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re-use existing potential file, fix screen/log output, plug memory leaks

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This commit is contained in:
Axel Kohlmeyer
2023-12-12 23:28:09 -05:00
parent e7c330db9d
commit 29cf012061
8 changed files with 283 additions and 6197 deletions
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6006
examples/PACKAGES/sna_nnn_slcsa/Zr_2.eam.fs
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1
examples/PACKAGES/sna_nnn_slcsa/Zr_mm.eam.fs Symbolic link
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@ -0,0 +1 @@
../../../potentials/Zr_mm.eam.fs

3
examples/PACKAGES/sna_nnn_slcsa/dir.inputs/Zr.potential
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@ -1,3 +0,0 @@
pair_style hybrid/overlay zero 9.0 eam/fs
pair_coeff * * zero
pair_coeff * * eam/fs dir.inputs/Zr_2.eam.fs Zr

2
examples/PACKAGES/sna_nnn_slcsa/in.slcsa
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@ -27,7 +27,7 @@ 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
pair_coeff * * eam/fs Zr_mm.eam.fs Zr
timestep 0.002

83
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.1
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@ -43,7 +43,8 @@ Changing box ...
pair_style hybrid/overlay zero 9.0 eam/fs
pair_coeff * * zero
pair_coeff * * eam/fs Zr_2.eam.fs Zr
pair_coeff * * eam/fs Zr_mm.eam.fs Zr
Reading eam/fs potential file Zr_mm.eam.fs with DATE: 2007-06-11
timestep 0.002
@ -60,6 +61,48 @@ compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1
# 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[*]
Files used:
database mean descriptor: dir.slcsa/mean_descriptor.dat
lda scalings : dir.slcsa/lda_scalings.dat
lr decision : dir.slcsa/lr_decision.dat
lr bias : dir.slcsa/lr_bias.dat
maha stats : dir.slcsa/mahalanobis_file.dat
For class 0 maha threshold = 5.054
mean B:
-23.8329
4.6638
3.9805
icov:
1.1377 0.1077 -0.0171
0.1077 0.8846 -0.2577
-0.0171 -0.2577 0.6783
For class 1 maha threshold = 5.234
mean B:
-21.2853
-6.1583
1.7948
icov:
1.7124 0.0341 0.1966
0.0341 0.6453 0.288
0.1966 0.288 1.8991
For class 2 maha threshold = 5.036
mean B:
-23.1593
1.3059
-5.7549
icov:
0.7496 -0.0806 -0.1101
-0.0806 1.1178 0.1667
-0.1101 0.1667 0.6711
For class 3 maha threshold = 7.994
mean B:
68.1971
0.1604
-0.0067
icov:
0.9663 -0.1846 0.6622
-0.1846 8.2371 0.9841
0.6622 0.9841 5.9601
#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
@ -101,37 +144,37 @@ Neighbor list info ...
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
0 -143297.23 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2
50 -142154.08 1007.7164 360.9442 8.8091564 19.23244 4.2093382 113.87959 2 5.0327148 9.6817454 0.02610585 106.71863 2
100 -142365.33 1406.6559 503.83647 8.6272189 17.908949 2.9294666 113.75167 2 6.2058895 11.913521 0.033775944 108.66893 2
150 -142188.18 1432.0075 512.91691 8.6441961 18.176321 2.9277374 114.27958 2 5.5899425 10.521867 0.014919473 108.14526 2
200 -142000.4 1481.7247 530.72462 8.5895692 18.65646 3.1725758 114.55015 2 5.5955774 10.776385 0.061469343 108.35384 2
Loop time of 36.3759 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
Performance: 0.950 ns/day, 25.261 hours/ns, 5.498 timesteps/s, 118.760 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
Pair | 9.0837 | 9.0837 | 9.0837 | 0.0 | 24.97
Neigh | 0.52896 | 0.52896 | 0.52896 | 0.0 | 1.45
Comm | 0.045416 | 0.045416 | 0.045416 | 0.0 | 0.12
Output | 26.548 | 26.548 | 26.548 | 0.0 | 72.98
Modify | 0.1493 | 0.1493 | 0.1493 | 0.0 | 0.41
Other | | 0.02088 | | | 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
Nghost: 36674 ave 36674 max 36674 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
Neighs: 2.61729e+06 ave 2.61729e+06 max 2.61729e+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
FullNghs: 5.24007e+06 ave 5.24007e+06 max 5.24007e+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
Total # of neighbors = 5240069
Ave neighs/atom = 242.59579
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:43

