diff --git a/MathLib/LinAlg/LinAlg.h b/MathLib/LinAlg/LinAlg.h
index 0dee45dd1353c2afce2853a24bd2edbe6a1dd95b..154d8b45a80118f40162828c2477f9a3715927d0 100644
--- a/MathLib/LinAlg/LinAlg.h
+++ b/MathLib/LinAlg/LinAlg.h
@@ -149,7 +149,7 @@ namespace LinAlg
// Vector
/// Set local accessible vector in order to get entries.
-/// Call this before call operator[] or get(...).
+/// Call this before call operator[] or get(...) of x.
void setLocalAccessibleVector(PETScVector const& x);
void set(PETScVector& x, double const a);
@@ -210,8 +210,14 @@ namespace LinAlg
// Vector
-/// Set local accessible vector in order to get entries.
-/// Call this before call operator[] or get(...). Not used for EIGEN
+/**
+ Set local accessible vector in order to get entries. Call this
+ before call operator[] or get(...) of x.
+ The function only has computation if DDC is appied,
+ e.g. parallel computing. Up to now, Eigen vector is not used for
+ global vectors in parallel computing. Therefore this function is
+ empty in the current status.
+*/
void setLocalAccessibleVector(EigenVector const& x);
void set(EigenVector& x, double const a);
diff --git a/MathLib/LinAlg/PETSc/PETScLinearSolver.cpp b/MathLib/LinAlg/PETSc/PETScLinearSolver.cpp
index e4fa6ee8052e066854a8e7fe16ed6c1524906a4c..a563e4e47c9f9cdb117f7aed1ba991216c3f9853 100644
--- a/MathLib/LinAlg/PETSc/PETScLinearSolver.cpp
+++ b/MathLib/LinAlg/PETSc/PETScLinearSolver.cpp
@@ -83,7 +83,7 @@ bool PETScLinearSolver::solve(PETScMatrix& A, PETScVector &b, PETScVector &x)
KSPSetOperators(_solver, A.getRawMatrix(), A.getRawMatrix(), DIFFERENT_NONZERO_PATTERN);
#endif
- KSPSolve(_solver, b.getData(), x.getData());
+ KSPSolve(_solver, b.getRawVector(), x.getRawVector());
KSPConvergedReason reason;
KSPGetConvergedReason(_solver, &reason);
diff --git a/MathLib/LinAlg/PETSc/PETScVector.cpp b/MathLib/LinAlg/PETSc/PETScVector.cpp
index ebd841c61a258bfe7114f36160a72da0875037aa..0ef9641355cd7f7df3fd309c657471c946600df0 100644
--- a/MathLib/LinAlg/PETSc/PETScVector.cpp
+++ b/MathLib/LinAlg/PETSc/PETScVector.cpp
@@ -200,13 +200,10 @@ PetscScalar PETScVector::get(const PetscInt idx) const
{
return _entry_array[getLocalIndex(idx)];
}
- else
- {
- // Ghost entries, and its original index is 0.
- const PetscInt id_p = (idx == -_size) ? 0 : std::abs(idx);
- return _entry_array[id_p];
- }
- return 0; // avoid warning.
+
+ // Ghost entries, and its original index is 0.
+ const PetscInt id_p = (idx == -_size) ? 0 : std::abs(idx);
+ return _entry_array[id_p];
}
diff --git a/MathLib/LinAlg/PETSc/PETScVector.h b/MathLib/LinAlg/PETSc/PETScVector.h
index 3a936f11ee6d21f0d6f3dfce8fcdc994ebb5eac2..706377cfa4d4d5af9fc2d21608253d2edf671638 100644
--- a/MathLib/LinAlg/PETSc/PETScVector.h
+++ b/MathLib/LinAlg/PETSc/PETScVector.h
@@ -17,7 +17,6 @@
#pragma once
#include <map>
-#include <memory>
#include <string>
#include <vector>
@@ -157,6 +156,14 @@ class PETScVector
VecSetValues(_v, e_idxs.size(), &e_idxs[0], &sub_vec[0], INSERT_VALUES);
}
+ // TODO preliminary
+ void setZero() { VecSet(_v, 0.0); }
+
+ /// Disallow moving.
+ /// \todo This operator should be implemented properly when doing a
+ /// general cleanup of all matrix and vector classes.
+ PETScVector& operator = (PETScVector &&) = delete;
+
/// Set local accessible vector in order to get entries.
/// Call this before call operator[] or get(...).
void setLocalAccessibleVector() const;
@@ -178,12 +185,6 @@ class PETScVector
*/
void getGlobalVector(std::vector<PetscScalar>& u) const;
- /*!
- Copy local entries including ghost ones to an array
- \param u Preallocated vector for the values of local entries.
- */
- void copyValues(std::vector<double>& u) const;
-
/* Get an entry value. This is an expensive operation,
and it only get local value. Use it for only test purpose
Get the value of an entry by [] operator.
@@ -191,21 +192,6 @@ class PETScVector
*/
PetscScalar get(const PetscInt idx) const;
- // TODO eliminate in favour of getRawVector()
- /// Get PETsc vector. Use it only for test purpose
- const PETSc_Vec &getData() const
- {
- return _v;
- }
-
- // TODO preliminary
- void setZero() { VecSet(_v, 0.0); }
-
- /// Disallow moving.
