shell mkdir out_Al_GTFE shell rm params_Al_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 4.05 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*(${latparam1}*sqrt(6)/2) variable x_displace equal -1/2*(4.05*sqrt(6)/2) variable y_displace equal -1/${nshiftsy}*(${latparam1}*sqrt(2)/2) variable y_displace equal -1/2*(${latparam1}*sqrt(2)/2) variable y_displace equal -1/2*(4.05*sqrt(2)/2) variable xdim equal ${latparam1}*sqrt(6)/2*${nx} # spacing in <112> direction variable xdim equal 4.05*sqrt(6)/2*${nx} variable xdim equal 4.05*sqrt(6)/2*20 variable ydim equal ${latparam1}*sqrt(2)/2*${ny} # spacing in <110> direction variable ydim equal 4.05*sqrt(2)/2*${ny} variable ydim equal 4.05*sqrt(2)/2*20 variable zdim equal ${latparam1}*sqrt(3)*${nz}/2 variable zdim equal 4.05*sqrt(3)*${nz}/2 variable zdim equal 4.05*sqrt(3)*20/2 variable zdim2 equal ${latparam1}*sqrt(3)*${nz} variable zdim2 equal 4.05*sqrt(3)*${nz} variable zdim2 equal 4.05*sqrt(3)*20 print "zdim: ${zdim}" zdim: 70.1480577065395 print "zdim2: ${zdim2}" zdim2: 140.296115413079 variable zplus equal (${zdim}+${latparam1}*sqrt(3)/3)-1 #for shifting on top of SF variable zplus equal (70.1480577065395+${latparam1}*sqrt(3)/3)-1 variable zplus equal (70.1480577065395+4.05*sqrt(3)/3)-1 variable xsf equal ${latparam1}*sqrt(6)/6*${nx} variable xsf equal 4.05*sqrt(6)/6*${nx} variable xsf equal 4.05*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 -2.48010836456797*${i} variable xs equal -2.48010836456797*0 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.385857 on 1 procs for 1 steps with 48000 atoms 97.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37543 | 0.37543 | 0.37543 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015078 | 0.0015078 | 0.0015078 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.14 Other | | 0.008383 | | | 2.17 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.122106 on 1 procs for 1 steps with 48000 atoms Performance: 0.708 ns/day, 33.918 hours/ns, 8.190 timesteps/s 98.4% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12102 | 0.12102 | 0.12102 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046921 | 0.00046921 | 0.00046921 | 0.0 | 0.38 Output | 0.00029588 | 0.00029588 | 0.00029588 | 0.0 | 0.24 Modify | 0.00018597 | 0.00018597 | 0.00018597 | 0.0 | 0.15 Other | | 0.0001311 | | | 0.11 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -0 ${ys} 0.0 units box displace_atoms upper_plus move -0 -0 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160659.32 -160659.32 3 -160661.68 -160661.68 Loop time of 0.395092 on 1 procs for 1 steps with 48000 atoms 98.4% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160659.315522 -160659.315522 -160661.677346 Force two-norm initial, final = 4.3937 3.7093 Force max component initial, final = 0.0974279 0.0742982 Final line search alpha, max atom move = 1 0.0742982 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38994 | 0.38994 | 0.38994 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097823 | 0.00097823 | 0.00097823 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00074577 | 0.00074577 | 0.00074577 | 0.0 | 0.19 Other | | 0.003424 | | | 0.87 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.1 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160661.68 -160661.68 4 -160661.68 -160661.68 Loop time of 0.222687 on 1 procs for 1 steps with 48000 atoms Performance: 0.388 ns/day, 61.858 hours/ns, 4.491 timesteps/s 96.2% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12109 | 0.12109 | 0.12109 | 0.0 | 54.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037503 | 0.00037503 | 0.00037503 | 0.0 | 0.17 Output | 0.1006 | 0.1006 | 0.1006 | 0.0 | 45.17 Modify | 0.00051022 | 0.00051022 | 0.00051022 | 0.0 | 0.23 Other | | 0.0001161 | | | 0.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.1 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.1 out_Al_GTFE/dump.Al_GTFE.1 next j jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*0 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*1 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 1+1 print "count: ${cnt}" count: 2 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.388372 on 1 procs for 1 steps with 48000 atoms 98.8% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38189 | 0.38189 | 0.38189 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094867 | 0.00094867 | 0.00094867 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00055838 | 