Merge branch 'main' of https://github.com/Huangzizhou/polyfem-python

Author: Huangzizhou

README.md

@@ -10,11 +10,18 @@
 The Python bindings are in alpha. Expect a lot of API changes and possible bugs. Use at your own peril!
 
 <br/>
-To use the Python bindings, clone the current repository and use `pip` to install:
+To use the Python bindings, clone the current repository and use anaconda to install:
 
 ```
+conda create -n diffipc python=3.9
+conda activate diffipc
+conda install numpy scipy conda-forge::cython pytorch::pytorch
+
+# optional
+export N_THREADS=16
+
 cd polyfem-python/
-pip install .
+pip install . -v
 ```
 
 For full documentation see [https://polyfem.github.io/](https://polyfem.github.io/).

pyproject.toml

@@ -0,0 +1,17 @@
+[build-system]
+requires = ["setuptools", "wheel", "pybind11", "cmake"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "polyfempy"
+version = "0.8"
+description="Polyfem Python Bindings"
+readme = "README.md"
+authors = [
+  { name = "Zizhou Huang", email = "zizhou@nyu.edu" },
+]
+requires-python = ">=3.6"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License"
+]

setup.py

@@ -37,25 +37,17 @@ def run(self):
             self.build_extension(ext)
 
     def build_extension(self, ext):
-        use_cholmod = os.environ.get( "USE_CHOLMOD", "1" )
         n_threads_str = os.environ.get( "N_THREADS", "1" )
         n_threads = int(n_threads_str)
 
-        cholmod_str = "-DPOLYSOLVE_WITH_CHOLMOD=OFF" if use_cholmod == "0" else "-DPOLYSOLVE_WITH_CHOLMOD=ON"
-
-
         extdir = os.path.join(os.path.abspath(os.path.dirname(
             self.get_ext_fullpath(ext.name))), "polyfempy")
 
         python_include_directory = str(get_python_inc())
 
         cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
                       '-DPYTHON_EXECUTABLE=' + sys.executable,
-                      '-DPYTHON_INCLUDE_DIR=' + python_include_directory,
-                      cholmod_str,
-                      '-DPOLYSOLVE_WITH_AMGCL=OFF',
-                      '-DPOLYSOLVE_WITH_MKL=OFF',
-                      '-DPOLYSOLVE_WITH_SPECTRA=OFF']
+                      '-DPYTHON_INCLUDE_DIR=' + python_include_directory]
 
         cfg = 'Debug' if self.debug else 'Release'
         build_args = ['--config', cfg]
@@ -93,9 +85,6 @@ def build_extension(self, ext):
 
 setup(
     name="polyfempy",
-    version="0.7",
-    author="Teseo Schneider",
-    author_email="",
     description="Polyfem Python Bindings",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -108,13 +97,5 @@ def build_extension(self, ext):
         "License :: OSI Approved :: MIT License"
     ],
     python_requires='>=3.6',
-    install_requires=[
-        'numpy',
-        'argparse'],
-    entry_points={
-        'console_scripts': [
-            'polyfem = polyfempy.command:polyfem'
-        ]
-    },
     test_suite="test"
 )

src/state/state.cpp

@@ -11,11 +11,6 @@
 #include <polyfem/time_integrator/ImplicitTimeIntegrator.hpp>
 #include <polyfem/State.hpp>
 
-// #include "raster.hpp"
-
-#include <igl/boundary_facets.h>
-#include <igl/remove_unreferenced.h>
-
 #include <stdexcept>
 
 #include <pybind11_json/pybind11_json.hpp>
@@ -285,7 +280,7 @@ void define_solver(py::module_ &m)
           py::arg("n_refs") = int(0),
           py::arg("boundary_id_threshold") = double(-1))
 
-      .def("nl_problem", [](State &s) { return s.solve_data.nl_problem; })
+      .def("nl_problem", [](State &s) { return *(s.solve_data.nl_problem); }, py::return_value_policy::reference)
 
       .def(
           "solve",

test/test.py

@@ -0,0 +1,63 @@
+# %%
+import polyfempy as pf
+import json
+import numpy as np
+
+# %%
+root = "../data/differentiable/input"
+with open(root + "/initial-contact.json", "r") as f:
+    config = json.load(f)
+
+config["contact"]["use_convergent_formulation"] = True
+config["root_path"] = root + "/initial-contact.json"
+
+solver = pf.Solver()
+solver.set_settings(json.dumps(config), True)
+solver.set_log_level(2)
+solver.load_mesh_from_settings()
+
+# %%
+mesh = solver.mesh()
+
+print(mesh.n_vertices())
+print(mesh.n_elements())
+print(mesh.n_cell_vertices(1))
+print(mesh.element_vertex(3, 0))
+print(mesh.boundary_element_vertex(3, 0))
+assert(mesh.is_boundary_vertex(1))
+
+min, max = mesh.bounding_box()
+
+# %%
+config = solver.settings()
+t0 = config["time"]["t0"]
+dt = config["time"]["dt"]
+
+# inits stuff
+solver.build_basis()
+solver.assemble()
+sol = solver.init_timestepping(t0, dt)
+
+for i in range(1, 5):
+    
+    # substepping
+    for t in range(1):
+        sol = solver.step_in_time(sol, t0, dt, t+1)
+
+    t0 += dt
+    solver.export_vtu("step_" + str(i) + ".vtu", sol, np.zeros((0, 0)), t0, dt)
+
+prob = solver.nl_problem()
+
+h = prob.hessian(sol)
+reduced_sol = prob.full_to_reduced(sol)
+full_sol = prob.reduced_to_full(reduced_sol)
+
+assert(np.linalg.norm(full_sol - sol.flatten()) < 1e-12)
+
+cache = solver.get_solution_cache()
+
+print(cache.solution(1).shape)
+print(cache.velocity(2).shape)
+print(cache.acceleration(3).shape)
+print(cache.hessian(4).shape)

test/test_basic.ipynb

@@ -119,7 +119,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,

test/test_differentiable.ipynb

@@ -140,7 +140,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,

test/test_sim.py

@@ -2,9 +2,9 @@
 import json
 import numpy as np
 
-pf.polyfem_command(json="/Users/zizhouhuang/Desktop/polyfem-python/data/contact/examples/2D/unit-tests/5-squares.json", log_level=2, max_threads=16)
+pf.polyfem_command(json="../data/contact/examples/2D/unit-tests/5-squares.json", log_level=2, max_threads=16)
 
-root = "/Users/zizhouhuang/Desktop/polyfem/data/contact/examples/2D/unit-tests"
+root = "../data/contact/examples/2D/unit-tests"
 with open(root + "/5-squares.json", "r") as f:
     config = json.load(f)