.. 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 = 154.948eV (T=299.682K) Etot = 152.543eV Energy per atom: Epot =117.373eV Ekin = 35.955eV (T=69.540K) Etot = 153.328eV Energy per atom: Epot =77.380eV Ekin = 75.796eV (T=146.595K) Etot = 153.176eV Energy per atom: Epot =71.548eV Ekin = 81.495eV (T=157.618K) Etot = 153.042eV Energy per atom: Epot =69.438eV Ekin = 83.552eV (T=161.597K) Etot = 152.990eV Energy per atom: Epot =80.249eV Ekin = 72.890eV (T=140.976K) Etot = 153.140eV Energy per atom: Epot =77.415eV Ekin = 75.718eV (T=146.446K) Etot = 153.133eV Energy per atom: Epot =73.806eV Ekin = 79.243eV (T=153.264K) Etot = 153.049eV Energy per atom: Epot =72.289eV Ekin = 80.763eV (T=156.203K) Etot = 153.052eV Energy per atom: Epot =79.168eV Ekin = 73.956eV (T=143.037K) Etot = 153.124eV Energy per atom: Epot =74.794eV Ekin = 78.290eV (T=151.419K) Etot = 153.083eV Energy per atom: Epot =74.348eV Ekin = 78.728eV (T=152.267K) Etot = 153.076eV Energy per atom: Epot =74.983eV Ekin = 78.097eV (T=151.046K) Etot = 153.080eV Energy per atom: Epot =77.079eV Ekin = 76.012eV (T=147.014K) Etot = 153.092eV Energy per atom: Epot =73.904eV Ekin = 79.174eV (T=153.129K) Etot = 153.078eV Energy per atom: Epot =76.139eV Ekin = 76.962eV (T=148.851K) Etot = 153.101eV Energy per atom: Epot =74.122eV Ekin = 78.955eV (T=152.705K) Etot = 153.077eV Energy per atom: Epot =77.108eV Ekin = 75.973eV (T=146.938K) Etot = 153.081eV Energy per atom: Epot =74.463eV Ekin = 78.619eV (T=152.055K) Etot = 153.082eV Energy per atom: Epot =74.883eV Ekin = 78.197eV (T=151.240K) Etot = 153.080eV Energy per atom: Epot =78.122eV Ekin = 74.977eV (T=145.012K) Etot = 153.099eV .. 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 =601.725eV Ekin = 80.694eV (T=156.069K) Etot = 682.418eV Energy per atom: Epot =669.463eV Ekin = 143.355eV (T=277.262K) Etot = 812.818eV Energy per atom: Epot =727.957eV Ekin = 202.534eV (T=391.718K) Etot = 930.490eV Energy per atom: Epot =783.096eV Ekin = 255.639eV (T=494.427K) Etot = 1038.735eV Energy per atom: Epot =831.946eV Ekin = 293.418eV (T=567.496K) Etot = 1125.364eV Energy per atom: Epot =890.000eV Ekin = 330.306eV (T=638.841K) Etot = 1220.306eV Energy per atom: Epot =920.016eV Ekin = 374.094eV (T=723.531K) Etot = 1294.111eV Energy per atom: Epot =960.199eV Ekin = 410.658eV (T=794.248K) Etot = 1370.857eV Energy per atom: Epot =1003.071eV Ekin = 436.900eV (T=845.003K) Etot = 1439.971eV Energy per atom: Epot =1041.591eV Ekin = 461.609eV (T=892.792K) Etot = 1503.200eV Energy per atom: Epot =1071.996eV Ekin = 488.972eV (T=945.714K) Etot = 1560.967eV Energy per atom: Epot =1101.252eV Ekin = 509.227eV (T=984.890K) Etot = 1610.479eV Energy per atom: Epot =1130.718eV Ekin = 534.254eV (T=1033.293K) Etot = 1664.972eV Energy per atom: Epot =1173.726eV Ekin = 535.697eV (T=1036.084K) Etot = 1709.423eV Energy per atom: Epot =1197.617eV Ekin = 548.383eV (T=1060.619K) Etot = 1746.000eV Energy per atom: Epot =1210.733eV Ekin = 573.038eV (T=1108.305K) Etot = 1783.771eV Energy per atom: Epot =1246.918eV Ekin = 576.407eV (T=1114.822K) Etot = 1823.325eV Energy per atom: Epot =1274.611eV Ekin = 591.580eV (T=1144.166K) Etot = 1866.191eV Energy per atom: Epot =1295.707eV Ekin = 605.086eV (T=1170.290K) Etot = 1900.793eV Energy per atom: Epot =1320.437eV Ekin = 610.015eV (T=1179.822K) Etot = 1930.452eV Energy per atom: Epot =1344.538eV Ekin = 615.678eV (T=1190.774K) Etot = 1960.215eV Energy per atom: Epot =1364.939eV Ekin = 626.751eV (T=1212.191K) Etot = 1991.690eV Energy per atom: Epot =1376.324eV Ekin = 644.630eV (T=1246.770K) Etot = 2020.954eV Energy per atom: Epot =1403.710eV Ekin = 646.117eV (T=1249.646K) Etot = 2049.827eV Energy per atom: Epot =1410.546eV Ekin = 666.396eV (T=1288.867K) Etot = 2076.942eV Energy per atom: Epot =1430.322eV Ekin = 664.966eV (T=1286.103K) Etot = 2095.289eV Energy per atom: Epot =1442.749eV Ekin = 674.001eV (T=1303.577K) Etot = 2116.750eV Energy per atom: Epot =1465.916eV Ekin = 678.670eV (T=1312.606K) Etot = 2144.585eV Energy per atom: Epot =1477.399eV Ekin = 679.004eV (T=1313.253K) Etot = 2156.403eV Energy per atom: Epot =1491.925eV Ekin = 675.996eV (T=1307.435K) Etot = 2167.921eV Energy per atom: Epot =1495.613eV Ekin = 694.062eV (T=1342.376K) Etot = 2189.675eV Energy per atom: Epot =1513.809eV