dmd/euler example (#12)

* bindings for AdaptiveDMD and NonuniformDMD. * added ci test for DMD class. * parallel test for DMD. * fix on parallel dmd test. * initial commit * initial commit * dg_euler.py in progress... * finished dg_euler testing example * minor changes and added mesh file * fom timer corrected * minor corrections to dg_euler.py * corrections to dg_euler.py and pyAdaptiveDMD.cpp --------- Co-authored-by: Kevin Chung <[email protected]> Co-authored-by: Henry Yu <[email protected]> Co-authored-by: Henry Yu <[email protected]> Co-authored-by: Henry Yu <[email protected]>
LLNL · Sep 5, 2023 · 72c8cdf · 72c8cdf
1 parent 4a8b2bc
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Showing 11 changed files with 1,192 additions and 302 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -63,6 +63,9 @@ jobs:
             pytest test_pyBasisReader.py --verbose
             echo run pyBasisWriter unit test
             pytest test_pyBasisWriter.py --verbose
+            echo run pyDMD unit test
+            pytest test_pyDMD.py --verbose
+            mpirun -n 2 pytest test_pyDMD.py --verbose
             echo run pyDEIM unit test
             pytest test_pyDEIM.py --verbose
             echo run pyGNAT unit test
@@ -127,6 +130,9 @@ jobs:
             pytest test_pyBasisReader.py --verbose
             echo run pyBasisWriter unit test
             pytest test_pyBasisWriter.py --verbose
+            echo run pyDMD unit test
+            pytest test_pyDMD.py --verbose
+            mpirun -n 2 pytest test_pyDMD.py --verbose
             echo run pyDEIM unit test
             pytest test_pyDEIM.py --verbose
             echo run pyGNAT unit test
@@ -188,6 +194,9 @@ jobs:
             pytest test_pyBasisReader.py --verbose
             echo run pyBasisWriter unit test
             pytest test_pyBasisWriter.py --verbose
+            echo run pyDMD unit test
+            pytest test_pyDMD.py --verbose
+            mpirun -n 2 pytest test_pyDMD.py --verbose
             echo run pyDEIM unit test
             pytest test_pyDEIM.py --verbose
             echo run pyGNAT unit test

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -128,22 +128,23 @@ link_libraries(
 add_subdirectory("extern/pybind11")
 
 pybind11_add_module(_pylibROM
-    bindings/pylibROM/pylibROM.cpp
+  bindings/pylibROM/pylibROM.cpp
 
-    bindings/pylibROM/linalg/pyMatrix.cpp
-    bindings/pylibROM/linalg/pyVector.cpp
-    bindings/pylibROM/linalg/pyBasisGenerator.cpp
-    bindings/pylibROM/linalg/pyBasisReader.cpp
+  bindings/pylibROM/linalg/pyMatrix.cpp
+  bindings/pylibROM/linalg/pyVector.cpp
+  bindings/pylibROM/linalg/pyBasisGenerator.cpp
+  bindings/pylibROM/linalg/pyBasisReader.cpp
 	bindings/pylibROM/linalg/pyBasisWriter.cpp
-    bindings/pylibROM/linalg/pyOptions.cpp
-    bindings/pylibROM/linalg/pyNNLS.cpp
-    bindings/pylibROM/linalg/svd/pySVD.cpp
-    bindings/pylibROM/linalg/svd/pyStaticSVD.cpp
-    bindings/pylibROM/linalg/svd/pyIncrementalSVD.cpp
+  bindings/pylibROM/linalg/pyOptions.cpp
+  bindings/pylibROM/linalg/pyNNLS.cpp
+  bindings/pylibROM/linalg/svd/pySVD.cpp
+  bindings/pylibROM/linalg/svd/pyStaticSVD.cpp
+  bindings/pylibROM/linalg/svd/pyIncrementalSVD.cpp
 
-    bindings/pylibROM/algo/pyDMD.cpp
+  bindings/pylibROM/algo/pyDMD.cpp
 	bindings/pylibROM/algo/pyParametricDMD.cpp
-
+	bindings/pylibROM/algo/pyNonuniformDMD.cpp
+  bindings/pylibROM/algo/pyAdaptiveDMD.cpp
 	bindings/pylibROM/hyperreduction/pyDEIM.cpp
 	bindings/pylibROM/hyperreduction/pyGNAT.cpp
 	bindings/pylibROM/hyperreduction/pyQDEIM.cpp

diff --git a/bindings/pylibROM/algo/pyAdaptiveDMD.cpp b/bindings/pylibROM/algo/pyAdaptiveDMD.cpp
@@ -0,0 +1,32 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include "algo/AdaptiveDMD.h"
+#include "linalg/Vector.h"
+#include "linalg/Matrix.h"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+void init_AdaptiveDMD(pybind11::module_ &m){
+
+    py::class_<AdaptiveDMD, DMD>(m, "AdaptiveDMD")
+        .def(py::init<int, double, std::string, std::string, double, bool, Vector*>(),
+            py::arg("dim"),
+            py::arg("desired_dt") = -1.0,
+            py::arg("rbf") = "G",
+            py::arg("interp_method") = "LS",
+            py::arg("closest_rbf_val") = 0.9,
+            py::arg("alt_output_basis") = false,
+            py::arg("state_offset") = nullptr)
+        .def("train", (void (AdaptiveDMD::*)(double, const Matrix*, double)) &AdaptiveDMD::train,
+            py::arg("energy_fraction").noconvert(),
+            py::arg("W0") = nullptr,
+            py::arg("linearity_tol") = 0.0)
+        .def("train", (void (AdaptiveDMD::*)(int, const Matrix*, double)) &AdaptiveDMD::train,
+            py::arg("k").noconvert(),
+            py::arg("W0") = nullptr,
+            py::arg("linearity_tol") = 0.0)
+        .def("getTrueDt", &AdaptiveDMD::getTrueDt)
+        .def("getInterpolatedSnapshots", &AdaptiveDMD::getInterpolatedSnapshots);
+}
+
diff --git a/bindings/pylibROM/algo/pyDMD.cpp b/bindings/pylibROM/algo/pyDMD.cpp
@@ -26,7 +26,7 @@ void init_DMD(pybind11::module_ &m) {
             return new DMD(dim, dt, alt_output_basis, vec);
         }), py::arg("dim"), py::arg("dt"), py::arg("alt_output_basis") = false, py::arg("vec") = nullptr)
 
