.. 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 = 158.622eV (T=306.789K) Etot = 156.218eV Energy per atom: Epot =119.719eV Ekin = 37.301eV (T=72.143K) Etot = 157.020eV Energy per atom: Epot =81.302eV Ekin = 75.588eV (T=146.195K) Etot = 156.891eV Energy per atom: Epot =71.793eV Ekin = 84.933eV (T=164.268K) Etot = 156.726eV Energy per atom: Epot =70.830eV Ekin = 85.844eV (T=166.030K) Etot = 156.674eV Energy per atom: Epot =82.532eV Ekin = 74.315eV (T=143.731K) Etot = 156.847eV Energy per atom: Epot =78.955eV Ekin = 77.874eV (T=150.614K) Etot = 156.829eV Energy per atom: Epot =76.247eV Ekin = 80.500eV (T=155.693K) Etot = 156.746eV Energy per atom: Epot =73.322eV Ekin = 83.417eV (T=161.336K) Etot = 156.739eV Energy per atom: Epot =81.273eV Ekin = 75.550eV (T=146.121K) Etot = 156.824eV Energy per atom: Epot =77.872eV Ekin = 78.918eV (T=152.633K) Etot = 156.789eV Energy per atom: Epot =75.291eV Ekin = 81.472eV (T=157.575K) Etot = 156.763eV Energy per atom: Epot =77.427eV Ekin = 79.352eV (T=153.474K) Etot = 156.779eV Energy per atom: Epot =78.864eV Ekin = 77.923eV (T=150.709K) Etot = 156.787eV Energy per atom: Epot =76.726eV Ekin = 80.051eV (T=154.825K) Etot = 156.777eV Energy per atom: Epot =77.236eV Ekin = 79.554eV (T=153.865K) Etot = 156.790eV Energy per atom: Epot =75.780eV Ekin = 80.987eV (T=156.636K) Etot = 156.767eV Energy per atom: Epot =79.190eV Ekin = 77.590eV (T=150.066K) Etot = 156.780eV Energy per atom: Epot =76.641eV Ekin = 80.142eV (T=155.002K) Etot = 156.783eV Energy per atom: Epot =76.284eV Ekin = 80.485eV (T=155.666K) Etot = 156.769eV Energy per atom: Epot =80.586eV Ekin = 76.211eV (T=147.399K) Etot = 156.797eV .. 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 =599.025eV Ekin = 80.269eV (T=155.248K) Etot = 679.294eV Energy per atom: Epot =667.632eV Ekin = 140.747eV (T=272.218K) Etot = 808.380eV Energy per atom: Epot =728.836eV Ekin = 195.984eV (T=379.050K) Etot = 924.820eV Energy per atom: Epot =780.872eV Ekin = 250.061eV (T=483.639K) Etot = 1030.932eV Energy per atom: Epot =829.368eV Ekin = 302.291eV (T=584.657K) Etot = 1131.659eV Energy per atom: Epot =878.144eV Ekin = 345.376eV (T=667.988K) Etot = 1223.520eV Energy per atom: Epot =916.561eV Ekin = 388.031eV (T=750.486K) Etot = 1304.592eV Energy per atom: Epot =972.857eV Ekin = 409.833eV (T=792.654K) Etot = 1382.690eV Energy per atom: Epot =1004.028eV Ekin = 440.334eV (T=851.645K) Etot = 1444.362eV Energy per atom: Epot =1037.810eV Ekin = 471.891eV (T=912.678K) Etot = 1509.700eV Energy per atom: Epot =1078.641eV Ekin = 485.479eV (T=938.958K) Etot = 1564.119eV Energy per atom: Epot =1107.238eV Ekin = 506.856eV (T=980.304K) Etot = 1614.094eV Energy per atom: Epot =1144.989eV Ekin = 523.962eV (T=1013.389K) Etot = 1668.952eV Energy per atom: Epot =1181.508eV Ekin = 547.390eV (T=1058.700K) Etot = 1728.898eV Energy per atom: Epot =1205.523eV Ekin = 567.171eV (T=1096.958K) Etot = 1772.694eV Energy per atom: Epot =1242.692eV Ekin = 563.439eV (T=1089.739K) Etot = 1806.130eV Energy per atom: Epot =1251.933eV Ekin = 590.634eV (T=1142.338K) Etot = 1842.567eV Energy per atom: Epot =1285.276eV Ekin = 602.851eV (T=1165.966K) Etot = 1888.127eV Energy per atom: Epot =1317.386eV Ekin = 601.356eV (T=1163.074K) Etot = 1918.741eV Energy per atom: Epot =1346.851eV Ekin = 611.551eV (T=1182.792K) Etot = 1958.402eV Energy per atom: Epot =1363.919eV Ekin = 627.271eV (T=1213.196K) Etot = 1991.190eV Energy per atom: Epot =1395.367eV Ekin = 627.013eV (T=1212.698K) Etot = 2022.380eV Energy per atom: Epot =1400.869eV Ekin = 642.389eV (T=1242.436K) Etot = 2043.258eV Energy per atom: Epot =1423.505eV Ekin = 644.506eV (T=1246.530K) Etot = 2068.011eV Energy per atom: Epot =1440.179eV Ekin = 650.648eV (T=1258.409K) Etot = 2090.826eV Energy per atom: Epot =1451.088eV Ekin = 668.110eV (T=1292.184K) Etot = 2119.199eV Energy per atom: Epot =1460.916eV Ekin = 670.276eV (T=1296.371K) Etot = 2131.191eV Energy per atom: Epot =1474.420eV Ekin = 674.329eV (T=1304.211K) Etot = 2148.748eV Energy per atom: Epot =1495.885eV Ekin = 675.958eV (T=1307.362K) Etot = 2171.843eV Energy per atom: Epot =1501.684eV Ekin = 687.957eV (T=1330.570K) Etot = 2189.642eV Energy per atom: Epot =1511.738eV Ekin = 693.865eV (T=1341.995K) Etot = 2205.603eV Energy per atom: Epot =1527.909eV Ekin = 696.826eV (T=1347.721K) Etot = 2224.734eV Energy per atom: Epot =1537.392eV Ekin = 701.525eV (T=1356.810K) Etot = 2238.917eV Energy per atom: Epot =1549.085eV Ekin = 701.302eV (T=1356.379K) Etot = 2250.387eV Energy per atom: Epot =1545.937eV Ekin = 708.283eV (T=1369.881K) Etot = 2254.220eV Energy per atom: Epot =1555.188eV Ekin = 712.464eV (T=1377.967K) Etot = 2267.652eV Energy per atom: Epot =1578.954eV Ekin = 702.915eV (T=1359.499K) Etot = 2281.869eV Energy per atom: Epot =1578.914eV Ekin = 710.948eV (T=1375.034K) Etot = 2289.861eV Energy per atom: Epot =1584.889eV Ekin = 714.611eV (T=1382.120K) Etot = 2299.500eV Energy per atom: Epot =1608.355eV Ekin = 700.889eV (T=1355.580K) Etot = 2309.244eV Energy per atom: Epot =1621.089eV Ekin = 705.608eV (T=1364.708K) Etot = 2326.697eV Energy per atom: Epot =1609.286eV Ekin = 730.353eV (T=1412.567K) Etot = 2339.639eV Energy per atom: Epot =1632.905eV Ekin = 711.377eV (T=1375.866K) Etot = 2344.283eV Energy per atom: Epot =1635.853eV Ekin = 722.824eV (T=1398.004K) Etot = 2358.676eV Energy per atom: Epot =1649.833eV Ekin = 729.122eV (T=1410.185K) Etot = 2378.955eV Energy per atom: Epot =1657.476eV Ekin = 737.249eV (T=1425.903K) Etot = 2394.725eV Energy per atom: Epot =1663.287eV Ekin = 734.565eV (T=1420.713K) Etot = 2397.852eV Energy per atom: Epot =1667.633eV Ekin = 738.012eV (T=1427.379K) Etot = 2405.645eV Energy per atom: Epot =1696.666eV Ekin = 720.288eV (T=1393.099K) Etot = 2416.954eV Energy per atom: Epot =1697.814eV Ekin = 738.912eV (T=1429.121K) Etot = 2436.726eV Energy per atom: Epot =1720.485eV Ekin = 726.515eV (T=1405.142K) Etot = 2447.000eV Energy per atom: Epot =1721.255eV Ekin = 741.883eV (T=1434.866K) Etot = 2463.138eV Energy per atom: Epot =1722.362eV Ekin = 741.308eV (T=1433.755K) Etot = 2463.670eV Energy per atom: Epot =1732.177eV Ekin = 737.459eV (T=1426.311K) Etot = 2469.636eV Energy per atom: Epot =1741.508eV Ekin = 741.845eV (T=1434.793K) Etot = 2483.354eV Energy per atom: Epot =1757.659eV Ekin = 732.081eV (T=1415.909K) Etot = 2489.740eV Energy per atom: Epot =1762.146eV Ekin = 728.835eV (T=1409.630K) Etot = 2490.981eV Energy per atom: Epot =1770.383eV Ekin = 719.426eV (T=1391.432K) Etot = 2489.809eV Energy per atom: Epot =1762.240eV Ekin = 737.809eV (T=1426.986K) Etot = 2500.049eV Energy per atom: Epot =1768.521eV Ekin = 730.459eV (T=1412.771K) Etot = 2498.980eV Energy per atom: Epot =1783.473eV Ekin = 721.606eV (T=1395.648K) Etot = 2505.078eV Energy per atom: Epot =1777.124eV Ekin = 741.081eV (T=1433.316K) Etot = 2518.205eV Energy per atom: Epot =1773.458eV Ekin = 746.303eV (T=1443.414K) Etot = 2519.761eV Energy per atom: Epot =1788.035eV Ekin = 735.671eV (T=1422.852K) Etot = 2523.706eV Energy per atom: Epot =1780.777eV Ekin = 744.202eV (T=1439.352K) Etot = 2524.979eV Energy per atom: Epot =1799.620eV Ekin = 739.943eV (T=1431.114K) Etot = 2539.563eV Energy per atom: Epot =1802.133eV Ekin = 739.164eV (T=1429.607K) Etot = 2541.296eV Energy per atom: Epot =1810.391eV Ekin = 749.035eV (T=1448.699K) Etot = 2559.426eV Energy per atom: Epot =1818.011eV Ekin = 746.306eV (T=1443.422K) Etot = 2564.318eV Energy per atom: Epot =1818.214eV Ekin = 748.738eV (T=1448.125K) Etot = 2566.953eV Energy per atom: Epot =1827.534eV Ekin = 739.210eV (T=1429.697K) Etot = 2566.744eV Energy per atom: Epot =1828.266eV Ekin = 744.207eV (T=1439.360K) Etot = 2572.473eV Energy per atom: Epot =1825.493eV Ekin = 747.191eV (T=1445.132K) Etot = 2572.683eV Energy per atom: Epot =1848.248eV Ekin = 728.190eV (T=1408.382K) Etot = 2576.438eV Energy per atom: Epot =1845.164eV Ekin = 736.864eV (T=1425.159K) Etot = 2582.028eV Energy per atom: Epot =1849.447eV Ekin = 740.280eV (T=1431.766K) Etot = 2589.727eV Energy per atom: Epot =1854.828eV Ekin = 739.171eV (T=1429.621K) Etot = 2593.999eV Energy per atom: Epot =1862.613eV Ekin = 744.530eV (T=1439.985K) Etot = 2607.142eV Energy per atom: Epot =1868.979eV Ekin = 738.269eV (T=1427.876K) Etot = 2607.248eV Energy per atom: Epot =1869.432eV Ekin = 740.004eV (T=1431.231K) Etot = 2609.436eV Energy per atom: Epot =1887.617eV Ekin = 742.399eV (T=1435.864K) Etot = 2630.016eV Energy per atom: Epot =1891.877eV Ekin = 741.153eV (T=1433.455K) Etot = 2633.030eV Energy per atom: Epot =1903.772eV Ekin = 738.551eV (T=1428.422K) Etot = 2642.323eV Energy per atom: Epot =1903.576eV Ekin = 755.759eV (T=1461.704K) Etot = 2659.335eV Energy per atom: Epot =1897.218eV Ekin = 764.669eV (T=1478.936K) Etot = 2661.887eV Energy per atom: Epot =1909.454eV Ekin = 761.305eV (T=1472.431K) Etot = 2670.759eV Energy per atom: Epot =1917.628eV Ekin = 764.375eV (T=1478.367K) Etot = 2682.003eV Energy per atom: Epot =1915.560eV Ekin = 759.840eV (T=1469.596K) Etot = 2675.399eV Energy per atom: Epot =1923.540eV Ekin = 755.621eV (T=1461.436K) Etot = 2679.161eV Energy per atom: Epot =1925.077eV Ekin = 755.730eV (T=1461.649K) Etot = 2680.807eV Energy per atom: Epot =1930.400eV Ekin = 752.675eV (T=1455.739K) Etot = 2683.076eV Energy per atom: Epot =1939.073eV Ekin = 744.448eV (T=1439.826K) Etot = 2683.520eV Energy per atom: Epot =1938.729eV Ekin = 756.875eV (T=1463.862K) Etot = 2695.604eV Energy per atom: Epot =1954.426eV Ekin = 749.423eV (T=1449.450K) Etot = 2703.849eV Energy per atom: Epot =1962.095eV Ekin = 743.707eV (T=1438.395K) Etot = 2705.802eV Energy per atom: Epot =1949.861eV Ekin = 755.869eV (T=1461.917K) Etot = 2705.730eV Energy per atom: Epot =1949.056eV Ekin = 761.144eV (T=1472.119K) Etot = 2710.200eV Energy per atom: Epot =1966.695eV Ekin = 751.995eV (T=1454.423K) Etot = 2718.690eV Energy per atom: Epot =1966.930eV Ekin = 749.993eV (T=1450.553K) Etot = 2716.923eV Energy per atom: Epot =1961.618eV Ekin = 763.295eV (T=1476.279K) Etot = 2724.913eV Energy per atom: Epot =1957.361eV Ekin = 767.144eV (T=1483.723K) Etot = 2724.505eV Energy per atom: Epot =1965.999eV Ekin = 753.679eV (T=1457.680K) Etot = 2719.678eV Energy per atom: Epot =1957.632eV Ekin = 773.014eV (T=1495.076K) Etot = 2730.646eV Energy per atom: Epot =1944.443eV Ekin = 776.289eV (T=1501.410K) Etot = 2720.732eV Energy per atom: Epot =1951.232eV Ekin = 769.641eV (T=1488.553K) Etot = 2720.873eV Energy per atom: Epot =1949.269eV Ekin = 777.160eV (T=1503.095K) Etot = 2726.429eV Energy per atom: Epot =1970.346eV Ekin = 757.404eV (T=1464.885K) Etot = 2727.750eV Energy per atom: Epot =1958.625eV Ekin = 768.141eV (T=1485.651K) Etot = 2726.766eV Energy per atom: Epot =1963.337eV Ekin = 765.545eV (T=1480.631K) Etot = 2728.882eV Energy per atom: Epot =1970.114eV Ekin = 774.025eV (T=1497.031K) Etot = 2744.138eV Energy per atom: Epot =1971.914eV Ekin = 781.029eV (T=1510.577K) Etot = 2752.943eV Energy per atom: Epot =1987.428eV Ekin = 755.333eV (T=1460.880K) Etot = 2742.761eV Energy per atom: Epot =1979.310eV Ekin = 769.154eV (T=1487.611K) Etot = 2748.465eV Energy per atom: Epot =1976.503eV Ekin = 783.690eV (T=1515.724K) Etot = 2760.192eV Energy per atom: Epot =1992.619eV Ekin = 769.696eV (T=1488.659K) Etot = 2762.315eV Energy per atom: Epot =1982.195eV Ekin = 778.332eV (T=1505.361K) Etot = 2760.527eV Energy per atom: Epot =1983.402eV Ekin = 770.277eV (T=1489.782K) Etot = 2753.678eV Energy per atom: Epot =2001.297eV Ekin = 761.862eV (T=1473.507K) Etot = 2763.159eV Energy per atom: Epot =1995.110eV Ekin = 762.604eV (T=1474.942K) Etot = 2757.713eV Energy per atom: Epot =1989.588eV Ekin = 769.476eV (T=1488.233K) Etot = 2759.063eV Energy per atom: Epot =1986.605eV Ekin = 775.895eV (T=1500.649K) Etot = 2762.501eV Energy per atom: Epot =2009.833eV Ekin = 764.081eV (T=1477.798K) Etot = 2773.914eV Energy per atom: Epot =2005.691eV Ekin = 770.046eV (T=1489.337K) Etot = 2775.737eV Energy per atom: Epot =2012.001eV Ekin = 760.389eV (T=1470.659K) Etot = 2772.390eV Energy per atom: Epot =2006.824eV Ekin = 779.203eV (T=1507.046K) Etot = 2786.027eV Energy per atom: Epot =2008.012eV Ekin = 767.657eV (T=1484.716K) Etot = 2775.669eV Energy per atom: Epot =2022.746eV Ekin = 756.772eV (T=1463.662K) Etot = 2779.517eV Energy per atom: Epot =2013.500eV Ekin = 765.608eV (T=1480.752K) Etot = 2779.108eV Energy per atom: Epot =2007.944eV Ekin = 776.182eV (T=1501.203K) Etot = 2784.126eV Energy per atom: Epot =2004.803eV Ekin = 774.400eV (T=1497.756K) Etot = 2779.202eV Energy per atom: Epot =2004.450eV Ekin = 777.854eV (T=1504.437K) Etot = 2782.303eV Energy per atom: Epot =2026.183eV Ekin = 760.150eV (T=1470.196K) Etot = 2786.333eV Energy per atom: Epot =2004.164eV Ekin = 781.398eV (T=1511.291K) Etot = 2785.562eV Energy per atom: Epot =2018.560eV Ekin = 773.400eV (T=1495.823K) Etot = 2791.960eV Energy per