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5249 lines (4733 loc) · 222 KB
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LAMMPS (15 Sep 2022)
### command to run:
### basic setting
units metal
dimension 3
boundary p p p # y need to be periodic, otherwise the empty region of the simulation box will be removed
atom_style atomic
atom_modify map array
comm_style tiled # for load balancing we need tiled
### neighbor setting
neighbor 2 bin
### global variables
variable nrun equal 4
variable ndump equal 2
variable nThermo equal 1
variable nrunIdle equal 0*${nrun}
variable nrunIdle equal 0*4
### set these parameters correctly, rest will be compited accordingly
variable Height equal 50 # Height of the newly created region.
variable lx equal 301 # add 1 so that 'floor' functions behave accordingly. lx>${DistanceLaserShot} for Laser
variable ly equal 501
variable lz equal 3
variable random01 equal random(0,1,123456)
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 ${lx} ${Height} ${ly} 0 ${lz}
region box block 0 301 ${Height} ${ly} 0 ${lz}
region box block 0 301 50 ${ly} 0 ${lz}
region box block 0 301 50 501 0 ${lz}
region box block 0 301 50 501 0 3
create_box 2 box
Created orthogonal box = (0 176 0) to (1059.52 1763.52 10.56)
2 by 3 by 1 MPI processor grid
### Initial atomic region
region BlockInitial block INF INF 45 200 INF INF
###create_atoms
#create_atoms 1 box
#delete_atoms group all
create_atoms 1 region BlockInitial
Created 543606 atoms
using lattice units in orthogonal box = (0 176 0) to (1059.52 1763.52 10.56)
create_atoms CPU = 0.097 seconds
mass 1 58.71
mass 2 58.71
### create other regions, dummy. So that it can be deleted in the recurssive block
variable y1 equal ${Height}
variable y1 equal 50
variable y2 equal 3*${Height}
variable y2 equal 3*50
variable y3 equal 4*${Height}
variable y3 equal 4*50
variable y_Inside equal ${y1}+2
variable y_Inside equal 50+2
variable z2 equal 0.0
variable z3 equal ${lz}
variable z3 equal 3
region BlockDeleteAtomsBottom_01 block INF INF INF ${y1} INF INF
region BlockDeleteAtomsBottom_01 block INF INF INF 50 INF INF
group GroupDeleteAtomsBottom_01 region BlockDeleteAtomsBottom_01
1806 atoms in group GroupDeleteAtomsBottom_01
region BlockCreateAtomsTop_01 block INF INF ${y2} ${y3} INF INF
region BlockCreateAtomsTop_01 block INF INF 150 ${y3} INF INF
region BlockCreateAtomsTop_01 block INF INF 150 200 INF INF
group GroupCreateAtomsTop_01 region BlockCreateAtomsTop_01
182406 atoms in group GroupCreateAtomsTop_01
region BlockInside block INF INF ${y_Inside} INF INF INF
region BlockInside block INF INF 52 INF INF INF
group GroupInside region BlockInside
536382 atoms in group GroupInside
variable nAtomsAll equal count(all)
variable nAtomsInitial equal ${nAtomsAll}
variable nAtomsInitial equal 543606
print "nAtomsInitial: ${nAtomsInitial}"
nAtomsInitial: 543606
variable nAtomsNew equal count(GroupCreateAtomsTop_01)
variable nAtomsDelete equal count(GroupDeleteAtomsBottom_01)
### EAM potentials
pair_style eam/alloy
#pair_coeff * * /home/schakraborty/MyRepository/LAMMPS_02/potentials/NiAlH_jea.eam.alloy Ni Ni # in GUIDO
pair_coeff * * /mnt/f/MyRepositories/LAMMPS_02/potentials/NiAlH_jea.eam.alloy Ni Ni # in WSL
Reading eam/alloy potential file /mnt/f/MyRepositories/LAMMPS_02/potentials/NiAlH_jea.eam.alloy with DATE: 2007-11-30
### initial velocities
variable T equal 800
variable T2 equal 2*$T # put twice the desired system temperature
variable T2 equal 2*800
compute Temperature all temp
velocity all create ${T2} 187723 temp Temperature
velocity all create 1600 187723 temp Temperature
### compute
### CNA and centro in region all, dump 2 times, 1 in all, 1 in dumpregion
compute CNA all cna/atom 3.00
compute CENTRO all centro/atom fcc
compute PE all pe/atom
compute KE all ke/atom
compute stress all stress/atom Temperature
compute p all pressure Temperature
### Compute temperature
variable TotalKE equal ke(GroupCreateAtomsTop_01)
variable Temp02 equal (v_TotalKE/(v_nAtomsNew*8.6*1.0e-05))*(2/3) # KE=(dim/2)*N*K_b*T);)K_b = 8.6*1.0e-05 eV/K
### run
timestep 0.005
thermo ${nThermo}
thermo 1
thermo_style custom step temp pe ke v_Temp02
####minimize the system energy and press, statistic equilibirum
#fix systemminimize all box/relax iso 0 nreset 5 vmax 0.001
#minimize 1E-10 1E-10 2000 2000
###define fix
fix 1 all npt temp $T $T 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix 1 all npt temp 800 $T 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix 1 all npt temp 800 800 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
#fix 1 all nve
dump dumpCFG all cfg ${ndump} dump_*.cfg mass type xs ys zs id c_CNA c_PE c_KE vy fy
dump dumpCFG all cfg 2 dump_*.cfg mass type xs ys zs id c_CNA c_PE c_KE vy fy
dump_modify dumpCFG first yes
dump dump02 all custom ${ndump} dump_*.dump id mass type xs ys zs id c_CNA c_PE c_KE vy fy
dump dump02 all custom 2 dump_*.dump id mass type xs ys zs id c_CNA c_PE c_KE vy fy
dump_modify dump02 first yes
### to output in a file using 'fix print'
variable Step equal step
variable Temp equal temp
variable PE equal pe
variable KE equal ke
fix extra all print ${nThermo} "${Step} ${Temp} ${PE} ${KE} ${Temp02}" file Output_Thermo.out screen no title "${Step} ${Temp} ${PE} ${KE} ${Temp02}"
fix extra all print 1 "${Step} ${Temp} ${PE} ${KE} ${Temp02}" file Output_Thermo.out screen no title "${Step} ${Temp} ${PE} ${KE} ${Temp02}"
balance 1.1 rcb # load balancing
Balancing ...
