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add pair_style nb3b/screened by Federica Lodesani

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This commit is contained in:
Axel Kohlmeyer
2023-10-30 11:01:57 -04:00
parent 1db5643d6e
commit 6056941688
15 changed files with 21536 additions and 17 deletions
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1
doc/src/Commands_pair.rst
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@ -221,6 +221,7 @@ OPT.
* :doc:`multi/lucy <pair_multi_lucy>`
* :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>`
* :doc:`nb3b/screened <pair_nb3b_screened>`
* :doc:`nm/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/long (o) <pair_nm>`

30
doc/src/pair_nb3b_harmonic.rst
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@ -1,14 +1,20 @@
.. index:: pair_style nb3b/harmonic
.. index:: pair_style nb3b/screened
pair_style nb3b/harmonic command
================================
pair_style nb3b/screened command
================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style nb3b/harmonic
pair_style style
* style = *nb3b/harmonic* or *nb3b/screened*
Examples
""""""""
@ -18,10 +24,14 @@ Examples
pair_style nb3b/harmonic
pair_coeff * * MgOH.nb3bharmonic Mg O H
pair_style nb3b/screened
pair_coeff * * PO.nb3b.screened P NULL O
pair_coeff * * SiOH.nb3b.screened Si O H
Description
"""""""""""
This pair style computes a non-bonded 3-body harmonic potential for the
The pair style *nb3b/harmonic* computes a non-bonded 3-body harmonic potential for the
energy E of a system of atoms as
.. math::
@ -33,7 +43,17 @@ prefactor. Note that the usual 1/2 factor is included in *K*\ . The form
of the potential is identical to that used in angle_style *harmonic*,
but in this case, the atoms do not need to be explicitly bonded.
Only a single pair_coeff command is used with this style which
Style *nb3b/screened* adds an additional exponentially decaying factor to
the harmonic term, given by
.. math::
E = K (\theta - \theta_0)^2 \exp \left(- \frac{r_{ij}}{\rho_{ij}} - \frac{r_{ik}}{\rho_{ik}} \right)
where :math:`\rho_ij` and :math:`\rho_ik` are the screening factors along
the two bonds. Note that the usual 1/2 factor is included in *K*.
Only a single pair_coeff command is used with these styles which
specifies a potential file with parameters for specified elements.
These are mapped to LAMMPS atom types by specifying N additional
arguments after the filename in the pair_coeff command, where N is the
@ -61,8 +81,8 @@ type 4 to the C element in the potential file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when the potential is used as part of the *hybrid* pair style. The
NULL values are placeholders for atom types that will be used with
other potentials. An example of a pair_coeff command for use with the
*hybrid* pair style is:
other potentials. Two examples of pair_coeff command for use with the
*hybrid* pair style are:
.. code-block:: LAMMPS

1
doc/src/pair_style.rst
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@ -298,6 +298,7 @@ accelerated styles exist.
* :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
* :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
* :doc:`nb3b/harmonic <pair_nb3b_harmonic>` - non-bonded 3-body harmonic potential
* :doc:`nb3b/screened <pair_nb3b_screened>` - non-bonded 3-body screened harmonic potential
* :doc:`nm/cut <pair_nm>` - N-M potential
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb

1
examples/nb3b/PSiO.nb3b.screened Symbolic link
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@ -0,0 +1 @@
../../potentials/PSiO.nb3b.screened

41
examples/nb3b/README.nb3b.screened Normal file
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@ -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
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File diff suppressed because it is too large Load Diff

6020
examples/nb3b/data.NaPO3 Normal file
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File diff suppressed because it is too large Load Diff

35
examples/nb3b/in.nb3b.screened Normal file
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@ -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
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@ -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
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@ -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

2
src/.gitignore vendored
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@ -1297,6 +1297,8 @@
/pair_morse_soft.h
/pair_nb3b_harmonic.cpp
/pair_nb3b_harmonic.h
/pair_nb3b_screened.cpp
/pair_nb3b_screened.h
/pair_nm_cut.cpp
/pair_nm_cut.h
/pair_nm_cut_coul_cut.cpp

26
src/MANYBODY/pair_nb3b_harmonic.cpp
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@ -37,18 +37,19 @@ using MathConst::MY_PI;
#define DELTA 4
#define SMALL 0.001
static const char *substyle[] = { "nb3n/harmonic", "nb3b/screened" };
/* ---------------------------------------------------------------------- */
PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp)
PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp), params(nullptr)
{
variant = HARMONIC;
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
centroidstressflag = CENTROID_NOTAVAIL;
unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
params = nullptr;
}
/* ----------------------------------------------------------------------
@ -191,9 +192,10 @@ void PairNb3bHarmonic::coeff(int narg, char **arg)
void PairNb3bHarmonic::init_style()
{
if (atom->tag_enable == 0) error->all(FLERR, "Pair style nb3b/harmonic requires atom IDs");
if (atom->tag_enable == 0)
error->all(FLERR, "Pair style {} requires atom IDs", substyle[variant]);
if (force->newton_pair == 0)
error->all(FLERR, "Pair style nb3b/harmonic requires newton pair on");
error->all(FLERR, "Pair style {} requires newton pair on", substyle[variant]);
// need a full neighbor list
@ -222,14 +224,14 @@ void PairNb3bHarmonic::read_file(char *file)
// open file on proc 0
if (comm->me == 0) {
PotentialFileReader reader(lmp, file, "nb3b/harmonic", unit_convert_flag);
PotentialFileReader reader(lmp, file, substyle[variant], unit_convert_flag);
char *line;
// transparently convert units for supported conversions
int unit_convert = reader.get_unit_convert();
double conversion_factor = utils::get_conversion_factor(utils::ENERGY, unit_convert);
while ((line = reader.next_line(NPARAMS_PER_LINE))) {
while ((line = reader.next_line(NPARAMS_PER_LINE + ((variant == SCREENED) ? 1 : 0)))) {
try {
ValueTokenizer values(line);
@ -269,6 +271,10 @@ void PairNb3bHarmonic::read_file(char *file)
params[nparams].kelement = kelement;
params[nparams].k_theta = values.next_double();
params[nparams].theta0 = values.next_double();
if (variant == SCREENED)
params[nparams].rho = values.next_double();
else
params[nparams].rho = 1.0; // dummy value
params[nparams].cutoff = values.next_double();
if (unit_convert) params[nparams].k_theta *= conversion_factor;
@ -276,9 +282,9 @@ void PairNb3bHarmonic::read_file(char *file)
error->one(FLERR, e.what());
}
if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 ||
params[nparams].cutoff < 0.0)
error->one(FLERR, "Illegal nb3b/harmonic parameter");
if ((params[nparams].k_theta < 0.0) || (params[nparams].theta0 < 0.0) ||
(params[nparams].cutoff < 0.0) || (params[nparams].rho <= 0.0))
error->one(FLERR, "Illegal {} parameter", substyle[variant]);
nparams++;
}

