.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples_generated/03-tutorials/md.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_generated_03-tutorials_md.py: .. _md_tutorial: ================== Molecular dynamics ================== .. note:: These examples *can* be run without ``asap3`` installed. In that case, ASE’s Python implementation of the EMT calculator can be used instead, but it is much slower. Goal ==== In this tutorial, we will learn how to perform basic molecular dynamics (MD) simulations using ASE. The key objectives are: - Understand how to set up a crystal structure (Cu atoms on an FCC lattice). - Initialize velocities from Maxwell–Boltzmann distribution corresponding to a chosen temperature. - Integrate Newton’s equations of motion using Velocity-Verlet algorithm and we monitor the temperature using Langevin thermostat. - Monitor and analyze thermodynamic quantities (potential energy, kinetic energy, total energy, temperature). - Save trajectories and visualize atomic motion with ASE’s GUI. - Explore MD in different scenarios: - Constant energy MD (NVE ensemble) - Constant temperature MD (NVT ensemble) - Isolated nanoparticle simulations By the end of this tutorial, you should be able to set up your own MD simulations, monitor energy conservation, and visualize system evolution. Part 1: Basic Molecular Dynamics Simulation =========================================== We start by creating a copper crystal, assigning random velocities corresponding to Maxwell Boltzmann Distribution at 300 K, and running dynamics in the NVE ensemble (constant energy). .. GENERATED FROM PYTHON SOURCE LINES 47-79 .. code-block:: Python import matplotlib.pyplot as plt import numpy as np # choose one of the following implementations of EMT: # included in ase # from ase.calculators.emt import EMT # faster performance from asap3 import EMT from ase import units from ase.cluster.cubic import FaceCenteredCubic as ClusterFCC from ase.io.trajectory import Trajectory from ase.lattice.cubic import FaceCenteredCubic as LatticeFCC from ase.md.langevin import Langevin # for later NPT simulations from ase.md.velocitydistribution import ( MaxwellBoltzmannDistribution, Stationary, ZeroRotation, ) from ase.md.verlet import VelocityVerlet from ase.optimize import QuasiNewton from ase.visualize.plot import plot_atoms # Set up initial positions of Cu atoms on Fcc crystal lattice size = 10 atoms = LatticeFCC( directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], symbol='Cu', size=(size, size, size), pbc=True, ) .. GENERATED FROM PYTHON SOURCE LINES 80-81 Before setting up the MD simulation, we take a look at the initial structure: .. GENERATED FROM PYTHON SOURCE LINES 83-89 .. code-block:: Python fig, ax = plt.subplots(figsize=(5, 5)) plot_atoms(atoms, ax, rotation=('45x,45y,0z'), show_unit_cell=2, radii=0.75) ax.set_axis_off() plt.tight_layout() plt.show() .. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_md_001.png :alt: md :srcset: /examples_generated/03-tutorials/images/sphx_glr_md_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 90-92 Now let's run the MD simulation and monitor the kinetic and potential energy of the whole system: .. GENERATED FROM PYTHON SOURCE LINES 92-149 .. code-block:: Python # Describe the interatomic interactions with the Effective Medium Theory (EMT) atoms.calc = EMT() # Set the initial velocities corresponding to T=300K from Maxwell Boltzmann # Distribution MaxwellBoltzmannDistribution(atoms, temperature_K=300) # We use Velocity Verlet algorithm to integrate the Newton's equations. timestep_fs = 5 dyn = VelocityVerlet(atoms, timestep_fs * units.fs) # 5 fs time step. def printenergy(a): """ Function to print the thermodynamical properties i.e potential energy, kinetic energy and total energy """ epot = a.get_potential_energy() ekin = a.get_kinetic_energy() temp = a.get_temperature() print( f'Energy per atom: Epot ={epot:6.3f}eV Ekin = {ekin:.3f}eV ' f'(T={temp:.3f}K) Etot = {epot + ekin:.3f}eV' ) # Now run the dynamics print('running a NVE simulation of fcc Cu') printenergy(atoms) # init lists to for energy vs time data time_ps, epot, ekin = [], [], [] mdind = 0 steps_per_block = 10 for i in range(20): dyn.run(steps_per_block) mdind += steps_per_block printenergy(atoms) # save the energies of the current MD step time_ps.append(mdind * timestep_fs / 1000.0) epot.append(atoms.get_potential_energy()) ekin.append(atoms.get_kinetic_energy()) etot = np.array(epot) + np.array(ekin) # Plot energies vs time fig, ax = plt.subplots(figsize=(6, 4)) ax.plot(time_ps, epot, label='Potential energy') ax.plot(time_ps, ekin, label='Kinetic energy') ax.plot(time_ps, etot, label='Total energy') ax.set_xlabel('Time (ps)') ax.set_ylabel('Energy (eV)') ax.legend(loc='best') ax.grid(True, linewidth=0.5, alpha=0.5) plt.tight_layout() plt.show() .. