update docs and references for name changes in USER-MOP package, remove obsoleted files
This commit is contained in:
Axel Kohlmeyer
@ -1,62 +0,0 @@
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variable T equal 0.8
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variable p_solid equal 0.05
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lattice fcc 1.0
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region box block 0.0 6.0 0.0 6.0 -2.0 12.0
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create_box 2 box
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mass * 1.0
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 0.5 1.0
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pair_coeff 2 2 0.0 0.0
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neigh_modify delay 0
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region solid_bottom block INF INF INF INF -1.1 0.1
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region liquid block INF INF INF INF 1.1 8.9
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region solid_up block INF INF INF INF 9.9 11.1
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create_atoms 1 region liquid
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delete_atoms porosity liquid 0.26 88765
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group liquid region liquid
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create_atoms 2 region solid_bottom
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group solid_bottom region solid_bottom
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create_atoms 2 region solid_up
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group solid_up region solid_up
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group solid union solid_bottom solid_up
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variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
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fix piston_up solid_up aveforce NULL NULL -${faSolid}
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fix freeze_up solid_up setforce 0.0 0.0 NULL
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fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
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fix nvesol solid nve
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compute Tliq liquid temp
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fix nvtliq liquid nvt temp $T $T 0.5
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fix_modify nvtliq temp Tliq
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thermo 10000
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thermo_modify flush yes temp Tliq
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# dump 1 all atom 10000 dump.lammpstrj
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fix fxbal all balance 1000 1.05 shift z 10 1.05
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velocity liquid create $T 47298 dist gaussian rot yes
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run 50000
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# undump 1
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reset_timestep 0
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compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
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compute liquidStress_ke liquid stress/atom NULL ke
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compute liquidStress_vir liquid stress/atom NULL virial
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fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
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compute mopz0 all mop z center kin conf
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fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
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compute moppz liquid mop/profile z 0.0 0.1 kin conf
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fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
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run 40000
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0
examples/USER/mop/in.compute_stress_mop
Executable file → Normal file
0
examples/USER/mop/in.compute_stress_mop
Executable file → Normal file
@ -1,186 +0,0 @@
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LAMMPS (31 Aug 2018)
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variable T equal 0.8
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variable p_solid equal 0.05
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
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region box block 0.0 6.0 0.0 6.0 -2.0 12.0
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create_box 2 box
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Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
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1 by 1 by 1 MPI processor grid
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mass * 1.0
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0
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pair_coeff 1 2 0.5 1.0
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pair_coeff 2 2 0.0 0.0
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neigh_modify delay 0
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region solid_bottom block INF INF INF INF -1.1 0.1
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region liquid block INF INF INF INF 1.1 8.9
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region solid_up block INF INF INF INF 9.9 11.1
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create_atoms 1 region liquid
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Created 1080 atoms
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Time spent = 0.000631094 secs
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delete_atoms porosity liquid 0.26 88765
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Deleted 257 atoms, new total = 823
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group liquid region liquid
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823 atoms in group liquid
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create_atoms 2 region solid_bottom
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Created 216 atoms
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Time spent = 0.000221014 secs
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group solid_bottom region solid_bottom
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216 atoms in group solid_bottom
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create_atoms 2 region solid_up
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Created 216 atoms
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Time spent = 0.000169039 secs
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group solid_up region solid_up
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216 atoms in group solid_up
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group solid union solid_bottom solid_up
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432 atoms in group solid
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variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
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variable faSolid equal 0.05*lx*ly/count(solid_up)
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fix piston_up solid_up aveforce NULL NULL -${faSolid}
