diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6810030143..9b20a8dd75 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -35,6 +35,12 @@ jobs: python -m pip install --upgrade pip pip install .[strict,docs] + - name: Copy tutorials + run: | + cp -r tutorials docs/ + jupyter nbconvert --to markdown docs/tutorials/*.ipynb + jupyter nbconvert --to markdown docs/tutorials/*/*.ipynb + - name: Build run: sphinx-build docs docs_build diff --git a/.gitignore b/.gitignore index d1f252c4f3..2500a708d8 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,8 @@ docs/_build/* docs/_build/*/* docs/_build/*/*/* docs_build/* +docs/tutorials/* +docs/tutorials/*/* # C extensions *.so diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fe2a771a13..44b0ec977e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,6 +7,7 @@ repos: hooks: - id: ruff args: [--fix] + exclude: tutorials/grueneisen_workflow.ipynb - id: ruff-format - repo: https://github.com/pre-commit/pre-commit-hooks rev: v5.0.0 diff --git a/docs/index.md b/docs/index.md index 085bf4de64..a40f5a5d39 100644 --- a/docs/index.md +++ b/docs/index.md @@ -9,6 +9,7 @@ user/docs-schemas-emmet user/fireworks user/atomate-1-vs-2 user/codes/index +tutorials/tutorials ``` ```{toctree} diff --git a/pyproject.toml b/pyproject.toml index d1f8818f29..a1bd875c7b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -82,6 +82,7 @@ docs = [ "sphinx-copybutton==0.5.2", "sphinx==8.1.3", "sphinx_design==0.6.1", + "jupyterlab==4.3.4" ] dev = ["pre-commit>=2.12.1"] tests = [ diff --git a/src/atomate2/common/flows/eos.py b/src/atomate2/common/flows/eos.py index 03fe6749cf..ba29f3215c 100644 --- a/src/atomate2/common/flows/eos.py +++ b/src/atomate2/common/flows/eos.py @@ -95,6 +95,12 @@ def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow: ) relax_flow.name = "EOS equilibrium relaxation" + try: + if len(relax_flow.jobs) > 1: + for job in relax_flow.jobs: + job.append_name(" EOS equilibrium relaxation") + except AttributeError: + pass flow_output["initial_relax"] = { "E0": relax_flow.output.output.energy, "V0": relax_flow.output.structure.volume, @@ -153,6 +159,12 @@ def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow: prev_dir=prev_dir, ) relax_job.name += f" deformation {frame_idx}" + try: + if len(relax_job.jobs) > 1: + for job in relax_job.jobs: + job.append_name(f" deformation {frame_idx}") + except AttributeError: + pass jobs["relax"].append(relax_job) if self.static_maker: diff --git a/src/atomate2/common/schemas/qha.py b/src/atomate2/common/schemas/qha.py index e85b173012..0f5acad6e2 100644 --- a/src/atomate2/common/schemas/qha.py +++ b/src/atomate2/common/schemas/qha.py @@ -37,8 +37,8 @@ class PhononQHADoc(StructureMetadata, extra="allow"): # type: ignore[call-arg] ) helmholtz_volume: Optional[list[list[float]]] = Field( None, - description="Free energies at temperatures and volumes." - "shape (temperatures, volumes)", + description="Free energies (eV) at temperatures and volumes (Angstrom^3)." + "shape (temperatures, volumes)", # TODO: add units here ) volume_temperature: Optional[list[float]] = Field( None, diff --git a/tests/aims/test_flows/test_eos.py b/tests/aims/test_flows/test_eos.py index e0170739f9..a363d59520 100644 --- a/tests/aims/test_flows/test_eos.py +++ b/tests/aims/test_flows/test_eos.py @@ -13,8 +13,8 @@ # mapping from job name to directory containing test files ref_paths = { - "Relaxation calculation 1": "double-relax-si/relax-1", - "Relaxation calculation 2": "double-relax-si/relax-2", + "Relaxation calculation 1 EOS equilibrium relaxation": "double-relax-si/relax-1", + "Relaxation calculation 2 EOS equilibrium relaxation": "double-relax-si/relax-2", "Relaxation calculation (fixed cell) deformation 0": "eos-si/0", "Relaxation calculation (fixed cell) deformation 1": "eos-si/1", "Relaxation calculation (fixed cell) deformation 2": "eos-si/2", diff 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100644 index 0000000000..75f0fc8805 Binary files /dev/null and b/tests/test_data/vasp/Si_qha_2/tight_relax_2_d5/outputs/vasprun.xml.gz