updating tensile_test notebook

9b802f8a · muhammad Hassani · 0dd7b667 · 9b802f8a · 9b802f8a
Commit 9b802f8a authored Sep 15, 2021 by muhammad Hassani
--- a/tensile_test/pyiron_tensile_test/__init__.py
+++ b/tensile_test/pyiron_tensile_test/__init__.py
 from pyiron_base import JOB_CLASS_DICT, Project
-from tensile_test_job import TensileJob
+from .tensile_test_job import TensileJob

 JOB_CLASS_DICT['TensileJob'] = 'pyiron_tensile_test.tensile_test_job'
--- a/tensile_test/sparql_tensile_test.ipynb
+++ b/tensile_test/sparql_tensile_test.ipynb
 {
 "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "30019591-6b6b-4093-b08e-b352c92293d1",
+   "metadata": {},
+   "source": [
+    "# Tensile test workflow\n",
+    "\n",
+    "Here, an examplary workflow of a tensile test is presented.\n",
+    "- The data source is obtained from a triple store via sparql queries.\n",
+    "- Then the elastic modulus is calculcated based on the given stress-strain data.\n",
+    "- The calculated elastic modulus is returned to the triple store.\n",
+    "\n",
+    "It must be mentioned that the sparql endpoint here is an instance of blazegraph, running on a personal cloud machine."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8f8eccf0-e01a-4ed8-ab63-23b7ca137a46",
+   "metadata": {},
+   "source": [
+    "### Importing and defining project from the custom defined module "
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 1,
@@ -7,7 +30,7 @@
   "metadata": {},
   "outputs": [],
   "source": [
-    "from pyiron_tensile_test import Project, TensileJob"
+    "from pyiron_tensile_test import Project"
   ]
  },
  {
@@ -21,6 +44,14 @@
    "pr.remove_jobs_silently(recursive=True)"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "d180d6c7-7ecc-4acf-859e-4ce029179df2",
+   "metadata": {},
+   "source": [
+    "### Creating a job of type tensile test"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 3,
@@ -31,6 +62,14 @@
    "job = pr.create.job.TensileJob(job_name='tensile_job')"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "c5e34bb4-f2d5-4027-a5b6-b00e3193e821",
+   "metadata": {},
+   "source": [
+    "### Defining the sparql endpoint and query for data source"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 4,
@@ -72,6 +111,14 @@
    "download_url"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "eed0e007-a990-4afe-b18d-ac7f19c0f5e0",
+   "metadata": {},
+   "source": [
+    "### Obtaining the experimental dataset"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 7,
@@ -210,6 +257,14 @@
    "job.experimental_json"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "640e6fc8-4b3e-447d-872f-01a75b1041a9",
+   "metadata": {},
+   "source": [
+    "### Extracting stress and strain data from the dataset"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 9,
@@ -287,6 +342,14 @@
    "job.plot_stress_strain()"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "3026e672-9c83-4d7b-9d33-547921c1d74b",
+   "metadata": {},
+   "source": [
+    "## Calculating the elastic modulus"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 13,
@@ -297,7 +360,7 @@
     "name": "stdout",
     "output_type": "stream",
     "text": [
-      "The job tensile_job was saved and received the ID: 342\n"
+      "The job tensile_job was saved and received the ID: 355\n"
     ]
    }
   ],
@@ -326,6 +389,14 @@
    "job.output.elastic_modulus"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "ba1ba3e5-7ebc-4d72-adb0-5735da75a21c",
+   "metadata": {},
+   "source": [
+    "### Return the calculated value to the triple store"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 15,
@@ -364,6 +435,14 @@
    "job.verify_update()"
   ]
  },
+  {
+   "cell_type": "markdown",
+   "id": "578ac891-c3c8-4fd7-b429-0296010f8533",
+   "metadata": {},
+   "source": [
+    "## Verifying the hdf5 file storage"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": 17,
@@ -463,7 +542,7 @@
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.7.11"
  }
 },
 "nbformat": 4,

