jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update kim_query & clear and update examples/kim

This commit is contained in:
Ryan S. Elliott 2019-07-25 14:03:35 -05:00
parent ca291f1015
commit fadb40051b
23 changed files with 86 additions and 1173 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
examples/kim/in.kim.lj.simulator_model → examples/kim/in.kim-ex.melt
View File

@ -14,15 +14,14 @@ variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode
newton on
kim_init LennardJones_Ar real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Au
kim_interactions Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
@ -31,5 +30,6 @@ neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

37
examples/kim/in.kim-pm-query.melt Normal file
View File

@ -0,0 +1,37 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
lattice fcc ${a0}
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

19
examples/kim/in.kim.lj.newton-off → examples/kim/in.kim-pm.melt
View File

@ -1,9 +1,10 @@
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
@ -14,20 +15,14 @@ variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton off
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
pair_style kim LennardJones_Ar
pair_coeff * * Ar
kim_interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom

36
examples/kim/in.kim-sm.melt Normal file
View File

@ -0,0 +1,36 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions O
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

35
examples/kim/in.kim.lj.lmp.newton-off
View File

@ -1,35 +0,0 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton off
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

41
examples/kim/in.kim.lj.newton-on
View File

@ -1,41 +0,0 @@
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton on
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
pair_style kim LennardJones_Ar
pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100

4
examples/kim/in.kim.lj.lmp.newton-on → examples/kim/in.lammps.melt
View File

@ -8,9 +8,7 @@ variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
newton on
units real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}

12
examples/kim/in.query
View File

@ -1,12 +0,0 @@
# example for performing a query to the OpenKIM test database to retrieve
# a parameter to be used in the input. here it requests the aluminium
# lattice constant for a specific test used for a specific model and then
# assigns it to the variable 'latconst'
kim_init EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002 metal
info variables out log
kim_query latconst split get_test_result test=TE_156715955670 species=["Al"] prop=structure-cubic-crystal-npt keys=["a","a"] units=["angstrom","angstrom"]
info variables out log
lattice fcc ${latconst_1}
lattice fcc ${latconst_2}

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1
View File

@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.004499 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms
Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54
Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90
Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23
Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00
Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95
Other | | 0.01091 | | | 0.37
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2370499
Ave neighs/atom = 74.0781
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4
View File

@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.001039 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms
Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/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 | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63
Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22
Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89
Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01
Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89
Other | | 0.02618 | | | 3.36
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 630904 ave 632094 max 628209 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 2523614
Ave neighs/atom = 78.8629
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1
View File

@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.003479 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms
Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26
Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65
Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08
Other | | 0.01094 | | | 0.50
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2126875
Ave neighs/atom = 66.4648
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

55
examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4
View File

@ -1,55 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000919 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms
Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/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 | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63
Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58
Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32
Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01
Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47
Other | | 0.006263 | | | 0.99
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 531719 ave 533273 max 529395 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 2126875
Ave neighs/atom = 66.4648
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

59
examples/kim/log.06Feb2019.in.kim.lj.newton-off.1
View File

@ -1,59 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.003446 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms
Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/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 | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05
Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58
Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82
Other | | 0.01032 | | | 0.34
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

65
examples/kim/log.06Feb2019.in.kim.lj.newton-off.4
View File

@ -1,65 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000921 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms
Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/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 | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52
Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91
Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74
Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01
Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17
Other | | 0.005874 | | | 0.66
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

59
examples/kim/log.06Feb2019.in.kim.lj.newton-on.1
View File

@ -1,59 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.003089 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms
Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58
Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82
Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41
Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00
Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81
Other | | 0.01132 | | | 0.37
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

65
examples/kim/log.06Feb2019.in.kim.lj.newton-on.4
View File

@ -1,65 +0,0 @@
LAMMPS (1 Feb 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000893 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms
Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53
Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85
Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82
Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00
Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04
Other | | 0.006797 | | | 0.75
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

34
examples/kim/log.22Mar2019.query.g++.1
View File

@ -1,34 +0,0 @@
LAMMPS (28 Feb 2019)
# example for performing a query to the OpenKIM test database to retrieve
# a parameter to be used in the input. here it requests the aluminium
# lattice constant for a specific test used for a specific model and then
# assigns it to the variable 'latconst'
units metal
info variables out log
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Fri Mar 22 20:00:56 2019
Variable information:
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
info variables out log
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
Printed on Fri Mar 22 20:00:57 2019
Variable information:
Variable[ 0]: latconst , style = string , def = 4.03208274841
Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
lattice fcc ${latconst}
lattice fcc 4.03208274841
Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
Total wall time: 0:00:00

