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@@ -33,6 +33,7 @@ env:
|
||||
HYPRE_ARCHIVE: v2.19.0.tar.gz
|
||||
HYPRE_TOP_DIR: hypre-2.19.0
|
||||
METIS_ARCHIVE: metis-4.0.3.tar.gz
|
||||
METIS_ARCHIVE_MAC: metis-4.0.3-mac.tgz
|
||||
METIS_TOP_DIR: metis-4.0.3
|
||||
MFEM_TOP_DIR: mfem
|
||||
|
||||
@@ -52,6 +53,7 @@ jobs:
|
||||
mpi: [seq, par]
|
||||
build-system: [make, cmake]
|
||||
hypre-target: [int32]
|
||||
precision: [fp64]
|
||||
exclude:
|
||||
- os: ubuntu-latest
|
||||
build-system: cmake
|
||||
@@ -75,6 +77,8 @@ jobs:
|
||||
- os: ubuntu-latest
|
||||
target: dbg
|
||||
config-opts: 'CPPFLAGS+=-Og'
|
||||
- os: macos-latest
|
||||
codecov: NO
|
||||
- os: windows-latest
|
||||
codecov: NO
|
||||
- os: windows-latest
|
||||
@@ -87,6 +91,7 @@ jobs:
|
||||
mpi: par
|
||||
build-system: cmake
|
||||
hypre-target: int32
|
||||
precision: fp64
|
||||
# This option can be set to pass additional configuration options to
|
||||
# the MFEM configuration command.
|
||||
# config-opts: '-DCMAKE_VERBOSE_MAKEFILE=ON'
|
||||
@@ -96,7 +101,15 @@ jobs:
|
||||
mpi: par
|
||||
build-system: make
|
||||
hypre-target: int64
|
||||
name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}
|
||||
precision: fp64
|
||||
- os: ubuntu-latest
|
||||
target: opt
|
||||
codecov: NO
|
||||
mpi: par
|
||||
build-system: make
|
||||
hypre-target: int32
|
||||
precision: fp32
|
||||
name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}-${{ matrix.precision }}
|
||||
|
||||
runs-on: ${{ matrix.os }}
|
||||
|
||||
@@ -126,6 +139,17 @@ jobs:
|
||||
# Fetch the complete history for codecov to access commits ID
|
||||
fetch-depth: 0
|
||||
|
||||
- name: Xcode version setup (MacOS)
|
||||
if: matrix.os == 'macos-latest'
|
||||
run: |
|
||||
XCODE_PATH="/Applications/Xcode_15.3.app"
|
||||
echo "> sudo xcode-select -s ${XCODE_PATH}"
|
||||
sudo xcode-select -s ${XCODE_PATH}
|
||||
echo "> g++ -v"
|
||||
g++ -v
|
||||
echo "> clang++ -v"
|
||||
clang++ -v
|
||||
|
||||
# Only get MPI if defined for the job.
|
||||
# TODO: It would be nice to have only one step, e.g. with a dedicated
|
||||
# action, but I (@adrienbernede) don't see how at the moment.
|
||||
@@ -169,25 +193,27 @@ jobs:
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ${{ env.HYPRE_TOP_DIR }}
|
||||
key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-v2.2
|
||||
key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-${{ matrix.hypre-target }}-${{ matrix.precision }}-v2.5
|
||||
|
||||
- name: get hypre
|
||||
if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest'
|
||||
uses: mfem/github-actions/build-hypre@v2.4
|
||||
uses: mfem/github-actions/build-hypre@v2.5
|
||||
with:
|
||||
archive: ${{ env.HYPRE_ARCHIVE }}
|
||||
dir: ${{ env.HYPRE_TOP_DIR }}
|
||||
target: ${{ matrix.hypre-target }}
|
||||
build-system: make
|
||||
precision: ${{ matrix.precision }}
|
||||
|
||||
- name: get hypre (Windows)
|
||||
if: matrix.mpi == 'par' && steps.hypre-cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
|
||||
uses: mfem/github-actions/build-hypre@v2.4
|
||||
uses: mfem/github-actions/build-hypre@v2.5
|
||||
with:
|
||||
archive: ${{ env.HYPRE_ARCHIVE }}
|
||||
dir: ${{ env.HYPRE_TOP_DIR }}
|
||||
target: ${{ matrix.hypre-target }}
|
||||
build-system: cmake
|
||||
precision: ${{ matrix.precision }}
|
||||
|
||||
# Get Metis through cache, or build it.
|
||||
# Install will only run on cache miss.
|
||||
@@ -197,13 +223,13 @@ jobs:
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ${{ env.METIS_TOP_DIR }}
|
||||
key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.2
|
||||
key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.5
|
||||
|
||||
- name: install metis
|
||||
if: matrix.mpi == 'par' && matrix.os != 'windows-latest' && steps.metis-cache.outputs.cache-hit != 'true'
|
||||
uses: mfem/github-actions/build-metis@v2.4
|
||||
uses: mfem/github-actions/build-metis@v2.5
|
||||
with:
|
||||
archive: ${{ env.METIS_ARCHIVE }}
|
||||
archive: ${{ matrix.os != 'macos-latest' && env.METIS_ARCHIVE || env.METIS_ARCHIVE_MAC }}
|
||||
dir: ${{ env.METIS_TOP_DIR }}
|
||||
|
||||
- name: cache vcpkg (Windows)
|
||||
@@ -228,7 +254,7 @@ jobs:
|
||||
|
||||
# MFEM build and test
|
||||
- name: build
|
||||
uses: mfem/github-actions/build-mfem@v2.4
|
||||
uses: mfem/github-actions/build-mfem@v2.5
|
||||
env:
|
||||
VCPKG_DEFAULT_BINARY_CACHE: ${{ github.workspace }}/vcpkg_cache
|
||||
with:
|
||||
@@ -240,6 +266,7 @@ jobs:
|
||||
hypre-dir: ${{ env.HYPRE_TOP_DIR }}
|
||||
metis-dir: ${{ env.METIS_TOP_DIR }}
|
||||
mfem-dir: ${{ env.MFEM_TOP_DIR }}
|
||||
precision: ${{ matrix.precision }}
|
||||
config-options: ${{ matrix.config-opts }}
|
||||
library-only: ${{ matrix.target == 'dbg' && matrix.os != 'ubuntu-latest' }}
|
||||
|
||||
@@ -282,7 +309,7 @@ jobs:
|
||||
# Code coverage (process and upload reports)
|
||||
- name: codecov
|
||||
if: matrix.codecov == 'YES'
|
||||
uses: mfem/github-actions/upload-coverage@v2.4
|
||||
uses: mfem/github-actions/upload-coverage@v2.5
|
||||
with:
|
||||
name: ${{ matrix.os }}-${{ matrix.build-system }}-${{ matrix.target }}-${{ matrix.mpi }}-${{ matrix.hypre-target }}
|
||||
project_dir: ${{ env.MFEM_TOP_DIR }}
|
||||
|
||||
@@ -53,11 +53,11 @@ jobs:
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ${{ env.HYPRE_TOP_DIR }}
|
||||
key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2.2
|
||||
key: ${{ runner.os }}-build-${{ env.HYPRE_TOP_DIR }}-v2.5
|
||||
|
||||
- name: Get Hypre
|
||||
if: steps.hypre-cache.outputs.cache-hit != 'true'
|
||||
uses: mfem/github-actions/build-hypre@v2.4
|
||||
uses: mfem/github-actions/build-hypre@v2.5
|
||||
with:
|
||||
archive: ${{ env.HYPRE_ARCHIVE }}
|
||||
dir: ${{ env.HYPRE_TOP_DIR }}
|
||||
@@ -68,18 +68,18 @@ jobs:
|
||||
uses: actions/cache@v4
|
||||
with:
|
||||
path: ${{ env.METIS_TOP_DIR }}
|
||||
key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.2
|
||||
key: ${{ runner.os }}-build-${{ env.METIS_TOP_DIR }}-v2.5
|
||||
|
||||
- name: Install Metis
|
||||
if: steps.metis-cache.outputs.cache-hit != 'true'
|
||||
uses: mfem/github-actions/build-metis@v2.4
|
||||
uses: mfem/github-actions/build-metis@v2.5
|
||||
with:
|
||||
archive: ${{ env.METIS_ARCHIVE }}
|
||||
dir: ${{ env.METIS_TOP_DIR }}
|
||||
|
||||
# MFEM build and test
|
||||
- name: build-mfem
|
||||
uses: mfem/github-actions/build-mfem@v2.4
|
||||
uses: mfem/github-actions/build-mfem@v2.5
|
||||
with:
|
||||
os: ${{ runner.os }}
|
||||
target: opt
|
||||
|
||||
@@ -44,7 +44,7 @@ jobs:
|
||||
path: mfem
|
||||
|
||||
- name: MFEM Build
|
||||
uses: mfem/github-actions/build-mfem@v2.4
|
||||
uses: mfem/github-actions/build-mfem@v2.5
|
||||
with:
|
||||
os: ${{ runner.os }}
|
||||
target: opt
|
||||
|
||||
+4
-2
@@ -57,6 +57,8 @@ examples/ex2[0-9]
|
||||
examples/ex2[0-9]p
|
||||
examples/ex3[0-9]
|
||||
examples/ex3[0-9]p
|
||||
examples/ex4[0-9]
|
||||
examples/ex4[0-9]p
|
||||
|
||||
examples/refined.mesh
|
||||
examples/displaced.mesh
|
||||
@@ -232,7 +234,7 @@ miniapps/meshing/mobius-strip.mesh
|
||||
miniapps/meshing/klein-bottle.mesh
|
||||
miniapps/meshing/toroid-*.mesh
|
||||
miniapps/meshing/twist-*.mesh
|
||||
miniapps/meshing/mesh-explorer.mesh
|
||||
miniapps/meshing/mesh-explorer.mesh*
|
||||
miniapps/meshing/partitioning.txt
|
||||
miniapps/meshing/mesh-explorer-visit*
|
||||
miniapps/meshing/mesh-explorer-paraview/
|
||||
@@ -369,7 +371,7 @@ miniapps/dpg/ParaView
|
||||
miniapps/spde/generate_random_field
|
||||
miniapps/spde/ParaView
|
||||
|
||||
miniapps/tribol/ContactPatchTest
|
||||
miniapps/tribol/contact-patch-test
|
||||
|
||||
# Unit test binary and outputs
|
||||
tests/unit/output_meshes
|
||||
|
||||
@@ -13,6 +13,9 @@
|
||||
# at Lawrence Livermore National Laboratory (LLNL). This entire pipeline is
|
||||
# LLNL-specific!
|
||||
|
||||
include:
|
||||
- project: 'lc-templates/id_tokens'
|
||||
file: 'id_tokens.yml'
|
||||
|
||||
# The pipeline is divided into stages. Usually, jobs in a given stage wait for
|
||||
# the preceding stages to complete before to start. However, we sometimes use
|
||||
|
||||
@@ -9,6 +9,10 @@
|
||||
# terms of the BSD-3 license. We welcome feedback and contributions, see file
|
||||
# CONTRIBUTING.md for details.
|
||||
|
||||
include:
|
||||
- project: 'lc-templates/id_tokens'
|
||||
file: 'id_tokens.yml'
|
||||
|
||||
# We define the following GitLab pipeline variables:
|
||||
variables:
|
||||
|
||||
|
||||
@@ -35,9 +35,8 @@ variables:
|
||||
- when: on_success
|
||||
|
||||
# Lassen uses a different job scheduler (spectrum lsf) that does not allow
|
||||
# pre-allocation the same way slurm does. We use pdebug queue on lassen
|
||||
# to speed-up the allocation. However this would not be scalable to
|
||||
# multiple builds.
|
||||
# pre-allocation the same way slurm does. We use the pci queue on lassen
|
||||
# to speed-up the allocation.
|
||||
.build_and_test_on_lassen:
|
||||
extends: [.on_lassen]
|
||||
stage: build_and_test
|
||||
@@ -45,5 +44,5 @@ variables:
|
||||
- echo ${MFEM_DATA_DIR}
|
||||
- echo ${SPEC}
|
||||
# Next script uses 'THREADS': leaving it empty --> it uses 'make all -j'
|
||||
- lalloc 1 -W 45 -q pdebug --atsdisable tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
|
||||
- lalloc 1 -W 45 -q pci --atsdisable tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
|
||||
needs: [setup]
|
||||
|
||||
@@ -52,4 +52,4 @@ variables:
|
||||
- echo ${JOBID}
|
||||
- echo ${MFEM_DATA_DIR}
|
||||
- echo ${SPEC}
|
||||
- srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) -t 45 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
|
||||
- srun $( [[ -n "${JOBID}" ]] && echo "--jobid=${JOBID}" ) --reservation=ci -t 45 -N 1 tests/gitlab/build_and_test --spec "${SPEC}" --data-dir "${MFEM_DATA_DIR}" --data
|
||||
|
||||
@@ -14,14 +14,14 @@ stages:
|
||||
- build_and_test
|
||||
- report
|
||||
|
||||
opt_mpi_cuda_xl_16_1_1_12:
|
||||
opt_mpi_cuda_gcc:
|
||||
variables:
|
||||
SPEC: "%xl@16.1.1.12 +mpi +cuda cuda_arch=70"
|
||||
SPEC: "%gcc@8.3.1 +mpi +cuda cuda_arch=70"
|
||||
extends: .build_and_test_on_lassen
|
||||
|
||||
opt_mpi_cuda_hypre_cuda_xl:
|
||||
opt_mpi_cuda_hypre_cuda_gcc:
|
||||
variables:
|
||||
SPEC: "%xl@16.1.1.12 +mpi +cuda cuda_arch=70 ^hypre+cuda~shared cuda_arch=70"
|
||||
SPEC: "%gcc@8.3.1 +mpi +cuda cuda_arch=70 ^hypre+cuda~shared cuda_arch=70"
|
||||
extends: .build_and_test_on_lassen
|
||||
|
||||
# Jobs report
|
||||
|
||||
@@ -32,11 +32,11 @@ mkdir _${BASELINE_TEST} && cd _${BASELINE_TEST}
|
||||
|
||||
# run
|
||||
if [[ "${MACHINE_NAME}" == "quartz" || "${MACHINE_NAME}" == "ruby" ]]; then
|
||||
salloc --nodes=1 -p pdebug ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
salloc --nodes=1 --reservation=ci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
elif [[ ${MACHINE_NAME} == "corona" ]]; then
|
||||
salloc --nodes=1 -t 60 -p pbatch ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
elif [[ ${MACHINE_NAME} == "lassen" ]]; then
|
||||
lalloc 1 -q pdebug ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
lalloc 1 -q pci ../runtest ../../mfem "${BASELINE_TEST} ${TPLS_DIR}"
|
||||
else
|
||||
echo "Unknown machine: MACHINE_NAME=$MACHINE_NAME"
|
||||
exit 1
|
||||
|
||||
@@ -8,82 +8,112 @@
|
||||
https://mfem.org
|
||||
|
||||
|
||||
Version 4.6.1 (development)
|
||||
Version 4.7.1 (development)
|
||||
===========================
|
||||
|
||||
- Added an MFEM example for the eikonal equation. This new solver is based on
|
||||
the proximal Galerkin method introduced by Keith and Surowiec.
|
||||
|
||||
- API change: in class GridFunction, 'fec' was renamed to 'fec_owned'.
|
||||
|
||||
|
||||
Version 4.7, released on May 7, 2024
|
||||
====================================
|
||||
|
||||
- Added support for single precision (with corresponding hypre build). The MFEM
|
||||
floating point type was generalized from `double` to `real_t`. For details see
|
||||
https://github.com/orgs/mfem/discussions/4207.
|
||||
|
||||
Meshing improvements
|
||||
--------------------
|
||||
- Added the capability to partition (big) serial meshes in serial code, see the
|
||||
new classes MeshPartitioner and MeshPart. This capability is also exposed as a
|
||||
menu option in the mesh-explorer miniapp in miniapps/meshing.
|
||||
|
||||
- Added named attribute sets and basic supporting methods to the Mesh class as a
|
||||
convenient means of referring to sets of domain or boundary attribute numbers.
|
||||
See the new Example 39/39p and data/compass.mesh.
|
||||
|
||||
- Introduced formulas for refinement of patches in NURBS meshes. Refinement by
|
||||
arbitrary integer factors is also enabled, e.g. in the mesh-explorer miniapp.
|
||||
NURBS coarsening and knot removal are also introduced.
|
||||
|
||||
Discretization improvements
|
||||
---------------------------
|
||||
- Introduced support for higher order non conformal Nedelec elements on
|
||||
simplices in ParMesh.
|
||||
|
||||
- Introduced support for internal boundary elements in nonconformal adapted
|
||||
meshes.
|
||||
|
||||
- Added functionality for construction of cut-surface and cut-volume
|
||||
IntegrationRules through a moment-fitting approach. The cut is specified by
|
||||
the zero level set of a Coefficient. See fem/intrules_cut.hpp and Example 38.
|
||||
|
||||
- Added a new nonlinear integrator, `HyperbolicFormIntegrator`. This implements
|
||||
both element-wise weak divergence and face-wise numerical flux for a general
|
||||
system of hyperbolic conservation laws. To use this integrator for a specific
|
||||
flux function, users can define a derived class of `FluxFunction`. Currently,
|
||||
advection, Burgers', shallow-water, Euler equations (see, Example 18) are
|
||||
available.
|
||||
|
||||
GPU support
|
||||
----------------------------
|
||||
- Added support for full assembly on simplices.
|
||||
|
||||
- Added functionality for BilinearFormIntegrators to use kernels that work for both
|
||||
tensor and unstructured elements.
|
||||
|
||||
- Added partial assembly for linear elasticity. Does not use sum factorization for now.
|
||||
|
||||
- Added partial assembly and GPU support for the DG diffusion integrator.
|
||||
|
||||
New and updated examples and miniapps
|
||||
-------------------------------------
|
||||
- Added a new block solver in miniapp/solvers for the Darcy problem.
|
||||
The new solver is based on a Bramble-Pasciak preconditioning. User can
|
||||
use and implement their own preconditioner for the mass matrix.
|
||||
|
||||
- Added miniapp to demonstrate new elasticity integrator and unstructured element GPU support,
|
||||
and a block diagonal preconditioner using low order refinement. Allows comparison with
|
||||
currently existing legacy mode integrator. See miniapps/solvers/lor_elast.
|
||||
|
||||
- Added a new mortar contact patch test miniapp using the Tribol interface
|
||||
physics library (see https://github.com/LLNL/Tribol). See miniapps/tribol.
|
||||
|
||||
Miscellaneous
|
||||
-------------
|
||||
- Added support for single and double precision, with corresponding hypre build.
|
||||
Generalized the floating point type from `double` to `real_t`. For more
|
||||
details see https://github.com/orgs/mfem/discussions/4207.
|
||||
- Added support for internal boundary elements in nonconforming meshes.
|
||||
|
||||
- The ReadCubit Genesis mesh importer has been rewritten to improve readability.
|
||||
|
||||
Discretization improvements
|
||||
---------------------------
|
||||
- Added a new nonlinear integrator, `HyperbolicFormIntegrator` that implements
|
||||
both element-wise weak divergence and face-wise numerical flux for a general
|
||||
system of hyperbolic conservation laws. To use the integrator for a specific
|
||||
flux function, users can define a derived class of `FluxFunction`. Currently,
|
||||
advection, Burgers, shallow-water and Euler equations (see Example 18/18p) are
|
||||
available.
|
||||
|
||||
- Added a capability to construct cut-surface and cut-volume IntegrationRules
|
||||
through a moment-fitting approach. The cut is specified by the zero level set
|
||||
of a Coefficient. See fem/intrules_cut.hpp and the new Example 38.
|
||||
|
||||
- Introduced support for high-order nonconforming Nedelec elements on simplices.
|
||||
|
||||
GPU computing
|
||||
-------------
|
||||
- Added partial assembly and GPU support for the DG diffusion integrator.
|
||||
|
||||
- Efficient GPU-accelerated LOR assembly is now supported on surface meshes.
|
||||
|
||||
- Added functionality to automatically configure hypre's compute policy to match
|
||||
MFEM's compute policy when hypre is built with GPU support. Requires version
|
||||
hypre-2.31.0 or later.
|
||||
|
||||
- Added support for full assembly on simplices.
|
||||
|
||||
- Added partial assembly for linear elasticity (no sum factorization for now).
|
||||
|
||||
- Added functionality for BilinearFormIntegrators to use kernels that work for
|
||||
both tensor and unstructured elements.
|
||||
|
||||
- The RAJA backend will use `seq_exec` for serial loop execution when RAJA
|
||||
v2023.06.00 and beyond is detected as `loop_exec` is deprecated.
|
||||
|
||||
- API change: The macro MFEM_HYPRE_FORALL (from hypre.hpp) which was intended
|
||||
for internal use, has been removed and replaced by the function template
|
||||
mfem::hypre_forall in general/forall.hpp.
|
||||
|
||||
New and updated examples and miniapps
|
||||
-------------------------------------
|
||||
- Added a new miniapp illustrating elastic contact based on the Tribol library,
|
||||
(https://github.com/LLNL/Tribol). See miniapps/tribol.
|
||||
|
||||
- Added a miniapp to demonstrate low order refined (LOR) block preconditioning
|
||||
for linear elasticity on GPUs. See miniapps/solvers/lor_elast.
|
||||
|
||||
- Added a new block solver in miniapp/solvers for the Darcy problem. The new
|
||||
solver is based on a Bramble-Pasciak preconditioning. User can use and
|
||||
implement their own preconditioner for the mass matrix.
|
||||
|
||||
- Added a small miniapp for printing the shape functions of a KnotVector. See
|
||||
miniapps/nurbs/nurbs_printfunc.cpp.
|
||||
|
||||
- Added two new example codes: 38 and 39/39p described above. Substantially
|
||||
updated Example 18/18p.
|
||||
|
||||
Miscellaneous
|
||||
-------------
|
||||
- Updated the Doxygen documentation style, which now requires Doxygen version
|
||||
1.9.8 or later. See the doc/ directory.
|
||||
|
||||
- Improved thread safety for global variables in the library, for example
|
||||
IntegrationRules IntRules, RefinedIntRules, GeometryRefiner
|
||||
GlobGeometryRefiner, and FiniteElement::dof2quad_array.
|
||||
- Improved thread safety for global variables in the library, e.g. for IntRules,
|
||||
RefinedIntRules, GlobGeometryRefiner, and FiniteElement::dof2quad_array.
|
||||
|
||||
- PETSc integration now generally requires PETSc version 3.21 or later, though
|
||||
depending on the functionality older versions may still work.
|
||||
|
||||
- RAJA backend will use seq_exec for serial loop execution when RAJA
|
||||
v2023.06.00 and beyond is detected as loop_exec is deprecated.
|
||||
- Various other simplifications, extensions, and bugfixes in the code.
|
||||
|
||||
- Added GSLIB-based gather-scatter operator.
|
||||
|
||||
- Adding named attribute sets and basic supporting methods to the Mesh class as
|
||||
a convenient means of referring to sets of domain or boundary attribute
|
||||
numbers. Also adding related serial and parallel examples which illustrate.
|
||||
|
||||
Version 4.6, released on September 27, 2023
|
||||
===========================================
|
||||
@@ -104,7 +134,6 @@ Meshing improvements
|
||||
* The edge to knot map for NURBS meshes can be determined automatically. It is
|
||||
no longer needed to specify this in the NURBS mesh.
|
||||
* Added curve interpolation method for NURBS.
|
||||
* Added new small miniapp for printing of shape functions of a KnotVector
|
||||
* See miniapps/nurbs for example meshes and miniapps.
|
||||
|
||||
Discretization improvements
|
||||
@@ -151,8 +180,6 @@ Linear and nonlinear solvers
|
||||
|
||||
- Added HIP support to the PETSc and SUNDIALS interfaces.
|
||||
|
||||
- Efficient GPU-accelerated LOR assembly now supports surface meshes.
|
||||
|
||||
New and updated examples and miniapps
|
||||
-------------------------------------
|
||||
- Added a new H(div) solver miniapp demonstrating the use of a matrix-free
|
||||
|
||||
+1
-1
@@ -58,7 +58,7 @@ project(mfem NONE)
|
||||
# Current version of MFEM, see also `makefile`.
|
||||
# mfem_VERSION = (string)
|
||||
# MFEM_VERSION = (int) [automatically derived from mfem_VERSION]
|
||||
set(${PROJECT_NAME}_VERSION 4.6.1)
|
||||
set(${PROJECT_NAME}_VERSION 4.7.1)
|
||||
|
||||
# Prohibit in-source build
|
||||
if (${PROJECT_SOURCE_DIR} STREQUAL ${PROJECT_BINARY_DIR})
|
||||
|
||||
@@ -75,6 +75,8 @@ and miniapps. See https://glvis.org and https://mfem.org/building.
|
||||
|
||||
Quick start with GNU make
|
||||
=========================
|
||||
See also: https://mfem.org/building
|
||||
|
||||
Serial build:
|
||||
make serial -j 4
|
||||
|
||||
@@ -83,6 +85,7 @@ Parallel build:
|
||||
(build METIS 4 in ../metis-4.0 relative to mfem/)
|
||||
(build hypre in ../hypre relative to mfem/)
|
||||
make parallel -j 4
|
||||
(For METIS 5, see https://mfem.org/building/#parallel-build-using-metis-5)
|
||||
|
||||
CUDA build:
|
||||
make cuda -j 4
|
||||
@@ -116,6 +119,7 @@ Parallel build:
|
||||
mkdir <mfem-build-dir> ; cd <mfem-build-dir>
|
||||
cmake <mfem-source-dir> -DMFEM_USE_MPI=YES
|
||||
make -j 4
|
||||
(For METIS 5, see https://mfem.org/building/#parallel-build-using-metis-5)
|
||||
|
||||
CUDA build:
|
||||
(this build requires CMake 3.8 or newer)
|
||||
@@ -612,9 +616,13 @@ The specific libraries and their options are:
|
||||
HYPRE >= 2.20.0 (HYPRE built with '--enable-mixedint')
|
||||
HYPRE >= 2.22.1 (HYPRE built with CUDA)
|
||||
HYPRE >= 2.23.0 (HYPRE built with HIP)
|
||||
HYPRE >= 2.31.0 (runtime selectable HYPRE execution on CPU/GPU)
|
||||
|
||||
- METIS, used when MFEM_USE_METIS = YES. If using METIS 5, set
|
||||
MFEM_USE_METIS_5 = YES (default is to use METIS 4).
|
||||
MFEM_USE_METIS_5 = YES (default is to use METIS 4). For building instructions,
|
||||
see the following:
|
||||
- METIS 4.0.3: https://mfem.org/building/#parallel-mpi-version-of-mfem
|
||||
- METIS 5.1.0: https://mfem.org/building/#parallel-build-using-metis-5
|
||||
URL: https://github.com/mfem/tpls (MFEM mirror, see above)
|
||||
Options: METIS_OPT, METIS_LIB.
|
||||
Versions: METIS 4.0.3 or 5.1.0.
|
||||
|
||||
@@ -120,6 +120,15 @@ constexpr real_t operator""_r(unsigned long long v)
|
||||
|
||||
// Check dependencies:
|
||||
|
||||
// Define MFEM_MPI_REAL_T to be the appropriate MPI real type
|
||||
#ifdef MFEM_USE_MPI
|
||||
#ifdef MFEM_USE_SINGLE
|
||||
#define MFEM_MPI_REAL_T MPI_FLOAT
|
||||
#elif defined MFEM_USE_DOUBLE
|
||||
#define MFEM_MPI_REAL_T MPI_DOUBLE
|
||||
#endif
|
||||
#endif
|
||||
|
||||
// Options that require MPI
|
||||
#ifndef MFEM_USE_MPI
|
||||
#ifdef MFEM_USE_SUPERLU
|
||||
|
||||
+1
-1
@@ -388,7 +388,7 @@ GINKGO_LIB = $(XLINKER)-rpath,$(GINKGO_LINK_LIB_DIR) -L$(GINKGO_LINK_LIB_DIR)\
|
||||
# AmgX library configuration
|
||||
AMGX_DIR = @MFEM_DIR@/../amgx
|
||||
AMGX_OPT = -I$(AMGX_DIR)/include
|
||||
AMGX_LIB = -lcusparse -lcusolver -lcublas -lnvToolsExt -L$(AMGX_DIR)/lib -lamgx
|
||||
AMGX_LIB = -L$(AMGX_DIR)/lib -lamgx -lcusparse -lcusolver -lcublas -lnvToolsExt
|
||||
|
||||
# GnuTLS library configuration
|
||||
GNUTLS_OPT =
|
||||
|
||||
+1
-1
@@ -110,4 +110,4 @@ config-mk:
|
||||
|
||||
clean:
|
||||
rm -f $(CONFIG_HPP) $(CONFIG_MK) sample-runs-build.log
|
||||
rm -f $(GHV) $(GHV).out $(GMV) $(GMV).out
|
||||
rm -f $(GHV) $(GHV).out $(GMV) $(GMV).out *.dSYM
|
||||
|
||||
@@ -92,4 +92,5 @@ vertices
|
||||
-0.70710678 -0.70710678
|
||||
0 -1
|
||||
0.70710678 -0.70710678
|
||||
|
||||
mfem_mesh_end
|
||||
|
||||
@@ -48,7 +48,7 @@ PROJECT_NAME = MFEM
|
||||
# could be handy for archiving the generated documentation or if some version
|
||||
# control system is used.
|
||||
|
||||
PROJECT_NUMBER = v4.6.1
|
||||
PROJECT_NUMBER = v4.7.1
|
||||
|
||||
# Using the PROJECT_BRIEF tag one can provide an optional one line description
|
||||
# for a project that appears at the top of each page and should give viewer a
|
||||
|
||||
@@ -110,9 +110,13 @@ namespace mfem {
|
||||
* - <a class="el" href="ex35p_8cpp_source.html">Example 35p</a>: parallel multi-domain damped harmonic oscillators
|
||||
* - <a class="el" href="ex36_8cpp_source.html">Example 36</a>: Proximal Galerkin FEM for the obstacle problem
|
||||
* - <a class="el" href="ex36p_8cpp_source.html">Example 36p</a>: parallel Proximal Galerkin FEM for the obstacle problem
|
||||
* - <a class="el" href="ex37_8cpp_source.html">Example 37</a>: Topology optimization
|
||||
* - <a class="el" href="ex37_8cpp_source.html">Example 37</a>: topology optimization
|
||||
* - <a class="el" href="ex37p_8cpp_source.html">Example 37p</a>: parallel topology optimization
|
||||
* - <a class="el" href="ex38_8cpp_source.html">Example 38</a>: cut-surface and cut-volume integration
|
||||
* - <a class="el" href="ex39_8cpp_source.html">Example 39</a>: named mesh attributes
|
||||
* - <a class="el" href="ex39p_8cpp_source.html">Example 39p</a>: parallel named mesh attributes
|
||||
* - <a class="el" href="ex40_8cpp_source.html">Example 40</a>: eikonal equation
|
||||
* - <a class="el" href="ex40p_8cpp_source.html">Example 40p</a>: parallel eikonal equation
|
||||
*
|
||||
* <H4>AmgX Examples</H4>
|
||||
* - Variants of Examples
|
||||
@@ -214,6 +218,8 @@ namespace mfem {
|
||||
* - <a class="el" href="miniapps_2performance_2ex1_8cpp_source.html">HPC Example 1</a>: high-performance nodal H1 FEM for the Laplace problem
|
||||
* - <a class="el" href="miniapps_2performance_2ex1p_8cpp_source.html">HPC Example 1p</a>: high-performance parallel nodal H1 FEM for the Laplace problem
|
||||
* - <a class="el" href="generate__random__field_8cpp_source.html">SPDE Solvers</a>: SPDE solver random field generation
|
||||
* - <a class="el" href="contact-patch-test_8cpp_source.html">Contact</a>: mortar contact patch test for elasticity
|
||||
* - <a class="el" href="multidomain_8cpp_source.html">Multidomain miniapp</a>: Multidomain and Submesh demonstration miniapp
|
||||
* - <a class="el" href="pdiffusion_8cpp_source.html">DPG Diffusion example</a>: DPG formulation for the diffusion problem
|
||||
* - <a class="el" href="pmaxwell_8cpp_source.html">DPG Maxwell example</a>: DPG formulation for the indefinite Maxwell problem
|
||||
* - <a class="el" href="lor__elast_8cpp_source.html">LOR Elasticity</a>: solve linear elasticity with LOR preconditioning on GPUs
|
||||
|
||||
@@ -46,7 +46,7 @@ class DoxygenAwesomeDarkModeToggle extends HTMLElement {
|
||||
DoxygenAwesomeDarkModeToggle.onSystemPreferenceChanged()
|
||||
})
|
||||
// Update the color scheme when the tab is made visible again.
|
||||
// It is possible that the appearance was changed in another tab
|
||||
// It is possible that the appearance was changed in another tab
|
||||
// while this tab was in the background.
|
||||
document.addEventListener("visibilitychange", visibilityState => {
|
||||
if (document.visibilityState === 'visible') {
|
||||
@@ -97,7 +97,7 @@ class DoxygenAwesomeDarkModeToggle extends HTMLElement {
|
||||
* @returns `true` for dark-mode, `false` for light-mode user preference
|
||||
*/
|
||||
static get userPreference() {
|
||||
return (!DoxygenAwesomeDarkModeToggle.systemPreference && localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersDarkModeInLightModeKey)) ||
|
||||
return (!DoxygenAwesomeDarkModeToggle.systemPreference && localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersDarkModeInLightModeKey)) ||
|
||||
(DoxygenAwesomeDarkModeToggle.systemPreference && !localStorage.getItem(DoxygenAwesomeDarkModeToggle.prefersLightModeInDarkModeKey))
|
||||
}
|
||||
|
||||
|
||||
+10
-3
@@ -45,6 +45,7 @@ list(APPEND ALL_EXE_SRCS
|
||||
ex37.cpp
|
||||
ex38.cpp
|
||||
ex39.cpp
|
||||
ex40.cpp
|
||||
)
|
||||
|
||||
if (MFEM_USE_MPI)
|
||||
@@ -87,6 +88,7 @@ if (MFEM_USE_MPI)
|
||||
ex36p.cpp
|
||||
ex37p.cpp
|
||||
ex39p.cpp
|
||||
ex40p.cpp
|
||||
)
|
||||
endif()
|
||||
|
||||
@@ -146,10 +148,10 @@ if (MFEM_ENABLE_TESTING)
|
||||
# Add CUDA/HIP tests.
|
||||
set(DEVICE_EXAMPLES
|
||||
# serial examples with device support:
|
||||
ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26 ex34
|
||||
ex1 ex3 ex4 ex5 ex6 ex9 ex14 ex22 ex24 ex25 ex26 ex34
|
||||
# parallel examples with device support:
|
||||
ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p ex24p ex25p ex26p
|
||||
ex34p ex35p)
|
||||
ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex14p ex22p ex24p ex25p
|
||||
ex26p ex34p ex35p)
|
||||
set(MFEM_TEST_DEVICE)
|
||||
if (MFEM_USE_CUDA)
|
||||
set(MFEM_TEST_DEVICE "cuda")
|
||||
@@ -159,6 +161,11 @@ if (MFEM_ENABLE_TESTING)
|
||||
if (MFEM_TEST_DEVICE)
|
||||
foreach(TEST_NAME ${DEVICE_EXAMPLES})
|
||||
set(THIS_TEST_OPTIONS "-no-vis" "-d" "${MFEM_TEST_DEVICE}")
|
||||
if (${TEST_NAME} MATCHES "ex14p")
|
||||
list(APPEND THIS_TEST_OPTIONS "-rs" "2" "-rp" "0" "-pa")
|
||||
elseif (${TEST_NAME} MATCHES "ex14")
|
||||
list(APPEND THIS_TEST_OPTIONS "-r" "2" "-pa")
|
||||
endif()
|
||||
if (NOT (${TEST_NAME} MATCHES ".*p$"))
|
||||
add_test(NAME ${TEST_NAME}_${MFEM_TEST_DEVICE}_ser
|
||||
COMMAND ${TEST_NAME} ${THIS_TEST_OPTIONS})
|
||||
|
||||
+1
-4
@@ -646,10 +646,7 @@ real_t HyperelasticOperator::ElasticEnergy(const ParGridFunction &x) const
|
||||
|
||||
real_t HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
|
||||
{
|
||||
real_t loc_energy = 0.5*M.InnerProduct(v, v);
|
||||
real_t energy;
|
||||
MPI_Allreduce(&loc_energy, &energy, 1, MPITypeMap<real_t>::mpi_type,
|
||||
MPI_SUM, fespace.GetComm());
|
||||
real_t energy = 0.5*M.ParInnerProduct(v, v);
|
||||
return energy;
|
||||
}
|
||||
|
||||
|
||||
+4
-4
@@ -39,8 +39,8 @@ private:
|
||||
// Base Nonlinear Form
|
||||
std::unique_ptr<NonlinearForm> nonlinearForm;
|
||||
// element-wise inverse mass matrix
|
||||
std::vector<DenseMatrix> invmass; // local scalar inverse mass.
|
||||
std::vector<DenseMatrix> weakdiv; // local weakdivergence. Trial space is ByDim.
|
||||
std::vector<DenseMatrix> invmass; // local scalar inverse mass
|
||||
std::vector<DenseMatrix> weakdiv; // local weak divergence (trial space ByDim)
|
||||
// global maximum characteristic speed. Updated by form integrators
|
||||
mutable real_t max_char_speed;
|
||||
// auxiliary variable used in Mult
|
||||
@@ -169,9 +169,9 @@ void DGHyperbolicConservationLaws::Mult(const Vector &x, Vector &y) const
|
||||
{
|
||||
// 0. Reset wavespeed computation before operator application.
|
||||
formIntegrator->ResetMaxCharSpeed();
|
||||
// 1. Apply Nonlinear form to obtain an axiliary result
|
||||
// 1. Apply Nonlinear form to obtain an auxiliary result
|
||||
// z = - <F̂(u_h,n), [[v]]>_e
|
||||
// If weak-divergencee is not preassembled, we also have weak-divergence
|
||||
// If weak-divergence is not preassembled, we also have weak-divergence
|
||||
// z = - <F̂(u_h,n), [[v]]>_e + (F(u_h), ∇v)
|
||||
nonlinearForm->Mult(x, z);
|
||||
if (!weakdiv.empty()) // if weak divergence is pre-assembled
|
||||
|
||||
@@ -0,0 +1,374 @@
|
||||
// MFEM Example 40
|
||||
//
|
||||
// Compile with: make ex40
|
||||
//
|
||||
// Sample runs: ex40 -step 10 -gr 2.0
|
||||
// ex40 -step 10 -gr 2.0 -o 3 -r 1
|
||||
// ex40 -step 10 -gr 2.0 -r 4 -m ../data/l-shape.mesh
|
||||
// ex40 -step 10 -gr 2.0 -r 2 -m ../data/fichera.mesh
|
||||
//
|
||||
// Description: This example code demonstrates how to use MFEM to solve the
|
||||
// eikonal equation,
|
||||
//
|
||||
// |∇𝑢| = 1 in Ω, 𝑢 = g on ∂Ω.
|
||||
//
|
||||
// The solution of this problem coincides with the unique optimum of
|
||||
// the nonlinear program
|
||||
//
|
||||
// maximize ∫_Ω 𝑢 d𝑥 subject to |∇𝑢| ≤ 1, 𝑢 = g on Ω, (⋆)
|
||||
//
|
||||
// which is the foundation for method implemented below.
|
||||
//
|
||||
// Following the proximal Galerkin methodology [1] (see also Example
|
||||
// 36), we construct a Legendre function for the unit ball
|
||||
// 𝐵₁ := {𝑥 ∈ Rⁿ | |𝑥| < 1}. Our choice is the Hellinger entropy,
|
||||
//
|
||||
// h(𝑥) = −( 1 − |𝑥|² )^{1/2},
|
||||
//
|
||||
// although other choices are possible, each leading to a slightly
|
||||
// different algorithm. We then adaptively regularize the optimization
|
||||
// problem (⋆) with the Bregman divergence of the Hellinger entropy,
|
||||
//
|
||||
// maximize ∫_Ω 𝑢 d𝑥 - αₖ⁻¹ Dₕ(∇𝑢,∇𝑢ₖ₋₁) subject to 𝑢 = g on Ω.
|
||||
//
|
||||
// This results in a sequence of functions ( 𝜓ₖ , 𝑢ₖ ),
|
||||
//
|
||||
// 𝑢ₖ → 𝑢, 𝜓ₖ/|𝜓ₖ| → ∇𝑢 as k → \infty,
|
||||
//
|
||||
// defined by the nonlinear saddle-point problems
|
||||
//
|
||||
// Find 𝜓ₖ ∈ H(div,Ω) and 𝑢ₖ ∈ L²(Ω) such that
|
||||
// ( Zₖ(𝜓ₖ) , τ ) + ( 𝑢ₖ , ∇⋅τ ) = ⟨ g , τ⋅n ⟩ ∀ τ ∈ H(div,Ω)
|
||||
// ( ∇⋅𝜓ₖ , v ) = ( ∇⋅𝜓ₖ₋₁ - 1 , v ) ∀ v ∈ L²(Ω)
|
||||
//
|
||||
// where Zₖ(𝜓) := ∇h⁻¹(αₖ 𝜓) = 𝜓 / ( αₖ⁻² + |𝜓|² )^{1/2} and step size
|
||||
// αₖ > 0. These saddle-point problems are solved using a damped Newton's
|
||||
// method. This example assumes that g = 0 and allows the step size to
|
||||
// grow geometrically, αₖ = α₀rᵏ, where r ≥ 1 is the growth rate.
|
||||
//
|
||||
// [1] Keith, B. and Surowiec, T. (2023) Proximal Galerkin: A structure-
|
||||
// preserving finite element method for pointwise bound constraints.
|
||||
// arXiv:2307.12444 [math.NA]
|
||||
|
||||
#include "mfem.hpp"
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
|
||||
using namespace std;
|
||||
using namespace mfem;
|
||||
|
||||
class ZCoefficient : public VectorCoefficient
|
||||
{
|
||||
protected:
|
||||
GridFunction *psi;
|
||||
real_t alpha;
|
||||
|
||||
public:
|
||||
ZCoefficient(int vdim, GridFunction &psi_, real_t alpha_ = 1.0)
|
||||
: VectorCoefficient(vdim), psi(&psi_), alpha(alpha_) { }
|
||||
|
||||
virtual void Eval(Vector &V, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
void SetAlpha(real_t alpha_) { alpha = alpha_; }
|
||||
};
|
||||
|
||||
class DZCoefficient : public MatrixCoefficient
|
||||
{
|
||||
protected:
|
||||
GridFunction *psi;
|
||||
real_t alpha;
|
||||
|
||||
public:
|
||||
DZCoefficient(int height, GridFunction &psi_, real_t alpha_ = 1.0)
|
||||
: MatrixCoefficient(height), psi(&psi_), alpha(alpha_) { }
|
||||
|
||||
virtual void Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
void SetAlpha(real_t alpha_) { alpha = alpha_; }
|
||||
};
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
// 1. Parse command-line options.
|
||||
const char *mesh_file = "../data/star.mesh";
|
||||
int order = 1;
|
||||
int max_it = 5;
|
||||
int ref_levels = 3;
|
||||
real_t alpha = 1.0;
|
||||
real_t growth_rate = 1.0;
|
||||
real_t newton_scaling = 0.9;
|
||||
real_t tichonov = 1e-1;
|
||||
real_t tol = 1e-4;
|
||||
bool visualization = 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(&ref_levels, "-r", "--refs",
|
||||
"Number of h-refinements.");
|
||||
args.AddOption(&max_it, "-mi", "--max-it",
|
||||
"Maximum number of iterations");
|
||||
args.AddOption(&tol, "-tol", "--tol",
|
||||
"Stopping criteria based on the difference between"
|
||||
"successive solution updates");
|
||||
args.AddOption(&alpha, "-step", "--step",
|
||||
"Initial size alpha");
|
||||
args.AddOption(&growth_rate, "-gr", "--growth-rate",
|
||||
"Growth rate of the step size alpha");
|
||||
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 mesh file.
|
||||
Mesh mesh(mesh_file, 1, 1);
|
||||
int dim = mesh.Dimension();
|
||||
int sdim = mesh.SpaceDimension();
|
||||
|
||||
MFEM_ASSERT(mesh.bdr_attributes.Size(),
|
||||
"This example does not currently support meshes"
|
||||
" without boundary attributes."
|
||||
)
|
||||
|
||||
// 3. Postprocess the mesh.
|
||||
// 3A. Refine the mesh to increase the resolution.
|
||||
for (int l = 0; l < ref_levels; l++)
|
||||
{
|
||||
mesh.UniformRefinement();
|
||||
}
|
||||
|
||||
// 3B. Interpolate the geometry after refinement to control geometry error.
|
||||
// NOTE: Minimum second-order interpolation is used to improve the accuracy.
|
||||
int curvature_order = max(order,2);
|
||||
mesh.SetCurvature(curvature_order);
|
||||
|
||||
// 4. Define the necessary finite element spaces on the mesh.
|
||||
RT_FECollection RTfec(order, dim);
|
||||
FiniteElementSpace RTfes(&mesh, &RTfec);
|
||||
|
||||
L2_FECollection L2fec(order, dim);
|
||||
FiniteElementSpace L2fes(&mesh, &L2fec);
|
||||
|
||||
cout << "Number of H(div) dofs: "
|
||||
<< RTfes.GetTrueVSize() << endl;
|
||||
cout << "Number of L² dofs: "
|
||||
<< L2fes.GetTrueVSize() << endl;
|
||||
|
||||
// 5. Define the offsets for the block matrices
|
||||
Array<int> offsets(3);
|
||||
offsets[0] = 0;
|
||||
offsets[1] = RTfes.GetVSize();
|
||||
offsets[2] = L2fes.GetVSize();
|
||||
offsets.PartialSum();
|
||||
|
||||
BlockVector x(offsets), rhs(offsets);
|
||||
x = 0.0; rhs = 0.0;
|
||||
|
||||
// 6. Define the solution vectors as a finite element grid functions
|
||||
// corresponding to the fespaces.
