IPS - The Inter Atomic Potential Suite

https://github.com/zincware/ipsuite
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### Install IPSuite from GitHub using Poetry

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/_get_started/quickstart.rst

Clones the latest IPSuite version from GitHub and installs dependencies using Poetry. This method is an alternative to using pip for installation.

```bash
git clone https://github.com/zincware/IPSuite.git
cd IPSuite
poetry install
```

--------------------------------

### Initialize Git and DVC for an IPS Project

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/_get_started/quickstart.rst

Initializes a new project directory with Git and DVC, which are necessary for IPSuite to function. This sets up version control and data management for the project.

```bash
mkdir project
cd project
git init
dvc init
```

--------------------------------

### Install xtb-python and packmol using Conda

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

Installs the necessary libraries 'xtb-python' and 'packmol' from the conda-forge channel. These are prerequisites for setting up initial configurations and performing calculations.

```bash
conda install -c conda-forge xtb-python
conda install -c conda-forge packmol
```

--------------------------------

### Node Example: Molecular Dynamics Simulation

Source: https://github.com/zincware/ipsuite/blob/main/AGENTS.md

An example demonstrating how to use an IPSuite Node to run a molecular dynamics simulation, starting from generating conformers and then executing the simulation. Assumes `project` and `ips` objects are available.

```python
with project:
    methanol_conformers = ips.Smiles2Conformers(smiles="CO", numConfs=5)
project.repro()
frames = methanol_conformers.frames
print(f"Generated {len(frames)} conformers.")
```

--------------------------------

### Initialize Project and Dependencies (Python)

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Imports necessary libraries from pathlib, ase, and zntrack for project management and molecular dynamics simulations. It also initializes a temporary directory for working files. This setup is crucial for subsequent data generation and manipulation within the IPS framework.

```python
from pathlib import Path

from ase import units
from ase.calculators.emt import EMT
from ase.io.trajectory import TrajectoryWriter
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.langevin import Langevin
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.visualize import view
from zntrack.utils import cwd_temp_dir

import ipsuite as ips

temp_dir = cwd_temp_dir()
```

--------------------------------

### Visualize Structures with ZnDraw

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/_get_started/quickstart.rst

Launches the ZnDraw application to visualize molecular structures generated by IPSuite nodes. This command specifically visualizes the single water molecule created by the Smiles2Atoms node.

```bash
zndraw nodes/Smiles2Atoms/structures.h5
```

--------------------------------

### Install Dependencies, Lint, and Test

Source: https://github.com/zincware/ipsuite/blob/main/AGENTS.md

Essential commands to run in sequence before committing code to ensure dependencies are installed, code is formatted and linted, and the test suite passes. These checks are enforced by CI.

```bash
uv sync
uvx pre-commit run --all-files
uv run pytest
```

--------------------------------

### Initialize Project Environment with Python Imports

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

Imports essential Python libraries for plotting, workflow management (znflow), temporary directory handling, and the IPSuite. It also sets up a temporary directory for operations.

```python
import matplotlib.pyplot as plt
import znflow
from zntrack.utils import cwd_temp_dir

import ipsuite as ips

temp_dir = cwd_temp_dir()
```

--------------------------------

### Docstring Example for IPSuite Node

Source: https://github.com/zincware/ipsuite/blob/main/CLAUDE.md

Demonstrates the expected format for Node docstrings in IPSuite, adhering to the numpy style. It includes an example showing how to use provided objects like `project` and `ips` to create and interact with a Node, illustrating expected output.

```python
Examples
--------
>>> with project:
...     methanol_conformers = ips.Smiles2Conformers(smiles="CO", numConfs=5)
>>> project.repro()
>>> frames = methanol_conformers.frames
>>> print(f"Generated {len(frames)} conformers.")
Generated 5 conformers.
```

--------------------------------

### Install IPSuite Package

Source: https://github.com/zincware/ipsuite/blob/main/README.md

Installs the IPSuite package using pip. This is a barebones installation and may require manual installation of third-party ML packages to avoid import errors.

```shell
pip install ipsuite
```

--------------------------------

### Generate Water Molecules using IPSuite and Packmol

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/_get_started/quickstart.rst

Generates a specified number of water molecules inside a box at a given density using IPSuite's Project, Smiles2Atoms, and Packmol nodes. The workflow is saved to DVC configuration files.

```python
import ipsuite as ips

with ips.Project() as project:
    # Generate a single water molecule
    mol = ips.Smiles2Atoms(smiles="O")
    # Duplicate water molecules
    packmol = ips.Packmol(
        data=[mol.frames], count=[10], density=876
        )

project.build()
```

