From a0525dff08add764161530f8b6e10eb2accf1407 Mon Sep 17 00:00:00 2001 From: singularitti Date: Sun, 19 Nov 2023 14:22:03 -0500 Subject: [PATCH 1/4] Rename `QuasiHarmonicApproxWorkflow` to `QuasiHarmonicApprox` --- docs/src/run/cli.md | 2 +- src/Express.jl | 2 +- .../Config.jl | 0 .../QuasiHarmonicApprox.jl} | 2 +- .../Recipes.jl | 2 +- .../actions.jl | 0 test/QuasiHarmonicApproxWorkflow.jl | 6 +++--- test/runtests.jl | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) rename src/{QuasiHarmonicApproxWorkflow => QuasiHarmonicApprox}/Config.jl (100%) rename src/{QuasiHarmonicApproxWorkflow/QuasiHarmonicApproxWorkflow.jl => QuasiHarmonicApprox/QuasiHarmonicApprox.jl} (66%) rename src/{QuasiHarmonicApproxWorkflow => QuasiHarmonicApprox}/Recipes.jl (93%) rename src/{QuasiHarmonicApproxWorkflow => QuasiHarmonicApprox}/actions.jl (100%) diff --git a/docs/src/run/cli.md b/docs/src/run/cli.md index 9c59f4a2..972c6a48 100644 --- a/docs/src/run/cli.md +++ b/docs/src/run/cli.md @@ -29,7 +29,7 @@ julia> run!(workflow); ``` For phonon and the QHA workflow, run `using Express.PhononWorkflow.Recipes` -and `using Express.QuasiHarmonicApproxWorkflow.Recipes` in the first step. +and `using Express.QuasiHarmonicApprox.Recipes` in the first step. In an EOS workflow, the final results include outputs returned by Quantum ESPRESSO, a list of raw data (volume-energy pairs), and a fitted EOS. If something goes wrong, the workflow diff --git a/src/Express.jl b/src/Express.jl index a95ef81a..490fbd28 100644 --- a/src/Express.jl +++ b/src/Express.jl @@ -6,6 +6,6 @@ include("ConvergenceTestWorkflow/ConvergenceTestWorkflow.jl") include("EquationOfStateWorkflow/EquationOfStateWorkflow.jl") # include("StaticElasticity/StaticElasticity.jl") include("PhononWorkflow/PhononWorkflow.jl") -# include("QuasiHarmonicApproxWorkflow/QuasiHarmonicApproxWorkflow.jl") +# include("QuasiHarmonicApprox/QuasiHarmonicApprox.jl") end diff --git a/src/QuasiHarmonicApproxWorkflow/Config.jl b/src/QuasiHarmonicApprox/Config.jl similarity index 100% rename from src/QuasiHarmonicApproxWorkflow/Config.jl rename to src/QuasiHarmonicApprox/Config.jl diff --git a/src/QuasiHarmonicApproxWorkflow/QuasiHarmonicApproxWorkflow.jl b/src/QuasiHarmonicApprox/QuasiHarmonicApprox.jl similarity index 66% rename from src/QuasiHarmonicApproxWorkflow/QuasiHarmonicApproxWorkflow.jl rename to src/QuasiHarmonicApprox/QuasiHarmonicApprox.jl index 637e6007..fdfdfc0b 100644 --- a/src/QuasiHarmonicApproxWorkflow/QuasiHarmonicApproxWorkflow.jl +++ b/src/QuasiHarmonicApprox/QuasiHarmonicApprox.jl @@ -1,4 +1,4 @@ -module QuasiHarmonicApproxWorkflow +module QuasiHarmonicApprox include("Config.jl") include("actions.jl") diff --git a/src/QuasiHarmonicApproxWorkflow/Recipes.jl b/src/QuasiHarmonicApprox/Recipes.jl similarity index 93% rename from src/QuasiHarmonicApproxWorkflow/Recipes.jl rename to src/QuasiHarmonicApprox/Recipes.jl index 19a15980..85220c9c 100644 --- a/src/QuasiHarmonicApproxWorkflow/Recipes.jl +++ b/src/QuasiHarmonicApprox/Recipes.jl @@ -6,7 +6,7 @@ using ExpressBase.Recipes: Recipe using EasyJobsBase: Job using SimpleWorkflows: Workflow, run!, → -using ..QuasiHarmonicApproxWorkflow: MakeInput, CalculateThermodyn, Plot +using ..QuasiHarmonicApprox: MakeInput, CalculateThermodyn, Plot import ...Express: jobify diff --git a/src/QuasiHarmonicApproxWorkflow/actions.jl b/src/QuasiHarmonicApprox/actions.jl similarity index 100% rename from src/QuasiHarmonicApproxWorkflow/actions.jl rename to src/QuasiHarmonicApprox/actions.jl diff --git a/test/QuasiHarmonicApproxWorkflow.jl b/test/QuasiHarmonicApproxWorkflow.jl index 30e3005b..d5f7f517 100644 --- a/test/QuasiHarmonicApproxWorkflow.jl +++ b/test/QuasiHarmonicApproxWorkflow.jl @@ -1,8 +1,8 @@ -module QuasiHarmonicApproxWorkflow +module QuasiHarmonicApprox using ExpressBase.Files: load -using Express.QuasiHarmonicApproxWorkflow: QuasiHarmonicApproximation -using Express.QuasiHarmonicApproxWorkflow.Config: ExpandConfig +using Express.QuasiHarmonicApprox: QuasiHarmonicApproximation +using Express.QuasiHarmonicApprox.Config: ExpandConfig using Test @testset "Load a configuration file: silicon" begin diff --git a/test/runtests.jl b/test/runtests.jl index 7fd8a2a5..88c79eab 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -2,5 +2,5 @@ using Express using Test @testset "Express.jl" begin - include("QuasiHarmonicApproxWorkflow.jl") + include("QuasiHarmonicApprox.jl") end From 7a6b3c6a55507dbcffa86e5fb74aefba41c40042 Mon Sep 17 00:00:00 2001 From: singularitti Date: Sun, 19 Nov 2023 14:23:21 -0500 Subject: [PATCH 2/4] Rename `ConvergenceTestWorkflow` to `ConvergenceTest` --- src/{ConvergenceTestWorkflow => ConvergenceTest}/Config.jl | 0 .../ConvergenceTest.jl} | 2 +- src/{ConvergenceTestWorkflow => ConvergenceTest}/Recipes.jl | 2 +- src/{ConvergenceTestWorkflow => ConvergenceTest}/actions.jl | 0 src/{ConvergenceTestWorkflow => ConvergenceTest}/think.jl | 0 src/Express.jl | 2 +- 6 files changed, 3 insertions(+), 3 deletions(-) rename src/{ConvergenceTestWorkflow => ConvergenceTest}/Config.jl (100%) rename src/{ConvergenceTestWorkflow/ConvergenceTestWorkflow.jl => ConvergenceTest/ConvergenceTest.jl} (74%) rename src/{ConvergenceTestWorkflow => ConvergenceTest}/Recipes.jl (98%) rename src/{ConvergenceTestWorkflow => ConvergenceTest}/actions.jl (100%) rename src/{ConvergenceTestWorkflow => ConvergenceTest}/think.jl (100%) diff --git a/src/ConvergenceTestWorkflow/Config.jl b/src/ConvergenceTest/Config.jl similarity index 100% rename from src/ConvergenceTestWorkflow/Config.jl rename to src/ConvergenceTest/Config.jl diff --git a/src/ConvergenceTestWorkflow/ConvergenceTestWorkflow.jl b/src/ConvergenceTest/ConvergenceTest.jl similarity index 74% rename from src/ConvergenceTestWorkflow/ConvergenceTestWorkflow.jl rename to src/ConvergenceTest/ConvergenceTest.jl index 9d06bae5..9fea4d72 100644 --- a/src/ConvergenceTestWorkflow/ConvergenceTestWorkflow.jl +++ b/src/ConvergenceTest/ConvergenceTest.jl @@ -1,4 +1,4 @@ -module ConvergenceTestWorkflow +module ConvergenceTest include("Config.jl") include("actions.jl") diff --git a/src/ConvergenceTestWorkflow/Recipes.jl b/src/ConvergenceTest/Recipes.jl similarity index 98% rename from src/ConvergenceTestWorkflow/Recipes.jl rename to src/ConvergenceTest/Recipes.jl index d1607d5f..faa441b5 100644 --- a/src/ConvergenceTestWorkflow/Recipes.jl +++ b/src/ConvergenceTest/Recipes.jl @@ -8,7 +8,7 @@ using ExpressBase.Recipes: Recipe using SimpleWorkflows: Workflow, run! using ..Config: StaticConfig, expand -using ..ConvergenceTestWorkflow: +using ..ConvergenceTest: DownloadPotentials, CreateInput, WriteInput, diff --git a/src/ConvergenceTestWorkflow/actions.jl b/src/ConvergenceTest/actions.jl similarity index 100% rename from src/ConvergenceTestWorkflow/actions.jl rename to src/ConvergenceTest/actions.jl diff --git a/src/ConvergenceTestWorkflow/think.jl b/src/ConvergenceTest/think.jl similarity index 100% rename from src/ConvergenceTestWorkflow/think.jl rename to src/ConvergenceTest/think.jl diff --git a/src/Express.jl b/src/Express.jl index 490fbd28..717baa9b 100644 --- a/src/Express.jl +++ b/src/Express.jl @@ -2,7 +2,7 @@ module Express # include("SelfConsistentField.jl") # include("BandStructure.jl") -include("ConvergenceTestWorkflow/ConvergenceTestWorkflow.jl") +include("ConvergenceTest/ConvergenceTest.jl") include("EquationOfStateWorkflow/EquationOfStateWorkflow.jl") # include("StaticElasticity/StaticElasticity.jl") include("PhononWorkflow/PhononWorkflow.jl") From