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Author SHA1 Message Date
Kenneth Weiss b86fb5308a style 2026-04-14 08:54:23 -07:00
Kenneth Weiss 4463d921f6 Updates CHANGELOG 2026-04-13 21:52:37 -07:00
Kenneth Weiss 20c657559d More fixes for building contact mini-app with make and cmake 2026-04-13 21:47:15 -07:00
Kenneth Weiss 7a999efb0d yAdds back FindAxom in support of contact mini-app 2026-04-13 18:54:17 -07:00
Kenneth Weiss 442ac18b65 Removes references to Axom in INSTALL 2026-04-13 12:40:24 -07:00
Kenneth Weiss 5097a44411 Removes Axom from make-based and cmake-based build systems 2026-04-13 12:37:18 -07:00
Kenneth Weiss e84fef4191 Removes SidreDataCollection from MFEM
This has been superseded by the MFEMSidreDataCollection in Axom.
2026-04-13 12:34:02 -07:00
92 changed files with 632 additions and 6604 deletions
-4
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@@ -443,10 +443,6 @@ miniapps/diag-smoothers/mg-abs-l1-jacobi
miniapps/contact/contact
miniapps/contact/ParaView
miniapps/plasma/pic/electrostatic-*
!miniapps/plasma/pic/electrostatic-*.cpp
miniapps/plasma/pic/*.csv
# Unit test binary and outputs
tests/unit/output_meshes
tests/unit/unit_tests
+5 -1
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@@ -23,7 +23,6 @@ Discretization improvements
Tet rules (d=14-20): Chuluunbaatar et al., Comput. Math. Appl. 124:89-97,
2022.
Version 4.9.1 (development)
===========================
@@ -46,6 +45,11 @@ New and updated examples and miniapps
- Electromagnetics/lorentz miniapp has been updated to leverage the ParticleSet
capability.
Miscellaneous
-------------
- Removes the SidreDataCollection class from MFEM in favor of the
MFEMSidreDataCollection class in the Axom library (https://github.com/llnl/axom).
Version 4.9, released on Dec 11, 2025
=====================================
+2 -9
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@@ -75,12 +75,10 @@ set(XSDK_ENABLE_Fortran OFF)
# Check if we need to enable C or Fortran.
if (MFEM_USE_CONDUIT OR
MFEM_USE_SIDRE OR
MFEM_USE_PETSC)
# This seems to be needed by:
# * find_package(BLAS REQUIRED) and
# * find_package(HDF5 REQUIRED) needed, in turn, by:
# - find_package(AXOM REQUIRED)
# * find_package(HDF5 REQUIRED) and
# * find_package(PETSc REQUIRED)
set(XSDK_ENABLE_C ON)
endif()
@@ -478,11 +476,6 @@ if (MFEM_USE_FMS)
find_package(FMS REQUIRED fms)
endif()
# Axom/Sidre
if (MFEM_USE_SIDRE)
find_package(Axom REQUIRED Axom)
endif()
# PUMI
if (MFEM_USE_PUMI)
# If PUMI_DIR was specified, only link to that directory,
@@ -629,7 +622,7 @@ find_package(Threads REQUIRED)
# integers, the METIS header (with 32-bit indices, as used by mfem) needs to
# be before SuiteSparse.
set(MFEM_TPLS OPENMP HYPRE LAPACK BLAS SuperLUDist STRUMPACK METIS SuiteSparse
SUNDIALS PETSC SLEPC MUMPS AXOM FMS CONDUIT Ginkgo GNUTLS GSLIB HDF5
SUNDIALS PETSC SLEPC MUMPS FMS CONDUIT Ginkgo GNUTLS GSLIB HDF5
NETCDF MPFR PUMI HIOP POSIXCLOCKS MFEMBacktrace ZLIB OCCA CEED RAJA UMPIRE
ADIOS2 MKL_CPARDISO MKL_PARDISO AMGX MAGMA CUSPARSE CUBLAS CALIPER CODIPACK
BENCHMARK PARELAG TRIBOL MPI_CXX HIP HIPBLAS HIPSPARSE MOONOLITH BLITZ
-17
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@@ -452,13 +452,6 @@ MFEM_USE_MPFR = YES/NO
quadrature rules. When enabled, this option uses the MPFR_* library options,
see below.
MFEM_USE_SIDRE = YES/NO
Sidre is a component of LLNL's axom project, https://github.com/LLNL/axom,
that provides an HDF5-based file format for visualization or restart
capability following the Conduit (https://github.com/LLNL/conduit) mesh
blueprint specification. When enabled, this option requires installation of
HDF5 (see also MFEM_USE_NETCDF), Conduit and LLNL's axom project.
MFEM_USE_SIMD = YES/NO
Enables the high performance templated classes to use architecture dependent
SIMD intrinsics instead of the generic implementation of class AutoSIMD in
@@ -778,14 +771,6 @@ The specific libraries and their options are:
Options: SLEPC_OPT, SLEPC_LIB.
Versions: SLEPc >= 3.8.0.
- Sidre (optional), part of LLNL's axom project, used when MFEM_USE_SIDRE = YES.
Starting with MFEM v4.1, Axom version 0.3.1 or later is required.
URL: https://github.com/LLNL/axom
https://github.com/LLNL/conduit (Conduit)
https://support.hdfgroup.org/HDF5 (HDF5)
Options: SIDRE_OPT, SIDRE_LIB.
Versions: Axom >= 0.3.1.
- Conduit (optional), used when MFEM_USE_CONDUIT = YES. Conduit Mesh Blueprint
support requires Conduit >= v0.3.1 and VisIt >= v2.13.1 to read the output.
URL: https://github.com/LLNL/conduit (Conduit)
@@ -1069,7 +1054,6 @@ MFEM_USE_OCCA
MFEM_USE_CEED
MFEM_USE_RAJA
MFEM_USE_UMPIRE
MFEM_USE_SIDRE
MFEM_USE_MOONOLITH
MFEM_USE_CALIPER
MFEM_USE_FMS
@@ -1133,7 +1117,6 @@ The CMake build system adds auto-detection for the following packages/libraries:
- OCCA
- RAJA
- UMPIRE
- AXOM - Used when MFEM_USE_SIDRE is enabled
- MOONOLITH
- CALIPER
- FMS
-4
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@@ -248,10 +248,6 @@ IF (DEFINED TPL_ENABLE_MPFR)
SET(MFEM_USE_MPFR ${TPL_ENABLE_MPFR} CACHE BOOL "Enable MPFR usage." FORCE)
ENDIF()
IF (DEFINED TPL_ENABLE_SIDRE)
SET(MFEM_USE_SIDRE ${TPL_ENABLE_SIDRE} CACHE BOOL "Enable Axom/Sidre usage" FORCE)
ENDIF()
IF (DEFINED TPL_ENABLE_FMS)
SET(MFEM_USE_FMS ${TPL_ENABLE_FMS} CACHE BOOL "Enable FMS usage" FORCE)
ENDIF()
-5
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@@ -46,7 +46,6 @@ set(MFEM_USE_NETCDF @MFEM_USE_NETCDF@)
set(MFEM_USE_PETSC @MFEM_USE_PETSC@)
set(MFEM_USE_SLEPC @MFEM_USE_SLEPC@)
set(MFEM_USE_MPFR @MFEM_USE_MPFR@)
set(MFEM_USE_SIDRE @MFEM_USE_SIDRE@)
set(MFEM_USE_FMS @MFEM_USE_FMS@)
set(MFEM_USE_CONDUIT @MFEM_USE_CONDUIT@)
set(MFEM_USE_PUMI @MFEM_USE_PUMI@)
@@ -109,10 +108,6 @@ if (MFEM_USE_RAJA)
find_dependency(RAJA)
endif()
if (MFEM_USE_UMPIRE)
find_dependency(umpire)
endif()
if (NOT TARGET mfem)
include(${CMAKE_CURRENT_LIST_DIR}/MFEMTargets.cmake)
endif (NOT TARGET mfem)
-3
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@@ -120,9 +120,6 @@
// Enable secure socket streams based on the GNUTLS library.
#cmakedefine MFEM_USE_GNUTLS
// Enable Sidre support.
#cmakedefine MFEM_USE_SIDRE
// Enable the use of SIMD in the high performance templated classes.
#cmakedefine MFEM_USE_SIMD
+24
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@@ -0,0 +1,24 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# Defines the following variables:
# - ADIAK_FOUND
# - ADIAK_LIBRARIES
# - ADIAK_INCLUDE_DIRS
include(MfemCmakeUtilities)
mfem_find_package(Adiak ADIAK ADIAK_DIR
"include" "adiak.h"
"lib" "adiak"
"Paths to headers required by Adiak."
"Libraries required by Adiak.")
+3
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@@ -13,6 +13,9 @@
# - AXOM_FOUND
# - AXOM_LIBRARIES
# - AXOM_INCLUDE_DIRS
#
# MFEM itself does not depend on Axom, however Tribol does. This module exists
# to support MFEM's Tribol integration (e.g. the contact miniapp).
include(MfemCmakeUtilities)
# Note: components are enabled based on the find_package() parameters.
+36
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@@ -0,0 +1,36 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# Defines the following variables:
# - CAMP_FOUND
# - CAMP_LIBRARIES
# - CAMP_INCLUDE_DIRS
include(MfemCmakeUtilities)
mfem_find_package(CAMP CAMP CAMP_DIR
"include" "camp/camp.hpp"
"lib" "camp"
"Paths to headers required by CAMP."
"Libraries required by CAMP.")
# RAJA commonly lists "camp" in INTERFACE_LINK_LIBRARIES. If there is no CMake
# target named "camp", CMake treats it as a bare library name (-lcamp).
if (CAMP_FOUND AND NOT TARGET camp)
list(GET CAMP_LIBRARIES 0 _camp_lib0)
add_library(camp UNKNOWN IMPORTED)
set_target_properties(camp PROPERTIES
IMPORTED_LOCATION "${_camp_lib0}"
INTERFACE_INCLUDE_DIRECTORIES "${CAMP_INCLUDE_DIRS}")
set(CAMP_LIBRARIES "camp" CACHE STRING "CAMP imported target." FORCE)
unset(_camp_lib0)
endif()
+15
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@@ -21,6 +21,21 @@ mfem_find_package(Caliper CALIPER CALIPER_DIR
"Paths to headers required by Caliper."
"Libraries required by Caliper.")
# Some downstream CMake packages (notably RAJA) may list "caliper" in their
# INTERFACE_LINK_LIBRARIES. If there is no CMake target named "caliper", CMake
# treats it as a bare library name and will pass -lcaliper to the linker.
# Create a minimal imported target when we only located the library by path.
if (CALIPER_FOUND AND NOT TARGET caliper)
list(GET CALIPER_LIBRARIES 0 _caliper_lib0)
add_library(caliper UNKNOWN IMPORTED)
set_target_properties(caliper PROPERTIES
IMPORTED_LOCATION "${_caliper_lib0}"
INTERFACE_INCLUDE_DIRECTORIES "${CALIPER_INCLUDE_DIRS}")
# Prefer linking via the target.
set(CALIPER_LIBRARIES "caliper" CACHE STRING "Caliper imported target." FORCE)
unset(_caliper_lib0)
endif()
# Append adiak path/lib if the user provided ADIAK_DIR
if(ADIAK_DIR AND EXISTS ${ADIAK_DIR})
find_package(adiak NO_DEFAULT_PATH REQUIRED PATHS ${ADIAK_DIR}/lib/cmake/adiak ${ADIAK_DIR})
+3 -3
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@@ -14,12 +14,12 @@
# - UMPIRE_LIBRARIES
# - UMPIRE_INCLUDE_DIRS
if (NOT umpire_ROOT AND UMPIRE_DIR)
set(umpire_ROOT ${UMPIRE_DIR})
if (NOT umpire_DIR AND UMPIRE_DIR)
set(umpire_DIR ${UMPIRE_DIR}/lib/cmake/umpire)
endif()
message(STATUS "Looking for UMPIRE ...")
message(STATUS " in UMPIRE_DIR = ${UMPIRE_DIR}")
message(STATUS " umpire_ROOT = ${umpire_ROOT}")
message(STATUS " umpire_DIR = ${umpire_DIR}")
find_package(umpire CONFIG)
set(UMPIRE_FOUND ${umpire_FOUND})
set(UMPIRE_LIBRARIES "umpire")
@@ -878,7 +878,7 @@ function(mfem_export_mk_files)
MFEM_USE_SUITESPARSE MFEM_USE_SUPERLU MFEM_USE_SUPERLU5 MFEM_USE_MUMPS
MFEM_USE_STRUMPACK MFEM_USE_GINKGO MFEM_USE_AMGX MFEM_USE_MAGMA
MFEM_USE_GNUTLS MFEM_USE_NETCDF MFEM_USE_PETSC MFEM_USE_SLEPC
MFEM_USE_MPFR MFEM_USE_SIDRE MFEM_USE_FMS MFEM_USE_CONDUIT MFEM_USE_PUMI
MFEM_USE_MPFR MFEM_USE_FMS MFEM_USE_CONDUIT MFEM_USE_PUMI
MFEM_USE_HIOP MFEM_USE_GSLIB MFEM_USE_CUDA MFEM_USE_HIP MFEM_USE_RAJA
MFEM_USE_OCCA MFEM_USE_CEED MFEM_USE_CALIPER MFEM_USE_UMPIRE MFEM_USE_SIMD
MFEM_USE_ADIOS2 MFEM_USE_MKL_CPARDISO MFEM_USE_MKL_PARDISO
-6
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@@ -97,9 +97,6 @@
// Enable MFEM functionality based on the SuiteSparse library.
// #define MFEM_USE_SUITESPARSE
// Enable MFEM functionality based on the ARPACK library.
// #define MFEM_USE_ARPACK
// Enable MFEM functionality based on the SuperLU_DIST library.
// #define MFEM_USE_SUPERLU
// #define MFEM_USE_SUPERLU5
@@ -123,9 +120,6 @@
// Enable secure socket streams based on the GNUTLS library.
// #define MFEM_USE_GNUTLS
// Enable Sidre support.
// #define MFEM_USE_SIDRE
// Enable the use of SIMD in the high performance templated classes.
// #define MFEM_USE_SIMD
-2
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@@ -32,7 +32,6 @@ MFEM_USE_MEMALLOC = @MFEM_USE_MEMALLOC@
MFEM_TIMER_TYPE = @MFEM_TIMER_TYPE@
MFEM_USE_SUNDIALS = @MFEM_USE_SUNDIALS@
MFEM_USE_SUITESPARSE = @MFEM_USE_SUITESPARSE@
MFEM_USE_ARPACK = @MFEM_USE_ARPACK@
MFEM_USE_SUPERLU = @MFEM_USE_SUPERLU@
MFEM_USE_SUPERLU5 = @MFEM_USE_SUPERLU5@
MFEM_USE_MUMPS = @MFEM_USE_MUMPS@
@@ -46,7 +45,6 @@ MFEM_USE_NETCDF = @MFEM_USE_NETCDF@
MFEM_USE_PETSC = @MFEM_USE_PETSC@
MFEM_USE_SLEPC = @MFEM_USE_SLEPC@
MFEM_USE_MPFR = @MFEM_USE_MPFR@
MFEM_USE_SIDRE = @MFEM_USE_SIDRE@
MFEM_USE_FMS = @MFEM_USE_FMS@
MFEM_USE_CONDUIT = @MFEM_USE_CONDUIT@
MFEM_USE_PUMI = @MFEM_USE_PUMI@
+9 -14
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@@ -48,7 +48,6 @@ option(MFEM_USE_NETCDF "Enable NETCDF usage" OFF)
option(MFEM_USE_PETSC "Enable PETSc support." OFF)
option(MFEM_USE_SLEPC "Enable SLEPc support." OFF)
option(MFEM_USE_MPFR "Enable MPFR usage." OFF)
option(MFEM_USE_SIDRE "Enable Axom/Sidre usage" OFF)
option(MFEM_USE_FMS "Enable FMS usage" OFF)
option(MFEM_USE_CONDUIT "Enable Conduit usage" OFF)
option(MFEM_USE_PUMI "Enable PUMI" OFF)
@@ -224,17 +223,8 @@ set(FMS_DIR "${MFEM_DIR}/../fms" CACHE PATH
set(CONDUIT_DIR "${MFEM_DIR}/../conduit" CACHE PATH
"Path to the Conduit library.")
set(AXOM_DIR "${MFEM_DIR}/../axom" CACHE PATH "Path to the Axom library.")
# May need to add "Boost" as requirement.
if (MFEM_USE_SIDRE)
if (MFEM_USE_MPI)
set(Axom_REQUIRED_PACKAGES "Conduit/blueprint/blueprint_mpi/relay/relay_mpi" CACHE STRING
"Additional packages required by Axom.")
elseif()
set(Axom_REQUIRED_PACKAGES "Conduit/blueprint/relay" CACHE STRING
"Additional packages required by Axom.")
endif()
endif()
set(AXOM_DIR "${MFEM_DIR}/../axom" CACHE PATH
"Path to the Axom library (required by Tribol for the contact mini-app).")
set(PUMI_DIR "${MFEM_DIR}/../pumi-2.1.0" CACHE STRING
"Directory where PUMI is installed")
@@ -252,6 +242,7 @@ set(MKL_PARDISO_DIR "" CACHE STRING "MKL installation path.")
set(OCCA_DIR "${MFEM_DIR}/../occa" CACHE PATH "Path to OCCA")
set(RAJA_DIR "${MFEM_DIR}/../raja" CACHE PATH "Path to RAJA")
set(CAMP_DIR "${MFEM_DIR}/../camp" CACHE PATH "Path to CAMP (required by RAJA/Umpire)")
set(CEED_DIR "${MFEM_DIR}/../libCEED" CACHE PATH "Path to libCEED")
set(UMPIRE_DIR "${MFEM_DIR}/../umpire" CACHE PATH "Path to Umpire")
set(CALIPER_DIR "${MFEM_DIR}/../caliper" CACHE PATH "Path to Caliper")
@@ -272,8 +263,12 @@ set(PARELAG_LIBRARIES "${PARELAG_DIR}/build/src/libParELAG.a" CACHE STRING
"The ParELAG library.")
set(TRIBOL_DIR "${MFEM_DIR}/../tribol" CACHE PATH "Path to Tribol")
set(Tribol_REQUIRED_PACKAGES "Axom/core/mint/slam/slic" CACHE STRING
"Additional packages required by Tribol")
# Tribol requires Axom. Many Tribol builds also enable optional TPLs like
# RAJA/UMPIRE/Caliper, and may pull additional Axom components (e.g. quest,
# lumberjack) via its exported targets.
set(Tribol_REQUIRED_PACKAGES
"REQUIRED:;Axom/core/primal/mint/slam/slic/quest/lumberjack;OPTIONAL:;Adiak;CAMP;RAJA;UMPIRE;Caliper"
CACHE STRING "Additional packages required by Tribol")
set(ENZYME_DIR "${MFEM_DIR}/../enzyme" CACHE PATH "Path to Enzyme")
+78 -24
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@@ -162,7 +162,6 @@ MFEM_USE_NETCDF = NO
MFEM_USE_PETSC = NO
MFEM_USE_SLEPC = NO
MFEM_USE_MPFR = NO
MFEM_USE_SIDRE = NO
MFEM_USE_FMS = NO
MFEM_USE_CONDUIT = NO
MFEM_USE_PUMI = NO
@@ -178,7 +177,6 @@ MFEM_USE_ALGOIM = NO
MFEM_USE_UMPIRE = NO
MFEM_USE_SIMD = NO
MFEM_USE_ADIOS2 = NO
MFEM_USE_ARPACK = NO
MFEM_USE_MKL_CPARDISO = NO
MFEM_USE_MKL_PARDISO = NO
MFEM_USE_MOONOLITH = NO
@@ -250,6 +248,15 @@ endif
# METIS library configuration
ifeq ($(MFEM_USE_SUPERLU)$(MFEM_USE_STRUMPACK)$(MFEM_USE_MUMPS),NONONO)
# MFEM_USE_METIS_5: when the user supplies METIS_DIR, try to auto-detect
# METIS 5 installs that follow the common <prefix>/{include,lib,lib64} layout.
ifeq ($(MFEM_USE_METIS_5),NO)
ifneq ($(wildcard $(METIS_DIR)/include/metis.h),)
ifneq ($(wildcard $(METIS_DIR)/lib/libmetis.* $(METIS_DIR)/lib64/libmetis.*),)
MFEM_USE_METIS_5 = YES
endif
endif
endif
ifeq ($(MFEM_USE_METIS_5),NO)
METIS_DIR = @MFEM_DIR@/../metis-4.0
METIS_OPT =
@@ -428,14 +435,6 @@ NETCDF_LIB = $(XLINKER)-rpath,$(NETCDF_DIR)/lib -L$(NETCDF_DIR)/lib\
$(XLINKER)-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib\
-lnetcdf -lhdf5_hl -lhdf5 $(ZLIB_LIB)
# ARPACK library configuration
ARPACK_DIR = @MFEM_DIR@/../ARPACK
ifeq ($(MFEM_USE_MPI),YES)
ARPACK_LIB = -L$(ARPACK_DIR) -lparpack -larpack
else
ARPACK_LIB = -L$(ARPACK_DIR) -larpack
endif
# PETSc library configuration (version greater or equal to 3.8 or the dev branch)
PETSC_ARCH := arch-linux2-c-debug
PETSC_DIR := $(MFEM_DIR)/../petsc/$(PETSC_ARCH)
@@ -496,17 +495,6 @@ ifneq (,$(wildcard $(CONDUIT_HDF5_HEADER)))
-lhdf5 $(ZLIB_LIB)
endif
# Sidre and required libraries configuration
# Be sure to check the HDF5_DIR (set above) is correct
SIDRE_DIR = @MFEM_DIR@/../axom
SIDRE_OPT = -I$(SIDRE_DIR)/include -I$(CONDUIT_DIR)/include/conduit\
-I$(HDF5_DIR)/include
SIDRE_LIB = \
$(XLINKER)-rpath,$(SIDRE_DIR)/lib -L$(SIDRE_DIR)/lib \
$(XLINKER)-rpath,$(CONDUIT_DIR)/lib -L$(CONDUIT_DIR)/lib \
$(XLINKER)-rpath,$(HDF5_DIR)/lib -L$(HDF5_DIR)/lib \
-laxom -lconduit -lconduit_relay -lconduit_blueprint -lhdf5 $(ZLIB_LIB) -ldl
# PUMI
# Note that PUMI_DIR is needed -- it is used to check for gmi_sim.h
PUMI_DIR = @MFEM_DIR@/../pumi-2.1.0
@@ -588,7 +576,13 @@ ifdef CUB_DIR
RAJA_OPT += -I$(CUB_DIR)
endif
# CAMP library configuration (required by RAJA/Umpire for most installs)
CAMP_LIB = -lcamp
# If the common sibling layout exists, use it as a default (handles versioned
# directories like camp-<hash>).
ifneq ($(wildcard $(RAJA_DIR)/../camp*/include/camp/camp.hpp),)
CAMP_DIR ?= $(patsubst %/include/camp/camp.hpp,%,$(firstword $(wildcard $(RAJA_DIR)/../camp*/include/camp/camp.hpp)))
endif
ifdef CAMP_DIR
RAJA_OPT += -I$(CAMP_DIR)/include
CAMP_LIB = $(XLINKER)-rpath,$(CAMP_DIR)/lib -L$(CAMP_DIR)/lib -lcamp
@@ -598,7 +592,12 @@ RAJA_LIB = $(XLINKER)-rpath,$(RAJA_DIR)/lib -L$(RAJA_DIR)/lib -lRAJA $(CAMP_LIB)
# UMPIRE library configuration
UMPIRE_DIR = @MFEM_DIR@/../umpire
UMPIRE_OPT = -I$(UMPIRE_DIR)/include $(if $(CAMP_DIR), -I$(CAMP_DIR)/include)
UMPIRE_LIB = -L$(UMPIRE_DIR)/lib -L$(UMPIRE_DIR)/lib64 -lumpire $(CAMP_LIB)
UMPIRE_LIB = -L$(UMPIRE_DIR)/lib -L$(UMPIRE_DIR)/lib64 -lumpire $(CAMP_LIB) -lpthread
# If the common sibling layout exists, use it as a default (handles versioned
# directories like fmt-<hash>).
ifneq ($(wildcard $(UMPIRE_DIR)/../fmt*/include/fmt/format.h),)
FMT_DIR ?= $(patsubst %/include/fmt/format.h,%,$(firstword $(wildcard $(UMPIRE_DIR)/../fmt*/include/fmt/format.h)))
endif
ifdef FMT_DIR
UMPIRE_OPT += -I$(FMT_DIR)/include
UMPIRE_LIB += -L$(FMT_DIR)/lib -L$(FMT_DIR)/lib64 -lfmt
@@ -630,8 +629,63 @@ PARELAG_LIB = -L$(PARELAG_DIR)/build/src -lParELAG
AXOM_DIR = @MFEM_DIR@/../axom
TRIBOL_DIR = @MFEM_DIR@/../tribol
TRIBOL_OPT = -I$(TRIBOL_DIR)/include -I$(AXOM_DIR)/include
TRIBOL_LIB = -L$(TRIBOL_DIR)/lib -ltribol -lredecomp -L$(AXOM_DIR)/lib -laxom_mint\
-laxom_slam -laxom_slic -laxom_core
# Tribol may be built with optional dependencies (e.g. RAJA/UMPIRE/CALIPER).
# Add those options only when the corresponding headers/libraries exist.
ifneq ($(wildcard $(RAJA_DIR)/include/RAJA/RAJA.hpp),)
TRIBOL_OPT += $(RAJA_OPT)
endif
ifneq ($(wildcard $(UMPIRE_DIR)/include/umpire/Umpire.hpp),)
TRIBOL_OPT += $(UMPIRE_OPT)
endif
ifneq ($(wildcard $(CALIPER_DIR)/include/caliper/cali.h),)
TRIBOL_OPT += $(CALIPER_OPT)
endif
TRIBOL_LIB = -L$(TRIBOL_DIR)/lib -L$(TRIBOL_DIR)/lib64
ifneq ($(wildcard $(TRIBOL_DIR)/lib/libtribol.* $(TRIBOL_DIR)/lib64/libtribol.*),)
TRIBOL_LIB += -ltribol
endif
ifneq ($(wildcard $(TRIBOL_DIR)/lib/libtribol_shared.* $(TRIBOL_DIR)/lib64/libtribol_shared.*),)
TRIBOL_LIB += -ltribol_shared
endif
ifneq ($(wildcard $(TRIBOL_DIR)/lib/libredecomp.* $(TRIBOL_DIR)/lib64/libredecomp.*),)
TRIBOL_LIB += -lredecomp
endif
TRIBOL_LIB += -L$(AXOM_DIR)/lib -L$(AXOM_DIR)/lib64
ifneq ($(wildcard $(AXOM_DIR)/lib/libaxom_quest.* $(AXOM_DIR)/lib64/libaxom_quest.*),)
TRIBOL_LIB += -laxom_quest
endif
ifneq ($(wildcard $(AXOM_DIR)/lib/libaxom_mint.* $(AXOM_DIR)/lib64/libaxom_mint.*),)
TRIBOL_LIB += -laxom_mint
endif
ifneq ($(wildcard $(AXOM_DIR)/lib/libaxom_slam.* $(AXOM_DIR)/lib64/libaxom_slam.*),)
TRIBOL_LIB += -laxom_slam
endif
ifneq ($(wildcard $(AXOM_DIR)/lib/libaxom_slic.* $(AXOM_DIR)/lib64/libaxom_slic.*),)
TRIBOL_LIB += -laxom_slic
endif
ifneq ($(wildcard $(AXOM_DIR)/lib/libaxom_lumberjack.* $(AXOM_DIR)/lib64/libaxom_lumberjack.*),)
TRIBOL_LIB += -laxom_lumberjack
endif
ifneq ($(wildcard $(AXOM_DIR)/lib/libaxom_core.* $(AXOM_DIR)/lib64/libaxom_core.*),)
TRIBOL_LIB += -laxom_core
endif
# Add common optional Tribol TPLs when their libraries are present.
ifneq ($(wildcard $(ADIAK_DIR)/lib/libadiak.* $(ADIAK_DIR)/lib64/libadiak.*),)
TRIBOL_LIB += $(XLINKER)-rpath,$(ADIAK_DIR)/lib64 $(XLINKER)-rpath,$(ADIAK_DIR)/lib \
-L$(ADIAK_DIR)/lib64 -L$(ADIAK_DIR)/lib -ladiak -ldl
endif
ifneq ($(wildcard $(UMPIRE_DIR)/lib/libumpire.* $(UMPIRE_DIR)/lib64/libumpire.*),)
TRIBOL_LIB += $(UMPIRE_LIB)
endif
ifneq ($(wildcard $(RAJA_DIR)/lib/libRAJA.* $(RAJA_DIR)/lib64/libRAJA.*),)
TRIBOL_LIB += $(RAJA_LIB)
endif
ifneq ($(wildcard $(CALIPER_DIR)/lib/libcaliper.* $(CALIPER_DIR)/lib64/libcaliper.*),)
TRIBOL_LIB += $(CALIPER_LIB)
endif
# Enzyme configuration
ENZYME_DIR = @MFEM_DIR@/../enzyme
-7
View File
@@ -49,13 +49,6 @@ list(APPEND ALL_EXE_SRCS
ex41.cpp
)
if (MFEM_USE_ARPACK)
list(APPEND ALL_EXE_SRCS
ex11.pp
ex13.pp
)
endif()
if (MFEM_USE_MPI)
list(APPEND ALL_EXE_SRCS
ex0p.cpp
-298
View File
@@ -1,298 +0,0 @@
// MFEM Example 11 - Serial Version
//
// Compile with: make ex11
//
// Sample runs: ex11 -m ../data/square-disc.mesh
// ex11 -m ../data/star.mesh
// ex11 -m ../data/star-mixed.mesh
// ex11 -m ../data/periodic-annulus-sector.msh
// ex11 -m ../data/square-disc-p2.vtk -o 2
// ex11 -m ../data/square-disc-p3.mesh -o 3
// ex11 -m ../data/square-disc-nurbs.mesh -o -1
// ex11 -m ../data/disc-nurbs.mesh -o -1 -n 20
// ex11 -m ../data/star-surf.mesh
// ex11 -m ../data/square-disc-surf.mesh
// ex11 -m ../data/inline-segment.mesh
// ex11 -m ../data/inline-quad.mesh
// ex11 -m ../data/inline-tri.mesh
// ex11 -m ../data/amr-quad.mesh
// ex11 -m ../data/amr-hex.mesh
// ex11 -m ../data/mobius-strip.mesh -n 8
//
// Description: This example code demonstrates the use of MFEM to solve the
// eigenvalue problem -Delta u = lambda u with homogeneous
// Dirichlet boundary conditions.
