229 lines
10 KiB
Groff
229 lines
10 KiB
Groff
LAMMPS (4 Feb 2025)
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Processor partition = 2
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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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# 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 = 0.001 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 188893 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/langevin ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
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fix pimdb all pimdb/langevin ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
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# Outputs
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variable prim_kinetic equal f_pimdb[5]
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variable virial equal f_pimdb[6]
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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 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) = 2.801 | 2.801 | 2.801 Mbytes
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Step PotEng v_virial v_prim_kinetic
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0 0 1.3661449e-08 0.0009918329
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1 8.3480048e-10 1.8742641e-09 0.00099182267
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2 2.8201389e-09 7.1801177e-09 0.00099180053
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3 7.3605781e-09 1.4372388e-08 0.00099176038
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4 1.4967393e-08 3.1274072e-08 0.00099170266
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5 2.4978087e-08 5.2470231e-08 0.00099162511
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6 3.5908849e-08 7.2301291e-08 0.00099153
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7 4.8226614e-08 9.5440683e-08 0.00099141194
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8 6.3621045e-08 1.1669162e-07 0.00099127168
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9 8.0119736e-08 1.3551097e-07 0.00099109846
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10 9.7965614e-08 1.6050328e-07 0.00099089759
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11 1.1538858e-07 1.8645705e-07 0.0009906735
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12 1.365443e-07 2.1181418e-07 0.00099042271
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13 1.5920175e-07 2.4218941e-07 0.00099012073
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14 1.8252589e-07 2.7507982e-07 0.00098977876
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15 2.0858909e-07 3.1771012e-07 0.00098940169
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16 2.3676046e-07 3.6075963e-07 0.00098900826
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17 2.689757e-07 4.0059005e-07 0.00098859985
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18 3.0022172e-07 4.3883585e-07 0.00098817535
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19 3.3127637e-07 4.8036287e-07 0.00098770764
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20 3.6044366e-07 5.2362451e-07 0.00098721266
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21 3.8484646e-07 5.7705077e-07 0.00098670407
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22 4.1435067e-07 6.3271105e-07 0.00098617081
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23 4.4508994e-07 6.9382916e-07 0.00098557406
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24 4.7879333e-07 7.5979853e-07 0.0009849612
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25 5.0918223e-07 8.232213e-07 0.00098434971
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26 5.4733661e-07 8.9901705e-07 0.0009836645
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27 5.7932115e-07 9.7033126e-07 0.0009830068
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28 6.1775401e-07 1.0444697e-06 0.00098229311
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29 6.6883535e-07 1.1208219e-06 0.00098150213
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30 7.0943445e-07 1.1899315e-06 0.00098077686
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31 7.4477897e-07 1.2560026e-06 0.00098003518
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32 7.8183156e-07 1.3287355e-06 0.00097921099
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33 8.1987667e-07 1.399856e-06 0.0009784037
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34 8.5514962e-07 1.4769272e-06 0.00097754491
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35 8.9607784e-07 1.5642459e-06 0.00097667479
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36 9.4986753e-07 1.6571388e-06 0.00097572641
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37 1.0024729e-06 1.7603492e-06 0.00097475881
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38 1.0526731e-06 1.8666516e-06 0.00097373763
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39 1.103419e-06 1.9696572e-06 0.0009727081
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40 1.1640352e-06 2.0910539e-06 0.00097155807
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41 1.2292837e-06 2.2198868e-06 0.00097030871
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42 1.3024454e-06 2.3576614e-06 0.00096896762
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43 1.3788736e-06 2.496284e-06 0.00096760456
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44 1.4503248e-06 2.637657e-06 0.00096619083
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45 1.5334106e-06 2.795845e-06 0.00096470693
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46 1.6246777e-06 2.9727162e-06 0.00096303835
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47 1.715884e-06 3.1451673e-06 0.00096140406
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48 1.8096683e-06 3.3241907e-06 0.00095971129
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49 1.916714e-06 3.5094834e-06 0.00095790964
