diff --git a/examples/sna_nnn_slcsa/dir.inputs/Zr_2.eam.fs b/examples/PACKAGES/sna_nnn_slcsa/Zr_2.eam.fs similarity index 100% rename from examples/sna_nnn_slcsa/dir.inputs/Zr_2.eam.fs rename to examples/PACKAGES/sna_nnn_slcsa/Zr_2.eam.fs diff --git a/examples/sna_nnn_slcsa/dir.inputs/Zr_cell.lmp b/examples/PACKAGES/sna_nnn_slcsa/data.zr_cell similarity index 100% rename from examples/sna_nnn_slcsa/dir.inputs/Zr_cell.lmp rename to examples/PACKAGES/sna_nnn_slcsa/data.zr_cell diff --git a/examples/sna_nnn_slcsa/dir.inputs/Zr.potential b/examples/PACKAGES/sna_nnn_slcsa/dir.inputs/Zr.potential similarity index 100% rename from examples/sna_nnn_slcsa/dir.inputs/Zr.potential rename to examples/PACKAGES/sna_nnn_slcsa/dir.inputs/Zr.potential diff --git a/examples/sna_nnn_slcsa/dir.slcsa/lda_scalings.dat b/examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lda_scalings.dat similarity index 100% rename from examples/sna_nnn_slcsa/dir.slcsa/lda_scalings.dat rename to examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lda_scalings.dat diff --git a/examples/sna_nnn_slcsa/dir.slcsa/lr_bias.dat b/examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lr_bias.dat similarity index 100% rename from examples/sna_nnn_slcsa/dir.slcsa/lr_bias.dat rename to examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lr_bias.dat diff --git a/examples/sna_nnn_slcsa/dir.slcsa/lr_decision.dat b/examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lr_decision.dat similarity index 100% rename from examples/sna_nnn_slcsa/dir.slcsa/lr_decision.dat rename to examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/lr_decision.dat diff --git a/examples/sna_nnn_slcsa/dir.slcsa/mahalanobis_file.dat b/examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/mahalanobis_file.dat similarity index 100% rename from examples/sna_nnn_slcsa/dir.slcsa/mahalanobis_file.dat rename to examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/mahalanobis_file.dat diff --git a/examples/sna_nnn_slcsa/dir.slcsa/mean_descriptor.dat b/examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/mean_descriptor.dat similarity index 100% rename from examples/sna_nnn_slcsa/dir.slcsa/mean_descriptor.dat rename to examples/PACKAGES/sna_nnn_slcsa/dir.slcsa/mean_descriptor.dat diff --git a/examples/PACKAGES/sna_nnn_slcsa/in.slcsa b/examples/PACKAGES/sna_nnn_slcsa/in.slcsa new file mode 100644 index 0000000000..9e65afefda --- /dev/null +++ b/examples/PACKAGES/sna_nnn_slcsa/in.slcsa @@ -0,0 +1,57 @@ +variable trequis equal 750.0 +variable prequis_low equal 0.0 +variable prequis_high equal 25.0e4 +variable equilSteps equal 200 +variable runSteps equal 2000 +variable freqdump equal 200 +variable pstime equal step*dt +variable sxx equal 1.e-4*pxx +variable syy equal 1.e-4*pyy +variable szz equal 1.e-4*pzz +variable sxy equal 1.e-4*pxy +variable sxz equal 1.e-4*pxz +variable syz equal 1.e-4*pyz +variable TK equal temp +variable PE equal pe +variable KE equal ke +variable V equal vol + +dimension 3 +boundary p p p +units metal +atom_style atomic +read_data data.zr_cell +replicate 1 5 5 + +change_box all triclinic + +pair_style hybrid/overlay zero 9.0 eam/fs +pair_coeff * * zero +pair_coeff * * eam/fs Zr_2.eam.fs Zr + +timestep 0.002 + +thermo 50 +thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz + +# fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat + +velocity all create ${trequis} 42345 dist gaussian + +# 1st step : compute the bispectrum on 24 nearest neighbors +compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25 + +# 2nd step : perform dimension reduction + logistic regression +compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*] + +#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*] + +# for testing only. in production use dump as shown above +compute max_slcsa all reduce max c_slcsa[*] +compute min_slcsa all reduce min