//
// We compute a number of the lowest eigenmodes by discretizing
// the Laplacian and Mass operators using a FE space of the
// specified order, or an isoparametric/isogeometric space if
// order < 1 (quadratic for quadratic curvilinear mesh, NURBS for
// NURBS mesh, etc.)
//
// The example highlights the use of the ARPACK eigenvalue solver
// (regular inverse mode). Reusing a single GLVis visualization
// window for multiple eigenfunctions is also illustrated.
//
// We recommend viewing Example 1 before viewing this example.
#include "mfem.hpp"
#include <fstream>
#include <iostream>
using namespace std;
using namespace mfem;
#ifdef MFEM_USE_ARPACK
int main(int argc, char *argv[])
{
// 1. Parse command-line options.
const char *mesh_file = "../data/star.mesh";
int ser_ref_levels = 3;
int order = 1;
int nev = 5;
double dbc_eig = 1e3;
bool visualization = 1;
bool arp_solver = true;
OptionsParser args(argc, argv);
args.AddOption(&mesh_file, "-m", "--mesh",
"Mesh file to use.");
args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
"Number of times to refine the mesh uniformly in serial.");
args.AddOption(&order, "-o", "--order",
"Finite element order (polynomial degree) or -1 for"
" isoparametric space.");
args.AddOption(&nev, "-n", "--num-eigs",
"Number of desired eigenmodes.");
args.AddOption(&dbc_eig, "-d", "--dbc-eig",
"Eigenvalues associated with Dirichlet BC "
"(should be larger than the maximum desired eigenvalue).");
args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.Parse();
if (!args.Good())
{
args.PrintUsage(cout);
return 1;
}
args.PrintOptions(cout);
// 2. Read the (serial) mesh from the given mesh file on all processors. We
// can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
// and volume meshes with the same code.
Mesh *mesh;
ifstream imesh(mesh_file);
if (!imesh)
{
cerr << "\nCan not open mesh file: " << mesh_file << '\n' << endl;
return 2;
}
mesh = new Mesh(imesh, 1, 1);
imesh.close();
int dim = mesh->Dimension();
// 3. Refine the serial mesh on all processors to increase the resolution. In
// this example we do 'ref_levels' of uniform refinement (2 by default, or
// specified on the command line with -rs).
for (int lev = 0; lev < ser_ref_levels; lev++)
{
mesh->UniformRefinement();
}
// 4. Define a finite element space on the mesh. Here we
// use continuous Lagrange finite elements of the specified order. If
// order < 1, we instead use an isoparametric/isogeometric space.
FiniteElementCollection *fec;
if (order > 0)
{
fec = new H1_FECollection(order, dim);
}
else if (mesh->GetNodes())
{
fec = mesh->GetNodes()->OwnFEC();
}
else
{
fec = new H1_FECollection(order = 1, dim);
}
FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
int size = fespace->GetVSize();
cout << "Number of unknowns: " << size << endl;
// 5. Set up the parallel bilinear forms a(.,.) and m(.,.) on the finite
// element space. The first corresponds to the Laplacian operator -Delta,
// while the second is a simple mass matrix needed on the right hand side
// of the generalized eigenvalue problem below. The boundary conditions
// are implemented by elimination with special values on the diagonal to
// shift the Dirichlet eigenvalues out of the computational range. After
// serial and parallel assembly we extract the corresponding parallel
// matrices A and M.
ConstantCoefficient one(1.0);
Array<int> ess_bdr;
if (mesh->bdr_attributes.Size())
{
ess_bdr.SetSize(mesh->bdr_attributes.Max());
ess_bdr = 1;
}
BilinearForm *a = new BilinearForm(fespace);
a->AddDomainIntegrator(new DiffusionIntegrator(one));
if (mesh->bdr_attributes.Size() == 0)
{
// Add a mass term if the mesh has no boundary, e.g. periodic mesh or
// closed surface.
a->AddDomainIntegrator(new MassIntegrator(one));
}
a->Assemble();
if (mesh->bdr_attributes.Size() != 0)
{
a->EliminateEssentialBCDiag(ess_bdr, dbc_eig);
}
a->Finalize();
BilinearForm *m = new BilinearForm(fespace);
m->AddDomainIntegrator(new MassIntegrator(one));
m->Assemble();
if (mesh->bdr_attributes.Size() != 0)
{
// shift the eigenvalue corresponding to eliminated dofs to a large value
m->EliminateEssentialBCDiag(ess_bdr, 1.0);
}
m->Finalize();
Solver * solver = NULL;
#ifndef MFEM_USE_SUITESPARSE
// 6. Define a simple symmetric Gauss-Seidel preconditioner and use it to
// solve the system A X = B with PCG.
cout << "Building CGSolver" << endl;
GSSmoother M(m->SpMat());
CGSolver * cg_solver = new CGSolver;
cg_solver->SetPreconditioner(M);
cg_solver->SetRelTol(1.0e-12);
solver = cg_solver;
#else
// 7. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
cout << "Building UMFPackSolver" << endl;
UMFPackSolver * umf_solver = new UMFPackSolver;
umf_solver->Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
solver = umf_solver;
#endif
solver->SetOperator(m->SpMat());
// 7. Define and configure the ARPACK eigensolver
SymGenEigensolver * eig_solver = NULL;
if (arp_solver)
{
// ArPackSymGen * arpack = new ArPackSymGen();
ArPackSAUPD * arpack = new ArPackSAUPD();
arpack->SetMode(2);
arpack->SetNumModes(nev);
arpack->SetMaxIter(400);
arpack->SetTol(1e-8);
arpack->SetPrintLevel(2);
arpack->SetSolver(*solver);
eig_solver = arpack;
}
eig_solver->SetOperators(*a, *m);
// 8. Compute the eigenmodes and extract the array of eigenvalues. Define a
// parallel grid function to represent each of the eigenmodes returned by
// the solver.
Array<double> eigenvalues;
eig_solver->Solve();
eig_solver->GetEigenvalues(eigenvalues);
cout << endl;
std::ios::fmtflags old_fmt = cout.flags();
cout.setf(std::ios::scientific);
std::streamsize old_prec = cout.precision(14);
for (int i=0; i<nev; i++)
{
cout << "Eigenvalue lambda " << eigenvalues[i] << endl;
}
cout.precision(old_prec);
cout.flags(old_fmt);
cout << endl;
GridFunction x(fespace);
// 9. Save the refined mesh and the modes in parallel. This output can be
// viewed later using GLVis: "glvis -np <np> -m mesh -g mode".
{
ostringstream mesh_name, mode_name;
mesh_name << "ex11.mesh";
ofstream mesh_ofs(mesh_name.str().c_str());
mesh_ofs.precision(8);
mesh->Print(mesh_ofs);
for (int i=0; i<nev; i++)
{
// convert eigenvector from Vector to GridFunction
x = eig_solver->GetEigenvector(i);
mode_name << "mode_" << setfill('0') << setw(2) << i;
ofstream mode_ofs(mode_name.str().c_str());
mode_ofs.precision(8);
x.Save(mode_ofs);
mode_name.str("");
}
}
// 10. Send the solution by socket to a GLVis server.
if (visualization)
{
char vishost[] = "localhost";
int visport = 19916;
socketstream mode_sock(vishost, visport);
mode_sock.precision(8);
for (int i=0; i<nev; i++)
{
cout << "Eigenmode " << i+1 << '/' << nev
<< ", Lambda = " << eigenvalues[i] << endl;
// convert eigenvector from Vector to GridFunction
x = eig_solver->GetEigenvector(i);
mode_sock << "solution\n" << *mesh << x << flush
<< "window_title 'Eigenmode " << i+1 << '/' << nev
<< ", Lambda = " << eigenvalues[i] << "'" << endl;
char c;
cout << "press (q)uit or (c)ontinue --> " << flush;
cin >> c;
if (c != 'c')
{
break;
}
}
mode_sock.close();
}
// 11. Free the used memory.
delete eig_solver;
delete solver;
delete m;
delete a;
delete fespace;
if (order > 0)
{
delete fec;
}
delete mesh;
return 0;
}
#endif // MFEM_USE_ARPACK
+40 -101
View File
@@ -72,8 +72,6 @@ int main(int argc, char *argv[])
int seed = 75;
bool slu_solver = false;
bool sp_solver = false;
bool lob_solver = true;
bool arp_solver = false;
bool cpardiso_solver = false;
bool visualization = 1;
@@ -99,10 +97,6 @@ int main(int argc, char *argv[])
args.AddOption(&sp_solver, "-sp", "--strumpack", "-no-sp",
"--no-strumpack", "Use the STRUMPACK Solver.");
#endif
#ifdef MFEM_USE_ARPACK
args.AddOption(&arp_solver, "-arp", "--arpack", "-no-arp",
"--no-arpack", "Use the Parallel ARPACK Solver.");
#endif
#ifdef MFEM_USE_MKL_CPARDISO
args.AddOption(&cpardiso_solver, "-cpardiso", "--cpardiso", "-no-cpardiso",
"--no-cpardiso", "Use the MKL CPardiso Solver.");
@@ -119,11 +113,6 @@ int main(int argc, char *argv[])
<< " Defaulting to SuperLU." << endl;
sp_solver = false;
}
if (arp_solver)
{
lob_solver = false;
}
// The command line options are also passed to the STRUMPACK
// solver. So do not exit if some options are not recognized.
if (!sp_solver)
@@ -254,119 +243,70 @@ int main(int argc, char *argv[])
// 8. Define and configure the LOBPCG eigensolver and the BoomerAMG
// preconditioner for A to be used within the solver. Set the matrices
// which define the generalized eigenproblem A x = lambda M x.
Solver * solver = NULL;
Solver * precond = NULL;
if (!slu_solver && !sp_solver && !cpardiso_solver)
{
HypreBoomerAMG * amg = new HypreBoomerAMG(*A);
amg->SetPrintLevel(0);
precond = amg;
if (arp_solver)
{
HyprePCG * pcg = new HyprePCG(*A);
pcg->SetTol(1e-12);
pcg->SetPreconditioner(*amg);
solver = pcg;
}
}
#ifdef MFEM_USE_SUPERLU
else if (slu_solver)
else
{
SuperLUSolver * superlu = new SuperLUSolver(MPI_COMM_WORLD);
superlu->SetPrintStatistics(false);
superlu->SetSymmetricPattern(true);
superlu->SetColumnPermutation(superlu::PARMETIS);
superlu->SetOperator(*Arow);
if (arp_solver)
{
solver = superlu;
}
else
#ifdef MFEM_USE_SUPERLU
if (slu_solver)
{
SuperLUSolver * superlu = new SuperLUSolver(MPI_COMM_WORLD);
superlu->SetPrintStatistics(false);
superlu->SetSymmetricPattern(true);
superlu->SetColumnPermutation(superlu::PARMETIS);
superlu->SetOperator(*Arow);
precond = superlu;
}
}
#endif
#ifdef MFEM_USE_STRUMPACK
else if (sp_solver)
{
STRUMPACKSolver * strumpack = new STRUMPACKSolver(argc, argv,
MPI_COMM_WORLD);
strumpack->SetPrintFactorStatistics(true);
strumpack->SetPrintSolveStatistics(false);
strumpack->SetKrylovSolver(strumpack::KrylovSolver::DIRECT);
strumpack->SetReorderingStrategy(strumpack::ReorderingStrategy::METIS);
strumpack->SetMatching(strumpack::MatchingJob::NONE);
strumpack->SetCompression(strumpack::CompressionType::NONE);
strumpack->SetOperator(*Arow);
strumpack->SetFromCommandLine();
if (arp_solver)
{
solver = strumpack;
}
else
if (sp_solver)
{
STRUMPACKSolver * strumpack = new STRUMPACKSolver(MPI_COMM_WORLD, argc, argv);
strumpack->SetPrintFactorStatistics(true);
strumpack->SetPrintSolveStatistics(false);
strumpack->SetKrylovSolver(strumpack::KrylovSolver::DIRECT);
strumpack->SetReorderingStrategy(strumpack::ReorderingStrategy::METIS);
strumpack->SetMatching(strumpack::MatchingJob::NONE);
strumpack->SetCompression(strumpack::CompressionType::NONE);
strumpack->SetOperator(*Arow);
strumpack->SetFromCommandLine();
precond = strumpack;
}
}
#endif
#ifdef MFEM_USE_MKL_CPARDISO
else if (cpardiso_solver)
{
auto cpardiso = new CPardisoSolver(A->GetComm());
cpardiso->SetMatrixType(CPardisoSolver::MatType::REAL_STRUCTURE_SYMMETRIC);
cpardiso->SetPrintLevel(1);
cpardiso->SetOperator(*A);
if (arp_solver)
{
solver = cpardiso;
}
else
if (cpardiso_solver)
{
auto cpardiso = new CPardisoSolver(A->GetComm());
cpardiso->SetMatrixType(CPardisoSolver::MatType::REAL_STRUCTURE_SYMMETRIC);
cpardiso->SetPrintLevel(1);
cpardiso->SetOperator(*A);
precond = cpardiso;
}
}
#endif
SymGenEigensolver * eig_solver = NULL;
if (lob_solver)
{
HypreLOBPCG * lobpcg = new HypreLOBPCG(MPI_COMM_WORLD);
lobpcg->SetNumModes(nev);
lobpcg->SetRandomSeed(seed);
lobpcg->SetPreconditioner(*precond);
lobpcg->SetMaxIter(200);
lobpcg->SetTol(1e-8);
lobpcg->SetPrecondUsageMode(1);
lobpcg->SetPrintLevel(1);
eig_solver = lobpcg;
}
#ifdef MFEM_USE_ARPACK
else if (arp_solver)
{
ArPackPSAUPD * arpack = new ArPackPSAUPD(MPI_COMM_WORLD);
arpack->SetNumModes(nev);
arpack->SetMaxIter(400);
arpack->SetTol(1e-8);
arpack->SetMode(3);
arpack->SetPrintLevel(2);
arpack->SetSolver(*solver);
eig_solver = arpack;
}
#endif
eig_solver->SetOperators(*A, *M);
HypreLOBPCG * lobpcg = new HypreLOBPCG(MPI_COMM_WORLD);
lobpcg->SetNumModes(nev);
lobpcg->SetRandomSeed(seed);
lobpcg->SetPreconditioner(*precond);
lobpcg->SetMaxIter(200);
lobpcg->SetTol(1e-8);
lobpcg->SetPrecondUsageMode(1);
lobpcg->SetPrintLevel(1);
lobpcg->SetMassMatrix(*M);
lobpcg->SetOperator(*A);
// 9. Compute the eigenmodes and extract the array of eigenvalues. Define a
// parallel grid function to represent each of the eigenmodes returned by
// the solver.
Array<real_t> eigenvalues;
eig_solver->Solve();
eig_solver->GetEigenvalues(eigenvalues);
lobpcg->Solve();
lobpcg->GetEigenvalues(eigenvalues);
ParGridFunction x(fespace);
// 10. Save the refined mesh and the modes in parallel. This output can be
@@ -381,8 +321,8 @@ int main(int argc, char *argv[])
for (int i=0; i<nev; i++)
{
// convert eigenvector from Vector to ParGridFunction
x.Distribute(eig_solver->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = lobpcg->GetEigenvector(i);
mode_name << "mode_" << setfill('0') << setw(2) << i << "."
<< setfill('0') << setw(6) << myid;
@@ -410,8 +350,8 @@ int main(int argc, char *argv[])
<< ", Lambda = " << eigenvalues[i] << endl;
}
// convert eigenvector from Vector to ParGridFunction
x.Distribute(eig_solver->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = lobpcg->GetEigenvector(i);
mode_sock << "parallel " << num_procs << " " << myid << "\n"
<< "solution\n" << *pmesh << x << flush
@@ -435,8 +375,7 @@ int main(int argc, char *argv[])
}
// 12. Free the used memory.
delete eig_solver;
delete solver;
delete lobpcg;
delete precond;
delete M;
delete A;
-381
View File
@@ -1,381 +0,0 @@
// MFEM Example 11 - Parallel Version
//
// Compile with: make ex11p
//
// Sample runs: mpirun -np 4 ex11p -m ../data/square-disc.mesh
// mpirun -np 4 ex11p -m ../data/star.mesh
// mpirun -np 4 ex11p -m ../data/escher.mesh
// mpirun -np 4 ex11p -m ../data/fichera.mesh
// mpirun -np 4 ex11p -m ../data/square-disc-p2.vtk -o 2
// mpirun -np 4 ex11p -m ../data/square-disc-p3.mesh -o 3
// mpirun -np 4 ex11p -m ../data/square-disc-nurbs.mesh -o -1
// mpirun -np 4 ex11p -m ../data/disc-nurbs.mesh -o -1 -n 20
// mpirun -np 4 ex11p -m ../data/pipe-nurbs.mesh -o -1
// mpirun -np 4 ex11p -m ../data/ball-nurbs.mesh -o 2
// mpirun -np 4 ex11p -m ../data/star-surf.mesh
// mpirun -np 4 ex11p -m ../data/square-disc-surf.mesh
// mpirun -np 4 ex11p -m ../data/inline-segment.mesh
// mpirun -np 4 ex11p -m ../data/amr-quad.mesh
// mpirun -np 4 ex11p -m ../data/amr-hex.mesh
// mpirun -np 4 ex11p -m ../data/mobius-strip.mesh -n 8
// mpirun -np 4 ex11p -m ../data/klein-bottle.mesh -n 10
//
// Description: This example code demonstrates the use of MFEM to solve the
// eigenvalue problem -Delta u = lambda u with homogeneous
// Dirichlet boundary conditions.
//
// We compute a number of the lowest eigenmodes by discretizing
// the Laplacian and Mass operators using a FE space of the
// specified order, or an isoparametric/isogeometric space if
// order < 1 (quadratic for quadratic curvilinear mesh, NURBS for
// NURBS mesh, etc.)
//
// The example highlights the use of the LOBPCG and ARPACK
// eigenvalue solvers together with the BoomerAMG preconditioner
// in HYPRE, as well as optionally the SuperLU parallel direct
// solver. Reusing a single GLVis visualization window for
// multiple eigenfunctions is also illustrated.
//
// We recommend viewing Example 1 before viewing this example.
#include "mfem.hpp"
#include <fstream>
#include <iostream>
using namespace std;
using namespace mfem;
int main(int argc, char *argv[])
{
// 1. Initialize MPI.
int num_procs, myid;
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
// 2. Parse command-line options.
const char *mesh_file = "../data/star.mesh";
int ser_ref_levels = 2;
int par_ref_levels = 1;
int order = 1;
int nev = 5;
bool slu_solver = false;
bool use_arpack = false;
bool visualization = 1;
OptionsParser args(argc, argv);
args.AddOption(&mesh_file, "-m", "--mesh",
"Mesh file to use.");
args.AddOption(&ser_ref_levels, "-rs", "--refine-serial",
"Number of times to refine the mesh uniformly in serial.");
args.AddOption(&par_ref_levels, "-rp", "--refine-parallel",
"Number of times to refine the mesh uniformly in parallel.");
args.AddOption(&order, "-o", "--order",
"Finite element order (polynomial degree) or -1 for"
" isoparametric space.");
args.AddOption(&nev, "-n", "--num-eigs",
"Number of desired eigenmodes.");
#ifdef MFEM_USE_SUPERLU
args.AddOption(&slu_solver, "-slu", "--superlu", "-no-slu",
"--no-superlu", "Use the SuperLU Solver.");
#endif
#ifdef MFEM_USE_ARPACK
args.AddOption(&use_arpack, "-arpack", "--use-arpack", "-no-arpack",
"--no-arpack",
"Enable or disable the use of ARPACK.");
#endif
args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.Parse();
if (!args.Good())
{
if (myid == 0)
{
args.PrintUsage(cout);
}
MPI_Finalize();
return 1;
}
if (myid == 0)
{
args.PrintOptions(cout);
}
// 3. Read the (serial) mesh from the given mesh file on all processors. We
// can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
// and volume meshes with the same code.
Mesh *mesh;
ifstream imesh(mesh_file);
if (!imesh)
{
if (myid == 0)
{
cerr << "\nCan not open mesh file: " << mesh_file << '\n' << endl;
}
MPI_Finalize();
return 2;
}
mesh = new Mesh(imesh, 1, 1);
imesh.close();
int dim = mesh->Dimension();
// 4. Refine the serial mesh on all processors to increase the resolution. In
// this example we do 'ref_levels' of uniform refinement (2 by default, or
// specified on the command line with -rs).
for (int lev = 0; lev < ser_ref_levels; lev++)
{
mesh->UniformRefinement();
}
// 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
// this mesh further in parallel to increase the resolution (1 time by
// default, or specified on the command line with -rp). Once the parallel
// mesh is defined, the serial mesh can be deleted.
ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
delete mesh;
for (int lev = 0; lev < par_ref_levels; lev++)
{
pmesh->UniformRefinement();
}
// 6. Define a parallel finite element space on the parallel mesh. Here we
// use continuous Lagrange finite elements of the specified order. If
// order < 1, we instead use an isoparametric/isogeometric space.
FiniteElementCollection *fec;
if (order > 0)
{
fec = new H1_FECollection(order, dim);
}
else if (pmesh->GetNodes())
{
fec = pmesh->GetNodes()->OwnFEC();
}
else
{
fec = new H1_FECollection(order = 1, dim);
}
ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
HYPRE_Int size = fespace->GlobalTrueVSize();
if (myid == 0)
{
cout << "Number of unknowns: " << size << endl;
}
// 7. Set up the parallel bilinear forms a(.,.) and m(.,.) on the finite
// element space. The first corresponds to the Laplacian operator -Delta,
// while the second is a simple mass matrix needed on the right hand side
// of the generalized eigenvalue problem below. The boundary conditions
// are implemented by elimination with special values on the diagonal to
// shift the Dirichlet eigenvalues out of the computational range. After
// serial and parallel assembly we extract the corresponding parallel
// matrices A and M.
ConstantCoefficient one(1.0);
Array<int> ess_bdr;
if (pmesh->bdr_attributes.Size())
{
ess_bdr.SetSize(pmesh->bdr_attributes.Max());
ess_bdr = 1;
}
ParBilinearForm *a = new ParBilinearForm(fespace);
a->AddDomainIntegrator(new DiffusionIntegrator(one));
if (pmesh->bdr_attributes.Size() == 0)
{
// Add a mass term if the mesh has no boundary, e.g. periodic mesh or
// closed surface.
a->AddDomainIntegrator(new MassIntegrator(one));
}
a->Assemble();
a->EliminateEssentialBCDiag(ess_bdr, 1.0);
a->Finalize();
ParBilinearForm *m = new ParBilinearForm(fespace);
m->AddDomainIntegrator(new MassIntegrator(one));
m->Assemble();
// shift the eigenvalue corresponding to eliminated dofs to a large value
m->EliminateEssentialBCDiag(ess_bdr, numeric_limits<double>::min());
m->Finalize();
HypreParMatrix *A = a->ParallelAssemble();
HypreParMatrix *M = m->ParallelAssemble();
#ifdef MFEM_USE_SUPERLU
Operator * Arow = NULL;
if (slu_solver)
{
Arow = new SuperLURowLocMatrix(*A);
}
#endif
delete a;
delete m;
// 8. Define and configure the LOBPCG eigensolver and the BoomerAMG
// preconditioner for A to be used within the solver. Set the matrices
// which define the generalized eigenproblem A x = lambda M x.
Eigensolver * esolver = NULL;
Solver * solver = NULL;
Solver * precond = NULL;
if (!slu_solver)
{
HypreBoomerAMG * amg = new HypreBoomerAMG(*A);
amg->SetPrintLevel(0);
precond = amg;
#ifdef MFEM_USE_ARPACK
if ( use_arpack )
{
HyprePCG * pcg = new HyprePCG(*A);
pcg->SetTol(1e-12);
pcg->SetMaxIter(200);
pcg->SetPreconditioner(*amg);
pcg->SetPrintLevel(0);
solver = pcg;
}
#endif
}
#ifdef MFEM_USE_SUPERLU
else
{
SuperLUSolver * superlu = new SuperLUSolver(MPI_COMM_WORLD);
superlu->SetPrintStatistics(false);
superlu->SetSymmetricPattern(true);
superlu->SetColumnPermutation(superlu::PARMETIS);
superlu->SetOperator(*Arow);
solver = use_arpack?superlu:NULL;
precond = use_arpack?NULL:superlu;
}
#endif
if ( use_arpack )
{
ParArPackSym * arpack = new ParArPackSym(MPI_COMM_WORLD);
arpack->SetMode(3);
arpack->SetPrintLevel(2);
arpack->SetSolver(*solver);
esolver = arpack;
}
else
{
HypreLOBPCG * lobpcg = new HypreLOBPCG(MPI_COMM_WORLD);
lobpcg->SetPreconditioner(*precond);
lobpcg->SetPrecondUsageMode(1);
lobpcg->SetPrintLevel(1);
esolver = lobpcg;
}
esolver->SetNumModes(nev);
esolver->SetMaxIter(100);
esolver->SetTol(1e-8);
esolver->SetMassMatrix(*M);
esolver->SetOperator(*A);
// 9. Compute the eigenmodes and extract the array of eigenvalues. Define a
// parallel grid function to represent each of the eigenmodes returned by
// the solver.
