Merge pull request #78 from kuanshi/refactorUQ

kz - adding a new example for PLoM

Examples/Examples.json

@@ -69,6 +69,11 @@
       "name": "Material Model: Deterministic Calibration",
       "description": "In this example, non-linear least squares minimization is used to calibrate the parameters values of a material model subjected to cyclic strain history.",
       "inputFile": "qfem-0018/src/input.json"
+    },
+    {
+      "name": "Two-Dimensional Truss: PLoM Modeling and Simulation",
+      "description": "In this example, the goal is to demonstrate the use of PLoM model method to predict the response of the example truss under the given load.",
+      "inputFile": "qfem-0022/src/input.json"
     }
   ]
 }

Examples/Examples_all.json

@@ -85,6 +85,10 @@
       "description": "~",
       "InputFile": "qfem-0018/input.json"
     },
+    {
+      "name": "Two-Dimensional Truss: PLoM Modeling and Simulation",
+      "description": "In this example, the goal is to demonstrate the use of PLoM model method to predict the response of the example truss under the given load.",
+      "inputFile": "qfem-0022/src/input.json"},
     {
       "name": "Surrogate modeling with design of experiments",
       "description": "In this example illustrates different design of experiments strategies.",

Examples/index.json

@@ -433,6 +433,35 @@
         "Simulation": "OpenSees",
         "Difficulty": "0"
       }
+    },
+    "qfem-0022": {
+      "id": "qfem-0022",
+      "title": "Two-Dimensional Truss: PLoM Modeling and Simulation",
+      "base": "qfem-0022",
+      "doc": [
+		"qfem-0022/README.rst",
+		"qfem-0022/src/input.tcl",
+		"qfem-0022/src/TrussModel.tcl",
+    "qfem-0022/src/TrussPost.tcl",
+    "qfem-0022/src/TrussPost.py",
+    "qfem-0022/figures/truss.png",
+		"qfem-0022/figures/UQ.png",
+		"qfem-0022/figures/FEM.png",
+    "qfem-0022/figures/RV.png",
+    "qfem-0022/figures/EDP.png",
+    "qfem-0022/figures/RES1.png",
+    "qfem-0022/figures/RES2.png",
+    "qfem-0022/figures/RES3.png",
+    "qfem-0022/figures/RES4.png"
+      ],
+      "entry_point": "qfem-0022/./input.json",
+      "summary": "In this example, the goal is to demonstrate the use of PLoM model method \nto predict the response of the example truss under the given load.\n",
+      "logo": "figures/truss.png",
+      "published": "2022-04-01T21:26:53.946381-08:00",
+      "categories": {
+        "Simulation": "OpenSees",
+        "Difficulty": "0"
+      }
     }
   },
   "categories": {

