From 34c3fa0a15e0760ac46647bdf99c19a2f1fbf281 Mon Sep 17 00:00:00 2001 From: jan-janssen Date: Tue, 30 Apr 2024 18:01:13 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20=20@=206b212?= =?UTF-8?q?0319ec18c287de522a198c7cab3a6cf9839=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.html | 1 + _sources/book/conclusion.md | 2 + _sources/conclusion.md | 2 + aiida.html | 1 + book/challenges.html | 1 + book/conclusion.html | 429 +++++++++++++++++++++++++++++++++++ book/introduction.html | 1 + challenges.html | 1 + conclusion.html | 437 ++++++++++++++++++++++++++++++++++++ genindex.html | 1 + introduction.html | 1 + jobflow.html | 1 + objects.inv | Bin 349 -> 368 bytes pyiron_base.html | 11 + search.html | 1 + searchindex.js | 2 +- 16 files changed, 891 insertions(+), 1 deletion(-) create mode 100644 _sources/book/conclusion.md create mode 100644 _sources/conclusion.md create mode 100644 book/conclusion.html create mode 100644 conclusion.html diff --git a/README.html b/README.html index 80dcdeb..e13077e 100644 --- a/README.html +++ b/README.html @@ -183,6 +183,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/_sources/book/conclusion.md b/_sources/book/conclusion.md new file mode 100644 index 0000000..8ed6fa9 --- /dev/null +++ b/_sources/book/conclusion.md @@ -0,0 +1,2 @@ +# Conclusion +The same workflow was implemented in four different simulation frameworks. On the one hand this simplifies the selection of a simulation framework for users who look for a simulation framework for their own code. On the other hand it also highlights how to develop transferable simulation protocols to improve the portability of a given simulation protocol from one framework to the next. diff --git a/_sources/conclusion.md b/_sources/conclusion.md new file mode 100644 index 0000000..8ed6fa9 --- /dev/null +++ b/_sources/conclusion.md @@ -0,0 +1,2 @@ +# Conclusion +The same workflow was implemented in four different simulation frameworks. On the one hand this simplifies the selection of a simulation framework for users who look for a simulation framework for their own code. On the other hand it also highlights how to develop transferable simulation protocols to improve the portability of a given simulation protocol from one framework to the next. diff --git a/aiida.html b/aiida.html index 751adb8..2d6b0b1 100644 --- a/aiida.html +++ b/aiida.html @@ -182,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/book/challenges.html b/book/challenges.html index 011d541..295ee61 100644 --- a/book/challenges.html +++ b/book/challenges.html @@ -182,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/book/conclusion.html b/book/conclusion.html new file mode 100644 index 0000000..d35cf62 --- /dev/null +++ b/book/conclusion.html @@ -0,0 +1,429 @@ + + + + + + + + + + + Conclusion — ADIS2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
    +
    +
    +
    + + + Ctrl+K +
    +
    + +
    +
    + + +
    +
    + + + + + +
    + + + +
    + + + + +
    + +
    +
    + + + +
    +
    + +
    +
    +
    + + +
    +
    + + + + +
    + +
    + + + +
    + +
    +
    + +
    +
    + +
    + +
    + +
    + + +
    + +
    + +
    + + + + + +
    + + +
    + + + + + + + + + + + + + +
    + +
    + +
    +
    + + + +
    +

    Conclusion

    + +
    +
    + +
    +
    +
    + + + + +
    + +
    +

    Conclusion#

    +

    The same workflow was implemented in four different simulation frameworks. On the one hand this simplifies the selection of a simulation framework for users who look for a simulation framework for their own code. On the other hand it also highlights how to develop transferable simulation protocols to improve the portability of a given simulation protocol from one framework to the next.

    +
    + + + + +
    + + + + + + +
    + +
    +
    +
    + +
    + + + +
    + + +
    +
    + +
    + +
    + +

    +By pyiron +

    + +
    + +
    + + +

    + + © Copyright 2023. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + + + + \ No newline at end of file diff --git a/book/introduction.html b/book/introduction.html index 8c86adf..b28f630 100644 --- a/book/introduction.html +++ b/book/introduction.html @@ -182,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/challenges.html b/challenges.html index d2f9d8f..ad1c747 100644 --- a/challenges.html +++ b/challenges.html @@ -182,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/conclusion.html b/conclusion.html new file mode 100644 index 0000000..7ee1c31 --- /dev/null +++ b/conclusion.html @@ -0,0 +1,437 @@ + + + + + + + + + + + Conclusion — ADIS2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
    +
    +
    +
    + + + Ctrl+K +
    +
    + +
    +
    + + +
    +
    + + + +
    + + + +
    + + + + +
    + +
    +
    + + + +
    +
    + +
    +
    +
    + + +
    +
    + + + + +
    + +
    + + + +
    + +
    +
    + +
    +
    + +
    + +
    + +
    + + +
    + +
    + +
    + + + + + +
    + + +
    + + + + + + + + + + + + + +
    + +
    + +
    +
    + + + +
    +

    Conclusion

    + +
    +
    + +
    +
    +
    + + + + +
    + +
    +

    Conclusion#

    +

    The same workflow was implemented in four different simulation frameworks. On the one hand this simplifies the selection of a simulation framework for users who look for a simulation framework for their own code. On the other hand it also highlights how to develop transferable simulation protocols to improve the portability of a given simulation protocol from one framework to the next.

    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + +
    + +
    + +

    +By pyiron +

    + +
    + +
    + + +

    + + © Copyright 2023. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html index d608a7e..7919f74 100644 --- a/genindex.html +++ b/genindex.html @@ -181,6 +181,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/introduction.html b/introduction.html index 079634f..ef0447f 100644 --- a/introduction.html +++ b/introduction.html @@ -182,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/jobflow.html b/jobflow.html index 8fc5b13..c5f19f6 100644 --- a/jobflow.html +++ b/jobflow.html @@ -182,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/objects.inv b/objects.inv index 5a7155d74dcc25d4a4fd74ee1ea32c577cae9a1d..ce838360738ade11d53a14417b6331617d4da300 100644 GIT binary patch delta 259 zcmV+e0sQ{m0`LNmb$^e+PQx$|MDP9z|3E-oxm6_x4wXtdaI74AlbAZ*%Im1~?@6*w zF(pumn>{mccXn5#t~yL7vhkSqIg@_@guuy?k~(S@b_gUaU0o@@Lfg z7|`@OF2T9U_;aR+XsyE=RH}EmVovOf%z^u+yho|`Mz8j~#V>Ok`h$L~i z5FMI@3deIX8ywsWBORnNnR^4yaHp;mgr;eOybn$&sva^xABrJ9MstVJXdNP9BHX051Q;lX)JQ>XGFyF zId3c}(Q2#kXQ(ldq3MezI$iFb;=j2smYyjaZbpd_u{jYnsV5VzZ88aL+;x=($1#!m qBDQZs)eWAdwIlnTfya1PggMJVcm$VM_jj1F?Zo;XN)*3Tdg&7E<#v?- diff --git a/pyiron_base.html b/pyiron_base.html index e8d810f..e264dfe 100644 --- a/pyiron_base.html +++ b/pyiron_base.html @@ -60,6 +60,7 @@ + @@ -181,6 +182,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • @@ -628,6 +630,15 @@