Array<double> eigenvalues;
esolver->Solve();
esolver->GetEigenvalues(eigenvalues);
if ( myid == 0 && use_arpack )
{
cout << endl;
for (int i=0; i<eigenvalues.Size(); i++)
{
cout << "Eigenvalue lambda " << eigenvalues[i] << endl;
}
cout << endl;
}
ParGridFunction x(fespace);
// 10. Save the refined mesh and the modes in parallel. This output can be
// viewed later using GLVis: "glvis -np <np> -m mesh -g mode".
{
ostringstream mesh_name, mode_name;
mesh_name << "mesh." << setfill('0') << setw(6) << myid;
ofstream mesh_ofs(mesh_name.str().c_str());
mesh_ofs.precision(8);
pmesh->Print(mesh_ofs);
for (int i=0; i<nev; i++)
{
// convert eigenvector from HypreParVector to ParGridFunction
x.Distribute(esolver->GetEigenvector(i));
mode_name << "mode_" << setfill('0') << setw(2) << i << "."
<< setfill('0') << setw(6) << myid;
ofstream mode_ofs(mode_name.str().c_str());
mode_ofs.precision(8);
x.Save(mode_ofs);
mode_name.str("");
}
}
// 11. Send the solution by socket to a GLVis server.
if (visualization)
{
char vishost[] = "localhost";
int visport = 19916;
socketstream mode_sock(vishost, visport);
mode_sock.precision(8);
for (int i=0; i<nev; i++)
{
if ( myid == 0 )
{
cout << "Eigenmode " << i+1 << '/' << nev
<< ", Lambda = " << eigenvalues[i] << endl;
}
// convert eigenvector from HypreParVector to ParGridFunction
x.Distribute(esolver->GetEigenvector(i));
mode_sock << "parallel " << num_procs << " " << myid << "\n"
<< "solution\n" << *pmesh << x << flush
<< "window_title 'Eigenmode " << i+1 << '/' << nev
<< ", Lambda = " << eigenvalues[i] << "'" << endl;
char c;
if (myid == 0)
{
cout << "press (q)uit or (c)ontinue --> " << flush;
cin >> c;
}
MPI_Bcast(&c, 1, MPI_CHAR, 0, MPI_COMM_WORLD);
if (c != 'c')
{
break;
}
}
mode_sock.close();
}
// 12. Free the used memory.
delete esolver;
delete solver;
delete precond;
delete M;
delete A;
delete fespace;
if (order > 0)
{
delete fec;
}
delete pmesh;
MPI_Finalize();
return 0;
}
+5 -5
View File
@@ -276,8 +276,8 @@ int main(int argc, char *argv[])
for (int i=0; i<nev; i++)
{
// convert eigenvector from Vector to ParGridFunction
x.Distribute(lobpcg->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = lobpcg->GetEigenvector(i);
mode_name << "mode_" << setfill('0') << setw(2) << i << "."
<< setfill('0') << setw(6) << myid;
@@ -303,7 +303,7 @@ int main(int argc, char *argv[])
pmesh->Print(adios2output);
for (int i=0; i<nev; i++)
{
x.Distribute(lobpcg->GetEigenvector(i));
x = lobpcg->GetEigenvector(i);
// x is a temporary that must be saved immediately
x.Save(adios2output, "mode_" + std::to_string(i));
}
@@ -326,8 +326,8 @@ int main(int argc, char *argv[])
<< ", Lambda = " << eigenvalues[i] << endl;
}
// convert eigenvector from Vector to ParGridFunction
x.Distribute(lobpcg->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = lobpcg->GetEigenvector(i);
mode_sock << "parallel " << num_procs << " " << myid << "\n"
<< "solution\n" << *pmesh << x << flush
-282
View File
@@ -1,282 +0,0 @@
// MFEM Example 13
//
// Compile with: make ex3p
//
// Sample runs: ex13 -m ../data/star.mesh -s 5
// ex13 -m ../data/square-disc.mesh -o 2 -n 4 // minres fails to conv.
// ex13 -m ../data/beam-hex.mesh
// ex13 -m ../data/square-disc.mesh -rs 1 -s 26
// ex13 -m ../data/square-disc-nurbs.mesh -rs 3 -s 26
// ex13 -m ../data/amr-quad.mesh -o 2 // minres fails to conv.
// ex13 -m ../data/mobius-strip.mesh -n 8
//
// Description: This example code solves a simple 3D electromagnetic
// eigenmode problem corresponding to the second order
// Maxwell equation curl curl E = lambda E with boundary
// condition E x n = 0. We discretize with Nedelec finite
// elements.
//
// The example demonstrates the use of H(curl) finite element
// spaces with the curl-curl and the (vector finite element) mass
// bilinear form, as well as the use of the ARPACK eigenmode
// solver for symmetric matrices using the shift-invert mode.
//
#include "mfem.hpp"
#include <fstream>
#include <iostream>
using namespace std;
using namespace mfem;
#ifdef MFEM_USE_ARPACK
int main(int argc, char *argv[])
{
// 1. Parse command-line options.
const char *mesh_file = "../data/beam-tet.mesh";
int order = 1;
int nev = 5;
int sr = 2;
double sigma = 11.0;
bool visualization = 1;
bool arp_solver = true;
OptionsParser args(argc, argv);
args.AddOption(&mesh_file, "-m", "--mesh",
"Mesh file to use.");
args.AddOption(&order, "-o", "--order",
"Finite element order (polynomial degree).");
args.AddOption(&nev, "-n", "--num-eigs",
"Number of desired eigenmodes.");
args.AddOption(&sr, "-rs", "--refine-serial",
"Number of times to refine the mesh uniformly in serial.");
args.AddOption(&sigma, "-s", "--shift",
"Average of the desired eigenvalue range.");
args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.Parse();
if (!args.Good())
{
args.PrintUsage(cout);
return 1;
}
args.PrintOptions(cout);
// 2. Read the mesh from the given mesh file. We can handle triangular,
// quadrilateral, tetrahedral, hexahedral, surface and volume meshes
// with the same code.
Mesh *mesh;
ifstream imesh(mesh_file);
if (!imesh)
{
cerr << "\nCan not open mesh file: " << mesh_file << '\n' << endl;
return 2;
}
mesh = new Mesh(imesh, 1, 1);
imesh.close();
int dim = mesh->Dimension();
// 3. Refine the mesh to increase the resolution. In this example we do
// 'ref_levels' of uniform refinement.
{
int ref_levels = sr;
for (int l = 0; l < ref_levels; l++)
{
mesh->UniformRefinement();
}
}
// 4. Define a finite element space on the mesh. Here we use the lowest
// order Nedelec finite elements, but we can easily switch
// to higher-order spaces by changing the value of p.
FiniteElementCollection *fec = new ND_FECollection(order, dim);
FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
int size = fespace->GetVSize();
cout << "Number of unknowns: " << size << endl;
cout << "Number of boundary attributes: " << mesh->bdr_attributes.Max()
<< endl;
// 5. Set up the parallel bilinear form corresponding to the EM diffusion
// operator curl muinv curl - sigma I, by adding the curl-curl and the
// mass domain integrators and finally imposing homogeneous Dirichlet
// boundary conditions. The boundary conditions are implemented by
// marking all the boundary attributes from the mesh as essential
// (Dirichlet). After serial and parallel assembly we extract the
// parallel matrices A and M.
Coefficient *muinv = new ConstantCoefficient(1.0);
Coefficient *negSigma = new ConstantCoefficient(-sigma);
BilinearForm *a = new BilinearForm(fespace);
a->AddDomainIntegrator(new CurlCurlIntegrator(*muinv));
a->AddDomainIntegrator(new VectorFEMassIntegrator(*negSigma));
a->Assemble();
Array<int> ess_bdr(mesh->bdr_attributes.Max());
ess_bdr = 1;
a->EliminateEssentialBC(ess_bdr);
a->Finalize();
BilinearForm *m = new BilinearForm(fespace);
m->AddDomainIntegrator(new VectorFEMassIntegrator());
m->Assemble();
m->EliminateEssentialBCDiag(ess_bdr, sqrt(numeric_limits<double>::min()));
m->Finalize();
// 6. Define a parallel grid function to approximate each of the
// eigenmodes returned by the solver. Use this as a template to
// create a special multi-vector object needed by the eigensolver
// which is then initialized with random values.
GridFunction x(fespace);
x = 0.0;
// 7. Define and configure the GMRES
// solver to be used within the eigensolver.
Solver * solver = NULL;
if ( false )
{
GMRESSolver * gmres = new GMRESSolver();
gmres->SetOperator(*a);
gmres->SetRelTol(1e-8);
gmres->SetMaxIter(1000);
gmres->SetPrintLevel(0);
solver = gmres;
}
else
{
#ifndef MFEM_USE_SUITESPARSE
cout << "Building MINRESSolver" << endl;
MINRESSolver * minres = new MINRESSolver();
minres->SetRelTol(1e-12);
minres->SetMaxIter(1000);
minres->SetPrintLevel(0);
solver = minres;
#else
// 7. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
cout << "Building UMFPackSolver" << endl;
UMFPackSolver * umf_solver = new UMFPackSolver;
umf_solver->Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
solver = umf_solver;
#endif
}
solver->SetOperator(a->SpMat());
// 7. Define and configure the ARPACK eigensolver
SymGenEigensolver * eig_solver = NULL;
if (arp_solver)
{
ArPackSAUPD * arpack = new ArPackSAUPD();
arpack->SetNumModes(nev);
arpack->SetMaxIter(400);
arpack->SetTol(1e-8);
arpack->SetShift(sigma);
arpack->SetMode(3);
arpack->SetPrintLevel(2);
arpack->SetSolver(*solver);
eig_solver = arpack;
}
eig_solver->SetOperators(*a, *m);
// Obtain the eigenvalues and eigenvectors
Array<double> eigenvalues(nev);
eigenvalues = -1.0;
// arpack->Solve(eigenvalues, *eigenvectors);
eig_solver->Solve();
eig_solver->GetEigenvalues(eigenvalues);
cout << endl;
std::ios::fmtflags old_fmt = cout.flags();
cout.setf(std::ios::scientific);
std::streamsize old_prec = cout.precision(14);
for (int i=0; i<min(nev,eigenvalues.Size()); i++)
{
cout << "Eigenvalue lambda " << eigenvalues[i] << endl;
}
cout.precision(old_prec);
cout.flags(old_fmt);
cout << endl;
VisItDataCollection visit_dc("Example13", mesh);
GridFunction ** mode = new GridFunction*[min(nev,eigenvalues.Size())];
for (int i=0; i<min(nev,eigenvalues.Size()); i++)
{
mode[i] = new GridFunction(fespace);
*mode[i] = eig_solver->GetEigenvector(i);
ostringstream modeName;
modeName << "mode_" << setfill('0') << setw(2) << i;
visit_dc.RegisterField(modeName.str().c_str(),mode[i]);
}
visit_dc.Save();
// 8. Save the refined mesh and the modes. This output can
// be viewed later using GLVis: "glvis -m mesh -g mode".
{
ofstream mesh_ofs("refined.mesh");
mesh_ofs.precision(8);
mesh->Print(mesh_ofs);
for (int i=0; i<min(nev,eigenvalues.Size()); i++)
{
x = eig_solver->GetEigenvector(i);
ostringstream modeName;
modeName << "mode_" << setfill('0') << setw(2) << i;
ofstream mode_ofs(modeName.str().c_str());
mode_ofs.precision(8);
x.Save(mode_ofs);
modeName.str("");
}
}
// 9. Send the solution by socket to a GLVis server.
if (visualization)
{
char vishost[] = "localhost";
int visport = 19916;
socketstream mode_sock(vishost, visport);
mode_sock.precision(8);
for (int i=0; i<min(nev,eigenvalues.Size()); i++)
{
x = eig_solver->GetEigenvector(i);
mode_sock << "solution\n" << *mesh << x << flush;
char c;
cout << "press (q)uit or (c)ontinue --> " << flush;
cin >> c;
if (c != 'c')
{
break;
}
}
mode_sock.close();
}
// 10. Free the used memory.
delete a;
delete m;
delete negSigma;
delete muinv;
delete eig_solver;
delete solver;
// delete X;
delete fespace;
delete fec;
delete mesh;
return 0;
}
#endif // MFEM_USE_ARPACK
+4 -4
View File
@@ -215,8 +215,8 @@ int main(int argc, char *argv[])
for (int i=0; i<nev; i++)
{
// convert eigenvector from Vector to ParGridFunction
x.Distribute(ame->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = ame->GetEigenvector(i);
mode_name << "mode_" << setfill('0') << setw(2) << i << "."
<< setfill('0') << setw(6) << myid;
@@ -244,8 +244,8 @@ int main(int argc, char *argv[])
<< ", Lambda = " << eigenvalues[i] << endl;
}
// convert eigenvector from Vector to ParGridFunction
x.Distribute(ame->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = ame->GetEigenvector(i);
mode_sock << "parallel " << num_procs << " " << myid << "\n"
<< "solution\n" << *pmesh << x << flush
+4 -4
View File
@@ -228,7 +228,7 @@ int main(int argc, char *argv[])
for (int i=0; i<nev; i++)
{
// convert eigenvector from HypreParVector to ParGridFunction
x.Distribute(ame->GetEigenvector(i));
x = ame->GetEigenvector(i);
curl.Mult(x, dx);
mode_name << "mode_" << setfill('0') << setw(2) << i << "."
@@ -295,7 +295,7 @@ int main(int argc, char *argv[])
}
// convert eigenvector from HypreParVector to ParGridFunction
x.Distribute(ame->GetEigenvector(i));
x = ame->GetEigenvector(i);
curl.Mult(x, dx);
{
@@ -469,7 +469,7 @@ int main(int argc, char *argv[])
}
// convert eigenvector from HypreParVector to ParGridFunction
x.Distribute(ame->GetEigenvector(i));
x = ame->GetEigenvector(i);
curl.Mult(x, dx);
{
@@ -599,7 +599,7 @@ int main(int argc, char *argv[])
}
// convert eigenvector from HypreParVector to ParGridFunction
x.Distribute(ame->GetEigenvector(i));
x = ame->GetEigenvector(i);
curl.Mult(x, dx);
mode_sock << "parallel " << num_procs << " " << myid << "\n"
+3 -3
View File
@@ -658,7 +658,7 @@ void ScalarWaveGuide(int mode, ParGridFunction &x)
lobpcg.SetOperator(*A);
lobpcg.Solve();
x.Distribute(lobpcg.GetEigenvector(mode));
x = lobpcg.GetEigenvector(mode);
delete A;
delete M;
@@ -714,7 +714,7 @@ void VectorWaveGuide(int mode, ParGridFunction &x)
ame.SetOperator(*A);
ame.Solve();
x.Distribute(ame.GetEigenvector(mode));
x = ame.GetEigenvector(mode);
delete A;
delete M;
@@ -780,7 +780,7 @@ void PseudoScalarWaveGuide(int mode, ParGridFunction &x_l2)
lobpcg.SetOperator(*A);
lobpcg.Solve();
x.Distribute(lobpcg.GetEigenvector(mode));
x = lobpcg.GetEigenvector(mode);
x_l2.ProjectCoefficient(xCoef);
+52 -11
View File
@@ -5,8 +5,8 @@
// Sample runs:
// ex37 -alpha 10
// ex37 -alpha 10 -pv
// ex37 -lambda 0.1 -mu 0.1 -growth 1
// ex37 -o 2 -alpha 10.0 -mi 50 -vf 0.4 -ntol 1e-5 -growth 1.5
// ex37 -lambda 0.1 -mu 0.1
// ex37 -o 2 -alpha 5.0 -mi 50 -vf 0.4 -ntol 1e-5
// ex37 -r 6 -o 1 -alpha 25.0 -epsilon 0.02 -mi 50 -ntol 1e-5
//
// Description: This example code demonstrates the use of MFEM to solve a
@@ -55,6 +55,53 @@
using namespace std;
using namespace mfem;
/**
* @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace
* ∫_Ω ρ dx = θ vol(Ω) as follows:
*
* 1. Compute the root of the R → R function
* f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω)
* 2. Set ψ ← ψ + c.
*
* @param psi a GridFunction to be updated
* @param target_volume θ vol(Ω)
* @param tol Newton iteration tolerance
* @param max_its Newton maximum iteration number
* @return real_t Final volume, ∫_Ω sigmoid(ψ)
*/
real_t proj(GridFunction &psi, real_t target_volume, real_t tol=1e-12,
int max_its=10)
{
MappedGridFunctionCoefficient sigmoid_psi(&psi, sigmoid);
MappedGridFunctionCoefficient der_sigmoid_psi(&psi, der_sigmoid);
LinearForm int_sigmoid_psi(psi.FESpace());
int_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(sigmoid_psi));
LinearForm int_der_sigmoid_psi(psi.FESpace());
int_der_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(
der_sigmoid_psi));
bool done = false;
for (int k=0; k<max_its; k++) // Newton iteration
{
int_sigmoid_psi.Assemble(); // Recompute f(c) with updated ψ
const real_t f = int_sigmoid_psi.Sum() - target_volume;
int_der_sigmoid_psi.Assemble(); // Recompute df(c) with updated ψ
const real_t df = int_der_sigmoid_psi.Sum();
const real_t dc = -f/df;
psi += dc;
if (abs(dc) < tol) { done = true; break; }
}
if (!done)
{
mfem_warning("Projection reached maximum iteration without converging. "
"Result may not be accurate.");
}
int_sigmoid_psi.Assemble();
return int_sigmoid_psi.Sum();
}
/*
* ---------------------------------------------------------------
* ALGORITHM PREAMBLE
@@ -133,11 +180,10 @@ int main(int argc, char *argv[])
int ref_levels = 5;
int order = 2;
real_t alpha = 1.0;
real_t growth = 2;
real_t epsilon = 0.01;
real_t vol_fraction = 0.5;
int max_it = 1e3;
real_t itol = 1e-2;
real_t itol = 1e-1;
real_t ntol = 1e-4;
real_t rho_min = 1e-6;
real_t lambda = 1.0;
@@ -152,8 +198,6 @@ int main(int argc, char *argv[])
"Order (degree) of the finite elements.");
args.AddOption(&alpha, "-alpha", "--alpha-step-length",
"Step length for gradient descent.");
args.AddOption(&growth, "-growth", "--alpha-growth-rate",
"Growth rate of step length for gradient descent.");
args.AddOption(&epsilon, "-epsilon", "--epsilon-thickness",
"Length scale for ρ.");
args.AddOption(&max_it, "-mi", "--max-it",
@@ -288,7 +332,6 @@ int main(int argc, char *argv[])
}
FilterSolver->SetEssentialBoundary(ess_bdr_filter);
FilterSolver->SetupFEM();
FilterSolver->AssembleDiffusionBilinear();
BilinearForm mass(&control_fes);
mass.AddDomainIntegrator(new InverseIntegrator(new MassIntegrator(one)));
@@ -342,7 +385,7 @@ int main(int argc, char *argv[])
// 11. Iterate:
for (int k = 1; k <= max_it; k++)
{
if (k > 1) { alpha = std::pow((real_t) k,growth); }
if (k > 1) { alpha *= ((real_t) k) / ((real_t) k-1); }
mfem::out << "\nStep = " << k << std::endl;
@@ -379,9 +422,7 @@ int main(int argc, char *argv[])
// Step 5 - Update design variable ψ ← proj(ψ - αG)
psi.Add(-alpha, grad);
GridFunction alpha_grad(grad);
alpha_grad *= alpha;
const real_t material_volume = proj(psi, alpha_grad, target_volume);
const real_t material_volume = proj(psi, target_volume);
// Compute ||ρ - ρ_old|| in control fes.
real_t norm_increment = zerogf.ComputeL1Error(succ_diff_rho);
+23 -183
View File
@@ -137,7 +137,7 @@ public:
exponent(exponent_), rho_min(rho_min_)
{
MFEM_ASSERT(rho_min_ >= 0.0, "rho_min must be >= 0");
MFEM_ASSERT(rho_min_ < 1.0, "rho_min must be < 1");
MFEM_ASSERT(rho_min_ < 1.0, "rho_min must be > 1");
MFEM_ASSERT(u, "displacement field is not set");
MFEM_ASSERT(rho_filter, "density field is not set");
}
@@ -231,12 +231,9 @@ private:
FiniteElementCollection * fec = nullptr;
FiniteElementSpace * fes = nullptr;
Array<int> ess_bdr;
Array<int> ess_tdof_list;
Array<int> neumann_bdr;
GridFunction * u = nullptr;
LinearForm * b = nullptr;
BilinearForm * a = nullptr;
OperatorPtr A;
bool parallel;
#ifdef MFEM_USE_MPI
ParMesh * pmesh = nullptr;
@@ -270,8 +267,6 @@ public:
void ResetFEM();
void SetupFEM();
void UpdateEssentialTDofs();
void AssembleDiffusionBilinear(bool update_ess_tdofs=true);
void Solve();
GridFunction * GetFEMSolution();
LinearForm * GetLinearForm() {return b;}
@@ -376,130 +371,6 @@ public:
};
/**
* @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace
* ∫_Ω ρ dx = θ vol(Ω) as follows:
*
* 1. Compute the root of the R → R function
* f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω)
* using the Illinois method
* 2. Set ψ ← ψ + c.
*
* @param psi a GridFunction to be updated
* @param alpha_grad alpha multiplied by gradient
* @param target_volume θ vol(Ω)
* @param tol Illinois iteration tolerance
* @param max_its Illinois maximum iteration number
* @return real_t Final volume (∫_Ω sigmoid(ψ) dx)
*/
real_t proj(GridFunction &psi, GridFunction &alpha_grad, real_t target_volume,
real_t tol = 1e-12, int max_its = 100)
{
#ifdef MFEM_USE_MPI
FiniteElementSpace *fes = psi.FESpace();
ParFiniteElementSpace *pfes = dynamic_cast<ParFiniteElementSpace*>(fes);
#endif
ConstantCoefficient zero_cf(0.0);
real_t a = -alpha_grad.ComputeMaxError(zero_cf);
real_t b = -a;
real_t y = 0.0;
MappedGridFunctionCoefficient sigmoid_psi(
&psi, [&y](const real_t x) { return sigmoid(x + y); });
std::unique_ptr<LinearForm> int_sigmoid_psi;
#ifdef MFEM_USE_MPI
ParGridFunction *par_psi = dynamic_cast<ParGridFunction *>(&psi);
if (par_psi)
{
int_sigmoid_psi.reset(new ParLinearForm(par_psi->ParFESpace()));
}
else
{
int_sigmoid_psi.reset(new LinearForm(psi.FESpace()));
}
#else
int_sigmoid_psi.reset(new LinearForm(psi.FESpace()));
#endif
int_sigmoid_psi->AddDomainIntegrator(new DomainLFIntegrator(sigmoid_psi));
y = a;
int_sigmoid_psi->Assemble();
real_t f_a = int_sigmoid_psi->Sum(); // f_a := f(a) + θ vol(Ω)
y = b;
int_sigmoid_psi->Assemble();
real_t f_b = int_sigmoid_psi->Sum(); // f_b := f(b) + θ vol(Ω)
#ifdef MFEM_USE_MPI
if (pfes)
{
MPI_Allreduce(MPI_IN_PLACE, &f_a, 1, MPITypeMap<real_t>::mpi_type,
MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(MPI_IN_PLACE, &f_b, 1, MPITypeMap<real_t>::mpi_type,
MPI_SUM, MPI_COMM_WORLD);
}
#endif
f_a -= target_volume; // f_a := f(a)
f_b -= target_volume; // f_b := f(b)
real_t c = 0.0;
real_t f_c = 0.0;
int side = 0;
bool done = false;
for (int k=0; k < max_its; k++)
{
c = (f_a * b - f_b * a) / (f_a - f_b);
if (abs(b - a) < tol * abs(b + a)) { done = true; break; }
y = c;
int_sigmoid_psi->Assemble();
f_c = int_sigmoid_psi->Sum(); // f_c := f(c) + θ vol(Ω)
#ifdef MFEM_USE_MPI
if (pfes)
{
MPI_Allreduce(MPI_IN_PLACE, &f_c, 1, MPITypeMap<real_t>::mpi_type,
MPI_SUM, MPI_COMM_WORLD);
}
#endif
f_c -= target_volume; // f_c := f(c)
if (f_c * f_b > 0)
{
b = c;
f_b = f_c;
if (side == -1) { f_a /= 2.0; }
side = -1;
}
else if (f_c * f_a > 0)
{
a = c;
f_a = f_c;
if (side == 1) { f_b /= 2.0; }
side = 1;
}
else
{
done = true; break;
}
}
if (!done)
{
mfem_warning("Projection reached maximum iteration without converging. "
"Result may not be accurate.");
}
y = 0.0;
psi += c;
int_sigmoid_psi->Assemble();
real_t material_volume = int_sigmoid_psi->Sum();
#ifdef MFEM_USE_MPI
if (pfes)
{
MPI_Allreduce(MPI_IN_PLACE, &material_volume, 1,
MPITypeMap<real_t>::mpi_type, MPI_SUM, MPI_COMM_WORLD);
}
#endif
return material_volume;
}
// Poisson solver
@@ -551,8 +422,12 @@ void DiffusionSolver::SetupFEM()
}
}
void DiffusionSolver::UpdateEssentialTDofs()
void DiffusionSolver::Solve()
{
OperatorPtr A;
Vector B, X;
Array<int> ess_tdof_list;
#ifdef MFEM_USE_MPI
if (parallel)
{
@@ -565,39 +440,7 @@ void DiffusionSolver::UpdateEssentialTDofs()
#else
fes->GetEssentialTrueDofs(ess_bdr,ess_tdof_list);
#endif
}
void DiffusionSolver::AssembleDiffusionBilinear(bool update_ess_tdofs)
{
if (update_ess_tdofs)
{
UpdateEssentialTDofs();
}
#ifdef MFEM_USE_MPI
if (parallel)
{
a = new ParBilinearForm(pfes);
}
else
{
a = new BilinearForm(fes);
}
#else
a = new BilinearForm(fes);
#endif
a->AddDomainIntegrator(new DiffusionIntegrator(*diffcf));
if (masscf)
{
a->AddDomainIntegrator(new MassIntegrator(*masscf));
}
a->Assemble();
a->FormSystemMatrix(ess_tdof_list, A);
}
void DiffusionSolver::Solve()
{
Vector B, X;
*u=0.0;
if (b)
{
delete b;
@@ -632,33 +475,31 @@ void DiffusionSolver::Solve()
b->Assemble();
*u=0.0;
if (essbdr_cf)
{
u->ProjectBdrCoefficient(*essbdr_cf,ess_bdr);
}
BilinearForm * a = nullptr;
#ifdef MFEM_USE_MPI
if (parallel)
{
X.SetSize(pfes->TrueVSize());
B.SetSize(pfes->TrueVSize());
dynamic_cast<ParGridFunction*>(u)->ParallelAssemble(X);
dynamic_cast<ParLinearForm*>(b)->ParallelAssemble(B);
dynamic_cast<ParBilinearForm*>(a)->ParallelEliminateTDofsInRHS(
ess_tdof_list, X, B);
a = new ParBilinearForm(pfes);
}
else
{
X.NewDataAndSize(u->GetData(), u->Size());
B.NewDataAndSize(b->GetData(), b->Size());
a->EliminateVDofsInRHS(ess_tdof_list, X, B);
a = new BilinearForm(fes);
}
#else
X.NewDataAndSize(u->GetData(), u->Size());
B.NewDataAndSize(b->GetData(), b->Size());
a->EliminateVDofsInRHS(ess_tdof_list, X, B);
a = new BilinearForm(fes);
#endif
a->AddDomainIntegrator(new DiffusionIntegrator(*diffcf));
if (masscf)
{
a->AddDomainIntegrator(new MassIntegrator(*masscf));
}
a->Assemble();
if (essbdr_cf)
{
u->ProjectBdrCoefficient(*essbdr_cf,ess_bdr);
}
a->FormLinearSystem(ess_tdof_list, *u, *b, A, X, B);
CGSolver * cg = nullptr;
Solver * M = nullptr;
@@ -687,6 +528,7 @@ void DiffusionSolver::Solve()
delete M;
delete cg;
a->RecoverFEMSolution(X, *b, *u);
delete a;
}
GridFunction * DiffusionSolver::GetFEMSolution()
@@ -718,8 +560,6 @@ DiffusionSolver::~DiffusionSolver()
#endif
delete fec; fec = nullptr;
delete b;
A.Clear();
delete a;
}
+60 -11
View File
@@ -4,8 +4,8 @@
//
// Sample runs:
// mpirun -np 4 ex37p -alpha 10 -pv
// mpirun -np 4 ex37p -lambda 0.1 -mu 0.1 -growth 1
// mpirun -np 4 ex37p -o 2 -alpha 10.0 -mi 50 -vf 0.4 -ntol 1e-5 -growth 1.5
// mpirun -np 4 ex37p -lambda 0.1 -mu 0.1
// mpirun -np 4 ex37p -o 2 -alpha 5.0 -mi 50 -vf 0.4 -ntol 1e-5
// mpirun -np 4 ex37p -r 6 -o 2 -alpha 10.0 -epsilon 0.02 -mi 50 -ntol 1e-5
//
// Description: This example code demonstrates the use of MFEM to solve a
@@ -54,6 +54,61 @@
using namespace std;
using namespace mfem;
/**
* @brief Bregman projection of ρ = sigmoid(ψ) onto the subspace
* ∫_Ω ρ dx = θ vol(Ω) as follows:
*
* 1. Compute the root of the R → R function
* f(c) = ∫_Ω sigmoid(ψ + c) dx - θ vol(Ω)
* 2. Set ψ ← ψ + c.
