From a79cf7fa2d98bae9ed02830022549de0584561f0 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Feb 2024 00:02:26 +0000 Subject: [PATCH 01/27] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 24.1.1 → 24.2.0](https://github.com/psf/black/compare/24.1.1...24.2.0) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1753282e..838f3470 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 24.1.1 + rev: 24.2.0 hooks: - id: black From 8595601263ffbd0eebee94e518485055e2576a81 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Feb 2024 00:02:33 +0000 Subject: [PATCH 02/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- apax/data/input_pipeline.py | 14 ++-- apax/train/trainer.py | 10 +-- apax/utils/jax_md_reduced/partition.py | 2 +- tests/conftest.py | 12 ++-- tests/integration_tests/md/test_md.py | 12 ++-- tests/unit_tests/model/test_apax.py | 94 +++++++++++++++----------- tests/unit_tests/train/test_loss.py | 88 +++++++++++++++--------- tests/unit_tests/train/test_metrics.py | 44 +++++++----- 8 files changed, 167 insertions(+), 109 deletions(-) diff --git a/apax/data/input_pipeline.py b/apax/data/input_pipeline.py index 6832c587..3e53fa33 100644 --- a/apax/data/input_pipeline.py +++ b/apax/data/input_pipeline.py @@ -134,12 +134,14 @@ def dataset_from_dicts( for key, val in labels["fixed"].items(): labels["fixed"][key] = tf.constant(val) - ds = tf.data.Dataset.from_tensor_slices(( - inputs["ragged"], - inputs["fixed"], - labels["ragged"], - labels["fixed"], - )) + ds = tf.data.Dataset.from_tensor_slices( + ( + inputs["ragged"], + inputs["fixed"], + labels["ragged"], + labels["fixed"], + ) + ) return ds diff --git a/apax/train/trainer.py b/apax/train/trainer.py index 0c96277b..684203eb 100644 --- a/apax/train/trainer.py +++ b/apax/train/trainer.py @@ -109,10 +109,12 @@ def fit( epoch_loss["val_loss"] /= val_steps_per_epoch epoch_loss["val_loss"] = float(epoch_loss["val_loss"]) - epoch_metrics.update({ - f"val_{key}": float(val) - for key, val in val_batch_metrics.compute().items() - }) + epoch_metrics.update( + { + f"val_{key}": float(val) + for key, val in val_batch_metrics.compute().items() + } + ) epoch_metrics.update({**epoch_loss}) diff --git a/apax/utils/jax_md_reduced/partition.py b/apax/utils/jax_md_reduced/partition.py index 0f799160..52e156e5 100644 --- a/apax/utils/jax_md_reduced/partition.py +++ b/apax/utils/jax_md_reduced/partition.py @@ -281,7 +281,7 @@ def neighbor_fn(position_and_error, max_occupancy=None): if not is_sparse(format): capacity_limit = N - 1 if mask_self else N elif format is NeighborListFormat.Sparse: - capacity_limit = N * (N - 1) if mask_self else N ** 2 + capacity_limit = N * (N - 1) if mask_self else N**2 else: capacity_limit = N * (N - 1) // 2 if max_occupancy > capacity_limit: diff --git a/tests/conftest.py b/tests/conftest.py index 599817ce..734a9ff5 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -143,11 +143,13 @@ def modify_xyz_file(file_path, target_string, replacement_string): @pytest.fixture() def get_sample_input(): - positions = np.array([ - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - [0.0, 0.0, 1.0], - ]) + positions = np.array( + [ + [1.0, 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 1.0], + ] + ) atomic_numbers = np.array([1, 1, 8]) box = np.diag(np.zeros(3)) offsets = np.full([3, 3], 0) diff --git a/tests/integration_tests/md/test_md.py b/tests/integration_tests/md/test_md.py index b04216d3..ce1a3893 100644 --- a/tests/integration_tests/md/test_md.py +++ b/tests/integration_tests/md/test_md.py @@ -115,11 +115,13 @@ def test_ase_calc(get_tmp_path): model_config.dump_config(model_config.data.model_version_path) cell_size = 10.0 - positions = np.array([ - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - [0.0, 0.0, 1.0], - ]) + positions = np.array( + [ + [1.0, 0.0, 0.0], + [0.0, 1.0, 0.0], + [0.0, 0.0, 1.0], + ] + ) atomic_numbers = np.array([1, 1, 8]) box = np.diag([cell_size] * 3) offsets = jnp.full([3, 3], 0) diff --git a/tests/unit_tests/model/test_apax.py b/tests/unit_tests/model/test_apax.py index 51d5cd11..67f28751 100644 --- a/tests/unit_tests/model/test_apax.py +++ b/tests/unit_tests/model/test_apax.py @@ -8,18 +8,22 @@ def test_apax_variable_size(): - R = np.array([ - [0.0, 0.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ]) + R = np.array( + [ + [0.0, 0.0, 0.0], + [1.0, 0.0, 0.0], + [0.0, 1.0, 0.0], + ] + ) Z = np.array([1, 2, 2]) - idx = np.array([ - [1, 2, 0, 2, 0, 1], - [0, 0, 1, 1, 2, 2], - ]) + idx = np.array( + [ + [1, 2, 0, 2, 0, 1], + [0, 0, 1, 1, 2, 2], + ] + ) offsets = jnp.full([6, 3], 0) box = np.array([0, 0, 0]) @@ -65,20 +69,24 @@ def test_apax_variable_size(): def test_atomistic_model(): key = jax.random.PRNGKey(0) - dR = np.array([ - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - [-1.0, 0.0, 0.0], - [-1.0, 1.0, 0.0], - [0.0, -1.0, 0.0], - [1.0, -1.0, 0.0], - ]) + dR = np.array( + [ + [1.0, 0.0, 0.0], + [0.0, 1.0, 0.0], + [-1.0, 0.0, 0.0], + [-1.0, 1.0, 0.0], + [0.0, -1.0, 0.0], + [1.0, -1.0, 0.0], + ] + ) Z = np.array([1, 2, 2]) - idx = np.array([ - [1, 2, 0, 2, 0, 1], - [0, 0, 1, 1, 2, 2], - ]) + idx = np.array( + [ + [1, 2, 0, 2, 0, 1], + [0, 0, 1, 1, 2, 2], + ] + ) model = AtomisticModel(mask_atoms=False) @@ -91,18 +99,22 @@ def test_atomistic_model(): def test_energy_model(): key = jax.random.PRNGKey(0) - R = np.array([ - [0.0, 0.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ]) + R = np.array( + [ + [0.0, 0.0, 0.0], + [1.0, 0.0, 0.0], + [0.0, 1.0, 0.0], + ] + ) Z = np.array([1, 2, 2]) - idx = np.array([ - [1, 2, 0, 2, 0, 1], - [0, 0, 1, 1, 2, 2], - ]) + idx = np.array( + [ + [1, 2, 0, 2, 0, 1], + [0, 0, 1, 1, 2, 2], + ] + ) offsets = jnp.full([6, 3], 0) box = np.array([0.0, 0.0, 0.0]) @@ -117,18 +129,22 @@ def test_energy_model(): def test_energy_force_model(): key = jax.random.PRNGKey(0) - R = np.array([ - [0.0, 0.0, 0.0], - [1.0, 0.0, 0.0], - [0.0, 1.0, 0.0], - ]) + R = np.array( + [ + [0.0, 0.0, 0.0], + [1.0, 0.0, 0.0], + [0.0, 1.0, 0.0], + ] + ) Z = np.array([1, 2, 2]) - idx = np.array([ - [1, 2, 0, 2, 0, 1], - [0, 0, 1, 1, 2, 2], - ]) + idx = np.array( + [ + [1, 2, 0, 2, 0, 1], + [0, 0, 1, 1, 2, 2], + ] + ) offsets = jnp.full([6, 3], 0) box = np.array([0.0, 0.0, 0.0]) diff --git a/tests/unit_tests/train/test_loss.py b/tests/unit_tests/train/test_loss.py index 26c18bc1..0d300c65 100644 --- a/tests/unit_tests/train/test_loss.py +++ b/tests/unit_tests/train/test_loss.py @@ -19,10 +19,12 @@ def test_weighted_squared_error(): assert loss.shape == () assert abs(loss - ref) < 1e-6 - pred = jnp.array([ - [0.6, 0.4, 0.2, -0.5], - [0.1, -0.1, 0.8, 0.6], - ]) + pred = jnp.array( + [ + [0.6, 0.4, 0.2, -0.5], + [0.1, -0.1, 0.8, 0.6], + ] + ) loss = weighted_squared_error(energy_label, pred, divisor=1.0) loss = jnp.sum(loss) ref = 0.25 @@ -35,23 +37,31 @@ def test_weighted_squared_error(): def test_force_angle_loss(): - F_pred = jnp.array([[ - [0.5, 0.0, 0.0], - [0.5, 0.0, 0.0], - [0.5, 0.5, 0.0], - [0.0, 0.5, 0.0], - [0.0, 0.5, 0.0], - [0.0, 0.0, 0.0], # padding - ]]) - - F_0 = jnp.array([[ - [0.5, 0.0, 0.0], - [0.9, 0.0, 0.0], - [0.5, 0.0, 0.0], - [0.5, 0.0, 0.0], - [0.9, 0.0, 0.0], - [0.0, 0.0, 0.0], # padding - ]]) + F_pred = jnp.array( + [ + [ + [0.5, 0.0, 0.0], + [0.5, 0.0, 0.0], + [0.5, 0.5, 0.0], + [0.0, 0.5, 0.0], + [0.0, 0.5, 0.0], + [0.0, 0.0, 0.0], # padding + ] + ] + ) + + F_0 = jnp.array( + [ + [ + [0.5, 0.0, 0.0], + [0.9, 0.0, 0.0], + [0.5, 0.0, 0.0], + [0.5, 0.0, 0.0], + [0.9, 0.0, 0.0], + [0.0, 0.0, 0.0], # padding + ] + ] + ) F_angle_loss = force_angle_loss(F_pred, F_0) F_angle_loss = jnp.arccos(-F_angle_loss + 1) * 360 / (2 * np.pi) @@ -74,17 +84,25 @@ def test_force_loss(): "n_atoms": jnp.array([2]), } label = { - name: jnp.array([[ - [0.4, 0.2, 0.5], - [0.3, 0.8, 0.1], - ]]), + name: jnp.array( + [ + [ + [0.4, 0.2, 0.5], + [0.3, 0.8, 0.1], + ] + ] + ), } pred = { - name: jnp.array([[ - [0.4, 0.2, 0.5], - [0.3, 0.8, 0.1], - ]]), + name: jnp.array( + [ + [ + [0.4, 0.2, 0.5], + [0.3, 0.8, 0.1], + ] + ] + ), } loss_func = Loss(name=name, loss_type=loss_type, weight=weight) loss = loss_func(inputs=inputs, label=label, prediction=pred) @@ -93,10 +111,14 @@ def test_force_loss(): assert abs(loss - ref_loss) < 1e-6 pred = { - name: jnp.array([[ - [0.4, 0.2, 0.5], - [0.3, 0.8, 0.6], - ]]), + name: jnp.array( + [ + [ + [0.4, 0.2, 0.5], + [0.3, 0.8, 0.6], + ] + ] + ), } loss_func = Loss(name=name, loss_type=loss_type, weight=weight) loss = loss_func(inputs=inputs, label=label, prediction=pred) diff --git a/tests/unit_tests/train/test_metrics.py b/tests/unit_tests/train/test_metrics.py index 66381e4f..2e2de005 100644 --- a/tests/unit_tests/train/test_metrics.py +++ b/tests/unit_tests/train/test_metrics.py @@ -6,17 +6,25 @@ def test_cosine_sim(): prediction = { - "forces": jnp.array([[ - [0.5, 0.0, 0.0], - [0.5, 0.0, 0.0], - ]]) + "forces": jnp.array( + [ + [ + [0.5, 0.0, 0.0], + [0.5, 0.0, 0.0], + ] + ] + ) } label = { - "forces": jnp.array([[ - [0.0, 0.5, 0.0], - [0.5, 0.0, 0.0], - ]]) + "forces": jnp.array( + [ + [ + [0.0, 0.5, 0.0], + [0.5, 0.0, 0.0], + ] + ] + ) } angle_error = cosine_sim(label, prediction, "forces") @@ -28,18 +36,22 @@ def test_cosine_sim(): def test_initialize_metrics_collection(): prediction = { "energy": jnp.array([1.0, 1.0]), - "forces": jnp.array([ - [[1.0, 0.0, 0.0], [1.0, 0.0, 0.0]], - [[1.0, 0.0, 0.0], [1.0, 0.0, 0.0]], - ]), + "forces": jnp.array( + [ + [[1.0, 0.0, 0.0], [1.0, 0.0, 0.0]], + [[1.0, 0.0, 0.0], [1.0, 0.0, 0.0]], + ] + ), } label = { "energy": jnp.array([1.0, 2.0]), - "forces": jnp.array([ - [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], - [[1.0, 0.0, 0.0], [2.0, 1.0, 0.0]], - ]), + "forces": jnp.array( + [ + [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], + [[1.0, 0.0, 0.0], [2.0, 1.0, 0.0]], + ] + ), } metrics_list = [ MetricsConfig(name="energy", reductions=["mae", "rmse"]), From 0e9fd78ec08b7ee4387a44c1c4e1a1cf67a5902b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 18 Mar 2024 22:07:42 +0000 Subject: [PATCH 03/27] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 838f3470..11bb3eba 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: - id: trailing-whitespace - repo: https://github.com/psf/black - rev: 24.2.0 + rev: 24.3.0 hooks: - id: black From 75afe9d5ad383a3d84a1503b9eef7181017ca424 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Wed, 3 Apr 2024 14:32:50 +0200 Subject: [PATCH 04/27] initial Node draft --- .github/workflows/pytest.yaml | 2 +- apax/nodes/__init__.py | 0 apax/nodes/bal.py | 98 ++ apax/nodes/md.py | 107 ++ apax/nodes/model.py | 172 +++ apax/nodes/utils.py | 80 ++ poetry.lock | 1896 ++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 8 files changed, 2343 insertions(+), 13 deletions(-) create mode 100644 apax/nodes/__init__.py create mode 100644 apax/nodes/bal.py create mode 100644 apax/nodes/md.py create mode 100644 apax/nodes/model.py create mode 100644 apax/nodes/utils.py diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml index bc45eb79..a72b0b1d 100644 --- a/.github/workflows/pytest.yaml +++ b/.github/workflows/pytest.yaml @@ -24,7 +24,7 @@ jobs: - name: Install package run: | poetry --version - poetry install + poetry install --all-extras - name: Unit Tests run: | diff --git a/apax/nodes/__init__.py b/apax/nodes/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/apax/nodes/bal.py b/apax/nodes/bal.py new file mode 100644 index 00000000..b40ccd0b --- /dev/null +++ b/apax/nodes/bal.py @@ -0,0 +1,98 @@ +import zntrack +import ase +import numpy as np +import matplotlib.pyplot as plt +from .utils import get_flat_data_from_dict, plot_with_uncertainty +import znflow + +from apax.bal import kernel_selection + +class BatchKernelSelection(zntrack.Node): + """Interface to the batch active learning methods implemented in apax. + Check the apax documentation for a list and explanation of implemented properties. + + Attributes + ---------- + models: Union[Apax, List[Apax]] + One or more Apax models to construct a feature map from. + base_feature_map: dict + Name and parameters for the feature map transformation. + selection_method: str + Name of the selection method to be used. Choose from: + ["max_dist", ] + n_configurations: int + Number of samples to be selected. + processing_batch_size: int + Number of samples to be processed in parallel. + Does not affect the result, just the speed of computing features. + """ + + models: list = zntrack.deps() + base_feature_map: dict = zntrack.params({"name": "ll_grad", "layer_name": "dense_2"}) + selection_method: str = zntrack.params("max_dist") + n_configurations: str = zntrack.params() + processing_batch_size: str = zntrack.meta.Text(64) + img_selection = zntrack.outs_path(zntrack.nwd / "selection.png") + + train_data: list[ase.Atoms] = zntrack.deps() + + def _post_init_(self): + if self.train_data is not None and not isinstance(self.train_data, dict): + try: + self.train_data = znflow.combine( + self.train_data, attribute="atoms", return_dict_attr="name" + ) + except TypeError: + self.train_data = znflow.combine(self.train_data, attribute="atoms") + + if self.data is not None and not isinstance(self.data, dict): + try: + self.data = znflow.combine( + self.data, attribute="atoms", return_dict_attr="name" + ) + except TypeError: + self.data = znflow.combine(self.data, attribute="atoms") + + def select_atoms(self, atoms_lst: list[ase.Atoms]) -> list[int]: + if isinstance(self.models, list): + param_files = [m._parameter["data"]["directory"] for m in self.models] + else: + param_files = self.models._parameter["data"]["directory"] + + if isinstance(self.train_data, dict): + self.train_data = get_flat_data_from_dict(self.train_data) + + selected = kernel_selection( + param_files, + self.train_data, + atoms_lst, + self.base_feature_map, + self.selection_method, + selection_batch_size=self.n_configurations, + processing_batch_size=self.processing_batch_size, + ) + self._get_plot(atoms_lst, selected) + + return list(selected) + + def _get_plot(self, atoms_lst: list[ase.Atoms], indices: list[int]): + energies = np.array([atoms.calc.results["energy"] for atoms in atoms_lst]) + + if "energy_uncertainty" in atoms_lst[0].calc.results.keys(): + uncertainty = np.array( + [atoms.calc.results["energy_uncertainty"] for atoms in atoms_lst] + ) + fig, ax, _ = plot_with_uncertainty( + {"mean": energies, "std": uncertainty}, + ylabel="energy", + xlabel="configuration", + ) + else: + fig, ax = plt.subplots() + ax.plot(energies, label="energy") + ax.set_ylabel("energy") + ax.set_xlabel("configuration") + + ax.plot(indices, energies[indices], "x", color="red") + + fig.savefig(self.img_selection, bbox_inches="tight") \ No newline at end of file diff --git a/apax/nodes/md.py b/apax/nodes/md.py new file mode 100644 index 00000000..2ca833d1 --- /dev/null +++ b/apax/nodes/md.py @@ -0,0 +1,107 @@ +import functools +import logging +import pathlib +import typing + +import ase.io +import h5py +import yaml +import znh5md +import zntrack.utils +from zntrack import dvc, zn + +from .utils import check_duplicate_keys +from .model import Apax + +log = logging.getLogger(__name__) + + +class ApaxJaxMD(zntrack.Node): + """Class to run a more performant JaxMD simulation with a apax Model. + + Attributes + ---------- + model: ApaxModel + model to use for the simulation + repeat: float + number of repeats + md_parameter: dict + parameter for the MD simulation + md_parameter_file: str + path to the MD simulation parameter file + """ + + model: Apax = zntrack.deps() + repeat = zn.params(None) + + md_parameter: dict = zn.params(None) + md_parameter_file: str = dvc.params(None) + + sim_dir: pathlib.Path = dvc.outs(zntrack.nwd / "md") + init_struc_dir: pathlib.Path = dvc.outs(zntrack.nwd / "initial_structure.extxyz") + + # def post_init(self): + # if not self.state.loaded: + # dict_supplied = self.md_parameter is None + # file_supplied = self.md_parameter_file is None + + # if dict_supplied and file_supplied: + # raise TypeError("Please specify either an input dict or a file") + # elif not dict_supplied and not file_supplied: + # raise TypeError( + # "Can not train apax model without a parameter dict or file" + # ) + # else: + # log.info( + # "Please keep track of the parameter file with git, just like the" + # " params.yaml" + # ) + + # if not isinstance(self.model, Apax): + # raise TypeError( + # "Performing simulations with JaxMD requires a apax model Node" + # ) + + # self.data = utils.helpers.get_deps_if_node(self.data, "atoms") + + def _post_load_(self) -> None: + self._handle_parameter_file() + + def _handle_parameter_file(self): + if self.md_parameter_file: + md_parameter_file_content = pathlib.Path(self.md_parameter_file).read_text() + self.md_parameter = yaml.safe_load(md_parameter_file_content) + + custom_parameters = { + "sim_dir": self.sim_dir.as_posix(), + "initial_structure": self.init_struc_dir.as_posix(), + } + check_duplicate_keys(custom_parameters, self.md_parameter, log) + self.md_parameter.update(custom_parameters) + + def run(self): + """Primary method to run which executes all steps of the model training""" + from apax.md.nvt import run_md + + # self._handle_parameter_file() + atoms = self.get_data() + if self.repeat is not None: + atoms = atoms.repeat(self.repeat) + ase.io.write(self.init_struc_dir.as_posix(), atoms) + + self.model._handle_parameter_file() + run_md(self.model._parameter, self.md_parameter) + + @functools.cached_property + def atoms(self) -> typing.List[ase.Atoms]: + # filename should be changeable + def