migration of mprans to xtensor (#1068)

* Added xtensor-python to environment.yaml * AddedMass based on xtensor * xtensor * SedClosure based on xtensor * VOF3P based on xtensor * NCLS3P based on xtensor * Moved mprans2/setup.py into proteus/setup.py * MCorr3P based on xtensor * Install xtensor for hashdist * Add PROTEUS_OPT compilation options for xtensor-based extensions * mprans.RANS3PSed * mprans.RANS3PSed2D * Moved RANS3PSed to mprans * Add calculateVelocityAverage * Dissipation2D * VOS3P * PresInc * Dissipation * CLSVOF * NCLS * MCorr * RANS2P * RANS2P2D * RANS2P_IB * Travis parallel compilation disabled * RDLS * VOF * MoveMesh * MoveMesh2D * SW2D * SW2DCV * GN_SW2DCV * Fixed AddedMass * Fixed VOF3P * Fixed NCLS3P * Fixed MCorr3P * Kappa and Kappa2D * RANS3PF * SedClosure.h * Splitted RANS3PF.h and RANS3PF2D.h * Disabled optimizations * Fixed build after rebase * Reverted RANS3PF and enabled optimizations again Co-authored-by: David Brochart <[email protected]> Co-authored-by: Alvin Zhang <[email protected]>
erdc · Feb 13, 2020 · cf9c7f9 · cf9c7f9
1 parent 5ee9138
commit cf9c7f9
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diff --git a/.gitignore b/.gitignore
@@ -31,11 +31,11 @@ linux2/
 garnet.gnu/
 Cygwin
 proteus.egg-info/
-proteus/ADR.cpp
 proteus/subsurfaceTransportFunctions.c
 cygwin_bootstrap.done
 matlab_setup.done
 dist/
+tmp/
 
 # Generated files
 
@@ -58,14 +58,12 @@ proteus/csparsity.cpp
 proteus/csubgridError.c
 proteus/ctimeIntegration.c
 proteus/ctransportCoefficients.c
-proteus/elastoplastic/cElastoPlastic.cpp
 proteus/equivalent_polynomials.cpp
 proteus/fenton/Fenton.cpp
 proteus/flcbdfWrappers.cpp
 proteus/mbd/CouplingFSI.cpp
 proteus/mprans/BoundaryConditions.cpp
 proteus/mprans/MeshSmoothing.cpp
-proteus/mprans/SedClosure.cpp
 proteus/mprans/cAddedMass.cpp
 proteus/mprans/cCLSVOF.cpp
 proteus/mprans/cGN_SW2DCV.cpp
@@ -79,5 +77,4 @@ proteus/mprans/cRANS3PF.cpp
 proteus/mprans/cRANS3PSed.cpp
 proteus/mprans/cVOF3P.cpp
 proteus/mprans/cVOS3P.cpp
-proteus/richards/cRichards.cpp
 proteus/superluWrappers.c
diff --git a/.travis.yml b/.travis.yml
@@ -32,6 +32,7 @@ jobs:
     env: TEST_PROFILE="proteus-hashdist"
     install:
       - git lfs pull
+      - ./get_xtensor.sh
       - ./stack/hit/bin/hit init-home
       - ./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_src --objects="source"
       - ./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_ubuntu_16_04 --objects="build"
@@ -51,7 +52,7 @@ jobs:
       - export PATHSAVE=$PATH
       - export PATH=$PWD/linux/bin:$PATH
       - export LD_LIBRARY_PATH=$PWD/linux/lib:$LD_LIBRARY_PATH
-      - PROTEUS_OPT="-w -O2 -UNDEBUG" FC=gfortran CC=mpicc CXX=mpicxx make develop N=2
+      - PROTEUS_OPT="-w -O2 -UNDEBUG" FC=gfortran CC=mpicc CXX=mpicxx make develop N=1
       - export SSL_CERT_DIR=/etc/ssl/certs
       - #./linux/bin/pip3 install matplotlib
     script:
@@ -76,7 +77,7 @@ jobs:
       - conda info -a
       - conda env create -f environment-dev.yml
       - conda activate proteus-dev
-      - pip install -v -e .
+      - make develop-conda N=1
     script:
       - export MPLBACKEND="AGG"
       - py.test -n 1 --dist=loadfile --forked -v proteus/tests --ignore proteus/tests/POD  --ignore proteus/tests/MeshAdaptPUMI --cov=proteus
@@ -108,4 +109,4 @@ jobs:
       - git lfs pull
       - cd proteus/tests/ci
       - parun poisson_3d_tetgen_p.py poisson_3d_tetgen_c0p1_n.py -l 5 -v
-#      - py.test -n 1 --dist=no --forked -v proteus/tests --ignore proteus/tests/POD  --ignore proteus/tests/MeshAdaptPUMI --cov=proteus
+#      - py.test -n 1 --dist=no --forked -v proteus/tests --ignore proteus/tests/POD  --ignore proteus/tests/MeshAdaptPUMI --cov=proteus
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -41,4 +41,5 @@ dependencies:
   - ipyparallel
   - pillow
   - recordtype
+  - xtensor-python
   - git-lfs
diff --git a/environment.yml b/environment.yml
@@ -11,5 +11,6 @@ dependencies:
   - cython
   - pillow
   - pip
+  - xtensor-python
   - pip:
     - recordtype
diff --git a/get_xtensor.sh b/get_xtensor.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+rm -rf proteus/xtensor
+mkdir -p proteus/xtensor
+cd proteus/xtensor
+mkdir xtl xtensor-python xtensor pybind11
+wget https://github.com/QuantStack/xtl/archive/0.6.11.tar.gz            -O xtl.tar.gz
+wget https://github.com/QuantStack/xtensor-python/archive/0.24.1.tar.gz -O xtensor-python.tar.gz
+wget https://github.com/xtensor-stack/xtensor/archive/0.21.2.tar.gz     -O xtensor.tar.gz
+wget https://github.com/pybind/pybind11/archive/v2.4.3.tar.gz           -O pybind11.tar.gz
+tar zxf xtl.tar.gz              --strip-components=1 -C xtl
+tar zxf xtensor-python.tar.gz   --strip-components=1 -C xtensor-python
+tar zxf xtensor.tar.gz          --strip-components=1 -C xtensor
+tar zxf pybind11.tar.gz         --strip-components=1 -C pybind11
+rm *.gz
diff --git a/proteus/ADR.cpp b/proteus/ADR.cpp
@@ -0,0 +1,29 @@
+#include "pybind11/pybind11.h"
+#include "pybind11/stl_bind.h"
+
+#define FORCE_IMPORT_ARRAY
+#include "ADR.h"
+
+#if defined(__GNUC__) && !defined(__clang__)
+    namespace workaround
+    {
+        inline void define_allocators()
+        {
+            std::allocator<int> a0;
+            std::allocator<double> a1;
+        }
+    }
+#endif
+
+namespace py = pybind11;
+using proteus::cppADR_base;
+
+PYBIND11_MODULE(ADR, m)
+{
+    xt::import_numpy();
+
+    py::class_<cppADR_base>(m, "ADR")
+        .def(py::init(&proteus::newADR))
+        .def("calculateResidual", &cppADR_base::calculateResidual)
+        .def("calculateJacobian", &cppADR_base::calculateJacobian);
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,5 +11,6 @@ dependencies: @@
       - cython
       - pillow
       - pip
+      - xtensor-python
       - pip:
         - recordtype