.. 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_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/tutorials/images/sphx_glr_md_001.png :alt: md :srcset: /examples_generated/tutorials/images/sphx_glr_md_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 90-92 Now let's run the MD simulation and monitor the kinetic and potential energy of the whole system: .. GENERATED FROM PYTHON SOURCE LINES 92-149 .. code-block:: Python # Describe the interatomic interactions with the Effective Medium Theory (EMT) atoms.calc = EMT() # Set the initial velocities corresponding to T=300K from Maxwell Boltzmann # Distribution MaxwellBoltzmannDistribution(atoms, temperature_K=300) # We use Velocity Verlet algorithm to integrate the Newton's equations. timestep_fs = 5 dyn = VelocityVerlet(atoms, timestep_fs * units.fs) # 5 fs time step. def printenergy(a): """ Function to print the thermodynamical properties i.e potential energy, kinetic energy and total energy """ epot = a.get_potential_energy() ekin = a.get_kinetic_energy() temp = a.get_temperature() print( f'Energy per atom: Epot ={epot:6.3f}eV Ekin = {ekin:.3f}eV ' f'(T={temp:.3f}K) Etot = {epot + ekin:.3f}eV' ) # Now run the dynamics print('running a NVE simulation of fcc Cu') printenergy(atoms) # init lists to for energy vs time data time_ps, epot, ekin = [], [], [] mdind = 0 steps_per_block = 10 for i in range(20): dyn.run(steps_per_block) mdind += steps_per_block printenergy(atoms) # save the energies of the current MD step time_ps.append(mdind * timestep_fs / 1000.0) epot.append(atoms.get_potential_energy()) ekin.append(atoms.get_kinetic_energy()) etot = np.array(epot) + np.array(ekin) # Plot energies vs time fig, ax = plt.subplots(figsize=(6, 4)) ax.plot(time_ps, epot, label='Potential energy') ax.plot(time_ps, ekin, label='Kinetic energy') ax.plot(time_ps, etot, label='Total energy') ax.set_xlabel('Time (ps)') ax.set_ylabel('Energy (eV)') ax.legend(loc='best') ax.grid(True, linewidth=0.5, alpha=0.5) plt.tight_layout() plt.show() .. image-sg:: /examples_generated/tutorials/images/sphx_glr_md_002.png :alt: md :srcset: /examples_generated/tutorials/images/sphx_glr_md_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none running a NVE simulation of fcc Cu Energy per atom: Epot =-2.405eV Ekin = 159.092eV (T=307.697K) Etot = 156.687eV Energy per atom: Epot =120.602eV Ekin = 36.894eV (T=71.357K) Etot = 157.496eV Energy per atom: Epot =79.794eV Ekin = 77.559eV (T=150.006K) Etot = 157.353eV Energy per atom: Epot =73.104eV Ekin = 84.103eV (T=162.663K) Etot = 157.207eV Energy per atom: Epot =71.113eV Ekin = 86.040eV (T=166.409K) Etot = 157.154eV Energy per atom: Epot =83.695eV Ekin = 73.626eV (T=142.399K) Etot = 157.321eV Energy per atom: Epot =78.776eV Ekin = 78.517eV (T=151.858K) Etot = 157.293eV Energy per atom: Epot =76.302eV Ekin = 80.914eV (T=156.494K) Etot = 157.216eV Energy per atom: Epot =73.950eV Ekin = 83.263eV (T=161.039K) Etot = 157.213eV Energy per atom: Epot =81.815eV Ekin = 75.486eV (T=145.996K) Etot = 157.300eV Energy per atom: Epot =76.506eV Ekin = 80.745eV (T=156.168K) Etot = 157.251eV Energy per atom: Epot =76.718eV Ekin = 80.525eV (T=155.743K) Etot = 157.243eV Energy per atom: Epot =77.498eV Ekin = 79.752eV (T=154.247K) Etot = 157.250eV Energy per atom: Epot =78.809eV Ekin = 78.445eV (T=151.719K) Etot = 157.254eV Energy per atom: Epot =75.463eV Ekin = 81.771eV (T=158.152K) Etot = 157.234eV Energy per atom: Epot =78.136eV Ekin = 79.133eV (T=153.051K) Etot = 157.269eV Energy per atom: Epot =76.723eV Ekin = 80.531eV (T=155.753K) Etot = 157.254eV Energy per atom: Epot =79.513eV Ekin = 77.733eV (T=150.342K) Etot = 157.246eV Energy per atom: Epot =75.966eV Ekin = 81.284eV (T=157.210K) Etot = 157.250eV Energy per atom: Epot =76.617eV Ekin = 80.634eV (T=155.953K) Etot = 157.250eV Energy per atom: Epot =80.895eV Ekin = 76.375eV (T=147.716K) Etot = 157.270eV .. 