    Publication of the workflowjobflow

     + +
    +

    next

    +

    Conclusion

    +
    + +     diff --git a/search.html b/search.html index 5776eaf..4ea6707 100644 --- a/search.html +++ b/search.html @@ -183,6 +183,7 @@
  • Aiida
  • jobflow
  • pyiron
    • +
  • Conclusion
    • diff --git a/searchindex.js b/searchindex.js index e25bbda..b57b1ce 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Aiida": [[1, "aiida"]], "Calc function to rescale structures": [[1, "calc-function-to-rescale-structures"]], "Challenges for workflow frameworks": [[2, "challenges-for-workflow-frameworks"], [4, "challenges-for-workflow-frameworks"]], "Data Storage / Data Sharing": [[7, "data-storage-data-sharing"]], "EOS: Work function version": [[1, "eos-work-function-version"]], "Equation of State curve - basic QE": [[1, "equation-of-state-curve-basic-qe"]], "Example Workflow": [[2, "example-workflow"], [4, "example-workflow"]], "Explanation": [[0, "explanation"]], "External Executable": [[2, "external-executable"], [4, "external-executable"]], "Implementation": [[2, "implementation"], [4, "implementation"]], "Implementation of a new simulation code": [[7, "implementation-of-a-new-simulation-code"]], "Importing a structure": [[1, "importing-a-structure"]], "Installation / Setup": [[7, "installation-setup"]], "Introduction": [[3, "introduction"], [5, "introduction"]], "Publication of the workflow": [[7, "publication-of-the-workflow"]], "Python Function": [[2, "python-function"], [4, "python-function"]], "Quantum Espresso Workflow": [[0, "quantum-espresso-workflow"]], "Relaxing the geometry": [[1, "relaxing-the-geometry"]], "Submission to an HPC / Check pointing / Error handling": [[7, "submission-to-an-hpc-check-pointing-error-handling"]], "Universal Interface": [[2, "universal-interface"], [4, "universal-interface"]], "Using the builder": [[1, "using-the-builder"]], "Work chain version": [[1, "work-chain-version"]], "jobflow": [[6, "jobflow"]], "pyiron": [[7, "pyiron"]]}, "docnames": ["README", "aiida", "book/challenges", "book/introduction", "challenges", "introduction", "jobflow", "pyiron_base"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1}, "filenames": ["README.md", "aiida.ipynb", "book/challenges.md", "book/introduction.md", "challenges.md", "introduction.md", "jobflow.ipynb", "pyiron_base.ipynb"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [2, 4], "0": [0, 1, 6, 7], "00139": 6, "00149": 6, "00159": 6, "00169": 6, "00179": 6, "00189": 6, "02": [1, 6, 7], "03": 6, "04": [1, 6], "045218924156295": 6, "045218941837687": 6, "05": [1, 7], "0623b121": 1, "078d": 1, "08390ab2207b": 1, "0982098b": 1, "0b8733b946c4": 6, "0e46d480": 6, "0x7f8d7be46b50": 1, "0x7f8d8d2dcf90": 1, "1": [0, 1, 2, 4, 6, 7], "10": [2, 4], "1073": 1, "1074": [1, 6], "11": 1, "111545777030954": 6, "114": 1, "116": 1, "125": 1, "128": 1, "131": 1, "134": 1, "137": 1, "14": 6, "15": 6, "154572126333": 1, "155b": 6, "15a": [2, 4], "16": 1, "1693": 1, "174": 6, "175799058074337": 6, "176": 6, "1900ab56": 1, "19513783416937": 6, "1951387021735": 6, "19862df7": 1, "1ab7cdcf9ae": 6, "1ae9": 6, "1e4e": 1, "2": [6, 7], "20": 1, "2024": [1, 6], "21": 1, "212ef6852ddf": 1, "2139a72b": 1, "22": 1, "220e": 1, "23": 1, "231834805659": 1, "24": 1, "2511": 1, "256": 6, "25b4d82f": 1, "27": 6, "2724d8c6306c": 1, "27999a687256": 1, "283007573324": 1, "2d23a147": 1, "2d4ksucf2d": 6, "2djanssen": 6, "2dqua": 6, "2dsso": 6, "3": [2, 4, 6, 7], "30c3": 1, "32": 6, "33cc": 1, "37": 6, "383573d8d4ed": 1, "39": 1, "395": 6, "396": 6, "39ad": 1, "3be7": 1, "3fd5b445578b": 1, "4": [1, 2, 4, 6, 7], "40": 1, "404": 6, "405a": 1, "406": 6, "40c0": 1, "40d6": 1, "41": 1, "416b": 1, "4172": 6, "41b2": 1, "41e5": 1, "42": 1, "420a": 1, "4244": 6, "4279": 6, "430124128914": 1, "4369": 6, "444fc6e6": 1, "4455": 1, "445c": 6, "448c": 1, "44c4": 1, "44f8": 1, "45": 6, "451028786": 1, "45c0": 1, "45dc": 1, "46": 1, "463e": 6, "4719": 1, "4739": 1, "4751": 1, "48": 1, "4804": 1, "48317b85b5a1": 1, "486e": 1, "48b3": 1, "48e5": 1, "497a082c": 1, "4aa3": 1, "4af3": 1, "4c5d1fc6": 1, "4d91": 1, "4dd0": 6, "4dd8": 1, "4ddf": 1, "4ded": 1, "4e03": 6, "4e29dd81c5f3": 1, "4e7095f36908": 1, "4e79": 6, "4edb": 6, "4fa7": 1, "5": [1, 6, 7], "50489472587755": 6, "514079e9": 6, "53": [1, 6], "53d5ed890a99": 6, "548ac2d51b93": 1, "55": 6, "5590": 1, "56": [1, 6], "563": 6, "564": 6, "57": 6, "575624050752516": 6, "59": [1, 6], "5a9342f9": 1, "5f32": 1, "5fbase": 6, "5ffc349a": 1, "5fpyiron": 6, "6": [1, 6, 7], "60": 1, "600": 6, "62": 6, "62741c3d2644": 1, "64": 7, "66": [1, 6], "67": 1, "671627766898": 1, "69": 6, "692a9438": 1, "6bd2": 6, "6da6feede4": 1, "6e3c5a28": 6, "7": [1, 7], "71": 1, "72": 6, "723a": 1, "7251942208": 1, "72ab2547": 6, "73b0118b": 1, "7503": 1, "76": 1, "7699": 6, "785519366503": 1, "7863009779": 1, "8": [1, 7], "80": 1, "809a": 1, "81465161758611": 6, "815": 6, "83": 1, "833a": 1, "8451830762128": 6, "8557": 1, "86": 1, "86c5": 1, "8741797823543": 6, "87ad6b9b": 6, "88": 1, "8844": 1, "88538094246082": 6, "889b": 6, "89": 1, "892": 6, "897de3c5b829": 1, "8a66": 6, "8b46": 1, "8b73": 1, "8b80": 6, "8d0b": 1, "8e31": 6, "9": [1, 6, 7], "9056159296787105": 6, "907": 6, "9075": 6, "908": 6, "9158947387848": 6, "9194989203452": 6, "92": 1, "9272223013": 1, "9273047095": 1, "936525208987": 6, "9365272693506": 6, "9421694118": 1, "95": 1, "9661": 1, "96d0": 1, "970c10a80dad4217a0f75cca3dd833b2": 1, "9766426435887574": 6, "979": 6, "980": 6, "980b72a5": 6, "9987ab9f": 6, "9b0f": 1, "9b10": 1, "9b72": 6, "9bf857a0a761": 1, "9cd7": 1, "9d24": 1, "9e35": 6, "9f34": 6, "A": [6, 7], "ASE": 6, "As": 7, "By": [0, 2, 4, 7], "For": [2, 3, 4, 5, 7], "If": 1, "In": [2, 4, 7], "It": [2, 4], "No": 6, "The": [0, 