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 277 416 3
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute cna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute centro/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
rebalancing time: 0.305 seconds
iteration count = 0
initial/final maximal load/proc = 271803 90601
initial/final imbalance factor = 3 1
run ${nrun} # Dynamics equiulibriation
run 4
Per MPI rank memory allocation (min/avg/max) = 225.1 | 232.7 | 247.5 Mbytes
Step Temp PotEng KinEng v_Temp02
0 1600 -2416145.4 112426.34 1605.4458
1 1529.5229 -2411188.5 107474.16 1534.7999
2 1334.7852 -2397443.9 93790.63 1339.6083
3 1061.8599 -2378077.4 74613.136 1066.0411
4 774.07854 -2357613.1 54391.759 777.5612
Loop time of 5.96587 on 6 procs for 4 steps with 543606 atoms
Performance: 0.290 ns/day, 82.859 hours/ns, 0.670 timesteps/s
94.7% CPU use with 6 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7748 | 1.79 | 1.8081 | 0.9 | 30.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.035575 | 0.047367 | 0.063409 | 3.9 | 0.79
Output | 4.0345 | 4.0346 | 4.0346 | 0.0 | 67.63
Modify | 0.079906 | 0.088492 | 0.1033 | 3.4 | 1.48
Other | | 0.005483 | | | 0.09
Nlocal: 90601 ave 91203 max 90000 min
Histogram: 2 0 0 0 2 0 0 0 0 2
Nghost: 157754 ave 161247 max 152962 min
Histogram: 2 0 0 0 0 0 0 1 2 1
Neighs: 7.93015e+06 ave 7.98435e+06 max 7.89965e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 2
FullNghs: 1.58603e+07 ave 1.59657e+07 max 1.57548e+07 min
Histogram: 2 0 0 0 0 2 0 0 0 2
Total # of neighbors = 95161752
Ave neighs/atom = 175.05648
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
unfix 1
#fix 1 GroupInside nve
fix 1 GroupInside npt temp $T $T 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix 1 GroupInside npt temp 800 $T 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix 1 GroupInside npt temp 800 800 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix fPushParticles GroupCreateAtomsTop_01 addforce 0.0 0.0 0.0 every 1
fix fLangevin GroupDeleteAtomsBottom_01 langevin ${T} ${T} 0.2 123456
fix fLangevin GroupDeleteAtomsBottom_01 langevin 800 ${T} 0.2 123456
fix fLangevin GroupDeleteAtomsBottom_01 langevin 800 800 0.2 123456
run ${nrun}
run 4
Per MPI rank memory allocation (min/avg/max) = 225.1 | 232.7 | 247.5 Mbytes
Step Temp PotEng KinEng v_Temp02
0 774.07854 -2357613.1 54391.759 777.5612
1 539.60387 -2340924.7 37916.054 539.39501
2 399.84261 -2331035.4 28095.525 397.32496
3 368.06128 -2328882.9 25862.363 364.88839
4 424.01234 -2332990.7 29793.847 421.57737
Loop time of 5.88292 on 6 procs for 4 steps with 543606 atoms
Performance: 0.294 ns/day, 81.707 hours/ns, 0.680 timesteps/s
97.0% CPU use with 6 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5339 | 1.5601 | 1.5855 | 1.2 | 26.52
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026283 | 0.046669 | 0.06174 | 5.2 | 0.79
Output | 4.1893 | 4.1893 | 4.1893 | 0.0 | 71.21
Modify | 0.074872 | 0.080407 | 0.090254 | 2.4 | 1.37
Other | | 0.006403 | | | 0.11
Nlocal: 90601 ave 91182 max 90017 min
Histogram: 1 1 0 0 0 1 2 0 0 1
Nghost: 157754 ave 161268 max 152713 min
Histogram: 2 0 0 0 0 0 0 1 2 1
Neighs: 7.84948e+06 ave 7.90232e+06 max 7.82316e+06 min
Histogram: 2 0 2 0 1 0 0 0 0 1
FullNghs: 1.5699e+07 ave 1.58001e+07 max 1.5618e+07 min
Histogram: 1 0 1 1 0 2 0 0 0 1
Total # of neighbors = 94193770
Ave neighs/atom = 173.27581
Neighbor list builds = 0
Dangerous builds = 0
print "*****LAMMPS Initilization DONE******"
*****LAMMPS Initilization DONE******
### to run AM script in loop
label labelSetAMLoop
variable nLoop equal floor((${ly}-${y3})/${Height})
variable nLoop equal floor((501-${y3})/${Height})
variable nLoop equal floor((501-200)/${Height})
variable nLoop equal floor((501-200)/50)
print "Total AM Loop: ${nLoop}"
Total AM Loop: 6
variable loop01 loop ${nLoop}
variable loop01 loop 6
label labelAMLoop
print "loop: ${loop01}"
loop: 1
next loop01
jump script_LAMMPS_AM.inp
### command to run recurssively for AM simulation
### Delete previous fix, region, group etc. before redefining
### delete the bottom atom righ at the begining and reassign before the next run for T-control
delete_atoms region BlockDeleteAtomsBottom_01
