lammps/doc/pair_reax_c.txt

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pair_style reax/c command :h3

[Syntax:]

pair_style reax/c cfile keyword value :pre

cfile = NULL or name of a control file :ul

one keyword value pair may be appended
keyword = {checkqeq} 
  {checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix :pre
:ule

[Examples:]

pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_coeff * * ffield.reax 1 2 2 3 :pre 

[Description:]

Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
co-workers.  ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. There is more than one version of ReaxFF.  The version
implemented in LAMMPS uses the functional forms documented in the
supplemental information of the following paper: "(Chenoweth et al.,
2008)"_#Chenoweth_2008.  The version integrated into LAMMPS matches
the most up-to-date version of ReaxFF as of summer 2010.  For more
technical details about the pair reax/c implementation of ReaxFF, see
the "(Aktulga)" paper.

The {reax/c} style differs from the "pair_style reax"_pair_reax.html
command in the lo-level implementation details.  The {reax} style is a
Fortran library, linked to LAMMPS.  The {reax/c} style was initially
implemented as stand-alone C code and is now integrated into LAMMPS as
a package.

LAMMPS provides several different versions of ffield.reax in its
potentials dir, each called potentials/ffield.reax.label.  These are
documented in potentials/README.reax.  The default ffield.reax
contains parameterizations for the following elements: C, H, O, N, S.

The format of these files is identical to that used originally by van
Duin.  We have tested the accuracy of {pair_style reax/c} potential
against the original ReaxFF code for the systems mentioned above.  You
can use other ffield files for specific chemical systems that may be
available elsewhere (but note that their accuracy may not have been
tested).

The {cfile} setting can be specified as NULL, in which case default
settings are used.  Or a control file can be specified which contains
cutoff values for the ReaxFF potential in addition to some performance
and output controls.  Each line in the control specifies the value for
a control variable.  The format of the control file is described
below.  

Two examples using {pair_style reax/c} are provided in the examples/reax
sub-directory, along with corresponding examples for 
"pair_style reax"_pair_reax.html.

Use of this pair style requires that a charge be defined for every
atom.  See the "atom_style"_atom_style.html and
"read_data"_read_data.html commands for details on how to specify
charges.

The ReaxFF parameter files provided were created using a charge
equilibration (QEq) model for handling the electrostatic interactions.
Therefore, by default, LAMMPS requires that the "fix
qeq/reax"_fix_qeq_reax.html command be used with {pair_style reax/c}
when simulating a ReaxFF model, to equilibrate charge each timestep.
Using the keyword {checkqeq} with the value {no} 
turns off the check for {fix qeq/reax},
allowing a simulation to be run without charge equilibration.
In this case, the static charges you
assign to each atom will be used for computing the electrostatic
interactions in the system.
See the "fix qeq/reax"_fix_qeq_reax.html command for details.

The thermo variable {evdwl} stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
{ecoul}.  The output of these quantities is controlled by the
"thermo"_thermo.html command.

This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html command as a vector of values of length 14.
The 14 values correspond to the following sub-categories (the variable
names in italics match those used in the original FORTRAN ReaxFF code):

{eb} = bond energy
{ea} = atom energy
{elp} = lone-pair energy
{emol} = molecule energy (always 0.0)
{ev} = valence angle energy
{epen} = double-bond valence angle penalty
{ecoa} = valence angle conjugation energy
{ehb} = hydrogen bond energy
{et} = torsion energy
{eco} = conjugation energy 
{ew} = van der Waals energy
{ep} = Coulomb energy
{efi} = electric field energy (always 0.0)
{eqeq} = charge equilibration energy :ol

To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:

compute reax all pair reax/c
variable eb  	 equal c_reax\[1\]
variable ea  	 equal c_reax\[2\] 
...
variable eqeq 	 equal c_reax\[14\]
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre

Only a single pair_coeff command is used with the {reax/c} style which
specifies a ReaxFF potential file with parameters for all needed
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 number of LAMMPS atom types:

filename
N indices = mapping of ReaxFF elements to atom types :ul

The filename is the ReaxFF potential file.  Unlike for the {reax}
pair style, any filename can be used.