*
* @param psi a GridFunction to be updated
* @param target_volume θ vol(Ω)
* @param tol Newton iteration tolerance
* @param max_its Newton maximum iteration number
* @return real_t Final volume, ∫_Ω sigmoid(ψ)
*/
real_t proj(ParGridFunction &psi, real_t target_volume, real_t tol=1e-12,
int max_its=10)
{
MappedGridFunctionCoefficient sigmoid_psi(&psi, sigmoid);
MappedGridFunctionCoefficient der_sigmoid_psi(&psi, der_sigmoid);
ParLinearForm int_sigmoid_psi(psi.ParFESpace());
int_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(sigmoid_psi));
ParLinearForm int_der_sigmoid_psi(psi.ParFESpace());
int_der_sigmoid_psi.AddDomainIntegrator(new DomainLFIntegrator(
der_sigmoid_psi));
bool done = false;
for (int k=0; k<max_its; k++) // Newton iteration
{
int_sigmoid_psi.Assemble(); // Recompute f(c) with updated ψ
real_t f = int_sigmoid_psi.Sum();
MPI_Allreduce(MPI_IN_PLACE, &f, 1, MPITypeMap<real_t>::mpi_type,
MPI_SUM, MPI_COMM_WORLD);
f -= target_volume;
int_der_sigmoid_psi.Assemble(); // Recompute df(c) with updated ψ
real_t df = int_der_sigmoid_psi.Sum();
MPI_Allreduce(MPI_IN_PLACE, &df, 1, MPITypeMap<real_t>::mpi_type,
MPI_SUM, MPI_COMM_WORLD);
const real_t dc = -f/df;
psi += dc;
if (abs(dc) < tol) { done = true; break; }
}
if (!done)
{
mfem_warning("Projection reached maximum iteration without converging. "
"Result may not be accurate.");
}
int_sigmoid_psi.Assemble();
real_t material_volume = int_sigmoid_psi.Sum();
MPI_Allreduce(MPI_IN_PLACE, &material_volume, 1,
MPITypeMap<real_t>::mpi_type, MPI_SUM, MPI_COMM_WORLD);
return material_volume;
}
/*
* ---------------------------------------------------------------
* ALGORITHM PREAMBLE
@@ -138,11 +193,10 @@ int main(int argc, char *argv[])
int ref_levels = 5;
int order = 2;
real_t alpha = 1.0;
real_t growth = 2;
real_t epsilon = 0.01;
real_t vol_fraction = 0.5;
int max_it = 1e3;
real_t itol = 1e-2;
real_t itol = 1e-1;
real_t ntol = 1e-4;
real_t rho_min = 1e-6;
real_t lambda = 1.0;
@@ -157,8 +211,6 @@ int main(int argc, char *argv[])
"Order (degree) of the finite elements.");
args.AddOption(&alpha, "-alpha", "--alpha-step-length",
"Step length for gradient descent.");
args.AddOption(&growth, "-growth", "--alpha-growth-rate",
"Growth rate of step length for gradient descent.");
args.AddOption(&epsilon, "-epsilon", "--epsilon-thickness",
"Length scale for ρ.");
args.AddOption(&max_it, "-mi", "--max-it",
@@ -307,7 +359,6 @@ int main(int argc, char *argv[])
}
FilterSolver->SetEssentialBoundary(ess_bdr_filter);
FilterSolver->SetupFEM();
FilterSolver->AssembleDiffusionBilinear();
ParBilinearForm mass(&control_fes);
mass.AddDomainIntegrator(new InverseIntegrator(new MassIntegrator(one)));
@@ -361,7 +412,7 @@ int main(int argc, char *argv[])
// 11. Iterate:
for (int k = 1; k <= max_it; k++)
{
if (k > 1) { alpha = std::pow((real_t) k,growth); }
if (k > 1) { alpha *= ((real_t) k) / ((real_t) k-1); }
if (myid == 0)
{
@@ -401,9 +452,7 @@ int main(int argc, char *argv[])
// Step 5 - Update design variable ψ ← proj(ψ - αG)
psi.Add(-alpha, grad);
ParGridFunction alpha_grad(grad);
alpha_grad *= alpha;
const real_t material_volume = proj(psi, alpha_grad, target_volume);
const real_t material_volume = proj(psi, target_volume);
// Compute ||ρ - ρ_old|| in control fes.
real_t norm_increment = zerogf.ComputeL1Error(succ_diff_rho);
+6 -4
View File
@@ -433,16 +433,18 @@ int main(int argc, char *argv[])
u.ProjectCoefficient(*u0);
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example41", &mesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example41", &mesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+5 -3
View File
@@ -518,10 +518,12 @@ int main(int argc, char *argv[])
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example41-Parallel", pmesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example41-Parallel", pmesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+6 -4
View File
@@ -305,16 +305,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9", &mesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9", &mesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+6 -4
View File
@@ -441,16 +441,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9-Parallel", pmesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9-Parallel", pmesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+6 -4
View File
@@ -354,16 +354,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9", mesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9", mesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+6 -4
View File
@@ -414,16 +414,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9-Parallel", pmesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9-Parallel", pmesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
-5
View File
@@ -31,9 +31,6 @@ SEQ_DEVICE_EXAMPLES = ex1 ex3 ex4 ex5 ex6 ex9 ex14 ex22 ex24 ex25 ex26 ex34
PAR_DEVICE_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex14p \
ex22p ex24p ex25p ex26p ex34p ex35p
ifeq ($(MFEM_USE_ARPACK),YES)
SEQ_EXAMPLES += ex11 ex13
endif
ifeq ($(MFEM_USE_LAPACK),YES)
SEQ_EXAMPLES += ex38
endif
@@ -160,8 +157,6 @@ ex37-test-seq: ex37
@$(call mfem-test,$<,, Serial example,-mi 3)
ex37p-test-par: ex37p
@$(call mfem-test,$<, $(RUN_MPI), Parallel example,-mi 3)
ex39-test-seq: ex39
@$(call mfem-test,$<,, Serial example,-m ../data/compass.mesh)
ex41-test-seq: ex41
@$(call mfem-test,$<,, Serial example,-tf 1.0)
ex41p-test-par: ex41p
+6 -4
View File
@@ -368,16 +368,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9-Parallel", pmesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9-Parallel", pmesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+6 -4
View File
@@ -316,16 +316,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9", &mesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9", &mesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
+6 -4
View File
@@ -453,16 +453,18 @@ int main(int argc, char *argv[])
}
// Create data collection for solution output: either VisItDataCollection for
// ascii data files, or SidreDataCollection for binary data files.
// ascii data files, or ConduitDataCollection for binary data files.
DataCollection *dc = NULL;
if (visit)
{
if (binary)
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection("Example9-Parallel", pmesh);
#ifdef MFEM_USE_CONDUIT
auto conduit_dc = new ConduitDataCollection("Example9-Parallel", pmesh);
conduit_dc->SetProtocol("hdf5");
dc = conduit_dc;
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for binary output.");
MFEM_ABORT("Must build with MFEM_USE_CONDUIT=YES for binary output.");
#endif
}
else
-5
View File
@@ -312,11 +312,6 @@ set(HDRS
particleset.hpp
)
if (MFEM_USE_SIDRE)
list(APPEND SRCS sidredatacollection.cpp)
list(APPEND HDRS sidredatacollection.hpp)
endif()
if (MFEM_USE_CONDUIT)
list(APPEND SRCS conduitdatacollection.cpp)
list(APPEND HDRS conduitdatacollection.hpp)
-3
View File
@@ -52,9 +52,6 @@ public:
/// Get the time for time dependent coefficients
real_t GetTime() { return time; }
/// Returns dimension of the vector.
int GetVDim() { return 1; }
/** @brief Evaluate the coefficient in the element described by @a T at the
point @a ip. */
/** @note When this method is called, the caller must make sure that the
-2
View File
@@ -1453,8 +1453,6 @@ ConduitDataCollection::LoadMeshAndFields(int domain_id,
std::string
ConduitDataCollection::ElementTypeToShapeName(Element::Type element_type)
{
// Adapted from SidreDataCollection
// Note -- the mapping from Element::Type to string is based on
// enum Element::Type { POINT, SEGMENT, TRIANGLE, QUADRILATERAL,
// TETRAHEDRON, HEXAHEDRON };
+4 -4
View File
@@ -34,10 +34,10 @@ namespace mfem
- HDF5 library, https://support.hdfgroup.org/HDF5
@note The ConduitDataCollection only wraps the mfem objects to save them and
creates them on load, Conduit does not own any of the data. The
SidreDataCollection provides more features, for example the
SidreDataCollection allocates and will own the data backing the mfem objects
in the data collection.
creates them on load, Conduit does not own any of the data.
The MFEMSidreDataCollection in the Axom package (https://github.com/LLNL/axom)
derives from mfem::DataCollection and provides more features, for example
it allocates and will own the data backing the mfem objects in the data collection.
This class also provides public static methods that convert between MFEM
Meshes and GridFunctions and Conduit Mesh Blueprint descriptions.
+5 -18
View File
@@ -492,8 +492,6 @@ void VisItDataCollection::SaveRootFile()
to_padded_string(cycle, pad_digits_cycle) +
".mfem_root";
std::ofstream root_file(root_name);
MFEM_VERIFY(root_file.is_open(),
"Failed to open ofstream " << root_name);
root_file << GetVisItRootString();
if (!root_file)
{
@@ -979,10 +977,7 @@ void ParaViewDataCollection::Save()
// Save the local part of the mesh and grid functions fields to the local
// VTU file. Also save coefficient fields.
{
std::string os_str = vtu_prefix + GenerateVTUFileName("proc", myid);
std::ofstream os(os_str);
MFEM_VERIFY(os.is_open(),
"Failed to open ofstream " << os_str);
std::ofstream os(vtu_prefix + GenerateVTUFileName("proc", myid));
os.precision(precision);
SaveDataVTU(os, levels_of_detail);
}
@@ -994,10 +989,7 @@ void ParaViewDataCollection::Save()
"QuadratureFunction output is not supported for "
"ParaViewDataCollection on domain boundary!");
const std::string &field_name = qfield.first;
std::string os_str = vtu_prefix + GenerateVTUFileName(field_name, myid);
std::ofstream os(os_str);
MFEM_VERIFY(os.is_open(),
"Failed to open ofstream " << os_str);
std::ofstream os(vtu_prefix + GenerateVTUFileName(field_name, myid));
qfield.second->SaveVTU(os, pv_data_format, GetCompressionLevel(), field_name);
}
@@ -1008,10 +1000,7 @@ void ParaViewDataCollection::Save()
{
// Create the main PVTU file
{
std::string os_str = vtu_prefix + GeneratePVTUFileName("data");
std::ofstream pvtu_out(os_str);
MFEM_VERIFY(pvtu_out.is_open(),
"Failed to open ofstream " << os_str);
std::ofstream pvtu_out(vtu_prefix + GeneratePVTUFileName("data"));
WritePVTUHeader(pvtu_out);
// Grid function fields and coefficient fields
@@ -1066,10 +1055,8 @@ void ParaViewDataCollection::Save()
const std::string &q_field_name = q_field.first;
std::string q_fname = GeneratePVTUPath() + "/"
+ GeneratePVTUFileName(q_field_name);
std::string os_str = col_path + "/" + q_fname;
std::ofstream pvtu_out(os_str);
MFEM_VERIFY(pvtu_out.is_open(),
"Failed to open ofstream " << os_str);
std::ofstream pvtu_out(col_path + "/" + q_fname);
WritePVTUHeader(pvtu_out);
int vec_dim = q_field.second->GetVDim();
pvtu_out << "<PPointData>\n";
+6 -6
View File
@@ -320,8 +320,8 @@ public:
error estimation procedure where the flux averaging is replaced by a global
L2 projection (requiring a mass matrix solve).
The required BilinearFormIntegrator must implement the method
ComputeElementFlux().
The required BilinearFormIntegrator must implement the methods
ComputeElementFlux() and ComputeFluxEnergy().
Implemented for the parallel case only.
*/
@@ -357,8 +357,8 @@ protected:
public:
/** @brief Construct a new L2ZienkiewiczZhuEstimator object.
@param integ This BilinearFormIntegrator must implement the method
ComputeElementFlux().
@param integ This BilinearFormIntegrator must implement the methods
ComputeElementFlux() and ComputeFluxEnergy().
@param sol The solution field whose error is to be estimated.
@param flux_fes The L2ZienkiewiczZhuEstimator assumes ownership of this
FiniteElementSpace and will call its Update() method when
@@ -382,8 +382,8 @@ public:
{ }
/** @brief Construct a new L2ZienkiewiczZhuEstimator object.
@param integ This BilinearFormIntegrator must implement the method
ComputeElementFlux().
@param integ This BilinearFormIntegrator must implement the methods
ComputeElementFlux() and ComputeFluxEnergy().
@param sol The solution field whose error is to be estimated.
@param flux_fes The L2ZienkiewiczZhuEstimator does NOT assume ownership
of this FiniteElementSpace; will call its Update() method
-4
View File
@@ -62,10 +62,6 @@
#include "pnonlinearform.hpp"
#endif
#ifdef MFEM_USE_SIDRE
#include "sidredatacollection.hpp"
#endif
#ifdef MFEM_USE_CONDUIT
#include "conduitdatacollection.hpp"
#endif
+11 -11
View File
@@ -3030,14 +3030,10 @@ void GridFunction::ProjectCoefficient(Coefficient *coeff[])
}
}
void GridFunction::ProjectDiscCoefficient(
std::variant<Coefficient*, VectorCoefficient*> coeff, Array<int> &dof_attr)
void GridFunction::ProjectDiscCoefficient(VectorCoefficient &coeff,
Array<int> &dof_attr)
{
std::visit([&](auto* c)
{
MFEM_VERIFY(VectorDim() == c->GetVDim(), "coeff vdim != VectorDim()");
}, coeff);
MFEM_VERIFY(VectorDim() == coeff.GetVDim(), "coeff vdim != VectorDim()");
Array<int> vdofs;
Vector vals;
@@ -3051,10 +3047,7 @@ void GridFunction::ProjectDiscCoefficient(
{
fes->GetElementVDofs(i, vdofs);
vals.SetSize(vdofs.Size());
std::visit([&](auto* c)
{
fes->GetFE(i)->Project(*c, *fes->GetElementTransformation(i), vals);
}, coeff);
fes->GetFE(i)->Project(coeff, *fes->GetElementTransformation(i), vals);
// the values in shared dofs are determined from the element with maximal
// attribute
@@ -3070,6 +3063,13 @@ void GridFunction::ProjectDiscCoefficient(
}
}
void GridFunction::ProjectDiscCoefficient(VectorCoefficient &coeff)
{
MFEM_VERIFY(VectorDim() == coeff.GetVDim(), "coeff vdim != VectorDim()");
Array<int> dof_attr;
ProjectDiscCoefficient(coeff, dof_attr);
}
void GridFunction::ProjectDiscCoefficient(Coefficient &coeff, AvgType type)
{
// Harmonic (x1 ... xn) = [ (1/x1 + ... + 1/xn) / n ]^-1.
+5 -21
View File
@@ -23,7 +23,6 @@
#include <limits>
#include <ostream>
#include <string>
#include <variant>
namespace mfem
{
@@ -80,18 +79,10 @@ protected:
bool wcoef,
int subdomain);
/** @brief Project a discontinuous (vector) coefficient as a grid function on
a continuous finite element space. Return in dof_attr the maximal
attribute of the elements containing each degree of freedom. */
virtual void ProjectDiscCoefficient(
std::variant<Coefficient*, VectorCoefficient*> coeff, Array<int> &dof_attr);
/** @brief Project a discontinuous (vector) coefficient as a grid function on
a continuous finite element space. The values in shared dofs are
determined from the element with maximal attribute. */
virtual void ProjectDiscCoefficient(
std::variant<Coefficient*, VectorCoefficient*> coeff)
{ Array<int> dof_attr; ProjectDiscCoefficient(coeff, dof_attr); };
/** Project a discontinuous vector coefficient in a continuous space and
return in dof_attr the maximal attribute of the elements containing each
degree of freedom. */
void ProjectDiscCoefficient(VectorCoefficient &coeff, Array<int> &dof_attr);
/** Helper function for ProjectCoefficientElementL2 */
void ProjectCoefficientElementL2_(Coefficient &coeff, Vector &sol, Vector &Va);
@@ -524,17 +515,10 @@ public:
but using an array of scalar coefficients for each component. */
void ProjectCoefficient(Coefficient *coeff[]);
/** @brief Project a discontinuous coefficient as a grid function on
a continuous finite element space. The values in shared dofs are
determined from the element with maximal attribute. */
virtual void ProjectDiscCoefficient(Coefficient &coeff)
{ ProjectDiscCoefficient(&coeff); }
/** @brief Project a discontinuous vector coefficient as a grid function on
a continuous finite element space. The values in shared dofs are
determined from the element with maximal attribute. */
virtual void ProjectDiscCoefficient(VectorCoefficient &coeff)
{ ProjectDiscCoefficient(&coeff); }
virtual void ProjectDiscCoefficient(VectorCoefficient &coeff);
enum AvgType {ARITHMETIC, HARMONIC};
/** @brief Projects a discontinuous coefficient so that the values in shared
+5 -6
View File
@@ -490,7 +490,7 @@ void FindPointsGSLIB::FindPointsOnDevice(const Vector &point_pos,
}
DEV.find_device = true;
const unsigned int id = gsl_comm->id, np = gsl_comm->np;
const int id = gsl_comm->id, np = gsl_comm->np;
gsl_mfem_ref.SetSize(points_cnt * dim);
gsl_mfem_elem.SetSize(points_cnt);
@@ -652,7 +652,7 @@ void FindPointsGSLIB::FindPointsOnDevice(const Vector &point_pos,
{
const int pp = hash_offset[i];
/* don't send back to where it just came from */
if (static_cast<unsigned>(pp) == p->proc)
if (pp == p->proc)
{
continue;
}
@@ -1068,7 +1068,7 @@ void FindPointsGSLIB::InterpolateOnDevice(const Vector &field_in_evec,
sarray_transfer(struct evalOutPt_t, &outpt, proc, 1, cr);
opt = (evalOutPt_t *)outpt.ptr;
for (size_t index = 0; index < outpt.n; index++)
for (int index = 0; index < outpt.n; index++)
{
int idx = ordering == Ordering::byNODES ?
opt->index + i*points_cnt :
@@ -1413,7 +1413,7 @@ void FindPointsGSLIB::SetupSplitMeshesAndIntegrationRules(const int order)
{
MFEM_VERIFY(mesh, "Setup FindPointsGSLIB with mesh first.");
const int dof1D = order+1;
dim = mesh->Dimension();
const int dim = mesh->Dimension();
SetupSplitMeshes();
if (dim == 2)
@@ -2254,8 +2254,7 @@ void FindPointsGSLIB::DistributeInterpolatedValues(const Vector &int_vals,
sarray_transfer(struct out_pt, outpt, proc, 1, cr);
// Store received data
MFEM_VERIFY(outpt->n == static_cast<size_t>(points_cnt),
"Incompatible size. Number of points "
MFEM_VERIFY(outpt->n == points_cnt, "Incompatible size. Number of points "
"received does not match the number of points originally "
"found using FindPoints.");
-6
View File
@@ -202,19 +202,13 @@ protected:
const int dof1dsol, const int ordering);
public:
/// Serial constructor
FindPointsGSLIB();
/// Serial constructor + setup with given Mesh (see \ref Setup)
FindPointsGSLIB(Mesh &mesh_in, const double bb_t = 0.1,
const double newt_tol = 1.0e-12,
const int npt_max = 256);
#ifdef MFEM_USE_MPI
/// Constructor for ParMesh
FindPointsGSLIB(MPI_Comm comm_);
/// Constructor + setup with given ParMesh (see \ref Setup)
FindPointsGSLIB(ParMesh &mesh_in, const double bb_t = 0.1,
const double newt_tol = 1.0e-12,
const int npt_max = 256);
+1 -1
View File
@@ -254,7 +254,7 @@ get_edge(const double *elx[2], const double *wtend, int ei,
edge.dxdn[d] = workspace + (2 + d) * pN; //dxdn and dydn at DOFs along edge
}
if (static_cast<unsigned>(side_init) != (1u << ei))
if (side_init != (1u << ei))
{
#define ELX(d, j, k) elx[d][j + k * pN] // assumes lexicographic ordering
for (int d = 0; d < 2; ++d)
+2 -2
View File
@@ -294,7 +294,7 @@ get_face(const double *elx[3], const double *wtend, int fi, double *workspace,
face.dxdn[d] = workspace+(3+d)*p_Nfr;
}
if (static_cast<unsigned>(side_init) != (1u << fi))
if (side_init != (1u << fi))
{
const int e_stride[3] = {1, pN, pN*pN};
#define ELX(d, j, k, l) elx[d][j*e_stride[d1]+k*e_stride[d2]+l*e_stride[dn]]
@@ -342,7 +342,7 @@ get_edge(const double *elx[3], const double *wtend, int ei, double *workspace,
if (jidx >= 3*pN) { return edge; }
if (static_cast<unsigned>(side_init) != (64u << ei))
if (side_init != (64u << ei))
{
const int e_stride[3] = {1, pN, pN*pN};
#define ELX(d, j, k, l) elx[d][j*e_stride[de]+k*e_stride[dn1]+l*e_stride[dn2]]
+37 -33
View File
@@ -43,52 +43,56 @@ public:
index = i;
}
void Set3w(const real_t x1, const real_t x2, const real_t x3, const real_t w)
{ x = x1; y = x2; z = x3; weight = w; }
void Set2w(const real_t x1, const real_t x2, const real_t w)
{ x = x1; y = x2; weight = w; }
void Set1w(const real_t x1, const real_t w)
{ x = x1; weight = w; }
void Set3w(const real_t *p) { Set3w(p[0], p[1], p[2], p[3]); }
void Set2w(const real_t *p) { Set2w(p[0], p[1], p[2]); }
void Set1w(const real_t *p) { Set1w(p[0], p[1]); }
void Set3(const real_t x1, const real_t x2, const real_t x3)
{ x = x1; y = x2; z = x3; }
void Set2(const real_t x1, const real_t x2)
{ x = x1; y = x2; }
void Set1(const real_t x1)
{ x = x1; }
void Set3(const real_t *p) { Set3(p[0], p[1], p[2]); }
void Set2(const real_t *p) { Set2(p[0], p[1]); }
void Set1(const real_t *p) { Set1(p[0]); }
void Set(const real_t x1, const real_t x2, const real_t x3, const real_t w)
{ Set3w(x1, x2, x3, w); }
void Set(const real_t *p, const int dim)
{
MFEM_ASSERT(1 <= dim && dim <= 3, "invalid dim: " << dim);
switch (dim)
x = p[0];
if (dim > 1)
{
case 3: Set3(p); break;
case 2: Set2(p); break;
case 1: Set1(p); break;
y = p[1];
if (dim > 2)
{
z = p[2];
}
}
}
void Get(real_t *p, const int dim) const
{
MFEM_ASSERT(1 <= dim && dim <= 3, "invalid dim: " << dim);
switch (dim)
p[0] = x;
if (dim > 1)
{
case 3: p[2] = z;
case 2: p[1] = y;
case 1: p[0] = x;
p[1] = y;
if (dim > 2)
{
p[2] = z;
}
}
}
void Set(const real_t x1, const real_t x2, const real_t x3, const real_t w)
{ x = x1; y = x2; z = x3; weight = w; }
void Set3w(const real_t *p) { x = p[0]; y = p[1]; z = p[2]; weight = p[3]; }
void Set3(const real_t x1, const real_t x2, const real_t x3)
{ x = x1; y = x2; z = x3; }
void Set3(const real_t *p) { x = p[0]; y = p[1]; z = p[2]; }
void Set2w(const real_t x1, const real_t x2, const real_t w)
{ x = x1; y = x2; weight = w; }
void Set2w(const real_t *p) { x = p[0]; y = p[1]; weight = p[2]; }
void Set2(const real_t x1, const real_t x2) { x = x1; y = x2; }
void Set2(const real_t *p) { x = p[0]; y = p[1]; }
void Set1w(const real_t x1, const real_t w) { x = x1; weight = w; }
void Set1w(const real_t *p) { x = p[0]; weight = p[1]; }
};
/// Class for an integration rule - an Array of IntegrationPoint.
+2 -2
View File
@@ -164,8 +164,8 @@ private:
public:
/// Constructs the domain integrator $ (Q, \nabla v) $
DomainLFGradIntegrator(VectorCoefficient &QF, const IntegrationRule *ir = NULL)
: DeltaLFIntegrator(QF, ir), Q(QF) { }
DomainLFGradIntegrator(VectorCoefficient &QF)
: DeltaLFIntegrator(QF), Q(QF) { }
bool SupportsDevice() const override { return true; }
+2 -2
View File
@@ -717,9 +717,9 @@ void ParGridFunction::ProjectCoefficientElementL2(VectorCoefficient &vcoeff)
}
void ParGridFunction::ProjectDiscCoefficient(
std::variant<Coefficient*, VectorCoefficient*> coeff)
void ParGridFunction::ProjectDiscCoefficient(VectorCoefficient &coeff)
{
MFEM_VERIFY(VectorDim() == coeff.GetVDim(), "coeff vdim != VectorDim()");
// local maximal element attribute for each dof
Array<int> ldof_attr;
+5 -6
View File
@@ -63,12 +63,6 @@ protected:
void ProjectBdrCoefficient(Coefficient *coeff[], VectorCoefficient *vcoeff,
const Array<int> &attr);
/** @brief Project a discontinuous (vector) coefficient as a grid function on
a continuous finite element space. The values in shared dofs are
determined from the element with maximal attribute. */
virtual void ProjectDiscCoefficient(
std::variant<Coefficient*, VectorCoefficient*> coeff) override;
public:
ParGridFunction() { pfes = NULL; }
@@ -274,6 +268,11 @@ public:
ProjectType type = ProjectType::DEFAULT) override;
using GridFunction::ProjectDiscCoefficient;
/** @brief Project a discontinuous vector coefficient as a grid function on
a continuous finite element space. The values in shared dofs are
determined from the element with maximal attribute. */
void ProjectDiscCoefficient(VectorCoefficient &coeff) override;
void ProjectDiscCoefficient(Coefficient &coeff, AvgType type) override;
void ProjectDiscCoefficient(VectorCoefficient &vcoeff, AvgType type) override;
File diff suppressed because it is too large Load Diff
-539
View File
@@ -1,539 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_SIDREDATACOLLECTION
#define MFEM_SIDREDATACOLLECTION
#include "../config/config.hpp"
#ifdef MFEM_USE_SIDRE
#include "datacollection.hpp"
// Ignore warnings from the axom/sidre header (GCC + Clang versions)
#ifdef MFEM_HAVE_GCC_PRAGMA_DIAGNOSTIC
# pragma GCC diagnostic push
# if defined(__clang__)
# pragma GCC diagnostic ignored "-Wextra-semi"
# else // real GCC?
# pragma GCC diagnostic ignored "-Wpedantic"
# endif
#endif
#include <axom/sidre.hpp>
#ifdef MFEM_HAVE_GCC_PRAGMA_DIAGNOSTIC
# pragma GCC diagnostic pop
#endif
namespace mfem
{
/** @brief Data collection with Sidre routines following the Conduit mesh
blueprint specification. */
/** SidreDataCollection provides an HDF5-based file format for visualization or
restart capability. This functionality is aimed primarily at customers of
LLNL's axom project that run problems at extreme scales.
