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Ta/mpas cell centers #35

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Ta/mpas cell centers #35

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e25498c
Added MeshCellCenter Implementation
tomeravgil Oct 13, 2023
d8a7441
Added read files in fortran changed function args
tomeravgil Oct 19, 2023
ac27d0d
added new mesh field elmCenterXYZ
Oct 25, 2023
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Please remove personal attribute files, and put this in .gitignore

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61 changes: 48 additions & 13 deletions src/pmpo_c.cpp
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Expand Up @@ -255,13 +255,6 @@ void polympo_setMeshNumVtxs(MPMesh_ptr p_mpmesh, int numVtxs){
p_mesh->setMeshVtxBasedFieldSize();
}

int polympo_getMeshNumVtxs(MPMesh_ptr p_mpmesh) {
checkMPMeshValid(p_mpmesh); //chech vailidity
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;
int nVtxs = p_mesh->getNumVertices();
return nVtxs;
}

void polympo_setMeshNumElms(MPMesh_ptr p_mpmesh, int numElms){
checkMPMeshValid(p_mpmesh);
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;
Expand All @@ -272,14 +265,10 @@ void polympo_setMeshNumElms(MPMesh_ptr p_mpmesh, int numElms){
p_mesh->setNumElms(numElms);
p_mesh->setElm2VtxConn(elm2Vtx);
p_mesh->setElm2ElmConn(elm2Elm);
p_mesh->setMeshVtxBasedFieldSize();
}

int polympo_getMeshNumElms(MPMesh_ptr p_mpmesh) {
checkMPMeshValid(p_mpmesh); //chech vailidity
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;
int nElms = p_mesh->getNumElements();
return nElms;
}

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Remove empty lines


void polympo_setMeshTypeGeneralPoly(MPMesh_ptr p_mpmesh){
//chech validity
Expand Down Expand Up @@ -375,6 +364,20 @@ void polympo_setMeshElm2ElmConn(MPMesh_ptr p_mpmesh, int maxEdges, int nCells, i
});
}

int polympo_getMeshNumVtxs(MPMesh_ptr p_mpmesh) {
checkMPMeshValid(p_mpmesh); //chech vailidity
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;
int nVtxs = p_mesh->getNumVertices();
return nVtxs;
}

int polympo_getMeshNumElms(MPMesh_ptr p_mpmesh) {
checkMPMeshValid(p_mpmesh); //chech vailidity
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;
int nElms = p_mesh->getNumElements();
return nElms;
}

void polympo_setMeshVtxCoords(MPMesh_ptr p_mpmesh, int nVertices, double* xArray, double* yArray, double* zArray){
//chech validity
checkMPMeshValid(p_mpmesh);
Expand Down Expand Up @@ -413,6 +416,38 @@ void polympo_getMeshVtxCoords(MPMesh_ptr p_mpmesh, int nVertices, double* xArray
}
}

/*
void polympo_setMeshCellCenters(MPMesh_ptr p_mpmesh, int nCells, double* xArray, double* yArray, double* zArray){

checkMPMeshValid(p_mpmesh);
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;

auto centersArray = p_mesh->getMeshField<polyMPO::MeshF_CellCenters>();
auto h_centersArray = Kokkos::create_mirror_view(centersArray);
for (int i =0; i<nCenters;i++){
xArray[i] = h_centersArray(i,0);
yArray[i] = h_centersArray(i,1);
zArray[i] = h_centersArray(i,2);
}
Kokkos::deep_copy(centersArray, h_centersArray);
}

void polympo_getMeshCellCenters(MPMesh_ptr p_mpmesh, int nCells, double* xArray, double* yArray, double* zArray){

checkMPMeshValid(p_mpmesh);
auto p_mesh = ((polyMPO::MPMesh*)p_mpmesh)->p_mesh;

auto centersArray = p_mesh->getMeshField<polyMPO::MeshF_CellCenters>();
auto h_centersArray = Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(),centersArray);

for (int i=0;i<nCenters;i++){
xArray[i] = h_centersArray(i,0);
yArray[i] = h_centersArray(i,1);
zArray[i] = h_centersArray(i,2);
}
}
*/
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If we don't need the code, please remove it.