In the ReaxFF potential file, near the top, after the general
parameters, is the atomic parameters section that contains element
names, each with a couple dozen numeric parameters.  If there are M
elements specified in the {ffield} file, think of these as numbered 1
to M. Each of the N indices you specify for the N atom types of LAMMPS
atoms must be an integer from 1 to M.  Atoms with LAMMPS type 1 will
be mapped to whatever element you specify as the first index value,
etc.  If a mapping value is specified as NULL, the mapping is not
performed.  This can be used when the {reax/c} style is used as part
of the {hybrid} pair style.  The NULL values are placeholders for atom
types that will be used with other potentials.

IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part
of the {hybrid} pair style.  Some additional work still need to be
done to enable this.

As an example, say your LAMMPS simulation has 4 atom types and the
elements are ordered as C, H, O, N in the {ffield} file.  If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:

pair_coeff * * ffield.reax 1 1 4 2 :pre

:line

The format of a line in the control file is as follows:

variable_name value :pre

and it may be followed by an "!" character and a trailing comment.

If the value of a control variable is not specified, then default
values are used.  What follows is the list of variables along with a
brief description of their use and default values.

simulation_name: Output files produced by {pair_style reax/c} carry
this name + extensions specific to their contents.  Partial energies
are reported with a ".pot" extension, while the trajectory file has
".trj" extension.
 
tabulate_long_range: To improve performance, long range interactions
can optionally be tabulated (0 means no tabulation). Value of this
variable denotes the size of the long range interaction table.  The
range from 0 to long range cutoff (defined in the {ffield} file) is
divided into {tabulate_long_range} points.  Then at the start of
simulation, we fill in the entries of the long range interaction table
by computing the energies and forces resulting from van der Waals and
Coulomb interactions between every possible atom type pairs present in
the input system.  During the simulation we consult to the long range
interaction table to estimate the energy and forces between a pair of
atoms. Linear interpolation is used for estimation. (default value =
0)

energy_update_freq: Denotes the frequency (in number of steps) of
writes into the partial energies file. (default value = 0)

nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
regarding the bonded interactions. (default value = 4)

hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
bond interactions.(default value = 0 - means no hydrogen bonds are
present)

bond_graph_cutoff: is the threshold used in determining what is a
physical bond, what is not. Bonds and angles reported in the
trajectory file rely on this cutoff. (default value = 0.3)

thb_cutoff: cutoff value for the strength of bonds to be considered in
three body interactions. (default value = 0.001)

write_freq: Frequency of writes into the trajectory file. (default
value = 0)

traj_title: Title of the trajectory - not the name of the trajectory
file.

atom_info: 1 means print only atomic positions + charge (default = 0)

atom_forces: 1 adds net forces to atom lines in the trajectory file
(default = 0)

atom_velocities: 1 adds atomic velocities to atoms line (default = 0)

bond_info: 1 prints bonds in the trajectory file (default = 0)

angle_info: 1 prints angles in the trajectory file (default = 0)

:line

[Mixing, shift, table, tail correction, restart, rRESPA info]:

This pair style does not support the "pair_modify"_pair_modify.html
mix, shift, table, and tail options.

This pair style does not write its information to "binary restart
files"_restart.html, since it is stored in potential files.  Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.

This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command.  It does not support the
{inner}, {middle}, {outer} keywords.

[Restrictions:]

This pair style is part of the USER-REAXC package.  It is only enabled
if LAMMPS was built with that package.  See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.

The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real "units"_units.html.  You can use
the ReaxFF potential with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation doesn't use "real" units.

This pair style cannot yet compute per-atom energy or stress.  If you
use another command that tries to calculate these quantities using
this pair style, a warning message will be printed and the quantities
will be 0.0.

[Related commands:]

"pair_coeff"_pair_coeff.html, "fix_qeq_reax"_fix_qeq_reax.html,
"pair_style reax"_pair_reax.html

[Default:]

The keyword default is checkqeq = yes.

:line

:link(Chenoweth_2008) 
[(Chenoweth_2008)] Chenoweth, van Duin and Goddard, 
Journal of Physical Chemistry A, 112, 1040-1053 (2008).

:link(Aktulga) [(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel
Computing, to appear (2011).