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Oct 28, 2025
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Fix compilation warnings #861

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122a81a
FIX: Eliminate compilation warnings.
baagaard-usgs Oct 28, 2025
8d8399f
Update list of changes.
baagaard-usgs Oct 28, 2025
f26c750
Update workspace spelling dictionary.
baagaard-usgs Oct 28, 2025
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1 change: 1 addition & 0 deletions .vscode/settings.json
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Expand Up @@ -39,6 +39,7 @@
"dm",
"drucker",
"elastoplastic",
"Gmsh",
"Knepley",
"neumann",
"nodeset",
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15 changes: 9 additions & 6 deletions CHANGES.md
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Expand Up @@ -13,16 +13,19 @@ The version numbers are in the form `MAJOR.MINOR.PATCH`, where major releases in
* Add displacement scale and improve the names of the other scales.
* The time scale for poroelasticity is derived from the other scales and nominal material properties.
* Add discussion of nondimensionalization for each of the governing equations.
* Update default solver tolerances consistent with new nondimensionalization scales.
* Update default solver tolerances consistent with the new nondimensionalization scales.
* Add option to use adaptive time stepping and update examples `reverse-2d` Steps 7 and 8 and `magma-2d` Step 1 to demonstrate its use.
* Update solver settings for elasticity for better scalability with problem size.
* ASCII mesh format
* Changed `group` to `vertex-group`; remove `group` `type`.
* Renamed `VertexGroup` to `BoundaryGroup` in `meshio.gmsh_utils` and changed default behavior to not be recursive (generate "face" groups, not "vertex" groups).
* Update multi-grid preconditioner solver settings for elasticity for better scalability with problem size.
* Mesh formats
* Add support for use of Cubit side sets and Gmsh physical groups with edges (2D) and surfaces (3D). Use of Cubit vertex sets and Gmsh physical groups with vertices are deprecated and support for them will be removed in version 6.0.0.
* Use of Cubit side sets and Gmsh physical groups with curves (2D) and surfaces (3D) are using
* ASCII mesh format
* Changed `group` to `vertex-group`; remove `group` `type`.
* Renamed `VertexGroup` to `BoundaryGroup` in `meshio.gmsh_utils` and changed default behavior to not be recursive (generate "face" groups, not "vertex" groups).
* Use the VTU (XML) format for VTK files instead of the legacy ASCII format.
* Material `description` property is no longer used; a deprecation warning is printed to stdout if it is specified. This feature will be removed in v6.0.
* Internal labels for meshes and fields are now derived from the Pyre component name and identifier.
* Update PETSc to 3.23.1
* Update PETSc to 3.24.0
* **Added**
* Improved documentation for `pylith_eqinfo` and illustrate use in `examples/strikdslip-2d`, `examples/crustal-strikeslip-2d`, and `examples/crustal-strikeslip-3d`.
* Added `pylith_convertmesh` for converting Cubit and Gmsh files to the PETSc HDF5 mesh format.
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2 changes: 1 addition & 1 deletion libsrc/pylith/fekernels/IsotropicLinearGenMaxwell.cc
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Expand Up @@ -14,6 +14,6 @@

#include "pylith/fekernels/IsotropicLinearGenMaxwell.hh" // Implementation of object methods.

const PylithInt pylith::fekernels::IsotropicLinearGenMaxwell::numParallel = 3;
// const PylithInt pylith::fekernels::IsotropicLinearGenMaxwell::numParallel = 3;

// End of file
2 changes: 1 addition & 1 deletion libsrc/pylith/fekernels/IsotropicLinearGenMaxwell.hh
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Expand Up @@ -84,7 +84,7 @@ class pylith::fekernels::IsotropicLinearGenMaxwell {
// PUBLIC MEMBERS /////////////////////////////////////////////////////////////////////////////
public:

static const PylithInt numParallel;
static const PylithInt numParallel = 3;