Deleted 0 atoms, new total = 543606
unfix 1
unfix fPushParticles
unfix fLangevin
region BlockInside delete
group GroupInside delete
region BlockDeleteAtomsBottom_01 delete
group GroupDeleteAtomsBottom_01 delete
region BlockCreateAtomsTop_01 delete
group GroupCreateAtomsTop_01 delete
variable delta_y equal (step/${nrun})*${Height}
variable delta_y equal (step/4)*${Height}
variable delta_y equal (step/4)*50
if "${nAtomsAll} > ${nAtomsInitial}" then "variable y1 equal ${y1}+${Height}" # This will make sure that total number of atom is close to initial atoms
variable y2 equal ${y2}+${Height}
variable y2 equal 150+${Height}
variable y2 equal 150+50
variable y3 equal ${y3}+${Height}
variable y3 equal 200+${Height}
variable y3 equal 200+50
variable y_Inside equal ${y1}+2
variable y_Inside equal 50+2
### update other regions
region BlockDeleteAtomsBottom_01 block INF INF INF ${y1} INF INF # delete all atom down the interface
region BlockDeleteAtomsBottom_01 block INF INF INF 50 INF INF
region BlockCreateAtomsTop_01 block INF INF ${y2} ${y3} INF INF
region BlockCreateAtomsTop_01 block INF INF 200 ${y3} INF INF
region BlockCreateAtomsTop_01 block INF INF 200 250 INF INF
region BlockInside block INF INF ${y_Inside} INF INF INF
region BlockInside block INF INF 52 INF INF INF
###----create atoms i.e, spherical powder particles in a loop-----
print "*** Powder particle creation begins***"
*** Powder particle creation begins***
variable nParticles equal floor(${lx}/(${Height})) # square box shaped
variable nParticles equal floor(301/(${Height}))
variable nParticles equal floor(301/(50))
variable radiusIdeal equal ${Height}/2
variable radiusIdeal equal 50/2
variable vloopParticle loop ${nParticles}
variable vloopParticle loop 6
label labelParticleCreation
print "Grain creation loop: ${vloopParticle}"
Grain creation loop: 1
variable perturb01 equal v_random01
if "(${vloopParticle} == 0) || (${vloopParticle} == ${nParticles})" then "variable perturb01 equal 0.00"
variable radius equal (0.75+0.25*${perturb01})*${radiusIdeal}
variable radius equal (0.75+0.25*0.543193161487579)*${radiusIdeal}
variable radius equal (0.75+0.25*0.543193161487579)*25
variable temp01 equal ${perturb01}*${radiusIdeal} #((step/${nrun})%2)*${radius}
variable temp01 equal 0.652336478233337*${radiusIdeal}
variable temp01 equal 0.652336478233337*25
variable temp02 equal 2*${radiusIdeal}*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(1-1)+${radiusIdeal}
variable temp02 equal 2*25*(1-1)+25
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopParticle} - 50
variable cx equal 16.3084119558334+${temp02}
variable cx equal 16.3084119558334+25
variable cy equal (${y2}+${y3})/2
variable cy equal (200+${y3})/2
variable cy equal (200+250)/2
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
print "Grain parameters cx: ${cx} cy: ${cy} cz: ${cz} radius: ${radius}"
Grain parameters cx: 41.3084119558334 cy: 225 cz: 1.5 radius: 22.1449572592974
region Particle sphere ${cx} ${cy} ${cz} ${radius}
region Particle sphere 41.3084119558334 ${cy} ${cz} ${radius}
region Particle sphere 41.3084119558334 225 ${cz} ${radius}
region Particle sphere 41.3084119558334 225 1.5 ${radius}
region Particle sphere 41.3084119558334 225 1.5 22.1449572592974
create_atoms 1 region Particle
Created 21530 atoms
using lattice units in orthogonal box = (-0.038088577 176 -0.00037930073) to (1059.5581 1763.52 10.560379)
create_atoms CPU = 0.013 seconds
group Particle region Particle
21530 atoms in group Particle
variable theta_z equal ${random01}*90 # angle to rotate the grain
variable theta_z equal 0.612226366996765*90
displace_atoms Particle rotate ${cx} ${cy} ${cz} 0 0 1 ${theta_z} # rotate wrt z-axis
displace_atoms Particle rotate 41.3084119558334 ${cy} ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 41.3084119558334 225 ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 41.3084119558334 225 1.5 0 0 1 ${theta_z}
displace_atoms Particle rotate 41.3084119558334 225 1.5 0 0 1 55.1003730297089
Displacing atoms ...