atom: Epot =2008.698eV Ekin = 792.032eV (T=1531.859K) Etot = 2800.730eV Energy per atom: Epot =2022.136eV Ekin = 775.795eV (T=1500.456K) Etot = 2797.931eV Energy per atom: Epot =2011.284eV Ekin = 785.480eV (T=1519.188K) Etot = 2796.764eV Energy per atom: Epot =2009.994eV Ekin = 784.401eV (T=1517.099K) Etot = 2794.394eV Energy per atom: Epot =2021.977eV Ekin = 777.682eV (T=1504.105K) Etot = 2799.660eV Energy per atom: Epot =2005.574eV Ekin = 789.702eV (T=1527.353K) Etot = 2795.276eV Energy per atom: Epot =2003.155eV Ekin = 796.299eV (T=1540.111K) Etot = 2799.454eV Energy per atom: Epot =2017.340eV Ekin = 790.090eV (T=1528.102K) Etot = 2807.429eV Energy per atom: Epot =2008.345eV Ekin = 795.126eV (T=1537.844K) Etot = 2803.472eV Energy per atom: Epot =2004.986eV Ekin = 793.529eV (T=1534.755K) Etot = 2798.515eV Energy per atom: Epot =2018.189eV Ekin = 781.057eV (T=1510.632K) Etot = 2799.246eV Energy per atom: Epot =2012.489eV Ekin = 786.287eV (T=1520.748K) Etot = 2798.776eV Energy per atom: Epot =2013.945eV Ekin = 781.815eV (T=1512.099K) Etot = 2795.761eV Energy per atom: Epot =2016.186eV Ekin = 795.814eV (T=1539.173K) Etot = 2811.999eV Energy per atom: Epot =2030.736eV Ekin = 779.794eV (T=1508.189K) Etot = 2810.530eV Energy per atom: Epot =2026.443eV Ekin = 790.085eV (T=1528.093K) Etot = 2816.528eV Energy per atom: Epot =2020.859eV Ekin = 783.287eV (T=1514.945K) Etot = 2804.146eV Energy per atom: Epot =2025.570eV Ekin = 773.212eV (T=1495.460K) Etot = 2798.782eV Energy per atom: Epot =2008.255eV Ekin = 786.929eV (T=1521.989K) Etot = 2795.184eV Energy per atom: Epot =2011.520eV Ekin = 778.654eV (T=1505.984K) Etot = 2790.174eV Energy per atom: Epot =2017.475eV Ekin = 769.213eV (T=1487.726K) Etot = 2786.688eV Energy per atom: Epot =2014.604eV Ekin = 772.691eV (T=1494.452K) Etot = 2787.296eV Energy per atom: Epot =2019.461eV Ekin = 766.847eV (T=1483.149K) Etot = 2786.307eV Energy per atom: Epot =2006.866eV Ekin = 774.978eV (T=1498.875K) Etot = 2781.844eV Energy per atom: Epot =2009.667eV Ekin = 773.779eV (T=1496.556K) Etot = 2783.446eV Energy per atom: Epot =2004.868eV Ekin = 778.380eV (T=1505.454K) Etot = 2783.248eV Energy per atom: Epot =2004.123eV Ekin = 774.775eV (T=1498.482K) Etot = 2778.897eV Energy per atom: Epot =2008.081eV Ekin = 776.020eV (T=1500.891K) Etot = 2784.102eV Energy per atom: Epot =2006.112eV Ekin = 784.277eV (T=1516.860K) Etot = 2790.390eV Energy per atom: Epot =1999.058eV Ekin = 793.149eV (T=1534.020K) Etot = 2792.208eV Energy per atom: Epot =2001.882eV Ekin = 789.627eV (T=1527.207K) Etot = 2791.509eV Energy per atom: Epot =2011.816eV Ekin = 782.466eV (T=1513.357K) Etot = 2794.282eV Energy per atom: Epot =2012.585eV Ekin = 777.223eV (T=1503.217K) Etot = 2789.808eV Energy per atom: Epot =2005.495eV Ekin = 776.898eV (T=1502.589K) Etot = 2782.393eV Energy per atom: Epot =2000.301eV Ekin = 788.398eV (T=1524.831K) Etot = 2788.700eV Energy per atom: Epot =2006.485eV Ekin = 780.395eV (T=1509.352K) Etot = 2786.880eV Energy per atom: Epot =2004.324eV Ekin = 787.685eV (T=1523.451K) Etot = 2792.008eV Energy per atom: Epot =1997.281eV Ekin = 794.963eV (T=1537.528K) Etot = 2792.244eV Energy per atom: Epot =2000.368eV Ekin = 792.918eV (T=1533.573K) Etot = 2793.286eV Energy per atom: Epot =1998.084eV Ekin = 795.040eV (T=1537.677K) Etot = 2793.124eV Energy per atom: Epot =2012.496eV Ekin = 783.626eV (T=1515.602K) Etot = 2796.123eV Energy per atom: Epot =2006.668eV Ekin = 782.097eV (T=1512.643K) Etot = 2788.765eV Energy per atom: Epot =2011.246eV Ekin = 772.106eV (T=1493.319K) Etot = 2783.352eV Energy per atom: Epot =1999.394eV Ekin = 779.412eV (T=1507.451K) Etot = 2778.806eV Energy per atom: Epot =2008.991eV Ekin = 771.023eV (T=1491.225K) Etot = 2780.013eV Energy per atom: Epot =1988.879eV Ekin = 785.380eV (T=1518.993K) Etot = 2774.260eV Energy per atom: Epot =1985.673eV Ekin = 789.931eV (T=1527.795K) Etot = 2775.604eV Energy per atom: Epot =2003.843eV Ekin = 778.225eV (T=1505.155K) Etot = 2782.068eV Energy per atom: Epot =2007.956eV Ekin = 774.978eV (T=1498.874K) Etot = 2782.934eV Energy per atom: Epot =2001.761eV Ekin = 786.649eV (T=1521.448K) Etot = 2788.410eV Energy per atom: Epot =2009.021eV Ekin = 773.766eV (T=1496.531K) Etot = 2782.787eV Energy per atom: Epot =2008.004eV Ekin = 775.101eV (T=1499.113K) Etot = 2783.105eV Energy per atom: Epot =1996.755eV Ekin = 778.372eV (T=1505.439K) Etot = 2775.127eV Energy per atom: Epot =1999.826eV Ekin = 777.895eV (T=1504.516K) Etot = 2777.721eV Energy per atom: Epot =2008.644eV Ekin = 767.439eV (T=1484.294K) Etot = 2776.083eV Energy per atom: Epot =2002.375eV Ekin = 779.719eV (T=1508.044K) Etot = 2782.094eV Energy per atom: Epot =2003.088eV Ekin = 772.662eV (T=1494.396K) Etot = 2775.751eV Energy per atom: Epot =2000.746eV Ekin = 770.028eV (T=1489.301K) Etot = 2770.773eV Energy per atom: Epot =2006.245eV Ekin = 761.312eV (T=1472.443K) Etot = 2767.557eV Energy per atom: Epot =1993.876eV Ekin = 775.093eV (T=1499.097K) Etot = 2768.968eV Energy per atom: Epot =1995.610eV Ekin = 768.416eV (T=1486.184K) Etot = 2764.027eV Energy per atom: Epot =1995.697eV Ekin = 769.008eV (T=1487.329K) Etot = 2764.705eV Energy per atom: Epot =1982.384eV Ekin = 780.437eV (T=1509.432K) Etot = 2762.821eV Energy per atom: Epot =1981.783eV Ekin = 782.023eV (T=1512.501K) Etot = 2763.806eV Energy per atom: Epot =1991.493eV Ekin = 773.094eV (T=1495.231K) Etot = 2764.587eV Energy per atom: Epot =1973.650eV Ekin = 791.075eV (T=1530.009K) Etot = 2764.725eV .. 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] 20:07:12 43.457006 1.0818 BFGSLineSearch: 1[ 1] 20:07:12 42.347659 0.2273 BFGSLineSearch: 2[ 2] 20:07:12 42.108454 0.1349 BFGSLineSearch: 3[ 3] 20:07:12 41.964817 0.1138 BFGSLineSearch: 4[ 4] 20:07:12 41.924933 0.0683 BFGSLineSearch: 5[ 5] 20:07:12 41.915346 0.0225 BFGSLineSearch: 6[ 6] 20:07:12 41.914920 0.0059 BFGSLineSearch: 7[ 7] 20:07:12 41.914872 0.0023 BFGSLineSearch: 8[ 9] 20:07:12 41.914855 0.0023 BFGSLineSearch: 9[ 10] 20:07:12 41.914851 0.0010 running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 15.215eV (T=1265.648K) Etot = 57.129eV Energy per atom: Epot =50.899eV Ekin = 6.277eV (T=522.149K) Etot = 57.176eV Energy per atom: Epot =51.203eV Ekin = 5.974eV (T=496.949K) Etot = 57.177eV Energy per atom: Epot =50.895eV Ekin = 6.279eV (T=522.359K) Etot = 57.175eV Energy per atom: Epot =51.951eV Ekin = 5.231eV (T=435.188K) Etot = 57.182eV Energy per atom: Epot =50.451eV Ekin = 6.723eV (T=559.266K) Etot = 57.174eV Energy per atom: Epot =49.546eV Ekin = 7.623eV (T=634.095K) Etot = 57.168eV Energy per atom: Epot =50.036eV Ekin = 7.139eV (T=593.833K) Etot = 57.174eV Energy per atom: Epot =50.117eV Ekin = 7.065eV (T=587.707K) Etot = 57.182eV Energy per atom: Epot =49.245eV Ekin = 7.930eV (T=659.689K) Etot = 57.175eV Energy per atom: Epot =50.013eV Ekin = 7.161eV (T=595.705K) Etot = 57.174eV Energy per atom: Epot =50.579eV Ekin = 6.595eV (T=548.638K) Etot = 57.174eV Energy per atom: Epot =50.477eV Ekin = 6.693eV (T=556.764K) Etot = 57.170eV Energy per atom: Epot =50.251eV Ekin = 6.923eV (T=575.889K) Etot = 57.174eV Energy per atom: Epot =49.763eV Ekin = 7.409eV (T=616.346K) Etot = 57.172eV Energy per atom: Epot =49.952eV Ekin = 7.224eV (T=600.950K) Etot = 57.176eV Energy per atom: Epot =49.981eV Ekin = 7.198eV (T=598.745K) Etot = 57.179eV Energy per atom: Epot =49.930eV Ekin = 7.251eV (T=603.194K) Etot = 57.181eV Energy per atom: Epot =50.421eV Ekin = 6.758eV (T=562.182K) Etot = 57.179eV Energy per atom: Epot =50.832eV Ekin = 6.345eV (T=527.796K) Etot = 57.177eV Energy per atom: Epot =50.141eV Ekin = 7.035eV (T=585.226K) Etot = 57.177eV Energy per atom: Epot =50.313eV Ekin = 6.866eV (T=571.147K) Etot = 57.179eV Energy per atom: Epot =49.391eV Ekin = 7.787eV (T=647.748K) Etot = 57.177eV Energy per atom: Epot =49.534eV Ekin = 7.636eV (T=635.220K) Etot = 57.170eV Energy per atom: Epot =49.786eV Ekin = 7.382eV (T=614.124K) Etot = 57.168eV Energy per atom: Epot =50.110eV Ekin = 7.066eV (T=587.788K) Etot = 57.176eV Energy per atom: Epot =49.598eV Ekin = 7.575eV (T=630.101K) Etot = 57.172eV Energy per atom: Epot =50.208eV Ekin = 6.967eV (T=579.560K) Etot = 57.175eV Energy per atom: Epot =50.069eV Ekin = 7.105eV (T=591.043K) Etot = 57.174eV Energy per atom: Epot =49.749eV Ekin = 7.423eV (T=617.513K) Etot = 57.173eV Energy per atom: Epot =50.022eV Ekin = 7.149eV (T=594.674K) Etot = 57.171eV Energy per atom: Epot =50.006eV Ekin = 7.168eV (T=596.254K) Etot = 57.174eV Energy per atom: Epot =50.437eV Ekin = 6.738eV (T=560.528K) Etot = 57.175eV Energy per atom: Epot =50.138eV Ekin = 7.033eV (T=585.031K) Etot = 57.171eV Energy per atom: Epot =50.005eV Ekin = 7.172eV (T=596.608K) Etot = 57.177eV Energy per atom: Epot =49.731eV Ekin = 7.440eV (T=618.916K) Etot = 57.171eV Energy per atom: Epot =49.364eV Ekin = 7.807eV (T=649.413K) Etot = 57.171eV Energy per atom: Epot =49.787eV Ekin = 7.386eV (T=614.436K) Etot = 57.173eV Energy per atom: Epot =50.453eV Ekin = 6.728eV (T=559.664K) Etot = 57.181eV Energy per atom: Epot =49.061eV Ekin = 8.104eV (T=674.157K) Etot = 57.165eV Energy per atom: Epot =50.256eV Ekin = 6.917eV (T=575.425K) Etot = 57.174eV Energy per atom: Epot =49.995eV Ekin = 7.178eV (T=597.132K) Etot = 57.173eV Energy per atom: Epot =49.693eV Ekin = 7.477eV (T=621.952K) Etot = 57.170eV Energy per atom: Epot =50.543eV Ekin = 6.633eV (T=551.794K) Etot = 57.177eV Energy per atom: Epot =49.281eV Ekin = 7.884eV (T=655.884K) Etot = 57.166eV Energy per atom: Epot =50.011eV Ekin = 7.162eV (T=595.747K) Etot = 57.172eV Energy per atom: Epot =50.894eV Ekin = 6.286eV (T=522.939K) Etot = 57.181eV Energy per atom: Epot =49.948eV Ekin = 7.227eV (T=601.172K) Etot = 57.175eV Energy per atom: Epot =49.594eV Ekin = 7.576eV (T=630.226K) Etot = 57.170eV Energy per atom: Epot =49.197eV Ekin = 7.974eV (T=663.346K) Etot = 57.171eV Energy per atom: Epot =50.275eV Ekin = 6.903eV (T=574.261K) Etot = 57.178eV Energy per atom: Epot =48.805eV Ekin = 8.366eV (T=695.925K) Etot = 57.171eV Energy per atom: Epot =50.601eV Ekin = 6.581eV (T=547.483K) Etot = 57.182eV Energy per atom: Epot =50.307eV Ekin = 6.876eV (T=571.962K) Etot = 57.182eV Energy per atom: Epot =49.590eV Ekin = 7.584eV (T=630.900K) Etot = 57.174eV Energy per atom: Epot =50.135eV Ekin = 7.037eV (T=585.358K) Etot = 57.172eV Energy per atom: Epot =49.972eV Ekin = 7.198eV (T=598.791K) Etot = 57.170eV Energy per atom: Epot =50.251eV Ekin = 6.926eV (T=576.120K) Etot = 57.177eV Energy per atom: Epot =50.000eV Ekin = 7.168eV (T=596.321K) Etot = 57.168eV Energy per atom: Epot =50.397eV Ekin = 6.776eV (T=563.661K) Etot = 57.173eV Energy per atom: Epot =50.725eV Ekin = 6.455eV (T=536.946K) Etot = 57.180eV Energy per atom: Epot =50.238eV Ekin = 6.938eV (T=577.130K) Etot = 57.175eV Energy per atom: Epot =50.156eV Ekin = 7.018eV (T=583.781K) Etot = 57.174eV Energy per atom: Epot =49.763eV Ekin = 7.411eV (T=616.537K) Etot = 57.175eV Energy per atom: Epot =50.270eV Ekin = 6.904eV (T=574.284K) Etot = 57.173eV Energy per atom: Epot =49.973eV Ekin = 7.196eV (T=598.651K) Etot = 57.169eV Energy per atom: Epot =49.607eV Ekin = 7.562eV (T=629.059K) Etot = 57.169eV Energy per atom: Epot =50.153eV Ekin = 7.023eV (T=584.199K) Etot = 57.176eV Energy per atom: Epot =50.020eV Ekin = 7.152eV (T=594.958K) Etot = 57.172eV Energy per atom: Epot =49.987eV Ekin = 7.184eV (T=597.616K) Etot = 57.172eV Energy per atom: Epot =49.876eV Ekin = 7.295eV (T=606.836K) Etot = 57.171eV Energy per atom: Epot =50.555eV Ekin = 6.623eV (T=550.909K) Etot = 57.177eV Energy per atom: Epot =50.260eV Ekin = 6.917eV (T=575.440K) Etot = 57.177eV Energy per atom: Epot =49.869eV Ekin = 7.303eV (T=607.511K) Etot = 57.172eV Energy per atom: Epot =50.855eV Ekin = 6.327eV (T=526.332K) Etot = 57.182eV Energy per atom: Epot =48.832eV Ekin = 8.339eV (T=693.732K) Etot = 57.172eV Energy per atom: Epot =49.386eV Ekin = 7.783eV (T=647.400K) Etot = 57.169eV Energy per atom: Epot =50.017eV Ekin = 7.155eV (T=595.232K) Etot = 57.173eV Energy per atom: Epot =49.586eV Ekin = 7.588eV (T=631.214K) Etot = 57.174eV Energy per atom: Epot =49.893eV Ekin = 7.280eV (T=605.588K) Etot = 57.173eV Energy per atom: Epot =49.999eV Ekin = 7.175eV (T=596.860K) Etot = 57.173eV Energy per atom: Epot =50.269eV Ekin = 6.905eV (T=574.399K) Etot = 57.174eV Energy per atom: Epot =49.613eV Ekin = 7.559eV (T=628.818K) Etot = 57.172eV Energy per atom: Epot =49.715eV Ekin = 7.461eV (T=620.676K) Etot = 57.176eV Energy per atom: Epot =50.418eV Ekin = 6.758eV (T=562.200K) Etot = 57.176eV Energy per atom: Epot =49.479eV Ekin = 7.693eV (T=639.925K) Etot = 57.171eV Energy per atom: Epot =49.141eV Ekin = 8.029eV (T=667.913K) Etot = 57.170eV Energy per atom: Epot =49.386eV Ekin = 7.786eV (T=647.664K) Etot = 57.171eV Energy per atom: Epot =50.743eV Ekin = 6.434eV (T=535.235K) Etot = 57.177eV Energy per atom: Epot =49.848eV