.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples_generated/03-tutorials/md.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_generated_03-tutorials_md.py: .. _md_tutorial: ================== Molecular dynamics ================== .. note:: These examples *can* be run without ``asap3`` installed. In that case, ASE’s Python implementation of the EMT calculator can be used instead, but it is much slower. Goal ==== In this tutorial, we will learn how to perform basic molecular dynamics (MD) simulations using ASE. The key objectives are: - Understand how to set up a crystal structure (Cu atoms on an FCC lattice). - Initialize velocities from Maxwell–Boltzmann distribution corresponding to a chosen temperature. - Integrate Newton’s equations of motion using Velocity-Verlet algorithm and we monitor the temperature using Langevin thermostat. - Monitor and analyze thermodynamic quantities (potential energy, kinetic energy, total energy, temperature). - Save trajectories and visualize atomic motion with ASE’s GUI. - Explore MD in different scenarios: - Constant energy MD (NVE ensemble) - Constant temperature MD (NVT ensemble) - Isolated nanoparticle simulations By the end of this tutorial, you should be able to set up your own MD simulations, monitor energy conservation, and visualize system evolution. Part 1: Basic Molecular Dynamics Simulation =========================================== We start by creating a copper crystal, assigning random velocities corresponding to Maxwell Boltzmann Distribution at 300 K, and running dynamics in the NVE ensemble (constant energy). .. GENERATED FROM PYTHON SOURCE LINES 47-79 .. code-block:: Python import matplotlib.pyplot as plt import numpy as np # choose one of the following implementations of EMT: # included in ase # from ase.calculators.emt import EMT # faster performance from asap3 import EMT from ase import units from ase.cluster.cubic import FaceCenteredCubic as ClusterFCC from ase.io.trajectory import Trajectory from ase.lattice.cubic import FaceCenteredCubic as LatticeFCC from ase.md.langevin import Langevin # for later NPT simulations from ase.md.velocitydistribution import ( MaxwellBoltzmannDistribution, Stationary, ZeroRotation, ) from ase.md.verlet import VelocityVerlet from ase.optimize import QuasiNewton from ase.visualize.plot import plot_atoms # Set up initial positions of Cu atoms on Fcc crystal lattice size = 10 atoms = LatticeFCC( directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], symbol='Cu', size=(size, size, size), pbc=True, ) .. GENERATED FROM PYTHON SOURCE LINES 80-81 Before setting up the MD simulation, we take a look at the initial structure: .. GENERATED FROM PYTHON SOURCE LINES 83-89 .. code-block:: Python fig, ax = plt.subplots(figsize=(5, 5)) plot_atoms(atoms, ax, rotation=('45x,45y,0z'), show_unit_cell=2, radii=0.75) ax.set_axis_off() plt.tight_layout() plt.show() .. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_md_001.png :alt: md :srcset: /examples_generated/03-tutorials/images/sphx_glr_md_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 90-92 Now let's run the MD simulation and monitor the kinetic and potential energy of the whole system: .. GENERATED FROM PYTHON SOURCE LINES 92-149 .. code-block:: Python # Describe the interatomic interactions with the Effective Medium Theory (EMT) atoms.calc = EMT() # Set the initial velocities corresponding to T=300K from Maxwell Boltzmann # Distribution MaxwellBoltzmannDistribution(atoms, temperature_K=300) # We use Velocity Verlet algorithm to integrate the Newton's equations. timestep_fs = 5 dyn = VelocityVerlet(atoms, timestep_fs * units.fs) # 5 fs time step. def printenergy(a): """ Function to print the thermodynamical properties i.e potential energy, kinetic energy and total energy """ epot = a.get_potential_energy() ekin = a.get_kinetic_energy() temp = a.get_temperature() print( f'Energy per atom: Epot ={epot:6.3f}eV Ekin = {ekin:.3f}eV ' f'(T={temp:.3f}K) Etot = {epot + ekin:.3f}eV' ) # Now run the dynamics print('running a NVE simulation of fcc Cu') printenergy(atoms) # init lists to for energy vs time data time_ps, epot, ekin = [], [], [] mdind = 0 steps_per_block = 10 for i in range(20): dyn.run(steps_per_block) mdind += steps_per_block printenergy(atoms) # save the energies of the current MD step time_ps.append(mdind * timestep_fs / 1000.0) epot.append(atoms.get_potential_energy()) ekin.append(atoms.get_kinetic_energy()) etot = np.array(epot) + np.array(ekin) # Plot energies vs time fig, ax = plt.subplots(figsize=(6, 4)) ax.plot(time_ps, epot, label='Potential energy') ax.plot(time_ps, ekin, label='Kinetic energy') ax.plot(time_ps, etot, label='Total energy') ax.set_xlabel('Time (ps)') ax.set_ylabel('Energy (eV)') ax.legend(loc='best') ax.grid(True, linewidth=0.5, alpha=0.5) plt.tight_layout() plt.show() .. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_md_002.png :alt: md :srcset: /examples_generated/03-tutorials/images/sphx_glr_md_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /builds/ase/ase/examples/03-tutorials/md.py:98: DeprecationWarning: Use thermalize_momenta MaxwellBoltzmannDistribution(atoms, temperature_K=300) running a NVE simulation of fcc Cu Energy per atom: Epot =-2.405eV Ekin = 155.997eV (T=301.711K) Etot = 153.592eV Energy per atom: Epot =117.849eV Ekin = 36.522eV (T=70.637K) Etot = 154.371eV Energy per atom: Epot =78.586eV Ekin = 75.649eV (T=146.311K) Etot = 154.235eV Energy per atom: Epot =71.419eV Ekin = 82.675eV (T=159.901K) Etot = 154.095eV Energy per atom: Epot =70.138eV Ekin = 83.898eV (T=162.266K) Etot = 154.037eV Energy per atom: Epot =80.028eV Ekin = 74.158eV (T=143.428K) Etot = 154.185eV Energy per atom: Epot =78.287eV Ekin = 75.898eV (T=146.794K) Etot = 154.185eV Energy per atom: Epot =75.359eV Ekin = 78.753eV (T=152.315K) Etot = 154.112eV Energy per atom: Epot =72.607eV Ekin = 81.494eV (T=157.616K) Etot = 154.100eV Energy per atom: Epot =78.260eV Ekin = 75.908eV (T=146.813K) Etot = 154.168eV Energy per atom: Epot =76.560eV Ekin = 77.584eV (T=150.054K) Etot = 154.144eV Energy per atom: Epot =74.600eV Ekin = 79.524eV (T=153.806K) Etot = 154.124eV Energy per atom: Epot =77.508eV Ekin = 76.640eV (T=148.227K) Etot = 154.147eV Energy per atom: Epot =75.473eV Ekin = 78.660eV (T=152.134K) Etot = 154.133eV Energy per atom: Epot =75.849eV Ekin = 78.287eV (T=151.413K) Etot = 154.135eV Energy per atom: Epot =75.273eV Ekin = 78.874eV (T=152.549K) Etot = 154.147eV Energy per atom: Epot =76.139eV Ekin = 78.000eV (T=150.858K) Etot = 154.138eV Energy per atom: Epot =77.511eV Ekin = 76.620eV (T=148.191K) Etot = 154.132eV Energy per atom: Epot =73.170eV Ekin = 80.957eV (T=156.579K) Etot = 154.128eV Energy per atom: Epot =76.166eV Ekin = 77.970eV (T=150.802K) Etot = 154.136eV Energy per atom: Epot =79.282eV Ekin = 74.871eV (T=144.807K) Etot = 154.153eV .. GENERATED FROM PYTHON SOURCE LINES 150-162 Note how the total energy is conserved, but the kinetic energy quickly drops to half the expected value. Why? What you learned here: - How to set up a basic MD run. - How to monitor the energy over time. - That total energy is approximately conserved in NVE simulations, what is the error in total energy? Exercise: Tune the time step from 5fs to 10fs and 50fs, what changes do you observe in total energy? .. GENERATED FROM PYTHON SOURCE LINES 165-196 Part 2: Constant temperature MD =============================== In many cases, you want to control temperature (NVT ensemble). This can be done using a thermostat, like -- in this tutorial -- Langevin thermostat. Compared to the previous example, we replace the line ``dyn = VelocityVerlet(...)`` with :: dyn = Langevin(atoms, timestep=5 * units.fs, temperature_K=T, friction=0.02) where ``T`` is the desired temperature in Kelvin. For that we also imported the Langevin in the beginning. The Langevin dynamics will then slowly adjust the total energy of the system so the temperature approaches the desired one. As a slightly less boring example, let us use this to melt a chunk of copper by starting the simulation without any momentum of the atoms (no kinetic energy), and with a desired temperature above the melting point. We will also save information about the atoms in a trajectory file called ``moldyn3.traj``. .. note:: It is recommended to use the ``asap3`` implementation of the ``EMT`` calculator here, because its performance benefits over the ``ase`` implementation. .. GENERATED FROM PYTHON SOURCE LINES 198-246 .. code-block:: Python size = 10 T = 1500 # Kelvin # Set up a crystal atoms = LatticeFCC( directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], symbol='Cu', size=(size, size, size), pbc=False, ) # Describe the interatomic interactions with the Effective Medium Theory atoms.calc = EMT() # We want to run MD with constant energy using the Langevin algorithm # with a time step of 5 fs, the temperature T and the friction # coefficient to 0.02 atomic units. timestep_fs = 5 dyn = Langevin( atoms, timestep=timestep_fs * units.fs, temperature_K=T, friction=0.02 ) # We also want to save the positions of all atoms after every 100th time step. traj = Trajectory('fccCu_NPT.traj', 'w', atoms) # Now run the dynamics print('running a NVT simulation of fcc Cu') printenergy(atoms) time_ps, temperature = [], [] mdind = 0 steps_per_block = 10 for i in range(200): dyn.run(steps_per_block) mdind += steps_per_block printenergy(atoms) # save the temperature of the current MD step time_ps.append(mdind * timestep_fs / 1000.0) temperature.append(atoms.get_temperature()) # Plot temperatures vs time fig, ax = plt.subplots(figsize=(6, 4)) ax.plot(time_ps, temperature) ax.set_xlabel('Time (ps)') ax.set_ylabel('Temperature (K)') ax.grid(True, linewidth=0.5, alpha=0.5) plt.tight_layout() plt.show() .. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_md_003.png :alt: md :srcset: /examples_generated/03-tutorials/images/sphx_glr_md_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/ase/.local/lib/python3.13/site-packages/ase/md/langevin.py:102: FutureWarning: The implementation of `fixcm=True` in `Langevin` does not strictly sample the correct NVT distributions. The deviations are typically small for large systems but can be more pronounced for small systems. Use `fixcm=False` together with `ase.constraints.FixCom`. `fixcm` is deprecated since ASE 3.28.0 and will be removed in a future release. warnings.warn(msg, FutureWarning) running a NVT simulation of fcc Cu Energy per atom: Epot =540.816eV Ekin = 0.000eV (T=0.000K) Etot = 540.816eV Energy per atom: Epot =600.029eV Ekin = 80.740eV (T=156.158K) Etot = 680.769eV Energy per atom: Epot =670.954eV Ekin = 139.408eV (T=269.627K) Etot = 810.361eV Energy per atom: Epot =728.898eV Ekin = 196.851eV (T=380.726K) Etot = 925.748eV Energy per atom: Epot =777.400eV Ekin = 254.754eV (T=492.717K) Etot = 1032.154eV Energy per atom: Epot =833.992eV Ekin = 295.082eV (T=570.714K) Etot = 1129.074eV Energy per atom: Epot =881.924eV Ekin = 339.427eV (T=656.482K) Etot = 1221.351eV Energy per atom: Epot =926.617eV Ekin = 377.545eV (T=730.204K) Etot = 1304.162eV Energy per atom: Epot =964.253eV Ekin = 415.048eV (T=802.740K) Etot = 1379.302eV Energy per atom: Epot =997.783eV Ekin = 446.135eV (T=862.864K) Etot = 1443.918eV Energy per atom: Epot =1036.714eV Ekin = 463.249eV (T=895.964K) Etot = 1499.962eV Energy per atom: Epot =1064.941eV Ekin = 482.117eV (T=932.455K) Etot = 1547.058eV Energy per atom: Epot =1095.130eV Ekin = 505.841eV (T=978.340K) Etot = 