group GroupCreateAtomsTop_01 union GroupCreateAtomsTop_01 Particle
21530 atoms in group GroupCreateAtomsTop_01
region Particle delete
group Particle delete
next vloopParticle
jump SELF labelParticleCreation
print "Grain creation loop: ${vloopParticle}"
Grain creation loop: 2
variable perturb01 equal v_random01
if "(${vloopParticle} == 0) || (${vloopParticle} == ${nParticles})" then "variable perturb01 equal 0.00"
variable radius equal (0.75+0.25*${perturb01})*${radiusIdeal}
variable radius equal (0.75+0.25*0.619038879871368)*${radiusIdeal}
variable radius equal (0.75+0.25*0.619038879871368)*25
variable temp01 equal ${perturb01}*${radiusIdeal} #((step/${nrun})%2)*${radius}
variable temp01 equal 0.0782623291015625*${radiusIdeal}
variable temp01 equal 0.0782623291015625*25
variable temp02 equal 2*${radiusIdeal}*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(2-1)+${radiusIdeal}
variable temp02 equal 2*25*(2-1)+25
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopParticle} - 50
variable cx equal 1.95655822753906+${temp02}
variable cx equal 1.95655822753906+75
variable cy equal (${y2}+${y3})/2
variable cy equal (200+${y3})/2
variable cy equal (200+250)/2
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
print "Grain parameters cx: ${cx} cy: ${cy} cz: ${cz} radius: ${radius}"
Grain parameters cx: 76.9565582275391 cy: 225 cz: 1.5 radius: 22.618992999196
region Particle sphere ${cx} ${cy} ${cz} ${radius}
region Particle sphere 76.9565582275391 ${cy} ${cz} ${radius}
region Particle sphere 76.9565582275391 225 ${cz} ${radius}
region Particle sphere 76.9565582275391 225 1.5 ${radius}
region Particle sphere 76.9565582275391 225 1.5 22.618992999196
create_atoms 1 region Particle
Created 22454 atoms
using lattice units in orthogonal box = (-0.038088577 176 -0.00037930073) to (1059.5581 1763.52 10.560379)
create_atoms CPU = 0.015 seconds
group Particle region Particle
24794 atoms in group Particle
variable theta_z equal ${random01}*90 # angle to rotate the grain
variable theta_z equal 0.358080863952637*90
displace_atoms Particle rotate ${cx} ${cy} ${cz} 0 0 1 ${theta_z} # rotate wrt z-axis
displace_atoms Particle rotate 76.9565582275391 ${cy} ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 76.9565582275391 225 ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 76.9565582275391 225 1.5 0 0 1 ${theta_z}
displace_atoms Particle rotate 76.9565582275391 225 1.5 0 0 1 32.2272777557373
Displacing atoms ...
group GroupCreateAtomsTop_01 union GroupCreateAtomsTop_01 Particle
43984 atoms in group GroupCreateAtomsTop_01
region Particle delete
group Particle delete
next vloopParticle
jump SELF labelParticleCreation
print "Grain creation loop: ${vloopParticle}"
Grain creation loop: 3
variable perturb01 equal v_random01
if "(${vloopParticle} == 0) || (${vloopParticle} == ${nParticles})" then "variable perturb01 equal 0.00"
variable radius equal (0.75+0.25*${perturb01})*${radiusIdeal}
variable radius equal (0.75+0.25*0.803503632545471)*${radiusIdeal}
variable radius equal (0.75+0.25*0.803503632545471)*25
variable temp01 equal ${perturb01}*${radiusIdeal} #((step/${nrun})%2)*${radius}
variable temp01 equal 0.0261417627334595*${radiusIdeal}
variable temp01 equal 0.0261417627334595*25
variable temp02 equal 2*${radiusIdeal}*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(3-1)+${radiusIdeal}
variable temp02 equal 2*25*(3-1)+25
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopParticle} - 50
variable cx equal 0.653544068336487+${temp02}
variable cx equal 0.653544068336487+125
variable cy equal (${y2}+${y3})/2
variable cy equal (200+${y3})/2
variable cy equal (200+250)/2
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
print "Grain parameters cx: ${cx} cy: ${cy} cz: ${cz} radius: ${radius}"
Grain parameters cx: 125.653544068336 cy: 225 cz: 1.5 radius: 23.7718977034092
region Particle sphere ${cx} ${cy} ${cz} ${radius}
region Particle sphere 125.653544068336 ${cy} ${cz} ${radius}
region Particle sphere 125.653544068336 225 ${cz} ${radius}
region Particle sphere 125.653544068336 225 1.5 ${radius}
region Particle sphere 125.653544068336 225 1.5 23.7718977034092
create_atoms 1 region Particle
Created 24807 atoms
using lattice units in orthogonal box = (-0.038088577 176 -0.00037930073) to (1059.5581 1763.52 10.560379)
create_atoms CPU = 0.015 seconds
group Particle region Particle
24807 atoms in group Particle
variable theta_z equal ${random01}*90 # angle to rotate the grain
variable theta_z equal 0.032852828502655*90
displace_atoms Particle rotate ${cx} ${cy} ${cz} 0 0 1 ${theta_z} # rotate wrt z-axis
displace_atoms Particle rotate 125.653544068336 ${cy} ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 125.653544068336 225 ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 125.653544068336 225 1.5 0 0 1 ${theta_z}
displace_atoms Particle rotate 125.653544068336 225 1.5 0 0 1 2.95675456523895
Displacing atoms ...
