Add an example for USER/adios based on the balance example
This commit is contained in:
Norbert Podhorszki
45
examples/USER/adios/adios2_config.xml
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45
examples/USER/adios/adios2_config.xml
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<?xml version="1.0"?>
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<adios-config>
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<!-- example engines
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<engine type="BPFile">
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<engine type="HDF5">
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<engine type="InSituMPI">
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<engine type="SST">
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<engine type="DataMan">
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-->
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<!-- example operations
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These operations go inside an IO group (but not inside engine group)
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<io name="custom">
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<variable name="T">
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<operation type="zfp">
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<parameter key="accuracy" value="0.01"/>
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</operation>
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</variable>
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</io>
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-->
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<!--====================================================
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Configuration for the dump atom/adios command
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====================================================-->
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<io name="atom">
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<engine type="BPFile">
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</engine>
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</io>
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<!--====================================================
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Configuration for the dump custom/adios command
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====================================================-->
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<io name="custom">
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<engine type="BPFile">
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</engine>
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</io>
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</adios-config>
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56
examples/USER/adios/in.adios_balance
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56
examples/USER/adios/in.adios_balance
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# 2d circle of particles inside a box with LJ walls
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variable b index 0
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variable x index 50
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variable y index 20
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variable d index 20
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variable v index 5
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variable w index 2
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units lj
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dimension 2
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atom_style atomic
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boundary f f p
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lattice hex 0.85
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region box block 0 $x 0 $y -0.5 0.5
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create_box 1 box
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region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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create_atoms 1 region circle
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mass 1 1.0
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velocity all create 0.5 87287 loop geom
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velocity all set $v $w 0 sum yes
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pair_style lj/cut 2.5
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pair_coeff 1 1 10.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
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comm_style tiled
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fix 10 all balance 50 0.9 rcb
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compute 1 all property/atom proc
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variable p atom c_1%10
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dump 2 all custom 50 balance.dump id v_p x y z
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dump 3 all custom/adios 50 balance_custom.bp id v_p x y z
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dump 4 all atom/adios 50 balance_atom.bp
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#dump 3 all image 50 image.*.jpg v_p type &
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# adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
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#variable colors string &
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# "red green blue yellow white &
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# purple pink orange lime gray"
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#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
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thermo_style custom step temp epair press f_10[3] f_10
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thermo 100
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run 200
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114
examples/USER/adios/log.balance
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114
examples/USER/adios/log.balance
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LAMMPS (4 Jan 2019)
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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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# 2d circle of particles inside a box with LJ walls
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variable b index 0
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variable x index 50
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variable y index 20
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variable d index 20
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variable v index 5
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variable w index 2
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units lj
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dimension 2
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atom_style atomic
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boundary f f p
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lattice hex 0.85
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Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
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region box block 0 $x 0 $y -0.5 0.5
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region box block 0 50 0 $y -0.5 0.5
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region box block 0 50 0 20 -0.5 0.5
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create_box 1 box
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Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
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2 by 2 by 1 MPI processor grid
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region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
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region circle sphere 11 6.7735026918962581988 0.0 10
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create_atoms 1 region circle
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Created 361 atoms
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Time spent = 0.00171804 secs
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mass 1 1.0
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velocity all create 0.5 87287 loop geom
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velocity all set $v $w 0 sum yes
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velocity all set 5 $w 0 sum yes
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velocity all set 5 2 0 sum yes
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pair_style lj/cut 2.5
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pair_coeff 1 1 10.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
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comm_style tiled
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fix 10 all balance 50 0.9 rcb
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compute 1 all property/atom proc
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variable p atom c_1%10
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dump 2 all custom 50 balance.dump id v_p x y z
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dump 3 all custom/adios 50 balance_custom.bp id v_p x y z
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dump 4 all atom/adios 50 balance_atom.bp
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#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
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#variable colors string # "red green blue yellow white # purple pink orange lime gray"
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#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
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thermo_style custom step temp epair press f_10[3] f_10
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thermo 100
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run 200
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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 = 42 29 1
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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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.933 | 4.944 Mbytes
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Step Temp E_pair Press f_10[3] f_10
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0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
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100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
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200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
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Loop time of 0.0992351 on 4 procs for 200 steps with 361 atoms
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Performance: 870660.046 tau/day, 2015.417 timesteps/s
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32.2% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0078368 | 0.0081607 | 0.0085468 | 0.3 | 8.22
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Neigh | 0.002804 | 0.0045915 | 0.0092173 | 3.9 | 4.63
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Comm | 0.044407 | 0.05352 | 0.062051 | 3.0 | 53.93
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Output | 0.011406 | 0.012025 | 0.01342 | 0.7 | 12.12
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Modify | 0.006305 | 0.0064294 | 0.0066617 | 0.2 | 6.48
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Other | | 0.01451 | | | 14.62
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Nlocal: 90.25 ave 91 max 90 min
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Histogram: 3 0 0 0 0 0 0 0 0 1
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Nghost: 58.25 ave 64 max 51 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 730.75 ave 801 max 671 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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Total # of neighbors = 2923
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Ave neighs/atom = 8.09695
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Neighbor list builds = 60
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Dangerous builds = 0
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Total wall time: 0:00:00
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