Merge pull request #198 from atztogo/master

Update tutorial document at ISSP Univ. Tokyo

docs/pages/2019_ISSP_Chiba_Japan/index.rst

@@ -6,27 +6,28 @@
 +-----------------+--------------------------------------------------------------------------------+
 | Related resources                                                                                |
 +=================+================================================================================+
-| Virtual Machine | `Quantum Mobile 19.09.0`_                                                      |
+| Virtual Machine | `Quantum Mobile (ISSP special)`_                                               |
 +-----------------+--------------------------------------------------------------------------------+
-| python packages | `aiida-core 1.0.0b6`_, `aiida-quantumespresso 3.0.0a5`_, `aiidalab 19.08.0a1`_ |
+| python packages | `aiida-core 1.0.1`_, `aiida-quantumespresso 3.0.0a5`_, `aiidalab 19.11.0a2`_   |
 +-----------------+--------------------------------------------------------------------------------+
 | codes           | `Quantum Espresso 6.4.1`_                                                      |
 +-----------------+--------------------------------------------------------------------------------+
 
-.. _Quantum Mobile 19.09.0: https://github.com/marvel-nccr/quantum-mobile/releases/tag/19.09.0
-.. _aiida-core 1.0.0b6: https://pypi.org/project/aiida-core/1.0.0b6
+.. _Quantum Mobile (ISSP special): http://phonondb.mtl.kyoto-u.ac.jp/aiida_tutorial/Quantum_Mobile_ISSP.ova
+.. _aiida-core 1.0.1: https://pypi.org/project/aiida-core/1.0.1
 .. _aiida-quantumespresso 3.0.0a5: https://pypi.org/project/aiida-quantumespresso/3.0.0a5
-.. _aiidalab 19.08.0a1: https://pypi.org/project/aiidalab/19.8.0a1
+.. _aiidalab 19.11.0a2: https://pypi.org/project/aiidalab/19.11.0a2
 .. _Quantum Espresso 6.4.1: https://github.com/QEF/q-e/releases/tag/qe-6.4.1
 
 These are the hands-on materials from the 2-day AiiDA tutorial
 |tutorial_name| from December 19-20, 2019.
 
-Participants of the tutorial use the Quantum Mobile VirtualBox image
-linked above or from `this mirror
-<http://phonondb.mtl.kyoto-u.ac.jp/quantum_mobile_19.09.0.ova>`_ on
-their own computer. The image already contains all the required
-software.
+Participants of the tutorial use the Quantum Mobile VirtualBox virtual
+machine (VM) image linked above on their own computer. The image
+already contains all the required software. This VM image can be
+imported from the GUI interface of VirtualBox by "File => Import
+Appliance" or from the Virtualbox window "[Tools] =>
+[Import]".
 
 Getting started
 ---------------

docs/pages/2019_ISSP_Chiba_Japan/notebooks/querybuilder-tutorial.ipynb

@@ -585,7 +585,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "generate_query_graph(qb.get_json_compatible_queryhelp(), 'query1.png')\n",
+    "generate_query_graph(qb.queryhelp, 'query1.png')\n",
     "Image(filename='query1.png')"
    ]
   },
@@ -629,7 +629,7 @@
    "source": [
     "qb = QueryBuilder()\n",
     "# Here I also visualize what's going on:\n",
-    "generate_query_graph(qb.get_json_compatible_queryhelp(), 'query2.png')\n",
+    "generate_query_graph(qb.queryhelp, 'query2.png')\n",
     "Image(filename='query2.png')"
    ]
   },
@@ -775,7 +775,7 @@
     "qb.append(Group, filters={'label':{'like':'tutorial_%'}}, project='label', tag='group')\n",
     "# Visualize:\n",
     "print(\"Groups:\", ', '.join([g for g, in qb.all()]))\n",
-    "generate_query_graph(qb.get_json_compatible_queryhelp(), 'query3.png')\n",
+    "generate_query_graph(qb.queryhelp, 'query3.png')\n",
     "Image(filename='query3.png')"
    ]
   },
@@ -795,7 +795,7 @@
     "# I want every PwCalculation that is a member of the specified groups:\n",
     "qb.append(PwCalculation, tag='calculation', with_group=) # Complete the function call with the correct relationship-tag!\n",
     "#Visualize\n",
-    "generate_query_graph(qb.get_json_compatible_queryhelp(), 'query4.png') \n",
+    "generate_query_graph(qb.queryhelp, 'query4.png') \n",
     "Image(filename='query4.png')"
    ]
   },
@@ -822,7 +822,7 @@
     "# Complete the function call with the correct relationship-tag!\n",
     "qb.append(StructureData, project=, tag='structure', with_outgoing=)\n",
     "# Visualize:\n",
-    "generate_query_graph(qb.get_json_compatible_queryhelp(), 'query5.png')\n",
+    "generate_query_graph(qb.queryhelp, 'query5.png')\n",
     "Image(filename='query5.png')"
    ]
   },
@@ -854,7 +854,7 @@
     "# Complete the function call with the correct relationship-tag!\n",
     "qb.append(Dict, tag='results', project=['attributes.energy_smearing', ...], with_incoming=)\n",
     "\n",
-    "generate_query_graph(qb.get_json_compatible_queryhelp(), 'query6.png') \n",
+    "generate_query_graph(qb.queryhelp, 'query6.png') \n",
     "Image(filename='query6.png')"
    ]
   },

