update polyfem

CMakeLists.txt

@@ -1,6 +1,6 @@
 ################################################################################
 # Check required CMake version
-set(REQUIRED_CMAKE_VERSION "3.14.0")
+set(REQUIRED_CMAKE_VERSION "3.25.0")
 cmake_minimum_required(VERSION ${REQUIRED_CMAKE_VERSION})
 
 if(INPUT_POLYFEMPY_DATA_ROOT)
@@ -13,11 +13,18 @@ if(NOT EXISTS ${POLYFEMPY_DATA_ROOT})
 endif()
 
 project(polyfempy)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
 ################################################################################
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/recipes/")
 
+include(polyfem_cpm_cache)
+
 # Color output
 include(UseColors)
 
@@ -51,11 +58,9 @@ include(polyfem_data)
 ################################################################################
 # Subdirectories
 ################################################################################
-add_library(polyfempy MODULE src/binding.cpp src/raster.cpp)
+pybind11_add_module(polyfempy)
+add_subdirectory(src)
+target_include_directories(polyfempy PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/src")
 target_link_libraries(polyfempy PRIVATE polyfem::polyfem pybind11::module pybind11::json)
 
 set_target_properties(polyfempy PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}" SUFFIX "${PYTHON_MODULE_EXTENSION}")
-
-
-
-

README.md

@@ -8,29 +8,12 @@
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/polyfempy/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge)
 
 
-
-
-The python bindings are in alpha. Expect a lot of API changes and possible bugs. Use at your own peril!
+The Python bindings are in alpha. Expect a lot of API changes and possible bugs. Use at your own peril!
 
 <br/>
-I am making efforts to provide a simple python interface to Polyfem.
-
-For doing so I am maintaining  a *conda* package which can be easily installed [https://anaconda.org/conda-forge/polyfempy](https://anaconda.org/conda-forge/polyfempy).
-
-Note that the conda deployment is slow and this tutorial will follow the deployment version.
-
-If you hare in a hurry for the juicy latest feature you can clone the repository [Polyfem-python](https://github.com/polyfem/polyfem-python) and use `pip` to install:
+To use the Python bindings, clone the current repository and use `pip` to install:
 ```
-python setup.py install
+pip install .
 ```
-and
-```
-python setup.py test
-```
-for testing.
-
-For python documentation [https://polyfem.github.io/python/](https://polyfem.github.io/python/).
-
-For python jupyter notebook [https://polyfem.github.io/python_examples/](https://polyfem.github.io/python_examples/).
 
 For full documentation see [https://polyfem.github.io/](https://polyfem.github.io/).

cmake/recipes/CPM.cmake

@@ -0,0 +1,33 @@
+set(CPM_DOWNLOAD_VERSION 0.39.0)
+
+if(CPM_SOURCE_CACHE)
+  set(CPM_DOWNLOAD_LOCATION "${CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+elseif(DEFINED ENV{CPM_SOURCE_CACHE})
+  set(CPM_DOWNLOAD_LOCATION "$ENV{CPM_SOURCE_CACHE}/cpm/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+else()
+  set(CPM_DOWNLOAD_LOCATION "${CMAKE_BINARY_DIR}/cmake/CPM_${CPM_DOWNLOAD_VERSION}.cmake")
+endif()
+
+# Expand relative path. This is important if the provided path contains a tilde (~)
+get_filename_component(CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE)
+
+function(download_cpm)
+  message(STATUS "Downloading CPM.cmake to ${CPM_DOWNLOAD_LOCATION}")
+  file(DOWNLOAD
+       https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake
+       ${CPM_DOWNLOAD_LOCATION}
+  )
+endfunction()
+
+if(NOT (EXISTS ${CPM_DOWNLOAD_LOCATION}))
+  download_cpm()
+else()
+  # resume download if it previously failed
+  file(READ ${CPM_DOWNLOAD_LOCATION} check)
+  if("${check}" STREQUAL "")
+    download_cpm()
+  endif()
+  unset(check)
+endif()
+
+include(${CPM_DOWNLOAD_LOCATION})

cmake/recipes/polyfem.cmake

@@ -7,13 +7,14 @@ endif()
 
 message(STATUS "Third-party: creating target 'polyfem::polyfem'")
 