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_md_002.png :alt: md :srcset: /examples_generated/03-tutorials/images/sphx_glr_md_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /builds/ase/ase/examples/03-tutorials/md.py:98: DeprecationWarning: Use thermalize_momenta MaxwellBoltzmannDistribution(atoms, temperature_K=300) running a NVE simulation of fcc Cu Energy per atom: Epot =-2.405eV Ekin = 156.300eV (T=302.298K) Etot = 153.895eV Energy per atom: Epot =119.284eV Ekin = 35.412eV (T=68.490K) Etot = 154.696eV Energy per atom: Epot =77.916eV Ekin = 76.626eV (T=148.202K) Etot = 154.543eV Energy per atom: Epot =71.706eV Ekin = 82.698eV (T=159.944K) Etot = 154.404eV Energy per atom: Epot =69.762eV Ekin = 84.585eV (T=163.595K) Etot = 154.347eV Energy per atom: Epot =81.355eV Ekin = 73.159eV (T=141.495K) Etot = 154.514eV Energy per atom: Epot =80.468eV Ekin = 74.043eV (T=143.206K) Etot = 154.511eV Energy per atom: Epot =71.689eV Ekin = 82.702eV (T=159.953K) Etot = 154.391eV Energy per atom: Epot =72.773eV Ekin = 81.636eV (T=157.891K) Etot = 154.409eV Energy per atom: Epot =80.820eV Ekin = 73.675eV (T=142.494K) Etot = 154.495eV Energy per atom: Epot =76.150eV Ekin = 78.309eV (T=151.456K) Etot = 154.459eV Energy per atom: Epot =74.786eV Ekin = 79.649eV (T=154.049K) Etot = 154.435eV Energy per atom: Epot =76.768eV Ekin = 77.678eV (T=150.236K) Etot = 154.446eV Energy per atom: Epot =76.976eV Ekin = 77.474eV (T=149.841K) Etot = 154.450eV Energy per atom: Epot =75.569eV Ekin = 78.877eV (T=152.554K) Etot = 154.445eV Energy per atom: Epot =75.189eV Ekin = 79.260eV (T=153.295K) Etot = 154.449eV Energy per atom: Epot =74.939eV Ekin = 79.497eV (T=153.753K) Etot = 154.435eV Energy per atom: Epot =78.459eV Ekin = 75.993eV (T=146.977K) Etot = 154.452eV Energy per atom: Epot =75.297eV Ekin = 79.158eV (T=153.099K) Etot = 154.456eV Energy per atom: Epot =74.212eV Ekin = 80.221eV (T=155.155K) Etot = 154.433eV Energy per atom: Epot =79.696eV Ekin = 74.761eV (T=144.594K) Etot = 154.457eV .. GENERATED FROM PYTHON SOURCE LINES 150-162 Note how the total energy is conserved, but the kinetic energy quickly drops to half the expected value. Why? What you learned here: - How to set up a basic MD run. - How to monitor the energy over time. - That total energy is approximately conserved in NVE simulations, what is the error in total energy? Exercise: Tune the time step from 5fs to 10fs and 50fs, what changes do you observe in total energy? .. GENERATED FROM PYTHON SOURCE LINES 165-196 Part 2: Constant temperature MD =============================== In many cases, you want to control temperature (NVT ensemble). This can be done using a thermostat, like -- in this tutorial -- Langevin thermostat. Compared to the previous example, we replace the line ``dyn = VelocityVerlet(...)`` with :: dyn = Langevin(atoms, timestep=5 * units.fs, temperature_K=T, friction=0.02) where ``T`` is the desired temperature in Kelvin. For that we also imported the Langevin in the beginning. The Langevin dynamics will then slowly adjust the total energy of the system so the temperature approaches the desired one. As a slightly less boring example, let us use this to melt a chunk of copper by starting the simulation without any momentum of the atoms (no kinetic energy), and with a desired temperature above the melting point. We will also save information about the atoms in a trajectory file called ``moldyn3.traj``. .. note:: It is recommended to use the ``asap3`` implementation of the ``EMT`` calculator here, because its performance benefits over the ``ase`` implementation. .. GENERATED FROM PYTHON SOURCE LINES 198-246 .. code-block:: Python size = 10 T = 1500 # Kelvin # Set up a crystal atoms = LatticeFCC( directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], symbol='Cu', size=(size, size, size), pbc=False, ) # Describe the interatomic interactions with the Effective Medium Theory atoms.calc = EMT() # We want to run MD with constant energy using the Langevin algorithm # with a time step of 5 fs, the temperature T and the friction # coefficient to 0.02 atomic units. timestep_fs = 5 dyn = Langevin( atoms, timestep=timestep_fs * units.fs, temperature_K=T, friction=0.02 ) # We also want to save the positions of all atoms after every 100th time step. traj = Trajectory('fccCu_NPT.traj', 'w', atoms) # Now run the dynamics print('running a NVT simulation of fcc Cu') printenergy(atoms) time_ps, temperature = [], [] mdind = 0 steps_per_block = 10 for i in range(200): dyn.run(steps_per_block) mdind += steps_per_block printenergy(atoms) # save the temperature of the current MD step time_ps.append(mdind * timestep_fs / 1000.0) temperature.append(atoms.get_temperature()) # Plot temperatures vs time fig, ax = plt.subplots(figsize=(6, 4)) ax.plot(time_ps, temperature) ax.set_xlabel('Time (ps)') ax.set_ylabel('Temperature (K)') ax.grid(True, linewidth=0.5, alpha=0.5) plt.tight_layout() plt.show() .. image-sg:: /examples_generated/03-tutorials/images/sphx_glr_md_003.png :alt: md :srcset: /examples_generated/03-tutorials/images/sphx_glr_md_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/ase/.local/lib/python3.14/site-packages/ase/md/langevin.py:102: FutureWarning: The implementation of `fixcm=True` in `Langevin` does not strictly sample the correct NVT distributions. The deviations are typically small for large systems but can be more pronounced for small systems. Use `fixcm=False` together with `ase.constraints.FixCom`. `fixcm` is deprecated since ASE 3.28.0 and will be removed in a future release. warnings.warn(msg, FutureWarning) running a NVT simulation of fcc Cu Energy per atom: Epot =540.816eV Ekin = 0.000eV (T=0.000K) Etot = 540.816eV Energy per atom: Epot =598.720eV Ekin = 82.148eV (T=158.881K) Etot = 680.868eV Energy per atom: Epot =668.922eV Ekin = 140.412eV (T=271.569K) Etot = 809.334eV Energy per atom: Epot =729.289eV Ekin = 198.779eV (T=384.456K) Etot = 928.068eV Energy per atom: Epot =781.930eV Ekin = 255.430eV (T=494.023K) Etot = 1037.360eV Energy per atom: Epot =837.359eV Ekin = 298.007eV (T=576.371K) Etot = 1135.365eV Energy