# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.866007231175899*${_u_distance} variable latticeconst_converted equal 2.866007231175899*1 lattice bcc ${latticeconst_converted} lattice bcc 2.8660072311759 Lattice spacing in x,y,z = 2.8660072 2.8660072 2.8660072 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.660072 28.660072 28.660072) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.660072 28.660072 28.660072) create_atoms CPU = 0.000 seconds variable mass_converted equal 51.9961*${_u_mass} variable mass_converted equal 51.9961*1 kim interactions Cr #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style hybrid/overlay eam/alloy eam/fs pair_coeff * * eam/alloy /tmp/kim-shared-library-parameter-file-directory-XXXXXXhF0bqx/FeCr_d.eam.alloy Cr pair_coeff * * eam/fs /tmp/kim-shared-library-parameter-file-directory-XXXXXXhF0bqx/FeCr_s.eam.fs Cr #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 51.9961 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 23541.3760861316 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23541.3760861316/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23541.3760861316/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 23541.3760861316/(1*1*${_u_distance}) variable V0_metal equal 23541.3760861316/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 23541.3760861316*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 23541.3760861316 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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/SM_237089298463_001#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 8 8 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair eam/alloy, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard (2) pair eam/fs, perpetual, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -8137.0598 -8137.0598 -8202.4715 -8202.4715 253.15 253.15 23541.376 23541.376 2967.8451 2967.8451 1000 -8069.2172 -8069.2172 -8137.1154 -8137.1154 262.77308 262.77308 23596.219 23596.219 160.92692 160.92692 Loop time of 5.39351 on 1 procs for 1000 steps with 2000 atoms Performance: 16.019 ns/day, 1.498 hours/ns, 185.408 timesteps/s, 370.816 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2962 | 5.2962 | 5.2962 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021408 | 0.021408 | 0.021408 | 0.0 | 0.40 Output | 7.1214e-05 | 7.1214e-05 | 7.1214e-05 | 0.0 | 0.00 Modify | 0.068759 | 0.068759 | 0.068759 | 0.0 | 1.27 Other | | 0.007084 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136000 ave 136000 max 136000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136000 Ave neighs/atom = 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 = ${P}" flag: Temp = 253.410223716012, Press = -14.4592530099452 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8069.2172 -8069.2172 -8137.1154 -8137.1154 262.77308 262.77308 23596.219 23596.219 160.92692 160.92692 2000 -8077.9461 -8077.9461 -8141.3241 -8141.3241 245.27932 245.27932 23622.347 23622.347 -2576.5279 -2576.5279 Loop time of 6.1308 on 1 procs for 1000 steps with 2000 atoms Performance: 14.093 ns/day, 1.703 hours/ns, 163.111 timesteps/s, 326.222 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0401 | 6.0401 | 6.0401 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019096 | 0.019096 | 0.019096 | 0.0 | 0.31 Output | 4.7759e-05 | 4.7759e-05 | 4.7759e-05 | 0.0 | 0.00 Modify | 0.064822 | 0.064822 | 0.064822 | 0.0 | 1.06 Other | | 0.006725 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5462 ave 5462 max 5462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136830 ave 136830 max 136830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136830 Ave neighs/atom = 68.415 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.139824790871, Press = -7.7836393059907 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8077.9461 -8077.9461 -8141.3241 -8141.3241 245.27932 245.27932 23622.347 23622.347 -2576.5279 -2576.5279 3000 -8068.0106 -8068.0106 -8131.4194 -8131.4194 245.39877 245.39877 23599.614 23599.614 -227.27429 -227.27429 Loop time of 5.87254 on 1 procs for 1000 steps with 2000 atoms Performance: 14.713 ns/day, 1.631 hours/ns, 170.284 timesteps/s, 340.568 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7884 | 5.7884 | 5.7884 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018041 | 0.018041 | 0.018041 | 0.0 | 0.31 Output | 4.0105e-05 | 4.0105e-05 | 4.0105e-05 | 0.0 | 0.00 Modify | 0.060351 | 0.060351 | 0.060351 | 0.0 | 1.03 Other | | 0.005687 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5442 ave 5442 max 5442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136551 ave 136551 max 136551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136551 Ave neighs/atom = 68.2755 Neighbor list builds = 0 Dangerous builds = 0 if "${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 23596.2591422244 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0