struct Context {
PylithReal shearModulus;
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40 changes: 20 additions & 20 deletions libsrc/pylith/materials/Elasticity.cc
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Expand Up @@ -472,30 +472,30 @@ pylith::materials::Elasticity::_setKernelsResidual(pylith::feassemble::Integrato
default:
PYLITH_COMPONENT_LOGICERROR("Unknown case (bitUse=" << bitUse << ") for residual kernels.");
} // switch
const PetscPointFn* r1 = _rheology->getKernelf1v(coordsys);
PetscPointFn* r1 = _rheology->getKernelf1v(coordsys);

std::vector<ResidualKernels> kernels;
switch (_formulation) {
case QUASISTATIC: {
const PetscPointFn* f0u = r0;
const PetscPointFn* f1u = r1;
PetscPointFn* f0u = r0;
PetscPointFn* f1u = r1;

kernels.resize(1);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
break;
} // QUASISTATIC
case DYNAMIC: {
// Displacement
const PetscPointFn* f0u = pylith::fekernels::DispVel::f0u;
const PetscPointFn* f1u = NULL;
const PetscPointFn* g0u = pylith::fekernels::DispVel::g0u;
const PetscPointFn* g1u = NULL;
PetscPointFn* f0u = pylith::fekernels::DispVel::f0u;
PetscPointFn* f1u = NULL;
PetscPointFn* g0u = pylith::fekernels::DispVel::g0u;
PetscPointFn* g1u = NULL;

// Velocity
const PetscPointFn* f0v = pylith::fekernels::Elasticity::f0v;
const PetscPointFn* f1v = NULL;
const PetscPointFn* g0v = r0;
const PetscPointFn* g1v = r1;
PetscPointFn* f0v = pylith::fekernels::Elasticity::f0v;
PetscPointFn* f1v = NULL;
PetscPointFn* g0v = r0;
PetscPointFn* g1v = r1;

kernels.resize(4);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
Expand All @@ -506,16 +506,16 @@ pylith::materials::Elasticity::_setKernelsResidual(pylith::feassemble::Integrato
} // DYNAMIC
case DYNAMIC_IMEX: {
// Displacement
const PetscPointFn* f0u = pylith::fekernels::DispVel::f0u;
const PetscPointFn* f1u = NULL;
const PetscPointFn* g0u = pylith::fekernels::DispVel::g0u;
const PetscPointFn* g1u = NULL;
PetscPointFn* f0u = pylith::fekernels::DispVel::f0u;
PetscPointFn* f1u = NULL;
PetscPointFn* g0u = pylith::fekernels::DispVel::g0u;
PetscPointFn* g1u = NULL;

// Velocity
const PetscPointFn* f0v = pylith::fekernels::DispVel::f0v;
const PetscPointFn* f1v = NULL;
const PetscPointFn* g0v = r0;
const PetscPointFn* g1v = r1;
PetscPointFn* f0v = pylith::fekernels::DispVel::f0v;
PetscPointFn* f1v = NULL;
PetscPointFn* g0v = r0;
PetscPointFn* g1v = r1;

kernels.resize(4);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
Expand Down Expand Up @@ -638,7 +638,7 @@ pylith::materials::Elasticity::_setKernelsDerivedField(pylith::feassemble::Integ
kernels[0] = ProjectKernels("cauchy_stress", _rheology->getKernelCauchyStressVector(coordsys));

const int spaceDim = coordsys->getSpaceDim();
const PetscPointFn* strainKernel =
PetscPointFn* strainKernel =
(3 == spaceDim) ? pylith::fekernels::Elasticity3D::infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::ElasticityPlaneStrain::infinitesimalStrain_asVector :
NULL;
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10 changes: 5 additions & 5 deletions libsrc/pylith/materials/IncompressibleElasticity.cc
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Expand Up @@ -328,12 +328,12 @@ pylith::materials::IncompressibleElasticity::_setKernelsResidual(pylith::feassem
} // switch

// Displacement
const PetscPointFn* f0u = r0;
const PetscPointFn* f1u = _rheology->getKernelf1u(coordsys);
PetscPointFn* f0u = r0;
PetscPointFn* f1u = _rheology->getKernelf1u(coordsys);

