Parametric_tw_csv example (#10)

* more bindings for Database classes. * initial loading for local_tw_csv.py * minor fix. * parametric_tw_csv example. * update the commands. * fixed the command.
LLNL · Sep 5, 2023 · 3199284 · 3199284
1 parent 72c8cdf
commit 3199284
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Showing 10 changed files with 1,731 additions and 5 deletions.
diff --git a/bindings/pylibROM/python_utils/cpp_utils.hpp b/bindings/pylibROM/python_utils/cpp_utils.hpp
@@ -50,4 +50,42 @@ T* getVectorPointer(py::array_t<T> &u_in)
 
     return static_cast<T*>(buf_info.ptr);
 }
+
+template<typename T>
+py::buffer_info
+get1DArrayBufferInfo(T *ptr, const int nelem)
+{
+    return py::buffer_info(
+        ptr,                         /* Pointer to buffer */
+        sizeof(T),                          /* Size of one scalar */
+        py::format_descriptor<T>::format(), /* Python struct-style format descriptor */
+        1,                                      /* Number of dimensions */
+        { nelem },                         /* Buffer dimensions */
+        { sizeof(T) }                       /* Strides (in bytes) for each index */
+    );
+}
+
+template<typename T>
+py::capsule
+get1DArrayBufferHandle(T *ptr, const bool free_when_done=false)
+{
+    if (free_when_done)
+        return py::capsule(ptr, [](void *f){
+            T *T_ptr = reinterpret_cast<T *>(f);
+            delete[] T_ptr;
+        });
+    else
+        return py::capsule([](){});
+}
+
+template<typename T>
+py::array_t<T>
+get1DArrayFromPtr(T *ptr, const int nelem, bool free_when_done=false)
+{
+    // if empty array, no need to free when done.
+    free_when_done = free_when_done && (nelem > 0);
+    return py::array(get1DArrayBufferInfo(ptr, nelem),
+                     get1DArrayBufferHandle(ptr, free_when_done));
+}
+
 #endif
diff --git a/bindings/pylibROM/utils/pyCSVDatabase.cpp b/bindings/pylibROM/utils/pyCSVDatabase.cpp
@@ -99,5 +99,68 @@ void init_CSVDatabase(pybind11::module_ &m) {
         self.putIntegerArray(key, getVectorPointer(data), nelements);
     });
 
+    csvdb.def("getIntegerArray", [](
+        CSVDatabase &self, const std::string& key, int nelements)
+    {
+        int *dataptr = new int[nelements];
+        self.getIntegerArray(key, dataptr, nelements);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    csvdb.def("getIntegerVector", [](
+        CSVDatabase &self, const std::string& key, bool append)
+    {
+        std::vector<int> *datavec = new std::vector<int>;
+        self.getIntegerVector(key, *datavec, append);
+        return get1DArrayFromPtr(datavec->data(), datavec->size(), true);
+    },
+    py::arg("key"), py::arg("append") = false);
+
+    csvdb.def("getDoubleArray", [](
+        CSVDatabase &self, const std::string& key, int nelements)
+    {
+        double *dataptr = new double[nelements];
+        self.getDoubleArray(key, dataptr, nelements);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    csvdb.def("getDoubleArray", [](
+        CSVDatabase &self, const std::string& key, int nelements, const std::vector<int>& idx)
+    {
+        double *dataptr = new double[nelements];
+        self.getDoubleArray(key, dataptr, nelements, idx);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    csvdb.def("getDoubleArray", [](
+        CSVDatabase &self, const std::string& key, int nelements,
+        int offset, int block_size, int stride)
+    {
+        double *dataptr = new double[nelements];
+        self.getDoubleArray(key, dataptr, nelements, offset, block_size, stride);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    csvdb.def("getDoubleVector", [](
+        CSVDatabase &self, const std::string& key, bool append)
+    {
+        std::vector<double> *datavec = new std::vector<double>();
+        self.getDoubleVector(key, *datavec, append);
+        return get1DArrayFromPtr(datavec->data(), datavec->size(), true);
+    },
+    py::arg("key"), py::arg("append") = false);
+
+    csvdb.def("getDoubleArraySize", &CSVDatabase::getDoubleArraySize);
+
+    csvdb.def("getStringVector", [](
+        CSVDatabase &self, const std::string& file_name, bool append)
+    {
+        std::vector<std::string> data;
+        self.getStringVector(file_name, data, append);
+        return py::cast(data);
+    }, py::arg("file_name"), py::arg("append") = false);
+
+    csvdb.def("getLineCount", &CSVDatabase::getLineCount);
+
 }
 
diff --git a/bindings/pylibROM/utils/pyDatabase.cpp b/bindings/pylibROM/utils/pyDatabase.cpp
@@ -24,5 +24,11 @@ void init_Database(pybind11::module_ &m) {
         .export_values();
 
     // TODO(kevin): finish binding of member functions.
-
+    db.def("getInteger", [](
+        Database &self, const std::string& key)
+    {
+        int data;
+        self.getInteger(key, data);
+        return data;
+    });
 }
diff --git a/bindings/pylibROM/utils/pyHDFDatabase.cpp b/bindings/pylibROM/utils/pyHDFDatabase.cpp
@@ -38,6 +38,41 @@ void init_HDFDatabase(pybind11::module_ &m) {
         self.putIntegerArray(key, getVectorPointer(data), nelements);
     });
 
