LAMMPS (23 Jun 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 10.514 10.514 10.514 Created orthogonal box = (0 0 0) to (10.514 10.514 10.514) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (10.514 10.514 10.514) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_282799919035_000#item-citation - pair reaxff command: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 10.514 0 10.514 0 10.514 -0.0058870609 -40.538882 -41.076022 -41.076022 -41.076022 -41.076022 0 1.6591553e-15 1.6591553e-15 Loop time of 1.303e-06 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.303e-06 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66 ave 66 max 66 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66 Ave neighs/atom = 16.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.00147176522160497 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 9.809529 9.809529 9.809529 Created orthogonal box = (0 0 0) to (9.809529 9.809529 9.809529) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (9.809529 9.809529 9.809529) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 9.809529 0 9.809529 0 9.809529 -0.015036708 -100.97682 -102.31477 -102.31477 -102.31477 -102.31477 -2.0428971e-15 0 0 Loop time of 4.71e-07 on 1 procs for 0 steps with 4 atoms 212.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.71e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66 ave 66 max 66 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66 Ave neighs/atom = 16.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.00375917706756653 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 9.372925 9.372925 9.372925 Created orthogonal box = (0 0 0) to (9.372925 9.372925 9.372925) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (9.372925 9.372925 9.372925) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 9.372925 0 9.372925 0 9.372925 -0.025022186 -166.35784 -168.56208 -168.56208 -168.56208 -168.56208 2.3418848e-15 4.6837697e-15 4.6837697e-15 Loop time of 4.9e-07 on 1 procs for 0 steps with 4 atoms 204.1% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.9e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162 Ave neighs/atom = 40.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0062555465936341 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 9.05571 9.05571 9.05571 Created orthogonal box = (0 0 0) to (9.05571 9.05571 9.05571) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (9.05571 9.05571 9.05571) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 9.05571 0 9.05571 0 9.05571 -0.03509728 -231.2662 -234.33048 -234.33048 -234.33048 -234.33048 0 0 0 Loop time of 4.81e-07 on 1 procs for 0 steps with 4 atoms 207.9% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162 Ave neighs/atom = 40.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.00877432000876188 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 8.806417 8.806417 8.806417 Created orthogonal box = (0 0 0) to (8.806417 8.806417 8.806417) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.806417 8.806417 8.806417) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 8.806417 0 8.806417 0 8.806417 -0.044947231 -292.94551 -296.82704 -296.82704 -296.82704 -296.82704 5.6470706e-15 1.1294141e-14 0 Loop time of 4.81e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162 Ave neighs/atom = 40.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0112368078660967 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 8.601027 8.601027 8.601027 Created orthogonal box = (0 0 0) to (8.601027 8.601027 8.601027) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.601027 8.601027 8.601027) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 8.601027 0 8.601027 0 8.601027 -0.054416048 -349.73184 -354.36579 -354.36579 -354.36579 -354.36579 6.0613592e-15 -1.2122718e-14 -1.2122718e-14 Loop time of 4.81e-07 on 1 procs for 0 steps with 4 atoms 207.9% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 162 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162 Ave neighs/atom = 40.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0136040120251617 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 8.426369 8.426369 8.426369 Created orthogonal box = (0 0 0) to (8.426369 8.426369 8.426369) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.426369 8.426369 8.426369) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 8.426369 0 8.426369 0 8.426369 -0.063419976 -400.51925 -405.82613 -405.82613 -405.82613 -405.82613 0 -1.2892274e-14 -1.2892274e-14 Loop time of 6.31e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.31e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0158549940191255 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 8.274431 8.274431 8.274431 Created orthogonal box = (0 0 0) to (8.274431 8.274431 8.274431) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.274431 8.274431 8.274431) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 8.274431 0 8.274431 0 8.274431 -0.071912784 -444.52559 -450.41555 -450.41555 -450.41555 -450.41555 0 0 -2.7231184e-14 Loop time of 4.71e-07 on 1 procs for 0 steps with 4 atoms 212.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.71e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0179781959036911 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 8.139977 8.139977 8.139977 Created orthogonal box = (0 0 0) to (8.139977 8.139977 8.139977) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.139977 8.139977 8.139977) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 8.139977 0 8.139977 0 8.139977 -0.07986908 -481.17085 -487.54636 -487.54636 -487.54636 -487.54636 5.7058349e-15 1.2081071e-14 -1.2081071e-14 Loop time of 4.7e-07 on 1 procs for 0 steps with 4 atoms 212.