1, 2, 4, 6, 7], "These": 7, "To": 1, "__init__": 6, "a193": 1, "a297": 1, "a37cc25c": 1, "a44a935f": 6, "a78": 1, "a880322c8261": 6, "a8d6": 1, "a95a": 6, "aa74ac59": 1, "aa93": 1, "abort": 7, "absolut": 1, "abstract": 1, "abstractcod": 1, "ac68": 1, "acceler": 7, "access": [2, 4], "act": 7, "ad3a": 1, "ad67": 1, "addit": [2, 4, 6, 7], "address": [2, 4, 7], "adis_tool": [0, 6, 7], "ae0d": 1, "ae4dad051635": 1, "afaa090a": 1, "afdd": 1, "afterward": 7, "again": 7, "aiida": [0, 2, 4], "aiida_qe_bas": [0, 1], "aiidadeprecationwarn": 1, "al": [0, 1, 6, 7], "al4": 6, "all": [1, 2, 4, 7], "allow": 7, "alreadi": [2, 4, 7], "also": [2, 4], "altern": 7, "aluminium": [0, 2, 4, 7], "an": [0, 1, 2, 4, 6], "analogi": [2, 4, 7], "angstrom": 6, "ani": [2, 4, 6, 7], "anoth": [2, 4], "append": [1, 2, 4, 6, 7], "appli": [2, 4], "approach": 7, "ar": [1, 2, 3, 4, 5, 6, 7], "archiv": 7, "arg": [2, 4], "as_posix": 1, "ase": [1, 6, 7], "ase_structur": [1, 2, 4, 6, 7], "aspect": [2, 4], "atom": [2, 4, 6], "atomist": 7, "attributedict": 1, "automat": 0, "b06f": 1, "b0759785": 6, "b2c9920d4791": 6, "b354499e": 1, "b4a2": 1, "b4ba65fe3d38": 6, "b6255a668cd8": 6, "b661": 1, "b67c2d2a83c3": 1, "b6e1": 1, "b705": 6, "b75c": 1, "b7eef2d75317": 1, "baac": 1, "base": [3, 5, 6, 7], "basemodel": 6, "baseqemak": 6, "bash": 7, "bb27de53": 1, "bbcb": 6, "bc77a827": 1, "be3a": 1, "been": [2, 4], "befor": 7, "below": [1, 2, 4], "best": [2, 4], "bf8ca7860540": 6, "bin": 7, "bind": [2, 4, 7], "block": 7, "both": [2, 4, 7], "bracket": 7, "briefli": 7, "broken": 7, "brows": 7, "build": [1, 6, 7], "bulk": [0, 1, 2, 4, 6, 7], "c626067d81e1": 6, "calcfunct": 1, "calcjob_dict": 1, "calcjobnod": 1, "calcul": [0, 1, 2, 3, 4, 5, 6, 7], "call": [1, 2, 4, 7], "can": [2, 4, 7], "cannot": 6, "case": [2, 4, 7], "caus": 7, "cb9e9befb761": 1, "cell": [2, 4, 6, 7], "centr": [2, 4], "certain": 7, "challeng": 7, "chdir": 7, "check_output": [1, 6], "choos": [2, 4], "chosen": [2, 4], "cl": [1, 6], "class": [1, 6], "classmethod": [1, 6], "cluster": 7, "code": [1, 2, 4], "cold": 1, "collect": [2, 4], "collect_output": [2, 4, 6, 7], "collect_output_funct": 7, "com": 1, "combin": 7, "come": [3, 5], "command": [3, 5, 7], "common": 1, "commonli": [3, 5], "commun": [2, 4], "compar": [1, 2, 4], "comparison": [2, 4], "complet": 7, "compon": 7, "compress": 7, "comput": [0, 1, 2, 4, 7], "computation": 7, "concern": [2, 4], "conclud": 7, "conda": [0, 1, 7], "configur": [1, 7], "connect": 7, "consist": [2, 4, 7], "constant": [2, 4], "construct": 7, "contain": 7, "context": [2, 4], "contrast": 7, "control": 1, "convers": 7, "convert": 7, "copi": [2, 4, 6, 7], "core": [1, 6, 7], "could": [2, 4, 7], "coupl": [3, 5, 7], "cover": [2, 4], "cpu": 7, "crash": 7, "creat": [1, 2, 4, 7], "create_eos_dictionari": 1, "create_fold": 6, "creation": 7, "crystal": [1, 2, 4, 6, 7], "ctx": 1, "cubic": [1, 2, 4, 6, 7], "curli": 7, "curv": [2, 4, 7], "d": 1, "d0d8a5391be2": 1, "d1ce257f": 1, "d428af731e8d": 1, "d6ae": 6, "d6d2e0c33994": 1, "data": [1, 2, 4], "databas": 7, "dataclass": 6, "debug": 7, "decor": [2, 4], "dedic": 7, "def": [1, 2, 4, 6, 7], "default_calc_job_plugin": 1, "default_factori": 6, "defb7c21acd3": 1, "defin": [0, 1, 2, 4, 7], "degauss": [1, 2, 4, 6, 7], "demonstr": [2, 4], "densiti": [2, 4], "depend": [0, 2, 4], "deprec": 1, "descript": 6, "detach": 1, "detect": 0, "detour": 6, "develop": [2, 4, 7], "dft": [2, 4, 6], "dict": [1, 6], "dictionari": [2, 4], "differ": [0, 1, 2, 4, 7], "direct": 1, "directori": [2, 4, 6, 7], "discuss": 7, "do": [3, 5], "doe": 7, "doubl": 7, "e": [1, 6], "e0fcc577": 1, "e4c3": 1, "e7c8": 1, "e7ec1c33": 1, "each": 7, "easili": [2, 4, 7], "eb9c": 1, "ec40843e6a86": 1, "ee507eb7": 1, "effici": [2, 4, 7], "either": 7, "element": [1, 2, 4], "email": 1, "enabl": 7, "energi": [0, 1, 2, 4, 6, 7], "energy_lst": [2, 4, 6, 7], "engin": 1, "enhanc": [2, 4], "enumer": [1, 7], "env": 1, "environ": [0, 3, 5, 7], "eos_dict": 1, "eos_result": 1, "equationofst": 1, "espresso": [1, 2, 4, 7], "ev": 6, "ev_curv": 6, "evalu": [2, 4, 7], "evcurv": [2, 4, 6, 7], "even": 7, "evolv": 7, "exampl": 7, "except": [1, 6], "execut": [6, 7], "executable_str": 7, "execute_job": 7, "exist": [2, 4, 7], "exist_ok": [2, 4, 6, 7], "expens": 7, "explan": 7, "export": 1, "extend": [2, 4], "extern": 7, "f": 1, "f0e400dc": 1, "f43a": 1, "f4cd": 1, "f698bcff99ea": 1, "f71ee458594": 1, "f85f": 1, "f89b8859": 1, "face": [2, 4], "factor_list": 1, "fail": [2, 4], "fals": 6, "fanci": 1, "fbea": 6, "featur": 1, "few": 7, "ffb6371e045d": 1, "ffd9": 1, "field": 6, "file": [1, 2, 3, 4, 5, 6, 7], "filenam": [2, 4, 6, 7], "filepath_execut": 1, "filesystem": 7, "final": 7, "finish": 6, "first": [2, 4, 7], "fit": [2, 4], "five": [2, 4], "flexibl": [2, 4], "float": 6, "flow": 6, "focu": 7, "focus": [2, 4], "folder": [1, 7], "folderdata": 1, "follow": [0, 2, 4, 6, 7], "format": [2, 4, 7], "four": [2, 4], "framework": [0, 3, 5], "from": [1, 2, 4, 6, 7], "from_directori": 6, "function": 7, "furthermor": 7, "g": 1, "gener": [2, 4, 6, 7], "generate_structur": [2, 4, 6, 7], "generate_structures81144f1592dde5715ec257eb7f425177": 7, "get_as": 1, "get_build": 1, "get_cel": 1, "get_dict": 1, "get_ev_curv": 6, "get_input_set": 6, "get_list": 1, "get_volum": [2, 4, 6, 7], "github": 7, "give": [2, 4, 7], "given": [1, 2, 4, 7], "ha": 7, "handl": [2, 4], "have": [2, 4, 7], "hdf": 7, "hdf5": 7, "here": [2, 4, 7], "hierach": 7, "hierarchi": 7, "high": [2, 4, 7], "highlight": [2, 4], "home": [1, 7], "hostnam": 1, "how": [2, 4], "hpc": [2, 4], "human": [2, 4], "hundr": [3, 5], "i": [0, 1, 2, 4, 6, 7], "id": 7, "ideal": [2, 4], "ieee_invalid_flag": 6, "ignor": 6, "imag": [2, 4, 6, 7], "implement": 0, "import": [6, 7], "increas": [2, 4], "independ": [0, 7], "index": [1, 