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Extended to handle gradgradflag 0/1 options

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This commit is contained in:
Aidan Thompson
2020-07-09 19:23:57 -06:00
parent 0d570f5577
commit e38f970676
6 changed files with 482 additions and 132 deletions
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30
examples/mliap/in.mliap.quadratic.compute
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@ -67,13 +67,6 @@ compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
variable db_2_100 equal c_db[2][100]
# set up compute snap generating global array
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
thermo 100
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
@ -81,15 +74,32 @@ thermo 100
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
thermo 100
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector
thermo_style custom &
pe 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]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
# dump_modify mydump_db sort id
run ${nsteps}
# Run MD
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector
thermo_style custom &
pe 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]
thermo_modify norm no
run ${nsteps}

26
examples/mliap/in.mliap.snap.compute
View File

@ -67,11 +67,6 @@ compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
variable db_2_25 equal c_db[2][25]
# set up compute snap generating global array
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
thermo 100
# test output: 1: total potential energy
@ -82,14 +77,29 @@ thermo 100
#
# followed by 5 counterparts from compute snap
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector
thermo_style custom &
pe 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]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
# dump_modify mydump_db sort id
run ${nsteps}
# Run MD
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector
thermo_style custom &
pe 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]
thermo_modify norm no
run ${nsteps}

134
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (15 Jun 2020)
LAMMPS (30 Jun 2020)
# Demonstrate MLIAP quadratic compute
# initialize simulation
@ -28,7 +28,7 @@ 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 2 box
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
Created orthogonal box = (0 0 0) to (2 2 2)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 2 atoms
@ -99,9 +99,18 @@ compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
variable db_2_100 equal c_db[2][100]
# set up compute snap generating global array
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
thermo 100
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -112,26 +121,11 @@ SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
thermo 100
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector
thermo_style custom pe 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]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
# dump_modify mydump_db sort id
# Run MD
run ${nsteps}
run 0
Neighbor list info ...
@ -171,7 +165,7 @@ PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_sn
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
100.0% CPU use with 1 MPI tasks x no OpenMP threads
200.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -183,17 +177,105 @@ Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1e-06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 853 ave 853 max 853 min
Nghost: 853.0 ave 853.0 max 853.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 330 ave 330 max 330 min
Neighs: 330.0 ave 330.0 max 330.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 660 ave 660 max 660 min
FullNghs: 660.0 ave 660.0 max 660.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660
Ave neighs/atom = 330
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector
thermo_style custom pe 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]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)
thermo_modify norm no
run ${nsteps}
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zbl, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute snav/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute snad/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute mliap, occasional
attributes: full, newton on
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
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
200.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 853.0 ave 853.0 max 853.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 330.0 ave 330.0 max 330.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 660.0 ave 660.0 max 660.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

137
examples/mliap/log.03Jul20.mliap.quadratic.compute.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (15 Jun 2020)
LAMMPS (30 Jun 2020)
# Demonstrate MLIAP quadratic compute
# initialize simulation
@ -28,7 +28,7 @@ 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 2 box
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
Created orthogonal box = (0 0 0) to (2 2 2)
1 by 2 by 2 MPI processor grid
create_atoms 2 box
Created 2 atoms
@ -99,9 +99,18 @@ compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
variable db_2_100 equal c_db[2][100]
# set up compute snap generating global array
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
thermo 100
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
@ -112,26 +121,11 @@ SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
thermo 100
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector
thermo_style custom pe 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]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
# dump_modify mydump_db sort id
# Run MD
run ${nsteps}
run 0
Neighbor list info ...
@ -170,7 +164,95 @@ WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../doma
Per MPI rank memory allocation (min/avg/max) = 22.18 | 22.18 | 22.18 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 2e-06 on 4 procs for 0 steps with 2 atoms
Loop time of 3.5e-06 on 4 procs for 0 steps with 2 atoms
92.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 734.5 ave 735.0 max 734.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 82.5 ave 177.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 165.0 ave 330.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 660
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21 gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector
thermo_style custom pe 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]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)
thermo_modify norm no
run ${nsteps}
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zbl, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute snav/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute snad/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute mliap, 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 (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 69.68 | 69.81 | 69.93 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
100.0% CPU use with 4 MPI tasks x no OpenMP threads
@ -182,19 +264,20 @@ 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 | | 2.75e-06 | | |100.00
Nlocal: 0.5 ave 1 max 0 min
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 734.5 ave 735 max 734 min
Nghost: 734.5 ave 735.0 max 734.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 82.5 ave 177 max 0 min
Neighs: 82.5 ave 177.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 165 ave 330 max 0 min
FullNghs: 165.0 ave 330.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 660
Ave neighs/atom = 330
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

