Merge pull request #131 from KratosMultiphysics/ContractionExpansionAllFiles

Adding all files for generating paper results (in branch)

Author: Rbravo555

rom_application/ContractionExpansionChannel/AllFiles_requireKratosBranch/Example1/Affine/ProblemFiles/.ipynb_checkpoints/Untitled-checkpoint.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bbeaaa45",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Copy the RomPython folder to your own drive and run this cell to use the notebook in google colab\n",
+    "\n",
+    "from google.colab import drive\n",
+    "drive.mount('/content/drive/')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a2a6c2f6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip install KratosMultiphysics\n",
+    "!pip install KratosRomApplication\n",
+    "!pip install KratosStructuralMechanicsApplication\n",
+    "!pip install KratosLinearSolversApplication\n",
+    "!pip install KratosConstitutiveLawsApplication"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "af25d338",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from KratosMultiphysics.StructuralMechanicsApplication.structural_mechanics_analysis import StructuralMechanicsAnalysis\n",
+    "from KratosMultiphysics.RomApplication.rom_testing_utilities import SetUpSimulationInstance\n",
+    "import KratosMultiphysics"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "98750e24",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(\"/content/drive/MyDrive/WinterSchool2023_Examples_test/stanford_bunny/ProjectParameters.json\",'r') as parameter_file:\n",
+    "    parameters = KratosMultiphysics.Parameters(parameter_file.read())\n",
+    "model = KratosMultiphysics.Model()\n",
+    "simulation = StructuralMechanicsAnalysis(model,parameters)\n",
+    "simulation.Run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e5bd6eb5",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

…tionKratosStructuredMeshWorkingRicc.mdpa …tionKratosStructuredMeshWorkingRicc.mdparom_application/ContractionExpansionChannel/Affine_Mapping/ProblemFiles/2DFlowBifurcationKratosStructuredMeshWorkingRicc.mdpa renamed to rom_application/ContractionExpansionChannel/AllFiles_requireKratosBranch/Example1/Affine/ProblemFiles/2DFlowBifurcationKratosStructuredMeshWorkingRicc.mdpa rom_application/ContractionExpansionChannel/Affine_Mapping/ProblemFiles/2DFlowBifurcationKratosStructuredMeshWorkingRicc.mdpa renamed to rom_application/ContractionExpansionChannel/AllFiles_requireKratosBranch/Example1/Affine/ProblemFiles/2DFlowBifurcationKratosStructuredMeshWorkingRicc.mdpa