-    // .def("setOffset", &PyDMD::setOffset, py::arg("offset_vector"), py::arg("order"))  //problem if we want to name the wrapper as DMD. Could get rid of the using namespace directive?
+    .def("setOffset", &DMD::setOffset, py::arg("offset_vector"), py::arg("order"))
     .def("takeSample", [](DMD &self, py::array_t<double> &u_in, double t) {
         self.takeSample(getVectorPointer(u_in), t);
     })

diff --git a/bindings/pylibROM/algo/pyNonuniformDMD.cpp b/bindings/pylibROM/algo/pyNonuniformDMD.cpp
@@ -0,0 +1,40 @@
+//
+// Created by barrow9 on 6/4/23.
+//
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include "librom.h"
+#include "python_utils/cpp_utils.hpp"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+void init_NonuniformDMD(pybind11::module_ &m) {
+
+    py::class_<NonuniformDMD, DMD>(m, "NonuniformDMD")
+
+	//constructor, default.
+	.def(py::init<std::string>()) //constructor a
+
+    .def(py::init([](int dim,
+                     bool alt_output_basis,
+                     Vector* state_offset,
+                     Vector* derivative_offset) {
+        return new NonuniformDMD(dim, alt_output_basis, state_offset, derivative_offset);
+    }), 
+    py::arg("dim"),
+    py::arg("alt_output_basis") = false,
+    py::arg("state_offset") = nullptr,
+    py::arg("derivative_offset") = nullptr)
+
+    //TODO: needed explicitly?
+    .def("__del__", [](NonuniformDMD& self) { self.~NonuniformDMD(); }) // Destructor
+
+    .def("setOffset", &NonuniformDMD::setOffset, py::arg("offset_vector"), py::arg("order"))
+
+    .def("load", &NonuniformDMD::load, py::arg("base_file_name"))
+    .def("save", &NonuniformDMD::save, py::arg("base_file_name"));
+
+}
diff --git a/bindings/pylibROM/pylibROM.cpp b/bindings/pylibROM/pylibROM.cpp
@@ -20,6 +20,8 @@ void init_IncrementalSVD(pybind11::module_ &m);
 //algo
 void init_DMD(pybind11::module_ &);
 void init_ParametricDMD(pybind11::module_ &m);
+void init_NonuniformDMD(pybind11::module_ &m);
+void init_AdaptiveDMD(pybind11::module_ &m);
 
 //hyperreduction
 void init_DEIM(pybind11::module_ &m);
@@ -64,6 +66,8 @@ PYBIND11_MODULE(_pylibROM, m) {
     py::module algo = m.def_submodule("algo");
     init_DMD(algo);
     init_ParametricDMD(algo);
+    init_AdaptiveDMD(algo);
+    init_NonuniformDMD(algo);
 
     py::module hyperreduction = m.def_submodule("hyperreduction");
     init_DEIM(hyperreduction);

diff --git a/examples/data/periodic-square.mesh b/examples/data/periodic-square.mesh
@@ -0,0 +1,85 @@
+MFEM mesh v1.0
+
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# POINT       = 0
+# SEGMENT     = 1
+# TRIANGLE    = 2
+# SQUARE      = 3
+# TETRAHEDRON = 4
+# CUBE        = 5
+#
+
+dimension
+2
+
+# format: <attribute> <geometry type> <vertex 0> <vertex 1> ...
+elements
+9
+1 3 0 1 4 3
+2 3 1 2 5 4
+3 3 2 0 3 5
+4 3 3 4 7 6
+5 3 4 5 8 7
+6 3 5 3 6 8
+7 3 6 7 1 0
+8 3 7 8 2 1
+9 3 8 6 0 2
+
+boundary
+0
+
+vertices
+9
+
+nodes
+FiniteElementSpace
+FiniteElementCollection: L2_T1_2D_P1
+VDim: 2
+Ordering: 1
+
+-1 -1
+-0.333333333 -1
+-1 -0.333333333
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+
+-0.333333333 -1
++0.333333333 -1
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++0.333333333 -0.333333333
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+
+-1 -0.333333333
+-0.333333333 -0.333333333
+-1 +0.333333333
+-0.333333333 +0.333333333
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+-0.333333333 -0.333333333
++0.333333333 -0.333333333
+-0.333333333 +0.333333333
++0.333333333 +0.333333333
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++0.333333333 -0.333333333
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+-1 +0.333333333
+-0.333333333 +0.333333333
+-1 +1
+-0.333333333 +1
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+-0.333333333 +1
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+
++0.333333333 +0.333333333
++1 +0.333333333
++0.333333333 +1
++1 +1