// Pressure
const PetscPointFn* f0p = _rheology->getKernelf0p(coordsys);
const PetscPointFn* f1p = NULL;
PetscPointFn* f0p = _rheology->getKernelf0p(coordsys);
PetscPointFn* f1p = NULL;

std::vector<ResidualKernels> kernels(2);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
Expand Down Expand Up @@ -429,7 +429,7 @@ pylith::materials::IncompressibleElasticity::_setKernelsDerivedField(pylith::fea
kernels[0] = ProjectKernels("cauchy_stress", _rheology->getKernelCauchyStressVector(coordsys));

const int spaceDim = coordsys->getSpaceDim();
const PetscPointFn* strainKernel =
PetscPointFn* strainKernel =
(3 == spaceDim) ? pylith::fekernels::Elasticity3D::infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::ElasticityPlaneStrain::infinitesimalStrain_asVector :
NULL;
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4 changes: 2 additions & 2 deletions libsrc/pylith/materials/IsotropicLinearGenMaxwell.cc
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Expand Up @@ -224,11 +224,11 @@ pylith::materials::IsotropicLinearGenMaxwell::addKernelsUpdateStateVars(std::vec
PYLITH_COMPONENT_DEBUG("addKernelsUpdateStateVars(kernels="<<kernels<<", coordsys="<<coordsys<<")");

const int spaceDim = coordsys->getSpaceDim();
const PetscPointFn* funcViscousStrain =
PetscPointFn* funcViscousStrain =
(3 == spaceDim) ? pylith::fekernels::IsotropicLinearGenMaxwell3D::viscousStrain_infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::IsotropicLinearGenMaxwellPlaneStrain::viscousStrain_infinitesimalStrain_asVector :
NULL;
const PetscPointFn* funcTotalStrain =
PetscPointFn* funcTotalStrain =
(3 == spaceDim) ? pylith::fekernels::Elasticity3D::infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::ElasticityPlaneStrain::infinitesimalStrain_asVector :
NULL;
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4 changes: 2 additions & 2 deletions libsrc/pylith/materials/IsotropicLinearMaxwell.cc
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Expand Up @@ -223,11 +223,11 @@ pylith::materials::IsotropicLinearMaxwell::addKernelsUpdateStateVars(std::vector
PYLITH_COMPONENT_DEBUG("addKernelsUpdateStateVars(kernels="<<kernels<<", coordsys="<<coordsys<<")");

const int spaceDim = coordsys->getSpaceDim();
const PetscPointFn* funcViscousStrain =
PetscPointFn* funcViscousStrain =
(3 == spaceDim) ? pylith::fekernels::IsotropicLinearMaxwell3D::viscousStrain_infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::IsotropicLinearMaxwellPlaneStrain::viscousStrain_infinitesimalStrain_asVector :
NULL;
const PetscPointFn* funcTotalStrain =
PetscPointFn* funcTotalStrain =
(3 == spaceDim) ? pylith::fekernels::Elasticity3D::infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::ElasticityPlaneStrain::infinitesimalStrain_asVector :
NULL;
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4 changes: 2 additions & 2 deletions libsrc/pylith/materials/IsotropicLinearPoroelasticity.cc
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Expand Up @@ -634,7 +634,7 @@ pylith::materials::IsotropicLinearPoroelasticity::addKernelsUpdateStateVarsImpli
if (_useStateVars) {
const int spaceDim = coordsys->getSpaceDim();

const PetscPointFn* funcPorosity =
PetscPointFn* funcPorosity =
(3 == spaceDim) ? pylith::fekernels::IsotropicLinearPoroelasticity3D::updatePorosityImplicit :
(2 == spaceDim) ? pylith::fekernels::IsotropicLinearPoroelasticityPlaneStrain::updatePorosityImplicit :
NULL;
Expand All @@ -660,7 +660,7 @@ pylith::materials::IsotropicLinearPoroelasticity::addKernelsUpdateStateVarsExpli
if (_useStateVars) {
const int spaceDim = coordsys->getSpaceDim();