7
src/MANYBODY/pair_nb3b_harmonic.h
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@ -35,23 +35,26 @@ class PairNb3bHarmonic : public Pair {
void init_style() override;
static constexpr int NPARAMS_PER_LINE = 6;
enum { HARMONIC = 0, SCREENED };
protected:
struct Param {
double k_theta, theta0, cutoff;
double rho; // added for screened harmonic style
double cut, cutsq;
int ielement, jelement, kelement;
};
double cutmax; // max cutoff for all elements
Param *params; // parameter set for an I-J-K interaction
int variant;
void allocate();
void read_file(char *);
void setup_params();
void twobody(Param *, double, double &, int, double &);
void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
int, double &);
virtual void threebody(Param *, Param *, Param *, double, double, double *, double *, double *,
double *, int, double &);
};
} // namespace LAMMPS_NS

89
src/MANYBODY/pair_nb3b_screened.cpp Normal file
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@ -0,0 +1,89 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Federica Lodesani
(based on nb3b harmonic by Todd R. Zeitler and Stillinger-Weber pair style)
------------------------------------------------------------------------- */
#include "pair_nb3b_screened.h"
#include <cmath>
#define SMALL 0.001
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairNb3bScreened::PairNb3bScreened(LAMMPS *lmp) : PairNb3bHarmonic(lmp)
{
variant = SCREENED;
}
/* ---------------------------------------------------------------------- */
void PairNb3bScreened::threebody(Param *paramij, Param *paramik, Param *paramijk, double rsq1,
double rsq2, double *delr1, double *delr2, double *fj, double *fk,
int eflag, double &eng)
{
double dtheta, tk;
double r1, r2, c, s, a, a11, a12, a22;
double scr, t00, rho1inv, rho2inv;
double ratio1, ratio2;
// angle (cos and sin)
r1 = sqrt(rsq1);
r2 = sqrt(rsq2);
c = delr1[0] * delr2[0] + delr1[1] * delr2[1] + delr1[2] * delr2[2];
c /= r1 * r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c * c);
if (s < SMALL) s = SMALL;
s = 1.0 / s;
// force & energy
// Harmonic function multiplied by a screening function
//
// Uijk=k/2(theta-theta0)**2 * exp[-(rij/rhoij+rik/rhoik)]
//
rho1inv = paramij->rho;
rho2inv = paramik->rho;
scr = exp(-r1 * rho1inv - r2 * rho2inv);
dtheta = acos(c) - paramijk->theta0;
tk = paramijk->k_theta * dtheta * scr;
t00 = tk * dtheta;
if (eflag) eng = t00;
a = -2.0 * tk * s;
a11 = a * c / rsq1;
a12 = -a / (r1 * r2);
a22 = a * c / rsq2;
ratio1 = rho1inv / r1;
ratio2 = rho2inv / r2;
fj[0] = a11 * delr1[0] + a12 * delr2[0] + t00 * ratio1 * delr1[0];
fj[1] = a11 * delr1[1] + a12 * delr2[1] + t00 * ratio1 * delr1[1];
fj[2] = a11 * delr1[2] + a12 * delr2[2] + t00 * ratio1 * delr1[2];
fk[0] = a22 * delr2[0] + a12 * delr1[0] + t00 * ratio2 * delr2[0];
fk[1] = a22 * delr2[1] + a12 * delr1[1] + t00 * ratio2 * delr2[1];
fk[2] = a22 * delr2[2] + a12 * delr1[2] + t00 * ratio2 * delr2[2];
}

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/* -*- c++ -*- ---------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(nb3b/screened,PairNb3bScreened);
// clang-format on
#else
#ifndef LMP_PAIR_NB3B_SCREENED_H
#define LMP_PAIR_NB3B_SCREENED_H
#include "pair_nb3b_harmonic.h"
namespace LAMMPS_NS {
class PairNb3bScreened : public PairNb3bHarmonic {
public:
PairNb3bScreened(class LAMMPS *);
protected:
void threebody(Param *, Param *, Param *, double, double, double *, double *, double *, double *,
int, double &) override;
};
} // namespace LAMMPS_NS
#endif
#endif