# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.8265378177165985*${_u_distance} variable latticeconst_converted equal 4.8265378177165985*1 lattice bcc ${latticeconst_converted} lattice bcc 4.8265378177166 Lattice spacing in x,y,z = 4.8265378 4.8265378 4.8265378 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (48.265378 48.265378 48.265378) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (48.265378 48.265378 48.265378) create_atoms CPU = 0.000 seconds variable mass_converted equal 132.90545*${_u_mass} variable mass_converted equal 132.90545*1 kim interactions Cs #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style eim variable kim_atom_type_sym_list string "Cs" variable kim_parameter_file_1 string /tmp/kim-shared-library-parameter-file-directory-XXXXXXYn2VXA/ffield_KIM.eim include /tmp/kim-shared-library-parameter-file-directory-XXXXXXYn2VXA/kim_coeff.lammps # Loop over all atoms to see which ones we need to include in the EIM pair_coeff command variable kim_atom_sym_i index ${kim_atom_type_sym_list} variable kim_atom_sym_i index Cs variable kim_atom_type_sym_list_unique string "" variable kim_seen_Li string false variable kim_seen_Na string false variable kim_seen_K string false variable kim_seen_Rb string false variable kim_seen_Cs string false variable kim_seen_F string false variable kim_seen_Cl string false variable kim_seen_Br string false variable kim_seen_I string false label loopi if "(${kim_atom_sym_i} == Li) && (${kim_seen_Li} == false)" then """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Li" """ "variable kim_seen_Li string true" elif "(${kim_atom_sym_i} == Na) && (${kim_seen_Na} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Na" """ "variable kim_seen_Na string true" elif "(${kim_atom_sym_i} == K) && (${kim_seen_K} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} K" """ "variable kim_seen_K string true" elif "(${kim_atom_sym_i} == Rb) && (${kim_seen_Rb} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Rb" """ "variable kim_seen_Rb string true" elif "(${kim_atom_sym_i} == Cs) && (${kim_seen_Cs} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Cs" """ "variable kim_seen_Cs string true" elif "(${kim_atom_sym_i} == F) && (${kim_seen_F} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} F" """ "variable kim_seen_F string true" elif "(${kim_atom_sym_i} == Cl) && (${kim_seen_Cl} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Cl" """ "variable kim_seen_Cl string true" elif "(${kim_atom_sym_i} == Br) && (${kim_seen_Br} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Br" """ "variable kim_seen_Br string true" elif "(${kim_atom_sym_i} == I) && (${kim_seen_I} == false)" """ variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} I" """ "variable kim_seen_I string true" variable kim_atom_type_sym_list_unique string "${kim_atom_type_sym_list_unique} Cs" Cs variable kim_seen_Cs string true next kim_atom_sym_i jump SELF loopi pair_coeff * * ${kim_atom_type_sym_list_unique} ${kim_parameter_file_1} ${kim_atom_type_sym_list} pair_coeff * * Cs ${kim_parameter_file_1} ${kim_atom_type_sym_list} pair_coeff * * Cs /tmp/kim-shared-library-parameter-file-directory-XXXXXXYn2VXA/ffield_KIM.eim ${kim_atom_type_sym_list} pair_coeff * * Cs /tmp/kim-shared-library-parameter-file-directory-XXXXXXYn2VXA/ffield_KIM.eim Cs Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXYn2VXA/ffield_KIM.eim with DATE: 2010-08-31 variable kim_atom_sym_i delete variable kim_atom_type_sym_list_unique delete variable kim_seen_Li delete variable kim_seen_Na delete variable kim_seen_K delete variable kim_seen_Rb delete variable kim_seen_Cs delete variable kim_seen_F delete variable kim_seen_Cl delete variable kim_seen_Br delete variable kim_seen_I delete variable kim_atom_type_sym_list delete variable kim_parameter_file_1 delete #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 132.90545 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 112436.453933059 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 112436.453933059/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 112436.453933059/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 112436.453933059/(1*1*${_u_distance}) variable V0_metal equal 112436.453933059/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 112436.453933059*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 112436.453933059 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_259779394709_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 = 9.6064 ghost atom cutoff = 9.6064 binsize = 4.8032, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair eim, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.444 | 3.444 | 3.444 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -1403.9545 -1403.9545 -1479.7019 -1479.7019 293.15 293.15 112436.45 112436.45 719.58164 719.58164 1000 -1332.7911 -1332.7911 -1408.8743 -1408.8743 294.44998 294.44998 115992.58 115992.58 -7.3820701 -7.3820701 Loop time of 3.79875 on 1 procs for 1000 steps with 2000 atoms Performance: 22.744 ns/day, 1.055 hours/ns, 263.244 timesteps/s, 526.489 katom-step/s 90.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6746 | 3.6746 | 3.6746 | 0.0 | 96.73 Neigh | 0.013257 | 0.013257 | 0.013257 | 0.0 | 0.35 Comm | 0.020869 | 0.020869 | 0.020869 | 0.0 | 0.55 Output | 0.00010385 | 0.00010385 | 0.00010385 | 0.0 | 0.00 Modify | 0.082591 | 0.082591 | 0.082591 | 0.0 | 2.17 Other | | 0.007347 | | | 0.19 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3222 ave 3222 max 3222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60110 ave 60110 max 60110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60110 Ave neighs/atom = 30.055 Neighbor list builds = 4 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 = ${P}" flag: Temp = 294.484863797576, Press = 1.36650443835484 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 3.447 | 3.447 | 3.447 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -1332.7911 -1332.7911 -1408.8743 -1408.8743 294.44998 294.44998 115992.58 115992.58 -7.3820701 -7.3820701 2000 -1336.6019 -1336.6019 -1414.8357 -1414.8357 302.77304 302.77304 116403.08 116403.08 -209.16791 -209.16791 Loop time of 3.30406 on 1 procs for 1000 steps with 2000 atoms Performance: 26.150 ns/day, 0.918 hours/ns, 302.658 timesteps/s, 605.315 katom-step/s 86.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2016 | 3.2016 | 3.2016 | 0.0 | 96.90 Neigh | 0.010639 | 0.010639 | 0.010639 | 0.0 | 0.32 Comm | 0.0125 | 0.0125 | 0.0125 | 0.0 | 0.38 Output | 6.1856e-05 | 6.1856e-05 | 6.1856e-05 | 0.0 | 0.00 Modify | 0.072953 | 0.072953 | 0.072953 | 0.0 | 2.21 Other | | 0.00628 | | | 0.19 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3340 ave 3340 max 3340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60425 ave 60425 max 60425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60425 Ave neighs/atom = 30.2125 Neighbor list builds = 4 Dangerous builds = 0 if "${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_T293.15.out" else "print 'not_converged' file output/vol_T293.15.out" print '${V}' file output/vol_T293.15.out 116127.036514053 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0