forked from lijiext/lammps
move fix to EXTRA-FIX package, update docs, add reference logs to example
This commit is contained in:
Axel Kohlmeyer
parent
e33590b2fc
commit
93fcf3cc75
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@ -42,6 +42,8 @@ Examples
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Description
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"""""""""""
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.. versionadded:: TBD
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This fix implements flow boundary conditions (FBC) introduced in :ref:`(Pavlov1) <fbc-Pavlov1>` and :ref:`(Pavlov2) <fbc-Pavlov2>`.
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The goal is to generate a stationary flow with a shifted Maxwell velocity distribution:
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@ -108,6 +110,10 @@ This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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Fix *wall_flow* is part of the EXTRA-FIX package. It is only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Flow boundary conditions should not be used with rigid bodies such as those
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defined by a "fix rigid" command.
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@ -1,4 +1,4 @@
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variable nrun equal 10000
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variable nrun equal 1000
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variable dump_count equal 10
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variable nwall equal 4
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@ -0,0 +1,182 @@
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-758-ge33590b2fc-modified)
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using 1 OpenMP thread(s) per MPI task
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variable nrun equal 1000
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variable dump_count equal 10
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variable nwall equal 4
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variable w1 equal 67
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variable w2 equal 71
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variable w3 equal 75
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variable w4 equal 79
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variable x_cylinder equal 20
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variable y_cylinder equal 17
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variable r_cylinder equal 4
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variable MASS equal 1
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variable TEMP equal 0.4
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variable VFLOW equal 0.5
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units lj
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atom_style atomic
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lattice fcc 0.3
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Lattice spacing in x,y,z = 2.3712622 2.3712622 2.3712622
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region sim_box block 0 84 0 34 0 10
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boundary p p p
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create_box 2 sim_box
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Created orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
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1 by 1 by 1 MPI processor grid
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region reg_cylinder cylinder z ${x_cylinder} ${y_cylinder} ${r_cylinder} EDGE EDGE
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region reg_cylinder cylinder z 20 ${y_cylinder} ${r_cylinder} EDGE EDGE
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region reg_cylinder cylinder z 20 17 ${r_cylinder} EDGE EDGE
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region reg_cylinder cylinder z 20 17 4 EDGE EDGE
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create_atoms 1 box
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Created 114240 atoms
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using lattice units in orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
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create_atoms CPU = 0.010 seconds
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## setup obstacle ##
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group g_obst region reg_cylinder
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1950 atoms in group g_obst
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group g_flow subtract all g_obst
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112290 atoms in group g_flow
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set group g_obst type 2
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Setting atom values ...
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1950 settings made for type
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mass 1 ${MASS}
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mass 1 1
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mass 2 ${MASS}
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mass 2 1
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velocity g_flow create ${TEMP} 4928459 rot yes dist gaussian
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velocity g_flow create 0.4 4928459 rot yes dist gaussian
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velocity g_obst set 0.0 0.0 0.0
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pair_style lj/cut 1.122462
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pair_coeff 1 1 1.0 1.0
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pair_coeff 1 2 1.0 1.0
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pair_coeff 2 2 1.0 1.0
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pair_modify shift yes
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 g_flow nve
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fix 2 g_flow wall/flow x ${VFLOW} ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 79
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variable dump_every equal ${nrun}/${dump_count}
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variable dump_every equal 1000/${dump_count}
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variable dump_every equal 1000/10
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variable thermo_every equal ${dump_every}
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variable thermo_every equal 100
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variable restart_every equal ${nrun}/10
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variable restart_every equal 1000/10
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##### uncomment for grid aggregation #####
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#variable gr_Nx equal 42
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#variable gr_Ny equal 17
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#variable gr_Nz equal 1
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#variable gr_Nevery equal ${dump_every}
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#variable gr_Nrepeat equal 1
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#variable gr_Nfreq equal ${dump_every}
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#fix 3 g_flow ave/grid ${gr_Nevery} ${gr_Nrepeat} ${gr_Nfreq} ${gr_Nx} ${gr_Ny} ${gr_Nz} vx vy vz density/mass norm all ave one
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#compute ct_gridId g_flow property/grid ${gr_Nx} ${gr_Ny} ${gr_Nz} id
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#dump dmp_grid g_flow grid ${dump_every} grid.lammpstrj c_ct_gridId:grid:data f_3:grid:data[*]
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##########################################