const PetscPointFn* funcPorosity =
PetscPointFn* funcPorosity =
(3 == spaceDim) ? pylith::fekernels::IsotropicLinearPoroelasticity3D::updatePorosityExplicit :
(2 == spaceDim) ? pylith::fekernels::IsotropicLinearPoroelasticityPlaneStrain::updatePorosityExplicit :
NULL;
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4 changes: 2 additions & 2 deletions libsrc/pylith/materials/IsotropicPowerLaw.cc
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Expand Up @@ -227,13 +227,13 @@ pylith::materials::IsotropicPowerLaw::addKernelsUpdateStateVars(std::vector<Proj
PYLITH_COMPONENT_DEBUG("addKernelsUpdateStateVars(kernels="<<kernels<<", coordsys="<<coordsys<<")");

const int spaceDim = coordsys->getSpaceDim();
const PetscPointFn* funcViscousStrain =
PetscPointFn* funcViscousStrain =
(!_useReferenceState && 3 == spaceDim) ? pylith::fekernels::IsotropicPowerLaw3D::viscousStrain_infinitesimalStrain_asVector :
(!_useReferenceState && 2 == spaceDim) ? pylith::fekernels::IsotropicPowerLawPlaneStrain::viscousStrain_infinitesimalStrain_asVector :
(_useReferenceState && 3 == spaceDim) ? pylith::fekernels::IsotropicPowerLaw3D::viscousStrain_infinitesimalStrain_refState_asVector :
(_useReferenceState && 2 == spaceDim) ? pylith::fekernels::IsotropicPowerLawPlaneStrain::viscousStrain_infinitesimalStrain_refState_asVector :
NULL;
const PetscPointFn* funcDeviatoricStress =
PetscPointFn* funcDeviatoricStress =
(!_useReferenceState && 3 == spaceDim) ? pylith::fekernels::IsotropicPowerLaw3D::deviatoricStress_infinitesimalStrain_asVector :
(!_useReferenceState && 2 == spaceDim) ? pylith::fekernels::IsotropicPowerLawPlaneStrain::deviatoricStress_infinitesimalStrain_asVector :
(_useReferenceState && 3 == spaceDim) ? pylith::fekernels::IsotropicPowerLaw3D::deviatoricStress_infinitesimalStrain_refState_asVector :
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54 changes: 27 additions & 27 deletions libsrc/pylith/materials/Poroelasticity.cc
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Expand Up @@ -421,17 +421,17 @@ pylith::materials::Poroelasticity::_setKernelsResidual(pylith::feassemble::Integ
case QUASISTATIC: {
if (!_useStateVars) {
// Displacement
const PetscPointFn* f0u = r0;
const PetscPointFn* f1u = _rheology->getKernelf1u_implicit(coordsys);
PetscPointFn* f0u = r0;
PetscPointFn* f1u = _rheology->getKernelf1u_implicit(coordsys);

// Pressure
PetscPointFn* f0p = _rheology->getKernelf0p_implicit(coordsys, _useBodyForce, _gravityField, _useSourceDensity);
PetscPointFn* f1p = _rheology->getKernelf1p_implicit(coordsys, _useBodyForce, _gravityField); // darcy
// velocity

// Volumetric Strain
const PetscPointFn* f0e = pylith::fekernels::Poroelasticity::f0e;
const PetscPointFn* f1e = NULL;
PetscPointFn* f0e = pylith::fekernels::Poroelasticity::f0e;
PetscPointFn* f1e = NULL;

kernels.resize(3);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
Expand All @@ -440,27 +440,27 @@ pylith::materials::Poroelasticity::_setKernelsResidual(pylith::feassemble::Integ
} else {
// Displacement
PetscPointFn* f0u = r0;
const PetscPointFn* f1u = _rheology->getKernelf1u_implicit(coordsys);
PetscPointFn* f1u = _rheology->getKernelf1u_implicit(coordsys);

// Pressure
PetscPointFn* f0p = _rheology->getKernelf0p_implicit(coordsys, _useBodyForce, _gravityField, _useSourceDensity);
PetscPointFn* f1p = _rheology->getKernelf1p_implicit(coordsys, _useBodyForce, _gravityField);

// Volumetric Strain
const PetscPointFn* f0e = pylith::fekernels::Poroelasticity::f0e;
const PetscPointFn* f1e = NULL;
PetscPointFn* f0e = pylith::fekernels::Poroelasticity::f0e;
PetscPointFn* f1e = NULL;

