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 = 9.69326 9.69326 9.69326 Created orthogonal box = (0 0 0) to (9.69326 9.69326 9.69326) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (9.69326 9.69326 9.69326) 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 9.69326 0 9.69326 0 9.69326 -0.43804065 -26.244198 -26.591934 -26.591934 -26.591934 -26.591934 0 -1.0586475e-15 -2.117295e-15 Loop time of 1.192e-06 on 1 procs for 0 steps with 4 atoms 83.9% 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 | | 1.192e-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: 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: -0.000857866580930247 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 = 9.043775 9.043775 9.043775 Created orthogonal box = (0 0 0) to (9.043775 9.043775 9.043775) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (9.043775 9.043775 9.043775) 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 9.043775 0 9.043775 0 9.043775 -0.44252077 -61.776824 -62.595367 -62.595367 -62.595367 -62.595367 0 0 0 Loop time of 4.91e-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 | | 4.91e-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: -0.00197789498677275 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 = 8.64125 8.64125 8.64125 Created orthogonal box = (0 0 0) to (8.64125 8.64125 8.64125) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.64125 8.64125 8.64125) 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 8.64125 0 8.64125 0 8.64125 -0.44726327 -100.18993 -101.51745 -101.51745 -101.51745 -101.51745 -1.4942775e-15 0 0 Loop time of 5.01e-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 | | 5.01e-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: -0.00316352132099651 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 = 8.348795 8.348795 8.348795 Created orthogonal box = (0 0 0) to (8.348795 8.348795 8.348795) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.348795 8.348795 8.348795) 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 8.348795 0 8.348795 0 8.348795 -0.45200471 -138.64044 -140.47742 -140.47742 -140.47742 -140.47742 0 0 -6.6274974e-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: -0.0043488806375965 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 = 8.11896 8.11896 8.11896 Created orthogonal box = (0 0 0) to (8.11896 8.11896 8.11896) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (8.11896 8.11896 8.11896) 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 8.11896 0 8.11896 0 8.11896 -0.45663014 -175.56025 -177.88642 -177.88642 -177.88642 -177.88642 -3.8945136e-15 -1.0318892e-14 -9.4987714e-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: -0.00550523836389526 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 = 7.929602 7.929602 7.929602 Created orthogonal box = (0 0 0) to (7.929602 7.929602 7.929602) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.929602 7.929602 7.929602) 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 7.929602 0 7.929602 0 7.929602 -0.46108005 -209.94278 -212.72452 -212.72452 -212.72452 -212.72452 9.2817606e-16 1.3846129e-14 1.3226848e-14 Loop time of 4.9e-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 | | 4.9e-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: -0.00661771568693001 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 = 7.768576 7.768576 7.768576 Created orthogonal box = (0 0 0) to (7.768576 7.768576 7.768576) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.768576 7.768576 7.768576) 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 7.768576 0 7.768576 0 7.768576 -0.46532108 -241.09456 -244.28906 -244.28906 -244.28906 -244.28906 -2.5365306e-15 -3.7121111e-14 -3.4857714e-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: 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: -0.0076779735489375 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 = 7.628498 7.628498 7.628498 Created orthogonal box = (0 0 0) to (7.628498 7.628498 7.628498) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.628498 7.628498 7.628498) 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 7.628498 0 7.628498 0 7.628498 -0.46933377 -268.49976 -272.05738 -272.05738 -272.05738 -272.05738 1.9205798e-15 1.5142462e-14 4.4061452e-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: 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: -0.00868114667372151 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 = 7.504538 7.504538 7.504538 Created orthogonal box = (0 0 0) to (7.504538 7.504538 7.504538) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.504538 7.504538 7.504538) 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 7.504538 0 7.504538 0 7.504538 -0.47310673 -291.75634 -295.62211 -295.62211 -295.62211 -295.62211 2.0941943e-16 2.6040415e-14 -5.5111843e-15 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: 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: -0.009624386120723 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 = 7.393368 7.393368 7.393368 Created orthogonal box = (0 0 0) to (7.393368 7.393368 7.393368) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.393368 7.393368 7.393368) 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 7.393368 0 7.393368 0 7.393368 -0.47663326 -310.53871 -314.65335 -314.65335 -314.65335 -314.65335 -6.2534049e-15 2.7289915e-14 1.2425264e-14 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: 