forked from lijiext/lammps
update AGNI potential for Al, reference runs and output and citation
This commit is contained in:
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49e83b4348
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File diff suppressed because it is too large
Load Diff
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@ -5,7 +5,7 @@ boundary p p f
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read_data adatom.data
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pair_style agni
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pair_coeff * * Al_prb.agni Al
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pair_coeff * * Al_jpc.agni Al
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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@ -4,7 +4,7 @@ boundary p p p
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read_data vacancy.data
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pair_style agni
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pair_coeff * * Al_prb.agni Al
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pair_coeff * * Al_jpc.agni Al
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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@ -0,0 +1,87 @@
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LAMMPS (21 Feb 2017)
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using 1 OpenMP thread(s) per MPI task
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processors * * 1
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units metal
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boundary p p f
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read_data adatom.data
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orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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181 atoms
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pair_style agni
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pair_coeff * * Al_jpc.agni Al
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Reading potential file Al_jpc.agni with DATE: 2017-02-24
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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timestep 0.0005
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velocity all create 500 12345
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fix 1 all nvt temp 250 250 0.2
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fix 5 all momentum 1 linear 1 1 1
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thermo 100
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thermo_style custom step ke temp
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# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 8.3
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ghost atom cutoff = 8.3
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binsize = 4.15, bins = 5 4 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair agni, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Memory usage per processor = 2.69795 Mbytes
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Step KinEng Temp
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0 11.633413 500
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100 4.6059939 197.964
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200 7.3700149 316.76065
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300 6.0443913 259.78581
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400 6.1631189 264.88868
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500 6.2647272 269.25577
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600 5.2732539 226.6426
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700 5.6514471 242.89721
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800 6.5572407 281.8279
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900 6.0576738 260.35669
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1000 6.5622233 282.04205
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Loop time of 51.9308 on 1 procs for 1000 steps with 181 atoms
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Performance: 0.832 ns/day, 28.850 hours/ns, 19.256 timesteps/s
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99.4% CPU use with 1 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 | 51.89 | 51.89 | 51.89 | 0.0 | 99.92
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Neigh | 0.023158 | 0.023158 | 0.023158 | 0.0 | 0.04
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Comm | 0.0049036 | 0.0049036 | 0.0049036 | 0.0 | 0.01
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Output | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.00
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Modify | 0.010244 | 0.010244 | 0.010244 | 0.0 | 0.02
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Other | | 0.002483 | | | 0.00
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Nlocal: 181 ave 181 max 181 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 563 ave 563 max 563 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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FullNghs: 19484 ave 19484 max 19484 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 19484
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Ave neighs/atom = 107.646
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Neighbor list builds = 33
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:52
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@ -0,0 +1,87 @@
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LAMMPS (21 Feb 2017)
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using 1 OpenMP thread(s) per MPI task
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processors * * 1
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units metal
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boundary p p f
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read_data adatom.data
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orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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181 atoms
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pair_style agni
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pair_coeff * * Al_jpc.agni Al
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Reading potential file Al_jpc.agni with DATE: 2017-02-24
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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timestep 0.0005
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velocity all create 500 12345
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fix 1 all nvt temp 250 250 0.2
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fix 5 all momentum 1 linear 1 1 1
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thermo 100
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thermo_style custom step ke temp
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# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 8.3
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ghost atom cutoff = 8.3
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binsize = 4.15, bins = 5 4 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair agni, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Memory usage per processor = 3.06041 Mbytes
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Step KinEng Temp
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0 11.633413 500
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100 4.6059941 197.96401
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200 7.3700154 316.76067
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300 6.0443913 259.78581
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400 6.1631193 264.8887
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500 6.2647281 269.25581
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600 5.2732537 226.64259
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700 5.651448 242.89725
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800 6.5572405 281.82789
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900 6.0576741 260.3567
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1000 6.562224 282.04208
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Loop time of 14.5263 on 4 procs for 1000 steps with 181 atoms
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Performance: 2.974 ns/day, 8.070 hours/ns, 68.841 timesteps/s
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99.3% CPU use with 4 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 | 12.858 | 13.227 | 13.574 | 8.0 | 91.06
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Neigh | 0.0056965 | 0.0058173 | 0.0060787 | 0.2 | 0.04
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Comm | 0.92934 | 1.276 | 1.6455 | 25.7 | 8.78
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Output | 0.00013971 | 0.00017625 | 0.00025463 | 0.0 | 0.00
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Modify | 0.012693 | 0.012756 | 0.012911 | 0.1 | 0.09
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Other | | 0.004066 | | | 0.03
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Nlocal: 45.25 ave 52 max 40 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Nghost: 376.5 ave 382 max 366 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 4871 ave 5578 max 4374 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Total # of neighbors = 19484
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Ave neighs/atom = 107.646
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Neighbor list builds = 33
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:14
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@ -0,0 +1,87 @@
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LAMMPS (21 Feb 2017)
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using 1 OpenMP thread(s) per MPI task
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units metal
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boundary p p p
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read_data vacancy.data