7], "individu": 7, "ineffici": [2, 4], "info": 6, "input": [1, 2, 4, 6, 7], "input_data": [2, 4, 6, 7], "input_dict": [2, 4, 6, 7], "input_set_gener": 6, "inputgener": 6, "inputset": 6, "insert": 7, "inspect": 7, "instal": [0, 1], "installedcod": 1, "instanc": 1, "integr": [2, 4, 7], "intend": [2, 4], "intens": [2, 4], "interact": 7, "interfac": [0, 7], "intern": [2, 4, 7], "io": [6, 7], "ipynb": 0, "isinst": 1, "istructur": 6, "item": 1, "iter": 7, "its": 7, "jan": 6, "jinja2": 7, "job": [6, 7], "job_decor": [2, 4], "job_nam": 7, "job_qe_minim": 7, "job_strain": 7, "job_strain_": 7, "job_strain_0": 7, "job_strain_1": 7, "job_strain_2": 7, "job_strain_3": 7, "job_strain_4": 7, "job_workflow": 7, "jobflow": [0, 2, 4], "join": [2, 4, 6, 7], "jovyan": 1, "jupyt": [6, 7], "jupyterbook": 7, "just": 1, "kei": 1, "kjpaw_psl": [0, 1, 6, 7], "kpt": [2, 4, 6, 7], "kwarg": [1, 2, 4], "label": 1, "lambda": 6, "languag": [2, 4, 7], "larg": 7, "latter": 7, "lattic": [2, 4, 7], "lead": [2, 4, 7], "learn": [3, 5], "legaci": 1, "len": 6, "lib": 1, "librdmacm": 6, "like": [2, 4, 7], "limit": [3, 5], "line": [1, 3, 5, 7], "line2d": 1, "link": 7, "linspac": [6, 7], "linux": [2, 4], "list": [1, 2, 4], "load_cod": 1, "load_comput": 1, "load_profil": 1, "local": [1, 6, 7], "localhost": 1, "locat": 7, "machin": [2, 3, 4, 5], "major": [2, 4], "make": 6, "makedir": [2, 4, 6, 7], "maker": 6, "manag": [1, 2, 4, 7], "mani": [2, 4], "manual": [2, 4], "mark": 7, "materi": 7, "matplotlib": [1, 6, 7], "mca_base_component_repository_open": 6, "mca_btl_openib": 6, "metadata": 1, "might": [2, 4, 7], "minimalist": 7, "modern": [2, 3, 4, 5], "modul": 7, "modulu": [0, 2, 4], "more": 7, "mpirun": [6, 7], "msonatom": 6, "multipl": 7, "my_funct": [2, 4], "my_queu": 7, "mybind": [0, 7], "n": [0, 1, 6, 7], "name": [1, 2, 4, 6, 7], "need": [2, 3, 4, 5, 6], "new": [2, 4], "new_cel": 1, "new_job": 6, "node": 1, "none": 6, "note": 6, "notebook": [1, 7], "notexist": 1, "np": [6, 7], "num_machin": 1, "num_mpiprocs_per_machin": 1, "number": [2, 4, 7], "numpi": [6, 7], "o": [2, 4, 6, 7], "object": [6, 7], "occup": [1, 2, 4, 6, 7], "omp_num_thread": 1, "one": [2, 4], "onli": [2, 4, 7], "open": [2, 4, 6], "opportun": 7, "optim": [0, 2, 4, 7], "option": [1, 2, 4, 6, 7], "orm": 1, "out": 1, "outlin": 1, "output": [1, 2, 4, 6, 7], "output_schema": 6, "outputrefer": 6, "over": [2, 4, 7], "packag": [1, 7], "parallel": [2, 4], "paramet": [1, 2, 4, 6, 7], "pars": [2, 4, 6, 7], "parse_pw": [2, 4, 6, 7], "parser": [0, 2, 4, 6, 7], "pass": 1, "path": [1, 2, 4, 6, 7], "pathlib": 1, "pbc": 6, "pbe": [0, 1, 6, 7], "per": 7, "perform": [2, 4, 7], "pk": 1, "place": 0, "plain": [2, 4], "plot": [1, 2, 4, 6, 7], "plot_energy_volume_curv": [2, 4, 6, 7], "plot_energy_volume_curve_job": 6, "plt": [1, 2, 4, 6, 7], "plugin": 1, "pm": 1, "png": [2, 4, 6, 7], "point": 6, "poor": 7, "portabl": 1, "portablecod": 1, "posit": [2, 4], "postbuild": 0, "potenti": 0, "pr": 7, "prepend_text": 1, "previou": 6, "primari": 7, "process": [1, 7], "profil": 1, "program": [2, 4], "project": 7, "properti": 1, "protocol": [2, 4, 7], "prototyp": 7, "provid": [2, 4, 7], "pseudo": 0, "pseudo_dir": 1, "pseudopotenti": [1, 2, 4, 6, 7], "publish": 7, "pw": [1, 6, 7], "pw_code": 1, "pwcalcul": 1, "pwi": [2, 4, 6, 7], "pwo": [6, 7], "pwscf": [2, 4, 6, 7], "py": 1, "pydant": 6, "pyiron": [2, 4], "pyiron_atomist": 7, "pyiron_bas": [0, 7], "pymatgen": 6, "pyplot": [1, 6, 7], "python": [1, 7], "python3": 1, "qe": 6, "qe_cmd": 6, "qeinputgener": 6, "qeinputset": 6, "qeinputstaticgener": 6, "qetaskdoc": 6, "qi": 6, "quantum": [1, 2, 4, 7], "quantumespresso": 1, "queri": 7, "queu": [2, 4, 7], "queue": 7, "qunatum": 0, "rabbitmq": 1, "rang": [2, 4, 6], "rapid": 7, "rather": [2, 4], "re": 7, "readabl": [2, 4], "receiv": [2, 4, 7], "recent": [2, 4], "recogn": 7, "recommend": [2, 4], "recomput": 7, "regular": 1, "relat": 7, "relax": [6, 7], "relax_param": 1, "relaxed_structur": 1, "releas": [2, 4], "reload": 7, "remain": [2, 4, 7], "remot": 1, "remote_fold": 1, "remotedata": 1, "remov": [1, 7], "remove_job": 7, "render": 7, "replac": 6, "report": 1, "repres": [2, 4, 7], "reproduc": 7, "reproducibl": 7, "requir": [2, 4, 7], "rescale_list": 1, "rescaled_structur": 1, "resourc": [1, 2, 4, 7], "respect": 1, "respons": 6, "rest": 7, "result": [1, 2, 4, 7], "retriev": 1, "return": [1, 2, 4, 6, 7], "run": [1, 6, 7], "run_eo": 1, "run_eos_wf": 1, "run_get_nod": 1, "run_loc": 6, "run_q": 6, "same": [2, 4, 7], "save": 7, "savefig": [2, 4, 6, 7], "sbatch": 7, "scale": [2, 4, 7], "scale_atom": [1, 2, 4, 6, 7], "scale_factor": 1, "scaled_structure_dict": 1, "scaling_factor": 1, "scf": [1, 6, 7], "scf_input": 1, "scheduler_typ": 1, "scienc": 7, "scientif": [2, 4], "script": [0, 7], "secondari": [2, 4], "select": 7, "self": [1, 6], "serial": [2, 4], "serializ": 6, "server": [1, 7], "servic": 7, "set": [1, 2, 4, 6], "set_cel": [1, 2, 4, 6, 7], "setup": 1, "share": 6, "shell": 6, "should": [2, 4], "signal": 6, "simpl": [0, 2, 4], "simplifi": [2, 4, 7], "simstack": [2, 4], "simul": [2, 3, 4, 5], "singl": [2, 4, 7], "site": 1, "sleep": 1, "slurm": [2, 4], "smear": [1, 2, 4, 6, 7], "so": 6, "softwar": [2, 4], "some": [2, 4, 7], "sourc": [2, 4], "spec": 1, "specif": [2, 4, 7], "specifi": [1, 2, 4, 7], "sql": 7, "sqlite_do": 1, "srv": 1, "start": 6, "static": [6, 7], "staticqemak": 6, "step": [2, 4, 7], "still": [2, 4, 7], "stop_children": 6, "stop_jobflow": 6, "storag": [2, 3, 4, 5], "store": [1, 7], "store_input": 6, "stored_data": 6, "str": [6, 7], "strain": [2, 4, 6, 7], "strain_lst": [2, 4, 6, 7], "structur": [0, 2, 4, 6, 7], "structure_": 1, "structure_0": 1, "structure_1": 1, "structure_2": 1, "structure_3": 1, "structure_4": 1, "structure_lst": [2, 4, 6, 