phiFEM 0.7.1.dev1__tar.gz → 0.7.2.dev1__tar.gz

{phifem-0.7.1.dev1 → phifem-0.7.2.dev1}/.gitignore

@@ -548,5 +548,6 @@ run_image.sh# pixi environments
 **/*.xdmf
 **/*.h5
 **/*.toml
+!pixi.toml
 **/*.sh
 **/*.prof

phifem-0.7.2.dev1/.vscode/settings.json

@@ -0,0 +1,70 @@
+{
+    "workbench.colorCustomizations": {
+        "activityBar.activeBackground": "#0eb103",
+        "activityBar.background": "#0eb103",
+        "activityBar.foreground": "#e7e7e7",
+        "activityBar.inactiveForeground": "#e7e7e799",
+        "activityBarBadge.background": "#e0e2fe",
+        "activityBarBadge.foreground": "#15202b",
+        "commandCenter.border": "#e7e7e799",
+        "sash.hoverBorder": "#0eb103",
+        "statusBar.background": "#0a7f02",
+        "statusBar.foreground": "#e7e7e7",
+        "statusBarItem.hoverBackground": "#0eb103",
+        "statusBarItem.remoteBackground": "#030fbc",
+        "statusBarItem.remoteForeground": "#e7e7e7",
+        "titleBar.activeBackground": "#0a7f02",
+        "titleBar.activeForeground": "#e7e7e7",
+        "titleBar.inactiveBackground": "#0a7f0299",
+        "titleBar.inactiveForeground": "#e7e7e799",
+        "activityBarTop.activeBackground": "#0eb103",
+        "activityBarTop.background": "#0eb103",
+        "activityBarTop.foreground": "#e7e7e7",
+        "activityBarTop.inactiveForeground": "#e7e7e799",
+        "commandCenter.foreground": "#e7e7e7",
+        "statusBar.debuggingBackground": "#0a7f02",
+        "statusBar.debuggingForeground": "#e7e7e7",
+        "activityBar.activeBorder": "#e7e7e7",
+        "activityBarTop.activeBorder": "#e7e7e7"
+    },
+    "peacock.color": "#0a7f02",
+    "peacock.favoriteColors": [
+
+        {
+            "name": "Angular Red",
+            "value": "#dd0531"
+        },
+        {
+            "name": "Azure Blue",
+            "value": "#007fff"
+        },
+        {
+            "name": "JavaScript Yellow",
+            "value": "#f9e64f"
+        },
+        {
+            "name": "Mandalorian Blue",
+            "value": "#1857a4"
+        },
+        {
+            "name": "Node Green",
+            "value": "#215732"
+        },
+        {
+            "name": "React Blue",
+            "value": "#61dafb"
+        },
+        {
+            "name": "Something Different",
+            "value": "#832561"
+        },
+        {
+            "name": "Svelte Orange",
+            "value": "#ff3d00"
+        },
+        {
+            "name": "Vue Green",
+            "value": "#42b883"
+        }
+    ]
+}

{phifem-0.7.1.dev1 → phifem-0.7.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: phiFEM
-Version: 0.7.1.dev1
+Version: 0.7.2.dev1
 Summary: phiFEM: convenience tools to use the phiFEM immersed boundary finite element method with dolfinx.
 Project-URL: Homepage, https://github.com/PhiFEM/phiFEM
 Project-URL: Issues, https://github.com/PhiFEM/phiFEM/issues

phifem-0.7.2.dev1/demo/interface-elasticity/plot.py

@@ -0,0 +1,18 @@
+import numpy as np
+import polars as pl
+import matplotlib.pyplot as plt
+
+eql = pl.read_csv("param1_output/results.csv")
+std = pl.read_csv("std_output/results.csv")
+
+fig = plt.figure()
+ax = fig.subplots()
+for name, data in zip(["eql", "std"], [eql, std]):
+    for norm in ["H10 relative error", "L2 relative error"]:
+        xs = data["dof"].to_numpy()
+        ys = data[norm].to_numpy()
+
+        ax.loglog(xs, ys, "-^", label=norm.split(sep=' ')[0] + ' ' + name)
+
+plt.legend()
+plt.savefig("convergence.png")