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 =600.332eV Ekin = 83.491eV (T=161.479K) Etot = 683.823eV Energy per atom: Epot =671.229eV Ekin = 141.061eV (T=272.824K) Etot = 812.290eV Energy per atom: Epot =726.493eV Ekin = 201.470eV (T=389.661K) Etot = 927.964eV Energy per atom: Epot =786.391eV Ekin = 252.822eV (T=488.980K) Etot = 1039.213eV Energy per atom: Epot =836.641eV Ekin = 295.782eV (T=572.068K) Etot = 1132.423eV Energy per atom: Epot =878.490eV Ekin = 337.853eV (T=653.437K) Etot = 1216.343eV Energy per atom: Epot =923.730eV Ekin = 378.527eV (T=732.103K) Etot = 1302.257eV Energy per atom: Epot =962.268eV Ekin = 419.241eV (T=810.848K) Etot = 1381.509eV Energy per atom: Epot =1003.285eV Ekin = 446.701eV (T=863.958K) Etot = 1449.986eV Energy per atom: Epot =1032.256eV Ekin = 468.895eV (T=906.884K) Etot = 1501.152eV Energy per atom: Epot =1072.253eV Ekin = 490.176eV (T=948.044K) Etot = 1562.429eV Energy per atom: Epot =1097.734eV Ekin = 517.133eV (T=1000.180K) Etot = 1614.867eV Energy per atom: Epot =1141.368eV Ekin = 521.653eV (T=1008.923K) Etot = 1663.022eV Energy per atom: Epot =1164.993eV Ekin = 543.205eV (T=1050.605K) Etot = 1708.198eV Energy per atom: Epot =1192.656eV Ekin = 567.210eV (T=1097.033K) Etot = 1759.865eV Energy per atom: Epot =1231.520eV Ekin = 563.206eV (T=1089.290K) Etot = 1794.726eV Energy per atom: Epot =1254.863eV Ekin = 569.826eV (T=1102.092K) Etot = 1824.689eV Energy per atom: Epot =1272.408eV Ekin = 587.111eV (T=1135.524K) Etot = 1859.519eV Energy per atom: Epot =1301.682eV Ekin = 595.417eV (T=1151.588K) Etot = 1897.099eV Energy per atom: Epot =1309.658eV Ekin = 618.859eV (T=1196.927K) Etot = 1928.517eV Energy per atom: Epot =1339.024eV Ekin = 616.908eV (T=1193.154K) Etot = 1955.932eV Energy per atom: Epot =1361.415eV Ekin = 618.529eV (T=1196.290K) Etot = 1979.944eV Energy per atom: Epot =1359.344eV Ekin = 648.561eV (T=1254.374K) Etot = 2007.906eV Energy per atom: Epot =1387.135eV Ekin = 637.737eV (T=1233.438K) Etot = 2024.871eV Energy per atom: Epot =1406.600eV Ekin = 641.018eV (T=1239.784K) Etot = 2047.618eV Energy per atom: Epot =1418.353eV Ekin = 647.675eV (T=1252.660K) Etot = 2066.028eV Energy per atom: Epot =1436.485eV Ekin = 654.434eV (T=1265.732K) Etot = 2090.919eV Energy per atom: Epot =1447.974eV Ekin = 661.095eV (T=1278.615K) Etot = 2109.069eV Energy per atom: Epot =1452.310eV Ekin = 675.398eV (T=1306.279K) Etot = 2127.708eV Energy per atom: Epot =1467.295eV Ekin = 675.402eV (T=1306.286K) Etot = 2142.697eV Energy per atom: Epot =1483.672eV Ekin = 679.538eV (T=1314.286K) Etot = 2163.210eV Energy per atom: Epot =1500.563eV Ekin = 685.993eV (T=1326.769K) Etot = 2186.555eV Energy per atom: Epot =1525.343eV Ekin = 685.679eV (T=1326.163K) Etot = 2211.023eV Energy per atom: Epot =1530.082eV Ekin = 693.014eV (T=1340.350K) Etot = 2223.096eV Energy per atom: Epot =1545.124eV Ekin = 685.582eV (T=1325.975K) Etot = 2230.706eV Energy per atom: Epot =1554.315eV Ekin = 681.503eV (T=1318.085K) Etot = 2235.817eV Energy per atom: Epot =1559.745eV Ekin = 695.155eV (T=1344.491K) Etot = 2254.901eV Energy per atom: Epot =1566.951eV Ekin = 704.504eV (T=1362.572K) Etot = 2271.454eV Energy per atom: Epot =1592.706eV Ekin = 694.612eV (T=1343.439K) Etot = 2287.318eV Energy per atom: Epot =1593.148eV Ekin = 707.354eV (T=1368.084K) Etot = 2300.502eV Energy per atom: Epot =1609.759eV Ekin = 697.030eV (T=1348.117K) Etot = 2306.790eV Energy per atom: Epot =1596.164eV Ekin = 718.903eV (T=1390.421K) Etot = 2315.067eV Energy per atom: Epot =1619.103eV Ekin = 706.161eV (T=1365.776K) Etot = 2325.264eV Energy per atom: Epot =1630.419eV Ekin = 708.988eV (T=1371.244K) Etot = 2339.407eV Energy per atom: Epot =1647.196eV Ekin = 719.132eV (T=1390.864K) Etot = 2366.328eV Energy per atom: Epot =1651.129eV Ekin = 714.111eV (T=1381.154K) Etot = 2365.240eV Energy per atom: Epot =1654.694eV Ekin = 713.629eV (T=1380.221K) Etot = 2368.323eV Energy per atom: Epot =1645.941eV Ekin = 731.221eV (T=1414.245K) Etot = 2377.162eV Energy per atom: Epot =1668.509eV Ekin = 720.085eV (T=1392.707K) Etot = 2388.594eV Energy per atom: Epot =1679.437eV Ekin = 724.501eV (T=1401.248K) Etot = 2403.938eV Energy per atom: Epot =1687.561eV Ekin = 737.494eV (T=1426.377K) Etot = 2425.054eV Energy per atom: Epot =1697.499eV Ekin = 725.777eV (T=1403.717K) Etot = 2423.276eV Energy per atom: Epot =1717.363eV Ekin = 712.217eV (T=1377.489K) Etot = 2429.580eV Energy per atom: Epot =1729.904eV Ekin = 716.208eV (T=1385.208K) Etot = 2446.112eV Energy per atom: Epot =1725.995eV Ekin = 727.183eV (T=1406.436K) Etot = 2453.179eV Energy per atom: Epot =1728.277eV Ekin = 728.911eV (T=1409.778K) Etot = 2457.188eV Energy per atom: Epot =1739.732eV Ekin = 720.348eV (T=1393.215K) Etot = 2460.080eV Energy per atom: Epot =1752.254eV Ekin = 720.190eV (T=1392.911K) Etot = 2472.445eV Energy per atom: Epot =1762.005eV Ekin = 721.652eV (T=1395.737K) Etot = 2483.657eV Energy per atom: Epot =1762.749eV Ekin = 729.327eV (T=1410.581K) Etot = 2492.076eV Energy per atom: Epot =1771.180eV Ekin = 730.017eV (T=1411.916K) Etot = 2501.197eV Energy per atom: Epot =1762.228eV Ekin = 750.300eV (T=1451.146K) Etot = 2512.528eV Energy per atom: Epot =1782.538eV Ekin = 738.097eV (T=1427.544K) Etot = 2520.634eV Energy per atom: Epot =1784.624eV Ekin = 745.578eV (T=1442.012K) Etot = 2530.202eV Energy per atom: Epot =1789.128eV Ekin = 748.783eV (T=1448.211K) Etot = 2537.911eV Energy per atom: Epot =1804.221eV Ekin = 731.157eV (T=1414.120K) Etot = 2535.377eV Energy per atom: Epot =1812.224eV Ekin = 730.998eV (T=1413.814K) Etot = 2543.222eV Energy per atom: Epot =1806.749eV Ekin = 738.791eV (T=1428.886K) Etot = 2545.540eV Energy per atom: Epot =1811.587eV Ekin = 750.550eV (T=1451.629K) Etot = 2562.136eV Energy per atom: Epot =1823.013eV Ekin = 750.593eV (T=1451.712K) Etot = 2573.606eV Energy per atom: Epot =1832.911eV Ekin = 737.067eV (T=1425.551K) Etot = 2569.978eV Energy per atom: Epot =1838.739eV Ekin = 731.904eV (T=1415.566K) Etot = 2570.643eV Energy per atom: Epot =1828.745eV Ekin = 740.524eV (T=1432.238K) Etot = 2569.269eV Energy per atom: Epot =1843.974eV Ekin = 731.877eV (T=1415.514K) Etot = 2575.851eV Energy per atom: Epot =1849.323eV Ekin = 733.702eV (T=1419.044K) Etot = 2583.025eV Energy per atom: Epot =1854.013eV Ekin = 732.967eV (T=1417.621K) Etot = 2586.980eV Energy per atom: Epot =1844.527eV Ekin = 745.295eV (T=1441.466K) Etot = 2589.822eV Energy per atom: Epot =1840.570eV Ekin = 744.009eV (T=1438.979K) Etot = 2584.579eV Energy per atom: Epot =1842.556eV Ekin = 745.780eV (T=1442.403K) Etot = 2588.335eV Energy per atom: Epot =1845.293eV Ekin = 746.807eV (T=1444.390K) Etot = 2592.100eV Energy per atom: Epot =1849.884eV Ekin = 747.306eV (T=1445.355K) Etot = 2597.190eV Energy per atom: Epot =1853.703eV Ekin = 747.865eV (T=1446.437K) Etot = 2601.568eV Energy per atom: Epot =1862.601eV Ekin = 744.490eV (T=1439.909K) Etot = 2607.092eV Energy per atom: Epot =1864.157eV Ekin = 752.334eV (T=1455.079K) Etot = 2616.491eV Energy per atom: Epot =1886.974eV Ekin = 729.430eV (T=1410.781K) Etot = 2616.404eV Energy per atom: Epot =1874.398eV Ekin = 744.173eV (T=1439.295K) Etot = 2618.570eV Energy per atom: Epot =1881.101eV Ekin = 738.820eV (T=1428.942K) Etot = 2619.920eV Energy per atom: Epot =1883.170eV Ekin = 736.730eV (T=1424.899K) Etot = 2619.899eV Energy per atom: Epot =1880.138eV Ekin = 738.753eV (T=1428.813K) Etot = 2618.891eV Energy per atom: Epot =1885.265eV Ekin = 744.379eV (T=1439.693K) Etot = 2629.644eV Energy per atom: Epot =1902.814eV Ekin = 735.776eV (T=1423.055K) Etot = 2638.590eV Energy per atom: Epot =1901.667eV Ekin = 738.004eV (T=1427.365K) Etot = 2639.672eV Energy per atom: Epot =1892.228eV Ekin = 753.943eV (T=1458.192K) Etot = 2646.171eV Energy per atom: Epot =1904.675eV Ekin = 754.592eV (T=1459.446K) Etot = 2659.267eV Energy per atom: Epot =1914.356eV Ekin = 749.396eV (T=1449.397K) Etot = 2663.752eV Energy per atom: Epot =1903.829eV Ekin = 760.330eV (T=1470.544K) Etot = 2664.159eV Energy per atom: Epot =1912.498eV Ekin = 742.192eV (T=1435.464K) Etot = 2654.690eV Energy per atom: Epot =1927.457eV Ekin = 731.134eV (T=1414.076K) Etot = 2658.591eV Energy per atom: Epot =1926.551eV Ekin = 748.736eV (T=1448.121K) Etot = 2675.287eV Energy per atom: Epot =1921.824eV Ekin = 748.483eV (T=1447.630K) Etot = 2670.306eV Energy per atom: Epot =1920.829eV Ekin = 758.828eV (T=1467.639K) Etot = 2679.657eV Energy per atom: Epot =1936.500eV Ekin = 749.790eV (T=1450.159K) Etot = 2686.289eV Energy per atom: Epot =1940.654eV Ekin = 744.925eV (T=1440.750K) Etot = 2685.579eV Energy per atom: Epot =1934.711eV Ekin = 755.958eV (T=1462.089K) Etot = 2690.669eV Energy per atom: Epot =1951.528eV Ekin = 741.175eV (T=1433.496K) Etot = 2692.702eV Energy per atom: Epot =1941.693eV Ekin = 766.586eV (T=1482.645K) Etot = 2708.279eV Energy per atom: Epot =1956.195eV Ekin = 753.960eV (T=1458.225K) Etot = 2710.155eV Energy per atom: Epot =1947.448eV Ekin = 769.465eV (T=1488.213K) Etot = 2716.913eV Energy per atom: Epot =1956.948eV Ekin = 765.814eV (T=1481.151K) Etot = 2722.762eV Energy per atom: Epot =1959.850eV Ekin = 760.446eV (T=1470.769K) Etot = 2720.296eV Energy per atom: Epot =1958.344eV Ekin = 760.351eV (T=1470.586K) Etot = 2718.695eV Energy per atom: Epot =1956.312eV Ekin = 767.254eV (T=1483.937K) Etot = 2723.566eV Energy per atom: Epot =1969.973eV Ekin = 765.568eV (T=1480.676K) Etot = 2735.541eV Energy per atom: Epot =1971.719eV Ekin = 765.278eV (T=1480.115K) Etot = 2736.997eV Energy per atom: Epot =1976.574eV Ekin = 759.342eV (T=1468.634K) Etot = 2735.917eV Energy per atom: Epot =1975.100eV Ekin = 766.815eV (T=1483.087K) Etot = 2741.915eV Energy per atom: Epot =1993.905eV Ekin = 759.006eV (T=1467.984K) Etot = 2752.912eV Energy per atom: Epot =2000.776eV