235 lines
10 KiB
Groff
235 lines
10 KiB
Groff
LAMMPS (4 Feb 2025)
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Processor partition = 1
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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 188892 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 8.5850843e-10 5.313724e-10 0.00024796083
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2 3.4339027e-09 1.4919466e-09 0.00024795841
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3 7.7257901e-09 2.8816048e-09 0.00024795438
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4 1.3733516e-08 4.7001635e-09 0.00024794873
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5 2.1456164e-08 6.9473741e-09 0.00024794148
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6 3.0892555e-08 9.6229225e-09 0.00024793261
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7 4.2041252e-08 1.2726429e-08 0.00024792214
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8 5.4900553e-08 1.6257449e-08 0.00024791006
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9 6.9468499e-08 2.0215473e-08 0.00024789638
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10 8.5742867e-08 2.4599926e-08 0.0002478811
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11 1.0372118e-07 2.9410168e-08 0.00024786422
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12 1.2340069e-07 3.4645495e-08 0.00024784576
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13 1.447784e-07 4.0305136e-08 0.0002478257
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14 1.6785106e-07 4.6388259e-08 0.00024780406
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15 1.9261515e-07 5.2893965e-08 0.00024778084
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16 2.190669e-07 5.9821291e-08 0.00024775605
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17 2.4720228e-07 6.7169211e-08 0.00024772969
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18 2.7701701e-07 7.4936635e-08 0.00024770176
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19 3.0850655e-07 8.312241e-08 0.00024767228
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20 3.416661e-07 9.1725317e-08 0.00024764125
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21 3.7649064e-07 1.0074408e-07 0.00024760868
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22 4.1297485e-07 1.1017735e-07 0.00024757457
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23 4.511132e-07 1.2002372e-07 0.00024753893
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24 4.9089989e-07 1.3028173e-07 0.00024750177
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25 5.3232887e-07 1.4094984e-07 0.0002474631
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26 5.7539386e-07 1.5202647e-07 0.00024742293
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27 6.2008832e-07 1.6350996e-07 0.00024738126
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28 6.6640547e-07 1.7539859e-07 0.00024733811
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29 7.1433828e-07 1.876906e-07 0.00024729348
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30 7.6387949e-07 2.0038414e-07 0.00024724738
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31 8.150216e-07 2.1347732e-07 0.00024719983
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32 8.6775685e-07 2.2696818e-07 0.00024715084
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33 9.2207727e-07 2.4085472e-07 0.0002471004
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34 9.7797464e-07 2.5513485e-07 0.00024704855
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35 1.0354405e-06 2.6980645e-07 0.00024699528
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36 1.0944662e-06 2.8486732e-07 0.00024694061
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37 1.1550427e-06 3.0031522e-07 0.00024688456
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38 1.2171611e-06 3.1614785e-07 0.00024682713
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39 1.2808118e-06 3.3236283e-07 0.00024676833
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40 1.3459853e-06 3.4895776e-07 0.00024670818
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41 1.4126717e-06 3.6593016e-07 0.0002466467
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42 1.4808611e-06 3.832775e-07 0.0002465839
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43 1.5505431e-06 4.009972e-07 0.00024651978
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44 1.6217074e-06 4.1908663e-07 0.00024645437
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45 1.6943431e-06 4.3754308e-07 0.00024638767
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46 1.7684394e-06 4.5636381e-07 0.00024631971
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47 1.8439852e-06 4.7554603e-07 0.0002462505
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48 1.9209691e-06 4.9508689e-07 0.00024618005
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49 1.9993796e-06 5.1498348e-07 0.00024610839
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50 2.079205e-06 5.3523286e-07 0.00024603551
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51 2.1604333e-06 5.5583202e-07 0.00024596145
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52 2.2430524e-06 5.7677791e-07 0.00024588621
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53 2.32705e-06 5.9806742e-07 0.00024580981
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54 2.4124135e-06 6.1969741e-07 0.00024573228
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55 2.4991302e-06 6.4166468e-07 0.00024565362