Examples/qfem-0022/README.rst

@@ -0,0 +1,99 @@
+.. _qfem-0022:
+
+Two-Dimensional Truss: PLoM Modeling and Simulation
+=====================================================
+
++----------------+------------------------------------------+
+| Problem files  | :github:`Download <Examples/qfem-0022>`  |
++----------------+------------------------------------------+
+
+Consider the problem simulating response of a two-dimensional truss structure with uncertain material properties shown in the following figure.
+The goal of the exercise is to demonstrate the use of ``PLoM model`` method under ``SimCenterUQ``.
+
+.. figure:: figures/truss.png
+   :align: center
+   :width: 600
+
+1. Elastic modulus(``E``): mean :math:`\mu_E=205 kN/{mm^2}` and standard deviation :math:`\sigma_E =15 kN/{mm^2}` (COV = 7.3%)
+2. Load (``P``): mean :math:`\mu_P =25 kN` and a standard deviation of :math:`\sigma_P = 3 kN`, (COV = 12%).
+3. Cross sectional area for the upper three bars (``Au``): mean :math:`\mu_{Au} = 500 mm^2`, and a standard deviation of :math:`\sigma_{Au} = 25mm^2`  (COV = 5%)
+4. Cross sectional area for the other six bars (``Ao``): mean :math:`\mu_{Ao} = 250mm^2`, and :math:`\sigma_{Ao} = 10mm^2` (COV = 4%)
+
+The exercise requires two files: 
+
+1. :qfem-0022:`TrussTemplate.tcl <src/TrussModel.tcl>`
+
+.. literalinclude:: ./src/TrussModel.tcl
+   :language: tcl
+
+2. :qfem-0001:`TrussPost.tcl </src/TrussPost.tcl>`. 
+
+The ``TrussPost.tcl`` script shown below will accept as input any of the 6 nodes in the domain and for each of the two dof directions.
+
+.. literalinclude:: ./src/TrussPost.tcl
+   :language: tcl
+
+PLoM Modeling
+^^^^^^^^^^^^^^^^^
+
+1. Start the application and the UQ Selection will be highlighted. In the panel for the UQ selection, select ``SimCenterUQ`` as the UQ engine. 
+   Select ``PLoM Model`` for the UQ method, and use ``Sampling and Simulation`` as the Training Dataset.
+   For sampling method, select ``LHS`` with 50 initial simulations for generating training data (with a random seed specified).
+   For the new sample number ratio, input 5 by which 250 new realizations will be created from the trained PLoM model.
+
+.. figure:: figures/UQ.png
+   :align: center
+   :figclass: align-center
+
+2. Next select the **FEM** panel from the input panel. This will default in the ``OpenSees`` engine. For the main script copy the path name to ``TrussModel.tcl`` or select **choose** and navigate to the file. For the **post-process script** field, repeat the same procedure for the ``TrussPost.tcl`` script.
+
+.. figure:: figures/FEM.png
+   :align: center
+   :figclass: align-center
+
+3. Next select the **RV** panel from the input panel. This should be pre-populated with four random variables with same names as those having ``pset`` in the tcl script. For each variable, from the drop down menu change them from having a constant distribution to a normal one and then provide the means and standard deviations specified for the problem.
+
+.. figure:: figures/RV.png
+   :align: center
+   :figclass: align-center
+
+4. Next select the **EDP** tab. Here two response variables ``Node_2_Disp_2`` and ``Node_3_Disp_2`` are defined, which should be consistent with the post-process script. 
+
+.. figure:: figures/EDP.png
+   :align: center
+   :figclass: align-center
+
+.. note::   
+
+   The user can add extra EDP by selecting add and then providing additional names. As seen from the post-process script any of the 6 nodes may be specified and for any node either the 1 or 2 DOF direction.
+
+5. Next click on the **Run** button. This will cause the backend application to launch the job. When done the **RES** panel will be selected and the results will be displayed. 
+   The landing page of **RES** will show summarize the training information including training sampling number along with two PLoM model trucation plots for PCA and KDE.
+
+.. figure:: figures/RES1.png
+   :align: center
+   :figclass: align-center
+
+   PCA representation error versus the PCA eigenvalues overlapped by the truncating PCA eigenvalue used in training
+
+.. figure:: figures/RES2.png
+   :align: center
+   :figclass: align-center
+
+   Diffusion map eigenvalue by components overlapped by the truncating eigenvalue used in training
+
+
+If the user selects the **Data** tab in the results panel, they will be presented with both a graphical plot and a tabular listing of the data.
+Various views of the graphical display can be obtained by left and right clicking in the columns of the tabular data. If a singular column of 
+the tabular data is pressed with both right and left buttons a frequency and CDF will be displayed, as shown in figure below.
+
+.. figure:: figures/RES3.png
+   :align: center
+   :figclass: align-center
+
+The PLoM model can be saved and be loaded back for future use. The ``Save PLoM Model`` button at the bottom of Summary 
+page would bring up a dialogue window for saving the model file to a user-defined directory.
+
+.. figure:: figures/RES4.png
+   :align: center
+   :figclass: align-center

Examples/qfem-0022/meta.yaml

@@ -0,0 +1,8 @@
+title:  Two-Dimensional Truss - PLoM Modeling and Simulation
+summary: |
+  Consider the problem simulating response of a two-dimensional truss structure with uncertain material properties. The goal of the exercise is to demonstrate the use of ``PLoM model`` method under ``SimCenterUQ`` to predict the response of the truss under the given load.
+author:
+- family: Zhong
+  given: Kuanshi
+collection-title: Surrogate training - building
+difficulty: 0

