delete log files for now
This commit is contained in:
Steve Plimpton
@ -1,82 +0,0 @@
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LAMMPS (23 Jun 2022)
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# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
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units metal
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atom_style full
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atom_modify sort 0 0.0
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read_data 2uo2.lmp
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Reading data file ...
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triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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6 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.037 seconds
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read_data CPU = 0.205 seconds
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velocity all create 300.0 87287 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.00025
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fix 1 all nve
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fix 2 all mdi/qm virial yes elements 92 8
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thermo_style custom step temp pe etotal press
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thermo 1
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dump 1 all custom 1 dump.aimd.mdi id type x y z vx vy vz fx fy fz
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run 2
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0
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ghost atom cutoff = 0
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binsize = 10.8, bins = 1 1 1
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0 neighbor lists, perpetual/occasional/extra = 0 0 0
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
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Step Temp PotEng TotEng Press
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0 300 -50.539035 -50.345145 -120197.6
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1 307.57345 -50.544722 -50.345937 -120123.27
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2 316.3757 -50.551342 -50.346868 -120035.12
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Loop time of 30.0573 on 1 procs for 2 steps with 6 atoms
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Performance: 0.001 ns/day, 16698.513 hours/ns, 0.067 timesteps/s
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100.0% 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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Bond | 0.00049455 | 0.00049455 | 0.00049455 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0024482 | 0.0024482 | 0.0024482 | 0.0 | 0.01
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Output | 0.0061712 | 0.0061712 | 0.0061712 | 0.0 | 0.02
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Modify | 30.044 | 30.044 | 30.044 | 0.0 | 99.95
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Other | | 0.004682 | | | 0.02
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Nlocal: 6 ave 6 max 6 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2 ave 2 max 2 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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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:52
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@ -1,100 +0,0 @@
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LAMMPS (23 Jun 2022)
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# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
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units metal
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atom_style full
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atom_modify sort 0 0.0
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read_data 2uo2.lmp
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Reading data file ...
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triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
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2 by 1 by 1 MPI processor grid
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reading atoms ...
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6 atoms
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.004 seconds
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velocity all create 300.0 87287 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.00025
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fix 1 all nve
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fix 2 all mdi/qm virial yes elements 92 8
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thermo_style custom step temp pe etotal press
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thermo 1
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dump 1 all custom 1 dump.aimd.mdi id type x y z vx vy vz fx fy fz
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run 20
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0
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ghost atom cutoff = 0
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binsize = 10.8, bins = 1 1 1
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0 neighbor lists, perpetual/occasional/extra = 0 0 0
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WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 5.485 | 5.987 | 6.489 Mbytes
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Step Temp PotEng TotEng Press
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0 300 -50.539035 -50.345145 -120197.6
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1 307.57345 -50.544722 -50.345937 -120123.27
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2 316.3757 -50.551342 -50.346868 -120035.12
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3 326.39203 -50.558885 -50.347938 -119933.11
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4 337.60559 -50.567341 -50.349146 -119817.17
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5 349.99734 -50.576697 -50.350493 -119687.24
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6 363.54606 -50.586939 -50.351979 -119543.23
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7 378.22834 -50.598054 -50.353605 -119385.07
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8 394.0186 -50.610024 -50.355369 -119212.67
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9 410.88903 -50.622831 -50.357273 -119025.94
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10 428.80963 -50.636457 -50.359317 -118824.77
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11 447.74819 -50.65088 -50.3615 -118609.06
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12 467.67027 -50.666079 -50.363823 -118378.7
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13 488.53922 -50.68203 -50.366287 -118133.58
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14 510.31617 -50.698708 -50.36889 -117873.58
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15 532.96002 -50.716086 -50.371633 -117598.57
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16 556.42747 -50.734137 -50.374517 -117308.44
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17 580.67298 -50.75283 -50.377541 -117003.05
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18 605.64879 -50.772136 -50.380705 -116682.27
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19 631.30497 -50.792023 -50.38401 -116345.95
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20 657.58937 -50.812455 -50.387454 -115993.97
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Loop time of 25.6068 on 2 procs for 20 steps with 6 atoms
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Performance: 0.017 ns/day, 1422.598 hours/ns, 0.781 timesteps/s
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100.0% CPU use with 2 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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Bond | 1.636e-06 | 2.023e-06 | 2.41e-06 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 4.199e-05 | 4.8295e-05 | 5.4599e-05 | 0.0 | 0.00
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Output | 0.0018384 | 0.002081 | 0.0023236 | 0.5 | 0.01
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Modify | 25.604 | 25.604 | 25.604 | 0.0 | 99.99
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Other | | 0.000287 | | | 0.00
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Nlocal: 3 ave 6 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 1 ave 2 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 2 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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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:27
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@ -1,82 +0,0 @@
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LAMMPS (23 Jun 2022)
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# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
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|
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units metal
|
||||
atom_style full
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atom_modify sort 0 0.0
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|
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read_data 2uo2.lmp
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Reading data file ...
