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LAMMPS (30 Aug 2013)
units metal
variable E equal 20.0
variable nx equal 16
# allow charges
atom_style full
dielectric 1.
dimension 3
boundary p p p
lattice fcc 4.08 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 4.08 4.08 4.08
region BOX block -8 8 0 3 0 3
create_box 3 BOX
Created orthogonal box = (-32.64 0 0) to (32.64 12.24 12.24)
4 by 1 by 1 MPI processor grid
create_atoms 1 region BOX
Created 576 atoms
pair_style lj/cut 10.
#pair_style lj/cut/coul/long 10.
#kspace_style pppm 1.e-4
#kspace_style ewald 1.e-4
pair_coeff * * 0.2381 3.405
mass * 39.948
group real region BOX
576 atoms in group real
region LEFT block -5 -2 INF INF INF INF
region RIGHT block 2 5 INF INF INF INF
set region LEFT type 2
Setting atom values ...
108 settings made for type
set region RIGHT type 3
Setting atom values ...
108 settings made for type
set region LEFT charge -1.
Setting atom values ...
108 settings made for charge
set region RIGHT charge 1.
Setting atom values ...
108 settings made for charge
group NION region LEFT
108 atoms in group NION
group PION region RIGHT
108 atoms in group PION
neighbor 2. bin
###########################################################################
#fix EFIELD all efield $E 0.0 0.0
###########################################################################
fix ATC real 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: WARNING: material units real do not match lammps
ATC: 1 materials defined from Ar_species.mat
ATC: creating fem_efield extrinsic model
ATC: WARNING: material units real do not match lammps
ATC: 1 materials defined from Ar_species.mat
fix_modify ATC add_species N group NION
fix_modify ATC add_species P group PION
fix_modify ATC include atomic_charge
fix_modify ATC internal_quadrature off
fix_modify ATC extrinsic short_range off
fix_modify ATC mesh create ${nx} 1 1 BOX p p p
fix_modify ATC mesh create 16 1 1 BOX p p p
ATC: created uniform mesh with 68 nodes, 16 unique nodes, and 16 elements
fix_modify ATC atom_element_map eulerian 1
fix_modify ATC atom_weight multiscale
fix_modify ATC initial mass_density all 0.
#fix_modify ATC initial charge_density all 0.
fix_modify ATC initial electric_potential all 0.
fix_modify ATC mesh create_nodeset left_end -8.01 -7.99 -.1 .1 -.1 .1
ATC: created nodeset left_end with 1 nodes
fix_modify ATC fix electric_potential left_end 0.
#fix_modify ATC mesh create_nodeset right_end 7.99 8.01 -.1 .1 -.1 .1
#fix_modify ATC fix electric_potential right_end 0.
# quick test for charged surfaces
#fix_modify ATC mesh create_faceset left_end box -8 10 -10 10 -10 10 outward
#fix_modify ATC extrinsic fix_charge left_end 0.
fix_modify ATC add_species NION type 2
fix_modify ATC add_species PION type 3
###########################################################################
variable n equal count(real)
print "number of atoms: $n"
number of atoms: 576
timestep 0.0005
thermo 100
compute Fn NION reduce sum fx
compute Fp PION reduce sum fx
thermo_style custom step etotal temp press pe c_Fn c_Fp
# initial thermo line should be:
#0 13699.992 0 12453927 13699.992 880.49388 -880.49388
fix_modify ATC output opp_forceFE 100 text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationNION
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationPION
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationN
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationP
species_concentration : species_concentrationNION
species_concentration : species_concentrationPION
species_concentration : species_concentrationN
species_concentration : species_concentrationP
run 1000
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 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: 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 = 50.4595 Mbytes
Step TotEng Temp Press PotEng Fn Fp
0 13699.992 0 12453927 13699.992 880.49388 -880.49388
100 18516.206 19920.46 14980264 17035.627 -29.468216 29.468216
200 18590.499 18996.496 15042503 17178.592 74.632418 -74.632418
300 16986.906 22207.446 13773775 15336.347 213.36855 -213.36855
400 17031.316 20483.897 13881842 15508.858 -1030.06 1030.06
500 18393.547 13569.054 15141293 17385.033 -881.32991 881.32991
600 17629.245 22129.326 14228700 15984.492 297.77405 -297.77405
700 17374.698 17398.728 14252085 16081.545 -1458.7112 1458.7112
800 17805.47 15491.378 14643513 16654.08 2644.7457 -2644.7457
900 20614.308 23711.81 16239209 18851.938 218.5282 -218.5282
1000 22067.741 26242.181 17175599 20117.302 -752.00587 752.00587
Loop time of 3.62172 on 4 procs for 1000 steps with 576 atoms
Pair time (%) = 1.48902 (41.1135)
Bond time (%) = 0.000212669 (0.00587205)
Neigh time (%) = 0.0337982 (0.933206)
Comm time (%) = 0.176507 (4.87357)
Outpt time (%) = 0.0090723 (0.250497)
Other time (%) = 1.91312 (52.8234)
Nlocal: 144 ave 144 max 144 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3096 ave 3096 max 3096 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 30906 ave 31490 max 30319 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 61812 ave 62964 max 60660 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 247248
Ave neighs/atom = 429.25
Ave special neighs/atom = 0
Neighbor list builds = 7
Dangerous builds = 0
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