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.7e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0199672699622866 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 8.019395 8.019395 8.019395 Created orthogonal box = (0 0 0) to (8.019395 8.019395 8.019395) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.019395 8.019395 8.019395) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 8.019395 0 8.019395 0 8.019395 -0.087276002 -510.02695 -516.78481 -516.78481 -516.78481 -516.78481 -6.7591892e-15 -3.0161206e-14 -3.4907358e-15 Loop time of 4.81e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 168 ave 168 max 168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0218190004044358 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.910089 7.910089 7.910089 Created orthogonal box = (0 0 0) to (7.910089 7.910089 7.910089) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.910089 7.910089 7.910089) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.910089 0 7.910089 0 7.910089 -0.094128746 -530.79574 -537.82878 -537.82878 -537.82878 -537.82878 -1.8267478e-14 -3.155763e-14 -7.4058244e-15 Loop time of 4.8e-07 on 1 procs for 0 steps with 4 atoms 208.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.8e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0235321865843907 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.810128 7.810128 7.810128 Created orthogonal box = (0 0 0) to (7.810128 7.810128 7.810128) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.810128 7.810128 7.810128) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.810128 0 7.810128 0 7.810128 -0.10042797 -543.24834 -550.44638 -550.44638 -550.44638 -550.44638 -2.3223326e-15 2.3949673e-14 -4.4191025e-14 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 216.9% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0251069914878265 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.718041 7.718041 7.718041 Created orthogonal box = (0 0 0) to (7.718041 7.718041 7.718041) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.718041 7.718041 7.718041) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.718041 0 7.718041 0 7.718041 -0.10617745 -547.20145 -554.45187 -554.45187 -554.45187 -554.45187 2.0234697e-15 -2.1170654e-14 2.117475e-14 Loop time of 4.91e-07 on 1 procs for 0 steps with 4 atoms 203.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.91e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0265443635353395 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.632676 7.632676 7.632676 Created orthogonal box = (0 0 0) to (7.632676 7.632676 7.632676) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.632676 7.632676 7.632676) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.632676 0 7.632676 0 7.632676 -0.11138337 -542.50622 -549.69443 -549.69443 -549.69443 -549.69443 3.3372346e-15 -2.8341084e-14 -3.23644e-14 Loop time of 4.71e-07 on 1 procs for 0 steps with 4 atoms 212.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.71e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210 ave 210 max 210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210 Ave neighs/atom = 52.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0278458424154653 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.553119 7.553119 7.553119 Created orthogonal box = (0 0 0) to (7.553119 7.553119 7.553119) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.553119 7.553119 7.553119) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.553119 0 7.553119 0 7.553119 -0.116053 -529.03953 -536.0493 -536.0493 -536.0493 -536.0493 -1.632747e-14 3.1081629e-14 3.5154756e-14 Loop time of 4.71e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.71e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0290132490414203 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.478629 7.478629 7.478629 Created orthogonal box = (0 0 0) to (7.478629 7.478629 7.478629) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.478629 7.478629 7.478629) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.478629 0 7.478629 0 7.478629 -0.12019453 -506.6979 -513.41165 -513.41165 -513.41165 -513.41165 -7.2935683e-15 3.5342291e-14 1.009844e-14 Loop time of 7.61e-07 on 1 procs for 0 steps with 4 atoms 394.2% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0300486313661688 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.4086 7.4086 7.4086 Created orthogonal box = (0 0 0) to (7.4086 7.4086 7.4086) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.4086 7.4086 7.4086) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.4086 0 7.4086 0 7.4086 -0.12381648 -475.39393 -481.6929 -481.6929 -481.6929 -481.6929 -5.4832023e-15 5.0923388e-14 2.9666718e-14 Loop time of 5.81e-07 on 1 procs for 0 steps with 4 atoms 172.1% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0309541190680045 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.342527 7.342527 7.342527 Created orthogonal box = (0 0 0) to (7.342527 7.342527 7.342527) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.342527 7.342527 7.342527) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.342527 0 7.342527 0 7.342527 -0.12692767 -435.05178 -440.81622 -440.81622 -440.81622 -440.81622 4.8714058e-15 -4.8714058e-15 2.9228435e-14 Loop time of 5.61e-07 on 1 procs for 0 steps with 4 atoms 178.