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Merged
glesur merged 5 commits into from
Oct 13, 2024
Merged

Simplify input file for DIMENSIONS < 3 setups #274

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ca7b229
do not require extra info on the grid and boundary conditions when
glesur Oct 4, 2024
8402f22
clean all tests with DIMENSIONS<3
glesur Oct 4, 2024
94ebf90
bring thermal diffusion test back to 3D
glesur Oct 4, 2024
1f1a76c
-ensure that planetarySystem doesn't think we're doing half-disk in 2D
glesur Oct 5, 2024
a75f6ef
update documentation
glesur Oct 6, 2024
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6 changes: 3 additions & 3 deletions doc/source/reference/idefix.ini.rst
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Expand Up @@ -16,7 +16,7 @@ allows for comments, which should start with ``#``.

``Grid`` section
--------------------
The grid section defines the grid total dimension. It consists of 3 entries ``X1-grid``, ``X2-grid`` and ``X3-grid``. Each entry defines the repartition of the grid points in the corresponding direction (the grid is always rectilinear).
The grid section defines the grid total dimension. It consists of 3 entries ``X1-grid``, ``X2-grid`` (when DIMENSIONS>=2) and ``X3-grid`` (when DIMENSIONS=3). Each entry defines the repartition of the grid points in the corresponding direction (the grid is always rectilinear).
Each entry defines a series of grid blocks which are concatenated along the direction. Each block in a direction can have a different spacing rule (uniform, log or stretched). The definition of the Grid entries is as follows

+----------------------------+-------------------------+------------------------------+
Expand Down Expand Up @@ -332,8 +332,8 @@ this block is simply ignored.
------------------------

This section describes the boundary conditions used by the code. There are 6 entries
which need to be defined: ``X1-beg``, ``X2-beg``, ``X3-beg`` for the left boundaries in the direction X1, X2, X3,
and ``X1-end``, ``X2-end``, ``X3-end`` for the right boundaries. Each boundary can be assigned the following types of conditions
that need to be defined: ``X1-beg``, ``X2-beg``, ``X3-beg`` for the left boundaries in the direction X1, X2, X3,
and ``X1-end``, ``X2-end``, ``X3-end`` for the right boundaries. ``X2`` boundaries are mandatory only when DIMENSIONS>=2 and ``X3`` when DIMENSIONS=3. Each boundary can be assigned the following types of conditions

+----------------+------------------------------------------------------------------------------------------------------------------+
| Boundary type | Comment |
Expand Down
14 changes: 9 additions & 5 deletions src/dataBlock/planetarySystem/planetarySystem.cpp
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Expand Up @@ -83,12 +83,16 @@ indirect term, with multiple planets that don't feel each others.");
IDEFIX_ERROR("need to define a planet-to-primary mass ratio via planetToPrimary");
}
#if GEOMETRY == POLAR || GEOMETRY == CARTESIAN
if ((this->data->mygrid->xbeg[KDIR] == 0)
|| (this->data->mygrid->xend[KDIR] == 0)) {
this->halfdisk = true;
} else {
#if DIMENSIONS == 3
if ((this->data->mygrid->xbeg[KDIR] == 0)
|| (this->data->mygrid->xend[KDIR] == 0)) {
this->halfdisk = true;
} else {
this->halfdisk = false;
}
#else // DIMENSIONS == 3
this->halfdisk = false;
}
#endif // DIMENSIONS == 3
#elif GEOMETRY == SPHERICAL
if ( (this->data->mygrid->xbeg[JDIR] == M_PI/2.0)
|| (this->data->mygrid->xend[JDIR] == M_PI/2.0)) {
Expand Down
9 changes: 8 additions & 1 deletion src/gravity/laplacian.hpp
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Expand Up @@ -19,7 +19,14 @@ class DataBlock;
class Laplacian {
public:
// Types of boundary which can be treated
enum LaplacianBoundaryType {internalgrav, periodic, nullgrad, nullpot, userdef, axis, origin};
enum LaplacianBoundaryType {internalgrav,
periodic,
nullgrad,
nullpot,
userdef,
axis,
origin,
undefined};

