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