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fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
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fix freeze_up solid_up setforce 0.0 0.0 NULL
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fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
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fix nvesol solid nve
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compute Tliq liquid temp
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fix nvtliq liquid nvt temp $T $T 0.5
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fix nvtliq liquid nvt temp 0.8 $T 0.5
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fix nvtliq liquid nvt temp 0.8 0.8 0.5
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fix_modify nvtliq temp Tliq
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WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1404)
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thermo 10000
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thermo_modify flush yes temp Tliq
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WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
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# dump 1 all atom 10000 dump.lammpstrj
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fix fxbal all balance 1000 1.05 shift z 10 1.05
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velocity liquid create $T 47298 dist gaussian rot yes
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velocity liquid create 0.8 47298 dist gaussian rot yes
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run 50000
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 7 7 16
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0.8 -3.7188573 0 -2.9328812 -0.65673631 2016
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10000 0.80645968 -3.2160592 0 -2.4237366 -0.17266146 2016
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20000 0.85787011 -3.2087113 0 -2.3658796 0.032152534 2016
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30000 0.76357074 -3.1761807 0 -2.4259953 -0.034009443 2016
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40000 0.8116632 -3.1965608 0 -2.399126 -0.030033303 2016
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50000 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
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Loop time of 40.6472 on 1 procs for 50000 steps with 1255 atoms
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Performance: 531401.825 tau/day, 1230.097 timesteps/s
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99.7% 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 | 28.102 | 28.102 | 28.102 | 0.0 | 69.14
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Neigh | 9.8377 | 9.8377 | 9.8377 | 0.0 | 24.20
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Comm | 0.91642 | 0.91642 | 0.91642 | 0.0 | 2.25
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Output | 0.00024581 | 0.00024581 | 0.00024581 | 0.0 | 0.00
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Modify | 1.4027 | 1.4027 | 1.4027 | 0.0 | 3.45
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Other | | 0.3879 | | | 0.95
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Nlocal: 1255 ave 1255 max 1255 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2268 ave 2268 max 2268 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 40149 ave 40149 max 40149 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 40149
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Ave neighs/atom = 31.9912
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Neighbor list builds = 5714
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Dangerous builds = 0
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# undump 1
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reset_timestep 0
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compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
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compute liquidStress_ke liquid stress/atom NULL ke
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compute liquidStress_vir liquid stress/atom NULL virial
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fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
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compute mopz0 all mop z center kin conf
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fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
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compute moppz liquid mop/profile z 0.0 0.1 kin conf
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fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
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run 40000
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 7 7 16
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3 neighbor lists, perpetual/occasional/extra = 1 2 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute mop, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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(3) compute mop/profile, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
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10000 0.80600425 -3.1900933 0 -2.3982182 -0.042750667 2016
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20000 0.78117978 -3.2121798 0 -2.444694 0.0092285451 2016
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||||
30000 0.81008494 -3.1728363 0 -2.376952 0.053347807 2016
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40000 0.80440016 -3.1768915 0 -2.3865924 -0.0075214347 2016
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||||
Loop time of 45.4499 on 1 procs for 40000 steps with 1255 atoms
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Performance: 380198.462 tau/day, 880.089 timesteps/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 | 25.456 | 25.456 | 25.456 | 0.0 | 56.01
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Neigh | 7.9422 | 7.9422 | 7.9422 | 0.0 | 17.47
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Comm | 0.73477 | 0.73477 | 0.73477 | 0.0 | 1.62
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Output | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 0.00
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Modify | 11.004 | 11.004 | 11.004 | 0.0 | 24.21
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Other | | 0.3131 | | | 0.69
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Nlocal: 1255 ave 1255 max 1255 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2269 ave 2269 max 2269 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 40325 ave 40325 max 40325 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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|
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Total # of neighbors = 40325
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Ave neighs/atom = 32.1315
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Neighbor list builds = 4587
|
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Dangerous builds = 0
|
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|
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Total wall time: 0:01:26
|
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@ -1,188 +0,0 @@
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LAMMPS (31 Aug 2018)
|
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
