237 lines
10 KiB
Plaintext
237 lines
10 KiB
Plaintext
LAMMPS (4 Feb 2025)
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Processor partition = 0
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# Units and dimensions
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units electron
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dimension 3
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boundary p p p
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atom_style atomic
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atom_modify map yes
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pair_style none
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# Time step (in femtoseconds)
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timestep 0.5
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# Temperature (in Kelvin)
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variable Temp equal 17.4
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# Number of Nose-Hoover chains
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variable nhc equal 4
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# Force constant (in Hartree energies per Bohr radius squared)
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variable k equal 1.2154614120000001e-08
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# Number of beads
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variable Nbeads equal 4
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variable ibead uloop ${Nbeads} pad
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variable ibead uloop 4 pad
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variable seed equal 18889
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# Create box and atoms. All distances are in Bohr
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region box block -1500 1500 -1500 1500 -1500 1500
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create_box 1 box
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Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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1 by 1 by 1 MPI processor grid
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variable a loop 3
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label loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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create_atoms 1 single -14.5 ${y1} ${z1}
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create_atoms 1 single -14.5 9.5 ${z1}
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create_atoms 1 single -14.5 9.5 1.5
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Created 1 atoms
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using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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create_atoms CPU = 0.000 seconds
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next a
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jump SELF loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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create_atoms 1 single -14 ${y1} ${z1}
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create_atoms 1 single -14 9 ${z1}
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create_atoms 1 single -14 9 2
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Created 1 atoms
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using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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create_atoms CPU = 0.000 seconds
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next a
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jump SELF loop
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variable x1 equal -15.0+0.5*v_a
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variable y1 equal 10.0-0.5*v_a
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variable z1 equal 1+0.5*v_a
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create_atoms 1 single ${x1} ${y1} ${z1}
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create_atoms 1 single -13.5 ${y1} ${z1}
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create_atoms 1 single -13.5 8.5 ${z1}
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create_atoms 1 single -13.5 8.5 2.5
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Created 1 atoms
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using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
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create_atoms CPU = 0.000 seconds
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next a
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jump SELF loop
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# Electron mass (in amu)
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mass 1 0.00054858
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# Initialize velocities
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velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
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velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
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velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
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velocity all create 17.4 188891 mom yes rot yes dist gaussian
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# Add harmonic external force
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fix harm all spring/self ${k}
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fix harm all spring/self 1.215461412e-08
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# Add harmonic potential energy to total energy and potential energy
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fix_modify harm energy yes
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# PIMD command
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fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
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fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
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fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
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# Outputs
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variable virial equal f_pimdb[3]
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variable prim_kinetic equal f_pimdb[4]
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thermo_style custom step pe v_virial v_prim_kinetic
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thermo 1
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run 100
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WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
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Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2)
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WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
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Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
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Step PotEng v_virial v_prim_kinetic
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0 0 0 0.00024794798
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1 8.5849317e-10 4.5664581e-10 0.00024794215
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2 3.4338094e-09 1.3424585e-09 0.00024793325
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3 7.7255501e-09 2.6573351e-09 0.00024792129
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4 1.3733112e-08 4.4011211e-09 0.00024790626
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5 2.1455686e-08 6.5736113e-09 0.00024788818
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6 3.0892259e-08 9.1745487e-09 0.00024786704
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7 4.2041614e-08 1.2203626e-08 0.00024784285
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8 5.4902328e-08 1.5660483e-08 0.0002478156
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9 6.9472776e-08 1.9544712e-08 0.00024778532
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10 8.5751128e-08 2.385585e-08 0.00024775199
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11 1.0373535e-07 2.8593386e-08 0.00024771564
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12 1.234232e-07 3.3756758e-08 0.00024767626
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13 1.4481225e-07 3.9345352e-08 0.00024763386
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14 1.6789985e-07 4.5358504e-08 0.00024758844
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15 1.9268316e-07 5.1795501e-08 0.00024754003
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16 2.1915914e-07 5.8655576e-08 0.00024748862
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17 2.4732452e-07 6.5937915e-08 0.00024743423
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18 2.7717588e-07 7.3641654e-08 0.00024737686
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19 3.0870956e-07 8.1765876e-08 0.00024731653