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orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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31 atoms
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pair_style agni
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pair_coeff * * Al_jpc.agni Al
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Reading potential file Al_jpc.agni with DATE: 2017-02-24
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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timestep 0.0005
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velocity all create 1000 12345
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fix 1 all nvt temp 900 900 200
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fix 5 all momentum 1 linear 1 1 1
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thermo 100
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thermo_style custom step ke etotal temp
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# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 8.3
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ghost atom cutoff = 8.3
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binsize = 4.15, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair agni, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Memory usage per processor = 2.73416 Mbytes
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Step KinEng TotEng Temp
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0 3.8778043 3.8778043 1000
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100 2.9986261 2.9986261 773.27937
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200 3.6860314 3.6860314 950.54599
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300 3.813315 3.813315 983.36961
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400 3.7330285 3.7330285 962.6655
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500 3.5875467 3.5875467 925.14896
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600 3.5331529 3.5331529 911.12202
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700 2.6509449 2.6509449 683.62008
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800 3.3763492 3.3763492 870.68582
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900 3.903673 3.903673 1006.6709
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1000 3.0884824 3.0884824 796.45133
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Loop time of 9.02712 on 1 procs for 1000 steps with 31 atoms
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Performance: 4.786 ns/day, 5.015 hours/ns, 110.777 timesteps/s
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99.4% CPU use with 1 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 | 9.0039 | 9.0039 | 9.0039 | 0.0 | 99.74
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Neigh | 0.011892 | 0.011892 | 0.011892 | 0.0 | 0.13
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Comm | 0.0061693 | 0.0061693 | 0.0061693 | 0.0 | 0.07
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Output | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.00
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Modify | 0.0035009 | 0.0035009 | 0.0035009 | 0.0 | 0.04
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Other | | 0.001521 | | | 0.02
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Nlocal: 31 ave 31 max 31 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 869 ave 869 max 869 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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FullNghs: 4360 ave 4360 max 4360 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 4360
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Ave neighs/atom = 140.645
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Neighbor list builds = 53
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:09
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@ -0,0 +1,87 @@
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LAMMPS (21 Feb 2017)
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using 1 OpenMP thread(s) per MPI task
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units metal
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boundary p p p
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read_data vacancy.data
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orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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31 atoms
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pair_style agni
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pair_coeff * * Al_jpc.agni Al
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Reading potential file Al_jpc.agni with DATE: 2017-02-24
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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timestep 0.0005
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velocity all create 1000 12345
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fix 1 all nvt temp 900 900 200
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fix 5 all momentum 1 linear 1 1 1
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thermo 100
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thermo_style custom step ke etotal temp
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# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 8.3
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ghost atom cutoff = 8.3
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binsize = 4.15, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair agni, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Memory usage per processor = 2.72175 Mbytes
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Step KinEng TotEng Temp
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0 3.8778044 3.8778044 1000
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100 2.9986263 2.9986263 773.27942
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200 3.6860315 3.6860315 950.54602
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300 3.8133145 3.8133145 983.3695
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400 3.7330282 3.7330282 962.66543
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500 3.5875466 3.5875466 925.14895
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600 3.5331523 3.5331523 911.12186
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700 2.6509448 2.6509448 683.62005
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800 3.3763493 3.3763493 870.68584
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900 3.9036733 3.9036733 1006.671
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1000 3.0884818 3.0884818 796.45116
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Loop time of 2.46785 on 4 procs for 1000 steps with 31 atoms
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Performance: 17.505 ns/day, 1.371 hours/ns, 405.212 timesteps/s
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99.2% CPU use with 4 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 | 2.0737 | 2.299 | 2.3902 | 8.7 | 93.16
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Neigh | 0.0025222 | 0.0027327 | 0.0028174 | 0.2 | 0.11
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Comm | 0.059817 | 0.15141 | 0.37684 | 33.8 | 6.14
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Output | 0.0001502 | 0.00016767 | 0.00021219 | 0.0 | 0.01
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Modify | 0.0098755 | 0.010248 | 0.010664 | 0.3 | 0.42
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Other | | 0.004321 | | | 0.18
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Nlocal: 7.75 ave 8 max 7 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Nghost: 617.25 ave 621 max 612 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 1090 ave 1131 max 993 min
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Histogram: 1 0 0 0 0 0 0 0 1 2
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Total # of neighbors = 4360
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Ave neighs/atom = 140.645
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Neighbor list builds = 53
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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File diff suppressed because it is too large
Load Diff
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@ -1,4 +1,5 @@
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# DATE: 2016-11-11 CONTRIBUTOR: Venkatesh Botu <botuvenkatesh@gmail.com> CITATION: Botu, V. and Ramprasad, R., Phys. Rev. B, 92, 094306 (2015)
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# This potential is deprecated. Please use Al_jpc.agni instead.
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# This potential file is parameterized for metal units
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generation 1
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@ -60,6 +60,14 @@ static const char cite_pair_agni[] =
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" pages = {094306},\n"
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" year = {2015},\n"
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" publisher = {APS}\n"
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"}\n\n"
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"@article{botu2017jpc,\n"
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" author = {Botu, V. and Batra, R. and Chapman, J. and Ramprasad, Rampi},\n"
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" journal = {J. Phys. Chem. C},\n"
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" volume = {121},\n"
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" number = {1},\n"
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" pages = {511},\n"
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" year = {2017},\n"
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"}\n\n";
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#define AGNI_VERSION 1
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Reference in New Issue