+%% Cell type:markdown id:30019591-6b6b-4093-b08e-b352c92293d1 tags:
+
+# Tensile test workflow
+
+Here, an examplary workflow of a tensile test is presented.
+- The data source is obtained from a triple store via sparql queries.
+- Then the elastic modulus is calculcated based on the given stress-strain data.
+- The calculated elastic modulus is returned to the triple store.
+
+It must be mentioned that the sparql endpoint here is an instance of blazegraph, running on a personal cloud machine.
+
+%% Cell type:markdown id:8f8eccf0-e01a-4ed8-ab63-23b7ca137a46 tags:
+
+### Importing and defining project from the custom defined module
+
 %% Cell type:code id:c4ed7e16-cde3-4a61-b882-2d5d0266f994 tags:

 ``` python
-from pyiron_tensile_test import Project, TensileJob
+from pyiron_tensile_test import Project
 ```

 %% Cell type:code id:1455a593-de89-4960-b569-cfadde7dc473 tags:

 ``` python
 pr = Project('test_tensile_job')
 pr.remove_jobs_silently(recursive=True)
 ```

+%% Cell type:markdown id:d180d6c7-7ecc-4acf-859e-4ce029179df2 tags:
+
+### Creating a job of type tensile test
+
 %% Cell type:code id:72765577-e5fc-467b-b9fa-9f29c1afa75e tags:

 ``` python
 job = pr.create.job.TensileJob(job_name='tensile_job')
 ```

+%% Cell type:markdown id:c5e34bb4-f2d5-4027-a5b6-b00e3193e821 tags:
+
+### Defining the sparql endpoint and query for data source
+
 %% Cell type:code id:8496725a-d729-4335-b91f-35844d2e3e7d tags:

 ``` python
 job.endpoint = 'https://blazegraph.workshop-virtual.de/bigdata/sparql'
 ```

 %% Cell type:code id:7531101b-73fb-4880-87f5-58f5de30e304 tags:

 ``` python
 download_url = job.query_data_source(test_name='Tensile_Test')
 ```

 %% Cell type:code id:ad71ed4e-56f7-42a9-a887-2f3119650d00 tags:

 ``` python
 download_url
 ```

 %% Output

    'https://datashare.mpcdf.mpg.de/s/9N5Z1YXxMv9g09p'

+%% Cell type:markdown id:eed0e007-a990-4afe-b18d-ac7f19c0f5e0 tags:
+
+### Obtaining the experimental dataset
+
 %% Cell type:code id:29b6c64a-99c5-4d0b-8aee-6be40e2b9a26 tags:

 ``` python
 job.get_dataset(url=download_url)
 ```

 %% Cell type:code id:376ce2f8-d36c-4099-b771-a34960b96423 tags:

 ``` python
 job.experimental_json
 ```

 %% Output

                                                   test.metadata  \
    object.identifier                                   RX5163DV
    test.start-timestamp                2009-05-13T10:23:00+0200
    object.length                    {'value': 50, 'unit': 'mm'}
    object.cross-section-area  {'value': 78.658, 'unit': 'mm^2'}
    test.speed-1                {'value': 0.1, 'unit': 'mm/sec'}
    test.speed-2                {'value': 0.4, 'unit': 'mm/sec'}
    Young's module               {'value': 202.1, 'unit': 'GPa'}
    yield stress                   {'value': 316, 'unit': 'MPa'}
    tensile strength               {'value': 607, 'unit': 'MPa'}
    fields                                                   NaN
    data                                                     NaN
    
                                                                                                                                                                                                                           test.series
    object.identifier                                                                                                                                                                                                              NaN
    test.start-timestamp                                                                                                                                                                                                           NaN
    object.length                                                                                                                                                                                                                  NaN
    object.cross-section-area                                                                                                                                                                                                      NaN
    test.speed-1                                                                                                                                                                                                                   NaN
    test.speed-2                                                                                                                                                                                                                   NaN
    Young's module                                                                                                                                                                                                                 NaN
    yield stress                                                                                                                                                                                                                   NaN
    tensile strength                                                                                                                                                                                                               NaN
    fields                                                                                       [[Time, s], [Crosshead Travel, mm], [Load, kN], [Tensile Stress, MPa], [Elongation_1, %], [Elongation_2, %], [Elongation Average, %]]
    data                       [[0.0, -4e-05, 0.00062, 0.007840000000000001, 0.0004900000000000001, 0.0, 0.0], [0.1, 0.00252, -0.00013000000000000002, -0.0016500000000000002, 0.00047000000000000004, 0.0, 0.0], [0.2, 0.00928, 0....