phifem-0.7.2.dev1/demo/multimaterial-cantilever/output/petsc_log.txt

@@ -0,0 +1,108 @@
+****************************************************************************************************************************************************************
+***                                WIDEN YOUR WINDOW TO 160 CHARACTERS.  Use 'enscript -r -fCourier9' to print this document                                 ***
+****************************************************************************************************************************************************************
+
+------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------
+
+Unknown Name on a  named fedora1.home with 1 process, by rbulle on Sat Jul  4 00:25:30 2026
+Using 20 OpenMP threads
+Using PETSc Release Version 3.24.4, Jan 30, 2026
+
+                         Max       Max/Min     Avg       Total
+Time (sec):           8.030e-01     1.000   8.030e-01
+Objects:              0.000e+00     0.000   0.000e+00
+Flops:                4.922e+07     1.000   4.922e+07  4.922e+07
+Flops/sec:            6.130e+07     1.000   6.130e+07  6.130e+07
+MPI Msg Count:        0.000e+00     0.000   0.000e+00  0.000e+00
+MPI Msg Len (bytes):  0.000e+00     0.000   0.000e+00  0.000e+00
+MPI Reductions:       0.000e+00     0.000
+
+Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract)
+                            e.g., VecAXPY() for real vectors of length N --> 2N flops
+                            and VecAXPY() for complex vectors of length N --> 8N flops
+
+Summary of Stages:   ----- Time ------  ----- Flop ------  --- Messages ---  -- Message Lengths --  -- Reductions --
+                        Avg     %Total     Avg     %Total    Count   %Total     Avg         %Total    Count   %Total
+ 0:      Main Stage: 3.8547e-01  48.0%  4.6737e+07  94.9%  0.000e+00   0.0%  0.000e+00        0.0%  0.000e+00   0.0%
+
+------------------------------------------------------------------------------------------------------------------------
+See the 'Profiling' chapter of the users' manual for details on interpreting output.
+Phase summary info:
+   Count: number of times phase was executed
+   Time and Flop: Max - maximum over all processes
+                  Ratio - ratio of maximum to minimum over all processes
+   Mess: number of messages sent
+   AvgLen: average message length (bytes)
+   Reduct: number of global reductions
+   Global: entire computation
+   Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop().
+      %T - percent time in this phase         %F - percent flop in this phase
+      %M - percent messages in this phase     %L - percent message lengths in this phase
+      %R - percent reductions in this phase
+   Total Mflop/s: 1e-6 * (sum of flop over all processes)/(max time over all processes)
+------------------------------------------------------------------------------------------------------------------------
+Event                Count      Time (sec)     Flop                              --- Global ---  --- Stage ----  Total
+                   Max Ratio  Max     Ratio   Max  Ratio  Mess   AvgLen  Reduct  %T %F %M %L %R  %T %F %M %L %R Mflop/s
+------------------------------------------------------------------------------------------------------------------------
+
+--- Event Stage 0: Main Stage
+
+BuildTwoSided          1 1.0 8.3500e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
+SFSetGraph             1 1.0 2.8300e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
+SFSetUp                1 1.0 3.2110e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
+VecMDot                1 1.0 1.5732e-05 1.0 4.18e+04 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  2658
+VecNorm                2 1.0 4.1922e-05 1.0 8.36e+04 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  1995
+VecScale               2 1.0 1.2051e-05 1.0 4.18e+04 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  3471
+VecCopy                3 1.0 4.1677e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
+VecSet                 2 1.0 1.9565e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
+VecAXPY                1 1.0 1.0378e-05 1.0 4.18e+04 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  4030
+VecMAXPY               2 1.0 1.1011e-05 1.0 8.36e+04 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  7597
+VecNormalize           2 1.0 5.7649e-05 1.0 1.25e+05 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  2176
+MatMult                1 1.0 1.4990e-03 1.0 3.38e+06 1.0 0.0e+00 0.0e+00 0.0e+00  0  7  0  0  0   0  7  0  0  0  2257
+MatSolve               2 1.0 1.2231e-02 1.0 3.24e+07 1.0 0.0e+00 0.0e+00 0.0e+00  2 66  0  0  0   3 69  0  0  0  2650
+MatLUFactorSym         1 1.0 4.5700e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  6  0  0  0  0  12  0  0  0  0     0
+MatLUFactorNum         1 1.0 3.2561e-01 1.0 1.06e+07 1.0 0.0e+00 0.0e+00 0.0e+00 41 22  0  0  0  84 23  0  0  0    33
+PCSetUp                1 1.0 3.7133e-01 1.0 1.06e+07 1.0 0.0e+00 0.0e+00 0.0e+00 46 22  0  0  0  96 23  0  0  0    29