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20 3.4192172e-07 9.0309618e-08 0.00024725324
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21 3.7680831e-07 9.9271863e-08 0.00024718701
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22 4.1336509e-07 1.0865155e-07 0.00024711785
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23 4.5158762e-07 1.1844756e-07 0.00024704578
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24 4.9147126e-07 1.2865874e-07 0.0002469708
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25 5.3301119e-07 1.3928387e-07 0.00024689293
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26 5.7620236e-07 1.5032169e-07 0.00024681218
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27 6.2103957e-07 1.6177089e-07 0.00024672857
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28 6.675174e-07 1.7363012e-07 0.00024664212
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29 7.1563024e-07 1.8589798e-07 0.00024655283
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30 7.6537229e-07 1.9857299e-07 0.00024646073
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31 8.1673756e-07 2.1165368e-07 0.00024636584
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32 8.6971988e-07 2.2513849e-07 0.00024626816
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33 9.2431288e-07 2.3902582e-07 0.00024616772
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34 9.8051001e-07 2.5331402e-07 0.00024606453
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35 1.0383045e-06 2.6800143e-07 0.00024595862
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36 1.0976895e-06 2.8308629e-07 0.00024585001
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37 1.1586578e-06 2.9856682e-07 0.0002457387
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38 1.2212021e-06 3.1444121e-07 0.00024562473
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39 1.2853151e-06 3.3070757e-07 0.00024550812
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40 1.350989e-06 3.4736399e-07 0.00024538888
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41 1.4182159e-06 3.644085e-07 0.00024526703
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42 1.4869879e-06 3.8183911e-07 0.00024514261
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43 1.5572969e-06 3.9965375e-07 0.00024501562
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44 1.6291343e-06 4.1785034e-07 0.0002448861
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45 1.7024917e-06 4.3642673e-07 0.00024475406
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46 1.7773604e-06 4.5538075e-07 0.00024461954
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47 1.8537315e-06 4.7471016e-07 0.00024448255
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48 1.9315959e-06 4.9441271e-07 0.00024434312
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49 2.0109445e-06 5.1448608e-07 0.00024420127
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50 2.0917677e-06 5.3492792e-07 0.00024405703
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51 2.1740562e-06 5.5573584e-07 0.00024391043
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52 2.2578001e-06 5.769074e-07 0.00024376149
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53 2.3429895e-06 5.9844014e-07 0.00024361023
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54 2.4296146e-06 6.2033154e-07 0.00024345669
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55 2.5176649e-06 6.4257904e-07 0.00024330088
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56 2.6071302e-06 6.6518005e-07 0.00024314285
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57 2.6980001e-06 6.8813194e-07 0.00024298261
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58 2.7902637e-06 7.1143203e-07 0.0002428202
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59 2.8839103e-06 7.3507763e-07 0.00024265563
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60 2.9789289e-06 7.5906598e-07 0.00024248895
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61 3.0753084e-06 7.833943e-07 0.00024232018
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62 3.1730376e-06 8.0805977e-07 0.00024214934
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63 3.2721049e-06 8.3305953e-07 0.00024197647
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64 3.372499e-06 8.5839069e-07 0.00024180161
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65 3.474208e-06 8.8405032e-07 0.00024162477
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66 3.5772201e-06 9.1003545e-07 0.00024144598
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67 3.6815235e-06 9.3634309e-07 0.00024126529
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68 3.7871058e-06 9.6297021e-07 0.00024108272
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69 3.893955e-06 9.8991374e-07 0.0002408983
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70 4.0020586e-06 1.0171706e-06 0.00024071206
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71 4.1114041e-06 1.0447376e-06 0.00024052403
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72 4.2219789e-06 1.0726116e-06 0.00024033425
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73 4.3337702e-06 1.1007895e-06 0.00024014274
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74 4.4467651e-06 1.1292679e-06 0.00023994955
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75 4.5609507e-06 1.1580437e-06 0.0002397547
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76 4.6763137e-06 1.1871136e-06 0.00023955822
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77 4.792841e-06 1.2164741e-06 0.00023936014
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78 4.9105191e-06 1.2461221e-06 0.00023916051
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79 5.0293346e-06 1.276054e-06 0.00023895935
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80 5.149274e-06 1.3062666e-06 0.00023875669
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81 5.2703234e-06 1.3367563e-06 0.00023855257
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82 5.392469e-06 1.3675198e-06 0.00023834703
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83 5.515697e-06 1.3985535e-06 0.00023814009
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84 5.6399934e-06 1.4298539e-06 0.00023793178
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85 5.7653439e-06 1.4614174e-06 0.00023772215
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86 5.8917344e-06 1.4932406e-06 0.00023751123
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87 6.0191505e-06 1.5253199e-06 0.00023729904
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88 6.1475779e-06 1.5576515e-06 0.00023708563
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89 6.277002e-06 1.590232e-06 0.00023687102
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90 6.4074081e-06 1.6230576e-06 0.00023665526
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91 6.5387817e-06 1.6561246e-06 0.00023643837
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92 6.6711079e-06 1.6894294e-06 0.00023622039
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93 6.8043718e-06 1.7229682e-06 0.00023600135
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94 6.9385585e-06 1.7567372e-06 0.00023578129
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95 7.0736529e-06 1.7907328e-06 0.00023556024
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96 7.2096401e-06 1.8249512e-06 0.00023533824
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97 7.3465046e-06 1.8593885e-06 0.00023511531
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98 7.4842314e-06 1.8940408e-06 0.0002348915
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99 7.622805e-06 1.9289045e-06 0.00023466684
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100 7.76221e-06 1.9639756e-06 0.00023444136
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Loop time of 0.00940749 on 1 procs for 100 steps with 3 atoms
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Performance: 459208566.791 fs/day, 0.000 hours/fs, 10629.828 timesteps/s, 31.889 katom-step/s
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90.3% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 8.466e-06 | 8.466e-06 | 8.466e-06 | 0.0 | 0.09
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Comm | 7.8365e-05 | 7.8365e-05 | 7.8365e-05 | 0.0 | 0.83
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Output | 0.0012482 | 0.0012482 | 0.0012482 | 0.0 | 13.27
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Modify | 0.0079193 | 0.0079193 | 0.0079193 | 0.0 | 84.18
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Other | | 0.0001532 | | | 1.63
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Nlocal: 3 ave 3 max 3 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Neighbor list builds = 24
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Dangerous builds = 0
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Total wall time: 0:00:00
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