Examples/qfem-0022/src/TrussModel.tcl

@@ -0,0 +1,69 @@
+
+# units kN & mm
+
+#
+# set some parameters
+#
+
+pset E 205
+pset P 25
+pset Au 500
+pset Ao 250
+
+#
+# build the model
+#
+
+model Basic -ndm 2 -ndf 2
+
+node 1     0    0
+node 2  4000    0
+node 3  8000    0
+node 4 12000    0
+node 5  4000 4000
+node 6  8000 4000
+
+fix 1 1 1
+fix 4 0 1
+
+uniaxialMaterial Elastic 1 $E
+
+element truss 1 1 2 $Ao 1
+element truss 2 2 3 $Ao 1
+element truss 3 3 4 $Ao 1
+element truss 4 1 5 $Au 1
+element truss 5 5 6 $Au 1
+element truss 6 6 4 $Au 1
+element truss 7 2 5 $Ao 1
+element truss 8 3 6 $Ao 1
+element truss 9 5 3 $Ao 1
+timeSeries Linear 1
+pattern Plain 1 1 {
+    load 2 0 [expr -$P]
+    load 3 0 [expr -$P]
+}
+
+#
+# create a recorder
+#
+
+recorder Node -file node.out -scientific -precision 10 -node 1 2 3 4 5 6 -dof 1 2 disp
+
+#
+# build and perform the analysis
+#
+
+algorithm Linear
+integrator LoadControl 1.0
+system ProfileSPD
+numberer RCM
+constraints Plain
+analysis Static
+analyze 1
+
+#
+# remove the recorders
+#
+
+remove recorders
+

Examples/qfem-0022/src/TrussPost.py

@@ -0,0 +1,67 @@
+#!/usr/bin/python
+
+# written: fmk, adamzs 01/18
+
+# import functions for Python 2.X support
+from __future__ import division, print_function
+import sys
+if sys.version.startswith('2'): 
+    range=xrange
+    string_types = basestring
+else:
+    string_types = str
+
+import sys
+
+def process_results(inputArgs):
+
+    #
+    # process output file "node.out" for nodal displacements
+    #
+
+    with open ('node.out', 'rt') as inFile:
+        line = inFile.readline()
+        displ = line.split()
+        numNode = len(displ)
+
+    inFile.close
+
+    # now process the input args and write the results file
+
+    outFile = open('results.out','w')
+
+    # note for now assuming no ERROR in user data
+    for i in inputArgs:
+
+        theList=i.split('_')
+
+        if (len(theList) == 4):
+            dof = int(theList[3])
+        else:
+            dof = 1
+
+        if (theList[0] == "Node"):
+            nodeTag = int(theList[1])
+
+            if (nodeTag > 0 and nodeTag <= numNode):
+                if (theList[2] == "Disp"):
+                    nodeDisp = abs(float(displ[((nodeTag-1)*2)+dof-1]))
+                    outFile.write(str(nodeDisp))
+                    outFile.write(' ')
+                else:
+                    outFile.write('0. ')
+            else:
+                outFile.write('0. ')
+        else:
+            outFile.write('0. ')
+
+    outFile.close
+
+
+if __name__ == "__main__":
+    n = len(sys.argv)
+    responses = []
+    for i in range(1,n):
+        responses.append(sys.argv[i])
+
+    process_results(responses)

Examples/qfem-0022/src/TrussPost.tcl

@@ -0,0 +1,31 @@
+# create file handler to write results to output & list into which we will put results
+set resultFile [open results.out w]
+set results []
+
+# get list of valid nodeTags
+set nodeTags [getNodeTags]
+
+# for each quanity in list of QoI passed
+#  - get nodeTag
+#  - get nodal displacement if valid node, output 0.0 if not
+#  - for valid node output displacement, note if dof not provided output 1'st dof
+
+foreach edp $listQoI {
+	set splitEDP [split $edp "_"]	
+	set nodeTag [lindex $splitEDP 1]
+	if {$nodeTag in $nodeTags} {
+	    set nodeDisp [nodeDisp $nodeTag]
+	    if {[llength $splitEDP] == 3} {
+		set result [expr abs([lindex $nodeDisp 0])]
+	    } else {
+		set result [expr abs([lindex $nodeDisp [expr [lindex $splitEDP 3]-1]])]
+	    }
+	} else {
+	    set result 0.
+	}
+	lappend results $result
+}
+
+# send results to output file & close the file
+puts $resultFile $results
+close $resultFile