docs/pages/2019_ISSP_Chiba_Japan/sections/calculations.rst

@@ -495,9 +495,9 @@ error code near the "Finished" status of the State should be non-zero,
 .. code:: bash
 
     $ verdi process list -a -p1
-      PK  Created    State             Process label    Process status
-    ----  ---------  ----------------  ---------------  ----------------
-      98  16h ago    Finished [115]    PwCalculation
+      PK  Created    Process label    Process State     Process status
+    ----  ---------  ---------------  ----------------  ----------------
+    2060  3m ago     PwCalculation    ⏹Finished [300]
     ...
     $ # Anything but [0] after the Finished state signals a failure
 
@@ -521,38 +521,38 @@ For any calculation, both successful and failed, you can get a summary by:
 .. code:: bash
 
     $ verdi process show <pk_number>
-    Property       Value
-    -------------  ---------------------------------------------------
-    type           CalcJobNode
-    pk             98
-    uuid           4c444afd-f6e2-4896-b9ae-8cb8a5ec75c5
-    label          PW test
-    description    My first AiiDA calc with Quantum ESPRESSO on Si
-    ctime          2019-05-01 15:59:39.180018+00:00
-    mtime          2019-05-01 16:01:44.870902+00:00
-    process state  Finished
-    exit status    115
-    computer       [1] localhost
+    Property     Value
+    -----------  --------------------------------------------------------------------------------
+    type         PwCalculation
+    state        Finished [300] Both the stdout and XML output files could not be read or parsed.
+    pk           2060
+    uuid         cd874e9d-94f7-4fc8-88c5-decdfc031491
+    label        PW test
+    description  My first AiiDA calc with Quantum ESPRESSO on Si
+    ctime        2019-12-13 06:14:07.374401+00:00
+    mtime        2019-12-13 06:14:19.775021+00:00
+    computer     [2] localhost
 
     Inputs      PK    Type
     ----------  ----  -------------
     pseudos
-        Si      50    UpfData
-    code        2     Code
-    kpoints     10    KpointsData
-    parameters  96    Dict
-    settings    97    Dict
-    structure   9     StructureData
-
-    Outputs          PK  Type
-    -------------  ----  ----------
-    remote_folder    99  RemoteData
-    retrieved       100  FolderData
+        Si      2003  UpfData
+    code        2056  Code
+    kpoints     2058  KpointsData
+    parameters  2059  Dict
+    structure   2057  StructureData
+
+    Outputs              PK  Type
+    -----------------  ----  --------------
+    output_parameters  2064  Dict
+    output_trajectory  2063  TrajectoryData
+    remote_folder      2061  RemoteData
+    retrieved          2062  FolderData
 
     Log messages
     ---------------------------------------------
-    There are 2 log messages for this calculation
-    Run 'verdi process report 98' to see them
+    There are 3 log messages for this calculation
+    Run 'verdi process report 2060' to see them
 
 The last part of the output alerts you to the fact that there
 are some log messages waiting for you, if you run
@@ -564,16 +564,18 @@ key and see if our calculation succeeds:
 .. code:: python
 
     parameters_dict = {
-        "CONTROL": {
-            "calculation": "scf",
+        'CONTROL': {
+            'calculation': 'scf',
+            'tstress': True,
+            'tprnfor': True,
+        },
+        'SYSTEM': {
+            'ecutwfc': 30.,
+            'ecutrho': 200.,
         },
-        "SYSTEM": {
-            "ecutwfc": 30.,
-            "ecutrho": 200.,
+        'ELECTRONS': {
+            'conv_thr': 1.e-8,
         },
-        "ELECTRONS": {
-            "conv_thr": 1.e-6,
-        }
     }
     builder.parameters = Dict(dict=parameters_dict)
     calculation = submit(builder)

docs/pages/2019_ISSP_Chiba_Japan/sections/first_taste.rst

@@ -32,7 +32,7 @@ There are a number of helpful resources available to you for getting more inform
 Please consider:
 
  * consulting the extensive `AiiDA documentation <https://aiida-core.readthedocs.io/en/latest/>`_
- * asking in the `Slack channel of the tutorial <https://aiida-tutorial-india.slack.com>`_
+ * asking in the `Slack channel of the tutorial <https://aiidatutorial-tck8243.slack.com>`_
  * asking your neighbor
  * asking a tutor
  * opening a new issue on the `tutorial issue tracker <https://github.com/aiidateam/aiida-tutorials/issues>`_
@@ -136,79 +136,8 @@ A few questions you could answer using these commands (optional)
 
 .. tip::
 
-    Use the ``grep`` command to filter the terminal output by keywords, e.g., ``verdi calc job res 175 | grep wall_time``.
+    Use the ``grep`` command to filter the terminal output by keywords, e.g., ``verdi calcjob res 175 | grep wall_time``.
 