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#dump dmp_coord all atom ${dump_every} dump.lammpstrj
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#compute ct_Temp g_flow temp/com
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#thermo_style custom step temp epair emol etotal press c_ct_Temp
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#restart ${restart_every} flow.restart
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timestep 0.005
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thermo ${thermo_every}
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thermo 100
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run ${nrun}
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run 1000
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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 wall/flow command: doi:10.1177/10943420231213013
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@Article{Pavlov-etal-IJHPCA-2024,
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author = {Daniil Pavlov and Vladislav Galigerov and Daniil Kolotinskii and Vsevolod Nikolskiy and Vladimir Stegailov},
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title = {GPU-based molecular dynamics of fluid flows: Reaching for turbulence},
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journal = {The International Journal of High Performance Computing Applications},
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year = 2024,
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volume = 38,
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number = 1,
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pages = 34-49
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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 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 20 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.422462
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ghost atom cutoff = 1.422462
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binsize = 0.711231, bins = 281 114 34
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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) = 26.69 | 26.69 | 26.69 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.39317221 0 0 0.58975315 0.11795063
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100 0.3671684 0.045118445 0 0.59586622 0.27378331
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200 0.3732041 0.036897471 0 0.59669873 0.24917809
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300 0.37432305 0.036501844 0 0.5979815 0.24715194
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400 0.37603886 0.035350565 0 0.59940392 0.24480762
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500 0.37617142 0.036949771 0 0.60120196 0.24862985
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600 0.37751983 0.036484268 0 0.60275905 0.24784635
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700 0.37787831 0.037327783 0 0.60414029 0.25060427
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800 0.37959242 0.036206184 0 0.60558983 0.2476903
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900 0.38019033 0.036874395 0 0.6071549 0.24984211
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1000 0.38070666 0.037068948 0 0.60812395 0.25041936
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Loop time of 5.61598 on 1 procs for 1000 steps with 114240 atoms
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Performance: 76923.319 tau/day, 178.063 timesteps/s, 20.342 Matom-step/s
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99.7% 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 | 2.6351 | 2.6351 | 2.6351 | 0.0 | 46.92
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Neigh | 1.2994 | 1.2994 | 1.2994 | 0.0 | 23.14
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Comm | 0.26576 | 0.26576 | 0.26576 | 0.0 | 4.73
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Output | 0.0030531 | 0.0030531 | 0.0030531 | 0.0 | 0.05
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Modify | 1.3019 | 1.3019 | 1.3019 | 0.0 | 23.18
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Other | | 0.1107 | | | 1.97
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Nlocal: 114240 ave 114240 max 114240 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 20119 ave 20119 max 20119 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 164018 ave 164018 max 164018 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 164018
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Ave neighs/atom = 1.4357318
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:05
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@ -0,0 +1,182 @@
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LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-758-ge33590b2fc-modified)
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using 1 OpenMP thread(s) per MPI task
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variable nrun equal 1000
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variable dump_count equal 10
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variable nwall equal 4
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variable w1 equal 67
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variable w2 equal 71
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variable w3 equal 75
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variable w4 equal 79
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variable x_cylinder equal 20
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variable y_cylinder equal 17
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variable r_cylinder equal 4
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variable MASS equal 1
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variable TEMP equal 0.4
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variable VFLOW equal 0.5
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units lj
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atom_style atomic
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lattice fcc 0.3
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Lattice spacing in x,y,z = 2.3712622 2.3712622 2.3712622
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region sim_box block 0 84 0 34 0 10
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boundary p p p
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create_box 2 sim_box
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Created orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
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4 by 1 by 1 MPI processor grid
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region reg_cylinder cylinder z ${x_cylinder} ${y_cylinder} ${r_cylinder} EDGE EDGE
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region reg_cylinder cylinder z 20 ${y_cylinder} ${r_cylinder} EDGE EDGE
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region reg_cylinder cylinder z 20 17 ${r_cylinder} EDGE EDGE
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region reg_cylinder cylinder z 20 17 4 EDGE EDGE
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create_atoms 1 box
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Created 114240 atoms
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using lattice units in orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622)
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create_atoms CPU = 0.003 seconds
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## setup obstacle ##
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group g_obst region reg_cylinder
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1950 atoms in group g_obst
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group g_flow subtract all g_obst
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112290 atoms in group g_flow
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set group g_obst type 2
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Setting atom values ...
