add pair_style nb3b/screened by Federica Lodesani
This commit is contained in:
Axel Kohlmeyer
1
examples/nb3b/PSiO.nb3b.screened
Symbolic link
1
examples/nb3b/PSiO.nb3b.screened
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/PSiO.nb3b.screened
|
||||
41
examples/nb3b/README.nb3b.screened
Normal file
41
examples/nb3b/README.nb3b.screened
Normal file
@ -0,0 +1,41 @@
|
||||
Additional information for pair style nb3b/screened example.
|
||||
|
||||
This input uses the BMP potential (Bertani, M., Menziani, M. C.,
|
||||
& Pedone, A. (2021). Improved empirical force field for multicomponent
|
||||
oxide glasses and crystals. Physical Review Materials, 5(4), 045602).
|
||||
|
||||
The interatomic potential is obtained by mixing coulombic interactions
|
||||
with other two-body functions (modified Morse and Buckingham), with a
|
||||
three-body interaction (screened harmonic function).
|
||||
|
||||
The modified Morse is introduce with Tables and it is combined with
|
||||
Buckingham and coul/dsf to complete the two-body force field.
|
||||
The three-body interaction is computed with pair style nb3b/screened
|
||||
only for P-O-P angle. With the pair_coeff command the atom types
|
||||
involved in the three-body potential are specified:
|
||||
|
||||
pair_coeff * * nb3b/screened PSiO.nb3b.screened P NULL O
|
||||
|
||||
And they appear in the same order as in the data file:
|
||||
type 1: P;
|
||||
type 2: Na, not involved in the three body so indicated as NULL;
|
||||
type 3: O.
|
||||
|
||||
In the potential file PSiO.nb3b.screened there are the parameters of
|
||||
all permutations of the required atom types. In the example, also
|
||||
parameters for Si permutations appear but they are not employed in
|
||||
the current case.
|
||||
|
||||
# i j k K theta0 rho cutoff
|
||||
O P P 65.0 109.47 1.0 3.3
|
||||
O P Si 120.0 109.47 1.0 0.000
|
||||
O P O 0.000 0.000 1.0 0.000
|
||||
O Si P 120.0 109.47 1.0 0.000
|
||||
O Si Si 25.0 109.47 1.0 3.3
|
||||
(...)
|
||||
|
||||
The rho value must be always higher than 0.0. Cutoff and rho are extracted
|
||||
only from symmetric interactions (e.g. O P P, O Si Si), because of that
|
||||
you do not need to specify those values for the asymmetric interactions
|
||||
(e.g. O P Si and O Si P).
|
||||
|
||||
14997
examples/nb3b/Table_NP.dat
Normal file
14997
examples/nb3b/Table_NP.dat
Normal file
File diff suppressed because it is too large
Load Diff
6020
examples/nb3b/data.NaPO3
Normal file
6020
examples/nb3b/data.NaPO3
Normal file
File diff suppressed because it is too large
Load Diff
35
examples/nb3b/in.nb3b.screened
Normal file
35
examples/nb3b/in.nb3b.screened
Normal file
@ -0,0 +1,35 @@
|
||||
### LAMMPS input file
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaPO3
|
||||
|
||||
pair_style hybrid/overlay coul/dsf 0.2 12.0 table spline 20000 buck 7.0 nb3b/screened
|
||||
|
||||
pair_coeff * * coul/dsf
|
||||
pair_coeff 1 3 table Table_NP.dat Pair_P-O 7.0
|
||||
pair_coeff 2 3 table Table_NP.dat Pair_Na-O 7.0
|
||||
pair_coeff 3 3 table Table_NP.dat Pair_O-O 7.0
|
||||
|
||||
# pair Buckingham
|
||||
pair_coeff 1 1 buck 5.093669 0.905598 0.0
|
||||
|
||||
# shrm
|
||||
pair_coeff * * nb3b/screened PSiO.nb3b.screened P NULL O
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 10 check no
|
||||
timestep 0.002
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step density lx press pe evdwl ecoul temp
|
||||
|
||||
#dump 2 all custom 10000 NaPO3-melt.lammpstrj id type element x y z
|
||||
#dump_modify 2 element P Na O
|
||||
variable temp equal 2500
|
||||
|
||||
fix 1 all npt temp ${temp} ${temp} $(100*dt) iso 1 1 $(1000*dt)
|
||||
run 1000
|
||||
132
examples/nb3b/log.30Oct23.nb3b.screened.g++.1
Normal file
132
examples/nb3b/log.30Oct23.nb3b.screened.g++.1
Normal file
@ -0,0 +1,132 @@
|
||||
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-700-g901ed98d31)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
### LAMMPS input file
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaPO3
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (34.33782 34.33782 34.33782)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
reading velocities ...