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: -0.0105060184347325 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 = 7.292594 7.292594 7.292594 Created orthogonal box = (0 0 0) to (7.292594 7.292594 7.292594) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.292594 7.292594 7.292594) 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 7.292594 0 7.292594 0 7.292594 -0.47990977 -324.57693 -328.87758 -328.87758 -328.87758 -328.87758 -1.8548477e-15 1.8499921e-15 1.9012189e-14 Loop time of 4.91e-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 | | 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: 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: -0.0113251452064138 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 = 7.200436 7.200436 7.200436 Created orthogonal box = (0 0 0) to (7.200436 7.200436 7.200436) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.200436 7.200436 7.200436) 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 7.200436 0 7.200436 0 7.200436 -0.48293468 -333.64204 -338.0628 -338.0628 -338.0628 -338.0628 -3.218365e-15 2.6811301e-14 -3.5790439e-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: 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: -0.0120813728490235 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 = 7.115536 7.115536 7.115536 Created orthogonal box = (0 0 0) to (7.115536 7.115536 7.115536) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.115536 7.115536 7.115536) 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 7.115536 0 7.115536 0 7.115536 -0.4857077 -337.53598 -342.00833 -342.00833 -342.00833 -342.00833 -1.2545252e-15 1.0454377e-15 -1.977968e-14 Loop time of 5.01e-07 on 1 procs for 0 steps with 4 atoms 199.6% 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 | | 5.01e-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: -0.0127746289022555 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 = 7.036834 7.036834 7.036834 Created orthogonal box = (0 0 0) to (7.036834 7.036834 7.036834) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (7.036834 7.036834 7.036834) 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 7.036834 0 7.036834 0 7.036834 -0.48822944 -336.08504 -340.53816 -340.53816 -340.53816 -340.53816 2.7455085e-14 1.0290252e-14 1.1846761e-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: -0.0134050619445635 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 = 6.963486 6.963486 6.963486 Created orthogonal box = (0 0 0) to (6.963486 6.963486 6.963486) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.963486 6.963486 6.963486) 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 6.963486 0 6.963486 0 6.963486 -0.4905011 -329.13556 -333.49661 -333.49661 -333.49661 -333.49661 8.2541546e-15 3.7110233e-14 2.8549336e-14 Loop time of 5.01e-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 | | 5.01e-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: -0.013972977834481 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 = 6.894811 6.894811 6.894811 Created orthogonal box = (0 0 0) to (6.894811 6.894811 6.894811) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.894811 6.894811 6.894811) 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 6.894811 0 6.894811 0 6.894811 -0.49252429 -316.55076 -320.74506 -320.74506 -320.74506 -320.74506 2.987633e-15 -3.385218e-14 -4.8434128e-14 Loop time of 5.01e-07 on 1 procs for 0 steps with 4 atoms 199.6% 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 | | 5.01e-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: -0.0144787756926533 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 = 6.830248 6.830248 6.830248 Created orthogonal box = (0 0 0) to (6.830248 6.830248 6.830248) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.830248 6.830248 6.830248) 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 6.830248 0 6.830248 0 6.830248 -0.49430098 -298.20648 -302.15772 -302.15772 -302.15772 -302.15772 9.3140336e-15 2.6405522e-14 6.8436871e-15 Loop time of 5.01e-07 on 1 procs for 0 steps with 4 atoms 199.6% 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 | | 5.01e-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: -0.0149229469913303 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 = 6.769332 6.769332 6.769332 Created orthogonal box = (0 0 0) to (6.769332 6.769332 6.769332) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.769332 6.769332 6.769332) 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 6.769332 0 6.769332 0 6.769332 -0.49583328 -273.98926 -277.61961 -277.61961 -277.61961 -277.61961 -3.1083043e-15 -2.979601e-14 -2.3008737e-14 Loop time of 4.8e-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 | | 4.8e-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: 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: -0.015306021979081 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 = 6.711673 6.711673 6.711673 Created orthogonal box = (0 0 0) to (6.711673 6.711673 6.711673) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.711673 6.711673 6.711673) 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 6.711673 0 6.711673 0 6.711673 -0.49712342 -243.79472 -247.025 -247.025 -247.025 -247.025 -4.0860387e-15 -2.6559252e-14 -1.631924e-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: 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: -0.0156285586959003 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 = 6.656941 6.656941 6.656941 Created orthogonal box = (0 0 0) to (6.656941 6.656941 6.656941) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.656941 6.656941 6.656941) 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 6.656941 0 6.656941 0 6.656941 -0.49817371 -207.52665 -210.27638 -210.27638 -210.27638 -210.27638 -3.0641366e-16 1.5065338e-14 6.1538076e-15 Loop time of 4.72e-07 on 1 procs for 0 steps with 4 atoms 211.9% 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 | | 4.72e-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: -0.0158911313852517 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 = 6.604853 6.604853 6.604853 Created orthogonal box = (0 0 0) to (6.604853 6.604853 6.604853) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.604853 6.604853 6.604853) 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 6.604853 0 6.604853 0 6.604853 -0.49898651 -165.09495 -167.28246 -167.28246 -167.28246 -167.28246 3.0326306e-15 7.68615e-15 4.7319495e-15 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: 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: -0.0160943295015903 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 = 6.555165 6.555165 6.555165 Created orthogonal box = (0 0 0) to (6.555165 6.555165 6.555165) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.555165 6.555165 6.555165) 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 6.555165 0 6.555165 0 6.555165 -0.49956417 -116.41495 -117.95745 -117.95745 -117.95745 -117.95745 3.209086e-16 -6.7390806e-15 -6.7390806e-15 Loop time of 4.91e-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 | | 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: 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: -0.0162387449663258 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 = 6.507666 6.507666 6.507666 Created orthogonal box = (0 0 0) to (6.507666 6.507666 6.507666) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.507666 6.507666 6.507666) 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 6.507666 0 6.507666 0 6.507666 -0.49990905 -61.407651 -62.221303 -62.221303 -62.221303 -62.221303 0 -1.6399344e-16 4.1818328e-15 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: -0.0163249655121283 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 = 6.46217 6.46217 6.46217 Created orthogonal box = (0 0 0) to (6.46217 6.46217 6.46217) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.46217 6.46217 6.46217) 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 6.46217 0 6.46217 0 6.46217 -0.50002349 0.0038768957 0.0039282645 0.0039282645 0.0039282645 0.0039282645 -3.7962497e-15 5.5827201e-15 -1.674816e-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: -0.0163535758019658 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 = 6.416176 6.416176 6.416176 Created orthogonal box = (0 0 0) to (6.416176 6.416176 6.416176) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.416176 6.416176 6.416176) 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 6.416176 0 6.416176 0 6.416176 -0.49989702 71.794994 72.746278 72.746278 72.746278 72.746278 -1.4829467e-14 -2.0533108e-15 -3.194039e-15 Loop time of 5.01e-07 on 1 procs for 0 steps with 4 atoms 199.6% 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 | | 5.01e-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: -0.01632195713428 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 = 6.368779 6.368779 6.368779 Created orthogonal box = (0 0 0) to (6.368779 6.368779 6.368779) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.368779 6.368779 6.368779) 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 6.368779 0 6.368779 0 6.368779 -0.49948043 157.18726 159.26999 159.26999 159.26999 159.26999 1.2130419e-14 1.3530082e-14 5.1321002e-15 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: 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: -0.0162178112167373 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 = 6.319891 6.319891 6.319891 Created orthogonal box = (0 0 0) to (6.319891 6.319891 6.319891) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.319891 6.319891 6.319891) 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 6.319891 0 6.319891 0 6.319891 -0.49870884 258.849 262.27875 262.27875 262.27875 262.27875 1.5084693e-14 -4.5512385e-14 -2.5220091e-14 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: 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: -0.0160249139343805 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 = 6.269414 6.269414 6.269414 Created orthogonal box = (0 0 0) to (6.269414 6.269414 6.269414) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.269414 6.269414 6.269414) 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 6.269414 0 6.269414 0 6.269414 -0.49750278 380.05592 385.09166 385.09166 385.09166 385.09166 7.9044008e-15 1.9669937e-14 -2.0496704e-14 Loop time of 5.01e-07 on 1 procs for 0 steps with 4 atoms 199.6% 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 | | 5.01e-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: 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: -0.01572339937082 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 = 6.217243 6.217243 6.217243 Created orthogonal box = (0 0 0) to (6.217243 6.217243 6.217243) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.217243 6.217243 6.217243) 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 6.217243 0 6.217243 