92
examples/kim/log.30Apr2019.kim.VOH.simulator_model.g++.1
View File

@ -1,92 +0,0 @@
LAMMPS (30 Apr 2019)
using 1 OpenMP thread(s) per MPI task
# REAX potential for VOH system
# .....
units real
atom_style charge
kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000
units real
atom_style charge
neigh_modify one 4000
read_data data.VOH
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
100 atoms
read_data CPU = 0.000217199 secs
kim_style define H C O V
Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913211_000
For Simulator : LAMMPS 28-Feb-2019
Running on : LAMMPS 30 Apr 2019
pair_style reax/c /tmp/kim-simulator-model-parameter-file-XXXXXXFRmlac safezone 2.0 mincap 100
pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXX363kge H C O V
Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXX363kge with DATE: 2011-02-18
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:311)
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /tmp/kim-simulator-model-parameter-file-XXXXXXzgDl49
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.voh
run 300
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 25.97 | 25.97 | 25.97 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10246.825 0 -10246.825 42.256089
300 199.45773 -10218.342 0 -10159.482 -66.730725
Loop time of 1.06721 on 1 procs for 300 steps with 100 atoms
Performance: 6.072 ns/day, 3.953 hours/ns, 281.107 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.93954 | 0.93954 | 0.93954 | 0.0 | 88.04
Neigh | 0.029087 | 0.029087 | 0.029087 | 0.0 | 2.73
Comm | 0.0018935 | 0.0018935 | 0.0018935 | 0.0 | 0.18
Output | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.00
Modify | 0.096112 | 0.096112 | 0.096112 | 0.0 | 9.01
Other | | 0.0005522 | | | 0.05
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 608 ave 608 max 608 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3441 ave 3441 max 3441 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3441
Ave neighs/atom = 34.41
Neighbor list builds = 30
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

132
examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.1
View File

@ -1,132 +0,0 @@
LAMMPS (30 Apr 2019)
using 1 OpenMP thread(s) per MPI task
units metal
kim_style init ex_sim_model_Si_mod_tersoff
units metal
newton on
atom_style atomic
atom_modify map array
boundary p p p
# temperatures
variable tlo equal 1800.0
variable thi equal 2400.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
create_atoms CPU = 0.000393867 secs
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
velocity all create 2400 5287286 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
kim_style define Si
Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff
For Simulator : LAMMPS 12-Dec-2018
Running on : LAMMPS 30 Apr 2019
pair_style tersoff/mod
pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV Si
Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXVWG8uV with DATE: 2013-07-26
thermo 10
fix 1 all nve
fix 2 all langevin ${thi} ${thi} 0.1 48278
fix 2 all langevin 2400 ${thi} 0.1 48278
fix 2 all langevin 2400 2400 0.1 48278
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.11 | 3.11 | 3.11 Mbytes
Step Temp E_pair E_mol TotEng Press
0 2397.3877 -2363.0694 0 -2205.0272 15086.224
10 1328.4035 -2289.1682 0 -2201.5963 29164.666
20 1086.1557 -2254.4447 0 -2182.8424 31906.878
30 1528.8439 -2270.2968 0 -2169.5113 21610.528
40 1345.227 -2250.3915 0 -2161.7105 22146.886
50 1300.3329 -2235.8593 0 -2150.1379 23557.875
60 1546.1664 -2241.3019 0 -2139.3744 21648.774
70 1662.2896 -2236.2369 0 -2126.6543 23958.738
80 1631.7284 -2223.45 0 -2115.8821 28842.194
90 1795.3629 -2225.2998 0 -2106.9447 29522.37
100 1830.156 -2224.3733 0 -2103.7245 28805.09
Loop time of 0.201725 on 1 procs for 100 steps with 511 atoms
Performance: 42.831 ns/day, 0.560 hours/ns, 495.724 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19292 | 0.19292 | 0.19292 | 0.0 | 95.63
Neigh | 0.0037313 | 0.0037313 | 0.0037313 | 0.0 | 1.85
Comm | 0.00074744 | 0.00074744 | 0.00074744 | 0.0 | 0.37
Output | 0.00026727 | 0.00026727 | 0.00026727 | 0.0 | 0.13
Modify | 0.0036564 | 0.0036564 | 0.0036564 | 0.0 | 1.81
Other | | 0.0004075 | | | 0.20
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 970 ave 970 max 970 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 9174 ave 9174 max 9174 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9174
Ave neighs/atom = 17.953
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:00