|
||||
GridFunction u_gf, delta_psi_gf;
|
||||
delta_psi_gf.MakeRef(&RTfes,x,offsets[0]);
|
||||
u_gf.MakeRef(&L2fes,x,offsets[1]);
|
||||
|
||||
GridFunction psi_old_gf(&RTfes);
|
||||
GridFunction psi_gf(&RTfes);
|
||||
GridFunction u_old_gf(&L2fes);
|
||||
|
||||
// 7. Define initial guesses for the solution variables.
|
||||
delta_psi_gf = 0.0;
|
||||
psi_gf = 0.0;
|
||||
u_gf = 0.0;
|
||||
psi_old_gf = psi_gf;
|
||||
u_old_gf = u_gf;
|
||||
|
||||
// 8. Prepare for glvis output.
|
||||
char vishost[] = "localhost";
|
||||
int visport = 19916;
|
||||
socketstream sol_sock;
|
||||
if (visualization)
|
||||
{
|
||||
sol_sock.open(vishost,visport);
|
||||
sol_sock.precision(8);
|
||||
}
|
||||
|
||||
// 9. Coefficients to be used later.
|
||||
ConstantCoefficient neg_one(-1.0);
|
||||
ConstantCoefficient zero(0.0);
|
||||
ConstantCoefficient tichonov_cf(tichonov);
|
||||
ConstantCoefficient neg_tichonov_cf(-1.0*tichonov);
|
||||
ZCoefficient Z(sdim, psi_gf, alpha);
|
||||
DZCoefficient DZ(sdim, psi_gf, alpha);
|
||||
ScalarVectorProductCoefficient neg_Z(-1.0, Z);
|
||||
DivergenceGridFunctionCoefficient div_psi_cf(&psi_gf);
|
||||
DivergenceGridFunctionCoefficient div_psi_old_cf(&psi_old_gf);
|
||||
SumCoefficient psi_old_minus_psi(div_psi_old_cf, div_psi_cf, 1.0, -1.0);
|
||||
|
||||
// 10. Assemble constant matrices/vectors to avoid reassembly in the loop.
|
||||
LinearForm b0, b1;
|
||||
b0.MakeRef(&RTfes,rhs.GetBlock(0),0);
|
||||
b1.MakeRef(&L2fes,rhs.GetBlock(1),0);
|
||||
|
||||
b0.AddDomainIntegrator(new VectorFEDomainLFIntegrator(neg_Z));
|
||||
b1.AddDomainIntegrator(new DomainLFIntegrator(neg_one));
|
||||
b1.AddDomainIntegrator(new DomainLFIntegrator(psi_old_minus_psi));
|
||||
|
||||
BilinearForm a00(&RTfes);
|
||||
a00.AddDomainIntegrator(new VectorFEMassIntegrator(DZ));
|
||||
a00.AddDomainIntegrator(new VectorFEMassIntegrator(tichonov_cf));
|
||||
|
||||
MixedBilinearForm a10(&RTfes,&L2fes);
|
||||
a10.AddDomainIntegrator(new VectorFEDivergenceIntegrator());
|
||||
a10.Assemble();
|
||||
a10.Finalize();
|
||||
SparseMatrix &A10 = a10.SpMat();
|
||||
SparseMatrix *A01 = Transpose(A10);
|
||||
|
||||
BilinearForm a11(&L2fes);
|
||||
a11.AddDomainIntegrator(new MassIntegrator(neg_tichonov_cf));
|
||||
a11.Assemble();
|
||||
a11.Finalize();
|
||||
SparseMatrix &A11 = a11.SpMat();
|
||||
|
||||
// 11. Iterate.
|
||||
int k;
|
||||
int total_iterations = 0;
|
||||
real_t increment_u = 0.1;
|
||||
GridFunction u_tmp(&L2fes);
|
||||
for (k = 0; k < max_it; k++)
|
||||
{
|
||||
u_tmp = u_old_gf;
|
||||
Z.SetAlpha(alpha);
|
||||
DZ.SetAlpha(alpha);
|
||||
|
||||
mfem::out << "\nOUTER ITERATION " << k+1 << endl;
|
||||
|
||||
int j;
|
||||
for ( j = 0; j < 5; j++)
|
||||
{
|
||||
total_iterations++;
|
||||
|
||||
b0.Assemble();
|
||||
b1.Assemble();
|
||||
|
||||
a00.Assemble(false);
|
||||
a00.Finalize(false);
|
||||
SparseMatrix &A00 = a00.SpMat();
|
||||
|
||||
// Construct Schur-complement preconditioner
|
||||
Vector A00_diag(a00.Height());
|
||||
A00.GetDiag(A00_diag);
|
||||
A00_diag.Reciprocal();
|
||||
SparseMatrix *S = Mult_AtDA(*A01, A00_diag);
|
||||
|
||||
BlockDiagonalPreconditioner prec(offsets);
|
||||
prec.SetDiagonalBlock(0,new DSmoother(A00));
|
||||
#ifndef MFEM_USE_SUITESPARSE
|
||||
prec.SetDiagonalBlock(1,new GSSmoother(*S));
|
||||
#else
|
||||
prec.SetDiagonalBlock(1,new UMFPackSolver(*S));
|
||||
#endif
|
||||
prec.owns_blocks = 1;
|
||||
|
||||
BlockOperator A(offsets);
|
||||
A.SetBlock(0,0,&A00);
|
||||
A.SetBlock(1,0,&A10);
|
||||
A.SetBlock(0,1,A01);
|
||||
A.SetBlock(1,1,&A11);
|
||||
|
||||
GMRES(A,prec,rhs,x,0,2000,500,1e-12,0.0);
|
||||
delete S;
|
||||
|
||||
u_tmp -= u_gf;
|
||||
real_t Newton_update_size = u_tmp.ComputeL2Error(zero);
|
||||
u_tmp = u_gf;
|
||||
|
||||
// Damped Newton update
|
||||
psi_gf.Add(newton_scaling, delta_psi_gf);
|
||||
a00.Update();
|
||||
|
||||
if (visualization)
|
||||
{
|
||||
sol_sock << "solution\n" << mesh << u_gf << "window_title 'Discrete solution'"
|
||||
<< flush;
|
||||
}
|
||||
|
||||
mfem::out << "Newton_update_size = " << Newton_update_size << endl;
|
||||
|
||||
if (Newton_update_size < increment_u)
|
||||
{
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
u_tmp = u_gf;
|
||||
u_tmp -= u_old_gf;
|
||||
increment_u = u_tmp.ComputeL2Error(zero);
|
||||
|
||||
mfem::out << "Number of Newton iterations = " << j+1 << endl;
|
||||
mfem::out << "Increment (|| uₕ - uₕ_prvs||) = " << increment_u << endl;
|
||||
|
||||
u_old_gf = u_gf;
|
||||
psi_old_gf = psi_gf;
|
||||
|
||||
if (increment_u < tol || k == max_it-1)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
alpha *= max(growth_rate, 1_r);
|
||||
|
||||
}
|
||||
|
||||
mfem::out << "\n Outer iterations: " << k+1
|
||||
<< "\n Total iterations: " << total_iterations
|
||||
<< "\n Total dofs: " << RTfes.GetTrueVSize() + L2fes.GetTrueVSize()
|
||||
<< endl;
|
||||
|
||||
delete A01;
|
||||
return 0;
|
||||
}
|
||||
|
||||
void ZCoefficient::Eval(Vector &V, ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
MFEM_ASSERT(psi != NULL, "grid function is not set");
|
||||
MFEM_ASSERT(alpha > 0, "alpha is not positive");
|
||||
|
||||
Vector psi_vals(vdim);
|
||||
psi->GetVectorValue(T, ip, psi_vals);
|
||||
real_t norm = psi_vals.Norml2();
|
||||
real_t phi = 1.0 / sqrt(1.0/(alpha*alpha) + norm*norm);
|
||||
|
||||
V = psi_vals;
|
||||
V *= phi;
|
||||
}
|
||||
|
||||
void DZCoefficient::Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
MFEM_ASSERT(psi != NULL, "grid function is not set");
|
||||
MFEM_ASSERT(alpha > 0, "alpha is not positive");
|
||||
|
||||
Vector psi_vals(height);
|
||||
psi->GetVectorValue(T, ip, psi_vals);
|
||||
real_t norm = psi_vals.Norml2();
|
||||
real_t phi = 1.0 / sqrt(1.0/(alpha*alpha) + norm*norm);
|
||||
|
||||
K = 0.0;
|
||||
for (int i = 0; i < height; i++)
|
||||
{
|
||||
K(i,i) = phi;
|
||||
for (int j = 0; j < height; j++)
|
||||
{
|
||||
K(i,j) -= psi_vals(i) * psi_vals(j) * pow(phi, 3);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,436 @@
|
||||
// MFEM Example 40 - Parallel Version
|
||||
//
|
||||
// Compile with: make ex40p
|
||||
//
|
||||
// Sample runs: mpirun -np 4 ex40p -step 10 -gr 2.0
|
||||
// mpirun -np 4 ex40p -step 10 -gr 2.0 -o 3 -r 1
|
||||
// mpirun -np 4 ex40p -step 10 -gr 2.0 -r 4 -m ../data/l-shape.mesh
|
||||
// mpirun -np 4 ex40p -step 10 -gr 2.0 -r 2 -m ../data/fichera.mesh
|
||||
//
|
||||
// Description: This example code demonstrates how to use MFEM to solve the
|
||||
// eikonal equation,
|
||||
//
|
||||
// |∇𝑢| = 1 in Ω, 𝑢 = g on ∂Ω.
|
||||
//
|
||||
// The solution of this problem coincides with the unique optimum of
|
||||
// the nonlinear program
|
||||
//
|
||||
// maximize ∫_Ω 𝑢 d𝑥 subject to |∇𝑢| ≤ 1, 𝑢 = g on Ω, (⋆)
|
||||
//
|
||||
// which is the foundation for method implemented below.
|
||||
//
|
||||
// Following the proximal Galerkin methodology [1] (see also Example
|
||||
// 36), we construct a Legendre function for the unit ball
|
||||
// 𝐵₁ := {𝑥 ∈ Rⁿ | |𝑥| < 1}. Our choice is the Hellinger entropy,
|
||||
//
|
||||
// h(𝑥) = −( 1 − |𝑥|² )^{1/2},
|
||||
//
|
||||
// although other choices are possible, each leading to a slightly
|
||||
// different algorithm. We then adaptively regularize the optimization
|
||||
// problem (⋆) with the Bregman divergence of the Hellinger entropy,
|
||||
//
|
||||
// maximize ∫_Ω 𝑢 d𝑥 - αₖ⁻¹ Dₕ(∇𝑢,∇𝑢ₖ₋₁) subject to 𝑢 = g on Ω.
|
||||
//
|
||||
// This results in a sequence of functions ( 𝜓ₖ , 𝑢ₖ ),
|
||||
//
|
||||
// 𝑢ₖ → 𝑢, 𝜓ₖ/|𝜓ₖ| → ∇𝑢 as k → \infty,
|
||||
//
|
||||
// defined by the nonlinear saddle-point problems
|
||||
//
|
||||
// Find 𝜓ₖ ∈ H(div,Ω) and 𝑢ₖ ∈ L²(Ω) such that
|
||||
// ( Zₖ(𝜓ₖ) , τ ) + ( 𝑢ₖ , ∇⋅τ ) = ⟨ g , τ⋅n ⟩ ∀ τ ∈ H(div,Ω)
|
||||
// ( ∇⋅𝜓ₖ , v ) = ( ∇⋅𝜓ₖ₋₁ - 1 , v ) ∀ v ∈ L²(Ω)
|
||||
//
|
||||
// where Zₖ(𝜓) := ∇h⁻¹(αₖ 𝜓) = 𝜓 / ( αₖ⁻² + |𝜓|² )^{1/2} and step size
|
||||
// αₖ > 0. These saddle-point problems are solved using a damped Newton's
|
||||
// method. This example assumes that g = 0 and allows the step size to
|
||||
// grow geometrically, αₖ = α₀rᵏ, where r ≥ 1 is the growth rate.
|
||||
//
|
||||
// [1] Keith, B. and Surowiec, T. (2023) Proximal Galerkin: A structure-
|
||||
// preserving finite element method for pointwise bound constraints.
|
||||
// arXiv:2307.12444 [math.NA]
|
||||
|
||||
#include "mfem.hpp"
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
|
||||
using namespace std;
|
||||
using namespace mfem;
|
||||
|
||||
class ZCoefficient : public VectorCoefficient
|
||||
{
|
||||
protected:
|
||||
ParGridFunction *psi;
|
||||
real_t alpha;
|
||||
|
||||
public:
|
||||
ZCoefficient(int vdim, ParGridFunction &psi_, real_t alpha_ = 1.0)
|
||||
: VectorCoefficient(vdim), psi(&psi_), alpha(alpha_) { }
|
||||
|
||||
virtual void Eval(Vector &V, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
void SetAlpha(real_t alpha_) { alpha = alpha_; }
|
||||
};
|
||||
|
||||
class DZCoefficient : public MatrixCoefficient
|
||||
{
|
||||
protected:
|
||||
ParGridFunction *psi;
|
||||
real_t alpha;
|
||||
|
||||
public:
|
||||
DZCoefficient(int height, ParGridFunction &psi_, real_t alpha_ = 1.0)
|
||||
: MatrixCoefficient(height), psi(&psi_), alpha(alpha_) { }
|
||||
|
||||
virtual void Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
void SetAlpha(real_t alpha_) { alpha = alpha_; }
|
||||
};
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
// 0. Initialize MPI and HYPRE.
|
||||
Mpi::Init();
|
||||
int num_procs = Mpi::WorldSize();
|
||||
int myid = Mpi::WorldRank();
|
||||
Hypre::Init();
|
||||
|
||||
// 1. Parse command-line options.
|
||||
const char *mesh_file = "../data/star.mesh";
|
||||
int order = 1;
|
||||
int max_it = 5;
|
||||
int ref_levels = 3;
|
||||
real_t alpha = 1.0;
|
||||
real_t growth_rate = 1.0;
|
||||
real_t newton_scaling = 0.9;
|
||||
real_t tichonov = 1e-1;
|
||||
real_t tol = 1e-4;
|
||||
bool visualization = 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(&ref_levels, "-r", "--refs",
|
||||
"Number of h-refinements.");
|
||||
args.AddOption(&max_it, "-mi", "--max-it",
|
||||
"Maximum number of iterations");
|
||||
args.AddOption(&tol, "-tol", "--tol",
|
||||
"Stopping criteria based on the difference between"
|
||||
"successive solution updates");
|
||||
args.AddOption(&alpha, "-step", "--step",
|
||||
"Initial size alpha");
|
||||
args.AddOption(&growth_rate, "-gr", "--growth-rate",
|
||||
"Growth rate of the step size alpha");
|
||||
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);
|
||||
}
|
||||
return 1;
|
||||
}
|
||||
if (myid == 0)
|
||||
{
|
||||
args.PrintOptions(cout);
|
||||
}
|
||||
|
||||
// 2. Read the mesh from the mesh file.
|
||||
Mesh mesh(mesh_file, 1, 1);
|
||||
int dim = mesh.Dimension();
|
||||
int sdim = mesh.SpaceDimension();
|
||||
|
||||
MFEM_ASSERT(mesh.bdr_attributes.Size(),
|
||||
"This example does not currently support meshes"
|
||||
" without boundary attributes."
|
||||
)
|
||||
|
||||
// 3. Postprocess the mesh.
|
||||
// 3A. Refine the mesh to increase the resolution.
|
||||
for (int l = 0; l < ref_levels; l++)
|
||||
{
|
||||
mesh.UniformRefinement();
|
||||
}
|
||||
|
||||
// 3B. Interpolate the geometry after refinement to control geometry error.
|
||||
// NOTE: Minimum second-order interpolation is used to improve the accuracy.
|
||||
int curvature_order = max(order,2);
|
||||
mesh.SetCurvature(curvature_order);
|
||||
|
||||
ParMesh pmesh(MPI_COMM_WORLD, mesh);
|
||||
mesh.Clear();
|
||||
|
||||
// 4. Define the necessary finite element spaces on the mesh.
|
||||
RT_FECollection RTfec(order, dim);
|
||||
ParFiniteElementSpace RTfes(&pmesh, &RTfec);
|
||||
|
||||
L2_FECollection L2fec(order, dim);
|
||||
ParFiniteElementSpace L2fes(&pmesh, &L2fec);
|
||||
|
||||
int num_dofs_RT = RTfes.GlobalTrueVSize();
|
||||
int num_dofs_L2 = L2fes.GlobalTrueVSize();
|
||||
if (myid == 0)
|
||||
{
|
||||
cout << "Number of H(div) dofs: "
|
||||
<< num_dofs_RT << endl;
|
||||
cout << "Number of L² dofs: "
|
||||
<< num_dofs_L2 << endl;
|
||||
}
|
||||
|
||||
// 5. Define the offsets for the block matrices
|
||||
Array<int> offsets(3);
|
||||
offsets[0] = 0;
|
||||
offsets[1] = RTfes.GetVSize();
|
||||
offsets[2] = L2fes.GetVSize();
|
||||
offsets.PartialSum();
|
||||
|
||||
Array<int> toffsets(3);
|
||||
toffsets[0] = 0;
|
||||
toffsets[1] = RTfes.GetTrueVSize();
|
||||
toffsets[2] = L2fes.GetTrueVSize();
|
||||
toffsets.PartialSum();
|
||||
|
||||
BlockVector x(offsets), rhs(offsets);
|
||||
x = 0.0; rhs = 0.0;
|
||||
|
||||
BlockVector tx(toffsets), trhs(toffsets);
|
||||
tx = 0.0; trhs = 0.0;
|
||||
|
||||
// 6. Define the solution vectors as a finite element grid functions
|
||||
// corresponding to the fespaces.
|
||||
ParGridFunction u_gf, delta_psi_gf;
|
||||
delta_psi_gf.MakeRef(&RTfes,x,offsets[0]);
|
||||
u_gf.MakeRef(&L2fes,x,offsets[1]);
|
||||
|
||||
ParGridFunction psi_old_gf(&RTfes);
|
||||
ParGridFunction psi_gf(&RTfes);
|
||||
ParGridFunction u_old_gf(&L2fes);
|
||||
|
||||
// 7. Define initial guesses for the solution variables.
|
||||
delta_psi_gf = 0.0;
|
||||
psi_gf = 0.0;
|
||||
u_gf = 0.0;
|
||||
psi_old_gf = psi_gf;
|
||||
u_old_gf = u_gf;
|
||||
|
||||
// 8. Prepare for glvis output.
|
||||
char vishost[] = "localhost";
|
||||
int visport = 19916;
|
||||
socketstream sol_sock;
|
||||
if (visualization)
|
||||
{
|
||||
sol_sock.open(vishost,visport);
|
||||
sol_sock.precision(8);
|
||||
}
|
||||
|
||||
// 9. Coefficients to be used later.
|
||||
ConstantCoefficient neg_one(-1.0);
|
||||
ConstantCoefficient zero(0.0);
|
||||
ConstantCoefficient tichonov_cf(tichonov);
|
||||
ConstantCoefficient neg_tichonov_cf(-1.0*tichonov);
|
||||
ZCoefficient Z(sdim, psi_gf, alpha);
|
||||
DZCoefficient DZ(sdim, psi_gf, alpha);
|
||||
ScalarVectorProductCoefficient neg_Z(-1.0, Z);
|
||||
DivergenceGridFunctionCoefficient div_psi_cf(&psi_gf);
|
||||
DivergenceGridFunctionCoefficient div_psi_old_cf(&psi_old_gf);
|
||||
SumCoefficient psi_old_minus_psi(div_psi_old_cf, div_psi_cf, 1.0, -1.0);
|
||||
|
||||
// 10. Assemble constant matrices/vectors to avoid reassembly in the loop.
|
||||
ParLinearForm b0, b1;
|
||||
b0.MakeRef(&RTfes,rhs.GetBlock(0),0);
|
||||
b1.MakeRef(&L2fes,rhs.GetBlock(1),0);
|
||||
|
||||
b0.AddDomainIntegrator(new VectorFEDomainLFIntegrator(neg_Z));
|
||||
b1.AddDomainIntegrator(new DomainLFIntegrator(neg_one));
|
||||
b1.AddDomainIntegrator(new DomainLFIntegrator(psi_old_minus_psi));
|
||||
|
||||
ParBilinearForm a00(&RTfes);
|
||||
a00.AddDomainIntegrator(new VectorFEMassIntegrator(DZ));
|
||||
a00.AddDomainIntegrator(new VectorFEMassIntegrator(tichonov_cf));
|
||||
|
||||
ParMixedBilinearForm a10(&RTfes,&L2fes);
|
||||
a10.AddDomainIntegrator(new VectorFEDivergenceIntegrator());
|
||||
a10.Assemble();
|
||||
a10.Finalize();
|
||||
HypreParMatrix *A10 = a10.ParallelAssemble();
|
||||
|
||||
HypreParMatrix *A01 = A10->Transpose();
|
||||
|
||||
ParBilinearForm a11(&L2fes);
|
||||
a11.AddDomainIntegrator(new MassIntegrator(neg_tichonov_cf));
|
||||
a11.Assemble();
|
||||
a11.Finalize();
|
||||
HypreParMatrix *A11 = a11.ParallelAssemble();
|
||||
|
||||
// 11. Iterate.
|
||||
int k;
|
||||
int total_iterations = 0;
|
||||
real_t increment_u = 0.1;
|
||||
ParGridFunction u_tmp(&L2fes);
|
||||
for (k = 0; k < max_it; k++)
|
||||
{
|
||||
u_tmp = u_old_gf;
|
||||
Z.SetAlpha(alpha);
|
||||
DZ.SetAlpha(alpha);
|
||||
|
||||
if (myid == 0)
|
||||
{
|
||||
mfem::out << "\nOUTER ITERATION " << k+1 << endl;
|
||||
}
|
||||
|
||||
int j;
|
||||
for ( j = 0; j < 5; j++)
|
||||
{
|
||||
total_iterations++;
|
||||
|
||||
b0.Assemble();
|
||||
b0.ParallelAssemble(trhs.GetBlock(0));
|
||||
|
||||
b1.Assemble();
|
||||
b1.ParallelAssemble(trhs.GetBlock(1));
|
||||
|
||||
a00.Assemble(false);
|
||||
a00.Finalize(false);
|
||||
HypreParMatrix *A00 = a00.ParallelAssemble();
|
||||
|
||||
// Construct Schur-complement preconditioner
|
||||
HypreParVector A00_diag(MPI_COMM_WORLD, A00->GetGlobalNumRows(),
|
||||
A00->GetRowStarts());
|
||||
A00->GetDiag(A00_diag);
|
||||
HypreParMatrix S_tmp(*A01);
|
||||
S_tmp.InvScaleRows(A00_diag);
|
||||
HypreParMatrix *S = ParMult(A10, &S_tmp, true);
|
||||
|
||||
BlockDiagonalPreconditioner prec(toffsets);
|
||||
HypreBoomerAMG P00(*A00);
|
||||
P00.SetPrintLevel(0);
|
||||
HypreBoomerAMG P11(*S);
|
||||
P11.SetPrintLevel(0);
|
||||
prec.SetDiagonalBlock(0,&P00);
|
||||
prec.SetDiagonalBlock(1,&P11);
|
||||
|
||||
BlockOperator A(toffsets);
|
||||
A.SetBlock(0,0,A00);
|
||||
A.SetBlock(1,0,A10);
|
||||
A.SetBlock(0,1,A01);
|
||||
A.SetBlock(1,1,A11);
|
||||
|
||||
GMRESSolver gmres(MPI_COMM_WORLD);
|
||||
gmres.SetPrintLevel(-1);
|
||||
gmres.SetRelTol(1e-8);
|
||||
gmres.SetMaxIter(2000);
|
||||
gmres.SetKDim(500);
|
||||
gmres.SetOperator(A);
|
||||
gmres.SetPreconditioner(prec);
|
||||
gmres.Mult(trhs,tx);
|
||||
delete S;
|
||||
delete A00;
|
||||
|
||||
delta_psi_gf.SetFromTrueDofs(tx.GetBlock(0));
|
||||
u_gf.SetFromTrueDofs(tx.GetBlock(1));
|
||||
|
||||
u_tmp -= u_gf;
|
||||
real_t Newton_update_size = u_tmp.ComputeL2Error(zero);
|
||||
u_tmp = u_gf;
|
||||
|
||||
// Damped Newton update
|
||||
psi_gf.Add(newton_scaling, delta_psi_gf);
|
||||
a00.Update();
|
||||
|
||||
if (visualization)
|
||||
{
|
||||
sol_sock << "parallel " << num_procs << " " << myid << "\n";
|
||||
sol_sock << "solution\n" << pmesh << u_gf << "window_title 'Discrete solution'"
|
||||
<< flush;
|
||||
}
|
||||
|
||||
if (myid == 0)
|
||||
{
|
||||
mfem::out << "Newton_update_size = " << Newton_update_size << endl;
|
||||
}
|
||||
|
||||
if (Newton_update_size < increment_u)
|
||||
{
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
u_tmp = u_gf;
|
||||
u_tmp -= u_old_gf;
|
||||
increment_u = u_tmp.ComputeL2Error(zero);
|
||||
|
||||
if (myid == 0)
|
||||
{
|
||||
mfem::out << "Number of Newton iterations = " << j+1 << endl;
|
||||
mfem::out << "Increment (|| uₕ - uₕ_prvs||) = " << increment_u << endl;
|
||||
}
|
||||
|
||||
u_old_gf = u_gf;
|
||||
psi_old_gf = psi_gf;
|
||||
|
||||
if (increment_u < tol || k == max_it-1)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
alpha *= max(growth_rate, 1_r);
|
||||
|
||||
}
|
||||
|
||||
// 12. Print stats.
|
||||
if (myid == 0)
|
||||
{
|
||||
mfem::out << "\n Outer iterations: " << k+1
|
||||
<< "\n Total iterations: " << total_iterations
|
||||
<< "\n Total dofs: " << RTfes.GetTrueVSize() + L2fes.GetTrueVSize()
|
||||
<< endl;
|
||||
}
|
||||
|
||||
// 13. Free the used memory.
|
||||
delete A01;
|
||||
delete A10;
|
||||
delete A11;
|
||||
return 0;
|
||||
}
|
||||
|
||||
void ZCoefficient::Eval(Vector &V, ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
MFEM_ASSERT(psi != NULL, "grid function is not set");
|
||||
MFEM_ASSERT(alpha > 0, "alpha is not positive");
|
||||
|
||||
Vector psi_vals(vdim);
|
||||
psi->GetVectorValue(T, ip, psi_vals);
|
||||
real_t norm = psi_vals.Norml2();
|
||||
real_t phi = 1.0 / sqrt(1.0/(alpha*alpha) + norm*norm);
|
||||
|
||||
V = psi_vals;
|
||||
V *= phi;
|
||||
}
|
||||
|
||||
void DZCoefficient::Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
MFEM_ASSERT(psi != NULL, "grid function is not set");
|
||||
MFEM_ASSERT(alpha > 0, "alpha is not positive");
|
||||
|
||||
Vector psi_vals(height);
|
||||
psi->GetVectorValue(T, ip, psi_vals);
|
||||
real_t norm = psi_vals.Norml2();
|
||||
real_t phi = 1.0 / sqrt(1.0/(alpha*alpha) + norm*norm);
|
||||
|
||||
K = 0.0;
|
||||
for (int i = 0; i < height; i++)
|
||||
{
|
||||
K(i,i) = phi;
|
||||
for (int j = 0; j < height; j++)
|
||||
{
|
||||
K(i,j) -= psi_vals(i) * psi_vals(j) * pow(phi, 3);
|
||||
}
|
||||
}
|
||||
}
|
||||
+13
-5
@@ -23,14 +23,14 @@ MFEM_LIB_FILE = mfem_is_not_built
|
||||
|
||||
SEQ_EXAMPLES = ex0 ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9 ex10 ex14 ex15 ex16 \
|
||||
ex17 ex18 ex19 ex20 ex21 ex22 ex23 ex24 ex25 ex26 ex27 ex28 ex29 ex30 \
|
||||
ex31 ex33 ex34 ex36 ex37 ex38 ex39
|
||||
ex31 ex33 ex34 ex36 ex37 ex38 ex39 ex40
|
||||
PAR_EXAMPLES = ex0p ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex8p ex9p ex10p ex11p \
|
||||
ex12p ex13p ex14p ex15p ex16p ex17p ex18p ex19p ex20p ex21p ex22p ex24p \
|
||||
ex25p ex26p ex27p ex28p ex29p ex30p ex31p ex32p ex33p ex34p ex35p ex36p \
|
||||
ex37p ex39p
|
||||
SEQ_DEVICE_EXAMPLES = ex1 ex3 ex4 ex5 ex6 ex9 ex22 ex24 ex25 ex26 ex34
|
||||
PAR_DEVICE_EXAMPLES = ex1p ex2p ex3p ex4p ex5p ex6p ex7p ex9p ex13p ex22p \
|
||||
ex24p ex25p ex26p ex34p ex35p
|
||||
ex37p ex39p ex40p
|
||||
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_LAPACK),YES)
|
||||
SEQ_EXAMPLES += ex38
|
||||
@@ -138,6 +138,14 @@ ex10-test-seq: ex10
|
||||
@$(call mfem-test,$<,, Serial example,-tf 5)
|
||||
ex10p-test-par: ex10p
|
||||
@$(call mfem-test,$<, $(RUN_MPI), Parallel example,-tf 5)
|
||||
ex14-test-seq-cuda: ex14
|
||||
@$(call mfem-test,$<,, Serial CUDA example,-r 2 -pa -d cuda)
|
||||
ex14p-test-par-cuda: ex14p
|
||||
@$(call mfem-test,$<, $(RUN_MPI), Parallel CUDA example,-rs 2 -rp 0 -pa -d cuda)
|
||||
ex14-test-seq-hip: ex14
|
||||
@$(call mfem-test,$<,, Serial HIP example,-r 2 -pa -d hip)
|
||||
ex14p-test-par-hip: ex14p
|
||||
@$(call mfem-test,$<, $(RUN_MPI), Parallel HIP example,-rs 2 -rp 0 -pa -d hip)
|
||||
ex15-test-seq: ex15
|
||||
@$(call mfem-test,$<,, Serial example,-e 1)
|
||||
ex15p-test-par: ex15p
|
||||
|
||||
@@ -1,3 +1,14 @@
|
||||
// Copyright (c) 2010-2024, 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 <algorithm>
|
||||
#include <assert.h>
|
||||
#include <cstdlib>
|
||||
|
||||
@@ -709,10 +709,7 @@ real_t HyperelasticOperator::ElasticEnergy(const ParGridFunction &x) const
|
||||
|
||||
real_t HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
|
||||
{
|
||||
real_t loc_energy = 0.5*M.InnerProduct(v, v);
|
||||
real_t energy;
|
||||
MPI_Allreduce(&loc_energy, &energy, 1, MPITypeMap<real_t>::mpi_type, MPI_SUM,
|
||||
fespace.GetComm());
|
||||
real_t energy = 0.5*M.ParInnerProduct(v, v);
|
||||
return energy;
|
||||
}
|
||||
|
||||
|
||||
@@ -66,7 +66,6 @@ int main(int argc, char *argv[])
|
||||
{
|
||||
// 1. Initialize MPI (required by PUMI) and HYPRE.
|
||||
Mpi::Init(argc, argv);
|
||||
int num_procs = Mpi::WorldSize();
|
||||
int myid = Mpi::WorldRank();
|
||||
Hypre::Init();
|
||||
|
||||
|
||||
@@ -80,8 +80,6 @@ int main(int argc, char *argv[])
|
||||
{
|
||||
// 1. Initialize MPI (required by PUMI) and HYPRE.
|
||||
Mpi::Init(argc, argv);
|
||||
int num_proc = Mpi::WorldSize();
|
||||
int myId = Mpi::WorldRank();
|
||||
Hypre::Init();
|
||||
|
||||
// 2. Parse command-line options.
|
||||
|
||||
@@ -856,10 +856,7 @@ double HyperelasticOperator::ElasticEnergy(const ParGridFunction &x) const
|
||||
|
||||
double HyperelasticOperator::KineticEnergy(const ParGridFunction &v) const
|
||||
{
|
||||
double loc_energy = 0.5*M.InnerProduct(v, v);
|
||||
double energy;
|
||||
MPI_Allreduce(&loc_energy, &energy, 1, MPI_DOUBLE, MPI_SUM,
|
||||
fespace.GetComm());
|
||||
double energy = 0.5*M.ParInnerProduct(v, v);
|
||||
return energy;
|
||||
}
|
||||
|
||||
|
||||
@@ -340,9 +340,9 @@ public:
|
||||
$ M^{-1} $ (currently returns NULL) */
|
||||
virtual MatrixInverse *Inverse() const;
|
||||
|
||||
/** @brief Finalizes the matrix initialization if the ::AssemblyLevel is
|
||||
/** @brief Finalizes the matrix initialization if the ::AssemblyLevel is
|
||||
AssemblyLevel::LEGACY.
|
||||
THe matrix that gets finalized is different if you are using static
|
||||
The matrix that gets finalized is different if you are using static
|
||||
condensation or hybridization.*/
|
||||
virtual void Finalize(int skip_zeros = 1);
|
||||
|
||||
@@ -643,7 +643,7 @@ public:
|
||||
void EliminateVDofs(const Array<int> &vdofs, const Vector &sol, Vector &rhs,
|
||||
DiagonalPolicy dpolicy = DIAG_ONE);
|
||||
|
||||
/** @brief Eliminate the given @a vdofs, storing the eliminated part
|
||||
/** @brief Eliminate the given @a vdofs, storing the eliminated part
|
||||
internally in $ M_e $.
|
||||
|
||||
This method works in conjunction with EliminateVDofsInRHS() and allows
|
||||
@@ -826,7 +826,7 @@ public:
|
||||
$ M^{-1} $ (currently unimplemented and returns NULL)*/
|
||||
virtual MatrixInverse *Inverse() const;
|
||||
|
||||
/** @brief Finalizes the matrix initialization if the ::AssemblyLevel is
|
||||
/** @brief Finalizes the matrix initialization if the ::AssemblyLevel is
|
||||
AssemblyLevel::LEGACY.*/
|
||||
virtual void Finalize(int skip_zeros = 1);
|
||||
|
||||
|
||||
+3
-3
@@ -1741,7 +1741,7 @@ public:
|
||||
{ vector_fe.CalcPhysDShape(Trans, shape); }
|
||||
};
|
||||
|
||||
/** Class for integrating the bilinear form $a(u,v) := (-\hat{V} \cdot \nabla \cdot u, \nabla \cdot v)$ in 2D
|
||||
/** Class for integrating the bilinear form $a(u,v) := (-\hat{V} \cdot \nabla u, \nabla \cdot v)$ in 2D
|
||||
or 3D and where $\hat{V}$ is a vector coefficient, $u$ is in $H^1$ and $v$ is in $H(div)$. */
|
||||
class MixedGradDivIntegrator : public MixedScalarVectorIntegrator
|
||||
{
|
||||
@@ -1780,7 +1780,7 @@ public:
|
||||
{ scalar_fe.CalcPhysDivShape(Trans, shape); }
|
||||
};
|
||||
|
||||
/** Class for integrating the bilinear form $a(u,v) := (-\hat{V} \nabla \cdot u, \nabla \cdot v)$ in 2D
|
||||
/** Class for integrating the bilinear form $a(u,v) := (-\hat{V} \nabla \cdot u, \nabla v)$ in 2D
|
||||
or 3D and where $\hat{V}$ is a vector coefficient, $u$ is in $H(div)$ and $v$ is in $H^1$. */
|
||||
class MixedDivGradIntegrator : public MixedScalarVectorIntegrator
|
||||
{
|
||||
@@ -1820,7 +1820,7 @@ public:
|
||||
{ scalar_fe.CalcPhysDivShape(Trans, shape); }
|
||||
};
|
||||
|
||||
/** Class for integrating the bilinear form $a(u,v) := (-\hat{V} u, \nabla \cdot v)$ in 2D or 3D
|
||||
/** Class for integrating the bilinear form $a(u,v) := (-\hat{V} u, \nabla v)$ in 2D or 3D
|
||||
and where $\hat{V}$ is a vector coefficient, $u$ is in $H^1$ or $L_2$ and $v$ is in $H^1$. */
|
||||
class MixedScalarWeakDivergenceIntegrator : public MixedScalarVectorIntegrator
|
||||
{
|
||||
|
||||
+118
-4
@@ -807,6 +807,7 @@ void SymmetricMatrixCoefficient::ProjectSymmetric(QuadratureFunction &qf)
|
||||
|
||||
QuadratureSpaceBase &qspace = *qf.GetSpace();
|
||||
const int ne = qspace.GetNE();
|
||||
qf.HostWrite();
|
||||
DenseMatrix values;
|
||||
DenseSymmetricMatrix matrix;
|
||||
for (int iel = 0; iel < ne; ++iel)
|
||||
@@ -818,7 +819,7 @@ void SymmetricMatrixCoefficient::ProjectSymmetric(QuadratureFunction &qf)
|
||||
{
|
||||
const IntegrationPoint &ip = ir[iq];
|
||||
T.SetIntPoint(&ip);
|
||||
matrix.UseExternalData(&values(0, iq), vdim);
|
||||
matrix.UseExternalData(&values(0, iq), height);
|
||||
Eval(matrix, T, ip);
|
||||
}
|
||||
}
|
||||
@@ -828,13 +829,12 @@ void SymmetricMatrixCoefficient::ProjectSymmetric(QuadratureFunction &qf)
|
||||
void SymmetricMatrixCoefficient::Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
mat.SetSize(height);
|
||||
Eval(mat, T, ip);
|
||||
Eval(mat_aux, T, ip);
|
||||
for (int j = 0; j < width; ++j)
|
||||
{
|
||||
for (int i = 0; i < height; ++ i)
|
||||
{
|
||||
K(i, j) = mat(i, j);
|
||||
K(i, j) = mat_aux(i, j);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -924,6 +924,75 @@ void MatrixArrayCoefficient::Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
}
|
||||
}
|
||||
|
||||
MatrixArrayVectorCoefficient::MatrixArrayVectorCoefficient (int dim)
|
||||
: MatrixCoefficient (dim)
|
||||
{
|
||||
Coeff.SetSize(height);
|
||||
ownCoeff.SetSize(height);
|
||||
for (int i = 0; i < height; i++)
|
||||
{
|
||||
Coeff[i] = NULL;
|
||||
ownCoeff[i] = true;
|
||||
}
|
||||
}
|
||||
|
||||
void MatrixArrayVectorCoefficient::SetTime(real_t t)
|
||||
{
|
||||
for (int i=0; i < height; i++)
|
||||
{
|
||||
if (Coeff[i]) { Coeff[i]->SetTime(t); }
|
||||
}
|
||||
this->MatrixCoefficient::SetTime(t);
|
||||
}
|
||||
|
||||
void MatrixArrayVectorCoefficient::Set(int i, VectorCoefficient * c, bool own)
|
||||
{
|
||||
MFEM_ASSERT(i < height && i >= 0, "Row "
|
||||
<< i << " does not exist. " <<
|
||||
"Matrix height = " << height << ".");
|
||||
if (ownCoeff[i]) { delete Coeff[i]; }
|
||||
Coeff[i] = c;
|
||||
ownCoeff[i] = own;
|
||||
}
|
||||
|
||||
MatrixArrayVectorCoefficient::~MatrixArrayVectorCoefficient ()
|
||||
{
|
||||
for (int i=0; i < height; i++)
|
||||
{
|
||||
if (ownCoeff[i]) { delete Coeff[i]; }
|
||||
}
|
||||
}
|
||||
|
||||
void MatrixArrayVectorCoefficient::Eval(int i, Vector &V,
|
||||
ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
MFEM_ASSERT(i < height && i >= 0, "Row "
|
||||
<< i << " does not exist. " <<
|
||||
"Matrix height = " << height << ".");
|
||||
if (Coeff[i])
|
||||
{
|
||||
Coeff[i] -> Eval(V, T, ip);
|
||||
}
|
||||
else
|
||||
{
|
||||
V = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
void MatrixArrayVectorCoefficient::Eval(DenseMatrix &K,
|
||||
ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
K.SetSize(height, width);
|
||||
Vector V(width);
|
||||
for (int i = 0; i < height; i++)
|
||||
{
|
||||
this->Eval(i, V, T, ip);
|
||||
K.SetRow(i, V);
|
||||
}
|
||||
}
|
||||
|
||||
void MatrixRestrictedCoefficient::SetTime(real_t t)
|
||||
{
|
||||
if (c) { c->SetTime(t); }
|
||||
@@ -1041,6 +1110,27 @@ real_t DeterminantCoefficient::Eval(ElementTransformation &T,
|
||||
return ma.Det();
|
||||
}
|
||||
|
||||
TraceCoefficient::TraceCoefficient(MatrixCoefficient &A)
|
||||
: a(&A), ma(A.GetHeight(), A.GetWidth())
|
||||
{
|
||||
MFEM_ASSERT(A.GetHeight() == A.GetWidth(),
|
||||
"TraceCoefficient: "
|
||||
"Argument must be a square matrix.");
|
||||
}
|
||||
|
||||
void TraceCoefficient::SetTime(real_t t)
|
||||
{
|
||||
if (a) { a->SetTime(t); }
|
||||
this->Coefficient::SetTime(t);
|
||||
}
|
||||
|
||||
real_t TraceCoefficient::Eval(ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
a->Eval(ma, T, ip);
|
||||
return ma.Trace();
|
||||
}
|
||||
|
||||
VectorSumCoefficient::VectorSumCoefficient(int dim)
|
||||
: VectorCoefficient(dim),
|
||||
ACoef(NULL), BCoef(NULL),
|
||||
@@ -1326,6 +1416,30 @@ void InverseMatrixCoefficient::Eval(DenseMatrix &M,
|
||||
M.Invert();
|
||||
}
|
||||
|
||||
ExponentialMatrixCoefficient::ExponentialMatrixCoefficient(MatrixCoefficient &A)
|
||||
: MatrixCoefficient(A.GetHeight(), A.GetWidth()), a(&A)
|
||||
{
|
||||
MFEM_ASSERT(A.GetHeight() == A.GetWidth() && A.GetHeight() == 2,
|
||||
"ExponentialMatrixCoefficient: "
|
||||
<< "Argument must be a square 2x2 matrix."
|
||||
<< " Height = " << A.GetHeight()
|
||||
<< ", Width = " << A.GetWidth());
|
||||
}
|
||||
|
||||
void ExponentialMatrixCoefficient::SetTime(real_t t)
|
||||
{
|
||||
if (a) { a->SetTime(t); }
|
||||
this->MatrixCoefficient::SetTime(t);
|
||||
}
|
||||
|
||||
void ExponentialMatrixCoefficient::Eval(DenseMatrix &M,
|
||||
ElementTransformation &T,
|
||||
const IntegrationPoint &ip)
|
||||
{
|
||||
a->Eval(M, T, ip);
|
||||
M.Exponential();
|
||||
}
|
||||
|
||||
OuterProductCoefficient::OuterProductCoefficient(VectorCoefficient &A,
|
||||
VectorCoefficient &B)
|
||||
: MatrixCoefficient(A.GetVDim(), B.GetVDim()), a(&A), b(&B),
|
||||
|
||||
+100
-6
@@ -1334,6 +1334,46 @@ public:
|
||||
virtual ~MatrixArrayCoefficient();
|
||||
};
|
||||
|
||||
/** @brief Matrix coefficient defined row-wise by an array of vector
|
||||
coefficients. Rows that are not set will evaluate to zero. The
|
||||
matrix coefficient is stored as an array indexing the rows of
|
||||
the matrix. */
|
||||
class MatrixArrayVectorCoefficient : public MatrixCoefficient
|
||||
{
|
||||
private:
|
||||
Array<VectorCoefficient *> Coeff;
|
||||
Array<bool> ownCoeff;
|
||||
|
||||
public:
|
||||
/** @brief Construct a coefficient matrix of dimensions @a dim * @a dim. The
|
||||
actual coefficients still need to be added with Set(). */
|
||||
explicit MatrixArrayVectorCoefficient (int dim);
|
||||
|
||||
/// Set the time for internally stored coefficients
|
||||
void SetTime(real_t t) override;
|
||||
|
||||
/// Get the vector coefficient located at the i-th row of the matrix
|
||||
VectorCoefficient* GetCoeff (int i) { return Coeff[i]; }
|
||||
|
||||
/** @brief Set the coefficient located at the i-th row of the matrix.
|
||||
By this will take ownership of the Coefficient passed in, but this
|
||||
can be overridden with the @a own parameter. */
|
||||
void Set(int i, VectorCoefficient * c, bool own=true);
|
||||
|
||||
using MatrixCoefficient::Eval;
|
||||
|
||||
/// Evaluate coefficient located at the i-th row of the matrix using integration
|
||||
/// point @a ip.
|
||||
void Eval(int i, Vector &V, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
|
||||
/// Evaluate the matrix coefficient @a ip.
|
||||
void Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip) override;
|
||||
|
||||
virtual ~MatrixArrayVectorCoefficient();
|
||||
};
|
||||
|
||||
|
||||
/** @brief Derived matrix coefficient that has the value of the parent matrix
|
||||
coefficient where it is active and is zero otherwise. */
|
||||
@@ -1426,12 +1466,13 @@ public:
|
||||
class SymmetricMatrixCoefficient : public MatrixCoefficient
|
||||
{
|
||||
protected:
|
||||
|
||||
/// Internal matrix used when evaluating this coefficient as a DenseMatrix.
|
||||
DenseSymmetricMatrix mat;
|
||||
mutable DenseSymmetricMatrix mat_aux;
|
||||
public:
|
||||
/// Construct a dim x dim matrix coefficient.
|
||||
explicit SymmetricMatrixCoefficient(int dimension)
|
||||
: MatrixCoefficient(dimension, true) { }
|
||||
: MatrixCoefficient(dimension, true), mat_aux(height) { }
|
||||
|
||||
/// Get the size of the matrix.
|
||||
int GetSize() const { return height; }
|
||||
@@ -1464,8 +1505,9 @@ public:
|
||||
virtual void Eval(DenseMatrix &K, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
|
||||
/// Return a reference to the constant matrix.
