# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.576890356838703*${_u_distance} variable latticeconst_converted equal 5.576890356838703*1 lattice bcc ${latticeconst_converted} lattice bcc 5.5768903568387 Lattice spacing in x,y,z = 5.5768904 5.5768904 5.5768904 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (55.768904 55.768904 55.768904) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (55.768904 55.768904 55.768904) create_atoms CPU = 0.000 seconds variable mass_converted equal 22.98977*${_u_mass} variable mass_converted equal 22.98977*1 kim interactions Na #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style reaxff NULL mincap 200 safezone 2 pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXxLTtnd/ReaxFF_HOSiCeNaCl.txt Na 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/reaxff 1 0.0 10.0 1.0e-6 reaxff #=== 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 173450.804563749 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 173450.804563749/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 173450.804563749/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 173450.804563749/(1*1*${_u_distance}) variable V0_metal equal 173450.804563749/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 173450.804563749*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 173450.804563749 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_282799919035_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 reaxff, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reaxff, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 147.6 | 147.6 | 147.6 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 361.10217 15.658872 -1504.8457 -65.256286 313.15 313.15 173450.8 173450.8 491.76321 498.27908 1000 1775.8617 77.00865 -76.38501 -3.3123675 310.85061 310.85061 1666876.4 1666876.4 49.105487 49.756135 Loop time of 6.35335 on 1 procs for 1000 steps with 2000 atoms Performance: 13.599 ns/day, 1.765 hours/ns, 157.397 timesteps/s, 314.795 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.53 | 4.53 | 4.53 | 0.0 | 71.30 Neigh | 0.58304 | 0.58304 | 0.58304 | 0.0 | 9.18 Comm | 0.015127 | 0.015127 | 0.015127 | 0.0 | 0.24 Output | 6.384e-05 | 6.384e-05 | 6.384e-05 | 0.0 | 0.00 Modify | 1.2187 | 1.2187 | 1.2187 | 0.0 | 19.18 Other | | 0.006424 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1459 ave 1459 max 1459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9233 ave 9233 max 9233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9233 Ave neighs/atom = 4.6165 Neighbor list builds = 105 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 = ${P}" flag: Temp = 310.820010535931, Press = 54.9729977614513 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 146.1 | 146.1 | 146.1 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 1775.8617 77.00865 -76.38501 -3.3123675 310.85061 310.85061 1666876.4 1666876.4 49.105487 49.756135 2000 1897.8993 82.300703 -13.322202 -0.57770537 320.74798 320.74798 13575196 13575196 6.4176084 6.5026417 Loop time of 1.35346 on 1 procs for 1000 steps with 2000 atoms Performance: 63.836 ns/day, 0.376 hours/ns, 738.845 timesteps/s, 1.478 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77456 | 0.77456 | 0.77456 | 0.0 | 57.23 Neigh | 0.26828 | 0.26828 | 0.26828 | 0.0 | 19.82 Comm | 0.010048 | 0.010048 | 0.010048 | 0.0 | 0.74 Output | 2.7581e-05 | 2.7581e-05 | 2.7581e-05 | 0.0 | 0.00 Modify | 0.29425 | 0.29425 | 0.29425 | 0.0 | 21.74 Other | | 0.006297 | | | 0.47 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 617 ave 617 max 617 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1207 ave 1207 max 1207 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1207 Ave neighs/atom = 0.6035 Neighbor list builds = 185 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.716380401471, Press = 23.9155234602549 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 146.4 | 146.4 | 146.4 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 1897.8993 82.300703 -13.322202 -0.57770537 320.74798 320.74798 13575196 13575196 6.4176084 6.5026417 3000 1898.6112 82.331573 -1.5874772 -0.068839526 318.89809 318.89809 1.0241344e+08 1.0241344e+08 0.84584364 0.85705107 Loop time of 0.841175 on 1 procs for 1000 steps with 2000 atoms Performance: 102.713 ns/day, 0.234 hours/ns, 1188.813 timesteps/s, 2.378 Matom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35528 | 0.35528 | 0.35528 | 0.0 | 42.24 Neigh | 0.28577 | 0.28577 | 0.28577 | 0.0 | 33.97 Comm | 0.0092676 | 0.0092676 | 0.0092676 | 0.0 | 1.10 Output | 2.6219e-05 | 2.6219e-05 | 2.6219e-05 | 0.0 | 0.00 Modify | 0.18327 | 0.18327 | 0.18327 | 0.0 | 21.79 Other | | 0.007562 | | | 0.90 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 285 ave 285 max 285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183 ave 183 max 183 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183 Ave neighs/atom = 0.0915 Neighbor list builds = 320 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.831568903374, Press = 13.8076282116732 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 148.4 | 148.4 | 148.4 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 1898.6112 82.331573 -1.5874774 -0.068839533 318.89809 318.89809 1.0241344e+08 1.0241344e+08 0.84584364 0.85705107 4000 1815.2178 78.715292 -0.18452678 -0.0080018387 304.66726 304.66726 7.3305505e+08 7.3305505e+08 0.11317711 0.11467671 Loop time of 1.33088 on 1 procs for 1000 steps with 2000 atoms Performance: 64.920 ns/day, 0.370 hours/ns, 751.384 timesteps/s, 1.503 Matom-step/s 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28572 | 0.28572 | 0.28572 | 0.0 | 21.47 Neigh | 0.85614 | 0.85614 | 0.85614 | 0.0 | 64.33 Comm | 0.015246 | 0.015246 | 0.015246 | 0.0 | 1.15 Output | 0.00012004 | 0.00012004 | 0.00012004 | 0.0 | 0.01 Modify | 0.16405 | 0.16405 | 0.16405 | 0.0 | 12.33 Other | | 0.009602 | | | 0.72 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 154 ave 154 max 154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23 ave 23 max 23 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23 Ave neighs/atom = 0.0115 Neighbor list builds = 500 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" jump SELF unstable print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation." ERROR: System volume 733055045.52627 A^3 has become larger than 173450804.563749 A^3. Aborting calculation. Total wall time: 0:00:09