Commit 410d79d8 authored by Norbert Podhorszki's avatar Norbert Podhorszki
Browse files

Add an example for USER/adios based on the balance example

parent 200fed9d

examples/USER/adios/adios2_config.xml

0 → 100644
+45 −0
Original line number Diff line number Diff line 
<?xml version="1.0"?>

<adios-config>



    <!-- example engines 



        <engine type="BPFile">

        <engine type="HDF5">

        <engine type="InSituMPI">

        <engine type="SST">

        <engine type="DataMan">



    -->



    <!-- example operations 

        These operations go inside an IO group (but not inside engine group)



    <io name="custom">

        <variable name="T">

            <operation type="zfp">

                <parameter key="accuracy" value="0.01"/>

            </operation>

        </variable>

    </io>

    -->



    <!--====================================================

           Configuration for the dump atom/adios command

        ====================================================-->



    <io name="atom">

        <engine type="BPFile">

        </engine>

    </io>



    <!--====================================================

           Configuration for the dump custom/adios command

        ====================================================-->



    <io name="custom">

        <engine type="BPFile">

        </engine>

    </io>





</adios-config>

examples/USER/adios/in.adios_balance

0 → 100644
+56 −0
Original line number Diff line number Diff line 
# 2d circle of particles inside a box with LJ walls



variable        b index 0



variable	x index 50

variable	y index 20

variable	d index 20

variable	v index 5

variable	w index 2

                

units		lj

dimension       2

atom_style	atomic

boundary        f f p



lattice		hex 0.85

region		box block 0 $x 0 $y -0.5 0.5

create_box	1 box

region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)

create_atoms	1 region circle

mass		1 1.0



velocity	all create 0.5 87287 loop geom

velocity        all set $v $w 0 sum yes



pair_style	lj/cut 2.5

pair_coeff	1 1 10.0 1.0 2.5



neighbor	0.3 bin

neigh_modify	delay 0 every 1 check yes



fix		1 all nve



fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5

fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5



comm_style      tiled

fix             10 all balance 50 0.9 rcb



compute         1 all property/atom proc

variable        p atom c_1%10

dump            2 all custom 50 balance.dump id v_p x y z

dump            3 all custom/adios 50 balance_custom.bp id v_p x y z

dump            4 all atom/adios 50 balance_atom.bp 



#dump            3 all image 50 image.*.jpg v_p type &

#                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02

#variable        colors string &

#                "red green blue yellow white &

#                purple pink orange lime gray"

#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}



thermo_style    custom step temp epair press f_10[3] f_10

thermo          100                



run		200

examples/USER/adios/log.balance

0 → 100644
+114 −0
Original line number Diff line number Diff line 
LAMMPS (4 Jan 2019)

OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)

  using 1 OpenMP thread(s) per MPI task

# 2d circle of particles inside a box with LJ walls



variable        b index 0



variable	x index 50

variable	y index 20

variable	d index 20

variable	v index 5

variable	w index 2



units		lj

dimension       2

atom_style	atomic

boundary        f f p



lattice		hex 0.85

Lattice spacing in x,y,z = 1.16553 2.01877 1.16553

region		box block 0 $x 0 $y -0.5 0.5

region		box block 0 50 0 $y -0.5 0.5

region		box block 0 50 0 20 -0.5 0.5

create_box	1 box

Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)

  2 by 2 by 1 MPI processor grid

region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)

region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)

region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)

region		circle sphere 11 6.7735026918962581988 0.0 10

create_atoms	1 region circle

Created 361 atoms

  Time spent = 0.00171804 secs

mass		1 1.0



velocity	all create 0.5 87287 loop geom

velocity        all set $v $w 0 sum yes

velocity        all set 5 $w 0 sum yes

velocity        all set 5 2 0 sum yes



pair_style	lj/cut 2.5

pair_coeff	1 1 10.0 1.0 2.5



neighbor	0.3 bin

neigh_modify	delay 0 every 1 check yes



fix		1 all nve



fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5

fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5

fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5

fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5



comm_style      tiled

fix             10 all balance 50 0.9 rcb



compute         1 all property/atom proc

variable        p atom c_1%10

dump            2 all custom 50 balance.dump id v_p x y z

dump            3 all custom/adios 50 balance_custom.bp id v_p x y z

dump            4 all atom/adios 50 balance_atom.bp



#dump            3 all image 50 image.*.jpg v_p type #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02

#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"

#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}



thermo_style    custom step temp epair press f_10[3] f_10

thermo          100



run		200

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 = 42 29 1

  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/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.933 | 4.944 Mbytes

Step Temp E_pair Press f_10[3] f_10 

       0    25.701528   -29.143179   -1.2407285    3.2354571    1.0526316 

     100    26.269576   -29.713313    7.9052334    1.2742382    1.0304709 

     200    26.368336   -29.809962    1.6412462    1.2520776    1.0083102 

Loop time of 0.0992351 on 4 procs for 200 steps with 361 atoms



Performance: 870660.046 tau/day, 2015.417 timesteps/s

32.2% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0078368  | 0.0081607  | 0.0085468  |   0.3 |  8.22

Neigh   | 0.002804   | 0.0045915  | 0.0092173  |   3.9 |  4.63

Comm    | 0.044407   | 0.05352    | 0.062051   |   3.0 | 53.93

Output  | 0.011406   | 0.012025   | 0.01342    |   0.7 | 12.12

Modify  | 0.006305   | 0.0064294  | 0.0066617  |   0.2 |  6.48

Other   |            | 0.01451    |            |       | 14.62



Nlocal:    90.25 ave 91 max 90 min

Histogram: 3 0 0 0 0 0 0 0 0 1

Nghost:    58.25 ave 64 max 51 min

Histogram: 1 0 0 0 0 0 2 0 0 1

Neighs:    730.75 ave 801 max 671 min

Histogram: 1 0 1 0 0 1 0 0 0 1



Total # of neighbors = 2923

Ave neighs/atom = 8.09695

Neighbor list builds = 60

Dangerous builds = 0

Total wall time: 0:00:00

CRA Git | Maintained and supported by SUSTech CRA and CCSE