Laplacian() = default;
Laplacian(DataBlock *, std::array<LaplacianBoundaryType,3>,
Expand Down
6 changes: 5 additions & 1 deletion src/gravity/selfGravity.cpp
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Expand Up @@ -42,7 +42,11 @@ void SelfGravity::Init(Input &input, DataBlock *datain) {
}

// Get the gravity-related boundary conditions
for(int dir = 0 ; dir < 3 ; dir++) {
for (int dir = 0 ; dir < 3 ; dir++) {
this->lbound[dir] = Laplacian::LaplacianBoundaryType::undefined;
this->rbound[dir] = Laplacian::LaplacianBoundaryType::undefined;
}
for(int dir = 0 ; dir < DIMENSIONS ; dir++) {
std::string label = std::string("boundary-X")+std::to_string(dir+1)+std::string("-beg");
std::string boundary = input.Get<std::string>("SelfGravity",label,0);

Expand Down
15 changes: 14 additions & 1 deletion src/grid.cpp
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Expand Up @@ -55,7 +55,7 @@ Grid::Grid(Input &input) {
npoints[dir] = 1;
nghost[dir] = 0;
std::string label = std::string("X")+std::to_string(dir+1)+std::string("-grid");
int numPatch = input.Get<int>("Grid",label,0);


if(dir<DIMENSIONS) {
#if ORDER < 4
Expand All @@ -64,6 +64,7 @@ Grid::Grid(Input &input) {
nghost[dir] = 3;
#endif
npoints[dir] = 0;
int numPatch = input.Get<int>("Grid",label,0);
for(int patch = 0; patch < numPatch ; patch++) {
npoints[dir] += input.Get<int>("Grid",label,2+3*patch );
}
Expand All @@ -73,7 +74,14 @@ Grid::Grid(Input &input) {
for(int dir = 0 ; dir < 3 ; dir++) {
np_tot[dir] = npoints[dir] + 2*nghost[dir];
np_int[dir] = npoints[dir];
lbound[dir] = undefined;
rbound[dir] = undefined;
}

// Default boundary conditions on each axis


for(int dir = 0 ; dir < DIMENSIONS ; dir++) {
std::string label = std::string("X")+std::to_string(dir+1)+std::string("-beg");
std::string boundary = input.Get<std::string>("Boundary",label,0);

Expand Down Expand Up @@ -337,6 +345,9 @@ void Grid::ShowConfig() {
case userdef:
lboundString="userdef";
break;
case undefined:
lboundString="undefined";
break;
default:
lboundString="unknown";
}
Expand All @@ -362,6 +373,8 @@ void Grid::ShowConfig() {
case userdef:
rboundString="userdef";
break;
case undefined:
lboundString="undefined";
default:
rboundString="unknown";
}
Expand Down
30 changes: 18 additions & 12 deletions src/gridHost.cpp
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Expand Up @@ -50,17 +50,17 @@ void GridHost::MakeGrid(Input &input) {

// Get grid parameters from input file, block [Grid]
for(int dir = 0 ; dir < 3 ; dir++) {
std::string label = std::string("X")+std::to_string(dir+1)+std::string("-grid");
int numPatch = input.Get<int>("Grid",label,0);
// These are extra dimensions that are not being used.

xstart[dir] = input.Get<real>("Grid",label,1);
xend[dir] = input.Get<real>("Grid",label,4+(numPatch-1)*3);

this->xbeg[dir] = xstart[dir];
this->xend[dir] = xend[dir];
if(dir<DIMENSIONS) {
std::string label = std::string("X")+std::to_string(dir+1)+std::string("-grid");
int numPatch = input.Get<int>("Grid",label,0);

xstart[dir] = input.Get<real>("Grid",label,1);
xend[dir] = input.Get<real>("Grid",label,4+(numPatch-1)*3);

if(dir<DIMENSIONS) {
this->xbeg[dir] = xstart[dir];
this->xend[dir] = xend[dir];
// First, we fill cells for any non strecthed patch
// Loop on all the patches
int idxstart = nghost[dir];
Expand Down Expand Up @@ -200,10 +200,16 @@ void GridHost::MakeGrid(Input &input) {
} else {
// dir >= DIMENSIONS/ Init simple uniform grid
for(int i = 0 ; i < np_tot[dir] ; i++) {
dx[dir](i) = (xend[dir]-xstart[dir])/(np_int[dir]);
x[dir](i)=xstart[dir] + (i-nghost[dir]+HALF_F)*dx[dir](i);
xl[dir](i)=xstart[dir] + (i-nghost[dir])*dx[dir](i);
xr[dir](i)=xstart[dir] + (i-nghost[dir]+1)*dx[dir](i);
// Initialize to default values
xstart[dir] = -0.5;
xend[dir] = 0.5;