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0317319185180543 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.279987 7.279987 7.279987 Created orthogonal box = (0 0 0) to (7.279987 7.279987 7.279987) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.279987 7.279987 7.279987) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.279987 0 7.279987 0 7.279987 -0.12953693 -385.6058 -390.71508 -390.71508 -390.71508 -390.71508 -1.6399797e-15 7.9265685e-15 1.1265099e-14 Loop time of 6.21e-07 on 1 procs for 0 steps with 4 atoms 161.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.21e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0323842314062468 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.220621 7.220621 7.220621 Created orthogonal box = (0 0 0) to (7.220621 7.220621 7.220621) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.220621 7.220621 7.220621) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.220621 0 7.220621 0 7.220621 -0.13165299 -326.99787 -331.3306 -331.3306 -331.3306 -331.3306 -3.3615272e-15 6.4429271e-15 -4.9222362e-15 Loop time of 6.01e-07 on 1 procs for 0 steps with 4 atoms 166.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.01e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.032913247573098 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.164123 7.164123 7.164123 Created orthogonal box = (0 0 0) to (7.164123 7.164123 7.164123) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.164123 7.164123 7.164123) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.164123 0 7.164123 0 7.164123 -0.13328446 -259.17739 -262.61149 -262.61149 -262.61149 -262.61149 8.1944892e-17 -4.8757211e-15 8.8705345e-15 Loop time of 5.91e-07 on 1 procs for 0 steps with 4 atoms 169.2% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.91e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0333211138732097 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.110228 7.110228 7.110228 Created orthogonal box = (0 0 0) to (7.110228 7.110228 7.110228) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.110228 7.110228 7.110228) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.110228 0 7.110228 0 7.110228 -0.13443977 -182.09747 -184.51026 -184.51026 -184.51026 -184.51026 1.0058695e-15 5.8675722e-16 -1.8021829e-15 Loop time of 6.01e-07 on 1 procs for 0 steps with 4 atoms 166.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.01e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0336099420097835 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.058707 7.058707 7.058707 Created orthogonal box = (0 0 0) to (7.058707 7.058707 7.058707) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.058707 7.058707 7.058707) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.058707 0 7.058707 0 7.058707 -0.13512713 -95.716882 -96.98513 -96.98513 -96.98513 -96.98513 -1.7134267e-15 -1.1394287e-14 -1.8590679e-14 Loop time of 6.11e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.11e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0337817816385508 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 7.00936 7.00936 7.00936 Created orthogonal box = (0 0 0) to (7.00936 7.00936 7.00936) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.00936 7.00936 7.00936) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 7.00936 0 7.00936 0 7.00936 -0.13535451 0.00036424111 0.00036906731 0.00036906731 0.00036906731 0.00036906731 -6.562014e-14 -4.1384435e-14 -3.9328337e-14 Loop time of 6.22e-07 on 1 procs for 0 steps with 4 atoms 321.5% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.22e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.033838627209476 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.959472 6.959472 6.959472 Created orthogonal box = (0 0 0) to (6.959472 6.959472 6.959472) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.959472 6.959472 6.959472) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.959472 0 6.959472 0 6.959472 -0.13510444 111.11212 112.58435 112.58435 112.58435 112.58435 -4.2906526e-14 -8.0717901e-14 -6.5343063e-14 Loop time of 6.01e-07 on 1 procs for 0 steps with 4 atoms 166.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.01e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306 Ave neighs/atom = 76.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0337761101824285 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.908061 6.908061 6.908061 Created orthogonal box = (0 0 0) to (6.908061 6.908061 6.908061) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.908061 6.908061 6.908061) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.908061 0 6.908061 0 6.908061 -0.13428339 242.36347 245.57479 245.57479 245.57479 245.57479 6.5807439e-15 1.6543259e-14 6.9920404e-15 Loop time of 8.01e-07 on 1 procs for 0 steps with 4 atoms 124.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.01e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0335708467706363 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.855033 6.855033 6.855033 Created orthogonal box = (0 0 0) to (6.855033 6.855033 6.855033) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.855033 6.855033 6.855033) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.855033 0 6.855033 0 6.855033 -0.13276838 397.53879 402.80618 402.80618 402.80618 402.80618 -9.7652381e-14 -8.7363337e-14 -1.1682742e-13 Loop time of 6.01e-07 on 1 procs for 0 steps with 4 atoms 332.