per atom: Epot =880.430eV Ekin = 336.803eV (T=651.407K) Etot = 1217.233eV Energy per atom: Epot =918.762eV Ekin = 381.057eV (T=736.998K) Etot = 1299.820eV Energy per atom: Epot =961.613eV Ekin = 411.814eV (T=796.483K) Etot = 1373.427eV Energy per atom: Epot =1001.328eV Ekin = 436.206eV (T=843.661K) Etot = 1437.534eV Energy per atom: Epot =1030.002eV Ekin = 479.364eV (T=927.131K) Etot = 1509.366eV Energy per atom: Epot =1080.852eV Ekin = 495.096eV (T=957.559K) Etot = 1575.948eV Energy per atom: Epot =1117.859eV Ekin = 516.296eV (T=998.562K) Etot = 1634.155eV Energy per atom: Epot =1150.939eV Ekin = 522.348eV (T=1010.266K) Etot = 1673.287eV Energy per atom: Epot =1173.392eV Ekin = 555.799eV (T=1074.964K) Etot = 1729.192eV Energy per atom: Epot =1204.756eV Ekin = 563.986eV (T=1090.799K) Etot = 1768.743eV Energy per atom: Epot =1232.626eV Ekin = 575.933eV (T=1113.905K) Etot = 1808.560eV Energy per atom: Epot =1256.234eV Ekin = 587.494eV (T=1136.264K) Etot = 1843.728eV Energy per atom: Epot =1264.151eV Ekin = 605.173eV (T=1170.458K) Etot = 1869.324eV Energy per atom: Epot =1299.254eV Ekin = 606.299eV (T=1172.636K) Etot = 1905.553eV Energy per atom: Epot =1340.382eV Ekin = 590.787eV (T=1142.633K) Etot = 1931.168eV Energy per atom: Epot =1359.545eV Ekin = 606.672eV (T=1173.356K) Etot = 1966.217eV Energy per atom: Epot =1359.046eV Ekin = 632.713eV (T=1223.723K) Etot = 1991.759eV Energy per atom: Epot =1385.240eV Ekin = 631.555eV (T=1221.483K) Etot = 2016.795eV Energy per atom: Epot =1412.174eV Ekin = 633.899eV (T=1226.016K) Etot = 2046.073eV Energy per atom: Epot =1411.849eV Ekin = 653.287eV (T=1263.514K) Etot = 2065.136eV Energy per atom: Epot =1428.906eV Ekin = 661.068eV (T=1278.563K) Etot = 2089.974eV Energy per atom: Epot =1456.099eV Ekin = 663.678eV (T=1283.612K) Etot = 2119.777eV Energy per atom: Epot =1459.140eV Ekin = 684.214eV (T=1323.330K) Etot = 2143.354eV Energy per atom: Epot =1485.667eV Ekin = 676.088eV (T=1307.613K) Etot = 2161.754eV Energy per atom: Epot =1487.843eV Ekin = 695.048eV (T=1344.284K) Etot = 2182.892eV Energy per atom: Epot =1523.647eV Ekin = 686.412eV (T=1327.581K) Etot = 2210.060eV Energy per atom: Epot =1519.686eV Ekin = 702.455eV (T=1358.609K) Etot = 2222.141eV Energy per atom: Epot =1538.585eV Ekin = 705.414eV (T=1364.332K) Etot = 2243.999eV Energy per atom: Epot =1553.861eV Ekin = 698.329eV (T=1350.629K) Etot = 2252.190eV Energy per atom: Epot =1559.306eV Ekin = 719.757eV (T=1392.072K) Etot = 2279.063eV Energy per atom: Epot =1590.454eV Ekin = 705.243eV (T=1364.001K) Etot = 2295.697eV Energy per atom: Epot =1589.293eV Ekin = 720.671eV (T=1393.841K) Etot = 2309.964eV Energy per atom: Epot =1593.407eV Ekin = 723.981eV (T=1400.243K) Etot = 2317.388eV Energy per atom: Epot =1619.914eV Ekin = 705.992eV (T=1365.449K) Etot = 2325.906eV Energy per atom: Epot =1628.407eV Ekin = 703.206eV (T=1360.062K) Etot = 2331.613eV Energy per atom: Epot =1644.970eV Ekin = 702.855eV (T=1359.382K) Etot = 2347.825eV Energy per atom: Epot =1648.951eV Ekin = 719.395eV (T=1391.373K) Etot = 2368.346eV Energy per atom: Epot =1652.819eV Ekin = 726.841eV (T=1405.775K) Etot = 2379.660eV Energy per atom: Epot =1686.241eV Ekin = 705.013eV (T=1363.557K) Etot = 2391.254eV Energy per atom: Epot =1675.251eV Ekin = 732.101eV (T=1415.947K) Etot = 2407.352eV Energy per atom: Epot =1683.029eV Ekin = 738.016eV (T=1427.386K) Etot = 2421.045eV Energy per atom: Epot =1695.076eV Ekin = 738.327eV (T=1427.989K) Etot = 2433.403eV Energy per atom: Epot =1711.346eV Ekin = 735.590eV (T=1422.694K) Etot = 2446.935eV Energy per atom: Epot =1726.938eV Ekin = 737.376eV (T=1426.149K) Etot = 2464.314eV Energy per atom: Epot =1731.488eV Ekin = 745.436eV (T=1441.738K) Etot = 2476.924eV Energy per atom: Epot =1729.798eV Ekin = 746.645eV (T=1444.077K) Etot = 2476.443eV Energy per atom: Epot =1751.787eV Ekin = 737.644eV (T=1426.667K) Etot = 2489.431eV Energy per atom: Epot =1756.531eV Ekin = 731.128eV (T=1414.065K) Etot = 2487.659eV Energy per atom: Epot =1744.433eV Ekin = 745.441eV (T=1441.748K) Etot = 2489.874eV Energy per atom: Epot =1752.050eV Ekin = 730.198eV (T=1412.266K) Etot = 2482.248eV Energy per atom: Epot =1757.561eV Ekin = 742.952eV (T=1436.934K) Etot = 2500.513eV Energy per atom: Epot =1753.362eV Ekin = 754.204eV (T=1458.697K) Etot = 2507.566eV Energy per atom: Epot =1759.149eV Ekin = 743.841eV (T=1438.653K) Etot = 2502.989eV Energy per atom: Epot =1758.834eV Ekin = 740.149eV (T=1431.513K) Etot = 2498.983eV Energy per atom: Epot =1780.281eV Ekin = 730.300eV (T=1412.464K) Etot = 2510.581eV Energy per atom: Epot =1776.996eV Ekin = 744.679eV (T=1440.274K) Etot = 2521.675eV Energy per atom: Epot =1785.240eV Ekin = 742.079eV (T=1435.244K) Etot = 2527.318eV Energy per atom: Epot =1787.193eV Ekin = 744.753eV (T=1440.418K) Etot = 2531.946eV Energy per atom: Epot =1791.241eV Ekin = 737.997eV (T=1427.351K) Etot = 2529.239eV Energy per atom: Epot =1787.258eV Ekin = 746.437eV (T=1443.673K) Etot = 2533.694eV Energy per atom: Epot =1813.978eV Ekin = 735.441eV (T=1422.407K) Etot = 2549.419eV Energy per atom: Epot =1811.308eV Ekin = 729.849eV (T=1411.591K) Etot = 2541.157eV Energy per atom: Epot =1815.331eV Ekin = 732.104eV (T=1415.953K) Etot = 2547.435eV Energy per atom: Epot =1815.761eV Ekin = 730.948eV (T=1413.718K) Etot = 2546.709eV Energy per atom: Epot =1815.295eV Ekin = 733.220eV (T=1418.112K) Etot = 2548.515eV Energy per atom: Epot =1809.491eV Ekin = 742.874eV (T=1436.782K) Etot = 2552.365eV Energy