update compute slcsa example to better align with LAMMPS conventions and move to more appropriate folder
This commit is contained in:
Axel Kohlmeyer
57
examples/PACKAGES/sna_nnn_slcsa/in.slcsa
Normal file
57
examples/PACKAGES/sna_nnn_slcsa/in.slcsa
Normal file
@ -0,0 +1,57 @@
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variable trequis equal 750.0
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variable prequis_low equal 0.0
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variable prequis_high equal 25.0e4
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variable equilSteps equal 200
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variable runSteps equal 2000
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variable freqdump equal 200
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variable pstime equal step*dt
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variable sxx equal 1.e-4*pxx
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variable syy equal 1.e-4*pyy
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variable szz equal 1.e-4*pzz
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variable sxy equal 1.e-4*pxy
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variable sxz equal 1.e-4*pxz
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variable syz equal 1.e-4*pyz
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variable TK equal temp
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variable PE equal pe
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variable KE equal ke
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variable V equal vol
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dimension 3
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boundary p p p
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units metal
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atom_style atomic
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read_data data.zr_cell
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replicate 1 5 5
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change_box all triclinic
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pair_style hybrid/overlay zero 9.0 eam/fs
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pair_coeff * * zero
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pair_coeff * * eam/fs Zr_2.eam.fs Zr
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timestep 0.002
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thermo 50
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thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz
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# 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
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velocity all create ${trequis} 42345 dist gaussian
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# 1st step : compute the bispectrum on 24 nearest neighbors
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compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25
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# 2nd step : perform dimension reduction + logistic regression
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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[*]
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#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
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# for testing only. in production use dump as shown above
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compute max_slcsa all reduce max c_slcsa[*]
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compute min_slcsa all reduce min c_slcsa[*]
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thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*]
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#fix 1 all nvt temp ${trequis} ${trequis} 0.100
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fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
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run ${equilSteps}
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137
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1
Normal file
137
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1
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@ -0,0 +1,137 @@
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LAMMPS (21 Nov 2023)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable trequis equal 750.0
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variable prequis_low equal 0.0
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variable prequis_high equal 25.0e4
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variable equilSteps equal 200
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variable runSteps equal 2000
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variable freqdump equal 200
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variable pstime equal step*dt
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variable sxx equal 1.e-4*pxx
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variable syy equal 1.e-4*pyy
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variable szz equal 1.e-4*pzz
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variable sxy equal 1.e-4*pxy
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variable sxz equal 1.e-4*pxz
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variable syz equal 1.e-4*pyz
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variable TK equal temp
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variable PE equal pe
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variable KE equal ke
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variable V equal vol
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dimension 3
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boundary p p p
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units metal
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atom_style atomic
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read_data data.zr_cell
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Reading data file ...
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orthogonal box = (0 0 0) to (19.374 33.556752 30.846)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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864 atoms
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read_data CPU = 0.002 seconds
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replicate 1 5 5
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Replication is creating a 1x5x5 = 25 times larger system...
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orthogonal box = (0 0 0) to (19.374 167.78376 154.23)
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1 by 1 by 1 MPI processor grid
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21600 atoms
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replicate CPU = 0.001 seconds
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change_box all triclinic
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Changing box ...
