Merge v5 into next - resolve conflicts #2658

dschwoerer · 2023-02-17T12:31:11Z

Merges next into master to resolve conflicts, so that #2655 can be merged

Solves `A + Div_par( B Grad_par )` in divergence form. Adapted from `InvertPar` which uses `Grad2_par2 = Grad_par(Grad_par)` in non-conservative form.

Enables the fluxes at the boundaries to be fixes to be the same as the Spitzer-Harm calculation.

The integral of Div(Q) over the domain should be the same for SNB and S-H methods, because the Neumann boundary conditions on H should ensure this.

Runs in open domain with boundaries, checking that the boundary fluxes are the same for SH and SNB calculations even with non-uniform mesh.

Strangely, changing calculation of dy, J from float to double makes difference between SNB and SH heat fluxes larger.

Forgot to add, so wouldn't be compiled in Autotools build

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

SNB and InvertParDiv for nonuniform grids

Fix error message

Expose mixed derivatives

Cleanup syntax

github-actions

clang-tidy made some suggestions

github-actions · 2023-02-17T12:42:09Z

include/bout/invert_pardiv.hxx

+ *
+ * Field3D result = inv->solve(rhs);
+ */
+class InvertParDiv {


warning: class 'InvertParDiv' defines a default destructor but does not define a copy constructor, a copy assignment operator, a move constructor or a move assignment operator [cppcoreguidelines-special-member-functions]

class InvertParDiv { ^

github-actions · 2023-02-17T12:42:09Z

include/bout/invert_pardiv.hxx

+  }
+
+protected:
+  CELL_LOC location;


warning: member variable 'location' has protected visibility [cppcoreguidelines-non-private-member-variables-in-classes]

CELL_LOC location; ^

github-actions · 2023-02-17T12:42:10Z

include/bout/invert_pardiv.hxx

+
+protected:
+  CELL_LOC location;
+  Mesh* localmesh; ///< Mesh object for this solver


warning: member variable 'localmesh' has protected visibility [cppcoreguidelines-non-private-member-variables-in-classes]

Mesh* localmesh; ///< Mesh object for this solver ^

github-actions · 2023-02-17T12:42:10Z

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx

+  nsys = 1 + (localmesh->LocalNz) / 2;
+}
+
+Field3D InvertParDivCR::solve(const Field3D& f) {


warning: function 'solve' has cognitive complexity of 88 (threshold 25) [readability-function-cognitive-complexity]

Field3D InvertParDivCR::solve(const Field3D& f) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:63: +1, including nesting penalty of 0, nesting level increased to 1

ASSERT1(localmesh == f.getMesh()); ^

include/bout/assert.hxx:39: expanded from macro 'ASSERT1'

if (!(condition)) { \ ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:64: +1, including nesting penalty of 0, nesting level increased to 1

ASSERT1(location == f.getLocation()); ^

include/bout/assert.hxx:39: expanded from macro 'ASSERT1'

if (!(condition)) { \ ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:78: +1, including nesting penalty of 0, nesting level increased to 1

for (surf.first(); !surf.isDone(); surf.next()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:80: +2, including nesting penalty of 1, nesting level increased to 2

if (!surf.closed()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:82: +3, including nesting penalty of 2, nesting level increased to 3

if (surf.firstY()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:83: +4, including nesting penalty of 3, nesting level increased to 4

if (location == CELL_YLOW) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:86: +1, nesting level increased to 4

} else { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:90: +3, including nesting penalty of 2, nesting level increased to 3

if (surf.lastY()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:94: +3, including nesting penalty of 2, nesting level increased to 3

if (n > size) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:113: +1, including nesting penalty of 0, nesting level increased to 1

for (surf.first(); !surf.isDone(); surf.next()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:124: +2, including nesting penalty of 1, nesting level increased to 2

if (!closed) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:125: +3, including nesting penalty of 2, nesting level increased to 3

if (surf.firstY()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:126: +4, including nesting penalty of 3, nesting level increased to 4

if (location == CELL_YLOW) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:131: +1, nesting level increased to 4

} else { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:136: +3, including nesting penalty of 2, nesting level increased to 3

if (surf.lastY()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:146: +2, including nesting penalty of 1, nesting level increased to 2

for (int y = 0; y < localmesh->LocalNy - localmesh->ystart - local_ystart; y++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:151: +2, including nesting penalty of 1, nesting level increased to 2

for (int k = 0; k < nsys; k++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:152: +3, including nesting penalty of 2, nesting level increased to 3

for (int y = 0; y < localmesh->LocalNy - localmesh->ystart - local_ystart; y++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:155: nesting level increased to 4

auto Left = [&](const Field2D& field) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:158: nesting level increased to 4

auto Right = [&](const Field2D& field) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:182: +2, including nesting penalty of 1, nesting level increased to 2

if (closed) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:189: +3, including nesting penalty of 2, nesting level increased to 3

if (rank == 0) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:190: +4, including nesting penalty of 3, nesting level increased to 4

for (int k = 0; k < nsys; k++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:196: +3, including nesting penalty of 2, nesting level increased to 3

if (rank == np - 1) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:197: +4, including nesting penalty of 3, nesting level increased to 4

for (int k = 0; k < nsys; k++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:203: +1, nesting level increased to 2

