diff --git a/examples/snap/log.15Jun22.grid.snap.g++.1 b/examples/snap/log.15Jun22.grid.snap.g++.1 index 71b884d1b6..ec2026b16e 100644 --- a/examples/snap/log.15Jun22.grid.snap.g++.1 +++ b/examples/snap/log.15Jun22.grid.snap.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (28 Jul 2021) +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task # Demonstrate calculation of SNAP bispectrum descriptors on a grid # CORRECTNESS: The two atom positions coincide with two of @@ -27,17 +28,17 @@ boundary p p p lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 -Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000 +Lattice spacing in x,y,z = 3.316 3.316 3.316 region box block 0 ${nx} 0 ${ny} 0 ${nz} region box block 0 1 0 ${ny} 0 ${nz} region box block 0 1 0 1 0 ${nz} region box block 0 1 0 1 0 1 create_box 1 box -Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000) +Created orthogonal box = (0 0 0) to (3.316 3.316 3.316) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2 atoms - using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000) + using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316) create_atoms CPU = 0.000 seconds mass 1 180.88 @@ -105,14 +106,15 @@ dump 2 all custom 1000 dump.batom id x y z c_b[*] # run run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.67637 ghost atom cutoff = 6.67637 binsize = 3.338185, bins = 1 1 1 - 4 neighbor lists, perpetual/occasional/extra = 1 3 0 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton @@ -123,22 +125,12 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (3) compute sna/grid, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (4) compute sna/grid/local, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.384 | 8.384 | 8.384 Mbytes -Step v_B5atom v_B5grid v_rmse_global - 0 1.0427295 1.0427295 0 -Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms +Per MPI rank memory allocation (min/avg/max) = 7.127 | 7.127 | 7.127 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 9.1551336e-16 +Loop time of 1.43e-06 on 1 procs for 0 steps with 2 atoms -100.0% CPU use with 1 MPI tasks x no OpenMP threads +139.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -148,19 +140,19 @@ 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 | | 1e-06 | | |100.00 +Other | | 1.43e-06 | | |100.00 -Nlocal: 2.00000 ave 2 max 2 min +Nlocal: 2 ave 2 max 2 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 339.000 ave 339 max 339 min +Nghost: 339 ave 339 max 339 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 64.0000 ave 64 max 64 min +Neighs: 64 ave 64 max 64 min Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 128.000 ave 128 max 128 min +FullNghs: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128 -Ave neighs/atom = 64.000000 +Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0 diff --git a/examples/snap/log.15Jun22.grid.snap.g++.4 b/examples/snap/log.15Jun22.grid.snap.g++.4 index 80761fc395..5be17ada7d 100644 --- a/examples/snap/log.15Jun22.grid.snap.g++.4 +++ b/examples/snap/log.15Jun22.grid.snap.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (28 Jul 2021) +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task # Demonstrate calculation of SNAP bispectrum descriptors on a grid # CORRECTNESS: The two atom positions coincide with two of @@ -27,17 +28,17 @@ boundary p p p lattice custom $a a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 lattice custom 3.316 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0 0 0 basis 0.5 0.5 0.5 -Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000 +Lattice spacing in x,y,z = 3.316 3.316 3.316 region box block 0 ${nx} 0 ${ny} 0 ${nz} region box block 0 1 0 ${ny} 0 ${nz} region box block 0 1 0 1 0 ${nz} region box block 0 1 0 1 0 1 create_box 1 box -Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000) +Created orthogonal box = (0 0 0) to (3.316 3.316 3.316) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 2 atoms - using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (3.3160000 3.3160000 3.3160000) + using lattice units in orthogonal box = (0 0 0) to (3.316 3.316 3.316) create_atoms CPU = 0.001 seconds mass 1 180.88 @@ -105,14 +106,15 @@ dump 2 all custom 1000 dump.batom id x y z c_b[*] # run run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.67637 ghost atom cutoff = 6.67637 binsize = 3.338185, bins = 1 1 1 - 4 neighbor lists, perpetual/occasional/extra = 1 3 0 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton @@ -123,23 +125,13 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (3) compute sna/grid, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (4) compute sna/grid/local, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:964) -Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.889 | 8.397 Mbytes -Step v_B5atom v_B5grid v_rmse_global - 0 1.0427295 1.0427295 0 -Loop time of 1.5e-06 on 4 procs for 0 steps with 2 atoms +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970) +Per MPI rank memory allocation (min/avg/max) = 6.123 | 6.631 | 7.139 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 1.6316879e-15 +Loop time of 2.57125e-06 on 4 procs for 0 steps with 2 atoms -83.3% CPU use with 4 MPI tasks x no OpenMP threads +107.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -149,19 +141,19 @@ 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 | | 1.5e-06 | | |100.00 +Other | | 2.571e-06 | | |100.00 -Nlocal: 0.500000 ave 1 max 0 min +Nlocal: 0.5 ave 1 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 274.500 ave 275 max 274 min +Nghost: 274.5 ave 275 max 274 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 16.0000 ave 40 max 0 min +Neighs: 16 ave 40 max 0 min Histogram: 2 0 0 0 0 0 1 0 0 1 -FullNghs: 32.0000 ave 64 max 0 min +FullNghs: 32 ave 64 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 128 -Ave neighs/atom = 64.000000 +Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0 diff --git a/examples/snap/log.15Jun22.grid.tri.g++.1 b/examples/snap/log.15Jun22.grid.tri.g++.1 index c261154367..e26315235b 100644 --- a/examples/snap/log.15Jun22.grid.tri.g++.1 +++ b/examples/snap/log.15Jun22.grid.tri.