235 lines
10 KiB
Groff
235 lines
10 KiB
Groff
LAMMPS (4 Feb 2025)
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Processor partition = 3
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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 188894 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 pimdb/nvt method pimd temp ${Temp} nhc ${nhc}
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fix pimdb all pimdb/nvt method pimd temp 17.4 nhc ${nhc}
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fix pimdb all pimdb/nvt 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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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 0.00024796164
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1 8.5847879e-10 4.4463719e-10 0.00024796024
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2 3.4336684e-09 1.3183829e-09 0.00024795602
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3 7.7250055e-09 2.6210625e-09 0.000247949
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4 1.3731669e-08 4.3524371e-09 0.00024793917
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5 2.1452581e-08 6.5122035e-09 0.00024792653
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6 3.0886407e-08 9.0999942e-09 0.0002479111
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7 4.2031554e-08 1.2115377e-08 0.00024789287
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8 5.4886174e-08 1.5557858e-08 0.00024787185
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9 6.9448162e-08 1.9426875e-08 0.00024784804
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10 8.5715159e-08 2.3721806e-08 0.00024782146
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11 1.0368455e-07 2.8441963e-08 0.0002477921
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12 1.2335346e-07 3.3586595e-08 0.00024775998
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13 1.4471878e-07 3.9154888e-08 0.0002477251
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14 1.6777712e-07 4.5145965e-08 0.00024768748
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15 1.9252485e-07 5.1558884e-08 0.00024764712
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16 2.1895809e-07 5.8392642e-08 0.00024760403
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17 2.4707272e-07 6.5646173e-08 0.00024755823
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18 2.7686434e-07 7.3318348e-08 0.00024750973
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19 3.0832834e-07 8.1407976e-08 0.00024745854
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20 3.4145982e-07 8.9913804e-08 0.00024740467
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21 3.7625367e-07 9.8834518e-08 0.00024734813
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22 4.127045e-07 1.0816874e-07 0.00024728895
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23 4.5080671e-07 1.1791504e-07 0.00024722714
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24 4.9055443e-07 1.2807191e-07 0.00024716271
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25 5.3194155e-07 1.3863779e-07 0.00024709568
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26 5.7496174e-07 1.4961107e-07 0.00024702607
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27 6.1960841e-07 1.6099007e-07 0.00024695389
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28 6.6587473e-07 1.7277305e-07 0.00024687917
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29 7.1375365e-07 1.8495821e-07 0.00024680191
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30 7.6323786e-07 1.975437e-07 0.00024672216
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31 8.1431984e-07 2.1052759e-07 0.00024663991
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32 8.6699183e-07 2.2390793e-07 0.0002465552
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33 9.2124582e-07 2.3768267e-07 0.00024646805
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34 9.7707361e-07 2.5184974e-07 0.00024637847
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35 1.0344667e-06 2.6640698e-07 0.0002462865
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36 1.0934165e-06 2.813522e-07 0.00024619215
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37 1.1539141e-06 2.9668313e-07 0.00024609545
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38 1.2159503e-06 3.1239747e-07 0.00024599643
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39 1.2795157e-06 3.2849286e-07 0.00024589511
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40 1.344601e-06 3.4496686e-07 0.00024579151
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41 1.4111961e-06 3.61817e-07 0.00024568566
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42 1.4792913e-06 3.7904076e-07 0.0002455776
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43 1.5488762e-06 3.9663555e-07 0.00024546734
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44 1.6199404e-06 4.1459874e-07 0.00024535492
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45 1.6924734e-06 4.3292764e-07 0.00024524035
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46 1.7664643e-06 4.5161952e-07 0.00024512369
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47 1.841902e-06 4.7067159e-07 0.00024500494
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48 1.9187753e-06 4.90081e-07 0.00024488415
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49 1.9970729e-06 5.0984488e-07 0.00024476135
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50 2.076783e-06 5.2996028e-07 0.00024463656
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51 2.1578939e-06 5.5042422e-07 0.00024450981
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52 2.2403935e-06 5.7123366e-07 0.00024438115
