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