per atom: Epot =1824.322eV Ekin = 731.820eV (T=1415.403K) Etot = 2556.142eV Energy per atom: Epot =1829.260eV Ekin = 737.516eV (T=1426.419K) Etot = 2566.776eV Energy per atom: Epot =1837.833eV Ekin = 724.427eV (T=1401.105K) Etot = 2562.260eV Energy per atom: Epot =1838.618eV Ekin = 726.430eV (T=1404.979K) Etot = 2565.049eV Energy per atom: Epot =1846.527eV Ekin = 734.261eV (T=1420.126K) Etot = 2580.789eV Energy per atom: Epot =1858.656eV Ekin = 733.162eV (T=1417.999K) Etot = 2591.818eV Energy per atom: Epot =1862.887eV Ekin = 724.441eV (T=1401.131K) Etot = 2587.328eV Energy per atom: Epot =1863.890eV Ekin = 733.853eV (T=1419.335K) Etot = 2597.743eV Energy per atom: Epot =1877.667eV Ekin = 719.787eV (T=1392.130K) Etot = 2597.454eV Energy per atom: Epot =1867.000eV Ekin = 743.254eV (T=1437.518K) Etot = 2610.254eV Energy per atom: Epot =1883.280eV Ekin = 736.844eV (T=1425.120K) Etot = 2620.124eV Energy per atom: Epot =1870.384eV Ekin = 754.720eV (T=1459.695K) Etot = 2625.104eV Energy per atom: Epot =1890.403eV Ekin = 743.714eV (T=1438.408K) Etot = 2634.117eV Energy per atom: Epot =1884.885eV Ekin = 759.225eV (T=1468.407K) Etot = 2644.110eV Energy per atom: Epot =1898.242eV Ekin = 739.623eV (T=1430.494K) Etot = 2637.865eV Energy per atom: Epot =1904.748eV Ekin = 741.880eV (T=1434.860K) Etot = 2646.628eV Energy per atom: Epot =1888.801eV Ekin = 758.337eV (T=1466.690K) Etot = 2647.138eV Energy per atom: Epot =1911.792eV Ekin = 745.908eV (T=1442.650K) Etot = 2657.700eV Energy per atom: Epot =1909.205eV Ekin = 751.016eV (T=1452.531K) Etot = 2660.222eV Energy per atom: Epot =1909.675eV Ekin = 759.166eV (T=1468.293K) Etot = 2668.841eV Energy per atom: Epot =1912.008eV Ekin = 763.765eV (T=1477.187K) Etot = 2675.773eV Energy per atom: Epot =1918.726eV Ekin = 757.142eV (T=1464.379K) Etot = 2675.868eV Energy per atom: Epot =1908.534eV Ekin = 763.271eV (T=1476.232K) Etot = 2671.805eV Energy per atom: Epot =1915.457eV Ekin = 761.036eV (T=1471.909K) Etot = 2676.493eV Energy per atom: Epot =1914.969eV Ekin = 762.645eV (T=1475.021K) Etot = 2677.614eV Energy per atom: Epot =1922.267eV Ekin = 759.592eV (T=1469.117K) Etot = 2681.859eV Energy per atom: Epot =1921.147eV Ekin = 751.202eV (T=1452.891K) Etot = 2672.349eV Energy per atom: Epot =1919.660eV Ekin = 759.755eV (T=1469.431K) Etot = 2679.415eV Energy per atom: Epot =1930.054eV Ekin = 752.789eV (T=1455.960K) Etot = 2682.843eV Energy per atom: Epot =1916.885eV Ekin = 776.317eV (T=1501.465K) Etot = 2693.202eV Energy per atom: Epot =1937.413eV Ekin = 761.304eV (T=1472.428K) Etot = 2698.716eV Energy per atom: Epot =1932.963eV Ekin = 775.836eV (T=1500.534K) Etot = 2708.799eV Energy per atom: Epot =1947.705eV Ekin = 766.495eV (T=1482.467K) Etot = 2714.200eV Energy per atom: Epot =1943.387eV Ekin = 769.882eV (T=1489.018K) Etot = 2713.269eV Energy per atom: Epot =1937.635eV Ekin = 773.207eV (T=1495.449K) Etot = 2710.842eV Energy per atom: Epot =1950.097eV Ekin = 764.992eV (T=1479.560K) Etot = 2715.089eV Energy per atom: Epot =1954.974eV Ekin = 760.096eV (T=1470.093K) Etot = 2715.070eV Energy per atom: Epot =1950.593eV Ekin = 758.713eV (T=1467.417K) Etot = 2709.306eV Energy per atom: Epot =1946.697eV Ekin = 772.217eV (T=1493.535K) Etot = 2718.914eV Energy per atom: Epot =1955.821eV Ekin = 768.284eV (T=1485.928K) Etot = 2724.105eV Energy per atom: Epot =1957.811eV Ekin = 771.214eV (T=1491.596K) Etot = 2729.025eV Energy per atom: Epot =1955.412eV Ekin = 773.022eV (T=1495.092K) Etot = 2728.434eV Energy per atom: Epot =1961.008eV Ekin = 755.084eV (T=1460.398K) Etot = 2716.092eV Energy per atom: Epot =1962.471eV Ekin = 758.204eV (T=1466.433K) Etot = 2720.676eV Energy per atom: Epot =1971.835eV Ekin = 753.891eV (T=1458.091K) Etot = 2725.726eV Energy per atom: Epot =1978.744eV Ekin = 753.920eV (T=1458.147K) Etot = 2732.664eV Energy per atom: Epot =1982.688eV Ekin = 744.045eV (T=1439.048K) Etot = 2726.733eV Energy per atom: Epot =1982.841eV Ekin = 745.433eV (T=1441.732K) Etot = 2728.273eV Energy per atom: Epot =1983.926eV Ekin = 750.583eV (T=1451.694K) Etot = 2734.510eV Energy per atom: Epot =1996.500eV Ekin = 757.717eV (T=1465.490K) Etot = 2754.216eV Energy per atom: Epot =1989.352eV Ekin = 765.384eV (T=1480.319K) Etot = 2754.736eV Energy per atom: Epot =1986.783eV Ekin = 763.912eV (T=1477.472K) Etot = 2750.695eV Energy per atom: Epot =1991.693eV Ekin = 767.206eV (T=1483.842K) Etot = 2758.899eV Energy per atom: Epot =1991.736eV Ekin = 770.444eV (T=1490.105K) Etot = 2762.179eV Energy per atom: Epot =1982.573eV Ekin = 775.460eV (T=1499.807K) Etot = 2758.033eV Energy per atom: Epot =1987.555eV Ekin = 755.364eV (T=1460.940K) Etot = 2742.919eV Energy per atom: Epot =1973.776eV Ekin = 771.590eV (T=1492.322K) Etot = 2745.366eV Energy per atom: Epot =1992.173eV Ekin = 751.241eV (T=1452.965K) Etot = 2743.413eV Energy per atom: Epot =1978.026eV Ekin = 768.925eV (T=1487.167K) Etot = 2746.951eV Energy per atom: Epot =1986.003eV Ekin = 771.591eV (T=1492.325K) Etot = 2757.595eV Energy per atom: Epot =1997.889eV Ekin = 762.366eV (T=1474.481K) Etot = 2760.255eV Energy per atom: Epot =1992.236eV Ekin = 769.265eV (T=1487.825K) Etot = 2761.500eV Energy per atom: Epot =1994.653eV Ekin = 767.728eV (T=1484.852K) Etot = 2762.380eV Energy per atom: Epot =1996.364eV Ekin = 768.051eV (T=1485.478K) Etot = 2764.415eV Energy per atom: Epot =1984.213eV Ekin = 772.839eV (T=1494.739K) Etot = 2757.052eV Energy per atom: Epot =1999.435eV Ekin = 766.885eV (T=1483.222K) Etot = 2766.320eV