.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/dynamics/03_nph_integration.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_dynamics_03_nph_integration.py: NPH Dynamics (MTK) with Lennard-Jones Potential ============================================== This example demonstrates **isothermal-free** (no thermostat) NPH dynamics using the Martyna-Tobias-Klein (MTK) barostat and the Lennard-Jones (LJ) potential. NPH maintains constant enthalpy and pressure (in the extended-system sense), and is useful for testing barostat mechanics and pressure coupling. .. GENERATED FROM PYTHON SOURCE LINES 28-44 .. code-block:: Python from __future__ import annotations import matplotlib.pyplot as plt import numpy as np import warp as wp from _dynamics_utils import ( DEFAULT_CUTOFF, DEFAULT_SKIN, EPSILON_AR, SIGMA_AR, MDSystem, create_fcc_argon, pressure_atm_to_ev_per_a3, run_nph_mtk, ) .. GENERATED FROM PYTHON SOURCE LINES 45-73 .. code-block:: Python print("=" * 95) print("NPH (MTK) DYNAMICS WITH LENNARD-JONES POTENTIAL") print("=" * 95) print() device = "cuda:0" if wp.is_cuda_available() else "cpu" print(f"Using device: {device}") print("\n--- Creating FCC Argon System ---") positions, cell = create_fcc_argon(num_unit_cells=4, a=5.26) # 256 atoms print(f"Created {len(positions)} atoms in {cell[0, 0]:.2f} ų box") print("\n--- Initializing MD System ---") system = MDSystem( positions=positions, cell=cell, epsilon=EPSILON_AR, sigma=SIGMA_AR, cutoff=DEFAULT_CUTOFF, skin=DEFAULT_SKIN, switch_width=0.0, device=device, dtype=np.float64, ) print("\n--- Setting Initial Temperature ---") system.initialize_temperature(temperature=94.4, seed=42) .. rst-class:: sphx-glr-script-out .. code-block:: none =============================================================================================== NPH (MTK) DYNAMICS WITH LENNARD-JONES POTENTIAL =============================================================================================== Using device: cuda:0 --- Creating FCC Argon System --- Created 256 atoms in 21.04 ų box --- Initializing MD System --- Initialized MD system with 256 atoms Cell: 21.04 x 21.04 x 21.04 Å Cutoff: 8.50 Å (+ 0.50 Å skin) LJ: ε = 0.0104 eV, σ = 3.40 Å Device: cuda:0, dtype: Units: x [Å], t [fs], E [eV], m [eV·fs²/Ų] (from amu), v [Å/fs] --- Setting Initial Temperature --- Initialized velocities: target=94.4 K, actual=90.4 K .. GENERATED FROM PYTHON SOURCE LINES 74-86 .. code-block:: Python print("\n--- NPH Run (3000 steps) ---") print(f"Pressure units sanity: 1 atm = {pressure_atm_to_ev_per_a3(1.0):.6e} eV/ų") stats = run_nph_mtk( system=system, num_steps=3000, dt_fs=1.0, target_pressure_atm=1.0, pdamp_fs=5000.0, reference_temperature_K=94.4, log_interval=200, ) .. rst-class:: sphx-glr-script-out .. code-block:: none --- NPH Run (3000 steps) --- Pressure units sanity: 1 atm = 6.324209e-07 eV/ų Running 3000 NPH (MTK) steps at P=1.000 atm dt = 1.000 fs, pdamp = 5000.0 fs (barostat timescale) ======================================================================================================================== Step KE (eV) PE (eV) Total (eV) T (K) P (atm) V (Å^3) Neighbors min r (Å) max|F| ======================================================================================================================== 0 2.9787 -21.5621 -18.5833 90.37 