file_handle(filename): + file = self.state.fs.open(filename, "rb") + return h5py.File(file) + + return znh5md.ASEH5MD( + self.sim_dir / "md.h5", + format_handler=functools.partial( + znh5md.FormatHandler, file_handle=file_handle + ), + ).get_atoms_list() \ No newline at end of file diff --git a/apax/nodes/model.py b/apax/nodes/model.py new file mode 100644 index 00000000..b9040ecd --- /dev/null +++ b/apax/nodes/model.py @@ -0,0 +1,172 @@ +import logging +import pathlib +import shutil +import typing as t +from typing import Optional + +import ase.io +import numpy as np +import pandas as pd +import yaml +import zntrack.utils + +from apax.md import ASECalculator +from apax.md.function_transformations import available_transformations +from apax.train.run import run as apax_run +from jax import config +from matplotlib import pyplot as plt +from zntrack import dvc, zn + +from .utils import check_duplicate_keys + +log = logging.getLogger(__name__) + + +class Apax(zntrack.Node): + """Class for the implementation of the apax model + + Attributes + ---------- + config: str + path to the apax config file + validation_data: ase.Atoms + atoms object with the validation data set + model_directory: pathlib.Path + model directory + train_data_file: pathlib.Path + path to the training data + validation_data_file: pathlib.Path + path to the valdidation data + """ + + config: str = dvc.params("apax.yaml") + validation_data = zntrack.deps() + model: Optional[t.Any] = zntrack.deps(None) + + model_directory: pathlib.Path = dvc.outs(zntrack.nwd / "apax_model") + + train_data_file: pathlib.Path = dvc.outs(zntrack.nwd / "train_atoms.extxyz") + validation_data_file: pathlib.Path = dvc.outs(zntrack.nwd / "val_atoms.extxyz") + + jax_enable_x64: bool = zn.params(True) + + metrics_epoch = dvc.plots( + zntrack.nwd / "log.csv", + # template=STATIC_PATH / "y_log.json", + # x="epoch", + # x_label="epochs", + # y="val_loss", + # y_label="validation loss", + ) + metrics = zn.metrics() + + _parameter: dict = None + + # def _post_init_(self): + # self.data = utils.helpers.get_deps_if_node(self.data, "atoms") + # self.validation_data = utils.helpers.get_deps_if_node( + # self.validation_data, "atoms" + # ) + # self._handle_parameter_file() + + def _post_load_(self) -> None: + self._handle_parameter_file() + + def _handle_parameter_file(self): + with self.state.use_tmp_path(): + self._parameter = yaml.safe_load(pathlib.Path(self.config).read_text()) + + custom_parameters = { + "directory": self.model_directory.resolve().as_posix(), + "experiment": "", + "train_data_path": self.train_data_file.as_posix(), + "val_data_path": self.validation_data_file.as_posix(), + } + + if self.model is not None: + param_files = self.model._parameter["data"]["directory"] + base_path = {"base_model_checkpoint": param_files} + try: + self._parameter["checkpoints"].update(base_path) + except KeyError: + self._parameter["checkpoints"] = base_path + + check_duplicate_keys(custom_parameters, self._parameter["data"], log) + self._parameter["data"].update(custom_parameters) + + def train_model(self): + """Train the model using `apax.train.run`""" + apax_run(self._parameter) + + def move_metrics(self): + """Move the metrics to the correct directories for DVC""" + path = self.model_directory / self.metrics_epoch.name + shutil.move(path, self.metrics_epoch) + + def get_metrics_from_plots(self): + """In addition to the plots write a model metric""" + metrics_df = pd.read_csv(self.metrics_epoch) + self.metrics = metrics_df.iloc[-1].to_dict() + + def run(self): + """Primary method to run which executes all steps of the model training""" + + config.update("jax_enable_x64", self.jax_enable_x64) + + ase.io.write(self.train_data_file, self.data) + ase.io.write(self.validation_data_file, self.validation_data) + + self.train_model() + self.move_metrics() + self.get_metrics_from_plots() + + def get_calculator(self, **kwargs): + """Get an apax ase calculator""" + with self.state.use_tmp_path(): + return ASECalculator(model_dir=self.model_directory) + + +class ApaxEnsemble(zntrack.Node): + """Parallel apax model ensemble in ASE. + + Attributes + ---------- + models: list + List of `ApaxModel` nodes to ensemble. + nl_skin: float + Neighborlist skin. + transformations: dict + Key-parameter dict with function transformations applied + to the model function within the ASE calculator. + See the apax documentation for available methods. + """ + + models: list[Apax] = zntrack.deps() + nl_skin: float = zntrack.params(0.5) + transformations: dict[str, dict] = zntrack.params(None) + + def run(self) -> None: + pass + + def get_calculator(self, **kwargs) -> ase.calculators.calculator.Calculator: + """Property to return a model specific ase calculator object. + + Returns + ------- + calc: + ase calculator object + """ + + param_files = [m._parameter["data"]["directory"] for m in self.models] + + transformations = [] + if self.transformations: + for transform, params in self.transformations.items(): + transformations.append(available_transformations[transform](**params)) + + calc = ASECalculator( + param_files, + dr=self.nl_skin, + transformations=transformations, + ) + return calc diff --git a/apax/nodes/utils.py b/apax/nodes/utils.py new file mode 100644 index 00000000..3fb363c0 --- /dev/null +++ b/apax/nodes/utils.py @@ -0,0 +1,80 @@ +import numpy as np +import matplotlib.pyplot as plt +import logging + +def get_flat_data_from_dict(data: dict, silent_ignore: bool = False) -> list: + """Flatten a dictionary of lists into a single list. + + Parameters + ---------- + data : dict + Dictionary of lists. + silent_ignore : bool, optional + If True, the function will return the input if it is not a + dictionary. If False, it will raise a TypeError. + + Example + ------- + >>> data = {'a': [1, 2, 3], 'b': [4, 5, 6]} + >>> get_flat_data_from_dict(data) + [1, 2, 3, 4, 5, 6] + """ + if not isinstance(data, dict): + if silent_ignore: + return data + else: + raise TypeError(f"data must be a dictionary and not {type(data)}") + + flat_data = [] + for x in data.values(): + flat_data.extend(x) + return flat_data + + +def plot_with_uncertainty(value, ylabel: str, xlabel: str, x=None, **kwargs) -> dict: + """Parameters + ---------- + value: data of shape (n, m) where n is the number of ensembles. + x: optional x values of shape (m,) + + Returns + ------- + + """ + if isinstance(value, dict): + data = value + else: + data = { + "mean": np.mean(value, axis=0), + "std": np.std(value, axis=0), + "max": np.max(value, axis=0), + "min": np.min(value, axis=0), + } + + fig, ax = plt.subplots(**kwargs) + if x is None: + x = np.arange(len(data["mean"])) + ax.fill_between( + x, + data["mean"] + data["std"], + data["mean"] - data["std"], + facecolor="lightblue", + ) + if "max" in data: + ax.plot(x, data["max"], linestyle="--", color="darkcyan") + if "min" in data: + ax.plot(x, data["min"], linestyle="--", color="darkcyan") + ax.plot(x, data["mean"], color="black") + ax.set_ylabel(ylabel) + ax.set_xlabel(xlabel) + + return fig, ax, data + +def check_duplicate_keys(dict_a: dict, dict_b: dict, log: logging.Logger) -> None: + """Check if a key of dict_a is present in dict_b and then log a warning.""" + for key in dict_a: + if key in dict_b: + log.warning( + f"Found <{key}> in given config file. 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@@ typer = {version = ">=0.7.0,<0.8.0", extras = ["all"]} [package.extras] dask = ["dask[array] (>=2022.11.1,<2023.0.0)"] +[[package]] +name = "zninit" +version = "0.1.11" +description = "Descriptor based dataclass implementation" +optional = true +python-versions = ">=3.8,<4.0" +files = [ + {file = "zninit-0.1.11-py3-none-any.whl", hash = "sha256:78e5c7e1d0d50c131cf8efab58aad4a213446a1c38f38360731bf11b778e29e1"}, + {file = "zninit-0.1.11.tar.gz", hash = "sha256:fc14a55bd85a38f8f1411bd319cac541c2e6e16ab402f3f11a94e182b0681965"}, +] + +[package.extras] +typeguard = ["typeguard (>=2.13.3,<3.0.0)"] + +[[package]] +name = "znjson" +version = "0.2.2" +description = "A Python Package to Encode/Decode some common file formats to json" +optional = true +python-versions = ">=3.8,<4.0" +files = [ + {file = "znjson-0.2.2-py3-none-any.whl", hash = "sha256:ee29bb63716f66d1d259a8e3565fb66b9c8b79aee896dc231df990ad26e7fb6b"}, + {file = "znjson-0.2.2.tar.gz", hash = "sha256:d421ff377d490d876ea016780ffd60a585949a29d6df28ae971da2a329f35b45"}, +] + +[[package]] +name = "zntrack" +version = "0.7.2" +description = "Create, Run and Benchmark DVC Pipelines in Python" +optional = true +python-versions = ">=3.8,<4.0.0" +files = [ + {file = "zntrack-0.7.2-py3-none-any.whl", hash = "sha256:42f23022d70b3597ae87318eaf552cfdf97305e8125ffd0e167dfe86920284a8"}, + {file = "zntrack-0.7.2.tar.gz", hash = "sha256:10ac7ab4b6cd70914fdefd5f91f65ac0426eb3c08238353cfe4dcc2975a0a180"}, +] + +[package.dependencies] +dot4dict = ">=0.1.1,<0.2.0" +dvc = ">=3.2.2,<4.0.0" +pandas = ">=2,<3" +pyyaml = ">=6.0,<7.0" +tqdm = ">=4.64.0,<5.0.0" +typer = ">=0.7.0,<0.8.0" +typing-extensions = ">=4.8.0,<5.0.0" +znflow = ">=0.1.14,<0.2.0" +zninit = ">=0.1.11,<0.2.0" +znjson = ">=0.2.2,<0.3.0" + [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.12" -content-hash = "02e6652599fb8121cb7d5fb59e151a32413f31c6a64e05904f147397d62687bf" +content-hash = "bfb4a82828c9b988a7954ccf86f7d5d1f4e8bfe142d4c1b373f566dc8edc18e7" diff --git a/pyproject.toml b/pyproject.toml index 217e22bb..7b2c4d4d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,7 @@ znh5md = "^0.1.7" pydantic = "^2.3.0" jax = "^0.4.14" jax-md = {git = "https://github.com/jax-md/jax-md.git"} +zntrack = {version = "^0.7.2", optional = true} [tool.poetry.scripts] apax = 'apax.cli.apax_app:app' From 1b7ea219011e8838ec895e01b52708172d3308cb Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 3 Apr 2024 12:34:06 +0000 Subject: [PATCH 05/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- apax/nodes/bal.py | 2 +- apax/nodes/md.