Set PETSc solve use command line option only according to the suggestion by Nori

MathLib/CMakeLists.txt

@@ -31,10 +31,6 @@ ENDIF ()
 IF (OGS_USE_PETSC)
     GET_SOURCE_FILES(SOURCES_LINALG_PETSC LinAlg/PETSc)
     SET ( SOURCES ${SOURCES} ${SOURCES_LINALG_PETSC})
-    GET_SOURCE_FILES(SOURCES_LINALG_PETSC_KSP LinAlg/PETSc/KSP_Option)
-    SET ( SOURCES ${SOURCES} ${SOURCES_LINALG_PETSC_KSP})
-    GET_SOURCE_FILES(SOURCES_LINALG_PETSC_PC LinAlg/PETSc/PC_Option)
-    SET ( SOURCES ${SOURCES} ${SOURCES_LINALG_PETSC_PC})
 ENDIF ()
 
 IF (METIS_FOUND)

MathLib/LinAlg/PETSc/KSP_Option/PETScKSP_Chebyshev_Option.cpp

-/*!
-   \file  PETScKSP_Chebyshev_Option.cpp
-   \brief Define the configuration data for the PETSc Chebyshev linear solver.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScKSP_Chebyshev_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScKSP_Chebyshev_Option::
-PETScKSP_Chebyshev_Option(const boost::property_tree::ptree &option)
-    : emin_chebyshev(0.01), emax_chebyshev(100.0)
-{
-    auto val = option.get_optional<double>("smallest_eignvalue");
-    emin_chebyshev = *val;
-
-    val = option.get_optional<double>("maximum_eignvalue");
-    emax_chebyshev = *val;
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/KSP_Option/PETScKSP_Chebyshev_Option.h

-/*!
-   \file  PETScKSP_Chebyshev_Option.h
-   \brief Define the configuration data for the PETSc Chebyshev linear solver.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCKSP_CHEBYSHEV_OPTION_H_
-#define PETSCKSP_CHEBYSHEV_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-/*!
-    PETSc KSP Chebyshev options
-
- */
-struct PETScKSP_Chebyshev_Option
-{
-    PETScKSP_Chebyshev_Option(const boost::property_tree::ptree &option);
-
-    /// Set Chebyshev option
-    void setOption(KSP &solver)
-    {
-        KSPChebyshevSetEigenvalues(solver, emax_chebyshev, emin_chebyshev);
-    }
-
-    /// Overloaded assign operator
-    void operator = (const PETScKSP_Chebyshev_Option& opt)
-    {
-        emin_chebyshev = opt.emin_chebyshev;
-        emax_chebyshev = opt.emax_chebyshev;
-    }
-
-    /// Smallest eignvalue for Chebyshev.
-    PetscReal emin_chebyshev;
-    /// maximum eignvalue for Chebyshev.
-    PetscReal emax_chebyshev;
-};
-
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/KSP_Option/PETScKSP_GMRES_Option.cpp

-/*!
-   \file  PETScKSP_GMRES_Option.cpp
-   \brief Define the configuration data for the PETSc GMRES linear solver.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScKSP_GMRES_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScKSP_GMRES_Option::
-PETScKSP_GMRES_Option(const boost::property_tree::ptree &option)
-    : restart_number(30), is_modified_gram_schmidt(false),
-      refine_type(KSP_GMRES_CGS_REFINE_NEVER)
-{
-    auto val = option.get_optional<double>("restart_number");
-    restart_number = *val;
-
-    boost::optional<bool> bool_vals = option.get_optional<bool>("modified_gram_schmidt");
-    is_modified_gram_schmidt = *bool_vals;
-
-    auto refine_type = option.get_optional<int>("refine_type");
-    switch(*refine_type)
-    {
-        case 0:
-            refine_type = KSP_GMRES_CGS_REFINE_NEVER;
-            break;
-        case 1:
-            refine_type = KSP_GMRES_CGS_REFINE_IFNEEDED;
-            break;
-        case 2:
-            refine_type = KSP_GMRES_CGS_REFINE_ALWAYS;
-            break;
-        default:
-            refine_type = KSP_GMRES_CGS_REFINE_NEVER;
-            break;
-    }
-}
-
-/// Set Chebyshev option
-void PETScKSP_GMRES_Option::setOption(KSP &solver)
-{
-    KSPGMRESSetRestart(solver, restart_number);
-
-    if(is_modified_gram_schmidt)
-    {
-        KSPGMRESSetOrthogonalization(solver, KSPGMRESClassicalGramSchmidtOrthogonalization);
-    }
-
-    KSPGMRESSetCGSRefinementType(solver, refine_type);
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/KSP_Option/PETScKSP_GMRES_Option.h

