 +10,15 @@
1010
//! Original implementation by CJ White.
1111
//!
1212
//! Notes:
13-
//! coordinates: t, r, theta, phi
14-
//! parameters: M (mass)
15-
//! metric:
16-
//! ds^2 = -\alpha^2 dt^2 + 1/\alpha^2 * dr^2 + r^2 (d\theta^2 + \sin^2\theta d\phi^2)
17-
//! where \alpha = \sqrt(1 - 2M/r)
13+
//! - coordinates: t, r, theta, phi
14+
//! - parameters: M (mass)
15+
//! - metric:
16+
//! \f[
17+
//! ds^2 = -\alpha^2 dt^2 + 1/\alpha^2 dr^2
18+
//! + r^2 (d\theta^2 + \sin^2\theta d\phi^2)
19+
//! \f]
20+
//! where \f$ \alpha = \sqrt{1 - 2M/r} \f$
21+
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1923
// C headers
2024

@@ -30,11 +34,22 @@
3034
#include "coordinates.hpp"
3135

3236
//----------------------------------------------------------------------------------------
33-
// Schwarzschild Constructor
34-
// Inputs:
35-
// pmb: pointer to MeshBlock containing this grid
36-
// pin: pointer to runtime inputs
37-
// flag: true if object is for coarse grid only in an AMR calculation
37+
//! \brief Schwarzschild Constructor
38+
//!
39+
//! Inputs:
40+
//! - pmb: pointer to MeshBlock containing this grid
41+
//! - pin: pointer to runtime inputs
42+
//! - flag: true if object is for coarse grid only in an AMR calculation
43+
//!
44+
//! Notes:
45+
//! - coordinates: t, r, theta, phi
46+
//! - parameters: M (mass)
47+
//! - metric:
48+
//! \f[
49+
//! ds^2 = -\alpha^2 dt^2 + 1/\alpha^2 dr^2
50+
//! + r^2 (d\theta^2 + \sin^2\theta d\phi^2)
51+
//! \f]
52+
//! where \f$ \alpha = \sqrt{1 - 2M/r} \f$
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3954
Schwarzschild::Schwarzschild(MeshBlock *pmb, ParameterInput *pin, bool flag)
4055
: Coordinates(pmb, pin, flag) {

Diff for: ‎src/field/field_diffusion/field_diffusion.cpp

+1-1
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@@ -138,7 +138,7 @@ void FieldDiffusion::AddEMF(const EdgeField &e_src, EdgeField &e_des) {
138138
}
139139

140140
//----------------------------------------------------------------------------------------
141-
//! \fn void FieldDiffusion::ClearFieldDiffusionEMF(EdgeField &e)
141+
//! \fn void FieldDiffusion::ClearEMF(EdgeField &e)
142142
//! \brief Clear EMF
143143

144144
// TODO(felker): move out of FieldDiffusion class. Completely general operation

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