235 lines
10 KiB
Groff
235 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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# 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 = 0.001 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/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 8.5850845e-10 -3.6831179e-10 0.0002479594
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2 3.4338783e-09 -3.0736303e-10 0.00024795267
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3 7.7256433e-09 1.8277487e-10 0.00024794145
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4 1.3733026e-08 1.1019528e-09 0.00024792576
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5 2.145494e-08 2.449944e-09 0.00024790558
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6 3.0889985e-08 4.226444e-09 0.00024788093
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7 4.2036455e-08 6.4310711e-09 0.00024785181
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8 5.4892332e-08 9.0633658e-09 0.00024781823
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9 6.9455288e-08 1.2122792e-08 0.00024778019
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10 8.572269e-08 1.5608734e-08 0.0002477377
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11 1.0369159e-07 1.9520504e-08 0.00024769077
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12 1.2335875e-07 2.3857331e-08 0.00024763941
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13 1.4472059e-07 2.8618373e-08 0.00024758363
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14 1.6777327e-07 3.3802708e-08 0.00024752344
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15 1.9251262e-07 3.940934e-08 0.00024745886
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16 2.1893415e-07 4.5437194e-08 0.00024738989
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17 2.4703311e-07 5.1885122e-08 0.00024731656
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18 2.768044e-07 5.8751899e-08 0.00024723887
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19 3.0824267e-07 6.6036227e-08 0.00024715685
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20 3.4134222e-07 7.3736729e-08 0.00024707051
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21 3.7609709e-07 8.1851958e-08 0.00024697986
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22 4.1250102e-07 9.0380389e-08 0.00024688494
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23 4.5054742e-07 9.9320426e-08 0.00024678575
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24 4.9022945e-07 1.086704e-07 0.00024668231
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25 5.3153996e-07 1.1842856e-07 0.00024657466
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26 5.744715e-07 1.285931e-07 0.00024646281
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27 6.1901635e-07 1.3916212e-07 0.00024634678
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28 6.6516648e-07 1.5013367e-07 0.0002462266
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29 7.1291361e-07 1.6150571e-07 0.00024610229
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30 7.6224914e-07 1.7327614e-07 0.00024597388
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31 8.1316422e-07 1.8544279e-07 0.0002458414
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32 8.6564969e-07 1.9800342e-07 0.00024570487
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33 9.1969614e-07 2.109557e-07 0.00024556432
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34 9.7529388e-07 2.2429727e-07 0.00024541978
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35 1.0324329e-06 2.3802567e-07 0.00024527128
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36 1.0911031e-06 2.5213838e-07 0.00024511886
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37 1.1512938e-06 2.6663282e-07 0.00024496253
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38 1.2129943e-06 2.8150634e-07 0.00024480234
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39 1.2761936e-06 2.9675622e-07 0.00024463831
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40 1.3408803e-06 3.1237968e-07 0.00024447049
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41 1.407043e-06 3.2837388e-07 0.0002442989
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42 1.4746698e-06 3.447359e-07 0.00024412359
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43 1.5437487e-06 3.6146277e-07 0.00024394458
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44 1.6142674e-06 3.7855146e-07 0.00024376192
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45 1.6862132e-06 3.9599886e-07 0.00024357564
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46 1.7595735e-06 4.1380182e-07 0.00024338577
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47 1.8343351e-06 4.3195711e-07 0.00024319237
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48 1.9104848e-06 4.5046147e-07 0.00024299547
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49 1.9880091e-06 4.6931154e-07 0.00024279511
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50 2.0668943e-06 4.8850394e-07 0.00024259132
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51 2.1471263e-06 5.0803521e-07 0.00024238416
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52 2.228691e-06 5.2790184e-07 0.00024217367
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53 2.311574e-06 5.4810027e-07 0.00024195988
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54 2.3957606e-06 5.6862687e-07 0.00024174285