--------------------------------

### Bootstrap Dataset Generation with IPSuite

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

Sets up and runs a data bootstrapping process using IPSuite. This involves creating initial atomic configurations, optimizing them with xTB, and generating diverse datasets through rattling, rotation, and translation of molecules, followed by volume scanning. The final dataset is combined and analyzed using energy and forces histograms.

```python
mapping = ips.geometry.BarycenterMapping()

with ips.Project() as project:
    water = ips.Smiles2Atoms(smiles="O")
    packmol = ips.Packmol(data=[water.atoms], count=[10], density=997)

    opt_calc = ips.xTBSinglePoint(data=packmol, method="gfn1-xtb", name="opt_calc")

    geopt = ips.ASEGeoOpt(
        model=opt_calc,
        data=packmol.atoms,
        optimizer="BFGS",
        run_kwargs={"fmax": 1.0},
    )

    n_configs = 5
    rattle = ips.bootstrap.RattleAtoms(
        data=geopt.atoms,
        data_id=-1,
        n_configurations=n_configs,
        maximum=0.08,  # Ang max atomic displacement
        include_original=True,
    )
    rotate = ips.bootstrap.RotateMolecules(
        data=geopt.atoms,
        data_id=-1,
        n_configurations=n_configs,
        maximum=15,  # deg max rotation
        include_original=False,
    )
    translate = ips.bootstrap.TranslateMolecules(
        data=geopt.atoms,
        data_id=-1,
        n_configurations=n_configs,
        maximum=0.3,  # Ang max molecular displacement
        include_original=False,
    )

    bootstrap_configurations = rattle.atoms + rotate.atoms + translate.atoms

    labeling_calc = ips.xTBSinglePoint(
        data=bootstrap_configurations, method="gfn1-xtb", name="label_calc"
    )
    volume_scan = ips.BoxScale(
        data=rattle.atoms,
        data_id=0,
        model=labeling_calc,
        mapping=mapping,
        start=0.8,
        stop=1.5,
        num=5,
    )
    bootstrap_dataset = znflow.combine([labeling_calc, volume_scan], attribute="atoms")

    energy_hist = ips.EnergyHistogram(data=bootstrap_dataset, bins=10)
    forces_hist = ips.ForcesHistogram(data=bootstrap_dataset, bins=10)

project.repro()
```

--------------------------------

### IPS Welcome Message and Progress Log

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

This snippet shows a welcome message from the Interatomic Potential Suite (IPS) along with progress indicators (e.g., percentage completion bars) and debug messages. It's typical output during the initialization or execution of IPS tasks.

```text
2023-05-30 16:18:23,396 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!

```

```
Output:
100%|██████████| 1/1 [00:00<00:00, 10.92it/s]

```

```
Output:
2023-05-30 16:18:24,687 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!
      Step     Time          Energy         fmax
BFGS:    0 16:18:24    -1452.227673      560.1183
BFGS:    1 16:18:25    -1525.179018       73.0175
BFGS:    2 16:18:25    -1541.432084       26.5437
BFGS:    3 16:18:25    -1548.847866       20.9261
BFGS:    4 16:18:25    -1553.041573       21.0507
BFGS:    5 16:18:25    -1557.985665       14.9412
BFGS:    6 16:18:25    -1560.632213        8.3526
BFGS:    7 16:18:25    -1562.409822        5.2405
BFGS:    8 16:18:25    -1563.889836        4.6672
BFGS:    9 16:18:26    -1565.320047       13.2885
BFGS:   10 16:18:26    -1566.448285        3.4639
BFGS:   11 16:18:26    -1567.953756        4.4025
BFGS:   12 16:18:26    -1568.948496        7.1006
BFGS:   13 16:18:26    -1569.550374        4.1206
BFGS:   14 16:18:26    -1570.227879        2.1917
BFGS:   15 16:18:26    -1570.532967        7.2313
BFGS:   16 16:18:26    -1570.847957        2.6559
BFGS:   17 16:18:27    -1571.138681        1.4818
BFGS:   18 16:18:27    -1571.662669        2.2882
BFGS:   19 16:18:27    -1571.800839        1.6854
BFGS:   20 16:18:27    -1571.956670        0.8907
2023-05-30 16:18:28,493 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!
2023-05-30 16:18:29,693 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!
2023-05-30 16:18:30,954 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!
2023-05-30 16:18:31,096 (WARNING): Setting maximum to 2 Pi.
2023-05-30 16:18:32,202 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!
2023-05-30 16:18:33,349 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!

```

```
Output:
100%|██████████| 16/16 [00:01<00:00,  8.80it/s]

```

```
Output:
2023-05-30 16:18:36,564 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!

```

```
Output:
Could not load field atoms for node BoxScale_mapping.
100%|███████████████████████████████████| 5/5 [00:00<00:00,  8.29it/s]

```

```
Output:
2023-05-30 16:18:38,818 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!
2023-05-30 16:18:40,299 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!

```
```

--------------------------------

### Visualizing DVC Workflow

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Displays the Directed Acyclic Graph (DAG) of the DVC (Data Version Control) workflow. This command helps visualize the dependencies between different stages and data nodes in the project, aiding in understanding the data processing pipeline.

```bash
!dvc dag
```

--------------------------------

### Run Molecular Dynamics Simulation (Python)

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Configures and runs a short molecular dynamics simulation using the Langevin thermostat. It sets up the simulation parameters like timestep, steps, temperature, assigns an EMT calculator, and saves the trajectory to a file. This generates the sample atomistic data.

```python
timestep = 5 * units.fs
steps = 100
temperature = 800
traj_path = Path(temp_dir.name) / "trajectory.traj"


atoms.calc = EMT()
MaxwellBoltzmannDistribution(atoms, temperature_K=temperature)

dyn = Langevin(atoms, timestep, temperature_K=temperature, friction=0.002)

writer = TrajectoryWriter(traj_path, "w", atoms=atoms)
dyn.attach(writer, interval=1)

dyn.run(steps)
```

--------------------------------

### Packmol Simulation Output and Success Message

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

This snippet displays the output of a Packmol simulation, indicating the packing process, objective function value, constraint violations, and a success message with final results. It also provides citation information for the Packmol tool.