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using 1 OpenMP thread(s) per MPI task
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variable T equal 0.8
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variable p_solid equal 0.05
|
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|
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
|
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region box block 0.0 6.0 0.0 6.0 -2.0 12.0
|
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create_box 2 box
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Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
|
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1 by 1 by 4 MPI processor grid
|
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|
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mass * 1.0
|
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pair_style lj/cut 2.5
|
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pair_coeff * * 1.0 1.0
|
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pair_coeff 1 2 0.5 1.0
|
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pair_coeff 2 2 0.0 0.0
|
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neigh_modify delay 0
|
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|
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region solid_bottom block INF INF INF INF -1.1 0.1
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region liquid block INF INF INF INF 1.1 8.9
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region solid_up block INF INF INF INF 9.9 11.1
|
||||
|
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create_atoms 1 region liquid
|
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Created 1080 atoms
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||||
Time spent = 0.000378132 secs
|
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delete_atoms porosity liquid 0.26 88765
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Deleted 288 atoms, new total = 792
|
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group liquid region liquid
|
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792 atoms in group liquid
|
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|
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create_atoms 2 region solid_bottom
|
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Created 216 atoms
|
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Time spent = 0.000345945 secs
|
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group solid_bottom region solid_bottom
|
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216 atoms in group solid_bottom
|
||||
create_atoms 2 region solid_up
|
||||
Created 216 atoms
|
||||
Time spent = 0.000124454 secs
|
||||
group solid_up region solid_up
|
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216 atoms in group solid_up
|
||||
group solid union solid_bottom solid_up
|
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432 atoms in group solid
|
||||
|
||||
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
|
||||
variable faSolid equal 0.05*lx*ly/count(solid_up)
|
||||
fix piston_up solid_up aveforce NULL NULL -${faSolid}
|
||||
fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
|
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fix freeze_up solid_up setforce 0.0 0.0 NULL
|
||||
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
|
||||
fix nvesol solid nve
|
||||
compute Tliq liquid temp
|
||||
fix nvtliq liquid nvt temp $T $T 0.5
|
||||
fix nvtliq liquid nvt temp 0.8 $T 0.5
|
||||
fix nvtliq liquid nvt temp 0.8 0.8 0.5
|
||||
fix_modify nvtliq temp Tliq
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404)
|
||||
|
||||
thermo 10000
|
||||
thermo_modify flush yes temp Tliq
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
# dump 1 all atom 10000 dump.lammpstrj
|
||||
|
||||
fix fxbal all balance 1000 1.05 shift z 10 1.05
|
||||
velocity liquid create $T 47298 dist gaussian rot yes
|
||||
velocity liquid create 0.8 47298 dist gaussian rot yes
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.122 | 3.135 | 3.147 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.8 -3.4905808 0 -2.7150906 -0.59565852 2016
|
||||
10000 0.82075861 -3.1822235 0 -2.3866107 0.013840263 2016
|
||||
20000 0.76467575 -3.0955084 0 -2.3542602 -0.076868925 2016
|
||||
30000 0.75803557 -3.1011543 0 -2.3663428 -0.052887049 2016
|
||||
40000 0.81732724 -3.064259 0 -2.2719724 0.070708808 2016
|
||||
50000 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016
|
||||
Loop time of 22.1566 on 4 procs for 50000 steps with 1224 atoms
|
||||
|
||||
Performance: 974879.887 tau/day, 2256.666 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.732 | 13.012 | 14.39 | 38.0 | 58.73
|
||||
Neigh | 2.47 | 3.7351 | 4.3661 | 38.4 | 16.86
|
||||
Comm | 1.881 | 3.4383 | 5.8722 | 79.7 | 15.52
|
||||
Output | 0.00014567 | 0.0003581 | 0.0009892 | 0.0 | 0.00
|
||||
Modify | 1.1006 | 1.5188 | 2.6121 | 51.3 | 6.85
|
||||
Other | | 0.4521 | | | 2.04
|
||||
|
||||
Nlocal: 306 ave 312 max 295 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 1242.75 ave 1373 max 944 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Neighs: 9770.25 ave 10807 max 8736 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 39081
|
||||
Ave neighs/atom = 31.9289
|
||||
Neighbor list builds = 5704
|
||||
Dangerous builds = 0
|
||||
# undump 1
|
||||
reset_timestep 0
|
||||
|
||||
compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
|
||||
|
||||
compute liquidStress_ke liquid stress/atom NULL ke
|
||||
compute liquidStress_vir liquid stress/atom NULL virial
|
||||
fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
|
||||
|
||||
compute mopz0 all mop z center kin conf
|
||||
fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
|
||||
|
||||
compute moppz liquid mop/profile z 0.0 0.1 kin conf
|
||||
fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
|
||||
|
||||
run 40000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 1 2 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute mop, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute mop/profile, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.147 | 4.15 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.75874551 -3.1070261 0 -2.3715265 -0.074970431 2016
|
||||
10000 0.82372476 -3.1299329 0 -2.3314448 -0.14706101 2016
|
||||
20000 0.80692892 -3.1278896 0 -2.3456828 -0.085123604 2016
|
||||
30000 0.78458951 -3.0966006 0 -2.3360488 0.13637007 2016
|
||||
40000 0.80106495 -3.1135836 0 -2.3370611 -0.14404185 2016
|
||||
Loop time of 31.4145 on 4 procs for 40000 steps with 1224 atoms
|
||||
|
||||
Performance: 550065.249 tau/day, 1273.299 timesteps/s
|
||||
92.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.199 | 12.307 | 13.428 | 35.4 | 39.18
|
||||
Neigh | 2.1261 | 3.1416 | 3.6373 | 33.5 | 10.00
|
||||
Comm | 3.5381 | 4.476 | 6.229 | 48.9 | 14.25
|
||||
Output | 0.00062943 | 0.0031546 | 0.0040004 | 2.6 | 0.01
|
||||
Modify | 10.186 | 10.862 | 12.26 | 24.8 | 34.58
|
||||
Other | | 0.6247 | | | 1.99
|
||||
|
||||
Nlocal: 306 ave 315 max 299 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 1221.5 ave 1347 max 912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
Neighs: 9710.25 ave 10301 max 8980 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 38841
|
||||
Ave neighs/atom = 31.7328
|
||||
Neighbor list builds = 4573
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:53
|
||||
Reference in New Issue
Block a user