Ekin = 760.718eV (T=1471.294K) Etot = 2761.493eV Energy per atom: Epot =1981.529eV Ekin = 769.163eV (T=1487.628K) Etot = 2750.692eV Energy per atom: Epot =1983.161eV Ekin = 768.950eV (T=1487.217K) Etot = 2752.111eV Energy per atom: Epot =1986.357eV Ekin = 776.183eV (T=1501.205K) Etot = 2762.539eV Energy per atom: Epot =1989.410eV Ekin = 775.807eV (T=1500.478K) Etot = 2765.217eV Energy per atom: Epot =1999.589eV Ekin = 765.383eV (T=1480.317K) Etot = 2764.971eV Energy per atom: Epot =1984.929eV Ekin = 775.509eV (T=1499.901K) Etot = 2760.438eV Energy per atom: Epot =1984.229eV Ekin = 776.585eV (T=1501.984K) Etot = 2760.814eV Energy per atom: Epot =2002.925eV Ekin = 777.251eV (T=1503.270K) Etot = 2780.176eV Energy per atom: Epot =2002.236eV Ekin = 783.963eV (T=1516.252K) Etot = 2786.198eV Energy per atom: Epot =1993.496eV Ekin = 795.022eV (T=1537.641K) Etot = 2788.518eV Energy per atom: Epot =2013.089eV Ekin = 779.684eV (T=1507.976K) Etot = 2792.773eV Energy per atom: Epot =1992.341eV Ekin = 786.466eV (T=1521.094K) Etot = 2778.807eV Energy per atom: Epot =1994.316eV Ekin = 769.163eV (T=1487.627K) Etot = 2763.478eV Energy per atom: Epot =1996.610eV Ekin = 772.086eV (T=1493.282K) Etot = 2768.697eV Energy per atom: Epot =1995.341eV Ekin = 774.458eV (T=1497.869K) Etot = 2769.799eV Energy per atom: Epot =2005.919eV Ekin = 775.742eV (T=1500.352K) Etot = 2781.661eV Energy per atom: Epot =2010.116eV Ekin = 772.040eV (T=1493.192K) Etot = 2782.156eV Energy per atom: Epot =1990.498eV Ekin = 783.531eV (T=1515.418K) Etot = 2774.030eV Energy per atom: Epot =2019.468eV Ekin = 761.587eV (T=1472.976K) Etot = 2781.055eV Energy per atom: Epot =2006.299eV Ekin = 778.882eV (T=1506.426K) Etot = 2785.181eV Energy per atom: Epot =2019.224eV Ekin = 772.558eV (T=1494.195K) Etot = 2791.783eV Energy per atom: Epot =2003.820eV Ekin = 786.149eV (T=1520.481K) Etot = 2789.969eV Energy per atom: Epot =2013.735eV Ekin = 770.048eV (T=1489.339K) Etot = 2783.783eV Energy per atom: Epot =2005.852eV Ekin = 771.805eV (T=1492.737K) Etot = 2777.657eV Energy per atom: Epot =2007.063eV Ekin = 773.657eV (T=1496.320K) Etot = 2780.720eV Energy per atom: Epot =2014.317eV Ekin = 773.258eV (T=1495.549K) Etot = 2787.575eV Energy per atom: Epot =2005.241eV Ekin = 768.705eV (T=1486.742K) Etot = 2773.946eV Energy per atom: Epot =2007.629eV Ekin = 765.413eV (T=1480.375K) Etot = 2773.042eV Energy per atom: Epot =2015.018eV Ekin = 763.951eV (T=1477.548K) Etot = 2778.969eV Energy per atom: Epot =2017.758eV Ekin = 771.316eV (T=1491.791K) Etot = 2789.073eV Energy per atom: Epot =2011.374eV Ekin = 769.791eV (T=1488.843K) Etot = 2781.165eV Energy per atom: Epot =2010.294eV Ekin = 767.755eV (T=1484.904K) Etot = 2778.049eV Energy per atom: Epot =2005.899eV Ekin = 769.263eV (T=1487.822K) Etot = 2775.163eV Energy per atom: Epot =2005.169eV Ekin = 786.017eV (T=1520.226K) Etot = 2791.187eV Energy per atom: Epot =2013.759eV Ekin = 774.021eV (T=1497.024K) Etot = 2787.780eV Energy per atom: Epot =1997.234eV Ekin = 792.204eV (T=1532.192K) Etot = 2789.439eV Energy per atom: Epot =2015.303eV Ekin = 769.240eV (T=1487.778K) Etot = 2784.543eV Energy per atom: Epot =2014.982eV Ekin = 773.096eV (T=1495.236K) Etot = 2788.078eV Energy per atom: Epot =2012.141eV Ekin = 774.638eV (T=1498.218K) Etot = 2786.779eV Energy per atom: Epot =2009.113eV Ekin = 780.619eV (T=1509.785K) Etot = 2789.732eV Energy per atom: Epot =2002.015eV Ekin = 781.577eV (T=1511.638K) Etot = 2783.592eV Energy per atom: Epot =1991.922eV Ekin = 781.276eV (T=1511.056K) Etot = 2773.198eV Energy per atom: Epot =1990.747eV Ekin = 773.953eV (T=1496.892K) Etot = 2764.700eV Energy per atom: Epot =1996.334eV Ekin = 768.928eV (T=1487.174K) Etot = 2765.262eV Energy per atom: Epot =1990.911eV Ekin = 775.330eV (T=1499.556K) Etot = 2766.242eV Energy per atom: Epot =1986.406eV Ekin = 777.454eV (T=1503.663K) Etot = 2763.859eV Energy per atom: Epot =1993.111eV Ekin = 767.524eV (T=1484.459K) Etot = 2760.635eV Energy per atom: Epot =1984.922eV Ekin = 775.304eV (T=1499.506K) Etot = 2760.226eV Energy per atom: Epot =1996.507eV Ekin = 767.918eV (T=1485.220K) Etot = 2764.424eV Energy per atom: Epot =1991.139eV Ekin = 769.102eV (T=1487.511K) Etot = 2760.241eV Energy per atom: Epot =1994.896eV Ekin = 772.759eV (T=1494.583K) Etot = 2767.655eV Energy per atom: Epot =1987.307eV Ekin = 772.767eV (T=1494.598K) Etot = 2760.074eV Energy per atom: Epot =2001.528eV Ekin = 756.602eV (T=1463.333K) Etot = 2758.129eV Energy per atom: Epot =2000.220eV Ekin = 762.545eV (T=1474.828K) Etot = 2762.765eV Energy per