From 462b7daa0a7b81013260612849a0de47bed3dad5 Mon Sep 17 00:00:00 2001 From: Chris Sewell Date: Thu, 18 Jul 2019 14:24:18 +0100 Subject: [PATCH] added documentation for `crystal17.main.base` workflow --- docs/source/index.rst | 1 + docs/source/user_guide/workflow_base.ipynb | 725 +++++++++++++++++++++ 2 files changed, 726 insertions(+) create mode 100644 docs/source/user_guide/workflow_base.ipynb diff --git a/docs/source/index.rst b/docs/source/index.rst index 4573dc5..6c34c59 100755 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -13,6 +13,7 @@ The aiida-crystal17 plugin for `AiiDA`_ user_guide/get_started user_guide/calc_basic user_guide/calc_main + user_guide/workflow_base user_guide/calc_main_immigrant user_guide/calc_gulp api_index diff --git a/docs/source/user_guide/workflow_base.ipynb b/docs/source/user_guide/workflow_base.ipynb new file mode 100644 index 0000000..30620fa --- /dev/null +++ b/docs/source/user_guide/workflow_base.ipynb @@ -0,0 +1,725 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Main Calculation Restart Workflow" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The `crystal17.main.base` workflow builds on the `crystal.main` calculation, by automating restarts of the calculation for known failure modes:\n", + "\n", + "- **No SCF convergence within maximum cycles**: the FMIXING value is lowered, and the calculation is restarted from the last known geometry and wave-function (using GUESSP)\n", + "- **No geometric convergence within maximum iterations**: the calculation is restarted from the last known geometry and wave-function (using GUESSP)\n", + "- **Reaches scheduler wall-time**: the calculation is restarted from the last known geometry.\n", + "\n", + "Additionally, new SHRINK terms can be computed, to adhere to a minimum desired k-point spacing, given the input structure." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32m ✓ \u001b[0mprofile: On profile test_crystal17\u001b[0m\n", + "\u001b[32m ✓ \u001b[0mrepository: /Users/cjs14/GitHub/aiida-cjs-working/databases/aiida/.aiida/repository/test_crystal17\u001b[0m\n", + "\u001b[32m ✓ \u001b[0mpostgres: Connected as cjs14@localhost:5432\u001b[0m\n", + "\u001b[32m ✓ \u001b[0mrabbitmq: Connected to amqp://127.0.0.1?heartbeat=600\u001b[0m\n", + "\u001b[32m ✓ \u001b[0mdaemon: Daemon is running as PID 35477 since 2019-07-18 12:57:21\u001b[0m\n" + ] + } + ], + "source": [ + "!verdi status" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[31m\u001b[1mInputs\u001b[0m\n", + "\u001b[1m cry: required \u001b[0m\n", + " basis_family: optional Str An alternative to specifying the basis sets manually: one can specify the n ...\u001b[0m\n", + " clean_workdir: optional Bool If `True`, work directories of all called calculation will be cleaned at th ...\u001b[0m\n", + " kpoints_distance: optional Float The minimum desired distance in 1/Å between k-points in reciprocal space. T ...\u001b[0m\n", + " kpoints_force_parity: optional Bool Optional input when constructing the k-points based on a desired `kpoints_d ...\u001b[0m\n", + " max_iterations: optional Int Maximum number of iterations the work chain will restart the calculation to ...\u001b[0m\n", + " metadata: optional \u001b[0m\n", + "\u001b[31m\u001b[1mOutputs\u001b[0m\n", + "\u001b[1m remote_folder: required RemoteData Input files necessary to run the process will be stored in this folder node ...\u001b[0m\n", + "\u001b[1m results: required Dict the data extracted from the main output file\u001b[0m\n", + " structure: optional StructureData the structure output from the calculation\u001b[0m\n", + " symmetry: optional SymmetryData the symmetry data from the calculation\u001b[0m\n", + "\u001b[31m\u001b[1mExit codes\u001b[0m\n", + " 1: The process has failed with an unspecified error.\u001b[0m\n", + " 2: The process failed with legacy failure mode.\u001b[0m\n", + " 10: The process returned an invalid output.\u001b[0m\n", + " 11: The process did not register a required output.\u001b[0m\n", + " 101: The maximum number of iterations was exceeded.\u001b[0m\n", + " 102: The calculation failed for an unknown reason, twice in a row.\u001b[0m\n", + " 201: The parameters could not be validated against the jsonschema.\u001b[0m\n", + " 202: The explicit `basis_sets` or `basis_family` could not be used to get the necessary basis sets.\u001b[0m\n", + " 204: The `metadata.options` did not specify both `resources.num_machines` and `max_wallclock_seconds`.\u001b[0m\n", + " 300: The calculation failed with an unrecoverable error.