264 lines
9.4 KiB
Groff
264 lines
9.4 KiB
Groff
LAMMPS (23 Jun 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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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 2uo2 3uo2 4uo2
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mdi connect
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label LOOP
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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 ${files}.lmp
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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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neighbor 0.3 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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fix 1 all mdi/qm virial yes elements 92 8 connect no
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thermo_style custom step temp pe etotal press
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thermo 1
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run 0
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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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. (src/comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -50.539035 -50.539035 -120855.2
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Loop time of 1.956e-06 on 2 procs for 0 steps with 6 atoms
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127.8% CPU use with 2 MPI tasks x 1 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 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 1.956e-06 | | |100.00
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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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write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
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write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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next files
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jump SELF LOOP
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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 ${files}.lmp
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read_data 3uo2.lmp
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Reading data file ...
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triclinic box = (0 0 0) to (16.2 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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9 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 = 0.001 seconds
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neighbor 0.3 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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fix 1 all mdi/qm virial yes elements 92 8 connect no
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thermo_style custom step temp pe etotal press
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thermo 1
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run 0
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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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 = 16.2, 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. (src/comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -78.155679 -78.155679 -99931.431
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Loop time of 2.375e-06 on 2 procs for 0 steps with 9 atoms
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147.4% CPU use with 2 MPI tasks x 1 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 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 2.375e-06 | | |100.00
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Nlocal: 4.5 ave 9 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 1.5 ave 3 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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write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
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write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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next files
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jump SELF LOOP
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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 ${files}.lmp
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read_data 4uo2.lmp
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Reading data file ...
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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 2 by 1 MPI processor grid
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reading atoms ...
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12 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 = 0.002 seconds
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neighbor 0.3 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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fix 1 all mdi/qm virial yes elements 92 8 connect no
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thermo_style custom step temp pe etotal press
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thermo 1
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run 0
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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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. (src/comm_brick.cpp:210)
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Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
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Step Temp PotEng TotEng Press
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0 0 -102.35713 -102.35713 -31036.168
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Loop time of 2.4445e-06 on 2 procs for 0 steps with 12 atoms
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122.7% CPU use with 2 MPI tasks x 1 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 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 2.444e-06 | | |100.00
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Nlocal: 6 ave 6 max 6 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Nghost: 2.5 ave 4 max 1 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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write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
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write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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next files
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jump SELF LOOP
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mdi exit
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Total wall time: 0:00:08
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