# periodic boundary conditions along all three dimensions boundary p p p # Set neighbor skin variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.248509056866169*${_u_distance} variable latticeconst_converted equal 5.248509056866169*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24850905686617 Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 pair_coeff * * Ar #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.948 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 144579.877647162 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144579.877647162*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144579.877647162 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 313.15 17 mom yes rot yes # set NPT ensemble for all atoms fix ensemble all npt temp ${temp_converted} ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/1 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/1 variable T_metal equal temp/${_u_temperature} variable T_metal equal temp/1 variable V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*1*${_u_distance}) variable V_metal equal vol/(1*1*1) variable P_metal equal press/${_u_pressure} variable P_metal equal press/1 fix avgmyTemp all ave/time 5 20 100 v_T_metal ave running start 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # extract fix quantities into variables so they can be used in if-else logic later. variable T equal f_avgmyTemp variable P equal f_avgmyPress variable V equal f_avgmyVol # set error bounds for temperature and pressure in original metal units (K and bar) variable T_low equal "313.15 - 1.0" variable T_up equal "313.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # print to logfile every 1000 timesteps thermo_style custom step etotal v_etotal_metal pe v_pe_metal temp v_T_metal vol v_V_metal press v_P_metal thermo 1000 # Run a simulation for at most 2000*1000 timesteps. At each 1000th time step, check # whether the temperature and pressure have converged. If yes, break. label top variable a loop 2000 run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.2 | 10.2 | 10.2 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -184.15125 -184.15125 -346.02203 -346.02203 313.15 313.15 144579.88 144579.88 1195.8589 1195.8589 1000 92.89724 92.89724 -68.391648 -68.391648 312.02429 312.02429 588091.81 588091.81 155.03173 155.03173 Loop time of 17.8931 on 1 procs for 1000 steps with 4000 atoms Performance: 4.829 ns/day, 4.970 hours/ns, 55.888 timesteps/s, 223.550 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.457 | 16.457 | 16.457 | 0.0 | 91.97 Neigh | 1.2602 | 1.2602 | 1.2602 | 0.0 | 7.04 Comm | 0.03849 | 0.03849 | 0.03849 | 0.0 | 0.22 Output | 0.00011907 | 0.00011907 | 0.00011907 | 0.0 | 0.00 Modify | 0.12217 | 0.12217 | 0.12217 | 0.0 | 0.68 Other | | 0.01544 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6302 ave 6302 max 6302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 423804 ave 423804 max 423804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423804 Ave neighs/atom = 105.951 Neighbor list builds = 56 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 311.668506866365, Press = 157.808505309707 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.214 | 5.214 | 5.214 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 92.89724 92.89724 -68.391648 -68.391648 312.02429 312.02429 588091.81 588091.81 155.03173 155.03173 2000 146.22589 146.22589 -15.838665 -15.838665 313.52486 313.52486 2794758.4 2794758.4 54.544959 54.544959 Loop time of 5.13799 on 1 procs for 1000 steps with 4000 atoms Performance: 16.816 ns/day, 1.427 hours/ns, 194.628 timesteps/s, 778.514 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1757 | 4.1757 | 4.1757 | 0.0 | 81.27 Neigh | 0.80548 | 0.80548 | 0.80548 | 0.0 | 15.68 Comm | 0.024573 | 0.024573 | 0.024573 | 0.0 | 0.48 Output | 6.1125e-05 | 6.1125e-05 | 6.1125e-05 | 0.0 | 0.00 Modify | 0.11994 | 0.11994 | 0.11994 | 0.0 | 2.33 Other | | 0.01227 | | | 0.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3250 ave 3250 max 3250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93108 ave 93108 max 93108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93108 Ave neighs/atom = 23.277 Neighbor list builds = 96 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 312.368047125574, Press = 109.430629785595 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.702 | 3.702 | 3.702 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 146.22589 146.22589 -15.838665 -15.838665 313.52486 313.52486 2794758.4 2794758.4 54.544959 54.544959 3000 158.76453 158.76453 -3.8029947 -3.8029947 314.4979 314.4979 15030221 15030221 11.313367 11.313367 Loop time of 1.75421 on 1 procs for 1000 steps with 4000 atoms Performance: 49.253 ns/day, 0.487 hours/ns, 570.057 timesteps/s, 2.280 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0529 | 1.0529 | 1.0529 | 0.0 | 60.02 Neigh | 0.55223 | 0.55223 | 0.55223 | 0.0 | 31.48 Comm | 0.019076 | 0.019076 | 0.019076 | 0.0 | 1.09 Output | 5.4182e-05 | 5.4182e-05 | 5.4182e-05 | 0.0 | 0.00 Modify | 0.11814 | 0.11814 | 0.11814 | 0.0 | 6.73 Other | | 0.01184 | | | 0.67 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1692 ave 1692 max 1692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 18834 ave 18834 max 18834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18834 Ave neighs/atom = 4.7085 Neighbor list builds = 165 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 312.539754724666, Press = 70.475632883655 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 32 32 32 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.83 | 3.83 | 3.83 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 158.76453 158.76453 -3.8029947 -3.8029947 314.4979 314.4979 15030221 15030221 11.313367 11.313367 4000 162.98258 162.98258 -0.88906627 -0.88906627 317.02081 317.02081 78401886 78401886 2.2196595 2.2196595 Loop time of 0.941129 on 1 procs for 1000 steps with 4000 atoms Performance: 91.805 ns/day, 0.261 hours/ns, 1062.554 timesteps/s, 4.250 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3968 | 0.3968 | 0.3968 | 0.0 | 42.16 Neigh | 0.3961 | 0.3961 | 0.3961 | 0.0 | 42.09 Comm | 0.017565 | 0.017565 | 0.017565 | 0.0 | 1.87 Output | 3.7831e-05 | 3.7831e-05 | 3.7831e-05 | 0.0 | 0.00 Modify | 0.11754 | 0.11754 | 0.11754 | 0.0 | 12.49 Other | | 0.01308 | | | 1.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 933 ave 933 max 933 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4246 ave 4246 max 4246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4246 Ave neighs/atom = 1.0615 Neighbor list builds = 270 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 312.657612578253, Press = 49.5111889177138 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 56 56 56 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.497 | 4.497 | 4.497 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 162.98258 162.98258 -0.88906627 -0.88906627 317.02081 317.02081 78401886 78401886 2.2196595 2.2196595 5000 162.09698 162.09698 -0.23551424 -0.23551424 314.04322 314.04322 3.9391045e+08 3.9391045e+08 0.44001268 0.44001268 Loop time of 0.965442 on 1 procs for 1000 steps with 4000 atoms Performance: 89.493 ns/day, 0.268 hours/ns, 1035.795 timesteps/s, 4.143 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23059 | 0.23059 | 0.23059 | 0.0 | 23.88 Neigh | 0.58116 | 0.58116 | 0.58116 | 0.0 | 60.20 Comm | 0.02019 | 0.02019 | 0.02019 | 0.0 | 2.09 Output | 5.7087e-05 | 5.7087e-05 | 5.7087e-05 | 0.0 | 0.01 Modify | 0.11788 | 0.11788 | 0.11788 | 0.0 | 12.21 Other | | 0.01557 | | | 1.61 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 503 ave 503 max 503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 982 ave 982 max 982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 982 Ave neighs/atom = 0.2455 Neighbor list builds = 425 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" jump SELF unstable print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation." ERROR: System volume 393910450.996022 A^3 has become larger than 144579877.647162 A^3. Aborting calculation. Total wall time: 0:00:27