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55 2.481236e-06 5.8947797e-07 0.00024152261
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56 2.5679851e-06 6.1064984e-07 0.00024129922
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57 2.6559926e-06 6.3213871e-07 0.00024107271
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58 2.7452431e-06 6.5394073e-07 0.00024084313
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59 2.8357209e-06 6.7605203e-07 0.00024061054
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60 2.9274101e-06 6.9846868e-07 0.00024037498
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61 3.0202947e-06 7.2118669e-07 0.00024013649
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62 3.1143583e-06 7.4420204e-07 0.00023989513
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63 3.2095846e-06 7.6751065e-07 0.00023965094
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64 3.3059569e-06 7.911084e-07 0.00023940398
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65 3.4034585e-06 8.1499113e-07 0.00023915429
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66 3.5020722e-06 8.3915461e-07 0.00023890193
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67 3.601781e-06 8.6359461e-07 0.00023864694
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68 3.7025676e-06 8.8830681e-07 0.00023838939
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69 3.8044144e-06 9.132869e-07 0.00023812931
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70 3.9073038e-06 9.3853048e-07 0.00023786677
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71 4.0112181e-06 9.6403314e-07 0.00023760182
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72 4.1161392e-06 9.8979043e-07 0.00023733451
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73 4.2220491e-06 1.0157978e-06 0.0002370649
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74 4.3289295e-06 1.0420509e-06 0.00023679303
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75 4.4367621e-06 1.068545e-06 0.00023651897
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76 4.5455283e-06 1.0952755e-06 0.00023624277
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77 4.6552095e-06 1.1222378e-06 0.00023596449
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78 4.7657869e-06 1.1494273e-06 0.00023568418
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79 4.8772416e-06 1.1768393e-06 0.0002354019
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80 4.9895545e-06 1.2044689e-06 0.00023511771
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81 5.1027067e-06 1.2323116e-06 0.00023483166
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82 5.2166788e-06 1.2603625e-06 0.00023454381
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83 5.3314515e-06 1.2886168e-06 0.00023425422
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84 5.4470054e-06 1.3170697e-06 0.00023396295
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85 5.5633208e-06 1.3457162e-06 0.00023367006
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86 5.6803783e-06 1.3745516e-06 0.0002333756
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87 5.798158e-06 1.403571e-06 0.00023307963
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88 5.9166402e-06 1.4327693e-06 0.00023278222
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89 6.0358049e-06 1.4621418e-06 0.00023248341
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90 6.1556323e-06 1.4916833e-06 0.00023218329
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91 6.2761023e-06 1.5213889e-06 0.00023188189
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92 6.3971948e-06 1.5512537e-06 0.00023157929
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93 6.5188897e-06 1.5812727e-06 0.00023127554
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94 6.6411667e-06 1.6114407e-06 0.0002309707
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95 6.7640056e-06 1.6417527e-06 0.00023066484
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96 6.8873862e-06 1.6722038e-06 0.00023035801
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97 7.011288e-06 1.7027888e-06 0.00023005028
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98 7.1356907e-06 1.7335027e-06 0.0002297417
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99 7.2605738e-06 1.7643404e-06 0.00022943234
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100 7.3859169e-06 1.7952968e-06 0.00022912226
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Loop time of 0.00507947 on 1 procs for 100 steps with 3 atoms
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Performance: 850481762.482 fs/day, 0.000 hours/fs, 19687.078 timesteps/s, 59.061 katom-step/s
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98.9% 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 | 3.1029e-05 | 3.1029e-05 | 3.1029e-05 | 0.0 | 0.61
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Comm | 0.00027821 | 0.00027821 | 0.00027821 | 0.0 | 5.48
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Output | 0.001016 | 0.001016 | 0.001016 | 0.0 | 20.00
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Modify | 0.0032013 | 0.0032013 | 0.0032013 | 0.0 | 63.02
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Other | | 0.0005529 | | | 10.89
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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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