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/apax/nodes/bal.py b/apax/nodes/bal.py index b40ccd0b..c69d52be 100644 --- a/apax/nodes/bal.py +++ b/apax/nodes/bal.py @@ -95,4 +95,4 @@ def _get_plot(self, atoms_lst: list[ase.Atoms], indices: list[int]): ax.plot(indices, energies[indices], "x", color="red") - fig.savefig(self.img_selection, bbox_inches="tight") \ No newline at end of file + fig.savefig(self.img_selection, bbox_inches="tight") diff --git a/apax/nodes/md.py b/apax/nodes/md.py index 2ca833d1..e35f380d 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -104,4 +104,4 @@ def file_handle(filename): format_handler=functools.partial( znh5md.FormatHandler, file_handle=file_handle ), - ).get_atoms_list() \ No newline at end of file + ).get_atoms_list() From 370795c34ccaf7f40c19786aefa8dafc3b436944 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Wed, 3 Apr 2024 14:34:39 +0200 Subject: [PATCH 06/27] isort --- apax/nodes/bal.py | 8 +++++--- apax/nodes/md.py | 2 +- apax/nodes/model.py | 6 +++--- apax/nodes/utils.py | 6 ++++-- 4 files changed, 13 insertions(+), 9 deletions(-) diff --git a/apax/nodes/bal.py b/apax/nodes/bal.py index c69d52be..cd2f523b 100644 --- a/apax/nodes/bal.py +++ b/apax/nodes/bal.py @@ -1,12 +1,14 @@ -import zntrack import ase -import numpy as np import matplotlib.pyplot as plt -from .utils import get_flat_data_from_dict, plot_with_uncertainty +import numpy as np import znflow +import zntrack from apax.bal import kernel_selection +from .utils import get_flat_data_from_dict, plot_with_uncertainty + + class BatchKernelSelection(zntrack.Node): """Interface to the batch active learning methods implemented in apax. Check the apax documentation for a list and explanation of implemented properties. diff --git a/apax/nodes/md.py b/apax/nodes/md.py index e35f380d..a1daf35e 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -10,8 +10,8 @@ import zntrack.utils from zntrack import dvc, zn -from .utils import check_duplicate_keys from .model import Apax +from .utils import check_duplicate_keys log = logging.getLogger(__name__) diff --git a/apax/nodes/model.py b/apax/nodes/model.py index b9040ecd..f949dda8 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -9,13 +9,13 @@ import pandas as pd import yaml import zntrack.utils +from jax import config +from matplotlib import pyplot as plt +from zntrack import dvc, zn from apax.md import ASECalculator from apax.md.function_transformations import available_transformations from apax.train.run import run as apax_run -from jax import config -from matplotlib import pyplot as plt -from zntrack import dvc, zn from .utils import check_duplicate_keys diff --git a/apax/nodes/utils.py b/apax/nodes/utils.py index 3fb363c0..59c6f05d 100644 --- a/apax/nodes/utils.py +++ b/apax/nodes/utils.py @@ -1,7 +1,9 @@ -import numpy as np -import matplotlib.pyplot as plt import logging +import matplotlib.pyplot as plt +import numpy as np + + def get_flat_data_from_dict(data: dict, silent_ignore: bool = False) -> list: """Flatten a dictionary of lists into a single list. From 8941b0a30286ad18c2e6e5a8597d8d1a8bb694a7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 3 Apr 2024 12:34:48 +0000 Subject: [PATCH 07/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- apax/nodes/utils.py | 1 + 1 file changed, 1 insertion(+) diff --git a/apax/nodes/utils.py b/apax/nodes/utils.py index 59c6f05d..5db8b107 100644 --- a/apax/nodes/utils.py +++ b/apax/nodes/utils.py @@ -72,6 +72,7 @@ def plot_with_uncertainty(value, ylabel: str, xlabel: str, x=None, **kwargs) -> return fig, ax, data + def check_duplicate_keys(dict_a: dict, dict_b: dict, log: logging.Logger) -> None: """Check if a key of dict_a is present in dict_b and then log a warning.""" for key in dict_a: From b3be0e7dda904d0a6ac6f294bf79d2e847e3eed3 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 09:57:33 +0200 Subject: [PATCH 08/27] test utils and training --- apax/nodes/model.py | 39 ++++++++++++++++++++------------------- apax/nodes/utils.py | 18 ++++++++++++++++++ poetry.lock | 5 ++++- pyproject.toml | 3 +++ tests/nodes/test_model.py | 25 +++++++++++++++++++++++++ tests/nodes/test_utils.py | 17 +++++++++++++++++ 6 files changed, 87 insertions(+), 20 deletions(-) create mode 100644 tests/nodes/test_model.py create mode 100644 tests/nodes/test_utils.py diff --git a/apax/nodes/model.py b/apax/nodes/model.py index f949dda8..727081df 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -39,6 +39,7 @@ class Apax(zntrack.Node): path to the valdidation data """ + data: list = zntrack.deps() config: str = dvc.params("apax.yaml") validation_data = zntrack.deps() model: Optional[t.Any] = zntrack.deps(None) @@ -50,15 +51,15 @@ class Apax(zntrack.Node): jax_enable_x64: bool = zn.params(True) - metrics_epoch = dvc.plots( - zntrack.nwd / "log.csv", - # template=STATIC_PATH / "y_log.json", - # x="epoch", - # x_label="epochs", - # y="val_loss", - # y_label="validation loss", - ) - metrics = zn.metrics() + # metrics_epoch = zntrack.plots_path( + # zntrack.nwd / "apax_model" / "log.csv", + # # template=STATIC_PATH / "y_log.json", + # # x="epoch", + # # x_label="epochs", + # # y="val_loss", + # # y_label="validation loss", + # ) + # metrics = zn.metrics() _parameter: dict = None @@ -98,15 +99,15 @@ def train_model(self): """Train the model using `apax.train.run`""" apax_run(self._parameter) - def move_metrics(self): - """Move the metrics to the correct directories for DVC""" - path = self.model_directory / self.metrics_epoch.name - shutil.move(path, self.metrics_epoch) + # def move_metrics(self): + # """Move the metrics to the correct directories for DVC""" + # path = self.model_directory / self.metrics_epoch.name + # shutil.move(path, self.metrics_epoch) - def get_metrics_from_plots(self): - """In addition to the plots write a model metric""" - metrics_df = pd.read_csv(self.metrics_epoch) - self.metrics = metrics_df.iloc[-1].to_dict() + # def get_metrics_from_plots(self): + # """In addition to the plots write a model metric""" + # metrics_df = pd.read_csv(self.metrics_epoch) + # self.metrics = metrics_df.iloc[-1].to_dict() def run(self): """Primary method to run which executes all steps of the model training""" @@ -117,8 +118,8 @@ def run(self): ase.io.write(self.validation_data_file, self.validation_data) self.train_model() - self.move_metrics() - self.get_metrics_from_plots() + # self.move_metrics() + # self.get_metrics_from_plots() def get_calculator(self, **kwargs): """Get an apax ase calculator""" diff --git a/apax/nodes/utils.py b/apax/nodes/utils.py index 5db8b107..af655543 100644 --- a/apax/nodes/utils.py +++ b/apax/nodes/utils.py @@ -2,6 +2,24 @@ import matplotlib.pyplot as plt import numpy as np +import ase.io +import zntrack +import functools + + +class AddData(zntrack.Node): + file: str = zntrack.deps_path() + + def run(self): + pass + + @functools.cached_property + def atoms(self) -> list[ase.Atoms]: + data = [] + for atoms in ase.io.iread(self.file): + data.append(atoms) + if len(data) == 50: + return data def get_flat_data_from_dict(data: dict, silent_ignore: bool = False) -> list: diff --git a/poetry.lock b/poetry.lock index da5dc13d..212cdb48 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5521,7 +5521,10 @@ znflow = ">=0.1.14,<0.2.0" zninit = ">=0.1.11,<0.2.0" znjson = ">=0.2.2,<0.3.0" +[extras] +zntrack = ["zntrack"] + [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.12" -content-hash = "bfb4a82828c9b988a7954ccf86f7d5d1f4e8bfe142d4c1b373f566dc8edc18e7" +content-hash = "0a034a99dea4a2718da2a248b0287f88ad1692030585737ddef5215c6422088f" diff --git