shell mkdir out_Ag_GTFE WARNING: Shell command 'mkdir' failed with error 'File exists' (../input.cpp:1262) shell rm params_Ag_GTFE.txt WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1283) # --------------------- Define Variables ------------------ # Defining variables here is important to run loops correctly variable latparam1 equal 4.09 variable nshiftsx equal 2 variable nshiftsy equal 2 variable nx equal 20 variable ny equal 20 variable nz equal 20 variable cnt equal 0 #total count variable x_displace equal -1/${nshiftsx}*(${latparam1}*sqrt(6)/2) variable x_displace equal -1/2*(${latparam1}*sqrt(6)/2) variable x_displace equal -1/2*(4.09*sqrt(6)/2) variable y_displace equal -1/${nshiftsy}*(${latparam1}*sqrt(2)/2) variable y_displace equal -1/2*(${latparam1}*sqrt(2)/2) variable y_displace equal -1/2*(4.09*sqrt(2)/2) variable xdim equal ${latparam1}*sqrt(6)/2*${nx} # spacing in <112> direction variable xdim equal 4.09*sqrt(6)/2*${nx} variable xdim equal 4.09*sqrt(6)/2*20 variable ydim equal ${latparam1}*sqrt(2)/2*${ny} # spacing in <110> direction variable ydim equal 4.09*sqrt(2)/2*${ny} variable ydim equal 4.09*sqrt(2)/2*20 variable zdim equal ${latparam1}*sqrt(3)*${nz}/2 variable zdim equal 4.09*sqrt(3)*${nz}/2 variable zdim equal 4.09*sqrt(3)*20/2 variable zdim2 equal ${latparam1}*sqrt(3)*${nz} variable zdim2 equal 4.09*sqrt(3)*${nz} variable zdim2 equal 4.09*sqrt(3)*20 print "zdim: ${zdim}" zdim: 70.8408780295671 print "zdim2: ${zdim2}" zdim2: 141.681756059134 variable zplus equal (${zdim}+${latparam1}*sqrt(3)/3) #for shifting on top of SF variable zplus equal (70.8408780295671+${latparam1}*sqrt(3)/3) variable zplus equal (70.8408780295671+4.09*sqrt(3)/3) variable xsf equal ${latparam1}*sqrt(6)/6*${nx} variable xsf equal 4.09*sqrt(6)/6*${nx} variable xsf equal 4.09*sqrt(6)/6*20 label loopi variable i loop 0 ${nshiftsx} variable i loop 0 2 label loopj variable j loop 0 ${nshiftsy} variable j loop 0 2 variable xs equal ${x_displace}*${i} # shift applied in x direction variable xs equal -2.5046032619958*${i} variable xs equal -2.5046032619958*0 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.44603336752649*${j} variable ys equal -1.44603336752649*0 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 0+1 print "count: ${cnt}" count: 1 #-------------------- Initialize Simulation ---------------- clear units metal dimension 3 boundary p p s #fixed surface along z atom_style atomic # --------------------- Initial structure definition--------------------- # block oriented s.t. <112> || x, <110> || y, <111> || z lattice fcc ${latparam1} lattice fcc 4.09 Lattice spacing in x,y,z = 4.09 4.09 4.09 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 100.184130479832 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 100.184130479832 -.001 57.8413347010596 -.001 ${zdim} units box region 1 block -.001 100.184130479832 -.001 57.8413347010596 -.001 70.8408780295671 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 100.184130479832 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 100.184130479832 -.001 57.8413347010596 ${zdim} ${zdim2} units box region 2 block -.001 100.184130479832 -.001 57.8413347010596 70.8408780295671 ${zdim2} units box region 2 block -.001 100.184130479832 -.001 57.8413347010596 70.8408780295671 141.681756059134 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 100.184130479832 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 100.184130479832 -.001 57.8413347010596 ${zplus} ${zdim2} units box region 3 block -.001 100.184130479832 -.001 57.8413347010596 73.2022406305527 ${zdim2} units box region 3 block -.001 100.184130479832 -.001 57.8413347010596 73.2022406305527 141.681756059134 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 100.184130479832 0 ${ydim} 0 ${zdim2} units box region whole block 0 100.184130479832 0 57.8413347010596 0 ${zdim2} units box region whole block 0 100.184130479832 0 57.8413347010596 0 141.681756059134 units box create_box 1 whole Created orthogonal box = (0 0 0) to (100.184 57.8413 141.682) 1 by 1 by 1 MPI processor grid lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.09 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.67894 5.78413 7.08409 create_atoms 1 region 1 Created 24800 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.09 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.67894 5.78413 7.08409 create_atoms 1 region 2 Created 23540 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Ag.eam Ag # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 25140 atoms in group bot group top region 2 23880 atoms in group top group upper_plus region 3 22400 atoms in group upper_plus shell cd out_Ag_GTFE compute peratom all pe/atom compute eatoms all reduce sum c_peratom compute csym all centro/atom fcc compute disp all displace/atom # compute dxtot bottom reduce sum c_disp[1] thermo 1 thermo_style custom step pe c_eatoms dump first all custom 1 dump.Ag_unmin id type xs ys zs run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4 -> bins = 26 15 36 Memory usage per processor = 22.1489 Mbytes Step PotEng c_eatoms 0 nan nan 1 nan nan Loop time of 0.147091 on 1 procs for 1 steps with 48340 atoms Performance: 0.587 ns/day, 40.859 hours/ns, 6.799 timesteps/s 96.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092363 | 0.092363 | 0.092363 | 0.0 | 62.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088096 | 0.00088096 | 0.00088096 | 0.0 | 0.60 Output | 0.05372 | 0.05372 | 0.05372 | 0.0 | 36.52 Modify | 2.861e-06 | 2.861e-06 | 2.861e-06 | 0.0 | 0.00 Other | | 0.000124 | | | 0.08 Nlocal: 48340 ave 48340 max 48340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23070 ave 23070 max 23070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.19718e+06 ave 3.19718e+06 max 3.19718e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3197179 Ave neighs/atom = 66.1394 Neighbor list builds = 0 Dangerous builds = 0