group GroupCreateAtomsTop_01 union GroupCreateAtomsTop_01 Particle
68791 atoms in group GroupCreateAtomsTop_01
region Particle delete
group Particle delete
next vloopParticle
jump SELF labelParticleCreation
print "Grain creation loop: ${vloopParticle}"
Grain creation loop: 4
variable perturb01 equal v_random01
if "(${vloopParticle} == 0) || (${vloopParticle} == ${nParticles})" then "variable perturb01 equal 0.00"
variable radius equal (0.75+0.25*${perturb01})*${radiusIdeal}
variable radius equal (0.75+0.25*0.0400077104568481)*${radiusIdeal}
variable radius equal (0.75+0.25*0.0400077104568481)*25
variable temp01 equal ${perturb01}*${radiusIdeal} #((step/${nrun})%2)*${radius}
variable temp01 equal 0.535777807235718*${radiusIdeal}
variable temp01 equal 0.535777807235718*25
variable temp02 equal 2*${radiusIdeal}*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(4-1)+${radiusIdeal}
variable temp02 equal 2*25*(4-1)+25
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopParticle} - 50
variable cx equal 13.3944451808929+${temp02}
variable cx equal 13.3944451808929+175
variable cy equal (${y2}+${y3})/2
variable cy equal (200+${y3})/2
variable cy equal (200+250)/2
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
print "Grain parameters cx: ${cx} cy: ${cy} cz: ${cz} radius: ${radius}"
Grain parameters cx: 188.394445180893 cy: 225 cz: 1.5 radius: 19.0000481903553
region Particle sphere ${cx} ${cy} ${cz} ${radius}
region Particle sphere 188.394445180893 ${cy} ${cz} ${radius}
region Particle sphere 188.394445180893 225 ${cz} ${radius}
region Particle sphere 188.394445180893 225 1.5 ${radius}
region Particle sphere 188.394445180893 225 1.5 19.0000481903553
create_atoms 1 region Particle
Created 15820 atoms
using lattice units in orthogonal box = (-0.038088577 176 -0.00037930073) to (1059.5581 1763.52 10.560379)
create_atoms CPU = 0.011 seconds
group Particle region Particle
15820 atoms in group Particle
variable theta_z equal ${random01}*90 # angle to rotate the grain
variable theta_z equal 0.0990321040153503*90
displace_atoms Particle rotate ${cx} ${cy} ${cz} 0 0 1 ${theta_z} # rotate wrt z-axis
displace_atoms Particle rotate 188.394445180893 ${cy} ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 188.394445180893 225 ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 188.394445180893 225 1.5 0 0 1 ${theta_z}
displace_atoms Particle rotate 188.394445180893 225 1.5 0 0 1 8.91288936138153
Displacing atoms ...
group GroupCreateAtomsTop_01 union GroupCreateAtomsTop_01 Particle
84611 atoms in group GroupCreateAtomsTop_01
region Particle delete
group Particle delete
next vloopParticle
jump SELF labelParticleCreation
print "Grain creation loop: ${vloopParticle}"
Grain creation loop: 5
variable perturb01 equal v_random01
if "(${vloopParticle} == 0) || (${vloopParticle} == ${nParticles})" then "variable perturb01 equal 0.00"
variable radius equal (0.75+0.25*${perturb01})*${radiusIdeal}
variable radius equal (0.75+0.25*0.359844505786896)*${radiusIdeal}
variable radius equal (0.75+0.25*0.359844505786896)*25
variable temp01 equal ${perturb01}*${radiusIdeal} #((step/${nrun})%2)*${radius}
variable temp01 equal 0.571093380451202*${radiusIdeal}
variable temp01 equal 0.571093380451202*25
variable temp02 equal 2*${radiusIdeal}*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(5-1)+${radiusIdeal}
variable temp02 equal 2*25*(5-1)+25
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopParticle} - 50
variable cx equal 14.27733451128+${temp02}
variable cx equal 14.27733451128+225
variable cy equal (${y2}+${y3})/2
variable cy equal (200+${y3})/2
variable cy equal (200+250)/2
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
print "Grain parameters cx: ${cx} cy: ${cy} cz: ${cz} radius: ${radius}"
Grain parameters cx: 239.27733451128 cy: 225 cz: 1.5 radius: 20.9990281611681
region Particle sphere ${cx} ${cy} ${cz} ${radius}
region Particle sphere 239.27733451128 ${cy} ${cz} ${radius}
region Particle sphere 239.27733451128 225 ${cz} ${radius}
region Particle sphere 239.27733451128 225 1.5 ${radius}
region Particle sphere 239.27733451128 225 1.5 20.9990281611681
create_atoms 1 region Particle
Created 19324 atoms
using lattice units in orthogonal box = (-0.038088577 176 -0.00037930073) to (1059.5581 1763.52 10.560379)
create_atoms CPU = 0.011 seconds
group Particle region Particle
19324 atoms in group Particle
variable theta_z equal ${random01}*90 # angle to rotate the grain
variable theta_z equal 0.289885520935059*90
displace_atoms Particle rotate ${cx} ${cy} ${cz} 0 0 1 ${theta_z} # rotate wrt z-axis
displace_atoms Particle rotate 239.27733451128 ${cy} ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 239.27733451128 225 ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 239.27733451128 225 1.5 0 0 1 ${theta_z}
displace_atoms Particle rotate 239.27733451128 225 1.5 0 0 1 26.0896968841553
Displacing atoms ...
