.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples_generated/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_tutorials_md.py: .. _md_tutorials_basic: ================== 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/tutorials/images/sphx_glr_md_001.png :alt: md :srcset: /examples_generated/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/tutorials/images/sphx_glr_md_002.png :alt: md :srcset: /examples_generated/tutorials/images/sphx_glr_md_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none running a NVE simulation of fcc Cu Energy per atom: Epot =-2.405eV Ekin = 159.735eV (T=308.942K) Etot = 157.331eV Energy per atom: Epot =121.861eV Ekin = 36.277eV (T=70.163K) Etot = 158.138eV Energy per atom: Epot =79.564eV Ekin = 78.417eV (T=151.666K) Etot = 157.982eV Energy per atom: Epot =72.612eV Ekin = 85.229eV (T=164.840K) Etot = 157.841eV Energy per atom: Epot =72.032eV Ekin = 85.764eV (T=165.875K) Etot = 157.797eV Energy per atom: Epot =83.742eV Ekin = 74.217eV (T=143.542K) Etot = 157.959eV Energy per atom: Epot =79.224eV Ekin = 78.706eV (T=152.224K) Etot = 157.930eV Energy per atom: Epot =77.021eV Ekin = 80.837eV (T=156.347K) Etot = 157.858eV Energy per atom: Epot =74.344eV Ekin = 83.510eV (T=161.516K) Etot = 157.854eV Energy per atom: Epot =81.745eV Ekin = 76.188eV (T=147.354K) Etot = 157.933eV Energy per atom: Epot =77.121eV Ekin = 80.762eV (T=156.201K) Etot = 157.884eV Energy per atom: Epot =76.431eV Ekin = 81.440eV (T=157.512K) Etot = 157.871eV Energy per atom: Epot =78.189eV Ekin = 79.708eV (T=154.163K) Etot = 157.897eV Energy per atom: Epot =79.647eV Ekin = 78.253eV (T=151.349K) Etot = 157.900eV Energy per atom: Epot =76.023eV Ekin = 81.853eV (T=158.310K) Etot = 157.875eV Energy per atom: Epot =77.988eV Ekin = 79.919eV (T=154.569K) Etot = 157.907eV Energy per atom: Epot =76.737eV Ekin = 81.149eV (T=156.949K) Etot = 157.886eV Energy per atom: Epot =81.069eV Ekin = 76.825eV (T=148.586K) Etot = 157.894eV Energy per atom: Epot =76.233eV Ekin = 81.658eV (T=157.934K) Etot = 157.891eV Energy per atom: Epot =76.980eV Ekin = 80.902eV (T=156.471K) Etot = 157.882eV Energy per atom: Epot =80.195eV Ekin = 77.703eV (T=150.284K) Etot = 157.898eV .. 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/tutorials/images/sphx_glr_md_003.png :alt: md :srcset: /examples_generated/tutorials/images/sphx_glr_md_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none 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 =599.972eV Ekin = 82.205eV (T=158.991K) Etot = 682.177eV Energy per atom: Epot =672.213eV Ekin = 140.843eV (T=272.403K) Etot = 813.057eV Energy per atom: Epot =727.158eV Ekin = 201.790eV (T=390.279K) Etot = 928.948eV Energy per atom: Epot =781.348eV Ekin = 256.759eV (T=496.594K) Etot = 1038.107eV Energy per atom: Epot =832.730eV Ekin = 301.707eV (T=583.528K) Etot = 1134.437eV Energy per atom: Epot =884.720eV Ekin = 341.319eV (T=660.141K) Etot = 1226.039eV Energy per atom: Epot =927.002eV Ekin = 381.965eV (T=738.754K) Etot = 1308.967eV Energy per atom: Epot =976.594eV Ekin = 417.843eV (T=808.145K) Etot = 1394.437eV Energy per atom: Epot =1015.387eV Ekin = 450.212eV (T=870.750K) Etot = 1465.599eV Energy per atom: Epot =1043.250eV Ekin = 480.295eV (T=928.933K) Etot = 1523.545eV Energy per atom: Epot =1082.070eV Ekin = 500.506eV (T=968.022K) Etot = 1582.576eV Energy per atom: Epot =1114.915eV Ekin = 513.489eV (T=993.133K) Etot = 1628.405eV Energy per atom: Epot =1146.345eV Ekin = 526.644eV (T=1018.576K) Etot = 1672.990eV Energy per atom: Epot =1180.541eV Ekin = 543.243eV (T=1050.679K) Etot = 1723.784eV Energy per atom: Epot =1201.107eV Ekin = 560.656eV (T=1084.357K) Etot = 1761.763eV Energy per atom: Epot =1240.142eV Ekin = 567.867eV (T=1098.304K) Etot = 1808.009eV Energy per atom: Epot =1256.063eV Ekin = 596.756eV (T=1154.178K) Etot = 1852.819eV Energy per atom: Epot =1292.784eV Ekin = 588.693eV (T=1138.584K) Etot = 1881.477eV Energy per atom: Epot =1313.310eV Ekin = 602.161eV (T=1164.631K) Etot = 1915.471eV Energy per atom: Epot =1339.652eV Ekin = 602.447eV (T=1165.185K) Etot = 1942.099eV Energy per atom: Epot =1342.616eV Ekin = 635.468eV (T=1229.050K) Etot = 1978.084eV Energy per atom: Epot =1376.010eV Ekin = 634.272eV (T=1226.737K) Etot = 2010.281eV Energy per atom: Epot =1390.225eV Ekin = 645.828eV (T=1249.088K) Etot = 2036.053eV Energy per atom: Epot =1415.532eV