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Added doc page for compute mliap and updated examples

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This commit is contained in:
Aidan Thompson
2020-07-03 13:43:51 -06:00
parent 28bbb6afbc
commit 9d0aee7426
12 changed files with 921 additions and 98 deletions
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4
examples/snap/in.snap.compute.quadratic
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@ -80,9 +80,9 @@ fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
thermo 100
# test output: 1: total potential energy
# 2: xz component of stress tensor
# 2: xy component of stress tensor
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
# 4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 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

26
examples/snap/log.27Nov18.snap.compute.g++.1 → examples/snap/log.03Jul20.snap.compute.g++.1
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@ -1,6 +1,4 @@
LAMMPS (20 Nov 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
LAMMPS (15 Jun 2020)
# Demonstrate bispectrum computes
# initialize simulation
@ -30,11 +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) to (2 2 2)
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 2 atoms
create_atoms CPU = 0.000478029 secs
create_atoms CPU = 0.000 seconds
mass * 180.88
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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_30 equal c_db[2][30]
variable db_2_25 equal c_db[2][25]
# set up compute snap generating global array
@ -118,12 +116,12 @@ thermo 100
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(B_{000}^i, all i of type 2)
# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
thermo_style custom pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
@ -166,11 +164,11 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
322.86952 1505558.1 364182.88 381.32218 -855.04473 322.86952 1505558.1 364182.88 381.32218 -855.04473
Loop time of 9.53674e-07 on 1 procs for 0 steps with 2 atoms
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
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
104.9% CPU use with 1 MPI tasks x 1 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
@ -180,7 +178,7 @@ 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 | | 9.537e-07 | | |100.00
Other | | 1e-06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0

30
examples/snap/log.27Nov18.snap.compute.g++.4 → examples/snap/log.03Jul20.snap.compute.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (20 Nov 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
LAMMPS (15 Jun 2020)
# Demonstrate bispectrum computes
# initialize simulation
@ -30,11 +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) to (2 2 2)
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
1 by 2 by 2 MPI processor grid
create_atoms 2 box
Created 2 atoms
create_atoms CPU = 0.000610113 secs
create_atoms CPU = 0.001 seconds
mass * 180.88
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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_30 equal c_db[2][30]
variable db_2_25 equal c_db[2][25]
# set up compute snap generating global array
@ -118,12 +116,12 @@ thermo 100
# test output: 1: total potential energy
# 2: xy component of stress tensor
# 3: Sum(B_{000}^i, all i of type 2)
# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
#
# followed by 5 counterparts from compute snap
thermo_style custom pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
@ -165,13 +163,13 @@ Neighbor list info ...
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:936)
Per MPI rank memory allocation (min/avg/max) = 8.211 | 8.254 | 8.295 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
322.86952 1505558.1 364182.88 381.32218 -855.04473 322.86952 1505558.1 364182.88 381.32218 -855.04473
Loop time of 2.38419e-06 on 4 procs for 0 steps with 2 atoms
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 9.945 | 9.988 | 10.03 Mbytes
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
Loop time of 2.75e-06 on 4 procs for 0 steps with 2 atoms
104.9% CPU use with 4 MPI tasks x 1 OpenMP threads
90.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -181,7 +179,7 @@ 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 | | 2.384e-06 | | |100.00
Other | | 2.75e-06 | | |100.00
Nlocal: 0.5 ave 1 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

26
examples/snap/log.27Nov18.snap.compute.quadratic.g++.1 → examples/snap/log.03Jul20.snap.compute.quadratic.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (20 Nov 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
LAMMPS (15 Jun 2020)
# Demonstrate bispectrum computes
# initialize simulation
@ -30,11 +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) to (2 2 2)
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
1 by 1 by 1 MPI processor grid
create_atoms 2 box
Created 2 atoms
create_atoms CPU = 0.000473976 secs
create_atoms CPU = 0.001 seconds
mass * 180.88
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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_120 equal c_db[2][120]
variable db_2_100 equal c_db[2][100]
# set up compute snap generating global array
@ -118,12 +116,12 @@ 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: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[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_style custom pe pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
@ -166,11 +164,11 @@ Neighbor list info ...
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 21.78 | 21.78 | 21.78 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699 322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699
Loop time of 2.14577e-06 on 1 procs for 0 steps with 2 atoms
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
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
93.2% CPU use with 1 MPI tasks x 1 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
@ -180,7 +178,7 @@ 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 | | 2.146e-06 | | |100.00
Other | | 1e-06 | | |100.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0

30
examples/snap/log.27Nov18.snap.compute.quadratic.g++.4 → examples/snap/log.03Jul20.snap.compute.quadratic.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (20 Nov 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
LAMMPS (15 Jun 2020)
# Demonstrate bispectrum computes
# initialize simulation
@ -30,11 +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) to (2 2 2)
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
1 by 2 by 2 MPI processor grid
create_atoms 2 box
Created 2 atoms
create_atoms CPU = 0.000118971 secs
create_atoms CPU = 0.001 seconds
mass * 180.88
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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_120 equal c_db[2][120]
variable db_2_100 equal c_db[2][100]
# set up compute snap generating global array
@ -118,12 +116,12 @@ 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: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
# 5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[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_style custom pe pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
thermo_modify norm no
# dump mydump_db all custom 1000 dump_db id c_db[*]
@ -165,13 +163,13 @@ Neighbor list info ...
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:936)
Per MPI rank memory allocation (min/avg/max) = 19.7 | 19.74 | 19.78 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699 322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699
Loop time of 2.80142e-06 on 4 procs for 0 steps with 2 atoms
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
Per MPI rank memory allocation (min/avg/max) = 21.43 | 21.47 | 21.52 Mbytes
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
Loop time of 2.25e-06 on 4 procs for 0 steps with 2 atoms
107.1% CPU use with 4 MPI tasks x 1 OpenMP threads
111.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
@ -181,7 +179,7 @@ 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 | | 2.801e-06 | | |100.00
Other | | 2.25e-06 | | |100.00
Nlocal: 0.5 ave 1 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2