```text
Current structure written to file: mixture.xyz
--------------------------------------------------------------------------------

  Packing solved for molecules of type           1
  Objective function value:    1.5567789525860229E-005
  Maximum violation of target distance:    0.0000000000000000     
  Max. constraint violation:    1.5567789525860229E-005
--------------------------------------------------------------------------------

################################################################################

  Packing all molecules together 

################################################################################


  Initial approximation is a solution. Nothing to do. 

  Solution written to file: mixture.xyz

################################################################################

                                 Success! 
              Final objective function value: .31847E-01
              Maximum violation of target distance:   0.000000
              Maximum violation of the constraints: .15568E-04

--------------------------------------------------------------------------------

              Please cite this work if Packmol was useful: 

           L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, 
         PACKMOL: A package for building initial configurations for
                   molecular dynamics simulations. 
          Journal of Computational Chemistry, 30:2157-2164,2009.

################################################################################

   Running time:    5.92000026E-04  seconds. 

--------------------------------------------------------------------------------
```

--------------------------------

### Temporal Data Splitting with IPS

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Implements a temporally aware data splitting strategy using IPS to ensure that validation and training splits do not temporally overlap with the test set. It uses `SplitSelection` for initial partitioning and `UniformTemporalSelection` and `UniformEnergeticSelection` for final data selection.

```python
with ips.Project() as project:
    trajectory = ips.AddData(file=traj_path, name="trajectory")
    test_split = ips.SplitSelection(data=trajectory, split=0.1, name="test_split")
    val_split = ips.SplitSelection(
        data=test_split.excluded_atoms, split=0.17, name="val_split"
    )  # 0.15 / 0.9 * 1.0 \approx 0.17
    train_split = val_split.excluded_atoms  # 0.8 of the total data

    test_data = ips.UniformTemporalSelection(
        data=test_split, n_configurations=10, name="test_data"
    )
    val_data = ips.UniformTemporalSelection(
        data=val_split, n_configurations=15, name="val_data"
    )
    train_data = ips.UniformEnergeticSelection(
        data=train_split, n_configurations=80, name="train_data"
    )

project.repro()
```

--------------------------------

### Load and Visualize Trajectory Data (Python)

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Demonstrates how to load the trajectory data processed by IPS and visualize it using ASE's `view` function. The loaded data is a list of ASE Atoms objects, suitable for further analysis or visualization.

```python
trajectory.load()  # requires the project to have been run
view(trajectory)
```

--------------------------------

### Load Trajectory Data with IPS (Python)

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Loads the previously generated trajectory data into the IPS project using the `AddData` Node. It then calls `project.repro()` to execute the data loading process and track the file with DVC. This makes the trajectory data accessible within the IPS environment.

```python
with ips.Project() as project:
    trajectory = ips.AddData(file=traj_path, name="trajectory")
project.repro()
```

--------------------------------

### Random Data Splitting with IPS

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/01_Data_Loading_and_Selection.ipynb

Demonstrates random partitioning of data into training, validation, and test sets using IPS. It utilizes `RandomSelection` nodes to iteratively exclude configurations for each split. This method is simple but may lead to temporal overlap between splits for sequential data.

```python
with project:
    random_test_selection = ips.RandomSelection(
        data=trajectory, n_configurations=10, name="random_test_selection"
    )
    random_val_selection = ips.RandomSelection(
        data=random_test_selection.excluded_atoms,
        n_configurations=15,
        name="random_val_selection",
    )
    random_train_selection = ips.RandomSelection(
        data=random_val_selection.excluded_atoms,
        n_configurations=75,
        name="random_train_selection",
    )
project.repro()
```

--------------------------------

### Cleanup Temporary Directory in Python

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

This Python snippet demonstrates how to clean up a temporary directory. It's typically used after data generation or processing to free up disk space. Ensure that the `temp_dir` object is properly initialized before calling this method.

```python
temp_dir.cleanup()
```

--------------------------------

### Configure PLUMED Metadynamics Input

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/07_metadyanmics_data_generating.ipynb

Defines the PLUMED input file content for metadynamics. It specifies collective variables (torsion angles phi and psi), the metadynamics bias parameters (height, sigma, pace), and output files (HILLS, COLVAR). This setup is crucial for guiding the simulation.

```python
thermostat = ips.LangevinThermostat(
    time_step=0.5,
    temperature=300,
    friction=0.01,
)

FILE = """
FLUSH STRIDE=10000
phi: TORSION ATOMS=8,7,5,3
psi: TORSION ATOMS=7,5,3,2
restraint: METAD ARG=phi,psi SIGMA=0.35,0.35 HEIGHT=1.2 BIASFACTOR=8 \
           PACE=400 FILE=HILLS GRID_MIN=-pi,-pi GRID_MAX=pi,pi
PRINT ARG=phi,psi FILE=COLVAR STRIDE=1
"""
with Path("plumed.dat").open("w") as f:
    f.write(FILE)
```

--------------------------------

### Create and Optimize Alanine Dipeptide System

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/07_metadyanmics_data_generating.ipynb

Constructs a system containing an alanine dipeptide molecule using SMILES notation and optimizes its geometry using the specified model and optimizer. The output 'geoopt.frames' serves as the starting point for further simulations.

