Add files via upload
This commit is contained in:
gplummer317
4
examples/NiO.ctip
Normal file
4
examples/NiO.ctip
Normal file
@ -0,0 +1,4 @@
|
||||
# CTIP potential parameters for Ni-O
|
||||
# X (eV) J (eV) gamma (1/ang) zeta (1/ang) Z (e) qmin qmax omega
|
||||
Ni -5.840000 14.157390 0.549290 0.000000 0.000000 0.000000 2.000000 100.000
|
||||
O 0.000000 15.655862 1.428571 0.000000 0.000000 -2.000000 0.000000 100.000
|
||||
18007
examples/NiO.eam.fs
Normal file
18007
examples/NiO.eam.fs
Normal file
File diff suppressed because it is too large
Load Diff
1745
examples/data.ctip
Normal file
1745
examples/data.ctip
Normal file
File diff suppressed because it is too large
Load Diff
43
examples/in.ctip
Normal file
43
examples/in.ctip
Normal file
@ -0,0 +1,43 @@
|
||||
#CTIP potential for NiO
|
||||
#Contributing author: Gabriel Plummer (NASA)
|
||||
|
||||
#Initialize
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
#Create Structure
|
||||
read_data data.ctip
|
||||
|
||||
#Define Charges
|
||||
group type1 type 1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
group type2 type 2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
|
||||
#Define Potential
|
||||
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
|
||||
pair_coeff * * eam/fs NiO.eam.fs Ni O
|
||||
pair_coeff * * coul/ctip NiO.ctip Ni O
|
||||
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
|
||||
|
||||
#Setup
|
||||
timestep 0.001
|
||||
thermo 100
|
||||
thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
|
||||
|
||||
#Minimization
|
||||
fix relax all box/relax iso 0
|
||||
minimize 1e-10 1e-10 100000 100000
|
||||
unfix relax
|
||||
|
||||
#Dynamics
|
||||
reset_timestep 0
|
||||
variable T equal 1000
|
||||
variable rnd equal round(random(0,999,${T}))
|
||||
velocity all create ${T} ${rnd} mom yes rot yes
|
||||
fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
|
||||
run 1000
|
||||
162
examples/log.ctip
Normal file
162
examples/log.ctip
Normal file
@ -0,0 +1,162 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-185-ge2e17b1326)
|
||||
#CTIP potential for NiO
|
||||
#Contributing author: Gabriel Plummer (NASA)
|
||||
|
||||
#Initialize
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
#Create Structure
|
||||
read_data data.ctip
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (24.719478 24.719478 24.719478)
|
||||
5 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1728 atoms
|
||||
read_data CPU = 0.411 seconds
|
||||
|
||||
#Define Charges
|
||||
group type1 type 1
|
||||
864 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
group type2 type 2
|
||||
864 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
|
||||
#Define Potential
|
||||
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
|
||||
pair_coeff * * eam/fs NiO.eam.fs Ni O
|
||||
pair_coeff * * coul/ctip NiO.ctip Ni O
|
||||
fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
|
||||
|
||||
#Setup
|
||||
timestep 0.001
|
||||
thermo 100
|
||||
thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
|
||||
|
||||
#Minimization
|
||||
fix relax all box/relax iso 0
|
||||
minimize 1e-10 1e-10 100000 100000
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 4 4 4
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair eam/fs, perpetual, trim from (2)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair coul/ctip, perpetual, half/full from (3)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix qeq/ctip, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
|
||||
(../min.cpp:219)
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.02 | 10.44 | 11.08 Mbytes
|
||||
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
|
||||
0 0 -9633.183 24.719478 24.719478 24.719478 -1482.4422 -1482.4422 -1482.4422 1.2374584 -1.2374584
|
||||
6 0 -9633.1929 24.70758 24.70758 24.70758 0.0058029496 0.0058029495 0.0058029496 1.2410596 -1.2410596
|
||||
Loop time of 0.141029 on 20 procs for 6 steps with 1728 atoms
|
||||
|
||||
99.0% CPU use with 20 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-9633.18301863317 -9633.19294375406 -9633.19294375059