void polympo_setMeshOnSurfVeloIncr(MPMesh_ptr p_mpmesh, int nComps, int nVertices, double* array) {
//check mpMesh is valid
checkMPMeshValid(p_mpmesh);
Expand Down
11 changes: 7 additions & 4 deletions src/pmpo_c.h
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Expand Up @@ -38,19 +38,22 @@ void polympo_setMeshGeomTypePlanar(MPMesh_ptr p_mpmesh);
void polympo_setMeshGeomTypeSpherical(MPMesh_ptr p_mpmesh);
void polympo_setMeshSphereRadius(MPMesh_ptr p_mpmesh, double sphereRadius);
void polympo_setMeshNumVtxs(MPMesh_ptr p_mpmesh, int numVtxs);
int polympo_getMeshNumVtxs(MPMesh_ptr p_mpmesh);
void polympo_setMeshNumElms(MPMesh_ptr p_mpmesh, int numElms);
int polympo_getMeshNumElms(MPMesh_ptr p_mpmesh);
void polympo_setMeshNumEdgesPerElm(MPMesh_ptr p_mpmesh, int nCells, int* array);
void polympo_setMeshElm2VtxConn(MPMesh_ptr p_mpmesh, int maxEdges, int nCells, int* array);
void polympo_setMeshElm2ElmConn(MPMesh_ptr p_mpmesh, int maxEdges, int nCells, int* array);
int polympo_getMeshNumVtxs(MPMesh_ptr p_mpmesh);
int polympo_getMeshNumElms(MPMesh_ptr p_mpmesh);

//Mesh fields
void polympo_setMeshVtxCoords(MPMesh_ptr p_mpmesh, int nVertices, double* xArray, double* yArray, double* zArray);
void polympo_getMeshVtxCoords(MPMesh_ptr p_mpmesh, int nVertices, double* xArray, double* yArray, double* zArray);
void polympo_setMeshVtxCoords(MPMesh_ptr p_mpmesh, int nCells, double* xArray, double* yArray, double* zArray);
void polympo_getMeshVtxCoords(MPMesh_ptr p_mpmesh, int nCells, double* xArray, double* yArray, double* zArray);
//void polympo_setMeshCellCenters(MPMesh_ptr p_mpmesh, int nCenters, double* xArray, double* yArray, double* zArray);
//void polympo_getMeshCellCenters(MPMesh_ptr p_mpmesh, int nCenters, double* xArray, double* yArray, double* zArray);
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Remove commented-out code.

void polympo_setMeshOnSurfVeloIncr(MPMesh_ptr p_mpmesh, int nComps, int nVertices, double* array);//vec2d
void polympo_getMeshOnSurfVeloIncr(MPMesh_ptr p_mpmesh, int nComps, int nVertices, double* array);//vec2d
void polympo_setMeshOnSurfDispIncr(MPMesh_ptr p_mpmesh, int nComps, int nVertices, double* array);//vec2d
void polympo_getMeshOnSurfDispIncr(MPMesh_ptr p_mpmesh, int nComps, int nVertices, double* array);//vec2d