// Velocity
const PetscPointFn* f0v = pylith::fekernels::Poroelasticity::f0v_implicit;
const PetscPointFn* f1v = NULL;
PetscPointFn* f0v = pylith::fekernels::Poroelasticity::f0v_implicit;
PetscPointFn* f1v = NULL;

// Time derivative of pressure
const PetscPointFn* f0pdot = pylith::fekernels::Poroelasticity::f0pdot;
const PetscPointFn* f1pdot = NULL;
PetscPointFn* f0pdot = pylith::fekernels::Poroelasticity::f0pdot;
PetscPointFn* f1pdot = NULL;

// Time derivative of Volumetric Strain
const PetscPointFn* f0edot = pylith::fekernels::Poroelasticity::f0edot;
const PetscPointFn* f1edot = NULL;
PetscPointFn* f0edot = pylith::fekernels::Poroelasticity::f0edot;
PetscPointFn* f1edot = NULL;

kernels.resize(6);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
Expand All @@ -475,22 +475,22 @@ pylith::materials::Poroelasticity::_setKernelsResidual(pylith::feassemble::Integ
case DYNAMIC_IMEX:
case DYNAMIC: {
// Displacement
const PetscPointFn* f0u = pylith::fekernels::DispVel::f0u;
const PetscPointFn* f1u = NULL;
const PetscPointFn* g0u = pylith::fekernels::Poroelasticity::g0u;
const PetscPointFn* g1u = NULL;
PetscPointFn* f0u = pylith::fekernels::DispVel::f0u;
PetscPointFn* f1u = NULL;
PetscPointFn* g0u = pylith::fekernels::Poroelasticity::g0u;
PetscPointFn* g1u = NULL;

// Pressure
const PetscPointFn* f0p = _rheology->getKernelf0p_explicit(coordsys);
const PetscPointFn* f1p = NULL;
const PetscPointFn* g0p = _rheology->getKernelg0p(coordsys, _useBodyForce, _gravityField, _useSourceDensity);
const PetscPointFn* g1p = _rheology->getKernelg1p_explicit(coordsys, _gravityField); // Darcy velocity
PetscPointFn* f0p = _rheology->getKernelf0p_explicit(coordsys);
PetscPointFn* f1p = NULL;
PetscPointFn* g0p = _rheology->getKernelg0p(coordsys, _useBodyForce, _gravityField, _useSourceDensity);
PetscPointFn* g1p = _rheology->getKernelg1p_explicit(coordsys, _gravityField); // Darcy velocity

// Velocity
const PetscPointFn* f0v = pylith::fekernels::Poroelasticity::f0v_explicit;
const PetscPointFn* f1v = NULL;
const PetscPointFn* g0v = r0;
const PetscPointFn* g1v = _rheology->getKernelg1v_explicit(coordsys);
PetscPointFn* f0v = pylith::fekernels::Poroelasticity::f0v_explicit;
PetscPointFn* f1v = NULL;
PetscPointFn* g0v = r0;
PetscPointFn* g1v = _rheology->getKernelg1v_explicit(coordsys);

kernels.resize(6);
kernels[0] = ResidualKernels("displacement", pylith::feassemble::Integrator::LHS, f0u, f1u);
Expand Down Expand Up @@ -775,13 +775,13 @@ pylith::materials::Poroelasticity::_setKernelsDerivedField(pylith::feassemble::I
kernels[0] = ProjectKernels("cauchy_stress", _rheology->getKernelCauchyStressVector(coordsys));

const int spaceDim = coordsys->getSpaceDim();
const PetscPointFn* strainKernel =
PetscPointFn* strainKernel =
(3 == spaceDim) ? pylith::fekernels::Elasticity3D::infinitesimalStrain_asVector :
(2 == spaceDim) ? pylith::fekernels::ElasticityPlaneStrain::infinitesimalStrain_asVector :
NULL;
kernels[1] = ProjectKernels("cauchy_strain", strainKernel);

const PetscPointFn* bulkDensity = pylith::fekernels::Poroelasticity::bulkDensity_asScalar;
PetscPointFn* bulkDensity = pylith::fekernels::Poroelasticity::bulkDensity_asScalar;

kernels[2] = ProjectKernels("bulk_density", bulkDensity);

Expand Down