|
||||
const DenseSymmetricMatrix& GetMatrix() { return mat; }
|
||||
|
||||
/// @deprecated Return a reference to the internal matrix used when evaluating this coefficient as a DenseMatrix.
|
||||
MFEM_DEPRECATED const DenseSymmetricMatrix& GetMatrix() { return mat_aux; }
|
||||
|
||||
virtual ~SymmetricMatrixCoefficient() { }
|
||||
};
|
||||
@@ -1485,6 +1527,10 @@ public:
|
||||
/// Evaluate the matrix coefficient at @a ip.
|
||||
virtual void Eval(DenseSymmetricMatrix &M, ElementTransformation &T,
|
||||
const IntegrationPoint &ip) { M = mat; }
|
||||
|
||||
/// Return a reference to the constant matrix.
|
||||
const DenseSymmetricMatrix& GetMatrix() { return mat; }
|
||||
|
||||
};
|
||||
|
||||
|
||||
@@ -1761,6 +1807,31 @@ public:
|
||||
const IntegrationPoint &ip);
|
||||
};
|
||||
|
||||
/// Scalar coefficient defined as the trace of a matrix coefficient
|
||||
class TraceCoefficient : public Coefficient
|
||||
{
|
||||
private:
|
||||
MatrixCoefficient * a;
|
||||
|
||||
mutable DenseMatrix ma;
|
||||
|
||||
public:
|
||||
/// Construct with the matrix.
|
||||
TraceCoefficient(MatrixCoefficient &A);
|
||||
|
||||
/// Set the time for internally stored coefficients
|
||||
void SetTime(real_t t);
|
||||
|
||||
/// Reset the matrix coefficient
|
||||
void SetACoef(MatrixCoefficient &A) { a = &A; }
|
||||
/// Return the matrix coefficient
|
||||
MatrixCoefficient * GetACoef() const { return a; }
|
||||
|
||||
/// Evaluate the trace coefficient at @a ip.
|
||||
virtual real_t Eval(ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
};
|
||||
|
||||
/// Vector coefficient defined as the linear combination of two vectors
|
||||
class VectorSumCoefficient : public VectorCoefficient
|
||||
{
|
||||
@@ -2112,7 +2183,7 @@ public:
|
||||
const IntegrationPoint &ip);
|
||||
};
|
||||
|
||||
/// Matrix coefficient defined as the transpose a matrix coefficient
|
||||
/// Matrix coefficient defined as the transpose of a matrix coefficient
|
||||
class TransposeMatrixCoefficient : public MatrixCoefficient
|
||||
{
|
||||
private:
|
||||
@@ -2135,7 +2206,7 @@ public:
|
||||
const IntegrationPoint &ip);
|
||||
};
|
||||
|
||||
/// Matrix coefficient defined as the inverse a matrix coefficient.
|
||||
/// Matrix coefficient defined as the inverse of a matrix coefficient.
|
||||
class InverseMatrixCoefficient : public MatrixCoefficient
|
||||
{
|
||||
private:
|
||||
@@ -2158,6 +2229,29 @@ public:
|
||||
const IntegrationPoint &ip);
|
||||
};
|
||||
|
||||
/// Matrix coefficient defined as the exponential of a matrix coefficient.
|
||||
class ExponentialMatrixCoefficient : public MatrixCoefficient
|
||||
{
|
||||
private:
|
||||
MatrixCoefficient * a;
|
||||
|
||||
public:
|
||||
/// Construct the matrix coefficient. Result is $ \exp(A) $.
|
||||
ExponentialMatrixCoefficient(MatrixCoefficient &A);
|
||||
|
||||
/// Set the time for internally stored coefficients
|
||||
void SetTime(real_t t);
|
||||
|
||||
/// Reset the matrix coefficient
|
||||
void SetACoef(MatrixCoefficient &A) { a = &A; }
|
||||
/// Return the matrix coefficient
|
||||
MatrixCoefficient * GetACoef() const { return a; }
|
||||
|
||||
/// Evaluate the matrix coefficient at @a ip.
|
||||
virtual void Eval(DenseMatrix &M, ElementTransformation &T,
|
||||
const IntegrationPoint &ip);
|
||||
};
|
||||
|
||||
/// Matrix coefficient defined as the outer product of two vector coefficients.
|
||||
class OuterProductCoefficient : public MatrixCoefficient
|
||||
{
|
||||
|
||||
+3
-12
@@ -1243,25 +1243,16 @@ ParSesquilinearForm::FormLinearSystem(const Array<int> &ess_tdof_list,
|
||||
HypreParMatrix * Ah;
|
||||
A_i.Get(Ah);
|
||||
hypre_ParCSRMatrix *Aih = *Ah;
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
ess_tdof_list.HostRead();
|
||||
for (int k = 0; k < n; k++)
|
||||
{
|
||||
const int j = ess_tdof_list[k];
|
||||
Aih->diag->data[Aih->diag->i[j]] = 0.0;
|
||||
}
|
||||
#else
|
||||
Ah->HypreReadWrite();
|
||||
const int *d_ess_tdof_list =
|
||||
ess_tdof_list.GetMemory().Read(MemoryClass::DEVICE, n);
|
||||
const int *d_diag_i = Aih->diag->i;
|
||||
ess_tdof_list.GetMemory().Read(GetHypreMemoryClass(), n);
|
||||
HYPRE_Int *d_diag_i = Aih->diag->i;
|
||||
real_t *d_diag_data = Aih->diag->data;
|
||||
MFEM_GPU_FORALL(k, n,
|
||||
mfem::hypre_forall(n, [=] MFEM_HOST_DEVICE (int k)
|
||||
{
|
||||
const int j = d_ess_tdof_list[k];
|
||||
d_diag_data[d_diag_i[j]] = 0.0;
|
||||
});
|
||||
#endif
|
||||
}
|
||||
else
|
||||
{
|
||||
|
||||
+11
-1
@@ -1,8 +1,18 @@
|
||||
// Copyright (c) 2010-2024, 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 "convergence.hpp"
|
||||
|
||||
using namespace std;
|
||||
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
|
||||
+2
-2
@@ -101,7 +101,7 @@ void DGMassInverse::SetRelTol(const real_t rel_tol_) { rel_tol = rel_tol_; }
|
||||
|
||||
void DGMassInverse::SetAbsTol(const real_t abs_tol_) { abs_tol = abs_tol_; }
|
||||
|
||||
void DGMassInverse::SetMaxIter(const real_t max_iter_) { max_iter = max_iter_; }
|
||||
void DGMassInverse::SetMaxIter(const int max_iter_) { max_iter = max_iter_; }
|
||||
|
||||
void DGMassInverse::Update()
|
||||
{
|
||||
@@ -137,7 +137,7 @@ void DGMassInverse::DGMassCGIteration(const Vector &b_, Vector &u_) const
|
||||
|
||||
const real_t RELTOL = rel_tol;
|
||||
const real_t ABSTOL = abs_tol;
|
||||
const real_t MAXIT = max_iter;
|
||||
const int MAXIT = max_iter;
|
||||
const bool IT_MODE = iterative_mode;
|
||||
const bool CHANGE_BASIS = (d2q != nullptr);
|
||||
|
||||
|
||||
+1
-1
@@ -96,7 +96,7 @@ public:
|
||||
/// Set the absolute tolerance.
|
||||
void SetAbsTol(const real_t abs_tol_);
|
||||
/// Set the maximum number of iterations.
|
||||
void SetMaxIter(const real_t max_iter_);
|
||||
void SetMaxIter(const int max_iter_);
|
||||
/// Recompute operator and preconditioner (when coefficient or mesh changes).
|
||||
void Update();
|
||||
|
||||
|
||||
+1
-1
@@ -316,7 +316,7 @@ public:
|
||||
int GetDim() const { return dim; }
|
||||
|
||||
/** @brief Returns the vector dimension for vector-valued finite elements,
|
||||
which is also the dimension of the interpolation operatrion. */
|
||||
which is also the dimension of the interpolation operation. */
|
||||
int GetRangeDim() const { return vdim; }
|
||||
|
||||
/// Returns the dimension of the curl for vector-valued finite elements.
|
||||
|
||||
+73
-51
@@ -39,7 +39,7 @@ GridFunction::GridFunction(Mesh *m, std::istream &input)
|
||||
UseDevice(true);
|
||||
|
||||
fes = new FiniteElementSpace;
|
||||
fec = fes->Load(m, input);
|
||||
fec_owned = fes->Load(m, input);
|
||||
|
||||
skip_comment_lines(input, '#');
|
||||
istream::int_type next_char = input.peek();
|
||||
@@ -81,10 +81,10 @@ GridFunction::GridFunction(Mesh *m, GridFunction *gf_array[], int num_pieces)
|
||||
int vdim, ordering;
|
||||
|
||||
fes = gf_array[0]->FESpace();
|
||||
fec = FiniteElementCollection::New(fes->FEColl()->Name());
|
||||
fec_owned = FiniteElementCollection::New(fes->FEColl()->Name());
|
||||
vdim = fes->GetVDim();
|
||||
ordering = fes->GetOrdering();
|
||||
fes = new FiniteElementSpace(m, fec, vdim, ordering);
|
||||
fes = new FiniteElementSpace(m, fec_owned, vdim, ordering);
|
||||
SetSize(fes->GetVSize());
|
||||
|
||||
if (m->NURBSext)
|
||||
@@ -153,11 +153,11 @@ GridFunction::GridFunction(Mesh *m, GridFunction *gf_array[], int num_pieces)
|
||||
|
||||
void GridFunction::Destroy()
|
||||
{
|
||||
if (fec)
|
||||
if (fec_owned)
|
||||
{
|
||||
delete fes;
|
||||
delete fec;
|
||||
fec = NULL;
|
||||
delete fec_owned;
|
||||
fec_owned = NULL;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -325,10 +325,9 @@ int GridFunction::VectorDim() const
|
||||
const FiniteElement *fe;
|
||||
if (!fes->GetNE())
|
||||
{
|
||||
const FiniteElementCollection *fe_coll = fes->FEColl();
|
||||
static const Geometry::Type geoms[3] =
|
||||
{ Geometry::SEGMENT, Geometry::TRIANGLE, Geometry::TETRAHEDRON };
|
||||
fe = fe_coll->
|
||||
fe = fes->FEColl()->
|
||||
FiniteElementForGeometry(geoms[fes->GetMesh()->Dimension()-1]);
|
||||
}
|
||||
else
|
||||
@@ -350,7 +349,8 @@ int GridFunction::CurlDim() const
|
||||
{
|
||||
static const Geometry::Type geoms[3] =
|
||||
{ Geometry::SEGMENT, Geometry::TRIANGLE, Geometry::TETRAHEDRON };
|
||||
fe = fec->FiniteElementForGeometry(geoms[fes->GetMesh()->Dimension()-1]);
|
||||
fe = fes->FEColl()->
|
||||
FiniteElementForGeometry(geoms[fes->GetMesh()->Dimension()-1]);
|
||||
}
|
||||
else
|
||||
{
|
||||
@@ -1321,9 +1321,9 @@ void GridFunction::ProjectVectorFieldOn(GridFunction &vec_field, int comp)
|
||||
}
|
||||
}
|
||||
|
||||
void GridFunction::AccumulateAndCountDerivativeValues(int comp, int der_comp,
|
||||
GridFunction &der,
|
||||
Array<int> &zones_per_dof)
|
||||
void GridFunction::AccumulateAndCountDerivativeValues(
|
||||
int comp, int der_comp, GridFunction &der,
|
||||
Array<int> &zones_per_dof) const
|
||||
{
|
||||
FiniteElementSpace * der_fes = der.FESpace();
|
||||
ElementTransformation * transf;
|
||||
@@ -1374,7 +1374,8 @@ void GridFunction::AccumulateAndCountDerivativeValues(int comp, int der_comp,
|
||||
}
|
||||
}
|
||||
|
||||
void GridFunction::GetDerivative(int comp, int der_comp, GridFunction &der)
|
||||
void GridFunction::GetDerivative(int comp, int der_comp,
|
||||
GridFunction &der) const
|
||||
{
|
||||
Array<int> overlap;
|
||||
AccumulateAndCountDerivativeValues(comp, der_comp, der, overlap);
|
||||
@@ -2061,41 +2062,37 @@ void GridFunction::AccumulateAndCountBdrValues(
|
||||
Coefficient *coeff[], VectorCoefficient *vcoeff, const Array<int> &attr,
|
||||
Array<int> &values_counter)
|
||||
{
|
||||
int i, j, fdof, d, ind, vdim;
|
||||
real_t val;
|
||||
const FiniteElement *fe;
|
||||
ElementTransformation *transf;
|
||||
Array<int> vdofs;
|
||||
Vector vc;
|
||||
|
||||
values_counter.SetSize(Size());
|
||||
values_counter = 0;
|
||||
|
||||
vdim = fes->GetVDim();
|
||||
|
||||
const int vdim = fes->GetVDim();
|
||||
HostReadWrite();
|
||||
|
||||
for (i = 0; i < fes->GetNBE(); i++)
|
||||
for (int i = 0; i < fes->GetNBE(); i++)
|
||||
{
|
||||
if (attr[fes->GetBdrAttribute(i) - 1] == 0) { continue; }
|
||||
|
||||
fe = fes->GetBE(i);
|
||||
fdof = fe->GetDof();
|
||||
transf = fes->GetBdrElementTransformation(i);
|
||||
const FiniteElement *fe = fes->GetBE(i);
|
||||
const int fdof = fe->GetDof();
|
||||
ElementTransformation *transf = fes->GetBdrElementTransformation(i);
|
||||
const IntegrationRule &ir = fe->GetNodes();
|
||||
fes->GetBdrElementVDofs(i, vdofs);
|
||||
|
||||
for (j = 0; j < fdof; j++)
|
||||
for (int j = 0; j < fdof; j++)
|
||||
{
|
||||
const IntegrationPoint &ip = ir.IntPoint(j);
|
||||
transf->SetIntPoint(&ip);
|
||||
if (vcoeff) { vcoeff->Eval(vc, *transf, ip); }
|
||||
for (d = 0; d < vdim; d++)
|
||||
for (int d = 0; d < vdim; d++)
|
||||
{
|
||||
if (!vcoeff && !coeff[d]) { continue; }
|
||||
|
||||
val = vcoeff ? vc(d) : coeff[d]->Eval(*transf, ip);
|
||||
if ( (ind = vdofs[fdof*d+j]) < 0 )
|
||||
real_t val = vcoeff ? vc(d) : coeff[d]->Eval(*transf, ip);
|
||||
int ind = vdofs[fdof*d+j];
|
||||
if ( ind < 0 )
|
||||
{
|
||||
val = -val, ind = -1-ind;
|
||||
}
|
||||
@@ -2117,10 +2114,11 @@ void GridFunction::AccumulateAndCountBdrValues(
|
||||
// iff A_ij != 0. It is sufficient to resolve just the first level of
|
||||
// dependency, since A is a projection matrix: A^n = A due to cR.cP = I.
|
||||
// Cases like these arise in 3D when boundary edges are constrained by
|
||||
// (depend on) internal faces/elements. We use the virtual method
|
||||
// GetBoundaryClosure from NCMesh to resolve the dependencies.
|
||||
|
||||
if (fes->Nonconforming() && fes->GetMesh()->Dimension() == 3)
|
||||
// (depend on) internal faces/elements, or for internal boundaries in 2 or
|
||||
// 3D. We use the virtual method GetBoundaryClosure from NCMesh to resolve
|
||||
// the dependencies.
|
||||
if (fes->Nonconforming() && (fes->GetMesh()->Dimension() == 2 ||
|
||||
fes->GetMesh()->Dimension() == 3))
|
||||
{
|
||||
Vector vals;
|
||||
Mesh *mesh = fes->GetMesh();
|
||||
@@ -2128,26 +2126,19 @@ void GridFunction::AccumulateAndCountBdrValues(
|
||||
Array<int> bdr_edges, bdr_vertices, bdr_faces;
|
||||
ncmesh->GetBoundaryClosure(attr, bdr_vertices, bdr_edges, bdr_faces);
|
||||
|
||||
for (i = 0; i < bdr_edges.Size(); i++)
|
||||
auto mark_dofs = [&](ElementTransformation &transf, const FiniteElement &fe)
|
||||
{
|
||||
int edge = bdr_edges[i];
|
||||
fes->GetEdgeVDofs(edge, vdofs);
|
||||
if (vdofs.Size() == 0) { continue; }
|
||||
|
||||
transf = mesh->GetEdgeTransformation(edge);
|
||||
transf->Attribute = -1; // TODO: set the boundary attribute
|
||||
fe = fes->GetEdgeElement(edge);
|
||||
if (!vcoeff)
|
||||
{
|
||||
vals.SetSize(fe->GetDof());
|
||||
for (d = 0; d < vdim; d++)
|
||||
vals.SetSize(fe.GetDof());
|
||||
for (int d = 0; d < vdim; d++)
|
||||
{
|
||||
if (!coeff[d]) { continue; }
|
||||
|
||||
fe->Project(*coeff[d], *transf, vals);
|
||||
fe.Project(*coeff[d], transf, vals);
|
||||
for (int k = 0; k < vals.Size(); k++)
|
||||
{
|
||||
ind = vdofs[d*vals.Size()+k];
|
||||
const int ind = vdofs[d*vals.Size()+k];
|
||||
if (++values_counter[ind] == 1)
|
||||
{
|
||||
(*this)(ind) = vals(k);
|
||||
@@ -2161,11 +2152,11 @@ void GridFunction::AccumulateAndCountBdrValues(
|
||||
}
|
||||
else // vcoeff != NULL
|
||||
{
|
||||
vals.SetSize(vdim*fe->GetDof());
|
||||
fe->Project(*vcoeff, *transf, vals);
|
||||
vals.SetSize(vdim*fe.GetDof());
|
||||
fe.Project(*vcoeff, transf, vals);
|
||||
for (int k = 0; k < vals.Size(); k++)
|
||||
{
|
||||
ind = vdofs[k];
|
||||
const int ind = vdofs[k];
|
||||
if (++values_counter[ind] == 1)
|
||||
{
|
||||
(*this)(ind) = vals(k);
|
||||
@@ -2176,6 +2167,26 @@ void GridFunction::AccumulateAndCountBdrValues(
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
for (auto edge : bdr_edges)
|
||||
{
|
||||
fes->GetEdgeVDofs(edge, vdofs);
|
||||
if (vdofs.Size() == 0) { continue; }
|
||||
|
||||
ElementTransformation *transf = mesh->GetEdgeTransformation(edge);
|
||||
const FiniteElement *fe = fes->GetEdgeElement(edge);
|
||||
mark_dofs(*transf, *fe);
|
||||
}
|
||||
|
||||
for (auto face : bdr_faces)
|
||||
{
|
||||
fes->GetFaceVDofs(face, vdofs);
|
||||
if (vdofs.Size() == 0) { continue; }
|
||||
|
||||
ElementTransformation *transf = mesh->GetFaceTransformation(face);
|
||||
const FiniteElement *fe = fes->GetFaceElement(face);
|
||||
mark_dofs(*transf, *fe);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -2228,26 +2239,37 @@ void GridFunction::AccumulateAndCountBdrTangentValues(
|
||||
accumulate_dofs(dofs, lvec, *this, values_counter);
|
||||
}
|
||||
|
||||
if (fes->Nonconforming() && fes->GetMesh()->Dimension() == 3)
|
||||
if (fes->Nonconforming() && (fes->GetMesh()->Dimension() == 2 ||
|
||||
fes->GetMesh()->Dimension() == 3))
|
||||
{
|
||||
Mesh *mesh = fes->GetMesh();
|
||||
NCMesh *ncmesh = mesh->ncmesh;
|
||||
Array<int> bdr_edges, bdr_vertices, bdr_faces;
|
||||
ncmesh->GetBoundaryClosure(bdr_attr, bdr_vertices, bdr_edges, bdr_faces);
|
||||
|
||||
for (int i = 0; i < bdr_edges.Size(); i++)
|
||||
for (auto edge : bdr_edges)
|
||||
{
|
||||
int edge = bdr_edges[i];
|
||||
fes->GetEdgeDofs(edge, dofs);
|
||||
if (dofs.Size() == 0) { continue; }
|
||||
|
||||
T = mesh->GetEdgeTransformation(edge);
|
||||
T->Attribute = -1; // TODO: set the boundary attribute
|
||||
fe = fes->GetEdgeElement(edge);
|
||||
lvec.SetSize(fe->GetDof());
|
||||
fe->Project(vcoeff, *T, lvec);
|
||||
accumulate_dofs(dofs, lvec, *this, values_counter);
|
||||
}
|
||||
|
||||
for (auto face : bdr_faces)
|
||||
{
|
||||
fes->GetFaceDofs(face, dofs);
|
||||
if (dofs.Size() == 0) { continue; }
|
||||
|
||||
T = mesh->GetFaceTransformation(face);
|
||||
fe = fes->GetFaceElement(face);
|
||||
lvec.SetSize(fe->GetDof());
|
||||
fe->Project(vcoeff, *T, lvec);
|
||||
accumulate_dofs(dofs, lvec, *this, values_counter);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -3904,7 +3926,7 @@ void GridFunction::LegacyNCReorder()
|
||||
mesh->GetEdgeVertices(i, ev);
|
||||
if (old_vertex[ev[0]] > old_vertex[ev[1]])
|
||||
{
|
||||
const int *ind = fec->DofOrderForOrientation(Geometry::SEGMENT, -1);
|
||||
const int *ind = fes->FEColl()->DofOrderForOrientation(Geometry::SEGMENT, -1);
|
||||
|
||||
fes->GetEdgeInteriorDofs(i, dofs);
|
||||
for (int k = 0; k < dofs.Size(); k++)
|
||||
|
||||
+13
-13
@@ -30,14 +30,14 @@ namespace mfem
|
||||
class GridFunction : public Vector
|
||||
{
|
||||
protected:
|
||||
/// FE space on which the grid function lives. Owned if #fec is not NULL.
|
||||
/// FE space on which the grid function lives. Owned if #fec_owned is not NULL.
|
||||
FiniteElementSpace *fes;
|
||||
|
||||
/** @brief Used when the grid function is read from a file. It can also be
|
||||
set explicitly, see MakeOwner().
|
||||
|
||||
If not NULL, this pointer is owned by the GridFunction. */
|
||||
FiniteElementCollection *fec;
|
||||
FiniteElementCollection *fec_owned;
|
||||
|
||||
long fes_sequence; // see FiniteElementSpace::sequence, Mesh::sequence
|
||||
|
||||
@@ -72,16 +72,16 @@ protected:
|
||||
|
||||
public:
|
||||
|
||||
GridFunction() { fes = NULL; fec = NULL; fes_sequence = 0; UseDevice(true); }
|
||||
GridFunction() { fes = NULL; fec_owned = NULL; fes_sequence = 0; UseDevice(true); }
|
||||
|
||||
/// Copy constructor. The internal true-dof vector #t_vec is not copied.
|
||||
GridFunction(const GridFunction &orig)
|
||||
: Vector(orig), fes(orig.fes), fec(NULL), fes_sequence(orig.fes_sequence)
|
||||
: Vector(orig), fes(orig.fes), fec_owned(NULL), fes_sequence(orig.fes_sequence)
|
||||
{ UseDevice(true); }
|
||||
|
||||
/// Construct a GridFunction associated with the FiniteElementSpace @a *f.
|
||||
GridFunction(FiniteElementSpace *f) : Vector(f->GetVSize())
|
||||
{ fes = f; fec = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
|
||||
{ fes = f; fec_owned = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
|
||||
|
||||
/// Construct a GridFunction using previously allocated array @a data.
|
||||
/** The GridFunction does not assume ownership of @a data which is assumed to
|
||||
@@ -91,13 +91,13 @@ public:
|
||||
*/
|
||||
GridFunction(FiniteElementSpace *f, real_t *data)
|
||||
: Vector(data, f->GetVSize())
|
||||
{ fes = f; fec = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
|
||||
{ fes = f; fec_owned = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
|
||||
|
||||
/** @brief Construct a GridFunction using previously allocated Vector @a base
|
||||
starting at the given offset, @a base_offset. */
|
||||
GridFunction(FiniteElementSpace *f, Vector &base, int base_offset = 0)
|
||||
: Vector(base, base_offset, f->GetVSize())
|
||||
{ fes = f; fec = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
|
||||
{ fes = f; fec_owned = NULL; fes_sequence = f->GetSequence(); UseDevice(true); }
|
||||
|
||||
/// Construct a GridFunction on the given Mesh, using the data from @a input.
|
||||
/** The content of @a input should be in the format created by the method
|
||||
@@ -116,12 +116,12 @@ public:
|
||||
GridFunction &operator=(const GridFunction &rhs)
|
||||
{ return operator=((const Vector &)rhs); }
|
||||
|
||||
/// Make the GridFunction the owner of #fec and #fes.
|
||||
/** If the new FiniteElementCollection, @a fec_, is NULL, ownership of #fec
|
||||
/// Make the GridFunction the owner of #fec_owned and #fes.
|
||||
/** If the new FiniteElementCollection, @a fec_, is NULL, ownership of #fec_owned
|
||||
and #fes is taken away. */
|
||||
void MakeOwner(FiniteElementCollection *fec_) { fec = fec_; }
|
||||
void MakeOwner(FiniteElementCollection *fec_) { fec_owned = fec_; }
|
||||
|
||||
FiniteElementCollection *OwnFEC() { return fec; }
|
||||
FiniteElementCollection *OwnFEC() { return fec_owned; }
|
||||
|
||||
int VectorDim() const;
|
||||
int CurlDim() const;
|
||||
@@ -321,7 +321,7 @@ public:
|
||||
@param[out] der The resulting derivative (scalar function). The
|
||||
FiniteElementSpace of this function must be set
|
||||
before the call. */
|
||||
void GetDerivative(int comp, int der_comp, GridFunction &der);
|
||||
void GetDerivative(int comp, int der_comp, GridFunction &der) const;
|
||||
|
||||
real_t GetDivergence(ElementTransformation &tr) const;
|
||||
|
||||
@@ -443,7 +443,7 @@ protected:
|
||||
GetDerivative() method; see its documentation. */
|
||||
void AccumulateAndCountDerivativeValues(int comp, int der_comp,
|
||||
GridFunction &der,
|
||||
Array<int> &zones_per_dof);
|
||||
Array<int> &zones_per_dof) const;
|
||||
|
||||
void AccumulateAndCountBdrValues(Coefficient *coeff[],
|
||||
VectorCoefficient *vcoeff,
|
||||
|
||||
@@ -1352,6 +1352,85 @@ void OversetFindPointsGSLIB::Interpolate(const Vector &point_pos,
|
||||
Interpolate(field_in, field_out);
|
||||
}
|
||||
|
||||
GSOPGSLIB::GSOPGSLIB(Array<long long> &ids)
|
||||
{
|
||||
gsl_comm = new gslib::comm;
|
||||
cr = new gslib::crystal;
|
||||
#ifdef MFEM_USE_MPI
|
||||
int initialized;
|
||||
MPI_Initialized(&initialized);
|
||||
if (!initialized) { MPI_Init(NULL, NULL); }
|
||||
MPI_Comm comm = MPI_COMM_WORLD;
|
||||
comm_init(gsl_comm, comm);
|
||||
#else
|
||||
comm_init(gsl_comm, 0);
|
||||
#endif
|
||||
crystal_init(cr, gsl_comm);
|
||||
UpdateIdentifiers(ids);
|
||||
}
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
GSOPGSLIB::GSOPGSLIB(MPI_Comm comm_, Array<long long> &ids)
|
||||
: cr(NULL), gsl_comm(NULL)
|
||||
{
|
||||
gsl_comm = new gslib::comm;
|
||||
cr = new gslib::crystal;
|
||||
comm_init(gsl_comm, comm_);
|
||||
crystal_init(cr, gsl_comm);
|
||||
UpdateIdentifiers(ids);
|
||||
}
|
||||
#endif
|
||||
|
||||
GSOPGSLIB::~GSOPGSLIB()
|
||||
{
|
||||
crystal_free(cr);
|
||||
gslib_gs_free(gsl_data);
|
||||
comm_free(gsl_comm);
|
||||
delete gsl_comm;
|
||||
delete cr;
|
||||
}
|
||||
|
||||
void GSOPGSLIB::UpdateIdentifiers(const Array<long long> &ids)
|
||||
{
|
||||
long long minval = ids.Min();
|
||||
#ifdef MFEM_USE_MPI
|
||||
MPI_Allreduce(MPI_IN_PLACE, &minval, 1, MPI_LONG_LONG_INT,
|
||||
MPI_MIN, gsl_comm->c);
|
||||
#endif
|
||||
MFEM_VERIFY(minval >= 0, "Unique identifier cannot be negative.");
|
||||
if (gsl_data != NULL) { gslib_gs_free(gsl_data); }
|
||||
num_ids = ids.Size();
|
||||
gsl_data = gslib_gs_setup(ids.GetData(),
|
||||
ids.Size(),
|
||||
gsl_comm, 0,
|
||||
gslib::gs_crystal_router, 0);
|
||||
}
|
||||
|
||||
void GSOPGSLIB::GS(Vector &senddata, GSOp op)
|
||||
{
|
||||
MFEM_VERIFY(senddata.Size() == num_ids,
|
||||
"Incompatible setup and GOP operation.");
|
||||
if (op == GSOp::ADD)
|
||||
{
|
||||
gslib_gs(senddata.GetData(),gslib::gs_double,gslib::gs_add,0,gsl_data,0);
|
||||
}
|
||||
else if (op == GSOp::MUL)
|
||||
{
|
||||
gslib_gs(senddata.GetData(),gslib::gs_double,gslib::gs_mul,0,gsl_data,0);
|
||||
}
|
||||
else if (op == GSOp::MAX)
|
||||
{
|
||||
gslib_gs(senddata.GetData(),gslib::gs_double,gslib::gs_max,0,gsl_data,0);
|
||||
}
|
||||
else if (op == GSOp::MIN)
|
||||
{
|
||||
gslib_gs(senddata.GetData(),gslib::gs_double,gslib::gs_min,0,gsl_data,0);
|
||||
}
|
||||
else
|
||||
{
|
||||
MFEM_ABORT("Invalid GSOp operation.");
|
||||
}
|
||||
}
|
||||
|
||||
} // namespace mfem
|
||||
|
||||
|
||||
+62
-1
@@ -23,13 +23,16 @@ struct comm;
|
||||
struct findpts_data_2;
|
||||
struct findpts_data_3;
|
||||
struct crystal;
|
||||
struct gs_data;
|
||||
}
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
/** \brief FindPointsGSLIB can robustly evaluate a GridFunction on an arbitrary
|
||||
* collection of points. There are three key functions in FindPointsGSLIB:
|
||||
* collection of points.
|
||||
*
|
||||
* There are three key functions in FindPointsGSLIB:
|
||||
*
|
||||
* 1. Setup - constructs the internal data structures of gslib.
|
||||
*
|
||||
@@ -226,6 +229,7 @@ public:
|
||||
|
||||
/** \brief OversetFindPointsGSLIB enables use of findpts for arbitrary number of
|
||||
overlapping grids.
|
||||
|
||||
The parameters in this class are the same as FindPointsGSLIB with the
|
||||
difference of additional inputs required to account for more than 1 mesh. */
|
||||
class OversetFindPointsGSLIB : public FindPointsGSLIB
|
||||
@@ -290,6 +294,63 @@ public:
|
||||
using FindPointsGSLIB::Interpolate;
|
||||
};
|
||||
|
||||
/** \brief Class for gather-scatter (gs) operations on Vectors based on
|
||||
corresponding global identifiers.
|
||||
|
||||
This functionality is useful for gs-ops on DOF values across processor
|
||||
boundary, where the global identifier would be the corresponding true DOF
|
||||
index. Operations currently supported are min, max, sum, and multiplication.
|
||||
Note: identifier 0 does not participate in the gather-scatter operation and
|
||||
a given identifier can be included multiple times on a given rank.
|
||||
For example, consider a vector, v:
|
||||
- v = [0.3, 0.4, 0.25, 0.7] on rank1,
|
||||
- v = [0.6, 0.1] on rank 2,
|
||||
- v = [-0.2, 0.3, 0.7, 0.] on rank 3.
|
||||
|
||||
Consider a corresponding Array<int>, a:
|
||||
- a = [1, 2, 3, 1] on rank 1,
|
||||
- a = [3, 2] on rank 2,
|
||||
- a = [1, 2, 0, 3] on rank 3.
|
||||
|
||||
A gather-scatter "minimum" operation, done as follows:
|
||||
GSOPGSLIB gs = GSOPGSLIB(MPI_COMM_WORLD, a);
|
||||
gs.GS(v, GSOp::MIN);
|
||||
would return into v:
|
||||
- v = [-0.2, 0.1, 0., -0.2] on rank 1,
|
||||
- v = [0., 0.1] on rank 2,
|
||||
- v = [-0.2, 0.1, 0.7, 0.] on rank 3,
|
||||
where the values have been compared across all processors based on the
|
||||
integer identifier. */
|
||||
class GSOPGSLIB
|
||||
{
|
||||
protected:
|
||||
struct gslib::crystal *cr; // gslib's internal data
|
||||
struct gslib::comm *gsl_comm; // gslib's internal data
|
||||
struct gslib::gs_data *gsl_data = NULL;
|
||||
int num_ids;
|
||||
|
||||
public:
|
||||
GSOPGSLIB(Array<long long> &ids);
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
GSOPGSLIB(MPI_Comm comm_, Array<long long> &ids);
|
||||
#endif
|
||||
|
||||
virtual ~GSOPGSLIB();
|
||||
|
||||
/// Supported operation types. See class description.
|
||||
enum GSOp {ADD, MUL, MIN, MAX};
|
||||
|
||||
/// Update the identifiers used for the gather-scatter operator.
|
||||
/// Same @a ids get grouped together and id == 0 does not participate.
|
||||
/// See class description.
|
||||
void UpdateIdentifiers(const Array<long long> &ids);
|
||||
|
||||
/// Gather-Scatter operation on senddata. Must match length of unique
|
||||
/// identifiers used in the constructor. See class description.
|
||||
void GS(Vector &senddata, GSOp op);
|
||||
};
|
||||
|
||||
} // namespace mfem
|
||||
|
||||
#endif // MFEM_USE_GSLIB
|
||||
|
||||
+5
-6
@@ -18,7 +18,6 @@
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
|
||||
void HyperbolicFormIntegrator::AssembleElementVector(const FiniteElement &el,
|
||||
ElementTransformation &Tr,
|
||||
const Vector &elfun,
|
||||
@@ -29,7 +28,7 @@ void HyperbolicFormIntegrator::AssembleElementVector(const FiniteElement &el,
|
||||
const int dof = el.GetDof();
|
||||
|
||||
#ifdef MFEM_THREAD_SAFE
|
||||
// Local storages for element integration
|
||||
// Local storage for element integration
|
||||
|
||||
// shape function value at an integration point
|
||||
Vector shape(dof);
|
||||
@@ -62,7 +61,7 @@ void HyperbolicFormIntegrator::AssembleElementVector(const FiniteElement &el,
|
||||
ir = &IntRules.Get(Tr.GetGeometryType(), order);
|
||||
}
|
||||
|
||||
// loop over interation points
|
||||
// loop over integration points
|
||||
for (int i = 0; i < ir->GetNPoints(); i++)
|
||||
{
|
||||
const IntegrationPoint &ip = ir->IntPoint(i);
|
||||
@@ -92,7 +91,7 @@ void HyperbolicFormIntegrator::AssembleFaceVector(
|
||||
const int dof2 = el2.GetDof();
|
||||
|
||||
#ifdef MFEM_THREAD_SAFE
|
||||
// Local storages for element integration
|
||||
// Local storage for element integration
|
||||
|
||||
// shape function value at an integration point - first elem
|
||||
Vector shape1(dof1);
|
||||
@@ -122,7 +121,7 @@ void HyperbolicFormIntegrator::AssembleFaceVector(
|
||||
DenseMatrix elvect2_mat(elvect.GetData() + dof1 * num_equations, dof2,
|
||||
num_equations);
|
||||
|
||||
// obtain integration rule. If integration is rule is given, then use it.
|
||||
// Obtain integration rule. If integration is rule is given, then use it.
|
||||
// Otherwise, get (2*p + IntOrderOffset) order integration rule
|
||||
const IntegrationRule *ir = IntRule;
|
||||
if (!ir)
|
||||
@@ -149,7 +148,7 @@ void HyperbolicFormIntegrator::AssembleFaceVector(
|
||||
if (nor.Size() == 1) // if 1D, use 1 or -1.
|
||||
{
|
||||
// This assume the 1D integration point is in (0,1). This may not work
|
||||
// if this chages.
|
||||
// if this changes.
|
||||
nor(0) = (Tr.GetElement1IntPoint().x - 0.5) * 2.0;
|
||||
}
|
||||
else
|
||||
|
||||
+27
-34
@@ -18,43 +18,36 @@
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
// MFEM Hyperbolic Conservation Laws
|
||||
// This file contains general hyperbolic conservation element/face form
|
||||
// integrators. HyperbolicFormIntegrator and RiemannSolver are defined.
|
||||
//
|
||||
// Description:
|
||||
// HyperbolicFormIntegrator is a NonlinearFormIntegrator that implements
|
||||
// element weak divergence and interface flux
|
||||
//
|
||||
// This file contains general hyperbolic conservation element/face form
|
||||
// integrators.
|
||||
// ∫_T F(u):∇v, -∫_e F̂(u)⋅[[v]]
|
||||
//
|
||||
// HyperbolicFormIntegrator and RiemannSolver are defined.
|
||||
// HyperbolicFormIntegrator is a NonlinearFormIntegrator that implements
|
||||
// element weak divergence and interface flux
|
||||
// Here, T is an element, e is an edge, and [[⋅]] is jump. This form integrator
|
||||
// is coupled with RiemannSolver that implements the numerical flux F̂. For
|
||||
// RiemannSolver, the Rusanov flux, also known as local Lax-Friedrichs flux, is
|
||||
// provided.
|
||||
//
|
||||
// ∫_T F(u):∇v, -∫_e F̂(u)⋅[[v]]
|
||||
// To implement a specific hyperbolic conservation laws, users can create
|
||||
// derived classes from FluxFunction with overloaded ComputeFlux. One can
|
||||
// optionally overload ComputeFluxDotN to avoid creating dense matrix when
|
||||
// computing normal flux. Several example equations are also defined including:
|
||||
// advection, Burgers', shallow water, and Euler equations. Users can control
|
||||
// the quadrature rule by either providing the integration rule, or integration
|
||||
// order offset. Integration will use 2*p + IntOrderOffset order quadrature
|
||||
// rule.
|
||||
//
|
||||
// Here, T is an element, e is an edge, and [[⋅]] is jump. This form
|
||||
// integrator is coupled with RiemannSolver that implements the numerical
|
||||
// flux F̂. For RiemannSolver, the Rusanov flux, also known as local
|
||||
// Lax-Friedrichs flux, is provided.
|
||||
//
|
||||
// To implement a specific hyperbolic conservation laws, users can create
|
||||
// derived classes from FluxFunction with overloaded ComputeFlux. One can
|
||||
// optionally overload ComputeFluxDotN to avoid creating dense matrix when
|
||||
// computing normal flux. Several example equations are also defined
|
||||
// including: advection, Burgers', shallow water, and Euler equations. Users
|
||||
// can control the quadrature rule by either providing the integration rule,
|
||||
// or integration order offset. Integration will use 2*p + IntOrderOffset
|
||||
// order quadrature rule.
|
||||
//
|
||||
// At each call of HyperbolicFormIntegrator::AssembleElementVector
|
||||
// HyperbolicFormIntegrator::AssembleFaceVector, the maximum characteristic
|
||||
// speed will be updated. This will not be reinitialized automatically.
|
||||
// To reinitialize, use HyperbolicFormIntegrator::ResetMaxCharSpeed. See,
|
||||
// ex18.hpp.
|
||||
//
|
||||
// Note: To avoid communication overhead, we update the maximum
|
||||
// characteristic speed within each process. Use a proper MPI routine to
|
||||
// gather the information.
|
||||
// At each call of HyperbolicFormIntegrator::AssembleElementVector
|
||||
// HyperbolicFormIntegrator::AssembleFaceVector, the maximum characteristic
|
||||
// speed will be updated. This will not be reinitialized automatically. To
|
||||
// reinitialize, use HyperbolicFormIntegrator::ResetMaxCharSpeed. See, ex18.hpp.
|
||||
//
|
||||
// Note: To avoid communication overhead, we update the maximum characteristic
|
||||
// speed within each MPI process only. Use the appropriate MPI routine to gather
|
||||
// the information.
|
||||
|
||||
/**
|
||||
* @brief Abstract class for hyperbolic flux for a system of hyperbolic
|
||||
@@ -88,7 +81,7 @@ public:
|
||||
virtual real_t ComputeFlux(const Vector &state, ElementTransformation &Tr,
|
||||
DenseMatrix &flux) const = 0;
|
||||
/**
|
||||
* @brief Compute normal flux. Optionally overloadded in the
|
||||
* @brief Compute normal flux. Optionally overloaded in the
|
||||
* derived class to avoid creating full dense matrix for flux.
|
||||
*
|
||||
* @param[in] state state at the current integration point
|
||||
@@ -168,13 +161,13 @@ protected:
|
||||
class HyperbolicFormIntegrator : public NonlinearFormIntegrator
|
||||
{
|
||||
private:
|
||||
// The maximum characterstic speed, updated during element/face vector assembly
|
||||
// The maximum characteristic speed, updated during element/face vector assembly
|
||||
real_t max_char_speed;
|
||||
const RiemannSolver &rsolver; // Numerical flux that maps F(u±,x) to hat(F)
|
||||
const FluxFunction &fluxFunction;
|
||||
const int IntOrderOffset; // integration order offset, 2*p + IntOrderOffset.
|
||||
#ifndef MFEM_THREAD_SAFE
|
||||
// Local storages for element integration
|
||||
// Local storage for element integration
|
||||
Vector shape; // shape function value at an integration point
|
||||
Vector state; // state value at an integration point
|
||||
DenseMatrix flux; // flux value at an integration point
|
||||
|
||||
@@ -307,7 +307,7 @@ static void PADGDiffusionSetupFaceInfo2D(const int nf, const Mesh &mesh,
|
||||
}
|
||||
}
|
||||
|
||||
// Assigns to perm the permuation:
|
||||
// Assigns to perm the permutation:
|
||||
// perm[0] <- normal component
|
||||
// perm[1] <- first tangential component
|
||||
// perm[2] <- second tangential component
|
||||
|
||||
@@ -563,7 +563,7 @@ void DiffusionIntegrator::AssemblePatchMatrix_fullQuadrature(
|
||||
cdofs.SetSize(maxw[0], maxw[1], maxw[2]);
|
||||
|
||||
// Compute sparsity of the sparse matrix
|
||||
smati = new int[ndof+1];
|
||||
smati = Memory<int>(ndof+1);
|
||||
smati[0] = 0;
|
||||
|
||||
for (int dof_j=0; dof_j<ndof; ++dof_j)
|
||||
@@ -586,8 +586,8 @@ void DiffusionIntegrator::AssemblePatchMatrix_fullQuadrature(
|
||||
nnz += ndd;
|
||||
}
|
||||
|
||||
smatj = new int[nnz];
|
||||
smata = new real_t[nnz];
|
||||
smatj = Memory<int>(nnz);
|
||||
smata = Memory<real_t>(nnz);
|
||||
|
||||
for (int i=0; i<nnz; ++i)
|
||||
{
|
||||
@@ -973,7 +973,7 @@ void DiffusionIntegrator::AssemblePatchMatrix_reducedQuadrature(
|
||||
cdofs.SetSize(maxw[0], maxw[1], maxw[2]);
|
||||
|
||||
// Compute sparsity of the sparse matrix
|
||||
smati = new int[ndof+1];
|
||||
smati = Memory<int>(ndof+1);
|
||||
smati[0] = 0;
|
||||
|
||||
for (int dof_j=0; dof_j<ndof; ++dof_j)
|
||||
@@ -996,8 +996,8 @@ void DiffusionIntegrator::AssemblePatchMatrix_reducedQuadrature(
|
||||
nnz += ndd;
|
||||
}
|
||||
|
||||
smatj = new int[nnz];
|
||||
smata = new real_t[nnz];
|
||||
smatj = Memory<int>(nnz);
|
||||
smata = Memory<real_t>(nnz);
|
||||
|
||||
for (int i=0; i<nnz; ++i)
|
||||
{
|
||||
|
||||
@@ -157,7 +157,7 @@ void ElasticityAddMultPA_(const int nDofs, const FiniteElementSpace &fespace,
|
||||
static constexpr int aSize = aUpper-aLower;
|
||||
static constexpr bool isComponent = (i_block >= 0);
|
||||
|
||||
//Assuming all elements are the same
|
||||
// Assuming all elements are the same
|
||||
const auto &ir = QVec.GetIntRule(0);
|
||||
const QuadratureInterpolator *E_To_Q_Map = fespace.GetQuadratureInterpolator(
|
||||
ir);
|
||||
@@ -180,7 +180,7 @@ void ElasticityAddMultPA_(const int nDofs, const FiniteElementSpace &fespace,
|
||||
auto invJ = inv(make_tensor<d, d>(
|
||||
[&](int i, int j) { return J(p, i, j, e); }));
|
||||
tensor<real_t, aSize, d> gradx;
|
||||
//load grad(x) into gradx
|
||||
// load grad(x) into gradx
|
||||
if (isComponent)
|
||||
{
|
||||
for (int i = 0; i < d; i++)
|
||||
@@ -198,11 +198,11 @@ void ElasticityAddMultPA_(const int nDofs, const FiniteElementSpace &fespace,
|
||||
}
|
||||
}
|
||||
}
|
||||
//compute divergence
|
||||
// compute divergence
|
||||
real_t div = 0.;
|
||||
for (int i = aLower; i < aUpper; i++)
|
||||
{
|
||||
//take size of gradx into account
|
||||
// take size of gradx into account
|
||||
const int iIndex = isComponent ? 0 : i;
|
||||
div += gradx(iIndex,i);
|
||||
}
|
||||
@@ -211,11 +211,11 @@ void ElasticityAddMultPA_(const int nDofs, const FiniteElementSpace &fespace,
|
||||
{
|
||||
for (int q = qLower; q < qUpper; q++)
|
||||
{
|
||||
//compute contraction of 4*sym(grad(u))sym(grad(v)) term.