differ diff --git a/tests/vasp/flows/test_eos.py b/tests/vasp/flows/test_eos.py index 86b4d541d8..20614e664d 100644 --- a/tests/vasp/flows/test_eos.py +++ b/tests/vasp/flows/test_eos.py @@ -23,7 +23,11 @@ expected_incar_deform = expected_incar_relax | {"ISIF": 2} -expected_incar_static = expected_incar_relax | {"NSW": 0, "IBRION": -1, "ISMEAR": -5} +expected_incar_static = expected_incar_relax | { + "NSW": 0, + "IBRION": -1, + "ISMEAR": -5, +} expected_incar_static.pop("ISIF") @@ -77,15 +81,17 @@ def test_mp_eos_maker( n_frames: int = 2, linear_strain: tuple = (-0.05, 0.05), ): + relax_job_name_1 = "EOS MP GGA relax 1 EOS equilibrium relaxation" + relax_job_name_2 = "EOS MP GGA relax 2 EOS equilibrium relaxation" base_ref_path = "Si_EOS_MP_GGA/" ref_paths = {} expected_incars = { - "EOS MP GGA relax 1": expected_incar_relax_1, - "EOS MP GGA relax 2": expected_incar_relax, + relax_job_name_1: expected_incar_relax_1, + relax_job_name_2: expected_incar_relax, } for idx in range(2): - ref_paths[f"EOS MP GGA relax {idx + 1}"] = ( + ref_paths[f"EOS MP GGA relax {idx + 1} EOS equilibrium relaxation"] = ( f"mp-149-PBE-EOS_MP_GGA_relax_{idx + 1}" ) @@ -118,7 +124,7 @@ def test_mp_eos_maker( ) structure = Structure.from_file( - f"{vasp_test_dir}/{ref_paths['EOS MP GGA relax 1']}/inputs/POSCAR.gz" + f"{vasp_test_dir}/{ref_paths[relax_job_name_1]}/inputs/POSCAR.gz" ) # cannot perform least-squares fit for four parameters with only 3 data points @@ -153,7 +159,10 @@ def test_mp_eos_maker( # deformation jobs not included in this assert len(job_output) == len(ref_paths) - ref_energies = {"EOS MP GGA relax 1": -10.849349, "EOS MP GGA relax 2": -10.849357} + ref_energies = { + "EOS MP GGA relax 1 EOS equilibrium relaxation": -10.849349, + "EOS MP GGA relax 2 EOS equilibrium relaxation": -10.849357, + } if do_statics: ref_energies["EOS equilibrium static"] = -10.849357 diff --git a/tutorials/force_fields/phonon_workflow.ipynb b/tutorials/force_fields/phonon_workflow.ipynb index e2537bb392..a231b1faef 100644 --- a/tutorials/force_fields/phonon_workflow.ipynb +++ b/tutorials/force_fields/phonon_workflow.ipynb @@ -4,6 +4,14 @@ "cell_type": "markdown", "id": "0", "metadata": {}, + "source": [ + "# Phonon Workflow Tutorial with Force Fields" + ] + }, + { + "cell_type": "markdown", + "id": "1", + "metadata": {}, "source": [ "We start with imports necessary to test the tutorial automatically. In practice, you can load a structure file from any other place and you are also not required to generate the data in a temporary directory." ] @@ -11,7 +19,7 @@ { "cell_type": "code", "execution_count": null, - "id": "1", + "id": "2", "metadata": {}, "outputs": [], "source": [ @@ -25,7 +33,7 @@ }, { "cell_type": "markdown", - "id": "2", + "id": "3", "metadata": {}, "source": [ "First, we load a structure from a file." @@ -34,7 +42,7 @@ { "cell_type": "code", "execution_count": null, - "id": "3", + "id": "4", "metadata": {}, "outputs": [], "source": [ @@ -45,7 +53,7 @@ }, { "cell_type": "markdown", - "id": "4", + "id": "5", "metadata": {}, "source": [ "Then, we load the `PhononMaker` and run_locally to perform the calculation directly here in the notebook." @@ -54,7 +62,7 @@ { "cell_type": "code", "execution_count": null, - "id": "5", + "id": "6", "metadata": {}, "outputs": [], "source": [ @@ -76,7 +84,7 @@ }, { "cell_type": "markdown", - "id": "6", + "id": "7", "metadata": {}, "source": [ "One can switch to a different force field as well!" @@ -85,7 +93,7 @@ { "cell_type": "code", "execution_count": null, - "id": "7", + "id": "8", "metadata": {}, "outputs": [], "source": [ @@ -108,7 +116,7 @@ }, { "cell_type": "markdown", - "id": "8", + "id": "9", "metadata": {}, "source": [ "Or by using the name only:" @@ -117,7 +125,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9", + "id": "10", "metadata": {}, "outputs": [], "source": [ @@ -127,7 +135,7 @@ }, { "cell_type": "markdown", - "id": "10", + "id": "11", "metadata": {}, "source": [ "Now, we clean up the temporary directory that we made. In reality, you might want to keep this data." @@ -136,7 +144,7 @@ { "cell_type": "code", "execution_count": null, - "id": "11", + "id": "12", "metadata": {}, "outputs": [], "source": [ diff --git a/tutorials/grueneisen_workflow.ipynb b/tutorials/grueneisen_workflow.ipynb new file mode 100644 index 0000000000..78cc45d2d2 --- /dev/null +++ b/tutorials/grueneisen_workflow.ipynb @@ -0,0 +1,283 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "This part is needed for the execution in the notebook.