```python
with project.group("System_Creation"):
    mol = ips.Smiles2Atoms(smiles="CNC(=O)[C@H](C)NC(C)=O")
    geoopt = ips.ASEGeoOpt(
        data=mol.frames, model=mace, optimizer="FIRE", run_kwargs={"fmax": 0.05}
    )
```

--------------------------------

### Fix Docker Permission Issues

Source: https://github.com/zincware/ipsuite/blob/main/README.md

Provides shell commands to resolve file permission issues that may arise when switching between Docker containers and a host system's DVC installation. It includes methods to change file ownership both from the host and within the Docker container.

```shell
echo $(id -u):$(id -g)
docker run -it -v "$(pwd):/app" pythonf/ipsuite /bin/bash
addgroup --gid $GROUP_ID user
adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID user
chown user:user -R .
```

--------------------------------

### Python: Load and Plot Energy Histogram using IPS Data

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

This Python snippet demonstrates how to load histogram data from an IPS energy histogram object and then visualize it using matplotlib. It assumes the `energy_hist` object has been previously defined and loaded, and it displays a log-scaled histogram of energy counts.

```python
energy_hist.load()
forces_hist.load()
```

```python
counts, bin_edges = energy_hist.get_hist()

plt.stairs(counts, bin_edges, fill=True)
plt.xlabel(energy_hist.xlabel)
plt.ylabel(energy_hist.ylabel)
plt.yscale("log")
plt.show()
```

--------------------------------

### Python: Load and Plot Forces Histogram using IPS Data

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/06_Bootstrapping_Datasets.ipynb

This Python snippet shows how to load histogram data for forces from an IPS object and plot it using matplotlib. Similar to the energy histogram, it assumes a `forces_hist` object is available and displays a log-scaled plot of force counts.

```python
counts, bin_edges = forces_hist.get_hist()

plt.stairs(counts, bin_edges, fill=True)
plt.xlabel(forces_hist.xlabel)
plt.ylabel(forces_hist.ylabel)
plt.yscale("log")
plt.show()
```

--------------------------------

### Initialize Git and DVC Repositories

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb

Initializes Git and DVC (Data Version Control) repositories in the current directory. This is a standard practice for versioning code and data in machine learning projects. No specific inputs or outputs are defined, but it sets up the project for version control.

```bash
!git init
!dvc init
```

--------------------------------

### Set up IPSuite Project and MACE-MP0 Model

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/07_metadyanmics_data_generating.ipynb

Initializes an IPSuite project and configures the MACE-MP0 model for subsequent calculations. This is a foundational step for running simulations within the IPSuite framework.

```python
import ipsuite as ips

project = ips.Project()
mace = ips.MACEMPModel()
```

--------------------------------

### Initialize Python Environment with IPS Utilities

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb

Sets up the Python environment for IPS analysis by importing necessary modules from pathlib, ase, and zntrack. It creates a temporary directory for operations. Dependencies include pathlib, ase, and zntrack.

```python
from pathlib import Path

from ase import units
from ase.calculators.emt import EMT
from ase.io.trajectory import TrajectoryWriter
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.langevin import Langevin
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from zntrack.utils import cwd_temp_dir

temp_dir = cwd_temp_dir()
```

--------------------------------

### Run NPT Simulations with Barostats in Python

Source: https://context7.com/zincware/ipsuite/llms.txt

This snippet demonstrates how to perform NPT (constant Number of particles, Pressure, and Temperature) simulations using Ipsuite's NPTThermostat and SVCRBarostat. It includes setting up the simulation parameters like time step, temperature, pressure, and coupling times, and analyzing the final density. Dependencies include the ipsuite and pandas libraries.

```python
import ipsuite as ips

project = ips.Project()

with project:
    initial = ips.AddData(file="liquid_box.xyz")

    model = ips.MACEMPModel(model="large", device="cuda")

    # Nose-Hoover + Parrinello-Rahman NPT
    npt_thermostat = ips.NPTThermostat(
        time_step=0.5,
        temperature=300,  # K
        pressure=1.01325,  # bar (converted internally)
        ttime=100,  # Temperature coupling (fs)
        pfactor=2000000,  # Pressure coupling
        tetragonal_strain=False  # Allow all cell deformations
    )

    # Stochastic cell rescaling barostat
    svcr_barostat = ips.SVCRBarostat(
        time_step=1.0,
        temperature=350,
        betaT=4.57e-5,  # Isothermal compressibility
        pressure_au=1.01325,
        taut=100,  # Temperature damping (fs)
        taup=1000  # Pressure damping (fs)
    )

    # NPT equilibration
    npt_md = ips.ASEMD(
        model=model,
        data=initial.frames,
        thermostat=npt_thermostat,
        steps=50000,
        sampling_rate=10,
        checks=[
            ips.DensityCheck(min_density=800, max_density=1200)
        ]
    )

project.repro()

# Analyze density evolution
import pandas as pd
metrics = pd.read_csv(npt_md.metrics[0])
print(f"Final density: {metrics['density'].iloc[-1]:.2f} kg/m³")
```

--------------------------------

### Create and Execute Workflows with Project Context Manager (Python)

Source: https://context7.com/zincware/ipsuite/llms.txt

Demonstrates defining and executing a complete atomistic simulation workflow using the IPSuite Project context manager. It includes steps for loading structures, creating an ensemble model, running MD simulations with temperature control, and analyzing force predictions. The workflow execution relies on ZnTrack and DVC for reproducibility.

