update examples to standard lammps conventions
This commit is contained in:
Colin Denniston
@ -2,13 +2,15 @@
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# Large colloidal sphere difusing around. #
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# #
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# In the first stage, the sphere is constructed by condensing atoms onto #
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# the surface of a spherica region. #
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# the surface of a spherical region. There are a flag you can change to #
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# either bond atoms into a spherical shell or integrate them as a rigid body#
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# #
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# To run this example, LAMMPS needs to be compiled with a the following #
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# packages: RIGID, LATBOTLZ #
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# #
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# Sample output from this run can be found in the file: #
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# 'dump.polymer.lammpstrj' #
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# If you uncomment the "dump..." line, sample output from this run #
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# can be found in the file: #
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# 'dump.trapnewsphere.lammpstrj' #
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# and viewed using, e.g., the VMD software. #
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# #
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#===========================================================================#
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@ -60,7 +62,7 @@ fix wall all wall/region mysphere lj93 15.0 1.5 5.28
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fix 2 all nve
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dump mydump all atom 10000 out.lammpstrj
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#dump mydump all atom 10000 dump.trapnewsphere.lammpstrj
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run 20000
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@ -191,7 +193,7 @@ if "${is_bonded} == 1" then &
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else &
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"variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out"
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fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
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#fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
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run 10000
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#run 25000000
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@ -0,0 +1,388 @@
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LAMMPS (17 Feb 2022)
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#===========================================================================#
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# Large colloidal sphere difusing around. #
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# #
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# In the first stage, the sphere is constructed by condensing atoms onto #
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# the surface of a spherical region. There are a flag you can change to #
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# either bond atoms into a spherical shell or integrate them as a rigid body#
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# #
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# To run this example, LAMMPS needs to be compiled with a the following #
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# packages: RIGID, LATBOTLZ #
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# #
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# If you uncomment the "dump..." line, sample output from this run #
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# can be found in the file: #
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# 'dump.trapnewsphere.lammpstrj' #
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# and viewed using, e.g., the VMD software. #
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# #
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#===========================================================================#
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units nano
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dimension 3
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boundary p p p
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region mybox block -24 24 -24 24 -24 24
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# flag indicating whether sphere will be bonded or rigid, 0 or 1
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variable is_bonded equal 0
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# timestep for the LB run (setup uses different timesteps)
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variable tstep equal 0.00025
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# number of stencil points in any direction. could be 2, 3, or 4
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variable stpts equal 2
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if "${is_bonded} == 1" then "create_box 1 mybox bond/types 10 extra/bond/per/atom 12" else "create_box 1 mybox"
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create_box 1 mybox
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Created orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 2 by 2 MPI processor grid
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#----------------------------------------------------------------------------
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# Create a spherical region and then fill it with atoms
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#----------------------------------------------------------------------------
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region mysphereinside sphere 0 0 0 4.0
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#variable n_nodes equal 216
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variable n_nodes equal 284
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create_atoms 1 random ${n_nodes} 1234 mysphereinside units box
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create_atoms 1 random 284 1234 mysphereinside units box
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Created 284 atoms
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using box units in orthogonal box = (-24 -24 -24) to (24 24 24)
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create_atoms CPU = 0.001 seconds
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pair_style soft 1.0
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pair_coeff * * 0.0
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variable prefactor equal ramp(0,30)
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fix 1 all adapt 1 pair soft a * * v_prefactor
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mass * 1.0
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#----------------------------------------------------------------------------
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# Set up and do an initial run to push the atoms apart as the random creation
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# could have them overlapping too much for stability.
