# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.639087498188019*${_u_distance} variable latticeconst_converted equal 3.639087498188019*1 lattice fcc ${latticeconst_converted} lattice fcc 3.63908749818802 Lattice spacing in x,y,z = 3.6390875 3.6390875 3.6390875 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (36.390875 36.390875 36.390875) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (36.390875 36.390875 36.390875) create_atoms CPU = 0.000 seconds variable mass_converted equal 63.546*${_u_mass} variable mass_converted equal 63.546*1 kim interactions Cu #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_MendelevKramerBecker_2008_Cu__MO_945691923444_006 pair_coeff * * Cu #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 63.546 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 48192.2822398585 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 48192.2822398585/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 48192.2822398585/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 48192.2822398585/(1*1*${_u_distance}) variable V0_metal equal 48192.2822398585/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 48192.2822398585*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 48192.2822398585 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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_945691923444_006#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 10 10 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) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -12991.271 -12991.271 -13132.465 -13132.465 273.15 273.15 48192.282 48192.282 3129.3353 3129.3353 1000 -12838.114 -12838.114 -12979.647 -12979.647 273.80638 273.80638 48761.683 48761.683 -2247.4953 -2247.4953 Loop time of 19.9255 on 1 procs for 1000 steps with 4000 atoms Performance: 4.336 ns/day, 5.535 hours/ns, 50.187 timesteps/s, 200.747 katom-step/s 49.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.53 | 19.53 | 19.53 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.038728 | 0.038728 | 0.038728 | 0.0 | 0.19 Output | 0.00012002 | 0.00012002 | 0.00012002 | 0.0 | 0.00 Modify | 0.34385 | 0.34385 | 0.34385 | 0.0 | 1.73 Other | | 0.01284 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 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: 704000 ave 704000 max 704000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 704000 Ave neighs/atom = 176 Neighbor list builds = 0 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 = ${P}" flag: Temp = 273.21955019254, Press = -28.9240908707699 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -12838.114 -12838.114 -12979.647 -12979.647 273.80638 273.80638 48761.683 48761.683 -2247.4953 -2247.4953 2000 -12848.839 -12848.839 -12989.575 -12989.575 272.26289 272.26289 48593.165 48593.165 1371.3015 1371.3015 Loop time of 18.3747 on 1 procs for 1000 steps with 4000 atoms Performance: 4.702 ns/day, 5.104 hours/ns, 54.423 timesteps/s, 217.690 katom-step/s 61.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.14 | 18.14 | 18.14 | 0.0 | 98.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.04679 | 0.04679 | 0.04679 | 0.0 | 0.25 Output | 5.1577e-05 | 5.1577e-05 | 5.1577e-05 | 0.0 | 0.00 Modify | 0.17632 | 0.17632 | 0.17632 | 0.0 | 0.96 Other | | 0.01173 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 709098 ave 709098 max 709098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 709098 Ave neighs/atom = 177.2745 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.551457663023, Press = 7.58993043223262 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -12848.839 -12848.839 -12989.575 -12989.575 272.26289 272.26289 48593.165 48593.165 1371.3015 1371.3015 3000 -12854.43 -12854.43 -12993.295 -12993.295 268.64322 268.64322 48672.765 48672.765 -1275.2854 -1275.2854 Loop time of 13.6954 on 1 procs for 1000 steps with 4000 atoms Performance: 6.309 ns/day, 3.804 hours/ns, 73.017 timesteps/s, 292.069 katom-step/s 82.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.501 | 13.501 | 13.501 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.028378 | 0.028378 | 0.028378 | 0.0 | 0.21 Output | 6.9811e-05 | 6.9811e-05 | 6.9811e-05 | 0.0 | 0.00 Modify | 0.15412 | 0.15412 | 0.15412 | 0.0 | 1.13 Other | | 0.01153 | | | 0.08 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 710160 ave 710160 max 710160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 710160 Ave neighs/atom = 177.54 Neighbor list builds = 0 Dangerous builds = 0 if "${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" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 48645.7625666559 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0