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.01e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0331920939367975 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.800282 6.800282 6.800282 Created orthogonal box = (0 0 0) to (6.800282 6.800282 6.800282) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.800282 6.800282 6.800282) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.800282 0 6.800282 0 6.800282 -0.13040985 581.25584 588.95748 588.95748 588.95748 588.95748 3.2193597e-14 1.3471487e-13 3.7367567e-14 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0326024615159883 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.743693 6.743693 6.743693 Created orthogonal box = (0 0 0) to (6.743693 6.743693 6.743693) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.743693 6.743693 6.743693) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.743693 0 6.743693 0 6.743693 -0.12702527 799.16627 809.75522 809.75522 809.75522 809.75522 3.3010864e-14 -1.8175625e-13 -2.8304851e-13 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.031756318562466 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.685137 6.685137 6.685137 Created orthogonal box = (0 0 0) to (6.685137 6.685137 6.685137) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.685137 6.685137 6.685137) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.685137 0 6.685137 0 6.685137 -0.12239072 1058.2437 1072.2654 1072.2654 1072.2654 1072.2654 8.4714809e-15 -4.6189741e-14 -6.8881208e-14 Loop time of 4.7e-07 on 1 procs for 0 steps with 4 atoms 212.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.7e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0305976788779318 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.624474 6.624474 6.624474 Created orthogonal box = (0 0 0) to (6.624474 6.624474 6.624474) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.624474 6.624474 6.624474) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.624474 0 6.624474 0 6.624474 -0.11623044 1367.1257 1385.2401 1385.2401 1385.2401 1385.2401 7.7113377e-14 5.2611223e-13 3.8784712e-13 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0290576107410782 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.561545 6.561545 6.561545 Created orthogonal box = (0 0 0) to (6.561545 6.561545 6.561545) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.561545 6.561545 6.561545) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.561545 0 6.561545 0 6.561545 -0.10820255 1736.6192 1759.6294 1759.6294 1759.6294 1759.6294 1.7065249e-14 2.0691615e-13 1.6105329e-13 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 433.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0270506374398095 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.496175 6.496175 6.496175 Created orthogonal box = (0 0 0) to (6.496175 6.496175 6.496175) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.496175 6.496175 6.496175) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal 0 4 0 6.496175 0 6.496175 0 6.496175 -0.097881221 2180.3135 2209.2026 2209.2026 2209.2026 2209.2026 5.2756877e-14 -1.0859124e-13 6.176951e-14 Loop time of 4.81e-07 on 1 procs for 0 steps with 4 atoms 207.9% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0244703052620485 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.428168 6.428168 6.428168 Created orthogonal box = (0 0 0) to (6.428168 6.428168 6.428168) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.428168 6.428168 6.428168) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. 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) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 102 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 6.428168 0 6.428168 0 6.428168 -0.084732521 2715.4503 2751.43 2751.43 2751.43 2751.43 -1.8784934e-13 6.1981206e-13 -2.2233376e-13 Loop time of 5.81e-07 on 1 procs for 0 steps with 4 atoms 172.1% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338 ave 338 max 338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338 Ave neighs/atom = 84.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0211831303330509 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.3573 6.3573 6.3573 Created orthogonal box = (0 0 0) to (6.3573 6.3573 6.3573) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.3573 6.3573 6.3573) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 105 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 6.3573 0 6.3573 0 6.3573 -0.068081337 3364.1346 3408.7093 3408.7093 3408.7093 3408.7093 -7.5053827e-15 -4.4000306e-13 -5.2256227e-13 Loop time of 5.91e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.91e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 530 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530 Ave neighs/atom = 132.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0170203343478383 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.283321 6.283321 6.283321 Created orthogonal box = (0 0 0) to (6.283321 6.283321 6.283321) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.283321 6.283321 6.283321) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 108 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 6.283321 0 6.283321 0 6.283321 -0.047068977 4154.916 4209.9687 4209.9687 4209.9687 4209.9687 -3.9276024e-14 2.9068718e-13 -2.8844739e-13 Loop time of 4.71e-07 on 1 procs for 0 steps with 4 atoms 212.