7], "structure_strain": [2, 4, 6, 7], "structuredata": 1, "studi": [2, 4], "submit": [1, 7], "subprocess": [1, 6], "success": [2, 4], "suffici": [3, 5], "suit": [2, 4], "summar": 7, "super": 1, "supercel": [2, 4], "symbol": 6, "system": [1, 2, 4, 7], "take": [1, 2, 4], "task": [2, 4, 7], "task_doc": 6, "templat": 7, "tensor": 7, "tenth": [3, 5], "test": [0, 1, 7], "text": [2, 4], "than": [2, 4], "thei": 7, "theori": [2, 4], "thi": [0, 1, 2, 4, 7], "thousand": [3, 5], "three": [0, 2, 4], "through": 7, "time": 7, "tprnfor": [2, 4, 6, 7], "track": [2, 4], "tradit": [2, 3, 4, 5], "trajectori": 7, "transfer": [2, 4], "transform": 6, "transport_typ": 1, "true": [1, 2, 4, 6, 7], "try": 1, "tstress": [2, 4, 6, 7], "tupl": 6, "two": 7, "type": [1, 6], "typic": 1, "unabl": 6, "union": 6, "unit": [2, 4], "universal_newlin": 6, "up": [2, 4, 7], "upf": [0, 1, 6, 7], "us": [2, 3, 4, 5, 6, 7], "user": [2, 4, 7], "userwarn": 1, "util": [2, 3, 4, 5], "uuid": [1, 6], "v": 1, "v3": 1, "valid_typ": 1, "valu": 1, "variabl": [2, 4, 7], "variou": [2, 4], "vc": [1, 6, 7], "verdi": 1, "veri": [2, 4], "version": 7, "via": 7, "volum": [0, 1, 2, 4, 6, 7], "volume_lst": [2, 4, 6, 7], "wa": [2, 4, 7], "wai": [2, 4], "warn": 1, "warn_deprec": 1, "we": [2, 3, 4, 5, 6], "websit": 7, "well": [2, 4, 7], "were": [2, 4], "when": [2, 3, 4, 5, 7], "which": [2, 4, 7], "while": [2, 4, 7], "why": [3, 5], "wide": [2, 4], "without": 1, "workchain": 1, "workchainnod": 1, "workdir": 1, "workflow": [1, 3, 5], "workflow895ba469e3d888839622dab8177e3746": 7, "workfunct": 1, "working_directori": [2, 4, 6, 7], "workstat": 7, "would": 1, "wrap": 7, "wrap_execut": 7, "wrap_python_funct": 7, "write": [2, 4, 6, 7], "write_input": [2, 4, 6, 7], "write_input_funct": 7, "write_qe_input_set": 6, "written": [2, 4], "x": [1, 6, 7], "xlabel": [2, 4, 6, 7], "xml": [2, 4, 6, 7], "year": [2, 4], "ylabel": [2, 4, 6, 7], "yml": [0, 7], "you": 1}, "titles": ["Quantum Espresso Workflow", "Aiida", "Challenges for workflow frameworks", "Introduction", "Challenges for workflow frameworks", "Introduction", "jobflow", "pyiron"], "titleterms": {"aiida": 1, "an": 7, "basic": 1, "builder": 1, "calc": 1, "chain": 1, "challeng": [2, 4], "check": 7, "code": 7, "curv": 1, "data": 7, "eo": 1, "equat": 1, "error": 7, "espresso": 0, "exampl": [2, 4], "execut": [2, 4], "explan": 0, "extern": [2, 4], "framework": [2, 4], "function": [1, 2, 4], "geometri": 1, "handl": 7, "hpc": 7, "implement": [2, 4, 7], "import": 1, "instal": 7, "interfac": [2, 4], "introduct": [3, 5], "jobflow": 6, "new": 7, "point": 7, "public": 7, "pyiron": 7, "python": [2, 4], "qe": 1, "quantum": 0, "relax": 1, "rescal": 1, "setup": 7, "share": 7, "simul": 7, "state": 1, "storag": 7, "structur": 1, "submiss": 7, "univers": [2, 4], "us": 1, "version": 1, "work": 1, "workflow": [0, 2, 4, 7]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"Aiida": [[1, "aiida"]], "Calc function to rescale structures": [[1, "calc-function-to-rescale-structures"]], "Challenges for workflow frameworks": [[2, "challenges-for-workflow-frameworks"], [5, "challenges-for-workflow-frameworks"]], "Conclusion": [[3, "conclusion"], [6, "conclusion"]], "Data Storage / Data Sharing": [[9, "data-storage-data-sharing"]], "EOS: Work function version": [[1, "eos-work-function-version"]], "Equation of State curve - basic QE": [[1, "equation-of-state-curve-basic-qe"]], "Example Workflow": [[2, "example-workflow"], [5, "example-workflow"]], "Explanation": [[0, "explanation"]], "External Executable": [[2, "external-executable"], [5, "external-executable"]], "Implementation": [[2, "implementation"], [5, "implementation"]], "Implementation of a new simulation code": [[9, "implementation-of-a-new-simulation-code"]], "Importing a structure": [[1, "importing-a-structure"]], "Installation / Setup": [[9, "installation-setup"]], "Introduction": [[4, "introduction"], [7, "introduction"]], "Publication of the workflow": [[9, "publication-of-the-workflow"]], "Python Function": [[2, "python-function"], [5, "python-function"]], "Quantum Espresso Workflow": [[0, "quantum-espresso-workflow"]], "Relaxing the geometry": [[1, "relaxing-the-geometry"]], "Submission to an HPC / Check pointing / Error handling": [[9, "submission-to-an-hpc-check-pointing-error-handling"]], "Universal Interface": [[2, "universal-interface"], [5, "universal-interface"]], "Using the builder": [[1, "using-the-builder"]], "Work chain version": [[1, "work-chain-version"]], "jobflow": [[8, "jobflow"]], "pyiron": [[9, "pyiron"]]}, "docnames": ["README", "aiida", "book/challenges", "book/conclusion", "book/introduction", "challenges", "conclusion", "introduction", "jobflow", "pyiron_base"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1}, "filenames": ["README.md", "aiida.ipynb", "book/challenges.md", "book/conclusion.md", "book/introduction.md", "challenges.md", "conclusion.md", "introduction.md", "jobflow.ipynb", "pyiron_base.ipynb"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"": [2, 5], "0": [0, 1, 8, 9], "00139": 8, "00149": 8, "00159": 8, "00169": 8, "00179": 8, "00189": 8, "02": [1, 8, 9], "03": 8, "04": [1, 8], "045218924156295": 8, "045218941837687": 8, "05": [1, 9], "0623b121": 1, "078d": 1, "08390ab2207b": 1, "0982098b": 1, "0b8733b946c4": 8, "0e46d480": 8, "0x7f8d7be46b50": 1, "0x7f8d8d2dcf90": 1, "1": [0, 1, 2, 5, 8, 9], "10": [2, 5], "1073": 1, "1074": [1, 8], "11": 1, "111545777030954": 8, "114": 1, "116": 1, "125": 1, "128": 1, "131": 1, "134": 1, "137": 1, "14": 8, "15": 8, "154572126333": 1, "155b": 8, "15a": [2, 5], "16": 1, "1693": 1, "174": 8, "175799058074337": 8, "176": 8, "1900ab56": 1, "19513783416937": 8, "1951387021735": 8, "19862df7": 1, "1ab7cdcf9ae": 8, "1ae9": 8, "1e4e": 1, "2": [8, 9], "20": 1, "2024": [1, 