\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "from mock_vasp import TEST_DIR, mock_vasp\n", + "\n", + "ref_paths = {\n", + " \"tight relax 1\": \"Si_gruneisen_tutorial/tight_relax_1_0\",\n", + " \"tight relax 2\": \"Si_gruneisen_tutorial/tight_relax_2_1\",\n", + " \"tight relax 1 plus\": \"Si_gruneisen_tutorial/tight_relax_1_plus_3\",\n", + " \"tight relax 2 plus\": \"Si_gruneisen_tutorial/tight_relax_2_plus_5\",\n", + " \"tight relax 1 minus\": \"Si_gruneisen_tutorial/tight_relax_1_minus_4\",\n", + " \"tight relax 2 minus\": \"Si_gruneisen_tutorial/tight_relax_2_minus_6\",\n", + " \"dft phonon static 1/1 ground\": \"Si_gruneisen_tutorial/dft_phonon_static_1_1_ground_24\",\n", + " \"dft phonon static 1/1 plus\": \"Si_gruneisen_tutorial/dft_phonon_static_1_1_plus_26\",\n", + " \"dft phonon static 1/1 minus\": \"Si_gruneisen_tutorial/dft_phonon_static_1_1_minus_28\",\n", + "}" + ] + }, + { + "cell_type": "markdown", + "id": "2", + "metadata": {}, + "source": [ + "Let's load all required Makers." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3", + "metadata": {}, + "outputs": [], + "source": [ + "from atomate2.vasp.flows.core import DoubleRelaxMaker\n", + "from atomate2.vasp.jobs.core import TightRelaxMaker\n", + "from atomate2.vasp.jobs.phonons import PhononDisplacementMaker\n", + "from atomate2.vasp.sets.core import StaticSetGenerator, TightRelaxSetGenerator" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4", + "metadata": {}, + "outputs": [], + "source": [ + "from jobflow import JobStore, run_locally\n", + "from maggma.stores import MemoryStore\n", + "from pymatgen.core import Structure\n", + "\n", + "from atomate2.vasp.flows.gruneisen import GruneisenMaker, PhononMaker\n", + "\n", + "job_store = JobStore(\n", + " MemoryStore(),\n", + " additional_stores={\"data\": MemoryStore()},\n", + ")\n", + "si_structure = Structure.from_file(TEST_DIR / \"structures\" / \"Si_diamond.cif\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": {}, + "outputs": [], + "source": [ + "phonon_displacement_maker = PhononDisplacementMaker(\n", + " name=\"dft phonon static\",\n", + " run_vasp_kwargs={\"handlers\": ()},\n", + " input_set_generator=StaticSetGenerator(\n", + " user_incar_settings={\n", + " \"GGA\": \"PE\",\n", + " \"IBRION\": -1,\n", + " \"ISPIN\": 1,\n", + " \"ISMEAR\": 0,\n", + " \"ISIF\": 3,\n", + " \"ENCUT\": 700,\n", + " \"EDIFF\": 1e-7,\n", + " \"LAECHG\": False,\n", + " \"LREAL\": False,\n", + " \"ALGO\": \"Normal\",\n", + " \"NSW\": 0,\n", + " \"LCHARG\": False,\n", + " \"LWAVE\": False,\n", + " \"LVTOT\": False,\n", + " \"LORBIT\": None,\n", + " \"LOPTICS\": False,\n", + " \"SIGMA\": 0.05,\n", + " \"ISYM\": 0,\n", + " \"KSPACING\": 0.1,\n", + " \"NPAR\": 4,\n", + " },\n", + " auto_ispin=False,\n", + " ),\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6", + "metadata": {}, + "outputs": [], + "source": [ + "phonon_bulk_relax_maker_isif3 = DoubleRelaxMaker.from_relax_maker(\n", + " TightRelaxMaker(\n", + " run_vasp_kwargs={\"handlers\": ()},\n", + " input_set_generator=TightRelaxSetGenerator(\n", + " user_incar_settings={\n", + " \"GGA\": \"PE\",\n", + " \"ISPIN\": 1,\n", + " \"KSPACING\": 0.1,\n", + " # \"EDIFFG\": 1e-5,\n", + " \"ALGO\": \"Normal\",\n", + " \"LAECHG\": False,\n", + " \"ISMEAR\": 0,\n", + " \"ENCUT\": 700,\n", + " \"IBRION\": 1,\n", + " \"ISYM\": 0,\n", + " \"SIGMA\": 0.05,\n", + " \"LCHARG\": False,\n", + " \"LWAVE\": False,\n", + " \"LVTOT\": False,\n", + " \"LORBIT\": None,\n", + " \"LOPTICS\": False,\n", + " \"LREAL\": False,\n", + " \"ISIF\": 3,\n", + " \"NPAR\": 