```python
import ipsuite as ips

# Define workflow
project = ips.Project()

with project:
    # Load molecular structures
    water = ips.Smiles2Conformers(smiles="O", numConfs=50, seed=42)

    # Create ensemble model for uncertainty quantification
    model = ips.MACEMPModel(model="medium", device="cuda")

    # Run MD simulation with temperature control
    thermostat = ips.LangevinThermostat(
        time_step=0.5,  # fs
        temperature=300,  # K
        friction=0.02
    )

    md_simulation = ips.ASEMD(
        model=model,
        data=water.frames,
        thermostat=thermostat,
        steps=10000,
        sampling_rate=10,
        checks=[ips.TemperatureCheck(max_temperature=500)]
    )

    # Analyze force predictions
    analysis = ips.ForcesHistogram(
        data=md_simulation.frames,
        bins=100,
        logy_scale=True
    )

# Execute all defined Nodes in dependency order
project.repro()  # Uses DVC to execute only changed nodes

# Access results after execution
frames = md_simulation.frames  # List[ase.Atoms]
print(f"Collected {len(frames)} MD frames")
```

--------------------------------

### Complete Active Learning Loop with Uncertainty-Driven Selection in Python

Source: https://context7.com/zincware/ipsuite/llms.txt

This Python script demonstrates a full active learning cycle. It uses IPSuite to generate initial structures, perform reference calculations, run molecular dynamics with ensemble uncertainty, select high-uncertainty configurations, retrain a model, and validate its performance. Dependencies include ipsuite, and potentially external ML training nodes (commented out).

```python
import ipsuite as ips

project = ips.Project()

with project:
    # 1. Initial structure generation
    water = ips.Smiles2Conformers(smiles="O", numConfs=100, seed=42)
    box = ips.Packmol(
        data=[water.frames],
        count=[64],
        density=1000
    )

    # 2. Initial reference calculations
    reference_calc = ips.CP2KModel(
        config="cp2k_pbe.yaml",
        files=["BASIS_MOLOPT", "GTH_POTENTIALS"],
        cmd="mpirun -np 16 cp2k_shell.psmp"
    )
    initial_training = ips.ApplyCalculator(
        data=box.frames,
        model=reference_calc
    )

    # 3. Train initial models (external ML training nodes)
    # model_v1 = TrainMACE(data=initial_training.frames, ...)
    # model_v2 = TrainMACE(data=initial_training.frames, ...)

    # 4. Run exploratory MD with ensemble uncertainty
    ensemble = ips.EnsembleModel(models=[model_v1, model_v2])

    thermostat = ips.LangevinThermostat(
        time_step=0.5,
        temperature=350,
        friction=0.02
    )

    md_exploration = ips.ASEMD(
        model=ensemble,
        data=box.frames,
        thermostat=thermostat,
        steps=50000,
        sampling_rate=5,
        checks=[
            ips.ThresholdCheck(
                key="forces_uncertainty",
                max_value=0.12,
                window_size=500
            ),
            ips.TemperatureCheck(max_temperature=500),
            ips.NaNCheck()
        ]
    )

    # 5. Select high-uncertainty configurations
    uncertain_configs = ips.ThresholdSelection(
        data=md_exploration.frames,
        key="forces_uncertainty",
        threshold=0.08,
        n_configurations=50,
        min_distance=10
    )

    # 6. Calculate reference for uncertain structures
    new_references = ips.ApplyCalculator(
        data=uncertain_configs.frames,
        model=reference_calc
    )

    # 7. Combine with original training data
    combined_training = ips.Flatten(
        data=[initial_training.frames, new_references.frames]
    )

    # 8. Retrain models with expanded dataset
    # model_v3 = TrainMACE(data=combined_training.frames, ...)

    # 9. Validate on held-out test set
    test_set = ips.RandomSelection(
        data=initial_training.frames,
        n_configurations=20,
        seed=999
    )

    final_predictions = ips.ApplyCalculator(
        data=test_set.frames,
        model=model_v3
    )

    validation_metrics = ips.PredictionMetrics(
        x=test_set.frames,
        y=final_predictions.frames
    )

project.repro()

print(f"Active learning cycle complete")
print(f"Initial training: {len(initial_training.frames)} configs")
print(f"New samples: {len(new_references.frames)} configs")
print(f"Total training: {len(combined_training.frames)} configs")
print(f"Final MAE: {validation_metrics.forces['mae']:.3f} meV/Å")

```

--------------------------------

### Implement Active Learning with Threshold Checks in Python

Source: https://context7.com/zincware/ipsuite/llms.txt

This Python snippet demonstrates how to set up a simulation with active learning using threshold checks. It defines an ensemble model, a molecular dynamics simulation with uncertainty-based stopping criteria, and a mechanism to select uncertain frames for retraining. Dependencies include the 'ipsuite' library.