1600.971eV Energy per atom: Epot =1140.331eV Ekin = 511.181eV (T=988.669K) Etot = 1651.512eV Energy per atom: Epot =1160.585eV Ekin = 540.505eV (T=1045.385K) Etot = 1701.090eV Energy per atom: Epot =1187.078eV Ekin = 555.272eV (T=1073.945K) Etot = 1742.351eV Energy per atom: Epot =1216.913eV Ekin = 569.596eV (T=1101.648K) Etot = 1786.509eV Energy per atom: Epot =1238.768eV Ekin = 591.691eV (T=1144.383K) Etot = 1830.459eV Energy per atom: Epot =1276.822eV Ekin = 590.860eV (T=1142.775K) Etot = 1867.682eV Energy per atom: Epot =1296.175eV Ekin = 600.154eV (T=1160.751K) Etot = 1896.329eV Energy per atom: Epot =1324.978eV Ekin = 613.763eV (T=1187.070K) Etot = 1938.740eV Energy per atom: Epot =1344.561eV Ekin = 627.462eV (T=1213.566K) Etot = 1972.023eV Energy per atom: Epot =1359.425eV Ekin = 640.140eV (T=1238.086K) Etot = 1999.564eV Energy per atom: Epot =1399.906eV Ekin = 635.830eV (T=1229.751K) Etot = 2035.736eV Energy per atom: Epot =1399.596eV Ekin = 671.936eV (T=1299.582K) Etot = 2071.531eV Energy per atom: Epot =1423.234eV Ekin = 668.482eV (T=1292.902K) Etot = 2091.716eV Energy per atom: Epot =1435.677eV Ekin = 673.163eV (T=1301.956K) Etot = 2108.840eV Energy per atom: Epot =1453.142eV Ekin = 662.513eV (T=1281.358K) Etot = 2115.655eV Energy per atom: Epot =1461.109eV Ekin = 672.313eV (T=1300.312K) Etot = 2133.422eV Energy per atom: Epot =1472.296eV Ekin = 672.708eV (T=1301.076K) Etot = 2145.004eV Energy per atom: Epot =1486.602eV Ekin = 676.455eV (T=1308.322K) Etot = 2163.057eV Energy per atom: Epot =1493.073eV Ekin = 683.986eV (T=1322.888K) Etot = 2177.059eV Energy per atom: Epot =1509.245eV Ekin = 680.954eV (T=1317.023K) Etot = 2190.199eV Energy per atom: Epot =1525.203eV Ekin = 684.370eV (T=1323.632K) Etot = 2209.574eV Energy per atom: Epot =1519.078eV Ekin = 691.607eV (T=1337.627K) Etot = 2210.684eV Energy per atom: Epot =1516.504eV Ekin = 697.736eV (T=1349.483K) Etot = 2214.241eV Energy per atom: Epot =1535.801eV Ekin = 699.131eV (T=1352.180K) Etot = 2234.931eV Energy per atom: Epot =1552.228eV Ekin = 697.065eV (T=1348.185K) Etot = 2249.294eV Energy per atom: Epot =1566.885eV Ekin = 704.694eV (T=1362.939K) Etot = 2271.579eV Energy per atom: Epot =1570.116eV Ekin = 714.645eV (T=1382.186K) Etot = 2284.761eV Energy per atom: Epot =1575.746eV Ekin = 713.337eV (T=1379.657K) Etot = 2289.084eV Energy per atom: Epot =1597.996eV Ekin = 707.814eV (T=1368.973K) Etot = 2305.810eV Energy per atom: Epot =1599.926eV Ekin = 714.188eV (T=1381.302K) Etot = 2314.114eV Energy per atom: Epot =1617.680eV Ekin = 708.909eV (T=1371.091K) Etot = 2326.588eV Energy per atom: Epot =1624.281eV Ekin = 705.284eV (T=1364.082K) Etot = 2329.565eV Energy per atom: Epot =1625.069eV Ekin = 707.955eV (T=1369.247K) Etot = 2333.024eV Energy per atom: Epot =1635.045eV Ekin = 713.437eV (T=1379.849K) Etot = 2348.482eV Energy per atom: Epot =1645.885eV Ekin = 715.434eV (T=1383.712K) Etot = 2361.319eV Energy per atom: Epot =1662.038eV Ekin = 719.220eV (T=1391.034K) Etot = 2381.258eV Energy per atom: Epot =1671.331eV Ekin = 711.695eV (T=1376.479K) Etot = 2383.026eV Energy per atom: Epot =1670.241eV Ekin = 718.591eV (T=1389.817K) Etot = 2388.831eV Energy per atom: Epot =1665.326eV Ekin = 727.665eV (T=1407.368K) Etot = 2392.992eV Energy per atom: Epot =1690.912eV Ekin = 715.237eV (T=1383.330K) Etot = 2406.149eV Energy per atom: Epot =1675.807eV Ekin = 735.642eV (T=1422.796K) Etot = 2411.449eV Energy per atom: Epot =1709.021eV Ekin = 711.385eV (T=1375.881K) Etot = 2420.406eV Energy per atom: Epot =1702.848eV Ekin = 725.713eV (T=1403.593K) Etot = 2428.562eV Energy per atom: Epot =1721.916eV Ekin = 717.005eV (T=1386.749K) Etot = 2438.920eV Energy per atom: Epot =1726.413eV Ekin = 719.669eV (T=1391.903K) Etot = 2446.082eV Energy per atom: Epot =1735.688eV Ekin = 708.447eV (T=1370.199K) Etot = 2444.135eV Energy per atom: Epot =1730.322eV Ekin = 724.620eV (T=1401.479K) Etot = 2454.942eV Energy per atom: Epot =1723.939eV Ekin = 736.310eV (T=1424.087K) Etot = 2460.248eV Energy per atom: Epot =1739.118eV Ekin = 728.218eV (T=1408.436K) Etot = 2467.336eV Energy per atom: Epot =1765.249eV Ekin = 704.381eV (T=1362.335K) Etot = 2469.630eV Energy per atom: Epot =1742.577eV Ekin = 725.619eV (T=1403.410K) Etot = 2468.196eV Energy per atom: Epot =1763.176eV Ekin = 720.677eV (T=1393.853K) Etot = 2483.854eV Energy per atom: Epot =1776.941eV Ekin = 719.695eV (T=1391.952K) Etot = 2496.636eV Energy per atom: Epot =1785.343eV Ekin = 721.405eV (T=1395.260K) Etot = 2506.748eV Energy per atom: Epot =1782.540eV Ekin = 733.416eV (T=1418.491K) Etot = 2515.956eV Energy per atom: Epot =1801.899eV Ekin = 716.571eV (T=1385.910K) Etot = 2518.470eV Energy per atom: Epot =1790.905eV Ekin = 733.426eV (T=1418.511K) Etot = 2524.332eV Energy per atom: Epot =1799.781eV Ekin = 740.276eV (T=1431.758K) Etot = 2540.057eV Energy per atom: Epot =1814.540eV Ekin = 722.310eV (T=1397.010K) Etot = 2536.850eV Energy per atom: Epot =1819.278eV Ekin = 739.234eV (T=1429.743K) Etot = 2558.512eV Energy per atom: Epot =1825.117eV Ekin = 748.901eV (T=1448.440K) Etot = 2574.019eV Energy per atom: Epot =1845.098eV Ekin = 731.037eV (T=1413.890K) Etot = 2576.135eV Energy per atom: Epot =1840.395eV Ekin = 746.879eV (T=1444.529K) Etot = 2587.275eV Energy per atom: Epot =1842.648eV Ekin = 752.921eV (T=1456.214K) Etot = 2595.568eV Energy per atom: Epot =1850.766eV Ekin = 745.082eV (T=1441.054K) Etot = 2595.849eV Energy per atom: Epot =1858.547eV Ekin = 740.476eV (T=1432.145K) Etot = 2599.023eV Energy per atom: Epot =1856.232eV Ekin = 745.698eV (T=1442.246K) Etot = 2601.931eV Energy per atom: Epot =1873.124eV Ekin = 734.302eV (T=1420.204K) Etot = 2607.426eV Energy per atom: Epot =1878.958eV Ekin = 738.414eV (T=1428.157K) Etot = 2617.372eV Energy per atom: Epot =1880.593eV Ekin = 746.670eV (T=1444.125K) Etot = 2627.263eV Energy per atom: Epot =1898.996eV Ekin = 739.824eV (T=1430.885K) Etot = 2638.821eV Energy per atom: Epot =1899.043eV Ekin = 745.310eV (T=1441.494K) Etot = 2644.353eV Energy per atom: Epot =1898.401eV Ekin = 745.511eV (T=1441.884K) Etot = 2643.913eV Energy per atom: Epot =1902.538eV Ekin = 750.413eV (T=1451.364K) Etot = 2652.951eV Energy per atom: Epot =1911.350eV Ekin = 747.427eV (T=1445.590K) Etot = 2658.778eV Energy per atom: Epot =1916.125eV Ekin = 739.768eV (T=1430.775K) Etot = 2655.893eV Energy per atom: Epot =1924.475eV Ekin = 747.033eV (T=1444.827K) Etot = 2671.508eV Energy per atom: Epot =1923.681eV Ekin = 747.638eV (T=1445.996K) Etot = 2671.319eV Energy per atom: Epot =1935.318eV Ekin = 726.415eV (T=1404.950K) Etot = 2661.733eV Energy per atom: Epot =1916.994eV Ekin = 751.797eV (T=1454.040K) Etot = 2668.791eV Energy per atom: Epot =1925.445eV Ekin = 747.611eV (T=1445.944K) Etot = 2673.056eV Energy per atom: Epot =1924.771eV Ekin = 751.217eV (T=1452.919K) Etot = 2675.988eV Energy per atom: Epot =1922.896eV Ekin = 755.154eV (T=1460.533K) Etot = 2678.050eV Energy per atom: Epot =1936.812eV Ekin = 747.654eV (T=1446.027K) Etot = 2684.466eV Energy per atom: Epot =1939.333eV Ekin = 752.595eV (T=1455.584K) Etot = 2691.928eV Energy per atom: Epot =1927.043eV Ekin = 767.438eV (T=1484.292K) Etot = 2694.481eV Energy per atom: Epot =1948.149eV Ekin = 746.392eV (T=1443.587K) Etot = 2694.541eV Energy per atom: Epot =1957.387eV Ekin = 742.627eV (T=1436.304K) Etot = 2700.014eV Energy per atom: Epot =1952.626eV Ekin = 752.207eV (T=1454.834K) Etot = 2704.834eV Energy per atom: Epot =1951.983eV Ekin = 762.433eV (T=1474.612K) Etot = 2714.416eV Energy per atom: Epot =1958.223eV Ekin = 760.351eV (T=1470.586K) Etot = 2718.574eV Energy per atom: Epot =1961.883eV Ekin = 763.700eV (T=1477.061K) Etot = 2725.582eV Energy per atom: Epot =1966.449eV Ekin = 760.877eV (T=1471.603K) Etot = 2727.326eV Energy per atom: Epot =1962.634eV Ekin = 768.545eV (T=1486.432K) Etot = 2731.178eV Energy per atom: Epot =1964.147eV Ekin = 768.039eV (T=1485.454K) Etot = 2732.185eV Energy per atom: Epot =1967.084eV Ekin = 762.285eV (T=1474.326K) Etot = 2729.369eV Energy per atom: Epot =1964.266eV Ekin = 768.682eV (T=1486.697K) Etot = 2732.948eV Energy per atom: Epot =1982.414eV Ekin = 755.952eV (T=1462.077K) Etot = 2738.366eV Energy per atom: Epot =1976.206eV Ekin = 768.027eV (T=1485.430K) Etot = 2744.233eV Energy per atom: Epot =1967.903eV Ekin = 781.265eV (T=1511.035K) Etot = 2749.169eV Energy per atom: Epot =1986.921eV Ekin = 765.513eV (T=1480.569K) Etot = 2752.434eV Energy per atom: Epot =1979.491eV Ekin = 777.247eV (T=1503.263K) Etot = 2756.738eV Energy per atom: Epot =1984.830eV Ekin = 770.125eV (T=1489.488K) Etot = 2754.954eV Energy per atom: Epot =1985.612eV Ekin = 763.120eV (T=1475.940K) Etot = 2748.731eV Energy per atom: Epot =1994.981eV Ekin = 751.633eV (T=1453.724K) Etot = 2746.614eV Energy per atom: Epot =1994.050eV Ekin = 764.952eV (T=1479.485K) Etot = 2759.002eV Energy per atom: Epot =1992.604eV Ekin = 778.285eV (T=1505.272K) Etot = 2770.890eV Energy per atom: Epot =1995.550eV Ekin = 771.791eV (T=1492.711K) Etot = 2767.341eV Energy per atom: Epot =1997.004eV Ekin = 775.420eV (T=1499.730K) Etot = 2772.425eV Energy per atom: Epot =1999.211eV Ekin = 773.900eV (T=1496.791K) Etot = 2773.112eV Energy per atom: Epot =1998.820eV Ekin = 769.542eV (T=1488.361K) Etot = 2768.361eV Energy per atom: Epot =1994.532eV Ekin = 767.886eV (T=1485.159K) Etot = 2762.418eV Energy per atom: Epot =2003.450eV Ekin = 768.761eV (T=1486.850K) Etot = 2772.211eV Energy per atom: Epot =1998.259eV Ekin = 777.137eV (T=1503.051K) Etot = 2775.396eV Energy per atom: Epot =2000.697eV Ekin = 779.368eV (T=1507.365K) Etot = 2780.064eV Energy per atom: Epot =2003.305eV Ekin = 768.379eV (T=1486.113K) Etot = 2771.685eV Energy per atom: Epot =2010.718eV Ekin = 766.304eV (T=1482.099K) Etot = 2777.022eV Energy per atom: Epot =2012.941eV Ekin = 758.220eV (T=1466.463K) Etot = 2771.161eV Energy per atom: Epot =1989.441eV Ekin = 776.872eV (T=1502.537K) Etot = 2766.313eV Energy per atom: Epot =1993.049eV Ekin = 778.032eV (T=1504.782K) Etot = 2771.081eV Energy per atom: Epot =2003.629eV Ekin = 770.818eV (T=1490.830K) Etot = 2774.447eV Energy per atom: Epot =2001.620eV Ekin = 778.832eV (T=1506.329K) Etot = 2780.452eV Energy per atom: Epot =1985.573eV Ekin = 788.199eV (T=1524.445K) Etot = 2773.771eV Energy per atom: Epot =2004.655eV Ekin = 768.687eV (T=1486.708K) Etot = 2773.342eV Energy per atom: Epot =1989.355eV Ekin = 779.992eV (T=1508.573K) Etot = 2769.347eV Energy per atom: Epot =1989.142eV Ekin = 764.648eV (T=1478.895K) Etot = 2753.789eV Energy per atom: Epot =1979.368eV Ekin = 774.271eV (T=1497.508K) Etot = 2753.639eV Energy per atom: Epot =1993.844eV Ekin = 761.820eV (T=1473.426K) Etot = 2755.664eV Energy per atom: Epot =1983.275eV Ekin = 777.541eV (T=1503.832K) Etot = 2760.815eV Energy per atom: Epot =1980.049eV Ekin = 786.832eV (T=1521.802K) Etot = 2766.881eV Energy per atom: Epot =1995.787eV Ekin = 773.705eV (T=1496.414K) Etot = 2769.493eV Energy per atom: Epot =1985.712eV Ekin = 774.882eV (T=1498.690K) Etot = 2760.595eV Energy per atom: Epot =1991.996eV Ekin = 762.372eV (T=1474.494K) Etot = 2754.368eV Energy per atom: Epot =1979.564eV Ekin = 765.354eV (T=1480.261K) Etot = 2744.918eV Energy per atom: Epot =1973.996eV Ekin = 775.940eV (T=1500.735K) Etot = 2749.936eV Energy per atom: Epot =1983.695eV Ekin = 759.691eV (T=1469.309K) Etot = 2743.387eV Energy per atom: Epot =1982.807eV Ekin = 765.930eV (T=1481.375K) Etot = 2748.737eV Energy per atom: Epot =1982.453eV Ekin = 766.594eV (T=1482.659K) Etot = 2749.047eV Energy per atom: Epot =1997.814eV