Ekin = 644.287eV (T=1246.108K) Etot = 2059.820eV Energy per atom: Epot =1425.901eV Ekin = 655.572eV (T=1267.934K) Etot = 2081.474eV Energy per atom: Epot =1444.253eV Ekin = 654.012eV (T=1264.917K) Etot = 2098.266eV Energy per atom: Epot =1448.299eV Ekin = 677.946eV (T=1311.206K) Etot = 2126.245eV Energy per atom: Epot =1464.841eV Ekin = 680.576eV (T=1316.294K) Etot = 2145.417eV Energy per atom: Epot =1487.571eV Ekin = 678.839eV (T=1312.934K) Etot = 2166.410eV Energy per atom: Epot =1505.883eV Ekin = 678.295eV (T=1311.881K) Etot = 2184.178eV Energy per atom: Epot =1508.757eV Ekin = 689.118eV (T=1332.814K) Etot = 2197.875eV Energy per atom: Epot =1523.368eV Ekin = 694.560eV (T=1343.340K) Etot = 2217.928eV Energy per atom: Epot =1537.434eV Ekin = 702.065eV (T=1357.854K) Etot = 2239.498eV Energy per atom: Epot =1558.578eV Ekin = 694.238eV (T=1342.717K) Etot = 2252.816eV Energy per atom: Epot =1564.139eV Ekin = 711.040eV (T=1375.214K) Etot = 2275.180eV Energy per atom: Epot =1578.612eV Ekin = 694.730eV (T=1343.669K) Etot = 2273.342eV Energy per atom: Epot =1583.579eV Ekin = 699.373eV (T=1352.648K) Etot = 2282.952eV Energy per atom: Epot =1592.511eV Ekin = 702.761eV (T=1359.201K) Etot = 2295.272eV Energy per atom: Epot =1599.974eV Ekin = 706.421eV (T=1366.279K) Etot = 2306.394eV Energy per atom: Epot =1621.183eV Ekin = 699.594eV (T=1353.076K) Etot = 2320.777eV Energy per atom: Epot =1624.637eV Ekin = 712.381eV (T=1377.807K) Etot = 2337.018eV Energy per atom: Epot =1634.119eV Ekin = 718.201eV (T=1389.063K) Etot = 2352.319eV Energy per atom: Epot =1646.660eV Ekin = 713.934eV (T=1380.811K) Etot = 2360.594eV Energy per atom: Epot =1659.033eV Ekin = 711.775eV (T=1376.634K) Etot = 2370.808eV Energy per atom: Epot =1668.405eV Ekin = 721.467eV (T=1395.379K) Etot = 2389.872eV Energy per atom: Epot =1682.209eV Ekin = 716.911eV (T=1386.568K) Etot = 2399.120eV Energy per atom: Epot =1681.150eV Ekin = 733.245eV (T=1418.159K) Etot = 2414.394eV Energy per atom: Epot =1683.937eV Ekin = 742.548eV (T=1436.153K) Etot = 2426.485eV Energy per atom: Epot =1699.882eV Ekin = 736.089eV (T=1423.660K) Etot = 2435.971eV Energy per atom: Epot =1715.110eV Ekin = 735.915eV (T=1423.324K) Etot = 2451.025eV Energy per atom: Epot =1711.320eV Ekin = 747.100eV (T=1444.956K) Etot = 2458.420eV Energy per atom: Epot =1739.657eV Ekin = 726.087eV (T=1404.316K) Etot = 2465.744eV Energy per atom: Epot =1747.252eV Ekin = 725.313eV (T=1402.818K) Etot = 2472.565eV Energy per atom: Epot =1749.302eV Ekin = 734.818eV (T=1421.202K) Etot = 2484.119eV Energy per atom: Epot =1756.435eV Ekin = 735.296eV (T=1422.126K) Etot = 2491.731eV Energy per atom: Epot =1746.243eV Ekin = 742.155eV (T=1435.392K) Etot = 2488.398eV Energy per atom: Epot =1766.746eV Ekin = 732.218eV (T=1416.173K) Etot = 2498.964eV Energy per atom: Epot =1784.506eV Ekin = 732.934eV (T=1417.558K) Etot = 2517.440eV Energy per atom: Epot =1774.907eV Ekin = 751.788eV (T=1454.024K) Etot = 2526.695eV Energy per atom: Epot =1791.829eV Ekin = 742.934eV (T=1436.899K) Etot = 2534.763eV Energy per atom: Epot =1799.170eV Ekin = 731.207eV (T=1414.218K) Etot = 2530.377eV Energy per atom: Epot =1799.415eV Ekin = 743.207eV (T=1437.428K) Etot = 2542.622eV Energy per atom: Epot =1808.356eV Ekin = 746.424eV (T=1443.650K) Etot = 2554.781eV Energy per atom: Epot =1816.898eV Ekin = 738.073eV (T=1427.498K) Etot = 2554.971eV Energy per atom: Epot =1808.646eV Ekin = 754.147eV (T=1458.585K) Etot = 2562.793eV Energy per atom: Epot =1826.674eV Ekin = 748.724eV (T=1448.097K) Etot = 2575.398eV Energy per atom: Epot =1834.495eV Ekin = 747.912eV (T=1446.528K) Etot = 2582.407eV Energy per atom: Epot =1842.792eV Ekin = 738.202eV (T=1427.746K) Etot = 2580.993eV Energy per atom: Epot =1846.995eV Ekin = 735.402eV (T=1422.332K) Etot = 2582.397eV Energy per atom: Epot =1853.659eV Ekin = 733.543eV (T=1418.737K) Etot = 2587.202eV Energy per atom: Epot =1852.353eV Ekin = 740.563eV (T=1432.312K) Etot = 2592.915eV Energy per atom: Epot =1852.427eV Ekin = 750.495eV (T=1451.522K) Etot = 2602.922eV Energy per atom: Epot =1855.454eV Ekin = 753.056eV (T=1456.475K) Etot = 2608.509eV Energy per atom: Epot =1859.903eV Ekin = 750.153eV (T=1450.861K) Etot = 2610.056eV Energy per atom: Epot =1866.650eV Ekin = 749.598eV (T=1449.787K) Etot = 2616.247eV Energy per atom: Epot =1854.392eV Ekin = 755.946eV (T=1462.065K) Etot = 2610.338eV