Ekin = 692.745eV (T=1339.830K) Etot = 2206.554eV Energy per atom: Epot =1531.970eV Ekin = 686.798eV (T=1328.327K) Etot = 2218.768eV Energy per atom: Epot =1544.264eV Ekin = 689.085eV (T=1332.750K) Etot = 2233.349eV Energy per atom: Epot =1557.569eV Ekin = 687.861eV (T=1330.384K) Etot = 2245.430eV Energy per atom: Epot =1564.734eV Ekin = 687.369eV (T=1329.432K) Etot = 2252.103eV Energy per atom: Epot =1566.922eV Ekin = 709.072eV (T=1371.407K) Etot = 2275.994eV Energy per atom: Epot =1578.269eV Ekin = 705.353eV (T=1364.215K) Etot = 2283.622eV Energy per atom: Epot =1600.029eV Ekin = 701.360eV (T=1356.492K) Etot = 2301.389eV Energy per atom: Epot =1602.564eV Ekin = 708.322eV (T=1369.956K) Etot = 2310.886eV Energy per atom: Epot =1601.896eV Ekin = 718.430eV (T=1389.507K) Etot = 2320.326eV Energy per atom: Epot =1619.465eV Ekin = 722.159eV (T=1396.719K) Etot = 2341.625eV Energy per atom: Epot =1636.084eV Ekin = 713.298eV (T=1379.580K) Etot = 2349.381eV Energy per atom: Epot =1649.205eV Ekin = 710.289eV (T=1373.760K) Etot = 2359.493eV Energy per atom: Epot =1663.154eV Ekin = 710.474eV (T=1374.119K) Etot = 2373.628eV Energy per atom: Epot =1662.579eV Ekin = 729.390eV (T=1410.704K) Etot = 2391.969eV Energy per atom: Epot =1672.067eV Ekin = 717.868eV (T=1388.419K) Etot = 2389.934eV Energy per atom: Epot =1669.671eV Ekin = 731.154eV (T=1414.115K) Etot = 2400.825eV Energy per atom: Epot =1681.732eV Ekin = 728.516eV (T=1409.014K) Etot = 2410.249eV Energy per atom: Epot =1689.519eV Ekin = 738.216eV (T=1427.775K) Etot = 2427.736eV Energy per atom: Epot =1692.172eV Ekin = 740.812eV (T=1432.794K) Etot = 2432.984eV Energy per atom: Epot =1691.845eV Ekin = 740.247eV (T=1431.701K) Etot = 2432.092eV Energy per atom: Epot =1704.530eV Ekin = 732.034eV (T=1415.817K) Etot = 2436.564eV Energy per atom: Epot =1727.371eV Ekin = 726.674eV (T=1405.451K) Etot = 2454.045eV Energy per atom: Epot =1727.350eV Ekin = 732.285eV (T=1416.304K) Etot = 2459.636eV Energy per atom: Epot =1738.200eV Ekin = 727.816eV (T=1407.659K) Etot = 2466.016eV Energy per atom: Epot =1739.794eV Ekin = 726.612eV (T=1405.331K) Etot = 2466.406eV Energy per atom: Epot =1746.728eV Ekin = 727.269eV (T=1406.601K) Etot = 2473.997eV Energy per atom: Epot =1767.648eV Ekin = 718.433eV (T=1389.512K) Etot = 2486.081eV Energy per atom: Epot =1755.131eV Ekin = 732.947eV (T=1417.582K) Etot = 2488.077eV Energy per atom: Epot =1790.069eV Ekin = 707.977eV (T=1369.290K) Etot = 2498.046eV Energy per atom: Epot =1781.675eV Ekin = 717.220eV (T=1387.167K) Etot = 2498.896eV Energy per atom: Epot =1790.789eV Ekin = 718.243eV (T=1389.144K) Etot = 2509.032eV Energy per atom: Epot =1787.431eV Ekin = 720.300eV (T=1393.123K) Etot = 2507.731eV Energy per atom: Epot =1789.525eV Ekin = 729.726eV (T=1411.354K) Etot = 2519.252eV Energy per atom: Epot =1800.888eV Ekin = 712.477eV (T=1377.993K) Etot = 2513.366eV Energy per atom: Epot =1807.820eV Ekin = 713.163eV (T=1379.319K) Etot = 2520.983eV Energy per atom: Epot =1797.710eV Ekin = 735.726eV (T=1422.958K) Etot = 2533.436eV Energy per atom: Epot =1814.247eV Ekin = 730.461eV (T=1412.776K) Etot = 2544.709eV Energy per atom: Epot =1818.121eV Ekin = 735.947eV (T=1423.385K) Etot = 2554.068eV Energy per atom: Epot =1816.730eV Ekin = 747.570eV (T=1445.866K) Etot = 2564.301eV Energy per atom: Epot =1824.273eV Ekin = 745.953eV (T=1442.737K) Etot = 2570.225eV Energy per atom: Epot =1822.268eV Ekin = 755.619eV (T=1461.433K) Etot = 2577.888eV Energy per atom: Epot =1834.546eV Ekin = 746.029eV (T=1442.884K) Etot = 2580.575eV Energy per atom: Epot =1844.301eV Ekin = 738.668eV (T=1428.649K) Etot = 2582.970eV Energy per atom: Epot =1836.705eV Ekin = 750.406eV (T=1451.351K) Etot = 2587.111eV Energy per atom: Epot =1841.868eV Ekin = 747.493eV (T=1445.717K) Etot = 2589.362eV Energy per atom: Epot =1848.663eV Ekin = 747.791eV (T=1446.293K) Etot = 2596.454eV Energy per atom: Epot =1843.547eV Ekin = 751.811eV (T=1454.067K) Etot = 2595.358eV Energy per atom: Epot =1856.589eV Ekin = 747.686eV (T=1446.090K) Etot = 2604.275eV Energy per atom: Epot =1868.226eV Ekin = 731.977eV (T=1415.707K) Etot = 2600.202eV Energy per atom: Epot =1865.448eV Ekin = 736.264eV (T=1423.999K) Etot = 2601.712eV Energy per atom: Epot =1877.425eV Ekin = 733.419eV (T=1418.497K) Etot = 2610.844eV Energy per atom: Epot =1875.556eV Ekin = 730.561eV (T=1412.968K) Etot = 2606.117eV Energy per atom: Epot =1877.085eV Ekin = 737.512eV (T=1426.413K) Etot = 2614.598eV Energy per atom: Epot =1884.608eV Ekin = 725.966eV (T=1404.081K) Etot = 2610.573eV Energy per atom: Epot =1872.576eV Ekin = 744.536eV (T=1439.997K) Etot = 2617.112eV Energy per atom: Epot =1886.497eV Ekin = 734.174eV (T=1419.957K) Etot = 2620.671eV Energy per atom: Epot =1891.968eV Ekin = 743.176eV (T=1437.368K) Etot = 2635.145eV Energy per atom: Epot =1899.550eV Ekin = 735.303eV (T=1422.140K) Etot = 2634.853eV Energy per atom: Epot =1888.664eV Ekin = 748.406eV (T=1447.483K) Etot = 2637.070eV Energy per atom: Epot =1898.589eV Ekin = 743.448eV (T=1437.894K) Etot = 2642.037eV Energy per atom: Epot =1905.101eV Ekin = 736.151eV (T=1423.780K) Etot = 2641.251eV Energy per atom: Epot =1897.729eV Ekin = 749.566eV (T=1449.726K) Etot = 2647.295eV Energy per atom: Epot =1912.900eV Ekin = 740.437eV (T=1432.070K) Etot = 2653.337eV Energy per atom: Epot =1922.873eV Ekin = 734.106eV (T=1419.824K) Etot = 2656.979eV Energy per atom: Epot =1924.181eV Ekin = 736.443eV (T=1424.346K) Etot = 2660.625eV Energy per atom: Epot =1917.984eV Ekin = 747.873eV (T=1446.451K) Etot = 2665.857eV Energy per atom: Epot =1921.152eV Ekin = 755.712eV (T=1461.613K) Etot = 2676.864eV Energy per atom: Epot =1917.868eV Ekin = 757.780eV (T=1465.613K) Etot = 2675.648eV Energy per atom: Epot =1927.606eV Ekin = 755.613eV (T=1461.421K) Etot = 2683.218eV Energy per atom: Epot =1932.034eV Ekin = 758.874eV (T=1467.729K) Etot = 2690.909eV Energy per atom: Epot =1933.650eV Ekin = 763.192eV (T=1476.079K) Etot = 2696.841eV Energy per atom: Epot =1944.037eV Ekin = 753.795eV (T=1457.906K) Etot = 2697.833eV Energy per atom: Epot =1937.597eV Ekin = 766.963eV (T=1483.372K) Etot = 2704.560eV Energy per atom: Epot =1937.261eV Ekin = 765.615eV (T=1480.767K) Etot = 2702.876eV Energy per atom: Epot =1937.212eV Ekin = 769.363eV (T=1488.016K) Etot = 2706.576eV Energy per atom: Epot =1962.150eV Ekin = 755.847eV (T=1461.874K) Etot = 2717.997eV Energy per atom: Epot =1959.176eV Ekin = 759.638eV (T=1469.205K) Etot = 2718.814eV Energy per atom: Epot =1971.729eV Ekin = 750.221eV (T=1450.994K) Etot = 2721.950eV Energy per atom: Epot =1978.494eV Ekin = 754.455eV (T=1459.182K) Etot = 2732.949eV Energy per atom: Epot =1964.131eV Ekin = 770.055eV (T=1489.353K) Etot = 2734.186eV Energy per atom: Epot =1967.850eV Ekin = 767.894eV (T=1485.174K) Etot = 2735.744eV Energy per atom: Epot =1984.437eV Ekin = 760.934eV (T=1471.713K) Etot = 2745.372eV Energy per atom: Epot =1998.026eV Ekin = 753.121eV (T=1456.601K) Etot = 2751.147eV Energy per atom: Epot =1987.299eV Ekin = 762.359eV (T=1474.469K) Etot = 2749.658eV Energy per atom: Epot =1993.802eV Ekin = 772.752eV (T=1494.569K) Etot = 2766.553eV Energy per atom: Epot =2012.373eV Ekin = 760.610eV (T=1471.085K) Etot = 2772.982eV Energy per atom: Epot =2005.164eV Ekin = 765.318eV (T=1480.191K) Etot = 2770.482eV Energy per atom: Epot =1994.051eV Ekin = 768.331eV (T=1486.020K) Etot = 2762.382eV Energy per atom: Epot =2004.475eV Ekin = 756.761eV (T=1463.642K) Etot = 2761.237eV Energy per atom: Epot =1986.739eV Ekin = 770.614eV (T=1490.434K) Etot = 2757.353eV Energy per atom: Epot =1987.064eV Ekin = 767.358eV (T=1484.137K) Etot = 2754.422eV Energy per atom: Epot =1979.511eV Ekin = 773.155eV (T=1495.350K) Etot = 2752.666eV Energy per atom: Epot =1980.698eV Ekin = 778.310eV (T=1505.318K) Etot = 2759.007eV Energy per atom: Epot =1977.633eV Ekin = 777.389eV (T=1503.539K) Etot = 2755.022eV Energy per atom: Epot =1976.971eV Ekin = 770.445eV (T=1490.108K) Etot = 2747.416eV Energy per atom: Epot =1989.532eV Ekin = 766.280eV (T=1482.053K) Etot = 2755.812eV Energy per atom: Epot =1969.363eV Ekin = 782.583eV (T=1513.584K) Etot = 2751.946eV Energy per atom: Epot =1983.265eV Ekin = 766.901eV (T=1483.254K) Etot = 2750.166eV Energy per atom: Epot =1998.345eV Ekin = 755.636eV (T=1461.466K) Etot = 2753.981eV Energy per atom: Epot =1990.847eV Ekin = 766.862eV (T=1483.178K) Etot = 2757.709eV Energy per atom: Epot =1992.031eV Ekin = 775.664eV (T=1500.201K) Etot = 2767.695eV Energy per atom: Epot =1989.817eV Ekin = 773.800eV (T=1496.597K) Etot = 2763.618eV Energy per atom: Epot =2008.932eV Ekin = 755.740eV (T=1461.666K) Etot = 2764.672eV Energy per atom: Epot =2022.830eV Ekin = 737.352eV (T=1426.104K) Etot = 2760.183eV Energy per atom: Epot =2008.282eV Ekin = 763.933eV (T=1477.513K) Etot = 2772.215eV Energy per atom: Epot =2014.928eV Ekin = 753.906eV (T=1458.119K) Etot = 2768.833eV Energy per atom: Epot =2007.366eV Ekin = 769.034eV (T=1487.379K) Etot = 2776.400eV Energy per atom: Epot =2000.610eV Ekin = 777.075eV (T=1502.930K) Etot = 2777.685eV Energy per atom: Epot =1996.002eV Ekin = 781.488eV (T=1511.467K) Etot = 2777.490eV Energy per atom: Epot =1994.812eV Ekin = 776.918eV (T=1502.627K) Etot = 2771.731eV Energy per atom: Epot =2004.624eV Ekin = 763.493eV (T=1476.661K) Etot = 2768.117eV Energy per atom: Epot =2008.430eV Ekin = 761.423eV (T=1472.659K) Etot = 2769.854eV Energy per atom: Epot =2000.048eV Ekin = 778.256eV (T=1505.216K) Etot = 2778.305eV Energy per atom: Epot =2001.928eV Ekin = 770.014eV (T=1489.274K) Etot = 2771.942eV Energy per atom: Epot =2003.301eV Ekin = 764.908eV (T=1479.399K) Etot = 2768.209eV Energy per atom: Epot =1993.946eV Ekin = 769.343eV (T=1487.977K) Etot = 2763.289eV Energy per atom: Epot =1996.352eV Ekin = 771.600eV (T=1492.342K) Etot = 2767.952eV Energy per atom: Epot =1986.728eV Ekin = 782.471eV (T=1513.366K) Etot = 2769.198eV Energy per atom: Epot =1986.188eV Ekin = 782.920eV (T=1514.235K) Etot = 2769.107eV Energy per atom: Epot =1991.066eV Ekin = 780.193eV (T=1508.961K) Etot = 2771.259eV Energy per atom: Epot =1999.196eV Ekin = 774.999eV (T=1498.915K) Etot = 2774.195eV Energy per atom: Epot =1991.880eV Ekin = 784.216eV (T=1516.742K) Etot = 2776.096eV Energy per atom: Epot =1995.820eV Ekin = 774.506eV (T=1497.962K) Etot = 2770.325eV Energy per atom: Epot =1992.932eV Ekin = 763.835eV (T=1477.323K) Etot = 2756.767eV Energy per atom: Epot =1989.726eV Ekin = 761.565eV (T=1472.932K) Etot = 2751.291eV Energy per atom: Epot =1990.505eV Ekin = 761.960eV (T=1473.696K) Etot = 2752.465eV Energy per atom: Epot =2000.201eV Ekin = 761.131eV (T=1472.094K) Etot = 2761.332eV Energy per atom: Epot =1997.915eV Ekin = 767.674eV (T=1484.748K) Etot = 2765.589eV Energy per atom: Epot =1989.931eV Ekin = 766.353eV (T=1482.193K) Etot = 2756.283eV Energy per atom: Epot =1989.930eV Ekin = 760.522eV (T=1470.916K) Etot = 2750.452eV Energy per atom: Epot =1978.694eV Ekin = 770.760eV (T=1490.717K) Etot = 2749.454eV Energy per atom: Epot =1976.283eV Ekin = 768.572eV (T=1486.485K) Etot = 2744.854eV Energy per atom: Epot =1973.535eV Ekin = 763.981eV (T=1477.606K) Etot = 2737.516eV Energy per atom: Epot =1974.517eV Ekin = 762.755eV (T=1475.234K) Etot = 2737.272eV Energy per atom: Epot =1966.245eV Ekin = 773.236eV (T=1495.506K) Etot = 2739.482eV Energy per atom: Epot =1968.523eV Ekin = 766.659eV (T=1482.784K) Etot = 2735.181eV Energy per atom: Epot =1971.274eV Ekin = 764.066eV (T=1477.771K) Etot = 2735.340eV Energy per atom: Epot =1977.214eV Ekin = 753.689eV (T=1457.700K) Etot = 2730.903eV Energy per atom: Epot =1973.680eV Ekin = 760.457eV (T=1470.789K) Etot = 2734.137eV Energy per atom: Epot =1975.782eV Ekin = 760.269eV (T=1470.426K) Etot = 2736.050eV Energy per atom: Epot =1971.286eV Ekin = 769.448eV (T=1488.179K) Etot = 2740.734eV Energy per atom: Epot =1979.965eV Ekin = 763.872eV (T=1477.395K) Etot = 2743.837eV Energy per atom: Epot =1978.278eV Ekin = 765.464eV (T=1480.474K) Etot = 2743.742eV Energy per atom: Epot =2001.038eV Ekin = 745.703eV (T=1442.254K) Etot = 2746.740eV Energy per atom: Epot =1978.346eV Ekin = 761.544eV (T=1472.893K) Etot = 2739.890eV Energy per atom: Epot =1975.693eV Ekin = 772.755eV (T=1494.576K) Etot = 2748.448eV Energy per atom: Epot =1979.589eV Ekin = 768.773eV (T=1486.873K) Etot = 2748.361eV Energy per atom: Epot =1991.103eV Ekin = 752.266eV (T=1454.949K) Etot = 2743.369eV Energy per atom: Epot =1995.970eV Ekin = 751.774eV (T=1453.996K) Etot = 2747.744eV Energy per atom: Epot =1989.678eV Ekin = 756.761eV (T=1463.642K) Etot = 2746.439eV Energy per atom: Epot =1994.004eV Ekin = 743.286eV (T=1437.581K) Etot = 2737.290eV Energy per atom: Epot =1989.764eV Ekin = 749.747eV (T=1450.075K) Etot = 2739.510eV Energy per atom: Epot =1981.304eV Ekin = 756.497eV (T=1463.132K) Etot = 2737.802eV Energy per atom: Epot =1978.634eV Ekin = 766.949eV (T=1483.346K) Etot = 2745.583eV Energy per atom: Epot =1994.008eV Ekin = 756.688eV (T=1463.501K) Etot = 2750.696eV Energy per atom: Epot =1988.387eV Ekin = 765.819eV (T=1481.160K) Etot = 2754.206eV Energy per atom: Epot =1986.540eV Ekin = 764.855eV (T=1479.297K) Etot = 2751.395eV Energy per atom: Epot =1978.068eV Ekin = 775.271eV (T=1499.441K) Etot = 2753.339eV Energy per atom: Epot =1994.321eV Ekin = 758.100eV (T=1466.231K) Etot = 2752.420eV Energy per atom: Epot =1980.630eV Ekin = 765.594eV (T=1480.725K) Etot = 2746.224eV Energy per atom: Epot =1981.201eV Ekin = 769.753eV (T=1488.769K) Etot = 2750.953eV Energy per atom: Epot =1991.726eV Ekin = 763.113eV (T=1475.928K) Etot = 2754.839eV Energy per atom: Epot =1981.482eV Ekin = 774.230eV (T=1497.429K) Etot = 2755.712eV Energy per atom: Epot =1982.761eV Ekin = 770.891eV (T=1490.971K) Etot = 2753.652eV Energy per atom: Epot =1981.508eV Ekin = 766.960eV (T=1483.368K) Etot = 2748.468eV Energy per atom: Epot =1986.226eV Ekin = 766.345eV (T=1482.178K) Etot = 2752.571eV Energy per atom: Epot =1989.858eV Ekin = 763.011eV (T=1475.730K) Etot = 2752.869eV Energy per atom: Epot =1987.789eV Ekin = 766.789eV (T=1483.037K) Etot = 2754.578eV .. 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] 10:12:26 43.457006 1.0818 BFGSLineSearch: 1[ 1] 10:12:26 42.347659 0.2273 BFGSLineSearch: 2[ 2] 10:12:26 42.108454 0.1349 BFGSLineSearch: 3[ 3] 10:12:26 41.964817 0.1138 BFGSLineSearch: 4[ 4] 10:12:26 41.924933 0.0683 BFGSLineSearch: 5[ 5] 10:12:26 41.915346 0.0225 BFGSLineSearch: 6[ 6] 10:12:26 41.914920 0.0059 BFGSLineSearch: 7[ 7] 10:12:26 41.914872 0.0023 BFGSLineSearch: 8[ 9] 10:12:26 41.914855 0.0023 BFGSLineSearch: 9[ 10] 10:12:26 41.914851 0.0010 running a NVE simulation of a Cu nanoparticle Energy per atom: Epot =41.915eV Ekin = 16.285eV (T=1354.728K) Etot = 58.200eV Energy per atom: Epot =50.557eV Ekin = 7.679eV (T=638.828K) Etot = 58.237eV Energy per atom: Epot =51.711eV Ekin = 6.545eV (T=544.426K) Etot = 58.255eV Energy per atom: Epot =52.026eV Ekin = 6.229eV (T=518.171K) Etot = 58.255eV Energy per atom: Epot =51.907eV Ekin = 6.346eV (T=527.927K) Etot = 58.254eV Energy per atom: Epot =51.543eV Ekin = 6.708eV (T=557.986K) Etot = 58.251eV Energy per atom: Epot =50.607eV Ekin = 7.640eV (T=635.543K) Etot = 58.247eV Energy per atom: Epot =50.120eV Ekin = 8.127eV (T=676.034K) Etot = 58.246eV Energy per atom: Epot =50.410eV Ekin = 7.837eV (T=651.946K) Etot = 58.247eV Energy per atom: Epot =50.592eV Ekin = 7.655eV (T=636.793K) Etot = 58.247eV Energy per atom: Epot =50.975eV Ekin = 7.278eV (T=605.417K) Etot = 58.253eV Energy per atom: Epot =50.978eV Ekin = 7.271eV (T=604.818K) Etot = 58.249eV Energy per atom: Epot =51.830eV Ekin = 6.423eV (T=534.274K) Etot = 58.253eV Energy per atom: Epot =50.476eV Ekin = 7.771eV (T=646.463K) Etot = 58.248eV Energy per atom: Epot =50.793eV Ekin = 7.455eV (T=620.167K) Etot = 58.248eV Energy per atom: Epot =49.964eV Ekin = 8.278eV (T=688.645K) Etot = 58.243eV Energy per atom: Epot =50.871eV Ekin = 7.376eV (T=613.596K) Etot = 58.247eV Energy per atom: Epot =51.383eV Ekin = 6.870eV (T=571.507K) Etot = 58.253eV Energy per atom: Epot =50.273eV Ekin = 7.972eV (T=663.124K) Etot = 58.245eV Energy per atom: Epot =50.542eV Ekin = 7.706eV (T=641.072K) Etot = 58.248eV Energy per atom: Epot =49.887eV Ekin = 8.363eV (T=695.674K) Etot = 58.249eV Energy per atom: Epot =49.643eV Ekin = 8.600eV (T=715.420K) Etot = 58.243eV Energy per atom: Epot =51.369eV Ekin = 6.878eV (T=572.164K) Etot = 58.247eV Energy per atom: Epot =50.537eV Ekin = 7.709eV (T=641.246K) Etot = 58.246eV Energy per atom: Epot =51.597eV Ekin = 6.656eV (T=553.712K) Etot = 58.253eV Energy per atom: Epot =49.501eV Ekin = 8.746eV (T=727.515K) Etot = 58.247eV Energy per atom: Epot =50.871eV Ekin = 7.382eV (T=614.052K) Etot = 58.253eV Energy per atom: Epot =51.517eV Ekin = 6.733eV (T=560.093K) Etot = 58.250eV Energy per atom: Epot =51.266eV Ekin = 6.983eV (T=580.871K) Etot = 58.249eV Energy per atom: Epot =50.558eV Ekin = 7.693eV (T=639.988K) Etot = 58.251eV Energy per atom: Epot =50.566eV Ekin = 7.684eV (T=639.181K) Etot = 58.250eV Energy per atom: Epot =50.652eV Ekin = 7.594eV (T=631.706K) Etot = 58.246eV Energy per atom: Epot =50.382eV Ekin = 7.871eV (T=654.761K) Etot = 58.253eV Energy per