- /// \todo This operator should be implemented properly when doing a
- /// general cleanup of all matrix and vector classes.
- PETScVector& operator = (PETScVector &&) = delete;
-
//! Exposes the underlying PETSc vector.
PETSc_Vec getRawVector() { return _v; }
@@ -217,6 +203,11 @@ class PETScVector
*/
PETSc_Vec getRawVector() const { return _v; }
+ /*!
+ Copy local entries including ghost ones to an array
+ \param u Preallocated vector for the values of local entries.
+ */
+ void copyValues(std::vector<double>& u) const;
/*! View the global vector for test purpose. Do not use it for output a big vector.
\param file_name File name for output
diff --git a/NumLib/DOF/MeshComponentMap.cpp b/NumLib/DOF/MeshComponentMap.cpp
index 160c30b8b9119677eef5f4ecd37687395cacf52b..c9be0069205f1c602c74e2cf08106a1e6a9c8aad 100644
--- a/NumLib/DOF/MeshComponentMap.cpp
+++ b/NumLib/DOF/MeshComponentMap.cpp
@@ -84,9 +84,6 @@ MeshComponentMap::MeshComponentMap(
OGS_FATAL("Global index in the system of equations"
" can only be numbered by the oder type"
" of ComponentOrder::BY_LOCATION");
- // _num_global_dof is used as the global index offset
- //global_id = static_cast<GlobalIndexType>(
- // _num_global_dof + mesh.getGlobalNodeID(j));
}
const bool is_ghost =
mesh.isGhostNode(mesh.getNode(j)->getID());
diff --git a/ProcessLib/Process.cpp b/ProcessLib/Process.cpp
index f003e2f42e0ff233280f4b87a3823b2c025262bc..25e265394bbc0180413bf33b88b40bec6bbc273e 100644
--- a/ProcessLib/Process.cpp
+++ b/ProcessLib/Process.cpp
@@ -122,8 +122,6 @@ void Process::assemble(const double t, GlobalVector const& x, GlobalMatrix& M,
GlobalMatrix& K, GlobalVector& b,
StaggeredCouplingTerm const& coupling_term)
{
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
assembleConcreteProcess(t, x, M, K, b, coupling_term);
@@ -138,8 +136,6 @@ void Process::assembleWithJacobian(const double t, GlobalVector const& x,
GlobalVector& b, GlobalMatrix& Jac,
StaggeredCouplingTerm const& coupling_term)
{
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
MathLib::LinAlg::setLocalAccessibleVector(xdot);
@@ -244,8 +240,6 @@ void Process::computeSparsityPattern()
void Process::preTimestep(GlobalVector const& x, const double t,
const double delta_t)
{
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
preTimestepConcreteProcess(x, t, delta_t);
_boundary_conditions.preTimestep(t);
@@ -253,8 +247,6 @@ void Process::preTimestep(GlobalVector const& x, const double t,
void Process::postTimestep(GlobalVector const& x)
{
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
postTimestepConcreteProcess(x);
}
@@ -263,8 +255,6 @@ void Process::computeSecondaryVariable(const double t, GlobalVector const& x,
StaggeredCouplingTerm const&
coupled_term)
{
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
computeSecondaryVariableConcrete(t, x, coupled_term);
@@ -277,16 +267,12 @@ void Process::preIteration(const unsigned iter, const GlobalVector &x)
cached_var->expire();
}
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
preIterationConcreteProcess(iter, x);
}
NumLib::IterationResult Process::postIteration(const GlobalVector &x)
{
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(x);
return postIterationConcreteProcess(x);
}
diff --git a/ProcessLib/TES/TESProcess.cpp b/ProcessLib/TES/TESProcess.cpp
index ffdeb5dd6beac2b80ee9bef2cb59ff29b36e0489..db778b975b82bc62ee2f695cc836e2a551a9153e 100644
--- a/ProcessLib/TES/TESProcess.cpp
+++ b/ProcessLib/TES/TESProcess.cpp
@@ -285,8 +285,6 @@ NumLib::IterationResult TESProcess::postIterationConcreteProcess(
std::vector<double> local_x_cache;
std::vector<double> local_x_prev_ts_cache;
- // The function only has computation if DDC is appied,
- // e.g. Parallel comuting.
MathLib::LinAlg::setLocalAccessibleVector(*_x_previous_timestep);
auto check_variable_bounds = [&](std::size_t id,
@@ -344,7 +342,6 @@ TESProcess::computeVapourPartialPressure(
auto const x_nV = Adsorption::AdsorptionReaction::getMolarFraction(
x_mV, _assembly_params.M_react, _assembly_params.M_inert);
- // TODO Problems with PETSc? (local vs. global index)
result_cache->set(node_id, p * x_nV);
}
@@ -382,7 +379,6 @@ TESProcess::computeRelativeHumidity(
auto const p_S =
Adsorption::AdsorptionReaction::getEquilibriumVapourPressure(T);
- // TODO Problems with PETSc? (local vs. global index)
result_cache->set(node_id, p * x_nV / p_S);
}
@@ -423,7 +419,6 @@ TESProcess::computeEquilibriumLoading(
: _assembly_params.react_sys->getEquilibriumLoading(
p_V, T, _assembly_params.M_react);
- // TODO Problems with PETSc? (local vs. global index)
result_cache->set(node_id, C_eq);
}