483.900 9314.02 9984 3.713 2.313e-03 200 1.2437 -19.7223 -18.4786 37.73 1874.371 9315.29 10304 3.324 1.421e-01 400 1.5568 -20.0382 -18.4814 47.23 1616.679 9320.21 10251 3.313 1.767e-01 600 1.3286 -19.8128 -18.4842 40.31 1759.341 9328.40 10272 3.345 1.635e-01 800 1.5427 -20.0477 -18.5050 46.80 1535.262 9339.90 10238 3.238 1.957e-01 1000 1.5328 -20.0559 -18.5231 46.50 1490.899 9354.50 10246 3.319 1.423e-01 1200 1.4868 -20.0141 -18.5273 45.11 1456.033 9372.10 10230 3.324 1.814e-01 1400 1.4602 -19.9886 -18.5284 44.30 1399.313 9392.63 10220 3.254 1.923e-01 1600 1.5267 -20.0742 -18.5475 46.32 1264.287 9416.05 10197 3.296 1.873e-01 1800 1.5781 -20.1337 -18.5556 47.88 1126.031 9442.13 10184 3.334 1.587e-01 2000 1.4324 -20.0079 -18.5755 43.46 1150.127 9470.71 10200 3.331 1.761e-01 2200 1.4594 -20.0437 -18.5843 44.28 1015.622 9501.66 10168 3.305 1.580e-01 2400 1.3964 -19.9745 -18.5781 42.36 957.259 9534.74 10164 3.332 2.141e-01 2600 1.4027 -19.9867 -18.5840 42.56 839.253 9569.86 10137 3.321 1.651e-01 2800 1.4522 -20.0477 -18.5954 44.06 682.781 9606.82 10105 3.376 1.269e-01 2999 1.4276 -20.0343 -18.6067 43.31 589.422 9645.21 10106 3.323 1.520e-01 .. GENERATED FROM PYTHON SOURCE LINES 87-112 .. code-block:: Python print("\n--- Analysis ---") temps = np.array([s.temperature for s in stats]) pressures_atm = np.array([s.pressure for s in stats]) volumes = np.array([s.volume for s in stats]) steps = np.array([s.step for s in stats]) print(f" Mean Temperature: {temps.mean():.2f} ± {temps.std():.2f} K") print(f" Mean Pressure: {pressures_atm.mean():.3f} ± {pressures_atm.std():.3f} atm") print(f" Mean Volume: {volumes.mean():.2f} ± {volumes.std():.2f} ų") fig, ax = plt.subplots(3, 1, figsize=(7.0, 6.5), sharex=True, constrained_layout=True) ax[0].plot(steps, temps, lw=1.5) ax[0].set_ylabel("Temperature (K)") ax[1].plot(steps, pressures_atm, lw=1.5) ax[1].axhline(1.0, color="k", ls="--", lw=1.0, label="target") ax[1].set_ylabel("Pressure (atm)") ax[1].legend(frameon=False, loc="best") ax[2].plot(steps, volumes, lw=1.5) ax[2].set_xlabel("Step") ax[2].set_ylabel(r"Volume ($\AA^3$)") fig.suptitle("NPH (MTK): Temperature, Pressure, and Volume") print("\n" + "=" * 95) print("SIMULATION COMPLETE") print("=" * 95) .. image-sg:: /examples/dynamics/images/sphx_glr_03_nph_integration_001.png :alt: NPH (MTK): Temperature, Pressure, and Volume :srcset: /examples/dynamics/images/sphx_glr_03_nph_integration_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none --- Analysis --- Mean Temperature: 47.04 ± 11.48 K Mean Pressure: 1202.536 ± 405.565 atm Mean Volume: 9432.77 ± 106.85 ų =============================================================================================== SIMULATION COMPLETE =============================================================================================== .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 12.831 seconds) .. _sphx_glr_download_examples_dynamics_03_nph_integration.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: 03_nph_integration.ipynb <03_nph_integration.ipynb>` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: 03_nph_integration.py <03_nph_integration.py>` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: 03_nph_integration.zip <03_nph_integration.zip>` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_