be03845089197b80ce4e61b9e39f458b4d2a6f52 Mon Sep 17 00:00:00 2001 From: singularitti Date: Sun, 19 Nov 2023 14:24:38 -0500 Subject: [PATCH 3/4] Rename `EquationOfStateWorkflow` to `EquationOfState` --- docs/src/run/cli.md | 2 +- src/{EquationOfStateWorkflow => EquationOfState}/Config.jl | 0 .../EquationOfState.jl} | 2 +- src/{EquationOfStateWorkflow => EquationOfState}/Recipes.jl | 2 +- src/{EquationOfStateWorkflow => EquationOfState}/actions.jl | 0 src/{EquationOfStateWorkflow => EquationOfState}/think.jl | 0 src/Express.jl | 2 +- 7 files changed, 4 insertions(+), 4 deletions(-) rename src/{EquationOfStateWorkflow => EquationOfState}/Config.jl (100%) rename src/{EquationOfStateWorkflow/EquationOfStateWorkflow.jl => EquationOfState/EquationOfState.jl} (74%) rename src/{EquationOfStateWorkflow => EquationOfState}/Recipes.jl (99%) rename src/{EquationOfStateWorkflow => EquationOfState}/actions.jl (100%) rename src/{EquationOfStateWorkflow => EquationOfState}/think.jl (100%) diff --git a/docs/src/run/cli.md b/docs/src/run/cli.md index 972c6a48..aa3cc34a 100644 --- a/docs/src/run/cli.md +++ b/docs/src/run/cli.md @@ -19,7 +19,7 @@ and submit it to a workload manager like [Slurm](https://www.schedmd.com/). However, users can also request an interactive session and run code Julia REPL. ```julia-repl -julia> using Express.EquationOfStateWorkflow.Recipes +julia> using Express.EquationOfState.Recipes julia> using QuantumESPRESSOExpress diff --git a/src/EquationOfStateWorkflow/Config.jl b/src/EquationOfState/Config.jl similarity index 100% rename from src/EquationOfStateWorkflow/Config.jl rename to src/EquationOfState/Config.jl diff --git a/src/EquationOfStateWorkflow/EquationOfStateWorkflow.jl b/src/EquationOfState/EquationOfState.jl similarity index 74% rename from src/EquationOfStateWorkflow/EquationOfStateWorkflow.jl rename to src/EquationOfState/EquationOfState.jl index 0da17d02..f46e1f37 100644 --- a/src/EquationOfStateWorkflow/EquationOfStateWorkflow.jl +++ b/src/EquationOfState/EquationOfState.jl @@ -1,4 +1,4 @@ -module EquationOfStateWorkflow +module EquationOfState include("Config.jl") include("actions.jl") diff --git a/src/EquationOfStateWorkflow/Recipes.jl b/src/EquationOfState/Recipes.jl similarity index 99% rename from src/EquationOfStateWorkflow/Recipes.jl rename to src/EquationOfState/Recipes.jl index ca7f8262..a31d7214 100644 --- a/src/EquationOfStateWorkflow/Recipes.jl +++ b/src/EquationOfState/Recipes.jl @@ -8,7 +8,7 @@ using ExpressBase.Recipes: Recipe using SimpleWorkflows: Workflow, run! using ..Config: StaticConfig, expand -using ..EquationOfStateWorkflow: +using ..EquationOfState: DownloadPotentials, ComputeVolume, CreateInput, diff --git a/src/EquationOfStateWorkflow/actions.jl b/src/EquationOfState/actions.jl similarity index 100% rename from src/EquationOfStateWorkflow/actions.jl rename to src/EquationOfState/actions.jl diff --git a/src/EquationOfStateWorkflow/think.jl b/src/EquationOfState/think.jl similarity index 100% rename from src/EquationOfStateWorkflow/think.jl rename to src/EquationOfState/think.jl diff --git a/src/Express.jl b/src/Express.jl index 717baa9b..61600dc1 100644 --- a/src/Express.jl +++ b/src/Express.jl @@ -3,7 +3,7 @@ module Express # include("SelfConsistentField.jl") # include("BandStructure.jl") include("ConvergenceTest/ConvergenceTest.jl") -include("EquationOfStateWorkflow/EquationOfStateWorkflow.jl") +include("EquationOfState/EquationOfState.jl") # include("StaticElasticity/StaticElasticity.jl") include("PhononWorkflow/PhononWorkflow.jl") # include("QuasiHarmonicApprox/QuasiHarmonicApprox.jl") From 