132
examples/kim/log.30Apr2019.kim.ex_si.simulator_model.g++.4
View File

@ -1,132 +0,0 @@
LAMMPS (30 Apr 2019)
using 1 OpenMP thread(s) per MPI task
units metal
kim_style init ex_sim_model_Si_mod_tersoff
units metal
newton on
atom_style atomic
atom_modify map array
boundary p p p
# temperatures
variable tlo equal 1800.0
variable thi equal 2400.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
create_atoms CPU = 0.102434 secs
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
velocity all create 2400 5287286 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
kim_style define Si
Using KIM Simulator Model : ex_sim_model_Si_mod_tersoff
For Simulator : LAMMPS 12-Dec-2018
Running on : LAMMPS 30 Apr 2019
pair_style tersoff/mod
pair_coeff * * /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL Si
Reading potential file /tmp/kim-simulator-model-parameter-file-XXXXXXqDlERL with DATE: 2013-07-26
thermo 10
fix 1 all nve
fix 2 all langevin ${thi} ${thi} 0.1 48278
fix 2 all langevin 2400 ${thi} 0.1 48278
fix 2 all langevin 2400 2400 0.1 48278
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes
Step Temp E_pair E_mol TotEng Press
0 2397.5824 -2363.0694 0 -2205.0143 15087.562
10 1298.5003 -2292.5456 0 -2206.945 28361.893
20 1114.7065 -2260.7006 0 -2187.2161 30574.077
30 1504.9472 -2271.8639 0 -2172.6537 20395.651
40 1357.5949 -2248.6066 0 -2159.1103 21779.773
50 1351.7212 -2235.0803 0 -2145.9713 23404.844
60 1582.4191 -2238.3233 0 -2134.006 21711.26
70 1654.3988 -2230.0965 0 -2121.0341 24276.504
80 1654.9629 -2218.6654 0 -2109.5658 27571.472
90 1815.7206 -2219.2065 0 -2099.5093 28475.757
100 1901.1544 -2216.5428 0 -2091.2137 28962.04
Loop time of 4.36959 on 4 procs for 100 steps with 511 atoms
Performance: 1.977 ns/day, 12.138 hours/ns, 22.885 timesteps/s
47.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.051784 | 0.056551 | 0.064825 | 2.1 | 1.29
Neigh | 0.00093389 | 0.001028 | 0.0011392 | 0.3 | 0.02
Comm | 2.8964 | 2.9342 | 3.016 | 2.8 | 67.15
Output | 0.673 | 0.68159 | 0.69707 | 1.1 | 15.60
Modify | 0.0011303 | 0.0029655 | 0.0081694 | 5.5 | 0.07
Other | | 0.6933 | | | 15.87
Nlocal: 127.75 ave 134 max 123 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 495 ave 498 max 489 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2302 ave 2443 max 2194 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 9208
Ave neighs/atom = 18.0196
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:05

104
examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.1
View File

@ -1,104 +0,0 @@
LAMMPS (30 Apr 2019)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units metal
atom_style atomic
newton on
kim_style init LennardJones_Ar
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.00314307 secs
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
kim_style define Ar
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985)
pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 4.91804 on 1 procs for 100 steps with 32000 atoms
Performance: 1.757 ns/day, 13.661 hours/ns, 20.333 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3033 | 4.3033 | 4.3033 | 0.0 | 87.50
Neigh | 0.53176 | 0.53176 | 0.53176 | 0.0 | 10.81
Comm | 0.024606 | 0.024606 | 0.024606 | 0.0 | 0.50
Output | 0.00016403 | 0.00016403 | 0.00016403 | 0.0 | 0.00
Modify | 0.038671 | 0.038671 | 0.038671 | 0.0 | 0.79
Other | | 0.01951 | | | 0.40
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:05

104
examples/kim/log.30Apr2019.kim.lj.simulator_model.g++.4
View File

@ -1,104 +0,0 @@
LAMMPS (30 Apr 2019)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units metal
atom_style atomic
newton on
kim_style init LennardJones_Ar
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.0979962 secs
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
kim_style define Ar
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985)
pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 6.29539 on 4 procs for 100 steps with 32000 atoms
Performance: 1.372 ns/day, 17.487 hours/ns, 15.885 timesteps/s
48.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9399 | 2.079 | 2.2181 | 9.1 | 33.02
Neigh | 0.25924 | 0.26632 | 0.2692 | 0.8 | 4.23
Comm | 2.5011 | 2.6605 | 2.751 | 5.9 | 42.26
Output | 0.069904 | 0.07097 | 0.071545 | 0.3 | 1.13
Modify | 0.011383 | 0.012206 | 0.01419 | 1.0 | 0.19
Other | | 1.206 | | | 19.16
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:07

3
src/KIM/kim_query.cpp
View File

@ -220,8 +220,9 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
url += qfunction;
std::string query(arg[0]);
query += "&model=";
query += "&model=[\"";
query += model_name;
query += "\"]";
for (int i=1; i < narg; ++i) {
query += '&';
query += arg[i];