Energy per atom: Epot =1998.465eV Ekin = 769.882eV (T=1489.018K) Etot = 2768.347eV Energy per atom: Epot =1997.526eV Ekin = 775.507eV (T=1499.898K) Etot = 2773.033eV Energy per atom: Epot =2004.990eV Ekin = 769.157eV (T=1487.616K) Etot = 2774.146eV Energy per atom: Epot =2004.105eV Ekin = 767.640eV (T=1484.682K) Etot = 2771.744eV Energy per atom: Epot =2007.293eV Ekin = 778.430eV (T=1505.552K) Etot = 2785.723eV Energy per atom: Epot =2008.152eV Ekin = 782.630eV (T=1513.674K) Etot = 2790.781eV Energy per atom: Epot =2007.870eV Ekin = 782.472eV (T=1513.369K) Etot = 2790.342eV Energy per atom: Epot =2008.217eV Ekin = 787.538eV (T=1523.167K) Etot = 2795.754eV Energy per atom: Epot =2008.968eV Ekin = 784.704eV (T=1517.685K) Etot = 2793.672eV Energy per atom: Epot =2009.908eV Ekin = 788.784eV (T=1525.578K) Etot = 2798.693eV Energy per atom: Epot =2009.510eV Ekin = 789.930eV (T=1527.793K) Etot = 2799.440eV Energy per atom: Epot =2020.866eV Ekin = 786.614eV (T=1521.380K) Etot = 2807.480eV Energy per atom: Epot =2010.608eV Ekin = 777.069eV (T=1502.918K) Etot = 2787.677eV Energy per atom: Epot =2023.918eV Ekin = 773.098eV (T=1495.239K) Etot = 2797.016eV Energy per atom: Epot =2006.440eV Ekin = 791.802eV (T=1531.414K) Etot = 2798.242eV Energy per atom: Epot =2014.949eV Ekin = 794.179eV (T=1536.011K) Etot = 2809.128eV Energy per atom: Epot =2033.511eV Ekin = 763.439eV (T=1476.558K) Etot = 2796.950eV Energy per atom: Epot =2028.223eV Ekin = 766.206eV (T=1481.910K) Etot = 2794.430eV Energy per atom: Epot =2022.881eV Ekin = 776.017eV (T=1500.884K) Etot = 2798.897eV Energy per atom: Epot =2016.132eV Ekin = 782.601eV (T=1513.618K) Etot = 2798.732eV Energy per atom: Epot =2018.608eV Ekin = 774.531eV (T=1498.011K) Etot = 2793.139eV Energy per atom: Epot =2019.563eV Ekin = 780.773eV (T=1510.084K) Etot = 2800.337eV Energy per atom: Epot =2028.866eV Ekin = 765.212eV (T=1479.987K) Etot = 2794.078eV Energy per atom: Epot =2024.775eV Ekin = 762.753eV (T=1475.231K) Etot = 2787.528eV Energy per atom: Epot =2022.851eV Ekin = 768.926eV (T=1487.171K) Etot = 2791.777eV Energy per atom: Epot =2027.133eV Ekin = 764.832eV (T=1479.252K) Etot = 2791.965eV Energy per atom: Epot =2028.004eV Ekin = 764.381eV (T=1478.379K) Etot = 2792.385eV Energy per atom: Epot =2025.218eV Ekin = 776.780eV (T=1502.360K) Etot = 2801.998eV Energy per atom: Epot =2006.958eV Ekin = 784.864eV (T=1517.995K) Etot = 2791.822eV Energy per atom: Epot =2010.634eV Ekin = 784.533eV (T=1517.355K) Etot = 2795.167eV Energy per atom: Epot =2017.261eV Ekin = 782.672eV (T=1513.755K) Etot = 2799.932eV Energy per atom: Epot =2027.510eV Ekin = 759.872eV (T=1469.660K) Etot = 2787.383eV Energy per atom: Epot =2014.679eV Ekin = 775.816eV (T=1500.495K) Etot = 2790.495eV Energy per atom: Epot =2021.236eV Ekin = 770.452eV (T=1490.122K) Etot = 2791.688eV Energy per atom: Epot =2010.359eV Ekin = 782.819eV (T=1514.040K) Etot = 2793.179eV Energy per atom: Epot =2023.153eV Ekin = 767.282eV (T=1483.991K) Etot = 2790.435eV Energy per atom: Epot =2019.367eV Ekin = 783.405eV (T=1515.173K) Etot = 2802.772eV Energy per atom: Epot =2028.410eV Ekin = 780.638eV (T=1509.822K) Etot = 2809.048eV Energy per atom: Epot =2021.046eV Ekin = 796.915eV (T=1541.304K) Etot = 2817.961eV Energy per atom: Epot =2035.117eV Ekin = 779.131eV (T=1506.908K) Etot = 2814.248eV Energy per atom: Epot =2026.594eV Ekin = 785.487eV (T=1519.200K) Etot = 2812.081eV Energy per atom: Epot =2028.565eV Ekin = 780.307eV (T=1509.182K) Etot = 2808.873eV Energy per atom: Epot =2024.202eV Ekin = 797.605eV (T=1542.638K) Etot = 2821.807eV Energy per atom: Epot =2028.546eV Ekin = 787.777eV (T=1523.630K) Etot = 2816.323eV Energy per atom: Epot =2027.708eV Ekin = 783.278eV (T=1514.927K) Etot = 2810.986eV Energy per atom: Epot =2025.709eV Ekin = 779.963eV (T=1508.517K) Etot = 2805.673eV Energy per atom: Epot =2020.067eV Ekin = 787.702eV (T=1523.483K) Etot = 2807.769eV Energy per atom: Epot =2012.048eV Ekin = 787.045eV (T=1522.213K) Etot = 2799.093eV Energy per atom: Epot =2014.302eV Ekin = 783.597eV (T=1515.545K) Etot = 2797.900eV Energy per atom: Epot =2021.601eV Ekin = 772.124eV (T=1493.354K) Etot = 2793.725eV Energy per atom: Epot =2006.703eV Ekin = 785.652eV (T=1519.519K) Etot = 2792.355eV Energy per atom: Epot =2020.463eV Ekin = 767.746eV (T=1484.887K) Etot = 2788.209eV Energy per atom: Epot =2015.229eV Ekin = 774.199eV (T=1497.369K) Etot = 2789.429eV Energy per atom: Epot =2007.424eV Ekin = 778.603eV (T=1505.885K) Etot = 2786.027eV Energy per atom: Epot =2013.613eV Ekin = 784.143eV (T=1516.601K) Etot = 2797.756eV Energy per atom: Epot =2015.415eV Ekin = 775.541eV (T=1499.963K) Etot = 2790.955eV Energy per atom: Epot =2022.417eV Ekin = 768.614eV (T=1486.566K) Etot = 2791.031eV Energy per atom: Epot =2027.980eV Ekin = 771.853eV (T=1492.831K) Etot = 2799.833eV Energy per atom: Epot =2032.536eV Ekin = 776.374eV (T=1501.574K) Etot = 2808.910eV Energy per atom: Epot =2030.605eV Ekin = 771.333eV (T=1491.825K) Etot = 2801.938eV Energy per atom: Epot =2008.630eV Ekin = 794.771eV (T=1537.155K) Etot = 2803.401eV Energy per atom: Epot =2023.040eV Ekin = 776.164eV (T=1501.168K) Etot = 2799.203eV Energy per atom: Epot =2008.830eV Ekin = 790.630eV (T=1529.146K) Etot = 2799.459eV .. 