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triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
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1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
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||||
6 atoms
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Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
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||||
0 = max # of 1-3 neighbors
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||||
0 = max # of 1-4 neighbors
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||||
1 = max # of special neighbors
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special bonds CPU = 0.034 seconds
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read_data CPU = 0.214 seconds
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velocity all create 300.0 87287 loop geom
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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||||
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timestep 0.00025
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||||
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||||
fix 1 all nve
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||||
|
||||
fix 2 all mdi/qm virial yes elements 92 8
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thermo_style custom step temp pe etotal press
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thermo 1
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dump 1 all custom 1 dump.aimd.mdi.plugin id type x y z vx vy vz fx fy fz
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mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 2"
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run 2
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Neighbor list info ...
|
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update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 300 -50.539035 -50.345145 -120197.6
|
||||
1 307.57345 -50.544722 -50.345937 -120123.27
|
||||
2 316.3757 -50.551342 -50.346868 -120035.12
|
||||
Loop time of 72.5549 on 1 procs for 2 steps with 6 atoms
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||||
|
||||
Performance: 0.001 ns/day, 40308.278 hours/ns, 0.028 timesteps/s
|
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32.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0.00041679 | 0.00041679 | 0.00041679 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
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Comm | 0.00238 | 0.00238 | 0.00238 | 0.0 | 0.00
|
||||
Output | 0.04814 | 0.04814 | 0.04814 | 0.0 | 0.07
|
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Modify | 72.499 | 72.499 | 72.499 | 0.0 | 99.92
|
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Other | | 0.004742 | | | 0.01
|
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|
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Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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Neighs: 0 ave 0 max 0 min
|
||||
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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Ave special neighs/atom = 0
|
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Neighbor list builds = 0
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Dangerous builds = 0
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@ -1,255 +0,0 @@
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LAMMPS (23 Jun 2022)
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# Series of single-point calcs of 2,3,4 UO2 molecules
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# with LATTE in MDI stand-alone mode
|
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variable files index 4uo2 3uo2 2uo2
|
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mdi connect
|
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|
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label LOOP
|
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|
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units metal
|
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atom_style full
|
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atom_modify sort 0 0.0
|
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|
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read_data ${files}.lmp
|
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read_data 4uo2.lmp
|
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Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
|
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1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
12 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -102.35713 -102.35713 -31036.168
|
||||
Loop time of 1.141e-06 on 1 procs for 0 steps with 12 atoms
|
||||
|
||||
175.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.141e-06 | | |100.00
|
||||
|
||||
Nlocal: 12 ave 12 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5 ave 5 max 5 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.4uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 3uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 16.2, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -78.155679 -78.155679 -99931.431
|
||||
Loop time of 9.62e-07 on 1 procs for 0 steps with 9 atoms
|
||||
|
||||
207.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.62e-07 | | |100.00
|
||||
|
||||
Nlocal: 9 ave 9 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.3uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 2uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -50.539035 -50.539035 -120855.2
|
||||
Loop time of 7.21e-07 on 1 procs for 0 steps with 6 atoms
|
||||
|
||||
138.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 7.21e-07 | | |100.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.2uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:02
|
||||
@ -1,255 +0,0 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
# Series of single-point calcs of 2,3,4 UO2 molecules
|
||||
# with LATTE in MDI stand-alone mode
|
||||
|
||||
variable files index 4uo2 3uo2 2uo2
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 4uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
12 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -102.35713 -102.35713 -31036.168
|
||||
Loop time of 1.654e-06 on 2 procs for 0 steps with 12 atoms
|
||||
|
||||
120.9% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.654e-06 | | |100.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2.5 ave 4 max 1 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.4uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 3uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 16.2, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -78.155679 -78.155679 -99931.431
|
||||
Loop time of 2.1225e-06 on 2 procs for 0 steps with 9 atoms
|
||||
|
||||
117.8% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.123e-06 | | |100.00
|
||||
|
||||
Nlocal: 4.5 ave 9 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1.5 ave 3 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.3uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 2uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -50.539035 -50.539035 -120855.2
|
||||
Loop time of 2.021e-06 on 2 procs for 0 steps with 6 atoms
|
||||
|
||||
123.7% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.021e-06 | | |100.00
|
||||
|
||||
Nlocal: 3 ave 6 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1 ave 2 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.2uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:08
|
||||
@ -1,81 +0,0 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
# Series of single-point calcs of 2,3,4 UO2 molecules
|
||||
# with LATTE in MDI plugin mode
|
||||
|
||||
variable files index 4uo2 3uo2 2uo2
|
||||
|
||||
label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 4uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
12 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.031 seconds
|
||||
read_data CPU = 0.184 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -102.35713 -102.35713 -31036.168
|
||||
Loop time of 0.000848374 on 1 procs for 0 steps with 12 atoms
|
||||
|
||||
122.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0008484 | | |100.00
|
||||
|
||||
Nlocal: 12 ave 12 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5 ave 5 max 5 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.plugin.4uo2 id type x y z fx fy fz modify sort id
|
||||
Reference in New Issue
Block a user