delete old log files

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macstein 2021-06-14 11:44:05 -07:00
parent 6a4420ba5c
commit ec0f47642a
8 changed files with 0 additions and 1028 deletions

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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Demonstrate MLIAP interface to SNAP nn Cu potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.621262
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice fcc $a
lattice fcc 3.621262
Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
create_atoms CPU = 0.000 seconds
mass 1 63.546
# choose potential
pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
SNAP keyword rcutfac 5.0
SNAP keyword twojmax 6
SNAP keyword nelems 1
SNAP keyword elems Cu
SNAP keyword radelems 0.5
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 1
pair_coeff * * Cu
# Setup output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
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 = 6
ghost atom cutoff = 6
binsize = 3, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 31.17 | 31.17 | 31.17 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
Loop time of 12.7584 on 1 procs for 100 steps with 256 atoms
Performance: 0.339 ns/day, 70.880 hours/ns, 7.838 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.755 | 12.755 | 12.755 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014069 | 0.0014069 | 0.0014069 | 0.0 | 0.01
Output | 0.00085897 | 0.00085897 | 0.00085897 | 0.0 | 0.01
Modify | 0.00075486 | 0.00075486 | 0.00075486 | 0.0 | 0.01
Other | | 0.0003242 | | | 0.00
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1431.00 ave 1431 max 1431 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 19968.0 ave 19968 max 19968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19968
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:12