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] 00:08:19 43.457006 1.0818 BFGSLineSearch: 1[ 1] 00:08:19 42.347659 0.2273 BFGSLineSearch: 2[ 2] 00:08:19 42.108454 0.1349 BFGSLineSearch: 3[ 3] 00:08:19 41.964817 0.1138 BFGSLineSearch: 4[ 4] 00:08:19 41.924933 0.0683 BFGSLineSearch: 5[ 5] 00:08:19 41.915346 0.0225 BFGSLineSearch: 6[ 6] 00:08:19 41.914920 0.0059 BFGSLineSearch: 7[ 7] 00:08:19 41.914872 0.0023 BFGSLineSearch: 8[ 9] 00:08:19 41.914855 0.0023 BFGSLineSearch: 9[ 10] 00:08:19 41.914851 0.0010 /builds/ase/ase/examples/03-tutorials/md.py:299: DeprecationWarning: Use thermalize_momenta MaxwellBoltzmannDistribution(atoms, temperature_K=1200) running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 13.132eV (T=1092.425K) Etot = 55.047eV Energy per atom: Epot =49.470eV Ekin = 5.612eV (T=466.816K) Etot = 55.081eV Energy per atom: Epot =49.472eV Ekin = 5.617eV (T=467.270K) Etot = 55.089eV Energy per atom: Epot =49.377eV Ekin = 5.711eV (T=475.117K) Etot = 55.089eV Energy per atom: Epot =49.753eV Ekin = 5.336eV (T=443.859K) Etot = 55.089eV Energy per atom: Epot =49.627eV Ekin = 5.461eV (T=454.310K) Etot = 55.088eV Energy per atom: Epot =48.963eV Ekin = 6.123eV (T=509.356K) Etot = 55.086eV Energy per atom: Epot =48.609eV Ekin = 6.473eV (T=538.440K) Etot = 55.082eV Energy per atom: Epot =47.589eV Ekin = 7.493eV (T=623.318K) Etot = 55.082eV Energy per atom: Epot =49.089eV Ekin = 6.002eV (T=499.256K) Etot = 55.090eV Energy per atom: Epot =49.752eV Ekin = 5.343eV (T=444.504K) Etot = 55.095eV Energy per atom: Epot =48.871eV Ekin = 6.215eV (T=517.019K) Etot = 55.086eV Energy per atom: Epot =48.135eV Ekin = 6.949eV (T=578.026K) Etot = 55.084eV Energy per atom: Epot =49.252eV Ekin = 5.840eV (T=485.792K) Etot = 55.092eV Energy per atom: Epot =48.959eV Ekin = 6.131eV (T=510.040K) Etot = 55.090eV Energy per atom: Epot =48.725eV Ekin = 6.363eV (T=529.284K) Etot = 55.088eV Energy per atom: Epot =49.057eV Ekin = 6.029eV (T=501.563K) Etot = 55.086eV Energy per atom: Epot =49.044eV Ekin = 6.047eV (T=503.020K) Etot = 55.091eV Energy per atom: Epot =48.619eV Ekin = 6.467eV (T=537.982K) Etot = 55.087eV Energy per atom: Epot =48.475eV Ekin = 6.609eV (T=549.819K) Etot = 55.085eV Energy per atom: Epot =48.434eV Ekin = 6.650eV (T=553.205K) Etot = 55.084eV Energy per atom: Epot =49.051eV Ekin = 6.034eV (T=501.958K) Etot = 55.085eV Energy per atom: Epot =49.411eV Ekin = 5.677eV (T=472.234K) Etot = 55.088eV Energy per atom: Epot =49.437eV Ekin = 5.650eV (T=469.978K) Etot = 55.087eV Energy per atom: Epot =49.004eV Ekin = 6.083eV (T=506.023K) Etot = 55.087eV Energy per atom: Epot =48.684eV Ekin = 6.406eV (T=532.862K) Etot = 55.089eV Energy per atom: Epot =48.753eV Ekin = 6.334eV (T=526.906K) Etot = 55.087eV Energy per atom: Epot =48.265eV Ekin = 6.814eV (T=566.820K) Etot = 55.079eV Energy per atom: Epot =48.115eV Ekin = 6.966eV (T=579.494K) Etot = 55.081eV Energy per atom: Epot =49.678eV Ekin = 5.412eV (T=450.206K) Etot = 55.090eV Energy per atom: Epot =49.037eV Ekin = 6.050eV (T=503.298K) Etot = 55.088eV Energy per atom: Epot =48.579eV Ekin = 6.509eV (T=541.459K) Etot = 55.088eV Energy per atom: Epot =48.311eV Ekin = 6.772eV (T=563.307K) Etot = 55.083eV Energy per atom: Epot =48.856eV Ekin = 6.227eV (T=517.998K) Etot = 55.083eV Energy per atom: Epot =48.197eV Ekin = 6.890eV (T=573.167K) Etot = 55.087eV Energy per atom: Epot =49.066eV Ekin = 6.023eV (T=501.029K) Etot = 55.089eV Energy per atom: Epot =49.479eV Ekin = 5.610eV (T=466.640K) Etot = 55.088eV Energy per atom: Epot =49.695eV Ekin = 5.395eV (T=448.831K) Etot = 55.090eV Energy per atom: Epot =49.045eV Ekin = 6.044eV (T=502.743K) Etot = 55.088eV Energy per atom: Epot =48.610eV Ekin = 6.477eV (T=538.828K) Etot = 55.087eV Energy per atom: Epot =48.512eV Ekin = 6.573eV (T=546.822K) Etot = 55.086eV Energy per atom: Epot =49.293eV Ekin = 5.797eV (T=482.258K) Etot = 55.091eV Energy per atom: Epot =49.199eV Ekin = 5.894eV (T=490.321K) Etot = 55.093eV Energy per atom: Epot =48.192eV Ekin = 6.896eV (T=573.623K) Etot = 55.087eV Energy per atom: Epot =48.866eV Ekin = 6.219eV (T=517.373K) Etot = 55.086eV Energy per atom: Epot =49.733eV Ekin = 5.356eV (T=445.585K) Etot = 55.089eV Energy per atom: Epot =49.784eV Ekin = 5.307eV (T=441.481K) Etot = 55.091eV Energy per atom: Epot =48.301eV Ekin = 6.783eV (T=564.236K) Etot = 55.084eV Energy per atom: Epot =48.934eV Ekin = 6.153eV (T=511.883K) Etot = 55.087eV Energy per atom: Epot =49.152eV Ekin = 5.936eV (T=493.809K) Etot = 55.088eV Energy per atom: Epot =48.776eV Ekin = 6.310eV (T=524.937K) Etot = 55.087eV Energy per atom: Epot =48.189eV Ekin = 6.897eV (T=573.762K) Etot = 55.086eV Energy per atom: Epot =49.201eV Ekin = 5.888eV (T=489.843K) Etot = 55.089eV Energy per atom: Epot =49.001eV Ekin = 6.085eV (T=506.195K) Etot = 55.086eV Energy per atom: Epot =50.015eV Ekin = 5.079eV (T=422.520K) Etot = 55.094eV Energy per atom: Epot =49.294eV Ekin = 5.796eV (T=482.126K) Etot = 55.090eV Energy per atom: Epot =48.764eV Ekin = 6.322eV (T=525.944K) Etot = 55.087eV Energy per atom: Epot =49.106eV Ekin = 5.983eV (T=497.705K) Etot = 55.089eV Energy per atom: Epot =48.717eV Ekin = 6.368eV (T=529.697K) Etot = 55.085eV Energy per atom: Epot =48.726eV Ekin = 6.357eV (T=528.837K) Etot = 55.084eV Energy per atom: Epot =48.470eV Ekin = 6.614eV (T=550.209K) Etot = 55.084eV Energy per atom: Epot =48.963eV Ekin = 6.125eV (T=509.482K) Etot = 55.088eV Energy per atom: Epot =48.559eV Ekin = 6.526eV (T=542.849K) Etot = 55.085eV Energy per atom: Epot =49.139eV Ekin = 5.951eV (T=495.002K) Etot = 55.089eV Energy per atom: Epot =48.880eV Ekin = 6.206eV (T=516.231K) Etot = 55.086eV Energy per atom: Epot =48.607eV Ekin = 6.478eV (T=538.908K) Etot = 55.086eV Energy