|
||||
3000 velocities
|
||||
read_data CPU = 0.019 seconds
|
||||
|
||||
pair_style hybrid/overlay coul/dsf 0.2 12.0 table spline 20000 buck 7.0 nb3b/screened
|
||||
|
||||
pair_coeff * * coul/dsf
|
||||
pair_coeff 1 3 table Table_NP.dat Pair_P-O 7.0
|
||||
WARNING: 1 of 4995 force values in table Pair_P-O are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 2 3 table Table_NP.dat Pair_Na-O 7.0
|
||||
WARNING: 2 of 4995 force values in table Pair_Na-O are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 3 3 table Table_NP.dat Pair_O-O 7.0
|
||||
|
||||
# pair Buckingham
|
||||
pair_coeff 1 1 buck 5.093669 0.905598 0.0
|
||||
|
||||
# shrm
|
||||
pair_coeff * * nb3b/screened PSiO.nb3b.screened P NULL O
|
||||
Reading nb3b/screened potential file PSiO.nb3b.screened with DATE: 2023-10-30
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 10 check no
|
||||
timestep 0.002
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step density lx press pe evdwl ecoul temp
|
||||
|
||||
#dump 2 all custom 10000 NaPO3-melt.lammpstrj id type element x y z
|
||||
#dump_modify 2 element P Na O
|
||||
variable temp equal 2500
|
||||
|
||||
fix 1 all npt temp ${temp} ${temp} $(100*dt) iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 ${temp} $(100*dt) iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 2500 $(100*dt) iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 2500 0.2000000000000000111 iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 2500 0.2000000000000000111 iso 1 1 2
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 10 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13
|
||||
ghost atom cutoff = 13
|
||||
binsize = 6.5, bins = 6 6 6
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair coul/dsf, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (5)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair buck, perpetual, skip from (5)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair nb3b/screened, perpetual, skip from (6)
|
||||
attributes: full, newton on, cut 4.3
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, trim from (1)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual
|
||||
attributes: full, newton on, cut 4.3
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.11 | 12.11 | 12.11 Mbytes
|
||||
Step Density Lx Press PotEng E_vdwl E_coul Temp
|
||||
0 2.509108 34.33782 46464.417 -50581.248 2292.3853 -52873.634 2500
|
||||
100 2.4533672 34.595928 33156.229 -50182.221 2373.5614 -52555.782 1666.1883
|
||||
200 2.3649528 35.021791 29182.391 -50158.578 2367.6353 -52526.213 1885.4424
|
||||
300 2.2932707 35.382952 14450.387 -50100.892 2239.9823 -52340.875 2045.1557
|
||||
400 2.2282371 35.723887 16680.683 -50048.753 2281.6385 -52330.392 2257.1768
|
||||
500 2.1753698 36.010969 15871.062 -49981.163 2285.6757 -52266.839 2396.7925
|
||||
600 2.1285968 36.272824 15066.532 -49934.767 2282.4577 -52217.225 2540.7515
|
||||
700 2.0841139 36.529076 7572.3436 -49895.93 2222.7473 -52118.677 2577.5774
|
||||
800 2.0485057 36.739517 6642.7187 -49870.601 2230.3801 -52100.981 2556.7855
|
||||
900 2.0180051 36.923689 8318.7918 -49890.3 2255.1538 -52145.454 2538.111
|
||||
1000 1.990678 37.091879 7724.2804 -49928.89 2250.855 -52179.745 2492.3778
|
||||
Loop time of 30.3284 on 1 procs for 1000 steps with 3000 atoms
|
||||
|
||||
Performance: 5.698 ns/day, 4.212 hours/ns, 32.972 timesteps/s, 98.917 katom-step/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 | 27.347 | 27.347 | 27.347 | 0.0 | 90.17
|
||||
Neigh | 2.8101 | 2.8101 | 2.8101 | 0.0 | 9.27
|
||||
Comm | 0.067332 | 0.067332 | 0.067332 | 0.0 | 0.22
|
||||
Output | 0.00047847 | 0.00047847 | 0.00047847 | 0.0 | 0.00
|
||||
Modify | 0.087652 | 0.087652 | 0.087652 | 0.0 | 0.29
|
||||
Other | | 0.01585 | | | 0.05
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11846 ave 11846 max 11846 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 811471 ave 811471 max 811471 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 811471
|
||||
Ave neighs/atom = 270.49033
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:30
|
||||
132
examples/nb3b/log.30Oct23.nb3b.screened.g++.4
Normal file
132
examples/nb3b/log.30Oct23.nb3b.screened.g++.4
Normal file
@ -0,0 +1,132 @@
|
||||
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-700-g901ed98d31)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
### LAMMPS input file
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style charge
|
||||
|
||||
read_data data.NaPO3
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (34.33782 34.33782 34.33782)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3000 atoms
|
||||
reading velocities ...