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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Demonstrate MLIAP interface to SNAP nn Cu potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.621262
units metal
# generate the box and atom positions using a FCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice fcc $a
lattice fcc 3.621262
Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
create_atoms CPU = 0.000 seconds
mass 1 63.546
# choose potential
pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
SNAP keyword rcutfac 5.0
SNAP keyword twojmax 6
SNAP keyword nelems 1
SNAP keyword elems Cu
SNAP keyword radelems 0.5
SNAP keyword welems 1.0
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
SNAP keyword switchflag 1
pair_coeff * * Cu
# Setup output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
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 = 6
ghost atom cutoff = 6
binsize = 3, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
Loop time of 3.22769 on 4 procs for 100 steps with 256 atoms
Performance: 1.338 ns/day, 17.932 hours/ns, 30.982 timesteps/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.19 | 3.2037 | 3.2196 | 0.7 | 99.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0061415 | 0.022081 | 0.035855 | 8.9 | 0.68
Output | 0.00093221 | 0.00094824 | 0.00098861 | 0.0 | 0.03
Modify | 0.0002173 | 0.00022773 | 0.00024477 | 0.0 | 0.01
Other | | 0.0006805 | | | 0.02
Nlocal: 64.0000 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 843.000 ave 843 max 843 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4992.00 ave 4992 max 4992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19968
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Demonstrate MLIAP interface to linear SNAP potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.316
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000 seconds
mass 1 180.88
# choose potential
include Ta06A.nn.mliap
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
Reading potential file Ta06A.nn.mliap.model with DATE: 2021-03-03
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword nelems 1
SNAP keyword elems Ta
SNAP keyword radelems 0.5
SNAP keyword welems 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * mliap Ta
# Setup output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
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 = 5.8
ghost atom cutoff = 5.8
binsize = 2.9, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527
30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131
40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684
50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899
60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757
70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 3.05207 on 1 procs for 100 steps with 128 atoms
Performance: 1.415 ns/day, 16.956 hours/ns, 32.765 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0503 | 3.0503 | 3.0503 | 0.0 | 99.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00072395 | 0.00072395 | 0.00072395 | 0.0 | 0.02
Output | 0.00050893 | 0.00050893 | 0.00050893 | 0.0 | 0.02
Modify | 0.00037375 | 0.00037375 | 0.00037375 | 0.0 | 0.01
Other | | 0.0001878 | | | 0.01
Nlocal: 128.000 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 727.000 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3712.00 ave 3712 max 3712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 7424.00 ave 7424 max 7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
# Demonstrate MLIAP interface to linear SNAP potential
# Initialize simulation
variable nsteps index 100
variable nrep equal 4
variable a equal 3.316
units metal
# generate the box and atom positions using a BCC lattice
variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4
boundary p p p
lattice bcc $a
lattice bcc 3.316
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
region box block 0 ${nx} 0 ${ny} 0 ${nz}
region box block 0 4 0 ${ny} 0 ${nz}
region box block 0 4 0 4 0 ${nz}
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000 seconds
mass 1 180.88
# choose potential
include Ta06A.nn.mliap
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73
# Specify hybrid with SNAP, ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model nn Ta06A.nn.mliap.model descriptor sna Ta06A.mliap.descriptor
Reading potential file Ta06A.nn.mliap.model with DATE: 2021-03-03
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
SNAP keyword nelems 1
SNAP keyword elems Ta
SNAP keyword radelems 0.5
SNAP keyword welems 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword bzeroflag 0
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * mliap Ta
# Setup output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run ${nsteps}
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 = 5.8
ghost atom cutoff = 5.8
binsize = 2.9, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair zbl, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.06 | 18.06 | 18.06 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527
30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131
40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684
50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899
60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757
70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 0.858301 on 4 procs for 100 steps with 128 atoms
Performance: 5.033 ns/day, 4.768 hours/ns, 116.509 timesteps/s
100.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.75351 | 0.79999 | 0.85429 | 4.2 | 93.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0026857 | 0.057019 | 0.10354 | 15.8 | 6.64
Output | 0.00078796 | 0.00080864 | 0.00085671 | 0.0 | 0.09
Modify | 0.00011437 | 0.00012275 | 0.00013339 | 0.0 | 0.01
Other | | 0.0003564 | | | 0.04
Nlocal: 32.0000 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 431.000 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 928.000 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1856.00 ave 1856 max 1856 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7424
Ave neighs/atom = 58.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# ---------- Initialize Simulation ---------------------
clear
using 1 OpenMP thread(s) per MPI task
units metal
dimension 3
boundary p p p
atom_style atomic
read_data Ni_Mo.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
read_data CPU = 0.000 seconds
#change_box all x scale 0.9 y scale 0.9 z scale 0.9
pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor
Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05
SO3 keyword rcutfac 4.1
SO3 keyword nmax 3
SO3 keyword lmax 2
SO3 keyword alpha 2.0
SO3 keyword nelems 2
SO3 keyword elems Mo
SO3 keyword radelems 0.5
SO3 keyword welems 42
pair_coeff * * Mo Ni
variable e equal pe
variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1
# dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run 3
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.22 | 17.22 | 17.22 Mbytes
PotEng Pxx Pyy Pzz Pxy Pxz Pyz
-60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498
-60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829
-60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456
-60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916
Loop time of 0.0093536 on 1 procs for 3 steps with 10 atoms
Performance: 27.711 ns/day, 0.866 hours/ns, 320.732 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0092137 | 0.0092137 | 0.0092137 | 0.0 | 98.50
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.5188e-05 | 1.5188e-05 | 1.5188e-05 | 0.0 | 0.16
Output | 0.00010311 | 0.00010311 | 0.00010311 | 0.0 | 1.10
Modify | 5.4e-06 | 5.4e-06 | 5.4e-06 | 0.0 | 0.06
Other | | 1.621e-05 | | | 0.17
Nlocal: 10.0000 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 423.000 ave 423 max 423 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 780.000 ave 780 max 780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 780
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
variable emin equal $e
variable emin equal -60.5087142406574
variable EperAtom equal (${emin}/${N})
variable EperAtom equal (-60.5087142406574/${N})
variable EperAtom equal (-60.5087142406574/10)
print "Total energy (eV/atom) = ${EperAtom} "
Total energy (eV/atom) = -6.05087142406574
Total wall time: 0:00:00