atom: Epot =50.251eV Ekin = 8.003eV (T=665.737K) Etot = 58.254eV Energy per atom: Epot =51.146eV Ekin = 7.108eV (T=591.292K) Etot = 58.254eV Energy per atom: Epot =50.669eV Ekin = 7.585eV (T=630.935K) Etot = 58.253eV Energy per atom: Epot =51.182eV Ekin = 7.077eV (T=588.684K) Etot = 58.259eV Energy per atom: Epot =50.419eV Ekin = 7.832eV (T=651.524K) Etot = 58.251eV Energy per atom: Epot =51.316eV Ekin = 6.937eV (T=577.078K) Etot = 58.253eV Energy per atom: Epot =51.047eV Ekin = 7.207eV (T=599.523K) Etot = 58.254eV Energy per atom: Epot =51.115eV Ekin = 7.134eV (T=593.455K) Etot = 58.250eV Energy per atom: Epot =50.858eV Ekin = 7.387eV (T=614.525K) Etot = 58.245eV Energy per atom: Epot =52.104eV Ekin = 6.150eV (T=511.595K) Etot = 58.254eV Energy per atom: Epot =51.204eV Ekin = 7.047eV (T=586.256K) Etot = 58.251eV Energy per atom: Epot =50.304eV Ekin = 7.941eV (T=660.592K) Etot = 58.246eV Energy per atom: Epot =50.497eV Ekin = 7.749eV (T=644.574K) Etot = 58.246eV Energy per atom: Epot =50.421eV Ekin = 7.825eV (T=650.909K) Etot = 58.245eV Energy per atom: Epot =51.788eV Ekin = 6.469eV (T=538.169K) Etot = 58.257eV Energy per atom: Epot =50.819eV Ekin = 7.429eV (T=618.031K) Etot = 58.248eV Energy per atom: Epot =50.652eV Ekin = 7.595eV (T=631.774K) Etot = 58.247eV Energy per atom: Epot =49.966eV Ekin = 8.277eV (T=688.504K) Etot = 58.242eV Energy per atom: Epot =50.230eV Ekin = 8.008eV (T=666.192K) Etot = 58.239eV Energy per atom: Epot =50.928eV Ekin = 7.320eV (T=608.900K) Etot = 58.247eV Energy per atom: Epot =51.586eV Ekin = 6.668eV (T=554.667K) Etot = 58.254eV Energy per atom: Epot =51.062eV Ekin = 7.191eV (T=598.153K) Etot = 58.252eV Energy per atom: Epot =50.272eV Ekin = 7.980eV (T=663.793K) Etot = 58.251eV Energy per atom: Epot =51.204eV Ekin = 7.050eV (T=586.429K) Etot = 58.253eV Energy per atom: Epot =50.966eV Ekin = 7.287eV (T=606.209K) Etot = 58.253eV Energy per atom: Epot =51.203eV Ekin = 7.055eV (T=586.907K) Etot = 58.258eV Energy per atom: Epot =51.540eV Ekin = 6.712eV (T=558.387K) Etot = 58.253eV Energy per atom: Epot =51.271eV Ekin = 6.984eV (T=580.953K) Etot = 58.254eV Energy per atom: Epot =50.411eV Ekin = 7.838eV (T=652.011K) Etot = 58.249eV Energy per atom: Epot =51.006eV Ekin = 7.239eV (T=602.190K) Etot = 58.245eV Energy per atom: Epot =51.420eV Ekin = 6.823eV (T=567.601K) Etot = 58.243eV Energy per atom: Epot =50.816eV Ekin = 7.432eV (T=618.215K) Etot = 58.248eV Energy per atom: Epot =51.479eV Ekin = 6.776eV (T=563.712K) Etot = 58.256eV Energy per atom: Epot =51.303eV Ekin = 6.949eV (T=578.083K) Etot = 58.252eV Energy per atom: Epot =51.619eV Ekin = 6.634eV (T=551.836K) Etot = 58.253eV Energy per atom: Epot =52.153eV Ekin = 6.102eV (T=507.571K) Etot = 58.254eV Energy per atom: Epot =51.124eV Ekin = 7.125eV (T=592.734K) Etot = 58.250eV Energy per atom: Epot =50.775eV Ekin = 7.473eV (T=621.680K) Etot = 58.248eV Energy per atom: Epot =50.862eV Ekin = 7.382eV (T=614.082K) Etot = 58.244eV Energy per atom: Epot =51.729eV Ekin = 6.521eV (T=542.426K) Etot = 58.250eV Energy per atom: Epot =51.474eV Ekin = 6.779eV (T=563.957K) Etot = 58.254eV Energy per atom: Epot =50.946eV Ekin = 7.305eV (T=607.687K) Etot = 58.251eV Energy per atom: Epot =50.704eV Ekin = 7.541eV (T=627.340K) Etot = 58.246eV Energy per atom: Epot =51.308eV Ekin = 6.943eV (T=577.582K) Etot = 58.251eV Energy per atom: Epot =50.678eV Ekin = 7.571eV (T=629.835K) Etot = 58.250eV Energy per atom: Epot =50.169eV Ekin = 8.076eV (T=671.832K) Etot = 58.245eV Energy per atom: Epot =50.585eV Ekin = 7.661eV (T=637.254K) Etot = 58.245eV Energy per atom: Epot =52.323eV Ekin = 5.932eV (T=493.460K) Etot = 58.255eV Energy per atom: Epot =50.118eV Ekin = 8.129eV (T=676.233K) Etot = 58.247eV Energy per atom: Epot =50.185eV Ekin = 8.062eV (T=670.616K) Etot = 58.247eV Energy per atom: Epot =51.730eV Ekin = 6.522eV (T=542.510K) Etot = 58.251eV Energy per atom: Epot =51.537eV Ekin = 6.718eV (T=558.827K) Etot = 58.255eV Energy per atom: Epot =50.996eV Ekin = 7.256eV (T=603.639K) Etot = 58.252eV Energy per atom: Epot =50.553eV Ekin = 7.698eV (T=640.394K) Etot = 58.251eV Energy per atom: Epot =50.708eV Ekin = 7.543eV (T=627.442K) Etot = 58.251eV Energy per atom: Epot =50.085eV Ekin = 8.162eV (T=678.976K) Etot = 58.247eV Energy per atom: Epot =50.983eV