group GroupCreateAtomsTop_01 union GroupCreateAtomsTop_01 Particle
103935 atoms in group GroupCreateAtomsTop_01
region Particle delete
group Particle delete
next vloopParticle
jump SELF labelParticleCreation
print "Grain creation loop: ${vloopParticle}"
Grain creation loop: 6
variable perturb01 equal v_random01
if "(${vloopParticle} == 0) || (${vloopParticle} == ${nParticles})" then "variable perturb01 equal 0.00"
variable perturb01 equal 0.00
variable radius equal (0.75+0.25*${perturb01})*${radiusIdeal}
variable radius equal (0.75+0.25*0)*${radiusIdeal}
variable radius equal (0.75+0.25*0)*25
variable temp01 equal ${perturb01}*${radiusIdeal} #((step/${nrun})%2)*${radius}
variable temp01 equal 0*${radiusIdeal}
variable temp01 equal 0*25
variable temp02 equal 2*${radiusIdeal}*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(${vloopParticle}-1)+${radiusIdeal}
variable temp02 equal 2*25*(6-1)+${radiusIdeal}
variable temp02 equal 2*25*(6-1)+25
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopParticle} - 50
variable cx equal 0+${temp02}
variable cx equal 0+275
variable cy equal (${y2}+${y3})/2
variable cy equal (200+${y3})/2
variable cy equal (200+250)/2
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
print "Grain parameters cx: ${cx} cy: ${cy} cz: ${cz} radius: ${radius}"
Grain parameters cx: 275 cy: 225 cz: 1.5 radius: 18.75
region Particle sphere ${cx} ${cy} ${cz} ${radius}
region Particle sphere 275 ${cy} ${cz} ${radius}
region Particle sphere 275 225 ${cz} ${radius}
region Particle sphere 275 225 1.5 ${radius}
region Particle sphere 275 225 1.5 18.75
create_atoms 1 region Particle
Created 15432 atoms
using lattice units in orthogonal box = (-0.038088577 176 -0.00037930073) to (1059.5581 1763.52 10.560379)
create_atoms CPU = 0.010 seconds
group Particle region Particle
16067 atoms in group Particle
variable theta_z equal ${random01}*90 # angle to rotate the grain
variable theta_z equal 0.542750537395477*90
displace_atoms Particle rotate ${cx} ${cy} ${cz} 0 0 1 ${theta_z} # rotate wrt z-axis
displace_atoms Particle rotate 275 ${cy} ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 275 225 ${cz} 0 0 1 ${theta_z}
displace_atoms Particle rotate 275 225 1.5 0 0 1 ${theta_z}
displace_atoms Particle rotate 275 225 1.5 0 0 1 48.8475483655929
Displacing atoms ...
group GroupCreateAtomsTop_01 union GroupCreateAtomsTop_01 Particle
119367 atoms in group GroupCreateAtomsTop_01
region Particle delete
group Particle delete
next vloopParticle
jump SELF labelParticleCreation
### Assign velocity/Temperature to the newly created atoms
#group GroupCreateAtomsTop_01 region BlockCreateAtomsTop_01
delete_atoms overlap 2.25 GroupCreateAtomsTop_01 all # atoms from the first group will be deleted
System init for delete_atoms ...
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 278 416 3
4 neighbor lists, perpetual/occasional/extra = 1 3 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(3) compute cna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute centro/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 19783 atoms, new total = 643190
velocity GroupCreateAtomsTop_01 create ${T2} 187723 #temp Temperature # assign velocity of the newly created atoms
velocity GroupCreateAtomsTop_01 create 1600 187723
### Redefine the group, fix etc.
group GroupDeleteAtomsBottom_01 region BlockDeleteAtomsBottom_01
0 atoms in group GroupDeleteAtomsBottom_01
group GroupInside region BlockInside
635902 atoms in group GroupInside
#fix 1 GroupInside nve
fix 1 GroupInside npt temp $T $T 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix 1 GroupInside npt temp 800 $T 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix 1 GroupInside npt temp 800 800 0.2 drag 0.5 x 0.0 0.0 5 z 0.0 0.0 5 couple none
fix fPushParticles GroupCreateAtomsTop_01 addforce 0.0 -0.2 0.0 every 1
fix fLangevin GroupDeleteAtomsBottom_01 langevin ${T} ${T} 0.5 123456
fix fLangevin GroupDeleteAtomsBottom_01 langevin 800 ${T} 0.5 123456
fix fLangevin GroupDeleteAtomsBottom_01 langevin 800 800 0.5 123456
print "nAtomsAll: ${nAtomsAll}; nAtomsInitial: ${nAtomsInitial}; nAtomsNew: ${nAtomsNew}"
nAtomsAll: 643190; nAtomsInitial: 543606; nAtomsNew: 99584
balance 1.1 rcb # load balancing
Balancing ...