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.71e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 530 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530 Ave neighs/atom = 132.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.0117672442519861 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.205945 6.205945 6.205945 Created orthogonal box = (0 0 0) to (6.205945 6.205945 6.205945) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.205945 6.205945 6.205945) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 111 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 6.205945 0 6.205945 0 6.205945 -0.020592675 5125.0825 5192.9899 5192.9899 5192.9899 5192.9899 1.6299536e-13 -4.0342633e-13 -1.5483033e-13 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 530 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530 Ave neighs/atom = 132.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: -0.00514816883443482 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.124845 6.124845 6.124845 Created orthogonal box = (0 0 0) to (6.124845 6.124845 6.124845) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.124845 6.124845 6.124845) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 114 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 6.124845 0 6.124845 0 6.124845 0.012776391 6323.8759 6407.6673 6407.6673 6407.6673 6407.6673 3.5637335e-13 6.6779535e-14 -1.9811952e-13 Loop time of 4.61e-07 on 1 procs for 0 steps with 4 atoms 216.9% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 530 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530 Ave neighs/atom = 132.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.00319409775674715 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 6.039644 6.039644 6.039644 Created orthogonal box = (0 0 0) to (6.039644 6.039644 6.039644) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.039644 6.039644 6.039644) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 2 2 2 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.45 | 16.45 | 16.45 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 117 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 6.039644 0 6.039644 0 6.039644 0.054909029 7817.2047 7920.7827 7920.7827 7920.7827 7920.7827 -2.0739653e-13 1.6528981e-13 4.8915082e-13 Loop time of 4.71e-07 on 1 procs for 0 steps with 4 atoms 212.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 4.71e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 360 ave 360 max 360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 530 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530 Ave neighs/atom = 132.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.0137272573307186 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.949906 5.949906 5.949906 Created orthogonal box = (0 0 0) to (5.949906 5.949906 5.949906) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.949906 5.949906 5.949906) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 120 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.949906 0 5.949906 0 5.949906 0.10828216 9694.5138 9822.9661 9822.9661 9822.9661 9822.9661 -2.6940339e-13 1.7815689e-12 1.1487261e-12 Loop time of 1.152e-06 on 1 procs for 0 steps with 4 atoms 260.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.152e-06 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 554 ave 554 max 554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554 Ave neighs/atom = 138.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.027070539873561 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.85512 5.85512 5.85512 Created orthogonal box = (0 0 0) to (5.85512 5.85512 5.85512) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.85512 5.85512 5.85512) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 123 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.85512 0 5.85512 0 5.85512 0.17621921 12079.185 12239.234 12239.234 12239.234 12239.234 1.1200865e-12 1.2250307e-12 -7.190169e-14 Loop time of 6.51e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.51e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 554 ave 554 max 554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554 Ave neighs/atom = 138.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.0440548033930667 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.754684 5.754684 5.754684 Created orthogonal box = (0 0 0) to (5.754684 5.754684 5.754684) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.754684 5.754684 5.754684) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 126 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.754684 0 5.754684 0 5.754684 0.26324291 15144.414 15345.077 15345.077 15345.077 15345.077 1.2958709e-13 4.2558006e-12 4.3785694e-12 Loop time of 6.11e-07 on 1 procs for 0 steps with 4 atoms 163.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.11e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 554 ave 554 max 554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 554 Ave neighs/atom = 138.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.065810726748892 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.647881 5.647881 5.647881 Created orthogonal box = (0 0 0) to (5.647881 5.647881 5.647881) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.647881 5.647881 5.647881) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 129 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.647881 0 5.647881 0 5.647881 0.3756095 19138.235 19391.816 19391.816 19391.816 19391.816 -8.4877078e-15 -1.2538393e-12 -1.1576732e-12 Loop time of 7.01e-07 on 1 procs for 0 steps with 4 atoms 142.