.. 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 = 151.071eV (T=292.185K) Etot = 148.667eV Energy per atom: Epot =114.117eV Ekin = 35.320eV (T=68.311K) Etot = 149.436eV Energy per atom: Epot =76.330eV Ekin = 72.974eV (T=141.138K) Etot = 149.303eV Energy per atom: Epot =68.960eV Ekin = 80.194eV (T=155.103K) Etot = 149.155eV Energy per atom: Epot =66.968eV Ekin = 82.135eV (T=158.856K) Etot = 149.103eV Energy per atom: Epot =78.841eV Ekin = 70.425eV (T=136.208K) Etot = 149.266eV Energy per atom: Epot =75.194eV Ekin = 74.054eV (T=143.227K) Etot = 149.249eV Energy per atom: Epot =72.195eV Ekin = 76.976eV (T=148.877K) Etot = 149.170eV Energy per atom: Epot =69.579eV Ekin = 79.587eV (T=153.928K) Etot = 149.166eV Energy per atom: Epot =77.377eV Ekin = 71.871eV (T=139.004K) Etot = 149.248eV Energy per atom: Epot =73.158eV Ekin = 76.043eV (T=147.074K) Etot = 149.201eV Energy per atom: Epot =71.991eV Ekin = 77.198eV (T=149.307K) Etot = 149.189eV Energy per atom: Epot =73.998eV Ekin = 75.215eV (T=145.471K) Etot = 149.212eV Energy per atom: Epot =74.930eV Ekin = 74.277eV (T=143.659K) Etot = 149.207eV Energy per atom: Epot =71.314eV Ekin = 77.875eV (T=150.617K) Etot = 149.189eV Energy per atom: Epot =74.402eV Ekin = 74.825eV (T=144.718K) Etot = 149.227eV Energy per atom: Epot =72.765eV Ekin = 76.434eV (T=147.831K) Etot = 149.199eV Energy per atom: Epot =75.121eV Ekin = 74.081eV (T=143.278K) Etot = 149.201eV Energy per atom: Epot =71.170eV Ekin = 78.027eV (T=150.911K) Etot = 149.197eV Energy per atom: Epot =74.493eV Ekin = 74.713eV (T=144.501K) Etot = 149.206eV Energy per atom: Epot =75.817eV Ekin = 73.397eV (T=141.956K) Etot = 149.214eV .. 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 =600.074eV Ekin = 82.644eV (T=159.840K) Etot = 682.718eV Energy per atom: Epot =673.134eV Ekin = 141.347eV (T=273.378K) Etot = 814.481eV Energy per atom: Epot =728.396eV Ekin = 201.057eV (T=388.861K) Etot = 929.453eV Energy per atom: Epot =787.047eV Ekin = 254.356eV (T=491.948K) Etot = 1041.404eV Energy per atom: Epot =836.533eV Ekin = 300.302eV (T=580.810K) Etot = 1136.835eV Energy per atom: Epot =879.926eV Ekin = 344.682eV (T=666.645K) Etot = 1224.607eV Energy per atom: Epot =920.931eV Ekin = 387.207eV (T=748.892K) Etot = 1308.138eV Energy per atom: Epot =964.997eV Ekin = 417.764eV (T=807.991K) Etot = 1382.761eV Energy per atom: Epot =1002.694eV Ekin = 443.727eV (T=858.206K) Etot = 1446.421eV Energy per atom: Epot =1041.790eV Ekin = 465.064eV (T=899.474K) Etot = 1506.854eV Energy per atom: Epot =1075.058eV Ekin = 490.570eV (T=948.806K) Etot = 1565.629eV Energy per atom: Epot =1103.164eV Ekin = 509.693eV (T=985.790K) Etot = 1612.857eV Energy per atom: Epot =1137.221eV Ekin = 522.503eV (T=1010.566K) Etot = 1659.724eV Energy per atom: Epot =1173.570eV Ekin = 529.448eV (T=1023.998K) Etot = 1703.018eV Energy per atom: Epot =1195.176eV Ekin = 554.115eV (T=1071.707K) Etot = 1749.291eV Energy per atom: Epot =1222.456eV Ekin = 560.668eV (T=1084.380K) Etot = 1783.124eV Energy per atom: Epot =1250.048eV Ekin = 575.409eV (T=1112.890K) Etot = 1825.456eV Energy per atom: Epot =1279.918eV Ekin = 590.243eV (T=1141.581K) Etot = 1870.161eV Energy per atom: Epot =1307.590eV Ekin = 596.985eV (T=1154.621K) Etot = 1904.575eV Energy per atom: Epot =1322.414eV Ekin = 616.789eV (T=1192.924K) Etot = 1939.203eV Energy per atom: Epot =1354.598eV Ekin = 613.064eV (T=1185.719K) Etot = 1967.662eV Energy per atom: Epot =1361.185eV Ekin = 640.965eV (T=1239.681K) Etot = 2002.150eV Energy per atom: Epot =1387.825eV Ekin = 643.665eV (T=1244.905K) Etot = 2031.490eV Energy per atom: Epot =1401.606eV Ekin = 654.726eV (T=1266.297K) Etot = 2056.332eV Energy per atom: Epot =1408.031eV Ekin = 663.287eV (T=1282.854K) Etot = 2071.318eV Energy per atom: Epot =1422.299eV Ekin = 665.836eV (T=1287.784K) Etot = 2088.135eV Energy per atom: Epot =1437.362eV Ekin = 677.106eV (T=1309.582K) Etot = 2114.468eV Energy per atom: Epot =1456.278eV Ekin = 670.798eV (T=1297.382K) Etot = 2127.076eV Energy per atom: Epot =1472.299eV Ekin = 679.869eV (T=1314.925K) Etot = 2152.168eV Energy per atom: Epot =1475.564eV Ekin = 689.009eV (T=1332.603K) Etot = 2164.573eV Energy per atom: Epot =1508.564eV Ekin = 679.957eV (T=1315.097K) Etot = 2188.521eV Energy per atom: Epot =1525.795eV Ekin = 679.153eV (T=1313.541K) Etot = 2204.949eV Energy per atom: Epot =1519.694eV Ekin = 705.567eV (T=1364.628K) Etot = 2225.261eV Energy per atom: Epot =1540.428eV Ekin = 698.182eV (T=1350.345K) Etot = 2238.610eV Energy per atom: Epot =1569.192eV Ekin = 684.637eV (T=1324.147K) Etot = 2253.829eV Energy per atom: Epot =1557.437eV Ekin = 715.361eV (T=1383.570K) Etot = 2272.797eV Energy per atom: Epot =1577.751eV Ekin = 713.137eV (T=1379.270K) Etot = 2290.888eV Energy per atom: Epot =1591.610eV Ekin = 703.184eV (T=1360.019K) Etot = 2294.794eV Energy per atom: Epot =1615.591eV Ekin = 695.289eV (T=1344.749K) Etot = 2310.880eV Energy per atom: Epot =1607.190eV Ekin = 714.247eV (T=1381.416K) Etot = 2321.437eV Energy per atom: Epot =1626.090eV Ekin = 715.537eV (T=1383.911K) Etot = 2341.627eV Energy per atom: Epot =1638.621eV Ekin = 707.588eV (T=1368.537K) Etot = 2346.209eV Energy per atom: Epot =1650.203eV Ekin = 709.008eV (T=1371.283K) Etot = 2359.211eV Energy per atom: Epot =1672.073eV Ekin = 705.967eV (T=1365.402K) Etot = 2378.040eV Energy per atom: Epot =1662.714eV Ekin = 730.239eV (T=1412.346K) Etot = 2392.953eV Energy per atom: Epot =1684.303eV Ekin = 714.929eV (T=1382.734K) Etot = 2399.232eV Energy per atom: Epot =1689.989eV Ekin = 724.603eV (T=1401.446K) Etot = 2414.592eV Energy per atom: Epot =1701.944eV Ekin = 718.447eV (T=1389.538K) Etot = 2420.390eV Energy per atom: Epot =1706.958eV Ekin = 729.585eV (T=1411.082K) Etot = 2436.543eV Energy per atom: Epot =1717.680eV Ekin = 728.611eV (T=1409.197K) Etot = 2446.291eV Energy per atom: Epot =1711.537eV Ekin = 742.015eV (T=1435.122K) Etot = 2453.552eV Energy per atom: Epot =1723.277eV Ekin = 743.054eV (T=1437.131K) Etot = 2466.331eV Energy per atom: Epot =1723.290eV Ekin = 747.090eV (T=1444.937K) Etot = 2470.380eV Energy per atom: Epot =1731.542eV Ekin = 740.717eV (T=1432.611K) Etot = 2472.259eV Energy per atom: Epot =1724.299eV Ekin = 750.080eV (T=1450.720K) Etot = 2474.379eV Energy per atom: Epot =1745.551eV Ekin = 740.874eV (T=1432.915K) Etot = 2486.425eV Energy per atom: Epot =1751.335eV Ekin = 740.024eV (T=1431.272K) Etot = 2491.359eV Energy per atom: Epot =1753.673eV Ekin = 742.359eV (T=1435.787K) Etot = 2496.032eV Energy per atom: Epot =1756.341eV Ekin = 743.574eV (T=1438.137K) Etot = 2499.915eV Energy per atom: Epot =1761.462eV Ekin = 738.356eV (T=1428.046K) Etot = 2499.818eV Energy per atom: Epot =1772.328eV Ekin = 741.133eV (T=1433.416K) Etot = 2513.461eV Energy per atom: Epot =1783.717eV Ekin = 733.343eV (T=1418.348K) Etot = 2517.060eV Energy per atom: Epot =1785.782eV Ekin = 743.130eV (T=1437.278K) Etot = 2528.912eV Energy per atom: Epot =1788.074eV Ekin = 739.698eV (T=1430.640K) Etot = 2527.772eV Energy per atom: Epot =1784.424eV Ekin = 747.003eV (T=1444.768K) Etot = 2531.427eV Energy per atom: Epot =1803.714eV Ekin = 733.874eV (T=1419.375K) Etot = 2537.587eV Energy per atom: Epot =1794.819eV Ekin = 741.155eV (T=1433.457K) Etot = 2535.974eV Energy per atom: Epot =1819.498eV Ekin = 729.059eV (T=1410.064K) Etot = 2548.558eV Energy per atom: Epot =1824.303eV Ekin = 736.475eV (T=1424.407K) Etot = 2560.778eV Energy per atom: Epot =1807.602eV Ekin = 750.135eV (T=1450.826K) Etot = 2557.737eV Energy per atom: Epot =1824.726eV Ekin = 732.117eV (T=1415.977K) Etot = 2556.843eV Energy per atom: Epot =1826.764eV Ekin = 733.609eV (T=1418.864K) Etot = 2560.373eV Energy per atom: Epot =1834.806eV Ekin = 731.635eV (T=1415.045K) Etot = 2566.440eV Energy per atom: Epot =1836.772eV Ekin = 733.049eV (T=1417.781K) Etot = 2569.821eV Energy per atom: Epot =1853.708eV Ekin = 729.067eV (T=1410.079K) Etot = 2582.775eV Energy per atom: Epot =1850.127eV Ekin = 741.090eV (T=1433.332K) Etot = 2591.217eV Energy per atom: Epot =1837.341eV Ekin = 752.310eV (T=1455.034K) Etot = 2589.652eV Energy per atom: Epot =1853.806eV Ekin = 739.404eV (T=1430.071K) Etot = 2593.210eV Energy per atom: Epot =1854.685eV Ekin = 747.978eV (T=1446.655K) Etot = 2602.664eV Energy per atom: Epot =1868.747eV Ekin = 737.128eV (T=1425.669K) Etot = 2605.874eV Energy per atom: Epot =1867.889eV Ekin = 744.992eV (T=1440.880K) Etot = 2612.881eV Energy per atom: Epot =1891.375eV Ekin = 737.165eV (T=1425.742K) Etot = 2628.540eV Energy per atom: Epot =1866.497eV Ekin = 756.837eV (T=1463.789K) Etot = 2623.334eV Energy per atom: Epot =1876.175eV Ekin = 746.347eV (T=1443.500K) Etot = 2622.522eV Energy per atom: Epot =1869.058eV Ekin = 759.962eV (T=1469.833K) Etot = 2629.021eV Energy per atom: Epot =1898.763eV Ekin = 741.007eV (T=1433.172K) Etot = 2639.770eV Energy per atom: Epot =1892.841eV Ekin = 748.720eV (T=1448.089K) Etot = 2641.561eV Energy per atom: Epot =1885.871eV Ekin = 753.239eV (T=1456.831K) Etot = 2639.110eV Energy per atom: Epot =1890.387eV Ekin = 753.714eV (T=1457.748K) Etot = 2644.101eV Energy per atom: Epot =1891.860eV Ekin = 749.860eV (T=1450.295K) Etot = 2641.720eV Energy per atom: Epot =1890.807eV Ekin = 752.056eV (T=1454.542K) Etot = 2642.863eV Energy per atom: Epot =1889.443eV Ekin = 750.871eV (T=1452.250K) Etot = 2640.314eV Energy per atom: Epot =1900.777eV Ekin = 745.028eV (T=1440.950K) Etot = 2645.806eV Energy per atom: Epot =1901.143eV Ekin = 752.984eV (T=1456.336K) Etot = 2654.126eV Energy per atom: Epot =1905.822eV Ekin = 758.745eV (T=1467.480K) Etot = 2664.568eV Energy per atom: Epot =1905.238eV Ekin = 765.192eV (T=1479.948K) Etot = 2670.431eV Energy per atom: Epot =1929.709eV Ekin = 739.435eV (T=1430.132K) Etot = 2669.144eV Energy per atom: Epot =1929.249eV Ekin = 746.950eV (T=1444.667K) Etot = 2676.199eV Energy per atom: Epot =1920.411eV Ekin = 757.924eV (T=1465.892K) Etot = 2678.335eV Energy per atom: Epot =1924.644eV Ekin = 761.233eV (T=1472.291K) Etot = 2685.877eV Energy per atom: Epot =1944.023eV Ekin = 740.601eV (T=1432.386K) Etot = 2684.624eV Energy per atom: Epot =1926.609eV Ekin = 759.805eV (T=1469.530K) Etot = 2686.415eV Energy per atom: Epot =1937.707eV Ekin = 751.194eV (T=1452.875K) Etot = 2688.901eV Energy per atom: Epot =1940.155eV Ekin = 750.559eV (T=1451.647K) Etot = 2690.715eV Energy per atom: Epot =1949.439eV Ekin = 748.113eV (T=1446.916K) Etot = 2697.552eV Energy per atom: Epot =1941.939eV Ekin = 767.837eV (T=1485.064K) Etot = 2709.777eV Energy per atom: Epot =1941.558eV Ekin = 764.488eV (T=1478.585K) Etot = 2706.045eV Energy per atom: Epot =1938.859eV Ekin = 774.898eV (T=1498.720K) Etot = 2713.757eV Energy per atom: Epot =1935.820eV Ekin = 778.210eV (T=1505.126K) Etot = 2714.031eV Energy per atom: Epot =1948.713eV Ekin = 768.428eV (T=1486.207K) Etot = 2717.141eV Energy per atom: Epot =1947.037eV Ekin = 762.062eV (T=1473.895K) Etot = 2709.099eV Energy per atom: Epot =1948.276eV Ekin = 758.882eV (T=1467.744K) Etot = 2707.158eV Energy per atom: Epot =1958.613eV Ekin = 744.537eV (T=1439.999K) Etot = 2703.150eV Energy per atom: Epot =1945.208eV Ekin = 760.988eV (T=1471.817K) Etot = 2706.196eV Energy per atom: Epot =1934.906eV Ekin = 772.363eV (T=1493.817K) Etot = 2707.268eV Energy per atom: Epot =1938.558eV Ekin = 762.054eV (T=1473.879K) Etot = 2700.612eV Energy per atom: Epot =1943.131eV Ekin = 755.765eV (T=1461.716K) Etot = 2698.896eV Energy per atom: Epot =1956.409eV Ekin = 757.269eV (T=1464.624K) Etot = 2713.678eV Energy per atom: Epot =1958.139eV Ekin = 760.784eV (T=1471.423K) Etot = 2718.923eV Energy per atom: Epot =1969.779eV Ekin = 751.439eV (T=1453.349K) Etot = 2721.218eV Energy per atom: Epot =1970.215eV Ekin = 764.195eV (T=1478.020K) Etot = 2734.410eV Energy per atom: Epot =1975.155eV Ekin = 763.043eV (T=1475.791K) Etot = 2738.198eV Energy per atom: Epot =1977.427eV Ekin = 766.455eV (T=1482.391K) Etot = 2743.882eV Energy per atom: Epot =1980.862eV Ekin = 768.848eV (T=1487.019K) Etot = 2749.710eV Energy per atom: Epot =1996.398eV Ekin = 756.641eV (T=1463.409K) Etot = 2753.039eV Energy per atom: Epot =1993.925eV Ekin = 762.829eV (T=1475.377K) Etot = 2756.754eV Energy per atom: Epot =2005.620eV Ekin = 738.315eV (T=1427.966K) Etot = 2743.935eV Energy per atom: Epot =1994.619eV Ekin = 764.064eV (T=1477.766K) Etot = 2758.683eV Energy per atom: Epot =1999.681eV Ekin = 762.188eV (T=1474.137K) Etot = 2761.869eV Energy per atom: Epot =1990.685eV Ekin = 772.741eV (T=1494.548K) Etot = 2763.426eV Energy per atom: Epot =1999.153eV Ekin = 777.553eV (T=1503.855K) Etot = 2776.706eV Energy per atom: Epot =1999.595eV Ekin = 787.994eV (T=1524.049K) Etot = 2787.589eV Energy per atom: Epot =2012.171eV Ekin = 772.706eV (T=1494.480K) Etot = 2784.877eV Energy per atom: Epot =2004.573eV Ekin = 780.243eV (T=1509.058K) Etot = 2784.816eV Energy per