144
examples/mliap/log.03Jul20.mliap.snap.compute.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (15 Jun 2020)
LAMMPS (30 Jun 2020)
# Demonstrate bispectrum computes
# initialize simulation
@ -28,11 +28,11 @@ 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 2 box
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
Created orthogonal box = (0 0 0) to (2 2 2)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 2 atoms
create_atoms CPU = 0.001 seconds
create_atoms CPU = 0.000 seconds
mass * 180.88
@ -99,21 +99,6 @@ compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
variable db_2_25 equal c_db[2][25]
# set up compute snap generating global array
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
thermo 100
# test output: 1: total potential energy
@ -124,14 +109,24 @@ thermo 100
#
# followed by 5 counterparts from compute snap
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector
thermo_style custom pe 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]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
# dump_modify mydump_db sort id
# Run MD
run ${nsteps}
run 0
Neighbor list info ...
@ -169,9 +164,9 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 10.73 | 10.73 | 10.73 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 0 on 1 procs for 0 steps with 2 atoms
Loop time of 2e-06 on 1 procs for 0 steps with 2 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
150.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -181,19 +176,106 @@ 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 | | 0 | | | 0.00
Other | | 2e-06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 853 ave 853 max 853 min
Nghost: 853.0 ave 853.0 max 853.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 330 ave 330 max 330 min
Neighs: 330.0 ave 330.0 max 330.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 660 ave 660 max 660 min
FullNghs: 660.0 ave 660.0 max 660.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660
Ave neighs/atom = 330
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector
thermo_style custom pe 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]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)
thermo_modify norm no
run ${nsteps}
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zbl, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute snav/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute snad/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute mliap, occasional
attributes: full, newton on
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
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
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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
Nlocal: 2.0 ave 2.0 max 2.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 853.0 ave 853.0 max 853.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 330.0 ave 330.0 max 330.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 660.0 ave 660.0 max 660.0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

143
examples/mliap/log.03Jul20.mliap.snap.compute.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (15 Jun 2020)
LAMMPS (30 Jun 2020)
# Demonstrate bispectrum computes
# initialize simulation
@ -28,7 +28,7 @@ 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 2 box
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
Created orthogonal box = (0 0 0) to (2 2 2)
1 by 2 by 2 MPI processor grid
create_atoms 2 box
Created 2 atoms
@ -99,21 +99,6 @@ compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
variable db_2_25 equal c_db[2][25]
# set up compute snap generating global array
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
thermo 100
# test output: 1: total potential energy
@ -124,14 +109,24 @@ thermo 100
#
# followed by 5 counterparts from compute snap
# run compute mliap with gradgradflag = 1
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 1
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector
thermo_style custom pe 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]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
# dump_modify mydump_db sort id
# Run MD
run ${nsteps}
run 0
Neighbor list info ...
@ -170,9 +165,9 @@ WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../doma
Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.7 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 3.25e-06 on 4 procs for 0 steps with 2 atoms
Loop time of 5.5e-06 on 4 procs for 0 steps with 2 atoms
115.4% CPU use with 4 MPI tasks x no OpenMP threads
104.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -182,19 +177,107 @@ 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 | | 3.25e-06 | | |100.00
Other | | 5.5e-06 | | |100.00
Nlocal: 0.5 ave 1 max 0 min
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 734.5 ave 735 max 734 min
Nghost: 734.5 ave 735.0 max 734.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 82.5 ave 177 max 0 min
Neighs: 82.5 ave 177.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 165 ave 330 max 0 min
FullNghs: 165.0 ave 330.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 660
Ave neighs/atom = 330
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
uncompute snap
unfix snap
# run compute mliap with gradgradflag = 0
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6 gradgradflag 0
SNAP keyword rcutfac 1.0
SNAP keyword twojmax 2
SNAP keyword nelems 2
SNAP keyword elems A
SNAP keyword radelems 2.3
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 0
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector
thermo_style custom pe 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]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:694)
thermo_modify norm no
run ${nsteps}
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 1 1 1
5 neighbor lists, perpetual/occasional/extra = 1 4 0
(1) pair zbl, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) compute sna/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute snav/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(4) compute snad/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(5) compute mliap, 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 (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 22.57 | 22.69 | 22.82 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
120.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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
Nlocal: 0.5 ave 1.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 734.5 ave 735.0 max 734.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 82.5 ave 177.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 165.0 ave 330.0 max 0.0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 660
Ave neighs/atom = 330.0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00