Energy per atom: Epot =1877.496eV Ekin = 744.598eV (T=1440.117K) Etot = 2622.094eV Energy per atom: Epot =1883.727eV Ekin = 736.629eV (T=1424.705K) Etot = 2620.356eV Energy per atom: Epot =1874.821eV Ekin = 751.835eV (T=1454.114K) Etot = 2626.656eV Energy per atom: Epot =1886.528eV Ekin = 745.656eV (T=1442.163K) Etot = 2632.183eV Energy per atom: Epot =1893.360eV Ekin = 743.892eV (T=1438.752K) Etot = 2637.251eV Energy per atom: Epot =1890.855eV Ekin = 747.017eV (T=1444.796K) Etot = 2637.872eV Energy per atom: Epot =1909.779eV Ekin = 745.131eV (T=1441.149K) Etot = 2654.910eV Energy per atom: Epot =1914.019eV Ekin = 757.012eV (T=1464.127K) Etot = 2671.030eV Energy per atom: Epot =1917.866eV Ekin = 758.486eV (T=1466.978K) Etot = 2676.352eV Energy per atom: Epot =1919.347eV Ekin = 751.706eV (T=1453.865K) Etot = 2671.053eV Energy per atom: Epot =1938.627eV Ekin = 741.735eV (T=1434.580K) Etot = 2680.362eV Energy per atom: Epot =1940.891eV Ekin = 733.910eV (T=1419.447K) Etot = 2674.801eV Energy per atom: Epot =1922.955eV Ekin = 750.931eV (T=1452.365K) Etot = 2673.886eV Energy per atom: Epot =1925.563eV Ekin = 748.837eV (T=1448.316K) Etot = 2674.400eV Energy per atom: Epot =1916.346eV Ekin = 756.748eV (T=1463.616K) Etot = 2673.094eV Energy per atom: Epot =1923.645eV Ekin = 756.321eV (T=1462.790K) Etot = 2679.966eV Energy per atom: Epot =1937.503eV Ekin = 752.427eV (T=1455.260K) Etot = 2689.930eV Energy per atom: Epot =1941.731eV Ekin = 750.863eV (T=1452.235K) Etot = 2692.594eV Energy per atom: Epot =1939.573eV Ekin = 759.057eV (T=1468.083K) Etot = 2698.630eV Energy per atom: Epot =1935.459eV Ekin = 775.987eV (T=1500.826K) Etot = 2711.446eV Energy per atom: Epot =1933.298eV Ekin = 773.844eV (T=1496.683K) Etot = 2707.143eV Energy per atom: Epot =1941.050eV Ekin = 771.418eV (T=1491.990K) Etot = 2712.468eV Energy per atom: Epot =1958.380eV Ekin = 764.832eV (T=1479.252K) Etot = 2723.212eV Energy per atom: Epot =1961.465eV Ekin = 766.329eV (T=1482.147K) Etot = 2727.794eV Energy per atom: Epot =1963.892eV Ekin = 765.240eV (T=1480.040K) Etot = 2729.132eV Energy per atom: Epot =1951.719eV Ekin = 777.302eV (T=1503.370K) Etot = 2729.021eV Energy per atom: Epot =1956.336eV Ekin = 786.069eV (T=1520.326K) Etot = 2742.405eV Energy per atom: Epot =1974.693eV Ekin = 765.940eV (T=1481.395K) Etot = 2740.634eV Energy per atom: Epot =1973.759eV Ekin = 772.418eV (T=1493.924K) Etot = 2746.177eV Energy per atom: Epot =1984.276eV Ekin = 760.904eV (T=1471.655K) Etot = 2745.180eV Energy per atom: Epot =1976.830eV Ekin = 759.420eV (T=1468.784K) Etot = 2736.250eV Energy per atom: Epot =1977.573eV Ekin = 763.511eV (T=1476.696K) Etot = 2741.084eV Energy per atom: Epot =1981.021eV Ekin = 760.084eV (T=1470.069K) Etot = 2741.105eV Energy per atom: Epot =1975.804eV Ekin = 761.456eV (T=1472.721K) Etot = 2737.260eV Energy per atom: Epot =1979.787eV Ekin = 755.630eV (T=1461.455K) Etot = 2735.418eV Energy per atom: Epot =1978.923eV Ekin = 758.583eV (T=1467.166K) Etot = 2737.507eV Energy per atom: Epot =1985.253eV Ekin = 752.148eV (T=1454.719K) Etot = 2737.401eV Energy per atom: Epot =1983.316eV Ekin = 763.861eV (T=1477.373K) Etot = 2747.176eV Energy per atom: Epot =1998.419eV Ekin = 749.643eV (T=1449.875K) Etot = 2748.062eV Energy per atom: Epot =1987.594eV Ekin = 750.346eV (T=1451.235K) Etot = 2737.941eV Energy per atom: Epot =1991.395eV Ekin = 753.040eV (T=1456.444K) Etot = 2744.434eV Energy per atom: Epot =1983.458eV Ekin = 766.995eV (T=1483.435K) Etot = 2750.453eV Energy per atom: Epot =1994.837eV Ekin = 761.061eV (T=1471.958K) Etot = 2755.898eV Energy per atom: Epot =2000.994eV Ekin = 757.303eV (T=1464.690K) Etot = 2758.297eV Energy per atom: Epot =1987.141eV Ekin = 769.171eV (T=1487.644K) Etot = 2756.313eV Energy per atom: Epot =1975.149eV Ekin = 780.372eV (T=1509.307K) Etot = 2755.521eV Energy per atom: Epot =1981.964eV Ekin = 769.916eV (T=1489.084K) Etot = 2751.879eV Energy per atom: Epot =1989.439eV Ekin = 765.594eV (T=1480.725K) Etot = 2755.032eV Energy per atom: Epot =2005.363eV Ekin = 752.074eV (T=1454.577K) Etot = 2757.437eV Energy per atom: Epot =2002.684eV Ekin = 756.710eV (T=1463.544K) Etot = 2759.395eV Energy per atom: Epot =1993.386eV Ekin = 761.663eV (T=1473.123K) Etot = 2755.049eV Energy per atom: Epot =1980.917eV Ekin = 780.383eV (T=1509.330K) Etot = 2761.300eV Energy per atom: Epot =1977.392eV Ekin = 787.211eV (T=1522.534K) Etot = 2764.603eV Energy per atom: Epot =1995.415eV Ekin = 778.280eV (T=1505.262K) Etot = 2773.696eV Energy per atom: Epot =1993.449eV Ekin = 778.039eV (T=1504.795K) Etot = 2771.488eV Energy per atom: Epot =1985.053eV Ekin = 797.943eV (T=1543.291K) Etot = 2782.995eV Energy per atom: Epot =1988.234eV Ekin = 789.594eV (T=1527.144K) Etot = 2777.828eV Energy per atom: Epot =1985.411eV Ekin = 782.933eV (T=1514.260K) Etot = 2768.343eV Energy per atom: Epot =1995.489eV Ekin = 776.919eV (T=1502.629K) Etot = 2772.408eV Energy per atom: Epot =2006.206eV Ekin = 765.235eV (T=1480.032K) Etot = 2771.442eV Energy per atom: Epot =1996.294eV Ekin = 786.024eV (T=1520.238K) Etot = 2782.318eV Energy per atom: Epot =1997.489eV Ekin = 793.180eV (T=1534.079K) Etot = 2790.669eV Energy per atom: Epot =1998.622eV Ekin = 783.420eV (T=1515.201K) Etot = 2782.042eV Energy per atom: Epot =2005.214eV Ekin = 786.863eV (T=1521.861K) Etot = 2792.077eV Energy per atom: Epot =2001.196eV Ekin = 791.080eV (T=1530.017K) Etot = 2792.276eV Energy per atom: Epot =2016.420eV Ekin = 778.103eV (T=1504.919K) Etot = 2794.523eV Energy per atom: Epot =1998.120eV Ekin = 793.205eV (T=1534.128K) Etot = 2791.325eV Energy per atom: Epot =2010.175eV Ekin = 778.309eV (T=1505.318K) Etot = 2788.485eV Energy per atom: Epot =2017.911eV Ekin = 773.286eV (T=1495.602K) Etot = 2791.197eV Energy per atom: Epot =2024.311eV Ekin = 770.302eV (T=1489.831K) Etot = 2794.613eV Energy per atom: Epot =2021.566eV Ekin = 780.156eV (T=1508.890K) Etot = 2801.723eV Energy per atom: Epot =2013.000eV Ekin = 782.398eV (T=1513.225K) Etot = 2795.398eV Energy per atom: Epot =2021.571eV Ekin = 772.061eV (T=1493.233K) Etot = 2793.631eV Energy per atom: Epot =2008.949eV Ekin = 779.231eV (T=1507.100K) Etot = 2788.180eV Energy per atom: Epot =2022.470eV Ekin = 770.087eV (T=1489.416K) Etot = 2792.557eV Energy per atom: Epot =2021.620eV Ekin = 769.653eV (T=1488.577K) Etot = 2791.273eV Energy per atom: Epot =2024.827eV Ekin = 767.776eV (T=1484.946K) Etot = 2792.603eV Energy per atom: Epot =2019.620eV Ekin = 776.707eV (T=1502.219K) Etot = 2796.327eV Energy per atom: Epot =2027.560eV Ekin = 771.229eV (T=1491.624K) Etot = 2798.790eV Energy per atom: Epot =2032.189eV Ekin = 764.244eV (T=1478.115K) Etot = 2796.433eV Energy per atom: Epot =2026.229eV Ekin = 768.485eV (T=1486.316K) Etot = 2794.713eV Energy per atom: Epot =2009.333eV Ekin = 771.036eV (T=1491.251K) Etot = 2780.369eV Energy per atom: Epot =2009.537eV Ekin = 766.541eV (T=1482.558K) Etot = 2776.079eV Energy per atom: Epot =2014.277eV Ekin = 766.552eV (T=1482.578K) Etot = 2780.829eV Energy per atom: Epot =2011.145eV Ekin = 767.570eV (T=1484.548K) Etot = 2778.715eV Energy per atom: Epot =2005.202eV Ekin = 767.751eV (T=1484.898K) Etot = 2772.953eV Energy per atom: Epot =2007.484eV Ekin = 766.669eV (T=1482.805K) Etot = 2774.153eV Energy per atom: Epot =1997.386eV Ekin = 778.021eV (T=1504.761K) Etot = 2775.408eV Energy per atom: Epot =2012.687eV Ekin = 762.384eV (T=1474.517K) Etot = 2775.071eV Energy per atom: Epot =1998.162eV Ekin = 785.032eV (T=1518.320K) Etot = 2783.193eV Energy per atom: Epot =2005.222eV Ekin = 782.687eV (T=1513.785K) Etot = 2787.909eV Energy per atom: Epot =2003.302eV Ekin = 787.121eV (T=1522.361K) Etot = 2790.423eV Energy per atom: Epot =1995.967eV Ekin = 800.707eV (T=1548.637K) Etot = 2796.674eV Energy per atom: Epot =2001.846eV Ekin = 785.164eV (T=1518.576K) Etot = 2787.010eV Energy per atom: Epot =2004.849eV Ekin = 791.180eV (T=1530.212K) Etot = 2796.029eV Energy per atom: Epot =2006.784eV Ekin = 788.572eV (T=1525.168K) Etot = 2795.356eV Energy per atom: Epot =2023.654eV Ekin = 767.103eV (T=1483.645K) Etot = 2790.757eV Energy per atom: Epot =2016.041eV Ekin = 783.147eV (T=1514.674K) Etot = 2799.188eV Energy per atom: Epot =2019.481eV Ekin = 778.667eV (T=1506.010K) Etot = 2798.148eV Energy per atom: Epot =2015.195eV Ekin = 777.456eV (T=1503.668K) Etot = 2792.651eV Energy per atom: Epot =2014.127eV Ekin = 786.521eV (T=1521.200K) Etot = 2800.648eV Energy per atom: Epot =2005.873eV Ekin = 778.663eV (T=1506.001K) Etot = 2784.536eV Energy per atom: Epot =2001.362eV Ekin = 777.581eV (T=1503.910K) Etot = 2778.943eV Energy per atom: Epot =2020.552eV Ekin = 762.301eV (T=1474.356K) Etot = 2782.853eV Energy per atom: Epot =2009.470eV Ekin = 781.001eV (T=1510.523K) Etot = 2790.471eV Energy per atom: Epot =2007.047eV Ekin = 774.344eV (T=1497.648K) Etot = 2781.391eV Energy per atom: Epot =2000.540eV Ekin = 770.265eV (T=1489.759K) Etot = 2770.805eV Energy per atom: Epot =2010.242eV Ekin = 757.575eV (T=1465.217K) Etot = 2767.818eV Energy per atom: Epot =2008.394eV Ekin = 768.143eV (T=1485.655K) Etot = 2776.537eV Energy per atom: Epot =2016.156eV Ekin = 771.519eV (T=1492.184K) Etot = 2787.674eV Energy per atom: Epot =2023.819eV Ekin = 773.332eV (T=1495.691K) Etot = 2797.151eV Energy per atom: Epot =2020.721eV Ekin = 771.654eV (T=1492.446K) Etot = 2792.375eV Energy per atom: Epot =2021.549eV Ekin = 767.943eV (T=1485.268K) Etot = 2789.492eV Energy per atom: Epot =2027.216eV Ekin = 767.241eV (T=1483.911K) Etot = 2794.457eV Energy per atom: Epot =2037.376eV Ekin = 759.184eV (T=1468.329K) Etot = 2796.560eV Energy per atom: Epot =2027.589eV Ekin = 773.847eV (T=1496.688K) Etot = 2801.436eV Energy per atom: Epot =2022.330eV Ekin = 784.223eV (T=1516.755K) Etot = 2806.553eV Energy per atom: Epot =2029.580eV Ekin = 778.269eV (T=1505.240K) Etot = 2807.848eV Energy per atom: Epot =2033.460eV Ekin = 773.991eV (T=1496.967K) Etot = 2807.451eV Energy per atom: Epot =2019.177eV Ekin = 784.671eV (T=1517.622K) Etot = 2803.847eV Energy per atom: Epot =2031.866eV Ekin = 773.281eV (T=1495.593K) Etot = 2805.147eV Energy per atom: Epot =2010.996eV Ekin = 790.458eV (T=1528.815K) Etot = 2801.454eV Energy per atom: Epot =2024.339eV Ekin = 763.395eV (T=1476.472K) Etot = 2787.734eV Energy per atom: Epot =2026.564eV Ekin = 757.083eV (T=1464.264K) Etot = 2783.646eV .. 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] 09:02:00 43.457006 1.0818 BFGSLineSearch: 1[ 1] 09:02:00 42.347659 0.2273 BFGSLineSearch: 2[ 2] 09:02:00 42.108454 0.1349 BFGSLineSearch: 3[ 3] 09:02:00 41.964817 0.1138 BFGSLineSearch: 4[ 4] 09:02:00 41.924933 0.0683 BFGSLineSearch: 5[ 5] 09:02:00 41.915346 0.0225 BFGSLineSearch: 6[ 6] 09:02:00 41.914920 0.0059 BFGSLineSearch: 7[ 7] 09:02:00 41.914872 0.0023 BFGSLineSearch: 8[ 9] 09:02:00 41.914855 0.0023 BFGSLineSearch: 9[ 10] 09:02:00 41.914851 0.0010 running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 17.668eV (T=1469.770K) Etot = 59.583eV Energy per atom: Epot =52.365eV Ekin = 7.276eV (T=605.297K) Etot = 59.642eV Energy per atom: Epot =52.238eV Ekin = 7.408eV (T=616.221K) Etot = 59.646eV Energy per atom: Epot =54.055eV Ekin = 5.593eV (T=465.247K) Etot = 59.647eV Energy per atom: Epot =52.595eV Ekin = 7.048eV (T=586.340K) Etot = 59.644eV Energy per atom: Epot =51.897eV Ekin = 7.744eV (T=644.222K) Etot = 59.641eV Energy per atom: Epot =52.083eV Ekin = 7.558eV (T=628.763K) Etot = 59.641eV Energy per atom: Epot =51.610eV Ekin = 8.029eV (T=667.920K) Etot = 59.639eV Energy per atom: Epot =51.248eV Ekin = 8.393eV (T=698.169K) Etot = 59.641eV Energy per atom: Epot =52.620eV Ekin = 7.032eV (T=585.007K) Etot = 59.652eV Energy per atom: Epot =52.913eV Ekin = 6.738eV (T=560.492K) Etot = 59.650eV Energy per atom: Epot =51.900eV Ekin = 7.741eV (T=643.929K) Etot = 59.641eV Energy per atom: Epot =52.288eV Ekin = 7.349eV (T=611.351K) Etot = 59.637eV Energy per atom: Epot =51.596eV Ekin = 8.037eV (T=668.573K) Etot = 59.633eV Energy per atom: Epot =51.346eV Ekin = 8.285eV (T=689.160K) Etot = 59.630eV Energy per atom: Epot =51.835eV Ekin = 7.804eV (T=649.163K) Etot = 59.639eV Energy per atom: Epot =51.900eV Ekin = 7.740eV (T=643.902K) Etot = 59.640eV Energy per atom: Epot =52.726eV Ekin = 6.918eV (T=575.477K) Etot = 59.644eV Energy per atom: Epot =52.327eV Ekin = 7.317eV (T=608.710K) Etot = 59.645eV Energy per atom: Epot =52.044eV Ekin = 7.598eV (T=632.010K) Etot = 59.642eV Energy per atom: Epot =51.961eV Ekin = 7.678eV (T=638.676K) Etot = 59.639eV Energy per atom: Epot =51.054eV Ekin = 8.581eV (T=713.848K) Etot = 59.635eV Energy per atom: Epot =51.876eV Ekin = 7.768eV (T=646.171K) Etot = 59.644eV Energy per atom: Epot =52.140eV Ekin = 7.501eV (T=623.999K) Etot = 59.641eV Energy per atom: Epot =52.474eV Ekin = 7.166eV (T=596.123K) Etot = 59.640eV Energy per atom: Epot =51.839eV Ekin = 7.800eV (T=648.843K) Etot = 59.638eV Energy per atom: Epot =52.029eV Ekin = 7.615eV (T=633.427K) Etot = 59.643eV Energy per atom: Epot =51.147eV Ekin = 8.489eV (T=706.145K) Etot = 59.636eV Energy per atom: Epot =51.472eV Ekin = 8.163eV (T=679.030K) Etot = 59.634eV Energy per atom: Epot =52.087eV Ekin = 7.555eV (T=628.475K) Etot = 59.642eV