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+import KratosMultiphysics
+from KratosMultiphysics.FluidDynamicsApplication.fluid_dynamics_analysis import FluidDynamicsAnalysis
+
+import json
+
+import numpy as np
+
+#for checking if paths exits
+import os
+
+#importing training trajectory
+from simulation_trajectories import TrainingTrajectory
+
+
+
+class FOM_Class(FluidDynamicsAnalysis):
+
+    def __init__(self, model, project_parameters):
+        super().__init__(model, project_parameters)
+        self.control_point = 538 #a node around the middle of the geometry to capture the bufurcation
+        self.velocity_y_at_control_point = []
+        self.narrowing_width = []
+        self.time_step_solution_container = []
+        self.reynolds_number_container = []
+
+
+    def InitialMeshPosition(self):
+        self.training_trajectory = TrainingTrajectory(self.project_parameters["solver_settings"]["fluid_solver_settings"]["time_stepping"]["time_step"].GetDouble())
+        self.w = self.training_trajectory.SetUpInitialNarrowing()
+        self.MoveAllPartsAccordingToW()
+
+    def ModifyInitialGeometry(self):
+        super().ModifyInitialGeometry()
+        self.InitialMeshPosition()
+
+
+
+    def MovePart(self, part_name, jacobian, centering_vector, extra_centering):
+        x_original = []
+        y_original = []
+        # first loop
+        for node in self.model.GetModelPart(f"FluidModelPart.{part_name}").Nodes:
+            if not node.IsFixed(KratosMultiphysics.MESH_DISPLACEMENT_X):
+                x_original.append(node.X0)
+            if not node.IsFixed(KratosMultiphysics.MESH_DISPLACEMENT_Y):
+                y_original.append(node.Y0)
+        x_original = np.array(x_original).reshape(1,-1)
+        y_original = np.array(y_original).reshape(1,-1)
+        matrix_of_coordinates = np.r_[x_original, y_original]
+        modified_matrix_of_coordinates = np.linalg.inv(jacobian) @ (matrix_of_coordinates - centering_vector)
+        modified_matrix_of_coordinates += centering_vector + extra_centering #re-locating
+        # second loop
+        i = 0
+        for node in self.model.GetModelPart(f"FluidModelPart.{part_name}").Nodes:
+            if not node.IsFixed(KratosMultiphysics.MESH_DISPLACEMENT_X):
+                x_disp = modified_matrix_of_coordinates[0,i] - node.X0
+                node.SetSolutionStepValue(KratosMultiphysics.MESH_DISPLACEMENT_X,0, x_disp )
+            if not node.IsFixed(KratosMultiphysics.MESH_DISPLACEMENT_Y):
+                y_disp = modified_matrix_of_coordinates[1,i] - node.Y0
+                node.SetSolutionStepValue(KratosMultiphysics.MESH_DISPLACEMENT_Y,0, y_disp )
+                i +=1
+            node.Fix(KratosMultiphysics.MESH_DISPLACEMENT_X)
+            node.Fix(KratosMultiphysics.MESH_DISPLACEMENT_Y)
+
+
+    def StoreBifurcationData(self):
+        # node =  self.model.GetModelPart("FluidModelPart").GetNode(self.control_point)
+        # self.velocity_y_at_control_point.append(node.GetSolutionStepValue(KratosMultiphysics.VELOCITY_Y))
+        # self.narrowing_width.append(self.w)
+        for node in self.model.GetModelPart("FluidModelPart.GENERIC_Meassure").Nodes:
+            pass
+        #node =  self.model.GetModelPart("Meassure").GetNode(self.control_point)
+        self.velocity_y_at_control_point.append(node.GetSolutionStepValue(KratosMultiphysics.VELOCITY_Y))
+        self.narrowing_width.append(self.w)
+
+
+    def MoveAllPartsAccordingToW(self):
+        #############################
+        ####    FREE ALL NODES   ####
+        #############################
+        for node in self.model.GetModelPart("FluidModelPart").Nodes:
+            node.Free(KratosMultiphysics.MESH_DISPLACEMENT_X)
+            node.Free(KratosMultiphysics.MESH_DISPLACEMENT_Y)
+
+        #############################
+        #### FIXING OUTSIDE PART ####
+        #############################
+        for node in self.model.GetModelPart("FluidModelPart.GENERIC_not_moving").Nodes:
+            node.SetSolutionStepValue(KratosMultiphysics.MESH_DISPLACEMENT_X,0, 0)
+            node.Fix(KratosMultiphysics.MESH_DISPLACEMENT_X)
+            node.SetSolutionStepValue(KratosMultiphysics.MESH_DISPLACEMENT_Y,0, 0)
+            node.Fix(KratosMultiphysics.MESH_DISPLACEMENT_Y)
+
+        #############################
+        ###  MOVE EACH SUB-PART   ###
+        #############################
+        self.MovePart('GENERIC_green', np.array([[1,0],[0,1/self.w]]), np.array([[0],[1.5]]), np.array([[0],[0]]))
+        self.MovePart('GENERIC_yellow_up', np.array([[1,0],[0, (2/(3-self.w))]]), np.array([[0],[3]]), np.array([[0],[0]]))
+        self.MovePart('GENERIC_yellow_down', np.array([[1,0],[0, 2/(3-self.w)]]), np.array([[0],[0]]), np.array([[0],[0]]))
+        self.MovePart('GENERIC_blue', np.array([[1,0],[(self.w-1)/2, 1]]), np.array([[0],[0]]), np.array([[0],[(self.w-1)/4]]))
+        self.MovePart('GENERIC_grey', np.array([[1,0],[(1-self.w)/2, 1]]), np.array([[0],[0]]), np.array([[0],[- (self.w-1)/4]]))
+
+
+
+    def UpdateNarrowing(self):
+        self.w = self.training_trajectory.UpdateW(self.w)