atom: Epot =2004.910eV Ekin = 782.943eV (T=1514.279K) Etot = 2787.853eV Energy per atom: Epot =2003.901eV Ekin = 779.161eV (T=1506.966K) Etot = 2783.063eV Energy per atom: Epot =2010.830eV Ekin = 778.132eV (T=1504.974K) Etot = 2788.961eV Energy per atom: Epot =2015.202eV Ekin = 777.114eV (T=1503.006K) Etot = 2792.316eV Energy per atom: Epot =2012.123eV Ekin = 778.258eV (T=1505.218K) Etot = 2790.381eV Energy per atom: Epot =2003.500eV Ekin = 787.334eV (T=1522.773K) Etot = 2790.835eV Energy per atom: Epot =2011.271eV Ekin = 783.630eV (T=1515.609K) Etot = 2794.901eV Energy per atom: Epot =2019.159eV Ekin = 780.611eV (T=1509.770K) Etot = 2799.770eV Energy per atom: Epot =2025.065eV Ekin = 771.099eV (T=1491.372K) Etot = 2796.164eV Energy per atom: Epot =2018.414eV Ekin = 783.007eV (T=1514.404K) Etot = 2801.421eV Energy per atom: Epot =2021.094eV Ekin = 780.602eV (T=1509.751K) Etot = 2801.696eV Energy per atom: Epot =2028.059eV Ekin = 788.761eV (T=1525.532K) Etot = 2816.820eV Energy per atom: Epot =2038.131eV Ekin = 771.266eV (T=1491.695K) Etot = 2809.396eV Energy per atom: Epot =2022.975eV Ekin = 780.359eV (T=1509.283K) Etot = 2803.335eV Energy per atom: Epot =2019.009eV Ekin = 776.257eV (T=1501.348K) Etot = 2795.266eV Energy per atom: Epot =2012.919eV Ekin = 782.077eV (T=1512.605K) Etot = 2794.996eV Energy per atom: Epot =2001.163eV Ekin = 774.657eV (T=1498.254K) Etot = 2775.820eV Energy per atom: Epot =1998.917eV Ekin = 770.158eV (T=1489.552K) Etot = 2769.075eV Energy per atom: Epot =2009.483eV Ekin = 767.284eV (T=1483.995K) Etot = 2776.767eV Energy per atom: Epot =1990.640eV Ekin = 787.881eV (T=1523.831K) Etot = 2778.521eV Energy per atom: Epot =2006.529eV Ekin = 768.663eV (T=1486.660K) Etot = 2775.191eV Energy per atom: Epot =2011.659eV Ekin = 764.267eV (T=1478.160K) Etot = 2775.927eV Energy per atom: Epot =1994.825eV Ekin = 770.493eV (T=1490.200K) Etot = 2765.318eV Energy per atom: Epot =1998.643eV Ekin = 772.531eV (T=1494.141K) Etot = 2771.174eV Energy per atom: Epot =2014.372eV Ekin = 749.250eV (T=1449.115K) Etot = 2763.622eV Energy per atom: Epot =1996.423eV Ekin = 767.883eV (T=1485.152K) Etot = 2764.306eV Energy per atom: Epot =2002.858eV Ekin = 771.548eV (T=1492.240K) Etot = 2774.405eV Energy per atom: Epot =1996.398eV Ekin = 773.551eV (T=1496.115K) Etot = 2769.949eV Energy per atom: Epot =2001.742eV Ekin = 774.239eV (T=1497.446K) Etot = 2775.981eV Energy per atom: Epot =2012.717eV Ekin = 769.309eV (T=1487.911K) Etot = 2782.026eV Energy per atom: Epot =2002.239eV Ekin = 769.456eV (T=1488.195K) Etot = 2771.696eV Energy per atom: Epot =1990.883eV Ekin = 783.538eV (T=1515.430K) Etot = 2774.420eV Energy per atom: Epot =2000.229eV Ekin = 771.505eV (T=1492.158K) Etot = 2771.734eV Energy per atom: Epot =1993.956eV Ekin = 776.421eV (T=1501.665K) Etot = 2770.377eV Energy per atom: Epot =1996.535eV Ekin = 776.921eV (T=1502.633K) Etot = 2773.456eV Energy per atom: Epot =2002.727eV Ekin = 773.762eV (T=1496.522K) Etot = 2776.488eV Energy per atom: Epot =2003.596eV Ekin = 777.052eV (T=1502.887K) Etot = 2780.648eV Energy per atom: Epot =2011.324eV Ekin = 774.147eV (T=1497.267K) Etot = 2785.471eV Energy per atom: Epot =2009.437eV Ekin = 778.034eV (T=1504.785K) Etot = 2787.471eV Energy per atom: Epot =2015.397eV Ekin = 766.079eV (T=1481.664K) Etot = 2781.476eV Energy per atom: Epot =2000.692eV Ekin = 769.447eV (T=1488.178K) Etot = 2770.139eV Energy per atom: Epot =2001.267eV Ekin = 778.629eV (T=1505.936K) Etot = 2779.896eV Energy per atom: Epot =2013.761eV Ekin = 774.403eV (T=1497.763K) Etot = 2788.164eV Energy per atom: Epot =2021.923eV Ekin = 766.545eV (T=1482.565K) Etot = 2788.469eV Energy per atom: Epot =2022.830eV Ekin = 764.531eV (T=1478.670K) Etot = 2787.361eV Energy per atom: Epot =2021.293eV Ekin = 763.347eV (T=1476.379K) Etot = 2784.640eV Energy per atom: Epot =2007.625eV Ekin = 776.539eV (T=1501.894K) Etot = 2784.164eV Energy per atom: Epot =2014.614eV Ekin = 769.429eV (T=1488.143K) Etot = 2784.043eV Energy per atom: Epot =2017.573eV Ekin = 769.171eV (T=1487.644K) Etot = 2786.745eV Energy per atom: Epot =2017.257eV Ekin = 771.868eV (T=1492.859K) Etot = 2789.125eV Energy per atom: Epot =2026.850eV Ekin = 763.762eV (T=1477.181K) Etot = 2790.611eV Energy per atom: Epot =2030.237eV Ekin = 770.222eV (T=1489.676K) Etot = 2800.458eV Energy per atom: Epot =2020.782eV Ekin = 786.990eV (T=1522.107K) Etot = 2807.772eV Energy per atom: Epot =2013.073eV Ekin = 792.184eV (T=1532.154K) Etot = 2805.257eV Energy per atom: Epot =2027.233eV Ekin = 779.507eV (T=1507.634K) Etot = 2806.740eV Energy per atom: Epot =2008.465eV Ekin = 787.996eV (T=1524.052K) Etot = 2796.461eV Energy per atom: Epot =2017.982eV Ekin = 774.275eV (T=1497.516K) Etot = 2792.258eV Energy per atom: Epot =2008.150eV Ekin = 779.716eV (T=1508.039K) Etot = 2787.866eV Energy per atom: Epot =2007.988eV Ekin = 772.816eV (T=1494.694K) Etot = 2780.804eV Energy per atom: Epot =2007.747eV Ekin = 773.871eV (T=1496.734K) Etot = 2781.618eV Energy per atom: Epot =2009.656eV Ekin = 768.972eV (T=1487.258K) Etot = 2778.628eV Energy per atom: Epot =1991.305eV Ekin = 776.540eV (T=1501.895K) Etot = 2767.844eV Energy per atom: Epot =1999.363eV Ekin = 765.839eV (T=1481.200K) Etot = 2765.202eV Energy per atom: Epot =1996.937eV Ekin = 781.922eV (T=1512.305K) Etot = 2778.859eV Energy per atom: Epot =2007.240eV Ekin = 773.613eV (T=1496.235K) Etot = 2780.853eV Energy per atom: Epot =2012.783eV Ekin = 759.555eV (T=1469.045K) Etot = 2772.338eV .. 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] 11:54:40 43.457006 1.0818 BFGSLineSearch: 1[ 1] 11:54:40 42.347659 0.2273 BFGSLineSearch: 2[ 2] 11:54:40 42.108454 0.1349 BFGSLineSearch: 3[ 3] 11:54:40 41.964817 0.1138 BFGSLineSearch: 4[ 4] 11:54:40 41.924933 0.0683 BFGSLineSearch: 5[ 5] 11:54:40 41.915346 0.0225 BFGSLineSearch: 6[ 6] 11:54:40 41.914920 0.0059 BFGSLineSearch: 7[ 7] 11:54:40 41.914872 0.0023 BFGSLineSearch: 8[ 9] 11:54:40 41.914855 0.0023 BFGSLineSearch: 9[ 10] 11:54:40 41.914851 0.0010 running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 14.351eV (T=1193.774K) Etot = 56.265eV Energy per atom: Epot =50.171eV Ekin = 6.132eV (T=510.101K) Etot = 56.303eV Energy per atom: Epot =49.466eV Ekin = 6.847eV (T=569.595K) Etot = 56.314eV Energy per atom: Epot =50.484eV Ekin = 5.831eV (T=485.053K) Etot = 56.315eV Energy per atom: Epot =50.730eV Ekin = 5.587eV (T=464.788K) Etot = 56.317eV Energy per atom: Epot =49.918eV Ekin = 6.398eV (T=532.256K) Etot = 56.316eV Energy per atom: Epot =48.950eV Ekin = 7.359eV (T=612.168K) Etot = 56.309eV Energy per atom: Epot =49.094eV Ekin = 7.216eV (T=600.236K) Etot = 56.309eV Energy per atom: Epot =50.022eV Ekin = 6.290eV (T=523.261K) Etot = 56.312eV Energy per atom: Epot =49.112eV Ekin = 7.195eV (T=598.558K) Etot = 56.308eV Energy per atom: Epot =49.951eV Ekin = 6.360eV (T=529.069K) Etot = 56.311eV Energy per atom: Epot =50.534eV Ekin = 5.778eV (T=480.675K) Etot = 56.312eV Energy per atom: Epot =49.397eV Ekin = 6.912eV (T=574.976K) Etot = 56.309eV Energy per atom: Epot =49.362eV Ekin = 6.948eV (T=578.016K) Etot = 56.310eV Energy per atom: Epot =49.413eV Ekin = 6.894eV (T=573.451K) Etot = 56.307eV Energy per atom: Epot =49.336eV Ekin = 6.971eV (T=579.859K) Etot = 56.306eV Energy per atom: Epot =49.875eV Ekin = 6.434eV (T=535.191K) Etot = 56.309eV Energy per atom: Epot =49.433eV Ekin = 6.875eV (T=571.928K) Etot = 56.308eV Energy per atom: Epot =50.257eV Ekin = 6.055eV (T=503.653K) Etot = 56.311eV Energy per atom: Epot =49.674eV Ekin = 6.639eV (T=552.315K) Etot = 56.313eV Energy per atom: Epot =49.536eV Ekin = 6.781eV (T=564.095K) Etot = 56.317eV Energy per atom: Epot =49.684eV Ekin = 6.636eV (T=552.027K) Etot = 56.320eV Energy per atom: Epot =49.300eV Ekin = 7.017eV (T=583.728K) Etot = 56.317eV Energy per atom: Epot =49.608eV Ekin = 6.706eV (T=557.841K) Etot = 56.314eV Energy per atom: Epot =48.885eV Ekin = 7.425eV (T=617.688K) Etot = 56.311eV Energy per atom: Epot =50.463eV Ekin = 5.858eV (T=487.300K) Etot = 56.321eV Energy per atom: Epot =49.691eV Ekin = 6.626eV (T=551.171K) Etot = 56.317eV Energy per atom: Epot =49.262eV Ekin = 7.047eV (T=586.202K) Etot = 56.309eV Energy per atom: Epot =48.944eV Ekin = 7.360eV (T=612.249K) Etot = 56.304eV Energy per atom: Epot =49.094eV Ekin = 7.215eV (T=600.175K) Etot = 56.309eV Energy per atom: Epot =49.501eV Ekin = 6.814eV (T=566.821K) Etot = 56.315eV Energy per atom: Epot =49.108eV Ekin = 7.203eV (T=599.233K) Etot = 56.311eV Energy per atom: Epot =50.292eV Ekin = 6.024eV (T=501.085K) Etot = 56.316eV Energy per atom: Epot =49.077eV Ekin = 7.235eV (T=601.849K) Etot = 56.312eV Energy per atom: Epot =48.960eV Ekin = 7.354eV (T=611.776K) Etot = 56.314eV Energy per atom: Epot =48.981eV Ekin = 7.331eV (T=609.876K) Etot = 56.312eV Energy per atom: Epot =49.235eV Ekin = 7.075eV (T=588.551K) Etot = 56.310eV Energy per atom: Epot =49.089eV Ekin = 7.226eV (T=601.085K) Etot = 56.315eV Energy per atom: Epot =49.111eV Ekin = 7.205eV (T=599.397K) Etot = 56.316eV Energy per atom: Epot =49.221eV Ekin = 7.088eV (T=589.649K) Etot = 56.309eV Energy per atom: Epot =48.989eV Ekin = 7.319eV (T=608.823K) Etot = 56.308eV Energy per atom: Epot =50.128eV Ekin = 6.185eV (T=514.522K) Etot = 56.313eV Energy per atom: Epot =49.094eV Ekin = 7.218eV (T=600.412K) Etot = 56.312eV Energy per atom: Epot =48.835eV Ekin = 7.477eV (T=621.989K) Etot = 56.312eV Energy per atom: Epot =49.883eV Ekin = 6.433eV (T=535.120K) Etot = 56.316eV Energy per atom: Epot =49.491eV Ekin = 6.826eV (T=567.843K) Etot = 56.317eV Energy per atom: Epot =49.915eV Ekin = 6.399eV (T=532.294K) Etot = 56.314eV Energy per atom: Epot =49.850eV Ekin = 6.466eV (T=537.856K) Etot = 56.316eV Energy per atom: Epot =48.888eV Ekin = 7.422eV (T=617.424K) Etot = 56.310eV Energy per atom: Epot =49.686eV Ekin = 6.619eV (T=550.592K) Etot = 56.305eV Energy per atom: Epot =49.005eV Ekin = 7.298eV (T=607.125K) Etot = 56.303eV Energy per atom: Epot =49.522eV Ekin = 6.789eV (T=564.781K) Etot = 56.311eV Energy per atom: Epot =49.513eV Ekin = 6.801eV (T=565.750K) Etot = 56.314eV Energy per atom: Epot =49.721eV Ekin = 6.591eV (T=548.312K) Etot = 56.313eV Energy per atom: Epot =49.856eV Ekin = 6.458eV (T=537.228K) Etot = 56.314eV Energy per atom: Epot =48.987eV Ekin = 7.321eV (T=609.047K) Etot = 56.308eV Energy per atom: Epot =48.936eV Ekin = 7.374eV (T=613.429K) Etot = 56.310eV Energy per atom: Epot =49.422eV Ekin = 6.886eV (T=572.812K) Etot = 56.308eV Energy per atom: Epot =49.075eV Ekin = 7.233eV (T=601.652K) Etot = 56.308eV Energy per atom: Epot =48.632eV Ekin = 7.679eV (T=638.778K) Etot = 56.310eV Energy per atom: Epot =49.890eV Ekin = 6.424eV (T=534.361K) Etot = 56.314eV Energy per atom: Epot =49.070eV Ekin = 7.236eV (T=601.934K) Etot = 56.306eV Energy per atom: Epot =50.069eV Ekin = 6.247eV (T=519.647K) Etot = 56.316eV Energy per atom: Epot =49.351eV Ekin = 6.960eV (T=578.969K) Etot = 56.311eV Energy per atom: Epot =50.365eV Ekin = 5.956eV (T=495.424K) Etot = 56.320eV Energy per atom: Epot =49.082eV Ekin = 7.231eV (T=601.486K) Etot = 56.313eV Energy per atom: Epot =49.196eV Ekin = 7.116eV (T=591.921K) Etot = 56.312eV Energy per atom: Epot =48.957eV Ekin = 7.354eV (T=611.773K) Etot = 56.311eV Energy per atom: Epot =48.631eV Ekin = 7.676eV (T=638.527K) Etot = 56.307eV Energy per atom: Epot =49.046eV Ekin = 7.266eV (T=604.443K) Etot = 56.312eV Energy per atom: Epot =49.698eV Ekin = 6.622eV (T=550.836K) Etot = 56.319eV Energy per atom: Epot =49.911eV Ekin = 6.408eV (T=533.090K) Etot = 56.319eV Energy per atom: Epot =49.434eV Ekin = 6.881eV (T=572.431K) Etot = 56.316eV Energy per atom: Epot =49.188eV Ekin = 7.127eV (T=592.891K) Etot = 56.316eV Energy per atom: Epot =49.368eV Ekin = 6.942eV (T=577.522K) Etot = 56.311eV Energy per atom: Epot =48.921eV Ekin = 7.387eV (T=614.488K) Etot = 56.308eV Energy per atom: Epot =49.382eV Ekin = 6.929eV (T=576.412K) Etot = 56.311eV Energy per atom: Epot =48.896eV Ekin = 7.416eV (T=616.878K) Etot = 56.311eV Energy per atom: Epot =48.952eV Ekin = 7.360eV (T=612.240K) Etot = 56.312eV Energy per atom: Epot =48.223eV Ekin = 8.085eV (T=672.530K) Etot = 56.307eV Energy per atom: Epot =49.766eV Ekin = 6.548eV (T=544.703K) Etot = 56.314eV Energy per atom: Epot =49.975eV Ekin = 6.339eV (T=527.339K) Etot = 56.315eV Energy per atom: Epot =48.113eV Ekin = 8.189eV (T=681.202K) Etot = 56.302eV Energy per atom: Epot =48.644eV Ekin = 7.664eV (T=637.574K) Etot = 56.308eV Energy per atom: Epot =48.631eV Ekin = 7.680eV (T=638.880K) Etot = 56.311eV Energy per atom: Epot =48.746eV Ekin = 7.559eV (T=628.776K) Etot = 56.304eV Energy per atom: Epot =49.265eV Ekin = 7.044eV (T=585.993K) Etot = 56.309eV Energy per atom: Epot =49.304eV Ekin = 7.011eV (T=583.185K) Etot = 56.314eV Energy per atom: Epot =49.476eV Ekin = 6.836eV (T=568.622K) Etot = 56.312eV Energy per atom: Epot =48.654eV