|
||||
Force two-norm initial, final = 41.928235 0.00016400809
|
||||
Force max component initial, final = 41.928235 0.00016396812
|
||||
Final line search alpha, max atom move = 0.0069092778 1.1329013e-06
|
||||
Iterations, force evaluations = 6 8
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.035558 | 0.041786 | 0.051032 | 3.7 | 29.63
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00095936 | 0.010188 | 0.0164 | 7.4 | 7.22
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0.087686 | 0.087716 | 0.087736 | 0.0 | 62.20
|
||||
Other | | 0.001339 | | | 0.95
|
||||
|
||||
Nlocal: 86.4 ave 108 max 72 min
|
||||
Histogram: 12 0 0 0 0 0 0 0 0 8
|
||||
Nghost: 5617.4 ave 5704 max 5307 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 16
|
||||
Neighs: 10800 ave 13500 max 9000 min
|
||||
Histogram: 12 0 0 0 0 0 0 0 0 8
|
||||
FullNghs: 117158 ave 146448 max 97632 min
|
||||
Histogram: 12 0 0 0 0 0 0 0 0 8
|
||||
|
||||
Total # of neighbors = 2343168
|
||||
Ave neighs/atom = 1356
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
unfix relax
|
||||
|
||||
#Dynamics
|
||||
reset_timestep 0
|
||||
variable T equal 1000
|
||||
variable rnd equal round(random(0,999,${T}))
|
||||
variable rnd equal round(random(0,999,1000))
|
||||
velocity all create ${T} ${rnd} mom yes rot yes
|
||||
velocity all create 1000 ${rnd} mom yes rot yes
|
||||
velocity all create 1000 233 mom yes rot yes
|
||||
fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
|
||||
fix npt all npt temp 1000 ${T} 0.1 iso 0 0 1
|
||||
fix npt all npt temp 1000 1000 0.1 iso 0 0 1
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.149 | 9.566 | 10.2 Mbytes
|
||||
Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
|
||||
0 1000 -9633.1929 24.70758 24.70758 24.70758 15934.845 15754.643 15735.458 1.2410596 -1.2410596
|
||||
100 600.77735 -9528.0587 24.816528 24.816528 24.816528 -16706.896 -15440.795 -17748.438 1.2181931 -1.2181931
|
||||
200 578.84855 -9490.9798 24.812601 24.812601 24.812601 -5870.3683 -4842.0362 -6712.6896 1.2254406 -1.2254406
|
||||
300 694.79571 -9478.5506 24.764327 24.764327 24.764327 14631.481 13819.893 13758.612 1.2372043 -1.2372043
|
||||
400 803.94245 -9462.254 24.866657 24.866657 24.866657 -4649.2497 -6021.9034 -7748.6267 1.2086116 -1.2086116
|
||||
500 893.70588 -9441.0062 24.891745 24.891745 24.891745 -5778.8391 -8212.3527 -4181.1625 1.2001221 -1.2001221
|
||||
600 947.22119 -9416.7533 24.863639 24.863639 24.863639 11263.656 12950.02 11329.777 1.2115052 -1.2115052
|
||||
700 1040.4867 -9409.838 24.933876 24.933876 24.933876 -6572.1906 -8531.0436 -3289.5795 1.1902748 -1.1902748
|
||||
800 1037.9461 -9398.4839 24.935134 24.935134 24.935134 -4681.5289 -2573.9057 -7152.37 1.1880294 -1.1880294
|
||||
900 1049.4492 -9411.1233 24.899755 24.899755 24.899755 3245.1762 8109.7345 5937.7248 1.2024012 -1.2024012
|
||||
1000 964.21897 -9412.4497 24.926456 24.926456 24.926456 -7644.82 -5151.3661 -8344.385 1.1908843 -1.1908843
|
||||
Loop time of 22.2998 on 20 procs for 1000 steps with 1728 atoms
|
||||
|
||||
Performance: 3.874 ns/day, 6.194 hours/ns, 44.843 timesteps/s, 77.489 katom-step/s
|
||||
99.7% CPU use with 20 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0411 | 4.7454 | 5.7909 | 34.0 | 21.28
|
||||
Neigh | 0.014489 | 0.017484 | 0.022231 | 1.9 | 0.08
|
||||
Comm | 0.1939 | 1.2368 | 1.9393 | 66.5 | 5.55
|
||||
Output | 0.00054344 | 0.00056061 | 0.00086343 | 0.0 | 0.00
|
||||
Modify | 16.272 | 16.28 | 16.286 | 0.1 | 73.01
|
||||
Other | | 0.01926 | | | 0.09
|
||||
|
||||
Nlocal: 86.4 ave 113 max 67 min
|
||||
Histogram: 4 3 1 3 0 3 1 1 3 1
|
||||
Nghost: 5641.65 ave 5713 max 5446 min
|
||||
Histogram: 4 0 0 0 0 0 0 1 7 8
|
||||
Neighs: 10519.6 ave 13753 max 8190 min
|
||||
Histogram: 4 3 0 4 0 3 1 1 3 1
|
||||
FullNghs: 111724 ave 146057 max 86634 min
|
||||
Histogram: 4 3 1 3 0 3 1 1 3 1
|
||||
|
||||
Total # of neighbors = 2234476
|
||||
Ave neighs/atom = 1293.0995
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
Reference in New Issue
Block a user