0.00055838 | 0.00055838 | 0.0 | 0.14 Other | | 0.004971 | | | 1.28 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.124924 on 1 procs for 1 steps with 48000 atoms Performance: 0.692 ns/day, 34.701 hours/ns, 8.005 timesteps/s 98.2% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12372 | 0.12372 | 0.12372 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050282 | 0.00050282 | 0.00050282 | 0.0 | 0.40 Output | 0.00035501 | 0.00035501 | 0.00035501 | 0.0 | 0.28 Modify | 0.00019789 | 0.00019789 | 0.00019789 | 0.0 | 0.16 Other | | 0.0001435 | | | 0.11 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -0 ${ys} 0.0 units box displace_atoms upper_plus move -0 -1.43189123190276 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160513.25 -160513.25 3 -160576.15 -160576.15 Loop time of 0.397336 on 1 procs for 1 steps with 48000 atoms 98.2% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160513.248863 -160513.248863 -160576.15223 Force two-norm initial, final = 36.3661 11.7808 Force max component initial, final = 0.918997 0.307643 Final line search alpha, max atom move = 0.108814 0.0334759 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39191 | 0.39191 | 0.39191 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001159 | 0.001159 | 0.001159 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00061011 | 0.00061011 | 0.00061011 | 0.0 | 0.15 Other | | 0.00366 | | | 0.92 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3032e+06 ave 3.3032e+06 max 3.3032e+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 = 3303200 Ave neighs/atom = 68.8167 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.2 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160576.15 -160576.15 4 -160576.15 -160576.15 Loop time of 0.229748 on 1 procs for 1 steps with 48000 atoms Performance: 0.376 ns/day, 63.819 hours/ns, 4.353 timesteps/s 96.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1285 | 0.1285 | 0.1285 | 0.0 | 55.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000453 | 0.000453 | 0.000453 | 0.0 | 0.20 Output | 0.1001 | 0.1001 | 0.1001 | 0.0 | 43.57 Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 0.25 Other | | 0.000123 | | | 0.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3e+06 ave 3.3e+06 max 3.3e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3300000 Ave neighs/atom = 68.75 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.2 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.2 out_Al_GTFE/dump.Al_GTFE.2 next j jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*0 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*2 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 2+1 print "count: ${cnt}" count: 3 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.37765 on 1 procs for 1 steps with 48000 atoms 98.8% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37225 | 0.37225 | 0.37225 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086021 | 0.00086021 | 0.00086021 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00058484 | 0.00058484 | 0.00058484 | 0.0 | 0.15 Other | | 0.003958 | | | 1.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.122889 on 1 procs for 1 steps with 48000 atoms Performance: 0.703 ns/day, 34.136 hours/ns, 8.137 timesteps/s 98.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12168 | 0.12168 | 0.12168 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005281 | 0.0005281 | 0.0005281 | 0.0 | 0.43 Output | 0.00035095 | 0.00035095 | 0.00035095 | 0.0 | 0.29 Modify | 0.00019884 | 0.00019884 | 0.00019884 | 0.0 | 0.16 Other | | 0.0001299 | | | 0.11 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -0 ${ys} 0.0 units box displace_atoms upper_plus move -0 -2.86378246380552 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160659.32 -160659.32 3 -160661.68 -160661.68 Loop time of 0.399815 on 1 procs for 1 steps with 48000 atoms 98.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160659.315522 -160659.315522 -160661.677346 Force two-norm initial, final = 4.3937 3.7093 Force max component initial, final = 0.0974279 0.0742982 Final line search alpha, max atom move = 1 0.0742982 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39332 | 0.39332 | 0.39332 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011997 | 0.0011997 | 0.0011997 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00071359 | 0.00071359 | 0.00071359 | 0.0 | 0.18 Other | | 0.004578 | | | 1.14 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.3 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160661.68 -160661.68 4 -160661.68 -160661.68 Loop time of 0.243697 on 1 procs for 1 steps with 48000 atoms Performance: 0.355 ns/day, 67.694 hours/ns, 4.103 timesteps/s 95.