4,\n", + " }\n", + " ),\n", + " )\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "7", + "metadata": {}, + "source": [ + "Then one can use the `GruneisenMaker` to generate a `Flow`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8", + "metadata": {}, + "outputs": [], + "source": [ + "flow = GruneisenMaker(\n", + " symprec=1e-4,\n", + " bulk_relax_maker=phonon_bulk_relax_maker_isif3,\n", + " phonon_maker=PhononMaker(\n", + " generate_frequencies_eigenvectors_kwargs={\n", + " \"tmin\": 0,\n", + " \"tmax\": 1000,\n", + " \"tstep\": 10,\n", + " },\n", + " min_length=10,\n", + " bulk_relax_maker=None,\n", + " born_maker=None,\n", + " static_energy_maker=None,\n", + " phonon_displacement_maker=phonon_displacement_maker,\n", + " ),\n", + ").make(structure=si_structure)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9", + "metadata": {}, + "outputs": [], + "source": [ + "flow.draw_graph().show()" + ] + }, + { + "cell_type": "markdown", + "id": "10", + "metadata": {}, + "source": [ + "We can then run the code with \"mock_vasp\"." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "11", + "metadata": { + "jupyter": { + "is_executing": true + } + }, + "outputs": [], + "source": [ + "with mock_vasp(ref_paths=ref_paths) as mf:\n", + " run_locally(\n", + " flow,\n", + " create_folders=True,\n", + " ensure_success=True,\n", + " raise_immediately=True,\n", + " store=job_store,\n", + " )" + ] + }, + { + "cell_type": "markdown", + "id": "12", + "metadata": {}, + "source": [ + "Let's then analyze outputs from the workflow." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "13", + "metadata": {}, + "outputs": [], + "source": [ + "job_store.connect()\n", + "\n", + "result = job_store.query_one(\n", + " {\"name\": \"compute_gruneisen_param\"},\n", + " properties=[\n", + " \"output.gruneisen_band_structure\",\n", + " \"output.gruneisen_parameter\",\n", + " ],\n", + " load=True,\n", + " sort={\"completed_at\": -1}, # to get the latest computation\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "14", + "metadata": {}, + "outputs": [], + "source": [ + "from pymatgen.phonon.gruneisen import GruneisenPhononBandStructureSymmLine\n", + "from pymatgen.phonon.plotter import GruneisenPhononBSPlotter\n", + "\n", + "bs = GruneisenPhononBandStructureSymmLine.from_dict(\n", + " result[\"output\"][\"gruneisen_band_structure\"]\n", + ")\n", + "plt = GruneisenPhononBSPlotter(bs=bs)\n", + "plt.get_plot_gs(plot_ph_bs_with_gruneisen=True)" + ] + } + ], + "metadata": { + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tutorials/openmm_tutorial.ipynb b/tutorials/openmm_tutorial.ipynb index 8cfb3baf9c..1d5124ad63 100644 --- a/tutorials/openmm_tutorial.ipynb +++ b/tutorials/openmm_tutorial.ipynb @@ -3,13 +3,21 @@ { "cell_type": "markdown", "id": "0", + "metadata": {}, + "source": [ + "# OpenMM Tutorial" + ] + }, + { + "cell_type": "markdown", + "id": "1", "metadata": { "jupyter": { "outputs_hidden": false } }, "source": [ - "### Installing Atomate2 From Source with OpenMM\n", + "## Installing Atomate2 From Source with OpenMM\n", "\n", "```bash\n", "# setting up our conda environment\n", @@ -50,20 +58,20 @@ }, { "cell_type": "markdown", - "id": "1", + "id": "2", "metadata": {}, "source": [ - "### Understanding Atomate2 OpenMM \n", + "## Understanding Atomate2 OpenMM\n", "\n", "Atomate2 is really just a collection of jobflow workflows relevant to materials science. In all the workflows, we pass our system of interest between different jobs to perform the desired simulation. Representing the intermediate state of a classical molecular dynamics simulation, however, is challenging. While the intermediate representation between stages of a periodic DFT simulation can include just the elements, xyz coordinates, and box vectors, classical molecular dynamics systems must also include velocities and forces. The latter is particularly challenging because all MD engines represent forces differently. Rather than implement our own representation, we use the `openff.interchange.Interchange` object, which catalogs the necessary system properties and interfaces with a variety