.. 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 90.37 483.899 9314.02 9984 3.713 2.313e-03 200 1.2314 -19.7368 -18.5055 37.36 1776.854 9340.55 10284 3.326 1.403e-01 400 1.4830 -20.0511 -18.5682 44.99 1205.924 9439.85 10192 3.322 1.694e-01 600 1.2378 -19.8628 -18.6249 37.55 870.716 9592.65 10132 3.358 1.480e-01 800 1.3245 -19.9646 -18.6402 40.18 225.838 9783.32 10059 3.253 2.009e-01 1000 1.2877 -19.8669 -18.5792 39.07 -245.812 9989.04 10000 3.408 1.109e-01 1200 1.1965 -19.6774 -18.4809 36.30 -581.964 10187.51 9937 3.403 1.097e-01 1400 1.0739 -19.4352 -18.3613 32.58 -810.741 10360.69 9825 3.378 1.070e-01 1600 1.0533 -19.3197 -18.2663 31.96 -1008.937 10493.73 9749 3.348 1.220e-01 1800 1.0086 -19.2108 -18.2022 30.60 -1087.767 10574.99 9680 3.379 1.175e-01 2000 1.0432 -19.2176 -18.1744 31.65 -1147.906 10597.64 9677 3.382 1.195e-01 2200 1.0819 -19.2963 -18.2144 32.82 -1125.141 10557.74 9693 3.362 1.151e-01 2400 1.0197 -19.3096 -18.2898 30.94 -913.656 10458.96 9794 3.383 1.163e-01 2600 1.1845 -19.5737 -18.3892 35.94 -804.347 10312.34 9913 3.411 1.100e-01 2800 1.1866 -19.7001 -18.5135 36.00 -470.461 10128.22 9955 3.393 9.997e-02 2999 1.2248 -19.8286 -18.6038 37.16 -52.197 9926.14 10012 3.402 1.492e-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: 39.09 ± 13.76 K Mean Pressure: -230.356 ± 878.663 atm Mean Volume: 10066.09 ± 440.19 ų =============================================================================================== SIMULATION COMPLETE =============================================================================================== .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 22.790 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 `_