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#----------------------------------------------------------------------------
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timestep 0.002
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# Define sphere where minimum of wall potential is at r=4 so
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# regions is 4 + (2/5)^(1/6) sigma
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region mysphere sphere 0 0 0 5.28756
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fix wall all wall/region mysphere lj93 15.0 1.5 5.28
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fix 2 all nve
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#dump mydump all atom 10000 dump.trapnewsphere.lammpstrj
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run 20000
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.1
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ghost atom cutoff = 1.1
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binsize = 0.55, bins = 88 88 88
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair soft, 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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.944 | 3.944 | 3.944 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 0 0 0 0
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20000 317.05614 618.63581 0 2476.8578 0.030715
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Loop time of 0.573686 on 4 procs for 20000 steps with 284 atoms
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Performance: 6024197.192 ns/day, 0.000 hours/ns, 34862.252 timesteps/s
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100.0% CPU use with 4 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 | 0.062609 | 0.070036 | 0.076149 | 1.8 | 12.21
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Neigh | 0.21074 | 0.2209 | 0.2305 | 1.5 | 38.51
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Comm | 0.17847 | 0.19084 | 0.21153 | 3.0 | 33.26
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Output | 1.74e-05 | 2.58e-05 | 5.02e-05 | 0.0 | 0.00
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Modify | 0.079214 | 0.082596 | 0.085481 | 0.8 | 14.40
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Other | | 0.009288 | | | 1.62
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Nlocal: 71 ave 73 max 69 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Nghost: 54.75 ave 57 max 53 min
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Histogram: 2 0 0 0 0 0 0 1 0 1
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Neighs: 107.25 ave 127 max 85 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Total # of neighbors = 429
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Ave neighs/atom = 1.5105634
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Neighbor list builds = 1996
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Dangerous builds = 1993
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unfix wall
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fix wall all wall/region mysphere lj93 50.0 1.5 5.68
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unfix 1
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#----------------------------------------------------------------------------
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# Do a run to condense the atoms onto the spherical surface and anneal them
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# so they will be orderly aranged onto a semi-triangular mesh on the sphere
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#----------------------------------------------------------------------------
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pair_style lj/cut 1.68359
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#pair_coeff * * 0.002 1.5 1.68369
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pair_coeff * * 0.0005 1.5 1.68369
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fix 3 all langevin 1.5 0.01 100.0 5678
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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comm_modify cutoff 2.5
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run 500000
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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 = 1.98369
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ghost atom cutoff = 2.5
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binsize = 0.991845, bins = 49 49 49
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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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.277 | 3.277 | 3.277 Mbytes
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Step Temp E_pair E_mol TotEng Press
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20000 317.05614 626.83186 0 2485.0538 0.034256287
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520000 0.20789564 780.54747 0 781.76592 0.028916791
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Loop time of 12.8226 on 4 procs for 500000 steps with 284 atoms
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Performance: 6738089.440 ns/day, 0.000 hours/ns, 38993.573 timesteps/s
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100.0% CPU use with 4 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 | 2.6508 | 3.1904 | 3.6443 | 20.0 | 24.88
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Neigh | 0.68551 | 0.75012 | 0.80362 | 5.1 | 5.85
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Comm | 3.7915 | 4.3143 | 4.922 | 19.6 | 33.65
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Output | 2.26e-05 | 3.335e-05 | 6.29e-05 | 0.0 | 0.00
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Modify | 3.1825 | 3.2495 | 3.3155 | 2.6 | 25.34
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Other | | 1.318 | | | 10.28
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Nlocal: 71 ave 74 max 69 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Nghost: 109.75 ave 113 max 105 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 613.25 ave 718 max 495 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Total # of neighbors = 2453
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Ave neighs/atom = 8.6373239
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Neighbor list builds = 13515
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Dangerous builds = 0
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minimize 0.0 1.0e-8 1000 100000
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
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Step Temp E_pair E_mol TotEng Press
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520000 0.20789564 780.54747 0 781.76592 0.028916791
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520004 0.20789564 780.00993 0 781.22838 0.02889732
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Loop time of 0.00296133 on 4 procs for 4 steps with 284 atoms
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99.8% CPU use with 4 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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780.547473373201 780.009929329778 780.009929329778
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Force two-norm initial, final = 40.166574 13.723713
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Force max component initial, final = 4.2404394 1.5423956
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Final line search alpha, max atom move = 6.0381565e-11 9.3132257e-11
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Iterations, force evaluations = 4 69
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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 | 0.0009509 | 0.0010909 | 0.0014002 | 0.5 | 36.84
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0007064 | 0.0010256 | 0.0011795 | 0.6 | 34.63
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0.000204 | 0.00024405 | 0.0002982 | 0.0 | 8.24
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Other | | 0.0006008 | | | 20.29
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Nlocal: 71 ave 72 max 69 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 109.75 ave 113 max 107 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 612.75 ave 726 max 504 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 2451
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Ave neighs/atom = 8.6302817
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix wall
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unfix 2
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unfix 3
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#----------------------------------------------------------------------------