-/*!
-   \file  PETScKSP_GMRES_Option.h
-   \brief Define the configuration data for the PETSc GMRES linear solver.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCKSP_GMRES_OPTION_H_
-#define PETSCKSP_GMRES_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-/*!
-    PETSc KSP GMRES options
-
- */
-struct PETScKSP_GMRES_Option
-{
-    PETScKSP_GMRES_Option(const boost::property_tree::ptree &option);
-
-    /// Set GMRES option
-    void setOption(KSP &solver);
-
-    /// Overloaded assign operator
-    void operator = (const PETScKSP_GMRES_Option& opt)
-    {
-        restart_number = opt.restart_number;
-        is_modified_gram_schmidt = opt.is_modified_gram_schmidt;
-        refine_type = opt.refine_type;
-    }
-
-    ///  Restart number of GMRES.
-    PetscInt restart_number;
-
-    /// Flag for the modified Gram-Schmidt orthogonalization.
-    bool is_modified_gram_schmidt;
-
-    /*!
-         \brief Refinement type for GMRES.
-         This iterative refinement is used to improve the stability
-         of orthogonalization.
-         KSPGMRESCGSRefinementType is a enum type of PETSc defined as
-         typedef enum {KSP_GMRES_CGS_REFINE_NEVER, KSP_GMRES_CGS_REFINE_IFNEEDED,
-                       KSP_GMRES_CGS_REFINE_ALWAYS} KSPGMRESCGSRefinementType;
-    */
-    KSPGMRESCGSRefinementType refine_type;
-};
-
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/KSP_Option/PETScKSP_Richards_Option.cpp

-/*!
-   \file  PETScKSP_Richards_Option.cpp
-   \brief Define the configuration data for the PETSc Richards linear solver.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScKSP_Richards_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScKSP_Richards_Option::
-PETScKSP_Richards_Option(const boost::property_tree::ptree &option)
-    : damping_factor_richards(1.0)
-{
-    auto damping_factor = option.get_optional<double>("damping_factor");
-    damping_factor_richards = *damping_factor;
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/KSP_Option/PETScKSP_Richards_Option.h

-/*!
-   \file  PETScKSP_Richards_Option.h
-   \brief Define the configuration data for the PETSc Richards linear solver.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCKSP_RICHARDS_OPTION_H_
-#define PETSCKSP_RICHARDS_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-
-/*!
-    PETSc KSP Richards options
-
- */
-struct PETScKSP_Richards_Option
-{
-    PETScKSP_Richards_Option(const boost::property_tree::ptree &option);
-
-    /// Set Richards option
-    void setOption(KSP &solver)
-    {
-        KSPRichardsonSetScale(solver, damping_factor_richards);
-    }
-
-    /// Overloaded assign operator
-    void operator = (const PETScKSP_Richards_Option& opt)
-    {
-        damping_factor_richards = opt.damping_factor_richards;
-    }
-
-    /// Damping factor for Richards.
-    PetscReal damping_factor_richards;
-};
-
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_AMG_Option.cpp

