.. 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-deploy/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 = 153.577eV (T=297.031K) Etot = 151.172eV Energy per atom: Epot =116.960eV Ekin = 34.993eV (T=67.679K) Etot = 151.952eV Energy per atom: Epot =77.259eV Ekin = 74.549eV (T=144.185K) Etot = 151.808eV Energy per atom: Epot =69.300eV Ekin = 82.364eV (T=159.300K) Etot = 151.665eV Energy per atom: Epot =69.345eV Ekin = 82.273eV (T=159.123K) Etot = 151.618eV Energy per atom: Epot =79.705eV Ekin = 72.066eV (T=139.381K) Etot = 151.771eV Energy per atom: Epot =77.169eV Ekin = 74.594eV (T=144.272K) Etot = 151.763eV Energy per atom: Epot =73.148eV Ekin = 78.530eV (T=151.884K) Etot = 151.678eV Energy per atom: Epot =70.732eV Ekin = 80.940eV (T=156.545K) Etot = 151.672eV Energy per atom: Epot =78.679eV Ekin = 73.083eV (T=141.349K) Etot = 151.762eV Energy per atom: Epot =75.083eV Ekin = 76.634eV (T=148.217K) Etot = 151.716eV Energy per atom: Epot =72.997eV Ekin = 78.691eV (T=152.196K) Etot = 151.688eV Energy per atom: Epot =74.382eV Ekin = 77.334eV (T=149.570K) Etot = 151.716eV Energy per atom: Epot =77.320eV Ekin = 74.408eV (T=143.911K) Etot = 151.728eV Energy per atom: Epot =73.395eV Ekin = 78.304eV (T=151.447K) Etot = 151.699eV Energy per atom: Epot =73.407eV Ekin = 78.308eV (T=151.454K) Etot = 151.715eV Energy per atom: Epot =75.643eV Ekin = 76.076eV (T=147.138K) Etot = 151.719eV Energy per atom: Epot =76.421eV Ekin = 75.290eV (T=145.617K) Etot = 151.711eV Energy per atom: Epot =72.944eV Ekin = 78.764eV (T=152.336K) Etot = 151.708eV Energy per atom: Epot =73.881eV Ekin = 77.823eV (T=150.517K) Etot = 151.704eV Energy per atom: Epot =78.395eV Ekin = 73.337eV (T=141.841K) Etot = 151.733eV .. 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 =600.443eV Ekin = 81.184eV (T=157.016K) Etot = 681.627eV Energy per atom: Epot =674.585eV Ekin = 142.140eV (T=274.911K) Etot = 816.725eV Energy per atom: Epot =726.187eV Ekin = 203.564eV (T=393.710K) Etot = 929.751eV Energy per atom: Epot =781.699eV Ekin = 250.632eV (T=484.745K) Etot = 1032.332eV Energy per atom: Epot =827.593eV Ekin = 298.980eV (T=578.252K) Etot = 1126.573eV Energy per atom: Epot =881.917eV Ekin = 329.256eV (T=636.810K) Etot = 1211.174eV Energy per atom: Epot =920.246eV Ekin = 375.654eV (T=726.548K) Etot = 1295.900eV Energy per atom: Epot =957.537eV Ekin = 408.226eV (T=789.544K) Etot = 1365.763eV Energy per atom: Epot =991.069eV Ekin = 441.968eV (T=854.804K) Etot = 1433.037eV Energy per atom: Epot =1031.237eV Ekin = 463.352eV (T=896.163K) Etot = 1494.589eV Energy per atom: Epot =1069.290eV Ekin = 486.280eV (T=940.508K) Etot = 1555.570eV Energy per atom: Epot =1109.849eV Ekin = 505.719eV (T=978.105K) Etot = 1615.568eV Energy per atom: Epot =1135.797eV Ekin = 532.835eV (T=1030.549K) Etot = 1668.632eV Energy per atom: Epot =1163.097eV Ekin = 552.623eV (T=1068.820K) Etot = 1715.720eV Energy per atom: Epot =1195.855eV Ekin = 558.102eV (T=1079.419K) Etot = 1753.957eV Energy per atom: Epot =1230.809eV Ekin = 562.726eV (T=1088.362K) Etot = 1793.535eV Energy per atom: Epot =1261.246eV Ekin = 566.582eV (T=1095.818K) Etot = 1827.827eV Energy per atom: Epot =1275.054eV Ekin = 583.921eV (T=1129.353K) Etot = 1858.975eV Energy per atom: Epot =1302.007eV Ekin = 590.569eV (T=1142.213K) Etot = 1892.577eV Energy per atom: Epot =1324.895eV Ekin = 603.953eV (T=1168.098K) Etot = 1928.849eV Energy per atom: Epot =1342.538eV Ekin = 620.972eV (T=1201.013K) Etot = 1963.509eV Energy per atom: Epot =1365.334eV Ekin = 623.667eV (T=1206.225K) Etot = 1989.001eV Energy per atom: Epot =1385.589eV Ekin = 637.651eV (T=1233.273K) Etot = 2023.240eV Energy per atom: Epot =1409.244eV Ekin = 631.626eV (T=1221.620K) Etot = 2040.870eV Energy per atom: Epot =1413.701eV Ekin = 654.475eV (T=1265.811K) Etot = 2068.176eV Energy per atom: Epot =1429.130eV Ekin = 656.960eV (T=1270.619K) Etot = 2086.091eV Energy per atom: Epot =1451.472eV Ekin = 662.080eV (T=1280.521K) Etot = 2113.552eV Energy per atom: Epot =1471.116eV Ekin = 661.301eV (T=1279.013K) Etot = 2132.416eV Energy per atom: Epot =1473.333eV Ekin = 671.418eV (T=1298.581K) Etot = 2144.751eV Energy per atom: Epot =1492.121eV Ekin = 675.173eV (T=1305.843K) Etot = 2167.294eV Energy per atom: Epot =1501.580eV Ekin = 679.375eV (T=1313.970K) Etot = 2180.955eV Energy per atom: Epot =1511.798eV Ekin = 683.124eV (T=1321.221K) Etot = 2194.922eV Energy per atom: Epot =1517.447eV Ekin = 697.910eV (T=1349.819K) Etot = 2215.358eV Energy per atom: Epot =1537.633eV Ekin = 688.127eV (T=1330.898K) Etot = 2225.761eV Energy per atom: Epot =1567.664eV Ekin = 673.295eV (T=1302.211K) Etot = 2240.958eV Energy per atom: Epot =1564.059eV Ekin = 681.311eV (T=1317.716K) Etot = 2245.370eV Energy per atom: Epot =1563.585eV Ekin = 701.929eV (T=1357.592K) Etot = 2265.514eV Energy per atom: Epot =1569.560eV Ekin = 701.645eV (T=1357.042K) Etot = 2271.205eV Energy per atom: Epot =1591.763eV Ekin = 698.776eV (T=1351.493K) Etot = 2290.538eV Energy per atom: Epot =1606.161eV Ekin = 691.021eV (T=1336.494K) Etot = 2297.181eV Energy per atom: Epot =1613.210eV Ekin = 700.612eV (T=1355.044K) Etot = 2313.821eV Energy per atom: Epot =1610.408eV Ekin = 729.229eV (T=1410.393K) Etot = 2339.638eV Energy per atom: Epot =1640.026eV Ekin = 717.108eV (T=1386.950K) Etot = 2357.134eV Energy per atom: Epot =1648.009eV Ekin = 731.138eV (T=1414.085K) Etot = 2379.148eV Energy per atom: Epot =1677.047eV Ekin = 704.599eV (T=1362.755K) Etot = 2381.646eV Energy per atom: Epot =1694.928eV Ekin = 698.279eV (T=1350.533K) Etot = 2393.208eV Energy per atom: Epot =1680.979eV Ekin = 707.724eV (T=1368.799K) Etot = 2388.703eV Energy per atom: Epot =1678.354eV Ekin = 718.017eV (T=1388.708K) Etot = 2396.372eV Energy per atom: Epot =1688.035eV Ekin = 721.236eV (T=1394.932K) Etot = 2409.270eV Energy per atom: Epot =1701.115eV Ekin = 718.328eV (T=1389.308K) Etot = 2419.442eV Energy per atom: Epot =1696.773eV Ekin = 728.450eV (T=1408.885K) Etot = 2425.222eV Energy per atom: Epot =1723.432eV Ekin = 717.881eV (T=1388.444K) Etot = 2441.313eV Energy per atom: Epot =1737.056eV Ekin = 725.087eV (T=1402.382K) Etot = 2462.143eV Energy per atom: Epot =1745.977eV Ekin = 725.070eV (T=1402.348K) Etot = 2471.047eV Energy per atom: Epot =1753.681eV Ekin = 720.492eV (T=1393.494K) Etot = 2474.173eV Energy per atom: Epot =1758.009eV Ekin = 724.394eV (T=1401.042K) Etot = 2482.403eV Energy per atom: Epot =1772.394eV Ekin = 737.709eV (T=1426.793K) Etot = 2510.103eV Energy per atom: Epot =1776.415eV Ekin = 733.254eV (T=1418.178K) Etot = 2509.670eV Energy per atom: Epot =1771.392eV Ekin = 740.327eV (T=1431.857K) Etot = 2511.719eV Energy per atom: Epot =1774.900eV Ekin = 758.057eV (T=1466.147K) Etot = 2532.957eV Energy per atom: Epot =1797.688eV Ekin = 736.186eV (T=1423.848K) Etot = 2533.874eV Energy per atom: Epot =1788.773eV Ekin = 751.949eV (T=1454.334K) Etot = 2540.722eV Energy per atom: Epot =1797.765eV Ekin = 743.937eV (T=1438.840K) Etot = 2541.702eV Energy per atom: Epot =1813.385eV Ekin = 742.145eV (T=1435.373K) Etot = 2555.530eV Energy per atom: Epot =1809.726eV Ekin = 744.696eV (T=1440.306K) Etot = 2554.422eV Energy per atom: Epot =1824.071eV Ekin = 750.872eV (T=1452.252K) Etot = 2574.944eV Energy per atom: Epot =1832.834eV Ekin = 746.761eV (T=1444.301K) Etot = 2579.595eV Energy per atom: Epot =1837.361eV Ekin = 758.120eV (T=1466.270K) Etot = 2595.481eV Energy per atom: Epot =1855.676eV Ekin = 739.108eV (T=1429.499K) Etot = 2594.784eV Energy per atom: Epot =1841.474eV Ekin = 757.010eV (T=1464.123K) Etot = 2598.483eV Energy per atom: Epot =1866.596eV Ekin = 735.294eV (T=1422.123K) Etot = 2601.890eV Energy per atom: Epot =1865.804eV Ekin = 737.586eV (T=1426.555K) Etot = 2603.389eV Energy per atom: Epot =1872.800eV Ekin = 746.672eV (T=1444.128K) Etot = 2619.471eV Energy per atom: Epot =1883.687eV Ekin = 742.210eV (T=1435.498K) Etot = 2625.896eV Energy per atom: Epot =1884.055eV Ekin = 751.641eV (T=1453.740K) Etot = 2635.697eV Energy per atom: Epot =1890.279eV Ekin = 745.250eV (T=1441.379K) Etot = 2635.529eV Energy per atom: Epot =1876.219eV Ekin = 766.889eV (T=1483.230K) Etot = 2643.108eV Energy per atom: Epot =1889.325eV Ekin = 747.443eV (T=1445.621K) Etot = 2636.769eV Energy per atom: Epot =1886.061eV Ekin = 741.165eV (T=1433.478K) Etot = 2627.226eV Energy per atom: Epot =1911.300eV Ekin = 725.300eV (T=1402.794K) Etot = 2636.600eV Energy per atom: Epot =1895.681eV Ekin = 739.275eV (T=1429.821K) Etot = 2634.956eV Energy per atom: Epot =1889.919eV Ekin = 758.947eV (T=1467.869K) Etot = 2648.866eV Energy per atom: Epot =1894.491eV Ekin = 768.468eV (T=1486.285K) Etot = 2662.960eV Energy per atom: Epot =1918.301eV Ekin = 748.986eV (T=1448.605K) Etot = 2667.288eV Energy per atom: Epot =1919.124eV Ekin = 753.757eV (T=1457.832K) Etot = 2672.881eV Energy per atom: Epot =1913.583eV Ekin = 763.658eV (T=1476.980K) Etot = 2677.240eV Energy per atom: Epot =1922.816eV Ekin = 762.860eV (T=1475.437K) Etot = 2685.676eV Energy per atom: Epot =1938.353eV Ekin = 755.480eV (T=1461.163K) Etot = 2693.832eV Energy per atom: Epot =1930.365eV Ekin = 764.955eV (T=1479.490K) Etot = 2695.320eV Energy per atom: Epot =1932.573eV Ekin = 760.958eV (T=1471.760K) Etot = 2693.532eV Energy per atom: Epot =1943.127eV Ekin = 754.455eV (T=1459.181K) Etot = 2697.582eV Energy per atom: Epot =1941.639eV Ekin = 756.054eV (T=1462.275K) Etot = 2697.694eV Energy per atom: Epot =1932.974eV Ekin = 768.861eV (T=1487.045K) Etot = 2701.835eV Energy per atom: Epot =1932.398eV Ekin = 769.938eV (T=1489.128K) Etot = 2702.336eV Energy per atom: Epot =1942.072eV Ekin = 764.830eV (T=1479.248K) Etot = 2706.902eV Energy per atom: Epot =1945.325eV Ekin = 769.087eV (T=1487.482K) Etot = 2714.412eV Energy per atom: Epot =1945.107eV Ekin = 778.168eV (T=1505.044K) Etot = 2723.275eV Energy per atom: Epot =1944.823eV Ekin = 780.565eV (T=1509.681K) Etot = 2725.388eV Energy per atom: Epot =1951.176eV Ekin = 774.621eV (T=1498.184K) Etot = 2725.797eV Energy per atom: Epot =1949.069eV Ekin = 769.304eV (T=1487.901K) Etot = 2718.373eV Energy per atom: Epot =1965.698eV Ekin = 759.480eV (T=1468.900K) Etot = 2725.178eV Energy per atom: Epot =1965.136eV Ekin = 768.062eV (T=1485.498K) Etot = 2733.198eV Energy per atom: Epot =1965.286eV Ekin = 759.646eV (T=1469.221K) Etot = 2724.931eV Energy per atom: Epot =1955.364eV Ekin = 774.557eV (T=1498.061K) Etot = 2729.921eV Energy per atom: Epot =1964.466eV Ekin = 779.562eV (T=1507.741K) Etot = 2744.028eV Energy per atom: Epot =1967.502eV Ekin = 768.296eV (T=1485.952K) Etot = 2735.798eV Energy per atom: Epot =1959.951eV Ekin = 776.614eV (T=1502.040K) Etot = 2736.566eV Energy per atom: Epot =1968.649eV Ekin = 774.229eV (T=1497.426K) Etot = 2742.878eV Energy per atom: Epot =1980.284eV Ekin = 765.861eV (T=1481.241K) Etot = 2746.145eV Energy per atom: Epot =1984.635eV Ekin = 768.125eV (T=1485.621K) Etot = 2752.760eV Energy per atom: Epot =1972.530eV Ekin = 784.795eV (T=1517.863K) Etot = 2757.325eV Energy per atom: Epot =1987.560eV Ekin = 763.660eV (T=1476.985K) Etot = 2751.220eV Energy per atom: Epot =1990.477eV Ekin = 763.973eV (T=1477.591K) Etot = 2754.450eV Energy per atom: Epot =2000.261eV Ekin = 757.904eV (T=1465.853K) Etot = 2758.165eV Energy per atom: Epot =1993.325eV Ekin = 761.450eV (T=1472.710K) Etot = 2754.774eV Energy per atom: Epot =1986.916eV Ekin = 766.821eV (T=1483.099K) Etot = 2753.737eV Energy per atom: Epot =1989.314eV Ekin = 766.233eV (T=1481.961K) Etot = 2755.547eV Energy per atom: Epot =1974.901eV Ekin = 776.553eV (T=1501.921K) Etot = 2751.454eV Energy per atom: Epot =1991.803eV Ekin = 760.978eV (T=1471.797K) Etot = 2752.781eV Energy per atom: Epot =1982.756eV Ekin = 779.998eV (T=1508.585K) Etot = 2762.754eV Energy per atom: Epot =1982.147eV Ekin = 779.734eV (T=1508.073K) Etot = 2761.881eV Energy per atom: Epot =1990.398eV Ekin = 783.774eV (T=1515.888K) Etot = 2774.172eV Energy per atom: Epot =1997.878eV Ekin = 777.591eV (T=1503.930K) Etot = 2775.469eV Energy per atom: Epot =1993.548eV Ekin = 773.790eV (T=1496.578K) Etot = 2767.338eV Energy per atom: Epot =2002.940eV Ekin = 768.812eV (T=1486.949K) Etot = 2771.752eV Energy per atom: Epot =1993.185eV Ekin = 787.369eV (T=1522.840K) Etot = 2780.555eV Energy per atom: Epot =1981.661eV Ekin = 791.603eV (T=1531.028K) Etot = 2773.264eV Energy per atom: Epot =1998.758eV Ekin = 773.714eV (T=1496.430K) Etot = 2772.472eV Energy per atom: Epot =1986.469eV Ekin = 785.824eV (T=1519.852K) Etot = 2772.293eV Energy per atom: Epot =1992.909eV Ekin = 776.152eV (T=1501.146K) Etot = 2769.061eV Energy per atom: Epot =1988.364eV Ekin = 777.901eV (T=1504.528K) Etot = 2766.265eV Energy per atom: Epot =1986.739eV Ekin = 777.556eV (T=1503.862K) Etot = 2764.296eV Energy per atom: Epot =1985.915eV Ekin = 776.528eV (T=1501.873K) Etot = 2762.443eV Energy per atom: Epot =1991.522eV Ekin = 780.820eV (T=1510.174K) Etot = 2772.342eV Energy per atom: Epot =1995.409eV Ekin = 774.235eV (T=1497.438K) Etot = 2769.644eV Energy per atom: Epot =1995.168eV Ekin = 771.594eV (T=1492.331K) Etot = 2766.762eV Energy per atom: Epot =1992.984eV Ekin = 768.739eV (T=1486.808K) Etot = 2761.723eV Energy per atom: Epot =1993.505eV Ekin = 764.890eV (T=1479.364K) Etot = 2758.395eV Energy per atom: Epot =1988.356eV Ekin = 769.997eV (T=1489.241K) Etot = 2758.353eV Energy per atom: Epot =1995.448eV Ekin = 768.702eV (T=1486.737K) Etot = 2764.150eV Energy per atom: Epot =1990.520eV Ekin = 767.820eV (T=1485.031K) Etot = 2758.341eV Energy per atom: Epot =1993.078eV Ekin = 767.627eV (T=1484.658K) Etot = 2760.705eV Energy per atom: Epot =1990.550eV Ekin = 774.707eV (T=1498.352K) Etot = 2765.258eV Energy per atom: Epot =1985.579eV Ekin = 791.009eV (T=1529.881K) Etot = 2776.588eV Energy per atom: Epot =1997.390eV Ekin = 785.903eV (T=1520.006K) Etot = 2783.294eV Energy per atom: Epot =2006.430eV Ekin = 772.538eV (T=1494.155K) Etot = 2778.968eV Energy per atom: Epot =1996.887eV Ekin = 782.964eV (T=1514.320K) Etot = 2779.850eV Energy per atom: Epot =2003.880eV Ekin = 778.535eV (T=1505.754K) Etot = 2782.415eV Energy per atom: Epot =1997.374eV Ekin = 778.272eV (T=1505.245K) Etot = 2775.646eV Energy per atom: Epot =1996.360eV Ekin = 775.456eV (T=1499.799K) Etot = 2771.816eV Energy per atom: Epot =2001.950eV Ekin = 774.834eV (T=1498.597K) Etot = 2776.785eV Energy per atom: Epot =1990.449eV Ekin = 785.332eV (T=1518.900K) Etot = 2775.780eV Energy per atom: Epot =1994.443eV Ekin = 768.992eV (T=1487.297K) Etot = 2763.435eV Energy per atom: Epot =1996.825eV Ekin = 767.062eV (T=1483.564K) Etot = 2763.887eV Energy per atom: Epot =1999.947eV Ekin = 770.722eV (T=1490.643K) Etot = 2770.669eV Energy per atom: Epot =1985.724eV Ekin = 776.811eV (T=1502.419K) Etot = 2762.534eV Energy per atom: Epot =1989.875eV Ekin = 779.192eV (T=1507.025K) Etot = 2769.067eV Energy per atom: Epot =2005.129eV Ekin = 761.369eV (T=1472.555K) Etot = 2766.499eV Energy per atom: Epot =2006.287eV Ekin = 757.080eV (T=1464.259K) Etot = 2763.367eV Energy per atom: Epot =1995.955eV Ekin = 765.907eV (T=1481.330K) Etot = 2761.861eV Energy per atom: Epot =2013.214eV Ekin = 742.373eV (T=1435.815K) Etot = 2755.587eV Energy per atom: Epot =1992.639eV Ekin = 770.071eV (T=1489.384K) Etot = 2762.710eV Energy per atom: Epot =2002.424eV Ekin = 755.831eV (T=1461.843K) Etot = 2758.255eV Energy per atom: Epot =1970.761eV Ekin = 775.714eV (T=1500.299K) Etot = 2746.475eV Energy per atom: Epot =1989.503eV Ekin = 755.192eV (T=1460.608K) Etot = 2744.695eV Energy per atom: Epot =1976.482eV Ekin = 763.637eV (T=1476.941K) Etot = 2740.120eV Energy per atom: Epot =1974.097eV Ekin = 771.177eV (T=1491.523K) Etot = 2745.274eV Energy per atom: Epot =1986.965eV Ekin = 765.665eV (T=1480.862K) Etot = 2752.630eV Energy per atom: Epot =1973.303eV Ekin = 786.637eV (T=1521.425K) Etot = 2759.940eV Energy per atom: Epot =1982.306eV Ekin = 777.588eV (T=1503.923K) Etot = 2759.894eV Energy per atom: Epot =1985.653eV Ekin = 771.388eV (T=1491.931K) Etot = 2757.040eV Energy per atom: Epot =1990.470eV Ekin = 771.886eV (T=1492.895K) Etot = 2762.357eV Energy per atom: Epot =1983.169eV Ekin = 780.933eV (T=1510.392K) Etot = 2764.101eV Energy per atom: Epot =1986.811eV Ekin = 774.160eV (T=1497.292K) Etot = 2760.971eV Energy per atom: Epot =1997.109eV Ekin = 765.478eV (T=1480.500K) Etot = 2762.586eV Energy per atom: Epot =1985.290eV Ekin = 773.744eV (T=1496.488K) Etot = 2759.034eV Energy per atom: Epot =1979.926eV Ekin = 777.983eV (T=1504.687K) Etot = 2757.909eV Energy per atom: Epot =1977.349eV Ekin = 782.457eV (T=1513.340K) Etot = 2759.806eV Energy per atom: Epot =1978.567eV Ekin = 777.364eV (T=1503.491K) Etot = 2755.932eV Energy per atom: Epot =1983.431eV Ekin = 780.938eV (T=1510.401K) Etot = 2764.369eV Energy per atom: Epot =1967.751eV Ekin = 800.365eV (T=1547.976K) Etot = 2768.116eV Energy per atom: Epot =1984.529eV Ekin = 778.706eV (T=1506.084K) Etot = 2763.234eV Energy per atom: Epot =1992.297eV Ekin = 769.084eV (T=1487.475K) Etot = 2761.381eV Energy per atom: Epot =1991.097eV Ekin = 768.057eV (T=1485.490K) Etot = 2759.154eV Energy per atom: Epot =1994.478eV Ekin = 770.958eV (T=1491.100K) Etot = 2765.436eV Energy per atom: Epot =1990.094eV Ekin = 786.548eV (T=1521.253K) Etot = 2776.643eV Energy per atom: Epot =1984.049eV Ekin = 793.026eV (T=1533.782K) Etot = 2777.075eV Energy per atom: Epot =1990.614eV Ekin = 791.764eV (T=1531.340K) Etot = 2782.378eV Energy per atom: Epot =2000.591eV Ekin = 783.923eV (T=1516.175K) Etot = 2784.514eV Energy per atom: Epot =1996.100eV Ekin = 782.368eV (T=1513.168K) Etot = 2778.469eV Energy per atom: Epot =1997.272eV Ekin = 782.876eV (T=1514.149K) Etot = 2780.147eV Energy per atom: Epot =2022.015eV Ekin = 758.552eV (T=1467.106K) Etot = 2780.567eV Energy per atom: Epot =2005.649eV Ekin = 772.703eV (T=1494.476K) Etot = 2778.353eV Energy per atom: Epot =2008.729eV Ekin = 772.762eV (T=1494.590K) Etot = 2781.491eV Energy per atom: Epot =2004.299eV Ekin = 774.836eV (T=1498.601K) Etot = 2779.135eV Energy per atom: Epot =2014.363eV Ekin = 769.549eV (T=1488.374K) Etot = 2783.912eV Energy per atom: Epot =2015.016eV Ekin = 773.638eV (T=1496.282K) Etot = 2788.654eV Energy per atom: Epot =2021.971eV Ekin = 767.489eV (T=1484.390K) Etot = 2789.460eV Energy per atom: Epot =2010.430eV Ekin = 779.371eV (T=1507.370K) Etot = 2789.800eV Energy per atom: Epot =2011.493eV Ekin = 771.532eV (T=1492.209K) Etot = 2783.024eV .. 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] 20:07:50 43.457006 1.0818 BFGSLineSearch: 1[ 1] 20:07:50 42.347659 0.2273 BFGSLineSearch: 2[ 2] 20:07:50 42.108454 0.1349 BFGSLineSearch: 3[ 3] 20:07:50 41.964817 0.1138 BFGSLineSearch: 4[ 4] 20:07:50 41.924933 0.0683 BFGSLineSearch: 5[ 5] 20:07:50 41.915346 0.0225 BFGSLineSearch: 6[ 6] 20:07:50 41.914920 0.0059 BFGSLineSearch: 7[ 7] 20:07:50 41.914872 0.0023 BFGSLineSearch: 8[ 9] 20:07:50 41.914855 0.0023 BFGSLineSearch: 9[ 10] 20:07:50 41.914851 0.0010 /builds/ase/ase-deploy/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 = 13.800eV (T=1147.940K) Etot = 55.714eV Energy per atom: Epot =49.621eV Ekin = 6.132eV (T=510.120K) Etot = 55.754eV Energy per atom: Epot =50.330eV Ekin = 5.436eV (T=452.216K) Etot = 55.766eV Energy per atom: Epot =50.369eV Ekin = 5.399eV (T=449.120K) Etot = 55.768eV Energy per atom: Epot =50.063eV Ekin = 5.701eV (T=474.288K) Etot = 55.764eV Energy per atom: Epot =50.296eV Ekin = 5.469eV (T=454.933K) Etot = 55.765eV Energy per atom: Epot =49.303eV Ekin = 6.458eV (T=537.233K) Etot = 55.761eV Energy per atom: Epot =48.994eV Ekin = 6.768eV (T=562.980K) Etot = 55.762eV Energy per atom: Epot =49.025eV Ekin = 6.739eV (T=560.604K) Etot = 55.764eV Energy per atom: Epot =48.799eV Ekin = 6.960eV (T=578.996K) Etot = 55.760eV Energy per atom: Epot =49.574eV Ekin = 6.185eV (T=514.536K) Etot = 55.760eV Energy per atom: Epot =49.640eV Ekin = 6.121eV (T=509.192K) Etot = 55.761eV Energy per atom: Epot =49.719eV Ekin = 6.046eV (T=502.962K) Etot = 55.765eV Energy per atom: Epot =48.702eV Ekin = 7.060eV (T=587.288K) Etot = 55.761eV Energy per atom: Epot =48.181eV Ekin = 7.575eV (T=630.120K) Etot = 55.756eV Energy per atom: Epot =49.073eV Ekin = 6.689eV (T=556.429K) Etot = 55.762eV Energy per atom: Epot =50.092eV Ekin = 5.676eV (T=472.171K) Etot = 55.768eV Energy per atom: Epot =50.247eV Ekin = 5.520eV (T=459.223K) Etot = 55.767eV Energy per atom: Epot =49.291eV Ekin = 6.469eV (T=538.163K) Etot = 55.761eV Energy per atom: Epot =49.500eV Ekin = 6.262eV (T=520.954K) Etot = 55.762eV Energy per atom: Epot =49.353eV Ekin = 6.407eV (T=532.959K) Etot = 55.760eV Energy per atom: Epot =48.337eV Ekin = 7.420eV (T=617.203K) Etot = 55.756eV Energy per atom: Epot =49.927eV Ekin = 5.842eV (T=485.951K) Etot = 55.769eV Energy per atom: Epot =49.436eV Ekin = 6.327eV (T=526.341K) Etot = 55.764eV Energy per atom: Epot =49.621eV Ekin = 6.144eV (T=511.080K) Etot = 55.765eV Energy per atom: Epot =48.322eV Ekin = 7.434eV (T=618.369K) Etot = 55.756eV Energy per atom: Epot =49.429eV Ekin = 6.330eV (T=526.559K) Etot = 55.759eV Energy per atom: Epot =49.266eV Ekin = 6.497eV (T=540.435K) Etot = 55.762eV Energy per atom: Epot =50.143eV Ekin = 5.625eV (T=467.965K) Etot = 55.768eV Energy per atom: Epot =49.655eV Ekin = 6.111eV (T=508.394K) Etot = 55.766eV Energy per atom: Epot =50.258eV Ekin = 5.511eV (T=458.425K) Etot = 55.769eV Energy per atom: Epot =49.986eV Ekin = 5.780eV (T=480.854K) Etot = 55.766eV Energy per atom: Epot =49.617eV Ekin = 6.148eV (T=511.408K) Etot = 