a/pyproject.toml b/pyproject.toml index 7b2c4d4d..3fd5554b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,6 +28,9 @@ jax = "^0.4.14" jax-md = {git = "https://github.com/jax-md/jax-md.git"} zntrack = {version = "^0.7.2", optional = true} +[tool.poetry.extras] +zntrack = ["zntrack"] + [tool.poetry.scripts] apax = 'apax.cli.apax_app:app' diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py new file mode 100644 index 00000000..3bcb25ac --- /dev/null +++ b/tests/nodes/test_model.py @@ -0,0 +1,25 @@ +from apax.nodes.utils import AddData +from apax.nodes.model import Apax +import zntrack, os +import pathlib +import shutil + +CONFIG_PATH = pathlib.Path(__file__).parent / "config.yaml" + +def test_add_data(tmp_path, get_md22_stachyose): + os.chdir(tmp_path) + shutil.copy(CONFIG_PATH, tmp_path) + proj = zntrack.Project() + with proj: + data = AddData(file=get_md22_stachyose) + model = Apax(data=data.atoms, validation_data=data.atoms, config="config.yaml") + + proj.run() + + model = model.from_rev() + data = data.from_rev() + + atoms = data.atoms[0] + atoms.calc = model.get_calculator() + + assert atoms.get_potential_energy() < 0 diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_utils.py new file mode 100644 index 00000000..a7e8af99 --- /dev/null +++ b/tests/nodes/test_utils.py @@ -0,0 +1,17 @@ +from apax.nodes.utils import AddData +import zntrack +import os +import ase.io +import shutil + +def test_add_data(tmp_path, get_md22_stachyose): + os.chdir(tmp_path) + proj = zntrack.Project() + with proj: + data = AddData(file=get_md22_stachyose) + + proj.run() + data = data.from_rev() + assert isinstance(data.atoms, list) + assert len(data.atoms) == 50 + assert all(isinstance(atoms, ase.Atoms) for atoms in data.atoms) From 085217dce194fd3d3473b080ede852be160112c9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 5 Apr 2024 07:57:42 +0000 Subject: [PATCH 09/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- tests/nodes/test_model.py | 2 +- tests/nodes/test_utils.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index 3bcb25ac..9d8d4ee8 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -13,7 +13,7 @@ def test_add_data(tmp_path, get_md22_stachyose): with proj: data = AddData(file=get_md22_stachyose) model = Apax(data=data.atoms, validation_data=data.atoms, config="config.yaml") - + proj.run() model = model.from_rev() diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_utils.py index a7e8af99..487f1cc0 100644 --- a/tests/nodes/test_utils.py +++ b/tests/nodes/test_utils.py @@ -9,7 +9,7 @@ def test_add_data(tmp_path, get_md22_stachyose): proj = zntrack.Project() with proj: data = AddData(file=get_md22_stachyose) - + proj.run() data = data.from_rev() assert isinstance(data.atoms, list) From f4a29749a2f28687c81fe084e707e06635bc166e Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 09:58:45 +0200 Subject: [PATCH 10/27] linting --- apax/nodes/model.py | 4 ---- tests/nodes/test_model.py | 3 ++- tests/nodes/test_utils.py | 1 - 3 files changed, 2 insertions(+), 6 deletions(-) diff --git a/apax/nodes/model.py b/apax/nodes/model.py index 727081df..7419bf2b 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -1,16 +1,12 @@ import logging import pathlib -import shutil import typing as t from typing import Optional import ase.io -import numpy as np -import pandas as pd import yaml import zntrack.utils from jax import config -from matplotlib import pyplot as plt from zntrack import dvc, zn from apax.md import ASECalculator diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index 3bcb25ac..fd6635e5 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -1,6 +1,7 @@ from apax.nodes.utils import AddData from apax.nodes.model import Apax -import zntrack, os +import zntrack +import os import pathlib import shutil diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_utils.py index a7e8af99..0f050fe1 100644 --- a/tests/nodes/test_utils.py +++ b/tests/nodes/test_utils.py @@ -2,7 +2,6 @@ import zntrack import os import ase.io -import shutil def test_add_data(tmp_path, get_md22_stachyose): os.chdir(tmp_path) From 8f0f25383ffa39f3c5648c03cb7f24d50a73a1eb Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 5 Apr 2024 07:58:54 +0000 Subject: [PATCH 11/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- tests/nodes/test_model.py | 1 + tests/nodes/test_utils.py | 1 + 2 files changed, 2 insertions(+) diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index d9326935..e0b7899d 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -7,6 +7,7 @@ CONFIG_PATH = pathlib.Path(__file__).parent / "config.yaml" + def test_add_data(tmp_path, get_md22_stachyose): os.chdir(tmp_path) shutil.copy(CONFIG_PATH, tmp_path) diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_utils.py index 665aefe3..5136f861 100644 --- a/tests/nodes/test_utils.py +++ b/tests/nodes/test_utils.py @@ -3,6 +3,7 @@ import os import ase.io + def test_add_data(tmp_path, get_md22_stachyose): os.chdir(tmp_path) proj = zntrack.Project() From 173543b860838bed9e4f0aa6ecd3f78953a8af3a Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 09:59:47 +0200 Subject: [PATCH 12/27] run isort --- apax/nodes/utils.py | 4 ++-- tests/nodes/test_model.py | 8 +++++--- tests/nodes/test_utils.py | 7 +++++-- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/apax/nodes/utils.py b/apax/nodes/utils.py index af655543..0014b697 100644 --- a/apax/nodes/utils.py +++ b/apax/nodes/utils.py @@ -1,10 +1,10 @@ +import functools import logging +import ase.io import matplotlib.pyplot as plt import numpy as np -import ase.io import zntrack -import functools class AddData(zntrack.Node): diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index d9326935..be81f1ae 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -1,10 +1,12 @@ -from apax.nodes.utils import AddData -from apax.nodes.model import Apax -import zntrack import os import pathlib import shutil +import zntrack + +from apax.nodes.model import Apax +from apax.nodes.utils import AddData + CONFIG_PATH = pathlib.Path(__file__).parent / "config.yaml" def test_add_data(tmp_path, get_md22_stachyose): diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_utils.py index 665aefe3..6f6690c8 100644 --- a/tests/nodes/test_utils.py +++ b/tests/nodes/test_utils.py @@ -1,7 +1,10 @@ -from apax.nodes.utils import AddData -import zntrack import os + import ase.io +import zntrack + +from apax.nodes.utils import AddData + def test_add_data(tmp_path, get_md22_stachyose): os.chdir(tmp_path) From 848efbbed73e19c31dc144488e4c9136623f5b66 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 5 Apr 2024 07:59:56 +0000 Subject: [PATCH 13/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- tests/nodes/test_utils.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_utils.py index da7a5957..6f6690c8 100644 --- a/tests/nodes/test_utils.py +++ b/tests/nodes/test_utils.py @@ -6,7 +6,6 @@ from apax.nodes.utils import AddData - def test_add_data(tmp_path, get_md22_stachyose): os.chdir(tmp_path) proj = zntrack.Project() From cfebbc3ddbd96a92a4e77dc8635a88ece6926d3a Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 10:03:50 +0200 Subject: [PATCH 14/27] rename config to example.yaml --- tests/nodes/example.yaml | 43 +++++++++++++++++++++++++++++++++++++++ tests/nodes/test_model.py | 4 ++-- 2 files changed, 45 insertions(+), 2 deletions(-) create mode 100644 tests/nodes/example.yaml diff --git a/tests/nodes/example.yaml b/tests/nodes/example.yaml new file mode 100644 index 00000000..a7de1dcf --- /dev/null +++ b/tests/nodes/example.yaml @@ -0,0 +1,43 @@ +n_epochs: 5 +seed: 1 +n_models: 1 + +data: + batch_size: 8 + scale_method: per_element_force_rms_scale + shift_method: per_element_regression_shift + shift_options: + energy_regularisation: 1.0 + valid_batch_size: 32 +loss: +- name: energy + +metrics: +- name: energy + reductions: + - mae + +model: + n_basis: 7 + n_radial: 5 + nn: + - 512 + - 512 + r_max: 5.5 + r_min: 0.7 + + b_init: zeros + emb_init: uniform + use_zbl: true + + descriptor_dtype: fp32 + readout_dtype: fp32 + scale_shift_dtype: fp32 + +optimizer: + opt_name: adam + emb_lr: 0.01 + nn_lr: 0.005 + scale_lr: 0.001 + shift_lr: 0.05 + zbl_lr: 0.001 \ No newline at end of file diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index 01ceb611..50ba86ac 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -7,7 +7,7 @@ from apax.nodes.model import Apax from apax.nodes.utils import AddData -CONFIG_PATH = pathlib.Path(__file__).parent / "config.yaml" +CONFIG_PATH = pathlib.Path(__file__).parent / "example.yaml" def test_add_data(tmp_path, get_md22_stachyose): @@ -16,7 +16,7 @@ def test_add_data(tmp_path, get_md22_stachyose): proj = zntrack.Project() with proj: data = AddData(file=get_md22_stachyose) - model = Apax(data=data.atoms, validation_data=data.atoms, config="config.yaml") + model = Apax(data=data.atoms, validation_data=data.atoms, config="example.yaml") proj.run() From de9ad948fdce2fec57934a761a98c374bff64923 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 5 Apr 2024 08:03:59 +0000 Subject: [PATCH 15/27] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- tests/nodes/example.