.. 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 -19.7224 -18.4787 37.73 1874.338 9315.29 10304 3.324 1.421e-01 400 1.5565 -20.0385 -18.4820 47.22 1616.424 9320.21 10251 3.313 1.767e-01 600 1.3279 -19.8136 -18.4857 40.29 1758.562 9328.40 10272 3.345 1.634e-01 800 1.5413 -20.0489 -18.5077 46.76 1534.009 9339.90 10238 3.238 1.956e-01 1000 1.5305 -20.0579 -18.5274 46.43 1488.875 9354.50 10245 3.320 1.421e-01 1200 1.4836 -20.0173 -18.5336 45.01 1453.012 9372.08 10230 3.324 1.812e-01 1400 1.4560 -19.9927 -18.5367 44.17 1395.335 9392.60 10221 3.255 1.918e-01 1600 1.5210 -20.0794 -18.5584 46.14 1259.430 9415.99 10198 3.296 1.870e-01 1800 1.5707 -20.1399 -18.5692 47.65 1120.123 9442.05 10183 3.334 1.584e-01 2000 1.4235 -20.0152 -18.5917 43.19 1143.202 9470.57 10199 3.332 1.754e-01 2200 1.4500 -20.0538 -18.6038 43.99 1006.484 9501.46 10166 3.306 1.569e-01 2400 1.3852 -19.9863 -18.6011 42.02 946.937 9534.46 10164 3.333 2.134e-01 2600 1.3896 -19.9992 -18.6097 42.16 828.089 9569.49 10135 3.322 1.641e-01 2800 1.4376 -20.0617 -18.6240 43.62 670.188 9606.32 10105 3.378 1.259e-01 2999 1.4092 -20.0481 -18.6389 42.75 577.191 9644.55 10104 3.324 1.515e-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: 46.84 ± 11.53 K Mean Pressure: 1197.256 ± 408.620 atm Mean Volume: 9432.62 ± 106.66 ų =============================================================================================== SIMULATION COMPLETE =============================================================================================== .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 24.224 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 `_