55.764eV Energy per atom: Epot =49.144eV Ekin = 6.616eV (T=550.370K) Etot = 55.760eV Energy per atom: Epot =49.784eV Ekin = 5.978eV (T=497.323K) Etot = 55.763eV Energy per atom: Epot =49.193eV Ekin = 6.567eV (T=546.299K) Etot = 55.761eV Energy per atom: Epot =49.690eV Ekin = 6.071eV (T=505.066K) Etot = 55.762eV Energy per atom: Epot =49.580eV Ekin = 6.181eV (T=514.186K) Etot = 55.761eV Energy per atom: Epot =49.215eV Ekin = 6.544eV (T=544.338K) Etot = 55.759eV Energy per atom: Epot =49.576eV Ekin = 6.185eV (T=514.472K) Etot = 55.760eV Energy per atom: Epot =49.530eV Ekin = 6.232eV (T=518.425K) Etot = 55.762eV Energy per atom: Epot =48.935eV Ekin = 6.825eV (T=567.761K) Etot = 55.760eV Energy per atom: Epot =48.739eV Ekin = 7.021eV (T=584.039K) Etot = 55.760eV Energy per atom: Epot =49.327eV Ekin = 6.435eV (T=535.342K) Etot = 55.763eV Energy per atom: Epot =49.305eV Ekin = 6.456eV (T=537.045K) Etot = 55.761eV Energy per atom: Epot =49.029eV Ekin = 6.731eV (T=559.915K) Etot = 55.759eV Energy per atom: Epot =49.970eV Ekin = 5.795eV (T=482.047K) Etot = 55.764eV Energy per atom: Epot =49.004eV Ekin = 6.755eV (T=561.906K) Etot = 55.758eV Energy per atom: Epot =49.018eV Ekin = 6.743eV (T=560.944K) Etot = 55.762eV Energy per atom: Epot =49.371eV Ekin = 6.391eV (T=531.616K) Etot = 55.761eV Energy per atom: Epot =49.453eV Ekin = 6.306eV (T=524.581K) Etot = 55.759eV Energy per atom: Epot =48.713eV Ekin = 7.042eV (T=585.787K) Etot = 55.755eV Energy per atom: Epot =49.400eV Ekin = 6.362eV (T=529.229K) Etot = 55.762eV Energy per atom: Epot =49.371eV Ekin = 6.392eV (T=531.754K) Etot = 55.763eV Energy per atom: Epot =48.928eV Ekin = 6.827eV (T=567.955K) Etot = 55.756eV Energy per atom: Epot =49.108eV Ekin = 6.652eV (T=553.387K) Etot = 55.761eV Energy per atom: Epot =49.166eV Ekin = 6.594eV (T=548.545K) Etot = 55.760eV Energy per atom: Epot =49.401eV Ekin = 6.361eV (T=529.158K) Etot = 55.762eV Energy per atom: Epot =49.332eV Ekin = 6.431eV (T=534.960K) Etot = 55.762eV Energy per atom: Epot =49.155eV Ekin = 6.609eV (T=549.750K) Etot = 55.764eV Energy per atom: Epot =48.250eV Ekin = 7.508eV (T=624.573K) Etot = 55.758eV Energy per atom: Epot =49.486eV Ekin = 6.279eV (T=522.324K) Etot = 55.765eV Energy per atom: Epot =48.628eV Ekin = 7.131eV (T=593.219K) Etot = 55.759eV Energy per atom: Epot =49.603eV Ekin = 6.159eV (T=512.352K) Etot = 55.762eV Energy per atom: Epot =49.165eV Ekin = 6.600eV (T=549.043K) Etot = 55.765eV Energy per atom: Epot =49.144eV Ekin = 6.618eV (T=550.556K) Etot = 55.762eV Energy per atom: Epot =49.054eV Ekin = 6.705eV (T=557.801K) Etot = 55.759eV Energy per atom: Epot =49.531eV Ekin = 6.229eV (T=518.199K) Etot = 55.760eV Energy per atom: Epot =49.676eV Ekin = 6.087eV (T=506.360K) Etot = 55.763eV Energy per atom: Epot =48.937eV Ekin = 6.827eV (T=567.882K) Etot = 55.763eV Energy per atom: Epot =49.156eV Ekin = 6.608eV (T=549.666K) Etot = 55.764eV Energy per atom: Epot =49.261eV Ekin = 6.495eV (T=540.258K) Etot = 55.756eV Energy per atom: Epot =49.578eV Ekin = 6.182eV (T=514.240K) Etot = 55.760eV Energy per atom: Epot =49.790eV Ekin = 5.977eV (T=497.180K) Etot = 55.767eV Energy per atom: Epot =49.140eV Ekin = 6.622eV (T=550.820K) Etot = 55.762eV Energy per atom: Epot =48.677eV Ekin = 7.084eV (T=589.287K) Etot = 55.761eV Energy per atom: Epot =49.639eV Ekin = 6.128eV (T=509.791K) Etot = 55.768eV Energy per atom: Epot =48.963eV Ekin = 6.791eV (T=564.934K) Etot = 55.754eV Energy per atom: Epot =48.934eV Ekin = 6.822eV (T=567.503K) Etot = 55.756eV Energy per atom: Epot =49.036eV Ekin = 6.726eV (T=559.494K) Etot = 55.761eV Energy per atom: Epot =48.291eV Ekin = 7.465eV (T=621.008K) Etot = 55.756eV Energy per atom: Epot =49.326eV Ekin = 6.435eV (T=535.286K) Etot = 55.761eV Energy per atom: Epot =48.575eV Ekin = 7.179eV (T=597.219K) Etot = 55.755eV Energy per atom: Epot =49.092eV Ekin = 6.671eV (T=554.904K) Etot = 55.763eV Energy per atom: Epot =49.763eV Ekin = 6.006eV (T=499.608K) Etot = 55.769eV Energy per atom: Epot =49.397eV Ekin = 6.367eV (T=529.664K) Etot = 55.764eV Energy per atom: Epot =47.995eV Ekin = 7.761eV (T=645.623K) Etot = 55.756eV Energy per atom: Epot =49.113eV Ekin = 6.645eV (T=552.756K) Etot = 55.758eV Energy per atom: Epot =49.678eV Ekin = 6.088eV (T=506.418K) Etot = 55.766eV Energy per atom: Epot =48.681eV Ekin = 7.080eV (T=588.993K) Etot = 55.761eV Energy per atom: Epot =49.228eV Ekin = 6.539eV (T=543.934K) Etot = 55.767eV Energy per atom: Epot =48.832eV Ekin = 6.928eV (T=576.324K) Etot = 55.760eV Energy per atom: Epot =49.700eV Ekin = 6.067eV (T=504.687K) Etot = 55.767eV Energy per atom: Epot =49.009eV Ekin = 6.753eV (T=561.762K) Etot = 55.762eV Energy per atom: Epot =48.833eV Ekin = 6.920eV (T=575.630K) Etot = 55.753eV Energy per atom: Epot =49.048eV Ekin = 6.705eV (T=557.780K) Etot = 55.753eV Energy per atom: Epot =49.105eV Ekin = 6.652eV (T=553.349K) Etot = 55.757eV Energy per atom: Epot =49.221eV Ekin = 6.539eV (T=543.989K) Etot = 55.760eV Energy per atom: Epot =48.774eV Ekin = 6.984eV (T=581.003K) Etot = 55.758eV Energy per atom: Epot =49.255eV Ekin = 6.506eV (T=541.193K) Etot = 55.761eV Energy per atom: Epot =48.659eV Ekin = 7.100eV (T=590.598K) Etot = 55.759eV Energy per atom: Epot =48.963eV Ekin = 6.797eV (T=565.406K) Etot = 55.760eV Energy per atom: Epot =49.269eV Ekin = 6.491eV (T=539.981K) Etot = 55.760eV Energy per atom: Epot =49.791eV Ekin = 5.975eV (T=497.016K) Etot = 55.766eV Energy per atom: Epot =48.746eV Ekin = 7.014eV (T=583.507K) Etot = 55.760eV Energy per atom: Epot =49.062eV Ekin = 6.700eV (T=557.338K) Etot = 55.762eV Energy per atom: Epot =48.994eV Ekin = 6.765eV (T=562.792K) Etot = 55.760eV Energy per atom: Epot =48.908eV Ekin = 6.853eV (T=570.108K) Etot = 55.762eV Energy per atom: Epot =49.309eV Ekin = 6.450eV (T=536.572K) Etot = 55.759eV Energy per atom: Epot =48.623eV Ekin = 7.135eV (T=593.565K) Etot = 55.759eV Energy per atom: Epot =48.841eV Ekin = 6.923eV (T=575.875K) Etot = 55.764eV Energy per atom: Epot =48.806eV Ekin = 6.956eV (T=578.659K) Etot = 55.762eV Energy per atom: Epot =49.692eV Ekin = 6.071eV (T=505.039K) Etot = 55.763eV Energy per atom: Epot =49.554eV Ekin = 6.205eV (T=516.186K) Etot = 55.759eV Energy per atom: Epot =49.572eV Ekin = 6.191eV (T=515.000K) Etot = 55.763eV Energy per atom: Epot =49.099eV Ekin = 6.661eV (T=554.065K) Etot = 55.759eV Energy per atom: Epot =49.567eV Ekin = 6.192eV (T=515.072K) Etot = 55.759eV Energy per atom: Epot =49.563eV Ekin = 6.195eV (T=515.364K) Etot = 55.758eV Energy per atom: Epot =49.083eV Ekin = 6.677eV (T=555.445K) Etot = 55.760eV Energy per atom: Epot =48.737eV Ekin = 7.021eV (T=584.044K) Etot = 55.758eV Energy per atom: Epot =48.857eV Ekin = 6.906eV (T=574.446K) Etot = 55.762eV Energy per atom: Epot =48.566eV Ekin = 7.192eV (T=598.313K) Etot = 55.758eV Energy per atom: Epot =48.752eV Ekin = 7.002eV (T=582.504K) Etot = 55.754eV Energy per atom: Epot =49.325eV Ekin = 6.437eV (T=535.445K) Etot = 55.762eV Energy per atom: Epot =48.982eV Ekin = 6.781eV (T=564.090K) Etot = 55.763eV Energy per atom: Epot =49.965eV Ekin = 5.803eV (T=482.767K) Etot = 55.768eV Energy per atom: Epot =49.678eV Ekin = 6.083eV (T=505.985K) Etot = 55.760eV Energy per atom: Epot =49.217eV Ekin = 6.543eV (T=544.309K) Etot = 55.760eV Energy per atom: Epot =48.925eV Ekin = 6.834eV (T=568.483K) Etot = 55.758eV Energy per atom: Epot =49.377eV Ekin = 6.385eV (T=531.124K) Etot = 55.761eV Energy per atom: Epot =49.590eV Ekin = 6.172eV (T=513.468K) Etot = 55.762eV Energy per atom: Epot =49.454eV Ekin = 6.308eV (T=524.703K) Etot = 55.762eV Energy per atom: Epot =49.231eV Ekin = 6.533eV (T=543.430K) Etot = 55.763eV Energy per atom: Epot =49.376eV Ekin = 6.389eV (T=531.505K) Etot = 55.766eV Energy per atom: Epot =49.601eV Ekin = 6.162eV (T=512.565K) Etot = 55.763eV Energy per atom: Epot =49.305eV Ekin = 6.456eV (T=537.067K) Etot = 55.762eV Energy per atom: Epot =49.012eV Ekin = 6.750eV (T=561.478K) Etot = 55.761eV Energy per atom: Epot =48.623eV Ekin = 7.139eV (T=593.904K) Etot = 55.763eV Energy per atom: Epot =48.951eV Ekin = 6.814eV (T=566.815K) Etot = 55.765eV Energy per atom: Epot =49.616eV Ekin = 6.149eV (T=511.506K) Etot = 55.765eV Energy per atom: Epot =49.277eV Ekin = 6.480eV (T=539.007K) Etot = 55.756eV Energy per atom: Epot =49.118eV Ekin = 6.644eV (T=552.677K) Etot = 55.762eV Energy per atom: Epot =48.874eV Ekin = 6.886eV (T=572.859K) Etot = 55.760eV Energy per atom: Epot =49.195eV Ekin = 6.567eV (T=546.266K) Etot = 55.762eV Energy per atom: Epot =48.723eV Ekin = 7.042eV (T=585.838K) Etot = 55.766eV Energy per atom: Epot =49.041eV Ekin = 6.719eV (T=558.948K) Etot = 55.760eV Energy per atom: Epot =48.987eV Ekin = 6.771eV (T=563.264K) Etot = 55.758eV Energy per atom: Epot =48.817eV Ekin = 6.941eV (T=577.378K) Etot = 55.758eV Energy per atom: Epot =49.215eV Ekin = 6.547eV (T=544.632K) Etot = 55.762eV Energy per atom: Epot =48.861eV Ekin = 6.899eV (T=573.916K) Etot = 55.760eV Energy per atom: Epot =49.525eV Ekin = 6.239eV (T=518.988K) Etot = 55.763eV Energy per atom: Epot =47.858eV Ekin = 7.897eV (T=656.896K) Etot = 55.755eV Energy per atom: Epot =48.111eV Ekin = 7.643eV (T=635.771K) Etot = 55.754eV Energy per atom: Epot =49.234eV Ekin = 6.525eV (T=542.822K) Etot = 55.759eV Energy per atom: Epot =49.099eV Ekin = 6.666eV (T=554.562K) Etot = 55.765eV Energy per atom: Epot =48.851eV Ekin = 6.912eV (T=574.950K) Etot = 55.763eV Energy per atom: Epot =49.887eV Ekin = 5.878eV (T=488.959K) Etot = 55.765eV Energy per atom: Epot =48.826eV Ekin = 6.937eV (T=577.096K) Etot = 55.763eV Energy per atom: Epot =48.178eV Ekin = 7.585eV (T=630.929K) Etot = 55.763eV Energy per atom: Epot =48.985eV Ekin = 6.779eV (T=563.882K) Etot = 55.764eV Energy per atom: Epot =48.710eV Ekin = 7.045eV (T=586.033K) Etot = 55.755eV Energy per atom: Epot =49.226eV Ekin = 6.530eV (T=543.226K) Etot = 55.757eV Energy per atom: Epot =49.347eV Ekin = 6.416eV (T=533.703K) Etot = 55.763eV Energy per atom: Epot =48.290eV Ekin = 7.466eV (T=621.090K) Etot = 55.756eV Energy per atom: Epot =49.189eV Ekin = 6.572eV (T=546.685K) Etot = 55.761eV Energy per atom: Epot =48.830eV Ekin = 6.932eV (T=576.651K) Etot = 55.762eV Energy per atom: Epot =48.444eV Ekin = 7.318eV (T=608.766K) Etot = 55.762eV Energy per atom: Epot =48.617eV Ekin = 7.142eV (T=594.136K) Etot = 55.759eV Energy per atom: Epot =49.318eV Ekin = 6.443eV (T=536.011K) Etot = 55.762eV Energy per atom: Epot =48.796eV Ekin = 6.964eV (T=579.285K) Etot = 55.760eV Energy per atom: Epot =49.080eV Ekin = 6.678eV (T=555.489K) Etot = 55.758eV Energy per atom: Epot =48.441eV Ekin = 7.315eV (T=608.545K) Etot = 55.756eV Energy per atom: Epot =48.558eV Ekin = 7.208eV (T=599.572K) Etot = 55.766eV Energy per atom: Epot =48.924eV Ekin = 6.842eV (T=569.166K) Etot = 55.766eV Energy per atom: Epot =49.345eV Ekin = 6.413eV (T=533.516K) Etot = 55.758eV Energy per atom: Epot =49.597eV Ekin = 6.164eV (T=512.803K) Etot = 55.761eV Energy per atom: Epot =47.615eV Ekin = 8.136eV (T=676.804K) Etot = 55.751eV Energy per atom: Epot =48.494eV Ekin = 7.265eV (T=604.359K) Etot = 55.759eV Energy per atom: Epot =49.288eV Ekin = 6.478eV (T=538.864K) Etot = 55.766eV Energy per atom: Epot =48.839eV Ekin = 6.922eV (T=575.780K) Etot = 55.761eV Energy per atom: Epot =48.389eV Ekin = 7.372eV (T=613.287K) Etot = 55.762eV Energy per atom: Epot =48.945eV Ekin = 6.819eV (T=567.220K) Etot = 55.764eV Energy per atom: Epot =48.720eV Ekin = 7.041eV (T=585.755K) Etot = 55.762eV Energy per atom: Epot =49.220eV Ekin = 6.545eV (T=544.431K) Etot = 55.764eV Energy per atom: Epot =48.474eV Ekin = 7.282eV (T=605.728K) Etot = 55.756eV Energy per atom: Epot =48.563eV Ekin = 7.192eV (T=598.268K) Etot = 55.755eV Energy per atom: Epot =49.137eV Ekin = 6.624eV (T=551.017K) Etot = 55.761eV Energy per atom: Epot =49.381eV Ekin = 6.378eV (T=530.598K) Etot = 55.760eV Energy per atom: Epot =49.264eV Ekin = 6.493eV (T=540.094K) Etot = 55.756eV Energy per atom: Epot =49.012eV Ekin = 6.744eV (T=561.048K) Etot = 55.756eV Energy per atom: Epot =48.776eV Ekin = 6.980eV (T=580.680K) Etot = 55.756eV Energy per atom: Epot =49.182eV Ekin = 6.575eV (T=546.965K) Etot = 55.757eV Energy per atom: Epot =48.967eV Ekin = 6.788eV (T=564.699K) Etot = 55.756eV Energy per atom: Epot =49.179eV Ekin = 6.584eV (T=547.736K) Etot = 55.764eV Energy per atom: Epot =49.567eV Ekin = 6.197eV (T=515.498K) Etot = 55.764eV Energy per atom: Epot =48.963eV Ekin = 6.794eV (T=565.197K) Etot = 55.757eV Energy per atom: Epot =49.374eV Ekin = 6.389eV (T=531.469K) Etot = 55.763eV Energy per atom: Epot =49.314eV Ekin = 6.449eV (T=536.481K) Etot = 55.764eV Energy per atom: Epot =48.945eV Ekin = 6.818eV (T=567.184K) Etot = 55.763eV Energy per atom: Epot =49.301eV Ekin = 6.463eV (T=537.653K) Etot = 55.764eV Energy per atom: Epot =49.028eV Ekin = 6.739eV (T=560.591K) Etot = 55.767eV .. 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 `_