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53 2.3242696e-06 5.9238553e-07 0.0002442506
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54 2.4095099e-06 6.138767e-07 0.00024411819
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55 2.4961017e-06 6.3570399e-07 0.00024398396
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56 2.5840323e-06 6.5786419e-07 0.00024384795
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57 2.6732887e-06 6.8035404e-07 0.00024371018
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58 2.7638579e-06 7.0317021e-07 0.0002435707
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59 2.8557265e-06 7.2630938e-07 0.00024342953
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60 2.9488811e-06 7.4976814e-07 0.00024328672
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61 3.0433081e-06 7.7354305e-07 0.0002431423
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62 3.1389936e-06 7.9763065e-07 0.00024299631
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63 3.2359238e-06 8.2202741e-07 0.00024284878
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64 3.3340844e-06 8.4672977e-07 0.00024269976
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65 3.4334612e-06 8.7173415e-07 0.00024254927
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66 3.5340397e-06 8.970369e-07 0.00024239736
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67 3.6358055e-06 9.2263435e-07 0.00024224406
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68 3.7387437e-06 9.4852279e-07 0.00024208942
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69 3.8428394e-06 9.7469849e-07 0.00024193348
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70 3.9480777e-06 1.0011576e-06 0.00024177626
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71 4.0544433e-06 1.0278964e-06 0.00024161782
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72 4.1619211e-06 1.054911e-06 0.0002414582
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73 4.2704954e-06 1.0821976e-06 0.00024129742
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74 4.3801508e-06 1.1097521e-06 0.00024113554
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75 4.4908716e-06 1.1375706e-06 0.0002409726
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76 4.6026419e-06 1.1656492e-06 0.00024080863
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77 4.7154459e-06 1.1939839e-06 0.00024064367
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78 4.8292673e-06 1.2225706e-06 0.00024047778
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79 4.9440901e-06 1.2514052e-06 0.00024031099
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80 5.059898e-06 1.2804837e-06 0.00024014333
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81 5.1766745e-06 1.309802e-06 0.00023997487
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82 5.2944032e-06 1.3393558e-06 0.00023980562
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83 5.4130674e-06 1.369141e-06 0.00023963565
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84 5.5326505e-06 1.3991534e-06 0.00023946499
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85 5.6531355e-06 1.4293887e-06 0.00023929369
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86 5.7745057e-06 1.4598429e-06 0.00023912178
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87 5.8967439e-06 1.4905114e-06 0.00023894931
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88 6.0198332e-06 1.5213902e-06 0.00023877633
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89 6.1437564e-06 1.5524748e-06 0.00023860287
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90 6.2684962e-06 1.5837609e-06 0.00023842898
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91 6.3940353e-06 1.6152441e-06 0.00023825471
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92 6.5203562e-06 1.6469202e-06 0.0002380801
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93 6.6474416e-06 1.6787847e-06 0.00023790518
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94 6.7752739e-06 1.7108332e-06 0.00023773001
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95 6.9038354e-06 1.7430613e-06 0.00023755463
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96 7.0331085e-06 1.7754645e-06 0.00023737908
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97 7.1630755e-06 1.8080385e-06 0.00023720341
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98 7.2937187e-06 1.8407787e-06 0.00023702765
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99 7.4250201e-06 1.8736806e-06 0.00023685186
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100 7.5569619e-06 1.9067398e-06 0.00023667607
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Loop time of 0.00510222 on 1 procs for 100 steps with 3 atoms
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Performance: 846690098.292 fs/day, 0.000 hours/fs, 19599.308 timesteps/s, 58.798 katom-step/s
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79.1% 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 | 1.5273e-05 | 1.5273e-05 | 1.5273e-05 | 0.0 | 0.30
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Comm | 0.00013505 | 0.00013505 | 0.00013505 | 0.0 | 2.65
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Output | 0.00046743 | 0.00046743 | 0.00046743 | 0.0 | 9.16
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Modify | 0.0042111 | 0.0042111 | 0.0042111 | 0.0 | 82.53
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Other | | 0.0002734 | | | 5.36
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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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