From fceeea1250a9aa1dc7517356a52c9376fb9c525a Mon Sep 17 00:00:00 2001
From: Ivan Kondov <ivan.kondov@kit.edu>
Date: Thu, 18 Feb 2021 15:53:02 +0100
Subject: [PATCH] extended the docs with example appending a workflow
---
docs/advanced.rst | 53 ++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 52 insertions(+), 1 deletion(-)
diff --git a/docs/advanced.rst b/docs/advanced.rst
index c29720c..13596d7 100644
--- a/docs/advanced.rst
+++ b/docs/advanced.rst
@@ -173,7 +173,7 @@ will return all completed workflows that have name *The coffee workflow*. The
empty selection means that no firework and no firework updates are selected.
This query is started with the command::
- lpad_-o yaml query -f query_sample_1.yaml
+ lpad_query -o yaml query -f query_sample_1.yaml
If, supposed, we have one workflow with that name and it is completed the output
is::
@@ -253,6 +253,57 @@ https://docs.mongodb.com/manual/tutorial/query-documents/
In the examples provided in this tutorial the queries are serialized to YAML and
to JSON.
+Building up a workflow as you go
+--------------------------------
+
+Very often in a research project one does not know the workflow final structure
+at the beginning. In FireWorks one can extend exiting workflows on the LaunchPad
+duting their whole lifetime, i.e. it does not matter whether the workflow has
+been just added, is running or completed. An simple example for extending a
+workflow is given in __ Exercise 4: Extending a workflow __. Here, the
+example shows how a workflow with a single Firework performing a structure
+relaxation can be exteded with a Firework performing normal mode analysis::
+
+ cd inputs
+ lpad add -c water-turbomole_relax.yaml
+ lpad get_wflows -q '{"name": "H2O normal modes - extend as you go"}'
+::
+ state: READY
+ name: H2O normal modes - extend as you go--2906
+ created_on": 2021-02-18T14:39:54.065000
+ states_list: REA
+
+ cd ../launches
+ qlaunch -q ../config/qadapter_fh2_turbomole.yaml -w ../config/fworker_fh2_turbomole.yaml singleshot
+
+After the job has been completed:
+
+ lpad -o yaml get_wflows -q '{"name": "H2O normal modes - extend as you go"}'
+::
+ created_on: '2021-02-18T14:39:54.065000'
+ name: H2O normal modes - extend as you go--2906
+ state: COMPLETED
+ states_list: C
+
+Now you decide to perform a normal mode anaysis and reuse the relaxed structure
+from the workflow::
+
+ cd ../inputs
+ lpad append_wflow -i 2906 -f water-turbomole_freqs.yaml
+ lpad -o yaml get_wflows -q '{"name": "H2O normal modes - extend as you go"}'
+::
+ name: H2O normal modes - extend as you go--2906
+ state: RUNNING
+ states_list: C-REA
+
+ cd ../launches
+ qlaunch -q ../config/qadapter_fh2_turbomole.yaml -w ../config/fworker_fh2_turbomole.yaml singleshot
+ lpad -o yaml get_wflows -q '{"name": "H2O normal modes - extend as you go"}'
+ created_on: '2021-02-18T14:39:54.065000'
+ name: H2O normal modes - extend as you go--2906
+ state: COMPLETED
+ states_list: C-C
+
Final remark
------------
--
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