-include(FetchContent)
-FetchContent_Declare(
-    polyfem
-    GIT_REPOSITORY https://github.com/polyfem/polyfem.git
-    GIT_TAG 12ac634833f91a3946cff26db01972fdb2ec3214
-    GIT_SHALLOW FALSE
-)
-FetchContent_MakeAvailable(polyfem)
-
+# include(FetchContent)
+# FetchContent_Declare(
+#     polyfem
+#     GIT_REPOSITORY https://github.com/polyfem/polyfem.git
+#     GIT_TAG 07ee824f836c445699bbc47ee6f19afbfe39bad4
+#     GIT_SHALLOW FALSE
+# )
+# FetchContent_MakeAvailable(polyfem)
 
+include(CPM)
+CPMAddPackage("gh:polyfem/polyfem#71b67e6416c59f498589ddc1633c11e6c246b392")

cmake/recipes/polyfem_cpm_cache.cmake

@@ -0,0 +1,24 @@
+#
+# Copyright 2021 Adobe. All rights reserved.
+# This file is licensed to you under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software distributed under
+# the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR REPRESENTATIONS
+# OF ANY KIND, either express or implied. See the License for the specific language
+# governing permissions and limitations under the License.
+#
+
+if(DEFINED ENV{CPM_SOURCE_CACHE})
+    set(CPM_SOURCE_CACHE_DEFAULT $ENV{CPM_SOURCE_CACHE})
+else()
+    # Set CPM cache folder if unset
+    file(REAL_PATH "~/.cache/CPM" CPM_SOURCE_CACHE_DEFAULT EXPAND_TILDE)
+endif()
+
+set(CPM_SOURCE_CACHE
+    ${CPM_SOURCE_CACHE_DEFAULT}
+    CACHE PATH "Directory to download CPM dependencies"
+)
+message(STATUS "Using CPM cache folder: ${CPM_SOURCE_CACHE}")

cmake/recipes/polyfem_data.cmake

@@ -7,7 +7,7 @@ include(FetchContent)
 FetchContent_Declare(
     polyfem_data
     GIT_REPOSITORY https://github.com/polyfem/polyfem-data
-    GIT_TAG 29a46df1fd90c237a82c219f346a956e72bd17d3
+    GIT_TAG f2089eb6eaa22071f7490e0f144e10afe85d4eba
     GIT_SHALLOW FALSE
     SOURCE_DIR ${POLYFEMPY_DATA_ROOT}
 )

cmake/recipes/pybind11.cmake

@@ -1,28 +1,11 @@
-#
-# Copyright 2020 Adobe. All rights reserved.
-# This file is licensed to you under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License. You may obtain a copy
-# of the License at http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software distributed under
-# the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR REPRESENTATIONS
-# OF ANY KIND, either express or implied. See the License for the specific language
-# governing permissions and limitations under the License.
-#
+# pybind11 (https://github.com/pybind/pybind11)
+# License: BSD-style
 if(TARGET pybind11::pybind11)
     return()
 endif()
 
 message(STATUS "Third-party: creating target 'pybind11::pybind11'")
 
-include(FetchContent)
-FetchContent_Declare(
-    pybind11
-    GIT_REPOSITORY https://github.com/pybind/pybind11.git
-    GIT_TAG v2.9.2
-    GIT_SHALLOW FALSE
-)
-
 if (POLICY CMP0094)  # https://cmake.org/cmake/help/latest/policy/CMP0094.html
     cmake_policy(SET CMP0094 NEW)  # FindPython should return the first matching Python
 endif ()
@@ -39,7 +22,8 @@ endif ()
 # Pybind11 still uses the deprecated FindPythonInterp. So let's call CMake's
 # new FindPython module and set PYTHON_EXECUTABLE for Pybind11 to pick up.
 # This works well with conda environments.
-find_package(Python REQUIRED COMPONENTS Interpreter Development)
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
 set(PYTHON_EXECUTABLE ${Python_EXECUTABLE})
 