Energy per atom: Epot =52.330eV Ekin = 7.316eV (T=608.602K) Etot = 59.647eV Energy per atom: Epot =50.718eV Ekin = 8.923eV (T=742.278K) Etot = 59.641eV Energy per atom: Epot =51.467eV Ekin = 8.171eV (T=679.678K) Etot = 59.638eV Energy per atom: Epot =51.314eV Ekin = 8.324eV (T=692.467K) Etot = 59.638eV Energy per atom: Epot =51.421eV Ekin = 8.221eV (T=683.867K) Etot = 59.642eV Energy per atom: Epot =51.497eV Ekin = 8.145eV (T=677.515K) Etot = 59.642eV Energy per atom: Epot =51.261eV Ekin = 8.376eV (T=696.789K) Etot = 59.638eV Energy per atom: Epot =51.324eV Ekin = 8.314eV (T=691.593K) Etot = 59.638eV Energy per atom: Epot =51.830eV Ekin = 7.812eV (T=649.858K) Etot = 59.642eV Energy per atom: Epot =51.866eV Ekin = 7.773eV (T=646.643K) Etot = 59.640eV Energy per atom: Epot =50.900eV Ekin = 8.730eV (T=726.245K) Etot = 59.630eV Energy per atom: Epot =52.076eV Ekin = 7.567eV (T=629.456K) Etot = 59.643eV Energy per atom: Epot =50.906eV Ekin = 8.730eV (T=726.208K) Etot = 59.636eV Energy per atom: Epot =51.594eV Ekin = 8.047eV (T=669.376K) Etot = 59.641eV Energy per atom: Epot =51.873eV Ekin = 7.773eV (T=646.634K) Etot = 59.646eV Energy per atom: Epot =51.514eV Ekin = 8.125eV (T=675.919K) Etot = 59.640eV Energy per atom: Epot =50.802eV Ekin = 8.834eV (T=734.862K) Etot = 59.636eV Energy per atom: Epot =52.400eV Ekin = 7.241eV (T=602.361K) Etot = 59.641eV Energy per atom: Epot =52.059eV Ekin = 7.578eV (T=630.420K) Etot = 59.637eV Energy per atom: Epot =51.582eV Ekin = 8.053eV (T=669.874K) Etot = 59.634eV Energy per atom: Epot =51.857eV Ekin = 7.781eV (T=647.246K) Etot = 59.638eV Energy per atom: Epot =52.174eV Ekin = 7.465eV (T=621.019K) Etot = 59.639eV Energy per atom: Epot =51.146eV Ekin = 8.487eV (T=705.995K) Etot = 59.633eV Energy per atom: Epot =51.774eV Ekin = 7.860eV (T=653.863K) Etot = 59.634eV Energy per atom: Epot =51.802eV Ekin = 7.838eV (T=652.019K) Etot = 59.640eV Energy per atom: Epot =51.127eV Ekin = 8.517eV (T=708.465K) Etot = 59.644eV Energy per atom: Epot =51.536eV Ekin = 8.104eV (T=674.121K) Etot = 59.639eV Energy per atom: Epot =51.957eV Ekin = 7.683eV (T=639.136K) Etot = 59.640eV Energy per atom: Epot =51.579eV Ekin = 8.056eV (T=670.138K) Etot = 59.635eV Energy per atom: Epot =51.922eV Ekin = 7.714eV (T=641.708K) Etot = 59.636eV Energy per atom: Epot =51.798eV Ekin = 7.840eV (T=652.143K) Etot = 59.637eV Energy per atom: Epot =51.715eV Ekin = 7.928eV (T=659.483K) Etot = 59.643eV Energy per atom: Epot =51.329eV Ekin = 8.305eV (T=690.866K) Etot = 59.634eV Energy per atom: Epot =51.192eV Ekin = 8.443eV (T=702.338K) Etot = 59.635eV Energy per atom: Epot =51.726eV Ekin = 7.918eV (T=658.688K) Etot = 59.644eV Energy per atom: Epot =51.608eV Ekin = 8.037eV (T=668.603K) Etot = 59.645eV Energy per atom: Epot =51.786eV Ekin = 7.856eV (T=653.503K) Etot = 59.642eV Energy per atom: Epot =52.938eV Ekin = 6.706eV (T=557.848K) Etot = 59.644eV Energy per atom: Epot =51.308eV Ekin = 8.327eV (T=692.713K) Etot = 59.635eV Energy per atom: Epot =50.449eV Ekin = 9.181eV (T=763.721K) Etot = 59.629eV Energy per atom: Epot =51.098eV Ekin = 8.541eV (T=710.515K) Etot = 59.639eV Energy per atom: Epot =51.798eV Ekin = 7.845eV (T=652.612K) Etot = 59.643eV Energy per atom: Epot =51.395eV Ekin = 8.237eV (T=685.244K) Etot = 59.633eV Energy per atom: Epot =51.865eV Ekin = 7.770eV (T=646.340K) Etot = 59.635eV Energy per atom: Epot =52.301eV Ekin = 7.338eV (T=610.427K) Etot = 59.639eV Energy per atom: Epot =50.838eV Ekin = 8.792eV (T=731.398K) Etot = 59.630eV Energy per atom: Epot =51.309eV Ekin = 8.326eV (T=692.575K) Etot = 59.634eV Energy per atom: Epot =51.623eV Ekin = 8.013eV (T=666.599K) Etot = 59.636eV Energy per atom: Epot =52.488eV Ekin = 7.153eV (T=595.055K) Etot = 59.641eV Energy per atom: Epot =51.124eV Ekin = 8.514eV (T=708.214K) Etot = 59.638eV Energy per atom: Epot =51.655eV Ekin = 7.982eV (T=664.016K) Etot = 59.637eV Energy per atom: Epot =51.304eV Ekin = 8.330eV (T=692.908K) Etot = 59.633eV Energy per atom: Epot =50.809eV Ekin = 8.828eV (T=734.406K) Etot = 59.637eV Energy per atom: Epot =51.976eV Ekin = 7.671eV (T=638.136K) Etot = 59.647eV Energy per atom: Epot =51.497eV Ekin = 8.145eV (T=677.556K) Etot = 59.642eV Energy per atom: Epot =51.608eV Ekin = 8.031eV (T=668.075K) Etot = 59.639eV Energy per atom: Epot =50.468eV Ekin = 9.164eV (T=762.321K) Etot = 59.632eV Energy per atom: Epot =51.829eV Ekin = 7.811eV (T=649.791K) Etot = 59.640eV Energy per atom: Epot =50.409eV Ekin = 9.221eV (T=767.057K) Etot = 59.630eV Energy per atom: Epot =52.040eV Ekin = 7.598eV (T=632.044K) Etot = 59.638eV Energy per atom: Epot =51.459eV Ekin = 8.177eV (T=680.185K) Etot = 59.636eV Energy per atom: Epot =51.301eV Ekin = 8.331eV (T=693.067K) Etot = 59.633eV Energy per atom: Epot =51.240eV Ekin = 8.395eV (T=698.321K) Etot = 59.634eV Energy per atom: Epot =51.443eV Ekin = 8.196eV (T=681.822K) Etot = 59.639eV Energy per atom: Epot =51.329eV Ekin = 8.313eV (T=691.490K) Etot = 59.641eV Energy per atom: Epot =51.523eV Ekin = 8.119eV (T=675.397K) Etot = 59.642eV Energy per atom: Epot =51.506eV Ekin = 8.138eV (T=676.950K) Etot = 59.644eV Energy per atom: Epot =51.041eV Ekin = 8.596eV (T=715.056K) Etot = 59.636eV Energy per atom: Epot =51.442eV Ekin = 8.192eV (T=681.482K) Etot = 59.634eV Energy per atom: Epot =52.366eV Ekin = 7.277eV (T=605.320K) Etot = 59.643eV Energy per atom: Epot =51.546eV Ekin = 8.096eV (T=673.514K) Etot = 59.643eV Energy per atom: Epot =51.862eV Ekin = 7.784eV (T=647.501K) Etot = 59.646eV Energy per atom: Epot =51.430eV Ekin = 8.212eV (T=683.149K) Etot = 59.642eV Energy per atom: Epot =51.890eV Ekin = 7.756eV (T=645.195K) Etot = 59.646eV Energy per atom: Epot =51.406eV Ekin = 8.236eV (T=685.116K) Etot = 59.642eV Energy per atom: Epot =51.069eV Ekin = 8.574eV (T=713.211K) Etot = 59.643eV Energy per atom: Epot =50.833eV Ekin = 8.805eV (T=732.470K) Etot = 59.638eV Energy per atom: Epot =50.893eV Ekin = 8.740eV (T=727.052K) Etot = 59.633eV Energy per atom: Epot =52.716eV Ekin = 6.931eV (T=576.602K) Etot = 59.648eV Energy per atom: Epot =51.711eV Ekin = 7.929eV (T=659.577K) Etot = 59.640eV Energy per atom: Epot =51.241eV Ekin = 8.394eV (T=698.280K) Etot = 59.636eV Energy per atom: Epot =52.023eV Ekin = 7.622eV (T=634.026K) Etot = 59.645eV Energy per atom: Epot =51.035eV Ekin = 8.605eV (T=715.827K) Etot = 59.640eV Energy per atom: Epot =51.398eV Ekin = 8.246eV (T=685.919K) Etot = 59.644eV Energy per atom: Epot =51.747eV Ekin = 7.897eV (T=656.935K) Etot = 59.644eV Energy per atom: Epot =50.635eV Ekin = 9.000eV (T=748.702K) Etot = 59.635eV Energy per atom: Epot =51.282eV Ekin = 8.357eV (T=695.176K) Etot = 59.639eV Energy per atom: Epot =50.778eV Ekin = 8.858eV (T=736.907K) Etot = 59.636eV Energy per atom: Epot =51.155eV Ekin = 8.482eV (T=705.603K) Etot = 59.637eV Energy per atom: Epot =50.374eV Ekin = 9.263eV (T=770.563K) Etot = 59.637eV Energy per atom: Epot =51.710eV Ekin = 7.931eV (T=659.715K) Etot = 59.641eV Energy per atom: Epot =51.318eV Ekin = 8.320eV (T=692.123K) Etot = 59.638eV Energy per atom: Epot =51.193eV Ekin = 8.443eV (T=702.340K) Etot = 59.636eV Energy per atom: Epot =51.116eV Ekin = 8.520eV (T=708.727K) Etot = 59.636eV Energy per atom: Epot =52.587eV Ekin = 7.053eV (T=586.691K) Etot = 59.640eV Energy per atom: Epot =52.101eV Ekin = 7.539eV (T=627.147K) Etot = 59.640eV Energy per atom: Epot =51.811eV Ekin = 7.832eV (T=651.506K) Etot = 59.642eV Energy per atom: Epot =52.131eV Ekin = 7.517eV (T=625.276K) Etot = 59.648eV Energy per atom: Epot =50.735eV Ekin = 8.898eV (T=740.233K) Etot = 59.634eV Energy per atom: Epot =51.095eV Ekin = 8.542eV (T=710.561K) Etot = 59.637eV Energy per atom: Epot =50.888eV Ekin = 8.754eV (T=728.197K) Etot = 59.641eV Energy per atom: Epot =51.156eV Ekin = 8.489eV (T=706.201K) Etot = 59.646eV Energy per atom: Epot =52.402eV Ekin = 7.253eV (T=603.361K) Etot = 59.655eV Energy per atom: Epot =51.441eV Ekin = 8.206eV (T=682.629K) Etot = 59.647eV Energy per atom: Epot =51.322eV Ekin = 8.316eV (T=691.795K) Etot = 59.638eV Energy per atom: Epot =50.557eV Ekin = 9.079eV (T=755.229K) Etot = 59.636eV Energy per atom: Epot =51.923eV Ekin = 7.720eV (T=642.232K) Etot = 59.643eV Energy per atom: Epot =51.827eV Ekin = 7.812eV (T=649.879K) Etot = 59.639eV Energy per atom: Epot =52.381eV Ekin = 7.263eV (T=604.215K) Etot = 59.644eV Energy per atom: Epot =50.760eV Ekin = 8.883eV (T=738.978K) Etot = 59.643eV Energy per atom: Epot =50.350eV Ekin = 9.292eV (T=772.980K) Etot = 59.642eV Energy per atom: Epot =51.915eV Ekin = 7.722eV (T=642.332K) Etot = 59.637eV Energy per atom: Epot =51.171eV Ekin = 8.468eV (T=704.398K) Etot = 59.639eV Energy per atom: Epot =51.222eV Ekin = 8.423eV (T=700.687K) Etot = 59.645eV Energy per atom: Epot =51.094eV Ekin = 8.547eV (T=710.957K) Etot = 59.641eV