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# If bonded, bond the atoms together at something close to their current
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# configuration
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#----------------------------------------------------------------------------
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variable total_mass equal 0.002398
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variable node_mass equal "v_total_mass / v_n_nodes"
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mass * ${node_mass}
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mass * 8.44366197183099e-06
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if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 25.0 0.869333" "bond_coeff 2 25.0 0.948" "bond_coeff 3 25.0 1.026666" "bond_coeff 4 25.0 1.105333" "bond_coeff 5 25.0 1.184" "bond_coeff 6 25.0 1.262666" "bond_coeff 7 25.0 1.341333" "bond_coeff 8 25.0 1.42" "bond_coeff 9 25.0 1.498666" "bond_coeff 10 25.0 1.577333" "create_bonds many all all 1 0.83 0.908666" "create_bonds many all all 2 0.908667 0.987333" "create_bonds many all all 3 0.987334 1.066" "create_bonds many all all 4 1.066001 1.144666" "create_bonds many all all 5 1.144667 1.223333" "create_bonds many all all 6 1.223334 1.302" "create_bonds many all all 7 1.302001 1.380666" "create_bonds many all all 8 1.380667 1.459333" "create_bonds many all all 9 1.459334 1.538" "create_bonds many all all 10 1.538001 1.61667"
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if "${is_bonded} == 1" then "pair_style lj/cut 5.05108" "pair_coeff * * 0.5 4.5" else "pair_style lj/cut 1.2" "pair_coeff * * 0.0 0.0"
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pair_style lj/cut 1.2
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pair_coeff * * 0.0 0.0
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timestep ${tstep}
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timestep 0.00025
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#----------------------------------------------------------------------------
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# You could uncomment the following lines and then turn off the noise and
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# comment out the trap (following) to instead do a run that drags the
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# sphere through the fluid to measure the drag force.
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#----------------------------------------------------------------------------
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#variable total_force equal 8.0
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#variable node_force equal "v_total_force / v_n_nodes"
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#variable oscillateY equal cos(step*0.0005)/(-0.004+50*v_tstep)/v_n_nodes
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#variable oscillateZ equal cos(step*0.0003)/(-0.004+50*v_tstep)/v_n_nodes
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#fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
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#----------------------------------------------------------------------------
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# Trap the sphere along x (could be done experimentally using optical
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# tweezers.
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#----------------------------------------------------------------------------
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variable fx atom -x*4.14195/284.0
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fix trap all addforce v_fx 0.0 0.0 # needs to go before fix lb/fluid and lb/viscous
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#----------------------------------------------------------------------------
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# Set up the lb/fluid parameters for water and at a temperature of 300 K. If
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# the colloid is integrated with the rigid fix, the dof are not
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# automatically calculated correctly but as this would then be a rigid
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# sphere it is clear it should have 6 degrees of freedom.
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#----------------------------------------------------------------------------
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if "${is_bonded} == 1" then "fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920" else "fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6"
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fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6
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fix FL all lb/fluid 1 1.0 0.0009982071 stencil 2 dx 1.2 noise 300.0 181920 dof 6
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Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:486)
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Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
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fix 2 all lb/viscous
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if "${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
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fix 3 all rigid group 1 all
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1 rigid bodies with 284 atoms
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#equilibration run
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
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Your simulation uses code contributions which should be cited:
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- fix lb/fluid command:
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@Article{Denniston et al.,
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author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
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title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
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year = 2022,
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volume = 275,
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pages = {108318}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes
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Step Temp E_pair E_mol TotEng Press
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520004 8.9102565e-07 0 0 1.8452924e-08 6.7761632e-05
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530004 3.474402 0 0 0.071954018 -0.00061159689
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Loop time of 238.57 on 4 procs for 10000 steps with 284 atoms
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Performance: 905.396 ns/day, 0.027 hours/ns, 41.916 timesteps/s
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100.0% CPU use with 4 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 | 0.07901 | 0.086329 | 0.095378 | 2.0 | 0.04
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Neigh | 0.012928 | 0.013445 | 0.013795 | 0.3 | 0.01
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Comm | 0.18848 | 0.1969 | 0.20455 | 1.3 | 0.08
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Output | 4.07e-05 | 5.9575e-05 | 0.0001157 | 0.0 | 0.00
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Modify | 238.01 | 238.02 | 238.03 | 0.1 | 99.77
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Other | | 0.2536 | | | 0.11
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Nlocal: 71 ave 84 max 59 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 110.75 ave 121 max 101 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Neighs: 243.25 ave 285 max 209 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Total # of neighbors = 973
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Ave neighs/atom = 3.4260563
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Neighbor list builds = 52
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Dangerous builds = 0
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# data gathering run
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reset_timestep 0
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#----------------------------------------------------------------------------
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# Create variables containing the positions/velocity of the colloids center
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# of mass.