atom: Epot =1976.761eV Ekin = 787.342eV (T=1522.788K) Etot = 2764.103eV Energy per atom: Epot =1992.619eV Ekin = 766.003eV (T=1481.517K) Etot = 2758.622eV Energy per atom: Epot =1987.990eV Ekin = 777.256eV (T=1503.281K) Etot = 2765.246eV Energy per atom: Epot =1972.394eV Ekin = 778.827eV (T=1506.320K) Etot = 2751.222eV Energy per atom: Epot =1976.587eV Ekin = 772.794eV (T=1494.650K) Etot = 2749.381eV Energy per atom: Epot =1973.462eV Ekin = 777.778eV (T=1504.291K) Etot = 2751.240eV Energy per atom: Epot =1977.540eV Ekin = 762.983eV (T=1475.676K) Etot = 2740.523eV Energy per atom: Epot =1978.698eV Ekin = 763.005eV (T=1475.718K) Etot = 2741.703eV Energy per atom: Epot =1987.225eV Ekin = 761.650eV (T=1473.097K) Etot = 2748.875eV Energy per atom: Epot =1985.961eV Ekin = 766.922eV (T=1483.293K) Etot = 2752.882eV Energy per atom: Epot =1968.490eV Ekin = 772.490eV (T=1494.062K) Etot = 2740.980eV Energy per atom: Epot =1970.733eV Ekin = 776.885eV (T=1502.564K) Etot = 2747.618eV Energy per atom: Epot =1987.989eV Ekin = 760.276eV (T=1470.440K) Etot = 2748.265eV Energy per atom: Epot =1975.596eV Ekin = 772.746eV (T=1494.558K) Etot = 2748.342eV Energy per atom: Epot =1975.297eV Ekin = 777.853eV (T=1504.436K) Etot = 2753.150eV Energy per atom: Epot =1988.022eV Ekin = 765.132eV (T=1479.833K) Etot = 2753.155eV Energy per atom: Epot =1990.993eV Ekin = 775.121eV (T=1499.152K) Etot = 2766.114eV Energy per atom: Epot =1980.966eV Ekin = 779.861eV (T=1508.319K) Etot = 2760.827eV Energy per atom: Epot =1982.746eV Ekin = 772.577eV (T=1494.231K) Etot = 2755.323eV Energy per atom: Epot =1989.417eV Ekin = 769.647eV (T=1488.565K) Etot = 2759.064eV Energy per atom: Epot =1991.006eV Ekin = 772.112eV (T=1493.332K) Etot = 2763.118eV Energy per atom: Epot =1993.232eV Ekin = 774.291eV (T=1497.546K) Etot = 2767.523eV Energy per atom: Epot =1989.250eV Ekin = 776.924eV (T=1502.639K) Etot = 2766.174eV Energy per atom: Epot =1981.952eV Ekin = 787.783eV (T=1523.641K) Etot = 2769.735eV Energy per atom: Epot =1986.845eV Ekin = 770.710eV (T=1490.619K) Etot = 2757.555eV Energy per atom: Epot =1980.789eV Ekin = 781.617eV (T=1511.715K) Etot = 2762.406eV Energy per atom: Epot =1992.867eV Ekin = 771.188eV (T=1491.544K) Etot = 2764.054eV Energy per atom: Epot =1999.025eV Ekin = 773.239eV (T=1495.511K) Etot = 2772.264eV .. 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] 21:08:06 43.457006 1.0818 BFGSLineSearch: 1[ 1] 21:08:06 42.347659 0.2273 BFGSLineSearch: 2[ 2] 21:08:06 42.108454 0.1349 BFGSLineSearch: 3[ 3] 21:08:06 41.964817 0.1138 BFGSLineSearch: 4[ 4] 21:08:06 41.924933 0.0683 BFGSLineSearch: 5[ 5] 21:08:06 41.915346 0.0225 BFGSLineSearch: 6[ 6] 21:08:06 41.914920 0.0059 BFGSLineSearch: 7[ 7] 21:08:06 41.914872 0.0023 BFGSLineSearch: 8[ 9] 21:08:06 41.914855 0.0023 BFGSLineSearch: 9[ 10] 21:08:06 41.914851 0.0010 running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 14.430eV (T=1200.376K) Etot = 56.345eV Energy per atom: Epot =49.879eV Ekin = 6.500eV (T=540.711K) Etot = 56.379eV Energy per atom: Epot =50.084eV Ekin = 6.305eV (T=524.510K) Etot = 56.389eV Energy per atom: Epot =50.885eV Ekin = 5.514eV (T=458.680K) Etot = 56.399eV Energy per atom: Epot =50.075eV Ekin = 6.315eV (T=525.336K) Etot = 56.391eV Energy per atom: Epot =49.201eV Ekin = 7.180eV (T=597.259K) Etot = 56.381eV Energy per atom: Epot =49.141eV Ekin = 7.240eV (T=602.295K) Etot = 56.382eV Energy per atom: Epot =50.116eV Ekin = 6.277eV (T=522.184K) Etot = 56.394eV Energy per atom: Epot =49.438eV Ekin = 6.955eV (T=578.522K) Etot = 56.392eV Energy per atom: Epot =49.508eV Ekin = 6.880eV (T=572.327K) Etot = 56.388eV Energy per atom: Epot =50.298eV Ekin = 6.092eV (T=506.768K) Etot = 56.390eV Energy per atom: Epot =50.873eV Ekin = 5.524eV (T=459.520K) Etot = 56.397eV Energy per atom: Epot =49.184eV Ekin = 7.206eV (T=599.474K) Etot = 56.390eV Energy per atom: Epot =49.783eV Ekin = 6.611eV (T=549.913K) Etot = 56.394eV Energy per atom: Epot =49.288eV Ekin = 7.103eV (T=590.845K) Etot = 56.390eV Energy per atom: Epot =48.839eV Ekin = 7.548eV (T=627.892K) Etot = 56.387eV Energy per atom: Epot =50.185eV Ekin = 6.208eV (T=516.391K) Etot = 56.393eV Energy per atom: Epot =50.027eV Ekin = 6.365eV (T=529.488K) Etot = 56.392eV Energy per atom: Epot =49.532eV Ekin = 6.854eV (T=570.148K) Etot = 56.386eV Energy per atom: Epot =49.506eV Ekin = 6.881eV (T=572.382K) Etot = 56.387eV Energy per atom: Epot =49.084eV Ekin = 7.301eV (T=607.383K) Etot = 56.386eV Energy per atom: Epot =48.932eV Ekin = 7.452eV (T=619.895K) Etot = 56.384eV Energy per atom: Epot =49.488eV Ekin = 6.900eV (T=573.993K) Etot = 56.388eV Energy per atom: Epot =49.501eV Ekin = 6.887eV (T=572.913K) Etot = 56.388eV Energy per atom: Epot =50.253eV Ekin = 6.142eV (T=510.925K) Etot = 56.395eV Energy per atom: Epot =49.553eV Ekin = 6.836eV (T=568.699K) Etot = 56.389eV Energy per atom: Epot =50.610eV Ekin = 5.785eV (T=481.255K) Etot = 56.396eV Energy per atom: Epot =49.863eV Ekin = 6.528eV (T=543.050K) Etot = 56.391eV Energy per atom: Epot =49.820eV Ekin = 6.568eV (T=546.377K) Etot = 56.389eV Energy per atom: Epot =49.801eV Ekin = 6.587eV (T=547.938K) Etot = 56.388eV Energy per atom: Epot =50.228eV Ekin = 6.163eV (T=512.662K) Etot = 56.391eV Energy per atom: Epot =49.284eV Ekin = 7.105eV (T=591.033K) Etot = 56.389eV Energy per atom: Epot =49.901eV Ekin = 6.486eV (T=539.577K) Etot = 56.387eV Energy per atom: Epot =49.962eV Ekin = 6.425eV (T=534.509K) Etot = 56.388eV Energy per atom: Epot =50.448eV Ekin = 5.941eV (T=494.232K) Etot = 56.390eV Energy per atom: Epot =49.370eV Ekin = 7.012eV (T=583.308K) Etot = 56.382eV Energy per atom: Epot =49.922eV Ekin = 6.467eV (T=537.998K) Etot = 56.389eV Energy per atom: Epot =50.389eV Ekin = 6.003eV (T=499.409K) Etot = 56.392eV Energy per atom: Epot =49.380eV Ekin = 7.006eV (T=582.844K) Etot = 56.387eV Energy per atom: Epot =49.471eV Ekin = 6.915eV (T=575.222K) Etot = 56.386eV Energy per atom: Epot =49.251eV Ekin = 7.132eV (T=593.323K) Etot = 56.383eV Energy per atom: Epot =50.069eV Ekin = 6.321eV (T=525.840K) Etot = 56.390eV Energy per atom: Epot =49.810eV Ekin = 6.579eV (T=547.304K) Etot = 56.389eV Energy per atom: Epot =49.908eV Ekin = 6.479eV (T=538.970K) Etot = 56.387eV Energy per atom: Epot =49.749eV Ekin = 6.637eV (T=552.074K) Etot = 56.386eV Energy per atom: Epot =50.057eV Ekin = 6.336eV (T=527.036K) Etot = 56.393eV Energy per atom: Epot =50.324eV Ekin = 6.070eV (T=504.936K) Etot = 56.393eV Energy per atom: Epot =49.599eV Ekin = 6.789eV (T=564.718K) Etot = 56.387eV Energy per atom: Epot =49.489eV Ekin = 6.893eV (T=573.430K) Etot = 56.382eV Energy per atom: Epot =49.858eV Ekin = 6.525eV (T=542.833K) Etot = 56.384eV Energy per atom: Epot =49.177eV Ekin = 7.208eV (T=599.579K) Etot = 56.384eV Energy per atom: Epot =49.714eV Ekin = 6.673eV (T=555.076K) Etot = 56.387eV Energy per atom: Epot =49.722eV Ekin = 6.667eV (T=554.597K) Etot = 56.389eV Energy per atom: Epot =49.563eV Ekin = 6.822eV (T=567.516K) Etot = 56.385eV Energy per atom: Epot =49.929eV Ekin = 6.461eV (T=537.504K) Etot = 56.391eV Energy per atom: Epot =49.377eV Ekin = 7.012eV (T=583.292K) Etot = 56.389eV Energy per atom: Epot =49.190eV Ekin = 7.196eV (T=598.644K) Etot = 56.386eV Energy per atom: Epot =50.371eV Ekin = 6.022eV (T=500.919K) Etot = 56.393eV Energy per atom: Epot =49.178eV Ekin = 7.210eV (T=599.757K) Etot = 56.388eV Energy per atom: Epot =49.523eV Ekin = 6.862eV (T=570.808K) Etot = 56.385eV Energy per atom: Epot =50.548eV Ekin = 5.843eV (T=486.089K) Etot = 56.391eV Energy per atom: Epot =50.444eV Ekin = 5.951eV (T=495.016K) Etot = 56.394eV Energy per atom: Epot =49.361eV Ekin = 7.029eV (T=584.678K) Etot = 56.390eV Energy per atom: Epot =49.813eV Ekin = 6.575eV (T=546.943K) Etot = 56.388eV Energy per atom: Epot =49.785eV Ekin = 6.599eV (T=548.920K) Etot = 56.384eV Energy per atom: Epot =50.171eV Ekin = 6.215eV (T=517.046K) Etot = 56.386eV Energy per atom: Epot =49.934eV Ekin = 6.454eV (T=536.916K) Etot = 56.389eV Energy per atom: Epot =49.179eV Ekin = 7.207eV (T=599.488K) Etot = 56.385eV Energy per atom: Epot =49.658eV Ekin = 6.730eV (T=559.847K) Etot = 56.388eV Energy per atom: Epot =49.337eV Ekin = 7.054eV (T=586.767K) Etot = 56.390eV Energy per atom: Epot =50.185eV Ekin = 6.209eV (T=516.524K) Etot = 56.394eV Energy per atom: Epot =48.509eV Ekin = 7.876eV (T=655.180K) Etot = 56.385eV Energy per atom: Epot =49.484eV Ekin = 6.904eV (T=574.321K) Etot = 56.388eV Energy per atom: Epot =49.650eV Ekin = 6.738eV (T=560.522K) Etot = 56.388eV Energy per atom: Epot =49.735eV Ekin = 6.653eV (T=553.399K) Etot = 56.387eV Energy per atom: Epot =50.034eV Ekin = 6.355eV (T=528.667K) Etot = 56.389eV Energy per atom: Epot =49.137eV Ekin = 7.246eV (T=602.761K) Etot = 56.383eV Energy per atom: Epot =49.907eV Ekin = 6.484eV (T=539.421K) Etot = 56.392eV Energy per atom: Epot =48.938eV Ekin = 7.450eV (T=619.739K) Etot = 56.388eV Energy per atom: Epot =50.001eV Ekin = 6.385eV (T=531.178K) Etot = 56.387eV Energy per atom: Epot =49.925eV Ekin = 6.460eV (T=537.368K) Etot = 56.385eV Energy per atom: Epot =50.227eV Ekin = 6.162eV (T=512.597K) Etot = 56.389eV Energy