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Finished cleaning up and testing. MLIAPData class is now fully integrated with ComputeMLIAP and PairMLIAP

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This commit is contained in:
Aidan Thompson
2020-07-11 19:01:16 -06:00
parent 6c6c47ce9c
commit 095c6a9850
24 changed files with 807 additions and 523 deletions
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4
examples/mliap/in.mliap.quadratic.compute
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@ -78,7 +78,7 @@ thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector
thermo_style custom &
@ -93,7 +93,7 @@ unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector
thermo_style custom &

4
examples/mliap/in.mliap.snap.compute
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@ -79,7 +79,7 @@ thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector
thermo_style custom &
@ -94,7 +94,7 @@ unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector
thermo_style custom &

14
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.1
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@ -110,7 +110,7 @@ thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -160,7 +160,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 22.45 | 22.45 | 22.45 Mbytes
Per MPI rank memory allocation (min/avg/max) = 22.47 | 22.47 | 22.47 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
@ -196,7 +196,7 @@ unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -247,12 +247,12 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 70.2 | 70.2 | 70.2 Mbytes
Per MPI rank memory allocation (min/avg/max) = 70.24 | 70.24 | 70.24 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
Loop time of 2e-06 on 1 procs for 0 steps with 2 atoms
200.0% CPU use with 1 MPI tasks x no OpenMP threads
50.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -262,7 +262,7 @@ 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 | | 2e-06 | | |100.00
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

20
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.4
View File

@ -110,7 +110,7 @@ thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -161,12 +161,12 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 22.18 | 22.18 | 22.18 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.429 | 6.43 | 6.432 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
Loop time of 3.5e-06 on 4 procs for 0 steps with 2 atoms
Loop time of 4.25e-06 on 4 procs for 0 steps with 2 atoms
92.9% CPU use with 4 MPI tasks x no OpenMP threads
82.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -176,7 +176,7 @@ 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 | | 3.5e-06 | | |100.00
Other | | 4.25e-06 | | |100.00
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -197,7 +197,7 @@ unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -249,12 +249,12 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 69.68 | 69.81 | 69.93 Mbytes
Per MPI rank memory allocation (min/avg/max) = 53.93 | 54.06 | 54.18 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
Loop time of 2.75e-06 on 4 procs for 0 steps with 2 atoms
Loop time of 4e-06 on 4 procs for 0 steps with 2 atoms
100.0% CPU use with 4 MPI tasks x no OpenMP threads
106.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -264,7 +264,7 @@ 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 | | 2.75e-06 | | |100.00
Other | | 4e-06 | | |100.00
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

14
examples/mliap/log.03Jul20.mliap.snap.compute.g++.1
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@ -111,7 +111,7 @@ thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -161,12 +161,12 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.73 | 10.73 | 10.73 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.75 | 10.75 | 10.75 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 2e-06 on 1 procs for 0 steps with 2 atoms
Loop time of 0 on 1 procs for 0 steps with 2 atoms
150.0% CPU use with 1 MPI tasks x no OpenMP threads
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -176,7 +176,7 @@ 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 | | 2e-06 | | |100.00
Other | | 0 | | | 0.00
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -197,7 +197,7 @@ unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -248,7 +248,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 22.85 | 22.85 | 22.85 Mbytes
Per MPI rank memory allocation (min/avg/max) = 22.89 | 22.89 | 22.89 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms

20
examples/mliap/log.03Jul20.mliap.snap.compute.g++.4
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@ -111,7 +111,7 @@ thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -162,12 +162,12 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.7 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.7 | 10.7 | 10.71 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 5.5e-06 on 4 procs for 0 steps with 2 atoms
Loop time of 3.75e-06 on 4 procs for 0 steps with 2 atoms
104.5% CPU use with 4 MPI tasks x no OpenMP threads
86.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -177,7 +177,7 @@ 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 | | 5.5e-06 | | |100.00
Other | | 3.75e-06 | | |100.00
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -198,7 +198,7 @@ unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -250,12 +250,12 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 22.57 | 22.69 | 22.82 Mbytes
Per MPI rank memory allocation (min/avg/max) = 22.57 | 22.71 | 22.85 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 2.5e-06 on 4 procs for 0 steps with 2 atoms
Loop time of 2e-06 on 4 procs for 0 steps with 2 atoms
120.0% CPU use with 4 MPI tasks x no OpenMP threads
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -265,7 +265,7 @@ 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 | | 2.5e-06 | | |100.00
Other | | 2e-06 | | |100.00
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

0
examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.1 → examples/mliap/log.21Jun20.mliap.snap.WBe.PRB2019.g++.1
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0
examples/mliap/log.21Jun20.mliap.snap.WBe.PRB201.g++.4 → examples/mliap/log.21Jun20.mliap.snap.WBe.PRB2019.g++.4
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