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 278 416 3
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute cna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute centro/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
rebalancing time: 0.126 seconds
iteration count = 0
initial/final maximal load/proc = 126203 107199
initial/final imbalance factor = 1.1772851 1.0000062
run ${nrun}
run 4
Per MPI rank memory allocation (min/avg/max) = 187.3 | 192.6 | 199.9 Mbytes
Step Temp PotEng KinEng v_Temp02
4 606.08628 -2771953.6 50389.227 1603.2105
5 681.26763 -2778379.6 56639.707 1535.8112
6 739.38073 -2783279.3 61471.155 1348.6289
7 759.823 -2784922.2 63170.699 1084.683
8 741.34255 -2783229.2 61634.259 805.68072
Loop time of 8.17425 on 6 procs for 4 steps with 643190 atoms
Performance: 0.211 ns/day, 113.531 hours/ns, 0.489 timesteps/s
95.4% CPU use with 6 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.996 | 2.0067 | 2.0316 | 0.8 | 24.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.029843 | 0.052668 | 0.063844 | 4.9 | 0.64
Output | 6.0156 | 6.0157 | 6.0157 | 0.0 | 73.59
Modify | 0.090753 | 0.091844 | 0.093361 | 0.3 | 1.12
Other | | 0.007348 | | | 0.09
Nlocal: 107198 ave 107199 max 107198 min
Histogram: 4 0 0 0 0 0 0 0 0 2
Nghost: 184327 ave 187770 max 182535 min
Histogram: 4 0 0 0 0 0 0 0 1 1
Neighs: 9.18984e+06 ave 9.24596e+06 max 9.06807e+06 min
Histogram: 1 1 0 0 0 0 0 0 0 4
FullNghs: 1.83745e+07 ave 1.84639e+07 max 1.81745e+07 min
Histogram: 1 1 0 0 0 0 0 0 0 4
Total # of neighbors = 1.1024679e+08
Ave neighs/atom = 171.40625
Neighbor list builds = 0
Dangerous builds = 0
###----mimic the short pulse of laser to a localized region----
print "*** Laser pulse begins***"
*** Laser pulse begins***
## Create ellipsoidal region of atoms
variable ellipse_a equal ${Height}/2 # spread of laser shot
variable ellipse_a equal 50/2
variable ellipse_b equal 2*${Height} # depth of laser shot, melt-pool depth for SLM
variable ellipse_b equal 2*50
variable ellipse_c equal ${ellipse_a}
variable ellipse_c equal 25
variable DistanceLaserShot equal 1.0*${Height} # center to center distance between laser shots
variable DistanceLaserShot equal 1.0*50
variable nLaserShot equal floor(${lx}/${DistanceLaserShot})
variable nLaserShot equal floor(301/${DistanceLaserShot})
variable nLaserShot equal floor(301/50)
variable vloopLaser loop ${nLaserShot}
variable vloopLaser loop 6
label labelLaserPulse
print "Laser loop: ${vloopLaser}"
Laser loop: 1
variable temp01 equal 0.00 #((step/${nrun})%2)*${Height}
variable temp02 equal ${DistanceLaserShot}*(${vloopLaser}-1)+${Height}/2
variable temp02 equal 50*(${vloopLaser}-1)+${Height}/2
variable temp02 equal 50*(1-1)+${Height}/2
variable temp02 equal 50*(1-1)+50/2
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopLaser} - 50
variable cx equal 0+${temp02}
variable cx equal 0+25
variable cy equal ${y3}
variable cy equal 250
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
region AreaLaser01 ellipsoid ${cx} ${cy} ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 25 ${cy} ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 25 250 ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 25 250 1.5 ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 25 250 1.5 25 ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 25 250 1.5 25 100 ${ellipse_c}
region AreaLaser01 ellipsoid 25 250 1.5 25 100 25
group AreaLaser01 region AreaLaser01
31734 atoms in group AreaLaser01
#delete_atoms group AreaLaser01
displace_atoms AreaLaser01 random 0.05 0.1 0.05 123456
Displacing atoms ...
run ${nrun}
run 4
Per MPI rank memory allocation (min/avg/max) = 268.5 | 274.2 | 288 Mbytes
Step Temp PotEng KinEng v_Temp02
8 741.34255 -2772606.8 61634.259 805.68072
9 708.2267 -2769667.6 58881.05 601.95966
10 689.04477 -2767921 57286.289 535.94845
11 694.80282 -2768285.8 57765.006 592.67901
12 726.93319 -2770867.7 60436.283 721.85156
Loop time of 9.15787 on 6 procs for 4 steps with 643190 atoms
Performance: 0.189 ns/day, 127.193 hours/ns, 0.437 timesteps/s
95.1% CPU use with 6 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2254 | 2.244 | 2.2659 | 1.0 | 24.50
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.036978 | 0.057922 | 0.077248 | 6.1 | 0.63
Output | 6.7546 | 6.7547 | 6.7549 | 0.0 | 73.76
Modify | 0.092908 | 0.094207 | 0.094971 | 0.2 | 1.03
Other | | 0.007023 | | | 0.08
Nlocal: 107198 ave 107267 max 107165 min
Histogram: 3 0 0 0 2 0 0 0 0 1
Nghost: 184324 ave 187752 max 182524 min
Histogram: 4 0 0 0 0 0 0 0 1 1
Neighs: 9.17075e+06 ave 9.25118e+06 max 9.01773e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 4
FullNghs: 1.83296e+07 ave 1.84845e+07 max 1.80288e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 4
Total # of neighbors = 1.0997735e+08
Ave neighs/atom = 170.98734
Neighbor list builds = 0
Dangerous builds = 0
region AreaLaser01 delete
group AreaLaser01 delete
next vloopLaser
jump SELF labelLaserPulse
print "Laser loop: ${vloopLaser}"
Laser loop: 2
variable temp01 equal 0.00 #((step/${nrun})%2)*${Height}
variable temp02 equal ${DistanceLaserShot}*(${vloopLaser}-1)+${Height}/2
variable temp02 equal 50*(${vloopLaser}-1)+${Height}/2
variable temp02 equal 50*(2-1)+${Height}/2
variable temp02 equal 50*(2-1)+50/2
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopLaser} - 50
variable cx equal 0+${temp02}
variable cx equal 0+75
variable cy equal ${y3}
variable cy equal 250
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
region AreaLaser01 ellipsoid ${cx} ${cy} ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 75 ${cy} ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 75 250 ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 75 250 1.5 ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 75 250 1.5 25 ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 75 250 1.5 25 100 ${ellipse_c}
region AreaLaser01 ellipsoid 75 250 1.5 25 100 25
group AreaLaser01 region AreaLaser01
39874 atoms in group AreaLaser01
#delete_atoms group AreaLaser01
displace_atoms AreaLaser01 random 0.05 0.1 0.05 123456
Displacing atoms ...
