# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.405484482645988*${_u_distance} variable latticeconst_converted equal 2.405484482645988*1 lattice bcc ${latticeconst_converted} lattice bcc 2.40548448264599 Lattice spacing in x,y,z = 2.4054845 2.4054845 2.4054845 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (24.054845 24.054845 24.054845) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (24.054845 24.054845 24.054845) create_atoms CPU = 0.000 seconds variable mass_converted equal 22.98977*${_u_mass} variable mass_converted equal 22.98977*1 kim interactions Na #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_Mendelev_2015_Na__MO_094065024556_000 pair_coeff * * Na #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 22.98977 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 13918.9885978527 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 13918.9885978527/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 13918.9885978527/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 13918.9885978527/(1*1*${_u_distance}) variable V0_metal equal 13918.9885978527/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 13918.9885978527*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 13918.9885978527 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_094065024556_000#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 = 11.2 ghost atom cutoff = 11.2 binsize = 5.6, bins = 5 5 5 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) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -16578.661 -16578.661 -16644.072 -16644.072 253.15 253.15 13918.989 13918.989 5019.824 5019.824 1000 -16513.857 -16513.857 -16576.526 -16576.526 242.53626 242.53626 13923.914 13923.914 2943.8376 2943.8376 Loop time of 42.3186 on 1 procs for 1000 steps with 2000 atoms Performance: 2.042 ns/day, 11.755 hours/ns, 23.630 timesteps/s, 47.261 katom-step/s 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.193 | 42.193 | 42.193 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.046635 | 0.046635 | 0.046635 | 0.0 | 0.11 Output | 9.6881e-05 | 9.6881e-05 | 9.6881e-05 | 0.0 | 0.00 Modify | 0.066557 | 0.066557 | 0.066557 | 0.0 | 0.16 Other | | 0.0127 | | | 0.03 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12859 ave 12859 max 12859 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: 1.736e+06 ave 1.736e+06 max 1.736e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1736000 Ave neighs/atom = 868 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 = ${P}" flag: Temp = 254.026894067015, Press = -149.889094895468 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.2 ghost atom cutoff = 11.2 binsize = 5.6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -16513.857 -16513.857 -16576.526 -16576.526 242.53626 242.53626 13923.914 13923.914 2943.8376 2943.8376 2000 -16513.425 -16513.425 -16577.441 -16577.441 247.74935 247.74935 13928.989 13928.989 -11357.397 -11357.397 Loop time of 56.8013 on 1 procs for 1000 steps with 2000 atoms Performance: 1.521 ns/day, 15.778 hours/ns, 17.605 timesteps/s, 35.210 katom-step/s 71.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.634 | 56.634 | 56.634 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.064103 | 0.064103 | 0.064103 | 0.0 | 0.11 Output | 5.8871e-05 | 5.8871e-05 | 5.8871e-05 | 0.0 | 0.00 Modify | 0.090474 | 0.090474 | 0.090474 | 0.0 | 0.16 Other | | 0.01256 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12859 ave 12859 max 12859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.73958e+06 ave 1.73958e+06 max 1.73958e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1739576 Ave neighs/atom = 869.788 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.275719707875, Press = -34.945661209057 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.2 ghost atom cutoff = 11.2 binsize = 5.6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -16513.425 -16513.425 -16577.441 -16577.441 247.74935 247.74935 13928.989 13928.989 -11357.397 -11357.397 3000 -16514.94 -16514.94 -16580.814 -16580.814 254.93901 254.93901 13928.722 13928.722 -11110.219 -11110.219 Loop time of 62.4051 on 1 procs for 1000 steps with 2000 atoms Performance: 1.385 ns/day, 17.335 hours/ns, 16.024 timesteps/s, 32.049 katom-step/s 65.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 62.214 | 62.214 | 62.214 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.055379 | 0.055379 | 0.055379 | 0.0 | 0.09 Output | 6.39e-05 | 6.39e-05 | 6.39e-05 | 0.0 | 0.00 Modify | 0.11642 | 0.11642 | 0.11642 | 0.0 | 0.19 Other | | 0.01897 | | | 0.03 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12859 ave 12859 max 12859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.73984e+06 ave 1.73984e+06 max 1.73984e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1739844 Ave neighs/atom = 869.922 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.333275359426, Press = -6.22339363528733 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.2 ghost atom cutoff = 11.2 binsize = 5.6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -16514.94 -16514.94 -16580.814 -16580.814 254.93901 254.93901 13928.722 13928.722 -11110.219 -11110.219 4000 -16513.492 -16513.492 -16580.084 -16580.084 257.71772 257.71772 13916.786 13916.786 22610.91 22610.91 Loop time of 61.001 on 1 procs for 1000 steps with 2000 atoms Performance: 1.416 ns/day, 16.945 hours/ns, 16.393 timesteps/s, 32.786 katom-step/s 66.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 60.795 | 60.795 | 60.795 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.085011 | 0.085011 | 0.085011 | 0.0 | 0.14 Output | 6.1155e-05 | 6.1155e-05 | 6.1155e-05 | 0.0 | 0.00 Modify | 0.078074 | 0.078074 | 0.078074 | 0.0 | 0.13 Other | | 0.04253 | | | 0.07 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12859 ave 12859 max 12859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.73936e+06 ave 1.73936e+06 max 1.73936e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1739360 Ave neighs/atom = 869.68 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.207482902711, Press = 22.8366743118723 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.2 ghost atom cutoff = 11.2 binsize = 5.6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -16513.492 -16513.492 -16580.084 -16580.084 257.71772 257.71772 13916.786 13916.786 22610.91 22610.91 5000 -16511.583 -16511.583 -16578.095 -16578.095 257.40969 257.40969 13922.865 13922.865 6080.7141 6080.7141 Loop time of 62.7591 on 1 procs for 1000 steps with 2000 atoms Performance: 1.377 ns/day, 17.433 hours/ns, 15.934 timesteps/s, 31.868 katom-step/s 64.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 62.599 | 62.599 | 62.599 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.051852 | 0.051852 | 0.051852 | 0.0 | 0.08 Output | 5.9742e-05 | 5.9742e-05 | 5.9742e-05 | 0.0 | 0.00 Modify | 0.095906 | 0.095906 | 0.095906 | 0.0 | 0.15 Other | | 0.01193 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12859 ave 12859 max 12859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.74009e+06 ave 1.74009e+06 max 1.74009e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1740088 Ave neighs/atom = 870.044 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 13924.9675401071 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0