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a04f267b54496befccb9082f31f01ff8f33e0e0c
lammps/examples/USER/atc/fluids/poisson.screen
jzimmer a04f267b54 ATC version 2.0, date: Aug22 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10655 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2013-08-22 23:31:13 +00:00

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LAMMPS (24 Aug 2013)
units metal
variable E equal 20.0
variable nx equal 32
# allow charges
atom_style full
dielectric 1.
dimension 3
boundary f 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 0 16 0 3 0 3
create_box 1 BOX
Created orthogonal box = (0 0 0) to (65.28 12.24 12.24)
4 by 1 by 1 MPI processor grid
create_atoms 1 region BOX
Created 576 atoms
pair_style lj/cut 13.
pair_coeff * * 0.2381 3.405
mass * 39.948
group real region BOX
576 atoms in group real
set group real charge 1
Setting atom values ...
576 settings made for charge
###########################################################################
#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 ion type 1 ### <<<<<
#fix_modify ATC add_species REAL group real
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 f p p
fix_modify ATC mesh create 32 1 1 BOX f p p
ATC: created uniform mesh with 132 nodes, 33 unique nodes, and 32 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.
###########################################################################
variable n equal count(real)
print "number of atoms: $n"
number of atoms: 576
timestep 0.0
thermo 1
compute Fx real reduce sum fx
compute Fy real reduce sum fy
thermo_style custom step etotal temp press pe c_Fx c_Fy
fix_modify ATC output poissonFE 1 text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
NodalAtomicSpeciesConcentration : NodalAtomicSpeciesConcentrationion
species_concentration : species_concentrationion
# (1) all fixed
fix_modify ATC fix electric_potential all linear 0 0 0 $E 0 0 0 0
fix_modify ATC fix electric_potential all linear 0 0 0 20 0 0 0 0
ATC: created function : 0 + 20(x-0)+0(y-0)+0(z-0)
run 1
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 = 48.9866 Mbytes
Step TotEng Temp Press PotEng Fx Fy
0 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13
1 13388.811 0 12185513 13388.811 -11520 -5.4091662e-13
Loop time of 0.00876236 on 4 procs for 1 steps with 576 atoms
Pair time (%) = 0.00293046 (33.4438)
Bond time (%) = 2.98023e-07 (0.00340118)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000374079 (4.26916)
Outpt time (%) = 0.00139093 (15.874)
Other time (%) = 0.00406659 (46.4097)
Nlocal: 144 ave 144 max 144 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3556 ave 4256 max 2856 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 58212 ave 63792 max 52524 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 116424 ave 127584 max 105264 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 465696
Ave neighs/atom = 808.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
# (2) Dirichlet
# NOTE with correct density solution is very close
#fix_modify ATC fix charge_density all 0.0588951459091903
fix_modify ATC unfix electric_potential all
fix_modify ATC mesh create_nodeset lbc 0.0 0.0 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify ATC mesh create_faceset lbc 0.0 INF -INF INF -INF INF
ATC: created faceset lbc with 1 faces
fix_modify ATC mesh create_faceset rbc -INF 16.0 -INF INF -INF INF
ATC: created faceset rbc with 1 faces
fix_modify ATC fix electric_potential lbc 100.0
run 1
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: 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 = 48.9866 Mbytes
Step TotEng Temp Press PotEng Fx Fy
1 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13
2 13388.811 0 12185513 13388.811 -200361.27 6.719863e-13
Loop time of 0.00804049 on 4 procs for 1 steps with 576 atoms
Pair time (%) = 0.00292277 (36.3507)
Bond time (%) = 7.7486e-07 (0.00963698)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000391722 (4.87187)
Outpt time (%) = 0.000965953 (12.0136)
Other time (%) = 0.00375926 (46.7542)
Nlocal: 144 ave 144 max 144 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3556 ave 4256 max 2856 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 58212 ave 63792 max 52524 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 116424 ave 127584 max 105264 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 465696
Ave neighs/atom = 808.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
# (3) Neumann
fix_modify ATC fix_flux electric_potential rbc 0.5
run 1
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: 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 = 48.9866 Mbytes
Step TotEng Temp Press PotEng Fx Fy
2 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12
3 13388.811 0 12185513 13388.811 -252475.24 1.1650611e-12
Loop time of 0.00827122 on 4 procs for 1 steps with 576 atoms
Pair time (%) = 0.00292873 (35.4087)
Bond time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000398278 (4.81523)
Outpt time (%) = 0.000935972 (11.316)
Other time (%) = 0.00400823 (48.46)
Nlocal: 144 ave 144 max 144 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3556 ave 4256 max 2856 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 58212 ave 63792 max 52524 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 116424 ave 127584 max 105264 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 465696
Ave neighs/atom = 808.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
# (4) Robin eps_1 phi'_1 = eps_2/L_2 (phi_{L_2} - phi)
fix_modify ATC unfix_flux electric_potential rbc
fix_modify ATC fix_robin electric_potential rbc 0.5 -0.00001
ATC: created function : 0.5 + -1e-05*u
run 1
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: 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 = 48.9866 Mbytes
Step TotEng Temp Press PotEng Fx Fy
3 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13
4 13388.811 0 12185513 13388.811 -225709.12 9.1181426e-13
Loop time of 0.00827569 on 4 procs for 1 steps with 576 atoms
Pair time (%) = 0.00293577 (35.4746)
Bond time (%) = 5.36442e-07 (0.00648214)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000405252 (4.8969)
Outpt time (%) = 0.000962913 (11.6354)
Other time (%) = 0.00397122 (47.9866)
Nlocal: 144 ave 144 max 144 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3556 ave 4256 max 2856 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 58212 ave 63792 max 52524 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 116424 ave 127584 max 105264 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 465696
Ave neighs/atom = 808.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
# (5) Robins on the left and Robins on the right
fix_modify ATC unfix electric_potential lbc
fix_modify ATC fix_robin electric_potential rbc 0.01 -0.0001
ATC: created function : 0.01 + -0.0001*u
fix_modify ATC fix_robin electric_potential lbc 0.01 -0.0001
ATC: created function : 0.01 + -0.0001*u
run 1
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: 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 = 48.9866 Mbytes
Step TotEng Temp Press PotEng Fx Fy
4 13388.811 0 12185513 13388.811 4.3291948e-09 -1.4571568e-12
5 13388.811 0 12185513 13388.811 4.3364707e-09 -1.4571568e-12
Loop time of 0.0088349 on 4 procs for 1 steps with 576 atoms
Pair time (%) = 0.0029276 (33.1368)
Bond time (%) = 7.15256e-07 (0.0080958)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000395775 (4.47968)
Outpt time (%) = 0.00099498 (11.2619)
Other time (%) = 0.00451583 (51.1135)
Nlocal: 144 ave 144 max 144 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3556 ave 4256 max 2856 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 58212 ave 63792 max 52524 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 116424 ave 127584 max 105264 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 465696
Ave neighs/atom = 808.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
#fix_modify ATC fix charge_density all 0.0
#run 1
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