0 6.217243 -0.49576466 524.84032 531.79445 531.79445 531.79445 531.79445 -3.4230659e-14 -6.4724254e-14 -7.3751389e-14 Loop time of 5.01e-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 | | 5.01e-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: 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: -0.0152888680203605 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 = 6.163259 6.163259 6.163259 Created orthogonal box = (0 0 0) to (6.163259 6.163259 6.163259) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.163259 6.163259 6.163259) 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 6.163259 0 6.163259 0 6.163259 -0.49337388 698.21461 707.46595 707.46595 707.46595 707.46595 1.4330168e-14 1.8297445e-14 -6.625856e-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: 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: -0.0146911723173487 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 = 6.107331 6.107331 6.107331 Created orthogonal box = (0 0 0) to (6.107331 6.107331 6.107331) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.107331 6.107331 6.107331) 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 6.107331 0 6.107331 0 6.107331 -0.49018078 906.44002 918.45035 918.45035 918.45035 918.45035 -9.4356306e-15 6.6371431e-14 4.0579063e-14 Loop time of 5.01e-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 | | 5.01e-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: 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: -0.013892898717315 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 = 6.049315 6.049315 6.049315 Created orthogonal box = (0 0 0) to (6.049315 6.049315 6.049315) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (6.049315 6.049315 6.049315) 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 6.049315 0 6.049315 0 6.049315 -0.48599873 1157.3892 1172.7246 1172.7246 1172.7246 1172.7246 -5.2971534e-15 1.1067504e-14 6.7825682e-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: 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: -0.0128473851192915 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 = 5.989048 5.989048 5.989048 Created orthogonal box = (0 0 0) to (5.989048 5.989048 5.989048) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.989048 5.989048 5.989048) 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 = 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 0 4 0 5.989048 0 5.989048 0 5.989048 -0.48059322 1461.0563 1480.4152 1480.4152 1480.4152 1480.4152 7.4431588e-15 -1.3707466e-13 -1.607788e-13 Loop time of 4.7e-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 | | 4.7e-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: -0.0114960085093173 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 = 5.92635 5.92635 5.92635 Created orthogonal box = (0 0 0) to (5.92635 5.92635 5.92635) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.92635 5.92635 5.92635) 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 = 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: 102 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.92635 0 5.92635 0 5.92635 -0.47366814 1830.2091 1854.4594 1854.4594 1854.4594 1854.4594 6.6679024e-14 1.2767847e-13 1.821083e-13 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: 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: -0.00976473761839926 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 = 5.861014 5.861014 5.861014 Created orthogonal box = (0 0 0) to (5.861014 5.861014 5.861014) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.861014 5.861014 5.861014) 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: 105 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.861014 0 5.861014 0 5.861014 -0.46484595 2281.3546 2311.5825 2311.5825 2311.5825 2311.5825 4.3688886e-14 3.0135475e-13 6.7592846e-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: 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: -0.00755919040847826 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 = 5.79281 5.79281 5.79281 Created orthogonal box = (0 0 0) to (5.79281 5.79281 5.79281) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.79281 5.79281 5.79281) 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: 108 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.79281 0 5.79281 0 5.79281 -0.4536426 2835.9854 2873.5622 2873.5622 2873.5622 2873.5622 1.2705249e-13 4.3505771e-13 2.9988446e-13 Loop time of 4.91e-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 | | 4.91e-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: -0.00475835240351501 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 = 5.721475 5.721475 5.721475 Created orthogonal box = (0 0 0) to (5.721475 5.721475 5.721475) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.721475 5.721475 5.721475) 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: 111 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.721475 0 5.721475 0 5.721475 -0.43943114 3522.436 3569.1083 3569.1083 3569.1083 3569.1083 4.2128987e-15 5.4651049e-13 3.4929857e-13 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: 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: -0.00120548826058825 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 = 5.646706 5.646706 5.646706 Created orthogonal box = (0 0 0) to (5.646706 5.646706 5.646706) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.646706 5.646706 5.646706) 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: 