-/*!
-   \file  PETScPC_AMG_Option.cpp
-   \brief Define the configuration data for PETSc AMG preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScPC_AMG_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScPC_AMG_Option::
-PETScPC_AMG_Option(const boost::property_tree::ptree &option)
-    : nsmooths(1), type(PCGAMGAGG), is_agg(true)
-{
-    auto val = option.get_optional<double>("agg_nsmooths");
-    nsmooths = *val;
-
-    auto type_name = option.get_optional<std::string>("type");
-    if(type_name->find("agg") != std::string::npos)
-    {
-        type = PCGAMGAGG;
-    }
-    if(type_name->find("geo") != std::string::npos)
-    {
-        type = PCGAMGGEO;
-        is_agg = false;
-    }
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_AMG_Option.h

-/*!
-   \file  PETScPC_AMG_Option.h
-   \brief Define the configuration data for PETSc AMG preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCPC_AMG_OPTION_H_
-#define PETSCPC_AMG_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-/*!
-    PETSc AMG preconditioner options
-
-*/
-struct PETScPC_AMG_Option
-{
-    PETScPC_AMG_Option(const boost::property_tree::ptree &option);
-
-    /// Set AMG option
-    void setOption(PC &pc)
-    {
-        PCGAMGSetType(pc, type);
-        if(is_agg)
-        {
-            PCGAMGSetNSmooths(pc, nsmooths);
-        }
-    }
-
-    /// Overloaded assign operator
-    void operator = (const PETScPC_AMG_Option& opt)
-    {
-        nsmooths = opt.nsmooths;
-        type = opt.type;
-    }
-
-    /// Number of smoothing steps
-    PetscInt nsmooths;
-
-    /*!
-        AMG type: PCGAMGAGG or PCGAMGGEO
-    */
-    PCGAMGType type;
-
-    /// Flag of agg type
-    bool is_agg;
-};
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_ASM_Option.cpp

-/*!
-   \file  PETScPC_ASM_Option.cpp
-   \brief Define the configuration data for PETSc ASM preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScPC_ASM_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScPC_ASM_Option::
-PETScPC_ASM_Option(const boost::property_tree::ptree &option)
-    : type(PC_ASM_BASIC)
-{
-    auto type_name = option.get_optional<std::string>("type");
-    if(type_name->find("base") != std::string::npos)
-    {
-        type = PC_ASM_BASIC;
-    }
-    if(type_name->find("interpolate") != std::string::npos)
-    {
-        type = PC_ASM_INTERPOLATE;
-    }
-    if(type_name->find("restrict") != std::string::npos)
-    {
-        type = PC_ASM_RESTRICT;
-    }
-    if(type_name->find("none") != std::string::npos)
-    {
-        type = PC_ASM_NONE;
-    }
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_ASM_Option.h

-/*!
-   \file  PETScPC_ASM_Option.h
-   \brief Define the configuration data for PETSc ASM preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCPC_ASM_OPTION_H_
-#define PETSCPC_ASM_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-/*!
-    PETSc ASM preconditioner options
-
-*/
-struct PETScPC_ASM_Option
-{
-    PETScPC_ASM_Option(const boost::property_tree::ptree &option);
-
-    /// Set ASM option
-    void setOption(PC &pc)
-    {
-        PCASMSetType(pc, type);
-    }
-
-    /// Overloaded assign operator
-    void operator = (const PETScPC_ASM_Option& opt)
-    {
-        type = opt.type;
-    }
-
-    /*!
-        ASM type:
-        PC_ASM_BASIC,
-        PC_ASM_INTERPOLATE,
-        PC_ASM_RESTRICT,
-        PC_ASM_NONE
-    */
-    PCASMType type;
-};
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_ILU_Option.cpp

