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Merged
krystophny merged 3 commits into from
Jan 14, 2026
Merged

Fix/spl per recursive #251

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6ac2278
refactor: modularize libneo_coordinates with proper OOP architecture
krystophny Jan 5, 2026
86b9b75
test: add comprehensive regression tests for coordinate systems
Jan 13, 2026
828680d
fix: mark procedures as recursive for OpenMP thread safety
krystophny Jan 13, 2026
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8 changes: 7 additions & 1 deletion CMakeSources.in
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,13 @@ add_library(neo STATIC
src/coordinates/vmec_coordinates.f90
src/coordinates/geoflux_coordinates.f90
src/coordinates/libneo_coordinate_conventions.f90
src/coordinates/libneo_coordinates_merged.f90
src/coordinates/libneo_coordinates_base.f90
src/coordinates/libneo_coordinates_vmec.f90
src/coordinates/libneo_coordinates_geoflux.f90
src/coordinates/libneo_coordinates_chartmap.f90
src/coordinates/libneo_coordinates_validator.f90
src/coordinates/libneo_coordinates_file_detection.f90
src/coordinates/libneo_coordinates.f90
src/coordinates/libneo_chartmap_vmec_generator.f90
src/coordinates/libneo_coordinates_mapping.f90
src/spline_vmec_data.f90
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7 changes: 7 additions & 0 deletions bind.toml
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@@ -0,0 +1,7 @@
[python]
package-name = "pylibneo"
# Exclude files that cause issues with f90wrap
exclude = [
"**/f2py_*.f90",
"**/local_rusage.c"
]
12 changes: 7 additions & 5 deletions fpm.toml
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Expand Up @@ -6,13 +6,15 @@ maintainer = "albert@tugraz.at"
copyright = "Copyright 2025, Plasma Physics at TU Graz"

[dependencies]
openmp = "*"
mpi = "*"
hdf5 = "*"
netcdf = "*"
# System libraries (openmp, mpi, hdf5, netcdf) handled via compiler flags

[build]
external-modules = ["fftw3.f03"]
external-modules = [
"fftw3", "fftw3.f03",
"netcdf", "hdf5", "h5lt",
"omp_lib", "mpi", "mpi_f08",
"openacc"
]
auto-executables = true
auto-tests = true
auto-examples = true
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274 changes: 18 additions & 256 deletions src/coordinates/libneo_coordinates.f90
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@@ -1,265 +1,27 @@
module libneo_coordinates
use, intrinsic :: iso_fortran_env, only: dp => real64
use interpolate, only: BatchSplineData3D
use libneo_coordinate_conventions
use libneo_coordinates_base
use libneo_coordinates_vmec
use libneo_coordinates_geoflux
use libneo_coordinates_chartmap
use libneo_coordinates_validator
use libneo_coordinates_file_detection
implicit none

public :: UNKNOWN
public :: CYL, VMEC, BOOZER
public :: coordinate_system_t
public :: UNKNOWN, CYL, VMEC, BOOZER
public :: RHO_TOR, RHO_POL, PSI_TOR_NORM, PSI_POL_NORM

character(len=*), parameter :: chartmap_netcdf_spec = &
"Chartmap NetCDF conventions:"//new_line('a')// &
"- Dimensions: rho, theta, zeta"//new_line('a')// &
"- Variables (required):"//new_line('a')// &
" rho(rho), theta(theta)"//new_line('a')// &
" zeta(zeta)"//new_line('a')// &
" x(zeta,theta,rho)"//new_line('a')// &
" y(zeta,theta,rho)"//new_line('a')// &
" z(zeta,theta,rho)"//new_line('a')// &
"- Optional: num_field_periods (integer >= 1)"// &
new_line('a')// &
"- Required: zeta_convention (global attribute)"// &
new_line('a')// &
" allowed: cyl, vmec"// &
new_line('a')// &
"- Ranges:"//new_line('a')// &
" rho in [0,1]"//new_line('a')// &
" theta in [0,2pi)"//new_line('a')// &
" zeta in [0,2pi/num_field_periods)"// &
new_line('a')// &
"periodic dims exclude endpoint"//new_line('a')// &
"- Storage order:"//new_line('a')// &
" file dims (zeta,theta,rho)"//new_line('a')// &
"Fortran reads x(rho,theta,zeta)"//new_line('a')// &
"- Units: x,y,z in cm"
public :: chartmap_netcdf_spec, chartmap_from_cyl_ierr_spec
public :: chartmap_from_cyl_ok, chartmap_from_cyl_err_max_iter
public :: chartmap_from_cyl_err_singular, chartmap_from_cyl_err_out_of_bounds
public :: chartmap_from_cyl_err_invalid
public :: refcoords_file_unknown, refcoords_file_chartmap, refcoords_file_vmec_wout