c_slcsa[*] +thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*] + +#fix 1 all nvt temp ${trequis} ${trequis} 0.100 +fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0 + +run ${equilSteps} diff --git a/examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1 b/examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1 new file mode 100644 index 0000000000..38b1f11251 --- /dev/null +++ b/examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1 @@ -0,0 +1,137 @@ +LAMMPS (21 Nov 2023) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable trequis equal 750.0 +variable prequis_low equal 0.0 +variable prequis_high equal 25.0e4 +variable equilSteps equal 200 +variable runSteps equal 2000 +variable freqdump equal 200 +variable pstime equal step*dt +variable sxx equal 1.e-4*pxx +variable syy equal 1.e-4*pyy +variable szz equal 1.e-4*pzz +variable sxy equal 1.e-4*pxy +variable sxz equal 1.e-4*pxz +variable syz equal 1.e-4*pyz +variable TK equal temp +variable PE equal pe +variable KE equal ke +variable V equal vol + +dimension 3 +boundary p p p +units metal +atom_style atomic +read_data data.zr_cell +Reading data file ... + orthogonal box = (0 0 0) to (19.374 33.556752 30.846) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 864 atoms + read_data CPU = 0.002 seconds +replicate 1 5 5 +Replication is creating a 1x5x5 = 25 times larger system... + orthogonal box = (0 0 0) to (19.374 167.78376 154.23) + 1 by 1 by 1 MPI processor grid + 21600 atoms + replicate CPU = 0.001 seconds + +change_box all triclinic +Changing box ... + triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0) + +pair_style hybrid/overlay zero 9.0 eam/fs +pair_coeff * * zero +pair_coeff * * eam/fs Zr_2.eam.fs Zr + +timestep 0.002 + +thermo 50 +thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz + +# fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat + +velocity all create ${trequis} 42345 dist gaussian +velocity all create 750 42345 dist gaussian + +# 1st step : compute the bispectrum on 24 nearest neighbors +compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25 + +# 2nd step : perform dimension reduction + logistic regression +compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*] + +#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*] + +# for testing only. in production use dump as shown above +compute max_slcsa all reduce max c_slcsa[*] +compute min_slcsa all reduce min c_slcsa[*] +thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*] + +#fix 1 all nvt temp ${trequis} ${trequis} 0.100 +fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0 +fix 1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0 +fix 1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0 +fix 1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0 +fix 1 all npt temp 750 750 0.100 tri 0 0 1.0 + +run ${equilSteps} +run 200 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 4 31 29 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard + (2) pair eam/fs, perpetual, trim from (1) + attributes: half, newton on, cut 9.6 + pair build: trim + stencil: none + bin: none + (3) compute sna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 31.9 | 31.9 | 31.9 Mbytes + Step PotEng KinEng Temp c_max_slcsa[1] c_max_slcsa[2] c_max_slcsa[3] c_max_slcsa[4] c_max_slcsa[5] c_min_slcsa[1] c_min_slcsa[2] c_min_slcsa[3] c_min_slcsa[4] c_min_slcsa[5] + 0 -139689.93 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2 + 50 -138733.53 1165.0291 417.29048 8.2778907 18.221432 3.019507 113.65218 2 5.2735872 10.834132 0.042702874 108.2674 2 + 100 -138821.33 1442.648 516.7281 8.3357676 17.470311 2.7073063 113.39999 2 6.145345 12.307441 0.034372881 108.61824 2 + 150 -138607.9 1435.9634 514.33383 8.3817341 17.984657 2.892662 113.40287 2 5.3635301 10.064171 0.030283213 107.5829 2 + 200 -138494.56 1560.9093 559.08699 8.5615388 18.429835 2.8130845 114.31517 2 