-/*!
-   \file  PETScPC_ILU_Option.cpp
-   \brief Define the configuration data for PETSc ILU preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScPC_ILU_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScPC_ILU_Option::
-PETScPC_ILU_Option(const boost::property_tree::ptree &option)
-    : levels(PETSC_DECIDE), reuse_ordering(false),
-      reuse_fill(false), use_in_place(false), allow_diagonal_fill(false)
-{
-    auto val = option.get_optional<double>("levels");
-    levels	= *val;
-
-    auto reuse_order = option.get_optional<bool>("reuse_ordering");
-    reuse_ordering = *reuse_order;
-
-    auto rfill = option.get_optional<bool>("reuse_fill");
-    reuse_fill = *rfill;
-
-    auto inplane = option.get_optional<bool>("use_in_place");
-    use_in_place = *inplane;
-
-    auto low_diag_fill = option.get_optional<bool>("allow_diagonal_fill");
-    allow_diagonal_fill = *low_diag_fill;
-}
-
-void PETScPC_ILU_Option::setOption(PC &pc)
-{
-    PCFactorSetLevels(pc, levels);
-
-    if(reuse_ordering)
-    {
-        PCFactorSetReuseOrdering(pc, PETSC_TRUE);
-    }
-
-    if(reuse_fill)
-    {
-        PCFactorSetReuseFill(pc, PETSC_TRUE);
-    }
-
-    if(use_in_place)
-    {
-        PCFactorSetUseInPlace(pc);
-    }
-
-    if(allow_diagonal_fill)
-    {
-        PCFactorSetAllowDiagonalFill(pc);
-    }
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_ILU_Option.h

-/*!
-   \file  PETScPC_ILU_Option.h
-   \brief Define the configuration data for PETSc ILU preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCPC_ILU_OPTION_H_
-#define PETSCPC_ILU_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-
-/*!
-    PETSc ILU preconditioner options
-
- */
-struct PETScPC_ILU_Option
-{
-    PETScPC_ILU_Option(const boost::property_tree::ptree &option);
-
-    /// Set ILU option
-    void setOption(PC &pc);
-
-    /// Overloaded assign operator
-    void operator = (const PETScPC_ILU_Option& opt)
-    {
-        levels = opt.levels;
-        reuse_ordering = opt.reuse_ordering;
-        reuse_fill = opt.reuse_fill;
-        use_in_place = opt.use_in_place;
-        allow_diagonal_fill = opt.allow_diagonal_fill;
-    }
-
-    /// Number of levels of fill for ILU(k)
-    int levels;
-
-    /// Reuse ordering of factorized matrix from previous factorization
-    bool reuse_ordering;
-
-    /// Use the fill ratio computed in the initial factorization.
-    bool reuse_fill;
-
-    /*! for ILU(0) with natural ordering, reuses the space of the matrix
-        for its factorization (overwrites original matrix)
-    */
-    bool use_in_place;
-
-    /// fill in a zero diagonal even if levels of fill indicate it wouldn't be fill
-    bool allow_diagonal_fill;
-};
-
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_LU_Option.cpp

-/*!
-   \file  PETScPC_LU_Option.cpp
-   \brief Define the configuration data for LU decompoistion preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScPC_LU_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScPC_LU_Option::
-PETScPC_LU_Option(const boost::property_tree::ptree &option)
-    : mat_type(MATORDERINGNATURAL)
-{
-    auto type_name = option.get_optional<std::string>("type");
-    if(type_name->find("natural") != std::string::npos)
-    {
-        mat_type = MATORDERINGNATURAL;
-    }
-    if(type_name->find("nd") != std::string::npos)
-    {
-        mat_type = MATORDERINGND;
-    }
-    if(type_name->find("1wd") != std::string::npos)
-    {
-        mat_type = MATORDERING1WD;
-    }
-    if(type_name->find("rcm") != std::string::npos)
-    {
-        mat_type = MATORDERINGRCM;
-    }
-    if(type_name->find("qmd") != std::string::npos)
-    {
-        mat_type = MATORDERINGQMD;
-    }
-    if(type_name->find("rowlength") != std::string::npos)
-    {
-        mat_type = MATORDERINGROWLENGTH;
-    }
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_LU_Option.h