|
||||
//this contraction could be made slightly cheaper using Voigt
|
||||
//notation, but repeated entries are summed for simplicity.
|
||||
// compute contraction of 4*sym(grad(u))sym(grad(v)) term.
|
||||
// this contraction could be made slightly cheaper using Voigt
|
||||
// notation, but repeated entries are summed for simplicity.
|
||||
real_t contraction = 0.;
|
||||
//not sure how to combine cases
|
||||
// not sure how to combine cases
|
||||
if (isComponent)
|
||||
{
|
||||
for (int a = 0; a < d; a++)
|
||||
@@ -276,7 +276,7 @@ void ElasticityAssembleDiagonalPA_(const int nDofs,
|
||||
const CoefficientVector &mu, const GeometricFactors &geom,
|
||||
const DofToQuad &maps, QuadratureFunction &QVec, Vector &diag)
|
||||
{
|
||||
//Assuming all elements are the same
|
||||
// Assuming all elements are the same
|
||||
const auto &ir = QVec.GetIntRule(0);
|
||||
static constexpr int d = dim;
|
||||
const int numPoints = ir.GetNPoints();
|
||||
@@ -299,9 +299,9 @@ void ElasticityAssembleDiagonalPA_(const int nDofs,
|
||||
{
|
||||
for (int q = 0; q < d; q++)
|
||||
{
|
||||
//compute contraction of 4*sym(grad(u))sym(grad(v)) term.
|
||||
//this contraction could be made slightly cheaper using Voigt
|
||||
//notation, but repeated entries are summed for simplicity.
|
||||
// compute contraction of 4*sym(grad(u))sym(grad(v)) term.
|
||||
// this contraction could be made slightly cheaper using Voigt
|
||||
// notation, but repeated entries are summed for simplicity.
|
||||
real_t contraction = 0.;
|
||||
for (int a = 0; a < d; a++)
|
||||
{
|
||||
@@ -321,7 +321,7 @@ void ElasticityAssembleDiagonalPA_(const int nDofs,
|
||||
}
|
||||
});
|
||||
|
||||
//Reduce quadrature function to an E-Vector
|
||||
// Reduce quadrature function to an E-Vector
|
||||
const auto QRead = Reshape(QVec.Read(), numPoints, d, d, d, numEls);
|
||||
auto diagDev = Reshape(diag.Write(), nDofs, d, numEls);
|
||||
const auto G = Reshape(maps.G.Read(), numPoints, d, nDofs);
|
||||
@@ -348,7 +348,7 @@ void ElasticityAssembleDiagonalPA_(const int nDofs,
|
||||
});
|
||||
}
|
||||
|
||||
//Templated implementation of ElasticityAssembleEA.
|
||||
// Templated implementation of ElasticityAssembleEA.
|
||||
template<int dim>
|
||||
void ElasticityAssembleEA_(const int i_block,
|
||||
const int j_block,
|
||||
@@ -360,7 +360,7 @@ void ElasticityAssembleEA_(const int i_block,
|
||||
const DofToQuad &maps,
|
||||
Vector &emat)
|
||||
{
|
||||
//Assuming all elements are the same
|
||||
// Assuming all elements are the same
|
||||
static constexpr int d = dim;
|
||||
const int numPoints = ir.GetNPoints();
|
||||
const int numEls = lambda.Size()/numPoints;
|
||||
@@ -386,7 +386,7 @@ void ElasticityAssembleEA_(const int i_block,
|
||||
{
|
||||
for (int m = 0; m < d; m++)
|
||||
{
|
||||
//compute contraction of 4*sym(grad(u))sym(grad(v)) term.
|
||||
// compute contraction of 4*sym(grad(u))sym(grad(v)) term.
|
||||
real_t contraction = 0.;
|
||||
for (int a = 0; a < d; a++)
|
||||
{
|
||||
|
||||
@@ -101,7 +101,7 @@ void MomentFittingIntRules::InitVolume(int order, Coefficient& levelset,
|
||||
}
|
||||
}
|
||||
|
||||
// assamble the matrix
|
||||
// assemble the matrix
|
||||
DenseMatrix Mat(nBasisVolume, ir.GetNPoints());
|
||||
for (int ip = 0; ip < ir.GetNPoints(); ip++)
|
||||
{
|
||||
@@ -118,7 +118,7 @@ void MomentFittingIntRules::InitVolume(int order, Coefficient& levelset,
|
||||
Mat.SetCol(ip, shape);
|
||||
}
|
||||
|
||||
// compute the svd for the matrix
|
||||
// compute the SVD for the matrix
|
||||
VolumeSVD = new DenseMatrixSVD(Mat, 'A', 'A');
|
||||
VolumeSVD->Eval(Mat);
|
||||
}
|
||||
@@ -1239,7 +1239,7 @@ void MomentFittingIntRules::OrthoBasis2D(const IntegrationPoint& ip,
|
||||
|
||||
shape.SetSize(nBasis, 2);
|
||||
|
||||
// evaluate basis inthe point
|
||||
// evaluate basis in the point
|
||||
DenseMatrix preshape(nBasis, 2);
|
||||
DivFreeBasis2D(ip, shape);
|
||||
|
||||
@@ -1597,6 +1597,6 @@ void MomentFittingIntRules::GetSurfaceWeights(ElementTransformation& Tr,
|
||||
}
|
||||
}
|
||||
|
||||
#endif //MFEM_USE_LAPACK
|
||||
#endif // MFEM_USE_LAPACK
|
||||
|
||||
}
|
||||
|
||||
+1
-1
@@ -291,7 +291,7 @@ void BatchedLOR_AMS::FormCoordinateVectors(const Vector &X_vert)
|
||||
const auto ltdof_ldof = HypreRead(R->GetMemoryJ());
|
||||
|
||||
// Go from E-vector format directly to T-vector format
|
||||
MFEM_HYPRE_FORALL(i, ntdofs,
|
||||
mfem::hypre_forall(ntdofs, [=] MFEM_HOST_DEVICE (int i)
|
||||
{
|
||||
const int j = d_offsets[ltdof_ldof[i]];
|
||||
for (int c = 0; c < sdim; ++c)
|
||||
|
||||
+15
-15
@@ -269,13 +269,13 @@ void BatchedLOR_H1::Assemble3D()
|
||||
real_t vx[8], vy[8], vz[8];
|
||||
LORVertexCoordinates3D<ORDER>(X, iel_ho, kx, ky, kz, vx, vy, vz);
|
||||
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iqz=0; iqz<2; ++iqz)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iqy=0; iqy<2; ++iqy)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iqx=0; iqx<2; ++iqx)
|
||||
{
|
||||
const real_t x = iqx;
|
||||
@@ -307,21 +307,21 @@ void BatchedLOR_H1::Assemble3D()
|
||||
}
|
||||
}
|
||||
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iqx=0; iqx<2; ++iqx)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int jz=0; jz<2; ++jz)
|
||||
{
|
||||
// Note loop starts at iz=jz here, taking advantage of
|
||||
// symmetries.
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iz=jz; iz<2; ++iz)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iqy=0; iqy<2; ++iqy)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iqz=0; iqz<2; ++iqz)
|
||||
{
|
||||
const real_t mq = const_mq ? MQ(0,0,0,0) : MQ(kx+iqx, ky+iqy, kz+iqz, iel_ho);
|
||||
@@ -356,10 +356,10 @@ void BatchedLOR_H1::Assemble3D()
|
||||
real_t wdetJ = Q(6,iqz,iqy,iqx);
|
||||
mass_A(iqy,iz,jz,iqx) += mq*wdetJ*biz*bjz;
|
||||
}
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int jy=0; jy<2; ++jy)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iy=0; iy<2; ++iy)
|
||||
{
|
||||
const real_t biy = (iy == iqy) ? 1.0 : 0.0;
|
||||
@@ -382,16 +382,16 @@ void BatchedLOR_H1::Assemble3D()
|
||||
}
|
||||
}
|
||||
}
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int jy=0; jy<2; ++jy)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int jx=0; jx<2; ++jx)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int iy=0; iy<2; ++iy)
|
||||
{
|
||||
//MFEM_UNROLL(2)
|
||||
// MFEM_UNROLL(2)
|
||||
for (int ix=0; ix<2; ++ix)
|
||||
{
|
||||
const real_t bix = (ix == iqx) ? 1.0 : 0.0;
|
||||
@@ -431,7 +431,7 @@ void BatchedLOR_H1::Assemble3D()
|
||||
// Assemble the local matrix into the macro-element sparse matrix
|
||||
// in a format similar to coordinate format. The (I,J) arrays
|
||||
// are implicit (not stored explicitly).
|
||||
//MFEM_UNROLL(8)
|
||||
// MFEM_UNROLL(8)
|
||||
for (int ii_loc=0; ii_loc<nv; ++ii_loc)
|
||||
{
|
||||
const int ix = ii_loc%2;
|
||||
|
||||
@@ -368,6 +368,72 @@ const
|
||||
y.Add(a, Ytmp);
|
||||
}
|
||||
|
||||
real_t ParBilinearForm::ParInnerProduct(const ParGridFunction &x,
|
||||
const ParGridFunction &y) const
|
||||
{
|
||||
MFEM_ASSERT(mat != NULL, "local matrix must be assembled");
|
||||
|
||||
real_t loc = InnerProduct(x, y);
|
||||
real_t glob = 0.;
|
||||
|
||||
MPI_Allreduce(&loc, &glob, 1, MPITypeMap<real_t>::mpi_type, MPI_SUM,
|
||||
pfes->GetComm());
|
||||
|
||||
return glob;
|
||||
}
|
||||
|
||||
real_t ParBilinearForm::TrueInnerProduct(const ParGridFunction &x,
|
||||
const ParGridFunction &y) const
|
||||
{
|
||||
MFEM_ASSERT(x.ParFESpace() == pfes, "the parallel spaces must match");
|
||||
MFEM_ASSERT(y.ParFESpace() == pfes, "the parallel spaces must match");
|
||||
|
||||
HypreParVector *x_p = x.ParallelProject();
|
||||
HypreParVector *y_p = y.ParallelProject();
|
||||
|
||||
real_t res = TrueInnerProduct(*x_p, *y_p);
|
||||
|
||||
delete x_p;
|
||||
delete y_p;
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
real_t ParBilinearForm::TrueInnerProduct(HypreParVector &x,
|
||||
HypreParVector &y) const
|
||||
{
|
||||
MFEM_VERIFY(p_mat.Ptr() != NULL, "parallel matrix must be assembled");
|
||||
|
||||
if (p_mat->GetType() != Operator::Hypre_ParCSR)
|
||||
{
|
||||
return TrueInnerProduct((const Vector&)x, (const Vector&)y);
|
||||
}
|
||||
|
||||
HypreParVector *Ax = new HypreParVector(pfes);
|
||||
HypreParMatrix *A = p_mat.As<HypreParMatrix>();
|
||||
|
||||
A->Mult(x, *Ax);
|
||||
|
||||
real_t res = mfem::InnerProduct(y, *Ax);
|
||||
|
||||
delete Ax;
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
real_t ParBilinearForm::TrueInnerProduct(const Vector &x,
|
||||
const Vector &y) const
|
||||
{
|
||||
MFEM_VERIFY(p_mat.Ptr() != NULL, "parallel matrix must be assembled");
|
||||
|
||||
Vector Ax(pfes->GetTrueVSize());
|
||||
p_mat->Mult(x, Ax);
|
||||
|
||||
real_t res = mfem::InnerProduct(pfes->GetComm(), y, Ax);
|
||||
|
||||
return res;
|
||||
}
|
||||
|
||||
void ParBilinearForm::FormLinearSystem(
|
||||
const Array<int> &ess_tdof_list, Vector &x, Vector &b,
|
||||
OperatorHandle &A, Vector &X, Vector &B, int copy_interior)
|
||||
|
||||
@@ -173,6 +173,37 @@ public:
|
||||
vectors on the true dofs. */
|
||||
void TrueAddMult(const Vector &x, Vector &y, const real_t a = 1.0) const;
|
||||
|
||||
/// Compute $ y^T M x $
|
||||
/** @warning The calculation is performed on local dofs, assuming that
|
||||
the local vectors are consistent with the prolongations of the true
|
||||
vectors (see ParGridFunction::Distribute()). If this is not the case,
|
||||
use TrueInnerProduct(const ParGridFunction &, const ParGridFunction &)
|
||||
instead.
|
||||
@note It is assumed that the local matrix is assembled and it has
|
||||
not been replaced by the parallel matrix through FormSystemMatrix().
|
||||
@see TrueInnerProduct(const ParGridFunction&, const ParGridFunction&) */
|
||||
real_t ParInnerProduct(const ParGridFunction &x,
|
||||
const ParGridFunction &y) const;
|
||||
|
||||
/// Compute $ y^T M x $ on true dofs (grid function version)
|
||||
/** @note The ParGridFunction%s are restricted to the true-vectors for
|
||||
for calculation.
|
||||
@note It is assumed that the parallel system matrix is assembled,
|
||||
see FormSystemMatrix().
|
||||
@see ParInnerProduct(const ParGridFunction&, const ParGridFunction&) */
|
||||
real_t TrueInnerProduct(const ParGridFunction &x,
|
||||
const ParGridFunction &y) const;
|
||||
|
||||
/// Compute $ y^T M x $ on true dofs (Hypre vector version)
|
||||
/** @note It is assumed that the parallel system matrix is assembled,
|
||||
see FormSystemMatrix(). */
|
||||
real_t TrueInnerProduct(HypreParVector &x, HypreParVector &y) const;
|
||||
|
||||
/// Compute $ y^T M x $ on true dofs (true-vector version)
|
||||
/** @note It is assumed that the parallel system matrix is assembled,
|
||||
see FormSystemMatrix(). */
|
||||
real_t TrueInnerProduct(const Vector &x, const Vector &y) const;
|
||||
|
||||
/// Return the parallel FE space associated with the ParBilinearForm.
|
||||
ParFiniteElementSpace *ParFESpace() const { return pfes; }
|
||||
|
||||
|
||||
+7
-7
@@ -861,17 +861,17 @@ void ParFiniteElementSpace::Build_Dof_TrueDof_Matrix() const // matrix P
|
||||
}
|
||||
}
|
||||
|
||||
HYPRE_Int *i_diag = new HYPRE_Int[ldof+1];
|
||||
HYPRE_Int *j_diag = new HYPRE_Int[ltdof];
|
||||
real_t *d_diag = new real_t[ltdof];
|
||||
HYPRE_Int *i_diag = Memory<HYPRE_Int>(ldof+1);
|
||||
HYPRE_Int *j_diag = Memory<HYPRE_Int>(ltdof);
|
||||
real_t *d_diag = Memory<real_t>(ltdof);
|
||||
int diag_counter;
|
||||
|
||||
HYPRE_Int *i_offd = new HYPRE_Int[ldof+1];
|
||||
HYPRE_Int *j_offd = new HYPRE_Int[nnz_offd];
|
||||
real_t *d_offd = new real_t[nnz_offd];
|
||||
HYPRE_Int *i_offd = Memory<HYPRE_Int>(ldof+1);
|
||||
HYPRE_Int *j_offd = Memory<HYPRE_Int>(nnz_offd);
|
||||
real_t *d_offd = Memory<real_t>(nnz_offd);
|
||||
int offd_counter;
|
||||
|
||||
HYPRE_BigInt *cmap = new HYPRE_BigInt[ldof-ltdof];
|
||||
HYPRE_BigInt *cmap = Memory<HYPRE_BigInt>(ldof-ltdof);
|
||||
|
||||
HYPRE_BigInt *col_starts = GetTrueDofOffsets();
|
||||
HYPRE_BigInt *row_starts = GetDofOffsets();
|
||||
|
||||
+11
-8
@@ -39,9 +39,10 @@ ParGridFunction::ParGridFunction(ParMesh *pmesh, const GridFunction *gf,
|
||||
{
|
||||
const FiniteElementSpace *glob_fes = gf->FESpace();
|
||||
// duplicate the FiniteElementCollection from 'gf'
|
||||
fec = FiniteElementCollection::New(glob_fes->FEColl()->Name());
|
||||
fec_owned = FiniteElementCollection::New(glob_fes->FEColl()->Name());
|
||||
// create a local ParFiniteElementSpace from the global one:
|
||||
fes = pfes = new ParFiniteElementSpace(pmesh, glob_fes, partitioning, fec);
|
||||
fes = pfes = new ParFiniteElementSpace(pmesh, glob_fes, partitioning,
|
||||
fec_owned);
|
||||
SetSize(pfes->GetVSize());
|
||||
|
||||
if (partitioning)
|
||||
@@ -81,7 +82,7 @@ ParGridFunction::ParGridFunction(ParMesh *pmesh, std::istream &input)
|
||||
: GridFunction(pmesh, input)
|
||||
{
|
||||
// Convert the FiniteElementSpace, fes, to a ParFiniteElementSpace:
|
||||
pfes = new ParFiniteElementSpace(pmesh, fec, fes->GetVDim(),
|
||||
pfes = new ParFiniteElementSpace(pmesh, fec_owned, fes->GetVDim(),
|
||||
fes->GetOrdering());
|
||||
delete fes;
|
||||
fes = pfes;
|
||||
@@ -249,6 +250,8 @@ void ParGridFunction::ExchangeFaceNbrData()
|
||||
auto send_data_ptr = mpi_gpu_aware ? send_data.Read() : send_data.HostRead();
|
||||
auto face_nbr_data_ptr = mpi_gpu_aware ? face_nbr_data.Write() :
|
||||
face_nbr_data.HostWrite();
|
||||
// Wait for the kernel to be done since it updates what's sent and it may be async
|
||||
if (mpi_gpu_aware) { MFEM_STREAM_SYNC; }
|
||||
for (int fn = 0; fn < num_face_nbrs; fn++)
|
||||
{
|
||||
int nbr_rank = pmesh->GetFaceNbrRank(fn);
|
||||
@@ -518,7 +521,7 @@ void ParGridFunction::CountElementsPerVDof(Array<int> &elem_per_vdof) const
|
||||
}
|
||||
|
||||
void ParGridFunction::GetDerivative(int comp, int der_comp,
|
||||
ParGridFunction &der)
|
||||
ParGridFunction &der) const
|
||||
{
|
||||
Array<int> overlap;
|
||||
AccumulateAndCountDerivativeValues(comp, der_comp, der, overlap);
|
||||
@@ -713,10 +716,10 @@ void ParGridFunction::ProjectBdrCoefficient(
|
||||
}
|
||||
}
|
||||
}
|
||||
gcomm.Bcast<int>(values_counter.HostReadWrite());
|
||||
for (int i = 0; i < values_counter.Size(); i++)
|
||||
{
|
||||
MFEM_ASSERT(pfes->GetLocalTDofNumber(i) == -1 ||
|
||||
bool(values_counter[i]) == bool(ess_vdofs_marker[i]),
|
||||
MFEM_ASSERT(bool(values_counter[i]) == bool(ess_vdofs_marker[i]),
|
||||
"internal error");
|
||||
}
|
||||
#endif
|
||||
@@ -753,10 +756,10 @@ void ParGridFunction::ProjectBdrCoefficientTangent(VectorCoefficient &vcoeff,
|
||||
#ifdef MFEM_DEBUG
|
||||
Array<int> ess_vdofs_marker;
|
||||
pfes->GetEssentialVDofs(bdr_attr, ess_vdofs_marker);
|
||||
gcomm.Bcast<int>(values_counter.HostReadWrite());
|
||||
for (int i = 0; i < values_counter.Size(); i++)
|
||||
{
|
||||
MFEM_ASSERT(pfes->GetLocalTDofNumber(i) == -1 ||
|
||||
bool(values_counter[i]) == bool(ess_vdofs_marker[i]),
|
||||
MFEM_ASSERT(bool(values_counter[i]) == bool(ess_vdofs_marker[i]),
|
||||
"internal error: " << pfes->GetLocalTDofNumber(i) << ' ' << bool(
|
||||
values_counter[i]));
|
||||
}
|
||||
|
||||
+1
-2
@@ -231,7 +231,7 @@ public:
|
||||
void CountElementsPerVDof(Array<int> &elem_per_vdof) const override;
|
||||
|
||||
/// Parallel version of GridFunction::GetDerivative(); see its documentation.
|
||||
void GetDerivative(int comp, int der_comp, ParGridFunction &der);
|
||||
void GetDerivative(int comp, int der_comp, ParGridFunction &der) const;
|
||||
|
||||
/** Sets the output vector @a dof_vals to the values of the degrees of
|
||||
freedom of element @a el. If @a el is greater than or equal to the number
|
||||
@@ -262,7 +262,6 @@ public:
|
||||
const Array<int> &attr) override
|
||||
{ ProjectBdrCoefficient(coeff, NULL, attr); }
|
||||
|
||||
// Only the values in the master are guaranteed to be correct!
|
||||
void ProjectBdrCoefficientTangent(VectorCoefficient &vcoeff,
|
||||
const Array<int> &bdr_attr) override;
|
||||
|
||||
|
||||
+238
-124
@@ -2949,6 +2949,15 @@ void TMOP_Integrator::EnableSurfaceFitting(const GridFunction &s0,
|
||||
MFEM_VERIFY(surf_fit_pos == NULL,
|
||||
"Using both fitting approaches is not supported.");
|
||||
|
||||
const int dim = s0.FESpace()->GetMesh()->Dimension();
|
||||
Mesh *mesh = s0.FESpace()->GetMesh();
|
||||
MFEM_VERIFY(mesh->GetNodes()->Size() == dim*s0.Size(),
|
||||
"Mesh and level-set polynomial order must be the same.");
|
||||
const H1_FECollection *fec = dynamic_cast<const H1_FECollection *>
|
||||
(s0.FESpace()->FEColl());
|
||||
MFEM_VERIFY(fec, "Only H1_FECollection is supported for the surface fitting "
|
||||
"grid function.");
|
||||
|
||||
delete surf_fit_gf;
|
||||
surf_fit_gf = new GridFunction(s0);
|
||||
surf_fit_gf->CountElementsPerVDof(surf_fit_dof_count);
|
||||
@@ -2987,12 +2996,24 @@ void TMOP_Integrator::EnableSurfaceFitting(const GridFunction &pos,
|
||||
void TMOP_Integrator::EnableSurfaceFitting(const ParGridFunction &s0,
|
||||
const Array<bool> &smarker,
|
||||
Coefficient &coeff,
|
||||
AdaptivityEvaluator &ae)
|
||||
AdaptivityEvaluator &ae,
|
||||
AdaptivityEvaluator *aegrad,
|
||||
AdaptivityEvaluator *aehess)
|
||||
{
|
||||
// To have both we must duplicate the markers.
|
||||
MFEM_VERIFY(surf_fit_pos == NULL,
|
||||
"Using both fitting approaches is not supported.");
|
||||
|
||||
const int dim = s0.FESpace()->GetMesh()->Dimension();
|
||||
ParMesh *pmesh = s0.ParFESpace()->GetParMesh();
|
||||
MFEM_VERIFY(pmesh->GetNodes()->Size() == dim*s0.Size(),
|
||||
"Mesh and level-set polynomial order must be the same.");
|
||||
const H1_FECollection *fec = dynamic_cast<const H1_FECollection *>
|
||||
(s0.FESpace()->FEColl());
|
||||
MFEM_VERIFY(fec, "Only H1_FECollection is supported for the surface fitting "
|
||||
"grid function.");
|
||||
|
||||
|
||||
delete surf_fit_gf;
|
||||
surf_fit_gf = new GridFunction(s0);
|
||||
s0.CountElementsPerVDof(surf_fit_dof_count);
|
||||
@@ -3000,11 +3021,80 @@ void TMOP_Integrator::EnableSurfaceFitting(const ParGridFunction &s0,
|
||||
surf_fit_coeff = &coeff;
|
||||
surf_fit_eval = &ae;
|
||||
|
||||
surf_fit_eval->SetParMetaInfo(*s0.ParFESpace()->GetParMesh(),
|
||||
*s0.ParFESpace());
|
||||
surf_fit_eval->SetParMetaInfo(*pmesh, *s0.ParFESpace());
|
||||
surf_fit_eval->SetInitialField
|
||||
(*surf_fit_gf->FESpace()->GetMesh()->GetNodes(), *surf_fit_gf);
|
||||
surf_fit_gf_bg = false;
|
||||
|
||||
if (!aegrad) { return; }
|
||||
|
||||
MFEM_VERIFY(aehess, "AdaptivityEvaluator for Hessians must be provided too.");
|
||||
|
||||
ParFiniteElementSpace *fes = s0.ParFESpace();
|
||||
|
||||
// FE space for gradients.
|
||||
delete surf_fit_grad;
|
||||
H1_FECollection *fec_grad = new H1_FECollection(fec->GetOrder(), dim,
|
||||
fec->GetBasisType());
|
||||
ParFiniteElementSpace *fes_grad = new ParFiniteElementSpace(pmesh, fec_grad,
|
||||
dim);
|
||||
// Initial gradients.
|
||||
surf_fit_grad = new GridFunction(fes_grad);
|
||||
surf_fit_grad->MakeOwner(fec_grad);
|
||||
for (int d = 0; d < dim; d++)
|
||||
{
|
||||
ParGridFunction surf_fit_grad_comp(fes, surf_fit_grad->GetData()+d*s0.Size());
|
||||
s0.GetDerivative(1, d, surf_fit_grad_comp);
|
||||
}
|
||||
surf_fit_eval_grad = aegrad;
|
||||
surf_fit_eval_grad->SetParMetaInfo(*pmesh, *fes_grad);
|
||||
surf_fit_eval_grad->SetInitialField(*pmesh->GetNodes(), *surf_fit_grad);
|
||||
|
||||
// FE space for Hessians.
|
||||
delete surf_fit_hess;
|
||||
H1_FECollection *fec_hess = new H1_FECollection(fec->GetOrder(), dim,
|
||||
fec->GetBasisType());
|
||||
ParFiniteElementSpace *fes_hess = new ParFiniteElementSpace(pmesh, fec_hess,
|
||||
dim*dim);
|
||||
// Initial Hessians.
|
||||
surf_fit_hess = new GridFunction(fes_hess);
|
||||
surf_fit_hess->MakeOwner(fec_hess);
|
||||
int id = 0;
|
||||
for (int d = 0; d < dim; d++)
|
||||
{
|
||||
for (int idir = 0; idir < dim; idir++)
|
||||
{
|
||||
ParGridFunction surf_fit_grad_comp(fes,
|
||||
surf_fit_grad->GetData()+d*s0.Size());
|
||||
ParGridFunction surf_fit_hess_comp(fes,
|
||||
surf_fit_hess->GetData()+id*s0.Size());
|
||||
surf_fit_grad_comp.GetDerivative(1, idir, surf_fit_hess_comp);
|
||||
id++;
|
||||
}
|
||||
}
|
||||
surf_fit_eval_hess = aehess;
|
||||
surf_fit_eval_hess->SetParMetaInfo(*pmesh, *fes_hess);
|
||||
surf_fit_eval_hess->SetInitialField(*pmesh->GetNodes(), *surf_fit_hess);
|
||||
|
||||
// Store DOF indices that are marked for fitting. Used to reduce work for
|
||||
// transferring information between source/background and current mesh.
|
||||
surf_fit_marker_dof_index.SetSize(0);
|
||||
#ifdef MFEM_USE_GSLIB
|
||||
if (dynamic_cast<InterpolatorFP *>(surf_fit_eval) &&
|
||||
dynamic_cast<InterpolatorFP *>(surf_fit_eval_grad) &&
|
||||
dynamic_cast<InterpolatorFP *>(surf_fit_eval_hess))
|
||||
{
|
||||
for (int i = 0; i < surf_fit_marker->Size(); i++)
|
||||
{
|
||||
if ((*surf_fit_marker)[i] == true)
|
||||
{
|
||||
surf_fit_marker_dof_index.Append(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
#endif
|
||||
|
||||
*surf_fit_grad = 0.0;
|
||||
*surf_fit_hess = 0.0;
|
||||
}
|
||||
|
||||
void TMOP_Integrator::EnableSurfaceFittingFromSource(
|
||||
@@ -3022,16 +3112,17 @@ void TMOP_Integrator::EnableSurfaceFittingFromSource(
|
||||
// Setup for level set function
|
||||
delete surf_fit_gf;
|
||||
surf_fit_gf = new GridFunction(s0);
|
||||
*surf_fit_gf = 0.0;
|
||||
surf_fit_marker = &smarker;
|
||||
surf_fit_coeff = &coeff;
|
||||
surf_fit_eval = &ae;
|
||||
|
||||
surf_fit_gf_bg = true;
|
||||
surf_fit_eval->SetParMetaInfo(*s_bg.ParFESpace()->GetParMesh(),
|
||||
*s_bg.ParFESpace());
|
||||
surf_fit_eval->SetInitialField
|
||||
(*s_bg.FESpace()->GetMesh()->GetNodes(), s_bg);
|
||||
GridFunction *nodes = s0.FESpace()->GetMesh()->GetNodes();
|
||||
surf_fit_eval->ComputeAtNewPosition(*nodes, *surf_fit_gf,
|
||||
nodes->FESpace()->GetOrdering());
|
||||
|
||||
// Setup for gradient on background mesh
|
||||
MFEM_VERIFY(s_bg_grad.ParFESpace()->GetOrdering() ==
|
||||
@@ -3041,11 +3132,11 @@ void TMOP_Integrator::EnableSurfaceFittingFromSource(
|
||||
delete surf_fit_grad;
|
||||
surf_fit_grad = new GridFunction(s0_grad);
|
||||
*surf_fit_grad = 0.0;
|
||||
surf_fit_eval_bg_grad = &age;
|
||||
surf_fit_eval_bg_hess = &ahe;
|
||||
surf_fit_eval_bg_grad->SetParMetaInfo(*s_bg_grad.ParFESpace()->GetParMesh(),
|
||||
*s_bg_grad.ParFESpace());
|
||||
surf_fit_eval_bg_grad->SetInitialField
|
||||
surf_fit_eval_grad = &age;
|
||||
surf_fit_eval_hess = &ahe;
|
||||
surf_fit_eval_grad->SetParMetaInfo(*s_bg_grad.ParFESpace()->GetParMesh(),
|
||||
*s_bg_grad.ParFESpace());
|
||||
surf_fit_eval_grad->SetInitialField
|
||||
(*s_bg_grad.FESpace()->GetMesh()->GetNodes(), s_bg_grad);
|
||||
|
||||
// Setup for Hessian on background mesh
|
||||
@@ -3056,9 +3147,9 @@ void TMOP_Integrator::EnableSurfaceFittingFromSource(
|
||||
delete surf_fit_hess;
|
||||
surf_fit_hess = new GridFunction(s0_hess);
|
||||
*surf_fit_hess = 0.0;
|
||||
surf_fit_eval_bg_hess->SetParMetaInfo(*s_bg_hess.ParFESpace()->GetParMesh(),
|
||||
*s_bg_hess.ParFESpace());
|
||||
surf_fit_eval_bg_hess->SetInitialField
|
||||
surf_fit_eval_hess->SetParMetaInfo(*s_bg_hess.ParFESpace()->GetParMesh(),
|
||||
*s_bg_hess.ParFESpace());
|
||||
surf_fit_eval_hess->SetInitialField
|
||||
(*s_bg_hess.FESpace()->GetMesh()->GetNodes(), s_bg_hess);
|
||||
|
||||
// Count number of zones that share each of the DOFs
|
||||
@@ -3863,7 +3954,7 @@ void TMOP_Integrator::AssembleElemVecSurfFit(const FiniteElement &el_x,
|
||||
|
||||
Vector sigma_e(dof_s);
|
||||
DenseMatrix surf_fit_grad_e(dof_s, dim);
|
||||
if (surf_fit_gf || surf_fit_gf_bg)
|
||||
if (surf_fit_gf)
|
||||
{
|
||||
surf_fit_gf->GetSubVector(vdofs, sigma_e);
|
||||
|
||||
@@ -3871,7 +3962,7 @@ void TMOP_Integrator::AssembleElemVecSurfFit(const FiniteElement &el_x,
|
||||
// The FE coefficients of the gradient go in surf_fit_grad_e.
|
||||
Vector grad_ptr(surf_fit_grad_e.GetData(), dof_s * dim);
|
||||
DenseMatrix grad_phys; // This will be (dof x dim, dof).
|
||||
if (surf_fit_gf_bg)
|
||||
if (surf_fit_grad)
|
||||
{
|
||||
surf_fit_grad->FESpace()->GetElementVDofs(el_id, dofs);
|
||||
surf_fit_grad->GetSubVector(dofs, grad_ptr);
|
||||
@@ -3945,7 +4036,7 @@ void TMOP_Integrator::AssembleElemGradSurfFit(const FiniteElement &el_x,
|
||||
Vector sigma_e(dof_s);
|
||||
DenseMatrix surf_fit_grad_e(dof_s, dim);
|
||||
DenseMatrix surf_fit_hess_e(dof_s, dim*dim);
|
||||
if (surf_fit_gf || surf_fit_gf_bg)
|
||||
if (surf_fit_gf)
|
||||
{
|
||||
surf_fit_gf->GetSubVector(vdofs, sigma_e);
|
||||
|
||||
@@ -3953,7 +4044,7 @@ void TMOP_Integrator::AssembleElemGradSurfFit(const FiniteElement &el_x,
|
||||
// The FE coefficients of the gradient go in surf_fit_grad_e.
|
||||
Vector grad_ptr(surf_fit_grad_e.GetData(), dof_s * dim);
|
||||
DenseMatrix grad_phys; // This will be (dof x dim, dof).
|
||||
if (surf_fit_gf_bg)
|
||||
if (surf_fit_grad)
|
||||
{
|
||||
surf_fit_grad->FESpace()->GetElementVDofs(el_id, dofs);
|
||||
surf_fit_grad->GetSubVector(dofs, grad_ptr);
|
||||
@@ -3967,7 +4058,7 @@ void TMOP_Integrator::AssembleElemGradSurfFit(const FiniteElement &el_x,
|
||||
// Project the Hessian of sigma in the same space.
|
||||
// The FE coefficients of the Hessian go in surf_fit_hess_e.
|
||||
Vector hess_ptr(surf_fit_hess_e.GetData(), dof_s*dim*dim);
|
||||
if (surf_fit_gf_bg)
|
||||
if (surf_fit_hess)
|
||||
{
|
||||
surf_fit_hess->FESpace()->GetElementVDofs(el_id, dofs);
|
||||
surf_fit_hess->GetSubVector(dofs, hess_ptr);
|
||||
@@ -3994,7 +4085,7 @@ void TMOP_Integrator::AssembleElemGradSurfFit(const FiniteElement &el_x,
|
||||
Tpr.SetIntPoint(&ip);
|
||||
real_t w = surf_fit_normal * surf_fit_coeff->Eval(Tpr, ip);
|
||||
|
||||
if (surf_fit_gf || surf_fit_gf_bg)
|
||||
if (surf_fit_gf)
|
||||
{
|
||||
Vector gg_ptr(surf_fit_hess_s.GetData(), dim * dim);
|
||||
surf_fit_hess_e.GetRow(s, gg_ptr);
|
||||
@@ -4376,6 +4467,130 @@ void TMOP_Integrator::ComputeMinJac(const Vector &x,
|
||||
dx = detv_avg_min / dxscale;
|
||||
}
|
||||
|
||||
void TMOP_Integrator::RemapSurfaceFittingLevelSetAtNodes(const Vector &new_x,
|
||||
int new_x_ordering)
|
||||
{
|
||||
if (!surf_fit_gf) { return; }
|
||||
|
||||
if (surf_fit_marker_dof_index.Size())
|
||||
{
|
||||
// Interpolate information only at DOFs marked for fitting.
|
||||
const int dim = surf_fit_gf->FESpace()->GetMesh()->Dimension();
|
||||
const int cnt = surf_fit_marker_dof_index.Size();
|
||||
const int total_cnt = new_x.Size()/dim;
|
||||
Vector new_x_sorted(cnt*dim);
|
||||
if (new_x_ordering == 0)
|
||||
{
|
||||
for (int d = 0; d < dim; d++)
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
new_x_sorted(i + d*cnt) = new_x(dof_index + d*total_cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
for (int d = 0; d < dim; d++)
|
||||
{
|
||||
new_x_sorted(d + i*dim) = new_x(d + dof_index*dim);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Interpolate values of the LS.
|
||||
Vector surf_fit_gf_int, surf_fit_grad_int, surf_fit_hess_int;
|
||||
surf_fit_eval->ComputeAtNewPosition(new_x_sorted, surf_fit_gf_int,
|
||||
new_x_ordering);
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
(*surf_fit_gf)[dof_index] = surf_fit_gf_int(i);
|
||||
}
|
||||
|
||||
// Interpolate gradients of the LS.
|
||||
surf_fit_eval_grad->ComputeAtNewPosition(new_x_sorted, surf_fit_grad_int,
|
||||
new_x_ordering);
|
||||
// Assumes surf_fit_grad and surf_fit_gf share the same space
|
||||
const int grad_dim = surf_fit_grad->VectorDim();
|
||||
const int grad_cnt = surf_fit_grad->Size()/grad_dim;
|
||||
if (surf_fit_grad->FESpace()->GetOrdering() == Ordering::byNODES)
|
||||
{
|
||||
for (int d = 0; d < grad_dim; d++)
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
(*surf_fit_grad)[dof_index + d*grad_cnt] =
|
||||
surf_fit_grad_int(i + d*cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
for (int d = 0; d < grad_dim; d++)
|
||||
{
|
||||
(*surf_fit_grad)[dof_index*grad_dim + d] =
|
||||
surf_fit_grad_int(i*grad_dim + d);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Interpolate Hessians of the LS.
|
||||
surf_fit_eval_hess->ComputeAtNewPosition(new_x_sorted, surf_fit_hess_int,
|
||||
new_x_ordering);
|
||||
// Assumes surf_fit_hess and surf_fit_gf share the same space
|
||||
const int hess_dim = surf_fit_hess->VectorDim();
|
||||
const int hess_cnt = surf_fit_hess->Size()/hess_dim;
|
||||
if (surf_fit_hess->FESpace()->GetOrdering() == Ordering::byNODES)
|
||||
{
|
||||
for (int d = 0; d < hess_dim; d++)
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
(*surf_fit_hess)[dof_index + d*hess_cnt] =
|
||||
surf_fit_hess_int(i + d*cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
for (int d = 0; d < hess_dim; d++)
|
||||
{
|
||||
(*surf_fit_hess)[dof_index*hess_dim + d] =
|
||||
surf_fit_hess_int(i*hess_dim + d);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
else
|
||||
{
|
||||
surf_fit_eval->ComputeAtNewPosition(new_x, *surf_fit_gf, new_x_ordering);
|
||||
if (surf_fit_eval_grad)
|
||||
{
|
||||
surf_fit_eval_grad->ComputeAtNewPosition(new_x, *surf_fit_grad,
|
||||
new_x_ordering);
|
||||
}
|
||||
if (surf_fit_eval_hess)
|
||||
{
|
||||
surf_fit_eval_hess->ComputeAtNewPosition(new_x, *surf_fit_hess,
|
||||
new_x_ordering);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void TMOP_Integrator::
|
||||
UpdateAfterMeshPositionChange(const Vector &x_new,
|
||||
const FiniteElementSpace &x_fes)
|
||||
@@ -4406,112 +4621,11 @@ UpdateAfterMeshPositionChange(const Vector &x_new,
|
||||
adapt_lim_eval->ComputeAtNewPosition(x_new, *adapt_lim_gf, ordering);
|
||||
}
|
||||
|
||||
// Update surf_fit_gf if surface fitting is enabled.
|
||||
// Update surf_fit_gf (and optionally its gradients) if surface
|
||||
// fitting is enabled.
|
||||
if (surf_fit_gf)
|
||||
{
|
||||
if (surf_fit_gf_bg)
|
||||
{
|
||||
// Interpolate information for only DOFs marked for fitting.
|
||||
const int dim = surf_fit_gf->FESpace()->GetMesh()->Dimension();
|
||||
const int cnt = surf_fit_marker_dof_index.Size();
|
||||
const int total_cnt = x_new.Size()/dim;
|
||||
Vector new_x_sorted(cnt*dim);
|
||||
if (ordering == 0)
|
||||
{
|
||||
for (int d = 0; d < dim; d++)
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
new_x_sorted(i + d*cnt) = x_new(dof_index + d*total_cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
for (int d = 0; d < dim; d++)
|
||||
{
|
||||
new_x_sorted(d + i*dim) = x_new(d + dof_index*dim);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Vector surf_fit_gf_int, surf_fit_grad_int, surf_fit_hess_int;
|
||||
surf_fit_eval->ComputeAtNewPosition(
|
||||
new_x_sorted, surf_fit_gf_int, ordering);
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
(*surf_fit_gf)[dof_index] = surf_fit_gf_int(i);
|
||||
}
|
||||
|
||||
surf_fit_eval_bg_grad->ComputeAtNewPosition(
|
||||
new_x_sorted, surf_fit_grad_int, ordering);
|
||||
// Assumes surf_fit_grad and surf_fit_gf share the same space
|
||||
const int grad_dim = surf_fit_grad->VectorDim();
|
||||
const int grad_cnt = surf_fit_grad->Size()/grad_dim;
|
||||
if (surf_fit_grad->FESpace()->GetOrdering() == Ordering::byNODES)
|
||||
{
|
||||
for (int d = 0; d < grad_dim; d++)
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
(*surf_fit_grad)[dof_index + d*grad_cnt] =
|
||||
surf_fit_grad_int(i + d*cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
for (int d = 0; d < grad_dim; d++)
|
||||
{
|
||||
(*surf_fit_grad)[dof_index*dim + d] =
|
||||
surf_fit_grad_int(i*dim + d);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
surf_fit_eval_bg_hess->ComputeAtNewPosition(
|
||||
new_x_sorted, surf_fit_hess_int, ordering);
|
||||
// Assumes surf_fit_hess and surf_fit_gf share the same space
|
||||
const int hess_dim = surf_fit_hess->VectorDim();
|
||||
const int hess_cnt = surf_fit_hess->Size()/hess_dim;
|
||||
if (surf_fit_hess->FESpace()->GetOrdering() == Ordering::byNODES)
|
||||
{
|
||||
for (int d = 0; d < hess_dim; d++)
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
(*surf_fit_hess)[dof_index + d*hess_cnt] =
|
||||
surf_fit_hess_int(i + d*cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
for (int i = 0; i < cnt; i++)
|
||||
{
|
||||
int dof_index = surf_fit_marker_dof_index[i];
|
||||
for (int d = 0; d < hess_dim; d++)
|
||||
{
|
||||
(*surf_fit_hess)[dof_index*dim + d] =
|
||||
surf_fit_hess_int(i*dim + d);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
surf_fit_eval->ComputeAtNewPosition(x_new, *surf_fit_gf, ordering);
|
||||
}
|
||||
RemapSurfaceFittingLevelSetAtNodes(x_new, ordering);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
+18
-10
@@ -1784,12 +1784,11 @@ protected:
|
||||
// Fitting to given physical positions.
|
||||
TMOP_QuadraticLimiter *surf_fit_limiter; // Owned. Created internally.
|
||||
const GridFunction *surf_fit_pos; // Not owned. Positions to fit.
|
||||
real_t surf_fit_normal;
|
||||
bool surf_fit_gf_bg;
|
||||
GridFunction *surf_fit_grad, *surf_fit_hess;
|
||||
AdaptivityEvaluator *surf_fit_eval_bg_grad, *surf_fit_eval_bg_hess;
|
||||
Array<int> surf_fit_dof_count;
|
||||
Array<int> surf_fit_marker_dof_index;
|
||||
real_t surf_fit_normal; // Normalization factor.
|
||||
GridFunction *surf_fit_grad, *surf_fit_hess; // Owned. Created internally.
|
||||
AdaptivityEvaluator *surf_fit_eval_grad, *surf_fit_eval_hess; // Not owned.
|
||||
Array<int> surf_fit_dof_count; // Number of dofs per node.
|
||||
Array<int> surf_fit_marker_dof_index; // Indices of nodes to fit.
|
||||
|
||||
DiscreteAdaptTC *discr_tc;
|
||||
|
||||
@@ -1985,6 +1984,10 @@ protected:
|
||||
real_t ComputeUntanglerMaxMuBarrier(const Vector &x,
|
||||
const FiniteElementSpace &fes);
|
||||
|
||||
// Remaps the internal surface fitting gridfunction object at provided
|
||||
// locations.
|
||||
void RemapSurfaceFittingLevelSetAtNodes(const Vector &new_x,
|
||||
int new_x_ordering);
|
||||
public:
|
||||
/** @param[in] m TMOP_QualityMetric for r-adaptivity (not owned).
|
||||
@param[in] tc Target-matrix construction algorithm to use (not owned).
|
||||
@@ -2000,9 +2003,8 @@ public:
|
||||
surf_fit_marker(NULL), surf_fit_coeff(NULL),
|
||||
surf_fit_gf(NULL), surf_fit_eval(NULL),
|
||||
surf_fit_limiter(NULL), surf_fit_pos(NULL),
|
||||
surf_fit_normal(1.0),
|
||||
surf_fit_gf_bg(false), surf_fit_grad(NULL), surf_fit_hess(NULL),
|
||||
surf_fit_eval_bg_grad(NULL), surf_fit_eval_bg_hess(NULL),
|
||||
surf_fit_normal(1.0), surf_fit_grad(NULL), surf_fit_hess(NULL),
|
||||
surf_fit_eval_grad(NULL), surf_fit_eval_hess(NULL),
|
||||
discr_tc(dynamic_cast<DiscreteAdaptTC *>(tc)),
|
||||
fdflag(false), dxscale(1.0e3), fd_call_flag(false), exact_action(false)
|
||||
{ PA.enabled = false; }
|
||||
@@ -2103,9 +2105,15 @@ public:
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
/// Parallel support for surface fitting to the zero level set of a function.