5.4711815 11.113891 0.074490923 107.87418 2 +Loop time of 36.3263 on 1 procs for 200 steps with 21600 atoms + +Performance: 0.951 ns/day, 25.227 hours/ns, 5.506 timesteps/s, 118.922 katom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.012 | 9.012 | 9.012 | 0.0 | 24.81 +Neigh | 0.67881 | 0.67881 | 0.67881 | 0.0 | 1.87 +Comm | 0.045066 | 0.045066 | 0.045066 | 0.0 | 0.12 +Output | 26.422 | 26.422 | 26.422 | 0.0 | 72.74 +Modify | 0.14726 | 0.14726 | 0.14726 | 0.0 | 0.41 +Other | | 0.02121 | | | 0.06 + +Nlocal: 21600 ave 21600 max 21600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 36652 ave 36652 max 36652 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.5961e+06 ave 2.5961e+06 max 2.5961e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 5.19109e+06 ave 5.19109e+06 max 5.19109e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5191091 +Ave neighs/atom = 240.32829 +Neighbor list builds = 5 +Dangerous builds = 0 +Total wall time: 0:00:43 diff --git a/examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4 b/examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4 new file mode 100644 index 0000000000..bda7ee0f39 --- /dev/null +++ b/examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4 @@ -0,0 +1,137 @@ +LAMMPS (21 Nov 2023) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable trequis equal 750.0 +variable prequis_low equal 0.0 +variable prequis_high equal 25.0e4 +variable equilSteps equal 200 +variable runSteps equal 2000 +variable freqdump equal 200 +variable pstime equal step*dt +variable sxx equal 1.e-4*pxx +variable syy equal 1.e-4*pyy +variable szz equal 1.e-4*pzz +variable sxy equal 1.e-4*pxy +variable sxz equal 1.e-4*pxz +variable syz equal 1.e-4*pyz +variable TK equal temp +variable PE equal pe +variable KE equal ke +variable V equal vol + +dimension 3 +boundary p p p +units metal +atom_style atomic +read_data data.zr_cell +Reading data file ... + orthogonal box = (0 0 0) to (19.374 33.556752 30.846) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 864 atoms + read_data CPU = 0.002 seconds +replicate 1 5 5 +Replication is creating a 1x5x5 = 25 times larger system... + orthogonal box = (0 0 0) to (19.374 167.78376 154.23) + 1 by 2 by 2 MPI processor grid + 21600 atoms + replicate CPU = 0.001 seconds + +change_box all triclinic +Changing box ... + triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0) + +pair_style hybrid/overlay zero 9.0 eam/fs +pair_coeff * * zero +pair_coeff * * eam/fs Zr_2.eam.fs Zr + +timestep 0.002 + +thermo 50 +thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz + +# fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat + +velocity all create ${trequis} 42345 dist gaussian +velocity all create 750 42345 dist gaussian + +# 1st step : compute the bispectrum on 24 nearest neighbors +compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25 + +# 2nd step : perform dimension reduction + logistic regression +compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*] + +#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*] + +# for testing only. in production use dump as shown above +compute max_slcsa all reduce max c_slcsa[*] +compute min_slcsa all reduce min c_slcsa[*] +thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*] + +#fix 1 all nvt temp ${trequis} ${trequis} 0.100 +fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0 +fix 1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0 +fix 1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0 +fix 1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0 +fix 1 all npt temp 750 750 0.100 tri 0 0 1.0 + +run ${equilSteps} +run 200 +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11 + ghost atom cutoff = 11 + binsize = 5.5, bins = 4 31 29 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/tri + bin: standard + (2) pair eam/fs, perpetual, trim from (1) + attributes: half, newton