+PCApply                2 1.0 1.2235e-02 1.0 3.24e+07 1.0 0.0e+00 0.0e+00 0.0e+00  2 66  0  0  0   3 69  0  0  0  2649
+KSPSetUp               1 1.0 1.0224e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
+KSPSolve               1 1.0 1.3936e-02 1.0 3.61e+07 1.0 0.0e+00 0.0e+00 0.0e+00  2 73  0  0  0   4 77  0  0  0  2590
+KSPGMRESOrthog         1 1.0 2.4189e-05 1.0 8.36e+04 1.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  3458
+------------------------------------------------------------------------------------------------------------------------
+
+Object Type          Creations   Destructions. Reports information only for process 0.
+
+--- Event Stage 0: Main Stage
+
+           Index Set     2              2
+   IS L to G Mapping     1              0
+   Star Forest Graph     3              0
+              Vector    21              1
+    Distributed Mesh     1              0
+     Discrete System     1              0
+           Weak Form     1              0
+========================================================================================================================
+Average time to get PetscTime(): 2.09e-08
+#No PETSc Option Table entries
+Compiled without FORTRAN kernels
+Compiled with full precision matrices (default)
+sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4
+Configure options: AR=${PREFIX}/bin/x86_64-conda-linux-gnu-ar CPP=${PREFIX}/bin/x86_64-conda-linux-gnu-cpp RANLIB=${PREFIX}/bin/x86_64-conda-linux-gnu-ranlib CC=mpicc CXX=mpicxx FC=mpifort CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include" LDFLAGS="-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib -Wl,-rpath-link,/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib -L/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib" --COPTFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda/petsc-3.24.4 -fdebug-prefix-map=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default=/usr/local/src/conda-prefix -O3" --CXXOPTFLAGS="-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda/petsc-3.24.4 -fdebug-prefix-map=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default=/usr/local/src/conda-prefix -O3" --FOPTFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -I${PREFIX}/include -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda/petsc-3.24.4 -fdebug-prefix-map=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default=/usr/local/src/conda-prefix -O3" --CUDAOPTFLAGS=-O3 --with-clib-autodetect=0 --with-cxxlib-autodetect=0 --with-fortranlib-autodetect=0 --with-debugging=0 --with-blas-lib=libblas.so --with-lapack-lib=liblapack.so --with-yaml=1 --with-hdf5=1 --with-fftw=1 --with-hwloc=1 --with-openmp=1 --with-hypre=1 --with-metis=1 --with-mpi=1 --with-mumps=1 --with-parmetis=1 --with-pthread=1 --with-ptscotch=1 --with-shared-libraries --with-ssl=0 --with-scalapack=1 --with-superlu=1 --with-superlu_dist=1 --with-superlu_dist-include=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include/superlu-dist --with-superlu_dist-lib=-lsuperlu_dist --with-suitesparse=1 --with-suitesparse-dir=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default --with-x=0 --with-scalar-type=real   --with-cuda=0 --prefix=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default
+-----------------------------------------
+Libraries compiled on 2026-01-31 17:50:54 on reproducible
+Machine characteristics: Linux-6.11.0-1018-azure-x86_64-with-glibc2.34
+Using PETSc directory: /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default
+Using PETSc arch: 
+-----------------------------------------
+
+Using C compiler: mpicc  -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda/petsc-3.24.4 -fdebug-prefix-map=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -fopenmp
+Using Fortran compiler: mpifort  -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -I${PREFIX}/include -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda/petsc-3.24.4 -fdebug-prefix-map=/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default=/usr/local/src/conda-prefix -O3   -fopenmp -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -fopenmp
+-----------------------------------------
+
+Using include paths: -I/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include -I/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include/suitesparse -I/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/include/superlu-dist
+-----------------------------------------
+
+Using C linker: mpicc
+Using Fortran linker: mpifort
+Using libraries: -Wl,-rpath,/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib -L/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib -lpetsc -Wl,-rpath,/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib -L/home/rbulle/Code/INRIA/phiFEM/.pixi/envs/default/lib -lHYPRE -lspqr -lumfpack -lklu -lcholmod -lamd -lfftw3_mpi -lfftw3 -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu_dist -lsuperlu -llapack -lblas -lptesmumps -lptscotchparmetisv3 -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lpthread -lhdf5_hl -lhdf5 -lparmetis -lmetis -lm -lyaml -lhwloc -lquadmath -ldl
+-----------------------------------------
+