integer, parameter :: chartmap_from_cyl_ok = 0
integer, parameter :: chartmap_from_cyl_err_max_iter = 1
integer, parameter :: chartmap_from_cyl_err_singular = 2
integer, parameter :: chartmap_from_cyl_err_out_of_bounds = 3
integer, parameter :: chartmap_from_cyl_err_invalid = 4
public :: vmec_coordinate_system_t, make_vmec_coordinate_system
public :: geoflux_coordinate_system_t, make_geoflux_coordinate_system
public :: chartmap_coordinate_system_t, make_chartmap_coordinate_system

integer, parameter :: refcoords_file_unknown = 0
integer, parameter :: refcoords_file_chartmap = 1
integer, parameter :: refcoords_file_vmec_wout = 2

character(len=*), parameter :: chartmap_from_cyl_ierr_spec = &
"chartmap_from_cyl ierr codes:"//new_line('a')// &
"0 ok"//new_line('a')// &
"1 max iterations or no progress"//new_line('a')// &
"2 singular normal equations"//new_line('a')// &
"3 step out of bounds for rho"//new_line('a')// &
"4 invalid mapping slice"

type, abstract :: coordinate_system_t
contains
procedure(evaluate_cart_if), deferred :: evaluate_cart
procedure(evaluate_cyl_if), deferred :: evaluate_cyl
procedure(covariant_basis_if), deferred :: covariant_basis
procedure(metric_tensor_if), deferred :: metric_tensor
procedure(from_cyl_if), deferred :: from_cyl
procedure :: cov_to_cart => coordinate_system_cov_to_cart
procedure :: ctr_to_cart => coordinate_system_ctr_to_cart
end type coordinate_system_t

abstract interface
subroutine evaluate_cart_if(self, u, x)
import :: coordinate_system_t, dp
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: x(3)
end subroutine

subroutine evaluate_cyl_if(self, u, x)
import :: coordinate_system_t, dp
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: x(3)
end subroutine

subroutine covariant_basis_if(self, u, e_cov)
import :: coordinate_system_t, dp
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: e_cov(3, 3)
end subroutine

subroutine metric_tensor_if(self, u, g, ginv, sqrtg)
import :: coordinate_system_t, dp
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: g(3, 3), ginv(3, 3), sqrtg
end subroutine

subroutine from_cyl_if(self, xcyl, u, ierr)
import :: coordinate_system_t, dp
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: xcyl(3)
real(dp), intent(out) :: u(3)
integer, intent(out) :: ierr
end subroutine
end interface

interface
module subroutine make_vmec_coordinate_system(cs)
class(coordinate_system_t), allocatable, intent(out) :: cs
end subroutine

module subroutine make_geoflux_coordinate_system(cs)
class(coordinate_system_t), allocatable, intent(out) :: cs
end subroutine

module subroutine make_chartmap_coordinate_system(cs, filename)
class(coordinate_system_t), allocatable, intent(out) :: cs
character(len=*), intent(in) :: filename
end subroutine

module subroutine validate_chartmap_file(filename, ierr, message)
character(len=*), intent(in) :: filename
integer, intent(out) :: ierr
character(len=*), intent(out) :: message
end subroutine validate_chartmap_file

module subroutine detect_refcoords_file_type(filename, file_type, ierr, message)
character(len=*), intent(in) :: filename
integer, intent(out) :: file_type
integer, intent(out) :: ierr
character(len=*), intent(out) :: message
end subroutine detect_refcoords_file_type
end interface

type, extends(coordinate_system_t) :: vmec_coordinate_system_t
contains
procedure :: evaluate_cart => vmec_evaluate_cart
procedure :: evaluate_cyl => vmec_evaluate_cyl
procedure :: covariant_basis => vmec_covariant_basis
procedure :: metric_tensor => vmec_metric_tensor
procedure :: from_cyl => vmec_from_cyl
end type vmec_coordinate_system_t