For more information, see:
- Sidre component of LLNL's axom project (to be open-sourced), http://goo.gl/cZyJdn
- LLNL conduit/blueprint library, https://github.com/LLNL/conduit
- HDF5 library, https://support.hdfgroup.org/HDF5
The layout created in the Sidre DataStore is: (`"──"` denote groups,
`"─•"` denote views, `"─>"` denote links, i.e. shallow-copy view)
<root>
<collection-name>_global (global group)
blueprint_index
<collection-name> (bp_index group)
state
cycle
time
number_of_domains = <mesh-mpi-comm-size>
coordsets
coords
path = "<bp-path>/coordsets/coords"
type > <bp-grp>/coordsets/coords/type = "explicit"
coord_system = "x"|"xy"|"xyz"
topologies
mesh
path = "<bp-path>/topologies/mesh"
type > <bp-grp>/topologies/mesh/type = "unstructured"
coordset > <bp-grp>/topologies/mesh/coordset = "coords"
grid_function > <bp-grp>/topologies/mesh/grid_function = "<nodes-field-name>"
boundary_topology > <bp-grp>/topologies/mesh/boundary_topology = "boundary"
boundary
path = "<bp-path>/topologies/mesh"
type > <bp-grp>/topologies/boundary/type = "unstructured"
coordset > <bp-grp>/topologies/boundary/coordset = "coords"
fields
mesh_material_attribute
path = "<bp-path>/fields/mesh_material_attribute"
association > <bp-grp>/fields/mesh_material_attribute/association = "element"
topology > <bp-grp>/fields/mesh_material_attribute/topology = "mesh"
number_of_components = 1
boundary_material_attribute
path = "<bp-path>/fields/boundary_material_attribute"
association > <bp-grp>/fields/boundary_material_attribute/association = "element"
topology > <bp-grp>/fields/boundary_material_attribute/topology = "boundary"
number_of_components = 1
grid-function-1
path = "<bp-path>/fields/grid-function-1"
basis > <bp-grp>/fields/grid-function-1/basis = "<fe-coll-name>"
topology > <bp-grp>/fields/grid-function-1/topology = "mesh"
number_of_components = gf1->VectorDim()
grid-function-2
path = "<bp-path>/fields/grid-function-2"
basis > <bp-grp>/fields/grid-function-2/basis = "<fe-coll-name>"
topology > <bp-grp>/fields/grid-function-2/topology = "mesh"
number_of_components = gf2->VectorDim()
...
...
<collection-name> (domain group)
blueprint (blueprint group)
state
cycle
time
domain = <mesh-mpi-rank>
time_step
coordsets
coords
type = "explicit"
values
x = view in <vertex-coords-buffer>/<ext-double-data>
y = view in <vertex-coords-buffer>/<ext-double-data>
z = view in <vertex-coords-buffer>/<ext-double-data>
topologies
mesh
type = "unstructured"
elements
shape = "points"|"lines"|...
connectivity = <vert-idx-array>
coordset = "coords"
grid_function = "<nodes-field-name>"
boundary_topology = "boundary"
boundary
type = "unstructured"
elements
shape = "points"|"lines"|...
connectivity = <vert-idx-array>
coordset = "coords"
fields
mesh_material_attribute
association = "element"
topology = "mesh"
values = <attr-array>
boundary_material_attribute
association = "element"
topology = "boundary"
values = <attr-array>
grid-function-1 (name can include path)
basis = "<fe-coll-name>"
topology = "mesh"
values = <ext-double-array>/<named-buffer> (vdim == 1)
grid-function-2 (name can include path)
basis = "<fe-coll-name>"
topology = "mesh"
values (vdim > 1)
x0 = view into <ext-double-array>/<named-buffer>
x1 = view into <ext-double-array>/<named-buffer>
x2 = view into <ext-double-array>/<named-buffer>
...
...
named_buffers (named_buffers group)
vertex_coords = <double-array>
grid-function-1 = <double-array>
grid-function-2 = <double-array>
...
@note blueprint_index is used both in serial and in parallel. In parallel,
only rank 0 will add entries to the blueprint index.
@note QuadratureFunction%s (q-fields) are not supported.
@note SidreDataCollection does not manage the FiniteElementSpace%s and
FiniteElementCollection%s associated with registered GridFunction%s.
Therefore, field registration is left to the user of SidreDataCollection and
there are no methods that automatically register GridFunction%s using just
the content of the Sidre DataStore. Such capabilities can be implemented in
a derived class, adding any desired object management routines.
@warning This class is still _experimental_, meaning that in future
releases, it may not be backward compatible, and the output files generated
by the current version may become unreadable.
*/
class SidreDataCollection : public DataCollection
{
public:
typedef NamedFieldsMap< Array<int> > AttributeFieldMap;
AttributeFieldMap attr_map;
public:
/// Constructor that allocates and initializes a Sidre DataStore.
/**
@param[in] collection_name Name of the collection used as a file name
when saving
@param[in] the_mesh Mesh shared by all grid functions in the
collection (can be NULL)
@param[in] owns_mesh_data Does the SidreDC own the mesh vertices?
With this constructor, the SidreDataCollection owns the allocated Sidre
DataStore.
*/
SidreDataCollection(const std::string& collection_name,
Mesh *the_mesh = NULL,
bool owns_mesh_data = false);
/// Constructor that links to an external Sidre DataStore.
/** Specifically, the global and domain groups can be at arbitrary paths.
@param[in] collection_name Name of the collection used as a file name
when saving
@param[in] bp_index_grp Pointer to the blueprint index group in the
datastore, see the above schematic
@param[in] domain_grp Pointer to the domain group in the datastore,
see the above schematic
@param[in] owns_mesh_data Does the SidreDC own the mesh vertices?
With this constructor, the SidreDataCollection does not own the Sidre
DataStore.
@note No mesh or fields are read from the given Groups. The mesh has
to be set with SetMesh() and fields registered with RegisterField().
*/
SidreDataCollection(const std::string& collection_name,
axom::sidre::Group * bp_index_grp,
axom::sidre::Group * domain_grp,
bool owns_mesh_data = false);
#ifdef MFEM_USE_MPI
/// Associate an MPI communicator with the collection.
/** If no mesh was associated with the collection, this method should be
called before using any of the Load() methods to read parallel data. */
void SetComm(MPI_Comm comm);
#endif
/// Register a GridFunction in the Sidre DataStore.
/** This method is a shortcut for the call
`RegisterField(field_name, gf, field_name, 0)`.
*/
virtual void RegisterField(const std::string &field_name, GridFunction *gf)
{
RegisterField(field_name, gf, field_name, 0);
}
/// Register a GridFunction in the Sidre DataStore.
/** The registration procedure is as follows:
- if (@a gf's data is NULL), allocate named buffer with the name
@a buffer_name with size _offset + gf->FESpace()->GetVSize()_ and use
its data (plus the given @a offset) to set @a gf's data;
- else, if (DataStore has a named buffer @a buffer_name), replace @a gf's
data array with that named buffer plus the given @a offset;
- else, use @a gf's data as external data associated with @a field_name
in the DataStore;
- register @a field_name in #field_map.
Both the @a field_name and @a buffer_name can contain a path prefix.
@note If @a field_name or @a buffer_name is empty, the method does
nothing.
@note If the GridFunction pointer @a gf or it's FiniteElementSpace
pointer are NULL, the method does nothing.
*/
void RegisterField(const std::string &field_name, GridFunction *gf,
const std::string &buffer_name,
axom::sidre::IndexType offset);
/// Registers an attribute field in the Sidre DataStore
/** The registration process is similar to that of RegisterField()
The attribute field is associated with the elements of the mesh
when @a is_bdry is false, and with the boundary elements, when
@a is_bdry is true.
@sa RegisterField() */
void RegisterAttributeField(const std::string& name, bool is_bdry);
void DeregisterAttributeField(const std::string& name);
/** Returns a pointer to the attribute field associated with
@a field_name, or NULL when there is no associated field */
Array<int>* GetAttributeField(const std::string& field_name) const
{ return attr_map.Get(field_name); }
/** Checks if there is an attribute field associated with @a field_name */
bool HasAttributeField(const std::string& field_name) const
{ return attr_map.Has(field_name); }
/** Checks if any rank in the mesh has boundary elements */
bool HasBoundaryMesh() const;
/// Set the name of the mesh nodes field.
/** This name will be used by SetMesh() to register the mesh nodes, if not
already registered. Also, this method should be called if the mesh nodes
GridFunction was or will be registered directly by the user. The default
value for the name is "mesh_nodes". */
void SetMeshNodesName(const std::string &nodes_name)
{
if (!nodes_name.empty()) { m_meshNodesGFName = nodes_name; }
}
/// De-register @a field_name from the SidreDataCollection.
/** The field is removed from the #field_map and the DataStore, including
deleting it from the named_buffers group, if allocated. */
virtual void DeregisterField(const std::string& field_name);
/// Delete all owned data.
virtual ~SidreDataCollection();
/// Set/change the mesh associated with the collection
/** Uses the field name "mesh_nodes" or the value set by SetMeshNodesName()
to register the mesh nodes GridFunction, if the mesh uses nodes. */
virtual void SetMesh(Mesh *new_mesh);
#ifdef MFEM_USE_MPI
/// Set/change the mesh associated with the collection
/** Uses the field name "mesh_nodes" or the value set by SetMeshNodesName()
to register the mesh nodes GridFunction, if the mesh uses nodes. */
virtual void SetMesh(MPI_Comm comm, Mesh *new_mesh);
#endif
/// Reset the domain and global datastore group pointers.
/** These are set in the constructor, but if a host code changes the
datastore contents ( such as wiping out the datastore and loading in new
contents from a file, i.e. a restart ) these pointers will need to be
reset to valid groups in the datastore.
@sa Load(const std::string &path, const std::string &protocol).
*/
void SetGroupPointers(axom::sidre::Group * global_grp,
axom::sidre::Group * domain_grp);
axom::sidre::Group * GetBPGroup() { return m_bp_grp; }
axom::sidre::Group * GetBPIndexGroup() { return m_bp_index_grp; }
/// Prepare the DataStore for writing
virtual void PrepareToSave();
/// Save the collection to file.
/** This method calls `Save(collection_name, "sidre_hdf5")`. */
virtual void Save();
/// Save the collection to @a filename.
/** The collection path prefix is prepended to the @a filename and the
current cycle is appended, if cycle >= 0. */
void Save(const std::string& filename, const std::string& protocol);
/// Load the Sidre DataStore from file.
/** No mesh or fields are read from the loaded DataStore.
If the data collection created the datastore, it knows the layout of
where the domain and global groups are, and can restore them after the
Load().
If, however, the data collection does not own the datastore (e.g. it did
not create the datastore), the host code must reset these pointers after
the load operation, using SetGroupPointers(), and also reset the state
variables, using UpdateStateFromDS().
*/
void Load(const std::string& path, const std::string& protocol);
/// Load SidreDataCollection from file.
/** The used file path is based on the current prefix path, collection name,
and the given @a cycle_. The protocol is "sidre_hdf5".
@sa Load(const std::string &path, const std::string &protocol).
*/
virtual void Load(int cycle_ = 0)
{
SetCycle(cycle_);
Load(get_file_path(name), "sidre_hdf5");
}
/// Load external data after registering externally owned fields.
void LoadExternalData(const std::string& path);
/** @brief Updates the DataCollection's cycle, time, and time-step variables
with the values from the data store. */
void UpdateStateFromDS();
/** @brief Updates the data store's cycle, time, and time-step variables with
the values from the SidreDataCollection. */
void UpdateStateToDS();
/** @name Methods for named buffer access and manipulation. */
///@{
/** @brief Get a pointer to the sidre::View holding the named buffer for
@a buffer_name. */
/** If such named buffer is not allocated, the method returns NULL.
@note To access the underlying pointer, use View::getData().
@note To query the size of the buffer, use View::getNumElements().
*/
axom::sidre::View *
GetNamedBuffer(const std::string& buffer_name) const
{
return named_buffers_grp()->hasView(buffer_name)
? named_buffers_grp()->getView(buffer_name)
: NULL;
}
/// Return newly allocated or existing named buffer for @a buffer_name.
/** The buffer is stored in the named_buffers group. If the currently
allocated buffer size is smaller than @a sz, then the buffer is
reallocated with size @a sz, destroying its contents.
@note To access the underlying pointer, use View::getData().
*/
axom::sidre::View *
AllocNamedBuffer(const std::string& buffer_name,
axom::sidre::IndexType sz,
axom::sidre::TypeID type =
axom::sidre::DOUBLE_ID);
/// Deallocate the named buffer @a buffer_name.
void FreeNamedBuffer(const std::string& buffer_name)
{ named_buffers_grp()->destroyViewAndData(buffer_name); }
///@}
private:
// Used if the Sidre data collection is providing the datastore itself.
const bool m_owns_datastore;
// TODO - Need to evaluate if this bool member can be combined with own_data
// in parent data collection class. m_owns_mesh_data indicates whether the
// Sidre dc owns the mesh element data and node positions gf. The DC base
// class own_data indicates if the dc owns the mesh object pointer itself and
// GF objects. Can we use one flag and just have DC own all objects vs none?
const bool m_owns_mesh_data;
// Name to be used for registering the mesh nodes in the SidreDataCollection.
// This name is used by SetMesh() and can be overwritten by the method
// SetMeshNodesName().
// Default value: "mesh_nodes".
std::string m_meshNodesGFName;
// If the data collection owns the datastore, it will store a pointer to it.
// Otherwise, this pointer is NULL.
axom::sidre::DataStore * m_datastore_ptr;
protected:
axom::sidre::Group *named_buffers_grp() const;
axom::sidre::View *
alloc_view(axom::sidre::Group *grp,
const std::string &view_name);
axom::sidre::View *
alloc_view(axom::sidre::Group *grp,
const std::string &view_name,
const axom::sidre::DataType &dtype);
axom::sidre::Group *
alloc_group(axom::sidre::Group *grp,
const std::string &group_name);
// return the filename based on prefix_path, collection name and cycle.
std::string get_file_path(const std::string &filename) const;
private:
// If the data collection does not own the datastore, it will need pointers
// to the blueprint and blueprint index group to use.
axom::sidre::Group * m_bp_grp;
axom::sidre::Group * m_bp_index_grp;
// This is stored for convenience.
axom::sidre::Group * m_named_bufs_grp;
// Private helper functions
void RegisterFieldInBPIndex(const std::string& field_name,
GridFunction *gf);
void DeregisterFieldInBPIndex(const std::string & field_name);
void RegisterAttributeFieldInBPIndex(const std::string& attr_name);
void DeregisterAttributeFieldInBPIndex(const std::string& attr_name);
/** @brief Return a string with the conduit blueprint name for the given
Element::Type. */
std::string getElementName( Element::Type elementEnum );
/**
* \brief A private helper function to set up the views associated with the
data of a scalar valued grid function in the blueprint style.
* \pre gf is not null
* \note This function is expected to be called by RegisterField()
* \note Handles cases where hierarchy is already set up,
* where the data was allocated by this data collection
* and where the grid function data is external to Sidre
*/
void addScalarBasedGridFunction(const std::string& field_name,
GridFunction* gf,
const std::string &buffer_name,
axom::sidre::IndexType offset);
/**
* \brief A private helper function to set up the views associated with the
data of a vector valued grid function in the blueprint style.
* \pre gf is not null
* \note This function is expected to be called by RegisterField()
* \note Handles cases where hierarchy is already set up,
* where the data was allocated by this data collection
* and where the grid function data is external to Sidre
*/
void addVectorBasedGridFunction(const std::string& field_name,
GridFunction* gf,
const std::string &buffer_name,
axom::sidre::IndexType offset);
/** @brief A private helper function to set up the Views associated with
attribute field named @a field_name */
void addIntegerAttributeField(const std::string& field_name, bool is_bdry);
/// Sets up the four main mesh blueprint groups.
/**
* \param hasBP Indicates whether the blueprint has already been set up.
*/
void createMeshBlueprintStubs(bool hasBP);
/// Sets up the mesh blueprint 'state' group.
/**
* \param hasBP Indicates whether the blueprint has already been set up.
*/
void createMeshBlueprintState(bool hasBP);
/// Sets up the mesh blueprint 'coordsets' group.
/**
* \param hasBP Indicates whether the blueprint has already been set up.
*/
void createMeshBlueprintCoordset(bool hasBP);
/// Sets up the mesh blueprint 'topologies' group.
/**
* This method is called from SetMesh().
* \param hasBP Indicates whether the blueprint has already been set up.
* \param mesh_name The name of the topology.
* \note Valid values for @a mesh_name are "mesh" and "boundary" and the
former has to be created with this method before the latter.
*/
void createMeshBlueprintTopologies(bool hasBP, const std::string& mesh_name);
#ifdef MFEM_USE_MPI
/// Sets up the mesh blueprint 'adjacencies' group.
/**
* \param hasBP Indicates whether the blueprint has already been set up.
* \note Only valid when using parallel meshes
*/
void createMeshBlueprintAdjacencies(bool hasBP);
#endif
/// Verifies that the contents of the mesh blueprint data is valid.
void verifyMeshBlueprint();
};
} // end namespace mfem
#endif
#endif
+27 -25
View File
@@ -14,7 +14,6 @@
#include "../config/config.hpp"
#include "array.hpp"
#include "text.hpp"
#include <iostream>
#include <map>
@@ -248,8 +247,7 @@ inline void ArraysByName<T>::Print(std::ostream &os, int width) const
os << data.size() << '\n';
for (auto const &it : data)
{
// Note: The method Load() can read any string formatted with std::quoted.
os << std::quoted(it.first) << '\n' << it.second.Size() << '\n';
os << '"' << it.first << '"' << '\n' << it.second.Size() << '\n';
it.second.Print(os, width > 0 ? width : it.second.Size());
}
}
@@ -260,36 +258,40 @@ void ArraysByName<T>::Load(std::istream &in)
int NumArrays;
in >> NumArrays;
for (int i = 0; i < NumArrays; i++)
std::string ArrayLine, ArrayName;
for (int i=0; i < NumArrays; i++)
{
in >> std::ws;
// Read the name:
// - If the stream 'in' starts with " then parse it with the function
// parse_quoted_string() from text.hpp. In this case, the name can be
// empty. Note: this case allows for reading any string formatted using
// std::quoted, e.g. as in the method Print().
// - If the name does not start with " then the name ends with the first
// white space character (and the white space character is not included
// in the name). Since white space characters are skipped before reading
// the name, there will be at least one non-white-space character in the
// name in this case.
std::string ArrayName;
if (in.peek() == '"')
getline(in, ArrayLine);
std::size_t q0 = ArrayLine.find('"');
std::size_t q1 = ArrayLine.rfind('"');
if (q0 != std::string::npos && q1 > q0)
{
if (parse_quoted_string(ArrayName, in) != 0)
{
MFEM_ABORT("error parsing input!");
}
// Locate set name between first and last double quote
ArrayName = ArrayLine.substr(q0+1,q1-q0-1);
}
else
{
in >> ArrayName;
MFEM_VERIFY(in.good(), "error parsing input!");
// If no double quotes found locate set name using white space
q1 = ArrayLine.find(' ');
ArrayName = ArrayLine.substr(0,q1-1);
}
if (q1+2 < ArrayLine.size())
{
// Read the remainder of the line which contains the array data
std::istringstream ArrayDataStream(ArrayLine.substr(q1+2,
ArrayLine.size()));
data[ArrayName].Load(ArrayDataStream, 0);
}
else
{
// Read the array data starting on the next line
data[ArrayName].Load(in, 0);
}
// Read the array
data[ArrayName].Load(in);
}
}
}
-42
View File
@@ -50,48 +50,6 @@ inline void filter_dos(std::string &line)
}
}
/** @brief Read a string formatted using std::quoted. Return nonzero on error.
The stream @a in must begin with @a delim. After clearing @a result and
extracting the opening @a delim, characters are extracted from @a in and
processed as follows:
- if the character is @a delim, return 0;
- if the character is different from @a escape, it is appended to @a result;
- if the character is @a escape, the next character from @a in is extracted
and if it is one of @a delim or @a escape, it is appended to @a result;
otherwise, both @a escape and the character after it are appended to
@a result; note that the latter case is not possible if the input was
formatted with std::quoted with the same @a delim and @a escape
characters.
If the stream @a in does not begin with @a delim, error code 1 is returned.
If reading the stream fails, error code 2 is returned. On success, zero is
returned and the closing @a delim character is the last character extracted
from @a in. */
inline int parse_quoted_string(std::string &result, std::istream &in,
char delim = '"', char escape = '\\')
{
using tt = std::string::traits_type; // std::char_traits<char>
auto equal = [](tt::int_type c1, tt::char_type c2) -> bool
{
return tt::eq_int_type(c1, tt::to_int_type(c2));
};
result.clear();
if (!equal(in.peek(), delim)) { return 1; }
in.get(); // extract delim
for (auto c = in.get(); !equal(c, delim); c = in.get())
{
if (equal(c, escape))
{
c = in.get();
if (!equal(c, escape) && !equal(c, delim)) { result += escape; }
}
if (!in) { return 2; }
result += tt::to_char_type(c);
}
return 0;
}
/// Convert an integer to a 0-padded string with the given number of @a digits
inline std::string to_padded_string(int i, int digits)
{
-3
View File
@@ -160,9 +160,6 @@ const char *GetConfigStr()
#ifdef MFEM_USE_RAJA
"MFEM_USE_RAJA\n"
#endif
#ifdef MFEM_USE_SIDRE
"MFEM_USE_SIDRE\n"
#endif
#ifdef MFEM_USE_SIMD
"MFEM_USE_SIMD\n"
#endif
-7
View File
@@ -23,7 +23,6 @@ list(APPEND SRCS
complex_operator.cpp
constraints.cpp
densemat.cpp
eigensolvers.cpp
filteredsolver.cpp
handle.cpp
matrix.cpp
@@ -56,7 +55,6 @@ list(APPEND HDRS
dinvariants.hpp
dtensor.hpp
dual.hpp
eigensolvers.hpp
filteredsolver.hpp
handle.hpp
invariants.hpp
@@ -103,11 +101,6 @@ if (MFEM_USE_MPI)
endif()
endif()
if (MFEM_USE_ARPACK)
list(APPEND SRCS arpack.cpp)
list(APPEND HDRS arpack.hpp)
endif()
if (MFEM_USE_SUNDIALS)
list(APPEND SRCS sundials.cpp)
list(APPEND HDRS sundials.hpp)
-1122
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File diff suppressed because it is too large Load Diff
-271
View File
@@ -1,271 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_ARPACK
#define MFEM_ARPACK
#include "../config/config.hpp"
#ifdef MFEM_USE_ARPACK
#include <string>
#ifdef MFEM_USE_MPI
#include <mpi.h>
#include "hypre.hpp"
#endif
#include "operator.hpp"
#define SSAUPD ssaupd_
#define SSEUPD sseupd_
#define DSAUPD dsaupd_
#define DSEUPD dseupd_
#ifdef MFEM_USE_MPI
#define PSSAUPD pssaupd_
#define PSSEUPD psseupd_
#define PDSAUPD pdsaupd_
#define PDSEUPD pdseupd_
#endif
extern "C" void SSAUPD(int *ido, char *bmat, int *n,
char *which, int *nev, float *tol, float *resid,
int *ncv, float *v, int *ldv,
int *iparam, int *ipntr,
float *workd, float *workl, int *lworkl, int *info);
extern "C" void SSEUPD(int *, char *, int *, float *,
float *, int *, float *, char *, int *, char *,
int *, float *, float *, int *, float *,
int *, int *, int *, float *,
float *, int *, int *);
extern "C" void DSAUPD(int *ido, char *bmat, int *n,
char *which, int *nev, double *tol, double *resid,
int *ncv, double *v, int *ldv,
int *iparam, int *ipntr,
double *workd, double *workl, int *lworkl, int *info);
extern "C" void DSEUPD(int *, char *, int *, double *,
double *, int *, double *, char *, int *, char *,
int *, double *, double *, int *, double *,
int *, int *, int *, double *,
double *, int *, int *);
#ifdef MFEM_USE_MPI
extern "C" void PSSAUPD(int *comm, int *ido, char *bmat, int *n,
char *which, int *nev, float *tol, float *resid,
int *ncv, float *v, int *ldv,
int *iparam, int *ipntr,
float *workd, float *workl, int *lworkl, int *info);
extern "C" void PSSEUPD(int *comm, int *, char *, int *, float *,
float *, int *, float *, char *, int *, char *,
int *, float *, float *, int *, float *,
int *, int *, int *, float *,
float *, int *, int *);
extern "C" void PDSAUPD(int *comm, int *ido, char *bmat, int *n,
char *which, int *nev, double *tol, double *resid,
int *ncv, double *v, int *ldv,
int *iparam, int *ipntr,
double *workd, double *workl, int *lworkl, int *info);
extern "C" void PDSEUPD(int *comm, int *, char *, int *, double *,
double *, int *, double *, char *, int *, char *,
int *, double *, double *, int *, double *,
int *, int *, int *, double *,
double *, int *, int *);
#endif
extern "C" {
void arpackgetcommdbg_(int *,int *,int *);
void arpacksetcommdbg_(int *,int *,int *);
void arpacksymdbg_(int *,int *,int *,int *,int *,int *,int *);
void arpacknonsymdbg_(int *,int *,int *,int *,int *,int *,int *);
void arpackcmplxdbg_(int *,int *,int *,int *,int *,int *,int *);
}
namespace mfem
{
/// Wrapper for the ARPACK routine SSAUPD or DSAUPD
class ArPackSAUPD : public SymEigensolver, public SymGenEigensolver
{
public:
ArPackSAUPD();
virtual ~ArPackSAUPD();
/** ARPACK modes are described in section 3.5 of the ARPACK manual.
Mode 1: regular mode to solve A x = lambda x
No solver and no mass matrix are needed.
Mode 2: regular inverse mode to solve A x = lambda M x
Both A and M are needed and the solver should compute M^{-1}.
Mode 3: shift-invert mode to solve either A x = lambda x
or A x = lambda M x
Mass matrix is optional. The solver should compute
(A-sigma I)^{-1} or (A-sigma M)^{-1}. The shift parameter,
sigma, also needs to be set with SetShift().
Mode 4: Buckling mode to solve K x = lambda K_G x
K is set using SetMassMatrix(), K_G is set using SetOperator(),
and the solver should compute (K-sigma K_G)^{-1}. The shift
parameter, sigma, also needs to be set with SetShift().
Mode 5: Cayley mode to solve A x = lambda M x
Both A and M are needed and the solver should compute
(A - sigma M)^{-1}. The shift parameter, sigma, also needs
to be set with SetShift().