|
||||
/// Here, we add two optional inputs: @a aegrad and @a aehess. When provided,
|
||||
/// the first and second derivative of the input level set are computed on
|
||||
/// the initial mesh, and @a aegrad and @a aehess are used to remap grad_s(x)
|
||||
/// from grad_s0(x0) and hess_s(x) from hess_s0(x0), respectively.
|
||||
void EnableSurfaceFitting(const ParGridFunction &s0,
|
||||
const Array<bool> &smarker, Coefficient &coeff,
|
||||
AdaptivityEvaluator &ae);
|
||||
AdaptivityEvaluator &ae,
|
||||
AdaptivityEvaluator *aegrad = NULL,
|
||||
AdaptivityEvaluator *aehess = NULL);
|
||||
|
||||
/** @brief Fitting of certain DOFs in the current mesh to the zero level set
|
||||
of a function defined on another (finer) source mesh.
|
||||
|
||||
+88
-36
@@ -429,11 +429,13 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
#endif
|
||||
|
||||
real_t scale = 1.0;
|
||||
real_t avg_surf_fit_err, max_surf_fit_err = 0.0;
|
||||
if (surf_fit_max_threshold > 0.0)
|
||||
bool fitting = IsSurfaceFittingEnabled();
|
||||
real_t init_fit_avg_err, init_fit_max_err = 0.0;
|
||||
if (fitting && surf_fit_converge_error)
|
||||
{
|
||||
GetSurfaceFittingError(x_out_loc, avg_surf_fit_err, max_surf_fit_err);
|
||||
if (max_surf_fit_err < surf_fit_max_threshold)
|
||||
GetSurfaceFittingError(x_out_loc, init_fit_avg_err, init_fit_max_err);
|
||||
// Check for convergence
|
||||
if (init_fit_max_err < surf_fit_max_err_limit)
|
||||
{
|
||||
if (print_options.iterations)
|
||||
{
|
||||
@@ -444,11 +446,12 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
return scale;
|
||||
}
|
||||
}
|
||||
if (adapt_inc_count >= max_adapt_inc_count)
|
||||
|
||||
if (surf_fit_adapt_count >= surf_fit_adapt_count_limit)
|
||||
{
|
||||
if (print_options.iterations)
|
||||
{
|
||||
mfem::out << "TMOPNewtonSolver converged "
|
||||
mfem::out << "TMOPNewtonSolver terminated "
|
||||
"based on max number of times surface fitting weight can"
|
||||
"be increased. \n";
|
||||
}
|
||||
@@ -467,7 +470,7 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
// reference to detect deteriorations.
|
||||
MFEM_VERIFY(min_det_ptr != NULL, " Initial mesh was valid, but"
|
||||
" intermediate mesh is invalid. Contact TMOP Developers.");
|
||||
MFEM_VERIFY(min_detJ_threshold == 0.0,
|
||||
MFEM_VERIFY(min_detJ_limit == 0.0,
|
||||
"This setup is not supported. Contact TMOP Developers.");
|
||||
*min_det_ptr = untangle_factor * min_detT_in;
|
||||
}
|
||||
@@ -478,6 +481,7 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
bool x_out_ok = false;
|
||||
real_t energy_out = 0.0, min_detT_out;
|
||||
const real_t norm_in = Norm(r);
|
||||
real_t avg_fit_err, max_fit_err = 0.0;
|
||||
|
||||
const real_t detJ_factor = (solver_type == 1) ? 0.25 : 0.5;
|
||||
compute_metric_quantile_flag = false;
|
||||
@@ -488,6 +492,9 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
// Perform the line search.
|
||||
for (int i = 0; i < 12; i++)
|
||||
{
|
||||
avg_fit_err = 0.0;
|
||||
max_fit_err = 0.0;
|
||||
|
||||
// Update the mesh and get the L-vector in x_out_loc.
|
||||
add(x, -scale, c, x_out);
|
||||
if (serial)
|
||||
@@ -502,7 +509,7 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
|
||||
// Check the changes in detJ.
|
||||
min_detT_out = ComputeMinDet(x_out_loc, *fes);
|
||||
if (untangling == false && min_detT_out <= min_detJ_threshold)
|
||||
if (untangling == false && min_detT_out <= min_detJ_limit)
|
||||
{
|
||||
// No untangling, and detJ got negative (or small) -- no good.
|
||||
if (print_options.iterations)
|
||||
@@ -529,18 +536,19 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
// Check the changes in total energy.
|
||||
ProcessNewState(x_out);
|
||||
|
||||
real_t avg_fit_err, max_fit_err = 0.0;
|
||||
if (surf_fit_max_threshold > 0.0)
|
||||
// Ensure sufficient decrease in fitting error if we are trying to
|
||||
// converge based on error.
|
||||
if (fitting && surf_fit_converge_error)
|
||||
{
|
||||
GetSurfaceFittingError(x_out_loc, avg_fit_err, max_fit_err);
|
||||
}
|
||||
if (surf_fit_max_threshold > 0.0 && max_fit_err >= 1.2*max_surf_fit_err)
|
||||
{
|
||||
if (print_options.iterations)
|
||||
if (max_fit_err >= 1.2*init_fit_max_err)
|
||||
{
|
||||
mfem::out << "Scale = " << scale << " Surf fit err increased.\n";
|
||||
if (print_options.iterations)
|
||||
{
|
||||
mfem::out << "Scale = " << scale << " Surf fit err increased.\n";
|
||||
}
|
||||
scale *= 0.5; continue;
|
||||
}
|
||||
scale *= 0.5; continue;
|
||||
}
|
||||
|
||||
if (serial)
|
||||
@@ -614,7 +622,7 @@ real_t TMOPNewtonSolver::ComputeScalingFactor(const Vector &x,
|
||||
|
||||
if (x_out_ok == false) { scale = 0.0; }
|
||||
|
||||
if (surf_fit_scale_factor > 0.0) { update_surf_fit_coeff = true; }
|
||||
if (surf_fit_scale_factor > 0.0) { surf_fit_coeff_update = true; }
|
||||
compute_metric_quantile_flag = true;
|
||||
|
||||
return scale;
|
||||
@@ -657,7 +665,7 @@ void TMOPNewtonSolver::GetSurfaceFittingWeight(Array<real_t> &weights) const
|
||||
for (int i = 0; i < integs.Size(); i++)
|
||||
{
|
||||
ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
|
||||
if (ti)
|
||||
if (ti && ti->IsSurfaceFittingEnabled())
|
||||
{
|
||||
weight = ti->GetSurfaceFittingWeight();
|
||||
weights.Append(weight);
|
||||
@@ -668,8 +676,11 @@ void TMOPNewtonSolver::GetSurfaceFittingWeight(Array<real_t> &weights) const
|
||||
Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
|
||||
for (int j = 0; j < ati.Size(); j++)
|
||||
{
|
||||
weight = ati[j]->GetSurfaceFittingWeight();
|
||||
weights.Append(weight);
|
||||
if (ati[j]->IsSurfaceFittingEnabled())
|
||||
{
|
||||
weight = ati[j]->GetSurfaceFittingWeight();
|
||||
weights.Append(weight);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -716,6 +727,39 @@ void TMOPNewtonSolver::GetSurfaceFittingError(const Vector &x_loc,
|
||||
}
|
||||
}
|
||||
|
||||
bool TMOPNewtonSolver::IsSurfaceFittingEnabled() const
|
||||
{
|
||||
const NonlinearForm *nlf = dynamic_cast<const NonlinearForm *>(oper);
|
||||
const Array<NonlinearFormIntegrator*> &integs = *nlf->GetDNFI();
|
||||
TMOP_Integrator *ti = NULL;
|
||||
TMOPComboIntegrator *co = NULL;
|
||||
|
||||
for (int i = 0; i < integs.Size(); i++)
|
||||
{
|
||||
ti = dynamic_cast<TMOP_Integrator *>(integs[i]);
|
||||
if (ti)
|
||||
{
|
||||
if (ti->IsSurfaceFittingEnabled())
|
||||
{
|
||||
return true;
|
||||
}
|
||||
}
|
||||
co = dynamic_cast<TMOPComboIntegrator *>(integs[i]);
|
||||
if (co)
|
||||
{
|
||||
Array<TMOP_Integrator *> ati = co->GetTMOPIntegrators();
|
||||
for (int j = 0; j < ati.Size(); j++)
|
||||
{
|
||||
if (ati[j]->IsSurfaceFittingEnabled())
|
||||
{
|
||||
return true;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
void TMOPNewtonSolver::ProcessNewState(const Vector &x) const
|
||||
{
|
||||
const NonlinearForm *nlf = dynamic_cast<const NonlinearForm *>(oper);
|
||||
@@ -801,38 +845,46 @@ void TMOPNewtonSolver::ProcessNewState(const Vector &x) const
|
||||
// adaptive surface fitting is enabled. The idea is to increase the
|
||||
// coefficient if the surface fitting error does not sufficiently
|
||||
// decrease between subsequent TMOPNewtonSolver iterations.
|
||||
if (update_surf_fit_coeff)
|
||||
if (surf_fit_coeff_update)
|
||||
{
|
||||
// Get surface fitting errors.
|
||||
GetSurfaceFittingError(x_loc, surf_fit_err_avg, surf_fit_err_max);
|
||||
GetSurfaceFittingError(x_loc, surf_fit_avg_err, surf_fit_max_err);
|
||||
// Get array with surface fitting weights.
|
||||
Array<real_t> weights;
|
||||
GetSurfaceFittingWeight(weights);
|
||||
Array<real_t> fitweights;
|
||||
GetSurfaceFittingWeight(fitweights);
|
||||
|
||||
if (print_options.iterations)
|
||||
{
|
||||
mfem::out << "Avg/Max surface fitting error: " <<
|
||||
surf_fit_err_avg << " " <<
|
||||
surf_fit_err_max << "\n";
|
||||
surf_fit_avg_err << " " <<
|
||||
surf_fit_max_err << "\n";
|
||||
mfem::out << "Min/Max surface fitting weight: " <<
|
||||
weights.Min() << " " << weights.Max() << "\n";
|
||||
fitweights.Min() << " " << fitweights.Max() << "\n";
|
||||
}
|
||||
|
||||
real_t change_surf_fit_err = surf_fit_err_avg_prvs-surf_fit_err_avg;
|
||||
real_t rel_change_surf_fit_err = change_surf_fit_err/surf_fit_err_avg_prvs;
|
||||
real_t change_surf_fit_err = surf_fit_avg_err_prvs-surf_fit_avg_err;
|
||||
real_t rel_change_surf_fit_err = change_surf_fit_err/surf_fit_avg_err_prvs;
|
||||
|
||||
// Increase the surface fitting coefficient if the surface fitting error
|
||||
// does not decrease sufficiently.
|
||||
if (rel_change_surf_fit_err < surf_fit_rel_change_threshold)
|
||||
// does not decrease sufficiently. If we are converging based on residual,
|
||||
// also make sure we have not reached the maximum fitting weight and
|
||||
// error threshold.
|
||||
if (rel_change_surf_fit_err < surf_fit_err_rel_change_limit &&
|
||||
(surf_fit_converge_error ||
|
||||
(fitweights.Max() < surf_fit_weight_limit &&
|
||||
surf_fit_max_err > surf_fit_max_err_limit)))
|
||||
{
|
||||
UpdateSurfaceFittingWeight(surf_fit_scale_factor);
|
||||
adapt_inc_count += 1;
|
||||
real_t scale_factor = std::min(surf_fit_scale_factor,
|
||||
surf_fit_weight_limit/fitweights.Max());
|
||||
UpdateSurfaceFittingWeight(scale_factor);
|
||||
surf_fit_adapt_count += 1;
|
||||
}
|
||||
else
|
||||
{
|
||||
adapt_inc_count = 0;
|
||||
surf_fit_adapt_count = 0;
|
||||
}
|
||||
surf_fit_err_avg_prvs = surf_fit_err_avg;
|
||||
update_surf_fit_coeff = false;
|
||||
surf_fit_avg_err_prvs = surf_fit_avg_err;
|
||||
surf_fit_coeff_update = false;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
+87
-26
@@ -134,18 +134,20 @@ protected:
|
||||
int solver_type;
|
||||
bool parallel;
|
||||
|
||||
// Line search step is rejected if min(detJ) <= min_detJ_threshold.
|
||||
real_t min_detJ_threshold = 0.0;
|
||||
// Line search step is rejected if min(detJ) <= min_detJ_limit.
|
||||
real_t min_detJ_limit = 0.0;
|
||||
|
||||
// Surface fitting variables.
|
||||
mutable real_t surf_fit_err_avg_prvs = 10000.0;
|
||||
mutable real_t surf_fit_err_avg, surf_fit_err_max;
|
||||
mutable bool update_surf_fit_coeff = false;
|
||||
real_t surf_fit_max_threshold = -1.0;
|
||||
real_t surf_fit_rel_change_threshold = 0.001;
|
||||
mutable real_t surf_fit_avg_err_prvs = 10000.0;
|
||||
mutable real_t surf_fit_avg_err, surf_fit_max_err;
|
||||
mutable bool surf_fit_coeff_update = false;
|
||||
real_t surf_fit_max_err_limit = -1.0;
|
||||
real_t surf_fit_err_rel_change_limit = 0.001;
|
||||
real_t surf_fit_scale_factor = 0.0;
|
||||
mutable int adapt_inc_count = 0;
|
||||
mutable int max_adapt_inc_count = 10;
|
||||
mutable int surf_fit_adapt_count = 0;
|
||||
mutable int surf_fit_adapt_count_limit = 10;
|
||||
mutable real_t surf_fit_weight_limit = 1e10;
|
||||
bool surf_fit_converge_error = false;
|
||||
|
||||
// Minimum determinant over the whole mesh. Used for mesh untangling.
|
||||
real_t *min_det_ptr = nullptr;
|
||||
@@ -191,6 +193,9 @@ protected:
|
||||
void GetSurfaceFittingWeight(Array<real_t> &weights) const;
|
||||
///@}
|
||||
|
||||
/// Check if surface fitting is enabled.
|
||||
bool IsSurfaceFittingEnabled() const;
|
||||
|
||||
public:
|
||||
#ifdef MFEM_USE_MPI
|
||||
TMOPNewtonSolver(MPI_Comm comm, const IntegrationRule &irule, int type = 0)
|
||||
@@ -224,38 +229,94 @@ public:
|
||||
/// (ii) surface fitting weight.
|
||||
virtual void ProcessNewState(const Vector &x) const;
|
||||
|
||||
/** @name Methods for adaptive surface fitting weight. (Experimental) */
|
||||
/// Enable/Disable adaptive surface fitting weight.
|
||||
/// The weight is modified after each TMOPNewtonSolver iteration as:
|
||||
/// w_{k+1} = w_{k} * @a surf_fit_scale_factor if relative change in
|
||||
/// max surface fitting error < @a surf_fit_rel_change_threshold.
|
||||
/// The solver terminates if the maximum surface fitting error does
|
||||
/// not sufficiently decrease for @a max_adapt_inc_count consecutive
|
||||
/// solver iterations or if the max error falls below @a surf_fit_max_threshold.
|
||||
void EnableAdaptiveSurfaceFitting()
|
||||
{
|
||||
surf_fit_scale_factor = 10.0;
|
||||
surf_fit_rel_change_threshold = 0.001;
|
||||
}
|
||||
/** @name Methods for adaptive surface fitting.
|
||||
\brief These methods control the behavior of the weight and the
|
||||
termination of the solver. (Experimental)
|
||||
|
||||
Adaptive fitting weight: The weight is modified after each
|
||||
TMOPNewtonSolver iteration as:
|
||||
w_{k+1} = w_{k} * \ref surf_fit_scale_factor if the relative
|
||||
change in average fitting error < \ref surf_fit_err_rel_change_limit.
|
||||
When converging based on the residual, we enforce the fitting weight
|
||||
to be at-most \ref surf_fit_weight_limit, and increase it only if the
|
||||
fitting error is below user prescribed threshold
|
||||
(\ref surf_fit_max_err_limit).
|
||||
See \ref SetAdaptiveSurfaceFittingScalingFactor and
|
||||
\ref SetAdaptiveSurfaceFittingRelativeChangeThreshold.
|
||||
|
||||
Note that the solver stops if the maximum surface fitting error
|
||||
does not sufficiently decrease for \ref surf_fit_adapt_count_limit (default 10)
|
||||
consecutive increments of the fitting weight during weight adaptation.
|
||||
This typically occurs when the mesh cannot align with the level-set
|
||||
without degrading element quality.
|
||||
See \ref SetMaxNumberofIncrementsForAdaptiveFitting.
|
||||
|
||||
Convergence criterion: There are two modes, residual- and error-based,
|
||||
which can be toggled using \ref SetSurfaceFittingConvergenceBasedOnError.
|
||||
|
||||
(i) Residual based (default): Stop when the norm of the gradient of the
|
||||
TMOP objective reaches the prescribed tolerance. This method is best used
|
||||
with a reasonable value for \ref surf_fit_weight_limit when the
|
||||
adaptive surface fitting scheme is used. See method
|
||||
\ref SetSurfaceFittingWeightLimit.
|
||||
|
||||
(ii) Error based: Stop when the maximum fitting error
|
||||
reaches the user-prescribed threshold, \ref surf_fit_max_err_limit.
|
||||
In this case, \ref surf_fit_weight_limit is ignored during weight
|
||||
adaptation.
|
||||
*/
|
||||
///@{
|
||||
void SetAdaptiveSurfaceFittingScalingFactor(real_t factor)
|
||||
{
|
||||
MFEM_VERIFY(factor > 1.0, "Scaling factor must be greater than 1.");
|
||||
surf_fit_scale_factor = factor;
|
||||
}
|
||||
void SetAdaptiveSurfaceFittingRelativeChangeThreshold(real_t threshold)
|
||||
{
|
||||
surf_fit_rel_change_threshold = threshold;
|
||||
surf_fit_err_rel_change_limit = threshold;
|
||||
}
|
||||
/// Used for stopping based on the number of consecutive failed weight
|
||||
/// adaptation iterations.
|
||||
// TODO: Rename to SetMaxNumberofIncrementsForAdaptiveSurfaceFitting
|
||||
// in future.
|
||||
void SetMaxNumberofIncrementsForAdaptiveFitting(int count)
|
||||
{
|
||||
max_adapt_inc_count = count;
|
||||
surf_fit_adapt_count_limit = count;
|
||||
}
|
||||
/// Used for error-based surface fitting termination.
|
||||
void SetTerminationWithMaxSurfaceFittingError(real_t max_error)
|
||||
{
|
||||
surf_fit_max_threshold = max_error;
|
||||
surf_fit_max_err_limit = max_error;
|
||||
surf_fit_converge_error = true;
|
||||
}
|
||||
/// Could be used with both error-based or residual-based convergence.
|
||||
void SetSurfaceFittingMaxErrorLimit(real_t max_error)
|
||||
{
|
||||
surf_fit_max_err_limit = max_error;
|
||||
}
|
||||
/// Used for residual-based surface fitting termination.
|
||||
void SetSurfaceFittingWeightLimit(real_t weight)
|
||||
{
|
||||
surf_fit_weight_limit = weight;
|
||||
}
|
||||
/// Toggle convergence based on residual or error.
|
||||
void SetSurfaceFittingConvergenceBasedOnError(bool mode)
|
||||
{
|
||||
surf_fit_converge_error = mode;
|
||||
if (surf_fit_converge_error)
|
||||
{
|
||||
MFEM_VERIFY(surf_fit_max_err_limit >= 0,
|
||||
"Fitting error based convergence requires the user to "
|
||||
"first set the error threshold."
|
||||
"See SetTerminationWithMaxSurfaceFittingError");
|
||||
}
|
||||
}
|
||||
///@}
|
||||
|
||||
/// Set minimum determinant enforced during line-search.
|
||||
void SetMinimumDeterminantThreshold(real_t threshold)
|
||||
{
|
||||
min_detJ_threshold = threshold;
|
||||
min_detJ_limit = threshold;
|
||||
}
|
||||
|
||||
virtual void Mult(const Vector &b, Vector &x) const
|
||||
|
||||
+1
-1
@@ -124,7 +124,7 @@ T Array<T>::Sum()
|
||||
}
|
||||
|
||||
template <class T>
|
||||
int Array<T>::IsSorted()
|
||||
int Array<T>::IsSorted() const
|
||||
{
|
||||
T val_prev = operator[](0), val;
|
||||
for (int i = 1; i < size; i++)
|
||||
|
||||
+28
-9
@@ -74,10 +74,14 @@ public:
|
||||
inline Array(int asize, MemoryType mt)
|
||||
: size(asize) { asize > 0 ? data.New(asize, mt) : data.Reset(mt); }
|
||||
|
||||
/** @brief Creates array using an externally allocated pointer @a data_ to
|
||||
@a asize elements. The data pointer will not be deleted by Array. */
|
||||
inline Array(T *data_, int asize)
|
||||
{ data.Wrap(data_, asize, false); size = asize; }
|
||||
/** @brief Creates array using an externally allocated host pointer @a data_
|
||||
to @a asize elements. If @a own_data is true, the array takes ownership
|
||||
of the pointer.
|
||||
|
||||
When @a own_data is true, the pointer @a data_ must be allocated with
|
||||
MemoryType given by MemoryManager::GetHostMemoryType(). */
|
||||
inline Array(T *data_, int asize, bool own_data = false)
|
||||
{ data.Wrap(data_, asize, own_data); size = asize; }
|
||||
|
||||
/// Copy constructor: deep copy from @a src
|
||||
/** This method supports source arrays using any MemoryType. */
|
||||
@@ -205,7 +209,14 @@ public:
|
||||
inline void Copy(Array ©) const;
|
||||
|
||||
/// Make this Array a reference to a pointer.
|
||||
inline void MakeRef(T *, int);
|
||||
/** When @a own_data is true, the pointer @a data_ must be allocated with
|
||||
MemoryType given by MemoryManager::GetHostMemoryType(). */
|
||||
inline void MakeRef(T *data_, int size_, bool own_data = false);
|
||||
|
||||
/// Make this Array a reference to a pointer.
|
||||
/** When @a own_data is true, the pointer @a data_ must be allocated with
|
||||
MemoryType given by @a mt. */
|
||||
inline void MakeRef(T *data_, int size, MemoryType mt, bool own_data);
|
||||
|
||||
/// Make this Array a reference to 'master'.
|
||||
inline void MakeRef(const Array &master);
|
||||
@@ -262,7 +273,7 @@ public:
|
||||
}
|
||||
|
||||
/// Return 1 if the array is sorted from lowest to highest. Otherwise return 0.
|
||||
int IsSorted();
|
||||
int IsSorted() const;
|
||||
|
||||
/// Fill the entries of the array with the cumulative sum of the entries.
|
||||
void PartialSum();
|
||||
@@ -868,11 +879,19 @@ inline void Array<T>::Copy(Array ©) const
|
||||
}
|
||||
|
||||
template <class T>
|
||||
inline void Array<T>::MakeRef(T *p, int s)
|
||||
inline void Array<T>::MakeRef(T *data_, int size_, bool own_data)
|
||||
{
|
||||
data.Delete();
|
||||
data.Wrap(p, s, false);
|
||||
size = s;
|
||||
data.Wrap(data_, size_, own_data);
|
||||
size = size_;
|
||||
}
|
||||
|
||||
template <class T>
|
||||
inline void Array<T>::MakeRef(T *data_, int size_, MemoryType mt, bool own_data)
|
||||
{
|
||||
data.Delete();
|
||||
data.Wrap(data_, size_, mt, own_data);
|
||||
size = size_;
|
||||
}
|
||||
|
||||
template <class T>
|
||||
|
||||
@@ -288,4 +288,3 @@ void ArraysByName<T>::Load(std::istream &in)
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@@ -275,7 +275,7 @@ void GroupTopology::Save(ostream &os) const
|
||||
os << "\ncommunication_groups\n";
|
||||
os << "number_of_groups " << NGroups() << "\n\n";
|
||||
|
||||
os << "# number of entities in each group, followed by group ids in group\n";
|
||||
os << "# number of entities in each group, followed by ranks in group\n";
|
||||
for (int group_id = 0; group_id < NGroups(); ++group_id)
|
||||
{
|
||||
int group_size = GetGroupSize(group_id);
|
||||
|
||||
@@ -14,6 +14,9 @@
|
||||
#ifdef MFEM_USE_CEED
|
||||
#include "../fem/ceed/interface/util.hpp"
|
||||
#endif
|
||||
#ifdef MFEM_USE_MPI
|
||||
#include "../linalg/hypre.hpp"
|
||||
#endif
|
||||
|
||||
#include <unordered_map>
|
||||
#include <string>
|
||||
@@ -250,6 +253,10 @@ void Device::Configure(const std::string &device, const int device_id)
|
||||
|
||||
// Only '*this' will call the MemoryManager::Destroy() method.
|
||||
destroy_mm = true;
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
Hypre::InitDevice();
|
||||
#endif
|
||||
}
|
||||
|
||||
// static method
|
||||
|
||||
@@ -19,6 +19,9 @@
|
||||
#include "device.hpp"
|
||||
#include "mem_manager.hpp"
|
||||
#include "../linalg/dtensor.hpp"
|
||||
#ifdef MFEM_USE_MPI
|
||||
#include <_hypre_utilities.h>
|
||||
#endif
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
@@ -780,6 +783,63 @@ inline void forall_3D_grid(int N, int X, int Y, int Z, int G, lambda &&body)
|
||||
ForallWrap<3>(true, N, body, X, Y, Z, G);
|
||||
}
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
|
||||
// Function mfem::hypre_forall_cpu() similar to mfem::forall, but it always
|
||||
// executes on the CPU using sequential or OpenMP-parallel execution based on
|
||||
// the hypre build time configuration.
|
||||
template<typename lambda>
|
||||
inline void hypre_forall_cpu(int N, lambda &&body)
|
||||
{
|
||||
#ifdef HYPRE_USING_OPENMP
|
||||
#pragma omp parallel for HYPRE_SMP_SCHEDULE
|
||||
#endif
|
||||
for (int i = 0; i < N; i++) { body(i); }
|
||||
}
|
||||
|
||||
// Function mfem::hypre_forall_gpu() similar to mfem::forall, but it always
|
||||
// executes on the GPU device that hypre was configured with at build time.
|
||||
#if defined(HYPRE_USING_GPU)
|
||||
template<typename lambda>
|
||||
inline void hypre_forall_gpu(int N, lambda &&body)
|
||||
{
|
||||
#if defined(HYPRE_USING_CUDA)
|
||||
CuWrap1D(N, body);
|
||||
#elif defined(HYPRE_USING_HIP)
|
||||
HipWrap1D(N, body);
|
||||
#else
|
||||
#error Unknown HYPRE GPU backend!
|
||||
#endif
|
||||
}
|
||||
#endif
|
||||
|
||||
// Function mfem::hypre_forall() similar to mfem::forall, but it executes on the
|
||||
// device, CPU or GPU, that hypre was configured with at build time (when the
|
||||
// HYPRE version is < 2.31.0) or at runtime (when HYPRE was configured with GPU
|
||||
// support at build time and HYPRE's version is >= 2.31.0). This selection is
|
||||
// generally independent of what device was selected in MFEM's runtime
|
||||
// configuration.
|
||||
template<typename lambda>
|
||||
inline void hypre_forall(int N, lambda &&body)
|
||||
{
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
hypre_forall_cpu(N, body);
|
||||
#elif MFEM_HYPRE_VERSION < 23100
|
||||
hypre_forall_gpu(N, body);
|
||||
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
|
||||
if (!HypreUsingGPU())
|
||||
{
|
||||
hypre_forall_cpu(N, body);
|
||||
}
|
||||
else
|
||||
{
|
||||
hypre_forall_gpu(N, body);
|
||||
}
|
||||
#endif
|
||||
}
|
||||
|
||||
#endif // MFEM_USE_MPI
|
||||
|
||||
} // namespace mfem
|
||||
|
||||
#endif // MFEM_FORALL_HPP
|
||||
|
||||
@@ -51,7 +51,7 @@ int isockstream::establish()
|
||||
{
|
||||
// char myname[129];
|
||||
char myname[] = "localhost";
|
||||
int sfd;
|
||||
int sfd = -1;
|
||||
struct addrinfo hints, *res, *rp;
|
||||
|
||||
memset(&hints, 0, sizeof(hints));
|
||||
|
||||
@@ -1154,6 +1154,10 @@ void MemoryManager::Copy_(void *dst_h_ptr, const void *src_h_ptr,
|
||||
// dest d | h2d d2d d2d
|
||||
// hd | h2h d2d d2d
|
||||
|
||||
MFEM_ASSERT(bytes != 0, "this method should not be called with bytes = 0");
|
||||
MFEM_ASSERT(dst_h_ptr != nullptr, "invalid dst_h_ptr = nullptr");
|
||||
MFEM_ASSERT(src_h_ptr != nullptr, "invalid src_h_ptr = nullptr");
|
||||
|
||||
const bool dst_on_host =
|
||||
(dst_flags & Mem::VALID_HOST) &&
|
||||
(!(dst_flags & Mem::VALID_DEVICE) ||
|
||||
@@ -1229,6 +1233,10 @@ void MemoryManager::Copy_(void *dst_h_ptr, const void *src_h_ptr,
|
||||
void MemoryManager::CopyToHost_(void *dest_h_ptr, const void *src_h_ptr,
|
||||
size_t bytes, unsigned src_flags)
|
||||
{
|
||||
MFEM_ASSERT(bytes != 0, "this method should not be called with bytes = 0");
|
||||
MFEM_ASSERT(dest_h_ptr != nullptr, "invalid dest_h_ptr = nullptr");
|
||||
MFEM_ASSERT(src_h_ptr != nullptr, "invalid src_h_ptr = nullptr");
|
||||
|
||||
const bool src_on_host = src_flags & Mem::VALID_HOST;
|
||||
if (src_on_host)
|
||||
{
|
||||
@@ -1255,6 +1263,10 @@ void MemoryManager::CopyToHost_(void *dest_h_ptr, const void *src_h_ptr,
|
||||
void MemoryManager::CopyFromHost_(void *dest_h_ptr, const void *src_h_ptr,
|
||||
size_t bytes, unsigned &dest_flags)
|
||||
{
|
||||
MFEM_ASSERT(bytes != 0, "this method should not be called with bytes = 0");
|
||||
MFEM_ASSERT(dest_h_ptr != nullptr, "invalid dest_h_ptr = nullptr");
|
||||
MFEM_ASSERT(src_h_ptr != nullptr, "invalid src_h_ptr = nullptr");
|
||||
|
||||
const bool dest_on_host = dest_flags & Mem::VALID_HOST;
|
||||
if (dest_on_host)
|
||||
{
|
||||
|
||||
+57
-8
@@ -18,8 +18,14 @@
|
||||
#include <cstring> // std::memcpy
|
||||
#include <type_traits> // std::is_const
|
||||
#include <cstddef> // std::max_align_t
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
#include <HYPRE_config.h> // HYPRE_USING_GPU
|
||||
// Enable internal hypre timing routines
|
||||
#define HYPRE_TIMING
|
||||
#include <HYPRE_utilities.h> // for HYPRE_GetMemoryLocation() and others
|
||||
#if (21400 <= MFEM_HYPRE_VERSION) && (MFEM_HYPRE_VERSION < 21900)
|
||||
#include <_hypre_utilities.h> // for HYPRE_MEMORY_HOST and others
|
||||
#endif
|
||||
#endif
|
||||
|
||||
namespace mfem
|
||||
@@ -869,6 +875,45 @@ public:
|
||||
};
|
||||
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
|
||||
#if MFEM_HYPRE_VERSION < 21400
|
||||
#define HYPRE_MEMORY_DEVICE (0)
|
||||
#define HYPRE_MEMORY_HOST (1)
|
||||
#endif
|
||||
#if MFEM_HYPRE_VERSION < 21900
|
||||
typedef int HYPRE_MemoryLocation;
|
||||
#endif
|
||||
|
||||
/// Return the configured HYPRE_MemoryLocation
|
||||
inline HYPRE_MemoryLocation GetHypreMemoryLocation()
|
||||
{
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
return HYPRE_MEMORY_HOST;
|
||||
#elif MFEM_HYPRE_VERSION < 23100
|
||||
return HYPRE_MEMORY_DEVICE;
|
||||
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
|
||||
HYPRE_MemoryLocation loc;
|
||||
HYPRE_GetMemoryLocation(&loc);
|
||||
return loc;
|
||||
#endif
|
||||
}
|
||||
|
||||
/// Return true if HYPRE is configured to use GPU
|
||||
inline bool HypreUsingGPU()
|
||||
{
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
return false;
|
||||
#elif MFEM_HYPRE_VERSION < 23100
|
||||
return true;
|
||||
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
|
||||
return GetHypreMemoryLocation() != HYPRE_MEMORY_HOST;
|
||||
#endif
|
||||
}
|
||||
|
||||
#endif // MFEM_USE_MPI
|
||||
|
||||
|
||||
// Inline methods
|
||||
|
||||
template <typename T>
|
||||
@@ -1004,10 +1049,12 @@ inline void Memory<T>::MakeAlias(const Memory &base, int offset, int size)
|
||||
// If the following condition is true then MemoryManager::Exists()
|
||||
// should also be true:
|
||||
IsDeviceMemory(MemoryManager::GetDeviceMemoryType())
|
||||
#else
|
||||
// When HYPRE_USING_GPU is defined we always register the 'base' if
|
||||
// the MemoryManager::Exists():
|
||||
#elif MFEM_HYPRE_VERSION < 23100
|
||||
// When HYPRE_USING_GPU is defined and HYPRE < 2.31.0, we always
|
||||
// register the 'base' if the MemoryManager::Exists():
|
||||
MemoryManager::Exists()
|
||||
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
|
||||
MemoryManager::Exists() && HypreUsingGPU()
|
||||
#endif
|
||||
)
|
||||
{
|
||||
@@ -1213,9 +1260,10 @@ template <typename T>
|
||||
inline void Memory<T>::CopyFrom(const Memory &src, int size)
|
||||
{
|
||||
MFEM_VERIFY(src.capacity>=size && capacity>=size, "Incorrect size");
|
||||
if (size <= 0) { return; }
|
||||
if (!(flags & Registered) && !(src.flags & Registered))
|
||||
{
|
||||
if (h_ptr != src.h_ptr && size != 0)
|
||||
if (h_ptr != src.h_ptr)
|
||||
{
|
||||
MFEM_ASSERT(h_ptr + size <= src.h_ptr || src.h_ptr + size <= h_ptr,
|
||||
"data overlaps!");
|
||||
@@ -1233,9 +1281,10 @@ template <typename T>
|
||||
inline void Memory<T>::CopyFromHost(const T *src, int size)
|
||||
{
|
||||
MFEM_VERIFY(capacity>=size, "Incorrect size");
|
||||
if (size <= 0) { return; }
|
||||
if (!(flags & Registered))
|
||||
{
|
||||
if (h_ptr != src && size != 0)
|
||||
if (h_ptr != src)
|
||||
{
|
||||
MFEM_ASSERT(h_ptr + size <= src || src + size <= h_ptr,
|
||||
"data overlaps!");
|
||||
@@ -1252,7 +1301,6 @@ inline void Memory<T>::CopyFromHost(const T *src, int size)
|
||||
template <typename T>
|
||||
inline void Memory<T>::CopyTo(Memory &dest, int size) const
|
||||
{
|
||||
MFEM_VERIFY(capacity>=size, "Incorrect size");
|
||||
dest.CopyFrom(*this, size);
|
||||
}
|
||||
|
||||
@@ -1260,9 +1308,10 @@ template <typename T>
|
||||
inline void Memory<T>::CopyToHost(T *dest, int size) const
|
||||
{
|
||||
MFEM_VERIFY(capacity>=size, "Incorrect size");
|
||||
if (size <= 0) { return; }
|
||||
if (!(flags & Registered))
|
||||
{
|
||||
if (h_ptr != dest && size != 0)
|
||||
if (h_ptr != dest)
|
||||
{
|
||||
MFEM_ASSERT(h_ptr + size <= dest || dest + size <= h_ptr,
|
||||
"data overlaps!");
|
||||
|
||||
@@ -134,7 +134,7 @@ int socketbuf::open(const char hostname[], int port)
|
||||
{
|
||||
closesocket(socket_descriptor);
|
||||
socket_descriptor = -2;
|
||||
return -1;
|
||||
continue;
|
||||
}
|
||||
#endif
|
||||
|
||||
@@ -148,7 +148,7 @@ int socketbuf::open(const char hostname[], int port)
|
||||
}
|
||||
|
||||
freeaddrinfo(res);
|
||||
return 0;
|
||||
return (socket_descriptor < 0) ? -1 : 0;
|
||||
}
|
||||
|
||||
int socketbuf::close()
|
||||
|
||||
+6
-1
@@ -207,7 +207,12 @@ template <> inline void Swap<Table>(Table &a, Table &b)
|
||||
void Transpose (const Table &A, Table &At, int ncols_A_ = -1);
|
||||
Table * Transpose (const Table &A);
|
||||
|
||||
/// Transpose an Array<int>
|
||||
/// @brief Transpose an Array<int>.
|
||||
///
|
||||
/// The array @a A represents a table where each row @a i has exactly one
|
||||
/// connection to the column (TYPE II) index specified by @a A[i].
|
||||
///
|
||||
/// @note The column (TYPE II) indices in each row of @a At will be sorted.
|
||||
void Transpose(const Array<int> &A, Table &At, int ncols_A_ = -1);
|
||||
|
||||
/// C = A * B (as boolean matrices)
|
||||
|
||||
@@ -400,6 +400,9 @@ inline double StopWatch::SystTime()
|
||||
|
||||
StopWatch::StopWatch() : M(new internal::StopWatch) { }
|
||||
|
||||
StopWatch::StopWatch(const StopWatch &sw)
|
||||
: M(new internal::StopWatch(*(sw.M))) { }
|
||||
|
||||
void StopWatch::Clear()
|
||||
{
|
||||
M->Clear();
|
||||
|
||||
@@ -40,6 +40,7 @@ private:
|
||||
public:
|
||||
/// Creates a new (stopped) StopWatch object.
|
||||
StopWatch();
|
||||
StopWatch(const StopWatch &);
|
||||
|
||||
/// Clear the elapsed time on the stopwatch and restart it if it's running.
|
||||
void Clear();
|
||||
|
||||
@@ -23,6 +23,10 @@
|
||||
#include "amgxsolver.hpp"
|
||||
#ifdef MFEM_USE_AMGX
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
#include "../general/communication.hpp"
|
||||
#endif
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
|
||||
@@ -81,7 +81,7 @@ void BlockOperator::Mult (const Vector & x, Vector & y) const
|
||||
tmp.SetSize(row_offsets[iRow+1] - row_offsets[iRow]);
|
||||
for (int jCol=0; jCol < nColBlocks; ++jCol)
|
||||
{
|
||||
if (op(iRow,jCol))
|
||||
if (op(iRow,jCol) && coef(iRow,jCol) != 0.)
|
||||
{
|
||||
op(iRow,jCol)->Mult(xblock.GetBlock(jCol), tmp);
|
||||
yblock.GetBlock(iRow).Add(coef(iRow,jCol), tmp);
|
||||
@@ -112,7 +112,7 @@ void BlockOperator::MultTranspose (const Vector & x, Vector & y) const
|
||||
tmp.SetSize(col_offsets[iRow+1] - col_offsets[iRow]);
|
||||
for (int jCol=0; jCol < nRowBlocks; ++jCol)
|
||||
{
|
||||
if (op(jCol,iRow))
|
||||
if (op(jCol,iRow) && coef(jCol,iRow) != 0.)
|
||||
{
|
||||
op(jCol,iRow)->MultTranspose(xblock.GetBlock(jCol), tmp);
|
||||
yblock.GetBlock(iRow).Add(coef(jCol,iRow), tmp);
|
||||
|
||||
@@ -1,3 +1,14 @@
|
||||
// Copyright (c) 2010-2024, 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 "cpardiso.hpp"
|
||||
#include "hypre.hpp"
|
||||
#include <algorithm>
|
||||
|
||||
@@ -532,6 +532,69 @@ MatrixInverse *DenseMatrix::Inverse() const
|
||||
return new DenseMatrixInverse(*this);
|
||||
}
|
||||
|
||||
void DenseMatrix::Exponential()
|
||||
{
|
||||
MFEM_ASSERT(Height() == Width() && Height() <= 2,
|
||||
"The matrix must be square and "
|
||||
<< "of size less than or equal to 2."
|
||||
<< " Height() = " << Height()
|
||||
<< ", Width() = " << Width());
|
||||
|
||||
switch (Height())
|
||||
{
|
||||
case 1:
|
||||
{
|
||||
data[0] = std::exp(data[0]);
|
||||
break;
|
||||
}
|
||||
case 2:
|
||||
{
|
||||
/// Formulas from Corollary 2.4 of doi:10.1109/9.233156
|
||||
/// Note typo in the paper, in the prefactor in the equation under (i).
|
||||
const real_t a = data[0];
|
||||
const real_t b = data[1];
|
||||
const real_t c = data[2];
|
||||
const real_t d = data[3];
|
||||
const real_t e = (a - d)*(a - d) + 4*b*c;
|
||||
const real_t f = std::exp((a + d)/2.0);
|
||||
const real_t g = std::sqrt(std::abs(e)) / 2.0;
|
||||
|
||||
if (e == 0)
|
||||
{
|
||||
data[0] = 1.0 + (a - d)/2.0;
|
||||
data[3] = 1.0 - (a - d)/2.0;
|
||||
}
|
||||
else if (e > 0)
|
||||
{
|
||||
data[0] = std::cosh(g) + (a - d)/2 * std::sinh(g) / g;
|
||||
data[1] = b * std::sinh(g) / g;
|
||||
data[2] = c * std::sinh(g) / g;
|
||||
data[3] = std::cosh(g) - (a - d)/2 * std::sinh(g) / g;
|
||||
}
|
||||
else
|
||||
{
|
||||
data[0] = std::cos(g) + (a - d)/2 * std::sin(g) / g;
|
||||
data[1] = b * std::sin(g) / g;
|
||||
data[2] = c * std::sin(g) / g;
|
||||
data[3] = std::cos(g) - (a - d)/2 * std::sin(g) / g;
|
||||
}
|
||||
for (int i = 0; i < 4; i++)
|
||||
{
|
||||
data[i] *= f;
|
||||
}
|
||||
break;
|
||||
}
|
||||
case 3:
|
||||
{
|
||||
MFEM_ABORT("3x3 matrices are not currently supported");
|
||||
}
|
||||
default:
|
||||
{
|
||||
MFEM_ABORT("Only 1x1 and 2x2 matrices are currently supported");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
real_t DenseMatrix::Det() const
|
||||
{
|
||||
MFEM_ASSERT(Height() == Width() && Height() > 0,
|
||||
@@ -3217,6 +3280,93 @@ void MultAtB(const DenseMatrix &A, const DenseMatrix &B, DenseMatrix &AtB)
|
||||
#endif
|
||||
}
|
||||
|
||||
void AddMultAtB(const DenseMatrix &A, const DenseMatrix &B,
|
||||
DenseMatrix &AtB)
|
||||
{
|
||||
MFEM_ASSERT(AtB.Height() == A.Width() && AtB.Width() == B.Width() &&
|
||||
A.Height() == B.Height(), "incompatible dimensions");
|
||||
|
||||
#ifdef MFEM_USE_LAPACK
|
||||
static char transa = 'T', transb = 'N';
|
||||
static real_t alpha = 1.0, beta = 1.0;
|
||||
int m = A.Width(), n = B.Width(), k = A.Height();
|
||||
|
||||
#ifdef MFEM_USE_SINGLE
|
||||
sgemm_(&transa, &transb, &m, &n, &k, &alpha, A.Data(), &k,
|
||||
#elif defined MFEM_USE_DOUBLE
|
||||
dgemm_(&transa, &transb, &m, &n, &k, &alpha, A.Data(), &k,
|
||||
#endif
|
||||
B.Data(), &k, &beta, AtB.Data(), &m);
|
||||
#else
|
||||
const int ah = A.Height();
|
||||
const int aw = A.Width();
|
||||
const int bw = B.Width();
|
||||
const real_t *ad = A.Data();
|
||||
const real_t *bd = B.Data();
|
||||
real_t *cd = AtB.Data();
|
||||
|
||||
for (int j = 0; j < bw; j++)
|
||||
{
|
||||
const real_t *ap = ad;
|
||||
for (int i = 0; i < aw; i++)
|
||||
{
|
||||
real_t d = 0.0;
|
||||
for (int k = 0; k < ah; k++)
|
||||
{
|
||||
d += ap[k] * bd[k];
|
||||
}
|
||||
*(cd++) += d;
|
||||
ap += ah;
|
||||
}
|
||||
bd += ah;
|
||||
}
|
||||
#endif
|
||||
}
|
||||
|
||||
void AddMult_a_AtB(real_t a, const DenseMatrix &A, const DenseMatrix &B,
|
||||
DenseMatrix &AtB)
|
||||
{
|
||||
MFEM_ASSERT(AtB.Height() == A.Width() && AtB.Width() == B.Width() &&
|
||||
A.Height() == B.Height(), "incompatible dimensions");
|
||||
|
||||
#ifdef MFEM_USE_LAPACK
|
||||
static char transa = 'T', transb = 'N';
|
||||
real_t alpha = a;
|
||||
static real_t beta = 1.0;
|
||||
int m = A.Width(), n = B.Width(), k = A.Height();
|
||||
|
||||
#ifdef MFEM_USE_SINGLE
|
||||
sgemm_(&transa, &transb, &m, &n, &k, &alpha, A.Data(), &k,
|
||||
#elif defined MFEM_USE_DOUBLE
|
||||
dgemm_(&transa, &transb, &m, &n, &k, &alpha, A.Data(), &k,
|
||||
#endif
|
||||
B.Data(), &k, &beta, AtB.Data(), &m);
|
||||
#else
|
||||
const int ah = A.Height();
|
||||
const int aw = A.Width();
|
||||
const int bw = B.Width();
|
||||
const real_t *ad = A.Data();
|
||||
const real_t *bd = B.Data();
|
||||
real_t *cd = AtB.Data();
|
||||
|
||||
for (int j = 0; j < bw; j++)
|
||||
{
|
||||
const real_t *ap = ad;
|
||||
for (int i = 0; i < aw; i++)
|
||||
{
|
||||
real_t d = 0.0;
|
||||
for (int k = 0; k < ah; k++)
|
||||
{
|
||||
d += ap[k] * bd[k];
|
||||
}
|
||||
*(cd++) += a * d;
|
||||
ap += ah;
|
||||
}
|
||||
bd += ah;
|
||||
}
|
||||
#endif
|
||||
}
|
||||
|
||||
void AddMult_a_AAt(real_t a, const DenseMatrix &A, DenseMatrix &AAt)
|
||||
{
|
||||
real_t d;
|
||||
|
||||
@@ -207,6 +207,10 @@ public:
|
||||
/// Replaces the current matrix with its square root inverse
|
||||
void SquareRootInverse();
|
||||
|
||||
/// Replaces the current matrix with its exponential
|
||||
/// (currently only supports 2x2 matrices)
|
||||
void Exponential();
|
||||
|
||||
/// Calculates the determinant of the matrix
|
||||
/// (optimized for 2x2, 3x3, and 4x4 matrices)
|
||||
real_t Det() const;
|
||||
@@ -580,6 +584,13 @@ void AddMult_a_ABt(real_t a, const DenseMatrix &A, const DenseMatrix &B,
|
||||
/// Multiply the transpose of a matrix A with a matrix B: At*B
|
||||
void MultAtB(const DenseMatrix &A, const DenseMatrix &B, DenseMatrix &AtB);
|
||||
|
||||
/// AtB += A^t * B
|
||||
void AddMultAtB(const DenseMatrix &A, const DenseMatrix &B, DenseMatrix &AtB);
|
||||
|
||||
/// AtB += a * A^t * B
|
||||
void AddMult_a_AtB(real_t a, const DenseMatrix &A, const DenseMatrix &B,
|
||||
DenseMatrix &AtB);
|
||||
|
||||
/// AAt += a * A * A^t
|
||||
void AddMult_a_AAt(real_t a, const DenseMatrix &A, DenseMatrix &AAt);
|
||||
|
||||
|
||||
+367
-256
File diff suppressed because it is too large
Load Diff
+141
-51
@@ -16,17 +16,19 @@
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
|
||||
#include "../general/globals.hpp"
|
||||
#include "sparsemat.hpp"
|
||||
#include "hypre_parcsr.hpp"
|
||||
#include <mpi.h>
|
||||
|
||||
// Enable internal hypre timing routines
|
||||
#define HYPRE_TIMING
|
||||
|
||||
// hypre header files
|
||||
#include "seq_mv.h"
|
||||
#include "_hypre_parcsr_mv.h"
|
||||
#include "_hypre_parcsr_ls.h"
|
||||
#include "temp_multivector.h"
|
||||
#include "../general/globals.hpp"
|
||||
#include <seq_mv.h>
|
||||
#include <temp_multivector.h>
|
||||
#include <_hypre_parcsr_mv.h>
|
||||
#include <_hypre_parcsr_ls.h>
|
||||
|
||||
#ifdef HYPRE_COMPLEX
|
||||
#error "MFEM does not work with HYPRE's complex numbers support"
|
||||
@@ -51,22 +53,6 @@
|
||||
#error "MFEM_USE_HIP=YES is required when HYPRE is built with HIP!"
