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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# 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/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
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fix pimdb all pimd/langevin/bosonic 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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Initializing PI Langevin equation thermostat...
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Bead ID | omega | tau | c1 | c2
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0 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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1 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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2 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
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PILE_L thermostat successfully initialized!
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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 1.3158398e-09 1.8742641e-09 0.00099182267
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2 5.0818396e-09 7.1801177e-09 0.00099180053
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3 1.2446727e-08 1.4372388e-08 0.00099176038
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4 2.1754941e-08 3.1274072e-08 0.00099170266
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5 3.2927703e-08 5.2470231e-08 0.00099162511
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6 4.7293056e-08 7.2301291e-08 0.00099153
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7 6.526455e-08 9.5440683e-08 0.00099141194
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8 8.6974168e-08 1.1669162e-07 0.00099127168
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9 1.1249595e-07 1.3551097e-07 0.00099109846
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10 1.4190482e-07 1.6050328e-07 0.00099089759
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11 1.7313555e-07 1.8645705e-07 0.0009906735
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12 2.0672874e-07 2.1181418e-07 0.00099042271
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13 2.4042615e-07 2.4218941e-07 0.00099012073
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14 2.7524432e-07 2.7507982e-07 0.00098977876
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15 3.1513375e-07 3.1771012e-07 0.00098940169
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16 3.6161087e-07 3.6075963e-07 0.00098900826
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17 4.0813191e-07 4.0059005e-07 0.00098859985
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18 4.5194598e-07 4.3883585e-07 0.00098817535
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19 4.9898075e-07 4.8036287e-07 0.00098770764
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20 5.5458728e-07 5.2362451e-07 0.00098721266
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21 6.1220768e-07 5.7705077e-07 0.00098670407
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22 6.6573849e-07 6.3271105e-07 0.00098617081
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23 7.2475089e-07 6.9382916e-07 0.00098557406
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24 7.804837e-07 7.5979853e-07 0.0009849612
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25 8.3194987e-07 8.232213e-07 0.00098434971
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26 8.8723792e-07 8.9901705e-07 0.0009836645
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27 9.3837241e-07 9.7033126e-07 0.0009830068
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28 9.897077e-07 1.0444697e-06 0.00098229311
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29 1.043431e-06 1.1208219e-06 0.00098150213
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30 1.0900368e-06 1.1899315e-06 0.00098077686
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31 1.1303314e-06 1.2560026e-06 0.00098003518
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32 1.1725968e-06 1.3287355e-06 0.00097921099
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33 1.2081344e-06 1.399856e-06 0.0009784037
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34 1.2449387e-06 1.4769272e-06 0.00097754491
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35 1.2852285e-06 1.5642459e-06 0.00097667479
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36 1.3234189e-06 1.6571388e-06 0.00097572641
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37 1.3666391e-06 1.7603492e-06 0.00097475881
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38 1.4102743e-06 1.8666516e-06 0.00097373763
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39 1.454172e-06 1.9696572e-06 0.0009727081
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40 1.5031422e-06 2.0910539e-06 0.00097155807
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41 1.5538491e-06 2.2198868e-06 0.00097030871
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42 1.6079193e-06 2.3576614e-06 0.00096896762
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43 1.6637051e-06 2.496284e-06 0.00096760456
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44 1.7189714e-06 2.637657e-06 0.00096619083
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45 1.7656688e-06 2.795845e-06 0.00096470693
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46 1.8092153e-06 2.9727162e-06 0.00096303835
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47 1.8415769e-06 3.1451673e-06 0.00096140406
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48 1.8664597e-06 3.3241907e-06 0.00095971129
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49 1.8940033e-06 3.5094834e-06 0.00095790964
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50 1.9211844e-06 3.7049195e-06 0.00095603039