Ekin = 759.293eV (T=1468.538K) Etot = 2757.106eV Energy per atom: Epot =2003.355eV Ekin = 761.571eV (T=1472.945K) Etot = 2764.926eV Energy per atom: Epot =1993.635eV Ekin = 762.333eV (T=1474.418K) Etot = 2755.968eV Energy per atom: Epot =2002.267eV Ekin = 756.646eV (T=1463.419K) Etot = 2758.913eV Energy per atom: Epot =1994.652eV Ekin = 760.656eV (T=1471.176K) Etot = 2755.309eV Energy per atom: Epot =1993.534eV Ekin = 758.502eV (T=1467.009K) Etot = 2752.036eV Energy per atom: Epot =1975.307eV Ekin = 776.334eV (T=1501.497K) Etot = 2751.641eV Energy per atom: Epot =1985.830eV Ekin = 762.320eV (T=1474.393K) Etot = 2748.150eV Energy per atom: Epot =1995.197eV Ekin = 750.767eV (T=1452.049K) Etot = 2745.964eV Energy per atom: Epot =1992.877eV Ekin = 752.004eV (T=1454.441K) Etot = 2744.880eV Energy per atom: Epot =2000.236eV Ekin = 750.485eV (T=1451.504K) Etot = 2750.721eV Energy per atom: Epot =1988.447eV Ekin = 762.185eV (T=1474.133K) Etot = 2750.632eV Energy per atom: Epot =1991.037eV Ekin = 763.614eV (T=1476.896K) Etot = 2754.651eV Energy per atom: Epot =1992.113eV Ekin = 760.137eV (T=1470.171K) Etot = 2752.250eV Energy per atom: Epot =1996.385eV Ekin = 757.903eV (T=1465.850K) Etot = 2754.288eV Energy per atom: Epot =1995.848eV Ekin = 759.575eV (T=1469.084K) Etot = 2755.423eV Energy per atom: Epot =1992.391eV Ekin = 758.922eV (T=1467.820K) Etot = 2751.313eV Energy per atom: Epot =1992.555eV Ekin = 761.658eV (T=1473.112K) Etot = 2754.213eV Energy per atom: Epot =1980.931eV Ekin = 773.800eV (T=1496.597K) Etot = 2754.731eV Energy per atom: Epot =1999.868eV Ekin = 762.953eV (T=1475.618K) Etot = 2762.821eV Energy per atom: Epot =1984.806eV Ekin = 773.778eV (T=1496.554K) Etot = 2758.584eV Energy per atom: Epot =1991.738eV Ekin = 771.909eV (T=1492.940K) Etot = 2763.648eV Energy per atom: Epot =1982.704eV Ekin = 785.012eV (T=1518.281K) Etot = 2767.716eV Energy per atom: Epot =1993.375eV Ekin = 769.586eV (T=1488.447K) Etot = 2762.962eV Energy per atom: Epot =1977.586eV Ekin = 795.167eV (T=1537.922K) Etot = 2772.753eV Energy per atom: Epot =1996.464eV Ekin = 776.632eV (T=1502.073K) Etot = 2773.095eV Energy per atom: Epot =2003.684eV Ekin = 772.034eV (T=1493.181K) Etot = 2775.718eV Energy per atom: Epot =1994.668eV Ekin = 782.091eV (T=1512.632K) Etot = 2776.758eV Energy per atom: Epot =2004.643eV Ekin = 766.196eV (T=1481.891K) Etot = 2770.839eV Energy per atom: Epot =2002.912eV Ekin = 768.580eV (T=1486.501K) Etot = 2771.492eV Energy per atom: Epot =2005.017eV Ekin = 764.824eV (T=1479.236K) Etot = 2769.841eV Energy per atom: Epot =1995.219eV Ekin = 771.699eV (T=1492.532K) Etot = 2766.917eV Energy per atom: Epot =2002.275eV Ekin = 761.949eV (T=1473.675K) Etot = 2764.224eV Energy per atom: Epot =2002.193eV Ekin = 762.399eV (T=1474.545K) Etot = 2764.592eV Energy per atom: Epot =1997.989eV Ekin = 777.582eV (T=1503.912K) Etot = 2775.571eV Energy per atom: Epot =2005.711eV Ekin = 775.655eV (T=1500.185K) Etot = 2781.366eV Energy per atom: Epot =1991.230eV Ekin = 776.734eV (T=1502.270K) Etot = 2767.964eV Energy per atom: Epot =1987.475eV Ekin = 766.601eV (T=1482.673K) Etot = 2754.076eV Energy per atom: Epot =1998.505eV Ekin = 762.947eV (T=1475.605K) Etot = 2761.451eV Energy per atom: Epot =1995.817eV Ekin = 760.810eV (T=1471.473K) Etot = 2756.627eV Energy per atom: Epot =1986.226eV Ekin = 769.300eV (T=1487.894K) Etot = 2755.527eV Energy per atom: Epot =1988.812eV Ekin = 769.050eV (T=1487.409K) Etot = 2757.862eV Energy per atom: Epot =1989.629eV Ekin = 776.319eV (T=1501.469K) Etot = 2765.948eV Energy per atom: Epot =1976.906eV Ekin = 787.333eV (T=1522.770K) Etot = 2764.239eV Energy per atom: Epot =1993.255eV Ekin = 770.426eV (T=1490.071K) Etot = 2763.681eV Energy per atom: Epot =1994.003eV Ekin = 760.818eV (T=1471.489K) Etot = 2754.821eV Energy per atom: Epot =1990.529eV Ekin = 764.859eV (T=1479.305K) Etot = 2755.388eV Energy per atom: Epot =1979.148eV Ekin = 786.965eV (T=1522.059K) Etot = 2766.113eV Energy per atom: Epot =2004.117eV Ekin = 763.465eV (T=1476.607K) Etot = 2767.581eV Energy per atom: Epot =1993.780eV Ekin = 762.892eV (T=1475.499K) Etot = 2756.671eV .. GENERATED FROM PYTHON SOURCE LINES 247-278 After running the simulation, you can study the result with the command :: ase gui fccCu_NPT.traj Try plotting the kinetic energy. Like in the temperature vs time plot you will *not* see a well-defined melting point due to finite size effects (including surface melting), but you will probably see an almost flat region where the inside of the system melts. The outermost layers melt at a lower temperature. .. note:: The Langevin dynamics will by default keep the position and momentum of the center of mass unperturbed. This is another improvement over just setting momenta corresponding to a temperature, as we did before. Part 3: Isolated particle MD ============================ When simulating isolated particles with MD, it is sometimes preferable to set random momenta corresponding to a specific temperature and let the system evolve freely. With a relatively high temperature, the is however a risk that the collection of atoms will drift out of the simulation box because the randomized momenta gave the center of mass a small but non-zero velocity too. Let us see what happens when we propagate a nanoparticle: .. GENERATED FROM PYTHON SOURCE LINES 280-313 .. code-block:: Python size = 4 atoms = ClusterFCC( 'Cu', surfaces=[[1, 0, 0], [1, 1, 0], [1, 1, 1]], layers=(size, size, size), vacuum=4, ) # asap3 requires a non-zero cell even if pbc are not applied atoms.cell = [40] * 3 atoms.set_pbc(False) # isolated cluster (explicit, for clarity) # Describe the interatomic interactions with the Effective Medium Theory atoms.calc = EMT() # Quick relaxation of the cluster qn = QuasiNewton(atoms) qn.run(fmax=0.001, steps=10) # Set the momenta corresponding to T=1200 K MaxwellBoltzmannDistribution(atoms, temperature_K=1200) Stationary(atoms) # zero linear momentum ZeroRotation(atoms) # zero angular momentum # Run MD using the Velocity Verlet algorithm and save trajectory dyn = VelocityVerlet(atoms, 5 * units.fs, trajectory='nanoparticleCu_NVE.traj') print('running a NVE simulation of a Cu nanoparticle') printenergy(atoms) steps_per_block = 10 for i in range(200): dyn.run(steps_per_block) printenergy(atoms) .. rst-class:: sphx-glr-script-out .. code-block:: none Step[ FC] Time Energy fmax BFGSLineSearch: 0[ 0] 00:07:59 43.457006 1.0818 BFGSLineSearch: 1[ 1] 00:07:59 42.347659 0.2273 BFGSLineSearch: 2[ 2] 00:07:59 42.108454 0.1349 BFGSLineSearch: 3[ 3] 00:07:59 41.964817 0.1138 BFGSLineSearch: 4[ 4] 00:07:59 41.924933 0.0683 BFGSLineSearch: 5[ 5] 00:07:59 41.915346 0.0225 BFGSLineSearch: 6[ 6] 00:07:59 41.914920 0.0059 BFGSLineSearch: 7[ 7] 00:07:59 41.914872 0.0023 BFGSLineSearch: 8[ 9] 00:07:59 41.914855 0.0023 BFGSLineSearch: 9[ 10] 00:07:59 41.914851 0.0010 /builds/ase/ase/examples/03-tutorials/md.py:299: DeprecationWarning: Use thermalize_momenta MaxwellBoltzmannDistribution(atoms, temperature_K=1200) running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 15.735eV (T=1308.955K) Etot = 57.650eV Energy per atom: Epot =50.389eV Ekin = 7.305eV (T=607.688K) Etot = 57.694eV Energy per atom: Epot =50.930eV Ekin = 6.775eV (T=563.556K) Etot = 57.704eV Energy per atom: Epot =52.287eV Ekin = 5.418eV (T=450.722K) Etot = 57.706eV Energy per atom: Epot =51.176eV Ekin = 6.525eV (T=542.827K) Etot = 57.701eV Energy per atom: Epot =50.388eV Ekin = 7.317eV (T=608.702K) Etot = 57.705eV Energy per atom: Epot =50.643eV Ekin = 7.062eV (T=587.467K) Etot = 57.705eV Energy per atom: Epot =49.324eV Ekin = 8.366eV (T=695.916K) Etot = 57.690eV Energy per atom: Epot =49.814eV Ekin = 7.880eV (T=655.530K) Etot = 57.694eV Energy per atom: Epot =49.821eV Ekin = 7.879eV (T=655.408K) Etot = 57.700eV Energy per atom: Epot =51.584eV Ekin = 6.122eV (T=509.296K) Etot = 57.707eV Energy per atom: Epot =51.540eV Ekin = 6.166eV (T=512.934K) Etot = 57.706eV Energy per atom: Epot =50.777eV Ekin = 6.925eV (T=576.080K) Etot = 57.702eV Energy per atom: Epot =50.535eV Ekin = 7.161eV (T=595.688K) Etot = 57.696eV Energy per atom: Epot =49.817eV Ekin = 7.879eV (T=655.389K) Etot = 57.695eV Energy per atom: Epot =50.914eV Ekin = 6.793eV (T=565.121K) Etot = 57.707eV Energy per atom: Epot =50.947eV Ekin = 6.763eV (T=562.581K) Etot = 57.710eV Energy per atom: Epot =51.553eV Ekin = 6.151eV (T=511.686K) Etot = 57.704eV Energy per atom: Epot =51.222eV Ekin = 6.478eV (T=538.889K) Etot = 57.700eV Energy per atom: Epot =50.586eV Ekin = 7.109eV (T=591.372K) Etot = 57.695eV Energy per atom: Epot =50.819eV Ekin = 6.879eV (T=572.212K) Etot = 57.698eV Energy per atom: Epot =50.308eV Ekin = 7.388eV (T=614.617K) Etot = 57.696eV Energy per atom: Epot =50.943eV Ekin = 6.756eV (T=562.038K) Etot = 57.699eV Energy per atom: Epot =51.150eV Ekin = 6.552eV (T=545.063K) Etot = 57.702eV Energy per atom: Epot =50.865eV Ekin = 6.837eV (T=568.737K) Etot = 57.701eV Energy per atom: Epot =50.656eV Ekin = 7.047eV (T=586.205K) Etot = 57.703eV Energy per atom: Epot =50.642eV Ekin = 7.055eV (T=586.879K) Etot = 57.697eV Energy per atom: Epot =50.152eV Ekin = 7.548eV (T=627.914K) Etot = 57.700eV Energy per atom: Epot =50.606eV Ekin = 7.098eV (T=590.455K) Etot = 57.704eV Energy per atom: Epot =50.849eV Ekin = 6.852eV (T=570.021K) Etot = 57.702eV Energy per atom: Epot =50.678eV Ekin = 7.024eV (T=584.343K) Etot = 57.702eV Energy per atom: Epot =51.087eV Ekin = 6.618eV (T=550.527K) Etot = 57.705eV Energy per atom: Epot =50.319eV Ekin = 7.382eV (T=614.115K) Etot = 57.702eV Energy per atom: Epot =51.465eV Ekin = 6.234eV (T=518.609K) Etot = 57.699eV Energy per atom: Epot =50.308eV Ekin = 7.386eV (T=614.407K) Etot = 57.694eV Energy per atom: Epot =51.320eV Ekin = 6.383eV (T=530.998K) Etot = 57.703eV Energy per atom: Epot =50.791eV Ekin = 6.910eV (T=574.800K) Etot = 57.701eV Energy per atom: Epot =50.900eV Ekin = 6.804eV (T=565.970K) Etot = 57.704eV Energy per atom: Epot =51.466eV Ekin = 6.240eV (T=519.056K) Etot = 57.706eV Energy per atom: Epot =50.699eV Ekin = 6.999eV (T=582.232K) Etot = 57.698eV Energy per atom: Epot =50.487eV Ekin = 7.210eV (T=599.737K) Etot = 57.697eV Energy per atom: Epot =51.667eV Ekin = 6.035eV (T=502.025K) Etot = 57.702eV Energy per atom: Epot =51.211eV Ekin = 6.491eV (T=539.987K) Etot = 57.702eV Energy per atom: Epot =51.599eV Ekin = 6.106eV (T=507.933K) Etot = 57.705eV Energy per atom: Epot =50.382eV Ekin = 7.316eV (T=608.633K) Etot = 57.698eV Energy per atom: Epot =50.620eV Ekin = 7.079eV (T=588.852K) Etot = 57.699eV Energy per atom: Epot =50.659eV Ekin = 7.047eV (T=586.249K) Etot = 57.707eV Energy per atom: Epot =49.904eV Ekin = 7.798eV (T=648.648K) Etot = 57.702eV Energy per atom: Epot =50.728eV Ekin = 6.971eV (T=579.859K) Etot = 57.699eV Energy per atom: Epot =50.490eV Ekin = 7.211eV (T=599.878K) Etot = 57.701eV Energy per atom: Epot =51.246eV Ekin = 6.462eV (T=537.510K) Etot = 57.707eV Energy per atom: Epot =50.317eV Ekin = 7.382eV (T=614.088K) Etot = 57.699eV Energy per atom: Epot =50.397eV Ekin = 7.295eV (T=606.859K) Etot = 57.692eV Energy per atom: Epot =50.954eV Ekin = 6.748eV (T=561.326K) Etot = 57.701eV Energy per atom: Epot =50.343eV Ekin = 7.358eV (T=612.114K) Etot = 57.701eV Energy per atom: Epot =50.359eV Ekin = 7.339eV (T=610.515K) Etot = 57.698eV Energy per atom: Epot =50.157eV Ekin = 7.539eV (T=627.139K) Etot = 57.696eV Energy per atom: Epot =50.122eV Ekin = 7.576eV (T=630.211K) Etot = 57.698eV Energy per atom: Epot =49.882eV Ekin = 7.816eV (T=650.147K) Etot = 57.698eV Energy per atom: Epot =50.539eV Ekin = 7.163eV (T=595.855K) Etot = 57.702eV Energy per atom: Epot =49.548eV Ekin = 8.150eV (T=677.933K) Etot = 57.698eV Energy per atom: Epot =49.585eV Ekin = 8.118eV (T=675.317K) Etot = 57.703eV Energy per atom: Epot =50.147eV Ekin = 7.553eV (T=628.298K) Etot = 57.700eV Energy per atom: Epot =50.217eV Ekin = 7.485eV (T=622.647K) Etot = 57.702eV Energy per atom: Epot =50.430eV Ekin = 7.270eV (T=604.745K) Etot = 57.699eV Energy per atom: Epot =50.144eV Ekin = 7.557eV (T=628.606K) Etot = 57.700eV Energy per atom: Epot =50.772eV Ekin = 6.928eV (T=576.323K) Etot = 57.700eV Energy per atom: Epot =50.324eV Ekin = 7.373eV (T=613.374K) Etot = 57.697eV Energy per atom: Epot =50.760eV Ekin = 6.941eV (T=577.412K) Etot = 57.701eV Energy per atom: Epot =49.760eV Ekin = 7.939eV (T=660.378K) Etot = 57.698eV Energy per atom: Epot =50.525eV Ekin = 7.179eV (T=597.179K) Etot = 57.704eV Energy per atom: Epot =50.379eV Ekin = 7.323eV (T=609.181K) Etot = 57.702eV Energy per atom: Epot =50.558eV Ekin = 7.150eV (T=594.745K) Etot = 57.707eV Energy per atom: Epot =49.404eV Ekin = 8.298eV (T=690.287K) Etot = 57.702eV Energy per atom: Epot =50.161eV Ekin = 7.538eV (T=627.022K) Etot = 57.698eV Energy per atom: Epot =50.036eV Ekin = 7.663eV (T=637.427K) Etot = 57.699eV Energy per atom: Epot =50.420eV Ekin = 7.282eV (T=605.750K) Etot = 57.702eV Energy per atom: Epot =51.005eV Ekin = 6.699eV (T=557.283K) Etot = 57.704eV Energy per atom: Epot =49.856eV Ekin = 7.838eV (T=652.038K) Etot = 57.694eV Energy per atom: Epot =50.002eV Ekin = 7.694eV (T=640.076K) Etot = 57.696eV Energy per atom: Epot =50.212eV Ekin = 7.485eV (T=622.676K) Etot = 57.697eV Energy per atom: Epot =50.100eV Ekin = 7.599eV (T=632.146K) Etot = 57.699eV Energy per atom: Epot =50.364eV Ekin = 7.341eV (T=610.681K) Etot = 57.706eV Energy per atom: Epot =49.485eV Ekin = 8.213eV (T=683.186K) Etot = 57.697eV Energy per atom: Epot =50.214eV Ekin = 7.489eV (T=622.966K) Etot = 57.703eV Energy per atom: Epot =50.026eV Ekin = 7.672eV (T=638.174K) Etot = 57.698eV Energy per atom: Epot =49.597eV Ekin = 8.098eV (T=673.613K) Etot = 57.695eV Energy per atom: Epot =49.538eV Ekin = 8.159eV (T=678.707K) Etot = 57.697eV Energy per atom: Epot =49.991eV Ekin = 7.713eV (T=641.584K) Etot = 57.704eV Energy per atom: Epot =50.119eV Ekin = 7.583eV (T=630.823K) Etot = 57.702eV Energy per atom: Epot =49.842eV Ekin = 7.860eV (T=653.884K) Etot = 57.703eV Energy per atom: Epot =49.708eV Ekin = 7.991eV (T=664.713K) Etot = 57.698eV Energy per atom: Epot =49.659eV Ekin = 8.037eV (T=668.580K) Etot = 57.696eV Energy per atom: Epot =50.540eV Ekin = 7.156eV (T=595.244K) Etot = 57.696eV Energy per atom: Epot =50.380eV Ekin = 7.320eV (T=608.938K) Etot = 57.700eV Energy per atom: Epot =50.291eV Ekin = 7.408eV (T=616.265K) Etot = 57.699eV Energy per atom: Epot =49.061eV Ekin = 8.635eV (T=718.343K) Etot = 57.697eV Energy per atom: Epot =49.994eV Ekin = 7.707eV (T=641.123K) Etot = 57.701eV Energy per atom: Epot =49.633eV Ekin = 8.064eV (T=670.804K) Etot = 57.697eV Energy per atom: Epot =49.611eV Ekin = 8.084eV (T=672.472K) Etot = 57.694eV Energy per atom: Epot =49.974eV Ekin = 7.724eV (T=642.547K) Etot = 57.699eV Energy per atom: Epot =50.200eV Ekin = 7.506eV (T=624.430K) Etot = 57.707eV Energy per atom: Epot =50.003eV Ekin = 7.699eV (T=640.418K) Etot = 57.701eV Energy per atom: Epot =49.917eV Ekin = 7.785eV (T=647.647K) Etot = 57.702eV Energy per atom: Epot =49.926eV Ekin = 7.772eV (T=646.507K) Etot = 57.698eV Energy per atom: Epot =50.208eV Ekin = 7.492eV (T=623.193K) Etot = 57.699eV Energy per atom: Epot =50.112eV Ekin = 7.590eV (T=631.369K) Etot = 57.702eV Energy per atom: Epot =49.398eV Ekin = 8.298eV (T=690.282K) Etot = 57.696eV Energy per atom: Epot =48.889eV Ekin = 8.800eV (T=732.012K) Etot = 57.689eV Energy per atom: Epot =48.470eV Ekin = 9.220eV (T=766.958K) Etot = 57.690eV Energy per atom: Epot =49.982eV Ekin = 7.722eV (T=642.360K) Etot = 57.704eV Energy per atom: Epot =49.851eV Ekin = 7.847eV (T=652.756K) Etot = 57.698eV Energy per atom: Epot =49.620eV Ekin = 8.075eV (T=671.738K) Etot = 57.695eV Energy per atom: Epot =50.245eV Ekin = 7.453eV (T=619.997K) Etot = 57.698eV Energy per atom: Epot =50.611eV Ekin = 7.093eV (T=590.030K) Etot = 57.704eV Energy per atom: Epot =49.923eV Ekin = 7.778eV (T=647.056K) Etot = 57.702eV Energy per atom: Epot =49.683eV Ekin = 8.017eV (T=666.913K) Etot = 57.701eV Energy per atom: Epot =49.633eV Ekin = 8.067eV (T=671.090K) Etot = 57.701eV Energy per atom: Epot =49.127eV Ekin = 8.574eV (T=713.242K) Etot = 57.701eV Energy per atom: Epot =49.184eV Ekin = 8.516eV (T=708.422K) Etot = 57.700eV Energy per atom: Epot =49.672eV Ekin = 8.022eV (T=667.287K) Etot = 57.693eV Energy per atom: Epot =49.449eV Ekin = 8.251eV (T=686.343K) Etot = 57.700eV Energy per atom: Epot =50.162eV Ekin = 7.539eV (T=627.170K) Etot = 57.702eV Energy per atom: Epot =50.456eV Ekin = 7.250eV (T=603.068K) Etot = 57.705eV Energy per atom: Epot =49.619eV Ekin = 8.079eV (T=672.088K) Etot = 57.698eV Energy per atom: Epot =49.719eV Ekin = 7.981eV (T=663.877K) Etot = 57.699eV Energy per atom: Epot =49.913eV Ekin = 7.789eV (T=647.946K) Etot = 57.702eV Energy per atom: Epot =49.435eV Ekin = 8.262eV (T=687.319K) Etot = 57.698eV Energy per atom: Epot =49.932eV Ekin = 7.771eV (T=646.437K) Etot = 57.703eV Energy per atom: Epot =50.385eV Ekin = 7.318eV (T=608.758K) Etot = 57.703eV Energy per atom: Epot =50.385eV Ekin = 7.314eV (T=608.454K) Etot = 57.699eV Energy per atom: Epot =49.605eV Ekin = 8.088eV (T=672.843K) Etot = 57.693eV Energy per atom: Epot =50.708eV Ekin = 6.992eV (T=581.622K) Etot = 57.700eV Energy per atom: Epot =51.448eV Ekin = 6.260eV (T=520.742K) Etot = 57.708eV Energy per atom: Epot =50.103eV Ekin = 7.603eV (T=632.450K) Etot = 57.706eV Energy per atom: Epot =49.197eV Ekin = 8.493eV (T=706.518K) Etot = 57.690eV Energy per atom: Epot =49.805eV Ekin = 7.884eV (T=655.854K) Etot = 57.689eV Energy per atom: Epot =49.951eV Ekin = 7.747eV (T=644.452K) Etot = 57.698eV Energy per atom: Epot =49.493eV Ekin = 8.204eV (T=682.487K) Etot = 57.697eV Energy per atom: Epot =49.313eV Ekin = 8.382eV (T=697.280K) Etot = 57.696eV Energy per atom: Epot =49.595eV Ekin = 8.104eV (T=674.179K) Etot = 57.699eV Energy per atom: Epot =49.858eV Ekin = 7.847eV (T=652.795K) Etot = 57.705eV Energy per atom: Epot =49.528eV Ekin = 8.169eV (T=679.533K) Etot = 57.697eV Energy per atom: Epot =49.529eV Ekin = 8.168eV (T=679.432K) Etot = 57.697eV Energy per atom: Epot =49.259eV Ekin = 8.437eV (T=701.886K) Etot = 57.696eV Energy per atom: Epot =49.709eV Ekin = 7.992eV (T=664.827K) Etot = 57.701eV Energy per atom: Epot =49.092eV Ekin = 8.603eV (T=715.679K) Etot = 57.695eV Energy per atom: Epot =49.473eV Ekin = 8.219eV (T=683.717K) Etot = 57.693eV Energy per atom: Epot =49.160eV Ekin = 8.525eV (T=709.149K) Etot = 57.685eV Energy per atom: Epot =49.451eV Ekin = 8.239eV (T=685.400K) Etot = 57.690eV Energy per atom: Epot =50.059eV Ekin = 7.640eV (T=635.519K) Etot = 57.699eV Energy per atom: Epot =49.984eV Ekin = 7.716eV (T=641.839K) Etot = 57.699eV Energy per atom: Epot =49.849eV Ekin = 7.848eV (T=652.860K) Etot = 57.697eV Energy per atom: Epot =49.708eV Ekin = 7.985eV (T=664.282K) Etot = 57.693eV Energy per atom: Epot =49.778eV Ekin = 7.914eV (T=658.344K) Etot = 57.692eV Energy per atom: Epot =50.078eV Ekin = 7.618eV (T=633.737K) Etot = 57.697eV Energy per atom: Epot =49.336eV Ekin = 8.361eV (T=695.484K) Etot = 57.696eV Energy per atom: Epot =50.085eV Ekin = 7.617eV (T=633.637K) Etot = 57.703eV Energy per atom: Epot =50.730eV Ekin = 6.971eV (T=579.858K) Etot = 57.701eV Energy per atom: Epot =49.803eV Ekin = 7.895eV (T=656.774K) Etot = 57.698eV Energy per atom: Epot =50.319eV Ekin = 7.383eV (T=614.184K) Etot = 57.703eV Energy per atom: Epot =49.900eV Ekin = 7.794eV (T=648.376K) Etot = 57.694eV Energy per atom: Epot =48.558eV Ekin = 9.134eV (T=759.808K) Etot = 57.692eV Energy per atom: Epot =50.595eV Ekin = 7.103eV (T=590.887K) Etot = 57.698eV Energy per atom: Epot =50.159eV Ekin = 7.535eV (T=626.835K) Etot = 57.694eV Energy per atom: Epot =50.286eV Ekin = 7.412eV (T=616.593K) Etot = 57.698eV Energy per atom: Epot =50.230eV Ekin = 7.467eV (T=621.124K) Etot = 57.697eV Energy per atom: Epot =49.802eV Ekin = 7.896eV (T=656.802K) Etot = 57.698eV Energy per atom: Epot =51.201eV Ekin = 6.507eV (T=541.268K) Etot = 57.707eV Energy per atom: Epot =50.580eV Ekin = 7.123eV (T=592.519K) Etot = 57.703eV Energy per atom: Epot =50.507eV Ekin = 7.192eV (T=598.282K) Etot = 57.699eV Energy per atom: Epot =49.711eV Ekin = 7.985eV (T=664.256K) Etot = 57.696eV Energy per atom: Epot =49.828eV Ekin = 7.872eV (T=654.851K) Etot = 57.700eV Energy per atom: Epot =49.241eV Ekin = 8.455eV (T=703.337K) Etot = 57.696eV Energy per atom: Epot =49.849eV Ekin = 7.852eV (T=653.167K) Etot = 57.700eV Energy per atom: Epot =49.596eV Ekin = 8.101eV (T=673.933K) Etot = 57.698eV Energy per atom: Epot =49.860eV Ekin = 7.840eV (T=652.208K) Etot = 57.701eV Energy per atom: Epot =49.849eV Ekin = 7.849eV (T=652.906K) Etot = 57.698eV Energy per atom: Epot =50.706eV Ekin = 6.997eV (T=582.070K) Etot = 57.703eV Energy per atom: Epot =50.181eV Ekin = 7.524eV (T=625.937K) Etot = 57.706eV Energy per atom: Epot =49.213eV Ekin = 8.489eV (T=706.168K) Etot = 57.702eV Energy per atom: Epot =49.460eV Ekin = 8.240eV (T=685.492K) Etot = 57.701eV Energy per atom: Epot =49.970eV Ekin = 7.734eV (T=643.374K) Etot = 57.704eV Energy per atom: Epot =50.187eV Ekin = 7.515eV (T=625.157K) Etot = 57.703eV Energy per atom: Epot =50.893eV Ekin = 6.811eV (T=566.571K) Etot = 57.704eV Energy per atom: Epot =49.844eV Ekin = 7.850eV (T=652.997K) Etot = 57.694eV Energy per atom: Epot =50.031eV Ekin = 7.665eV (T=637.610K) Etot = 57.696eV Energy per atom: Epot =49.171eV Ekin = 8.524eV (T=709.088K) Etot = 57.695eV Energy per atom: Epot =49.739eV Ekin = 7.962eV (T=662.343K) Etot = 57.701eV Energy per atom: Epot =50.214eV Ekin = 7.491eV (T=623.138K) Etot = 57.705eV Energy per atom: Epot =50.561eV Ekin = 7.142eV (T=594.117K) Etot = 57.703eV Energy per atom: Epot =49.879eV Ekin = 7.823eV (T=650.740K) Etot = 57.702eV Energy per atom: Epot =49.931eV Ekin = 7.768eV (T=646.198K) Etot = 57.699eV Energy per atom: Epot =49.560eV Ekin = 8.142eV (T=677.292K) Etot = 57.702eV Energy per atom: Epot =49.031eV Ekin = 8.667eV (T=721.003K) Etot = 57.698eV Energy per atom: Epot =48.994eV Ekin = 8.698eV (T=723.541K) Etot = 57.692eV Energy per atom: Epot =50.186eV Ekin = 7.513eV (T=624.984K) Etot = 57.699eV Energy per atom: Epot =49.925eV Ekin = 7.777eV (T=646.940K) Etot = 57.702eV Energy per atom: Epot =49.097eV Ekin = 8.599eV (T=715.350K) Etot = 57.696eV Energy per atom: Epot =49.646eV Ekin = 8.047eV (T=669.369K) Etot = 57.693eV Energy per atom: Epot =50.042eV Ekin = 7.657eV (T=636.918K) Etot = 57.699eV .. GENERATED FROM PYTHON SOURCE LINES 314-324 After running the simulation, use :ref:`ase-gui` to compare the resulting trajectory with how it looks if you comment out either the line that says ``Stationary(atoms)``, ``ZeroRotation(atoms)`` or both: :: ase gui nanoparticleCu_NVE.traj Try playing the movie with a high frame rate and set frame skipping to a low number. Can you spot the subtle difference? .. _sphx_glr_download_examples_generated_03-tutorials_md.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: md.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: md.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: md.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_