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Fixes to compile with BOUT++ next branch #1

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Fixes to compile with BOUT++ next branch #1

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d70ed64
CMakeList add C language support
bendudson Oct 8, 2024
5d8df73
SpecificInd: Replace zpm with offset
bendudson Oct 8, 2024
349b6b2
Atomic++: Upgrade nlohmann::json dependency
bendudson Oct 8, 2024
2edfb03
BOUT++ header locations
bendudson Oct 9, 2024
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.9...3.12)

project(hermes-2 LANGUAGES CXX)
project(hermes-2 LANGUAGES CXX C)
set(CMAKE_CXX_STANDARD 14)
find_package(bout++ REQUIRED)
add_executable(hermes-2 main.cxx hermes-2.cxx div_ops.cxx loadmetric.cxx radiation.cxx neutral-model.cxx diffusion2d.cxx atomicpp/ImpuritySpecies.cxx atomicpp/Prad.cxx atomicpp/RateCoefficient.cxx atomicpp/sharedFunctions.cxx)
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32,255 changes: 22,009 additions & 10,246 deletions atomicpp/json.hxx
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2 changes: 1 addition & 1 deletion diffusion2d.hxx
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Expand Up @@ -3,7 +3,7 @@
#define __NEUTRAL_DIFFUSION2D_H__

#include "neutral-model.hxx"
#include <invert_laplace.hxx>
#include <bout/invert_laplace.hxx>

class Diffusion2D : public NeutralModel {
public:
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12 changes: 6 additions & 6 deletions div_ops.cxx
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Expand Up @@ -27,11 +27,11 @@

#include <bout/assert.hxx>
#include <bout/mesh.hxx>
#include <derivs.hxx>
#include <difops.hxx>
#include <globals.hxx>
#include <output.hxx>
#include <utils.hxx>
#include <bout/derivs.hxx>
#include <bout/difops.hxx>
#include <bout/globals.hxx>
#include <bout/output.hxx>
#include <bout/utils.hxx>

#include <bout/index_derivs.hxx>

Expand Down Expand Up @@ -1430,7 +1430,7 @@ Field3D CustomStencil::apply(const Field3D &a, const std::string &region) {
BoutReal CustomStencil::apply(const Field3D &a, const Ind3D &i) {
BoutReal result = 0;
for (size_t c = 0; c < coefs.size(); ++c) {
result += coefs[c][i] * a[i.xp(xoffset[c]).zpm(zoffset[c])];
result += coefs[c][i] * a[i.offset(xoffset[c], 0, zoffset[c])];
}
return result;
}
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4 changes: 2 additions & 2 deletions div_ops.hxx
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Expand Up @@ -26,8 +26,8 @@
#ifndef __DIV_OPS_H__
#define __DIV_OPS_H__

#include <field3d.hxx>
#include <vector3d.hxx>
#include <bout/field3d.hxx>
#include <bout/vector3d.hxx>

class CustomStencil {
public:
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12 changes: 6 additions & 6 deletions hermes-2.cxx
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Expand Up @@ -21,13 +21,13 @@
*/
#include "hermes-2.hxx"

#include <derivs.hxx>
#include <field_factory.hxx>
#include <initialprofiles.hxx>
#include <bout/derivs.hxx>
#include <bout/field_factory.hxx>
#include <bout/initialprofiles.hxx>

#include <invert_parderiv.hxx>
#include "parallel_boundary_region.hxx"
#include "boundary_region.hxx"
#include <bout/invert_parderiv.hxx>
#include <bout/parallel_boundary_region.hxx>
#include <bout/boundary_region.hxx>

#include "div_ops.hxx"
#include "loadmetric.hxx"
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4 changes: 2 additions & 2 deletions hermes-2.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,11 @@ class Hermes;

#include <bout/physicsmodel.hxx>

#include <invert_laplace.hxx>
#include <bout/invert_laplace.hxx>
#include <bout/invert/laplacexy.hxx>
#include <bout/invert/laplacexz.hxx>
#include <bout/constants.hxx>
#include <mask.hxx>
#include <bout/mask.hxx>

#include "neutral-model.hxx"

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8 changes: 4 additions & 4 deletions loadmetric.cxx
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@@ -1,7 +1,7 @@
#include <globals.hxx>
#include <output.hxx>
#include <utils.hxx>
#include <field2d.hxx>
#include <bout/globals.hxx>
#include <bout/output.hxx>
#include <bout/utils.hxx>
#include <bout/field2d.hxx>
#include <bout/mesh.hxx>

#include "loadmetric.hxx"
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2 changes: 1 addition & 1 deletion loadmetric.hxx
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Expand Up @@ -2,7 +2,7 @@
#ifndef __LOADMETRIC_H__
#define __LOADMETRIC_H__

#include <bout_types.hxx>
#include <bout/bout_types.hxx>

void LoadMetric(BoutReal Lnorm, BoutReal Bnorm);

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4 changes: 2 additions & 2 deletions neutral-model.hxx
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Expand Up @@ -5,8 +5,8 @@
#ifndef __NEUTRAL_MODEL_H__
#define __NEUTRAL_MODEL_H__

#include <field3d.hxx>
#include <options.hxx>
#include <bout/field3d.hxx>
#include <bout/options.hxx>
#include <bout/solver.hxx>
#include <bout/mesh.hxx>

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8 changes: 4 additions & 4 deletions radiation.cxx
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@@ -1,7 +1,7 @@
#include <boutexception.hxx>
#include <globals.hxx> // for mesh object
#include <output.hxx>
#include <utils.hxx>
#include <bout/boutexception.hxx>
#include <bout/globals.hxx> // for mesh object
#include <bout/output.hxx>
#include <bout/utils.hxx>

#include "radiation.hxx"

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4 changes: 2 additions & 2 deletions radiation.hxx
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Expand Up @@ -2,8 +2,8 @@
#ifndef __RADIATION_H__
#define __RADIATION_H__

#include <field3d.hxx>
#include <bout_types.hxx>
#include <bout/field3d.hxx>
#include <bout/bout_types.hxx>

#include <vector>
#include <cmath>
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