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13192 | 0.13192 | 0.13192 | 0.0 | 54.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042582 | 0.00042582 | 0.00042582 | 0.0 | 0.17 Output | 0.11067 | 0.11067 | 0.11067 | 0.0 | 45.41 Modify | 0.00054908 | 0.00054908 | 0.00054908 | 0.0 | 0.23 Other | | 0.0001287 | | | 0.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.3 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.3 out_Al_GTFE/dump.Al_GTFE.3 next j jump SELF loopj variable j delete next i jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*1 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*0 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 3+1 print "count: ${cnt}" count: 4 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.383884 on 1 procs for 1 steps with 48000 atoms 98.6% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37753 | 0.37753 | 0.37753 | 0.0 | 98.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089097 | 0.00089097 | 0.00089097 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00057697 | 0.00057697 | 0.00057697 | 0.0 | 0.15 Other | | 0.004881 | | | 1.27 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.124942 on 1 procs for 1 steps with 48000 atoms Performance: 0.692 ns/day, 34.706 hours/ns, 8.004 timesteps/s 98.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12396 | 0.12396 | 0.12396 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040603 | 0.00040603 | 0.00040603 | 0.0 | 0.32 Output | 0.00029111 | 0.00029111 | 0.00029111 | 0.0 | 0.23 Modify | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.14 Other | | 0.000113 | | | 0.09 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -2.48010836456797 ${ys} 0.0 units box displace_atoms upper_plus move -2.48010836456797 -0 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160513.25 -160513.25 3 -160576.15 -160576.15 Loop time of 0.380688 on 1 procs for 1 steps with 48000 atoms 99.2% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160513.248863 -160513.248863 -160576.15223 Force two-norm initial, final = 36.3661 11.7808 Force max component initial, final = 0.918997 0.307643 Final line search alpha, max atom move = 0.108814 0.0334759 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37559 | 0.37559 | 0.37559 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009129 | 0.0009129 | 0.0009129 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00055981 | 0.00055981 | 0.00055981 | 0.0 | 0.15 Other | | 0.003626 | | | 0.95 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3032e+06 ave 3.3032e+06 max 3.3032e+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 = 3303200 Ave neighs/atom = 68.8167 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.4 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160576.15 -160576.15 4 -160576.15 -160576.15 Loop time of 0.215654 on 1 procs for 1 steps with 48000 atoms Performance: 0.401 ns/day, 59.904 hours/ns, 4.637 timesteps/s 96.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12291 | 0.12291 | 0.12291 | 0.0 | 57.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042486 | 0.00042486 | 0.00042486 | 0.0 | 0.20 Output | 0.091676 | 0.091676 | 0.091676 | 0.0 | 42.51 Modify | 0.00052691 | 0.00052691 | 0.00052691 | 0.0 | 0.24 Other | | 0.0001132 | | | 0.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3e+06 ave 3.3e+06 max 3.3e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3300000 Ave neighs/atom = 68.75 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.4 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.4 out_Al_GTFE/dump.Al_GTFE.4 next j jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*1 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*1 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 4+1 print "count: ${cnt}" count: 5 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.381591 on 1 procs for 1 steps with 48000 atoms 96.8% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37394 | 0.37394 | 0.37394 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014842 | 0.0014842 | 0.0014842 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00057697 | 0.00057697 | 0.00057697 | 0.0 | 0.15 Other | | 0.005592 | | | 1.47 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.124301 on 1 procs for 1 steps with 48000 atoms Performance: 0.695 ns/day, 34.528 hours/ns, 8.045 timesteps/s 97.