95
examples/PACKAGES/sna_nnn_slcsa/log.12Dec23.slcsa.g++.4
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@ -43,7 +43,8 @@ Changing box ...
pair_style hybrid/overlay zero 9.0 eam/fs
pair_coeff * * zero
pair_coeff * * eam/fs Zr_2.eam.fs Zr
pair_coeff * * eam/fs Zr_mm.eam.fs Zr
Reading eam/fs potential file Zr_mm.eam.fs with DATE: 2007-06-11
timestep 0.002
@ -60,6 +61,48 @@ compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1
# 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[*]
Files used:
database mean descriptor: dir.slcsa/mean_descriptor.dat
lda scalings : dir.slcsa/lda_scalings.dat
lr decision : dir.slcsa/lr_decision.dat
lr bias : dir.slcsa/lr_bias.dat
maha stats : dir.slcsa/mahalanobis_file.dat
For class 0 maha threshold = 5.054
mean B:
-23.8329
4.6638
3.9805
icov:
1.1377 0.1077 -0.0171
0.1077 0.8846 -0.2577
-0.0171 -0.2577 0.6783
For class 1 maha threshold = 5.234
mean B:
-21.2853
-6.1583
1.7948
icov:
1.7124 0.0341 0.1966
0.0341 0.6453 0.288
0.1966 0.288 1.8991
For class 2 maha threshold = 5.036
mean B:
-23.1593
1.3059
-5.7549
icov:
0.7496 -0.0806 -0.1101
-0.0806 1.1178 0.1667
-0.1101 0.1667 0.6711
For class 3 maha threshold = 7.994
mean B:
68.1971
0.1604
-0.0067
icov:
0.9663 -0.1846 0.6622
-0.1846 8.2371 0.9841
0.6622 0.9841 5.9601
#dump d1 all custom ${freqdump} slcsa_demo.dump id x y z c_slcsa[*]
@ -101,37 +144,37 @@ Neighbor list info ...
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
0 -143297.23 2093.9174 750 7.6195146 15.787294 1.2169942 111.01919 2 7.6195146 15.787294 1.2169942 111.01919 2
50 -142154.08 1007.7164 360.9442 8.8091564 19.23244 4.2093382 113.87959 2 5.0327148 9.6817454 0.02610585 106.71863 2
100 -142365.33 1406.6559 503.83647 8.6272189 17.908949 2.9294666 113.75167 2 6.2058895 11.913521 0.033775944 108.66893 2
150 -142188.18 1432.0075 512.91691 8.6441961 18.176321 2.9277374 114.27958 2 5.5899425 10.521867 0.014919473 108.14526 2
200 -142000.4 1481.7247 530.72462 8.5895692 18.65646 3.1725758 114.55015 2 5.5955774 10.776385 0.061469343 108.35384 2
Loop time of 9.81677 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
Performance: 3.521 ns/day, 6.817 hours/ns, 20.373 timesteps/s, 440.063 katom-step/s
99.7% 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
Pair | 2.6508 | 2.6589 | 2.6698 | 0.5 | 27.09
Neigh | 0.1516 | 0.15276 | 0.15406 | 0.3 | 1.56
Comm | 0.047132 | 0.058969 | 0.066095 | 3.2 | 0.60
Output | 6.8886 | 6.8886 | 6.8886 | 0.0 | 70.17
Modify | 0.046437 | 0.04661 | 0.046825 | 0.1 | 0.47
Other | | 0.01091 | | | 0.11
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
Nlocal: 5400 ave 5416 max 5393 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 12902.8 ave 12911 max 12888 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 654322 ave 655602 max 650912 min
Histogram: 1 0 0 0 0 0 0 0 0 3
FullNghs: 1.31002e+06 ave 1.31507e+06 max 1.30683e+06 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 5191084
Ave neighs/atom = 240.32796
Neighbor list builds = 5
Total # of neighbors = 5240065
Ave neighs/atom = 242.5956
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:11