|
||||
#endif
|
||||
|
||||
// MFEM_HYPRE_FORALL is a macro similar to mfem::forall, but it executes on the
|
||||
// device that hypre was configured with (no matter what device was selected
|
||||
// in MFEM's runtime configuration).
|
||||
#if defined(HYPRE_USING_CUDA)
|
||||
#define MFEM_HYPRE_FORALL(i, N,...) CuWrap1D(N, [=] MFEM_DEVICE \
|
||||
(int i) {__VA_ARGS__})
|
||||
#elif defined(HYPRE_USING_HIP)
|
||||
#define MFEM_HYPRE_FORALL(i, N,...) HipWrap1D(N, [=] MFEM_DEVICE \
|
||||
(int i) {__VA_ARGS__})
|
||||
#else
|
||||
#define MFEM_HYPRE_FORALL(i, N,...) for (int i = 0; i < N; i++) { __VA_ARGS__ }
|
||||
#endif
|
||||
|
||||
#include "sparsemat.hpp"
|
||||
#include "hypre_parcsr.hpp"
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
|
||||
@@ -87,6 +73,22 @@ public:
|
||||
/// Calling HYPRE_Finalize() manually is not compatible with this class.
|
||||
static void Init() { Instance(); }
|
||||
|
||||
/// @brief Configure HYPRE's compute and memory policy.
|
||||
///
|
||||
/// By default HYPRE will be configured with the same policy as MFEM unless
|
||||
/// `Hypre::configure_runtime_policy_from_mfem` is false, in which case
|
||||
/// HYPRE's default will be used; if HYPRE is built for the GPU and the
|
||||
/// aforementioned variable is false then HYPRE will use the GPU even if MFEM
|
||||
/// is not.
|
||||
///
|
||||
/// This function is no-op if HYPRE is built without GPU support or the HYPRE
|
||||
/// version is less than 2.31.0.
|
||||
///
|
||||
/// This function is NOT called by Init(). Instead it is called by
|
||||
/// Device::Configure() (when MFEM_USE_MPI=YES) after the MFEM device
|
||||
/// configuration is complete.
|
||||
static void InitDevice();
|
||||
|
||||
/// @brief Finalize hypre (called automatically at program exit if
|
||||
/// Hypre::Init() has been called).
|
||||
///
|
||||
@@ -94,6 +96,13 @@ public:
|
||||
/// called manually to more precisely control when hypre is finalized.
|
||||
static void Finalize();
|
||||
|
||||
/// @brief Use MFEM's device policy to configure HYPRE's device policy, true
|
||||
/// by default. This variable is used by InitDevice().
|
||||
///
|
||||
/// This value is not used if HYPRE is build without GPU support or the HYPRE
|
||||
/// version is less than 2.31.0.
|
||||
static bool configure_runtime_policy_from_mfem;
|
||||
|
||||
private:
|
||||
/// Calls HYPRE_Init() when the singleton is constructed.
|
||||
Hypre();
|
||||
@@ -142,15 +151,28 @@ inline int to_int(HYPRE_Int i)
|
||||
|
||||
|
||||
/// The MemoryClass used by Hypre objects.
|
||||
inline constexpr MemoryClass GetHypreMemoryClass()
|
||||
inline MemoryClass GetHypreMemoryClass()
|
||||
{
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
return MemoryClass::HOST;
|
||||
#elif defined(HYPRE_USING_UNIFIED_MEMORY)
|
||||
#elif MFEM_HYPRE_VERSION < 23100
|
||||
#if defined(HYPRE_USING_UNIFIED_MEMORY)
|
||||
return MemoryClass::MANAGED;
|
||||
#else
|
||||
return MemoryClass::DEVICE;
|
||||
#endif
|
||||
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
|
||||
if (GetHypreMemoryLocation() == HYPRE_MEMORY_HOST)
|
||||
{
|
||||
return MemoryClass::HOST;
|
||||
}
|
||||
// Return the actual memory location, see hypre_GetActualMemLocation():
|
||||
#if defined(HYPRE_USING_UNIFIED_MEMORY)
|
||||
return MemoryClass::MANAGED;
|
||||
#else
|
||||
return MemoryClass::DEVICE;
|
||||
#endif
|
||||
#endif
|
||||
}
|
||||
|
||||
/// The MemoryType used by MFEM when allocating arrays for Hypre objects.
|
||||
@@ -158,13 +180,27 @@ inline MemoryType GetHypreMemoryType()
|
||||
{
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
return Device::GetHostMemoryType();
|
||||
#elif defined(HYPRE_USING_UNIFIED_MEMORY)
|
||||
#elif MFEM_HYPRE_VERSION < 23100
|
||||
#if defined(HYPRE_USING_UNIFIED_MEMORY)
|
||||
return MemoryType::MANAGED;
|
||||
#else
|
||||
return MemoryType::DEVICE;
|
||||
#endif
|
||||
#else // HYPRE_USING_GPU is defined and MFEM_HYPRE_VERSION >= 23100
|
||||
if (GetHypreMemoryLocation() == HYPRE_MEMORY_HOST)
|
||||
{
|
||||
return Device::GetHostMemoryType();
|
||||
}
|
||||
// Return the actual memory location, see hypre_GetActualMemLocation():
|
||||
#if defined(HYPRE_USING_UNIFIED_MEMORY)
|
||||
return MemoryType::MANAGED;
|
||||
#else
|
||||
return MemoryType::DEVICE;
|
||||
#endif
|
||||
#endif
|
||||
}
|
||||
|
||||
|
||||
/// Wrapper for hypre's parallel vector class
|
||||
class HypreParVector : public Vector
|
||||
{
|
||||
@@ -328,10 +364,10 @@ public:
|
||||
HYPRE_Int Randomize(HYPRE_Int seed);
|
||||
|
||||
/// Prints the locally owned rows in parallel
|
||||
void Print(const char *fname) const;
|
||||
void Print(const std::string &fname) const;
|
||||
|
||||
/// Reads a HypreParVector from files saved with HypreParVector::Print
|
||||
void Read(MPI_Comm comm, const char *fname);
|
||||
void Read(MPI_Comm comm, const std::string &fname);
|
||||
|
||||
/// Calls hypre's destroy function
|
||||
~HypreParVector();
|
||||
@@ -883,12 +919,14 @@ public:
|
||||
const Memory<HYPRE_Int> &GetDiagMemoryJ() const { return mem_diag.J; }
|
||||
const Memory<real_t> &GetDiagMemoryData() const { return mem_diag.data; }
|
||||
|
||||
/// Prints the locally owned rows in parallel
|
||||
void Print(const char *fname, HYPRE_Int offi = 0, HYPRE_Int offj = 0) const;
|
||||
/// @brief Prints the locally owned rows in parallel. The resulting files can
|
||||
/// be read with Read_IJMatrix().
|
||||
void Print(const std::string &fname, HYPRE_Int offi = 0,
|
||||
HYPRE_Int offj = 0) const;
|
||||
/// Reads the matrix from a file
|
||||
void Read(MPI_Comm comm, const char *fname);
|
||||
void Read(MPI_Comm comm, const std::string &fname);
|
||||
/// Read a matrix saved as a HYPRE_IJMatrix
|
||||
void Read_IJMatrix(MPI_Comm comm, const char *fname);
|
||||
void Read_IJMatrix(MPI_Comm comm, const std::string &fname);
|
||||
|
||||
/// Print information about the hypre_ParCSRCommPkg of the HypreParMatrix.
|
||||
void PrintCommPkg(std::ostream &out = mfem::out) const;
|
||||
@@ -1037,29 +1075,40 @@ protected:
|
||||
bool A_is_symmetric;
|
||||
|
||||
public:
|
||||
/** Hypre smoother types:
|
||||
0 = Jacobi
|
||||
1 = l1-scaled Jacobi
|
||||
2 = l1-scaled block Gauss-Seidel/SSOR
|
||||
4 = truncated l1-scaled block Gauss-Seidel/SSOR
|
||||
5 = lumped Jacobi
|
||||
6 = Gauss-Seidel
|
||||
10 = On-processor forward solve for matrix w/ triangular structure
|
||||
16 = Chebyshev
|
||||
1001 = Taubin polynomial smoother
|
||||
1002 = FIR polynomial smoother. */
|
||||
enum Type { Jacobi = 0, l1Jacobi = 1, l1GS = 2, l1GStr = 4, lumpedJacobi = 5,
|
||||
GS = 6, OPFS = 10, Chebyshev = 16, Taubin = 1001, FIR = 1002
|
||||
};
|
||||
/// HYPRE smoother types
|
||||
enum Type
|
||||
{
|
||||
Jacobi = 0, ///< Jacobi
|
||||
l1Jacobi = 1, ///< l1-scaled Jacobi
|
||||
l1GS = 2, ///< l1-scaled block Gauss-Seidel/SSOR
|
||||
l1GStr = 4, ///< truncated l1-scaled block Gauss-Seidel/SSOR
|
||||
lumpedJacobi = 5, ///< lumped Jacobi
|
||||
GS = 6, ///< Gauss-Seidel
|
||||
OPFS = 10, /**< On-processor forward solve for matrix w/ triangular
|
||||
structure */
|
||||
Chebyshev = 16, ///< Chebyshev
|
||||
Taubin = 1001, ///< Taubin polynomial smoother
|
||||
FIR = 1002 ///< FIR polynomial smoother
|
||||
};
|
||||
|
||||
/// @deprecated Use DefaultType() instead
|
||||
#if !defined(HYPRE_USING_GPU)
|
||||
static constexpr Type default_type = l1GS;
|
||||
MFEM_DEPRECATED static constexpr Type default_type = l1GS;
|
||||
#else
|
||||
static constexpr Type default_type = l1Jacobi;
|
||||
MFEM_DEPRECATED static constexpr Type default_type = l1Jacobi;
|
||||
#endif
|
||||
|
||||
/** @brief Default value for the smoother type used by the constructors:
|
||||
Type::l1GS when HYPRE is running on CPU and Type::l1Jacobi when HYPRE is
|
||||
running on GPU. */
|
||||
static Type DefaultType()
|
||||
{
|
||||
return HypreUsingGPU() ? l1Jacobi : l1GS;
|
||||
}
|
||||
|
||||
HypreSmoother();
|
||||
|
||||
HypreSmoother(const HypreParMatrix &A_, int type = default_type,
|
||||
HypreSmoother(const HypreParMatrix &A_, int type = DefaultType(),
|
||||
int relax_times = 1, real_t relax_weight = 1.0,
|
||||
real_t omega = 1.0, int poly_order = 2,
|
||||
real_t poly_fraction = .3, int eig_est_cg_iter = 10);
|
||||
@@ -1474,13 +1523,54 @@ public:
|
||||
|
||||
virtual void SetOperator(const Operator &op);
|
||||
|
||||
void SetParams(real_t threshold, int max_levels);
|
||||
/// Set the threshold and levels parameters
|
||||
/** The accuracy and cost of ParaSails are parametrized by the real
|
||||
* @a thresh and integer @a nlevels parameters (0<=thresh<=1, 0<=nlevels).
|
||||
* Lower values of @a thresh and higher values of @a nlevels lead to
|
||||
* more accurate, but more expensive preconditioners. More accurate
|
||||
* preconditioners are also more expensive per iteration. The default
|
||||
* values are @a thresh = 0.1 and @a nlevels = 1.
|
||||
*/
|
||||
void SetParams(real_t thresh, int nlevels);
|
||||
|
||||
/// Set the filter parameter
|
||||
/** The filter parameter is used to drop small nonzeros in the preconditioner,
|
||||
* to reduce the cost of applying the preconditioner. Values from 0.055
|
||||
* to 0.1 are recommended. The default value is 0.1.
|
||||
*/
|
||||
void SetFilter(real_t filter);
|
||||
void SetLoadBal(real_t loadbal);
|
||||
void SetReuse(int reuse);
|
||||
void SetLogging(int logging);
|
||||
|
||||
/// Set symmetry parameter
|
||||
/** The recognized options are:
|
||||
* 0 = nonsymmetric and/or indefinite problem, and nonsymmetric preconditioner
|
||||
* 1 = SPD problem, and SPD (factored) preconditioner
|
||||
* 2 = nonsymmetric, definite problem, and SPD (factored) preconditioner
|
||||
*/
|
||||
void SetSymmetry(int sym);
|
||||
|
||||
/// Set the load balance parameter
|
||||
/** A zero value indicates that no load balance is attempted; a value
|
||||
* of unity indicates that perfect load balance will be attempted. The
|
||||
* recommended value is 0.9 to balance the overhead of data exchanges
|
||||
* for load balancing. No load balancing is needed if the preconditioner
|
||||
* is very sparse and fast to construct. The default value is 0.
|
||||
*/
|
||||
void SetLoadBal(real_t loadbal);
|
||||
|
||||
/// Set the pattern reuse parameter
|
||||
/** A nonzero value indicates that the pattern of the preconditioner
|
||||
* should be reused for subsequent constructions of the proconditioner.
|
||||
* A zero value inicates that the peconditioner should be constructed
|
||||
* from scratch. The default value is 0.
|
||||
*/
|
||||
void SetReuse(int reuse);
|
||||
|
||||
/// Set the logging parameter
|
||||
/** A nonzero value prints statistics of the setup procedure to stdout.
|
||||
* The default value of this parameter is 1.
|
||||
*/
|
||||
void SetLogging(int logging);
|
||||
|
||||
/// The typecast to HYPRE_Solver returns the internal sai_precond
|
||||
virtual operator HYPRE_Solver() const { return sai_precond; }
|
||||
|
||||
|
||||
@@ -16,11 +16,10 @@
|
||||
|
||||
#ifdef MFEM_USE_MPI
|
||||
|
||||
// Enable internal hypre timing routines
|
||||
#define HYPRE_TIMING
|
||||
|
||||
#include "../general/mem_manager.hpp"
|
||||
#include "_hypre_parcsr_mv.h"
|
||||
|
||||
// hypre header files
|
||||
#include <_hypre_parcsr_mv.h>
|
||||
|
||||
// Older hypre versions do not define HYPRE_BigInt and HYPRE_MPI_BIG_INT, so we
|
||||
// define them here for backward compatibility.
|
||||
@@ -46,10 +45,10 @@ typedef HYPRE_Int HYPRE_BigInt;
|
||||
#else // MFEM_HYPRE_VERSION >= 21400
|
||||
|
||||
#define mfem_hypre_TAlloc(type, size) \
|
||||
hypre_TAlloc(type, size, HYPRE_MEMORY_DEVICE)
|
||||
hypre_TAlloc(type, size, mfem::GetHypreMemoryLocation())
|
||||
#define mfem_hypre_CTAlloc(type, size) \
|
||||
hypre_CTAlloc(type, size, HYPRE_MEMORY_DEVICE)
|
||||
#define mfem_hypre_TFree(ptr) hypre_TFree(ptr, HYPRE_MEMORY_DEVICE)
|
||||
hypre_CTAlloc(type, size, mfem::GetHypreMemoryLocation())
|
||||
#define mfem_hypre_TFree(ptr) hypre_TFree(ptr, mfem::GetHypreMemoryLocation())
|
||||
|
||||
#define mfem_hypre_TAlloc_host(type, size) \
|
||||
hypre_TAlloc(type, size, HYPRE_MEMORY_HOST)
|
||||
|
||||
+130
-52
@@ -309,18 +309,51 @@ public:
|
||||
|
||||
|
||||
/// Base abstract class for first order time dependent operators.
|
||||
/** Operator of the form: (x,t) -> f(x,t), where k = f(x,t) generally solves the
|
||||
algebraic equation F(x,k,t) = G(x,t). The functions F and G represent the
|
||||
_implicit_ and _explicit_ parts of the operator, respectively. For explicit
|
||||
operators, F(x,k,t) = k, so f(x,t) = G(x,t). */
|
||||
/** Operator of the form: (u,t) -> k(u,t), where k generally solves the
|
||||
algebraic equation F(u,k,t) = G(u,t). The functions F and G represent the
|
||||
_implicit_ and _explicit_ parts of the operator, respectively.
|
||||
|
||||
A common use for this class is representing a differential algebraic
|
||||
equation of the form $ F(y,\frac{dy}{dt},t) = G(y,t) $.
|
||||
|
||||
For example, consider an ordinary differential equation of the form
|
||||
$ M \frac{dy}{dt} = g(y,t) $. There are various ways of expressing this ODE
|
||||
as a TimeDependentOperator depending on the choices for F and G. Here are
|
||||
some common choices:
|
||||
|
||||
1. F(u,k,t) = k and G(u,t) = inv(M) g(u,t),
|
||||
2. F(u,k,t) = M k and G(u,t) = g(u,t),
|
||||
3. F(u,k,t) = M k - g(u,t) and G(u,t) = 0.
|
||||
|
||||
Note that depending on the ODE solver, some of the above choices may be
|
||||
preferable to the others.
|
||||
*/
|
||||
class TimeDependentOperator : public Operator
|
||||
{
|
||||
public:
|
||||
/// Enum used to describe the form of the time-dependent operator.
|
||||
/** The type should be set by classes derived from TimeDependentOperator to
|
||||
describe the form, in terms of the functions F and G, used by the
|
||||
specific derived class. This information can be queried by classes or
|
||||
functions (like time stepping algorithms) to make choices about the
|
||||
algorithm to use, or to ensure that the TimeDependentOperator uses the
|
||||
form expected by the class/function.
|
||||
|
||||
For example, assume that a derived class is implementing the ODE
|
||||
$M \frac{dy}{dt} = g(y,t)$ and chooses to define $F(u,k,t) = M k$ and
|
||||
$G(u,t) = g(u,t)$. Then it cannot use type EXPLICIT, unless $M = I$, or
|
||||
type HOMOGENEOUS, unless $g(u,t) = 0$. If, on the other hand, the derived
|
||||
class chooses to define $F(u,k,t) = k$ and $G(u,t) = M^{-1} g(y,t)$, then
|
||||
the natural choice is to set the type to EXPLICIT, even though setting it
|
||||
to IMPLICIT is also not wrong -- doing so will simply fail to inform
|
||||
methods that query this information that it uses a more specific
|
||||
implementation, EXPLICIT, that may allow the use of algorithms that
|
||||
support only the EXPLICIT type. */
|
||||
enum Type
|
||||
{
|
||||
EXPLICIT, ///< This type assumes F(x,k,t) = k, i.e. k = f(x,t) = G(x,t).
|
||||
EXPLICIT, ///< This type assumes F(u,k,t) = k.
|
||||
IMPLICIT, ///< This is the most general type, no assumptions on F and G.
|
||||
HOMOGENEOUS ///< This type assumes that G(x,t) = 0.
|
||||
HOMOGENEOUS ///< This type assumes that G(u,t) = 0.
|
||||
};
|
||||
|
||||
/// Evaluation mode. See SetEvalMode() for details.
|
||||
@@ -328,29 +361,30 @@ public:
|
||||
{
|
||||
/** Normal evaluation. */
|
||||
NORMAL,
|
||||
/** Assuming additive split, f(x,t) = f1(x,t) + f2(x,t), evaluate the
|
||||
first term, f1. */
|
||||
/** Assuming additive split, k(u,t) = k1(u,t) + k2(u,t), evaluate the
|
||||
first term, k1. */
|
||||
ADDITIVE_TERM_1,
|
||||
/** Assuming additive split, f(x,t) = f1(x,t) + f2(x,t), evaluate the
|
||||
second term, f2. */
|
||||
/** Assuming additive split, k(u,t) = k1(u,t) + k2(u,t), evaluate the
|
||||
second term, k2. */
|
||||
ADDITIVE_TERM_2
|
||||
};
|
||||
|
||||
protected:
|
||||
real_t t; ///< Current time.
|
||||
Type type; ///< Describes the form of the TimeDependentOperator.
|
||||
Type type; /**< @brief Describes the form of the TimeDependentOperator, see
|
||||
the documentation of #Type. */
|
||||
EvalMode eval_mode; ///< Current evaluation mode.
|
||||
|
||||
public:
|
||||
/** @brief Construct a "square" TimeDependentOperator y = f(x,t), where x and
|
||||
y have the same dimension @a n. */
|
||||
/** @brief Construct a "square" TimeDependentOperator (u,t) -> k(u,t), where
|
||||
u and k have the same dimension @a n. */
|
||||
explicit TimeDependentOperator(int n = 0, real_t t_ = 0.0,
|
||||
Type type_ = EXPLICIT)
|
||||
: Operator(n) { t = t_; type = type_; eval_mode = NORMAL; }
|
||||
|
||||
/** @brief Construct a TimeDependentOperator y = f(x,t), where x and y have
|
||||
dimensions @a w and @a h, respectively. */
|
||||
TimeDependentOperator(int h, int w, real_t t_ = 0.0, Type type_ = EXPLICIT)
|
||||
/** @brief Construct a TimeDependentOperator (u,t) -> k(u,t), where u and k
|
||||
have dimensions @a w and @a h, respectively. */
|
||||
TimeDependentOperator(int h, int w, double t_ = 0.0, Type type_ = EXPLICIT)
|
||||
: Operator(h, w) { t = t_; type = type_; eval_mode = NORMAL; }
|
||||
|
||||
/// Read the currently set time.
|
||||
@@ -373,7 +407,7 @@ public:
|
||||
/** The evaluation mode is a switch that allows time-stepping methods to
|
||||
request evaluation of separate components/terms of the time-dependent
|
||||
operator. For example, IMEX methods typically assume additive split of
|
||||
the operator: f(x,t) = f1(x,t) + f2(x,t) and they rely on the ability to
|
||||
the operator: k(u,t) = k1(u,t) + k2(u,t) and they rely on the ability to
|
||||
evaluate the two terms separately.
|
||||
|
||||
Generally, setting the evaluation mode should affect the behavior of all
|
||||
@@ -384,62 +418,104 @@ public:
|
||||
{ eval_mode = new_eval_mode; }
|
||||
|
||||
/** @brief Perform the action of the explicit part of the operator, G:
|
||||
@a y = G(@a x, t) where t is the current time.
|
||||
@a v = G(@a u, t) where t is the current time.
|
||||
|
||||
Presently, this method is used by some PETSc ODE solvers, for more
|
||||
details, see the PETSc Manual. */
|
||||
virtual void ExplicitMult(const Vector &x, Vector &y) const;
|
||||
virtual void ExplicitMult(const Vector &u, Vector &v) const;
|
||||
|
||||
/** @brief Perform the action of the implicit part of the operator, F:
|
||||
@a y = F(@a x, @a k, t) where t is the current time.
|
||||
@a v = F(@a u, @a k, t) where t is the current time.
|
||||
|
||||
Presently, this method is used by some PETSc ODE solvers, for more
|
||||
details, see the PETSc Manual.*/
|
||||
virtual void ImplicitMult(const Vector &x, const Vector &k, Vector &y) const;
|
||||
virtual void ImplicitMult(const Vector &u, const Vector &k, Vector &v) const;
|
||||
|
||||
/** @brief Perform the action of the operator: @a y = k = f(@a x, t), where
|
||||
k solves the algebraic equation F(@a x, k, t) = G(@a x, t) and t is the
|
||||
current time. */
|
||||
virtual void Mult(const Vector &x, Vector &y) const;
|
||||
/** @brief Perform the action of the operator (u,t) -> k(u,t) where t is the
|
||||
current time set by SetTime() and @a k satisfies
|
||||
F(@a u, @a k, t) = G(@a u, t).
|
||||
|
||||
/** @brief Solve the equation: @a k = f(@a x + @a dt @a k, t), for the
|
||||
unknown @a k at the current time t.
|
||||
For solving an ordinary differential equation of the form
|
||||
$ M \frac{dy}{dt} = g(y,t) $, recall that F and G can be defined in
|
||||
various ways, e.g.:
|
||||
|
||||
For general F and G, the equation for @a k becomes:
|
||||
F(@a x + @a dt @a k, @a k, t) = G(@a x + @a dt @a k, t).
|
||||
1. F(u,k,t) = k and G(u,t) = inv(M) g(u,t)
|
||||
2. F(u,k,t) = M k and G(u,t) = g(u,t)
|
||||
3. F(u,k,t) = M k - g(u,t) and G(u,t) = 0.
|
||||
|
||||
The input vector @a x corresponds to time index (or cycle) n, while the
|
||||
currently set time, #t, and the result vector @a k correspond to time
|
||||
index n+1. The time step @a dt corresponds to the time interval between
|
||||
cycles n and n+1.
|
||||
Regardless of the choice of F and G, this function should always compute
|
||||
@a k = inv(M) g(@a u, t). */
|
||||
virtual void Mult(const Vector &u, Vector &v) const override;
|
||||
|
||||
This method allows for the abstract implementation of some time
|
||||
integration methods, including diagonal implicit Runge-Kutta (DIRK)
|
||||
methods and the backward Euler method in particular.
|
||||
/** @brief Solve for the unknown @a k, at the current time t, the following
|
||||
equation:
|
||||
F(@a u + @a gamma @a k, @a k, t) = G(@a u + @a gamma @a k, t).
|
||||
|
||||
For solving an ordinary differential equation of the form
|
||||
$ M \frac{dy}{dt} = g(y,t) $, recall that F and G can be defined in
|
||||
various ways, e.g.:
|
||||
|
||||
1. F(u,k,t) = k and G(u,t) = inv(M) g(u,t)
|
||||
2. F(u,k,t) = M k and G(u,t) = g(u,t)
|
||||
3. F(u,k,t) = M k - g(u,t) and G(u,t) = 0
|
||||
|
||||
Regardless of the choice of F and G, this function should solve for @a k
|
||||
in M @a k = g(@a u + @a gamma @a k, t).
|
||||
|
||||
To see how @a k can be useful, consider the backward Euler method defined
|
||||
by $ y(t + \Delta t) = y(t) + \Delta t k_0 $ where
|
||||
$ M k_0 = g \big( y(t) + \Delta t k_0, t + \Delta t \big) $. A backward
|
||||
Euler integrator can use @a k from this function for $k_0$, with the call
|
||||
using @a u set to $ y(t) $, @a gamma set to $ \Delta t$, and time set to
|
||||
$t + \Delta t$. See class BackwardEulerSolver.
|
||||
|
||||
Generalizing further, consider a diagonally implicit Runge-Kutta (DIRK)
|
||||
method defined by
|
||||
$ y(t + \Delta t) = y(t) + \Delta t \sum_{i=1}^s b_i k_i $ where
|
||||
$ M k_i = g \big( y(t) + \Delta t \sum_{j=1}^i a_{ij} k_j,
|
||||
t + c_i \Delta t \big) $.
|
||||
A DIRK integrator can use @a k from this function, with @a u set to
|
||||
$ y(t) + \Delta t \sum_{j=1}^{i-1} a_{ij} k_j $ and @a gamma set to
|
||||
$ a_{ii} \Delta t $, for $ k_i $. For example, see class SDIRK33Solver.
|
||||
|
||||
If not re-implemented, this method simply generates an error. */
|
||||
virtual void ImplicitSolve(const real_t dt, const Vector &x, Vector &k);
|
||||
virtual void ImplicitSolve(const real_t gamma, const Vector &u, Vector &k);
|
||||
|
||||
/** @brief Return an Operator representing (dF/dk @a shift + dF/dx) at the
|
||||
given @a x, @a k, and the currently set time.
|
||||
/** @brief Return an Operator representing (dF/dk @a shift + dF/du) at the
|
||||
given @a u, @a k, and the currently set time.
|
||||
|
||||
Presently, this method is used by some PETSc ODE solvers, for more
|
||||
details, see the PETSc Manual. */
|
||||
virtual Operator& GetImplicitGradient(const Vector &x, const Vector &k,
|
||||
virtual Operator& GetImplicitGradient(const Vector &u, const Vector &k,
|
||||
real_t shift) const;
|
||||
|
||||
/** @brief Return an Operator representing dG/dx at the given point @a x and
|
||||
/** @brief Return an Operator representing dG/du at the given point @a u and
|
||||
the currently set time.
|
||||
|
||||
Presently, this method is used by some PETSc ODE solvers, for more
|
||||
details, see the PETSc Manual. */
|
||||
virtual Operator& GetExplicitGradient(const Vector &x) const;
|
||||
virtual Operator& GetExplicitGradient(const Vector &u) const;
|
||||
|
||||
/** @brief Setup the ODE linear system $ A(x,t) = (I - gamma J) $ or
|
||||
$ A = (M - gamma J) $, where $ J(x,t) = \frac{df}{dt(x,t)} $.
|
||||
/** @brief Setup a linear system as needed by some SUNDIALS ODE solvers.
|
||||
|
||||
@param[in] x The state at which $A(x,t)$ should be evaluated.
|
||||
@param[in] fx The current value of the ODE rhs function, $f(x,t)$.
|
||||
For solving an ordinary differential equation of the form
|
||||
$ M \frac{dy}{dt} = g(y,t) $, recall that F and G can be defined as one
|
||||
of the following:
|
||||
|
||||
1. F(u,k,t) = k and G(u,t) = inv(M) g(u,t)
|
||||
2. F(u,k,t) = M k and G(u,t) = g(u,t)
|
||||
3. F(u,k,t) = M k - g(u,t) and G(u,t) = 0
|
||||
|
||||
This function performs setup to solve $ A x = b $ where A is either
|
||||
|
||||
1. A(@a y,t) = I - @a gamma inv(M) J(@a y,t)
|
||||
2. A(@a y,t) = M - @a gamma J(@a y,t)
|
||||
3. A(@a y,t) = M - @a gamma J(@a y,t)
|
||||
|
||||
with J = dg/dy (or a reasonable approximation thereof).
|
||||
|
||||
@param[in] y The state at which A(@a y,t) should be evaluated.
|
||||
@param[in] v The value of inv(M) g(y,t) for 1 or g(y,t) for 2 & 3.
|
||||
@param[in] jok Flag indicating if the Jacobian should be updated.
|
||||
@param[out] jcur Flag to signal if the Jacobian was updated.
|
||||
@param[in] gamma The scaled time step value.
|
||||
@@ -448,10 +524,10 @@ public:
|
||||
|
||||
Presently, this method is used by SUNDIALS ODE solvers, for more
|
||||
details, see the SUNDIALS User Guides. */
|
||||
virtual int SUNImplicitSetup(const Vector &x, const Vector &fx,
|
||||
virtual int SUNImplicitSetup(const Vector &y, const Vector &v,
|
||||
int jok, int *jcur, real_t gamma);
|
||||
|
||||
/** @brief Solve the ODE linear system $ A x = b $ as setup by
|
||||
/** @brief Solve the ODE linear system A @a x = @a b, where A is defined by
|
||||
the method SUNImplicitSetup().
|
||||
|
||||
@param[in] b The linear system right-hand side.
|
||||
@@ -464,7 +540,8 @@ public:
|
||||
details, see the SUNDIALS User Guides. */
|
||||
virtual int SUNImplicitSolve(const Vector &b, Vector &x, real_t tol);
|
||||
|
||||
/** @brief Setup the mass matrix in the ODE system $ M y' = f(y,t) $ .
|
||||
/** @brief Setup the mass matrix in the ODE system
|
||||
$ M \frac{dy}{dt} = g(y,t) $ .
|
||||
|
||||
If not re-implemented, this method simply generates an error.
|
||||
|
||||
@@ -472,8 +549,8 @@ public:
|
||||
details, see the ARKode User Guide. */
|
||||
virtual int SUNMassSetup();
|
||||
|
||||
/** @brief Solve the mass matrix linear system $ M x = b $
|
||||
as setup by the method SUNMassSetup().
|
||||
/** @brief Solve the mass matrix linear system M @a x = @a b, where M is
|
||||
defined by the method SUNMassSetup().
|
||||
|
||||
@param[in] b The linear system right-hand side.
|
||||
@param[in,out] x On input, the initial guess. On output, the solution.
|
||||
@@ -485,7 +562,8 @@ public:
|
||||
details, see the ARKode User Guide. */
|
||||
virtual int SUNMassSolve(const Vector &b, Vector &x, real_t tol);
|
||||
|
||||
/** @brief Compute the mass matrix-vector product $ v = M x $ .
|
||||
/** @brief Compute the mass matrix-vector product @a v = M @a x, where M is
|
||||
defined by the method SUNMassSetup().
|
||||
|
||||
@param[in] x The vector to multiply.
|
||||
@param[out] v The result of the matrix-vector product.
|
||||
|
||||
+6
-4
@@ -1188,6 +1188,8 @@ void FGMRESSolver::Mult(const Vector &b, Vector &x) const
|
||||
|
||||
final_norm = std::max(rel_tol*beta, abs_tol);
|
||||
|
||||
converged = false;
|
||||
|
||||
if (beta <= final_norm)
|
||||
{
|
||||
final_norm = beta;
|
||||
@@ -1303,8 +1305,6 @@ void FGMRESSolver::Mult(const Vector &b, Vector &x) const
|
||||
MFEM_ASSERT(IsFinite(beta), "beta = " << beta);
|
||||
if (beta <= final_norm)
|
||||
{
|
||||
final_norm = beta;
|
||||
final_iter = j;
|
||||
converged = true;
|
||||
|
||||
break;
|
||||
@@ -1317,7 +1317,9 @@ void FGMRESSolver::Mult(const Vector &b, Vector &x) const
|
||||
if (v[i]) { delete v[i]; }
|
||||
if (z[i]) { delete z[i]; }
|
||||
}
|
||||
converged = false;
|
||||
|
||||
final_norm = beta;
|
||||
final_iter = converged ? j : max_iter;
|
||||
|
||||
// Note: j is off by one when we arrive here
|
||||
if (!print_options.iterations && print_options.first_and_last)
|
||||
@@ -1328,7 +1330,7 @@ void FGMRESSolver::Mult(const Vector &b, Vector &x) const
|
||||
}
|
||||
if (print_options.summary || (print_options.warnings && !converged))
|
||||
{
|
||||
mfem::out << "FGMRES: Number of iterations: " << j-1 << '\n';
|
||||
mfem::out << "FGMRES: Number of iterations: " << final_iter << '\n';
|
||||
}
|
||||
if (print_options.warnings && !converged)
|
||||
{
|
||||
|
||||
+14
-5
@@ -58,6 +58,20 @@ DenseSymmetricMatrix &DenseSymmetricMatrix::operator=(real_t c)
|
||||
return *this;
|
||||
}
|
||||
|
||||
DenseSymmetricMatrix &DenseSymmetricMatrix::operator=(const DenseSymmetricMatrix
|
||||
&m)
|
||||
{
|
||||
SetSize(m.height);
|
||||
|
||||
const int hw = m.GetStoredSize();
|
||||
for (int i = 0; i < hw; i++)
|
||||
{
|
||||
data[i] = m.data[i];
|
||||
}
|
||||
|
||||
return *this;
|
||||
}
|
||||
|
||||
real_t &DenseSymmetricMatrix::Elem(int i, int j)
|
||||
{
|
||||
return (*this)(i,j);
|
||||
@@ -89,11 +103,6 @@ MatrixInverse *DenseSymmetricMatrix::Inverse() const
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
void DenseSymmetricMatrix::Print (std::ostream & os, int width_) const
|
||||
{
|
||||
mfem_error("DenseSymmetricMatrix::Print() not implemented!");
|
||||
}
|
||||
|
||||
DenseSymmetricMatrix::~DenseSymmetricMatrix()
|
||||
{
|
||||
data.Delete();
|
||||
|
||||
+3
-3
@@ -102,6 +102,9 @@ public:
|
||||
|
||||
DenseSymmetricMatrix &operator*=(real_t c);
|
||||
|
||||
/// Sets the matrix size and elements equal to those of m
|
||||
DenseSymmetricMatrix &operator=(const DenseSymmetricMatrix &m);
|
||||
|
||||
std::size_t MemoryUsage() const { return data.Capacity() * sizeof(real_t); }
|
||||
|
||||
/// Shortcut for mfem::Read( GetMemory(), TotalSize(), on_dev).
|
||||
@@ -134,9 +137,6 @@ public:
|
||||
/// Returns a pointer to (an approximation) of the matrix inverse.
|
||||
virtual MatrixInverse *Inverse() const;
|
||||
|
||||
/// Prints matrix to stream out.
|
||||
virtual void Print (std::ostream & out = mfem::out, int width_ = 4) const;
|
||||
|
||||
/// Destroys the symmetric matrix.
|
||||
virtual ~DenseSymmetricMatrix();
|
||||
};
|
||||
|
||||
+1
-7
@@ -716,13 +716,7 @@ inline real_t InnerProduct(MPI_Comm comm, const Vector &x, const Vector &y)
|
||||
{
|
||||
real_t loc_prod = x * y;
|
||||
real_t glb_prod;
|
||||
#ifdef MFEM_USE_SINGLE
|
||||
MPI_Allreduce(&loc_prod, &glb_prod, 1, MPI_FLOAT, MPI_SUM, comm);
|
||||
#elif defined MFEM_USE_DOUBLE
|
||||
MPI_Allreduce(&loc_prod, &glb_prod, 1, MPI_DOUBLE, MPI_SUM, comm);
|
||||
#else
|
||||
MFEM_ABORT("Floating point type undefined");
|
||||
#endif
|
||||
MPI_Allreduce(&loc_prod, &glb_prod, 1, MFEM_MPI_REAL_T, MPI_SUM, comm);
|
||||
return glb_prod;
|
||||
}
|
||||
#endif
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
# CONTRIBUTING.md for details.
|
||||
|
||||
# The current MFEM version as an integer, see also `CMakeLists.txt`.
|
||||
MFEM_VERSION = 40601
|
||||
MFEM_VERSION = 40701
|
||||
MFEM_VERSION_STRING = $(shell printf "%06d" $(MFEM_VERSION) | \
|
||||
sed -e 's/^0*\(.*.\)\(..\)\(..\)$$/\1.\2.\3/' -e 's/\.0/./g' -e 's/\.0$$//')
|
||||
|
||||
@@ -205,6 +205,14 @@ MFEM_SHARED_BUILD = $(MFEM_SHARED)
|
||||
override static = $(if $(MFEM_STATIC:YES=),,YES)
|
||||
override shared = $(if $(MFEM_SHARED:YES=),,YES)
|
||||
|
||||
# Error for package integrations that currently don't support single precision
|
||||
ifeq ($(MFEM_USE_SINGLE),YES)
|
||||
PKGS_NO_SINGLE = SUNDIALS SUITESPARSE SUPERLU STRUMPACK GINKGO AMGX SLEPC\
|
||||
PUMI GSLIB ALGOIM CEED MOONOLITH TRIBOL
|
||||
$(foreach pkg,$(PKGS_NO_SINGLE),$(if $(MFEM_USE_$(pkg):NO=),\
|
||||
$(error Package $(pkg) is NOT supported with single precision)))
|
||||
endif
|
||||
|
||||
# The default value of CXXFLAGS is based on the value of MFEM_DEBUG
|
||||
ifeq ($(MFEM_DEBUG),YES)
|
||||
CXXFLAGS ?= $(DEBUG_FLAGS)
|
||||
|
||||
+884
-3
@@ -20,9 +20,10 @@
|
||||
#include "../general/tic_toc.hpp"
|
||||
#include "../general/gecko.hpp"
|
||||
#include "../general/kdtree.hpp"
|
||||
#include "../general/sets.hpp"
|
||||
#include "../fem/quadinterpolator.hpp"
|
||||
|
||||
#include <iostream>
|
||||
// headers already included by mesh.hpp: <iostream>, <array>, <map>, <memory>
|
||||
#include <sstream>
|
||||
#include <fstream>
|
||||
#include <limits>
|
||||
@@ -1338,7 +1339,7 @@ Mesh::FaceInformation::operator Mesh::FaceInfo() const
|
||||
return res;
|
||||
}
|
||||
|
||||
std::ostream& operator<<(std::ostream& os, const Mesh::FaceInformation& info)
|
||||
std::ostream &operator<<(std::ostream &os, const Mesh::FaceInformation& info)
|
||||
{
|
||||
os << "face topology=";
|
||||
switch (info.topology)
|
||||
@@ -6209,6 +6210,12 @@ const FiniteElementSpace *Mesh::GetNodalFESpace() const
|
||||
|
||||
void Mesh::SetCurvature(int order, bool discont, int space_dim, int ordering)
|
||||
{
|
||||
if (order <= 0)
|
||||
{
|
||||
delete Nodes;
|
||||
Nodes = nullptr;
|
||||
return;
|
||||
}
|
||||
space_dim = (space_dim == -1) ? spaceDim : space_dim;
|
||||
FiniteElementCollection* nfec;
|
||||
if (discont)
|
||||
@@ -11419,7 +11426,8 @@ void Mesh::Printer(std::ostream &os, std::string section_delimiter,
|
||||
|
||||
if (!section_delimiter.empty())
|
||||
{
|
||||
os << section_delimiter << endl; // only with formats v1.2 and above
|
||||
os << '\n'
|
||||
<< section_delimiter << endl; // only with formats v1.2 and above
|
||||
}
|
||||
}
|
||||
|
||||
@@ -13299,6 +13307,879 @@ void Mesh::GetGeometricParametersFromJacobian(const DenseMatrix &J,
|
||||
}
|
||||
|
||||
|
||||
MeshPart::EntityHelper::EntityHelper(
|
||||
int dim_, const Array<int> (&entity_to_vertex_)[Geometry::NumGeom])
|
||||
: dim(dim_),
|
||||
entity_to_vertex(entity_to_vertex_)
|
||||
{
|
||||
int geom_offset = 0;
|
||||
for (int g = Geometry::DimStart[dim]; g < Geometry::DimStart[dim+1]; g++)
|
||||
{
|
||||
geom_offsets[g] = geom_offset;
|
||||
geom_offset += entity_to_vertex[g].Size()/Geometry::NumVerts[g];
|
||||
}
|
||||
geom_offsets[Geometry::DimStart[dim+1]] = geom_offset;
|
||||
num_entities = geom_offset;
|
||||
}
|
||||
|
||||
MeshPart::Entity MeshPart::EntityHelper::FindEntity(int bytype_entity_id)
|
||||
{
|
||||
// Find the 'geom' that corresponds to 'bytype_entity_id'
|
||||
int geom = Geometry::DimStart[dim];
|
||||
while (geom_offsets[geom+1] <= bytype_entity_id) { geom++; }
|
||||
MFEM_ASSERT(geom < Geometry::NumGeom, "internal error");
|
||||
MFEM_ASSERT(Geometry::Dimension[geom] == dim, "internal error");
|
||||
const int nv = Geometry::NumVerts[geom];
|
||||
const int geom_elem_id = bytype_entity_id - geom_offsets[geom];
|
||||
const int *v = &entity_to_vertex[geom][nv*geom_elem_id];
|
||||
return { geom, nv, v };
|
||||
}
|
||||
|
||||
void MeshPart::Print(std::ostream &os) const
|
||||
{
|
||||
os << "MFEM mesh v1.2\n";
|
||||
|
||||
// optional
|
||||
os <<
|
||||
"\n#\n# MFEM Geometry Types (see mesh/geom.hpp):\n#\n"
|
||||
"# POINT = 0\n"
|
||||
"# SEGMENT = 1\n"
|
||||
"# TRIANGLE = 2\n"
|
||||
"# SQUARE = 3\n"
|
||||
"# TETRAHEDRON = 4\n"
|
||||
"# CUBE = 5\n"
|
||||
"# PRISM = 6\n"
|
||||
"# PYRAMID = 7\n"
|
||||
"#\n";
|
||||
|
||||
const int dim = dimension;
|
||||
os << "\ndimension\n" << dim;
|
||||
|
||||
os << "\n\nelements\n" << num_elements << '\n';
|
||||
{
|
||||
const bool have_element_map = (element_map.Size() == num_elements);
|
||||
MFEM_ASSERT(have_element_map || element_map.Size() == 0,
|
||||
"invalid MeshPart state");
|
||||
EntityHelper elem_helper(dim, entity_to_vertex);
|
||||
MFEM_ASSERT(elem_helper.num_entities == num_elements,
|
||||
"invalid MeshPart state");
|
||||
for (int nat_elem_id = 0; nat_elem_id < num_elements; nat_elem_id++)
|
||||
{
|
||||
const int bytype_elem_id = have_element_map ?