-/*!
-   \file  PETScPC_LU_Option.h
-   \brief Define the configuration data for LU decompoistion preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSSPC_LU_OPTION_H_
-#define PETSSPC_LU_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-
-/*!
-    PETSc LU preconditioner options
-
-*/
-struct PETScPC_LU_Option
-{
-    PETScPC_LU_Option(const boost::property_tree::ptree &option);
-
-    /// Set LU option
-    void setOption(PC &pc)
-    {
-        PCFactorSetMatOrderingType(pc, mat_type);
-    }
-
-    /// Overloaded assign operator
-    void operator = (const PETScPC_LU_Option& opt)
-    {
-        mat_type = opt.mat_type;
-    }
-
-    /// Ordering routine (to reduce fill) to be used in the LU factorization.
-    MatOrderingType mat_type;
-};
-
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_SOR_Option.cpp

-/*!
-   \file  PETScPC_SOR_Option.cpp
-   \brief Define the configuration data for PETSc SOR/SSOR preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScPC_SOR_Option.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScPC_SOR_Option::
-PETScPC_SOR_Option(const boost::property_tree::ptree &option)
-    : omega(1.), its(PETSC_DEFAULT),
-      lits(PETSC_DEFAULT), type(SOR_FORWARD_SWEEP)
-{
-    auto val = option.get_optional<double>("omega");
-    omega	= *val;
-
-    auto n_its = option.get_optional<int>("local_iterations");
-    lits = *n_its;
-
-    n_its = option.get_optional<int>("parallel_iterations");
-    its = *n_its;
-
-    auto type_name = option.get_optional<std::string>("type");
-    if(type_name->find("pc_sor_symmetric") != std::string::npos)
-    {
-        type = SOR_FORWARD_SWEEP;
-    }
-    if(type_name->find("pc_sor_backward") != std::string::npos)
-    {
-        type = SOR_BACKWARD_SWEEP;
-    }
-    if(type_name->find("pc_sor_local_forward") != std::string::npos)
-    {
-        type = SOR_LOCAL_FORWARD_SWEEP;
-    }
-    if(type_name->find("pc_sor_local_symmetric") != std::string::npos)
-    {
-        type = SOR_LOCAL_SYMMETRIC_SWEEP;
-    }
-    if(type_name->find("pc_sor_local_backward") != std::string::npos)
-    {
-        type = SOR_LOCAL_BACKWARD_SWEEP;
-    }
-}
-
-void PETScPC_SOR_Option::setOption(PC &pc)
-{
-    PCSORSetOmega(pc, omega);
-    PCSORSetIterations(pc, its, lits);
-    PCSORSetSymmetric(pc, type);
-}
-
-} // end namespace
-

MathLib/LinAlg/PETSc/PC_Option/PETScPC_SOR_Option.h

-/*!
-   \file  PETScPC_SOR_Option.h
-   \brief Define the configuration data for PETSc SOR/SSOR preconditioner.
-
-   \author Wenqing Wang
-   \date 04-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-#ifndef PETSCPC_SOR_OPTION_H_
-#define PETSCPC_SOR_OPTION_H_
-
-#include <boost/property_tree/ptree.hpp>
-
-#include <petscksp.h>
-
-namespace MathLib
-{
-/*!
-    PETSc SOR//SSOR preconditioner options
-
-*/
-struct PETScPC_SOR_Option
-{
-    PETScPC_SOR_Option(const boost::property_tree::ptree &option);
-
-    /// Set SOR/SSOR option
-    void setOption(PC &pc);
-
-    /// Overloaded assign operator
-    void operator = (const PETScPC_SOR_Option& opt)
-    {
-        omega = opt.omega;
-        its = opt.its;
-        lits = opt.lits;
-        type = opt.type;
-    }
-
-    /// Relaxation number
-    PetscReal omega;
-
-    /// Number of parelllel iterations, each parallel iteration
-    /// has 'lits' local iterations
-    PetscInt its;
-
-    /// Number of local iterations
-    PetscInt lits;
-
-    /*!
-        SOR type:
-        SOR_FORWARD_SWEEP
-        SOR_BACKWARD_SWEEP
-        SOR_SYMMETRIC_SWEEP
-        SOR_LOCAL_FORWARD_SWEEP
-        SOR_LOCAL_BACKWARD_SWEEP
-        SOR_LOCAL_SYMMETRIC_SWEEP
-    */
-    MatSORType type;
-};
-} // end namespace
-#endif
-