Ekin = 7.653eV (T=636.603K) Etot = 56.306eV Energy per atom: Epot =48.716eV Ekin = 7.596eV (T=631.887K) Etot = 56.312eV Energy per atom: Epot =49.103eV Ekin = 7.209eV (T=599.724K) Etot = 56.312eV Energy per atom: Epot =48.697eV Ekin = 7.607eV (T=632.766K) Etot = 56.304eV Energy per atom: Epot =48.706eV Ekin = 7.604eV (T=632.560K) Etot = 56.310eV Energy per atom: Epot =49.133eV Ekin = 7.179eV (T=597.167K) Etot = 56.312eV Energy per atom: Epot =49.506eV Ekin = 6.801eV (T=565.775K) Etot = 56.307eV Energy per atom: Epot =48.930eV Ekin = 7.382eV (T=614.103K) Etot = 56.312eV Energy per atom: Epot =48.279eV Ekin = 8.026eV (T=667.670K) Etot = 56.305eV Energy per atom: Epot =48.961eV Ekin = 7.342eV (T=610.766K) Etot = 56.303eV Energy per atom: Epot =49.210eV Ekin = 7.102eV (T=590.803K) Etot = 56.312eV Energy per atom: Epot =49.572eV Ekin = 6.740eV (T=560.672K) Etot = 56.312eV Energy per atom: Epot =49.809eV Ekin = 6.504eV (T=541.046K) Etot = 56.313eV Energy per atom: Epot =49.072eV Ekin = 7.243eV (T=602.545K) Etot = 56.315eV Energy per atom: Epot =48.835eV Ekin = 7.477eV (T=622.018K) Etot = 56.313eV Energy per atom: Epot =49.041eV Ekin = 7.276eV (T=605.281K) Etot = 56.317eV Energy per atom: Epot =48.975eV Ekin = 7.336eV (T=610.284K) Etot = 56.312eV Energy per atom: Epot =48.471eV Ekin = 7.834eV (T=651.683K) Etot = 56.305eV Energy per atom: Epot =49.568eV Ekin = 6.747eV (T=561.289K) Etot = 56.315eV Energy per atom: Epot =49.171eV Ekin = 7.142eV (T=594.134K) Etot = 56.313eV Energy per atom: Epot =49.490eV Ekin = 6.820eV (T=567.341K) Etot = 56.311eV Energy per atom: Epot =49.448eV Ekin = 6.865eV (T=571.035K) Etot = 56.312eV Energy per atom: Epot =49.045eV Ekin = 7.263eV (T=604.151K) Etot = 56.308eV Energy per atom: Epot =48.463eV Ekin = 7.841eV (T=652.243K) Etot = 56.304eV Energy per atom: Epot =49.227eV Ekin = 7.081eV (T=589.050K) Etot = 56.308eV Energy per atom: Epot =48.790eV Ekin = 7.519eV (T=625.449K) Etot = 56.308eV Energy per atom: Epot =49.243eV Ekin = 7.068eV (T=587.921K) Etot = 56.310eV Energy per atom: Epot =49.407eV Ekin = 6.899eV (T=573.943K) Etot = 56.307eV Energy per atom: Epot =48.712eV Ekin = 7.598eV (T=632.052K) Etot = 56.310eV Energy per atom: Epot =48.695eV Ekin = 7.614eV (T=633.385K) Etot = 56.309eV Energy per atom: Epot =48.943eV Ekin = 7.363eV (T=612.523K) Etot = 56.307eV Energy per atom: Epot =48.879eV Ekin = 7.428eV (T=617.877K) Etot = 56.307eV Energy per atom: Epot =49.991eV Ekin = 6.322eV (T=525.926K) Etot = 56.313eV Energy per atom: Epot =49.071eV Ekin = 7.240eV (T=602.254K) Etot = 56.311eV Energy per atom: Epot =48.423eV Ekin = 7.879eV (T=655.439K) Etot = 56.302eV Energy per atom: Epot =48.129eV Ekin = 8.175eV (T=680.049K) Etot = 56.304eV Energy per atom: Epot =48.621eV Ekin = 7.688eV (T=639.526K) Etot = 56.309eV Energy per atom: Epot =49.404eV Ekin = 6.909eV (T=574.741K) Etot = 56.313eV Energy per atom: Epot =49.095eV Ekin = 7.219eV (T=600.498K) Etot = 56.314eV Energy per atom: Epot =48.837eV Ekin = 7.477eV (T=621.951K) Etot = 56.314eV Energy per atom: Epot =49.776eV Ekin = 6.539eV (T=543.936K) Etot = 56.314eV Energy per atom: Epot =49.435eV Ekin = 6.877eV (T=572.083K) Etot = 56.312eV Energy per atom: Epot =48.736eV Ekin = 7.576eV (T=630.198K) Etot = 56.312eV Energy per atom: Epot =48.444eV Ekin = 7.867eV (T=654.469K) Etot = 56.311eV Energy per atom: Epot =49.486eV Ekin = 6.832eV (T=568.309K) Etot = 56.318eV Energy per atom: Epot =49.098eV Ekin = 7.214eV (T=600.133K) Etot = 56.313eV Energy per atom: Epot =49.266eV Ekin = 7.041eV (T=585.701K) Etot = 56.307eV Energy per atom: Epot =48.559eV Ekin = 7.745eV (T=644.315K) Etot = 56.304eV Energy per atom: Epot =48.441eV Ekin = 7.868eV (T=654.471K) Etot = 56.308eV Energy per atom: Epot =48.695eV Ekin = 7.612eV (T=633.213K) Etot = 56.307eV Energy per atom: Epot =49.510eV Ekin = 6.798eV (T=565.481K) Etot = 56.307eV Energy per atom: Epot =49.265eV Ekin = 7.041eV (T=585.703K) Etot = 56.306eV Energy per atom: Epot =49.619eV Ekin = 6.693eV (T=556.768K) Etot = 56.312eV Energy per atom: Epot =49.202eV Ekin = 7.110eV (T=591.416K) Etot = 56.312eV Energy per atom: Epot =49.075eV Ekin = 7.236eV (T=601.910K) Etot = 56.310eV Energy per atom: Epot =48.867eV Ekin = 7.442eV (T=619.036K) Etot = 56.308eV Energy per atom: Epot =48.747eV Ekin = 7.566eV (T=629.368K) Etot = 56.313eV Energy per atom: Epot =49.072eV Ekin = 7.241eV (T=602.359K) Etot = 56.313eV Energy per atom: Epot =48.334eV Ekin = 7.968eV (T=662.835K) Etot = 56.302eV Energy per atom: Epot =48.910eV Ekin = 7.396eV (T=615.227K) Etot = 56.306eV Energy per atom: Epot =49.132eV Ekin = 7.175eV (T=596.850K) Etot = 56.307eV Energy per atom: Epot =48.591eV Ekin = 7.714eV (T=641.728K) Etot = 56.305eV Energy per atom: Epot =50.091eV Ekin = 6.222eV (T=517.628K) Etot = 56.314eV Energy per atom: Epot =49.162eV Ekin = 7.151eV (T=594.833K) Etot = 56.313eV Energy per atom: Epot =48.514eV Ekin = 7.791eV (T=648.095K) Etot = 56.305eV Energy per atom: Epot =49.320eV Ekin = 6.995eV (T=581.854K) Etot = 56.315eV Energy per atom: Epot =49.324eV Ekin = 6.989eV (T=581.422K) Etot = 56.313eV Energy per atom: Epot =48.239eV Ekin = 8.071eV (T=671.401K) Etot = 56.310eV Energy per atom: Epot =48.766eV Ekin = 7.544eV (T=627.549K) Etot = 56.310eV Energy per atom: Epot =48.504eV Ekin = 7.798eV (T=648.723K) Etot = 56.302eV Energy per atom: Epot =48.973eV Ekin = 7.337eV (T=610.322K) Etot = 56.310eV Energy per atom: Epot =49.580eV Ekin = 6.737eV (T=560.438K) Etot = 56.317eV Energy per atom: Epot =48.647eV Ekin = 7.660eV (T=637.190K) Etot = 56.307eV Energy per atom: Epot =48.411eV Ekin = 7.897eV (T=656.937K) Etot = 56.308eV Energy per atom: Epot =49.024eV Ekin = 7.290eV (T=606.410K) Etot = 56.314eV Energy per atom: Epot =49.770eV Ekin = 6.545eV (T=544.487K) Etot = 56.315eV Energy per atom: Epot =49.452eV Ekin = 6.860eV (T=570.697K) Etot = 56.312eV Energy per atom: Epot =48.769eV Ekin = 7.542eV (T=627.393K) Etot = 56.311eV Energy per atom: Epot =50.078eV Ekin = 6.238eV (T=518.935K) Etot = 56.316eV Energy per atom: Epot =49.889eV Ekin = 6.423eV (T=534.346K) Etot = 56.313eV Energy per atom: Epot =49.866eV Ekin = 6.452eV (T=536.760K) Etot = 56.318eV Energy per atom: Epot =48.884eV Ekin = 7.427eV (T=617.838K) Etot = 56.311eV Energy per atom: Epot =49.193eV Ekin = 7.120eV (T=592.268K) Etot = 56.313eV Energy per atom: Epot =49.612eV Ekin = 6.704eV (T=557.690K) Etot = 56.316eV Energy per atom: Epot =49.018eV Ekin = 7.294eV (T=606.746K) Etot = 56.311eV Energy per atom: Epot =49.266eV Ekin = 7.041eV (T=585.738K) Etot = 56.308eV Energy per atom: Epot =50.388eV Ekin = 5.926eV (T=492.968K) Etot = 56.314eV Energy per atom: Epot =49.266eV Ekin = 7.044eV (T=585.981K) Etot = 56.310eV Energy per atom: Epot =49.622eV Ekin = 6.692eV (T=556.704K) Etot = 56.314eV Energy per atom: Epot =49.420eV Ekin = 6.896eV (T=573.620K) Etot = 56.316eV Energy per atom: Epot =49.168eV Ekin = 7.143eV (T=594.202K) Etot = 56.311eV Energy per atom: Epot =50.108eV Ekin = 6.205eV (T=516.183K) Etot = 56.313eV Energy per atom: Epot =48.848eV Ekin = 7.459eV (T=620.469K) Etot = 56.307eV Energy per atom: Epot =49.235eV Ekin = 7.079eV (T=588.838K) Etot = 56.313eV Energy per atom: Epot =49.132eV Ekin = 7.183eV (T=597.553K) Etot = 56.315eV Energy per atom: Epot =49.777eV Ekin = 6.540eV (T=544.031K) Etot = 56.317eV Energy per atom: Epot =49.103eV Ekin = 7.204eV (T=599.269K) Etot = 56.307eV Energy per atom: Epot =48.914eV Ekin = 7.399eV (T=615.482K) Etot = 56.313eV Energy per atom: Epot =48.917eV Ekin = 7.399eV (T=615.506K) Etot = 56.316eV Energy per atom: Epot =49.569eV Ekin = 6.746eV (T=561.156K) Etot = 56.315eV Energy per atom: Epot =49.514eV Ekin = 6.798eV (T=565.470K) Etot = 56.311eV Energy per atom: Epot =49.015eV Ekin = 7.292eV (T=606.596K) Etot = 56.307eV Energy per atom: Epot =49.146eV Ekin = 7.166eV (T=596.099K) Etot = 56.312eV Energy per atom: Epot =49.106eV Ekin = 7.203eV (T=599.227K) Etot = 56.310eV Energy per atom: Epot =48.945eV Ekin = 7.363eV (T=612.541K) Etot = 56.309eV Energy per atom: Epot =48.947eV Ekin = 7.364eV (T=612.626K) Etot = 56.311eV Energy per atom: Epot =49.147eV Ekin = 7.167eV (T=596.163K) Etot = 56.314eV Energy per atom: Epot =48.992eV Ekin = 7.318eV (T=608.737K) Etot = 56.309eV Energy per atom: Epot =48.868eV Ekin = 7.441eV (T=619.017K) Etot = 56.309eV Energy per atom: Epot =48.944eV Ekin = 7.369eV (T=612.973K) Etot = 56.313eV Energy per atom: Epot =48.166eV Ekin = 8.141eV (T=677.257K) Etot = 56.308eV Energy per atom: Epot =47.891eV Ekin = 8.416eV (T=700.130K) Etot = 56.308eV .. 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 `_