|
||||
element_map[nat_elem_id] : nat_elem_id;
|
||||
const Entity ent = elem_helper.FindEntity(bytype_elem_id);
|
||||
// Print the element
|
||||
os << attributes[nat_elem_id] << ' ' << ent.geom;
|
||||
for (int i = 0; i < ent.num_verts; i++)
|
||||
{
|
||||
os << ' ' << ent.verts[i];
|
||||
}
|
||||
os << '\n';
|
||||
}
|
||||
}
|
||||
|
||||
os << "\nboundary\n" << num_bdr_elements << '\n';
|
||||
{
|
||||
const bool have_boundary_map = (boundary_map.Size() == num_bdr_elements);
|
||||
MFEM_ASSERT(have_boundary_map || boundary_map.Size() == 0,
|
||||
"invalid MeshPart state");
|
||||
EntityHelper bdr_helper(dim-1, entity_to_vertex);
|
||||
MFEM_ASSERT(bdr_helper.num_entities == num_bdr_elements,
|
||||
"invalid MeshPart state");
|
||||
for (int nat_bdr_id = 0; nat_bdr_id < num_bdr_elements; nat_bdr_id++)
|
||||
{
|
||||
const int bytype_bdr_id = have_boundary_map ?
|
||||
boundary_map[nat_bdr_id] : nat_bdr_id;
|
||||
const Entity ent = bdr_helper.FindEntity(bytype_bdr_id);
|
||||
// Print the boundary element
|
||||
os << bdr_attributes[nat_bdr_id] << ' ' << ent.geom;
|
||||
for (int i = 0; i < ent.num_verts; i++)
|
||||
{
|
||||
os << ' ' << ent.verts[i];
|
||||
}
|
||||
os << '\n';
|
||||
}
|
||||
}
|
||||
|
||||
os << "\nvertices\n" << num_vertices << '\n';
|
||||
if (!nodes)
|
||||
{
|
||||
const int sdim = space_dimension;
|
||||
os << sdim << '\n';
|
||||
for (int i = 0; i < num_vertices; i++)
|
||||
{
|
||||
os << vertex_coordinates[i*sdim];
|
||||
for (int d = 1; d < sdim; d++)
|
||||
{
|
||||
os << ' ' << vertex_coordinates[i*sdim+d];
|
||||
}
|
||||
os << '\n';
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
os << "\nnodes\n";
|
||||
nodes->Save(os);
|
||||
}
|
||||
|
||||
os << "\nmfem_serial_mesh_end\n";
|
||||
|
||||
// Start: GroupTopology::Save
|
||||
const int num_groups = my_groups.Size();
|
||||
os << "\ncommunication_groups\n";
|
||||
os << "number_of_groups " << num_groups << "\n\n";
|
||||
|
||||
os << "# number of entities in each group, followed by ranks in group\n";
|
||||
for (int group_id = 0; group_id < num_groups; ++group_id)
|
||||
{
|
||||
const int group_size = my_groups.RowSize(group_id);
|
||||
const int *group_ptr = my_groups.GetRow(group_id);
|
||||
os << group_size;
|
||||
for (int group_member_index = 0; group_member_index < group_size;
|
||||
++group_member_index)
|
||||
{
|
||||
os << ' ' << group_ptr[group_member_index];
|
||||
}
|
||||
os << '\n';
|
||||
}
|
||||
// End: GroupTopology::Save
|
||||
|
||||
const Table &g2v = group_shared_entity_to_vertex[Geometry::POINT];
|
||||
const Table &g2ev = group_shared_entity_to_vertex[Geometry::SEGMENT];
|
||||
const Table &g2tv = group_shared_entity_to_vertex[Geometry::TRIANGLE];
|
||||
const Table &g2qv = group_shared_entity_to_vertex[Geometry::SQUARE];
|
||||
|
||||
MFEM_VERIFY(g2v.RowSize(0) == 0, "internal erroor");
|
||||
os << "\ntotal_shared_vertices " << g2v.Size_of_connections() << '\n';
|
||||
if (dimension >= 2)
|
||||
{
|
||||
MFEM_VERIFY(g2ev.RowSize(0) == 0, "internal erroor");
|
||||
os << "total_shared_edges " << g2ev.Size_of_connections()/2 << '\n';
|
||||
}
|
||||
if (dimension >= 3)
|
||||
{
|
||||
MFEM_VERIFY(g2tv.RowSize(0) == 0, "internal erroor");
|
||||
MFEM_VERIFY(g2qv.RowSize(0) == 0, "internal erroor");
|
||||
const int total_shared_faces =
|
||||
g2tv.Size_of_connections()/3 + g2qv.Size_of_connections()/4;
|
||||
os << "total_shared_faces " << total_shared_faces << '\n';
|
||||
}
|
||||
os << "\n# group 0 has no shared entities\n";
|
||||
for (int gr = 1; gr < num_groups; gr++)
|
||||
{
|
||||
{
|
||||
const int nv = g2v.RowSize(gr);
|
||||
const int *sv = g2v.GetRow(gr);
|
||||
os << "\n# group " << gr << "\nshared_vertices " << nv << '\n';
|
||||
for (int i = 0; i < nv; i++)
|
||||
{
|
||||
os << sv[i] << '\n';
|
||||
}
|
||||
}
|
||||
if (dimension >= 2)
|
||||
{
|
||||
const int ne = g2ev.RowSize(gr)/2;
|
||||
const int *se = g2ev.GetRow(gr);
|
||||
os << "\nshared_edges " << ne << '\n';
|
||||
for (int i = 0; i < ne; i++)
|
||||
{
|
||||
const int *v = se + 2*i;
|
||||
os << v[0] << ' ' << v[1] << '\n';
|
||||
}
|
||||
}
|
||||
if (dimension >= 3)
|
||||
{
|
||||
const int nt = g2tv.RowSize(gr)/3;
|
||||
const int *st = g2tv.GetRow(gr);
|
||||
const int nq = g2qv.RowSize(gr)/4;
|
||||
const int *sq = g2qv.GetRow(gr);
|
||||
os << "\nshared_faces " << nt+nq << '\n';
|
||||
for (int i = 0; i < nt; i++)
|
||||
{
|
||||
os << Geometry::TRIANGLE;
|
||||
const int *v = st + 3*i;
|
||||
for (int j = 0; j < 3; j++) { os << ' ' << v[j]; }
|
||||
os << '\n';
|
||||
}
|
||||
for (int i = 0; i < nq; i++)
|
||||
{
|
||||
os << Geometry::SQUARE;
|
||||
const int *v = sq + 4*i;
|
||||
for (int j = 0; j < 4; j++) { os << ' ' << v[j]; }
|
||||
os << '\n';
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Write out section end tag for mesh.
|
||||
os << "\nmfem_mesh_end" << endl;
|
||||
}
|
||||
|
||||
Mesh &MeshPart::GetMesh()
|
||||
{
|
||||
if (mesh) { return *mesh; }
|
||||
|
||||
mesh.reset(new Mesh(dimension,
|
||||
num_vertices,
|
||||
num_elements,
|
||||
num_bdr_elements,
|
||||
space_dimension));
|
||||
|
||||
// Add elements
|
||||
{
|
||||
const bool have_element_map = (element_map.Size() == num_elements);
|
||||
MFEM_ASSERT(have_element_map || element_map.Size() == 0,
|
||||
"invalid MeshPart state");
|
||||
EntityHelper elem_helper(dimension, entity_to_vertex);
|
||||
MFEM_ASSERT(elem_helper.num_entities == num_elements,
|
||||
"invalid MeshPart state");
|
||||
const bool have_tet_refine_flags = (tet_refine_flags.Size() > 0);
|
||||
for (int nat_elem_id = 0; nat_elem_id < num_elements; nat_elem_id++)
|
||||
{
|
||||
const int bytype_elem_id = have_element_map ?
|
||||
element_map[nat_elem_id] : nat_elem_id;
|
||||
const Entity ent = elem_helper.FindEntity(bytype_elem_id);
|
||||
Element *el = mesh->NewElement(ent.geom);
|
||||
el->SetVertices(ent.verts);
|
||||
el->SetAttribute(attributes[nat_elem_id]);
|
||||
if (ent.geom == Geometry::TETRAHEDRON && have_tet_refine_flags)
|
||||
{
|
||||
constexpr int geom_tet = Geometry::TETRAHEDRON;
|
||||
const int tet_id = (ent.verts - entity_to_vertex[geom_tet])/4;
|
||||
const int ref_flag = tet_refine_flags[tet_id];
|
||||
static_cast<Tetrahedron*>(el)->SetRefinementFlag(ref_flag);
|
||||
}
|
||||
mesh->AddElement(el);
|
||||
}
|
||||
}
|
||||
|
||||
// Add boundary elements
|
||||
{
|
||||
const bool have_boundary_map = (boundary_map.Size() == num_bdr_elements);
|
||||
MFEM_ASSERT(have_boundary_map || boundary_map.Size() == 0,
|
||||
"invalid MeshPart state");
|
||||
EntityHelper bdr_helper(dimension-1, entity_to_vertex);
|
||||
MFEM_ASSERT(bdr_helper.num_entities == num_bdr_elements,
|
||||
"invalid MeshPart state");
|
||||
for (int nat_bdr_id = 0; nat_bdr_id < num_bdr_elements; nat_bdr_id++)
|
||||
{
|
||||
const int bytype_bdr_id = have_boundary_map ?
|
||||
boundary_map[nat_bdr_id] : nat_bdr_id;
|
||||
const Entity ent = bdr_helper.FindEntity(bytype_bdr_id);
|
||||
Element *bdr = mesh->NewElement(ent.geom);
|
||||
bdr->SetVertices(ent.verts);
|
||||
bdr->SetAttribute(bdr_attributes[nat_bdr_id]);
|
||||
mesh->AddBdrElement(bdr);
|
||||
}
|
||||
}
|
||||
|
||||
// Add vertices
|
||||
if (vertex_coordinates.Size() == space_dimension*num_vertices)
|
||||
{
|
||||
MFEM_ASSERT(!nodes, "invalid MeshPart state");
|
||||
for (int vert_id = 0; vert_id < num_vertices; vert_id++)
|
||||
{
|
||||
mesh->AddVertex(vertex_coordinates + space_dimension*vert_id);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
MFEM_ASSERT(vertex_coordinates.Size() == 0, "invalid MeshPart state");
|
||||
for (int vert_id = 0; vert_id < num_vertices; vert_id++)
|
||||
{
|
||||
mesh->AddVertex(0., 0., 0.);
|
||||
}
|
||||
// 'mesh.Nodes' cannot be set here -- they can be set later, if needed
|
||||
}
|
||||
|
||||
mesh->FinalizeTopology(/* generate_bdr: */ false);
|
||||
|
||||
return *mesh;
|
||||
}
|
||||
|
||||
|
||||
MeshPartitioner::MeshPartitioner(Mesh &mesh_,
|
||||
int num_parts_,
|
||||
int *partitioning_,
|
||||
int part_method)
|
||||
: mesh(mesh_)
|
||||
{
|
||||
if (partitioning_)
|
||||
{
|
||||
partitioning.MakeRef(partitioning_, mesh.GetNE(), false);
|
||||
}
|
||||
else
|
||||
{
|
||||
partitioning_ = mesh.GeneratePartitioning(num_parts_, part_method);
|
||||
// Mesh::GeneratePartitioning always uses new[] to allocate the,
|
||||
// partitioning, so we need to tell the memory manager to free it with
|
||||
// delete[] (even if a different host memory type has been selected).
|
||||
const MemoryType mt = MemoryType::HOST;
|
||||
partitioning.MakeRef(partitioning_, mesh.GetNE(), mt, true);
|
||||
}
|
||||
|
||||
Transpose(partitioning, part_to_element, num_parts_);
|
||||
// Note: the element ids in each row of 'part_to_element' are sorted.
|
||||
|
||||
const int dim = mesh.Dimension();
|
||||
if (dim >= 2)
|
||||
{
|
||||
Transpose(mesh.ElementToEdgeTable(), edge_to_element, mesh.GetNEdges());
|
||||
}
|
||||
|
||||
Array<int> boundary_to_part(mesh.GetNBE());
|
||||
// Same logic as in ParMesh::BuildLocalBoundary
|
||||
if (dim >= 3)
|
||||
{
|
||||
for (int i = 0; i < boundary_to_part.Size(); i++)
|
||||
{
|
||||
int face, o, el1, el2;
|
||||
mesh.GetBdrElementFace(i, &face, &o);
|
||||
mesh.GetFaceElements(face, &el1, &el2);
|
||||
boundary_to_part[i] =
|
||||
partitioning[(o % 2 == 0 || el2 < 0) ? el1 : el2];
|
||||
}
|
||||
}
|
||||
else if (dim == 2)
|
||||
{
|
||||
for (int i = 0; i < boundary_to_part.Size(); i++)
|
||||
{
|
||||
int edge = mesh.GetBdrElementFaceIndex(i);
|
||||
int el1 = edge_to_element.GetRow(edge)[0];
|
||||
boundary_to_part[i] = partitioning[el1];
|
||||
}
|
||||
}
|
||||
else if (dim == 1)
|
||||
{
|
||||
for (int i = 0; i < boundary_to_part.Size(); i++)
|
||||
{
|
||||
int vert = mesh.GetBdrElementFaceIndex(i);
|
||||
int el1, el2;
|
||||
mesh.GetFaceElements(vert, &el1, &el2);
|
||||
boundary_to_part[i] = partitioning[el1];
|
||||
}
|
||||
}
|
||||
Transpose(boundary_to_part, part_to_boundary, num_parts_);
|
||||
// Note: the boundary element ids in each row of 'part_to_boundary' are
|
||||
// sorted.
|
||||
boundary_to_part.DeleteAll();
|
||||
|
||||
Table *vert_element = mesh.GetVertexToElementTable(); // we must delete this
|
||||
vertex_to_element.Swap(*vert_element);
|
||||
delete vert_element;
|
||||
}
|
||||
|
||||
void MeshPartitioner::ExtractPart(int part_id, MeshPart &mesh_part) const
|
||||
{
|
||||
const int num_parts = part_to_element.Size();
|
||||
|
||||
MFEM_VERIFY(0 <= part_id && part_id < num_parts,
|
||||
"invalid part_id = " << part_id
|
||||
<< ", num_parts = " << num_parts);
|
||||
|
||||
const int dim = mesh.Dimension();
|
||||
const int sdim = mesh.SpaceDimension();
|
||||
const int num_elems = part_to_element.RowSize(part_id);
|
||||
const int *elem_list = part_to_element.GetRow(part_id); // sorted
|
||||
const int num_bdr_elems = part_to_boundary.RowSize(part_id);
|
||||
const int *bdr_elem_list = part_to_boundary.GetRow(part_id); // sorted
|
||||
|
||||
// Initialize 'mesh_part'
|
||||
mesh_part.dimension = dim;
|
||||
mesh_part.space_dimension = sdim;
|
||||
mesh_part.num_vertices = 0;
|
||||
mesh_part.num_elements = num_elems;
|
||||
mesh_part.num_bdr_elements = num_bdr_elems;
|
||||
for (int g = 0; g < Geometry::NumGeom; g++)
|
||||
{
|
||||
mesh_part.entity_to_vertex[g].SetSize(0); // can reuse Array allocation
|
||||
}
|
||||
mesh_part.tet_refine_flags.SetSize(0);
|
||||
mesh_part.element_map.SetSize(0); // 0 or 'num_elements', if needed
|
||||
mesh_part.boundary_map.SetSize(0); // 0 or 'num_bdr_elements', if needed
|
||||
mesh_part.attributes.SetSize(num_elems);
|
||||
mesh_part.bdr_attributes.SetSize(num_bdr_elems);
|
||||
mesh_part.vertex_coordinates.SetSize(0);
|
||||
|
||||
mesh_part.num_parts = num_parts;
|
||||
mesh_part.my_part_id = part_id;
|
||||
mesh_part.my_groups.Clear();
|
||||
for (int g = 0; g < Geometry::NumGeom; g++)
|
||||
{
|
||||
mesh_part.group_shared_entity_to_vertex[g].Clear();
|
||||
}
|
||||
mesh_part.nodes.reset(nullptr);
|
||||
mesh_part.nodal_fes.reset(nullptr);
|
||||
mesh_part.mesh.reset(nullptr);
|
||||
|
||||
// Initialize:
|
||||
// - 'mesh_part.entity_to_vertex' for the elements (boundary elements are
|
||||
// set later); vertex ids are global at this point - they will be mapped to
|
||||
// local ids later
|
||||
// - 'mesh_part.attributes'
|
||||
// - 'mesh_part.tet_refine_flags' if needed
|
||||
int geom_marker = 0, num_geom = 0;
|
||||
for (int i = 0; i < num_elems; i++)
|
||||
{
|
||||
const Element *elem = mesh.GetElement(elem_list[i]);
|
||||
const int geom = elem->GetGeometryType();
|
||||
const int nv = Geometry::NumVerts[geom];
|
||||
const int *v = elem->GetVertices();
|
||||
MFEM_VERIFY(numeric_limits<int>::max() - nv >=
|
||||
mesh_part.entity_to_vertex[geom].Size(),
|
||||
"overflow in 'entity_to_vertex[geom]', geom: "
|
||||
<< Geometry::Name[geom]);
|
||||
mesh_part.entity_to_vertex[geom].Append(v, nv);
|
||||
mesh_part.attributes[i] = elem->GetAttribute();
|
||||
if (geom == Geometry::TETRAHEDRON)
|
||||
{
|
||||
// Create 'mesh_part.tet_refine_flags' but only if we find at least one
|
||||
// non-zero flag in a tetrahedron.
|
||||
const Tetrahedron *tet = static_cast<const Tetrahedron*>(elem);
|
||||
const int ref_flag = tet->GetRefinementFlag();
|
||||
if (mesh_part.tet_refine_flags.Size() == 0)
|
||||
{
|
||||
if (ref_flag)
|
||||
{
|
||||
// This is the first time we encounter non-zero 'ref_flag'
|
||||
const int num_tets = mesh_part.entity_to_vertex[geom].Size()/nv;
|
||||
mesh_part.tet_refine_flags.SetSize(num_tets, 0);
|
||||
mesh_part.tet_refine_flags.Last() = ref_flag;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
mesh_part.tet_refine_flags.Append(ref_flag);
|
||||
}
|
||||
}
|
||||
if ((geom_marker & (1 << geom)) == 0)
|
||||
{
|
||||
geom_marker |= (1 << geom);
|
||||
num_geom++;
|
||||
}
|
||||
}
|
||||
MFEM_ASSERT(mesh_part.tet_refine_flags.Size() == 0 ||
|
||||
mesh_part.tet_refine_flags.Size() ==
|
||||
mesh_part.entity_to_vertex[Geometry::TETRAHEDRON].Size()/4,
|
||||
"internal error");
|
||||
// Initialize 'mesh_part.element_map' if needed
|
||||
if (num_geom > 1)
|
||||
{
|
||||
int offsets[Geometry::NumGeom];
|
||||
int offset = 0;
|
||||
for (int g = Geometry::DimStart[dim]; g < Geometry::DimStart[dim+1]; g++)
|
||||
{
|
||||
offsets[g] = offset;
|
||||
offset += mesh_part.entity_to_vertex[g].Size()/Geometry::NumVerts[g];
|
||||
}
|
||||
mesh_part.element_map.SetSize(num_elems);
|
||||
for (int i = 0; i < num_elems; i++)
|
||||
{
|
||||
const int geom = mesh.GetElementGeometry(elem_list[i]);
|
||||
mesh_part.element_map[i] = offsets[geom]++;
|
||||
}
|
||||
}
|
||||
|
||||
// Initialize:
|
||||
// - 'mesh_part.entity_to_vertex' for the boundary elements; vertex ids are
|
||||
// global at this point - they will be mapped to local ids later
|
||||
// - 'mesh_part.bdr_attributes'
|
||||
geom_marker = 0; num_geom = 0;
|
||||
for (int i = 0; i < num_bdr_elems; i++)
|
||||
{
|
||||
const Element *bdr_elem = mesh.GetBdrElement(bdr_elem_list[i]);
|
||||
const int geom = bdr_elem->GetGeometryType();
|
||||
const int nv = Geometry::NumVerts[geom];
|
||||
const int *v = bdr_elem->GetVertices();
|
||||
MFEM_VERIFY(numeric_limits<int>::max() - nv >=
|
||||
mesh_part.entity_to_vertex[geom].Size(),
|
||||
"overflow in 'entity_to_vertex[geom]', geom: "
|
||||
<< Geometry::Name[geom]);
|
||||
mesh_part.entity_to_vertex[geom].Append(v, nv);
|
||||
mesh_part.bdr_attributes[i] = bdr_elem->GetAttribute();
|
||||
if ((geom_marker & (1 << geom)) == 0)
|
||||
{
|
||||
geom_marker |= (1 << geom);
|
||||
num_geom++;
|
||||
}
|
||||
}
|
||||
// Initialize 'mesh_part.boundary_map' if needed
|
||||
if (num_geom > 1)
|
||||
{
|
||||
int offsets[Geometry::NumGeom];
|
||||
int offset = 0;
|
||||
for (int g = Geometry::DimStart[dim-1]; g < Geometry::DimStart[dim]; g++)
|
||||
{
|
||||
offsets[g] = offset;
|
||||
offset += mesh_part.entity_to_vertex[g].Size()/Geometry::NumVerts[g];
|
||||
}
|
||||
mesh_part.boundary_map.SetSize(num_bdr_elems);
|
||||
for (int i = 0; i < num_bdr_elems; i++)
|
||||
{
|
||||
const int geom = mesh.GetBdrElementGeometry(bdr_elem_list[i]);
|
||||
mesh_part.boundary_map[i] = offsets[geom]++;
|
||||
}
|
||||
}
|
||||
|
||||
// Create the vertex id map, 'vertex_loc_to_glob', which maps local ids to
|
||||
// global ones; the map is sorted, preserving the global ordering.
|
||||
Array<int> vertex_loc_to_glob;
|
||||
{
|
||||
std::unordered_set<int> vertex_set;
|
||||
for (int i = 0; i < num_elems; i++)
|
||||
{
|
||||
const Element *elem = mesh.GetElement(elem_list[i]);
|
||||
const int geom = elem->GetGeometryType();
|
||||
const int nv = Geometry::NumVerts[geom];
|
||||
const int *v = elem->GetVertices();
|
||||
vertex_set.insert(v, v + nv);
|
||||
}
|
||||
vertex_loc_to_glob.SetSize(vertex_set.size());
|
||||
std::copy(vertex_set.begin(), vertex_set.end(), // src
|
||||
vertex_loc_to_glob.begin()); // dest
|
||||
}
|
||||
vertex_loc_to_glob.Sort();
|
||||
|
||||
// Initialize 'mesh_part.num_vertices'
|
||||
mesh_part.num_vertices = vertex_loc_to_glob.Size();
|
||||
|
||||
// Update the vertex ids in the arrays 'mesh_part.entity_to_vertex' from
|
||||
// global to local.
|
||||
for (int g = 0; g < Geometry::NumGeom; g++)
|
||||
{
|
||||
Array<int> &vert_array = mesh_part.entity_to_vertex[g];
|
||||
for (int i = 0; i < vert_array.Size(); i++)
|
||||
{
|
||||
const int glob_id = vert_array[i];
|
||||
const int loc_id = vertex_loc_to_glob.FindSorted(glob_id);
|
||||
MFEM_ASSERT(loc_id >= 0, "internal error: global vertex id not found");
|
||||
vert_array[i] = loc_id;
|
||||
}
|
||||
}
|
||||
|
||||
// Initialize one of 'mesh_part.vertex_coordinates' or 'mesh_part.nodes'
|
||||
if (!mesh.GetNodes())
|
||||
{
|
||||
MFEM_VERIFY(numeric_limits<int>::max()/sdim >= vertex_loc_to_glob.Size(),
|
||||
"overflow in 'vertex_coordinates', num_vertices = "
|
||||
<< vertex_loc_to_glob.Size() << ", sdim = " << sdim);
|
||||
mesh_part.vertex_coordinates.SetSize(sdim*vertex_loc_to_glob.Size());
|
||||
for (int i = 0; i < vertex_loc_to_glob.Size(); i++)
|
||||
{
|
||||
const real_t *coord = mesh.GetVertex(vertex_loc_to_glob[i]);
|
||||
for (int d = 0; d < sdim; d++)
|
||||
{
|
||||
mesh_part.vertex_coordinates[i*sdim+d] = coord[d];
|
||||
}
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
const GridFunction &glob_nodes = *mesh.GetNodes();
|
||||
mesh_part.nodal_fes = ExtractFESpace(mesh_part, *glob_nodes.FESpace());
|
||||
// Initialized 'mesh_part.mesh'.
|
||||
// Note: the nodes of 'mesh_part.mesh' are not set.
|
||||
|
||||
mesh_part.nodes = ExtractGridFunction(mesh_part, glob_nodes,
|
||||
*mesh_part.nodal_fes);
|
||||
|
||||
// Attach the 'mesh_part.nodes' to the 'mesh_part.mesh'.
|
||||
mesh_part.mesh->NewNodes(*mesh_part.nodes, /* make_owner: */ false);
|
||||
// Note: the vertices of 'mesh_part.mesh' are not set.
|
||||
}
|
||||
|
||||
// Begin constructing the "neighbor" groups, i.e. the groups that contain
|
||||
// 'part_id'.
|
||||
ListOfIntegerSets groups;
|
||||
{
|
||||
// the first group is the local one
|
||||
IntegerSet group;
|
||||
group.Recreate(1, &part_id);
|
||||
groups.Insert(group);
|
||||
}
|
||||
|
||||
// 'shared_faces' : shared face id -> (global_face_id, group_id)
|
||||
// Note: 'shared_faces' will be sorted by 'global_face_id'.
|
||||
Array<Pair<int,int>> shared_faces;
|
||||
|
||||
// Add "neighbor" groups defined by faces
|
||||
// Construct 'shared_faces'.
|
||||
if (dim >= 3)
|
||||
{
|
||||
std::unordered_set<int> face_set;
|
||||
// Construct 'face_set'
|
||||
const Table &elem_to_face = mesh.ElementToFaceTable();
|
||||
for (int loc_elem_id = 0; loc_elem_id < num_elems; loc_elem_id++)
|
||||
{
|
||||
const int glob_elem_id = elem_list[loc_elem_id];
|
||||
const int nfaces = elem_to_face.RowSize(glob_elem_id);
|
||||
const int *faces = elem_to_face.GetRow(glob_elem_id);
|
||||
face_set.insert(faces, faces + nfaces);
|
||||
}
|
||||
// Construct 'shared_faces'; add "neighbor" groups defined by faces.
|
||||
IntegerSet group;
|
||||
for (int glob_face_id : face_set)
|
||||
{
|
||||
int el[2];
|
||||
mesh.GetFaceElements(glob_face_id, &el[0], &el[1]);
|
||||
if (el[1] < 0) { continue; }
|
||||
el[0] = partitioning[el[0]];
|
||||
el[1] = partitioning[el[1]];
|
||||
MFEM_ASSERT(el[0] == part_id || el[1] == part_id, "internal error");
|
||||
if (el[0] != part_id || el[1] != part_id)
|
||||
{
|
||||
group.Recreate(2, el);
|
||||
const int group_id = groups.Insert(group);
|
||||
shared_faces.Append(Pair<int,int>(glob_face_id, group_id));
|
||||
}
|
||||
}
|
||||
shared_faces.Sort(); // sort the shared faces by 'glob_face_id'
|
||||
}
|
||||
|
||||
// 'shared_edges' : shared edge id -> (global_edge_id, group_id)
|
||||
// Note: 'shared_edges' will be sorted by 'global_edge_id'.
|
||||
Array<Pair<int,int>> shared_edges;
|
||||
|
||||
// Add "neighbor" groups defined by edges.
|
||||
// Construct 'shared_edges'.
|
||||
if (dim >= 2)
|
||||
{
|
||||
std::unordered_set<int> edge_set;
|
||||
// Construct 'edge_set'
|
||||
const Table &elem_to_edge = mesh.ElementToEdgeTable();
|
||||
for (int loc_elem_id = 0; loc_elem_id < num_elems; loc_elem_id++)
|
||||
{
|
||||
const int glob_elem_id = elem_list[loc_elem_id];
|
||||
const int nedges = elem_to_edge.RowSize(glob_elem_id);
|
||||
const int *edges = elem_to_edge.GetRow(glob_elem_id);
|
||||
edge_set.insert(edges, edges + nedges);
|
||||
}
|
||||
// Construct 'shared_edges'; add "neighbor" groups defined by edges.
|
||||
IntegerSet group;
|
||||
for (int glob_edge_id : edge_set)
|
||||
{
|
||||
const int nelem = edge_to_element.RowSize(glob_edge_id);
|
||||
const int *elem = edge_to_element.GetRow(glob_edge_id);
|
||||
Array<int> &gr = group; // reference to the 'group' internal Array
|
||||
gr.SetSize(nelem);
|
||||
for (int j = 0; j < nelem; j++)
|
||||
{
|
||||
gr[j] = partitioning[elem[j]];
|
||||
}
|
||||
gr.Sort();
|
||||
gr.Unique();
|
||||
MFEM_ASSERT(gr.FindSorted(part_id) >= 0, "internal error");
|
||||
if (group.Size() > 1)
|
||||
{
|
||||
const int group_id = groups.Insert(group);
|
||||
shared_edges.Append(Pair<int,int>(glob_edge_id, group_id));
|
||||
}
|
||||
}
|
||||
shared_edges.Sort(); // sort the shared edges by 'glob_edge_id'
|
||||
}
|
||||
|
||||
// 'shared_verts' : shared vertex id -> (global_vertex_id, group_id)
|
||||
// Note: 'shared_verts' will be sorted by 'global_vertex_id'.
|
||||
Array<Pair<int,int>> shared_verts;
|
||||
|
||||
// Add "neighbor" groups defined by vertices.
|
||||
// Construct 'shared_verts'.
|
||||
{
|
||||
IntegerSet group;
|
||||
for (int i = 0; i < vertex_loc_to_glob.Size(); i++)
|
||||
{
|
||||
// 'vertex_to_element' maps global vertex ids to global element ids
|
||||
const int glob_vertex_id = vertex_loc_to_glob[i];
|
||||
const int nelem = vertex_to_element.RowSize(glob_vertex_id);
|
||||
const int *elem = vertex_to_element.GetRow(glob_vertex_id);
|
||||
Array<int> &gr = group; // reference to the 'group' internal Array
|
||||
gr.SetSize(nelem);
|
||||
for (int j = 0; j < nelem; j++)
|
||||
{
|
||||
gr[j] = partitioning[elem[j]];
|
||||
}
|
||||
gr.Sort();
|
||||
gr.Unique();
|
||||
MFEM_ASSERT(gr.FindSorted(part_id) >= 0, "internal error");
|
||||
if (group.Size() > 1)
|
||||
{
|
||||
const int group_id = groups.Insert(group);
|
||||
shared_verts.Append(Pair<int,int>(glob_vertex_id, group_id));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Done constructing the "neighbor" groups in 'groups'.
|
||||
const int num_groups = groups.Size();
|
||||
|
||||
// Define 'mesh_part.my_groups'
|
||||
groups.AsTable(mesh_part.my_groups);
|
||||
|
||||
// Construct 'mesh_part.group_shared_entity_to_vertex[Geometry::POINT]'
|
||||
Table &group__shared_vertex_to_vertex =
|
||||
mesh_part.group_shared_entity_to_vertex[Geometry::POINT];
|
||||
group__shared_vertex_to_vertex.MakeI(num_groups);
|
||||
for (int sv = 0; sv < shared_verts.Size(); sv++)
|
||||
{
|
||||
const int group_id = shared_verts[sv].two;
|
||||
group__shared_vertex_to_vertex.AddAColumnInRow(group_id);
|
||||
}
|
||||
group__shared_vertex_to_vertex.MakeJ();
|
||||
for (int sv = 0; sv < shared_verts.Size(); sv++)
|
||||
{
|
||||
const int glob_vertex_id = shared_verts[sv].one;
|
||||
const int group_id = shared_verts[sv].two;
|
||||
const int loc_vertex_id = vertex_loc_to_glob.FindSorted(glob_vertex_id);
|
||||
MFEM_ASSERT(loc_vertex_id >= 0, "internal error");
|
||||
group__shared_vertex_to_vertex.AddConnection(group_id, loc_vertex_id);
|
||||
}
|
||||
group__shared_vertex_to_vertex.ShiftUpI();
|
||||
|
||||
// Construct 'mesh_part.group_shared_entity_to_vertex[Geometry::SEGMENT]'
|
||||
if (dim >= 2)
|
||||
{
|
||||
Table &group__shared_edge_to_vertex =
|
||||
mesh_part.group_shared_entity_to_vertex[Geometry::SEGMENT];
|
||||
group__shared_edge_to_vertex.MakeI(num_groups);
|
||||
for (int se = 0; se < shared_edges.Size(); se++)
|
||||
{
|
||||
const int group_id = shared_edges[se].two;
|
||||
group__shared_edge_to_vertex.AddColumnsInRow(group_id, 2);
|
||||
}
|
||||
group__shared_edge_to_vertex.MakeJ();
|
||||
const Table &edge_to_vertex = *mesh.GetEdgeVertexTable();
|
||||
for (int se = 0; se < shared_edges.Size(); se++)
|
||||
{
|
||||
const int glob_edge_id = shared_edges[se].one;
|
||||
const int group_id = shared_edges[se].two;
|
||||
const int *v = edge_to_vertex.GetRow(glob_edge_id);
|
||||
for (int i = 0; i < 2; i++)
|
||||
{
|
||||
const int loc_vertex_id = vertex_loc_to_glob.FindSorted(v[i]);
|
||||
MFEM_ASSERT(loc_vertex_id >= 0, "internal error");
|
||||
group__shared_edge_to_vertex.AddConnection(group_id, loc_vertex_id);
|
||||
}
|
||||
}
|
||||
group__shared_edge_to_vertex.ShiftUpI();
|
||||
}
|
||||
|
||||
// Construct 'mesh_part.group_shared_entity_to_vertex[Geometry::TRIANGLE]'
|
||||
// and 'mesh_part.group_shared_entity_to_vertex[Geometry::SQUARE]'.
|
||||
if (dim >= 3)
|
||||
{
|
||||
Table &group__shared_tria_to_vertex =
|
||||
mesh_part.group_shared_entity_to_vertex[Geometry::TRIANGLE];
|
||||
Table &group__shared_quad_to_vertex =
|
||||
mesh_part.group_shared_entity_to_vertex[Geometry::SQUARE];
|
||||
Array<int> vertex_ids;
|
||||
group__shared_tria_to_vertex.MakeI(num_groups);
|
||||
group__shared_quad_to_vertex.MakeI(num_groups);
|
||||
for (int sf = 0; sf < shared_faces.Size(); sf++)
|
||||
{
|
||||
const int glob_face_id = shared_faces[sf].one;
|
||||
const int group_id = shared_faces[sf].two;
|
||||
const int geom = mesh.GetFaceGeometry(glob_face_id);
|
||||
mesh_part.group_shared_entity_to_vertex[geom].
|
||||
AddColumnsInRow(group_id, Geometry::NumVerts[geom]);
|
||||
}
|
||||
group__shared_tria_to_vertex.MakeJ();
|
||||
group__shared_quad_to_vertex.MakeJ();
|
||||
for (int sf = 0; sf < shared_faces.Size(); sf++)
|
||||
{
|
||||
const int glob_face_id = shared_faces[sf].one;
|
||||
const int group_id = shared_faces[sf].two;
|
||||
const int geom = mesh.GetFaceGeometry(glob_face_id);
|
||||
mesh.GetFaceVertices(glob_face_id, vertex_ids);
|
||||
// Rotate shared triangles that have an adjacent tetrahedron with a
|
||||
// nonzero refinement flag.
|
||||
// See also ParMesh::BuildSharedFaceElems.
|
||||
if (geom == Geometry::TRIANGLE)
|
||||
{
|
||||
int glob_el_id[2];
|
||||
mesh.GetFaceElements(glob_face_id, &glob_el_id[0], &glob_el_id[1]);
|
||||
int side = 0;
|
||||
const Element *el = mesh.GetElement(glob_el_id[0]);
|
||||
const Tetrahedron *tet = nullptr;
|
||||
if (el->GetGeometryType() == Geometry::TETRAHEDRON)
|
||||
{
|
||||
tet = static_cast<const Tetrahedron*>(el);
|
||||
}
|
||||
else
|
||||
{
|
||||
side = 1;
|
||||
el = mesh.GetElement(glob_el_id[1]);
|
||||
if (el->GetGeometryType() == Geometry::TETRAHEDRON)
|
||||
{
|
||||
tet = static_cast<const Tetrahedron*>(el);
|
||||
}
|
||||
}
|
||||
if (tet && tet->GetRefinementFlag())
|
||||
{
|
||||
// mark the shared face for refinement by reorienting
|
||||
// it according to the refinement flag in the tetrahedron
|
||||
// to which this shared face belongs to.
|
||||
int info[2];
|
||||
mesh.GetFaceInfos(glob_face_id, &info[0], &info[1]);
|
||||
tet->GetMarkedFace(info[side]/64, &vertex_ids[0]);
|
||||
}
|
||||
}
|
||||
for (int i = 0; i < vertex_ids.Size(); i++)
|
||||
{
|
||||
const int glob_id = vertex_ids[i];
|
||||
const int loc_id = vertex_loc_to_glob.FindSorted(glob_id);
|
||||
MFEM_ASSERT(loc_id >= 0, "internal error");
|
||||
vertex_ids[i] = loc_id;
|
||||
}
|
||||
mesh_part.group_shared_entity_to_vertex[geom].
|
||||
AddConnections(group_id, vertex_ids, vertex_ids.Size());
|
||||
}
|
||||
group__shared_tria_to_vertex.ShiftUpI();
|
||||
group__shared_quad_to_vertex.ShiftUpI();
|
||||
}
|
||||
}
|
||||
|
||||
std::unique_ptr<FiniteElementSpace>
|
||||
MeshPartitioner::ExtractFESpace(MeshPart &mesh_part,
|
||||
const FiniteElementSpace &global_fespace) const
|
||||
{
|
||||
mesh_part.GetMesh(); // initialize 'mesh_part.mesh'
|
||||
// Note: the nodes of 'mesh_part.mesh' are not set by GetMesh() unless they
|
||||
// were already constructed, e.g. by ExtractPart().
|
||||
|
||||
return std::unique_ptr<FiniteElementSpace>(
|
||||
new FiniteElementSpace(mesh_part.mesh.get(),
|
||||
global_fespace.FEColl(),
|
||||
global_fespace.GetVDim(),
|
||||
global_fespace.GetOrdering()));
|
||||
}
|
||||
|
||||
std::unique_ptr<GridFunction>
|
||||
MeshPartitioner::ExtractGridFunction(const MeshPart &mesh_part,
|
||||
const GridFunction &global_gf,
|
||||
FiniteElementSpace &local_fespace) const
|
||||
{
|
||||
std::unique_ptr<GridFunction> local_gf(new GridFunction(&local_fespace));
|
||||
|
||||
// Transfer data from 'global_gf' to 'local_gf'.
|
||||
Array<int> gvdofs, lvdofs;
|
||||
Vector loc_vals;
|
||||
const int part_id = mesh_part.my_part_id;
|
||||
const int num_elems = part_to_element.RowSize(part_id);
|
||||
const int *elem_list = part_to_element.GetRow(part_id); // sorted
|
||||
for (int loc_elem_id = 0; loc_elem_id < num_elems; loc_elem_id++)
|
||||
{
|
||||
const int glob_elem_id = elem_list[loc_elem_id];
|
||||
auto glob_dt = global_gf.FESpace()->GetElementVDofs(glob_elem_id, gvdofs);
|
||||
global_gf.GetSubVector(gvdofs, loc_vals);
|
||||
if (glob_dt) { glob_dt->InvTransformPrimal(loc_vals); }
|
||||
auto local_dt = local_fespace.GetElementVDofs(loc_elem_id, lvdofs);
|
||||
if (local_dt) { local_dt->TransformPrimal(loc_vals); }
|
||||
local_gf->SetSubVector(lvdofs, loc_vals);
|
||||
}
|
||||
return local_gf;
|
||||
}
|
||||
|
||||
|
||||
GeometricFactors::GeometricFactors(const Mesh *mesh, const IntegrationRule &ir,
|
||||
int flags, MemoryType d_mt)
|
||||
{
|
||||
|
||||
+352
-18
@@ -30,6 +30,7 @@
|
||||
#include <iostream>
|
||||
#include <array>
|
||||
#include <map>
|
||||
#include <memory>
|
||||
|
||||
namespace mfem
|
||||
{
|
||||
@@ -75,8 +76,10 @@ protected:
|
||||
visualization purpose in GLVis. */
|
||||
mutable int nbInteriorFaces, nbBoundaryFaces;
|
||||
|
||||
int meshgen; // see MeshGenerator()
|
||||
int mesh_geoms; // sum of (1 << geom) for all geom of all dimensions
|
||||
// see MeshGenerator(); global in parallel
|
||||
int meshgen;
|
||||
// sum of (1 << geom) for all geom of all dimensions; local in parallel
|
||||
int mesh_geoms;
|
||||
|
||||
// Counter for Mesh transformations: refinement, derefinement, rebalancing.
|
||||
// Used for checking during Update operations on objects depending on the
|
||||
@@ -307,11 +310,11 @@ protected:
|
||||
void Destroy(); // Delete all owned data.
|
||||
void ResetLazyData();
|
||||
|
||||
Element *ReadElementWithoutAttr(std::istream &);
|
||||
static void PrintElementWithoutAttr(const Element *, std::ostream &);
|
||||
Element *ReadElementWithoutAttr(std::istream &input);
|
||||
static void PrintElementWithoutAttr(const Element *el, std::ostream &os);
|
||||
|
||||
Element *ReadElement(std::istream &);
|
||||
static void PrintElement(const Element *, std::ostream &);
|
||||
Element *ReadElement(std::istream &input);
|
||||
static void PrintElement(const Element *el, std::ostream &os);
|
||||
|
||||
// Readers for different mesh formats, used in the Load() method.
|
||||
// The implementations of these methods are in mesh_readers.cpp.
|
||||
@@ -558,7 +561,7 @@ protected:
|
||||
mfem v1.2 format with the given section_delimiter at the end.
|
||||
If @a comments is non-empty, it will be printed after the first line of
|
||||
the file, and each line should begin with '#'. */
|
||||
void Printer(std::ostream &out = mfem::out,
|
||||
void Printer(std::ostream &os = mfem::out,
|
||||
std::string section_delimiter = "",
|
||||
const std::string &comments = "") const;
|
||||
|
||||
@@ -854,7 +857,9 @@ public:
|
||||
vectors using Mesh::CreatePeriodicVertexMapping.
|
||||
@note MFEM requires that each edge of the resulting mesh be uniquely
|
||||
identifiable by a pair of distinct vertices. As a consequence, periodic
|
||||
boundaries must be connected by at least three edges. */
|
||||
boundaries must be separated by at least two interior vertices.
|
||||
@note The resulting mesh uses a discontinuous nodal function, see
|
||||
SetCurvature() for further details. */
|
||||
static Mesh MakePeriodic(const Mesh &orig_mesh, const std::vector<int> &v2v);
|
||||
|
||||
///@}
|
||||
@@ -2124,7 +2129,11 @@ public:
|
||||
/// Set the curvature of the mesh nodes using the given polynomial degree.
|
||||
/** Creates a nodal GridFunction if one doesn't already exist.
|
||||
|
||||
@param[in] order Polynomial degree of the nodal FE space.
|
||||
@param[in] order Polynomial degree of the nodal FE space. If this
|
||||
value is <= 0 then the method will remove the
|
||||
nodal GridFunction and the Mesh will use the
|
||||
vertices array instead; the other arguments are
|
||||
ignored in this case.
|
||||
@param[in] discont Whether to use a discontinuous or continuous
|
||||
finite element space (continuous is default).
|
||||
@param[in] space_dim The space dimension (optional).
|
||||
@@ -2330,7 +2339,7 @@ public:
|
||||
std::ostream &os, int elem_attr = 0) const;
|
||||
|
||||
void PrintElementsWithPartitioning (int *partitioning,
|
||||
std::ostream &out,
|
||||
std::ostream &os,
|
||||
int interior_faces = 0);
|
||||
|
||||
/// Print set of disjoint surfaces:
|
||||
@@ -2338,13 +2347,13 @@ public:
|
||||
* If Aface_face(i,j) != 0, print face j as a boundary
|
||||
* element with attribute i+1.
|
||||
*/
|
||||
void PrintSurfaces(const Table &Aface_face, std::ostream &out) const;
|
||||
void PrintSurfaces(const Table &Aface_face, std::ostream &os) const;
|
||||
|
||||
/// Auxiliary method used by PrintCharacteristics().