MathLib/LinAlg/PETSc/PETScLinearSolver.cpp

@@ -18,118 +18,19 @@
 
 namespace MathLib
 {
-using boost::property_tree::ptree;
-
-PETScLinearSolver::PETScLinearSolver(PETScMatrix &A,
-                                     const boost::property_tree::ptree &option)
+PETScLinearSolver::PETScLinearSolver(PETScMatrix &A, const std::string prefix)
 {
     KSPCreate(PETSC_COMM_WORLD, &_solver);
     KSPSetOperators(_solver, A.getRawMatrix(), A.getRawMatrix(), DIFFERENT_NONZERO_PATTERN);
 
-    boost::optional<const ptree&> pt_solver = option.get_child_optional("linear_solver");
-    if(!pt_solver)
-    {
-       PetscPrintf(PETSC_COMM_WORLD,"\n*** PETSc linear solver is not specified, bcgs + bjacobi are used.\n");
-       // Base configuration
-       PETScLinearSolverOption opt;          
-       opt.setOption(_solver, _pc);
-       KSPSetFromOptions(_solver);  // set running time option 
-       return;
-    }
-
-    // Preconditioners:
-    boost::optional<const ptree&> pt_pc = option.get_child_optional("preconditioner");
-    if(!pt_pc)
-    {
-        PetscPrintf(PETSC_COMM_WORLD,"\n*** PETSc preconditioner is not specified, bjacobi is used.");
-       // Base configuration
-       PETScLinearSolverOption opt(*pt_solver);          
-       opt.setOption(_solver, _pc);
-       KSPSetFromOptions(_solver);  // set running time option         
-       return;
-    }
-
-    // Base configuration
-    PETScLinearSolverOption opt(*pt_solver, *pt_pc);
-          
-    opt.setOption(_solver, _pc);
-
-    //----------------------------------------------------------------------
-    // Specific configuration, solver
-    boost::optional<const ptree&> pt_solver_spec = pt_solver->get_child_optional("Richards");
-  
-    if(pt_solver_spec)
-    {		
-        PETScKSP_Richards_Option ksp_opt(*pt_solver_spec);
-        setKSP_Option(ksp_opt);
-    }
-
-    pt_solver_spec = pt_solver->get_child_optional("Chebyshev");
-    if(pt_solver_spec)
-    {
-        PETScKSP_Chebyshev_Option ksp_opt(*pt_solver_spec);
-        setKSP_Option(ksp_opt);
-    }
-
-    pt_solver_spec = pt_solver->get_child_optional("gmres");
-    if(pt_solver_spec)
-    {		
-        PETScKSP_GMRES_Option ksp_opt(*pt_solver_spec);
-        setKSP_Option(ksp_opt);
-    }
-
-    //----------------------------------------------------------------------
-    // Specific configuration, preconditioner
-    boost::optional<const ptree&> pt_pc_spec = pt_pc->get_child_optional("sor");
-    if(pt_pc_spec)
-    {
-        PETScPC_SOR_Option pc_opt(*pt_pc_spec);
-        setPC_Option(pc_opt);
-    }
- 
-    pt_pc_spec = pt_pc->get_child_optional("asm");
-    if(pt_pc_spec)
-    {
-        PETScPC_ASM_Option pc_opt(*pt_pc_spec);
-        setPC_Option(pc_opt);
-    }
-
-    pt_pc_spec = pt_pc->get_child_optional("amg");
-    if(pt_pc_spec)
-    {
-        PETScPC_AMG_Option pc_opt(*pt_pc_spec);
-        setPC_Option(pc_opt);
-    }  
-   
-    //----------------------------------------------------------------------------
-    // Only for sub-block preconditioner or sequential computation if it is needed.          
-    // ILU or ICC
-    pt_pc_spec = pt_pc->get_child_optional("ilu");
-    if(pt_pc_spec)
-    {
-        PETScPC_ILU_Option pc_opt(*pt_pc_spec);
-        setPC_Option(pc_opt);
-    }
-    else
-    {
-        pt_pc_spec = pt_pc->get_child_optional("icc");
-        if(pt_pc_spec)
-        {
-            PETScPC_ILU_Option pc_opt(*pt_pc_spec);
-            setPC_Option(pc_opt);
-        }
-    }
-
-    pt_pc_spec = pt_pc->get_child_optional("lu");
-    if(pt_pc_spec)
-    {
-        PETScPC_LU_Option pc_opt(*pt_pc_spec);
-        setPC_Option(pc_opt);
-    }
-    //----------------------------------------------------------------------------
-            
     //
+    KSPSetOptionsPrefix(_solver, prefix.c_str());    
     KSPSetFromOptions(_solver);  // set running time option
+    
+    KSPGetPC(_solver, &_pc);
+     
+    PCSetOptionsPrefix(_pc, prefix.c_str());    
+    PCSetFromOptions(_pc);  // set running time option
 }
 