|
||||
3000 velocities
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
pair_style hybrid/overlay coul/dsf 0.2 12.0 table spline 20000 buck 7.0 nb3b/screened
|
||||
|
||||
pair_coeff * * coul/dsf
|
||||
pair_coeff 1 3 table Table_NP.dat Pair_P-O 7.0
|
||||
WARNING: 1 of 4995 force values in table Pair_P-O are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 2 3 table Table_NP.dat Pair_Na-O 7.0
|
||||
WARNING: 2 of 4995 force values in table Pair_Na-O are inconsistent with -dE/dr.
|
||||
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
|
||||
pair_coeff 3 3 table Table_NP.dat Pair_O-O 7.0
|
||||
|
||||
# pair Buckingham
|
||||
pair_coeff 1 1 buck 5.093669 0.905598 0.0
|
||||
|
||||
# shrm
|
||||
pair_coeff * * nb3b/screened PSiO.nb3b.screened P NULL O
|
||||
Reading nb3b/screened potential file PSiO.nb3b.screened with DATE: 2023-10-30
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 10 delay 10 check no
|
||||
timestep 0.002
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step density lx press pe evdwl ecoul temp
|
||||
|
||||
#dump 2 all custom 10000 NaPO3-melt.lammpstrj id type element x y z
|
||||
#dump_modify 2 element P Na O
|
||||
variable temp equal 2500
|
||||
|
||||
fix 1 all npt temp ${temp} ${temp} $(100*dt) iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 ${temp} $(100*dt) iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 2500 $(100*dt) iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 2500 0.2000000000000000111 iso 1 1 $(1000*dt)
|
||||
fix 1 all npt temp 2500 2500 0.2000000000000000111 iso 1 1 2
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update: every = 10 steps, delay = 10 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 13
|
||||
ghost atom cutoff = 13
|
||||
binsize = 6.5, bins = 6 6 6
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair coul/dsf, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (5)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair buck, perpetual, skip from (5)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair nb3b/screened, perpetual, skip from (6)
|
||||
attributes: full, newton on, cut 4.3
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) neighbor class addition, perpetual, trim from (1)
|
||||
attributes: half, newton on, cut 8
|
||||
pair build: trim
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) neighbor class addition, perpetual
|
||||
attributes: full, newton on, cut 4.3
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.188 | 7.188 | 7.189 Mbytes
|
||||
Step Density Lx Press PotEng E_vdwl E_coul Temp
|
||||
0 2.509108 34.33782 46464.417 -50581.248 2292.3853 -52873.634 2500
|
||||
100 2.4533672 34.595928 33156.229 -50182.221 2373.5614 -52555.782 1666.1883
|
||||
200 2.3649528 35.021791 29182.391 -50158.578 2367.6353 -52526.213 1885.4424
|
||||
300 2.2932707 35.382952 14450.387 -50100.892 2239.9823 -52340.875 2045.1557
|
||||
400 2.2282371 35.723887 16680.683 -50048.753 2281.6385 -52330.392 2257.1768
|
||||
500 2.1753698 36.010969 15871.062 -49981.163 2285.6757 -52266.839 2396.7925
|
||||
600 2.1285968 36.272824 15066.532 -49934.767 2282.4577 -52217.225 2540.7515
|
||||
700 2.0841139 36.529076 7572.3446 -49895.929 2222.7474 -52118.677 2577.5774
|
||||
800 2.0485057 36.739517 6642.7277 -49870.601 2230.3802 -52100.981 2556.7856
|
||||
900 2.0180051 36.923689 8318.7257 -49890.301 2255.153 -52145.454 2538.1115
|
||||
1000 1.990678 37.091879 7730.4071 -49928.905 2250.9166 -52179.822 2492.4197
|
||||
Loop time of 9.72954 on 4 procs for 1000 steps with 3000 atoms
|
||||
|
||||
Performance: 17.760 ns/day, 1.351 hours/ns, 102.780 timesteps/s, 308.339 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.1441 | 8.0123 | 8.622 | 19.6 | 82.35
|
||||
Neigh | 0.7458 | 0.78431 | 0.80001 | 2.5 | 8.06
|
||||
Comm | 0.26061 | 0.88607 | 1.7928 | 61.3 | 9.11
|
||||
Output | 0.00024827 | 0.00027521 | 0.00035196 | 0.0 | 0.00
|
||||
Modify | 0.03802 | 0.038395 | 0.038805 | 0.1 | 0.39
|
||||
Other | | 0.008186 | | | 0.08
|
||||
|
||||
Nlocal: 750 ave 765 max 731 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 6607.5 ave 6671 max 6552 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 202867 ave 217674 max 182729 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 811469
|
||||
Ave neighs/atom = 270.48967
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:09
|
||||
Reference in New Issue
Block a user