+
+
+
+
+
+    def InitializeSolutionStep(self):
+        super().InitializeSolutionStep()
+
+        if self.time>10.0: # start modifying narrowing from 10 seconds onwards   (How long does it take to close????)
+            self.UpdateNarrowing()
+            self.MoveAllPartsAccordingToW()
+
+        print('The current Reynolds Number is: ', self.GetReynolds())
+
+
+
+    def GetReynolds(self):
+        #TODO Make values agree with papers. Parameter to modify: dunamic viscosity niu
+        velocities = []
+        for node in self.model.GetModelPart("FluidModelPart.GENERIC_narrowing_zone").Nodes:
+            velocities.append(node.GetSolutionStepValue(KratosMultiphysics.VELOCITY_X, 0))
+        vel_np = np.array(velocities)
+
+        vx =  np.max(vel_np) #np.mean(vel_np)
+        Re = (vx*self.w) / 0.1 #TODO retrieve dynamic viscosity in a more robust way
+        return Re
+
+
+
+    def FinalizeSolutionStep(self):
+        super().FinalizeSolutionStep()
+        self.StoreBifurcationData()
+        self.reynolds_number_container.append(self.GetReynolds())
+
+        ArrayOfResults = []
+        for node in self._GetSolver().fluid_solver.GetComputingModelPart().Nodes:
+            ArrayOfResults.append(node.GetSolutionStepValue(KratosMultiphysics.VELOCITY_X, 0))
+            ArrayOfResults.append(node.GetSolutionStepValue(KratosMultiphysics.VELOCITY_Y, 0))
+            ArrayOfResults.append(node.GetSolutionStepValue(KratosMultiphysics.PRESSURE, 0))
+        self.time_step_solution_container.append(ArrayOfResults)
+
+    def GetBifuracationData(self):
+        return np.array(self.velocity_y_at_control_point) ,  np.array(self.narrowing_width)
+
+    def GetReynoldsData(self):
+        return np.array(self.reynolds_number_container)
+
+    def GetSnapshotsMatrix(self):
+        SnapshotMatrix = np.zeros((len(self.time_step_solution_container[0]), len(self.time_step_solution_container)))
+        for i in range(len(self.time_step_solution_container)):
+            Snapshot_i= np.array(self.time_step_solution_container[i])
+            SnapshotMatrix[:,i] = Snapshot_i.transpose()
+        return SnapshotMatrix
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+def prepare_files(working_path):
+    """pre-pending the absolut path of the files in the Project Parameters"""
+    with open(working_path+'/ProblemFiles/ProjectParameters.json','r') as f:
+        updated_project_parameters = json.load(f)
+        file_input_name = updated_project_parameters["solver_settings"]["fluid_solver_settings"]["model_import_settings"]["input_filename"]
+        materials_filename = updated_project_parameters["solver_settings"]["fluid_solver_settings"]["material_import_settings"]["materials_filename"]
+        gid_output_name = updated_project_parameters["output_processes"]["gid_output"][0]["Parameters"]["output_name"]
+
+        updated_project_parameters["solver_settings"]["fluid_solver_settings"]["model_import_settings"]["input_filename"] = working_path + '/ProblemFiles/'+ file_input_name
+        updated_project_parameters["solver_settings"]["fluid_solver_settings"]["material_import_settings"]["materials_filename"] = working_path +'/ProblemFiles/'+ materials_filename
+        updated_project_parameters["output_processes"]["gid_output"][0]["Parameters"]["output_name"] = working_path +'/Results/FOM'
+        updated_project_parameters["output_processes"]["vtk_output"] = []
+
+    with open(working_path+'/ProblemFiles/ProjectParameters_modified.json','w') as f:
+        json.dump(updated_project_parameters, f, indent = 4)
+
+
+
+
+
+
+
+
+
+def convert_to_nd(SnapshotsMatrix, number_of_dimensions=2):
+    for i in range(np.shape(SnapshotsMatrix)[1]):
+        column_mean = np.mean( SnapshotsMatrix[:,i].reshape(-1,number_of_dimensions).reshape(-1,number_of_dimensions),0).reshape(-1,1)
+        if i ==0:
+            columns_means = column_mean
+        else:
+            columns_means = np.c_[columns_means,column_mean]
+
+    return columns_means
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+def Train_ROM():
+
+    if not os.path.exists(f'./Results/FOM.post.bin'):
+
+        with open("ProblemFiles/ProjectParameters_modified.json", 'r') as parameter_file:
+            parameters = KratosMultiphysics.Parameters(parameter_file.read())
+        global_model = KratosMultiphysics.Model()
+        simulation = FOM_Class(global_model, parameters)
+        simulation.Run()
+        SnapshotsMatrix = simulation.GetSnapshotsMatrix()
+        velocity_y, narrowing = simulation.GetBifuracationData()
+        reynolds = simulation.GetReynoldsData()
+        np.save('Results/reynolds.npy', reynolds)
+        np.save('Results/narrowing.npy', narrowing)
+        np.save('Results/Velocity_y.npy', velocity_y)
+        np.save('Results/SnapshotMatrix.npy', SnapshotsMatrix )
+
+
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+
+
+if __name__=="__main__":
+    #library for passing arguments to the script from bash
+    from sys import argv
+
+    working_path = argv[1]
+
+    prepare_files(working_path)
+
+    Train_ROM()