this->xbeg[dir] = xstart[dir];
this->xend[dir] = xend[dir];
dx[dir](i) = 1.0;
x[dir](i)=0.0;
xl[dir](i)=-0.5;
xr[dir](i)=0.5;
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion src/idefix.hpp
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Expand Up @@ -216,7 +216,7 @@ using IdfxFileHandler = FILE*;
#endif

// Types of boundary which can be treated
enum BoundaryType { internal, periodic, reflective, outflow, shearingbox, axis, userdef};
enum BoundaryType { internal, periodic, reflective, outflow, shearingbox, axis, userdef, undefined};
enum BoundarySide { left, right};
enum class SliceType {Cut, Average};

Expand Down
3 changes: 0 additions & 3 deletions test/HD/FargoPlanet/setup.cpp
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Expand Up @@ -43,7 +43,6 @@ void UserdefBoundary(Hydro *hydro, int dir, BoundarySide side, real t) {
IdefixArray4D<real> Vc = hydro->Vc;
auto *data = hydro->data;
IdefixArray1D<real> x1 = data->x[IDIR];
IdefixArray1D<real> x3 = data->x[KDIR];
if(dir==IDIR) {
int ighost,ibeg,iend;
if(side == left) {
Expand All @@ -56,7 +55,6 @@ void UserdefBoundary(Hydro *hydro, int dir, BoundarySide side, real t) {
ibeg, iend,
KOKKOS_LAMBDA (int k, int j, int i) {
real R=x1(i);
real z=x3(k);
real Vk = 1.0/sqrt(R);

Vc(RHO,k,j,i) = Vc(RHO,k,j,2*ighost - i +1);
Expand All @@ -75,7 +73,6 @@ void UserdefBoundary(Hydro *hydro, int dir, BoundarySide side, real t) {
ibeg, iend,
KOKKOS_LAMBDA (int k, int j, int i) {
real R=x1(i);
real z=x3(k);
real Vk = 1.0/sqrt(R);

Vc(RHO,k,j,i) = Vc(RHO,k,j,ighost);
Expand Down
3 changes: 0 additions & 3 deletions test/HD/VSI/idefix.ini
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@@ -1,7 +1,6 @@
[Grid]
X1-grid 1 1.0 1024 l 3.0
X2-grid 1 1.2707963267948965 512 u 1.8707963267948966
X3-grid 1 0.0 1 u 6.283185307179586

[TimeIntegrator]
CFL 0.8
Expand All @@ -22,8 +21,6 @@ X1-beg userdef
X1-end outflow
X2-beg outflow
X2-end outflow
X3-beg periodic
X3-end periodic

[Setup]
epsilon 0.1
Expand Down
3 changes: 0 additions & 3 deletions test/HD/ViscousDisk/idefix-rkl.ini
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@@ -1,7 +1,6 @@
[Grid]
X1-grid 1 1.0 64 u 3.0
X2-grid 1 1.2707963267948965 64 u 1.8707963267948966
X3-grid 1 0.0 1 u 6.283185307179586

[TimeIntegrator]
CFL 0.5
Expand All @@ -23,8 +22,6 @@ X1-beg userdef
X1-end userdef
X2-beg userdef
X2-end userdef
X3-beg periodic
X3-end periodic

[Setup]
epsilon 0.1
Expand Down
3 changes: 0 additions & 3 deletions test/HD/ViscousDisk/idefix.ini
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@@ -1,7 +1,6 @@
[Grid]
X1-grid 1 1.0 64 u 3.0
X2-grid 1 1.2707963267948965 64 u 1.8707963267948966
X3-grid 1 0.0 1 u 6.283185307179586

[TimeIntegrator]
CFL 0.5
Expand All @@ -23,8 +22,6 @@ X1-beg userdef
X1-end userdef
X2-beg userdef
X2-end userdef
X3-beg periodic
X3-end periodic

