# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.526318043470383*${_u_distance} variable latticeconst_converted equal 5.526318043470383*1 lattice fcc ${latticeconst_converted} lattice fcc 5.52631804347038 Lattice spacing in x,y,z = 5.526318 5.526318 5.526318 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (55.26318 55.26318 55.26318) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (55.26318 55.26318 55.26318) create_atoms CPU = 0.001 seconds variable mass_converted equal 40.078*${_u_mass} variable mass_converted equal 40.078*1 kim interactions Ca #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style reax/c NULL safezone 3.0 mincap 100 pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXVtm4ME/ffield-CaSiOH-lammps.reax.txt Ca WARNING: Van der Waals parameters for element SI indicate inner wall+shielding, but earlier atoms indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (src/REAXFF/reaxff_ffield.cpp:251) WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:296) fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 reax/c #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 40.078 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 168774.809224151 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 168774.809224151/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 168774.809224151/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 168774.809224151/(1*1*${_u_distance}) variable V0_metal equal 168774.809224151/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 168774.809224151*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 168774.809224151 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1000 timestep ${timestep_converted} timestep 1 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1000 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*0.986923266716013 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1000 # 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 10 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 10 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 10 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 10 iso 0 0 100 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/23.0605480120695 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/23.0605480120695 variable T_metal equal temp/${_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/0.986923266716013 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/SM_714124634215_000#item-citation - pair reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, number = {4--5}, pages = {245--259} } - fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } 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: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 10 10 10 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 443 | 443 | 443 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -308455.96 -13375.916 -312188.79 -13537.787 313.15 313.15 168774.81 168774.81 1011.0097 1024.4055 1000 -304421.33 -13200.958 -308243.62 -13366.708 320.65495 320.65495 169697.52 169697.52 -419.58099 -425.14044 Loop time of 163.356 on 1 procs for 1000 steps with 4000 atoms Performance: 0.529 ns/day, 45.377 hours/ns, 6.122 timesteps/s, 24.486 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 149.51 | 149.51 | 149.51 | 0.0 | 91.53 Neigh | 0.27667 | 0.27667 | 0.27667 | 0.0 | 0.17 Comm | 0.043982 | 0.043982 | 0.043982 | 0.0 | 0.03 Output | 0.00012074 | 0.00012074 | 0.00012074 | 0.0 | 0.00 Modify | 13.501 | 13.501 | 13.501 | 0.0 | 8.26 Other | | 0.02159 | | | 0.01 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: 420452 ave 420452 max 420452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420452 Ave neighs/atom = 105.113 Neighbor list builds = 9 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 = ${P}" flag: Temp = 313.241153404673, Press = 8.02322115751772 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 442.7 | 442.7 | 442.7 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -304421.33 -13200.958 -308243.62 -13366.708 320.65495 320.65495 169697.52 169697.52 -419.58099 -425.14044 2000 -304492.69 -13204.053 -308241.07 -13366.598 314.45505 314.45505 169589.43 169589.43 -87.133712 -88.288234 Loop time of 158.438 on 1 procs for 1000 steps with 4000 atoms Performance: 0.545 ns/day, 44.010 hours/ns, 6.312 timesteps/s, 25.247 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 144.89 | 144.89 | 144.89 | 0.0 | 91.45 Neigh | 0.30526 | 0.30526 | 0.30526 | 0.0 | 0.19 Comm | 0.04395 | 0.04395 | 0.04395 | 0.0 | 0.03 Output | 6.7747e-05 | 6.7747e-05 | 6.7747e-05 | 0.0 | 0.00 Modify | 13.178 | 13.178 | 13.178 | 0.0 | 8.32 Other | | 0.0204 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 420503 ave 420503 max 420503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420503 Ave neighs/atom = 105.12575 Neighbor list builds = 10 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 169582.91482425 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0