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56 2.5871872e-06 6.6396597e-07 0.00024557386
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57 2.6765714e-06 6.8659801e-07 0.00024549301
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58 2.7672695e-06 7.0955745e-07 0.00024541108
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59 2.859268e-06 7.328409e-07 0.00024532811
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60 2.9525533e-06 7.5644494e-07 0.00024524409
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61 3.0471115e-06 7.8036609e-07 0.00024515907
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62 3.1429287e-06 8.0460083e-07 0.00024507304
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63 3.2399907e-06 8.2914562e-07 0.00024498603
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64 3.3382831e-06 8.5399683e-07 0.00024489807
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65 3.4377915e-06 8.7915084e-07 0.00024480916
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66 3.5385011e-06 9.0460395e-07 0.00024471933
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67 3.6403972e-06 9.3035245e-07 0.0002446286
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68 3.7434648e-06 9.5639257e-07 0.00024453698
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69 3.8476886e-06 9.8272051e-07 0.0002444445
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70 3.9530535e-06 1.0093324e-06 0.00024435118
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71 4.0595439e-06 1.0362244e-06 0.00024425703
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72 4.1671443e-06 1.0633926e-06 0.00024416208
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73 4.275839e-06 1.0908331e-06 0.00024406635
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74 4.3856121e-06 1.1185418e-06 0.00024396985
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75 4.4964475e-06 1.1465147e-06 0.00024387262
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76 4.6083292e-06 1.1747478e-06 0.00024377466
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77 4.7212408e-06 1.2032371e-06 0.00024367601
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78 4.835166e-06 1.2319783e-06 0.00024357668
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79 4.9500883e-06 1.2609674e-06 0.00024347669
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80 5.0659909e-06 1.2902001e-06 0.00024337607
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81 5.1828572e-06 1.3196723e-06 0.00024327483
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82 5.3006702e-06 1.3493797e-06 0.000243173
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83 5.419413e-06 1.379318e-06 0.0002430706
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84 5.5390685e-06 1.4094831e-06 0.00024296765
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85 5.6596194e-06 1.4398705e-06 0.00024286417
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86 5.7810485e-06 1.4704759e-06 0.00024276019
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87 5.9033384e-06 1.501295e-06 0.00024265573
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88 6.0264715e-06 1.5323234e-06 0.00024255081
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89 6.1504303e-06 1.5635565e-06 0.00024244545
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90 6.275197e-06 1.5949902e-06 0.00024233967
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91 6.400754e-06 1.6266197e-06 0.0002422335
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92 6.5270834e-06 1.6584408e-06 0.00024212696
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93 6.6541672e-06 1.6904488e-06 0.00024202007
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94 6.7819875e-06 1.7226394e-06 0.00024191285
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95 6.9105262e-06 1.7550078e-06 0.00024180534
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96 7.0397651e-06 1.7875497e-06 0.00024169754
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97 7.169686e-06 1.8202604e-06 0.00024158948
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98 7.3002707e-06 1.8531354e-06 0.00024148118
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99 7.4315008e-06 1.88617e-06 0.00024137268
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100 7.563358e-06 1.9193596e-06 0.00024126398
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Loop time of 0.0050955 on 1 procs for 100 steps with 3 atoms
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Performance: 847807054.814 fs/day, 0.000 hours/fs, 19625.163 timesteps/s, 58.875 katom-step/s
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99.8% 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 | 2.3358e-05 | 2.3358e-05 | 2.3358e-05 | 0.0 | 0.46
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Comm | 0.00022527 | 0.00022527 | 0.00022527 | 0.0 | 4.42
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Output | 0.00078435 | 0.00078435 | 0.00078435 | 0.0 | 15.39
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Modify | 0.0036209 | 0.0036209 | 0.0036209 | 0.0 | 71.06
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Other | | 0.0004416 | | | 8.67
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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 = 23
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Dangerous builds = 0
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Total wall time: 0:00:00
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