Ekin = 7.269eV (T=604.716K) Etot = 58.252eV Energy per atom: Epot =49.846eV Ekin = 8.396eV (T=698.465K) Etot = 58.243eV Energy per atom: Epot =50.120eV Ekin = 8.121eV (T=675.538K) Etot = 58.241eV Energy per atom: Epot =50.170eV Ekin = 8.073eV (T=671.554K) Etot = 58.243eV Energy per atom: Epot =50.812eV Ekin = 7.436eV (T=618.569K) Etot = 58.248eV Energy per atom: Epot =50.623eV Ekin = 7.618eV (T=633.696K) Etot = 58.241eV Energy per atom: Epot =50.702eV Ekin = 7.545eV (T=627.611K) Etot = 58.246eV Energy per atom: Epot =50.704eV Ekin = 7.547eV (T=627.818K) Etot = 58.251eV Energy per atom: Epot =50.934eV Ekin = 7.317eV (T=608.648K) Etot = 58.250eV Energy per atom: Epot =50.618eV Ekin = 7.629eV (T=634.615K) Etot = 58.247eV Energy per atom: Epot =51.197eV Ekin = 7.052eV (T=586.643K) Etot = 58.250eV Energy per atom: Epot =51.424eV Ekin = 6.824eV (T=567.635K) Etot = 58.247eV Energy per atom: Epot =51.126eV Ekin = 7.126eV (T=592.816K) Etot = 58.253eV Energy per atom: Epot =50.996eV Ekin = 7.258eV (T=603.789K) Etot = 58.254eV Energy per atom: Epot =50.923eV Ekin = 7.331eV (T=609.802K) Etot = 58.254eV Energy per atom: Epot =51.195eV Ekin = 7.058eV (T=587.105K) Etot = 58.253eV Energy per atom: Epot =51.523eV Ekin = 6.727eV (T=559.608K) Etot = 58.250eV Energy per atom: Epot =51.268eV Ekin = 6.986eV (T=581.105K) Etot = 58.254eV Energy per atom: Epot =51.402eV Ekin = 6.850eV (T=569.823K) Etot = 58.252eV Energy per atom: Epot =51.808eV Ekin = 6.446eV (T=536.212K) Etot = 58.254eV Energy per atom: Epot =51.029eV Ekin = 7.222eV (T=600.754K) Etot = 58.251eV Energy per atom: Epot =50.463eV Ekin = 7.781eV (T=647.294K) Etot = 58.245eV Energy per atom: Epot =51.346eV Ekin = 6.904eV (T=574.303K) Etot = 58.250eV Energy per atom: Epot =51.129eV Ekin = 7.121eV (T=592.331K) Etot = 58.249eV Energy per atom: Epot =51.293eV Ekin = 6.957eV (T=578.753K) Etot = 58.250eV Energy per atom: Epot =50.863eV Ekin = 7.386eV (T=614.441K) Etot = 58.249eV Energy per atom: Epot =50.864eV Ekin = 7.390eV (T=614.708K) Etot = 58.253eV Energy per atom: Epot =50.098eV Ekin = 8.149eV (T=677.882K) Etot = 58.247eV Energy per atom: Epot =50.378eV Ekin = 7.868eV (T=654.473K) Etot = 58.246eV Energy per atom: Epot =51.194eV Ekin = 7.056eV (T=586.977K) Etot = 58.250eV Energy per atom: Epot =51.070eV Ekin = 7.184eV (T=597.592K) Etot = 58.254eV Energy per atom: Epot =49.947eV Ekin = 8.297eV (T=690.166K) Etot = 58.243eV Energy per atom: Epot =50.267eV Ekin = 7.977eV (T=663.544K) Etot = 58.244eV Energy per atom: Epot =50.214eV Ekin = 8.032eV (T=668.130K) Etot = 58.246eV Energy per atom: Epot =50.808eV Ekin = 7.437eV (T=618.624K) Etot = 58.245eV Energy per atom: Epot =50.069eV Ekin = 8.174eV (T=680.008K) Etot = 58.243eV Energy per atom: Epot =51.542eV Ekin = 6.711eV (T=558.298K) Etot = 58.254eV Energy per atom: Epot =50.910eV Ekin = 7.339eV (T=610.536K) Etot = 58.249eV Energy per atom: Epot =51.315eV Ekin = 6.939eV (T=577.198K) Etot = 58.254eV Energy per atom: Epot =49.492eV Ekin = 8.751eV (T=728.000K) Etot = 58.243eV Energy per atom: Epot =50.413eV Ekin = 7.833eV (T=651.584K) Etot = 58.246eV Energy per atom: Epot =50.627eV Ekin = 7.621eV (T=633.963K) Etot = 58.248eV Energy per atom: Epot =51.158eV Ekin = 7.093eV (T=590.032K) Etot = 58.251eV Energy per atom: Epot =51.065eV Ekin = 7.185eV (T=597.718K) Etot = 58.250eV Energy per atom: Epot =50.739eV Ekin = 7.505eV (T=624.325K) Etot = 58.244eV Energy per atom: Epot =50.000eV Ekin = 8.246eV (T=685.990K) Etot = 58.247eV Energy per atom: Epot =50.865eV Ekin = 7.387eV (T=614.502K) Etot = 58.252eV Energy per atom: Epot =50.910eV Ekin = 7.343eV (T=610.808K) Etot = 58.253eV Energy per atom: Epot =51.376eV Ekin = 6.879eV (T=572.228K) Etot = 58.255eV Energy per atom: Epot =50.652eV Ekin = 7.592eV (T=631.529K) Etot = 58.244eV Energy per atom: Epot =50.237eV Ekin = 8.005eV (T=665.937K) Etot = 58.242eV Energy per atom: Epot =51.310eV Ekin = 6.946eV (T=577.843K) Etot = 58.257eV Energy per atom: Epot =50.642eV Ekin = 7.610eV (T=633.084K) Etot = 58.252eV Energy per atom: Epot =49.859eV Ekin = 8.388eV (T=697.733K) Etot = 58.247eV Energy per atom: Epot =50.745eV Ekin = 7.506eV (T=624.395K) Etot = 58.251eV Energy per atom: Epot =51.078eV Ekin = 7.168eV (T=596.282K) Etot = 58.246eV Energy per atom: Epot =51.008eV Ekin = 7.237eV (T=602.014K) Etot = 58.244eV Energy per atom: Epot =50.585eV Ekin = 7.666eV (T=637.744K) Etot = 58.252eV Energy per atom: Epot =49.670eV Ekin = 8.574eV (T=713.241K) Etot = 58.244eV Energy per atom: Epot =51.136eV Ekin = 7.111eV (T=591.499K) Etot = 58.246eV Energy per atom: Epot =50.088eV Ekin = 8.152eV (T=678.139K) Etot = 58.240eV Energy per atom: Epot =50.602eV Ekin = 7.649eV (T=636.257K) Etot = 58.251eV Energy per atom: Epot =51.493eV Ekin = 6.763eV (T=562.615K) Etot = 58.256eV Energy per atom: Epot =50.663eV Ekin = 7.588eV (T=631.220K) Etot = 58.251eV Energy per atom: Epot =50.484eV Ekin = 7.767eV (T=646.071K) Etot = 58.250eV Energy per atom: Epot =50.897eV Ekin = 7.354eV (T=611.772K) Etot = 58.251eV Energy per atom: Epot =50.721eV Ekin = 7.533eV (T=626.606K) Etot = 58.253eV Energy per atom: Epot =50.749eV Ekin = 7.502eV (T=624.040K) Etot = 58.250eV Energy per atom: Epot =50.837eV Ekin = 7.411eV (T=616.531K) Etot = 58.248eV Energy per atom: Epot =50.622eV Ekin = 7.628eV (T=634.557K) Etot = 58.250eV Energy per atom: Epot =50.560eV Ekin = 7.693eV (T=639.953K) Etot = 58.253eV Energy per atom: Epot =49.799eV Ekin = 8.446eV (T=702.604K) Etot = 58.246eV Energy per atom: Epot =49.640eV Ekin = 8.603eV (T=715.688K) Etot = 58.243eV Energy per atom: Epot =51.590eV Ekin = 6.662eV (T=554.159K) Etot = 58.252eV Energy per atom: Epot =50.597eV Ekin = 7.651eV (T=636.427K) Etot = 58.247eV Energy per atom: Epot =50.088eV Ekin = 8.162eV (T=678.945K) Etot = 58.249eV Energy per atom: Epot =49.753eV Ekin = 8.493eV (T=706.485K) Etot = 58.246eV Energy per atom: Epot =51.125eV Ekin = 7.128eV (T=592.978K) Etot = 58.253eV Energy per atom: Epot =50.210eV Ekin = 8.040eV (T=668.796K) Etot = 58.249eV Energy per atom: Epot =51.080eV Ekin = 7.169eV (T=596.383K) Etot = 58.250eV Energy per atom: Epot =51.046eV Ekin = 7.202eV (T=599.111K) Etot = 58.248eV Energy per atom: Epot =50.449eV Ekin = 7.800eV (T=648.892K) Etot = 58.249eV Energy per atom: Epot =51.051eV Ekin = 7.201eV (T=599.057K) Etot = 58.252eV Energy per atom: Epot =50.784eV Ekin = 7.466eV (T=621.106K) Etot = 58.251eV Energy per atom: Epot =49.506eV Ekin = 8.727eV (T=726.006K) Etot = 58.233eV Energy per atom: Epot =49.453eV Ekin = 8.787eV (T=730.954K) Etot = 58.240eV Energy per atom: Epot =50.536eV Ekin = 7.712eV (T=641.563K) Etot = 58.249eV Energy per atom: Epot =50.507eV Ekin = 7.744eV (T=644.163K) Etot = 58.251eV Energy per atom: Epot =50.663eV Ekin = 7.587eV (T=631.132K) Etot = 58.250eV Energy per atom: Epot =50.939eV Ekin = 7.310eV (T=608.110K) Etot = 58.249eV Energy per atom: Epot =50.454eV Ekin = 7.796eV (T=648.535K) Etot = 58.250eV Energy per atom: Epot =49.567eV Ekin = 8.678eV (T=721.901K) Etot = 58.245eV Energy per atom: Epot =50.129eV Ekin = 8.120eV (T=675.440K) Etot = 58.249eV Energy per atom: Epot =50.344eV Ekin = 7.907eV (T=657.796K) Etot = 58.251eV Energy per atom: Epot =51.163eV Ekin = 7.088eV (T=589.604K) Etot = 58.251eV Energy per atom: Epot =50.972eV Ekin = 7.277eV (T=605.346K) Etot = 58.249eV Energy per atom: Epot =51.041eV Ekin = 7.207eV (T=599.522K) Etot = 58.248eV Energy per atom: Epot =50.525eV Ekin = 7.719eV (T=642.109K) Etot = 58.244eV Energy per atom: Epot =50.989eV Ekin = 7.257eV (T=603.724K) Etot = 58.246eV Energy per atom: Epot =51.477eV Ekin = 6.774eV (T=563.510K) Etot = 58.251eV Energy per atom: Epot =51.328eV Ekin = 6.921eV (T=575.772K) Etot = 58.250eV Energy per atom: Epot =50.851eV Ekin = 7.401eV (T=615.679K) Etot = 58.252eV Energy per atom: Epot =50.772eV Ekin = 7.483eV (T=622.525K) Etot = 58.256eV Energy per atom: Epot =50.322eV Ekin = 7.926eV (T=659.314K) Etot = 58.248eV Energy per atom: Epot =50.132eV Ekin = 8.114eV (T=675.011K) Etot = 58.246eV Energy per atom: Epot =49.836eV Ekin = 8.411eV (T=699.651K) Etot = 58.247eV Energy per atom: Epot =49.940eV Ekin = 8.306eV (T=690.960K) Etot = 58.246eV Energy per atom: Epot =50.535eV Ekin = 7.712eV (T=641.520K) Etot = 58.247eV Energy per atom: Epot =50.874eV Ekin = 7.372eV (T=613.283K) Etot = 58.247eV Energy per atom: Epot =50.523eV Ekin = 7.725eV (T=642.598K) Etot = 58.248eV Energy per atom: Epot =50.388eV Ekin = 7.858eV (T=653.650K) Etot = 58.245eV Energy per atom: Epot =51.024eV Ekin = 7.227eV (T=601.157K) Etot = 58.250eV .. 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 `_