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triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0)
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pair_style hybrid/overlay zero 9.0 eam/fs
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pair_coeff * * zero
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pair_coeff * * eam/fs Zr_2.eam.fs Zr
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timestep 0.002
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thermo 50
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thermo_style custom step pe ke temp vol pxx pyy pzz pxy pyz pxz
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# 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
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velocity all create ${trequis} 42345 dist gaussian
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velocity all create 750 42345 dist gaussian
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# 1st step : compute the bispectrum on 24 nearest neighbors
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compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.25
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# 2nd step : perform dimension reduction + logistic regression
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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[*]
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#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
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# for testing only. in production use dump as shown above
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compute max_slcsa all reduce max c_slcsa[*]
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compute min_slcsa all reduce min c_slcsa[*]
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thermo_style custom step pe ke temp c_max_slcsa[*] c_min_slcsa[*]
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#fix 1 all nvt temp ${trequis} ${trequis} 0.100
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fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
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fix 1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
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fix 1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0
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fix 1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0
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fix 1 all npt temp 750 750 0.100 tri 0 0 1.0
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run ${equilSteps}
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run 200
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5, bins = 4 31 29
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3 neighbor lists, perpetual/occasional/extra = 2 1 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton/tri
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stencil: half/bin/3d/tri
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bin: standard
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(2) pair eam/fs, perpetual, trim from (1)
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attributes: half, newton on, cut 9.6
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pair build: trim
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stencil: none
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bin: none
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(3) compute sna/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 31.9 | 31.9 | 31.9 Mbytes
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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]
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0 -139689.93 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2
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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
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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
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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
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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
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Loop time of 36.3263 on 1 procs for 200 steps with 21600 atoms
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Performance: 0.951 ns/day, 25.227 hours/ns, 5.506 timesteps/s, 118.922 katom-step/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.012 | 9.012 | 9.012 | 0.0 | 24.81
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Neigh | 0.67881 | 0.67881 | 0.67881 | 0.0 | 1.87
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Comm | 0.045066 | 0.045066 | 0.045066 | 0.0 | 0.12
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Output | 26.422 | 26.422 | 26.422 | 0.0 | 72.74
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Modify | 0.14726 | 0.14726 | 0.14726 | 0.0 | 0.41
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Other | | 0.02121 | | | 0.06
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Nlocal: 21600 ave 21600 max 21600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 36652 ave 36652 max 36652 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.5961e+06 ave 2.5961e+06 max 2.5961e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 5.19109e+06 ave 5.19109e+06 max 5.19109e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5191091
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Ave neighs/atom = 240.32829
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Neighbor list builds = 5
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Dangerous builds = 0
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Total wall time: 0:00:43
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137
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4
Normal file
137
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4
Normal file
@ -0,0 +1,137 @@
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LAMMPS (21 Nov 2023)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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variable trequis equal 750.0
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variable prequis_low equal 0.0
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variable prequis_high equal 25.0e4
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variable equilSteps equal 200
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variable runSteps equal 2000
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variable freqdump equal 200
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variable pstime equal step*dt
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variable sxx equal 1.e-4*pxx
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variable syy equal 1.e-4*pyy
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variable szz equal 1.e-4*pzz
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variable sxy equal 1.e-4*pxy
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variable sxz equal 1.e-4*pxz
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variable syz equal 1.e-4*pyz
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variable TK equal temp
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variable PE equal pe
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variable KE equal ke
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variable V equal vol
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dimension 3
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boundary p p p
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units metal
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atom_style atomic
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read_data data.zr_cell
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Reading data file ...
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orthogonal box = (0 0 0) to (19.374 33.556752 30.846)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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864 atoms
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read_data CPU = 0.002 seconds
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replicate 1 5 5
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Replication is creating a 1x5x5 = 25 times larger system...
|
||||||
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orthogonal box = (0 0 0) to (19.374 167.78376 154.23)
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1 by 2 by 2 MPI processor grid
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21600 atoms
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replicate CPU = 0.001 seconds
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|
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change_box all triclinic
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Changing box ...
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triclinic box = (0 0 0) to (19.374 167.78376 154.23) with tilt (0 0 0)
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||||||
|
|
||||||
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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
|
||||||
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|
||||||
|
velocity all create ${trequis} 42345 dist gaussian
|
||||||
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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
|
||||||
|
|
||||||
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# 2nd step : perform dimension reduction + logistic regression
|
||||||
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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[*]
|
||||||
|
|
||||||
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#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[*]
|
||||||
|
|
||||||
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#fix 1 all nvt temp ${trequis} ${trequis} 0.100
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||||||
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fix 1 all npt temp ${trequis} ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
|
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fix 1 all npt temp 750 ${trequis} 0.100 tri ${prequis_low} ${prequis_low} 1.0
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fix 1 all npt temp 750 750 0.100 tri ${prequis_low} ${prequis_low} 1.0
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fix 1 all npt temp 750 750 0.100 tri 0 ${prequis_low} 1.0
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fix 1 all npt temp 750 750 0.100 tri 0 0 1.0
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|
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run ${equilSteps}
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run 200
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Neighbor list info ...
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||||||
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update: every = 1 steps, delay = 0 steps, check = yes
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||||||
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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
|
||||||
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stencil: half/bin/3d/tri
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||||||
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bin: standard
|
||||||
|
(2) pair eam/fs, perpetual, trim from (1)
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||||||
|
attributes: half, newton on, cut 9.6
|
||||||
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pair build: trim
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||||||
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stencil: none
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||||||
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bin: none
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(3) compute sna/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 11.26 | 11.45 | 11.64 Mbytes
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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]
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0 -139689.93 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2
|
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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
|
||||||
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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
|
||||||
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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
|
||||||
@ -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
|
|
||||||
Reference in New Issue
Block a user