of MD engines. This is the object that we pass between stages of a classical MD simulation and it is the starting point of our workflow." ] }, { "cell_type": "markdown", - "id": "2", + "id": "3", "metadata": {}, "source": [ - "### Pouring a Glass of Wine\n", + "## Pouring a Glass of Wine\n", "\n", "The first job we need to create generates the `Interchange` object. To specify the system of interest, we use give it the SMILES strings, counts, and names (optional) of the molecules we want to include." ] @@ -71,7 +79,7 @@ { "cell_type": "code", "execution_count": null, - "id": "3", + "id": "4", "metadata": { "jupyter": { "outputs_hidden": false @@ -92,7 +100,7 @@ }, { "cell_type": "markdown", - "id": "4", + "id": "5", "metadata": {}, "source": [ "If you are wondering what arguments are allowed in the dictionaries, check out the `create_mol_spec` function in the `atomate2.openff.utils` module. Under the hood, this is being called on each mol_spec dict. Meaning the code below is functionally identical to the code above." @@ -101,7 +109,7 @@ { "cell_type": "code", "execution_count": null, - "id": "5", + "id": "6", "metadata": {}, "outputs": [], "source": [ @@ -114,7 +122,7 @@ }, { "cell_type": "markdown", - "id": "6", + "id": "7", "metadata": {}, "source": [ "In a more complex simulation we might want to scale the ion charges and include custom partial charges. An example with the Gen2 electrolyte is shown below. This yields the `elyte_interchange_job` object, which we can pass to the next stage of the simulation.\n", @@ -125,7 +133,7 @@ { "cell_type": "code", "execution_count": null, - "id": "7", + "id": "8", "metadata": { "jupyter": { "outputs_hidden": false @@ -170,10 +178,10 @@ }, { "cell_type": "markdown", - "id": "8", + "id": "9", "metadata": {}, "source": [ - "### The basic simulation\n", + "## The basic simulation\n", "\n", "To run a production simulation, we will create a production flow, link it to our `elyte_interchange_job`, and then run both locally.\n", "\n", @@ -184,7 +192,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9", + "id": "10", "metadata": {}, "outputs": [], "source": [ @@ -215,7 +223,7 @@ }, { "cell_type": "markdown", - "id": "10", + "id": "11", "metadata": {}, "source": [ "When the above code is executed, you should expect to see something like this:\n", @@ -242,10 +250,10 @@ }, { "cell_type": "markdown", - "id": "11", + "id": "12", "metadata": {}, "source": [ - "### Configuring the Simulation\n", + "## Configuring the Simulation\n", "\n", "All OpenMM jobs, i.e. anything in `atomate2.openmm.jobs`, inherits from the `BaseOpenMMMaker` class. `BaseOpenMMMaker` is highly configurable, you can change the timestep, temperature, reporting frequencies, output types, and a range of other properties. See the docstring for the full list of options.\n", "\n", @@ -255,7 +263,7 @@ { "cell_type": "code", "execution_count": null, - "id": "12", + "id": "13", "metadata": {}, "outputs": [], "source": [ @@ -266,7 +274,7 @@ }, { "cell_type": "markdown", - "id": "13", + "id": "14", "metadata": {}, "source": [ "Perhaps we want to record a trajectory with velocities but only for the final NVT run. " @@ -274,10 +282,10 @@ }, { "cell_type": "markdown", - "id": "14", + "id": "15", "metadata": {}, "source": [ - "### Running with Databases\n", + "## Running with Databases\n", "\n", "Before trying this, you should have a basic understanding of JobFlow and [Stores](https://materialsproject.github.io/jobflow/stores.html).