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12314 | 0.12314 | 0.12314 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052595 | 0.00052595 | 0.00052595 | 0.0 | 0.42 Output | 0.00031495 | 0.00031495 | 0.00031495 | 0.0 | 0.25 Modify | 0.00018406 | 0.00018406 | 0.00018406 | 0.0 | 0.15 Other | | 0.0001402 | | | 0.11 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -2.48010836456797 ${ys} 0.0 units box displace_atoms upper_plus move -2.48010836456797 -1.43189123190276 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160659.32 -160659.32 3 -160661.68 -160661.68 Loop time of 0.48719 on 1 procs for 1 steps with 48000 atoms 94.7% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160659.315522 -160659.315522 -160661.677346 Force two-norm initial, final = 4.3937 3.7093 Force max component initial, final = 0.0974279 0.0742982 Final line search alpha, max atom move = 1 0.0742982 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48074 | 0.48074 | 0.48074 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012298 | 0.0012298 | 0.0012298 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00072074 | 0.00072074 | 0.00072074 | 0.0 | 0.15 Other | | 0.004496 | | | 0.92 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.5 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160661.68 -160661.68 4 -160661.68 -160661.68 Loop time of 0.284444 on 1 procs for 1 steps with 48000 atoms Performance: 0.304 ns/day, 79.012 hours/ns, 3.516 timesteps/s 86.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14071 | 0.14071 | 0.14071 | 0.0 | 49.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050712 | 0.00050712 | 0.00050712 | 0.0 | 0.18 Output | 0.14141 | 0.14141 | 0.14141 | 0.0 | 49.72 Modify | 0.001652 | 0.001652 | 0.001652 | 0.0 | 0.58 Other | | 0.0001612 | | | 0.06 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.5 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.5 out_Al_GTFE/dump.Al_GTFE.5 next j jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*1 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*2 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 5+1 print "count: ${cnt}" count: 6 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.4281 on 1 procs for 1 steps with 48000 atoms 91.6% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42073 | 0.42073 | 0.42073 | 0.0 | 98.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014141 | 0.0014141 | 0.0014141 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00071406 | 0.00071406 | 0.00071406 | 0.0 | 0.17 Other | | 0.005238 | | | 1.22 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.137829 on 1 procs for 1 steps with 48000 atoms Performance: 0.627 ns/day, 38.286 hours/ns, 7.255 timesteps/s 92.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13677 | 0.13677 | 0.13677 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044227 | 0.00044227 | 0.00044227 | 0.0 | 0.32 Output | 0.00031614 | 0.00031614 | 0.00031614 | 0.0 | 0.23 Modify | 0.00018787 | 0.00018787 | 0.00018787 | 0.0 | 0.14 Other | | 0.0001109 | | | 0.08 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -2.48010836456797 ${ys} 0.0 units box displace_atoms upper_plus move -2.48010836456797 -2.86378246380552 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160513.25 -160513.25 3 -160576.15 -160576.15 Loop time of 0.425412 on 1 procs for 1 steps with 48000 atoms 95.4% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160513.248863 -160513.248863 -160576.15223 Force two-norm initial, final = 36.3661 11.7808 Force max component initial, final = 0.918997 0.307643 Final line search alpha, max atom move = 0.108814 0.0334759 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41928 | 0.41928 | 0.41928 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013039 | 0.0013039 | 0.0013039 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00086808 | 0.00086808 | 0.00086808 | 0.0 | 0.20 Other | | 0.003961 | | | 0.93 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3032e+06 ave 3.3032e+06 max 3.3032e+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 = 3303200 Ave neighs/atom = 68.8167 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.6 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160576.15 -160576.15 4 -160576.15 -160576.15 Loop time of 0.253463 on 1 procs for 1 steps with 48000 atoms Performance: 0.341 ns/day, 70.406 hours/ns, 3.945 timesteps/s 94.1% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13716 | 0.13716 | 0.13716 | 0.0 | 54.