8], "21": 1, "212ef6852ddf": 1, "2139a72b": 1, "22": 1, "220e": 1, "23": 1, "231834805659": 1, "24": 1, "2511": 1, "256": 8, "25b4d82f": 1, "27": 8, "2724d8c6306c": 1, "27999a687256": 1, "283007573324": 1, "2d23a147": 1, "2d4ksucf2d": 8, "2djanssen": 8, "2dqua": 8, "2dsso": 8, "3": [2, 5, 8, 9], "30c3": 1, "32": 8, "33cc": 1, "37": 8, "383573d8d4ed": 1, "39": 1, "395": 8, "396": 8, "39ad": 1, "3be7": 1, "3fd5b445578b": 1, "4": [1, 2, 5, 8, 9], "40": 1, "404": 8, "405a": 1, "406": 8, "40c0": 1, "40d6": 1, "41": 1, "416b": 1, "4172": 8, "41b2": 1, "41e5": 1, "42": 1, "420a": 1, "4244": 8, "4279": 8, "430124128914": 1, "4369": 8, "444fc6e6": 1, "4455": 1, "445c": 8, "448c": 1, "44c4": 1, "44f8": 1, "45": 8, "451028786": 1, "45c0": 1, "45dc": 1, "46": 1, "463e": 8, "4719": 1, "4739": 1, "4751": 1, "48": 1, "4804": 1, "48317b85b5a1": 1, "486e": 1, "48b3": 1, "48e5": 1, "497a082c": 1, "4aa3": 1, "4af3": 1, "4c5d1fc6": 1, "4d91": 1, "4dd0": 8, "4dd8": 1, "4ddf": 1, "4ded": 1, "4e03": 8, "4e29dd81c5f3": 1, "4e7095f36908": 1, "4e79": 8, "4edb": 8, "4fa7": 1, "5": [1, 8, 9], "50489472587755": 8, "514079e9": 8, "53": [1, 8], "53d5ed890a99": 8, "548ac2d51b93": 1, "55": 8, "5590": 1, "56": [1, 8], "563": 8, "564": 8, "57": 8, "575624050752516": 8, "59": [1, 8], "5a9342f9": 1, "5f32": 1, "5fbase": 8, "5ffc349a": 1, "5fpyiron": 8, "6": [1, 8, 9], "60": 1, "600": 8, "62": 8, "62741c3d2644": 1, "64": 9, "66": [1, 8], "67": 1, "671627766898": 1, "69": 8, "692a9438": 1, "6bd2": 8, "6da6feede4": 1, "6e3c5a28": 8, "7": [1, 9], "71": 1, "72": 8, "723a": 1, "7251942208": 1, "72ab2547": 8, "73b0118b": 1, "7503": 1, "76": 1, "7699": 8, "785519366503": 1, "7863009779": 1, "8": [1, 9], "80": 1, "809a": 1, "81465161758611": 8, "815": 8, "83": 1, "833a": 1, "8451830762128": 8, "8557": 1, "86": 1, "86c5": 1, "8741797823543": 8, "87ad6b9b": 8, "88": 1, "8844": 1, "88538094246082": 8, "889b": 8, "89": 1, "892": 8, "897de3c5b829": 1, "8a66": 8, "8b46": 1, "8b73": 1, "8b80": 8, "8d0b": 1, "8e31": 8, "9": [1, 8, 9], "9056159296787105": 8, "907": 8, "9075": 8, "908": 8, "9158947387848": 8, "9194989203452": 8, "92": 1, "9272223013": 1, "9273047095": 1, "936525208987": 8, "9365272693506": 8, "9421694118": 1, "95": 1, "9661": 1, "96d0": 1, "970c10a80dad4217a0f75cca3dd833b2": 1, "9766426435887574": 8, "979": 8, "980": 8, "980b72a5": 8, "9987ab9f": 8, "9b0f": 1, "9b10": 1, "9b72": 8, "9bf857a0a761": 1, "9cd7": 1, "9d24": 1, "9e35": 8, "9f34": 8, "A": [8, 9], "ASE": 8, "As": 9, "By": [0, 2, 5, 9], "For": [2, 4, 5, 7, 9], "If": 1, "In": [2, 5, 9], "It": [2, 5], "No": 8, "On": [3, 6], "The": [0, 1, 2, 3, 5, 6, 8, 9], "These": 9, "To": 1, "__init__": 8, "a193": 1, "a297": 1, "a37cc25c": 1, "a44a935f": 8, "a78": 1, "a880322c8261": 8, "a8d6": 1, "a95a": 8, "aa74ac59": 1, "aa93": 1, "abort": 9, "absolut": 1, "abstract": 1, "abstractcod": 1, "ac68": 1, "acceler": 9, "access": [2, 5], "act": 9, "ad3a": 1, "ad67": 1, "addit": [2, 5, 8, 9], "address": [2, 5, 9], "adis_tool": [0, 8, 9], "ae0d": 1, "ae4dad051635": 1, "afaa090a": 1, "afdd": 1, "afterward": 9, "again": 9, "aiida": [0, 2, 5], "aiida_qe_bas": [0, 1], "aiidadeprecationwarn": 1, "al": [0, 1, 8, 9], "al4": 8, "all": [1, 2, 5, 9], "allow": 9, "alreadi": [2, 5, 9], "also": [2, 3, 5, 6], "altern": 9, "aluminium": [0, 2, 5, 9], "an": [0, 1, 2, 5, 8], "analogi": [2, 5, 9], "angstrom": 8, "ani": [2, 5, 8, 9], "anoth": [2, 5], "append": [1, 2, 5, 8, 9], "appli": [2, 5], "approach": 9, "ar": [1, 2, 4, 5, 7, 8, 9], "archiv": 9, "arg": [2, 5], "as_posix": 1, "ase": [1, 8, 9], "ase_structur": [1, 2, 5, 8, 9], "aspect": [2, 5], "atom": [2, 5, 8], "atomist": 9, "attributedict": 1, "automat": 0, "b06f": 1, "b0759785": 8, "b2c9920d4791": 8, "b354499e": 1, "b4a2": 1, "b4ba65fe3d38": 8, "b6255a668cd8": 8, "b661": 1, "b67c2d2a83c3": 1, "b6e1": 1, "b705": 8, "b75c": 1, "b7eef2d75317": 1, "baac": 1, "base": [4, 7, 8, 9], "basemodel": 8, "baseqemak": 8, "bash": 9, "bb27de53": 1, "bbcb": 8, "bc77a827": 1, "be3a": 1, "been": [2, 5], "befor": 9, "below": [1, 2, 5], "best": [2, 5], "bf8ca7860540": 8, "bin": 9, "bind": [2, 5, 9], "block": 9, "both": [2, 5, 9], "bracket": 9, "briefli": 9, "broken": 9, "brows": 9, "build": [1, 8, 9], "bulk": [0, 1, 2, 5, 8, 9], "c626067d81e1": 8, "calcfunct": 1, "calcjob_dict": 1, "calcjobnod": 1, "calcul": [0, 1, 2, 4, 5, 7, 8, 9], "call": [1, 2, 5, 9], "can": [2, 5, 9], "cannot": 8, "case": [2, 5, 9], "caus": 9, "cb9e9befb761": 1, "cell": [2, 5, 8, 9], "centr": [2, 5], "certain": 9, "challeng": 9, "chdir": 9, "check_output": [1, 8], "choos": [2, 5], "chosen": [2, 5], "cl": [1, 8], "class": [1, 8], "classmethod": [1, 8], "cluster": 9, "code": [1, 2, 3, 5, 6], "cold": 1, "collect": [2, 5], "collect_output": [2, 5, 8, 9], "collect_output_funct": 9, "com": 1, "combin": 9, "come": [4, 7], "command": [4, 7, 9], "common": 1, "commonli": [4, 7], "commun": [2, 5], "compar": [1, 2, 5], "comparison": [2, 5], "complet": 9, "compon": 9, "compress": 9, "comput": [0, 1, 2, 5, 9], "computation": 9, "concern": [2, 5], "conclud": 9, "conda": [0, 1, 9], "configur": [1, 9], "connect": 9, "consist": [2, 5, 9], "constant": [2, 5], "construct": 9, "contain": 9, "context": [2, 5], "contrast": 9, "control": 1, "convers": 9, "convert": 9, "copi": [2, 5, 8, 9], "core": [1, 8, 9], "could": [2, 5, 9], "coupl": [4, 7, 9], "cover": [2, 5], "cpu": 9, "crash": 9, "creat": [1, 2, 5, 9], "create_eos_dictionari": 1, "create_fold": 8, "creation": 9, "crystal": [1, 2, 5, 8, 9], "ctx": 1, "cubic": [1, 2, 5, 8, 9], "curli": 9, "curv": [2, 5, 9], "d": 1, "d0d8a5391be2": 1, "d1ce257f": 1, "d428af731e8d": 1, "d6ae": 8, "d6d2e0c33994": 1, "data": [1, 2, 5], "databas": 9, "dataclass": 8, "debug": 9, "decor": [2, 5], "dedic": 9, "def": [1, 2, 5, 8, 9], "default_calc_job_plugin": 