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50 2.0374848e-06 3.7049195e-06 0.00095603039
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51 2.1747488e-06 3.9139587e-06 0.0009540918
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52 2.3236882e-06 4.1289537e-06 0.0009520767
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53 2.4790586e-06 4.3481079e-06 0.00095003676
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54 2.6478101e-06 4.5702968e-06 0.00094802906
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55 2.8275135e-06 4.7928135e-06 0.00094600351
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56 3.0338638e-06 5.0253448e-06 0.0009438419
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57 3.2428318e-06 5.2569331e-06 0.00094169256
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58 3.4414566e-06 5.4997767e-06 0.00093948055
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59 3.6324968e-06 5.7547729e-06 0.00093714003
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60 3.8269172e-06 6.0074589e-06 0.00093480857
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61 4.0183315e-06 6.2647899e-06 0.00093244785
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62 4.2263009e-06 6.5384938e-06 0.00092998209
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63 4.4382735e-06 6.8124372e-06 0.00092751453
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64 4.6488232e-06 7.0913777e-06 0.00092505171
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65 4.8707403e-06 7.3773956e-06 0.00092256944
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66 5.1178339e-06 7.6811232e-06 0.00091984092
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67 5.377713e-06 7.9951107e-06 0.0009170037
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68 5.63843e-06 8.3096758e-06 0.00091414977
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69 5.8975743e-06 8.6232285e-06 0.00091137219
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70 6.168921e-06 8.9388929e-06 0.00090857909
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71 6.4488238e-06 9.2524846e-06 0.00090583473
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72 6.7115203e-06 9.5688611e-06 0.00090308342
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73 6.995134e-06 9.8873586e-06 0.00090026584
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74 7.284199e-06 1.0203245e-05 0.00089755256
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75 7.6029528e-06 1.0523755e-05 0.00089485804
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76 7.9431391e-06 1.0848398e-05 0.00089217189
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77 8.2768015e-06 1.1164286e-05 0.00088956967
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78 8.6058917e-06 1.1466652e-05 0.00088700311
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79 8.9683477e-06 1.177381e-05 0.00088439373
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80 9.3324487e-06 1.2059606e-05 0.00088199635
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81 9.6876036e-06 1.233837e-05 0.0008797438
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82 1.0061754e-05 1.261531e-05 0.00087745162
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83 1.0457019e-05 1.2899972e-05 0.00087506863
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84 1.0866064e-05 1.3160246e-05 0.00087288444
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85 1.1298832e-05 1.3438712e-05 0.00087052617
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86 1.1762526e-05 1.372546e-05 0.00086818634
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87 1.2264941e-05 1.4017631e-05 0.00086572407
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88 1.2784125e-05 1.4328439e-05 0.000862992
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89 1.332533e-05 1.4640964e-05 0.00086017364
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90 1.3897966e-05 1.4978644e-05 0.0008570595
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91 1.4473024e-05 1.5307214e-05 0.00085411601
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92 1.5067033e-05 1.5649328e-05 0.00085112325
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93 1.5677943e-05 1.6015833e-05 0.0008479391
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94 1.6254294e-05 1.6393131e-05 0.00084474237
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95 1.6791089e-05 1.674573e-05 0.00084165639
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96 1.7362795e-05 1.7094435e-05 0.00083858996
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97 1.7961498e-05 1.7451741e-05 0.00083536142
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98 1.8568337e-05 1.780703e-05 0.00083221292
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99 1.9188379e-05 1.8141862e-05 0.00082913227
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100 1.9789011e-05 1.8457846e-05 0.00082619877
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Loop time of 0.00829826 on 1 procs for 100 steps with 3 atoms
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Performance: 520591251.874 fs/day, 0.000 hours/fs, 12050.723 timesteps/s, 36.152 katom-step/s
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79.5% 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 | 4.6257e-05 | 4.6257e-05 | 4.6257e-05 | 0.0 | 0.56
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Comm | 0.00029611 | 0.00029611 | 0.00029611 | 0.0 | 3.57
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Output | 0.00096988 | 0.00096988 | 0.00096988 | 0.0 | 11.69
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Modify | 0.0064529 | 0.0064529 | 0.0064529 | 0.0 | 77.76
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Other | | 0.0005331 | | | 6.42
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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 = 41
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Dangerous builds = 0
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