 void PETScLinearSolver::solve(const PETScVector &b, PETScVector &x)

MathLib/LinAlg/PETSc/PETScLinearSolver.h

@@ -17,20 +17,12 @@
 #ifndef PETSCLINEARSOLVER_H_
 #define PETSCLINEARSOLVER_H_
 
-#include "PETScMatrix.h"
-#include "PETScVector.h"
-
-#include "PETScLinearSolverOption.h"
+#include<string>
 
-#include "KSP_Option/PETScKSP_Chebyshev_Option.h"
-#include "KSP_Option/PETScKSP_Richards_Option.h"
-#include "KSP_Option/PETScKSP_GMRES_Option.h"
+#include "petscksp.h"
 
-#include "PC_Option/PETScPC_ILU_Option.h"
-#include "PC_Option/PETScPC_SOR_Option.h"
-#include "PC_Option/PETScPC_LU_Option.h"
-#include "PC_Option/PETScPC_ASM_Option.h"
-#include "PC_Option/PETScPC_AMG_Option.h"
+#include "PETScMatrix.h"
+#include "PETScVector.h"
 
 namespace MathLib
 {
@@ -38,6 +30,7 @@ namespace MathLib
 /*!
      A class of linear solver based on PETSc rountines.
 
+     All options for KSP and PC must given in the command line.
 */
 class PETScLinearSolver
 {
@@ -45,28 +38,12 @@ class PETScLinearSolver
 
         /*!
             Constructor
-            \param A      Matrix, cannot be constant.
-            \param option Configuration data for solver and preconditioner.
+            \param A       Matrix, cannot be constant.
+            \param prefix  Name used to distinguish the options in the command
+                           line for this solver. It can be the name of the PDE
+                           that owns an instance of this class.
         */
-        PETScLinearSolver(PETScMatrix &A, const boost::property_tree::ptree &option);
-
-        /*!
-            Set Krylov subspace parameters with given option
-            \param  ksp_opt Given parameters 
-        */ 
-        template <typename T_KSP_OPTION> void setKSP_Option(T_KSP_OPTION &ksp_opt)
-        {
-            ksp_opt.setOption(_solver);
-        }
-        
-        /*!
-            Set preconditioner parameters with given option
-            \param  pc_opt Given parameters 
-        */ 
-        template <typename T_PC_OPTION> void setPC_Option(T_PC_OPTION &pc_opt)
-        {
-            pc_opt.setOption(_pc);
-        }
+        PETScLinearSolver(PETScMatrix &A, const std::string prefix);
 