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (28 Jul 2021) +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task # Demonstrate calculation of SNAP bispectrum # descriptors on a grid for triclinic cell @@ -51,7 +52,7 @@ boundary p p p lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 -Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000 +Lattice spacing in x,y,z = 3.316 3.316 3.316 box tilt large region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} @@ -62,13 +63,13 @@ region box prism 0 3 0 2 0 1 2 ${nz} ${nz} region box prism 0 3 0 2 0 1 2 1 ${nz} region box prism 0 3 0 2 0 1 2 1 1 create_box 1 box -Created triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000) -WARNING: Triclinic box skew is large (src/domain.cpp:219) +Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) +WARNING: Triclinic box skew is large (src/domain.cpp:224) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 12 atoms - using lattice units in triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000) - create_atoms CPU = 0.001 seconds + using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) + create_atoms CPU = 0.000 seconds mass 1 180.88 @@ -138,14 +139,15 @@ dump 2 all custom 1000 dump.batom.tri id x y z c_b[*] # run run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.67637 ghost atom cutoff = 6.67637 binsize = 3.338185, bins = 6 3 1 - 4 neighbor lists, perpetual/occasional/extra = 1 3 0 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/newton/tri @@ -156,22 +158,12 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (3) compute sna/grid, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (4) compute sna/grid/local, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.435 | 8.435 | 8.435 Mbytes -Step v_B5atom v_B5grid v_rmse_global - 0 1.0427295 1.0427295 7.2262471e-14 -Loop time of 1e-06 on 1 procs for 0 steps with 12 atoms +Per MPI rank memory allocation (min/avg/max) = 7.183 | 7.183 | 7.183 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 7.2262471e-14 +Loop time of 1.414e-06 on 1 procs for 0 steps with 12 atoms -100.0% CPU use with 1 MPI tasks x no OpenMP threads +70.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -181,19 +173,19 @@ 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 | | 1e-06 | | |100.00 +Other | | 1.414e-06 | | |100.00 -Nlocal: 12.0000 ave 12 max 12 min +Nlocal: 12 ave 12 max 12 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 604.000 ave 604 max 604 min +Nghost: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 384.000 ave 384 max 384 min +Neighs: 384 ave 384 max 384 min Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 768.000 ave 768 max 768 min +FullNghs: 768 ave 768 max 768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 768 -Ave neighs/atom = 64.000000 +Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0 diff --git a/examples/snap/log.15Jun22.grid.tri.g++.4 b/examples/snap/log.15Jun22.grid.tri.g++.4 index bac7ecaa5a..cee3ce7f12 100644 --- a/examples/snap/log.15Jun22.grid.tri.g++.4 +++ b/examples/snap/log.15Jun22.grid.tri.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (28 Jul 2021) +LAMMPS (2 Jun 2022) + using 1 OpenMP thread(s) per MPI task # Demonstrate calculation of SNAP bispectrum # descriptors on a grid for triclinic cell @@ -51,7 +52,7 @@ boundary p p p lattice custom $a a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 lattice custom 3.316 a1 1 0 0 a2 1 1 0 a3 1 1 1 basis 0 0 0 basis 0.0 0.0 0.5 spacing 1 1 1 -Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000 +Lattice spacing in x,y,z = 3.316 3.316 3.316 box tilt large region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz} @@ -62,13 +63,13 @@ region box prism 0 3 0 2 0 1 2 ${nz} ${nz} region box prism 0 3 0 2 0 1 2 1 ${nz} region box prism 0 3 0 2 0 1 2 1 1 create_box 1 box -Created triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000) -WARNING: Triclinic box skew is large (src/domain.cpp:219) +Created triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) +WARNING: Triclinic box skew is large (src/domain.cpp:224) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 12 atoms - using lattice units in triclinic box = (0.0000000 0.0000000 0.0000000) to (9.9480000 6.6320000 3.3160000) with tilt (6.6320000 3.3160000 3.3160000) - create_atoms CPU = 0.001 seconds + using lattice units in triclinic box = (0 0 0) to (9.948 6.632 3.316) with tilt (6.632 3.316 3.316) + create_atoms CPU = 0.000 seconds mass 1 180.88 @@ -138,14 +139,15 @@ dump 2 all custom 1000 dump.batom.tri id x y z c_b[*] # run run 0 -WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.67637 ghost atom cutoff = 6.67637 binsize = 3.338185, bins = 6 3 1 - 4 neighbor lists, perpetual/occasional/extra = 1 3 0 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/newton/tri @@ -156,22 +158,12 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard - (3) compute sna/grid, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (4) compute sna/grid/local, occasional - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.405 | 8.405 | 8.405 Mbytes -Step v_B5atom v_B5grid v_rmse_global - 0 1.0427295 1.0427295 2.1052124e-14 -Loop time of 1.25e-06 on 4 procs for 0 steps with 12 atoms +Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes + Step v_B5atom v_B5grid v_rmse_global + 0 1.0427295 1.0427295 1.9367585e-14 +Loop time of 2.65825e-06 on 4 procs for 0 steps with 12 atoms -140.0% CPU use with 4 MPI tasks x no OpenMP threads +84.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -181,19 +173,19 @@ 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 | | 1.25e-06 | | |100.00 +Other | | 2.658e-06 | | |100.00 -Nlocal: 3.00000 ave 4 max 2 min +Nlocal: 3 ave 4 max 2 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 459.000 ave 460 max 458 min +Nghost: 459 ave 460 max 458 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 96.0000 ave 128 max 64 min +Neighs: 96 ave 128 max 64 min Histogram: 2 0 0 0 0 0 0 0 0 2 -FullNghs: 192.000 ave 256 max 128 min +FullNghs: 192 ave 256 max 128 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 768 -Ave neighs/atom = 64.000000 +Ave neighs/atom = 64 Neighbor list builds = 0 Dangerous builds = 0