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#----------------------------------------------------------------------------
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variable cmx equal xcm(all,x)
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variable cmy equal xcm(all,y)
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variable cmz equal xcm(all,z)
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variable vcmx equal vcm(all,x)
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variable vcmy equal vcm(all,y)
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variable vcmz equal vcm(all,z)
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if "${is_bonded} == 1" then "variable comdatafile string trap_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out"
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variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out
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variable comdatafile string trap_n284_st${stpts}_dt${tstep}.out
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variable comdatafile string trap_n284_st2_dt${tstep}.out
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variable comdatafile string trap_n284_st2_dt0.00025.out
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#fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.474402 0 0 0.071954018 0.00181615
|
||||
10000 2.6284662 0 0 0.054434894 0.00098091301
|
||||
Loop time of 237.772 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 908.435 ns/day, 0.026 hours/ns, 42.057 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.079283 | 0.087287 | 0.095198 | 2.6 | 0.04
|
||||
Neigh | 0.0133 | 0.013789 | 0.014439 | 0.3 | 0.01
|
||||
Comm | 0.18949 | 0.1975 | 0.20661 | 1.8 | 0.08
|
||||
Output | 2.88e-05 | 4.3675e-05 | 8.58e-05 | 0.0 | 0.00
|
||||
Modify | 237.21 | 237.22 | 237.22 | 0.0 | 99.77
|
||||
Other | | 0.253 | | | 0.11
|
||||
|
||||
Nlocal: 71 ave 87 max 54 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 110 ave 125 max 100 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 243.25 ave 264 max 207 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
#run 25000000
|
||||
Total wall time: 0:08:09
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,218 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 284 atoms
|
||||
using box units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.1
|
||||
ghost atom cutoff = 1.1
|
||||
binsize = 0.55, bins = 88 88 88
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.002
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.947 | 4.947 | 4.947 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
20000 317.05614 618.63581 0 2476.8578 0.030715
|
||||
Loop time of 1.04979 on 4 procs for 20000 steps with 284 atoms
|
||||
|
||||
Performance: 3292081.736 ns/day, 0.000 hours/ns, 19051.399 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10763 | 0.11963 | 0.13214 | 2.9 | 11.40
|
||||
Neigh | 0.38332 | 0.41159 | 0.43122 | 2.8 | 39.21
|
||||
Comm | 0.31394 | 0.34969 | 0.3981 | 5.1 | 33.31
|
||||
Output | 0.0029418 | 0.0035883 | 0.0043197 | 0.8 | 0.34
|
||||
Modify | 0.13951 | 0.14727 | 0.15199 | 1.3 | 14.03
|
||||
Other | | 0.01802 | | | 1.72
|
||||
|
||||
Nlocal: 71.0000 ave 73 max 69 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 54.7500 ave 57 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 107.250 ave 127 max 85 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 429
|
||||
Ave neighs/atom = 1.5105634
|
||||
Neighbor list builds = 1996
|
||||
Dangerous builds = 1993
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.98369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 0.991845, bins = 49 49 49
|
||||
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
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 20000
|
||||
Time step : 0.002
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.279 | 4.280 | 4.280 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 317.05614 626.83186 0 2485.0538 0.034256287
|
||||
520000 0.20789564 780.54747 0 781.76592 0.028916791
|
||||
Loop time of 20.94 on 4 procs for 500000 steps with 284 atoms
|
||||
|
||||
Performance: 4126072.144 ns/day, 0.000 hours/ns, 23877.732 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.3543 | 5.0458 | 5.6845 | 21.6 | 24.10
|
||||
Neigh | 1.3816 | 1.444 | 1.5232 | 4.7 | 6.90
|
||||
Comm | 6.2693 | 7.0156 | 7.7783 | 21.0 | 33.50
|
||||
Output | 0.038337 | 0.072704 | 0.11121 | 10.0 | 0.35
|
||||
Modify | 4.9433 | 5.027 | 5.1022 | 2.9 | 24.01
|
||||
Other | | 2.335 | | | 11.15
|
||||
|
||||
Nlocal: 71.0000 ave 74 max 69 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 109.750 ave 113 max 105 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 613.250 ave 718 max 495 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2453
|
||||
Ave neighs/atom = 8.6373239
|
||||
Neighbor list builds = 13515
|
||||
Dangerous builds = 0
|
||||
Setting up cg style minimization ...