*/
void SetMode(int mode);
inline void SetTol(real_t tol) override { tol_ = tol; }
inline void SetMaxIter(int max_iter) override { max_iter_ = max_iter; }
inline void SetPrintLevel(int logging) override { logging_ = logging; }
inline void SetShift(real_t sigma) { sigma_ = sigma; }
inline void SetNumModes(int num_eigs) override { nev_ = num_eigs; }
virtual void SetSolver(Solver & solver);
virtual void SetOperator(const Operator & A) override;
virtual void SetMassMatrix(const Operator & M);
virtual void SetOperators(const Operator & A, const Operator & B) override
{ SetOperator(A); SetMassMatrix(B); }
void Solve() override;
virtual int GetNumConverged() const override { return iparam_[4]; }
/// Collect the converged eigenvalues
virtual void GetEigenvalues(Array<real_t> & eigenvalues) const override;
/// Extract a single eigenvector
virtual const Vector & GetEigenvector(unsigned int i) const override;
/// Transfer ownership of the converged eigenvectors
Vector ** StealEigenvectors() override;
protected:
int myid_; // Index of this processor
int max_iter_;
int logging_;
// The following variables are for ARPACK
int nloc_; // number of items stored locally
int nev_; // number of requested eigenvalues
int ncv_; // number of ritz vectors
int rvec_; // boolean to return eigenvectors as well
int mode_; // 1 = standard, 2 = generalized, 3 = shift invert,
// 4 = buckling, 5 = Cayley
int lworkl_; // length of lworkl_ work array
int iparam_[12]; // arpack parameters
int ipntr_[12]; // arpack pointers
char bmat_; // I for standard problem, G for generalized
char which_[3]; // spectrum portion: LA, SA, LM, SM, BE
char hwmny_; // DSEUPD: A for all eigenvalues, S for some
real_t tol_; // relative accuracy bound for Ritz values
real_t sigma_; // eigenvalue shift parameter
int * select_;// workspace used during eigenvalue computation
real_t * dv_; // Ritz values
real_t * v_; // ncv Lanczos basis vectors
real_t * resid_; // residual vector
real_t * workd_; // work array for 3 vectors used in Arnoldi iteration
real_t * workl_; // work array
// Operators and Vectors needed outside of ARPACK
Solver * solver_;
const Operator * A_;
const Operator * B_;
Vector * w_;
Vector * x_;
Vector * y_;
Vector * z_;
mutable Vector ** eigenvectors_;
std::string solverName_;
void reverseComm();
int reverseCommMode1();
int reverseCommMode2();
int reverseCommMode3();
int reverseCommMode4();
int reverseCommMode5();
virtual void prepareEigenvectors() const;
void printErrors(const int & info, const int iparam[],
const char & bmat, const int & n,
const char which[],
const int & nev, const int & ncv,
const int & lworkl );
private:
virtual int computeNlocf() { return nloc_; }
virtual int computeIter(int & ido);
virtual int computeEigs();
};
#ifdef MFEM_USE_MPI
class ArPackPSAUPD : public ArPackSAUPD
{
public:
ArPackPSAUPD(MPI_Comm comm);
virtual ~ArPackPSAUPD() {}
void SetOperator(const Operator & A);
void SetMassMatrix(const Operator & M);
/// Collect the converged eigenvalues
void GetEigenvalues(Array<real_t> & eigenvalues) const;
/// Extract a single eigenvector
const Vector & GetEigenvector(unsigned int i) const;
/// Transfer ownership of the converged eigenvectors
// HypreParVector ** StealEigenvectors();
Vector ** StealEigenvectors();
protected:
void prepareEigenvectors() const;
private:
MPI_Comm comm_;
MPI_Fint commf_; // Fortran style MPI communicator
int numProcs_; // Number of processors
mutable HYPRE_Int * part_; // parallel partitioning for eigenvectors
int computeNlocf();
int computeIter(int & ido);
int computeEigs();
};
#endif // MFEM_USE_MPI
};
#endif // MFEM_USE_ARPACK
#endif // MFEM_ARPACK
-20
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@@ -1,20 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "linalg.hpp"
#include "eigensolvers.hpp"
using namespace std;
namespace mfem
{
};
-396
View File
@@ -1,396 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#ifndef MFEM_EIGENSOLVERS
#define MFEM_EIGENSOLVERS
#include "vector.hpp"
namespace mfem
{
/// Abstract Eigenequation
/// Defines the operator of the linear eigenvalue equation
/// A x_i = lambda_i x_i
/// Where A is a real-valued operator, the lambda_i are the eigenvalues,
/// and x_i are the eigenvectors.
class Eigenequation
{
protected:
Eigenequation() = default;
public:
virtual ~Eigenequation() = default;
/// @brief Set the operator A of the eigenvalue equation
virtual void SetOperator(const Operator & A) = 0;
};
/// Abstract Complex-valued Eigenequation
/// Defines the operator of the linear eigenvalue equation
/// A x_i = lambda_i x_i
/// Where A is a complex-valued operator, the lambda_i are the eigenvalues,
/// and x_i are the eigenvectors.
class ComplexEigenequation
{
protected:
ComplexEigenequation() = default;
public:
virtual ~ComplexEigenequation() = default;
/// @brief Set the real and imaginary parts of the operator A
virtual void SetOperator(const Operator & Ar, const Operator & Ai) = 0;
};
/// Abstract Generalized Eigenequation
/// Defines the operator of the linear eigenvalue equation
/// A x_i = lambda_i B x_i
/// Where A and B are real-valued operators, the lambda_i are the eigenvalues,
/// and x_i are the eigenvectors.
class GenEigenequation
{
protected:
GenEigenequation() = default;
public:
virtual ~GenEigenequation() = default;
/// @brief Set the operators A and B of the generalized eigenvalue equation
virtual void SetOperators(const Operator & A, const Operator & B) = 0;
};
/// Abstract Complex-valued Generalized Eigenequation
/// Defines the operator of the linear eigenvalue equation
/// A x_i = lambda_i B x_i
/// Where A and B are complex-valued operators, the lambda_i are the
/// eigenvalues, and x_i are the eigenvectors.
class ComplexGenEigenequation
{
protected:
ComplexGenEigenequation() = default;
public:
virtual ~ComplexGenEigenequation() = default;
/// @brief Set the real and imaginary parts of the operators A and B
virtual void SetOperators(const Operator & Ar, const Operator & Ai,
const Operator & Br, const Operator & Bi) = 0;
};
/// Abstract Eigensolver
/// Computes eigenvalue/eigenvector pairs for the linear system
/// A x_i = lambda_i x_i
/// Where the lambda_i are the eigenvalues and x_i are the eigenvectors.
class EigensolverBase
{
protected:
EigensolverBase() = default;
public:
virtual ~EigensolverBase() = default;
/// @brief Stopping criteria based on numerical tolerance
///
/// @note This may be defined differently by different solvers.
virtual void SetTol(real_t tol) = 0;
/// @brief Stopping criteria based on number of iterations required to
/// reach convergence.
///
/// @note This may also be defined differently in different solvers.
virtual void SetMaxIter(int max_iter) = 0;
/// @brief Controls the type and amount of information printed to
/// standard output.
virtual void SetPrintLevel(int logging) = 0;
/// @brief Set the number of desired eigenmodes to compute
virtual void SetNumModes(int num_eigs) = 0;
/// @brief Get the number of converged eigenmodes
virtual int GetNumConverged() const = 0;
/// @brief Perform the eigenvalue solve
virtual void Solve() = 0;
};
/// Symmetric Eigensolver
/// If A^T = A the linear system must have real-valued eigenvalues
/// and eigenvectors.
class SymEigensolver : public EigensolverBase, public Eigenequation
{
protected:
SymEigensolver() = default;
public:
virtual ~SymEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should equal the number of converged eigenvalues.
virtual void GetEigenvalues(Array<real_t> & eigenvalues) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, numConverged). The
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain numConverged vectors.
virtual Vector ** StealEigenvectors() = 0;
};
/// Symmetric Generalized Eigensolver
/// If A^T = A and M^T = M the linear system must have real-valued eigenvalues
/// and eigenvectors.
class SymGenEigensolver : public EigensolverBase, public GenEigenequation
{
protected:
SymGenEigensolver() = default;
public:
virtual ~SymGenEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should equal the number of converged eigenvalues.
virtual void GetEigenvalues(Array<real_t> & eigenvalues) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, numConverged). The
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain numConverged vectors.
virtual Vector ** StealEigenvectors() = 0;
};
/// Hermetian Eigensolver
/// If A^H = A the linear system must have real-valued eigenvalues
/// but may have complex-valued eigenvectors.
class HermEigensolver : public EigensolverBase, public ComplexEigenequation
{
protected:
HermEigensolver() = default;
public:
virtual ~HermEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should equal the number of converged eigenvalues.
virtual void GetEigenvalues(Array<real_t> & eigenvalues) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, 2*numConverged). The
/// vectors corresponding to even indices are the real parts of the
/// converged eigenvectors and the odd indices correspond to the
/// imaginary parts.
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain 2*numConverged vectors with the even
/// indices corresponding to the real parts of the converged
/// eigenvectors and the odd indices corresponding to the imaginary
/// parts.
virtual Vector ** StealEigenvectors() = 0;
};
/// Hermetian Generalized Eigensolver
/// If A^H = A and M^H = M the linear system must have real-valued eigenvalues
/// but may have complex-valued eigenvectors.
class HermGenEigensolver :
public EigensolverBase, public ComplexGenEigenequation
{
protected:
HermGenEigensolver() = default;
public:
virtual ~HermGenEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should equal the number of converged eigenvalues.
virtual void GetEigenvalues(Array<real_t> & eigenvalues) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, 2*numConverged). The
/// vectors corresponding to even indices are the real parts of the
/// converged eigenvectors and the odd indices correspond to the
/// imaginary parts.
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain 2*numConverged vectors with the even
/// indices corresponding to the real parts of the converged
/// eigenvectors and the odd indices corresponding to the imaginary
/// parts.
virtual Vector ** StealEigenvectors() = 0;
};
/// Non-Symmetric Eigensolver
/// For general real-valued operators A the linear system must have
/// eigenvalues and eigenvectors which form complex conjugate pairs.
class NonSymEigensolver : public EigensolverBase, public Eigenequation
{
protected:
NonSymEigensolver() = default;
public:
virtual ~NonSymEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should be the number of converged
/// eigenvalues. The complex-valued eigenvalues can be constructed
/// as: lambda_{2*j} = eig[2*j]+i*eig[2*j+1] and
/// lambda_{2*j+1} = eig[2*j]-i*eig[2*j+1]
/// With j in the range [0, numConverged/2)
virtual void GetEigenvalues(Array<real_t> & eig) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, numConverged). The
/// vectors corresponding to even indices are the real parts of the
/// converged eigenvectors and the odd indices correspond to the
/// imaginary parts. If needed, the complex conjugate pairs of
/// eigenvectors can be constructed in the same manner described
/// for the eigenvalues.
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain numConverged vectors with the even
/// indices corresponding to the real parts of the converged
/// eigenvectors and the odd indices corresponding to the imaginary
/// parts.
virtual Vector ** StealEigenvectors() = 0;
};
/// Non-Symmetric Eigensolver
/// For general real-valued operators A and M the linear system must have
/// eigenvalues and eigenvectors which form complex conjugate pairs.
class NonSymGenEigensolver : public EigensolverBase, public GenEigenequation
{
protected:
NonSymGenEigensolver() = default;
public:
virtual ~NonSymGenEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should be the number of converged
/// eigenvalues. The complex-valued eigenvalues can be constructed
/// as: lambda_{2*j} = eig[2*j]+i*eig[2*j+1] and
/// lambda_{2*j+1} = eig[2*j]-i*eig[2*j+1]
/// With j in the range [0, numConverged/2)
virtual void GetEigenvalues(Array<real_t> & eig) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, numConverged). The
/// vectors corresponding to even indices are the real parts of the
/// converged eigenvectors and the odd indices correspond to the
/// imaginary parts. If needed, the complex conjugate pairs of
/// eigenvectors can be constructed in the same manner described
/// for the eigenvalues.
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain numConverged vectors with the even
/// indices corresponding to the real parts of the converged
/// eigenvectors and the odd indices corresponding to the imaginary
/// parts.
virtual Vector ** StealEigenvectors() = 0;
};
/// Complex Eigensolver
/// Can have arbitrary complex-valued eigenvalues and eigenvectors
class ComplexEigensolver : public EigensolverBase, public ComplexEigenequation
{
protected:
ComplexEigensolver() = default;
public:
virtual ~ComplexEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should be twice the number of converged
/// eigenvalues. The complex-valued eigenvalues can be constructed
/// as: lambda_j = eig[2*j]+i*eig[2*j+1]
virtual void GetEigenvalues(Array<real_t> & eig) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, 2*numConverged). The
/// vectors corresponding to even indices are the real parts of the
/// converged eigenvectors and the odd indices correspond to the
/// imaginary parts.
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain 2*numConverged vectors with the even
/// indices corresponding to the real parts of the converged
/// eigenvectors and the odd indices corresponding to the imaginary
/// parts.
virtual Vector ** StealEigenvectors() = 0;
};
/// Complex Generalized Eigensolver
/// Can have arbitrary complex-valued eigenvalues and eigenvectors
class ComplexGenEigensolver :
public EigensolverBase, public ComplexGenEigenequation
{
protected:
ComplexGenEigensolver() = default;
public:
virtual ~ComplexGenEigensolver() = default;
/// @brief Collect the converged eigenvalues
///
/// The length of the array should be twice the number of converged
/// eigenvalues. The complex-valued eigenvalues can be constructed
/// as: lambda_j = eig[2*j]+i*eig[2*j+1]
virtual void GetEigenvalues(Array<real_t> & eig) const = 0;
/// @brief Extract a single eigenvector
///
/// The index i should be in the range [0, 2*numConverged). The
/// vectors corresponding to even indices are the real parts of the
/// converged eigenvectors and the odd indices correspond to the
/// imaginary parts.
virtual const Vector & GetEigenvector(unsigned int i) const = 0;
/// @brief Transfer ownership of the converged eigenvectors
///
/// The array should contain 2*numConverged vectors with the even
/// indices corresponding to the real parts of the converged
/// eigenvectors and the odd indices corresponding to the imaginary
/// parts.
virtual Vector ** StealEigenvectors() = 0;
};
}
#endif
+7 -25
View File
@@ -6556,7 +6556,7 @@ HypreLOBPCG::SetPreconditioner(Solver & precond)
}
void
HypreLOBPCG::SetOperator(const Operator & A)
HypreLOBPCG::SetOperator(Operator & A)
{
HYPRE_BigInt locSize = A.Width();
@@ -6603,7 +6603,7 @@ HypreLOBPCG::SetOperator(const Operator & A)
}
void
HypreLOBPCG::SetMassMatrix(const Operator & M)
HypreLOBPCG::SetMassMatrix(Operator & M)
{
matvec_fn.MatvecCreate = this->OperatorMatvecCreate;
matvec_fn.Matvec = this->OperatorMatvec;
@@ -6624,7 +6624,7 @@ HypreLOBPCG::GetEigenvalues(Array<real_t> & eigs) const
}
}
const Vector &
const HypreParVector &
HypreLOBPCG::GetEigenvector(unsigned int i) const
{
return multi_vec->GetVector(i);
@@ -6866,24 +6866,6 @@ HypreAME::SetPreconditioner(HypreSolver & precond)
ams_precond = &precond;
}
void
HypreAME::SetOperators(const Operator & opA, const Operator & opB)
{
const HypreParMatrix * A = dynamic_cast<const HypreParMatrix *>(&opA);
if (A == NULL)
{
mfem_error("HypreAME::SetOperator : first operator not HypreParMatrix!");
}
SetOperator(*A);
const HypreParMatrix * B = dynamic_cast<const HypreParMatrix *>(&opB);
if (B == NULL)
{
mfem_error("HypreAME::SetOperator : second operator not HypreParMatrix!");
}
SetMassMatrix(*B);
}
void
HypreAME::SetOperator(const HypreParMatrix & A)
{
@@ -6942,7 +6924,7 @@ HypreAME::createDummyVectors() const
}
}
const Vector &
const HypreParVector &
HypreAME::GetEigenvector(unsigned int i) const
{
if ( eigenvectors == NULL )
@@ -6953,7 +6935,7 @@ HypreAME::GetEigenvector(unsigned int i) const
return *eigenvectors[i];
}
Vector **
HypreParVector **
HypreAME::StealEigenvectors()
{
if ( eigenvectors == NULL )
@@ -6962,11 +6944,11 @@ HypreAME::StealEigenvectors()
}
// Set the local pointers to NULL so that they won't be deleted later
Vector ** vecs = (Vector**)eigenvectors;
HypreParVector ** vecs = eigenvectors;
eigenvectors = NULL;
multi_vec = NULL;
return (Vector**)vecs;
return vecs;
}
}
+20 -30
View File
@@ -18,9 +18,7 @@
#include "../general/globals.hpp"
#include "sparsemat.hpp"
#include "eigensolvers.hpp"
#include "hypre_parcsr.hpp"
#include "eigensolvers.hpp"
#include <mpi.h>
// Enable internal hypre timing routines
@@ -2148,7 +2146,7 @@ public:
A. Knyazev, M. Argentati, I. Lashuk, and E. Ovtchinnikov, SISC, 29(5),
2224-2239, 2007.
*/
class HypreLOBPCG : public SymGenEigensolver
class HypreLOBPCG
{
private:
MPI_Comm comm;
@@ -2238,43 +2236,38 @@ public:
HypreLOBPCG(MPI_Comm comm);
~HypreLOBPCG();
void SetTol(real_t tol) override;
void SetTol(real_t tol);
// not implemented in HYPRE
// real_t GetTol() const;
void SetRelTol(real_t rel_tol);
// not implemented in HYPRE
// real_t GetRelTol() const;
void SetMaxIter(int max_iter) override;
void SetMaxIter(int max_iter);
// not implemented in HYPRE
// int GetMaxIter() const;
void SetPrintLevel(int logging) override;
void SetNumModes(int num_eigs) override { nev = num_eigs; }
void SetPrintLevel(int logging);
void SetNumModes(int num_eigs) { nev = num_eigs; }
void SetPrecondUsageMode(int pcg_mode);
void SetRandomSeed(int s) { seed = s; }
void SetInitialVectors(int num_vecs, HypreParVector ** vecs);
// The following four methods support general operators
void SetPreconditioner(Solver & precond);
void SetOperators(const Operator & A, const Operator & B) override
{ SetOperator(A); SetMassMatrix(B); }
void SetOperator(const Operator & A);
void SetMassMatrix(const Operator & M);
void SetOperator(Operator & A);
void SetMassMatrix(Operator & M);
void SetSubSpaceProjector(Operator & proj) { subSpaceProj = &proj; }
/// Solve the eigenproblem
void Solve() override;
int GetNumConverged() const override { return nev; }
void Solve();
/// Collect the converged eigenvalues
void GetEigenvalues(Array<real_t> & eigenvalues) const override;
void GetEigenvalues(Array<real_t> & eigenvalues) const;
/// Extract a single eigenvector
const Vector & GetEigenvector(unsigned int i) const override;
const HypreParVector & GetEigenvector(unsigned int i) const;
/// Transfer ownership of the converged eigenvectors
Vector ** StealEigenvectors() override
{ return (Vector**)multi_vec->StealVectors(); }
HypreParVector ** StealEigenvectors() { return multi_vec->StealVectors(); }
};
/** AME eigenvalue solver in hypre
@@ -2299,7 +2292,7 @@ public:
mass matrix but it seems unlikely that this would be useful so it is not the
default behavior.
*/
class HypreAME : public SymGenEigensolver
class HypreAME
{
private:
int myid;
@@ -2328,31 +2321,28 @@ public:
HypreAME(MPI_Comm comm);
~HypreAME();
void SetTol(real_t tol) override;
void SetTol(real_t tol);
void SetRelTol(real_t rel_tol);
void SetMaxIter(int max_iter) override;
void SetPrintLevel(int logging) override;
void SetNumModes(int num_eigs) override;
void SetMaxIter(int max_iter);
void SetPrintLevel(int logging);
void SetNumModes(int num_eigs);
// The following four methods support operators of type HypreParMatrix.
void SetPreconditioner(HypreSolver & precond);
void SetOperators(const Operator & opA, const Operator & opB) override;
void SetOperator(const HypreParMatrix & A);
void SetMassMatrix(const HypreParMatrix & M);
/// Solve the eigenproblem
void Solve() override;
int GetNumConverged() const override { return nev; }
void Solve();
/// Collect the converged eigenvalues
void GetEigenvalues(Array<real_t> & eigenvalues) const override;
void GetEigenvalues(Array<real_t> & eigenvalues) const;
/// Extract a single eigenvector
const Vector & GetEigenvector(unsigned int i) const override;
const HypreParVector & GetEigenvector(unsigned int i) const;
/// Transfer ownership of the converged eigenvectors
Vector ** StealEigenvectors() override;
HypreParVector ** StealEigenvectors();
};
}
-5
View File
@@ -28,7 +28,6 @@
#include "symmat.hpp"
#include "ode.hpp"
#include "solvers.hpp"
#include "eigensolvers.hpp"
#include "handle.hpp"
#include "invariants.hpp"
#include "constraints.hpp"
@@ -58,10 +57,6 @@
#include "ginkgo.hpp"
#endif
#ifdef MFEM_USE_ARPACK
#include "arpack.hpp"
#endif
#ifdef MFEM_USE_MKL_PARDISO
#include "pardiso.hpp"
#endif
-16
View File
@@ -844,22 +844,6 @@ public:
};
/// Zero Operator N: x -> 0.
class ZeroOperator : public Operator
{
public:
/// Create an zero operator of size @a n.
explicit ZeroOperator(int n) : Operator(n) { }
/// Operator application
void Mult(const Vector &x, Vector &y) const override
{ y.SetSize(width); y = 0_r; }
/// Application of the transpose
void MultTranspose(const Vector &x, Vector &y) const override
{ y.SetSize(width); y = 0_r; }
};
/// Identity Operator I: x -> x.
class IdentityOperator : public Operator
{
+6 -9
View File
@@ -126,11 +126,11 @@ EXAMPLE_TEST_DIRS := examples
MINIAPP_SUBDIRS = common electromagnetics meshing performance tools \
toys nurbs gslib adjoint solvers shifted mtop parelag tribol autodiff dfem \
hooke multidomain dpg hdiv-linear-solver spde diag-smoothers contact \
fluids/navier fluids/schrodinger-flow plasma plasma/pic
fluids/navier fluids/schrodinger-flow plasma
MINIAPP_DIRS := $(addprefix miniapps/,$(MINIAPP_SUBDIRS))
MINIAPP_TEST_DIRS := $(filter-out %/common,$(MINIAPP_DIRS))
MINIAPP_USE_COMMON := $(addprefix miniapps/,electromagnetics meshing tools \
toys shifted dpg diag-smoothers fluids/navier plasma plasma/pic)
toys shifted dpg diag-smoothers fluids/navier plasma)
EM_DIRS = $(EXAMPLE_DIRS) $(MINIAPP_DIRS)
@@ -299,10 +299,10 @@ ifeq ($(MFEM_USE_LEGACY_OPENMP),YES)
endif
# List of MFEM dependencies, that require the *_LIB variable to be non-empty
MFEM_REQ_LIB_DEPS = SUPERLU MUMPS METIS FMS CONDUIT SIDRE LAPACK SUNDIALS\
MFEM_REQ_LIB_DEPS = SUPERLU MUMPS METIS FMS CONDUIT LAPACK SUNDIALS\
SUITESPARSE STRUMPACK GINKGO GNUTLS HDF5 NETCDF SLEPC PETSC MPFR PUMI HIOP\
GSLIB OCCA CEED RAJA UMPIRE MKL_CPARDISO MKL_PARDISO AMGX MAGMA CALIPER PARELAG\
TRIBOL BENCHMARK MOONOLITH ALGOIM ARPACK
TRIBOL BENCHMARK MOONOLITH ALGOIM
PETSC_ERROR_MSG = $(if $(PETSC_FOUND),,. PETSC config not found: $(PETSC_VARS))
@@ -365,14 +365,13 @@ MFEM_DEFINES = MFEM_VERSION MFEM_VERSION_STRING MFEM_GIT_STRING MFEM_USE_MPI\
MFEM_USE_LEGACY_OPENMP MFEM_USE_MEMALLOC MFEM_TIMER_TYPE MFEM_USE_SUNDIALS\
MFEM_USE_SUITESPARSE MFEM_USE_GINKGO MFEM_USE_SUPERLU MFEM_USE_SUPERLU5\
MFEM_USE_STRUMPACK MFEM_USE_GNUTLS MFEM_USE_HDF5 MFEM_USE_NETCDF MFEM_USE_PETSC\
MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_SIDRE MFEM_USE_FMS MFEM_USE_CONDUIT\
MFEM_USE_SLEPC MFEM_USE_MPFR MFEM_USE_FMS MFEM_USE_CONDUIT\
MFEM_USE_PUMI MFEM_USE_HIOP MFEM_USE_GSLIB MFEM_USE_CUDA MFEM_USE_HIP\
MFEM_USE_OCCA MFEM_USE_MOONOLITH MFEM_USE_CEED MFEM_USE_RAJA MFEM_USE_UMPIRE\
MFEM_USE_SIMD MFEM_USE_ADIOS2 MFEM_USE_MKL_CPARDISO MFEM_USE_MKL_PARDISO MFEM_USE_AMGX\
MFEM_USE_MAGMA MFEM_USE_MUMPS MFEM_USE_ADFORWARD MFEM_USE_CODIPACK MFEM_USE_CALIPER\
MFEM_USE_BENCHMARK MFEM_USE_PARELAG MFEM_USE_TRIBOL MFEM_USE_ALGOIM MFEM_USE_ENZYME\
MFEM_SOURCE_DIR MFEM_INSTALL_DIR MFEM_SHARED_BUILD MFEM_USE_DOUBLE MFEM_USE_SINGLE\
MFEM_USE_ARPACK
MFEM_SOURCE_DIR MFEM_INSTALL_DIR MFEM_SHARED_BUILD MFEM_USE_DOUBLE MFEM_USE_SINGLE
# List of makefile variables that will be written to config.mk:
MFEM_CONFIG_VARS = MFEM_CXX MFEM_HOST_CXX MFEM_CPPFLAGS MFEM_CXXFLAGS\
@@ -734,7 +733,6 @@ status info:
$(info MFEM_TIMER_TYPE = $(MFEM_TIMER_TYPE))
$(info MFEM_USE_SUNDIALS = $(MFEM_USE_SUNDIALS))
$(info MFEM_USE_SUITESPARSE = $(MFEM_USE_SUITESPARSE))
$(info MFEM_USE_ARPACK = $(MFEM_USE_ARPACK))
$(info MFEM_USE_SUPERLU = $(MFEM_USE_SUPERLU))
$(info MFEM_USE_SUPERLU5 = $(MFEM_USE_SUPERLU5))
$(info MFEM_USE_MUMPS = $(MFEM_USE_MUMPS))
@@ -748,7 +746,6 @@ status info:
$(info MFEM_USE_PETSC = $(MFEM_USE_PETSC))
$(info MFEM_USE_SLEPC = $(MFEM_USE_SLEPC))
$(info MFEM_USE_MPFR = $(MFEM_USE_MPFR))
$(info MFEM_USE_SIDRE = $(MFEM_USE_SIDRE))
$(info MFEM_USE_FMS = $(MFEM_USE_FMS))
$(info MFEM_USE_CONDUIT = $(MFEM_USE_CONDUIT))
$(info MFEM_USE_PUMI = $(MFEM_USE_PUMI))
+1 -3
View File
@@ -1616,9 +1616,7 @@ Element::Type Mesh::GetFaceElementType(int Face) const
Array<int> Mesh::GetFaceToBdrElMap() const
{
Array<int> face_to_be(Dim == 1 ? NumOfVertices :
Dim == 2 ? NumOfEdges :
Dim == 3 ? NumOfFaces : 0);
Array<int> face_to_be(Dim == 2 ? NumOfEdges : NumOfFaces);
face_to_be = -1;
for (int i = 0; i < NumOfBdrElements; i++)
{
+3
View File
@@ -63,6 +63,7 @@ ThresholdRefiner::ThresholdRefiner(ErrorEstimator &est)
threshold = 0.0;
num_marked_elements = 0LL;
current_sequence = -1;
non_conforming = -1;
nc_limit = 0;
@@ -86,6 +87,7 @@ int ThresholdRefiner::MarkWithoutRefining(Mesh & mesh,
threshold = 0.0;
num_marked_elements = 0LL;
refinements.SetSize(0);
current_sequence = mesh.GetSequence();
const long long num_elements = mesh.GetGlobalNE();
if (num_elements >= max_elements) { return STOP; }
@@ -147,6 +149,7 @@ int ThresholdRefiner::ApplyImpl(Mesh &mesh)
void ThresholdRefiner::Reset()
{
estimator.Reset();
current_sequence = -1;
num_marked_elements = 0LL;
// marked_elements.SetSize(0); // not necessary
}
+1
View File
@@ -188,6 +188,7 @@ protected:
long long num_marked_elements;
Array<Refinement> marked_elements;
long current_sequence;
int non_conforming;
int nc_limit;
+3 -17
View File
@@ -227,29 +227,15 @@ public:
const ParGridFunction &dst);
/**
* @brief Check if Mesh @a m is a ParSubMesh.