} else { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:205: +3, including nesting penalty of 2, nesting level increased to 3

if (surf.firstY()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:206: +4, including nesting penalty of 3, nesting level increased to 4

for (int k = 0; k < nsys; k++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:207: +5, including nesting penalty of 4, nesting level increased to 5

for (int y = 0; y < localmesh->ystart; y++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:216: +3, including nesting penalty of 2, nesting level increased to 3

if (surf.lastY()) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:217: +4, including nesting penalty of 3, nesting level increased to 4

for (int k = 0; k < nsys; k++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:218: +5, including nesting penalty of 4, nesting level increased to 5

for (int y = size - localmesh->ystart; y < size; y++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:234: +2, including nesting penalty of 1, nesting level increased to 2

for (int k = 0; k < nsys; k++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:235: +3, including nesting penalty of 2, nesting level increased to 3

for (int y = 0; y < size; y++) { ^

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:241: +2, including nesting penalty of 1, nesting level increased to 2

for (int y = 0; y < size; y++) { ^

github-actions · 2023-02-17T12:42:10Z

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx

+    int x = surf.xpos;
+
+    // Test if open or closed field-lines
+    BoutReal ts;


warning: variable 'ts' is not initialized [cppcoreguidelines-init-variables]

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx:42:

- #include <bout/constants.hxx> + #include <math.h> + + #include <bout/constants.hxx>

Suggested change

BoutReal ts;

BoutReal ts = NAN;

github-actions · 2023-02-17T12:42:10Z

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx

+
+    if (closed) {
+      // Twist-shift
+      int rank;


warning: variable 'rank' is not initialized [cppcoreguidelines-init-variables]

Suggested change

int rank;

int rank = 0;

github-actions · 2023-02-17T12:42:10Z

src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx

+    if (closed) {
+      // Twist-shift
+      int rank;
+      int np;


warning: variable 'np' is not initialized [cppcoreguidelines-init-variables]

Suggested change

int np;

int np = 0;

github-actions · 2023-02-17T12:42:11Z

src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx

+};
+
+namespace {
+RegisterInvertParDiv<InvertParDivCR> registerinvertpardivcyclic{PARDIVCYCLIC};


warning: variable 'registerinvertpardivcyclic' is non-const and globally accessible, consider making it const [cppcoreguidelines-avoid-non-const-global-variables]

RegisterInvertParDiv<InvertParDivCR> registerinvertpardivcyclic{PARDIVCYCLIC}; ^

github-actions · 2023-02-17T12:42:11Z

src/invert/pardiv/impls/cyclic/pardiv_cyclic.hxx

+};
+
+namespace {
+RegisterInvertParDiv<InvertParDivCR> registerinvertpardivcyclic{PARDIVCYCLIC};


warning: variable 'registerinvertpardivcyclic' defined in a header file; variable definitions in header files can lead to ODR violations [misc-definitions-in-headers]

RegisterInvertParDiv<InvertParDivCR> registerinvertpardivcyclic{PARDIVCYCLIC}; ^

github-actions · 2023-02-17T12:42:11Z

tests/integrated/test-snb/test_snb.cxx

@@ -19,6 +20,16 @@
    throw BoutException("Line " S__LINE__ " Expected false, got true: " #expr); \
  }

+#define EXPECT_LT(expr1, expr2)                                                         \


warning: function-like macro 'EXPECT_LT' used; consider a 'constexpr' template function [cppcoreguidelines-macro-usage]

#define EXPECT_LT(expr1, expr2) \ ^

bendudson

Thanks @dschwoerer !

bendudson and others added 20 commits August 18, 2022 17:58

Add InvertParDiv solver class

f100c34

Solves `A + Div_par( B Grad_par )` in divergence form. Adapted from `InvertPar` which uses `Grad2_par2 = Grad_par(Grad_par)` in non-conservative form.

Modify SNB solver to use InvertParDiv

47f8cd5

Enables the fluxes at the boundaries to be fixes to be the same as the Spitzer-Harm calculation.

Add SNB test of heat flux through boundaries

9071038

The integral of Div(Q) over the domain should be the same for SNB and S-H methods, because the Neumann boundary conditions on H should ensure this.

Apply clang-format changes

9d9c3ba

Update SNB test

61051d4

Runs in open domain with boundaries, checking that the boundary fluxes are the same for SH and SNB calculations even with non-uniform mesh.

Apply clang-format changes

25cf1bd

Implementing clang-tidy suggestions

9602fbb

Strangely, changing calculation of dy, J from float to double makes difference between SNB and SH heat fluxes larger.

Add pardiv to makefile

947254b

Forgot to add, so wouldn't be compiled in Autotools build

Apply suggestions from clang-tidy

4c7132d

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Apply clang-format changes

0d03e73

Merge pull request #2572 from boutproject/snb-nonuniform

23af1b8

SNB and InvertParDiv for nonuniform grids

Cleanup syntax

c81c70b

Expose mixed derivatives

c0a85a2

Apply clang-format changes

11edde3

Fix error message

59f665e

Apply clang-format changes

4aabdea

Merge pull request #2642 from boutproject/getField_error

e6c4d81

Fix error message

Merge pull request #2639 from boutproject/boutpp-mixed-deriv

a3248cf

Expose mixed derivatives

Merge pull request #2638 from boutproject/cleanup-difops

0f106d3

Cleanup syntax

Merge remote-tracking branch 'origin/next' into HEAD

ffa0890

github-actions bot reviewed Feb 17, 2023

View reviewed changes

bendudson approved these changes Feb 17, 2023

View reviewed changes

bendudson merged commit 6d19d7e into master Feb 17, 2023

bendudson deleted the master-next-merge-v5 branch February 17, 2023 19:13

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Merge v5 into next - resolve conflicts #2658

Merge v5 into next - resolve conflicts #2658

dschwoerer commented Feb 17, 2023

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bendudson left a comment

Merge v5 into next - resolve conflicts #2658

Merge v5 into next - resolve conflicts #2658

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