forked from lijiext/lammps
170 lines
6.9 KiB
Plaintext
170 lines
6.9 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style full # charge
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### NOTE p p p is required for both lammps & atc since periodic images are employed in ExtrinsicModelElectrostatic::correct_electrostatic_forces
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########### BEGIN PARAMETERS ####################################
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variable T equal 300
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variable a equal 1.0 # 5.719025032
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variable i equal 10 # thermo
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variable f equal 50 # neighbor & conc interval
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variable s equal 100 # 10 # 100 # output
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variable n equal 800 # 20 # 200 # 300 # duration
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variable x equal 4 # 40 # 2 # 4 # exchanges
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variable e equal 100. # 1. # 100. # 10. # energy
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variable h equal 5 # nelems
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variable dt equal 4. #1. # 0 # 4.0
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############## END PARAMETERS #################################
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dimension 3
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boundary p p p
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pair_style lj/cut/coul/cut 13.0
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lattice sc $a
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lattice sc 1
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Lattice spacing in x,y,z = 1 1 1
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read_data concentration_init.data
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Scanning data file ...
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Reading data file ...
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orthogonal box = (0 0 0) to (114.381 22.8761 22.8761)
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4 by 1 by 1 MPI processor grid
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544 atoms
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544 velocities
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Finding 1-2 1-3 1-4 neighbors ...
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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atom_modify sort 0 1
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mass * 39.948
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pair_coeff * * 0.2381 3.405
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pair_coeff 1 * 0.4 3.405
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dielectric 80.0
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variable xlo equal xlo
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variable xhi equal xhi
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variable xmid equal 0.5*(${xhi}+${xlo})
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variable xmid equal 0.5*(114.38050064000000816+${xlo})
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variable xmid equal 0.5*(114.38050064000000816+0)
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print "reservior x ${xmid}:${xhi}"
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reservior x 57.190250320000004081:114.38050064000000816
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variable ylo equal ylo
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variable yhi equal yhi
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variable zlo equal zlo
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variable zhi equal zhi
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region BOX block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
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region BOX block 0 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
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region BOX block 0 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box
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region BOX block 0 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box
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region BOX block 0 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box
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region BOX block 0 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box
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region BOX block 0 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box
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region FLUID block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
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region FLUID block 0 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
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region FLUID block 0 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box
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region FLUID block 0 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box
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region FLUID block 0 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box
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region FLUID block 0 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box
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region FLUID block 0 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box
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region R block ${xmid} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
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region R block 57.190250320000004081 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} units box
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region R block 57.190250320000004081 114.38050064000000816 ${ylo} ${yhi} ${zlo} ${zhi} units box
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region R block 57.190250320000004081 114.38050064000000816 0 ${yhi} ${zlo} ${zhi} units box
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region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 ${zlo} ${zhi} units box
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region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 0 ${zhi} units box
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region R block 57.190250320000004081 114.38050064000000816 0 22.876100128000000922 0 22.876100128000000922 units box
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group SOLID type 1
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288 atoms in group SOLID
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variable xdof equal 3*count(SOLID)
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compute_modify thermo_temp extra ${xdof}
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compute_modify thermo_temp extra 864
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#set group SOLID charge 0
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group NEUTRAL type 2
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114 atoms in group NEUTRAL
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group FLUID type 2 3 4
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256 atoms in group FLUID
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group NION type 3
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66 atoms in group NION
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group PION type 4
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76 atoms in group PION
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#group tPION type 5 # not dynamic
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#group tNION type 6 # not dynamic
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#variable typeP atom type[]==5
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set group PION charge 1
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Setting atom values ...
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76 settings made for charge
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set group NION charge -1
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Setting atom values ...
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66 settings made for charge
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variable O equal count(NEUTRAL)
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variable S equal count(SOLID)
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variable F equal count(FLUID)
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variable P equal count(PION)
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variable N equal count(NION)
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variable Pr equal count(PION,R)
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variable Nr equal count(NION,R)
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#variable tP equal count(tPION)
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#variable tN equal count(tNION)
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variable V equal vol
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variable cO equal v_O/v_V
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variable cS equal v_S/v_V
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variable cN equal v_N/v_V
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variable cP equal v_P/v_V
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compute q all property/atom q
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compute m all property/atom mass
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compute Q all reduce sum c_q
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compute M all reduce sum c_m
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compute Qf FLUID reduce sum c_q
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compute Mf FLUID reduce sum c_m
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compute PMIN PION reduce min x
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compute PMAX PION reduce max x
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compute NMIN NION reduce min x
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compute NMAX NION reduce max x
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timestep ${dt}
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timestep 4
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#neighbor 13 bin
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neigh_modify every $i check no
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neigh_modify every 10 check no
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# coulombic interactions
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fix ATC FLUID atc species_electrostatic Ar_electrostatic.mat
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ATC: constructing electrostatic species coupling with parameter file Ar_electrostatic.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 13
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ATC: 1 materials defined from Ar_electrostatic.mat
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ATC: creating fem_efield extrinsic model
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ATC: 1 materials defined from Ar_electrostatic.mat
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#fix_modify ATC parallel_consistency off
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fix_modify ATC extrinsic short_range off
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#fix_modify ATC boundary SOLID
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fix_modify ATC atom_element_map eulerian $i
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fix_modify ATC atom_element_map eulerian 10
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fix_modify ATC internal_quadrature off
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fix_modify ATC consistent_fe_initialization on
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fix_modify ATC filter type exponential
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fix_modify ATC filter scale $i
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fix_modify ATC filter scale 10
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fix_modify ATC filter equilibrate
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# mesh
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print "x = ${xlo}:${xhi}"
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x = 0:114.38050064000000816
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fix_modify ATC mesh create $h 1 1 BOX p p p # f p p ExtrinsicModelElectrostatic::correct_electrostatic_forces iterates through ghosts
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fix_modify ATC mesh create 5 1 1 BOX p p p
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ATC: created uniform mesh with 24 nodes, 5 unique nodes, and 5 elements
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fix_modify ATC mesh create_nodeset LBC ${xlo} ${xlo} -INF INF -INF INF
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fix_modify ATC mesh create_nodeset LBC 0 ${xlo} -INF INF -INF INF
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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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fix_modify ATC mesh create_elementset FLUID FLUID
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ATC: created elementset FLUID with 5 elements
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fix_modify ATC mesh create_elementset R R
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ATC: created elementset R with 2 elements
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fix_modify ATC mesh create_elementset BOX BOX
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ATC: created elementset BOX with 5 elements
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## NOTE tag instead of type, what about transition tyme
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fix_modify ATC mass_matrix fe
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fix_modify ATC internal_element_set FLUID
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fix_modify ATC include atomic_charge
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fix_modify ATC add_species N type 3
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fix_modify ATC add_species P type 4
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fix_modify ATC add_species Nt type 5
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fix_modify ATC add_species Pt type 6
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## CC
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fix_modify ATC control concentration N R 0.001 Nt # deletions R
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ERROR: Illegal fix_modify command (../fix.cpp:104)
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