144 lines
5.8 KiB
Plaintext
144 lines
5.8 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style full
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########### BEGIN PARAMETERS ####################################
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variable T equal 115.607
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print "reference temperature $T [K]"
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reference temperature 115.60699999999999932 [K]
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variable a equal 5.719025032
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variable i equal 1
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variable s equal 100
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variable dt equal 4.0
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############## END PARAMETERS #################################
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dimension 3
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boundary f p p
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pair_style lj/cut 13.0
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lattice sc $a
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lattice sc 5.7190250320000002304
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Lattice spacing in x,y,z = 5.71903 5.71903 5.71903
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region BOX block 0 12 0 4 0 4
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read_data velocities.init
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Scanning data file ...
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Reading data file ...
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orthogonal box = (0 0 0) to (68.6283 22.8761 22.8761)
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4 by 1 by 1 MPI processor grid
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192 atoms
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192 velocities
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Finding 1-2 1-3 1-4 neighbors ...
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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mass * 39.948
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pair_coeff * * 0.2381 3.405
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set group all charge 0.1
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Setting atom values ...
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192 settings made for charge
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dielectric 80.0
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timestep ${dt}
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timestep 4
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neigh_modify every $i check no
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neigh_modify every 1 check no
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thermo $s
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thermo 100
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# ------------- Equilibration and thermalisation ----------------
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fix WALL all wall/reflect xlo EDGE xhi EDGE
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fix NVT all nvt temp $T $T 10 drag 0.2
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fix NVT all nvt temp 115.60699999999999932 $T 10 drag 0.2
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fix NVT all nvt temp 115.60699999999999932 115.60699999999999932 10 drag 0.2
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thermo_style custom step temp press etotal pe
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#run 400
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unfix NVT
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# ------------- Post processing ---------------------------------
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fix PP all atc field
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ATC: constructing shape function field estimate
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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fix_modify PP fields add mass_density charge_density electric_potential velocity
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#fix_modify PP mesh create 50 1 1 BOX f p p
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fix_modify PP mesh create 25 1 1 BOX f p p
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ATC: created uniform mesh with 104 nodes, 26 unique nodes, and 25 elements
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#fix_modify PP mesh create 6 1 1 BOX f p p
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fix_modify PP atom_element_map eulerian $i
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fix_modify PP atom_element_map eulerian 1
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# ------------- Coupling ----------------------------------------
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fix AtC all atc species_electrostatic Ar_species.mat
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ATC: constructing electrostatic species coupling with parameter file Ar_species.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: 1 materials defined from Ar_species.mat
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ATC: creating fem_efield extrinsic model
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ATC: 1 materials defined from Ar_species.mat
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fix_modify AtC add_species ALL group all
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fix_modify AtC internal_quadrature off
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fix_modify AtC mesh create 6 1 1 BOX f p p
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ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements
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fix_modify AtC atom_element_map eulerian $i
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fix_modify AtC atom_element_map eulerian 1
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fix_modify AtC extrinsic short_range off
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fix_modify AtC mesh create_nodeset rbc 12. 12. -INF INF -INF INF
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ATC: created nodeset rbc with 1 nodes
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fix_modify AtC mesh create_nodeset lbc 0. 0. -INF INF -INF INF
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ATC: created nodeset lbc with 1 nodes
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# ------------- run ---------------------------------------------
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thermo_style custom step cpu etotal ke
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fix_modify AtC output liquid_electrostaticFE $s full_text # binary
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fix_modify AtC output liquid_electrostaticFE 100 full_text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationALL
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species_concentration : species_concentrationALL
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fix_modify PP output liquid_electrostaticPP $s full_text
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fix_modify PP output liquid_electrostaticPP 100 full_text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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log liquid_electrostatic.log
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fix_modify AtC fix electric_potential lbc linear 0 0 0 0 0 0 0
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ATC: created function : 0 + 0(x-0)+0(y-0)+0(z-0)
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run 800
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Setting up run ...
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ATC: WARNING: material: [ar] cannot find mass_density
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ATC: WARNING: physics model: [species], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
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ATC: WARNING: all initial conditions for mass_density have not been defined and the undefined are assumed zero
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ATC: WARNING: all initial conditions for charge_density have not been defined and the undefined are assumed zero
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ATC: WARNING: all initial conditions for species_concentration have not been defined and the undefined are assumed zero
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ATC: WARNING: all initial conditions for electric_potential have not been defined and the undefined are assumed zero
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ATC: WARNING: material: [ar] cannot find mass_density
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ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
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Memory usage per processor = 63.7188 Mbytes
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Step CPU TotEng KinEng
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0 0 35.202587 65.819079
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100 0.13389993 35.132776 72.573174
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200 0.25630498 37.926061 85.105883
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300 0.37974381 43.306749 97.61592
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400 0.50396085 50.460579 107.44276
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500 0.62712884 58.987352 111.76417
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600 0.75213289 68.996097 125.58655
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700 0.87788391 79.481129 137.54934
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800 1.009974 89.704034 154.18784
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Loop time of 1.01001 on 4 procs for 800 steps with 192 atoms
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Pair time (%) = 0.0733553 (7.26285)
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Bond time (%) = 0.000121653 (0.0120448)
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Neigh time (%) = 0.0668846 (6.62219)
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Comm time (%) = 0.0512613 (5.07534)
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Outpt time (%) = 0.00374603 (0.370892)
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Other time (%) = 0.814638 (80.6567)
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Nlocal: 48 ave 73 max 35 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 505 ave 641 max 343 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Neighs: 1650.75 ave 2905 max 855 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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FullNghs: 3301.5 ave 5798 max 1724 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 13206
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Ave neighs/atom = 68.7812
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Ave special neighs/atom = 0
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Neighbor list builds = 80
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Dangerous builds = 0
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