}
#endif
70 changes: 48 additions & 22 deletions src/pmpo_fortran.f90
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Expand Up @@ -223,17 +223,6 @@ subroutine polympo_setMeshNumVtxs(mpMesh,numVtxs) &
integer(c_int), value :: numVtxs
end subroutine
!---------------------------------------------------------------------------
!> @brief get the number of vertices from the mesh holding by polyMPO
!> @param mpMesh(in) mpMesh object
!> @param numVtxs(return)) the number of vertices
!---------------------------------------------------------------------------
function polympo_getMeshNumVtxs(mpMesh) result(numVtxs) &
bind(C, NAME = 'polympo_getMeshNumVtxs')
use :: iso_c_binding
type(c_ptr), intent(in), value :: mpMesh
integer(c_int) :: numVtxs
end function
!---------------------------------------------------------------------------
!> @brief set the number of elements of the mesh
!> modifies mesh topology polympo_startMeshFill required
!> @param mpMesh(in/out) mpMesh object
Expand All @@ -246,17 +235,6 @@ subroutine polympo_setMeshNumElms(mpMesh,numElms) &
integer(c_int), value :: numElms
end subroutine
!---------------------------------------------------------------------------
!> @brief get the number of elements from the mesh holding by polyMPO
!> @param mpMesh(in) mpMesh object
!> @param numVtxs(return)) the number of elements
!---------------------------------------------------------------------------
function polympo_getMeshNumElms(mpMesh) result(numElms) &
bind(C, NAME = 'polympo_getMeshNumElms')
use :: iso_c_binding
type(c_ptr), intent(in), value :: mpMesh
integer(c_int) :: numElms
end function
!---------------------------------------------------------------------------
!> @brief set the polympo mesh element to vertices connectivity
!> modifies mesh topology polympo_startMeshFill required
!> @param mpmesh(in/out) MPMesh object
Expand Down Expand Up @@ -285,6 +263,28 @@ subroutine polympo_setMeshElm2ElmConn(mpMesh, maxEdges, nCells, cellsOnCell) &
type(c_ptr), intent(in), value :: cellsOnCell
end subroutine
!---------------------------------------------------------------------------
!> @brief get the number of vertices from the mesh holding by polyMPO
!> @param mpMesh(in) mpMesh object
!> @param numVtxs(return)) the number of vertices
!---------------------------------------------------------------------------
function polympo_getMeshNumVtxs(mpMesh) result(numVtxs) &
bind(C, NAME = 'polympo_getMeshNumVtxs')
use :: iso_c_binding
type(c_ptr), intent(in), value :: mpMesh
integer(c_int) :: numVtxs
end function
!---------------------------------------------------------------------------
!> @brief get the number of elements from the mesh holding by polyMPO
!> @param mpMesh(in) mpMesh object
!> @param numVtxs(return)) the number of elements
!---------------------------------------------------------------------------
function polympo_getMeshNumElms(mpMesh) result(numElms) &
bind(C, NAME = 'polympo_getMeshNumElms')
use :: iso_c_binding
type(c_ptr), intent(in), value :: mpMesh
integer(c_int) :: numElms
end function
!---------------------------------------------------------------------------
!> @brief set the polympo mesh number of edges per element
!> modifies mesh topology polympo_startMeshFill required
!> @param mpmesh(in/out) MPMesh object
Expand Down Expand Up @@ -325,6 +325,32 @@ subroutine polympo_getMeshVtxCoords(mpMesh, nVertices, xArray, yArray, zArray) &
type(c_ptr), value :: xArray, yArray, zArray
end subroutine
!---------------------------------------------------------------------------
!> @brief set the polympo mesh cell centers
!> @param mpmesh(in/out) MPMesh object
!> @param nVertices(in) length of array in
!> @param x/y/zArray(in) the 1D arrays of cell coordinates
!---------------------------------------------------------------------------
!subroutine polympo_setMeshCellCenters(mpMesh, nCenters, xArray, yArray, zArray) &
! bind(C, NAME='polympo_setMeshCellCenters')
! use :: iso_c_binding
! type(c_ptr), value :: mpMesh
! integer(c_int), value:: nVertices
! type(c_ptr), value :: xArray, yArray, zArray
!end subroutine
!---------------------------------------------------------------------------
!> @brief get the polympo mesh cell centers
!> @param mpmesh(in/out) MPMesh object
!> @param nVertices(in) length of array in, use for assertion
!> @param x/y/zArray(in/out) the 1D arrays of vertices coordinates
!---------------------------------------------------------------------------
!subroutine polympo_getMeshCellCenters(mpMesh, nCenters, xArray, yArray, zArray) &
! bind(C, NAME='polympo_getMeshCellCenters')
! use :: iso_c_binding
! type(c_ptr), value :: mpMesh
! integer(c_int), value :: nVertices
! type(c_ptr), value :: xArray, yArray, zArray
!end subroutine
!---------------------------------------------------------------------------
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Remove commented-out code.

!> @brief set the spherical velocity increment mesh array
!> from a host array
!> @param mpmesh(in/out) MPMesh object
Expand Down
9 changes: 9 additions & 0 deletions src/pmpo_mesh.cpp
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Expand Up @@ -31,4 +31,13 @@ namespace polyMPO{
vtxOnSurfDispIncr_ = DoubleVec2dView(vtxOnSurfDispIncrMapEntry.second,numVtxs_);
}

void Mesh::setMeshElmBasedFieldSize(){
PMT_ALWAYS_ASSERT(meshEdit_);

auto elmCoordsMapEntry = meshFields2TypeAndString.at(MeshF_ElmCenterXYZ);
PMT_ALWAYS_ASSERT(elmCoordsMapEntry.first == MeshFType_ElmBased);
elmCenterXYZ_ = DoubleVec3dView(elmCoordsMapEntry.second, numElms_);

}

} // namespace polyMPO
13 changes: 11 additions & 2 deletions src/pmpo_mesh.hpp
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Expand Up @@ -22,7 +22,8 @@ enum MeshFieldIndex{
MeshF_VtxCoords,
MeshF_Vel,
MeshF_OnSurfVeloIncr,
MeshF_OnSurfDispIncr
MeshF_OnSurfDispIncr,
MeshF_ElmCenterXYZ
};
enum MeshFieldType{
MeshFType_Invalid = -2,
Expand All @@ -37,7 +38,8 @@ const std::map<MeshFieldIndex, std::pair<MeshFieldType,
{MeshF_VtxCoords, {MeshFType_VtxBased,"MeshField_VerticesCoords"}},
{MeshF_Vel, {MeshFType_VtxBased,"MeshField_Velocity"}},
{MeshF_OnSurfVeloIncr, {MeshFType_VtxBased,"MeshField_OnSurfaceVelocityIncrement"}},
{MeshF_OnSurfDispIncr, {MeshFType_VtxBased,"MeshField_OnSurfaceDisplacementIncrement"}}};
{MeshF_OnSurfDispIncr, {MeshFType_VtxBased,"MeshField_OnSurfaceDisplacementIncrement"}},
{MeshF_ElmCenterXYZ, {MeshFType_ElmBased,"MeshField_ElementCenterXYZ"}}};