-FetchContent_MakeAvailable(pybind11)
+include(CPM)
+CPMAddPackage("gh:pybind/[email protected]")

polyfempy/Settings.py

@@ -14,8 +14,7 @@ def __init__(self, discr_order=1, pressure_discr_order=1, pde=polyfempy.PDEs.Lap
 
         self.BDF_order = 1
 
-        self.scalar_formulation = "Laplacian"
-        self.tensor_formulation = "LinearElasticity"
+        self.formulation = "Laplacian"
         self.has_collision = contact_problem
         self.BDF_order = BDF_order
 
@@ -39,7 +38,6 @@ def __init__(self, discr_order=1, pressure_discr_order=1, pde=polyfempy.PDEs.Lap
         self.pde = pde
 
         self.selection = None
-        raise RuntimeError("Old Version Deprecated. Use version <0.5.2 on conda for the old interface")
 
     def get_problem(self):
         """Get the problem"""
@@ -62,23 +60,13 @@ def set_problem(self, problem):
 
     def get_pde(self, pde):
         """Get the PDE"""
-        if self._is_scalar:
-            return self.scalar_formulation
-        else:
-            self.tensor_formulation
+        return self.formulation
 
     def set_pde(self, pde):
         """Sets the PDE to solve, use any of the polyfempy.PDEs"""
 
-        if pde == "NonLinearElasticity":
-            pde = "NeoHookean"
-
         self._is_scalar = not polyfempy.polyfempy.is_tensor(pde)
-
-        if self._is_scalar:
-            self.scalar_formulation = pde
-        else:
-            self.tensor_formulation = pde
+        self.formulation = pde
 
     def set_material_params(self, name, value):
         """set the material parameters, for instance set_material_params("E", 200) sets the Young's modulus E to 200. See https://polyfem.github.io/documentation/#formulations for full list"""

polyfempy/__init__.py

@@ -1,9 +1,4 @@
-from .polyfempy import Solver
-from .polyfempy import PDEs
-from .polyfempy import ScalarFormulations
-from .polyfempy import TensorFormulations
-from .polyfempy import solve_febio
-from .polyfempy import solve
+from .polyfempy import *
 
 from .Settings import Settings
 from .Selection import Selection

polyfempy/command.py

@@ -6,80 +6,30 @@ def polyfem():
     parser = argparse.ArgumentParser()
 
     parser.add_argument("-j", "--json", type=str,
-                        default="", help="Simulation json file")
-    parser.add_argument("-m", "--mesh", type=str, default="", help="Mesh path")
-    parser.add_argument("-b", "--febio", type=str,
-                        default="", help="FEBio file path")
+                        default="", help="Simulation JSON file")
 
-    parser.add_argument("--n_refs", type=int, default=0,
-                        help="Number of refinements")
-    parser.add_argument("--not_norm", type=bool, default=True,
-                        help="Skips mesh normalization")
+    parser.add_argument("-y", "--yaml", type=str,
+                        default="", help="Simulation YAML file")
 
-    parser.add_argument("--problem", type=str,
-                        default="", help="Problem name")
-    parser.add_argument("--sform", type=str,
-                        default="", help="Scalar formulation")
-    parser.add_argument("--tform", type=str,
-                        default="", help="Tensor formulation")
+    parser.add_argument("--max_threads", type=int, default=1,
+                        help="Maximum number of threads")
 
-    parser.add_argument("--solver", type=str, default="", help="Solver to use")
+    parser.add_argument("-s", "--strict_validation", action='store_true',
+                        help="Enables strict validation of input JSON")
 