per atom: Epot =49.106eV Ekin = 5.987eV (T=498.040K) Etot = 55.093eV Energy per atom: Epot =48.552eV Ekin = 6.534eV (T=543.518K) Etot = 55.086eV Energy per atom: Epot =49.315eV Ekin = 5.775eV (T=480.427K) Etot = 55.091eV Energy per atom: Epot =49.238eV Ekin = 5.855eV (T=487.036K) Etot = 55.093eV Energy per atom: Epot =49.099eV Ekin = 5.992eV (T=498.429K) Etot = 55.091eV Energy per atom: Epot =48.338eV Ekin = 6.749eV (T=561.442K) Etot = 55.087eV Energy per atom: Epot =49.200eV Ekin = 5.894eV (T=490.313K) Etot = 55.094eV Energy per atom: Epot =48.452eV Ekin = 6.632eV (T=551.717K) Etot = 55.084eV Energy per atom: Epot =48.435eV Ekin = 6.650eV (T=553.178K) Etot = 55.085eV Energy per atom: Epot =48.558eV Ekin = 6.527eV (T=542.946K) Etot = 55.085eV Energy per atom: Epot =48.590eV Ekin = 6.495eV (T=540.319K) Etot = 55.085eV Energy per atom: Epot =49.054eV Ekin = 6.035eV (T=502.054K) Etot = 55.090eV Energy per atom: Epot =48.108eV Ekin = 6.971eV (T=579.927K) Etot = 55.080eV Energy per atom: Epot =48.562eV Ekin = 6.522eV (T=542.572K) Etot = 55.084eV Energy per atom: Epot =48.080eV Ekin = 7.005eV (T=582.714K) Etot = 55.085eV Energy per atom: Epot =48.334eV Ekin = 6.753eV (T=561.717K) Etot = 55.086eV Energy per atom: Epot =48.669eV Ekin = 6.418eV (T=533.900K) Etot = 55.087eV Energy per atom: Epot =49.216eV Ekin = 5.872eV (T=488.475K) Etot = 55.088eV Energy per atom: Epot =49.105eV Ekin = 5.981eV (T=497.565K) Etot = 55.086eV Energy per atom: Epot =48.596eV Ekin = 6.494eV (T=540.203K) Etot = 55.089eV Energy per atom: Epot =48.860eV Ekin = 6.231eV (T=518.338K) Etot = 55.091eV Energy per atom: Epot =48.925eV Ekin = 6.160eV (T=512.408K) Etot = 55.085eV Energy per atom: Epot =49.244eV Ekin = 5.844eV (T=486.163K) Etot = 55.088eV Energy per atom: Epot =48.723eV Ekin = 6.361eV (T=529.176K) Etot = 55.084eV Energy per atom: Epot =48.426eV Ekin = 6.659eV (T=553.928K) Etot = 55.085eV Energy per atom: Epot =48.270eV Ekin = 6.815eV (T=566.898K) Etot = 55.085eV Energy per atom: Epot =48.269eV Ekin = 6.817eV (T=567.062K) Etot = 55.085eV Energy per atom: Epot =47.881eV Ekin = 7.200eV (T=598.963K) Etot = 55.081eV Energy per atom: Epot =48.452eV Ekin = 6.632eV (T=551.678K) Etot = 55.084eV Energy per atom: Epot =48.983eV Ekin = 6.108eV (T=508.079K) Etot = 55.091eV Energy per atom: Epot =48.762eV Ekin = 6.326eV (T=526.257K) Etot = 55.088eV Energy per atom: Epot =48.883eV Ekin = 6.206eV (T=516.284K) Etot = 55.089eV Energy per atom: Epot =49.746eV Ekin = 5.346eV (T=444.674K) Etot = 55.092eV Energy per atom: Epot =49.468eV Ekin = 5.617eV (T=467.250K) Etot = 55.085eV Energy per atom: Epot =49.262eV Ekin = 5.827eV (T=484.731K) Etot = 55.089eV Energy per atom: Epot =48.598eV Ekin = 6.487eV (T=539.651K) Etot = 55.086eV Energy per atom: Epot =48.403eV Ekin = 6.682eV (T=555.817K) Etot = 55.085eV Energy per atom: Epot =49.222eV Ekin = 5.868eV (T=488.162K) Etot = 55.090eV Energy per atom: Epot =48.442eV Ekin = 6.646eV (T=552.841K) Etot = 55.088eV Energy per atom: Epot =48.514eV Ekin = 6.572eV (T=546.729K) Etot = 55.086eV Energy per atom: Epot =48.935eV Ekin = 6.151eV (T=511.715K) Etot = 55.087eV Energy per atom: Epot =49.485eV Ekin = 5.604eV (T=466.149K) Etot = 55.089eV Energy per atom: Epot =49.026eV Ekin = 6.061eV (T=504.154K) Etot = 55.087eV Energy per atom: Epot =48.680eV Ekin = 6.404eV (T=532.725K) Etot = 55.084eV Energy per atom: Epot =48.377eV Ekin = 6.710eV (T=558.177K) Etot = 55.087eV Energy per atom: Epot =48.302eV Ekin = 6.784eV (T=564.379K) Etot = 55.087eV Energy per atom: Epot =47.721eV Ekin = 7.362eV (T=612.410K) Etot = 55.082eV Energy per atom: Epot =49.129eV Ekin = 5.961eV (T=495.884K) Etot = 55.091eV Energy per atom: Epot =49.407eV Ekin = 5.682eV (T=472.673K) Etot = 55.089eV Energy per atom: Epot =49.244eV Ekin = 5.848eV (T=486.438K) Etot = 55.091eV Energy per atom: Epot =48.520eV Ekin = 6.573eV (T=546.748K) Etot = 55.092eV Energy per atom: Epot =48.538eV Ekin = 6.550eV (T=544.907K) Etot = 55.089eV Energy per atom: Epot =48.884eV Ekin = 6.206eV (T=516.292K) Etot = 55.090eV Energy per atom: Epot =48.850eV Ekin = 6.243eV (T=519.292K) Etot = 55.092eV Energy per atom: Epot =48.477eV Ekin = 6.611eV (T=549.912K) Etot = 55.088eV Energy per atom: Epot =48.595eV Ekin = 6.492eV (T=540.078K) Etot = 55.087eV Energy per atom: Epot =49.191eV Ekin = 5.898eV (T=490.633K) Etot = 55.089eV Energy per atom: Epot =48.993eV Ekin = 6.094eV (T=506.977K) Etot = 55.088eV Energy per atom: Epot =48.299eV Ekin = 6.787eV (T=564.616K) Etot = 55.086eV Energy per atom: Epot =48.764eV Ekin = 6.325eV (T=526.163K) Etot = 55.089eV Energy per atom: Epot =49.004eV Ekin = 6.083eV (T=506.016K) Etot = 55.087eV Energy per atom: Epot =48.824eV Ekin = 6.262eV (T=520.898K) Etot = 55.085eV Energy per atom: Epot =48.604eV Ekin = 6.480eV (T=539.010K) Etot = 55.084eV Energy per atom: Epot =48.702eV Ekin = 6.383eV (T=530.980K) Etot = 55.085eV Energy per atom: Epot =48.744eV Ekin = 6.346eV (T=527.910K) Etot = 55.090eV Energy per atom: Epot =49.030eV Ekin = 6.064eV (T=504.451K) Etot = 55.094eV Energy per atom: Epot =48.206eV Ekin = 6.881eV (T=572.426K) Etot = 55.087eV Energy per atom: Epot =48.287eV Ekin = 6.797eV (T=565.403K) Etot = 55.084eV Energy per atom: Epot =49.253eV Ekin = 5.839eV (T=485.761K) Etot = 55.092eV Energy per atom: Epot =48.795eV Ekin = 6.290eV (T=523.223K) Etot = 55.085eV Energy per atom: Epot =49.077eV Ekin = 6.013eV (T=500.168K) Etot = 55.089eV Energy per atom: Epot =48.302eV Ekin = 6.783eV (T=564.238K) Etot = 55.084eV Energy