+    hdfdb.def("getIntegerArray", [](
+        HDFDatabase &self, const std::string& key, int nelements)
+    {
+        int *dataptr = new int[nelements];
+        self.getIntegerArray(key, dataptr, nelements);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    hdfdb.def("getDoubleArray", [](
+        HDFDatabase &self, const std::string& key, int nelements)
+    {
+        double *dataptr = new double[nelements];
+        self.getDoubleArray(key, dataptr, nelements);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    hdfdb.def("getDoubleArray", [](
+        HDFDatabase &self, const std::string& key, int nelements, const std::vector<int>& idx)
+    {
+        double *dataptr = new double[nelements];
+        self.getDoubleArray(key, dataptr, nelements, idx);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    hdfdb.def("getDoubleArray", [](
+        HDFDatabase &self, const std::string& key, int nelements,
+        int offset, int block_size, int stride)
+    {
+        double *dataptr = new double[nelements];
+        self.getDoubleArray(key, dataptr, nelements, offset, block_size, stride);
+        return get1DArrayFromPtr(dataptr, nelements, true);
+    });
+
+    hdfdb.def("getDoubleArraySize", &HDFDatabase::getDoubleArraySize);
+
     // hdfdb.def("__del__", [](HDFDatabase& self) { self.~HDFDatabase(); }); // Destructor
 
 }

diff --git a/examples/data/inline-quad.mesh b/examples/data/inline-quad.mesh
@@ -0,0 +1,7 @@
+MFEM INLINE mesh v1.0
+
+type = quad
+nx = 4
+ny = 4
+sx = 1.0
+sy = 1.0
diff --git a/examples/dmd/heat_conduction_csv.sh b/examples/dmd/heat_conduction_csv.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+#SBATCH -N 1
+#SBATCH -t 0:05:00
+#SBATCH -p pdebug
+#SBATCH -o sbatch.log
+#SBATCH --open-mode truncate
+
+rm -rf parameters.txt dmd_list dmd_data run/dmd_data
+
+python3 ./parametric_heat_conduction.py -r 0.40 -save -csv -out dmd_data/dmd_par1 -no-vis > hc_par1.log
+python3 ./parametric_heat_conduction.py -r 0.45 -save -csv -out dmd_data/dmd_par2 -no-vis > hc_par2.log
+python3 ./parametric_heat_conduction.py -r 0.55 -save -csv -out dmd_data/dmd_par3 -no-vis > hc_par3.log
+python3 ./parametric_heat_conduction.py -r 0.60 -save -csv -out dmd_data/dmd_par4 -no-vis > hc_par4.log
+python3 ./parametric_heat_conduction.py -r 0.50 -save -csv -out dmd_data/dmd_par5 -no-vis > hc_par5.log
+
+mkdir dmd_list
+mv -f run/dmd_data .
+
+awk 'END{print NR}' dmd_data/dmd_par1/step0/sol.csv > dmd_data/dim.csv
+
+mv dmd_data/dmd_par1/snap_list.csv dmd_list/dmd_par1.csv
+mv dmd_data/dmd_par2/snap_list.csv dmd_list/dmd_par2.csv
+mv dmd_data/dmd_par3/snap_list.csv dmd_list/dmd_par3.csv
+mv dmd_data/dmd_par4/snap_list.csv dmd_list/dmd_par4.csv
+mv dmd_data/dmd_par5/snap_list.csv dmd_list/dmd_par5.csv
+
+echo "dmd_par1,0.40,0.01,0,0"  > dmd_list/dmd_train_parametric.csv
+echo "dmd_par2,0.45,0.01,0,0" >> dmd_list/dmd_train_parametric.csv
+echo "dmd_par3,0.55,0.01,0,0" >> dmd_list/dmd_train_parametric.csv
+echo "dmd_par4,0.60,0.01,0,0" >> dmd_list/dmd_train_parametric.csv
+echo "dmd_par5,0.50,0.01,0,0"  > dmd_list/dmd_train_local.csv
+echo "dmd_par5,0.50,0.01,0,0"  > dmd_list/dmd_test.csv
diff --git a/examples/dmd/heat_conduction_hdf.sh b/examples/dmd/heat_conduction_hdf.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+#SBATCH -N 1
+#SBATCH -t 0:05:00
+#SBATCH -p pdebug
+#SBATCH -o sbatch.log
+#SBATCH --open-mode truncate
+
+rm -rf parameters.txt dmd_list dmd_data run/dmd_data
+
+python3 ./parametric_heat_conduction.py -r 0.40 -save -hdf -out dmd_data/sim0 -no-vis > hc_par0.log
+python3 ./parametric_heat_conduction.py -r 0.45 -save -hdf -out dmd_data/sim1 -no-vis > hc_par1.log
+python3 ./parametric_heat_conduction.py -r 0.55 -save -hdf -out dmd_data/sim2 -no-vis > hc_par2.log
+python3 ./parametric_heat_conduction.py -r 0.60 -save -hdf -out dmd_data/sim3 -no-vis > hc_par3.log
+python3 ./parametric_heat_conduction.py -r 0.50 -save -hdf -out dmd_data/sim4 -no-vis > hc_par4.log
+
+mkdir dmd_list
+mv -f run/dmd_data .
+
+echo "0,0.40,0.01,0,0"  > dmd_list/dmd_train_parametric.csv
+echo "1,0.45,0.01,0,0" >> dmd_list/dmd_train_parametric.csv
+echo "2,0.55,0.01,0,0" >> dmd_list/dmd_train_parametric.csv
+echo "3,0.60,0.01,0,0" >> dmd_list/dmd_train_parametric.csv
+echo "4,0.50,0.01,0,0"  > dmd_list/dmd_train_local.csv
+echo "4,0.50,0.01,0,0"  > dmd_list/dmd_test.csv