1, "default_factori": 8, "defb7c21acd3": 1, "defin": [0, 1, 2, 5, 9], "degauss": [1, 2, 5, 8, 9], "demonstr": [2, 5], "densiti": [2, 5], "depend": [0, 2, 5], "deprec": 1, "descript": 8, "detach": 1, "detect": 0, "detour": 8, "develop": [2, 3, 5, 6, 9], "dft": [2, 5, 8], "dict": [1, 8], "dictionari": [2, 5], "differ": [0, 1, 2, 3, 5, 6, 9], "direct": 1, "directori": [2, 5, 8, 9], "discuss": 9, "do": [4, 7], "doe": 9, "doubl": 9, "e": [1, 8], "e0fcc577": 1, "e4c3": 1, "e7c8": 1, "e7ec1c33": 1, "each": 9, "easili": [2, 5, 9], "eb9c": 1, "ec40843e6a86": 1, "ee507eb7": 1, "effici": [2, 5, 9], "either": 9, "element": [1, 2, 5], "email": 1, "enabl": 9, "energi": [0, 1, 2, 5, 8, 9], "energy_lst": [2, 5, 8, 9], "engin": 1, "enhanc": [2, 5], "enumer": [1, 9], "env": 1, "environ": [0, 4, 7, 9], "eos_dict": 1, "eos_result": 1, "equationofst": 1, "espresso": [1, 2, 5, 9], "ev": 8, "ev_curv": 8, "evalu": [2, 5, 9], "evcurv": [2, 5, 8, 9], "even": 9, "evolv": 9, "exampl": 9, "except": [1, 8], "execut": [8, 9], "executable_str": 9, "execute_job": 9, "exist": [2, 5, 9], "exist_ok": [2, 5, 8, 9], "expens": 9, "explan": 9, "export": 1, "extend": [2, 5], "extern": 9, "f": 1, "f0e400dc": 1, "f43a": 1, "f4cd": 1, "f698bcff99ea": 1, "f71ee458594": 1, "f85f": 1, "f89b8859": 1, "face": [2, 5], "factor_list": 1, "fail": [2, 5], "fals": 8, "fanci": 1, "fbea": 8, "featur": 1, "few": 9, "ffb6371e045d": 1, "ffd9": 1, "field": 8, "file": [1, 2, 4, 5, 7, 8, 9], "filenam": [2, 5, 8, 9], "filepath_execut": 1, "filesystem": 9, "final": 9, "finish": 8, "first": [2, 5, 9], "fit": [2, 5], "five": [2, 5], "flexibl": [2, 5], "float": 8, "flow": 8, "focu": 9, "focus": [2, 5], "folder": [1, 9], "folderdata": 1, "follow": [0, 2, 5, 8, 9], "format": [2, 5, 9], "four": [2, 3, 5, 6], "framework": [0, 3, 4, 6, 7], "from": [1, 2, 3, 5, 6, 8, 9], "from_directori": 8, "function": 9, "furthermor": 9, "g": 1, "gener": [2, 5, 8, 9], "generate_structur": [2, 5, 8, 9], "generate_structures81144f1592dde5715ec257eb7f425177": 9, "get_as": 1, "get_build": 1, "get_cel": 1, "get_dict": 1, "get_ev_curv": 8, "get_input_set": 8, "get_list": 1, "get_volum": [2, 5, 8, 9], "github": 9, "give": [2, 5, 9], "given": [1, 2, 3, 5, 6, 9], "ha": 9, "hand": [3, 6], "handl": [2, 5], "have": [2, 5, 9], "hdf": 9, "hdf5": 9, "here": [2, 5, 9], "hierach": 9, "hierarchi": 9, "high": [2, 5, 9], "highlight": [2, 3, 5, 6], "home": [1, 9], "hostnam": 1, "how": [2, 3, 5, 6], "hpc": [2, 5], "human": [2, 5], "hundr": [4, 7], "i": [0, 1, 2, 5, 8, 9], "id": 9, "ideal": [2, 5], "ieee_invalid_flag": 8, "ignor": 8, "imag": [2, 5, 8, 9], "implement": [0, 3, 6], "import": [8, 9], "improv": [3, 6], "increas": [2, 5], "independ": [0, 9], "index": [1, 9], "individu": 9, "ineffici": [2, 5], "info": 8, "input": [1, 2, 5, 8, 9], "input_data": [2, 5, 8, 9], "input_dict": [2, 5, 8, 9], "input_set_gener": 8, "inputgener": 8, "inputset": 8, "insert": 9, "inspect": 9, "instal": [0, 1], "installedcod": 1, "instanc": 1, "integr": [2, 5, 9], "intend": [2, 5], "intens": [2, 5], "interact": 9, "interfac": [0, 9], "intern": [2, 5, 9], "io": [8, 9], "ipynb": 0, "isinst": 1, "istructur": 8, "item": 1, "iter": 9, "its": 9, "jan": 8, "jinja2": 9, "job": [8, 9], "job_decor": [2, 5], "job_nam": 9, "job_qe_minim": 9, "job_strain": 9, "job_strain_": 9, "job_strain_0": 9, "job_strain_1": 9, "job_strain_2": 9, "job_strain_3": 9, "job_strain_4": 9, "job_workflow": 9, "jobflow": [0, 2, 5], "join": [2, 5, 8, 9], "jovyan": 1, "jupyt": [8, 9], "jupyterbook": 9, "just": 1, "kei": 1, "kjpaw_psl": [0, 1, 8, 9], "kpt": [2, 5, 8, 9], "kwarg": [1, 2, 5], "label": 1, "lambda": 8, "languag": [2, 5, 9], "larg": 9, "latter": 9, "lattic": [2, 5, 9], "lead": [2, 5, 9], "learn": [4, 7], "legaci": 1, "len": 8, "lib": 1, "librdmacm": 8, "like": [2, 5, 9], "limit": [4, 7], "line": [1, 4, 7, 9], "line2d": 1, "link": 9, "linspac": [8, 9], "linux": [2, 5], "list": [1, 2, 5], "load_cod": 1, "load_comput": 1, "load_profil": 1, "local": [1, 8, 9], "localhost": 1, "locat": 9, "look": [3, 6], "machin": [2, 4, 5, 7], "major": [2, 5], "make": 8, "makedir": [2, 5, 8, 9], "maker": 8, "manag": [1, 2, 5, 9], "mani": [2, 5], "manual": [2, 5], "mark": 9, "materi": 9, "matplotlib": [1, 8, 9], "mca_base_component_repository_open": 8, "mca_btl_openib": 8, "metadata": 1, "might": [2, 5, 9], "minimalist": 9, "modern": [2, 4, 5, 7], "modul": 9, "modulu": [0, 2, 5], "more": 9, "mpirun": [8, 9], "msonatom": 8, "multipl": 9, "my_funct": [2, 5], "my_queu": 9, "mybind": [0, 9], "n": [0, 1, 8, 9], "name": [1, 2, 5, 8, 9], "need": [2, 4, 5, 7, 8], "new": [2, 5], "new_cel": 1, "new_job": 8, "next": [3, 6], "node": 1, "none": 8, "note": 8, "notebook": [1, 9], "notexist": 1, "np": [8, 9], "num_machin": 1, "num_mpiprocs_per_machin": 1, "number": [2, 5, 9], "numpi": [8, 9], "o": [2, 5, 8, 9], "object": [8, 9], "occup": [1, 2, 5, 8, 9], "omp_num_thread": 1, "one": [2, 3, 5, 6], "onli": [2, 5, 9], "open": [2, 5, 8], "opportun": 9, "optim": [0, 2, 5, 9], "option": [1, 2, 5, 8, 9], "orm": 1, "other": [3, 6], "out": 1, "outlin": 1, "output": [1, 2, 5, 8, 9], "output_schema": 8, "outputrefer": 8, "over": [2, 5, 9], "own": [3, 6], "packag": [1, 9], "parallel": [2, 5], "paramet": [1, 2, 5, 8, 9], "pars": [2, 5, 8, 9], "parse_pw": [2, 5, 8, 9], "parser": [0, 2, 5, 8, 9], "pass": 1, "path": [1, 2, 5, 8, 9], "pathlib": 1, "pbc": 8, "pbe": [0, 1, 8, 9], "per": 9, "perform": [2, 5, 9], "pk": 1, "place": 0, "plain": [2, 5], "plot": [1, 2, 5, 8, 9], "plot_energy_volume_curv": [2, 5, 8, 9], "plot_energy_volume_curve_job": 8, "plt": [1, 2, 5, 8, 9], "plugin": 1, "pm": 1, "png": [2, 5, 8, 9], "point": 8, "poor": 9, "portabl": [1, 3, 6], "portablecod": 1, "posit": [2, 5], "postbuild": 0, "potenti": 0, "pr": 9, "prepend_text": 