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51 1.9533838e-06 3.9139587e-06 0.0009540918
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52 1.9833776e-06 4.1289537e-06 0.0009520767
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53 2.0106231e-06 4.3481079e-06 0.00095003676
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54 2.0429292e-06 4.5702968e-06 0.00094802906
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55 2.0747842e-06 4.7928135e-06 0.00094600351
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56 2.1043981e-06 5.0253448e-06 0.0009438419
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57 2.1474343e-06 5.2569331e-06 0.00094169256
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58 2.2115003e-06 5.4997767e-06 0.00093948055
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59 2.2773037e-06 5.7547729e-06 0.00093714003
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60 2.3402972e-06 6.0074589e-06 0.00093480857
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61 2.4107157e-06 6.2647899e-06 0.00093244785
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62 2.4953095e-06 6.5384938e-06 0.00092998209
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63 2.58923e-06 6.8124372e-06 0.00092751453
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64 2.682021e-06 7.0913777e-06 0.00092505171
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65 2.7538688e-06 7.3773956e-06 0.00092256944
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66 2.8444661e-06 7.6811232e-06 0.00091984092
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67 2.9532286e-06 7.9951107e-06 0.0009170037
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68 3.0551339e-06 8.3096758e-06 0.00091414977
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69 3.1625164e-06 8.6232285e-06 0.00091137219
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70 3.2717759e-06 8.9388929e-06 0.00090857909
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71 3.3924986e-06 9.2524846e-06 0.00090583473
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72 3.5236727e-06 9.5688611e-06 0.00090308342
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73 3.6440162e-06 9.8873586e-06 0.00090026584
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74 3.7692169e-06 1.0203245e-05 0.00089755256
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75 3.8946044e-06 1.0523755e-05 0.00089485804
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76 4.0498738e-06 1.0848398e-05 0.00089217189
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77 4.2099346e-06 1.1164286e-05 0.00088956967
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78 4.3589564e-06 1.1466652e-05 0.00088700311
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79 4.5069481e-06 1.177381e-05 0.00088439373
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80 4.6635354e-06 1.2059606e-05 0.00088199635
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81 4.8398269e-06 1.233837e-05 0.0008797438
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82 5.0191539e-06 1.261531e-05 0.00087745162
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83 5.205285e-06 1.2899972e-05 0.00087506863
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84 5.3708116e-06 1.3160246e-05 0.00087288444
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85 5.5534416e-06 1.3438712e-05 0.00087052617
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86 5.7613e-06 1.372546e-05 0.00086818634
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87 5.9645662e-06 1.4017631e-05 0.00086572407
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88 6.1830289e-06 1.4328439e-05 0.000862992
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89 6.423646e-06 1.4640964e-05 0.00086017364
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90 6.688219e-06 1.4978644e-05 0.0008570595
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91 6.9305603e-06 1.5307214e-05 0.00085411601
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92 7.1857573e-06 1.5649328e-05 0.00085112325
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93 7.4653538e-06 1.6015833e-05 0.0008479391
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94 7.8132911e-06 1.6393131e-05 0.00084474237
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95 8.1540941e-06 1.674573e-05 0.00084165639
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96 8.4943231e-06 1.7094435e-05 0.00083858996
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97 8.8504733e-06 1.7451741e-05 0.00083536142
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98 9.2042324e-06 1.780703e-05 0.00083221292
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99 9.5058078e-06 1.8141862e-05 0.00082913227
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100 9.8087647e-06 1.8457846e-05 0.00082619877
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Loop time of 0.122922 on 1 procs for 100 steps with 3 atoms
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Performance: 35144210.362 fs/day, 0.000 hours/fs, 813.523 timesteps/s, 2.441 katom-step/s
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70.1% 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 | 1.1593e-05 | 1.1593e-05 | 1.1593e-05 | 0.0 | 0.01
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Comm | 9.2183e-05 | 9.2183e-05 | 9.2183e-05 | 0.0 | 0.07
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Output | 0.023243 | 0.023243 | 0.023243 | 0.0 | 18.91
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Modify | 0.099386 | 0.099386 | 0.099386 | 0.0 | 80.85
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Other | | 0.0001896 | | | 0.15
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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 = 33
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Dangerous builds = 0
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