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.01e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 698 ave 698 max 698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 698 Ave neighs/atom = 174.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.0939023744513842 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.53385 5.53385 5.53385 Created orthogonal box = (0 0 0) to (5.53385 5.53385 5.53385) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.53385 5.53385 5.53385) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 132 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.53385 0 5.53385 0 5.53385 0.52213091 24423.857 24747.473 24747.473 24747.473 24747.473 -2.0839798e-12 -2.5837722e-12 2.9009653e-12 Loop time of 5.61e-07 on 1 procs for 0 steps with 4 atoms 178.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 698 ave 698 max 698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 698 Ave neighs/atom = 174.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.130532728265848 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.411539 5.411539 5.411539 Created orthogonal box = (0 0 0) to (5.411539 5.411539 5.411539) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.411539 5.411539 5.411539) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 135 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.411539 0 5.411539 0 5.411539 0.71548977 31547.503 31965.508 31965.508 31965.508 31965.508 -7.1488544e-14 1.5856768e-12 1.5765506e-12 Loop time of 5.21e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.21e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 698 ave 698 max 698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 698 Ave neighs/atom = 174.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.178872441604476 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.279653 5.279653 5.279653 Created orthogonal box = (0 0 0) to (5.279653 5.279653 5.279653) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.279653 5.279653 5.279653) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 138 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.279653 0 5.279653 0 5.279653 0.97437437 41355.221 41903.178 41903.178 41903.178 41903.178 -2.8658987e-12 3.4296948e-12 4.6139849e-12 Loop time of 6.61e-07 on 1 procs for 0 steps with 4 atoms 151.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.61e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 794 ave 794 max 794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 794 Ave neighs/atom = 198.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.243593591284189 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 5.136564 5.136564 5.136564 Created orthogonal box = (0 0 0) to (5.136564 5.136564 5.136564) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.136564 5.136564 5.136564) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 141 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.136564 0 5.136564 0 5.136564 1.3271237 55203.767 55935.217 55935.217 55935.217 55935.217 1.7541662e-12 3.9749697e-13 1.8293337e-12 Loop time of 5.21e-07 on 1 procs for 0 steps with 4 atoms 191.9% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.21e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 794 ave 794 max 794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 794 Ave neighs/atom = 198.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.331780928188243 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.98019 4.98019 4.98019 Created orthogonal box = (0 0 0) to (4.98019 4.98019 4.98019) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.98019 4.98019 4.98019) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 144 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.98019 0 4.98019 0 4.98019 1.8181467 75360.128 76358.649 76358.649 76358.649 76358.649 -1.7320875e-13 -6.8048887e-12 -6.6261152e-12 Loop time of 5.11e-07 on 1 procs for 0 steps with 4 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 5.11e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 890 ave 890 max 890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 890 Ave neighs/atom = 222.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.454536680200993 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.80781 4.80781 4.80781 Created orthogonal box = (0 0 0) to (4.80781 4.80781 4.80781) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.80781 4.80781 4.80781) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 23.33 | 23.33 | 23.33 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 147 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.80781 0 4.80781 0 4.80781 2.519842 105807.55 107209.5 107209.5 107209.5 107209.5 -8.2981106e-12 -6.7923518e-12 -2.2394223e-12 Loop time of 7.32e-07 on 1 procs for 0 steps with 4 atoms 136.6% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.32e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 662 ave 662 max 662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 986 ave 986 max 986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 986 Ave neighs/atom = 246.