run ${nrun}
run 4
Per MPI rank memory allocation (min/avg/max) = 268.5 | 274.2 | 288.1 Mbytes
Step Temp PotEng KinEng v_Temp02
12 726.93319 -2757444.6 60436.283 721.85156
13 791.87189 -2762803.8 65835.203 910.76593
14 884.50788 -2770506 73536.839 1133.3393
15 978.51002 -2778302.8 81352.054 1319.6766
16 1049.6767 -2784147.5 87268.761 1426.8924
Loop time of 10.0403 on 6 procs for 4 steps with 643190 atoms
Performance: 0.172 ns/day, 139.448 hours/ns, 0.398 timesteps/s
95.4% CPU use with 6 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4556 | 2.4889 | 2.53 | 1.5 | 24.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.037414 | 0.079397 | 0.11397 | 8.6 | 0.79
Output | 7.3644 | 7.3645 | 7.3646 | 0.0 | 73.35
Modify | 0.098233 | 0.099063 | 0.099853 | 0.2 | 0.99
Other | | 0.008387 | | | 0.08
Nlocal: 107198 ave 107232 max 107168 min
Histogram: 1 0 2 0 0 0 1 1 0 1
Nghost: 184324 ave 187751 max 182521 min
Histogram: 4 0 0 0 0 0 0 0 1 1
Neighs: 9.16145e+06 ave 9.25167e+06 max 8.96888e+06 min
Histogram: 1 1 0 0 0 0 0 0 0 4
FullNghs: 1.83327e+07 ave 1.84941e+07 max 1.79858e+07 min
Histogram: 1 1 0 0 0 0 0 0 0 4
Total # of neighbors = 1.0999634e+08
Ave neighs/atom = 171.01687
Neighbor list builds = 0
Dangerous builds = 0
region AreaLaser01 delete
group AreaLaser01 delete
next vloopLaser
jump SELF labelLaserPulse
print "Laser loop: ${vloopLaser}"
Laser loop: 3
variable temp01 equal 0.00 #((step/${nrun})%2)*${Height}
variable temp02 equal ${DistanceLaserShot}*(${vloopLaser}-1)+${Height}/2
variable temp02 equal 50*(${vloopLaser}-1)+${Height}/2
variable temp02 equal 50*(3-1)+${Height}/2
variable temp02 equal 50*(3-1)+50/2
variable cx equal ${temp01}+${temp02} #((step/${nrun})%2)*10 + 100*${vloopLaser} - 50
variable cx equal 0+${temp02}
variable cx equal 0+125
variable cy equal ${y3}
variable cy equal 250
variable cz equal (${z2}+${z3})/2
variable cz equal (0+${z3})/2
variable cz equal (0+3)/2
region AreaLaser01 ellipsoid ${cx} ${cy} ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 125 ${cy} ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 125 250 ${cz} ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 125 250 1.5 ${ellipse_a} ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 125 250 1.5 25 ${ellipse_b} ${ellipse_c}
region AreaLaser01 ellipsoid 125 250 1.5 25 100 ${ellipse_c}
region AreaLaser01 ellipsoid 125 250 1.5 25 100 25
group AreaLaser01 region AreaLaser01
39767 atoms in group AreaLaser01
#delete_atoms group AreaLaser01
displace_atoms AreaLaser01 random 0.05 0.1 0.05 123456
Displacing atoms ...
run ${nrun}
run 4
Per MPI rank memory allocation (min/avg/max) = 268.5 | 274.2 | 288.1 Mbytes
Step Temp PotEng KinEng v_Temp02
16 1049.6767 -2770997.5 87268.761 1426.8924
17 1095.7618 -2774741.8 91100.218 1490.2623
18 1121.5026 -2776799.4 93240.276 1558.7254
19 1123.3307 -2776838.8 93392.257 1629.7312
20 1103.3469 -2775009.8 91730.827 1695.4986
Loop time of 10.236 on 6 procs for 4 steps with 643190 atoms
Performance: 0.169 ns/day, 142.167 hours/ns, 0.391 timesteps/s
94.1% CPU use with 6 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5996 | 2.6376 | 2.7062 | 2.1 | 25.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.034564 | 0.10365 | 0.14084 | 10.9 | 1.01
Output | 7.38 | 7.3801 | 7.3801 | 0.0 | 72.10
Modify | 0.10671 | 0.10789 | 0.1092 | 0.2 | 1.05
Other | | 0.006777 | | | 0.07
Nlocal: 107198 ave 107253 max 107135 min
Histogram: 1 0 0 0 1 2 0 1 0 1
Nghost: 184326 ave 187770 max 182480 min
Histogram: 4 0 0 0 0 0 0 0 0 2
Neighs: 9.1673e+06 ave 9.26566e+06 max 8.95138e+06 min
Histogram: 1 1 0 0 0 0 0 0 0 4
FullNghs: 1.83364e+07 ave 1.85111e+07 max 1.79469e+07 min