per atom: Epot =49.244eV Ekin = 7.144eV (T=594.287K) Etot = 56.388eV Energy per atom: Epot =49.255eV Ekin = 7.130eV (T=593.143K) Etot = 56.386eV Energy per atom: Epot =50.209eV Ekin = 6.182eV (T=514.236K) Etot = 56.391eV Energy per atom: Epot =49.806eV Ekin = 6.583eV (T=547.638K) Etot = 56.389eV Energy per atom: Epot =49.515eV Ekin = 6.869eV (T=571.435K) Etot = 56.385eV Energy per atom: Epot =50.000eV Ekin = 6.387eV (T=531.348K) Etot = 56.388eV Energy per atom: Epot =49.812eV Ekin = 6.576eV (T=547.038K) Etot = 56.388eV Energy per atom: Epot =49.716eV Ekin = 6.672eV (T=555.040K) Etot = 56.389eV Energy per atom: Epot =49.537eV Ekin = 6.852eV (T=569.962K) Etot = 56.388eV Energy per atom: Epot =48.994eV Ekin = 7.394eV (T=615.123K) Etot = 56.389eV Energy per atom: Epot =49.507eV Ekin = 6.881eV (T=572.442K) Etot = 56.388eV Energy per atom: Epot =49.362eV Ekin = 7.023eV (T=584.198K) Etot = 56.384eV Energy per atom: Epot =49.217eV Ekin = 7.168eV (T=596.297K) Etot = 56.385eV Energy per atom: Epot =48.690eV Ekin = 7.695eV (T=640.106K) Etot = 56.385eV Energy per atom: Epot =49.118eV Ekin = 7.265eV (T=604.367K) Etot = 56.383eV Energy per atom: Epot =49.575eV Ekin = 6.810eV (T=566.489K) Etot = 56.385eV Energy per atom: Epot =49.158eV Ekin = 7.221eV (T=600.721K) Etot = 56.380eV Energy per atom: Epot =49.288eV Ekin = 7.096eV (T=590.296K) Etot = 56.384eV Energy per atom: Epot =49.487eV Ekin = 6.901eV (T=574.067K) Etot = 56.388eV Energy per atom: Epot =49.679eV Ekin = 6.712eV (T=558.319K) Etot = 56.390eV Energy per atom: Epot =50.020eV Ekin = 6.368eV (T=529.742K) Etot = 56.388eV Energy per atom: Epot =50.402eV Ekin = 5.989eV (T=498.166K) Etot = 56.390eV Energy per atom: Epot =49.380eV Ekin = 7.006eV (T=582.814K) Etot = 56.387eV Energy per atom: Epot =49.606eV Ekin = 6.781eV (T=564.121K) Etot = 56.388eV Energy per atom: Epot =49.664eV Ekin = 6.727eV (T=559.588K) Etot = 56.391eV Energy per atom: Epot =49.827eV Ekin = 6.564eV (T=546.009K) Etot = 56.391eV Energy per atom: Epot =48.883eV Ekin = 7.501eV (T=623.990K) Etot = 56.384eV Energy per atom: Epot =49.593eV Ekin = 6.797eV (T=565.411K) Etot = 56.390eV Energy per atom: Epot =49.606eV Ekin = 6.785eV (T=564.453K) Etot = 56.391eV Energy per atom: Epot =49.731eV Ekin = 6.660eV (T=554.046K) Etot = 56.391eV Energy per atom: Epot =48.705eV Ekin = 7.681eV (T=638.972K) Etot = 56.386eV Energy per atom: Epot =49.624eV Ekin = 6.764eV (T=562.656K) Etot = 56.388eV Energy per atom: Epot =49.265eV Ekin = 7.123eV (T=592.561K) Etot = 56.388eV Energy per atom: Epot =49.797eV Ekin = 6.592eV (T=548.372K) Etot = 56.389eV Energy per atom: Epot =49.341eV Ekin = 7.040eV (T=585.618K) Etot = 56.381eV Energy per atom: Epot =49.150eV Ekin = 7.232eV (T=601.606K) Etot = 56.382eV Energy per atom: Epot =50.342eV Ekin = 6.051eV (T=503.335K) Etot = 56.392eV Energy per atom: Epot =49.082eV Ekin = 7.305eV (T=607.644K) Etot = 56.387eV Energy per atom: Epot =49.726eV Ekin = 6.665eV (T=554.402K) Etot = 56.391eV Energy per atom: Epot =49.777eV Ekin = 6.619eV (T=550.596K) Etot = 56.396eV Energy per atom: Epot =49.444eV Ekin = 6.946eV (T=577.829K) Etot = 56.390eV Energy per atom: Epot =49.706eV Ekin = 6.684eV (T=556.027K) Etot = 56.390eV Energy per atom: Epot =49.925eV Ekin = 6.467eV (T=538.007K) Etot = 56.393eV Energy per atom: Epot =49.779eV Ekin = 6.609eV (T=549.763K) Etot = 56.388eV Energy per atom: Epot =48.793eV Ekin = 7.588eV (T=631.242K) Etot = 56.381eV Energy per atom: Epot =49.263eV Ekin = 7.122eV (T=592.436K) Etot = 56.385eV Energy per atom: Epot =50.079eV Ekin = 6.307eV (T=524.664K) Etot = 56.386eV Energy per atom: Epot =48.925eV Ekin = 7.457eV (T=620.321K) Etot = 56.382eV Energy per atom: Epot =50.220eV Ekin = 6.169eV (T=513.215K) Etot = 56.390eV Energy per atom: Epot =49.482eV Ekin = 6.906eV (T=574.520K) Etot = 56.388eV Energy per atom: Epot =49.346eV Ekin = 7.042eV (T=585.800K) Etot = 56.388eV Energy per atom: Epot =49.572eV Ekin = 6.817eV (T=567.046K) Etot = 56.388eV Energy per atom: Epot =49.164eV Ekin = 7.220eV (T=600.604K) Etot = 56.384eV Energy per atom: Epot =49.271eV Ekin = 7.117eV (T=592.059K) Etot = 56.389eV Energy per atom: Epot =49.605eV Ekin = 6.782eV (T=564.183K) Etot = 56.388eV Energy per atom: Epot =49.433eV Ekin = 6.955eV (T=578.599K) Etot = 56.389eV Energy per atom: Epot =49.723eV Ekin = 6.668eV (T=554.672K) Etot = 56.391eV Energy per atom: Epot =49.313eV Ekin = 7.072eV (T=588.295K) Etot = 56.385eV Energy per atom: Epot =48.857eV Ekin = 7.525eV (T=625.960K) Etot = 56.382eV Energy per atom: Epot =50.042eV Ekin = 6.349eV (T=528.150K) Etot = 56.391eV