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/nodes/example.yaml b/tests/nodes/example.yaml index a7de1dcf..a83af51e 100644 --- a/tests/nodes/example.yaml +++ b/tests/nodes/example.yaml @@ -40,4 +40,4 @@ optimizer: nn_lr: 0.005 scale_lr: 0.001 shift_lr: 0.05 - zbl_lr: 0.001 \ No newline at end of file + zbl_lr: 0.001 From 6930533fbb4e09df558ca4be1a7ef6df08509137 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 10:13:32 +0200 Subject: [PATCH 16/27] cleanup --- apax/nodes/model.py | 51 ++++++++++++++------------------------------- 1 file changed, 16 insertions(+), 35 deletions(-) diff --git a/apax/nodes/model.py b/apax/nodes/model.py index 7419bf2b..ff794207 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -1,13 +1,12 @@ import logging import pathlib import typing as t -from typing import Optional import ase.io +import pandas as pd import yaml import zntrack.utils from jax import config -from zntrack import dvc, zn from apax.md import ASECalculator from apax.md.function_transformations import available_transformations @@ -36,36 +35,24 @@ class Apax(zntrack.Node): """ data: list = zntrack.deps() - config: str = dvc.params("apax.yaml") + config: str = zntrack.params_path() validation_data = zntrack.deps() - model: Optional[t.Any] = zntrack.deps(None) + model: t.Optional[t.Any] = zntrack.deps(None) - model_directory: pathlib.Path = dvc.outs(zntrack.nwd / "apax_model") + model_directory: pathlib.Path = zntrack.outs_path(zntrack.nwd / "apax_model") - train_data_file: pathlib.Path = dvc.outs(zntrack.nwd / "train_atoms.extxyz") - validation_data_file: pathlib.Path = dvc.outs(zntrack.nwd / "val_atoms.extxyz") + train_data_file: pathlib.Path = zntrack.outs_path(zntrack.nwd / "train_atoms.extxyz") + validation_data_file: pathlib.Path = zntrack.outs_path( + zntrack.nwd / "val_atoms.extxyz" + ) - jax_enable_x64: bool = zn.params(True) + # TODO: why is this an extra parameter? + jax_enable_x64: bool = zntrack.params(True) - # metrics_epoch = zntrack.plots_path( - # zntrack.nwd / "apax_model" / "log.csv", - # # template=STATIC_PATH / "y_log.json", - # # x="epoch", - # # x_label="epochs", - # # y="val_loss", - # # y_label="validation loss", - # ) - # metrics = zn.metrics() + metrics = zntrack.metrics() _parameter: dict = None - # def _post_init_(self): - # self.data = utils.helpers.get_deps_if_node(self.data, "atoms") - # self.validation_data = utils.helpers.get_deps_if_node( - # self.validation_data, "atoms" - # ) - # self._handle_parameter_file() - def _post_load_(self) -> None: self._handle_parameter_file() @@ -95,15 +82,10 @@ def train_model(self): """Train the model using `apax.train.run`""" apax_run(self._parameter) - # def move_metrics(self): - # """Move the metrics to the correct directories for DVC""" - # path = self.model_directory / self.metrics_epoch.name - # shutil.move(path, self.metrics_epoch) - - # def get_metrics_from_plots(self): - # """In addition to the plots write a model metric""" - # metrics_df = pd.read_csv(self.metrics_epoch) - # self.metrics = metrics_df.iloc[-1].to_dict() + def get_metrics_from_plots(self): + """In addition to the plots write a model metric""" + metrics_df = pd.read_csv(self.model_directory / "log.csv") + self.metrics = metrics_df.iloc[-1].to_dict() def run(self): """Primary method to run which executes all steps of the model training""" @@ -114,8 +96,7 @@ def run(self): ase.io.write(self.validation_data_file, self.validation_data) self.train_model() - # self.move_metrics() - # self.get_metrics_from_plots() + self.get_metrics_from_plots() def get_calculator(self, **kwargs): """Get an apax ase calculator""" From 99d921b39e0a0d053eaf2d090981f228fd75f945 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 10:21:36 +0200 Subject: [PATCH 17/27] remove jax_enable_x64 --- apax/nodes/model.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/apax/nodes/model.py b/apax/nodes/model.py index ff794207..306e10d0 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -46,9 +46,6 @@ class Apax(zntrack.Node): zntrack.nwd / "val_atoms.extxyz" ) - # TODO: why is this an extra parameter? - jax_enable_x64: bool = zntrack.params(True) - metrics = zntrack.metrics() _parameter: dict = None @@ -89,9 +86,6 @@ def get_metrics_from_plots(self): def run(self): """Primary method to run which executes all steps of the model training""" - - config.update("jax_enable_x64", self.jax_enable_x64) - ase.io.write(self.train_data_file, self.data) ase.io.write(self.validation_data_file, self.validation_data) From 6907a98778160af279a94c4f0f8b4a3038daa80b Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 10:54:35 +0200 Subject: [PATCH 18/27] test md --- apax/nodes/md.py | 5 ++++- tests/nodes/md.yaml | 9 +++++++++ tests/nodes/test_md.py | 28 ++++++++++++++++++++++++++ tests/nodes/test_model.py | 41 ++++++++++++++++++++++++++++++++++++--- 4 files changed, 79 insertions(+), 4 deletions(-) create mode 100644 tests/nodes/md.yaml create mode 100644 tests/nodes/test_md.py diff --git a/apax/nodes/md.py b/apax/nodes/md.py index a1daf35e..9fdec8d9 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -31,6 +31,9 @@ class ApaxJaxMD(zntrack.Node): path to the MD simulation parameter file """ + data: list[ase.Atoms] = zntrack.deps() + data_id: int = zntrack.params(-1) + model: Apax = zntrack.deps() repeat = zn.params(None) @@ -84,7 +87,7 @@ def run(self): from apax.md.nvt import run_md # self._handle_parameter_file() - atoms = self.get_data() + atoms = self.data[self.data_id] if self.repeat is not None: atoms = atoms.repeat(self.repeat) ase.io.write(self.init_struc_dir.as_posix(), atoms) diff --git a/tests/nodes/md.yaml b/tests/nodes/md.yaml new file mode 100644 index 00000000..6a85a983 --- /dev/null +++ b/tests/nodes/md.yaml @@ -0,0 +1,9 @@ +ensemble: + name: nvt + dt: 0.1 # fs time step + temperature: 1 + +duration: 5 # fs +n_inner: 5 # compiled innner steps +sampling_rate: 1 # dump interval +dr_threshold: 0.5 # Neighborlist skin diff --git a/tests/nodes/test_md.py b/tests/nodes/test_md.py new file mode 100644 index 00000000..4d0ee88b --- /dev/null +++ b/tests/nodes/test_md.py @@ -0,0 +1,28 @@ +import os +import pathlib +import shutil + +import zntrack +import yaml + +from apax.nodes.model import Apax +from apax.nodes.md import ApaxJaxMD +from apax.nodes.utils import AddData + +CONFIG_PATH = pathlib.Path(__file__).parent / "example.yaml" +MD_CONFIG_PATH = pathlib.Path(__file__).parent / "md.yaml" + +def test_n_jax_md(tmp_path, get_md22_stachyose): + os.chdir(tmp_path) + shutil.copy(CONFIG_PATH, tmp_path / "example.yaml") + shutil.copy(MD_CONFIG_PATH, tmp_path / "md.yaml") + proj = zntrack.Project() + with proj: + data = AddData(file=get_md22_stachyose) + model = Apax(data=data.atoms, validation_data=data.atoms, config="example.yaml") + md = ApaxJaxMD(model=model, md_parameter_file="md.yaml", data=data.atoms) + + proj.run() + + md = md.from_rev() + assert len(md.atoms) == 50 diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index 50ba86ac..624db1dc 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -3,16 +3,26 @@ import shutil import zntrack +import yaml -from apax.nodes.model import Apax +from apax.nodes.model import Apax, ApaxEnsemble from apax.nodes.utils import AddData CONFIG_PATH = pathlib.Path(__file__).parent / "example.yaml" +def save_config_with_seed(path: str, seed: int=1) -> None: + with open(CONFIG_PATH, "r") as f: + config = yaml.safe_load(f) + + config["seed"] = seed -def test_add_data(tmp_path, get_md22_stachyose): + with open(path, "w") as f: + yaml.dump(config, f) + + +def test_n_train_model(tmp_path, get_md22_stachyose): os.chdir(tmp_path) - shutil.copy(CONFIG_PATH, tmp_path) + save_config_with_seed(tmp_path / "example.yaml") proj = zntrack.Project() with proj: data = AddData(file=get_md22_stachyose) @@ -27,3 +37,28 @@ def test_add_data(tmp_path, get_md22_stachyose): atoms.calc = model.get_calculator() assert atoms.get_potential_energy() < 0 + +def test_n_train_2_model(tmp_path, get_md22_stachyose): + os.chdir(tmp_path) + + save_config_with_seed(tmp_path / "example.yaml") + save_config_with_seed(tmp_path / "example2.yaml", seed=2) + + + proj = zntrack.Project(automatic_node_names=True) + with proj: + data = AddData(file=get_md22_stachyose) + model1 = Apax(data=data.atoms, validation_data=data.atoms, config="example.yaml") + model2 = Apax(data=data.atoms, validation_data=data.atoms, config="example2.yaml") + ensemble = ApaxEnsemble(models=[model1, model2]) + + proj.run() + + model = ensemble.from_rev() + data = data.from_rev() + + atoms = data.atoms[0] + atoms.calc = model.get_calculator() + + assert atoms.get_potential_energy() < 0 + assert atoms.calc.results["energy_uncertainty"] > 0 From cc7f2dd8a373ac47e54925fcb126d4d0ab0b2b8a Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 10:54:59 +0200 Subject: [PATCH 19/27] linting --- apax/nodes/model.py | 1 - tests/nodes/test_md.py | 4 ++-- tests/nodes/test_model.py | 12 ++++++------ 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/apax/nodes/model.py b/apax/nodes/model.py index 306e10d0..7cc7db9a 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -6,7 +6,6 @@ import pandas as pd import yaml import zntrack.utils -from jax import config from apax.md import ASECalculator from apax.md.function_transformations import available_transformations diff --git a/tests/nodes/test_md.py b/tests/nodes/test_md.py index 4d0ee88b..aa027551 100644 --- a/tests/nodes/test_md.py +++ b/tests/nodes/test_md.py @@ -3,15 +3,15 @@ import shutil import zntrack -import yaml -from apax.nodes.model import Apax from apax.nodes.md import ApaxJaxMD +from apax.nodes.model import Apax from apax.nodes.utils import AddData CONFIG_PATH = pathlib.Path(__file__).parent / "example.yaml" MD_CONFIG_PATH = pathlib.Path(__file__).parent / "md.yaml" + def test_n_jax_md(tmp_path, get_md22_stachyose): os.chdir(tmp_path) shutil.copy(CONFIG_PATH, tmp_path / "example.yaml") diff --git a/tests/nodes/test_model.py b/tests/nodes/test_model.py index 624db1dc..06b13899 100644 --- a/tests/nodes/test_model.py +++ b/tests/nodes/test_model.py @@ -1,19 +1,19 @@ import os import pathlib -import shutil -import zntrack import yaml +import zntrack from apax.nodes.model import Apax, ApaxEnsemble from apax.nodes.utils import AddData CONFIG_PATH = pathlib.Path(__file__).parent / "example.yaml" -def save_config_with_seed(path: str, seed: int=1) -> None: + +def save_config_with_seed(path: str, seed: int = 1) -> None: with open(CONFIG_PATH, "r") as f: config = yaml.safe_load(f) - + config["seed"] = seed with open(path, "w") as f: @@ -38,13 +38,13 @@ def test_n_train_model(tmp_path, get_md22_stachyose): assert atoms.get_potential_energy() < 0 + def test_n_train_2_model(tmp_path, get_md22_stachyose): os.chdir(tmp_path) - + save_config_with_seed(tmp_path / "example.yaml") save_config_with_seed(tmp_path / "example2.yaml", seed=2) - proj = zntrack.Project(automatic_node_names=True) with proj: data = AddData(file=get_md22_stachyose) From 706b2d19c94a4ff2ad4a00774d4a64c9e7ff0370 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:07:04 +0200 Subject: [PATCH 20/27] remove BAL --- apax/nodes/bal.py | 100 ---------------------------------------------- 1 file changed, 100 deletions(-) delete mode 100644 apax/nodes/bal.py diff --git a/apax/nodes/bal.py b/apax/nodes/bal.py deleted file mode 100644 index cd2f523b..00000000 --- a/apax/nodes/bal.py +++ /dev/null @@ -1,100 +0,0 @@ -import ase -import matplotlib.pyplot as plt -import numpy as np -import znflow -import zntrack - -from apax.bal import kernel_selection - -from .utils import get_flat_data_from_dict, plot_with_uncertainty - - -class BatchKernelSelection(zntrack.Node): - """Interface to the batch active learning methods implemented in apax. - Check the apax documentation for a list and explanation of implemented properties. - - Attributes - ---------- - models: Union[Apax, List[Apax]] - One or more Apax models to construct a feature map from. - base_feature_map: dict - Name and parameters for the feature map transformation. - selection_method: str - Name of the selection method to be used. Choose from: - ["max_dist", ] - n_configurations: int - Number of samples to be selected. - processing_batch_size: int - Number of samples to be processed in parallel. - Does not affect the result, just the speed of computing features. - """ - - models: list = zntrack.deps() - base_feature_map: dict = zntrack.params({"name": "ll_grad", "layer_name": "dense_2"}) - selection_method: str = zntrack.params("max_dist") - n_configurations: str = zntrack.params() - processing_batch_size: str = zntrack.meta.Text(64) - img_selection = zntrack.outs_path(zntrack.nwd / "selection.png") - - train_data: list[ase.Atoms] = zntrack.deps() - - def _post_init_(self): - if self.train_data is not None and not isinstance(self.train_data, dict): - try: - self.train_data = znflow.combine( - self.train_data, attribute="atoms", return_dict_attr="name" - ) - except TypeError: - self.train_data = znflow.combine(self.train_data, attribute="atoms") - - if self.data is not None and not isinstance(self.data, dict): - try: - self.data = znflow.combine( - self.data, attribute="atoms", return_dict_attr="name" - ) - except TypeError: - self.data = znflow.combine(self.data, attribute="atoms") - - def select_atoms(self, atoms_lst: list[ase.Atoms]) -> list[int]: - if isinstance(self.models, list): - param_files = [m._parameter["data"]["directory"] for m in self.models] - else: - param_files = self.models._parameter["data"]["directory"] - - if isinstance(self.train_data, dict): - self.train_data = get_flat_data_from_dict(self.train_data) - - selected = kernel_selection( - param_files, - self.train_data, - atoms_lst, - self.base_feature_map, - self.selection_method, - selection_batch_size=self.n_configurations, - processing_batch_size=self.processing_batch_size, - ) - self._get_plot(atoms_lst, selected) - - return list(selected) - - def _get_plot(self, atoms_lst: list[ase.Atoms], indices: list[int]): - energies = np.array([atoms.calc.results["energy"] for atoms in atoms_lst]) - - if "energy_uncertainty" in atoms_lst[0].calc.results.keys(): - uncertainty = np.array( - [atoms.calc.results["energy_uncertainty"] for atoms in atoms_lst] - ) - fig, ax, _ = plot_with_uncertainty( - {"mean": energies, "std": uncertainty}, - ylabel="energy", - xlabel="configuration", - ) - else: - fig, ax = plt.subplots() - ax.plot(energies, label="energy") - ax.set_ylabel("energy") - ax.set_xlabel("configuration") - - ax.plot(indices, energies[indices], "x", color="red") - - fig.savefig(self.img_selection, bbox_inches="tight") From e8b9af97546583105ad61d279afe037af6315add Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:08:42 +0200 Subject: [PATCH 21/27] clean up --- apax/nodes/md.py | 25 ---------------- apax/nodes/utils.py | 71 --------------------------------------------- 2 files changed, 96 deletions(-) diff --git a/apax/nodes/md.py b/apax/nodes/md.py index 9fdec8d9..0872b7a3 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -43,30 +43,6 @@ class ApaxJaxMD(zntrack.Node): sim_dir: pathlib.Path = dvc.outs(zntrack.nwd / "md") init_struc_dir: pathlib.Path = dvc.outs(zntrack.nwd / "initial_structure.extxyz") - # def post_init(self): - # if not self.state.loaded: - # dict_supplied = self.md_parameter is None - # file_supplied = self.md_parameter_file is None - - # if dict_supplied and file_supplied: - # raise TypeError("Please specify either an input dict or a file") - # elif not dict_supplied and not file_supplied: - # raise TypeError( - # "Can not train apax model without a parameter dict or file" - # ) - # else: - # log.info( - # "Please keep track of the parameter file with git, just like the" - # " params.yaml" - # ) - - # if not isinstance(self.model, Apax): - # raise TypeError( - # "Performing simulations with JaxMD requires a apax model Node" - # ) - - # self.data = utils.helpers.get_deps_if_node(self.data, "atoms") - def _post_load_(self) -> None: self._handle_parameter_file() @@ -97,7 +73,6 @@ def run(self): @functools.cached_property def atoms(self) -> typing.List[ase.Atoms]: - # filename should be changeable def file_handle(filename): file = self.state.fs.open(filename, "rb") return h5py.File(file) diff --git a/apax/nodes/utils.py b/apax/nodes/utils.py index 0014b697..8efef777 100644 --- a/apax/nodes/utils.py +++ b/apax/nodes/utils.py @@ -2,8 +2,6 @@ import logging import ase.io -import matplotlib.pyplot as plt -import numpy as np import zntrack @@ -22,75 +20,6 @@ def atoms(self) -> list[ase.Atoms]: return data -def get_flat_data_from_dict(data: dict, silent_ignore: bool = False) -> list: - """Flatten a dictionary of lists into a single list. - - Parameters - ---------- - data : dict - Dictionary of lists. - silent_ignore : bool, optional - If True, the function will return the input if it is not a - dictionary. If False, it will raise a TypeError. - - Example - ------- - >>> data = {'a': [1, 2, 3], 'b': [4, 5, 6]} - >>> get_flat_data_from_dict(data) - [1, 2, 3, 4, 5, 6] - """ - if not isinstance(data, dict): - if silent_ignore: - return data - else: - raise TypeError(f"data must be a dictionary and not {type(data)}") - - flat_data = [] - for