-Moving to a different computer
-------------------------------
-
-The Quantum ESPRESSO calculation we just ran, was directly executed on the virtual machine.
-This is fine for tests, but production calculations should typically be run on a remote compute cluster.
-With AiiDA, moving a calculation from one computer to another means changing one line of code.
-
-For the purposes of this tutorial, you'll run on your neighbor's computer.
-Ask your neighbor for the IP address of their VM.
-Then, download the :download:`neighbor.yml <include/configuration/neighbor.yml>` setup template, replace the placeholder by the IP address and let AiiDA know about this computer by running:
-
-.. .. literalinclude:: include/configuration/neighbor.yml
-
-.. code:: bash
-
-  verdi computer setup --config neighbor.yml
-
-.. note::
-
-    If you do not have a partner machine available, for example because you are completing this
-    tutorial at a later time, simply use "localhost" instead of the IP address.
-
-AiiDA is now aware of the existence of the computer but you'll still need to let AiiDA
-know how to connect to it.
-AiiDA does this via `SSH <https://en.wikipedia.org/wiki/Secure_Shell>`_ keys.
-Your tutorial VM already contains a private SSH key for connecting to the ``compute`` user of your neighbor's machine,
-so all that is left is to configure it in AiiDA.
-
-Download the :download:`neighbor-config.yml <include/configuration/neighbor-config.yml>` configuration template and run:
-
-.. .. literalinclude:: include/configuration/neighbor-config.yml
-
-.. code:: bash
-
-  verdi computer configure ssh neighbor --config neighbor-config.yml --non-interactive
-
-.. note:: Both ``verdi computer setup`` and ``verdi computer configure`` can be used interactively without
-  configuration files, which are provided here just to avoid typing errors.
-
-AiiDA should now have access to your neighbor's computer. Let's quickly test this:
-
-.. code:: bash
-
-  verdi computer test neighbor
-
-Finally, let AiiDA know about the **code** we are going to use.
-We've again prepared a template that looks as follows:
-
-.. literalinclude:: include/configuration/qe.yml
-
-Download the :download:`qe.yml <include/configuration/qe.yml>` code template and run:
-
-.. code:: bash
-
-  verdi code setup --config qe.yml
-  verdi code list  # note the label of the new code you just set up!
-
-Now modify the code label in your ``demo_calcjob.py`` script to the label of your new code and simply run another calculation using ``verdi run demo_calcjob.py``.
-
-To see what is going on, AiiDA provides a command that lets you jump to the folder of the directory of the calculation on the remote computer:
-
-.. code:: bash
-
-  verdi process list --all  # get PK of new calculation
-  verdi calcjob gotocomputer <PK>
-
-Have a look around.
- * Do you recognize the different files?
- * Have a look at the submission script ``_aiidasubmit.sh``.
-   Compare it to the submission script of your previous calculation.
-   What are the differences?
 
 From calculations to workflows
 ------------------------------
@@ -268,11 +197,13 @@ Start the AiiDA REST API:
 
   verdi restapi
 
-and open the |provenance browser|.
+and open the |provenance browser|. If you can't see any useful
+information, please ask to tutors, because restapi v4 may have some
+issue on the day of this tutorial.
 
 .. |provenance browser| raw:: html
 
-   <a href="https://www.materialscloud.org/explore/ownrestapi?base_url=http://127.0.0.1:5000/api/v3" target="_blank">Materials Cloud provenance browser</a>
+   <a href="https://www.materialscloud.org/explore/ownrestapi?base_url=http://127.0.0.1:5000/api/v4" target="_blank">Materials Cloud provenance browser</a>
 
 .. note::
 

docs/pages/2019_ISSP_Chiba_Japan/sections/include/configuration/computer.yml

@@ -6,7 +6,7 @@ transport: local
 scheduler: "direct"
 work_dir: "/home/max/.aiida_run"
 mpirun_command: "mpirun -np {tot_num_mpiprocs}"
-mpiprocs_per_machine: "2"
+mpiprocs_per_machine: "1"
 shebang: "#!/bin/bash"
 prepend_text: " "
-append_text: " "
+append_text: " "