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051618 | 0.00051618 | 0.00051618 | 0.0 | 0.20 Output | 0.1151 | 0.1151 | 0.1151 | 0.0 | 45.41 Modify | 0.00056601 | 0.00056601 | 0.00056601 | 0.0 | 0.22 Other | | 0.0001199 | | | 0.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3e+06 ave 3.3e+06 max 3.3e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3300000 Ave neighs/atom = 68.75 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.6 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.6 out_Al_GTFE/dump.Al_GTFE.6 next j jump SELF loopj variable j delete next i jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*2 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*0 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 6+1 print "count: ${cnt}" count: 7 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.414622 on 1 procs for 1 steps with 48000 atoms 94.5% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40737 | 0.40737 | 0.40737 | 0.0 | 98.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00061297 | 0.00061297 | 0.00061297 | 0.0 | 0.15 Other | | 0.00512 | | | 1.23 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.123076 on 1 procs for 1 steps with 48000 atoms Performance: 0.702 ns/day, 34.188 hours/ns, 8.125 timesteps/s 97.2% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12199 | 0.12199 | 0.12199 | 0.0 | 99.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049019 | 0.00049019 | 0.00049019 | 0.0 | 0.40 Output | 0.00028801 | 0.00028801 | 0.00028801 | 0.0 | 0.23 Modify | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.14 Other | | 0.0001318 | | | 0.11 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -4.96021672913594 ${ys} 0.0 units box displace_atoms upper_plus move -4.96021672913594 -0 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160659.32 -160659.32 3 -160661.68 -160661.68 Loop time of 0.504332 on 1 procs for 1 steps with 48000 atoms 93.7% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160659.315522 -160659.315522 -160661.677346 Force two-norm initial, final = 4.3937 3.7093 Force max component initial, final = 0.0974279 0.0742982 Final line search alpha, max atom move = 1 0.0742982 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49836 | 0.49836 | 0.49836 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012262 | 0.0012262 | 0.0012262 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00082612 | 0.00082612 | 0.00082612 | 0.0 | 0.16 Other | | 0.003924 | | | 0.78 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160661.6773459--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.7 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160661.68 -160661.68 4 -160661.68 -160661.68 Loop time of 0.230832 on 1 procs for 1 steps with 48000 atoms Performance: 0.374 ns/day, 64.120 hours/ns, 4.332 timesteps/s 93.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1266 | 0.1266 | 0.1266 | 0.0 | 54.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051785 | 0.00051785 | 0.00051785 | 0.0 | 0.22 Output | 0.10298 | 0.10298 | 0.10298 | 0.0 | 44.61 Modify | 0.00057411 | 0.00057411 | 0.00057411 | 0.0 | 0.25 Other | | 0.0001559 | | | 0.07 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.7 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.7 out_Al_GTFE/dump.Al_GTFE.7 next j jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*2 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*1 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 7+1 print "count: ${cnt}" count: 8 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.372569 on 1 procs for 1 steps with 48000 atoms 97.6% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36528 | 0.36528 | 0.36528 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010569 | 0.0010569 | 0.0010569 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00057006 | 0.00057006 | 0.00057006 | 0.0 | 0.15 Other | | 0.005667 | | | 1.52 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.133341 on 1 procs for 1 steps with 48000 atoms Performance: 0.648 ns/day, 37.039 hours/ns, 7.500 timesteps/s 95.