1, "previou": 8, "primari": 9, "process": [1, 9], "profil": 1, "program": [2, 5], "project": 9, "properti": 1, "protocol": [2, 3, 5, 6, 9], "prototyp": 9, "provid": [2, 5, 9], "pseudo": 0, "pseudo_dir": 1, "pseudopotenti": [1, 2, 5, 8, 9], "publish": 9, "pw": [1, 8, 9], "pw_code": 1, "pwcalcul": 1, "pwi": [2, 5, 8, 9], "pwo": [8, 9], "pwscf": [2, 5, 8, 9], "py": 1, "pydant": 8, "pyiron": [2, 5], "pyiron_atomist": 9, "pyiron_bas": [0, 9], "pymatgen": 8, "pyplot": [1, 8, 9], "python": [1, 9], "python3": 1, "qe": 8, "qe_cmd": 8, "qeinputgener": 8, "qeinputset": 8, "qeinputstaticgener": 8, "qetaskdoc": 8, "qi": 8, "quantum": [1, 2, 5, 9], "quantumespresso": 1, "queri": 9, "queu": [2, 5, 9], "queue": 9, "qunatum": 0, "rabbitmq": 1, "rang": [2, 5, 8], "rapid": 9, "rather": [2, 5], "re": 9, "readabl": [2, 5], "receiv": [2, 5, 9], "recent": [2, 5], "recogn": 9, "recommend": [2, 5], "recomput": 9, "regular": 1, "relat": 9, "relax": [8, 9], "relax_param": 1, "relaxed_structur": 1, "releas": [2, 5], "reload": 9, "remain": [2, 5, 9], "remot": 1, "remote_fold": 1, "remotedata": 1, "remov": [1, 9], "remove_job": 9, "render": 9, "replac": 8, "report": 1, "repres": [2, 5, 9], "reproduc": 9, "reproducibl": 9, "requir": [2, 5, 9], "rescale_list": 1, "rescaled_structur": 1, "resourc": [1, 2, 5, 9], "respect": 1, "respons": 8, "rest": 9, "result": [1, 2, 5, 9], "retriev": 1, "return": [1, 2, 5, 8, 9], "run": [1, 8, 9], "run_eo": 1, "run_eos_wf": 1, "run_get_nod": 1, "run_loc": 8, "run_q": 8, "same": [2, 3, 5, 6, 9], "save": 9, "savefig": [2, 5, 8, 9], "sbatch": 9, "scale": [2, 5, 9], "scale_atom": [1, 2, 5, 8, 9], "scale_factor": 1, "scaled_structure_dict": 1, "scaling_factor": 1, "scf": [1, 8, 9], "scf_input": 1, "scheduler_typ": 1, "scienc": 9, "scientif": [2, 5], "script": [0, 9], "secondari": [2, 5], "select": [3, 6, 9], "self": [1, 8], "serial": [2, 5], "serializ": 8, "server": [1, 9], "servic": 9, "set": [1, 2, 5, 8], "set_cel": [1, 2, 5, 8, 9], "setup": 1, "share": 8, "shell": 8, "should": [2, 5], "signal": 8, "simpl": [0, 2, 5], "simplifi": [2, 3, 5, 6, 9], "simstack": [2, 5], "simul": [2, 3, 4, 5, 6, 7], "singl": [2, 5, 9], "site": 1, "sleep": 1, "slurm": [2, 5], "smear": [1, 2, 5, 8, 9], "so": 8, "softwar": [2, 5], "some": [2, 5, 9], "sourc": [2, 5], "spec": 1, "specif": [2, 5, 9], "specifi": [1, 2, 5, 9], "sql": 9, "sqlite_do": 1, "srv": 1, "start": 8, "static": [8, 9], "staticqemak": 8, "step": [2, 5, 9], "still": [2, 5, 9], "stop_children": 8, "stop_jobflow": 8, "storag": [2, 4, 5, 7], "store": [1, 9], "store_input": 8, "stored_data": 8, "str": [8, 9], "strain": [2, 5, 8, 9], "strain_lst": [2, 5, 8, 9], "structur": [0, 2, 5, 8, 9], "structure_": 1, "structure_0": 1, "structure_1": 1, "structure_2": 1, "structure_3": 1, "structure_4": 1, "structure_lst": [2, 5, 8, 9], "structure_strain": [2, 5, 8, 9], "structuredata": 1, "studi": [2, 5], "submit": [1, 9], "subprocess": [1, 8], "success": [2, 5], "suffici": [4, 7], "suit": [2, 5], "summar": 9, "super": 1, "supercel": [2, 5], "symbol": 8, "system": [1, 2, 5, 9], "take": [1, 2, 5], "task": [2, 5, 9], "task_doc": 8, "templat": 9, "tensor": 9, "tenth": [4, 7], "test": [0, 1, 9], "text": [2, 5], "than": [2, 5], "thei": 9, "theori": [2, 5], "thi": [0, 1, 2, 3, 5, 6, 9], "thousand": [4, 7], "three": [0, 2, 5], "through": 9, "time": 9, "tprnfor": [2, 5, 8, 9], "track": [2, 5], "tradit": [2, 4, 5, 7], "trajectori": 9, "transfer": [2, 3, 5, 6], "transform": 8, "transport_typ": 1, "true": [1, 2, 5, 8, 9], "try": 1, "tstress": [2, 5, 8, 9], "tupl": 8, "two": 9, "type": [1, 8], "typic": 1, "unabl": 8, "union": 8, "unit": [2, 5], "universal_newlin": 8, "up": [2, 5, 9], "upf": [0, 1, 8, 9], "us": [2, 4, 5, 7, 8, 9], "user": [2, 3, 5, 6, 9], "userwarn": 1, "util": [2, 4, 5, 7], "uuid": [1, 8], "v": 1, "v3": 1, "valid_typ": 1, "valu": 1, "variabl": [2, 5, 9], "variou": [2, 5], "vc": [1, 8, 9], "verdi": 1, "veri": [2, 5], "version": 9, "via": 9, "volum": [0, 1, 2, 5, 8, 9], "volume_lst": [2, 5, 8, 9], "wa": [2, 3, 5, 6, 9], "wai": [2, 5], "warn": 1, "warn_deprec": 1, "we": [2, 4, 5, 7, 8], "websit": 9, "well": [2, 5, 9], "were": [2, 5], "when": [2, 4, 5, 7, 9], "which": [2, 5, 9], "while": [2, 5, 9], "who": [3, 6], "why": [4, 7], "wide": [2, 5], "without": 1, "workchain": 1, "workchainnod": 1, "workdir": 1, "workflow": [1, 3, 4, 6, 7], "workflow895ba469e3d888839622dab8177e3746": 9, "workfunct": 1, "working_directori": [2, 5, 8, 9], "workstat": 9, "would": 1, "wrap": 9, "wrap_execut": 9, "wrap_python_funct": 9, "write": [2, 5, 8, 9], "write_input": [2, 5, 8, 9], "write_input_funct": 9, "write_qe_input_set": 8, "written": [2, 5], "x": [1, 8, 9], "xlabel": [2, 5, 8, 9], "xml": [2, 5, 8, 9], "year": [2, 5], "ylabel": [2, 5, 8, 9], "yml": [0, 9], "you": 1}, "titles": ["Quantum Espresso Workflow", "Aiida", "Challenges for workflow frameworks", "Conclusion", "Introduction", "Challenges for workflow frameworks", "Conclusion", "Introduction", "jobflow", "pyiron"], "titleterms": {"aiida": 1, "an": 9, "basic": 1, "builder": 1, "calc": 1, "chain": 1, "challeng": [2, 5], "check": 9, "code": 9, "conclus": [3, 6], "curv": 1, "data": 9, "eo": 1, "equat": 1, "error": 9, "espresso": 0, "exampl": [2, 5], "execut": [2, 5], "explan": 0, "extern": [2, 5], "framework": [2, 5], "function": [1, 2, 5], "geometri": 1, "handl": 9, "hpc": 9, "implement": [2, 5, 9], "import": 1, "instal": 9, "interfac": [2, 5], "introduct": [4, 7], "jobflow": 8, "new": 9, "point": 9, "public": 9, "pyiron": 9, "python": [2, 5], "qe": 1, "quantum": 0, "relax": 1, "rescal": 1, "setup": 9, "share": 9, "simul": 9, "state": 1, "storag": 9, "structur": 1, "submiss": 9, "univers": [2, 5], "us": 1, "version": 1, "work": 1, "workflow": [0, 2, 5, 9]}}) \ No newline at end of file