114 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.646706 0 5.646706 0 5.646706 -0.42139127 4378.5226 4436.538 4436.538 4436.538 4436.538 2.0118596e-14 4.503595e-13 9.0588593e-13 Loop time of 5.01e-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 | | 5.01e-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: 0.00330447894250524 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 = 5.568157 5.568157 5.568157 Created orthogonal box = (0 0 0) to (5.568157 5.568157 5.568157) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.568157 5.568157 5.568157) 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: 117 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 5.568157 0 5.568157 0 5.568157 -0.39843931 5455.3237 5527.6067 5527.6067 5527.6067 5527.6067 -9.8894537e-14 -9.4814838e-14 5.2796113e-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: 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: 0.00904246918912524 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 = 5.485425 5.485425 5.485425 Created orthogonal box = (0 0 0) to (5.485425 5.485425 5.485425) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.485425 5.485425 5.485425) 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 5.485425 0 5.485425 0 5.485425 -0.36912505 6822.9142 6913.3178 6913.3178 6913.3178 6913.3178 5.9625161e-14 5.4974718e-13 1.1737919e-13 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: 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: 0.016371033315746 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 = 5.398038 5.398038 5.398038 Created orthogonal box = (0 0 0) to (5.398038 5.398038 5.398038) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.398038 5.398038 5.398038) 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 5.398038 0 5.398038 0 5.398038 -0.33148168 8579.0038 8692.6756 8692.6756 8692.6756 8692.6756 -1.187428e-13 -3.8091561e-13 -6.7744936e-13 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: 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: 0.0257818756218645 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 = 5.305443 5.305443 5.305443 Created orthogonal box = (0 0 0) to (5.305443 5.305443 5.305443) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.305443 5.305443 5.305443) 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 5.305443 0 5.305443 0 5.305443 -0.28280374 10862.231 11006.156 11006.156 11006.156 11006.156 7.2323958e-13 5.1546777e-13 -9.3362592e-13 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: 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: 0.0379513616693612 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 = 5.206978 5.206978 5.206978 Created orthogonal box = (0 0 0) to (5.206978 5.206978 5.206978) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.206978 5.206978 5.206978) 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 5.206978 0 5.206978 0 5.206978 -0.21930237 13873.545 14057.369 14057.369 14057.369 14057.369 7.7715024e-13 -1.0155782e-12 2.0763489e-15 Loop time of 5.01e-07 on 1 procs for 0 steps with 4 atoms 199.6% 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 | | 5.01e-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: 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: 0.0538267034500337 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 = 5.101848 5.101848 5.101848 Created orthogonal box = (0 0 0) to (5.101848 5.101848 5.101848) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (5.101848 5.101848 5.101848) 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 5.101848 0 5.101848 0 5.101848 -0.13557268 17910.86 18148.179 18148.179 18148.179 18148.179 -1.4098758e-13 -2.5107916e-12 -1.082781e-13 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: 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: 0.074759125960843 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 = 4.989086 4.989086 4.989086 Created orthogonal box = (0 0 0) to (4.989086 4.989086 4.989086) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.989086 4.989086 4.989086) 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 4.989086 0 4.989086 0 4.989086 -0.023735081 23427.763 23738.181 23738.181 23738.181 23738.181 5.4816437e-13 3.1188823e-12 3.9026442e-12 Loop time of 4.91e-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 | | 4.91e-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: 0.102718526701746 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 = 4.867496 4.867496 4.867496 Created orthogonal box = (0 0 0) to (4.867496 4.867496 4.867496) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.867496 4.867496 4.867496) 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 4.867496 0 4.867496 0 4.867496 0.12799294 31136.548 31549.107 31549.107 31549.107 31549.107 2.102458e-12 3.3324772e-12 6.5736927e-12 Loop time of 4.92e-07 on 1 procs for 0 steps with 4 atoms 203.3% 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 | | 4.92e-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: 0.140650532030862 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 = 4.735578 4.735578 4.735578 Created orthogonal box = (0 0 0) to (4.735578 4.735578 4.735578) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.735578 4.735578 4.735578) 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) = 33.14 | 33.14 | 33.14 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 4.735578 0 4.735578 0 4.735578 0.33774813 