+%% Cell type:markdown id:640e6fc8-4b3e-447d-872f-01a75b1041a9 tags:
+
+### Extracting stress and strain data from the dataset
+
 %% Cell type:code id:edb0e1d0-89f2-48e1-8551-87f0634a2edc tags:

 ``` python
 job.extract_stress_strain()
 ```

 %% Cell type:code id:9502757f-f379-44fa-bbdf-74062087114f tags:

 ``` python
 job.input.strains
 ```

 %% Output

    array([4.90000000e-04, 4.70000000e-04, 5.00000000e-04, ...,
           5.51814239e+01, 5.51907786e+01, 5.51935194e+01])

 %% Cell type:code id:483ba441-eedb-480e-af52-1f912b7c6e0a tags:

 ``` python
 job.input.stresses
 ```

 %% Output

    array([ 7.8400000e-03, -1.6500000e-03,  1.7400000e-03, ...,
            3.8407181e+02,  3.8266739e+02,  3.8133539e+02])

 %% Cell type:code id:c5daa08a-c8f2-4e84-ac72-7d811da6d46e tags:

 ``` python
 job.plot_stress_strain()
 ```

 %% Output



+%% Cell type:markdown id:3026e672-9c83-4d7b-9d33-547921c1d74b tags:
+
+## Calculating the elastic modulus
+
 %% Cell type:code id:13c1a787-2596-4ec1-954b-30869f000971 tags:

 ``` python
 job.run()
 ```

 %% Output

-    The job tensile_job was saved and received the ID: 342
+    The job tensile_job was saved and received the ID: 355

 %% Cell type:code id:3610242f-f53b-4664-bd17-9c77acf79edd tags:

 ``` python
 job.output.elastic_modulus
 ```

 %% Output

    201.21019550851148

+%% Cell type:markdown id:ba1ba3e5-7ebc-4d72-adb0-5735da75a21c tags:
+
+### Return the calculated value to the triple store
+
 %% Cell type:code id:26aacc0c-6fde-461d-881b-293d000415a5 tags:

 ``` python
 job.update_triple_store()
 ```

 %% Cell type:code id:5f7e1c4f-6b3c-46c3-9c13-7797cb610e14 tags:

 ``` python
 job.verify_update()
 ```

 %% Output

    correctly updated!

    True

+%% Cell type:markdown id:578ac891-c3c8-4fd7-b429-0296010f8533 tags:
+
+## Verifying the hdf5 file storage
+
 %% Cell type:code id:376a7daa-4cae-4a3d-89d7-bc05da6b49d4 tags:

 ``` python
 job_load = pr.load(job.name)
 ```

 %% Cell type:code id:95c6590b-0b7e-4847-9a90-a1292127913c tags:

 ``` python
 job_load.output
 ```

 %% Output

    DataContainer({'elastic_modulus': 201.21019550851148})

 %% Cell type:code id:8d12770b-9b73-4a9f-a481-f067585e2daa tags:

 ``` python
 job_load.input
 ```

 %% Output

    DataContainer({'test_name': 'Tensile_Test', 'strains': array([4.90000000e-04, 4.70000000e-04, 5.00000000e-04, ...,
           5.51814239e+01, 5.51907786e+01, 5.51935194e+01]), 'stresses': array([ 7.8400000e-03, -1.6500000e-03,  1.7400000e-03, ...,
            3.8407181e+02,  3.8266739e+02,  3.8133539e+02])})

 %% Cell type:code id:450946ff-19d0-4bea-b993-ec26c9a15b1e tags:

 ``` python
 ```