         ~PETScLinearSolver()
         {

MathLib/LinAlg/PETSc/PETScLinearSolverOption.cpp

-/*!
-   \file  PETScLinearSolverOption.cpp
-   \brief Define members of PETScLinearSolverOption
-
-   \author Wenqing Wang
-   \date 02-2014
-
-   \copyright
-    Copyright (c) 2013, OpenGeoSys Community (http://www.opengeosys.org)
-               Distributed under a Modified BSD License.
-               See accompanying file LICENSE.txt or
-               http://www.opengeosys.org/project/license
-*/
-
-#include "PETScLinearSolverOption.h"
-
-namespace MathLib
-{
-
-using boost::property_tree::ptree;
-
-PETScLinearSolverOption::
-PETScLinearSolverOption(const boost::property_tree::ptree &ksp_option)
-    : _solver_name("bcgs"), _pc_name("bjacobi"), _preco_side(PC_LEFT),
-      _max_it(2000), _rtol(1.e-5), _atol(PETSC_DEFAULT), _dtol(PETSC_DEFAULT)
-{
-    auto solver_type = ksp_option.get_optional<std::string>("solver_type");       
-    if(solver_type)
-    {
-        _solver_name = *solver_type;
-    }
-
-    auto max_iteration_step = ksp_option.get_optional<int>("max_it");
-    if(max_iteration_step)
-    {
-        _max_it = *max_iteration_step;
-    }
-
-    auto error_tolerance = ksp_option.get_optional<double>("rtol");
-    if(error_tolerance)
-    {
-        _rtol = *error_tolerance;
-    }
-
-    error_tolerance = ksp_option.get_optional<double>("atol");
-    if(error_tolerance)
-    {
-        _atol = *error_tolerance;
-    }
-
-    error_tolerance = ksp_option.get_optional<double>("dtol");
-    if(error_tolerance)
-    {
-        _dtol = *error_tolerance;
-    }
-}
-
-PETScLinearSolverOption::
-PETScLinearSolverOption(const boost::property_tree::ptree &ksp_option,
-                        const boost::property_tree::ptree &pc_option)
-    : _solver_name("bcgs"), _pc_name("bjacobi"), _preco_side(PC_LEFT),
-      _max_it(2000), _rtol(1.e-5), _atol(PETSC_DEFAULT), _dtol(PETSC_DEFAULT)
-{
-    auto solver_type = ksp_option.get_optional<std::string>("solver_type");       
-    if(solver_type)
-    {
-        _solver_name = *solver_type;
-    }
-
-    auto max_iteration_step = ksp_option.get_optional<int>("max_it");
-    if(max_iteration_step)
-    {
-        _max_it = *max_iteration_step;
-    }
-
-    auto error_tolerance = ksp_option.get_optional<double>("rtol");
-    if(error_tolerance)
-    {
-        _rtol = *error_tolerance;
-    }
-
-    error_tolerance = ksp_option.get_optional<double>("atol");
-    if(error_tolerance)
-    {
-        _atol = *error_tolerance;
-    }
-
-    error_tolerance = ksp_option.get_optional<double>("dtol");
-    if(error_tolerance)
-    {
-        _dtol = *error_tolerance;
-    }
-
-    // Preconditioners:
-    auto pc_type = pc_option.get_optional<std::string>("pc_type");
-    if(pc_type)
-    {
-        _pc_name = *pc_type;
-    }
-    
-    auto pc_side = pc_option.get_optional<std::string>("pc_side");
-    if(pc_side)
-    {
-        if(pc_side->find("left") != std::string::npos)
-            _preco_side = PC_LEFT;
-        if(pc_side->find("right") != std::string::npos)
-            _preco_side = PC_RIGHT;
-        if(pc_side->find("symmetric") != std::string::npos)
-            _preco_side = PC_SYMMETRIC;
-    }
-}
-
-} // end namespace
-