-    parser.add_argument("-q", "-p", type=int, default=1,
-                        help="Discretization order")
-    parser.add_argument("--p_ref", type=bool,
-                        default=False, help="Use p refimenet")
-    # parser.add_argument("--spline", use_splines, "Use spline for quad/hex meshes");
-    parser.add_argument("--count_flipped_els", type=bool,
-                        default=False, help="Count flippsed elements")
-    parser.add_argument("--lin_geom", type=bool, default=False,
-                        help="Force use linear geometric mapping")
-    # parser.add_argument("--isoparametric", isoparametric, "Force use isoparametric basis");
-    # parser.add_argument("--serendipity", serendipity, "Use of serendipity elements, only for Q2");
-    # parser.add_argument("--stop_after_build_basis", stop_after_build_basis, "Stop after build bases");
-    parser.add_argument("--vis_mesh_res", type=float,
-                        default=-1.0, help="Vis mesh resolution")
-    parser.add_argument("--project_to_psd", type=bool,
-                        default=False, help="Project local matrices to psd")
-    parser.add_argument("--n_incr_load", type=int, default=-
-                        1, help="Number of incremeltal load")
-
-    parser.add_argument("--output", type=str, default="",
-                        help="Output json file")
-    parser.add_argument("--vtu", type=str, default="", help="Vtu output file")
-
-    parser.add_argument("--quiet", type=bool, default=False,
-                        help="Disable cout for logging")
-    parser.add_argument("--log_file", type=str,
-                        default="", help="Log to a file")
     parser.add_argument("--log_level", type=int, default=1,
                         help="Log level 1 debug 2 info")
 
-    parser.add_argument("--export_material_params", type=bool,
-                        default=False, help="Export material parameters")
+    parser.add_argument("-o", "--output_dir", type=str,
+                        default="", help="Directory for output files")
 
     args = parser.parse_args()
 
     polyfem_command(
-        args.json,
-        args.febio,
-        args.mesh,
-        args.problem,
-        args.sform,
-        args.tform,
-        args.n_refs,
-        args.not_norm,
-        args.solver,
-        args.q,
-        args.p_ref,
-        args.count_flipped_els,
-        args.lin_geom,
-        args.vis_mesh_res,
-        args.project_to_psd,
-        args.n_incr_load,
-        args.output,
-        args.vtu,
-        args.log_level,
-        args.log_file,
-        args.quiet,
-        args.export_material_params)
+        json=args.json,
+        yaml=args.yaml,
+        log_level=args.log_level,
+        strict_validation=args.strict_validation,
+        max_threads=args.max_threads,
+        output_dir=args.output_dir
+        )

setup.py

@@ -52,10 +52,7 @@ def build_extension(self, ext):
         cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
                       '-DPYTHON_EXECUTABLE=' + sys.executable,
                       '-DPYTHON_INCLUDE_DIR=' + python_include_directory,
-                      '-DPOLYSOLVE_WITH_PARDISO=OFF',
                       cholmod_str,
-                      #   '-DPOLYFEM_THREADING=NONE',
-                      '-DPOLYFEM_NO_UI=ON',
                       '-DPOLYSOLVE_WITH_AMGCL=OFF',
                       '-DPOLYSOLVE_WITH_MKL=OFF',
                       '-DPOLYSOLVE_WITH_SPECTRA=OFF']

src/CMakeLists.txt

@@ -0,0 +1,16 @@
+set(SOURCES
+  binding.cpp
+  raster.cpp
+)
+
+source_group(TREE "${CMAKE_CURRENT_SOURCE_DIR}" PREFIX "Source Files" FILES ${SOURCES})
+target_sources(polyfempy PRIVATE ${SOURCES})
+
+################################################################################
+# Subfolders
+################################################################################
+
+add_subdirectory(differentiable)
+add_subdirectory(mesh)
+add_subdirectory(state)
+add_subdirectory(solver)