type, extends(coordinate_system_t) :: chartmap_coordinate_system_t
type(BatchSplineData3D) :: spl_cart
type(BatchSplineData3D) :: spl_rz
logical :: has_spl_rz = .false.
integer :: nrho = 0
integer :: ntheta = 0
integer :: nzeta = 0
integer :: num_field_periods = 1
integer :: zeta_convention = UNKNOWN
integer :: rho_convention = UNKNOWN
real(dp) :: tol_newton = 1.0e-12_dp
contains
procedure :: evaluate_cart => chartmap_evaluate_cart
procedure :: evaluate_cyl => chartmap_evaluate_cyl
procedure :: covariant_basis => chartmap_covariant_basis
procedure :: metric_tensor => chartmap_metric_tensor
procedure :: from_cyl => chartmap_from_cyl
procedure :: from_cart => chartmap_from_cart
end type chartmap_coordinate_system_t

interface
module subroutine vmec_evaluate_cart(self, u, x)
class(vmec_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: x(3)
end subroutine vmec_evaluate_cart

module subroutine vmec_evaluate_cyl(self, u, x)
class(vmec_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: x(3)
end subroutine vmec_evaluate_cyl

module subroutine vmec_covariant_basis(self, u, e_cov)
class(vmec_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: e_cov(3, 3)
end subroutine vmec_covariant_basis

module subroutine vmec_metric_tensor(self, u, g, ginv, sqrtg)
class(vmec_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: g(3, 3), ginv(3, 3), sqrtg
end subroutine vmec_metric_tensor

module subroutine vmec_from_cyl(self, xcyl, u, ierr)
class(vmec_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: xcyl(3)
real(dp), intent(out) :: u(3)
integer, intent(out) :: ierr
end subroutine vmec_from_cyl

module subroutine chartmap_evaluate_cart(self, u, x)
class(chartmap_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: x(3)
end subroutine chartmap_evaluate_cart

module subroutine chartmap_evaluate_cyl(self, u, x)
class(chartmap_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: x(3)
end subroutine chartmap_evaluate_cyl

module subroutine chartmap_covariant_basis(self, u, e_cov)
class(chartmap_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: e_cov(3, 3)
end subroutine chartmap_covariant_basis

module subroutine chartmap_metric_tensor(self, u, g, ginv, sqrtg)
class(chartmap_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(out) :: g(3, 3), ginv(3, 3), sqrtg
end subroutine chartmap_metric_tensor

module subroutine chartmap_from_cyl(self, xcyl, u, ierr)
class(chartmap_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: xcyl(3)
real(dp), intent(out) :: u(3)
integer, intent(out) :: ierr
end subroutine chartmap_from_cyl

module subroutine chartmap_from_cart(self, x, u, ierr)
class(chartmap_coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: x(3)
real(dp), intent(out) :: u(3)
integer, intent(out) :: ierr
end subroutine chartmap_from_cart
end interface

contains

subroutine coordinate_system_cov_to_cart(self, u, v_cov, v_cart)
!> Convert covariant vector components to Cartesian.
!> v_cart_i = e_cov(i,j) * ginv(j,k) * v_cov(k)
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(in) :: v_cov(3)
real(dp), intent(out) :: v_cart(3)

real(dp) :: e_cov(3, 3), g(3, 3), ginv(3, 3), sqrtg
real(dp) :: v_ctr(3)

call self%metric_tensor(u, g, ginv, sqrtg)
call self%covariant_basis(u, e_cov)
v_ctr = matmul(ginv, v_cov)
v_cart = matmul(e_cov, v_ctr)
end subroutine coordinate_system_cov_to_cart

subroutine coordinate_system_ctr_to_cart(self, u, v_ctr, v_cart)
!> Convert contravariant vector components to Cartesian.
!> v_cart_i = e_cov(i,j) * v_ctr(j)
class(coordinate_system_t), intent(in) :: self
real(dp), intent(in) :: u(3)
real(dp), intent(in) :: v_ctr(3)
real(dp), intent(out) :: v_cart(3)

real(dp) :: e_cov(3, 3)

call self%covariant_basis(u, e_cov)
v_cart = matmul(e_cov, v_ctr)
end subroutine coordinate_system_ctr_to_cart
public :: validate_chartmap_file
public :: detect_refcoords_file_type

end module libneo_coordinates
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