42196.402 42755.505 42755.505 42755.505 42755.505 -1.0691861e-12 1.1362685e-12 -1.106194e-12 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: 1094 ave 1094 max 1094 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: 0.193089329451282 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 = 4.591412 4.591412 4.591412 Created orthogonal box = (0 0 0) to (4.591412 4.591412 4.591412) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.591412 4.591412 4.591412) 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: 144 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.591412 0 4.591412 0 4.591412 0.63443005 58575.885 59352.015 59352.015 59352.015 59352.015 1.0190916e-12 7.2642747e-12 6.0019345e-12 Loop time of 5.01e-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 | | 5.01e-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: 0.267259808366442 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 = 4.432489 4.432489 4.432489 Created orthogonal box = (0 0 0) to (4.432489 4.432489 4.432489) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.432489 4.432489 4.432489) 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: 147 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 4.432489 0 4.432489 0 4.432489 1.0660109 83792.391 84902.64 84902.64 84902.64 84902.64 9.6362444e-13 -2.8955659e-12 -1.3453472e-11 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: 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: 0.375155026421241 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 = 4.25544 4.25544 4.25544 Created orthogonal box = (0 0 0) to (4.25544 4.25544 4.25544) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.25544 4.25544 4.25544) 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 4.25544 0 4.25544 0 4.25544 1.7162028 124536.71 126186.82 126186.82 126186.82 126186.82 3.0868179e-12 -2.0722368e-11 -2.355636e-11 Loop time of 6.01e-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 | | 6.01e-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: 1466 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1466 Ave neighs/atom = 366.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.537703003798494 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 = 4.055591 4.055591 4.055591 Created orthogonal box = (0 0 0) to (4.055591 4.055591 4.055591) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (4.055591 4.055591 4.055591) 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 4.055591 0 4.055591 0 4.055591 2.7404456 194576.8 197154.94 197154.94 197154.94 197154.94 8.3304739e-13 -2.3513868e-11 -2.0049275e-11 Loop time of 4.91e-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 | | 4.91e-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: 1706 ave 1706 max 1706 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1706 Ave neighs/atom = 426.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 0.793763688975659 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 = 3.826191 3.826191 3.826191 Created orthogonal box = (0 0 0) to (3.826191 3.826191 3.826191) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (3.826191 3.826191 3.826191) 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: 156 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 3.826191 0 3.826191 0 3.826191 4.4512134 325279.81 329589.76 329589.76 329589.76 329589.76 1.2635195e-11 4.8341315e-11 8.2356368e-11 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: 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: 1.22145564970253 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 = 3.556958 3.556958 3.556958 Created orthogonal box = (0 0 0) to (3.556958 3.556958 3.556958) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (3.556958 3.556958 3.556958) 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: 159 vs 100. All future warnings will be suppressed (src/thermo.cpp:465) 0 4 0 3.556958 0 3.556958 0 3.556958 7.2357263 423268.86 428877.17 428877.17 428877.17 428877.17 1.7440777e-11 1.2929307e-10 -7.9232603e-12 Loop time of 9.01e-07 on 1 procs for 0 steps with 4 atoms 111.0% 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 | | 9.01e-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: 2498 ave 2498 max 2498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2498 Ave neighs/atom = 624.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 1.91758386119797 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 = 3.23109 3.23109 3.23109 Created orthogonal box = (0 0 0) to (3.23109 3.23109 3.23109) 1 by 1 by 1 MPI processor grid Created 4 atoms using lattice units in orthogonal box = (0 0 0) to (3.23109 3.23109 3.23109) 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) = 68.58 | 68.58 | 68.58 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 3.23109 0 3.23109 0 3.23109 9.915843 398076.21 403350.72 403350.72 403350.72 403350.72 -2.1342463e-11 -6.7514377e-11 -9.0305447e-11 Loop time of 8.81e-07 on 1 procs for 0 steps with 4 atoms 227.0% 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 | | 8.81e-07 | | |100.00 Nlocal: 4 ave 4 max 4 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2452 ave 2452 max 2452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3538 ave 3538 max 3538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3538 Ave neighs/atom = 884.5 Neighbor list builds = 0 Dangerous builds = 0 Cohesive energy: 2.58761305525443 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