```python
import ipsuite as ips

project = ips.Project()

with project:
    initial = ips.Smiles2Conformers(smiles="CCO", numConfs=1)

    box = ips.Packmol(data=[initial.frames], count=[50], density=800)

    # Ensemble for uncertainty quantification
    model1 = ips.MACEMPModel(model_path="model_v1.pth", device="cuda")
    model2 = ips.MACEMPModel(model_path="model_v2.pth", device="cuda")
    ensemble = ips.EnsembleModel(models=[model1, model2])

    thermostat = ips.LangevinThermostat(
        time_step=0.5,
        temperature=350,
        friction=0.02
    )

    # MD with uncertainty-based stopping
    md = ips.ASEMD(
        model=ensemble,
        data=box.frames,
        thermostat=thermostat,
        steps=100000,
        sampling_rate=5,
        checks=[
            # Stop if force uncertainty too high
            ips.ThresholdCheck(
                key="forces_uncertainty",
                max_value=0.15,  # meV/Å threshold
                window_size=500,  # Average over 500 frames
                minimum_window_size=100,
                larger_only=False
            ),
            # Stop if energy uncertainty too high
            ips.ThresholdCheck(
                key="energy_uncertainty",
                max_value=10.0,  # meV/atom threshold
                window_size=500
            ),
            # Standard safety checks
            ips.NaNCheck(),
            ips.TemperatureCheck(max_temperature=600)
        ]
    )

    # Select uncertain frames for labeling
    uncertain = ips.ThresholdSelection(
        data=md.frames,
        key="forces_uncertainty",
        threshold=0.1,
        n_configurations=20
    )

    # Label with reference method
    reference = ips.CP2KModel(config="cp2k.yaml", files=["BASIS", "POT"])
    labeled = ips.ApplyCalculator(
        data=uncertain.frames,
        model=reference
    )

project.repro()

print(f"MD stopped after {len(md.frames)} frames")
print(f"Selected {len(uncertain.frames)} frames for retraining")

```

--------------------------------

### Listing Available Models in ipsuite

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/02_Training_Models.ipynb

This code snippet shows how to access and display a list of all available models within the ipsuite library. This is useful for understanding the scope of models you can use.

```python
ips.__all__
```

--------------------------------

### Importing ipsuite Library

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/02_Training_Models.ipynb

This snippet demonstrates the basic import statement for the ipsuite library in Python. It's the first step to utilizing any functionality within the library.

```python
import ipsuite as ips
```

--------------------------------

### Run IPSuite Docker Commands

Source: https://github.com/zincware/ipsuite/blob/main/README.md

Demonstrates various commands to run IPSuite within a Docker container on Linux. These commands allow for tasks such as running dvc repro, executing Python code, listing zntrack, and launching Jupyter Lab.

```shell
docker run -it -v "$(pwd):/app" --gpus all pythonf/ipsuite dvc repro
docker run -it -v "$(pwd):/app" --gpus all pythonf/ipsuite python
docker run -it -v "$(pwd):/app" --gpus all pythonf/ipsuite zntrack list
docker run -it -v "$(pwd):/app" --gpus all --rm -p 8888:8888 pythonf/ipsuite jupyter lab --ip=0.0.0.0 --port=8888 --allow-root
```

--------------------------------

### Build IPSuite Project

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/07_metadyanmics_data_generating.ipynb

Builds the IPSuite project, which triggers the execution of all defined nodes and saves the project's configuration. This command initiates the actual simulation and data generation process.

```python
project.build()
```

--------------------------------

### Initialize PLUMED Calculator and Run MD Simulation

Source: https://github.com/zincware/ipsuite/blob/main/docs/source/examples/07_metadyanmics_data_generating.ipynb

Initializes the PLUMED calculator using the previously defined input file and the optimized geometry. It then sets up and runs an Adaptive String Method (ASE) Molecular Dynamics simulation using the PLUMED calculator as the model.

```python
with project.group("METAD"):
    calc = ips.PlumedModel(
        model=mace,
        data=geoopt.frames,
        data_id=-1,
        config="plumed.dat",
        timestep=0.5,
        temperature=300,
    )

    md = ips.ASEMD(
        model=calc,
        data=geoopt.frames,
        thermostat=thermostat,
        steps=4_000_000,
    )
```

--------------------------------

### Run Geometry Optimization with ipSuite

Source: https://context7.com/zincware/ipsuite/llms.txt

This snippet demonstrates how to perform geometry optimizations using ipSuite's ASEGeoOpt, which integrates with ASE optimizers. It allows for optimization of multiple structures, setting convergence criteria, step sizes, and applying constraints or checks.