\u001b[0m\n", + " 320: The initialization calculation failed.\u001b[0m\n" + ] + } + ], + "source": [ + "!verdi plugin list aiida.workflows crystal17.main.base" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "\n", + "from aiida.engine import run_get_node\n", + "from aiida.plugins import (\n", + " DataFactory, WorkflowFactory, CalculationFactory)\n", + "from aiida.tools.visualization import Graph\n", + "\n", + "from aiida_crystal17.tests import get_test_structure_and_symm, TEST_FILES\n", + "from aiida_crystal17.tests.utils import get_default_metadata\n", + "from aiida_crystal17.tests.utils import get_or_create_local_computer, get_or_create_code" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'test_crystal17'" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from aiida import load_profile\n", + "profile = load_profile()\n", + "profile.name" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "aiida_crystal17.data.basis_set.BasisSetData" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "DataFactory('crystal17.basisset')" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "computer = get_or_create_local_computer('work_directory', 'localhost')\n", + "code = get_or_create_code('crystal17.main', computer, 'mock_crystal17')\n", + "\n", + "params = {\n", + " \"title\": \"NiO Bulk with AFM spin\",\n", + " \"scf.single\": \"UHF\",\n", + " \"scf.k_points\": (8, 8),\n", + " \"scf.spinlock.SPINLOCK\": (0, 15),\n", + " \"scf.numerical.FMIXING\": 50,\n", + " \"scf.numerical.MAXCYCLE\": 10,\n", + " \"scf.post_scf\": [\"PPAN\"]\n", + " }\n", + "\n", + "instruct, symmetry = get_test_structure_and_symm(\"NiO_afm\")\n", + "\n", + "kind_data = DataFactory('crystal17.kinds')(data={\n", + " \"kind_names\": [\"Ni1\", \"Ni2\", \"O\"],\n", + " \"spin_alpha\": [True, False, False], \"spin_beta\": [False, True, False]})\n", + "\n", + "DataFactory('crystal17.basisset').upload_basisset_family(\n", + " os.path.join(TEST_FILES, \"basis_sets\", \"sto3g\"),\n", + " \"sto3g\",\n", + " \"minimal basis sets\",\n", + " stop_if_existing=False,\n", + " extension=\".basis\")\n", + "\n", + "# set up calculation\n", + "process_class = code.get_builder().process_class\n", + "calc_builder = process_class.create_builder(\n", + " params, instruct, \"sto3g\", \n", + " symmetry=symmetry, \n", + " kinds=kind_data, \n", + " code=code,\n", + " metadata=get_default_metadata(),\n", + " unflatten=True)\n", + "\n", + "wc_builder = WorkflowFactory('crystal17.main.base').get_builder()\n", + "wc_builder.cry = dict(calc_builder)\n", + "wc_builder.clean_workdir = True" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [], + "source": [ + "outputs, wc_node = run_get_node(wc_builder)" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[22mCryMainBaseWorkChain<240> Finished [5:results]\n", + " ├── CryMainCalculation<242> Finished [411]\n", + " └── CryMainCalculation<247> Finished [0]\u001b[0m\n" + ] + } + ], + "source": [ + "!verdi process status {wc_node.pk}" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[22m2019-07-18 13:02:05 [20 | REPORT]: [240|CryMainBaseWorkChain|run_calculation]: launching CryMainCalculation<242> iteration #1\n", + "2019-07-18 13:02:19 [23 | REPORT]: [240|CryMainBaseWorkChain|report_error_handled]: CryMainCalculation<242> failed with exit status 411: SCF convergence did not finalise (usually due to reaching step limit)\n", + "2019-07-18 13:02:19 [24 | REPORT]: [240|CryMainBaseWorkChain|report_error_handled]: Action taken: reduced fmixing from 50 to 40 and restarting from last calculation\n", + "2019-07-18 13:02:20 [25 | REPORT]: [240|CryMainBaseWorkChain|run_calculation]: launching CryMainCalculation<247> iteration #2\n", + "2019-07-18 13:02:30 [26 | REPORT]: [240|CryMainBaseWorkChain|inspect_calculation]: CryMainCalculation<247> completed successfully\n", + "2019-07-18 13:02:30 [27 | REPORT]: [240|CryMainBaseWorkChain|results]: work chain completed after 2 iterations\n", + "2019-07-18 13:02:30 [28 | REPORT]: [240|CryMainBaseWorkChain|on_terminated]: cleaned remote folders of calculations: 242 247\u001b[0m\n" + ] + } + ], + "source": [ + "!verdi process report {wc_node.pk}" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "N240\n", + "\n", + "CryMainBaseWorkChain (240)\n", + "State: finished\n", + "Exit Code: 0\n", + "\n", + "\n", + "\n", + "N242\n", + "\n", + "CryMainCalculation (242)\n", + "State: finished\n", + "Exit Code: 411\n", + "\n", + "\n", + "\n", + "N240->N242\n", + "\n", + "\n", + "CALL_CALC\n", + 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