Energy per atom: Epot =51.600eV Ekin = 8.040eV (T=668.816K) Etot = 59.640eV Energy per atom: Epot =50.454eV Ekin = 9.179eV (T=763.565K) Etot = 59.633eV Energy per atom: Epot =50.226eV Ekin = 9.409eV (T=782.723K) Etot = 59.636eV Energy per atom: Epot =51.046eV Ekin = 8.598eV (T=715.205K) Etot = 59.643eV Energy per atom: Epot =51.957eV Ekin = 7.692eV (T=639.900K) Etot = 59.649eV Energy per atom: Epot =51.101eV Ekin = 8.539eV (T=710.370K) Etot = 59.641eV Energy per atom: Epot =50.065eV Ekin = 9.563eV (T=795.490K) Etot = 59.628eV Energy per atom: Epot =50.802eV Ekin = 8.834eV (T=734.876K) Etot = 59.636eV Energy per atom: Epot =50.845eV Ekin = 8.791eV (T=731.263K) Etot = 59.636eV Energy per atom: Epot =50.415eV Ekin = 9.220eV (T=766.964K) Etot = 59.634eV Energy per atom: Epot =51.322eV Ekin = 8.316eV (T=691.763K) Etot = 59.637eV Energy per atom: Epot =50.372eV Ekin = 9.262eV (T=770.461K) Etot = 59.634eV Energy per atom: Epot =51.018eV Ekin = 8.617eV (T=716.854K) Etot = 59.636eV Energy per atom: Epot =49.920eV Ekin = 9.714eV (T=808.093K) Etot = 59.634eV Energy per atom: Epot =51.129eV Ekin = 8.518eV (T=708.611K) Etot = 59.648eV Energy per atom: Epot =51.005eV Ekin = 8.631eV (T=718.015K) Etot = 59.637eV Energy per atom: Epot =50.052eV Ekin = 9.575eV (T=796.522K) Etot = 59.627eV Energy per atom: Epot =51.564eV Ekin = 8.079eV (T=672.026K) Etot = 59.642eV Energy per atom: Epot =51.182eV Ekin = 8.458eV (T=703.590K) Etot = 59.640eV Energy per atom: Epot =51.771eV Ekin = 7.873eV (T=654.940K) Etot = 59.645eV Energy per atom: Epot =51.120eV Ekin = 8.518eV (T=708.542K) Etot = 59.638eV Energy per atom: Epot =51.578eV Ekin = 8.062eV (T=670.675K) Etot = 59.640eV Energy per atom: Epot =50.835eV Ekin = 8.796eV (T=731.675K) Etot = 59.630eV Energy per atom: Epot =51.045eV Ekin = 8.587eV (T=714.327K) Etot = 59.632eV Energy per atom: Epot =51.773eV Ekin = 7.867eV (T=654.395K) Etot = 59.640eV Energy per atom: Epot =51.997eV Ekin = 7.650eV (T=636.390K) Etot = 59.647eV Energy per atom: Epot =51.423eV Ekin = 8.224eV (T=684.160K) Etot = 59.647eV Energy per atom: Epot =51.674eV Ekin = 7.967eV (T=662.769K) Etot = 59.641eV Energy per atom: Epot =50.921eV Ekin = 8.714eV (T=724.925K) Etot = 59.636eV Energy per atom: Epot =50.414eV Ekin = 9.227eV (T=767.524K) Etot = 59.641eV Energy per atom: Epot =51.323eV Ekin = 8.319eV (T=692.033K) Etot = 59.642eV Energy per atom: Epot =51.159eV Ekin = 8.477eV (T=705.180K) Etot = 59.636eV Energy per atom: Epot =50.197eV Ekin = 9.438eV (T=785.122K) Etot = 59.635eV Energy per atom: Epot =51.059eV Ekin = 8.584eV (T=714.069K) Etot = 59.643eV Energy per atom: Epot =50.583eV Ekin = 9.052eV (T=752.992K) Etot = 59.635eV Energy per atom: Epot =50.340eV Ekin = 9.293eV (T=773.088K) Etot = 59.633eV Energy per atom: Epot =50.865eV Ekin = 8.776eV (T=730.073K) Etot = 59.642eV Energy per atom: Epot =51.432eV Ekin = 8.212eV (T=683.160K) Etot = 59.645eV Energy per atom: Epot =51.464eV Ekin = 8.179eV (T=680.372K) Etot = 59.642eV Energy per atom: Epot =51.752eV Ekin = 7.888eV (T=656.154K) Etot = 59.639eV Energy per atom: Epot =50.834eV Ekin = 8.800eV (T=732.062K) Etot = 59.634eV Energy per atom: Epot =50.232eV Ekin = 9.408eV (T=782.608K) Etot = 59.640eV Energy per atom: Epot =50.639eV Ekin = 9.007eV (T=749.299K) Etot = 59.646eV Energy per atom: Epot =50.581eV Ekin = 9.059eV (T=753.559K) Etot = 59.640eV Energy per atom: Epot =51.730eV Ekin = 7.912eV (T=658.170K) Etot = 59.642eV Energy per atom: Epot =51.514eV Ekin = 8.125eV (T=675.874K) Etot = 59.639eV Energy per atom: Epot =51.076eV Ekin = 8.560eV (T=712.115K) Etot = 59.637eV Energy per atom: Epot =51.623eV Ekin = 8.014eV (T=666.693K) Etot = 59.638eV Energy per atom: Epot =51.172eV Ekin = 8.468eV (T=704.437K) Etot = 59.640eV Energy per atom: Epot =52.076eV Ekin = 7.571eV (T=629.806K) Etot = 59.647eV Energy per atom: Epot =50.398eV Ekin = 9.239eV (T=768.563K) Etot = 59.637eV Energy per atom: Epot =50.725eV Ekin = 8.912eV (T=741.324K) Etot = 59.636eV Energy per atom: Epot =50.496eV Ekin = 9.143eV (T=760.566K) Etot = 59.639eV Energy per atom: Epot =50.727eV Ekin = 8.913eV (T=741.455K) Etot = 59.640eV Energy per atom: Epot =50.601eV Ekin = 9.039eV (T=751.886K) Etot = 59.640eV Energy per atom: Epot =51.128eV Ekin = 8.513eV (T=708.203K) Etot = 59.641eV .. 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_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 `_