From 139e9c3f13543b9b2cd484854170ba20f2a1cf5a Mon Sep 17 00:00:00 2001 From: richard gowers Date: Wed, 10 Apr 2024 09:56:25 +0100 Subject: [PATCH] docs: final tweaks to userguide quickrun clarify can run single sim locally homogenise quickrun examples add link to working with results page --- docs/guide/execution/quickrun_execution.rst | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/docs/guide/execution/quickrun_execution.rst b/docs/guide/execution/quickrun_execution.rst index 4b680c996..30987a096 100644 --- a/docs/guide/execution/quickrun_execution.rst +++ b/docs/guide/execution/quickrun_execution.rst @@ -5,8 +5,9 @@ Execution with Quickrun The planning and preparation of a campaign of alchemical simulations using the ``openfe`` package is intended to be achievable on a local workstation in a matter of minutes. -The **execution** of these simulations however requires a large amount of computational power and is intended to be -distributed across a HPC environment. +The **execution** of these simulations however requires a large amount of computational power, +and beyond running single calculations locally, +is intended to be distributed across a HPC environment. Doing this requires storing and sending the details of the simulation from the local workstation to a HPC environment, this can be done via the :func:`.Transformation.dump` function which :ref:`creates a saved "json" version of the data`. @@ -20,8 +21,10 @@ therefore this command would execute a simulation saved to a file called "transf :: - openfe quickrun transformation.json + openfe quickrun transformation.json -o results.json + +Which will produce a results file called ``results.json``. Executing within a job submission script ---------------------------------------- @@ -40,3 +43,9 @@ The ``quickrun`` command can be integrated into as: conda activate openfe_env openfe quickrun transformation.json -o results.json + + +See Also +-------- + +For details on inspecting these results, refer to :ref:`userguide_results`.