Energy per atom: Epot =49.888eV Ekin = 6.502eV (T=540.910K) Etot = 56.390eV Energy per atom: Epot =48.559eV Ekin = 7.822eV (T=650.717K) Etot = 56.381eV Energy per atom: Epot =50.097eV Ekin = 6.290eV (T=523.225K) Etot = 56.387eV Energy per atom: Epot =50.085eV Ekin = 6.299eV (T=523.952K) Etot = 56.383eV Energy per atom: Epot =49.646eV Ekin = 6.745eV (T=561.106K) Etot = 56.391eV Energy per atom: Epot =49.183eV Ekin = 7.205eV (T=599.396K) Etot = 56.388eV Energy per atom: Epot =49.560eV Ekin = 6.833eV (T=568.445K) Etot = 56.393eV Energy per atom: Epot =49.050eV Ekin = 7.337eV (T=610.317K) Etot = 56.386eV Energy per atom: Epot =49.470eV Ekin = 6.916eV (T=575.301K) Etot = 56.385eV Energy per atom: Epot =49.412eV Ekin = 6.974eV (T=580.147K) Etot = 56.386eV Energy per atom: Epot =49.838eV Ekin = 6.550eV (T=544.912K) Etot = 56.389eV Energy per atom: Epot =49.401eV Ekin = 6.984eV (T=581.009K) Etot = 56.385eV Energy per atom: Epot =49.730eV Ekin = 6.661eV (T=554.119K) Etot = 56.391eV Energy per atom: Epot =49.604eV Ekin = 6.788eV (T=564.696K) Etot = 56.392eV Energy per atom: Epot =49.735eV Ekin = 6.654eV (T=553.558K) Etot = 56.389eV Energy per atom: Epot =49.627eV Ekin = 6.761eV (T=562.432K) Etot = 56.388eV Energy per atom: Epot =49.266eV Ekin = 7.122eV (T=592.449K) Etot = 56.388eV Energy per atom: Epot =49.703eV Ekin = 6.687eV (T=556.236K) Etot = 56.390eV Energy per atom: Epot =49.612eV Ekin = 6.776eV (T=563.661K) Etot = 56.388eV Energy per atom: Epot =49.569eV Ekin = 6.819eV (T=567.251K) Etot = 56.388eV Energy per atom: Epot =49.792eV Ekin = 6.597eV (T=548.766K) Etot = 56.389eV Energy per atom: Epot =49.945eV Ekin = 6.443eV (T=535.968K) Etot = 56.388eV Energy per atom: Epot =48.930eV Ekin = 7.457eV (T=620.288K) Etot = 56.387eV Energy per atom: Epot =50.710eV Ekin = 5.687eV (T=473.053K) Etot = 56.397eV Energy per atom: Epot =49.879eV Ekin = 6.512eV (T=541.732K) Etot = 56.391eV Energy per atom: Epot =49.542eV Ekin = 6.844eV (T=569.320K) Etot = 56.385eV Energy per atom: Epot =48.597eV Ekin = 7.782eV (T=647.392K) Etot = 56.379eV Energy per atom: Epot =49.282eV Ekin = 7.102eV (T=590.774K) Etot = 56.384eV Energy per atom: Epot =49.807eV Ekin = 6.581eV (T=547.460K) Etot = 56.388eV Energy per atom: Epot =49.001eV Ekin = 7.384eV (T=614.209K) Etot = 56.385eV Energy per atom: Epot =49.703eV Ekin = 6.692eV (T=556.673K) Etot = 56.394eV Energy per atom: Epot =49.008eV Ekin = 7.383eV (T=614.137K) Etot = 56.390eV Energy per atom: Epot =49.305eV Ekin = 7.081eV (T=589.074K) Etot = 56.386eV Energy per atom: Epot =48.804eV Ekin = 7.577eV (T=630.263K) Etot = 56.380eV Energy per atom: Epot =48.731eV Ekin = 7.651eV (T=636.495K) Etot = 56.383eV Energy per atom: Epot =48.844eV Ekin = 7.539eV (T=627.184K) Etot = 56.384eV Energy per atom: Epot =49.951eV Ekin = 6.439eV (T=535.625K) Etot = 56.390eV Energy per atom: Epot =49.683eV Ekin = 6.706eV (T=557.820K) Etot = 56.389eV Energy per atom: Epot =49.817eV Ekin = 6.570eV (T=546.531K) Etot = 56.387eV Energy per atom: Epot =49.507eV Ekin = 6.880eV (T=572.314K) Etot = 56.387eV Energy per atom: Epot =49.719eV Ekin = 6.676eV (T=555.321K) Etot = 56.394eV Energy per atom: Epot =48.988eV Ekin = 7.400eV (T=615.546K) Etot = 56.388eV Energy per atom: Epot =49.495eV Ekin = 6.893eV (T=573.389K) Etot = 56.388eV Energy per atom: Epot =48.875eV Ekin = 7.511eV (T=624.844K) Etot = 56.387eV Energy per atom: Epot =49.297eV Ekin = 7.092eV (T=589.965K) Etot = 56.389eV Energy per atom: Epot =50.002eV Ekin = 6.391eV (T=531.686K) Etot = 56.393eV Energy per atom: Epot =50.161eV Ekin = 6.236eV (T=518.740K) Etot = 56.397eV Energy per atom: Epot =49.350eV Ekin = 7.040eV (T=585.636K) Etot = 56.390eV Energy per atom: Epot =49.211eV Ekin = 7.180eV (T=597.260K) Etot = 56.391eV Energy per atom: Epot =48.847eV Ekin = 7.536eV (T=626.898K) Etot = 56.383eV Energy per atom: Epot =49.068eV Ekin = 7.313eV (T=608.338K) Etot = 56.381eV Energy per atom: Epot =48.984eV Ekin = 7.401eV (T=615.667K) Etot = 56.385eV Energy per atom: Epot =49.315eV Ekin = 7.071eV (T=588.216K) Etot = 56.386eV Energy per atom: Epot =49.851eV Ekin = 6.540eV (T=544.041K) Etot = 56.391eV Energy per atom: Epot =49.945eV Ekin = 6.447eV (T=536.266K) Etot = 56.391eV Energy per atom: Epot =49.032eV Ekin = 7.354eV (T=611.791K) Etot = 56.386eV Energy per atom: Epot =48.955eV Ekin = 7.433eV (T=618.360K) Etot = 56.389eV Energy per atom: Epot =49.340eV Ekin = 7.048eV (T=586.313K) Etot = 56.388eV Energy per atom: Epot =48.975eV Ekin = 7.407eV (T=616.173K) Etot = 56.382eV .. 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 `_