1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
|
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/gromacs command :h3
pair_style lj/gromacs/cuda command :h3
pair_style lj/gromacs/omp command :h3
pair_style lj/gromacs/coul/gromacs command :h3
pair_style lj/gromacs/coul/gromacs/cuda command :h3
pair_style lj/gromacs/coul/gromacs/omp command :h3
[Syntax:]
pair_style style args :pre
style = {lj/gromacs} or {lj/gromacs/coul/gromacs}
args = list of arguments for a particular style :ul
{lj/gromacs} args = inner outer
inner, outer = global switching cutoffs for Lennard Jones
{lj/gromacs/coul/gromacs} args = inner outer (inner2) (outer2)
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
inner2, outer2 = global switching cutoffs for Coulombic (optional) :pre
[Examples:]
pair_style lj/gromacs 9.0 12.0
pair_coeff * * 100.0 2.0
pair_coeff 2 2 100.0 2.0 8.0 10.0 :pre
pair_style lj/gromacs/coul/gromacs 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0 :pre
[Description:]
The {lj/gromacs} styles compute shifted LJ and Coulombic interactions
with an additional switching function S(r) that ramps the energy and force
smoothly to zero between an inner and outer cutoff. It is a commonly
used potential in the "GROMACS"_http://www.gromacs.org MD code and for
the coarse-grained models of "(Marrink)"_#Marrink.
:c,image(Eqs/pair_gromacs.jpg)
R1 is the inner cutoff; Rc is the outer cutoff. The coefficients A, B,
and C are computed by LAMMPS to perform the shifting and smoothing.
The function
S(r) is actually applied once to each term of the LJ formula and once
to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
depending on which pair_style is used. The boundary conditions
applied to the smoothing function are as follows: S(r1) = S'(r1) = 0,
S(rc) = -F(rc), S'(rc) = -F'(rc), where F(r) is the corresponding term
in the LJ or Coulombic potential energy function and a
single quote represents a derivative with respect to r.
The inner and outer cutoff for the LJ and Coulombic terms can be the
same or different depending on whether 2 or 4 arguments are used in
the pair_style command. The inner LJ cutoff must be > 0, but the
inner Coulombic cutoff can be >= 0.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
inner (distance units)
outer (distance units) :ul
Note that sigma is defined in the LJ formula as the zero-crossing
distance for the potential, not as the energy minimum at 2^(1/6)
sigma.
The last 2 coefficients are optional inner and outer cutoffs for style
{lj/gromacs}. If not specified, the global {inner} and {outer} values
are used.
The last 2 coefficients cannot be used with style
{lj/gromacs/coul/gromacs} because this force field does not allow
varying cutoffs for individual atom pairs; all pairs use the global
cutoff(s) specified in the pair_style command.
:line
Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in "Section_accelerate"_Section_accelerate.html of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
None of the GROMACS pair styles support the
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
portion of the pair interaction is already smoothed to 0.0 at the
cutoff.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
None of the GROMACS pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure, since there are no corrections for
a potential that goes to 0.0 at the cutoff.
All of the GROMACS pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
All of the GROMACS pair styles can only be used via the {pair}
keyword of the "run_style respa"_run_style.html command. They do not
support the {inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Marrink)
[(Marrink)] Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
|