* @brief Check if ParMesh @a m is a ParSubMesh.
*
* @param m The input Mesh
* @param m The input ParMesh
*/
static bool IsParSubMesh(const Mesh *m)
static bool IsParSubMesh(const ParMesh *m)
{
return dynamic_cast<const ParSubMesh *>(m) != nullptr;
}
/**
* @brief Check if Mesh @a sub is a ParSubMesh of Mesh @a parent.
*
* @param sub The potential submesh Mesh
* @param parent The potential parent Mesh
*/
static bool IsParSubMesh(const Mesh* sub, const Mesh* parent)
{
while (IsParSubMesh(sub) &&
(sub = static_cast<const ParSubMesh *>(sub)->GetParent()) &&
sub != parent);
return sub == parent;
}
private:
ParSubMesh(const ParMesh &parent, SubMesh::From from,
const Array<int> &attributes);
-14
View File
@@ -225,20 +225,6 @@ public:
return dynamic_cast<const SubMesh *>(m) != nullptr;
}
/**
* @brief Check if Mesh @a sub is a SubMesh of Mesh @a parent.
*
* @param sub The potential submesh Mesh
* @param parent The potential parent Mesh
*/
static bool IsSubMesh(const Mesh* sub, const Mesh* parent)
{
while (IsSubMesh(sub) &&
(sub = static_cast<const SubMesh *>(sub)->GetParent()) &&
sub != parent);
return sub == parent;
}
private:
/// Private constructor
SubMesh(const Mesh &parent, From from, const Array<int> &attributes);
+38 -1
View File
@@ -82,6 +82,43 @@ Although Tribol can be built automatically via **uberenv** and **Spack**,
for this miniapp it is simpler to build **Axom** and **MFEM** manually and
point Tribol to them. The steps are as follows:
### Using pre-built Tribol/Axom installs
If you already have compatible installs of Tribol and Axom, point MFEM to the install prefixes.
- Hypre install prefix: `<path/to/hypre>`
- METIS install prefix: `<path/to/metis>`
- Axom install prefix: `<path/to/axom>`
- Tribol install prefix: `<path/to/tribol>`
**MFEM make build (configure):**
```bash
make config MFEM_USE_MPI=YES MFEM_USE_METIS=YES MFEM_USE_TRIBOL=YES \
HYPRE_DIR=<path/to/hypre> METIS_DIR=<path/to/metis> \
AXOM_DIR=<path/to/axom> TRIBOL_DIR=<path/to/tribol> ADIAK_DIR=<path/to/adiak> CAMP_DIR=<path/to/camp> RAJA_DIR=<path/to/raja> \
UMPIRE_DIR=<path/to/umpire> FMT_DIR=<path/to/fmt> CALIPER_DIR=<path/to/caliper>
```
**MFEM CMake build (configure):**
```bash
cmake -S . -B <mfem-build-dir> -DMFEM_USE_MPI=YES -DMFEM_USE_METIS=YES -DMFEM_USE_TRIBOL=YES \
HYPRE_DIR=<path/to/hypre> METIS_DIR=<path/to/metis> \
AXOM_DIR=<path/to/axom> TRIBOL_DIR=<path/to/tribol> ADIAK_DIR=<path/to/adiak> CAMP_DIR=<path/to/camp> RAJA_DIR=<path/to/raja> \
UMPIRE_DIR=<path/to/umpire> FMT_DIR=<path/to/fmt> CALIPER_DIR=<path/to/caliper>
```
Note: RAJA/UMPIRE/CALIPER are optional for MFEM itself, but many Tribol builds
enable them. If your Tribol install does not depend on them, you can omit the
corresponding `*_DIR` entries above.
Note: `FMT_DIR` only needs to be added for the make-based build (and only when
the Umpire install uses `fmt`). If `FMT_DIR` is not set and a sibling `fmt-*`
directory exists next to your `UMPIRE_DIR`, MFEM's make configuration will try
to pick it up automatically.
Note: when using pre-built Tribol/Axom, you typically need to use a compatible
compiler/MPI wrapper (same C++ standard library ABI).
### Manual Build Steps
1. Pull axom and tribol (starting from the mfem folder):
@@ -99,7 +136,7 @@ point Tribol to them. The steps are as follows:
TRIBOL_DIR = @MFEM_DIR@/../tribol-repo/tribol
TRIBOL_OPT = -I$(TRIBOL_DIR)/include -I$(AXOM_DIR)/include
TRIBOL_LIB = -L$(TRIBOL_DIR)/lib -ltribol -lredecomp -L$(AXOM_DIR)/lib \
-laxom_mint -laxom_slam -laxom_slic -laxom_core
-laxom_quest -laxom_mint -laxom_slam -laxom_slic -laxom_lumberjack -laxom_core
```
3. [**Axom:**](https://github.com/LLNL/axom.git) Starting from the MFEM root
directory (we assume this directory is named mfem):
+6 -55
View File
@@ -43,39 +43,19 @@ endif()
# Add the corresponding tests to the "test" target
if (MFEM_ENABLE_TESTING)
add_test(NAME tesla_1_np=${MFEM_MPI_NP}
add_test(NAME tesla_np=4
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:tesla> -no-vis -maxit 2 -cr "0 0 -0.2 0 0 0.2 0.2 0.4 1"
${MPIEXEC_POSTFLAGS})
add_test(NAME tesla_2_np=${MFEM_MPI_NP}
add_test(NAME volta_np=4
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:tesla>
-no-vis -maxit 2 -m ../../data/inline-hex.mesh -ubbc "0 0 1"
$<TARGET_FILE:volta> -no-vis -maxit 2 -dbcs 1 -dbcg -ds "0.0 0.0 0.0 0.2 8.0"
${MPIEXEC_POSTFLAGS})
add_test(NAME volta_1_np=${MFEM_MPI_NP}
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:volta>
-no-vis -maxit 2 -dbcs 1 -dbcg -ds "0.0 0.0 0.0 0.2 8.0"
${MPIEXEC_POSTFLAGS})
add_test(NAME volta_2_np=${MFEM_MPI_NP}
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:volta>
-no-vis -maxit 2 -m ../../data/square-disc.mesh -dbcs "1 2 3 4 5 6 7 8"
-dbcv "0 0 0 0 1 1 1 1"
${MPIEXEC_POSTFLAGS})
add_test(NAME volta_3_np=${MFEM_MPI_NP}
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:volta>
-no-vis -maxit 2 -m ../../data/inline-hex.mesh -dbcs "1 6" -dbcv "0 1"
${MPIEXEC_POSTFLAGS})
add_test(NAME joule_np=${MFEM_MPI_NP}
add_test(NAME joule_np=4
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:joule>
@@ -83,41 +63,12 @@ endif()
${MPIEXEC_POSTFLAGS})
if (MFEM_USE_DOUBLE) # otherwise returns MFEM_SKIP_RETURN_VALUE
add_test(NAME maxwell_np=${MFEM_MPI_NP}
add_test(NAME maxwell_np=4
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:maxwell>
-no-vis -abcs "-1" -dp "-0.3 0.0 0.0 0.3 0.0 0.0 0.1 1 .5 .5"
${MPIEXEC_POSTFLAGS})
endif()
if (MFEM_USE_GSLIB)
add_test(NAME lorentz_1_np=${MFEM_MPI_NP}
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:lorentz>
-no-vis -er Volta-AMR-Parallel -ec 2 -npt 100 -xmin "0.0 0.0 0.0"
-xmax "1.0 1.0 1.0" -pmin "1 0 0" -pmax "1 0 0" -rdf 0 -vt 0 -nt 100
${MPIEXEC_POSTFLAGS})
# Setup dependency on volta_3_np=<np>
set_tests_properties(volta_3_np=${MFEM_MPI_NP}
PROPERTIES FIXTURES_SETUP Volta3)
set_tests_properties(lorentz_1_np=${MFEM_MPI_NP}
PROPERTIES FIXTURES_REQUIRED Volta3)
add_test(NAME lorentz_2_np=${MFEM_MPI_NP}
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:lorentz>
-no-vis -br Tesla-AMR-Parallel -bc 2 -npt 10 -xmin "0.0 0.0 0.0"
-xmax "1.0 1.0 1.0" -pmin "0 0.1 0.05" -pmax "0 0.4 0.1" -nt 1000 -rdf 0
-vt 0
${MPIEXEC_POSTFLAGS})
# Setup dependency on tesla_2_np=<np>
set_tests_properties(tesla_2_np=${MFEM_MPI_NP}
PROPERTIES FIXTURES_SETUP Tesla2)
set_tests_properties(lorentz_2_np=${MFEM_MPI_NP}
PROPERTIES FIXTURES_REQUIRED Tesla2)
endif()
endif()
endif()
+2 -2
View File
@@ -117,10 +117,10 @@ joule-test-par: joule
lorentz-test-par: lorentz-test-1 lorentz-test-2
lorentz-test-1: lorentz volta-test-3
@$(call mfem-test,$<, $(RUN_MPI), Electromagnetic miniapp,\
-er Volta-AMR-Parallel -ec 2 -npt 100 -xmin '0.0 0.0 0.0' -xmax '1.0 1.0 1.0' -pmin '1 0 0' -pmax '1 0 0' -rdf 0 -vt 0 -nt 100)
-er Volta-AMR-Parallel -ec 2 -npt 100 -xmin '0.0 0.0 0.0' -xmax '1.0 1.0 1.0' -pmin '1 0 0' -pmax '1 0 0' -rdf 0 -vt 0 -nt 100')
lorentz-test-2: lorentz tesla-test-2
@$(call mfem-test,$<, $(RUN_MPI), Electromagnetic miniapp,\
-br Tesla-AMR-Parallel -bc 2 -npt 10 -xmin '0.0 0.0 0.0' -xmax '1.0 1.0 1.0' -pmin '0 0.1 0.05' -pmax '0 0.4 0.1' -nt 1000 -rdf 0 -vt 0)
-br Tesla-AMR-Parallel -bc 2 -br Tesla-AMR-Parallel -npt 10 -xmin '0.0 0.0 0.0' -xmax '1.0 1.0 1.0' -pmin '0 0.1 0.05' -pmax '0 0.4 0.1' -nt 1000 -rdf 0 -vt 0)
# Testing: "test" target and mfem-test* variables are defined in config/test.mk
+2 -2
View File
@@ -22,7 +22,7 @@ void ComputeInverse(const Array<real_t> &A, Array<real_t> &Ainv)
{
Array<real_t> A2 = A;
const int n2 = A.Size();
const int n = static_cast<int>(sqrt(n2));
const int n = static_cast<const int>(sqrt(n2));
Array<int> ipiv(n);
LUFactors lu(A2.GetData(), ipiv.GetData());
lu.Factor(n);
@@ -58,7 +58,7 @@ void SubcellIntegrals(int n, const Poly_1D::Basis &basis, Array<real_t> &B)
void Transpose(const Array<real_t> &B, Array<real_t> &Bt)
{
const int n = static_cast<int>(sqrt(B.Size()));
const int n = static_cast<const int>(sqrt(B.Size()));
Bt.SetSize(n*n);
for (int i=0; i<n; ++i) for (int j=0; j<n; ++j) { Bt[i+j*n] = B[j+i*n]; }
}
+4 -4
View File
@@ -329,8 +329,8 @@ int main(int argc, char *argv[])
for (int i=0; i<nev; i++)
{
// convert eigenvector from Vector to ParGridFunction
x.Distribute(lobpcg->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = lobpcg->GetEigenvector(i);
mode_name << "mode_" << setfill('0') << setw(2) << i << "."
<< setfill('0') << setw(6) << myid;
@@ -357,8 +357,8 @@ int main(int argc, char *argv[])
<< ", Lambda = " << eigenvalues[i] << endl;
}
// convert eigenvector from Vector to ParGridFunction
x.Distribute(lobpcg->GetEigenvector(i));
// convert eigenvector from HypreParVector to ParGridFunction
x = lobpcg->GetEigenvector(i);
mode_sock << "parallel " << num_procs << " " << myid << "\n"
<< "solution\n" << *pmesh << x << flush
-2
View File
@@ -23,5 +23,3 @@ if (MFEM_USE_MPI)
EXTRA_HEADERS ${PLASMA_COMMON_HEADERS})
endif()
add_subdirectory(pic)
+6 -14
View File
@@ -14,6 +14,9 @@ MFEM_DIR ?= ../..
MFEM_BUILD_DIR ?= ../..
SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/miniapps/plasma/,)
CONFIG_MK = $(MFEM_BUILD_DIR)/config/config.mk
# Use the MFEM install directory
# MFEM_INSTALL_DIR = ../../mfem
# CONFIG_MK = $(MFEM_INSTALL_DIR)/share/mfem/config.mk
MFEM_LIB_FILE = mfem_is_not_built
-include $(CONFIG_MK)
@@ -26,8 +29,6 @@ else
MINIAPPS = $(PAR_MINIAPPS) $(SEQ_MINIAPPS)
endif
PLASMA_SUBDIRS = pic
.SUFFIXES:
.SUFFIXES: .o .cpp .mk
.PHONY: all lib-common clean clean-build clean-exec
@@ -46,12 +47,7 @@ COMMON_O=
%: %.cpp
%.o: %.cpp
all: $(MINIAPPS) subdirs
.PHONY: subdirs $(PLASMA_SUBDIRS)
subdirs: $(PLASMA_SUBDIRS)
$(PLASMA_SUBDIRS): lib-common
$(MAKE) -C $(BLD)$(@)
all: $(MINIAPPS)
# Rules for building the miniapps
%: $(SRC)%.cpp $(COMMON_O) $(MFEM_LIB_FILE) $(CONFIG_MK) | lib-common
@@ -79,15 +75,11 @@ RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
$(MFEM_LIB_FILE):
$(error The MFEM library is not built)
ALL_CLEAN_SUBDIRS = $(addsuffix /clean,$(PLASMA_SUBDIRS))
.PHONY: $(ALL_CLEAN_SUBDIRS)
$(ALL_CLEAN_SUBDIRS):
$(MAKE) -C $(BLD)$(@D) $(@F)
clean: clean-build clean-exec
clean-build: $(addsuffix /clean,$(PLASMA_SUBDIRS))
clean-build:
rm -f *.o *~ $(SEQ_MINIAPPS) $(PAR_MINIAPPS)
rm -rf *.dSYM *.TVD.*breakpoints
clean-exec:
-28
View File
@@ -1,28 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
if (MFEM_USE_MPI AND MFEM_USE_GSLIB)
add_mfem_miniapp(electrostatic-pic
MAIN electrostatic-pic.cpp
EXTRA_HEADERS ${MFEM_MINIAPPS_COMMON_HEADERS}
LIBRARIES mfem-common)
# Add the corresponding tests to the "test" target
if (MFEM_ENABLE_TESTING)
add_test(NAME electrostatic-pic_np=${MFEM_MPI_NP}
COMMAND ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${MFEM_MPI_NP}
${MPIEXEC_PREFLAGS}
$<TARGET_FILE:electrostatic-pic> -rdi 2 -npt 40960 -k 0.2855993321 -a 0.05
-nt 200 -nx 16 -ny 16 -O 1 -q 0.01181640625 -m 0.01181640625 -oci 1000
-dt 0.1
${MPIEXEC_POSTFLAGS})
endif()
endif()
-788
View File
@@ -1,788 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
//
// -----------------------------------------------------
// Particle-In-Cell (PIC) Simulation (2D/3D)
// -----------------------------------------------------
//
// This miniapp performs a Particle-In-Cell simulation (supports 2D or 3D
// spatial dimensions) of multiple charged particles subject to electric
// field forces.
//
// dp/dt = q E
//
// The method used is explicit time integration with a leap-frog scheme.
//
// The electric field is computed from the particle charge distribution using
// a Poisson solver. The particle trajectories are computed within a periodic
// domain (2D or 3D).
//
// Solution process (per timestep, repeating steps 1-6):
// (1) Deposit charge from particles to grid via Dirac delta function
// to form the RHS of the Poisson equation
// (2) Solve Poisson equation (-Δφ = ρ - ρ_0) to compute potential φ, where
// ρ_0 is a constant neutralizing term that enforces global charge
// neutrality.
// (3) Compute electric field E = -∇φ from the potential
// (4) Interpolate E-field to particle positions
// (5) Push particles using leap-frog scheme (update momentum and position)
// (6) Redistribute particles across processors
//
// Compile with: make electrostatic-pic
//
// Sample runs:
//
// 2D2V Linear Landau damping test case (Ricketson & Hu, 2025):
// mpirun -n 4 ./electrostatic-pic -rdi 1 -npt 409600 -k 0.2855993321 -a 0.05 -nt 200 -nx 32 -ny 32 -O 1 -q 0.001181640625 -m 0.001181640625 -oci 1000 -dt 0.1
// 3D3V Linear Landau damping test case (Zheng et al., 2025):
// * mpirun -n 128 ./electrostatic-pic -dim 3 -rdi 1 -npt 40960000 -k 0.5 -a 0.01 -nt 100 -nx 32 -ny 32 -nz 32 -O 1 -q 0.00004844730731 -m 0.00004844730731 -oci 1000 -dt 0.02 -no-vis
#include "mfem.hpp"
#include "../../../general/text.hpp"
#include "../../common/fem_extras.hpp"
#include "../../common/particles_extras.hpp"
#include "../../common/pfem_extras.hpp"
#include <ctime>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <random>
#include <string>
#include <vector>
#define EPSILON 1 // ε_0
using namespace std;
using namespace mfem;
using namespace mfem::common;
struct PICContext
{
int dim = 2; ///< Spatial dimension.
int order = 1; ///< FE order for spatial discretization.
int nx = 100; ///< Number of grid cells in x-direction.
int ny = 100; ///< Number of grid cells in y-direction.
int nz = 100; ///< Number of grid cells in z-direction.
real_t L = 1.0; ///< Domain length.
int ordering = 1; ///< Ordering of particles.
int npt = 1000; ///< Number of particles.
real_t q = 1.0; ///< Particle charge.
real_t m = 1.0; ///< Particle mass.
real_t k = 1.0; ///< Wave number (Landau damping init).
real_t alpha = 0.1; ///< Perturbation amplitude (Landau damping init).
real_t dt = 1e-2; ///< Time step size.
int nt = 1000; ///< Number of time steps to run.
int redist_interval = 5; ///< Redistribution and update E_gf interval.
int output_csv_interval = 1000; ///< Interval for outputting CSV data files.
bool visualization = true; ///< Enable visualization.
int visport = 19916; ///< Port number for visualization server.
bool reproduce = true; ///< Enable reproducible results.
} ctx;
/** This class implements explicit time integration for charged particles
in an electric field using ParticleSet. */
class ParticleMover
{
public:
enum Fields
{
MASS, // vdim = 1
CHARGE, // vdim = 1
MOM, // vdim = dim
EFIELD // vdim = dim
};
protected:
/// Pointers to E field GridFunctions
ParGridFunction* E_gf;
/// FindPointsGSLIB object for E field mesh
FindPointsGSLIB& E_finder;
/// ParticleSet of charged particles
std::unique_ptr<ParticleSet> charged_particles;
/// Temporary vectors for particle computation
mutable Vector pm_, pp_;
public:
ParticleMover(MPI_Comm comm, ParGridFunction* E_gf_,
FindPointsGSLIB& E_finder_, int num_particles,
Ordering::Type pdata_ordering);
/// Initialize charged particles with given parameters
void InitializeChargedParticles(const real_t& k, const real_t& alpha,
real_t m, real_t q, real_t L,
bool reproduce = false);
/// Find Particles in mesh corresponding to E and field
void FindParticles();
/// Advance particles one time step using Boris algorithm
void Step(real_t& t, real_t dt, real_t L, bool first_step = false);
/// Redistribute particles across processors
void Redistribute();
/// Get reference to ParticleSet
ParticleSet& GetParticles() { return *charged_particles; }
/// Compute (global) kinetic energy from particles
/** Optionally, advance the particle momenta by time step @a dt. */
real_t ComputeKineticEnergy(real_t dt = 0.) const;
};
/** Field solver responsible for updating the electrostatic potential and field
from the particle charge density. Assembles and solves the periodic Poisson
problem, computes the electric field via a discrete gradient operator, and
provides utilities for field diagnostics (e.g. global field energy). */
class FieldSolver
{
private:
real_t domain_volume;
real_t neutralizing_const;
ParLinearForm* precomputed_neutralizing_lf = nullptr;
bool precompute_neutralizing_const = false;
// Diffusion matrix
HypreParMatrix* diffusion_matrix;
// Gradient operator for computing E = -∇φ
ParDiscreteLinearOperator* grad_interpolator;
FindPointsGSLIB& E_finder;
ParLinearForm b;
protected:
/** Compute neutralizing constant and initialize with the constant.
Returns a reference to the precomputed neutralizing ParLinearForm. */
const ParLinearForm& ComputeNeutralizingRHS(ParFiniteElementSpace* pfes,
const ParticleVector& Q,
MPI_Comm comm);
/** Deposit charge from particles into a ParLinearForm (RHS b).
b_i = sum_p q_p * φ_i(x_p) */
void DepositCharge(ParFiniteElementSpace* pfes, const ParticleVector& Q);
public:
FieldSolver(ParFiniteElementSpace* phi_fes, ParFiniteElementSpace* E_fes,
FindPointsGSLIB& E_finder_,
bool precompute_neutralizing_const_ = false);
~FieldSolver();
/** Update the phi_gf grid function from the particles.
Solve periodic Poisson: diffusion_matrix * phi = (rho - <rho>)
with zero-mean enforcement via OrthoSolver. */
void UpdatePhiGridFunction(ParticleSet& particles, ParGridFunction& phi_gf);
/** Update E_gf grid function from phi_gf grid function.
Compute the gradient: E = -φ. */
void UpdateEGridFunction(ParGridFunction& phi_gf, ParGridFunction& E_gf);
/// Compute (global) field energy: 0.5 * ∫ ||E||^2 dx
real_t ComputeFieldEnergy(const ParGridFunction& E_gf) const;
};
/// Prints the program's logo to the given output stream
void display_banner(ostream& os);
int main(int argc, char* argv[])
{
Mpi::Init(argc, argv);
int num_ranks = Mpi::WorldSize();
int rank = Mpi::WorldRank();
Hypre::Init();
if (Mpi::Root()) { display_banner(cout); }
OptionsParser args(argc, argv);
args.AddOption(&ctx.dim, "-dim", "--dimension",
"Spatial dimension (2 or 3)");
args.AddOption(&ctx.order, "-O", "--order",
"Finite element polynomial degree");
args.AddOption(&ctx.nx, "-nx", "--num-x",
"Number of elements in the x direction.");
args.AddOption(&ctx.ny, "-ny", "--num-y",
"Number of elements in the y direction.");
args.AddOption(&ctx.nz, "-nz", "--num-z",
"Number of elements in the z direction.");
args.AddOption(&ctx.q, "-q", "--charge", "Particle charge.");
args.AddOption(&ctx.m, "-m", "--mass", "Particle mass.");
args.AddOption(&ctx.dt, "-dt", "--time-step", "Time Step.");
args.AddOption(&ctx.nt, "-nt", "--num-timesteps", "Number of timesteps.");
args.AddOption(&ctx.npt, "-npt", "--num-particles",
"Total number of particles.");
args.AddOption(&ctx.k, "-k", "--k", "Wave number for initial distribution.");
args.AddOption(&ctx.alpha, "-a", "--alpha",
"Perturbation amplitude for initial distribution.");
args.AddOption(&ctx.ordering, "-o", "--ordering",
"Ordering of particle data. 0 = byNODES, 1 = byVDIM.");
args.AddOption(&ctx.redist_interval, "-rdi", "--redist-interval",
"Redistribution and update E_gf interval. Disabled if < 0.");
args.AddOption(&ctx.output_csv_interval, "-oci", "--output-csv-interval",
"Output CSV interval. Disabled if < 0.");
args.AddOption(&ctx.visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.AddOption(&ctx.visport, "-p", "--send-port", "Socket for GLVis.");
args.AddOption(&ctx.reproduce, "-rep", "--reproduce", "-no-rep",
"--no-reproduce",
"Enable or disable reproducible random seed.");
args.Parse();
if (!args.Good())
{
if (Mpi::Root()) { args.PrintUsage(cout); }
return 1;
}
if (Mpi::Root()) { args.PrintOptions(cout); }
// Assert that dimension is 2 or 3
MFEM_VERIFY(ctx.dim == 2 || ctx.dim == 3,
"Dimension must be 2 or 3, got " << ctx.dim);
MFEM_VERIFY(ctx.alpha >= -1.0 && ctx.alpha < 1.0,
"Alpha should be in range [-1, 1).");
MFEM_VERIFY(ctx.k > 0.0,
"k must be nonzero for displacement initialization.");
ctx.L = 2.0 * M_PI / ctx.k;
// 1. make a Cartesian Mesh (2D or 3D)
Mesh serial_mesh;
std::vector<Vector> translations;
if (ctx.dim == 2)
{
serial_mesh = Mesh(Mesh::MakeCartesian2D(
ctx.nx, ctx.ny, Element::QUADRILATERAL, false, ctx.L, ctx.L));
translations = {Vector({ctx.L, 0.0}), Vector({0.0, ctx.L})};
}
else // ctx.dim == 3
{
serial_mesh = Mesh(Mesh::MakeCartesian3D(
ctx.nx, ctx.ny, ctx.nz, Element::HEXAHEDRON, ctx.L, ctx.L, ctx.L));
translations = {Vector({ctx.L, 0.0, 0.0}), Vector({0.0, ctx.L, 0.0}),
Vector({0.0, 0.0, ctx.L})
};
}
Mesh periodic_mesh(Mesh::MakePeriodic(
serial_mesh, serial_mesh.CreatePeriodicVertexMapping(translations)));
// 2. Partition and distribute the mesh
ParMesh mesh(MPI_COMM_WORLD, periodic_mesh);
serial_mesh.Clear(); // the serial mesh is no longer needed
periodic_mesh.Clear(); // the periodic mesh is no longer needed
// 3. Build the interpolator of E field
mesh.EnsureNodes();
FindPointsGSLIB E_finder(mesh);
// 4. Define finite element spaces on the parallel mesh
H1_FECollection phi_fec(ctx.order, ctx.dim);
ParFiniteElementSpace phi_fespace(&mesh, &phi_fec);
ND_FECollection E_fec(ctx.order, ctx.dim);
ParFiniteElementSpace E_fespace(&mesh, &E_fec);
// 5. Initialize the grid functions for the electric field and potential
ParGridFunction phi_gf(&phi_fespace);
ParGridFunction E_gf(&E_fespace);
phi_gf = 0.0; // Initialize phi_gf to zero
E_gf = 0.0; // Initialize E_gf to zero
// 6. Construct the field solver
FieldSolver field_solver(&phi_fespace, &E_fespace, E_finder, true);
// 7. Initialize ParticleMover
Ordering::Type ordering_type =
ctx.ordering == 0 ? Ordering::byNODES : Ordering::byVDIM;
int num_particles =
ctx.npt / num_ranks + (rank < (ctx.npt % num_ranks) ? 1 : 0);
ParticleMover particle_mover(MPI_COMM_WORLD, &E_gf, E_finder, num_particles,
ordering_type);
particle_mover.InitializeChargedParticles(ctx.k, ctx.alpha, ctx.m, ctx.q,
ctx.L, ctx.reproduce);
// 8. Start the main loop
real_t t = 0;
real_t dt = ctx.dt;
mfem::StopWatch sw;
sw.Start();
for (int step = 1; step <= ctx.nt; step++)
{
// Step the FieldSolver
if (ctx.redist_interval > 0 &&
(step % ctx.redist_interval == 0 || step == 1) &&
particle_mover.GetParticles().GetGlobalNParticles() > 0)
{
// Redistribute
particle_mover.Redistribute();
// Update phi_gf from particles
field_solver.UpdatePhiGridFunction(particle_mover.GetParticles(),
phi_gf);
// Update E_gf from phi_gf
field_solver.UpdateEGridFunction(phi_gf, E_gf);
// Visualize fields if requested
if (ctx.visualization)
{
static socketstream vis_e, vis_phi;
common::VisualizeField(vis_e, "localhost", ctx.visport, E_gf,
"E_field", 0, 0, 500, 500);
common::VisualizeField(vis_phi, "localhost", ctx.visport, phi_gf,
"Potential", 500, 0, 500, 500);
}
}
// Step the ParticleMover
particle_mover.Step(t, dt, ctx.L, step == 1);
if (Mpi::Root())
{
mfem::out << "Step: " << step << " | Time: " << t;
mfem::out << " | Time per step: " << sw.RealTime() / step;
mfem::out << endl;
}
// Output particle data to CSV
if (ctx.output_csv_interval > 0 &&
(step % ctx.output_csv_interval == 0 || step == 1))
{
std::string csv_prefix = "PIC_Part_";
Array<int> field_idx{2}, tag_idx;
std::string file_name =
csv_prefix + mfem::to_padded_string(step, 6) + ".csv";
particle_mover.GetParticles().PrintCSV(file_name.c_str(), field_idx,
tag_idx);
}
if (ctx.redist_interval > 0 &&
(step % ctx.redist_interval == 0 || step == 1) &&
particle_mover.GetParticles().GetGlobalNParticles() > 0)
{
// Compute energies
// Note that particle momenta are a half time step ahead of the field
// after particle_mover.Step(). Therefore they are returned to the
// time level of the field for calculation of kinetic energy.