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13198 | 0.13198 | 0.13198 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052691 | 0.00052691 | 0.00052691 | 0.0 | 0.40 Output | 0.00043797 | 0.00043797 | 0.00043797 | 0.0 | 0.33 Modify | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.20 Other | | 0.0001311 | | | 0.10 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 variable E equal "c_eatoms" variable Eo equal $E variable Eo equal -160659.315522634 # ------------------- Displace top block with specified (xs,ys) coordinates ------------------- #displace_atoms is the command neccessary to move atoms into the next stacking arrangement (ie: A -> B) displace_atoms upper_plus move ${xs} ${ys} 0.0 units box displace_atoms upper_plus move -4.96021672913594 ${ys} 0.0 units box displace_atoms upper_plus move -4.96021672913594 -1.43189123190276 0.0 units box #only relax forces in z direction during energy minimization fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 #change 1 1 to 10000 10000 for relaxed structures. Should be similar, but adds computational time WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 23.2978 Mbytes Step PotEng c_eatoms 2 -160513.25 -160513.25 3 -160576.15 -160576.15 Loop time of 0.40282 on 1 procs for 1 steps with 48000 atoms 96.7% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160513.248863 -160513.248863 -160576.15223 Force two-norm initial, final = 36.3661 11.7808 Force max component initial, final = 0.918997 0.307643 Final line search alpha, max atom move = 0.108814 0.0334759 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39714 | 0.39714 | 0.39714 | 0.0 | 98.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011621 | 0.0011621 | 0.0011621 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.00063705 | 0.00063705 | 0.00063705 | 0.0 | 0.16 Other | | 0.003886 | | | 0.96 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3032e+06 ave 3.3032e+06 max 3.3032e+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 = 3303200 Ave neighs/atom = 68.8167 Neighbor list builds = 0 Dangerous builds = 0 variable Ef equal "c_eatoms" variable Cf equal 1.60217657e-16 variable A equal (${xdim}*${ydim})*1e-20 variable A equal (99.2043345827187*${ydim})*1e-20 variable A equal (99.2043345827187*57.2756492761104)*1e-20 variable SFE equal ((${Ef}-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965-${Eo})*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*${Cf})/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*${A}) variable SFE equal ((-160576.15222965--160659.315522634)*1.60217657e-16)/(1*5.68199267422971e-17) #variable Ef equal "c_eatoms" computes the final energy of the system after sliding is done #variable A is the area of the Stacking fault plane in m^2 #variable Cf is the conversion factor of electro volts to millijoules #variable SFE is the stacking-fault energy of the system in mJ/m^2 dump 2 all custom 1 dump.Al_GTFE.${cnt} id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom dump 2 all custom 1 dump.Al_GTFE.8 id type x y z c_disp[1] c_disp[2] c_disp[3] c_peratom shell cd .. fix print all print 1 "$(v_cnt) $(v_i) $(v_j) $(v_xs) $(v_ys) $(v_Ef) $(v_Eo) $(v_A) $(v_SFE)" append params_Al_GTFE.txt screen no title " " run 1 Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 27.7187 Mbytes Step PotEng c_eatoms 3 -160576.15 -160576.15 4 -160576.15 -160576.15 Loop time of 0.241203 on 1 procs for 1 steps with 48000 atoms Performance: 0.358 ns/day, 67.001 hours/ns, 4.146 timesteps/s 95.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13873 | 0.13873 | 0.13873 | 0.0 | 57.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000422 | 0.000422 | 0.000422 | 0.0 | 0.17 Output | 0.10135 | 0.10135 | 0.10135 | 0.0 | 42.02 Modify | 0.00058007 | 0.00058007 | 0.00058007 | 0.0 | 0.24 Other | | 0.0001187 | | | 0.05 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23909 ave 23909 max 23909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.3e+06 ave 3.3e+06 max 3.3e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3300000 Ave neighs/atom = 68.75 Neighbor list builds = 0 Dangerous builds = 0 undump 2 shell mv dump.Al_GTFE.${cnt} out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.8 out_Al_GTFE/dump.Al_GTFE.