```python
import ipsuite as ips

project = ips.Project()

with project:
    structures = ips.Smiles2Conformers(smiles="CCO", numConfs=10)

    model = ips.MACEMPModel(model="medium")

    # Optimize structures
    optimization = ips.ASEGeoOpt(
        data=structures.frames,
        data_id=-1,  # Optimize all structures (-1 means all)
        model=model,
        optimizer="FIRE",  # FIRE, BFGS, LBFGS, etc.
        run_kwargs={"fmax": 0.05},  # Force convergence: 0.05 eV/Å
        maxstep=0.2,  # Maximum step size (Å)
        sampling_rate=10,  # Save every 10th step
        dump_rate=1000  # Checkpoint every 1000 steps
    )

    # Optimize with constraints
    constrained_opt = ips.ASEGeoOpt(
        data=structures.frames,
        data_id=0,  # Optimize only first structure
        model=model,
        optimizer="BFGS",
        run_kwargs={"fmax": 0.01},
        constraints=[
            ips.FixedLayerConstraint(upper_limit=5.0, lower_limit=0.0)
        ],
        checks=[
            ips.EnergySpikeCheck(max_factor=2.0)
        ]
    )

project.repro()

# Access optimization trajectory
trajectory = optimization.frames  # All optimization steps
final_structures = [traj[-1] for traj in trajectory]
print(f"Optimized {len(final_structures)} structures")
```

--------------------------------

### Use CP2K and ORCA Quantum Chemistry Codes

Source: https://context7.com/zincware/ipsuite/llms.txt

Provides interfaces to CP2K (CP2KModel) and ORCA (ORCAModel) for quantum chemistry calculations. Supports configuration files, basis sets, potentials, and command-line execution. TBLiteModel is also available for tight-binding DFTB.

```python
import ipsuite as ips

project = ips.Project()

with project:
    structures = ips.Smiles2Conformers(smiles="CO", numConfs=5)

    # CP2K model with configuration file
    cp2k = ips.CP2KModel(
        config="cp2k_config.yaml",  # Contains CP2K input parameters
        files=["BASIS_MOLOPT", "GTH_POTENTIALS"],
        cmd="mpirun -np 4 cp2k_shell.psmp"
    )

    # ORCA model with inline configuration
    orca = ips.ORCAModel(
        simpleinput="B3LYP def2-TZVP TightSCF",
        blocks="%pal nprocs 8 end\n%scf maxiter 200 end",
        cmd="/opt/orca/orca"
    )

    # Tight-binding DFTB with TBLite
    tblite = ips.TBLiteModel()

    # Calculate reference energies and forces
    cp2k_calc = ips.ApplyCalculator(
        data=structures.frames,
        model=cp2k
    )

    orca_calc = ips.ApplyCalculator(
        data=structures.frames,
        model=orca
    )

project.repro()

# Compare results
for cp2k_atoms, orca_atoms in zip(cp2k_calc.frames, orca_calc.frames):
    e_cp2k = cp2k_atoms.get_potential_energy()
    e_orca = orca_atoms.get_potential_energy()
    print(f"CP2K: {e_cp2k:.3f} eV, ORCA: {e_orca:.3f} eV")
```

--------------------------------

### Load Atomic Configurations from Files with ipsuite

Source: https://context7.com/zincware/ipsuite/llms.txt

Imports structures from ASE-compatible formats for use in workflows. Supports various file types including XYZ and H5MD, and allows loading a specific number of configurations. Requires the 'ipsuite' library.

```python
import ipsuite as ips

project = ips.Project()

with project:
    # Load trajectory file
    trajectory = ips.AddData(
        file="md_trajectory.xyz",
        name="trajectory"
    )

    # Load specific number of configurations
    partial_data = ips.AddData(
        file="large_dataset.extxyz",
        lines_to_read=1000,
        name="partial"
    )

    # Load H5MD format (faster I/O)
    h5md_data = ips.AddDataH5MD(
        file="simulation.h5",
        name="h5md"
    )

project.repro()

# Access loaded configurations
structures = trajectory.frames  # List[ase.Atoms]
print(f"Loaded {len(structures)} structures")
print(f"First structure has {len(structures[0])} atoms")
```

--------------------------------

### Run Molecular Dynamics with ipSuite

Source: https://context7.com/zincware/ipsuite/llms.txt

This snippet demonstrates running molecular dynamics (MD) simulations using ipSuite's ASEMD. It allows for various thermostats (e.g., Langevin), safety checks (e.g., NaN, temperature, energy spikes), and configuration of simulation parameters like time step, temperature, and friction.

```python
import ipsuite as ips
import pandas as pd

project = ips.Project()

with project:
    initial = ips.Smiles2Conformers(smiles="O", numConfs=1)

    box = ips.Packmol(
        data=[initial.frames],
        count=[100],
        density=1000  # Water density
    )

    model = ips.MACEMPModel(model="medium", device="cuda")

    # Langevin thermostat for NVT
    thermostat = ips.LangevinThermostat(
        time_step=0.5,  # fs
        temperature=300,  # K
        friction=0.02
    )

    # MD simulation with safety checks
    md = ips.ASEMD(
        model=model,
        data=box.frames,
        data_ids=-1,  # Run all configurations
        thermostat=thermostat,
        steps=100000,
        sampling_rate=10,  # Save every 10 steps
        dump_rate=1000,  # Checkpoint every 1000 steps
        repeat=(1, 1, 1),  # Cell repetition
        seed=42,
        checks=[
            ips.NaNCheck(),
            ips.TemperatureCheck(max_temperature=500),
            ips.EnergySpikeCheck(min_factor=0.5, max_factor=2.0),
            ips.ConnectivityCheck(bonded_min_dist=0.6, bonded_max_dist=2.0)
        ]
    )

project.repro()

# Access trajectory
trajectory = md.frames
print(f"Collected {len(trajectory)} MD frames")

# Access metrics CSV
metrics = pd.read_csv(md.metrics[0])
print(metrics[["step", "temperature", "energy"]].head())
```

--------------------------------

### Analyze Uncertainty Calibration in Python

Source: https://context7.com/zincware/ipsuite/llms.txt

This Python snippet demonstrates how to analyze the calibration of uncertainty estimates using the 'ipsuite' library. It involves setting up reference calculations and ensemble predictions, then using the 'CalibrationMetrics' class to evaluate metrics like MACE, Miscalibration Area, and NLL. Plots visualizing the calibration curve are also generated.