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1950 settings made for type
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mass 1 ${MASS}
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mass 1 1
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mass 2 ${MASS}
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mass 2 1
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velocity g_flow create ${TEMP} 4928459 rot yes dist gaussian
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velocity g_flow create 0.4 4928459 rot yes dist gaussian
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velocity g_obst set 0.0 0.0 0.0
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pair_style lj/cut 1.122462
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pair_coeff 1 1 1.0 1.0
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pair_coeff 1 2 1.0 1.0
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pair_coeff 2 2 1.0 1.0
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pair_modify shift yes
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 g_flow nve
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fix 2 g_flow wall/flow x ${VFLOW} ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 ${nwall} ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 ${w1} ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 ${w2} ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 ${w3} ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 ${w4}
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fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 79
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variable dump_every equal ${nrun}/${dump_count}
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variable dump_every equal 1000/${dump_count}
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variable dump_every equal 1000/10
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variable thermo_every equal ${dump_every}
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variable thermo_every equal 100
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variable restart_every equal ${nrun}/10
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variable restart_every equal 1000/10
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##### uncomment for grid aggregation #####
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#variable gr_Nx equal 42
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#variable gr_Ny equal 17
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#variable gr_Nz equal 1
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#variable gr_Nevery equal ${dump_every}
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#variable gr_Nrepeat equal 1
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#variable gr_Nfreq equal ${dump_every}
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#fix 3 g_flow ave/grid ${gr_Nevery} ${gr_Nrepeat} ${gr_Nfreq} ${gr_Nx} ${gr_Ny} ${gr_Nz} vx vy vz density/mass norm all ave one
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#compute ct_gridId g_flow property/grid ${gr_Nx} ${gr_Ny} ${gr_Nz} id
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#dump dmp_grid g_flow grid ${dump_every} grid.lammpstrj c_ct_gridId:grid:data f_3:grid:data[*]
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##########################################
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#dump dmp_coord all atom ${dump_every} dump.lammpstrj
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#compute ct_Temp g_flow temp/com
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#thermo_style custom step temp epair emol etotal press c_ct_Temp
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#restart ${restart_every} flow.restart
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timestep 0.005
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thermo ${thermo_every}
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thermo 100
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run ${nrun}
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run 1000
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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 wall/flow command: doi:10.1177/10943420231213013
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@Article{Pavlov-etal-IJHPCA-2024,
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author = {Daniil Pavlov and Vladislav Galigerov and Daniil Kolotinskii and Vsevolod Nikolskiy and Vladimir Stegailov},
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title = {GPU-based molecular dynamics of fluid flows: Reaching for turbulence},
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journal = {The International Journal of High Performance Computing Applications},
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year = 2024,
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volume = 38,
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number = 1,
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pages = 34-49
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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 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 20 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.422462
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ghost atom cutoff = 1.422462
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binsize = 0.711231, bins = 281 114 34
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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) = 8.496 | 8.496 | 8.496 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.39317221 0 0 0.58975315 0.11795063
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100 0.36726398 0.045386014 0 0.59627716 0.27402111
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200 0.37384538 0.036574547 0 0.5973377 0.24836729
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300 0.37487455 0.036519645 0 0.59882654 0.24691726
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400 0.37591417 0.036405755 0 0.60027207 0.24700641
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500 0.37654714 0.037008829 0 0.60182459 0.24883444
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600 0.3778008 0.03663706 0 0.6033333 0.24874392
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700 0.37851338 0.036714175 0 0.60447928 0.24881829
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800 0.37984876 0.036237049 0 0.6060052 0.24843003
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900 0.38022763 0.036847615 0 0.60718407 0.24987198
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1000 0.38084717 0.037139994 0 0.60840575 0.25070072
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Loop time of 2.20347 on 4 procs for 1000 steps with 114240 atoms
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Performance: 196054.093 tau/day, 453.829 timesteps/s, 51.845 Matom-step/s
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95.6% 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 | 0.67927 | 0.70882 | 0.73473 | 2.4 | 32.17
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Neigh | 0.32928 | 0.34467 | 0.36084 | 2.0 | 15.64
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Comm | 0.3211 | 0.36609 | 0.40741 | 6.1 | 16.61
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Output | 0.0017748 | 0.0032465 | 0.0046508 | 2.1 | 0.15
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Modify | 0.71135 | 0.74424 | 0.76001 | 2.3 | 33.78
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Other | | 0.03641 | | | 1.65
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Nlocal: 28560 ave 29169 max 27884 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Nghost: 6452.25 ave 6546 max 6368 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Neighs: 40893 ave 42032 max 39445 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Total # of neighbors = 163572
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Ave neighs/atom = 1.4318277
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Neighbor list builds = 50
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Dangerous builds not checked
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Total wall time: 0:00:02
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@ -1023,6 +1023,8 @@
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/fix_wall_colloid.h
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/fix_wall_ees.cpp
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/fix_wall_ees.h
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/fix_wall_flow.cpp
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/fix_wall_flow.h
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/fix_wall_region_ees.cpp
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/fix_wall_region_ees.h
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/fix_wall_reflect_stochastic.cpp
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Reference in New Issue