enum mesh_type {mesh_unrecognized_lower = -1,
mesh_general_polygonal, //other meshes
Expand All @@ -64,6 +66,7 @@ class Mesh {

//start of meshFields
DoubleVec3dView vtxCoords_;
DoubleVec3dView elmCenterXYZ_;
DoubleVec2dView vtxVel_;
DoubleVec2dView vtxOnSurfVeloIncr_;
DoubleVec2dView vtxOnSurfDispIncr_;
Expand All @@ -88,6 +91,7 @@ class Mesh {
elm2ElmConn_(elm2ElmConn){
meshEdit_ = true;
setMeshVtxBasedFieldSize();
setMeshElmBasedFieldSize();
meshEdit_ = false;
vtxCoords_ = vtxCoords;
}
Expand All @@ -105,6 +109,8 @@ class Mesh {
IntElm2ElmView getElm2ElmConn() { return elm2ElmConn_; }
template<MeshFieldIndex index> auto getMeshField();
void setMeshVtxBasedFieldSize();

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Please remove the empty line.

void setMeshElmBasedFieldSize();

void setMeshEdit(bool meshEdit) { meshEdit_ = meshEdit; }
//onec MeshType/GeomType is set to valid types, we can't change them anymore
Expand Down Expand Up @@ -146,6 +152,9 @@ auto Mesh::getMeshField(){
else if constexpr (index==MeshF_OnSurfDispIncr){
return vtxOnSurfDispIncr_;
}
else if constexpr (index==MeshF_ElmCenterXYZ){
return elmCenterXYZ_;
}
fprintf(stderr,"Mesh Field Index error!\n");
exit(1);
}
Expand Down
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Please remove this .mod file.

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15 changes: 12 additions & 3 deletions test/readMPAS.f90
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Expand Up @@ -125,7 +125,8 @@ subroutine readMPASMesh(filename, maxEdges, vertexDegree, &
nCells, nVertices, nEdgesOnCell, &
onSphere, sphereRadius, &
xVertex, yVertex, zVertex, &
verticesOnCell, cellsOnCell)
verticesOnCell, cellsOnCell)!,&
!cellCenters)
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Remove commented-out code.

use :: netcdf
use :: iso_c_binding
implicit none
Expand All @@ -142,7 +143,7 @@ subroutine readMPASMesh(filename, maxEdges, vertexDegree, &

integer :: ncid, status, nCellsID, nVerticesID, maxEdgesID, vertexDegreeID, &
nEdgesOnCellID, xVertexID, yVertexID, zVertexID, &
verticesOnCellID, cellsOnCellID
verticesOnCellID, cellsOnCellID, cellCentersID

status = nf90_open(path=trim(filename), mode=nf90_nowrite, ncid=ncid)
if (status /= nf90_noerr) then
Expand Down Expand Up @@ -211,9 +212,10 @@ subroutine readMPASMesh(filename, maxEdges, vertexDegree, &
allocate(yVertex(nVertices))
allocate(zVertex(nVertices))
allocate(nEdgesOnCell(nCells))
!allocate(cellCenters(nCells))
allocate(verticesOnCell(maxEdges, nCells))
allocate(cellsOnCell(maxEdges, nCells))

status = nf90_get_att(ncid, nf90_global, "on_a_sphere", onSphere)
if (status /= nf90_noerr) then
write(0, *) "readMPASMesh: Error on get attribute 'on_a_sphere'"
Expand Down Expand Up @@ -315,6 +317,13 @@ subroutine readMPASMesh(filename, maxEdges, vertexDegree, &
stop
end if

!status = nf90_get_var(ncid, cellCentersID, cellCenters)
!if (status /= nf90_noerr) then
! write(0, *) "readMPASMesh: Error on get var of 'cellCenters'"
! write(0, *) trim(nf90_strerror(status))
! stop
!end if

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Remove commented-out code.

status = nf90_close(ncid)
end subroutine readMPASMesh
subroutine setWithMPASMeshByFortran(mpMesh, fileName, n) bind(C, name="setWithMPASMeshByFortran")
Expand Down