x in data.values(): - flat_data.extend(x) - return flat_data - - -def plot_with_uncertainty(value, ylabel: str, xlabel: str, x=None, **kwargs) -> dict: - """Parameters - ---------- - value: data of shape (n, m) where n is the number of ensembles. - x: optional x values of shape (m,) - - Returns - ------- - - """ - if isinstance(value, dict): - data = value - else: - data = { - "mean": np.mean(value, axis=0), - "std": np.std(value, axis=0), - "max": np.max(value, axis=0), - "min": np.min(value, axis=0), - } - - fig, ax = plt.subplots(**kwargs) - if x is None: - x = np.arange(len(data["mean"])) - ax.fill_between( - x, - data["mean"] + data["std"], - data["mean"] - data["std"], - facecolor="lightblue", - ) - if "max" in data: - ax.plot(x, data["max"], linestyle="--", color="darkcyan") - if "min" in data: - ax.plot(x, data["min"], linestyle="--", color="darkcyan") - ax.plot(x, data["mean"], color="black") - ax.set_ylabel(ylabel) - ax.set_xlabel(xlabel) - - return fig, ax, data - - def check_duplicate_keys(dict_a: dict, dict_b: dict, log: logging.Logger) -> None: """Check if a key of dict_a is present in dict_b and then log a warning.""" for key in dict_a: From 2ce3c06f99f03ecb1f35066f465887bef8a75ead Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:20:42 +0200 Subject: [PATCH 22/27] clean up --- apax/nodes/md.py | 38 ++++++++++++++++++++------------------ apax/nodes/model.py | 10 +++++++--- tests/nodes/test_md.py | 2 +- 3 files changed, 28 insertions(+), 22 deletions(-) diff --git a/apax/nodes/md.py b/apax/nodes/md.py index 0872b7a3..075ae612 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -8,7 +8,8 @@ import yaml import znh5md import zntrack.utils -from zntrack import dvc, zn + +from apax.md.nvt import run_md from .model import Apax from .utils import check_duplicate_keys @@ -21,13 +22,15 @@ class ApaxJaxMD(zntrack.Node): Attributes ---------- + data: list[ase.Atoms] + MD starting structure + data_id: int, default=-1 + index of the configuration from the data list to use model: ApaxModel model to use for the simulation repeat: float number of repeats - md_parameter: dict - parameter for the MD simulation - md_parameter_file: str + config: str path to the MD simulation parameter file """ @@ -35,41 +38,40 @@ class ApaxJaxMD(zntrack.Node): data_id: int = zntrack.params(-1) model: Apax = zntrack.deps() - repeat = zn.params(None) + repeat = zntrack.params(None) + + config: str = zntrack.params_path(None) - md_parameter: dict = zn.params(None) - md_parameter_file: str = dvc.params(None) + sim_dir: pathlib.Path = zntrack.outs_path(zntrack.nwd / "md") + init_struc_dir: pathlib.Path = zntrack.outs_path( + zntrack.nwd / "initial_structure.extxyz" + ) - sim_dir: pathlib.Path = dvc.outs(zntrack.nwd / "md") - init_struc_dir: pathlib.Path = dvc.outs(zntrack.nwd / "initial_structure.extxyz") + _parameter: dict = None def _post_load_(self) -> None: self._handle_parameter_file() def _handle_parameter_file(self): - if self.md_parameter_file: - md_parameter_file_content = pathlib.Path(self.md_parameter_file).read_text() - self.md_parameter = yaml.safe_load(md_parameter_file_content) + with self.state.use_tmp_path(): + self._parameter = yaml.safe_load(pathlib.Path(self.config).read_text()) custom_parameters = { "sim_dir": self.sim_dir.as_posix(), "initial_structure": self.init_struc_dir.as_posix(), } - check_duplicate_keys(custom_parameters, self.md_parameter, log) - self.md_parameter.update(custom_parameters) + check_duplicate_keys(custom_parameters, self._parameter, log) + self._parameter.update(custom_parameters) def run(self): """Primary method to run which executes all steps of the model training""" - from apax.md.nvt import run_md - # self._handle_parameter_file() atoms = self.data[self.data_id] if self.repeat is not None: atoms = atoms.repeat(self.repeat) ase.io.write(self.init_struc_dir.as_posix(), atoms) - self.model._handle_parameter_file() - run_md(self.model._parameter, self.md_parameter) + run_md(self.model._parameter, self._parameter) @functools.cached_property def atoms(self) -> typing.List[ase.Atoms]: diff --git a/apax/nodes/model.py b/apax/nodes/model.py index 7cc7db9a..e61ad97a 100644 --- a/apax/nodes/model.py +++ b/apax/nodes/model.py @@ -23,14 +23,18 @@ class Apax(zntrack.Node): ---------- config: str path to the apax config file - validation_data: ase.Atoms + data: list[ase.Atoms] + the training data set + validation_data: list[ase.Atoms] atoms object with the validation data set + model: t.Optional[Apax] + model to be used as a base model model_directory: pathlib.Path model directory train_data_file: pathlib.Path - path to the training data + output path to the training data validation_data_file: pathlib.Path - path to the valdidation data + output path to the validation data """ data: list = zntrack.deps() diff --git a/tests/nodes/test_md.py b/tests/nodes/test_md.py index aa027551..033ea147 100644 --- a/tests/nodes/test_md.py +++ b/tests/nodes/test_md.py @@ -20,7 +20,7 @@ def test_n_jax_md(tmp_path, get_md22_stachyose): with proj: data = AddData(file=get_md22_stachyose) model = Apax(data=data.atoms, validation_data=data.atoms, config="example.yaml") - md = ApaxJaxMD(model=model, md_parameter_file="md.yaml", data=data.atoms) + md = ApaxJaxMD(model=model, config="md.yaml", data=data.atoms) proj.run() From a6140e151e7ec75f9337fd77327028d44b55d994 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:23:44 +0200 Subject: [PATCH 23/27] module import --- apax/nodes/__init__.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/apax/nodes/__init__.py b/apax/nodes/__init__.py index e69de29b..ae635831 100644 --- a/apax/nodes/__init__.py +++ b/apax/nodes/__init__.py @@ -0,0 +1,4 @@ +from .md import ApaxJaxMD +from .model import Apax, ApaxEnsemble + +__all__ = ["Apax", "ApaxEnsemble", "ApaxJaxMD"] From 0335fa79ad0dc47d75086e5b6d1d2e20ced65685 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:31:15 +0200 Subject: [PATCH 24/27] bugfix ? --- apax/nodes/md.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/apax/nodes/md.py b/apax/nodes/md.py index 075ae612..ea4b89c6 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -9,8 +9,6 @@ import znh5md import zntrack.utils -from apax.md.nvt import run_md - from .model import Apax from .utils import check_duplicate_keys @@ -65,6 +63,7 @@ def _handle_parameter_file(self): def run(self): """Primary method to run which executes all steps of the model training""" + from apax.md.nvt import run_md atoms = self.data[self.data_id] if self.repeat is not None: From 742f3d955eadfcfc582c6c34b74fa76d7afe5086 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:34:46 +0200 Subject: [PATCH 25/27] not a bugfix --- apax/nodes/md.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/apax/nodes/md.py b/apax/nodes/md.py index ea4b89c6..075ae612 100644 --- a/apax/nodes/md.py +++ b/apax/nodes/md.py @@ -9,6 +9,8 @@ import znh5md import zntrack.utils +from apax.md.nvt import run_md + from .model import Apax from .utils import check_duplicate_keys @@ -63,7 +65,6 @@ def _handle_parameter_file(self): def run(self): """Primary method to run which executes all steps of the model training""" - from apax.md.nvt import run_md atoms = self.data[self.data_id] if self.repeat is not None: From ab0bc7cfb34917f4cdbc61eba08e9b45380b98a6 Mon Sep 17 00:00:00 2001 From: PythonFZ Date: Fri, 5 Apr 2024 11:36:10 +0200 Subject: [PATCH 26/27] rename files --- tests/nodes/{test_md.py => test_n_md.py} | 0 tests/nodes/{test_model.py => test_n_model.py} | 0 tests/nodes/{test_utils.py => test_n_utils.py} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename tests/nodes/{test_md.py => test_n_md.py} (100%) rename tests/nodes/{test_model.py => test_n_model.py} (100%) rename tests/nodes/{test_utils.py => test_n_utils.py} (100%) diff --git a/tests/nodes/test_md.py b/tests/nodes/test_n_md.py similarity index 100% rename from tests/nodes/test_md.py rename to tests/nodes/test_n_md.py diff --git a/tests/nodes/test_model.py b/tests/nodes/test_n_model.py similarity index 100% rename from tests/nodes/test_model.py rename to tests/nodes/test_n_model.py diff --git a/tests/nodes/test_utils.py b/tests/nodes/test_n_utils.py similarity index 100% rename from tests/nodes/test_utils.py rename to tests/nodes/test_n_utils.py From 286f80e8932c2377e622ef66cb0d6599ea16dd3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Fri, 5 Apr 2024 15:58:08 +0200 Subject: [PATCH 27/27] properly added mlflow dependency --- poetry.lock | 1436 +++++++++++++++++++++++++++++++++++++++++------- pyproject.toml | 6 +- 2 files changed, 1246 insertions(+), 196 deletions(-) diff --git a/poetry.lock b/poetry.lock index be1a69da..7327a27e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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