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.629960503377895 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.615769 4.615769 4.615769 Created orthogonal box = (0 0 0) to (4.615769 4.615769 4.615769) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.615769 4.615769 4.615769) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 33.91 | 33.91 | 33.91 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 150 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.615769 0 4.615769 0 4.615769 3.556102 153989.42 156029.78 156029.78 156029.78 156029.78 7.7793443e-13 -1.9775217e-11 -3.8478669e-11 Loop time of 8.02e-07 on 1 procs for 0 steps with 4 atoms 124.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.02e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1094 ave 1094 max 1094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1274 ave 1274 max 1274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1274 Ave neighs/atom = 318.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.889025510261217 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.398998 4.398998 4.398998 Created orthogonal box = (0 0 0) to (4.398998 4.398998 4.398998) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.398998 4.398998 4.398998) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 33.91 | 33.91 | 33.91 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 153 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.398998 0 4.398998 0 4.398998 5.1521024 234929.71 238042.53 238042.53 238042.53 238042.53 1.2841967e-11 4.7589706e-11 4.7490587e-11 Loop time of 9.42e-07 on 1 procs for 0 steps with 4 atoms 212.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.42e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1094 ave 1094 max 1094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1274 ave 1274 max 1274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1274 Ave neighs/atom = 318.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 1.28802560111552 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.150173 4.150173 4.150173 Created orthogonal box = (0 0 0) to (4.150173 4.150173 4.150173) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.150173 4.150173 4.150173) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 33.91 | 33.91 | 33.91 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 156 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.150173 0 4.150173 0 4.150173 7.7499913 382151.77 387215.28 387215.28 387215.28 387215.28 -2.2478914e-11 -4.6802453e-11 -7.8278643e-12 Loop time of 1.193e-06 on 1 procs for 0 steps with 4 atoms 167.6% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.193e-06 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1094 ave 1094 max 1094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1514 ave 1514 max 1514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1514 Ave neighs/atom = 378.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 1.93749781996917 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.858142 3.858142 3.858142 Created orthogonal box = (0 0 0) to (3.858142 3.858142 3.858142) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (3.858142 3.858142 3.858142) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 48.1 | 48.1 | 48.1 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 159 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 3.858142 0 3.858142 0 3.858142 12.312269 681363.34 690391.41 690391.41 690391.41 690391.41 -5.4168323e-11 -1.0637003e-10 -1.0991384e-10 Loop time of 1.123e-06 on 1 procs for 0 steps with 4 atoms 178.1% 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 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.123e-06 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1684 ave 1684 max 1684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2114 ave 2114 max 2114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2114 Ave neighs/atom = 528.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 3.07806724348855 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task WARNING: 'kim_' has been renamed to 'kim '. Please update your input. # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.50468 3.50468 3.50468 Created orthogonal box = (0 0 0) to (3.50468 3.50468 3.50468) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (3.50468 3.50468 3.50468) create_atoms CPU = 0.000 seconds WARNING: 'kim_' has been renamed to 'kim '. Please update your input. Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 1 1 1 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 48.86 | 48.86 | 48.86 Mbytes Step Atoms v_xlo_metal v_xhi_metal v_ylo_metal v_yhi_metal v_zlo_metal v_zhi_metal v_pe_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_pxy_metal v_pxz_metal v_pyz_metal WARNING: Too many warnings: 162 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 3.50468 0 3.50468 0 3.50468 21.261975 1399000.2 1417536.9 1417536.9 1417536.9 1417536.9 -7.3718431e-12 -4.1715707e-12 1.024192e-10 Loop time of 8.22e-07 on 1 procs for 0 steps with 4 atoms 243.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.22e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1684 ave 1684 max 1684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2690 ave 2690 max 2690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2690 Ave neighs/atom = 672.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 5.31549386928462 eV/atom OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Total wall time: 0:00:00