on, cut 9.6 + pair build: trim + stencil: none + bin: none + (3) compute sna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.26 | 11.45 | 11.64 Mbytes + Step PotEng KinEng Temp c_max_slcsa[1] c_max_slcsa[2] c_max_slcsa[3] c_max_slcsa[4] c_max_slcsa[5] c_min_slcsa[1] c_min_slcsa[2] c_min_slcsa[3] c_min_slcsa[4] c_min_slcsa[5] + 0 -139689.93 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2 + 50 -138733.53 1165.0291 417.29048 8.2778907 18.221432 3.019507 113.65218 2 5.2735872 10.834132 0.042702874 108.2674 2 + 100 -138821.33 1442.648 516.7281 8.3357676 17.470311 2.7073063 113.39999 2 6.145345 12.307441 0.034372881 108.61824 2 + 150 -138607.9 1435.9634 514.33383 8.3817341 17.984657 2.892662 113.40287 2 5.3635301 10.064171 0.030283213 107.5829 2 + 200 -138494.56 1560.9093 559.08699 8.5615388 18.429835 2.8130845 114.31517 2 5.4711815 11.113891 0.074490923 107.87418 2 +Loop time of 9.89929 on 4 procs for 200 steps with 21600 atoms + +Performance: 3.491 ns/day, 6.875 hours/ns, 20.203 timesteps/s, 436.395 katom-step/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.61 | 2.618 | 2.622 | 0.3 | 26.45 +Neigh | 0.19338 | 0.19618 | 0.19967 | 0.5 | 1.98 +Comm | 0.051086 | 0.055818 | 0.065206 | 2.4 | 0.56 +Output | 6.9725 | 6.9725 | 6.9725 | 0.0 | 70.43 +Modify | 0.04635 | 0.046617 | 0.046825 | 0.1 | 0.47 +Other | | 0.01018 | | | 0.10 + +Nlocal: 5400 ave 5431 max 5376 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 12889.2 ave 12909 max 12847 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 649026 ave 652559 max 642783 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +FullNghs: 1.29777e+06 ave 1.30656e+06 max 1.29086e+06 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 5191084 +Ave neighs/atom = 240.32796 +Neighbor list builds = 5 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/sna_nnn_slcsa/dir.inputs/in_lammps_npt b/examples/sna_nnn_slcsa/dir.inputs/in_lammps_npt deleted file mode 100644 index c325e0572f..0000000000 --- a/examples/sna_nnn_slcsa/dir.inputs/in_lammps_npt +++ /dev/null @@ -1,61 +0,0 @@ -variable trequis equal 750.0 -variable prequis_low equal 0.0 -variable prequis_high equal 25.0e4 -variable equilSteps equal 2000 -variable runSteps equal 20000 -variable freqdump equal 200 -variable pstime equal step*dt -variable sxx equal 1.e-4*pxx -variable syy equal 1.e-4*pyy -variable szz equal 1.e-4*pzz -variable sxy equal 1.e-4*pxy -variable sxz equal 1.e-4*pxz -variable syz equal 1.e-4*pyz -variable TK equal temp -variable PE equal pe -variable KE equal ke -variable V equal vol - -dimension 3 -boundary p p p -units metal -atom_style atomic -read_data dir.inputs/Zr_cell.lmp -replicate 1 10 10 - -#neighbor 0.0 bin -# neigh_modify delay 0 every 1 check no - -change_box all triclinic - -include dir.inputs/Zr.potential - -timestep 2.0e-3 - -thermo 1000 -thermo_style custom step pe ke temp pxx pyy pzz pxy pyz pxz - -fix extra all print 50 "${pstime} ${TK} ${PE} ${KE} ${V} ${sxx} ${syy} ${szz} ${sxy} ${sxz} ${syz}" file thermo_global_npt_low_temperature_Zr_hcp.dat - -velocity all create ${trequis} 42345 dist gaussian - -# 1st step : compute the bispectrum on 24 nearest neighbors -compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25 - -# 2nd step : perform dimension reduction + logistic regression -compute slcsa all slcsa/atom 8 4 dir.slcsa/mean_descriptor.dat dir.slcsa/lda_scalings.dat dir.slcsa/lr_decision.dat dir.slcsa/lr_bias.dat dir.slcsa/mahalanobis_file.dat c_bnnn[*] - -dump d1 all custom ${freqdump} dir.dumps/slcsa_demo.*.dump id x y z c_slcsa[*] - -#fix 1 all nvt temp ${trequis} ${trequis} 0.100 -fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0 - -run ${equilSteps} - -unfix 1 -#fix 1 all nvt temp ${trequis} ${trequis} 0.100 -fix 1 all npt temp ${trequis} ${trequis} 0.100 aniso ${prequis_high} ${prequis_high} 1.0 - -run ${runSteps} - -unfix 1 \ No newline at end of file