Ekin = 7.325eV (T=609.369K) Etot = 57.173eV Energy per atom: Epot =49.401eV Ekin = 7.770eV (T=646.392K) Etot = 57.171eV Energy per atom: Epot =49.754eV Ekin = 7.416eV (T=616.927K) Etot = 57.170eV Energy per atom: Epot =50.318eV Ekin = 6.859eV (T=570.546K) Etot = 57.176eV Energy per atom: Epot =50.000eV Ekin = 7.173eV (T=596.694K) Etot = 57.173eV Energy per atom: Epot =49.573eV Ekin = 7.599eV (T=632.109K) Etot = 57.172eV Energy per atom: Epot =50.882eV Ekin = 6.299eV (T=523.993K) Etot = 57.182eV Energy per atom: Epot =50.515eV Ekin = 6.664eV (T=554.395K) Etot = 57.180eV Energy per atom: Epot =50.705eV Ekin = 6.474eV (T=538.534K) Etot = 57.179eV Energy per atom: Epot =49.887eV Ekin = 7.291eV (T=606.491K) Etot = 57.177eV Energy per atom: Epot =50.485eV Ekin = 6.693eV (T=556.765K) Etot = 57.178eV Energy per atom: Epot =49.825eV Ekin = 7.352eV (T=611.600K) Etot = 57.177eV Energy per atom: Epot =50.762eV Ekin = 6.419eV (T=533.959K) Etot = 57.181eV Energy per atom: Epot =50.910eV Ekin = 6.268eV (T=521.380K) Etot = 57.178eV Energy per atom: Epot =49.700eV Ekin = 7.477eV (T=621.995K) Etot = 57.177eV Energy per atom: Epot =49.345eV Ekin = 7.831eV (T=651.433K) Etot = 57.176eV Energy per atom: Epot =50.731eV Ekin = 6.446eV (T=536.240K) Etot = 57.177eV Energy per atom: Epot =50.653eV Ekin = 6.520eV (T=542.338K) Etot = 57.172eV Energy per atom: Epot =50.143eV Ekin = 7.031eV (T=584.908K) Etot = 57.174eV Energy per atom: Epot =50.221eV Ekin = 6.955eV (T=578.556K) Etot = 57.176eV Energy per atom: Epot =50.910eV Ekin = 6.269eV (T=521.500K) Etot = 57.179eV Energy per atom: Epot =50.838eV Ekin = 6.342eV (T=527.546K) Etot = 57.180eV Energy per atom: Epot =50.085eV Ekin = 7.090eV (T=589.824K) Etot = 57.176eV Energy per atom: Epot =50.541eV Ekin = 6.635eV (T=551.924K) Etot = 57.175eV Energy per atom: Epot =50.158eV Ekin = 7.022eV (T=584.172K) Etot = 57.181eV Energy per atom: Epot =50.253eV Ekin = 6.925eV (T=576.067K) Etot = 57.178eV Energy per atom: Epot =50.163eV Ekin = 7.013eV (T=583.360K) Etot = 57.176eV Energy per atom: Epot =49.875eV Ekin = 7.301eV (T=607.362K) Etot = 57.176eV Energy per atom: Epot =50.614eV Ekin = 6.565eV (T=546.088K) Etot = 57.178eV Energy per atom: Epot =49.747eV Ekin = 7.425eV (T=617.670K) Etot = 57.173eV Energy per atom: Epot =50.614eV Ekin = 6.564eV (T=546.073K) Etot = 57.179eV Energy per atom: Epot =49.712eV Ekin = 7.461eV (T=620.694K) Etot = 57.174eV Energy per atom: Epot =50.214eV Ekin = 6.958eV (T=578.820K) Etot = 57.172eV Energy per atom: Epot =50.425eV Ekin = 6.749eV (T=561.452K) Etot = 57.175eV Energy per atom: Epot =50.108eV Ekin = 7.070eV (T=588.100K) Etot = 57.177eV Energy per atom: Epot =50.114eV Ekin = 7.062eV (T=587.465K) Etot = 57.176eV Energy per atom: Epot =49.458eV Ekin = 7.712eV (T=641.546K) Etot = 57.170eV Energy per atom: Epot =49.513eV Ekin = 7.658eV (T=637.011K) Etot = 57.170eV Energy per atom: Epot =50.331eV Ekin = 6.845eV (T=569.439K) Etot = 57.176eV Energy per atom: Epot =50.230eV Ekin = 6.946eV (T=577.773K) Etot = 57.175eV Energy per atom: Epot =50.091eV Ekin = 7.083eV (T=589.208K) Etot = 57.174eV Energy per atom: Epot =50.704eV Ekin = 6.477eV (T=538.781K) Etot = 57.181eV Energy per atom: Epot =50.140eV Ekin = 7.027eV (T=584.556K) Etot = 57.167eV Energy per atom: Epot =50.075eV Ekin = 7.099eV (T=590.514K) Etot = 57.173eV Energy per atom: Epot =49.937eV Ekin = 7.238eV (T=602.095K) Etot = 57.175eV Energy per atom: Epot =49.715eV Ekin = 7.454eV (T=620.071K) Etot = 57.169eV Energy per atom: Epot =50.134eV Ekin = 7.040eV (T=585.647K) Etot = 57.174eV Energy per atom: Epot =50.644eV Ekin = 6.533eV (T=543.453K) Etot = 57.177eV Energy per atom: Epot =50.713eV Ekin = 6.465eV (T=537.780K) Etot = 57.178eV Energy per atom: Epot =50.528eV Ekin = 6.654eV (T=553.532K) Etot = 57.182eV Energy per atom: Epot =49.790eV Ekin = 7.384eV (T=614.244K) Etot = 57.174eV Energy per atom: Epot =49.651eV Ekin = 7.522eV (T=625.699K) Etot = 57.173eV Energy per atom: Epot =50.440eV Ekin = 6.736eV (T=560.351K) Etot = 57.176eV Energy per atom: Epot =50.312eV Ekin = 6.864eV (T=570.994K) Etot = 57.176eV Energy per atom: Epot =49.631eV Ekin = 7.542eV (T=627.402K) Etot = 57.173eV Energy per atom: Epot =49.707eV Ekin = 7.467eV (T=621.159K) Etot = 57.174eV Energy per atom: Epot =50.184eV Ekin = 6.993eV (T=581.697K) Etot = 57.177eV Energy per atom: Epot =49.630eV Ekin = 7.548eV (T=627.884K) Etot = 57.177eV Energy per atom: Epot =49.268eV Ekin = 7.904eV (T=657.531K) Etot = 57.172eV Energy per atom: Epot =49.734eV Ekin = 7.439eV (T=618.840K) Etot = 57.173eV Energy per atom: Epot =50.971eV Ekin = 6.208eV (T=516.420K) Etot = 57.179eV Energy per atom: Epot =50.210eV Ekin = 6.967eV (T=579.547K) Etot = 57.177eV Energy per atom: Epot =50.166eV Ekin = 7.009eV (T=583.054K) Etot = 57.175eV Energy per atom: Epot =50.523eV Ekin = 6.654eV (T=553.515K) Etot = 57.177eV Energy per atom: Epot =50.980eV Ekin = 6.197eV (T=515.540K) Etot = 57.177eV Energy per atom: Epot =49.840eV Ekin = 7.334eV (T=610.053K) Etot = 57.173eV Energy per atom: Epot =49.718eV Ekin = 7.456eV (T=620.271K) Etot = 57.174eV Energy per atom: Epot =49.441eV Ekin = 7.732eV (T=643.235K) Etot = 57.174eV Energy per atom: Epot =49.638eV Ekin = 7.535eV (T=626.847K) Etot = 57.173eV Energy per atom: Epot =49.620eV Ekin = 7.550eV (T=628.051K) Etot = 57.170eV Energy per atom: Epot =49.012eV Ekin = 8.164eV (T=679.154K) Etot = 57.176eV Energy per atom: Epot =50.109eV Ekin = 7.073eV (T=588.385K) Etot = 57.182eV Energy per atom: Epot =49.555eV Ekin = 7.623eV (T=634.138K) Etot = 57.179eV Energy per atom: Epot =49.929eV Ekin = 7.248eV (T=602.896K) Etot = 57.176eV Energy per atom: Epot =49.539eV Ekin = 7.633eV (T=634.985K) Etot = 57.172eV Energy per atom: Epot =50.021eV Ekin = 7.154eV (T=595.141K) Etot = 57.175eV Energy per atom: Epot =49.434eV Ekin = 7.737eV (T=643.636K) Etot = 57.171eV Energy per atom: Epot =49.241eV Ekin = 7.936eV (T=660.139K) Etot = 57.176eV Energy per atom: Epot =48.598eV Ekin = 8.572eV (T=713.038K) Etot = 57.169eV Energy per atom: Epot =50.294eV Ekin = 6.884eV (T=572.618K) Etot = 57.178eV Energy per atom: Epot =48.147eV Ekin = 9.023eV (T=750.596K) Etot = 57.170eV Energy per atom: Epot =49.797eV Ekin = 7.373eV (T=613.365K) Etot = 57.171eV Energy per atom: Epot =49.923eV Ekin = 7.256eV (T=603.570K) Etot = 57.178eV Energy per atom: Epot =49.502eV Ekin = 7.677eV (T=638.618K) Etot = 57.179eV Energy per atom: Epot =49.242eV Ekin = 7.935eV (T=660.121K) Etot = 57.177eV Energy per atom: Epot =49.062eV Ekin = 8.112eV (T=674.776K) Etot = 57.173eV Energy per atom: Epot =50.193eV Ekin = 6.981eV (T=580.737K) Etot = 57.174eV Energy per atom: Epot =49.361eV Ekin = 7.812eV (T=649.853K) Etot = 57.173eV Energy per atom: Epot =49.888eV Ekin = 7.291eV (T=606.500K) Etot = 57.179eV Energy per atom: Epot =50.339eV Ekin = 6.839eV (T=568.935K) Etot = 57.179eV Energy per atom: Epot =49.123eV Ekin = 8.044eV (T=669.132K) Etot = 57.167eV Energy per atom: Epot =49.897eV Ekin = 7.278eV (T=605.401K) Etot = 57.175eV Energy per atom: Epot =49.193eV Ekin = 7.981eV (T=663.878K) Etot = 57.173eV Energy per atom: Epot =49.165eV Ekin = 8.005eV (T=665.948K) Etot = 57.170eV Energy per atom: Epot =48.442eV Ekin = 8.719eV (T=725.264K) Etot = 57.161eV Energy per atom: Epot =49.716eV Ekin = 7.460eV (T=620.578K) Etot = 57.176eV Energy per atom: Epot =50.047eV Ekin = 7.133eV (T=593.386K) Etot = 57.180eV Energy per atom: Epot =49.387eV Ekin = 7.783eV (T=647.453K) Etot = 57.170eV Energy per atom: Epot =49.996eV Ekin = 7.179eV (T=597.188K) Etot = 57.175eV Energy per atom: Epot =49.562eV Ekin = 7.614eV (T=633.348K) Etot = 57.175eV Energy per atom: Epot =49.316eV Ekin = 7.855eV (T=653.468K) Etot = 57.171eV Energy per atom: Epot =49.240eV Ekin = 7.932eV (T=659.875K) Etot = 57.172eV Energy per atom: Epot =49.171eV Ekin = 8.005eV (T=665.922K) Etot = 57.176eV Energy per atom: Epot =50.083eV Ekin = 7.099eV (T=590.570K) Etot = 57.182eV Energy per atom: Epot =48.415eV Ekin = 8.750eV (T=727.911K) Etot = 57.166eV Energy per atom: Epot =49.312eV Ekin = 7.861eV (T=653.917K) Etot = 57.173eV Energy per atom: Epot =49.566eV Ekin = 7.612eV (T=633.228K) Etot = 57.178eV Energy per atom: Epot =49.510eV Ekin = 7.666eV (T=637.722K) Etot = 57.176eV Energy per atom: Epot =49.392eV Ekin = 7.778eV (T=647.043K) Etot = 57.170eV Energy per atom: Epot =49.337eV Ekin = 7.837eV (T=651.911K) Etot = 57.174eV Energy per atom: Epot =49.338eV Ekin = 7.833eV (T=651.631K) Etot = 57.172eV Energy per atom: Epot =48.636eV Ekin = 8.536eV (T=710.100K) Etot = 57.172eV .. 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 `_