real_t kinetic_energy = particle_mover.ComputeKineticEnergy(-dt/2.);
real_t field_energy = field_solver.ComputeFieldEnergy(E_gf);
// Output energies
if (Mpi::Root())
{
cout << "Kinetic energy: " << kinetic_energy << "\t"
<< "Field energy: " << field_energy << "\t"
<< "Total energy: " << kinetic_energy + field_energy
<< endl;
}
// Write energies to a CSV file
if (Mpi::Root())
{
std::ofstream energy_file("energy.csv", std::ios::app);
energy_file << setprecision(10) << kinetic_energy << ","
<< field_energy << "," << kinetic_energy + field_energy
<< "\n";
}
}
}
}
ParticleMover::ParticleMover(MPI_Comm comm, ParGridFunction* E_gf_,
FindPointsGSLIB& E_finder_, int num_particles,
Ordering::Type pdata_ordering)
: E_gf(E_gf_), E_finder(E_finder_)
{
MFEM_ASSERT(E_gf, "Must pass an E field to ParticleMover.");
int dim = E_gf->ParFESpace()->GetMesh()->SpaceDimension();
pm_.SetSize(dim);
pp_.SetSize(dim);
// Create particle set: 2 scalars of mass and charge,
// 2 vectors of size space dim for momentum and e field
Array<int> field_vdims({1, 1, dim, dim});
charged_particles = std::make_unique<ParticleSet>(
comm, num_particles, dim, field_vdims, 1, pdata_ordering);
}
void ParticleMover::InitializeChargedParticles(const real_t& k,
const real_t& alpha, real_t m,
real_t q, real_t L,
bool reproduce)
{
int rank;
MPI_Comm_rank(charged_particles->GetComm(), &rank);
// use time-based seed for randomness
std::mt19937 gen(
reproduce ? rank : (rank + static_cast<unsigned int>(time(nullptr))));
std::uniform_real_distribution<> real_dist(0.0, 1.0);
std::normal_distribution<> norm_dist(0.0, 1.0);
int dim = charged_particles->Coords().GetVDim();
ParticleVector& X = charged_particles->Coords();
ParticleVector& P = charged_particles->Field(ParticleMover::MOM);
ParticleVector& M = charged_particles->Field(ParticleMover::MASS);
ParticleVector& Q = charged_particles->Field(ParticleMover::CHARGE);
for (int i = 0; i < charged_particles->GetNParticles(); i++)
{
// Initialize momentum
for (int d = 0; d < dim; d++) { P(i, d) = m * norm_dist(gen); }
// Uniform positions (no accept-reject)
for (int d = 0; d < dim; d++) { X(i, d) = real_dist(gen) * L; }
// Displacement along x for perturbation ~ cos(k x)
for (int d = 0; d < dim; d++)
{
real_t x = X(i, d);
x -= (alpha / k) * std::sin(k * x);
// periodic wrap to [0, L)
x = std::fmod(x, L);
if (x < 0) { x += L; }
X(i, d) = x;
}
// Initialize mass + charge
M(i) = m;
Q(i) = q;
}
FindParticles();
}
void ParticleMover::FindParticles()
{
E_finder.FindPoints(charged_particles->Coords());
}
void ParticleMover::Step(real_t& t, real_t dt, real_t L, bool first_step)
{
// Update E field at particles
ParticleVector& E = charged_particles->Field(EFIELD);
E_finder.Interpolate(*E_gf, E, E.GetOrdering());
// Extract particle data
ParticleVector& X = charged_particles->Coords();
ParticleVector& P = charged_particles->Field(MOM);
ParticleVector& M = charged_particles->Field(MASS);
ParticleVector& Q = charged_particles->Field(CHARGE);
// Accelerate the particles by the electric field
const int npt = charged_particles->GetNParticles();
const int dim = X.GetVDim();
for (int particle = 0; particle < npt; ++particle)
{
for (int d = 0; d < dim; ++d)
{
P(particle, d) +=
(first_step ? dt / 2.0 : dt) * Q(particle) * E(particle, d);
}
}
// Periodic boundary: wrap coordinates to [0, L)
for (int particle = 0; particle < npt; ++particle)
{
for (int d = 0; d < dim; ++d)
{
X(particle, d) += dt / M(particle) * P(particle, d);
while (X(particle, d) > L) { X(particle, d) -= L; }
while (X(particle, d) < 0.0) { X(particle, d) += L; }
}
}
FindParticles();
// Update time
t += dt;
}
void ParticleMover::Redistribute()
{
charged_particles->Redistribute(E_finder.GetProc());
FindParticles();
}
real_t ParticleMover::ComputeKineticEnergy(real_t dt) const
{
const ParticleVector& P = charged_particles->Field(MOM);
const ParticleVector& M = charged_particles->Field(MASS);
const ParticleVector& Q = charged_particles->Field(CHARGE);
const ParticleVector& E = charged_particles->Field(EFIELD);
// Note the electric field is not reinterpolated here and the last
// update from Step() is used directly.
real_t kinetic_energy = 0.0;
for (int p = 0; p < charged_particles->GetNParticles(); ++p)
{
real_t p_square_p = 0.0;
for (int d = 0; d < P.GetVDim(); ++d)
{
const real_t P_m = P(p, d) + dt * Q(p) * E(p, d);
p_square_p += P_m * P_m;
}
kinetic_energy += 0.5 * p_square_p / M(p);
}
real_t global_kinetic_energy = 0.0;
MPI_Allreduce(&kinetic_energy, &global_kinetic_energy, 1, MPI_DOUBLE,
MPI_SUM, charged_particles->GetComm());
return global_kinetic_energy;
}
FieldSolver::FieldSolver(ParFiniteElementSpace* phi_fes,
ParFiniteElementSpace* E_fes,
FindPointsGSLIB& E_finder_,
bool precompute_neutralizing_const_)
: precompute_neutralizing_const(precompute_neutralizing_const_),
E_finder(E_finder_),
b(phi_fes)
{
// compute domain volume
ParMesh* pmesh = phi_fes->GetParMesh();
real_t local_domain_volume = 0.0;
for (int i = 0; i < pmesh->GetNE(); i++)
{
local_domain_volume += pmesh->GetElementVolume(i);
}
MPI_Allreduce(&local_domain_volume, &domain_volume, 1, MPI_DOUBLE, MPI_SUM,
phi_fes->GetParMesh()->GetComm());
{
// Par bilinear form for the gradgrad matrix
ParBilinearForm dm(phi_fes);
ConstantCoefficient epsilon(EPSILON); // ε_0
dm.AddDomainIntegrator(
new DiffusionIntegrator(epsilon)); // ∫ ∇φ_i · ∇φ_j
dm.Assemble();
dm.Finalize();
diffusion_matrix = dm.ParallelAssemble(); // global gradgrad matrix
}
{
// Compute E = -∇φ using DiscreteLinearOperator
grad_interpolator = new ParDiscreteLinearOperator(phi_fes, E_fes);
grad_interpolator->AddDomainInterpolator(new GradientInterpolator);
grad_interpolator->Assemble();
}
}
FieldSolver::~FieldSolver()
{
delete diffusion_matrix;
delete precomputed_neutralizing_lf;
delete grad_interpolator;
}
const ParLinearForm& FieldSolver::ComputeNeutralizingRHS(
ParFiniteElementSpace* pfes, const ParticleVector& Q, MPI_Comm comm)
{
int npt = Q.Size();
// Get E_finder references
const Array<unsigned int>& code = E_finder.GetCode();
if (!precompute_neutralizing_const || precomputed_neutralizing_lf == nullptr)
{
// compute neutralizing constant
real_t local_sum = 0.0;
for (int p = 0; p < npt; ++p)
{
// Skip particles not successfully found
MFEM_ASSERT(code[p] != 2, "Particle " << p << " not found.");
local_sum += Q(p);
}
real_t global_sum = 0.0;
MPI_Allreduce(&local_sum, &global_sum, 1, MPI_DOUBLE, MPI_SUM, comm);
neutralizing_const = -global_sum / domain_volume;
if (Mpi::Root())
{
cout << "Total charge: " << global_sum
<< ", Domain volume: " << domain_volume
<< ", Neutralizing constant: " << neutralizing_const << endl;
if (precompute_neutralizing_const)
{
cout << "Further updates will use this precomputed neutralizing "
"constant."
<< endl;
}
}
delete precomputed_neutralizing_lf;
precomputed_neutralizing_lf = new ParLinearForm(pfes);
*precomputed_neutralizing_lf = 0.0;
ConstantCoefficient neutralizing_coeff(neutralizing_const);
precomputed_neutralizing_lf->AddDomainIntegrator(
new DomainLFIntegrator(neutralizing_coeff));
precomputed_neutralizing_lf->Assemble();
}
return *precomputed_neutralizing_lf;
}
void FieldSolver::DepositCharge(ParFiniteElementSpace* pfes,
const ParticleVector& Q)
{
int npt = Q.Size();
ParMesh* pmesh = pfes->GetParMesh();
int dim = pmesh->SpaceDimension();
int curr_rank;
MPI_Comm_rank(pmesh->GetComm(), &curr_rank);
// Get E_finder references
// 0: inside, 1: boundary, 2: not found
const Array<unsigned int>& code = E_finder.GetCode();
const Array<unsigned int>& proc = E_finder.GetProc(); // owning MPI rank
const Array<unsigned int>& elem = E_finder.GetElem(); // local element id
const Vector& rref = E_finder.GetReferencePosition(); // (r,s,t) byVDIM
Array<int> dofs;
for (int p = 0; p < npt; ++p)
{
// Skip particles not successfully found
MFEM_ASSERT(code[p] != 2, "Particle " << p << " not found.");
// Assert particle is on the current rank
MFEM_ASSERT((int)proc[p] == curr_rank,
"Particle " << p << " found in element owned by rank "
<< proc[p] << " but current rank is " << curr_rank
<< "." << endl
<< "You must call redistribute everytime before "
"updating the density grid function.");
const int e = elem[p];
// Reference coordinates for this particle (r,s[,t]) with byVDIM layout
IntegrationPoint ip;
ip.Set(rref.GetData() + dim * p, dim);
const FiniteElement& fe = *pfes->GetFE(e);
const int ldofs = fe.GetDof();
Vector shape(ldofs);
fe.CalcShape(ip, shape); // φ_i(x_p) in this element
pfes->GetElementDofs(e, dofs); // local dof indices
const real_t q_p = Q(p);
// Add q_p * φ_i(x_p) to b_i
b.AddElementVector(dofs, q_p, shape);
}
}
void FieldSolver::UpdatePhiGridFunction(ParticleSet& particles,
ParGridFunction& phi_gf)
{
// FE space / mesh
ParFiniteElementSpace* pfes = phi_gf.ParFESpace();
// Particle data: Q - charges (npt x 1)
ParticleVector& Q = particles.Field(ParticleMover::CHARGE);
// --------------------------------------------------------
// 1) Make RHS and pre-subtract averaged charge density for zero-mean RHS
// --------------------------------------------------------
MPI_Comm comm = pfes->GetComm();
b = ComputeNeutralizingRHS(pfes, Q, comm);
// --------------------------------------------------------
// 2) Deposit q_p * phi_i(x_p) into a ParLinearForm (RHS b)
// b_i = sum_p q_p * φ_i(x_p)
// --------------------------------------------------------
DepositCharge(pfes, Q);
// Assemble to a global true-dof RHS vector compatible with MassMatrix
HypreParVector B(pfes);
b.ParallelAssemble(B);
// ------------------------------------------------------------------
// 3) Solve A * phi = B with zero-mean enforcement via OrthoSolver
// ------------------------------------------------------------------
phi_gf = 0.0;
HypreParVector Phi_true(pfes);
Phi_true = 0.0;
HyprePCG solver(diffusion_matrix->GetComm());
solver.SetOperator(*diffusion_matrix);
solver.SetTol(1e-12);
solver.SetMaxIter(200);
solver.SetPrintLevel(0);
HypreBoomerAMG prec(*diffusion_matrix);
prec.SetPrintLevel(0);
solver.SetPreconditioner(prec);
OrthoSolver ortho(comm);
ortho.SetSolver(solver);
ortho.Mult(B, Phi_true);
// Map true-dof solution back to the ParGridFunction
phi_gf.Distribute(Phi_true);
}
void FieldSolver::UpdateEGridFunction(ParGridFunction& phi_gf,
ParGridFunction& E_gf)
{
// Compute ∇φ using precomputed gradient operator
grad_interpolator->Mult(phi_gf, E_gf);
// Scale by -1 to get E = -∇φ
E_gf.Neg();
}
real_t FieldSolver::ComputeFieldEnergy(const ParGridFunction& E_gf) const
{
// ---- Field energy: 0.5 * ∫ ||E||^2 dx ----
const ParFiniteElementSpace* fes = E_gf.ParFESpace();
const ParMesh* pmesh = fes->GetParMesh();
const int order = fes->GetMaxElementOrder();
const int qorder = std::max(2, 2 * order + 1);
const IntegrationRule* irs[Geometry::NumGeom];
for (int g = 0; g < Geometry::NumGeom; g++)
{
irs[g] = &IntRules.Get(g, qorder);
}
real_t field_energy = 0.0;
Vector zero(pmesh->Dimension());
zero = 0.0;
VectorConstantCoefficient zero_vec(zero);
const real_t E_l2 = E_gf.ComputeL2Error(zero_vec, irs);
field_energy = 0.5 * EPSILON * E_l2 * E_l2;
return field_energy;
}
void display_banner(ostream& os)
{
os << R"(
)"
<< endl
<< flush;
}
-85
View File
@@ -1,85 +0,0 @@
# Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
# at the Lawrence Livermore National Laboratory. All Rights reserved. See files
# LICENSE and NOTICE for details. LLNL-CODE-806117.
#
# This file is part of the MFEM library. For more information and source code
# availability visit https://mfem.org.
#
# MFEM is free software; you can redistribute it and/or modify it under the
# terms of the BSD-3 license. We welcome feedback and contributions, see file
# CONTRIBUTING.md for details.
# Use the MFEM build directory
MFEM_DIR ?= ../../..
MFEM_BUILD_DIR ?= ../../..
MFEM_INSTALL_DIR ?= ../../../mfem
SRC = $(if $(MFEM_DIR:../..=),$(MFEM_DIR)/miniapps/plasma/pic/,)
CONFIG_MK = $(or $(wildcard $(MFEM_BUILD_DIR)/config/config.mk),\
$(wildcard $(MFEM_INSTALL_DIR)/share/mfem/config.mk))
MFEM_LIB_FILE = mfem_is_not_built
-include $(CONFIG_MK)
PAR_MINIAPPS =
ifeq ($(MFEM_USE_GSLIB),YES)
PAR_MINIAPPS += electrostatic-pic
endif
ifeq ($(MFEM_USE_MPI),NO)
MINIAPPS =
else
MINIAPPS = $(PAR_MINIAPPS)
endif
.SUFFIXES:
.SUFFIXES: .o .cpp .mk
.PHONY: all lib-common clean clean-build clean-exec
.PRECIOUS: %.o
COMMON_LIB = -L$(MFEM_BUILD_DIR)/miniapps/common -lmfem-common
# If MFEM_SHARED is set, add the ../common rpath
COMMON_LIB += $(if $(MFEM_SHARED:YES=),,\
$(MFEM_XLINKER)-rpath,$(abspath $(MFEM_BUILD_DIR)/miniapps/common))
# Remove built-in rules
%: %.cpp
%.o: %.cpp
all: $(MINIAPPS)
# Rules for building the miniapps
electrostatic-pic: electrostatic-pic.cpp $(MFEM_LIB_FILE) $(CONFIG_MK) | lib-common
$(MFEM_CXX) $(MFEM_FLAGS) -c $<
$(MFEM_CXX) $(MFEM_LINK_FLAGS) -o $@ $@.o $(COMMON_LIB) $(MFEM_LIBS)
# Rule for building lib-common
lib-common:
$(MAKE) -C $(MFEM_BUILD_DIR)/miniapps/common
MFEM_TESTS = MINIAPPS
include $(MFEM_TEST_MK)
# Testing: "test" target and mfem-test* variables are defined in config/test.mk
# Testing: Specific execution options
RUN_MPI = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP) $(MFEM_MPI_NP)
electrostatic-pic-test-par: electrostatic-pic
@$(call mfem-test,$<, $(RUN_MPI), PIC miniapp,\
-rdi 2 -npt 40960 -k 0.2855993321 -a 0.05 -nt 200 -nx 16 -ny 16\
-O 1 -q 0.01181640625 -m 0.01181640625 -oci 1000 -dt 0.1)
# Generate an error message if the MFEM library is not built and exit
$(MFEM_LIB_FILE):
$(error The MFEM library is not built)
clean: clean-build clean-exec
clean-build:
rm -f *.o *~ $(SEQ_MINIAPPS) $(PAR_MINIAPPS)
rm -rf *.dSYM *.TVD.*breakpoints
clean-exec:
@rm -rf electrostatic-pic_* *.csv energy.csv
-11
View File
@@ -18,7 +18,6 @@
//
// Currently supported data collection type options:
// visit: VisItDataCollection (default)
// sidre or sidre_hdf5: SidreDataCollection
// json: ConduitDataCollection w/ protocol json
// conduit_json: ConduitDataCollection w/ protocol conduit_json
// conduit_bin: ConduitDataCollection w/ protocol conduit_bin
@@ -52,14 +51,6 @@ DataCollection *create_data_collection(const std::string &dc_name,
dc = new VisItDataCollection(MPI_COMM_WORLD, dc_name);
#else
dc = new VisItDataCollection(dc_name);
#endif
}
else if ( dc_type == "sidre" || dc_type == "sidre_hdf5")
{
#ifdef MFEM_USE_SIDRE
dc = new SidreDataCollection(dc_name);
#else
MFEM_ABORT("Must build with MFEM_USE_SIDRE=YES for sidre support.");
#endif
}
else if ( dc_type == "json" ||
@@ -140,7 +131,6 @@ int main(int argc, char *argv[])
args.AddOption(&src_coll_type, "-st", "--source-type",
"Set the source data collection type. Options:\n"
"\t visit: VisItDataCollection (default)\n"
"\t sidre or sidre_hdf5: SidreDataCollection\n"
"\t json: ConduitDataCollection w/ protocol json\n"
"\t conduit_json: ConduitDataCollection w/ protocol conduit_json\n"
"\t conduit_bin: ConduitDataCollection w/ protocol conduit_bin\n"
@@ -152,7 +142,6 @@ int main(int argc, char *argv[])
args.AddOption(&out_coll_type, "-ot", "--output-type",
"Set the output data collection type. Options:\n"
"\t visit: VisItDataCollection (default)\n"
"\t sidre or sidre_hdf5: SidreDataCollection\n"
"\t json: ConduitDataCollection w/ protocol json\n"
"\t conduit_json: ConduitDataCollection w/ protocol conduit_json\n"
"\t conduit_bin: ConduitDataCollection w/ protocol conduit_bin\n"
-1
View File
@@ -76,7 +76,6 @@ set(UNIT_TESTS_SRCS
linalg/test_vector.cpp
mesh/mesh_test_utils.cpp
mesh/test_exodus_reader.cpp
mesh/test_mfem_mesh_reader.cpp
mesh/test_exodus_writer.cpp
mesh/test_face_orientations.cpp
mesh/test_fms.cpp
-118
View File
@@ -1,118 +0,0 @@
MFEM mesh v1.3
#
# MFEM Geometry Types (see mesh/geom.hpp):
#
# POINT = 0
# SEGMENT = 1
# TRIANGLE = 2
# SQUARE = 3
# TETRAHEDRON = 4
# CUBE = 5
# PRISM = 6
#
dimension
2
elements
12
10 2 7 0 1
11 2 0 7 2
12 2 9 0 2
13 2 0 9 3
14 2 11 0 3
15 2 0 11 4
16 2 5 0 4
17 2 0 5 1
9 3 1 5 6 7
9 3 2 7 8 9
9 3 3 9 10 11
9 3 4 11 12 5
attribute_sets
16
"Base" 1 9
"E Even" 1 16
"E Odd" 1 17
"East"
2
16
17
"N Even" 1 10
"N Odd" 1 11
"North" 2 10 11
"Rose" 8 10 11 12
13 14
15 16 17
"Rose Even" 4
10
12
14
16
"Rose Odd"
4
11
13
15
17
"S Even" 1 14
"S Odd" 1 15
South 2
14
15
"W Even" 1 12
"W Odd" 1 13
West 2 12 13
boundary
8
1 1 5 6
2 1 6 7
3 1 7 8
4 1 8 9
5 1 9 10
6 1 10 11
7 1 11 12
8 1 12 5
bdr_attribute_sets
13
"Boundary" 8 1 2 3 4 5 6 7 8
"ENE" 1 1
"ESE" 1 8
"Eastern Boundary" 2 1 8
"NNE" 1 2
"NNW" 1 3
"Northern Boundary"
2
2
3
"SSE" 1 7
"SSW" 1 6
"Southern Boundary" 2
6
7
"WNW" 1 4
"WSW" 1 5
"Western Boundary" 2 4
5
vertices
13
2
0 0
0.14142136 0.14142136
-0.14142136 0.14142136
-0.14142136 -0.14142136
0.14142136 -0.14142136
1 0
0.70710678 0.70710678
0 1
-0.70710678 0.70710678
-1 0
-0.70710678 -0.70710678
0 -1
0.70710678 -0.70710678
mfem_mesh_end
+1 -1
View File
@@ -296,7 +296,7 @@ void TestRedistribute(Ordering::Type ordering)
int wrong_proc_count = 0;
for (int i = 0; i < procs.Size(); i++)
{
if (static_cast<unsigned>(rank) != procs[i])
if (rank != procs[i])
{
wrong_proc_count++;
}
-26
View File
@@ -30,29 +30,3 @@ TEST_CASE("String Manipulation", "[General]")
}
}
}
TEST_CASE("Quoted String Input", "[General]")
{
const auto test_strings =
{
"Test",
"Test with spaces",
"Test with \"quoted text\"",
"Test string ending with \\",
"\nTest with\tvarious white\v\rspace characters.",
"Test with some unicode characters: ∆, ∉, ∑, 🍎."
};
for (const auto c_str : test_strings)
{
CAPTURE(c_str);
const std::string str(c_str);
std::stringstream ss;
ss << std::quoted(str);
std::string read_str;
int error = parse_quoted_string(read_str, ss);
CHECK(error == 0);
CHECK(read_str == str);
}
}
-108
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@@ -1,108 +0,0 @@
// Copyright (c) 2010-2025, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
#include "mfem.hpp"
#include "unit_tests.hpp"
#include <algorithm>
#include <string>
#include <utility>
#include <vector>
using namespace mfem;
TEST_CASE("MFEM Mesh Named Attributes", "[Mesh]")
{
// Path relative to the directory tests/unit
Mesh mesh("data/compass-testing.mesh");
REQUIRE(mesh.Dimension() == 2);
REQUIRE(mesh.GetNE() == 12);
REQUIRE(mesh.GetNV() == 13);
REQUIRE(mesh.attribute_sets.attr_sets.Size() == 16);
REQUIRE(mesh.bdr_attribute_sets.attr_sets.Size() == 13);
std::vector<std::pair<std::string, std::vector<int>>> expected_attr_sets =
{
{"Base", {9}},
{"E Even", {16}},
{"E Odd", {17}},
{"East", {16, 17}},
{"N Even", {10}},
{"N Odd", {11}},
{"North", {10, 11}},
{"Rose", {10, 11, 12, 13, 14, 15, 16, 17}},
{"Rose Even", {10, 12, 14, 16}},
{"Rose Odd", {11, 13, 15, 17}},
{"S Even", {14}},
{"S Odd", {15}},
{"South", {14, 15}},
{"W Even", {12}},
{"W Odd", {13}},
{"West", {12, 13}}
};
for (auto const &attr_name_index_pair: expected_attr_sets )
{
REQUIRE(mesh.attribute_sets.AttributeSetExists(
attr_name_index_pair.first));
auto const &attr_set = mesh.attribute_sets.GetAttributeSet(
attr_name_index_pair.first);
auto const &expected_attr_set = attr_name_index_pair.second;
REQUIRE(static_cast<std::size_t>(attr_set.Size()) ==
expected_attr_set.size());
bool const elements_equal = std::equal(attr_set.begin(), attr_set.end(),
expected_attr_set.begin());
REQUIRE(elements_equal);
}
std::vector<std::pair<std::string, std::vector<int>>> expected_bdr_attr_sets
=
{
{"Boundary", {1, 2, 3, 4, 5, 6, 7, 8}},
{"ENE", { 1}},
{"ESE", { 8}},
{"Eastern Boundary", {1, 8}},
{"NNE", { 2}},
{"NNW", { 3}},
{"Northern Boundary", {2, 3}},
{"SSE", { 7}},
{"SSW", { 6}},
{"Southern Boundary", {6,7}},
{"WNW", { 4}},
{"WSW", { 5}},
{"Western Boundary", {4,5}}
};
for (auto const &attr_bdr_name_index_pair: expected_bdr_attr_sets )
{
REQUIRE(mesh.bdr_attribute_sets.AttributeSetExists(
attr_bdr_name_index_pair.first));
auto const &bdr_attr_set = mesh.bdr_attribute_sets.GetAttributeSet(
attr_bdr_name_index_pair.first);
auto const &expected_bdr_attr_set = attr_bdr_name_index_pair.second;
REQUIRE(static_cast<std::size_t>(bdr_attr_set.Size()) ==
expected_bdr_attr_set.size());
bool const elements_equal = std::equal(bdr_attr_set.begin(),
bdr_attr_set.end(),
expected_bdr_attr_set.begin());
REQUIRE(elements_equal);
}
}