${cnt} shell mv dump.Al_GTFE.8 out_Al_GTFE/dump.Al_GTFE.8 next j jump SELF 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 -2.48010836456797*${i} variable xs equal -2.48010836456797*2 variable ys equal ${y_displace}*${j} # shift applied in z direction variable ys equal -1.43189123190276*${j} variable ys equal -1.43189123190276*2 # Increment counter variable cnt equal ${cnt}+1 variable cnt equal 8+1 print "count: ${cnt}" count: 9 #-------------------- 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 4.05 Lattice spacing in x,y,z = 4.05 4.05 4.05 region 1 block -.001 ${xdim} -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 ${ydim} -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 ${zdim} units box region 1 block -.001 99.2043345827187 -.001 57.2756492761104 -.001 70.1480577065395 units box region 2 block -.001 ${xdim} -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 ${ydim} ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 ${zdim} ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 ${zdim2} units box region 2 block -.001 99.2043345827187 -.001 57.2756492761104 70.1480577065395 140.296115413079 units box region 3 block -.001 ${xdim} -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 ${ydim} ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 ${zplus} ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 ${zdim2} units box region 3 block -.001 99.2043345827187 -.001 57.2756492761104 71.4863262967575 140.296115413079 units box region whole block 0 ${xdim} 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 ${ydim} 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 ${zdim2} units box region whole block 0 99.2043345827187 0 57.2756492761104 0 140.296115413079 units box create_box 1 whole Created orthogonal box = (0 0 0) to (99.2043 57.2756 140.296) 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 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 1 Created 24000 atoms lattice fcc ${latparam1} orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 lattice fcc 4.05 orient x 1 1 2 orient y -1 1 0 orient z -1 -1 1 Lattice spacing in x,y,z = 6.61362 5.72756 7.01481 create_atoms 1 region 2 Created 24000 atoms # --------------------- Associate structure with interatomic potential --------------------- pair_style eam/alloy pair_coeff * * Al.eam Al # --------------------- Define groups, computes, minimize initial structure --------------------- group bot region 1 24000 atoms in group bot group top region 2 24000 atoms in group top group upper_plus region 3 23200 atoms in group upper_plus shell cd out_Al_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 100 thermo_style custom step pe c_eatoms #create stacking fault to start displace_atoms top move ${xsf} 0.0 0.0 units box displace_atoms top move 33.0681115275729 0.0 0.0 units box fix 1 all setforce 0 0 NULL min_style cg minimize 1e-10 1e-10 1 1 #10000 10000 WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) Neighbor list info ... 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 22.6728 Mbytes Step PotEng c_eatoms 0 -160651.8 -160651.8 1 -160659.32 -160659.32 Loop time of 0.450189 on 1 procs for 1 steps with 48000 atoms 87.8% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max force evaluations Energy initial, next-to-last, final = -160651.800226 -160651.800226 -160659.315522 Force two-norm initial, final = 6.85786 4.3937 Force max component initial, final = 0.154943 0.0974279 Final line search alpha, max atom move = 0.645399 0.0628799 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43958 | 0.43958 | 0.43958 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002389 | 0.002389 | 0.002389 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.0010788 | 0.0010788 | 0.0010788 | 0.0 | 0.24 Other | | 0.007137 | | | 1.59 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0 dump 1 all custom 1 dump.Al_GTFE.0 id type xs ys zs c_peratom c_csym undump 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25 -> bins = 24 14 33 Memory usage per processor = 17.6728 Mbytes Step PotEng c_eatoms 1 -160659.32 -160659.32 2 -160659.32 -160659.32 Loop time of 0.140208 on 1 procs for 1 steps with 48000 atoms Performance: 0.616 ns/day, 38.947 hours/ns, 7.132 timesteps/s 98.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1391 | 0.1391 | 0.1391 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004499 | 0.0004499 | 0.0004499 | 0.0 | 0.32 Output | 0.00033402 | 0.00033402 | 0.00033402 | 0.0 | 0.24 Modify | 0.000211 | 0.000211 | 0.000211 | 0.0 | 0.15 Other | | 0.0001099 | | | 0.08 Nlocal: 48000 ave 48000 max 48000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23900 ave 23900 max 23900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.2968e+06 ave 3.2968e+06 max 3.2968e+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 = 3296800 Ave neighs/atom = 68.6833 Neighbor list builds = 0 Dangerous builds = 0