|
||||
Unit style : nano
|
||||
Current step : 520000
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.404 | 5.405 | 5.405 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
520000 0.20789564 780.54747 0 781.76592 0.028916791
|
||||
520004 0.20789564 780.00993 0 781.22838 0.02889732
|
||||
Loop time of 0.0052249 on 4 procs for 4 steps with 284 atoms
|
||||
|
||||
90.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
780.547473373201 780.009929329778 780.009929329778
|
||||
Force two-norm initial, final = 40.166574 13.723713
|
||||
Force max component initial, final = 4.2404394 1.5423956
|
||||
Final line search alpha, max atom move = 6.0381565e-11 9.3132257e-11
|
||||
Iterations, force evaluations = 4 69
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.000733 | 0.00099598 | 0.0013314 | 0.0 | 19.06
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0006855 | 0.0010138 | 0.0012766 | 0.7 | 19.40
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0.0002038 | 0.00023407 | 0.0003163 | 0.0 | 4.48
|
||||
Other | | 0.002981 | | | 57.05
|
||||
|
||||
Nlocal: 71.0000 ave 72 max 69 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 109.750 ave 113 max 107 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 612.750 ave 726 max 504 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2451
|
||||
Ave neighs/atom = 8.6302817
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
1 rigid bodies with 284 atoms
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 520004
|
||||
Time step : 0.00025
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
520004 8.9102565e-07 0 0 1.8452924e-08 6.7761632e-05
|
||||
530004 3.474402 0 0 0.071954018 -0.00061159689
|
||||
Loop time of 252.92 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 854.024 ns/day, 0.028 hours/ns, 39.538 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.083731 | 0.090623 | 0.098802 | 1.8 | 0.04
|
||||
Neigh | 0.016581 | 0.017116 | 0.018055 | 0.4 | 0.01
|
||||
Comm | 0.18954 | 0.19805 | 0.20528 | 1.3 | 0.08
|
||||
Output | 0.0011027 | 0.0018302 | 0.002624 | 1.3 | 0.00
|
||||
Modify | 252.35 | 252.37 | 252.39 | 0.1 | 99.78
|
||||
Other | | 0.2466 | | | 0.10
|
||||
|
||||
Nlocal: 71.0000 ave 84 max 59 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 110.750 ave 121 max 101 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 243.250 ave 285 max 209 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 52
|
||||
Dangerous builds = 0
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.00025
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.474402 0 0 0.071954018 0.00181615
|
||||
10000 2.6284662 0 0 0.054434894 0.00098091301
|
||||
Loop time of 296.345 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 728.880 ns/day, 0.033 hours/ns, 33.744 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.097394 | 0.10852 | 0.12099 | 3.3 | 0.04
|
||||
Neigh | 0.014447 | 0.015052 | 0.015762 | 0.4 | 0.01
|
||||
Comm | 0.23755 | 0.24986 | 0.26167 | 2.3 | 0.08
|
||||
Output | 0.0022544 | 0.0025083 | 0.0025944 | 0.3 | 0.00
|
||||
Modify | 295.67 | 295.69 | 295.72 | 0.1 | 99.78
|
||||
Other | | 0.28 | | | 0.09
|
||||
|
||||
Nlocal: 71.0000 ave 87 max 54 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 110.000 ave 125 max 100 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 243.250 ave 264 max 207 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 288.718806
|
||||
LB update time: 135.577114
|
||||
LB PCalc time: 76.637579
|
||||
LB fluidForce time: 25.590260
|
||||
LB CorrectU time: 19.713186
|
||||
Total wall time: 0:09:31
|
||||
Reference in New Issue
Block a user