\n", "\n", @@ -363,10 +371,10 @@ }, { "cell_type": "markdown", - "id": "15", + "id": "16", "metadata": {}, "source": [ - "### Running on GPU(s)\n", + "## Running on GPU(s)\n", "\n", "Running on a GPU is nearly as simple as running on a CPU. The only difference is that you need to specify the `platform_properties` argument in the `EnergyMinimizationMaker` with the `DeviceIndex` of the GPU you want to use." ] @@ -374,7 +382,7 @@ { "cell_type": "code", "execution_count": null, - "id": "16", + "id": "17", "metadata": {}, "outputs": [], "source": [ @@ -394,7 +402,7 @@ }, { "cell_type": "markdown", - "id": "17", + "id": "18", "metadata": {}, "source": [ "To run on a system with multiple GPUs, the 'DeviceIndex' can be changed to a different number for each job." diff --git a/tutorials/phonon_workflow.ipynb b/tutorials/phonon_workflow.ipynb index f4186583c2..16608d1999 100644 --- a/tutorials/phonon_workflow.ipynb +++ b/tutorials/phonon_workflow.ipynb @@ -31,11 +31,11 @@ "id": "2", "metadata": {}, "source": [ - "# Phonon Workflow" + "# Phonon Workflow Tutorial with VASP" ] }, { - "cell_type": "raw", + "cell_type": "markdown", "id": "3", "metadata": {}, "source": [ diff --git a/tutorials/qha_workflow.ipynb b/tutorials/qha_workflow.ipynb new file mode 100644 index 0000000000..7cfd64db2b --- /dev/null +++ b/tutorials/qha_workflow.ipynb @@ -0,0 +1,387 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Quasi-harmonic Workflow Tutorial with VASP" + ] + }, + { + "cell_type": "markdown", + "id": "1", + "metadata": {}, + "source": [ + "This first part is only needed as we have to mock VASP here as we cannot run it directly in a jupyter notebook:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "from mock_vasp import TEST_DIR, mock_vasp\n", + "\n", + "ref_paths = {\n", + " \"phonon static 1/1\": \"Si_qha_2/phonon_static_1_1\",\n", + " \"static\": \"Si_qha_2/static\",\n", + " \"tight relax 1 EOS equilibrium relaxation\": \"Si_qha_2/tight_relax_1\",\n", + " \"tight relax 2 EOS equilibrium relaxation\": \"Si_qha_2/tight_relax_2\",\n", + " \"tight relax 1 deformation 0\": \"Si_qha_2/tight_relax_1_d0\",\n", + " \"tight relax 1 deformation 1\": \"Si_qha_2/tight_relax_1_d1\",\n", + " \"tight relax 1 deformation 2\": \"Si_qha_2/tight_relax_1_d2\",\n", + " \"tight relax 1 deformation 3\": \"Si_qha_2/tight_relax_1_d3\",\n", + " \"tight relax 1 deformation 4\": \"Si_qha_2/tight_relax_1_d4\",\n", + " \"tight relax 1 deformation 5\": \"Si_qha_2/tight_relax_1_d5\",\n", + " \"tight relax 2 deformation 0\": \"Si_qha_2/tight_relax_2_d0\",\n", + " \"tight relax 2 deformation 1\": \"Si_qha_2/tight_relax_2_d1\",\n", + " \"tight relax 2 deformation 2\": \"Si_qha_2/tight_relax_2_d2\",\n", + " \"tight relax 2 deformation 3\": \"Si_qha_2/tight_relax_2_d3\",\n", + " \"tight relax 2 deformation 4\": \"Si_qha_2/tight_relax_2_d4\",\n", + " \"tight relax 2 deformation 5\": \"Si_qha_2/tight_relax_2_d5\",\n", + " \"dft phonon static eos deformation 1\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_1\",\n", + " \"dft phonon static eos deformation 2\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_2\",\n", + " \"dft phonon static eos deformation 3\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_3\",\n", + " \"dft phonon static eos deformation 4\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_4\",\n", + " \"dft phonon static eos deformation 5\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_5\",\n", + " \"dft phonon static eos deformation 6\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_6\",\n", + " \"dft phonon static eos deformation 7\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_eos_deformation_7\",\n", + " \"dft phonon static 1/1 eos deformation 1\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_1\",\n", + " \"dft phonon static 1/1 eos deformation 2\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_2\",\n", + " \"dft phonon static 1/1 eos deformation 3\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_3\",\n", + " \"dft phonon static 1/1 eos deformation 4\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_4\",\n", + " \"dft phonon static 1/1 eos deformation 5\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_5\",\n", + " \"dft phonon static 1/1 eos deformation 6\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_6\",\n", + " \"dft phonon static 1/1 eos deformation 7\": \"Si_qha_2/\"\n", + " \"dft_phonon_static_1_1_eos_deformation_7\",\n", + "}" + ] + }, + { + "cell_type": "markdown", + "id": "3", + "metadata": {}, + "source": [ + "This tutorial will make use of a quasi-harmonic workflow\n", + " that allows to include volume-dependent anharmonicity \n", + " into the calculation of phonon free energies.