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@ -1,98 +0,0 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# ---------- Initialize Simulation ---------------------
clear
using 1 OpenMP thread(s) per MPI task
units metal
dimension 3
boundary p p p
atom_style atomic
read_data Ni_Mo.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620)
2 by 2 by 1 MPI processor grid
reading atoms ...
10 atoms
read_data CPU = 0.001 seconds
#change_box all x scale 0.9 y scale 0.9 z scale 0.9
pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor
Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05
SO3 keyword rcutfac 4.1
SO3 keyword nmax 3
SO3 keyword lmax 2
SO3 keyword alpha 2.0
SO3 keyword nelems 2
SO3 keyword elems Mo
SO3 keyword radelems 0.5
SO3 keyword welems 42
pair_coeff * * Mo Ni
variable e equal pe
variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1
# dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run 3
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.23 | 17.23 | 17.23 Mbytes
PotEng Pxx Pyy Pzz Pxy Pxz Pyz
-60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498
-60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829
-60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456
-60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916
Loop time of 0.00731116 on 4 procs for 3 steps with 10 atoms
Performance: 35.453 ns/day, 0.677 hours/ns, 410.331 timesteps/s
84.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0027137 | 0.0039915 | 0.0065214 | 2.5 | 54.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00021023 | 0.002945 | 0.0044067 | 3.0 | 40.28
Output | 9.7476e-05 | 0.00030125 | 0.00043822 | 0.0 | 4.12
Modify | 4.574e-06 | 5.1632e-06 | 6.299e-06 | 0.0 | 0.07
Other | | 6.82e-05 | | | 0.93
Nlocal: 2.50000 ave 3 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 303.500 ave 304 max 303 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 195.000 ave 234 max 156 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 780
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
variable emin equal $e
variable emin equal -60.5087142406574
variable EperAtom equal (${emin}/${N})
variable EperAtom equal (-60.5087142406574/${N})
variable EperAtom equal (-60.5087142406574/10)
print "Total energy (eV/atom) = ${EperAtom} "
Total energy (eV/atom) = -6.05087142406574
Total wall time: 0:00:00

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@ -1,125 +0,0 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
#read_data Si.data
lattice diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region box block 0 2 0 2 0 2
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 64 atoms
create_atoms CPU = 0.001 seconds
mass 1 29.0
# temperature
variable t equal 500.
# Potential
#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
SO3 keyword rcutfac 5.0
SO3 keyword nmax 3
SO3 keyword lmax 4
SO3 keyword alpha 2.0
SO3 keyword nelems 1
SO3 keyword elems Si
SO3 keyword radelems 0.5
SO3 keyword welems 14
pair_coeff * * Si Si
# Set-up output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create $t 5287287 loop geom
velocity all create 500 5287287 loop geom
fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2
run ${nsteps}
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 = 6
ghost atom cutoff = 6
binsize = 3, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 298.3 | 298.3 | 298.3 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456
10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624
20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165
30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641
40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177
50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008
60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639
70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391
80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675
90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78
100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458
Loop time of 5.83795 on 1 procs for 100 steps with 64 atoms
Performance: 0.740 ns/day, 32.433 hours/ns, 17.129 timesteps/s
91.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.8338 | 5.8338 | 5.8338 | 0.0 | 99.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00053236 | 0.00053236 | 0.00053236 | 0.0 | 0.01
Output | 0.0006904 | 0.0006904 | 0.0006904 | 0.0 | 0.01
Modify | 0.0025477 | 0.0025477 | 0.0025477 | 0.0 | 0.04
Other | | 0.0003419 | | | 0.01
Nlocal: 64.0000 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 557.000 ave 557 max 557 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2944.00 ave 2944 max 2944 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2944
Ave neighs/atom = 46.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

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@ -1,125 +0,0 @@
LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
#read_data Si.data
lattice diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region box block 0 2 0 2 0 2
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 64 atoms
create_atoms CPU = 0.000 seconds
mass 1 29.0
# temperature
variable t equal 500.
# Potential
#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
SO3 keyword rcutfac 5.0
SO3 keyword nmax 3
SO3 keyword lmax 4
SO3 keyword alpha 2.0
SO3 keyword nelems 1
SO3 keyword elems Si
SO3 keyword radelems 0.5
SO3 keyword welems 14
pair_coeff * * Si Si
# Set-up output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create $t 5287287 loop geom
velocity all create 500 5287287 loop geom
fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2
run ${nsteps}
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 = 6
ghost atom cutoff = 6
binsize = 3, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 298.2 | 298.2 | 298.2 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456
10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624
20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165
30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641
40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177
50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008
60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639
70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391
80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675
90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78
100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458
Loop time of 2.61422 on 4 procs for 100 steps with 64 atoms
Performance: 1.653 ns/day, 14.523 hours/ns, 38.252 timesteps/s
91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4136 | 2.4671 | 2.569 | 3.9 | 94.37
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.037437 | 0.13954 | 0.19315 | 16.2 | 5.34
Output | 0.00088435 | 0.0013739 | 0.0028352 | 2.3 | 0.05
Modify | 0.004319 | 0.0054199 | 0.0059273 | 0.9 | 0.21
Other | | 0.0007924 | | | 0.03
Nlocal: 16.0000 ave 16 max 16 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 349.000 ave 349 max 349 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 736.000 ave 736 max 736 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2944
Ave neighs/atom = 46.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02