```python
import ipsuite as ips

project = ips.Project()

with project:
    structures = ips.AddData(file="validation.xyz")

    # Reference
    reference = ips.ApplyCalculator(
        data=structures.frames,
        model=ips.CP2KModel(config="cp2k.yaml", files=["BASIS", "POT"])
    )

    # Ensemble predictions with uncertainty
    ensemble = ips.EnsembleModel(models=[
        ips.MACEMPModel(model_path="model1.pth"),
        ips.MACEMPModel(model_path="model2.pth"),
        ips.MACEMPModel(model_path="model3.pth")
    ])
    predictions = ips.ApplyCalculator(
        data=structures.frames,
        model=ensemble
    )

    # Calibration analysis
    calibration = ips.CalibrationMetrics(
        x=reference.frames,
        y=predictions.frames,
        force_dist_slices=[(0, 50), (50, 100), (100, 200)]  # meV/Å bins
    )

project.repro()

# Calibration metrics
print(f"MACE (Mean Abs Calibration Error): {calibration.mace:.4f}")
print(f"Miscalibration Area: {calibration.miscalibration_area:.4f}")
print(f"NLL (Negative Log-Likelihood): {calibration.nll:.4f}")

# Plots in calibration.plots_dir:
# - calibration_curve.png: Expected vs observed error

```

--------------------------------

### Compare Model Predictions with Reference Data in Python

Source: https://context7.com/zincware/ipsuite/llms.txt

This Python snippet outlines the process of comparing machine learning model predictions against reference data using the 'ipsuite' library. It involves loading structures, applying reference and ML models, and computing various error metrics such as MAE, RMSE, and R². The output includes printed metrics and generated plots for energy and forces.

```python
import ipsuite as ips

project = ips.Project()

with project:
    structures = ips.AddData(file="test_set.xyz")

    # Reference calculations
    reference_model = ips.CP2KModel(
        config="cp2k_ref.yaml",
        files=["BASIS", "POTENTIALS"]
    )
    reference = ips.ApplyCalculator(
        data=structures.frames,
        model=reference_model
    )

    # ML predictions
    ml_model = ips.MACEMPModel(model_path="trained_model.pth")
    predictions = ips.ApplyCalculator(
        data=structures.frames,
        model=ml_model
    )

    # Compute metrics
    metrics = ips.PredictionMetrics(
        x=reference.frames,  # Reference
        y=predictions.frames,  # Predictions
        figure_ymax={
            "energy": 50,  # meV/atom
            "forces": 200  # meV/Å
        }
    )

project.repro()

# Access computed metrics
print(f"Energy MAE: {metrics.energy['mae']:.3f} meV/atom")
print(f"Energy RMSE: {metrics.energy['rmse']:.3f} meV/atom")
print(f"Energy R²: {metrics.energy['r2']:.4f}")
print(f"Forces MAE: {metrics.forces['mae']:.3f} meV/Å")
print(f"Forces RMSE: {metrics.forces['rmse']:.3f} meV/Å")
print(f"Forces R²: {metrics.forces['r2']:.4f}")

# Plots automatically saved to metrics.plots_dir
# - energy_scatter.png: Energy correlation plot
# - forces_scatter.png: Forces correlation plot
# - energy_histogram.png: Error distribution

```

--------------------------------

### Apply Constraints During Simulations in Python

Source: https://context7.com/zincware/ipsuite/llms.txt

This Python snippet demonstrates how to apply various constraints during molecular dynamics simulations using Ipsuite. It covers fixing layers, spherical regions, bond lengths, and applying spring forces. Dependencies include the ipsuite library.

```python
import ipsuite as ips

project = ips.Project()

with project:
    surface = ips.AddData(file="surface_system.xyz")

    model = ips.MACEMPModel(model="medium")

    thermostat = ips.LangevinThermostat(
        time_step=1.0,
        temperature=300,
        friction=0.02
    )

    # Constrained MD simulation
    md = ips.ASEMD(
        model=model,
        data=surface.frames,
        thermostat=thermostat,
        steps=10000,
        constraints=[
            # Fix bottom layer of surface
            ips.FixedLayerConstraint(
                lower_limit=0.0,
                upper_limit=5.0
            ),
            # Fix atoms in spherical region
            ips.FixedSphereConstraint(
                radius=3.0,
                atom_id=0  # Center on atom 0
            ),
            # Fix specific bond length
            ips.FixedBondLengthConstraint(
                atom_id_1=10,
                atom_id_2=11
            ),
            # Apply spring forces between atom pairs
            ips.HookeanConstraint(
                atom_ids=[(5, 6), (7, 8)],
                k=10.0,  # Spring constant (eV/Å²)
                rt=2.5   # Threshold distance (Å)
            )
        ]
    )

project.repro()

print(f"Constrained MD: {len(md.frames)} frames")
```
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