13e18a9ff39aa6babb8792b1c552451c21c838ee Mon Sep 17 00:00:00 2001 From: singularitti Date: Sun, 19 Nov 2023 14:25:42 -0500 Subject: [PATCH 4/4] Rename `PhononWorkflow` to `Phonon` --- docs/src/run/cli.md | 2 +- docs/src/troubleshooting.md | 2 +- src/Express.jl | 2 +- src/{PhononWorkflow => Phonon}/Config.jl | 0 src/{PhononWorkflow/PhononWorkflow.jl => Phonon/Phonon.jl} | 2 +- src/{PhononWorkflow => Phonon}/Recipes.jl | 2 +- src/{PhononWorkflow => Phonon}/actions.jl | 0 src/{PhononWorkflow => Phonon}/think.jl | 0 8 files changed, 5 insertions(+), 5 deletions(-) rename src/{PhononWorkflow => Phonon}/Config.jl (100%) rename src/{PhononWorkflow/PhononWorkflow.jl => Phonon/Phonon.jl} (80%) rename src/{PhononWorkflow => Phonon}/Recipes.jl (99%) rename src/{PhononWorkflow => Phonon}/actions.jl (100%) rename src/{PhononWorkflow => Phonon}/think.jl (100%) diff --git a/docs/src/run/cli.md b/docs/src/run/cli.md index aa3cc34a..ce66cd32 100644 --- a/docs/src/run/cli.md +++ b/docs/src/run/cli.md @@ -28,7 +28,7 @@ julia> workflow = buildworkflow("eos.toml"); julia> run!(workflow); ``` -For phonon and the QHA workflow, run `using Express.PhononWorkflow.Recipes` +For phonon and the QHA workflow, run `using Express.Phonon.Recipes` and `using Express.QuasiHarmonicApprox.Recipes` in the first step. In an EOS workflow, the final results include outputs returned by Quantum ESPRESSO, a list diff --git a/docs/src/troubleshooting.md b/docs/src/troubleshooting.md index 3843cb27..1fcce5e3 100644 --- a/docs/src/troubleshooting.md +++ b/docs/src/troubleshooting.md @@ -223,7 +223,7 @@ workflow (an equation of state workflow in this case). And after the following J commands: ```julia -using Express.PhononWorkflow.Recipes +using Express.Phonon.Recipes using QuantumESPRESSOExpress wf = buildworkflow("phonon.yaml") diff --git a/src/Express.jl b/src/Express.jl index 61600dc1..feb11a54 100644 --- a/src/Express.jl +++ b/src/Express.jl @@ -5,7 +5,7 @@ module Express include("ConvergenceTest/ConvergenceTest.jl") include("EquationOfState/EquationOfState.jl") # include("StaticElasticity/StaticElasticity.jl") -include("PhononWorkflow/PhononWorkflow.jl") +include("Phonon/Phonon.jl") # include("QuasiHarmonicApprox/QuasiHarmonicApprox.jl") end diff --git a/src/PhononWorkflow/Config.jl b/src/Phonon/Config.jl similarity index 100% rename from src/PhononWorkflow/Config.jl rename to src/Phonon/Config.jl diff --git a/src/PhononWorkflow/PhononWorkflow.jl b/src/Phonon/Phonon.jl similarity index 80% rename from src/PhononWorkflow/PhononWorkflow.jl rename to src/Phonon/Phonon.jl index 108e2555..5139a326 100644 --- a/src/PhononWorkflow/PhononWorkflow.jl +++ b/src/Phonon/Phonon.jl @@ -1,4 +1,4 @@ -module PhononWorkflow +module Phonon include("Config.jl") include("actions.jl") diff --git a/src/PhononWorkflow/Recipes.jl b/src/Phonon/Recipes.jl similarity index 99% rename from src/PhononWorkflow/Recipes.jl rename to src/Phonon/Recipes.jl index 46bf231f..3fe78de0 100644 --- a/src/PhononWorkflow/Recipes.jl +++ b/src/Phonon/Recipes.jl @@ -15,7 +15,7 @@ using SimpleWorkflows: Workflow, run! using Thinkers: Thunk, setargs! using ..Config: StaticConfig, expand -using ..PhononWorkflow: DownloadPotentials, CreateInput, WriteInput, RunCmd +using ..Phonon: DownloadPotentials, CreateInput, WriteInput, RunCmd struct PhononDispersionRecipe <: Recipe config diff --git a/src/PhononWorkflow/actions.jl b/src/Phonon/actions.jl similarity index 100% rename from src/PhononWorkflow/actions.jl rename to src/Phonon/actions.jl diff --git a/src/PhononWorkflow/think.jl b/src/Phonon/think.jl similarity index 100% rename from src/PhononWorkflow/think.jl rename to src/Phonon/think.jl