\n", + " Please check out the paper by Togo to learn about the\n", + "exact implementation as we will rely on Phonopy to perform the quasi-harmonic approximation.\n", + " https://doi.org/10.7566/JPSJ.92.012001.\n", + " At the moment, we perform harmonic free\n", + " energy calculation along a volume curve\n", + " to arrive at free energy-volume curves\n", + " that are the starting point for the q\n", + " uasi-harmonic approximation." + ] + }, + { + "cell_type": "markdown", + "id": "4", + "metadata": {}, + "source": [ + "## Let's run the workflow\n", + "Now, we load a structure and other important functions and classes for running the qha workflow." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": {}, + "outputs": [], + "source": [ + "from jobflow import JobStore, run_locally\n", + "from maggma.stores import MemoryStore\n", + "from pymatgen.core import Structure\n", + "\n", + "from atomate2.vasp.flows.qha import QhaMaker\n", + "\n", + "job_store = JobStore(MemoryStore(), additional_stores={\"data\": MemoryStore()})\n", + "si_structure = Structure.from_file(TEST_DIR / \"structures\" / \"Si_diamond.cif\")" + ] + }, + { + "cell_type": "markdown", + "id": "6", + "metadata": {}, + "source": [ + "Then one can use the `QhaMaker` to generate a `Flow`.\n", + "First, the structure will be optimized than the\n", + "structures will be optimized at constant volume\n", + "along an energy volume curve. Please make sure the structural optimizations are tight enough. At each of these\n", + "volumes, a phonon run will then be performed.\n", + "The quasi-harmonic approximation is only valid\n", + "if the harmonic phonon curves don't show any\n", + "imaginary modes. However, for testing, you\n", + "can also switch off this option." + ] + }, + { + "cell_type": "markdown", + "id": "7", + "metadata": {}, + "source": [ + "Before we start the quasi-harmonic workflow,\n", + "we adapt the first relaxation, the relaxation\n", + "with different volumes and the static runs for\n", + "the phonon calculation. As we deal with Si,\n", + "we will not add the non-analytical term correction." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8", + "metadata": {}, + "outputs": [], + "source": [ + "from atomate2.vasp.flows.core import DoubleRelaxMaker\n", + "from atomate2.vasp.flows.phonons import PhononMaker\n", + "from atomate2.vasp.jobs.core import TightRelaxMaker\n", + "from atomate2.vasp.jobs.phonons import PhononDisplacementMaker\n", + "from atomate2.vasp.sets.core import StaticSetGenerator, TightRelaxSetGenerator\n", + "\n", + "phonon_bulk_relax_maker_isif3 = DoubleRelaxMaker.from_relax_maker(\n", + " TightRelaxMaker(\n", + " run_vasp_kwargs={\"handlers\": ()},\n", + " input_set_generator=TightRelaxSetGenerator(\n", + " user_incar_settings={\n", + " \"GGA\": \"PE\",\n", + " \"ISPIN\": 1,\n", + " \"KSPACING\": 0.1,\n", + " # \"EDIFFG\": 1e-5,\n", + " \"ALGO\": \"Normal\",\n", + " \"LAECHG\": False,\n", + " \"ISMEAR\": 0,\n", + " \"ENCUT\": 700,\n", + " \"IBRION\": 1,\n", + " \"ISYM\": 0,\n", + " \"SIGMA\": 0.05,\n", + " \"LCHARG\": False,\n", + " \"LWAVE\": False,\n", + " \"LVTOT\": False,\n", + " \"LORBIT\": None,\n", + " \"LOPTICS\": False,\n", + " \"LREAL\": False,\n", + " \"ISIF\": 3,\n", + " \"NPAR\": 4,\n", + " }\n", + " ),\n", + " )\n", + ")\n", + "\n", + "phonon_displacement_maker = PhononDisplacementMaker(\n", + " run_vasp_kwargs={\"handlers\": ()},\n", + " input_set_generator=StaticSetGenerator(\n", + " user_incar_settings={\n", + " \"GGA\": \"PE\",\n", + " \"IBRION\": -1,\n", + " \"ISPIN\": 1,\n", + " \"ISMEAR\": 0,\n", + " \"ISIF\": 3,\n", + " \"ENCUT\": 700,\n", + " \"EDIFF\": 1e-7,\n", + " \"LAECHG\": False,\n", + " \"LREAL\": False,\n", + " \"ALGO\": \"Normal\",\n", + " \"NSW\": 0,\n", + " \"LCHARG\": False,\n", + " \"LWAVE\": False,\n", + " \"LVTOT\": False,\n", + " \"LORBIT\": None,\n", + " \"LOPTICS\": False,\n", + " \"SIGMA\": 0.05,\n", + " \"ISYM\": 0,\n", + " \"KSPACING\": 0.1,\n", + " \"NPAR\": 4,\n", + " },\n", + " auto_ispin=False,\n", + " ),\n", + ")\n", + "\n", + "\n", + "phonon_bulk_relax_maker_isif4 = DoubleRelaxMaker.from_relax_maker(\n", + " TightRelaxMaker(\n", + " run_vasp_kwargs={\"handlers\": ()},\n", + " input_set_generator=TightRelaxSetGenerator(\n", + " user_incar_settings={\n", + " \"GGA\": \"PE\",\n", + " \"ISPIN\": 1,\n", + " \"KSPACING\": 0.1,\n", + " \"ALGO\": \"Normal\",\n", + " \"LAECHG\": False,\n", + " \"ISMEAR\": 0,\n", + " \"ENCUT\": 700,\n", + " \"IBRION\": 1,\n", + " \"ISYM\": 0,\n", + " \"SIGMA\": 0.05,\n", + " \"LCHARG\": False,\n", + " \"LWAVE\": False,\n", + " \"LVTOT\": False,\n", + " \"LORBIT\": None,\n", + " \"LOPTICS\": False,\n", + " \"LREAL\": False,\n", + " \"ISIF\": 4,\n", + " \"NPAR\": 4,\n", + " }\n", + " ),\n", + " )\n", + ")\n", + "\n", + "phonon_displacement_maker.name = \"dft phonon static\"" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9", + "metadata": {}, + "outputs": [], + "source": [ + "flow = QhaMaker(\n", + " initial_relax_maker=phonon_bulk_relax_maker_isif3,\n", + " eos_relax_maker=phonon_bulk_relax_maker_isif4,\n", + " min_length=10,\n", + " phonon_maker=PhononMaker(\n", + " generate_frequencies_eigenvectors_kwargs={\n", + " \"tmin\": 0,\n", + " \"tmax\": 1000,\n", + " \"tstep\": 10,\n", + " },\n", + " bulk_relax_maker=None,\n", + " born_maker=None,\n", + " static_energy_maker=phonon_displacement_maker,\n", + " phonon_displacement_maker=phonon_displacement_maker,\n", + " ),\n", + " linear_strain=(-0.15, 0.15),\n", + " number_of_frames=6,\n", + " pressure=None,\n", + " t_max=None,\n", + " ignore_imaginary_modes=False,\n", + " skip_analysis=False,\n", + " eos_type=\"vinet\",\n", + ").make(structure=si_structure)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "10", + "metadata": { + "jupyter": { + "is_executing": true + } + }, + "outputs": [], + "source": [ + "with mock_vasp(ref_paths=ref_paths) as mf:\n", + " run_locally(\n", + " flow,\n", + " create_folders=True,\n", + " ensure_success=True,\n", + " raise_immediately=True,\n", + " store=job_store,\n", + " )" + ] + }, + { + "cell_type": "markdown", + "id": "11", + "metadata": {}, + "source": [ + "## Let's retrieve the data and analyze it" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "12", + "metadata": {}, + "outputs": [], + "source": [ + "job_store.connect()\n", + "\n", + "result = job_store.query_one(\n", + " {\"name\": \"analyze_free_energy\"},\n", + " properties=[\n", + " \"output.helmholtz_volume\",\n", + " \"output.temperatures\",\n", + " \"output.volumes\",\n", + " ],\n", + " load=True,\n", + " sort={\"completed_at\": -1}, # to get the latest computation\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "13", + "metadata": {}, + "source": [ + "You can then plot some of the output free energy volume curves" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "14", + "metadata": {}, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "\n", + "for temp, energy_list in zip(\n", + " result[\"output\"][\"temperatures\"],\n", + " result[\"output\"][\"helmholtz_volume\"],\n", + " strict=False,\n", + "):\n", + " # Create the plot\n", + " plt.plot(\n", + " result[\"output\"][\"volumes\"],\n", + " energy_list,\n", + " marker=\"o\",\n", + " label=temp,\n", + " )\n", + " # Add labels and title\n", + "plt.xlabel(\"Volume\")\n", + "plt.ylabel(\"Free Energy\")\n", + "\n", + "# Show the plot\n", + "plt.show()" + ] + } + ], + "metadata": { + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/tutorials/tutorials.md b/tutorials/tutorials.md new file mode 100644 index 0000000000..6f3b61d53f --- /dev/null +++ b/tutorials/tutorials.md @@ -0,0 +1,16 @@ +(tutorials)= +[comment]: # This file will be copied to the docs to help including the tutorials +# Tutorials + +The section includes tutorials for workflows in atomate2. +They can also be found in the form of jupyternotebooks in: +[https://github.com/materialsproject/atomate2/tree/main/tutorials](https://github.com/materialsproject/atomate2/tree/main/tutorials) + +```{toctree} +blob_storage +lobster_workflow +openmm_tutorial +phonon_workflow +qha_workflow +force_fields/phonon_workflow +```