|
||||
/** It is also used in the `mesh-explorer` miniapp. */
|
||||
static void PrintElementsByGeometry(int dim,
|
||||
const Array<int> &num_elems_by_geom,
|
||||
std::ostream &out);
|
||||
std::ostream &os);
|
||||
|
||||
/** @brief Compute and print mesh characteristics such as number of vertices,
|
||||
number of elements, number of boundary elements, minimal and maximal
|
||||
@@ -2364,7 +2373,7 @@ public:
|
||||
|
||||
#ifdef MFEM_DEBUG
|
||||
/// Output an NCMesh-compatible debug dump.
|
||||
void DebugDump(std::ostream &out) const;
|
||||
void DebugDump(std::ostream &os) const;
|
||||
#endif
|
||||
|
||||
/// @}
|
||||
@@ -2445,7 +2454,334 @@ public:
|
||||
|
||||
/** Overload operator<< for std::ostream and Mesh; valid also for the derived
|
||||
class ParMesh */
|
||||
std::ostream &operator<<(std::ostream &out, const Mesh &mesh);
|
||||
std::ostream &operator<<(std::ostream &os, const Mesh &mesh);
|
||||
|
||||
/// @brief Print function for Mesh::FaceInformation.
|
||||
std::ostream& operator<<(std::ostream &os, const Mesh::FaceInformation& info);
|
||||
|
||||
|
||||
/** @brief Class containing a minimal description of a part (a subset of the
|
||||
elements) of a Mesh and its connectivity to other parts.
|
||||
|
||||
The main purpose of this class is to facilitate the partitioning of serial
|
||||
meshes (in serial, i.e. on one processor) and save the parts in parallel
|
||||
MFEM mesh format.
|
||||
|
||||
Another potential futrure purpose of this class could be to facilitate
|
||||
exchange of MeshParts between MPI ranks for repartitioning purposes. It can
|
||||
also potentially be used to implement parallel mesh I/O functions with
|
||||
partitionings that have number of parts different from the number of MPI
|
||||
tasks.
|
||||
|
||||
@note Parts of NURBS or non-conforming meshes cannot be fully described by
|
||||
this class alone with its current data members. Such extensions may be added
|
||||
in the future.
|
||||
*/
|
||||
class MeshPart
|
||||
{
|
||||
protected:
|
||||
struct Entity { int geom; int num_verts; const int *verts; };
|
||||
struct EntityHelper
|
||||
{
|
||||
int dim, num_entities;
|
||||
int geom_offsets[Geometry::NumGeom+1];
|
||||
typedef const Array<int> entity_to_vertex_type[Geometry::NumGeom];
|
||||
entity_to_vertex_type &entity_to_vertex;
|
||||
|
||||
EntityHelper(int dim_,
|
||||
const Array<int> (&entity_to_vertex_)[Geometry::NumGeom]);
|
||||
Entity FindEntity(int bytype_entity_id);
|
||||
};
|
||||
|
||||
public:
|
||||
/// Reference space dimension of the elements
|
||||
int dimension;
|
||||
|
||||
/// Dimension of the physical space into which the MeshPart is embedded.
|
||||
int space_dimension;
|
||||
|
||||
/// Number of vertices
|
||||
int num_vertices;
|
||||
|
||||
/// Number of elements with reference space dimension equal to 'dimension'.
|
||||
int num_elements;
|
||||
|
||||
/** @brief Number of boundary elements with reference space dimension equal
|
||||
to 'dimension'-1. */
|
||||
int num_bdr_elements;
|
||||
|
||||
/**
|
||||
Each 'entity_to_vertex[geom]' describes the entities of Geometry::Type
|
||||
'geom' in terms of their vertices. The number of entities of type 'geom'
|
||||
is:
|
||||
|
||||
num_entities[geom] = size('entity_to_vertex[geom]')/num_vertices[geom]
|
||||
|
||||
The number of all elements, 'num_elements', is:
|
||||
|
||||
'num_elements' = sum_{dim[geom]=='dimension'} num_entities[geom]
|
||||
|
||||
and the number of all boundary elements, 'num_bdr_elements' is:
|
||||
|
||||
'num_bdr_elements' = sum_{dim[geom]=='dimension'-1} num_entities[geom]
|
||||
|
||||
Note that 'entity_to_vertex' does NOT describe all "faces" in the mesh
|
||||
part (i.e. all 'dimension'-1 entities) but only the boundary elements.
|
||||
Also, note that lower dimesional entities ('dimension'-2 and lower) are
|
||||
NOT described by the respective array, i.e. the array will be empty.
|
||||
*/
|
||||
Array<int> entity_to_vertex[Geometry::NumGeom];
|
||||
|
||||
/** @brief Store the refinement flags for tetraheral elements. If all tets
|
||||
have zero refinement flags then this array is empty, i.e. has size 0. */
|
||||
Array<int> tet_refine_flags;
|
||||
|
||||
/**
|
||||
Terminology: "by-type" element/boundary ordering: ordered by
|
||||
Geometry::Type and within each Geometry::Type 'geom' ordered as in
|
||||
'entity_to_vertex[geom]'.
|
||||
|
||||
Optional re-ordering of the elements that will be used by (Par)Mesh
|
||||
objects constructed from this MeshPart. This array maps "natural" element
|
||||
ids (used by the Mesh/ParMesh objects) to "by-type" element ids (see
|
||||
above):
|
||||
|
||||
"by-type" element id = element_map["natural" element id]
|
||||
|
||||
The size of the array is either 'num_elements' or 0 when no re-ordering is
|
||||
needed (then "by-type" id == "natural" id).
|
||||
*/
|
||||
Array<int> element_map;
|
||||
|
||||
/// Optional re-ordering for the boundary elements, similar to 'element_map'.
|
||||
Array<int> boundary_map;
|
||||
|
||||
/**
|
||||
Element attributes. Ordered using the "natural" element ordering defined
|
||||
by the array 'element_map'. The size of this array is 'num_elements'.
|
||||
*/
|
||||
Array<int> attributes;
|
||||
|
||||
/**
|
||||
Boundary element attributes. Ordered using the "natural" boundary element
|
||||
ordering defined by the array 'boundary_map'. The size of this array is
|
||||
'num_bdr_elements'.
|
||||
*/
|
||||
Array<int> bdr_attributes;
|
||||
|
||||
/**
|
||||
Optional vertex coordinates. The size of the array is either
|
||||
|
||||
size = 'space_dimension' * 'num_vertices'
|
||||
|
||||
or 0 when the vertex coordinates are not used, i.e. when the MeshPart uses
|
||||
a nodal GridFunction to describe its location in physical space. This
|
||||
array uses Ordering::byVDIM: "X0,Y0,Z0, X1,Y1,Z1, ...".
|
||||
*/
|
||||
Array<real_t> vertex_coordinates;
|
||||
|
||||
/**
|
||||
Optional serial Mesh object constructed on demand using the method
|
||||
GetMesh(). One use case for it is when one wants to construct FE spaces
|
||||
and GridFunction%s on the MeshPart for saving or MPI communication.
|
||||
*/
|
||||
std::unique_ptr<Mesh> mesh;
|
||||
|
||||
/**
|
||||
Nodal FE space defined on 'mesh' used by the GridFunction 'nodes'. Uses
|
||||
the FE collection from the global nodal FE space.
|
||||
*/
|
||||
std::unique_ptr<FiniteElementSpace> nodal_fes;
|
||||
|
||||
/**
|
||||
'nodes': pointer to a GridFunction describing the physical location of the
|
||||
MeshPart. Used for describing high-order and periodic meshes. This
|
||||
GridFunction is defined on the FE space 'nodal_fes' which, in turn, is
|
||||
defined on the Mesh 'mesh'.
|
||||
*/
|
||||
std::unique_ptr<GridFunction> nodes;
|
||||
|
||||
/** @name Connectivity to other MeshPart objects */
|
||||
///@{
|
||||
|
||||
/// Total number of MeshParts
|
||||
int num_parts;
|
||||
|
||||
/** @brief Index of the part described by this MeshPart:
|
||||
0 <= 'my_part_id' < 'num_parts' */
|
||||
int my_part_id;
|
||||
|
||||
/**
|
||||
A group G is a subset of the set { 0, 1, ..., 'num_parts'-1 } for which
|
||||
there is a mesh entity E (of any dimension) in the global mesh such that
|
||||
G is the set of the parts assigned (by the partitioning array) to the
|
||||
elements adjacent to E. The MeshPart describes only the "neighbor" groups,
|
||||
i.e. the groups that contain 'my_part_id'. The Table 'my_groups' defines
|
||||
the "neighbor" groups in terms of their part ids. In other words, it maps
|
||||
"neighbor" group ids to a (sorted) list of part ids. In particular, the
|
||||
number of "neighbor" groups is given by 'my_groups.Size()'. The "local"
|
||||
group { 'my_part_id' } has index 0 in 'my_groups'.
|
||||
*/
|
||||
Table my_groups;
|
||||
|
||||
/**
|
||||
Shared entities for this MeshPart are mesh entities of all dimensions less
|
||||
than 'dimension' that are generated by the elements of this MeshPart and
|
||||
at least one other MeshPart.
|
||||
|
||||
The Table 'group_shared_entity_to_vertex[geom]' defines, for each group,
|
||||
the shared entities of Geometry::Type 'geom'. Each row (corresponding to a
|
||||
"neighbor" group, as defined by 'my_groups') in the Table defines the
|
||||
shared entities in a way similar to the arrays 'entity_to_vertex[geom]'.
|
||||
The "local" group (with index 0) does not have any shared entities, so the
|
||||
0-th row in the Table is always empty.
|
||||
|
||||
IMPORTANT: the descriptions of the groups in this MeshPart must match
|
||||
their descriptions in all neighboring MeshParts. This includes the
|
||||
ordering of the shared entities within the group, as well as the vertex
|
||||
ordering of each shared entity.
|
||||
*/
|
||||
Table group_shared_entity_to_vertex[Geometry::NumGeom];
|
||||
|
||||
///@}
|
||||
|
||||
/** @brief Write the MeshPart to a stream using the parallel format
|
||||
"MFEM mesh v1.2". */
|
||||
void Print(std::ostream &os) const;
|
||||
|
||||
/** @brief Construct a serial Mesh object from the MeshPart.
|
||||
|
||||
The nodes of 'mesh' are NOT initialized by this method, however, the
|
||||
nodal FE space and nodal GridFunction can be created and then attached to
|
||||
the 'mesh'. The Mesh is constructed only if 'mesh' is empty, otherwise
|
||||
the method simply returns the object held by 'mesh'.
|
||||
*/
|
||||
Mesh &GetMesh();
|
||||
};
|
||||
|
||||
|
||||
/** @brief Class that allows serial meshes to be partitioned into MeshPart
|
||||
objects, typically one MeshPart at a time, which can then be used to write
|
||||
the local mesh in parallel MFEM mesh format.
|
||||
|
||||
Sample usage of this class: partition a serial mesh and save it in parallel
|
||||
MFEM format:
|
||||
\code
|
||||
// The array 'partitioning' can be obtained e.g. from
|
||||
// mesh->GeneratePartitioning():
|
||||
void usage1(Mesh *mesh, int num_parts, int *partitioning)
|
||||
{
|
||||
MeshPartitioner partitioner(*mesh, num_parts, partitioning);
|
||||
MeshPart mesh_part;
|
||||
for (int i = 0; i < num_parts; i++)
|
||||
{
|
||||
partitioner.ExtractPart(i, mesh_part);
|
||||
ofstream omesh(MakeParFilename("my-mesh.", i));
|
||||
mesh_part.Print(omesh);
|
||||
}
|
||||
}
|
||||
\endcode
|
||||
|
||||
This class can also be used to partition a mesh and GridFunction(s) and save
|
||||
them in parallel:
|
||||
\code
|
||||
// The array 'partitioning' can be obtained e.g. from
|
||||
// mesh->GeneratePartitioning():
|
||||
void usage2(Mesh *mesh, int num_parts, int *partitioning,
|
||||
GridFunction *gf)
|
||||
{
|
||||
MeshPartitioner partitioner(*mesh, num_parts, partitioning);
|
||||
MeshPart mesh_part;
|
||||
for (int i = 0; i < num_parts; i++)
|
||||
{
|
||||
partitioner.ExtractPart(i, mesh_part);
|
||||
ofstream omesh(MakeParFilename("my-mesh.", i));
|
||||
mesh_part.Print(omesh);
|
||||
auto lfes = partitioner.ExtractFESpace(mesh_part, *gf->FESpace());
|
||||
auto lgf = partitioner.ExtractGridFunction(mesh_part, *gf, *lfes);
|
||||
ofstream ofield(MakeParFilename("my-field.", i));
|
||||
lgf->Save(ofield);
|
||||
}
|
||||
}
|
||||
\endcode
|
||||
*/
|
||||
class MeshPartitioner
|
||||
{
|
||||
protected:
|
||||
Mesh &mesh;
|
||||
Array<int> partitioning;
|
||||
Table part_to_element;
|
||||
Table part_to_boundary;
|
||||
Table edge_to_element;
|
||||
Table vertex_to_element;
|
||||
|
||||
public:
|
||||
/** @brief Construct a MeshPartitioner.
|
||||
|
||||
@param[in] mesh_ Mesh to be partitioned into MeshPart%s.
|
||||
@param[in] num_parts_ Number of parts to partition the mesh into.
|
||||
@param[in] partitioning_ Partitioning array: for every element in the
|
||||
mesh gives the partition it belongs to; if NULL,
|
||||
partitioning will be generated internally by
|
||||
calling Mesh::GeneratePartitioning().
|
||||
@param[in] part_method Partitioning method to be used in the call to
|
||||
Mesh::GeneratePartitioning() when the provided
|
||||
input partitioning is NULL.
|
||||
*/
|
||||
MeshPartitioner(Mesh &mesh_, int num_parts_, int *partitioning_ = NULL,
|
||||
int part_method = 1);
|
||||
|
||||
/** @brief Construct a MeshPart corresponding to the given @a part_id.
|
||||
|
||||
@param[in] part_id Partition index to extract; valid values are in
|
||||
the range [0, num_parts).
|
||||
@param[out] mesh_part Output MeshPart object; its contents is
|
||||
overwritten, while potentially reusing existing
|
||||
dynamic memory allocations.
|
||||
*/
|
||||
void ExtractPart(int part_id, MeshPart &mesh_part) const;
|
||||
|
||||
/** @brief Construct a local version of the given FiniteElementSpace
|
||||
@a global_fespace corresponding to the given @a mesh_part.
|
||||
|
||||
@param[in,out] mesh_part MeshPart on which to construct the local
|
||||
FiniteElementSpace; this object is
|
||||
generally modified by this call since it
|
||||
calls mesh_part.GetMesh() to ensure the
|
||||
local mesh is constructed.
|
||||
@param[in] global_fespace The global FiniteElementSpace that should
|
||||
be restricted to the @a mesh_part.
|
||||
|
||||
@returns A FiniteElementSpace pointer stored in a unique_ptr. The
|
||||
returned local FiniteElementSpace is built on the Mesh object
|
||||
contained in @a mesh_part (MeshPart::mesh) and it reuses the
|
||||
FiniteElementCollection of the @a global_fespace.
|
||||
*/
|
||||
std::unique_ptr<FiniteElementSpace>
|
||||
ExtractFESpace(MeshPart &mesh_part,
|
||||
const FiniteElementSpace &global_fespace) const;
|
||||
|
||||
/** @brief Construct a local version of the given GridFunction, @a global_gf,
|
||||
corresponding to the given @a mesh_part. The respective data is copied
|
||||
from @a global_gf to the returned local GridFunction.
|
||||
|
||||
@param[in] mesh_part MeshPart on which to construct the local
|
||||
GridFunction.
|
||||
@param[in] global_gf The global GridFunction that should be
|
||||
restricted to the @a mesh_part.
|
||||
@param[in,out] local_fespace The local FiniteElementSpace corresponding
|
||||
to @a mesh_part, e.g. constructed by the
|
||||
method ExtractFESpace().
|
||||
|
||||
@returns A GridFunction pointer stored in a unique_ptr. The returned
|
||||
local GridFunction is initialized with data appropriately copied
|
||||
from @a global_gf.
|
||||
*/
|
||||
std::unique_ptr<GridFunction>
|
||||
ExtractGridFunction(const MeshPart &mesh_part,
|
||||
const GridFunction &global_gf,
|
||||
FiniteElementSpace &local_fespace) const;
|
||||
};
|
||||
|
||||
|
||||
/** @brief Structure for storing mesh geometric factors: coordinates, Jacobians,
|
||||
@@ -2454,7 +2790,6 @@ std::ostream &operator<<(std::ostream &out, const Mesh &mesh);
|
||||
Mesh. See Mesh::GetGeometricFactors(). */
|
||||
class GeometricFactors
|
||||
{
|
||||
|
||||
private:
|
||||
void Compute(const GridFunction &nodes,
|
||||
MemoryType d_mt = MemoryType::DEFAULT);
|
||||
@@ -2502,6 +2837,7 @@ public:
|
||||
Vector detJ;
|
||||
};
|
||||
|
||||
|
||||
/** @brief Structure for storing face geometric factors: coordinates, Jacobians,
|
||||
determinants of the Jacobians, and normal vectors. */
|
||||
/** Typically objects of this type are constructed and owned by objects of class
|
||||
@@ -2556,6 +2892,7 @@ public:
|
||||
Vector normal;
|
||||
};
|
||||
|
||||
|
||||
/// Class used to extrude the nodes of a mesh
|
||||
class NodeExtrudeCoefficient : public VectorCoefficient
|
||||
{
|
||||
@@ -2587,9 +2924,6 @@ inline void ShiftRight(int &a, int &b, int &c)
|
||||
a = c; c = b; b = t;
|
||||
}
|
||||
|
||||
/// @brief Print function for Mesh::FaceInformation.
|
||||
std::ostream& operator<<(std::ostream& os, const Mesh::FaceInformation& info);
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
+16
-4
@@ -1151,15 +1151,24 @@ void Mesh::ReadXML_VTKMesh(std::istream &input, int &curved, int &read_gf,
|
||||
}
|
||||
if (cells_xml == NULL) { MFEM_ABORT(erstr); }
|
||||
|
||||
// Read the element attributes, which are stored as CellData named "material"
|
||||
// Read the element attributes, which are stored as CellData named either
|
||||
// "material" or "attribute". We prioritize "material" over "attribute" for
|
||||
// backwards compatibility.
|
||||
Array<int> cell_attributes;
|
||||
bool found_attributes = false;
|
||||
for (const XMLElement *cell_data_xml = piece->FirstChildElement();
|
||||
cell_data_xml != NULL;
|
||||
cell_data_xml = cell_data_xml->NextSiblingElement())
|
||||
{
|
||||
if (StringCompare(cell_data_xml->Name(), "CellData")
|
||||
&& StringCompare(cell_data_xml->Attribute("Scalars"), "material"))
|
||||
const bool is_cell_data =
|
||||
StringCompare(cell_data_xml->Name(), "CellData");
|
||||
const bool is_material =
|
||||
StringCompare(cell_data_xml->Attribute("Scalars"), "material");
|
||||
const bool is_attribute =
|
||||
StringCompare(cell_data_xml->Attribute("Scalars"), "attribute");
|
||||
if (is_cell_data && (is_material || (is_attribute && !found_attributes)))
|
||||
{
|
||||
found_attributes = true;
|
||||
const XMLElement *data_xml = cell_data_xml->FirstChildElement();
|
||||
if (data_xml != NULL && StringCompare(data_xml->Name(), "DataArray"))
|
||||
{
|
||||
@@ -1274,6 +1283,7 @@ void Mesh::ReadVTKMesh(std::istream &input, int &curved, int &read_gf,
|
||||
// Read the cell materials
|
||||
// bool found_material = false;
|
||||
Array<int> cell_attributes;
|
||||
bool found_attributes = false;
|
||||
while ((input.good()))
|
||||
{
|
||||
getline(input, buff);
|
||||
@@ -1281,8 +1291,10 @@ void Mesh::ReadVTKMesh(std::istream &input, int &curved, int &read_gf,
|
||||
{
|
||||
break; // We have entered the POINT_DATA block. Quit.
|
||||
}
|
||||
else if (buff.rfind("SCALARS material") == 0)
|
||||
else if (buff.rfind("SCALARS material") == 0 ||
|
||||
(buff.rfind("SCALARS attribute") == 0 && !found_attributes))
|
||||
{
|
||||
found_attributes = true;
|
||||
getline(input, buff); // LOOKUP_TABLE default
|
||||
if (buff.rfind("LOOKUP_TABLE default") != 0)
|
||||
{
|
||||
|
||||
+53
-49
@@ -35,9 +35,9 @@ KnotVector::KnotVector(istream &input)
|
||||
GetElements();
|
||||
}
|
||||
|
||||
KnotVector::KnotVector(int Order_, int NCP)
|
||||
KnotVector::KnotVector(int order, int NCP)
|
||||
{
|
||||
Order = Order_;
|
||||
Order = order;
|
||||
NumOfControlPoints = NCP;
|
||||
knot.SetSize(NumOfControlPoints + Order + 1);
|
||||
NumOfElements = 0;
|
||||
@@ -276,18 +276,18 @@ void KnotVector::PrintFunctions(std::ostream &os, int samples) const
|
||||
|
||||
for (int j = 0; j <samples; j++)
|
||||
{
|
||||
x =j*dx;
|
||||
os<< x + e;
|
||||
x = j*dx;
|
||||
os << x + e;
|
||||
|
||||
CalcShape ( shape, cnt, x);
|
||||
CalcShape(shape, cnt, x);
|
||||
for (int d = 0; d < Order+1; d++) { os<<"\t"<<shape[d]; }
|
||||
|
||||
CalcDShape ( shape, cnt, x);
|
||||
CalcDShape(shape, cnt, x);
|
||||
for (int d = 0; d < Order+1; d++) { os<<"\t"<<shape[d]; }
|
||||
|
||||
CalcD2Shape ( shape, cnt, x);
|
||||
CalcD2Shape(shape, cnt, x);
|
||||
for (int d = 0; d < Order+1; d++) { os<<"\t"<<shape[d]; }
|
||||
os<<endl;
|
||||
os << endl;
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -378,6 +378,7 @@ void KnotVector::CalcDShape(Vector &grad, int i, real_t xi) const
|
||||
}
|
||||
|
||||
// Routine from "The NURBS book" - 2nd ed - Piegl and Tiller
|
||||
// Algorithm A2.3 p. 72
|
||||
void KnotVector::CalcDnShape(Vector &gradn, int n, int i, real_t xi) const
|
||||
{
|
||||
int p = Order, rk, pk, j1, j2,r,j,k;
|
||||
@@ -522,7 +523,7 @@ void KnotVector::FindMaxima(Array<int> &ks, Vector &xi, Vector &u) const
|
||||
}
|
||||
|
||||
arg = (arg1 + arg2)/2;
|
||||
CalcShape ( shape, i, arg);
|
||||
CalcShape(shape, i, arg);
|
||||
max = shape[d];
|
||||
}
|
||||
|
||||
@@ -556,7 +557,7 @@ void KnotVector::FindInterpolant(Array<Vector*> &x)
|
||||
A = 0.0;
|
||||
for (int i = 0; i < ncp; i++)
|
||||
{
|
||||
CalcShape ( shape, i_args[i], xi_args[i]);
|
||||
CalcShape(shape, i_args[i], xi_args[i]);
|
||||
for (int p = 0; p < order+1; p++)
|
||||
{
|
||||
A(i,i_args[i] + p) = shape[p];
|
||||
@@ -637,9 +638,9 @@ void KnotVector::Difference(const KnotVector &kv, Vector &diff) const
|
||||
}
|
||||
}
|
||||
|
||||
void NURBSPatch::init(int dim_)
|
||||
void NURBSPatch::init(int dim)
|
||||
{
|
||||
Dim = dim_;
|
||||
Dim = dim;
|
||||
sd = nd = -1;
|
||||
|
||||
if (kv.Size() == 1)
|
||||
@@ -751,32 +752,32 @@ NURBSPatch::NURBSPatch(std::istream &input)
|
||||
}
|
||||
}
|
||||
|
||||
NURBSPatch::NURBSPatch(const KnotVector *kv0, const KnotVector *kv1, int dim_)
|
||||
NURBSPatch::NURBSPatch(const KnotVector *kv0, const KnotVector *kv1, int dim)
|
||||
{
|
||||
kv.SetSize(2);
|
||||
kv[0] = new KnotVector(*kv0);
|
||||
kv[1] = new KnotVector(*kv1);
|
||||
init(dim_);
|
||||
init(dim);
|
||||
}
|
||||
|
||||
NURBSPatch::NURBSPatch(const KnotVector *kv0, const KnotVector *kv1,
|
||||
const KnotVector *kv2, int dim_)
|
||||
const KnotVector *kv2, int dim)
|
||||
{
|
||||
kv.SetSize(3);
|
||||
kv[0] = new KnotVector(*kv0);
|
||||
kv[1] = new KnotVector(*kv1);
|
||||
kv[2] = new KnotVector(*kv2);
|
||||
init(dim_);
|
||||
init(dim);
|
||||
}
|
||||
|
||||
NURBSPatch::NURBSPatch(Array<const KnotVector *> &kv_, int dim_)
|
||||
NURBSPatch::NURBSPatch(Array<const KnotVector *> &kvs, int dim)
|
||||
{
|
||||
kv.SetSize(kv_.Size());
|
||||
kv.SetSize(kvs.Size());
|
||||
for (int i = 0; i < kv.Size(); i++)
|
||||
{
|
||||
kv[i] = new KnotVector(*kv_[i]);
|
||||
kv[i] = new KnotVector(*kvs[i]);
|
||||
}
|
||||
init(dim_);
|
||||
init(dim);
|
||||
}
|
||||
|
||||
NURBSPatch::NURBSPatch(NURBSPatch *parent, int dir, int Order, int NCP)
|
||||
@@ -859,7 +860,7 @@ void NURBSPatch::Print(std::ostream &os) const
|
||||
|
||||
int NURBSPatch::SetLoopDirection(int dir)
|
||||
{
|
||||
if (nj == -1)
|
||||
if (nj == -1) // 1D case
|
||||
{
|
||||
if (dir == 0)
|
||||
{
|
||||
@@ -875,7 +876,7 @@ int NURBSPatch::SetLoopDirection(int dir)
|
||||
mfem_error();
|
||||
}
|
||||
}
|
||||
else if (nk == -1)
|
||||
else if (nk == -1) // 2D case
|
||||
{
|
||||
if (dir == 0)
|
||||
{
|
||||
@@ -898,7 +899,7 @@ int NURBSPatch::SetLoopDirection(int dir)
|
||||
mfem_error();
|
||||
}
|
||||
}
|
||||
else
|
||||
else // 3D case
|
||||
{
|
||||
if (dir == 0)
|
||||
{
|
||||
@@ -992,6 +993,7 @@ void NURBSPatch::GetCoarseningFactors(Array<int> & f) const
|
||||
|
||||
void NURBSPatch::KnotInsert(Array<KnotVector *> &newkv)
|
||||
{
|
||||
MFEM_ASSERT(newkv.Size() == kv.Size(), "Invalid input to KnotInsert");
|
||||
for (int dir = 0; dir < kv.Size(); dir++)
|
||||
{
|
||||
KnotInsert(dir, *newkv[dir]);
|
||||
@@ -1026,6 +1028,7 @@ void NURBSPatch::KnotInsert(int dir, const KnotVector &newkv)
|
||||
|
||||
void NURBSPatch::KnotInsert(Array<Vector *> &newkv)
|
||||
{
|
||||
MFEM_ASSERT(newkv.Size() == kv.Size(), "Invalid input to KnotInsert");
|
||||
for (int dir = 0; dir < kv.Size(); dir++)
|
||||
{
|
||||
KnotInsert(dir, *newkv[dir]);
|
||||
@@ -1143,7 +1146,7 @@ void NURBSPatch::KnotInsert(int dir, const Vector &knot)
|
||||
for (int ll = 0; ll < size; ll++)
|
||||
{
|
||||
newp.slice(ind-1,ll) = alfa*newp.slice(ind-1,ll) +
|
||||
(1.0-alfa)*newp.slice(ind, ll);
|
||||
(1.0-alfa)*newp.slice(ind,ll);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -1372,6 +1375,8 @@ void NURBSPatch::DegreeElevate(int dir, int t)
|
||||
mfem_error("NURBSPatch::DegreeElevate : Incorrect direction!");
|
||||
}
|
||||
|
||||
MFEM_ASSERT(t >= 0, "DegreeElevate cannot decrease the degree.");
|
||||
|
||||
int i, j, k, kj, mpi, mul, mh, kind, cind, first, last;
|
||||
int r, a, b, oldr, save, s, tr, lbz, rbz, l;
|
||||
real_t inv, ua, ub, numer, alf, den, bet, gam;
|
||||
@@ -1715,8 +1720,10 @@ void NURBSPatch::Get3DRotationMatrix(real_t n[], real_t angle, real_t r,
|
||||
DenseMatrix &T)
|
||||
{
|
||||
real_t c, s, c1;
|
||||
real_t l2 = n[0]*n[0] + n[1]*n[1] + n[2]*n[2];
|
||||
real_t l = sqrt(l2);
|
||||
const real_t l2 = n[0]*n[0] + n[1]*n[1] + n[2]*n[2];
|
||||
const real_t l = sqrt(l2);
|
||||
|
||||
MFEM_ASSERT(l2 > 0.0, "3D rotation axis is undefined");
|
||||
|
||||
if (fabs(angle) == (real_t)(M_PI_2))
|
||||
{
|
||||
@@ -1973,7 +1980,7 @@ NURBSExtension::NURBSExtension(std::istream &input, bool spacing)
|
||||
// Read topology
|
||||
patchTopo = new Mesh;
|
||||
patchTopo->LoadPatchTopo(input, edge_to_knot);
|
||||
own_topo = 1;
|
||||
own_topo = true;
|
||||
|
||||
CheckPatches();
|
||||
// CheckBdrPatches();
|
||||
@@ -2172,7 +2179,7 @@ NURBSExtension::NURBSExtension(std::istream &input, bool spacing)
|
||||
NURBSExtension::NURBSExtension(NURBSExtension *parent, int newOrder)
|
||||
{
|
||||
patchTopo = parent->patchTopo;
|
||||
own_topo = 0;
|
||||
own_topo = false;
|
||||
|
||||
parent->edge_to_knot.Copy(edge_to_knot);
|
||||
|
||||
@@ -2229,7 +2236,7 @@ NURBSExtension::NURBSExtension(NURBSExtension *parent,
|
||||
SetOrderFromOrders();
|
||||
|
||||
patchTopo = parent->patchTopo;
|
||||
own_topo = 0;
|
||||
own_topo = false;
|
||||
|
||||
parent->edge_to_knot.Copy(edge_to_knot);
|
||||
|
||||
@@ -2287,8 +2294,8 @@ NURBSExtension::NURBSExtension(Mesh *mesh_array[], int num_pieces)
|
||||
" parent does not own the patch topology!");
|
||||
}
|
||||
patchTopo = parent->patchTopo;
|
||||
own_topo = 1;
|
||||
parent->own_topo = 0;
|
||||
own_topo = true;
|
||||
parent->own_topo = false;
|
||||
|
||||
parent->edge_to_knot.Copy(edge_to_knot);
|
||||
|
||||
@@ -2442,7 +2449,7 @@ void NURBSExtension::PrintFunctions(const char *basename, int samples) const
|
||||
for (int i = 0; i < NumOfKnotVectors; i++)
|
||||
{
|
||||
std::ostringstream filename;
|
||||
filename << basename<<"_"<<i<<".dat";
|
||||
filename << basename << "_" << i << ".dat";
|
||||
os.open(filename.str().c_str());
|
||||
knotVectors[i]->PrintFunctions(os,samples);
|
||||
os.close();
|
||||
@@ -2889,7 +2896,6 @@ void NURBSExtension::CheckKVDirection(int p, Array <int> &kvdir)
|
||||
// -1: direction is flipped
|
||||
// 1: direction is not flipped
|
||||
|
||||
|
||||
for (int i = 0; i < edges.Size(); i++)
|
||||
{
|
||||
// First side
|
||||
@@ -3069,7 +3075,7 @@ void NURBSExtension::UpdateUniqueKV()
|
||||
bool NURBSExtension::ConsistentKVSets()
|
||||
{
|
||||
// patchTopo->GetElementEdges is not yet implemented for 1D
|
||||
MFEM_VERIFY(Dimension()>1, "1D not yet implemented.");
|
||||
MFEM_VERIFY(Dimension() > 1, "1D not yet implemented.");
|
||||
|
||||
Array<int> edges, orient, kvdir;
|
||||
Vector diff;
|
||||
@@ -3180,7 +3186,7 @@ const
|
||||
}
|
||||
}
|
||||
|
||||
void NURBSExtension::GetBdrPatchKnotVectors(int p, Array<KnotVector *> &kv)
|
||||
void NURBSExtension::GetBdrPatchKnotVectors(int bp, Array<KnotVector *> &kv)
|
||||
{
|
||||
Array<int> edges;
|
||||
Array<int> orient;
|
||||
@@ -3189,19 +3195,19 @@ void NURBSExtension::GetBdrPatchKnotVectors(int p, Array<KnotVector *> &kv)
|
||||
|
||||
if (Dimension() == 2)
|
||||
{
|
||||
patchTopo->GetBdrElementEdges(p, edges, orient);
|
||||
patchTopo->GetBdrElementEdges(bp, edges, orient);
|
||||
kv[0] = KnotVec(edges[0]);
|
||||
}
|
||||
else if (Dimension() == 3)
|
||||
{
|
||||
patchTopo->GetBdrElementEdges(p, edges, orient);
|
||||
patchTopo->GetBdrElementEdges(bp, edges, orient);
|
||||
kv[0] = KnotVec(edges[0]);
|
||||
kv[1] = KnotVec(edges[1]);
|
||||
}
|
||||
}
|
||||
|
||||
void NURBSExtension::GetBdrPatchKnotVectors(
|
||||
int p, Array<const KnotVector *> &kv) const
|
||||
int bp, Array<const KnotVector *> &kv) const
|
||||
{
|
||||
Array<int> edges;
|
||||
Array<int> orient;
|
||||
@@ -3210,12 +3216,12 @@ void NURBSExtension::GetBdrPatchKnotVectors(
|
||||
|
||||
if (Dimension() == 2)
|
||||
{
|
||||
patchTopo->GetBdrElementEdges(p, edges, orient);
|
||||
patchTopo->GetBdrElementEdges(bp, edges, orient);
|
||||
kv[0] = KnotVec(edges[0]);
|
||||
}
|
||||
else if (Dimension() == 3)
|
||||
{
|
||||
patchTopo->GetBdrElementEdges(p, edges, orient);
|
||||
patchTopo->GetBdrElementEdges(bp, edges, orient);
|
||||
kv[0] = KnotVec(edges[0]);
|
||||
kv[1] = KnotVec(edges[1]);
|
||||
}
|
||||
@@ -3305,8 +3311,6 @@ void NURBSExtension::GenerateOffsets()
|
||||
p_meshOffsets[p] = meshCounter;
|
||||
p_spaceOffsets[p] = spaceCounter;
|
||||
|
||||
|
||||
|
||||
if (dim == 1)
|
||||
{
|
||||
meshCounter += KnotVec(0)->GetNE() - 1;
|
||||
@@ -4748,8 +4752,8 @@ ParNURBSExtension::ParNURBSExtension(MPI_Comm comm, NURBSExtension *parent,
|
||||
mfem_error("ParNURBSExtension::ParNURBSExtension :\n"
|
||||
" parent does not own the patch topology!");
|
||||
}
|
||||
own_topo = 1;
|
||||
parent->own_topo = 0;
|
||||
own_topo = true;
|
||||
parent->own_topo = false;
|
||||
|
||||
parent->edge_to_knot.Copy(edge_to_knot);
|
||||
|
||||
@@ -4812,7 +4816,7 @@ ParNURBSExtension::ParNURBSExtension(NURBSExtension *parent,
|
||||
|
||||
patchTopo = parent->patchTopo;
|
||||
own_topo = parent->own_topo;
|
||||
parent->own_topo = 0;
|
||||
parent->own_topo = false;
|
||||
|
||||
Swap(edge_to_knot, parent->edge_to_knot);
|
||||
|
||||
@@ -5057,7 +5061,7 @@ Table *ParNURBSExtension::Get3DGlobalElementDofTable()
|
||||
return (new Table(GetGNE(), gel_dof_list));
|
||||
}
|
||||
|
||||
void ParNURBSExtension::SetActive(const int *partitioning_,
|
||||
void ParNURBSExtension::SetActive(const int *partition,
|
||||
const Array<bool> &active_bel)
|
||||
{
|
||||
activeElem.SetSize(GetGNE());
|
||||
@@ -5065,7 +5069,7 @@ void ParNURBSExtension::SetActive(const int *partitioning_,
|
||||
NumOfActiveElems = 0;
|
||||
const int MyRank = gtopo.MyRank();
|
||||
for (int i = 0; i < GetGNE(); i++)
|
||||
if (partitioning_[i] == MyRank)
|
||||
if (partition[i] == MyRank)
|
||||
{
|
||||
activeElem[i] = true;
|
||||
NumOfActiveElems++;
|
||||
@@ -5080,7 +5084,7 @@ void ParNURBSExtension::SetActive(const int *partitioning_,
|
||||
}
|
||||
}
|
||||
|
||||
void ParNURBSExtension::BuildGroups(const int *partitioning_,
|
||||
void ParNURBSExtension::BuildGroups(const int *partition,
|
||||
const Table &elem_dof)
|
||||
{
|
||||
Table dof_proc;
|
||||
@@ -5092,7 +5096,7 @@ void ParNURBSExtension::BuildGroups(const int *partitioning_,
|
||||
// convert elements to processors
|
||||
for (int i = 0; i < dof_proc.Size_of_connections(); i++)
|
||||
{
|
||||
dof_proc.GetJ()[i] = partitioning_[dof_proc.GetJ()[i]];
|
||||
dof_proc.GetJ()[i] = partition[dof_proc.GetJ()[i]];
|
||||
}
|
||||
|
||||
// the first group is the local one
|
||||
|
||||
+442
-143
File diff suppressed because it is too large
Load Diff
+7
-8
@@ -256,9 +256,6 @@ ParMesh::ParMesh(MPI_Comm comm, Mesh &mesh, int *partitioning_,
|
||||
// build svert_lvert mapping
|
||||
BuildSharedVertMapping(nsvert, vert_element, vert_global_local);
|
||||
delete vert_element;
|
||||
|
||||
SetMeshGen();
|
||||
meshgen = mesh.meshgen; // copy the global 'meshgen'
|
||||
}
|
||||
|
||||
if (mesh.NURBSext)
|
||||
@@ -1527,6 +1524,7 @@ ParMesh ParMesh::MakeSimplicial(ParMesh &orig_mesh)
|
||||
void ParMesh::Finalize(bool refine, bool fix_orientation)
|
||||
{
|
||||
const int meshgen_save = meshgen; // Mesh::Finalize() may call SetMeshGen()
|
||||
// 'mesh_geoms' is local, so there's no need to save and restore it.
|
||||
|
||||
Mesh::Finalize(refine, fix_orientation);
|
||||
|
||||
@@ -4807,7 +4805,7 @@ void ParMesh::Print(std::ostream &os, const std::string &comments) const
|
||||
|
||||
if (NURBSext)
|
||||
{
|
||||
Printer(os, comments); // does not print shared boundary
|
||||
Printer(os, "", comments); // does not print shared boundary
|
||||
return;
|
||||
}
|
||||
|
||||
@@ -4935,7 +4933,7 @@ void ParMesh::Print(std::ostream &os, const std::string &comments) const
|
||||
|
||||
if (set_names)
|
||||
{
|
||||
os << "mfem_mesh_end\n";
|
||||
os << "\nmfem_mesh_end" << endl;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -5286,7 +5284,7 @@ void ParMesh::PrintAsSerial(std::ostream &os, const std::string &comments) const
|
||||
Mesh serialmesh = GetSerialMesh(save_rank);
|
||||
if (MyRank == save_rank)
|
||||
{
|
||||
serialmesh.Printer(os, comments);
|
||||
serialmesh.Printer(os, "", comments);
|
||||
}
|
||||
MPI_Barrier(MyComm);
|
||||
}
|
||||
@@ -6325,11 +6323,11 @@ void ParMesh::ParPrint(ostream &os, const std::string &comments) const
|
||||
if (Nonconforming())
|
||||
{
|
||||
// the NC mesh format works both in serial and in parallel
|
||||
Printer(os, comments);
|
||||
Printer(os, "", comments);
|
||||
return;
|
||||
}
|
||||
|
||||
// Write out serial mesh. Tell serial mesh to deliniate the end of it's
|
||||
// Write out serial mesh. Tell serial mesh to delineate the end of its
|
||||
// output with 'mfem_serial_mesh_end' instead of 'mfem_mesh_end', as we will
|
||||
// be adding additional parallel mesh information.
|
||||
Printer(os, "mfem_serial_mesh_end", comments);
|
||||
@@ -6346,6 +6344,7 @@ void ParMesh::ParPrint(ostream &os, const std::string &comments) const
|
||||
{
|
||||
os << "total_shared_faces " << sface_lface.Size() << '\n';
|
||||
}
|
||||
os << "\n# group 0 has no shared entities\n";
|
||||
for (int gr = 1; gr < GetNGroups(); gr++)
|
||||
{
|
||||
{
|
||||
|
||||
+3
-3
@@ -819,7 +819,7 @@ ParPumiMesh::ParPumiMesh(MPI_Comm comm, apf::Mesh2* apf_mesh,
|
||||
apf::Downward verts;
|
||||
apf_mesh->getDownward(ent,0,verts);
|
||||
|
||||
int *v, nv = 0;
|
||||
int *v = nullptr, nv = 0;
|
||||
apf::Mesh::Type ftype = apf_mesh->getType(ent);
|
||||
if (ftype == apf::Mesh::TRIANGLE)
|
||||
{
|
||||
@@ -890,9 +890,9 @@ GridFunctionPumi::GridFunctionPumi(Mesh* m, apf::Mesh2* PumiM,
|
||||
{
|
||||
int spDim = m->SpaceDimension();
|
||||
// Note: default BasisType for 'fec' is GaussLobatto.
|
||||
fec = new H1_FECollection(mesh_order, m->Dimension());
|
||||
fec_owned = new H1_FECollection(mesh_order, m->Dimension());
|
||||
int ordering = Ordering::byVDIM; // x1y1z1/x2y2z2/...
|
||||
fes = new FiniteElementSpace(m, fec, spDim, ordering);
|
||||
fes = new FiniteElementSpace(m, fec_owned, spDim, ordering);
|
||||
int data_size = fes->GetVSize();
|
||||
|
||||
// Read PUMI mesh data
|
||||
|
||||
@@ -401,6 +401,7 @@ ParSubMesh::ParSubMesh(const ParMesh &parent, SubMesh::From from,
|
||||
|
||||
// Copy boundary attribute numbers into local portion of a parallel
|
||||
// grid function
|
||||
parent_bdr_attr_gf.HostReadWrite(); // not modifying all entries
|
||||
for (int i=0; i<parent.GetNBE(); i++)
|
||||
{
|
||||
faceIdx = parent.GetBdrElementFaceIndex(i);
|
||||
|
||||
@@ -53,7 +53,7 @@ void Tetrahedron::Init(int ind1, int ind2, int ind3, int ind4, int attr,
|
||||
}
|
||||
|
||||
void Tetrahedron::ParseRefinementFlag(int refinement_edges[2], int &type,
|
||||
int &flag)
|
||||
int &flag) const
|
||||
{
|
||||
int i, f = refinement_flag;
|
||||
|
||||
@@ -134,9 +134,10 @@ void Tetrahedron::CreateRefinementFlag(int refinement_edges[2], int type,
|
||||
refinement_flag |= refinement_edges[0];
|
||||
}
|
||||
|
||||
void Tetrahedron::GetMarkedFace(const int face, int *fv)
|
||||
void Tetrahedron::GetMarkedFace(const int face, int *fv) const
|
||||
{
|
||||
int re[2], type, flag, *tv = this->indices;
|
||||
int re[2], type, flag;
|
||||
const int *tv = this->indices;
|
||||
ParseRefinementFlag(re, type, flag);
|
||||
switch (face)
|
||||
{
|
||||
|
||||
@@ -58,12 +58,13 @@ public:
|
||||
/// Return element's type.
|
||||
Type GetType() const override { return Element::TETRAHEDRON; }
|
||||
|
||||
void ParseRefinementFlag(int refinement_edges[2], int &type, int &flag);
|
||||
void ParseRefinementFlag(int refinement_edges[2], int &type,
|
||||
int &flag) const;
|
||||
void CreateRefinementFlag(int refinement_edges[2], int type, int flag = 0);
|
||||
|
||||
void GetMarkedFace(const int face, int *fv);
|
||||
void GetMarkedFace(const int face, int *fv) const;
|
||||
|
||||
int GetRefinementFlag() { return refinement_flag; }
|
||||
int GetRefinementFlag() const { return refinement_flag; }
|
||||
|
||||
void SetRefinementFlag(int rf) { refinement_flag = rf; }
|
||||
|
||||
|
||||
@@ -797,13 +797,7 @@ void MagneticDiffusionEOperator::buildGrad()
|
||||
|
||||
real_t MagneticDiffusionEOperator::ElectricLosses(ParGridFunction &E_gf) const
|
||||
{
|
||||
real_t el = m1->InnerProduct(E_gf,E_gf);
|
||||
|
||||
real_t global_el;
|
||||
MPI_Allreduce(&el, &global_el, 1, MPITypeMap<real_t>::mpi_type, MPI_SUM,
|
||||
m2->ParFESpace()->GetComm());
|
||||
|
||||
return el;
|
||||
return m1->ParInnerProduct(E_gf, E_gf);
|
||||
}
|
||||
|
||||
// E is the input GF, w is the output GF which is assumed to be an L2 scalar
|
||||
|
||||
@@ -307,6 +307,7 @@ int main(int argc, char *argv[])
|
||||
}
|
||||
|
||||
// Send the solution by socket to a GLVis server.
|
||||
if (visualization)
|
||||
{
|
||||
char vishost[] = "localhost";
|
||||
int visport = 19916;
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user