per atom: Epot =48.376eV Ekin = 6.708eV (T=557.979K) Etot = 55.083eV Energy per atom: Epot =48.940eV Ekin = 6.147eV (T=511.348K) Etot = 55.087eV Energy per atom: Epot =49.036eV Ekin = 6.051eV (T=503.402K) Etot = 55.088eV Energy per atom: Epot =48.852eV Ekin = 6.239eV (T=518.967K) Etot = 55.090eV Energy per atom: Epot =48.397eV Ekin = 6.691eV (T=556.588K) Etot = 55.088eV Energy per atom: Epot =48.287eV Ekin = 6.797eV (T=565.434K) Etot = 55.084eV Energy per atom: Epot =47.956eV Ekin = 7.127eV (T=592.849K) Etot = 55.083eV Energy per atom: Epot =48.475eV Ekin = 6.609eV (T=549.816K) Etot = 55.085eV Energy per atom: Epot =48.281eV Ekin = 6.806eV (T=566.147K) Etot = 55.087eV Energy per atom: Epot =49.211eV Ekin = 5.880eV (T=489.146K) Etot = 55.092eV Energy per atom: Epot =48.207eV Ekin = 6.877eV (T=572.096K) Etot = 55.085eV Energy per atom: Epot =49.076eV Ekin = 6.013eV (T=500.182K) Etot = 55.089eV Energy per atom: Epot =48.508eV Ekin = 6.580eV (T=547.340K) Etot = 55.088eV Energy per atom: Epot =48.335eV Ekin = 6.750eV (T=561.534K) Etot = 55.085eV Energy per atom: Epot =48.902eV Ekin = 6.183eV (T=514.371K) Etot = 55.086eV Energy per atom: Epot =49.617eV Ekin = 5.473eV (T=455.277K) Etot = 55.090eV Energy per atom: Epot =48.619eV Ekin = 6.466eV (T=537.854K) Etot = 55.085eV Energy per atom: Epot =48.398eV Ekin = 6.687eV (T=556.247K) Etot = 55.085eV Energy per atom: Epot =47.572eV Ekin = 7.512eV (T=624.929K) Etot = 55.084eV Energy per atom: Epot =47.599eV Ekin = 7.485eV (T=622.664K) Etot = 55.085eV Energy per atom: Epot =48.324eV Ekin = 6.765eV (T=562.789K) Etot = 55.090eV Energy per atom: Epot =48.074eV Ekin = 7.015eV (T=583.525K) Etot = 55.089eV Energy per atom: Epot =49.343eV Ekin = 5.748eV (T=478.115K) Etot = 55.091eV Energy per atom: Epot =48.639eV Ekin = 6.448eV (T=536.377K) Etot = 55.087eV Energy per atom: Epot =48.357eV Ekin = 6.734eV (T=560.211K) Etot = 55.091eV Energy per atom: Epot =48.286eV Ekin = 6.804eV (T=566.000K) Etot = 55.090eV Energy per atom: Epot =48.534eV Ekin = 6.554eV (T=545.211K) Etot = 55.089eV Energy per atom: Epot =47.824eV Ekin = 7.261eV (T=604.024K) Etot = 55.085eV Energy per atom: Epot =48.936eV Ekin = 6.153eV (T=511.824K) Etot = 55.089eV Energy per atom: Epot =49.533eV Ekin = 5.558eV (T=462.320K) Etot = 55.091eV Energy per atom: Epot =49.032eV Ekin = 6.057eV (T=503.870K) Etot = 55.089eV Energy per atom: Epot =48.171eV Ekin = 6.911eV (T=574.918K) Etot = 55.082eV Energy per atom: Epot =48.247eV Ekin = 6.838eV (T=568.789K) Etot = 55.084eV Energy per atom: Epot =48.238eV Ekin = 6.845eV (T=569.419K) Etot = 55.083eV Energy per atom: Epot =48.302eV Ekin = 6.782eV (T=564.206K) Etot = 55.084eV Energy per atom: Epot =48.462eV Ekin = 6.625eV (T=551.073K) Etot = 55.087eV Energy per atom: Epot =48.907eV Ekin = 6.182eV (T=514.263K) Etot = 55.089eV Energy per atom: Epot =49.037eV Ekin = 6.052eV (T=503.446K) Etot = 55.089eV Energy per atom: Epot =48.305eV Ekin = 6.779eV (T=563.923K) Etot = 55.084eV Energy per atom: Epot =48.721eV Ekin = 6.361eV (T=529.190K) Etot = 55.083eV Energy per atom: Epot =48.311eV Ekin = 6.768eV (T=563.040K) Etot = 55.080eV Energy per atom: Epot =48.228eV Ekin = 6.857eV (T=570.448K) Etot = 55.086eV Energy per atom: Epot =48.110eV Ekin = 6.975eV (T=580.243K) Etot = 55.085eV Energy per atom: Epot =49.253eV Ekin = 5.838eV (T=485.637K) Etot = 55.091eV Energy per atom: Epot =48.673eV Ekin = 6.414eV (T=533.520K) Etot = 55.086eV Energy per atom: Epot =48.434eV Ekin = 6.651eV (T=553.267K) Etot = 55.085eV Energy per atom: Epot =48.161eV Ekin = 6.922eV (T=575.824K) Etot = 55.083eV Energy per atom: Epot =48.167eV Ekin = 6.920eV (T=575.622K) Etot = 55.086eV Energy per atom: Epot =48.551eV Ekin = 6.539eV (T=543.991K) Etot = 55.091eV Energy per atom: Epot =49.093eV Ekin = 6.000eV (T=499.156K) Etot = 55.094eV Energy per atom: Epot =48.654eV Ekin = 6.433eV (T=535.114K) Etot = 55.087eV Energy per atom: Epot =49.198eV Ekin = 5.890eV (T=489.968K) Etot = 55.088eV Energy per atom: Epot =48.162eV Ekin = 6.925eV (T=576.101K) Etot = 55.088eV Energy per atom: Epot =48.123eV Ekin = 6.958eV (T=578.794K) Etot = 55.081eV Energy per atom: Epot =48.524eV Ekin = 6.561eV (T=545.770K) Etot = 55.085eV Energy per atom: Epot =48.542eV Ekin = 6.546eV (T=544.567K) Etot = 55.089eV Energy per atom: Epot =48.737eV Ekin = 6.349eV (T=528.141K) Etot = 55.086eV Energy per atom: Epot =48.715eV Ekin = 6.370eV (T=529.877K) Etot = 55.085eV Energy per atom: Epot =48.900eV Ekin = 6.188eV (T=514.754K) Etot = 55.088eV Energy per atom: Epot =48.799eV Ekin = 6.289eV (T=523.160K) Etot = 55.088eV Energy per atom: Epot =48.201eV Ekin = 6.881eV (T=572.438K) Etot = 55.082eV Energy per atom: Epot =48.629eV Ekin = 6.454eV (T=536.862K) Etot = 55.083eV Energy per atom: Epot =48.475eV Ekin = 6.610eV (T=549.824K) Etot = 55.085eV .. GENERATED FROM PYTHON SOURCE LINES 314-324 After running the simulation, use :ref:`ase-gui` to compare the resulting trajectory with how it looks if you comment out either the line that says ``Stationary(atoms)``, ``ZeroRotation(atoms)`` or both: :: ase gui nanoparticleCu_NVE.traj Try playing the movie with a high frame rate and set frame skipping to a low number. Can you spot the subtle difference? .. _sphx_glr_download_examples_generated_03-tutorials_md.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: md.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: md.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: md.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_