[Setup]
epsilon 0.1
Expand Down
5 changes: 0 additions & 5 deletions test/HD/ViscousFlowPastCylinder/idefix-rkl.ini
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@@ -1,9 +1,6 @@
[Grid]
X1-grid 1 1.0 128 l 10.0
# X2-grid 3 -3.141592653589793 64 s+ -0.2 128 u 0.2 64 s- 3.141592653589793
# X2-grid 1 -3.141592653589793 256 u 3.141592653589793
X2-grid 1 0.0 64 u 6.28318530717958
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.4
Expand All @@ -21,8 +18,6 @@ X1-beg userdef
X1-end userdef
X2-beg periodic
X2-end periodic
X3-beg outflow
X3-end outflow

[Output]
vtk 1.0
Expand Down
5 changes: 0 additions & 5 deletions test/HD/ViscousFlowPastCylinder/idefix.ini
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@@ -1,9 +1,6 @@
[Grid]
X1-grid 1 1.0 128 l 10.0
# X2-grid 3 -3.141592653589793 64 s+ -0.2 128 u 0.2 64 s- 3.141592653589793
# X2-grid 1 -3.141592653589793 256 u 3.141592653589793
X2-grid 1 0.0 64 u 6.28318530717958
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.4
Expand All @@ -21,8 +18,6 @@ X1-beg userdef
X1-end userdef
X2-beg periodic
X2-end periodic
X3-beg outflow
X3-end outflow

[Output]
vtk 1.0
Expand Down
6 changes: 0 additions & 6 deletions test/HD/sod-iso/idefix-hll.ini
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@@ -1,7 +1,5 @@
[Grid]
X1-grid 1 0.0 500 u 1.0
X2-grid 1 0.0 1 u 1.0
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.8
Expand All @@ -16,10 +14,6 @@ csiso constant 1.0
[Boundary]
X1-beg outflow
X1-end outflow
X2-beg outflow
X2-end outflow
X3-beg outflow
X3-end outflow

[Output]
vtk 0.1
Expand Down
6 changes: 0 additions & 6 deletions test/HD/sod-iso/idefix-hllc-rk3.ini
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@@ -1,7 +1,5 @@
[Grid]
X1-grid 1 0.0 500 u 1.0
X2-grid 1 0.0 1 u 1.0
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.8
Expand All @@ -16,10 +14,6 @@ csiso constant 1.0
[Boundary]
X1-beg outflow
X1-end outflow
X2-beg outflow
X2-end outflow
X3-beg outflow
X3-end outflow

[Output]
vtk 0.1
Expand Down
6 changes: 0 additions & 6 deletions test/HD/sod-iso/idefix-hllc.ini
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@@ -1,7 +1,5 @@
[Grid]
X1-grid 1 0.0 500 u 1.0
X2-grid 1 0.0 1 u 1.0
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.8
Expand All @@ -16,10 +14,6 @@ csiso constant 1.0
[Boundary]
X1-beg outflow
X1-end outflow
X2-beg outflow
X2-end outflow
X3-beg outflow
X3-end outflow

[Output]
vtk 0.1
Expand Down
6 changes: 0 additions & 6 deletions test/HD/sod-iso/idefix-rk3.ini
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@@ -1,7 +1,5 @@
[Grid]
X1-grid 1 0.0 500 u 1.0
X2-grid 1 0.0 1 u 1.0
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.8
Expand All @@ -16,10 +14,6 @@ csiso constant 1.0
[Boundary]
X1-beg outflow
X1-end outflow
X2-beg outflow
X2-end outflow
X3-beg outflow
X3-end outflow

[Output]
vtk 0.1
Expand Down
6 changes: 0 additions & 6 deletions test/HD/sod-iso/idefix-tvdlf.ini
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@@ -1,7 +1,5 @@
[Grid]
X1-grid 1 0.0 500 u 1.0
X2-grid 1 0.0 1 u 1.0
X3-grid 1 0.0 1 u 1.0

[TimeIntegrator]
CFL 0.8
Expand All @@ -16,10 +14,6 @@ csiso constant 1.0
[Boundary]
X1-beg outflow
X1-end outflow
X2-beg outflow
X2-end outflow
X3-beg outflow
X3-end outflow

[Output]
vtk 0.1
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