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doc/html/_sources/pair_reax.txt
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.. index:: pair_style reax
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pair_style reax command
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=======================
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Syntax
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""""""
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.. parsed-literal::
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pair_style reax hbcut hbnewflag tripflag precision
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* hbcut = hydrogen-bond cutoff (optional) (distance units)
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* hbnewflag = use old or new hbond function style (0 or 1) (optional)
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* tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
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* precision = precision for charge equilibration (optional)
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Examples
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""""""""
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.. parsed-literal::
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pair_style reax
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pair_style reax 10.0 0 1 1.0e-5
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pair_coeff * * ffield.reax 3 1 2 2
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pair_coeff * * ffield.reax 3 NULL NULL 3
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Description
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"""""""""""
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Style *reax* computes the ReaxFF potential of van Duin, Goddard and
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co-workers. ReaxFF uses distance-dependent bond-order functions to
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represent the contributions of chemical bonding to the potential
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energy. There is more than one version of ReaxFF. The version
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implemented in LAMMPS uses the functional forms documented in the
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supplemental information of the following paper:
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:ref:`(Chenoweth) <Chenoweth_2008>`. The version integrated into LAMMPS matches
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the most up-to-date version of ReaxFF as of summer 2010.
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WARNING: pair style reax is now deprecated and will soon be retired. Users
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should switch to :doc:`pair_style reax/c <pair_reax_c>`. The *reax* style
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differs from the *reax/c* style in the lo-level implementation details.
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The *reax* style is a
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Fortran library, linked to LAMMPS. The *reax/c* style was initially
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implemented as stand-alone C code and is now integrated into LAMMPS as
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a package.
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LAMMPS requires that a file called ffield.reax be provided, containing
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the ReaxFF parameters for each atom type, bond type, etc. The format
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is identical to the ffield file used by van Duin and co-workers. The
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filename is required as an argument in the pair_coeff command. Any
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value other than "ffield.reax" will be rejected (see below).
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LAMMPS provides several different versions of ffield.reax in its
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potentials dir, each called potentials/ffield.reax.label. These are
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documented in potentials/README.reax. The default ffield.reax
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contains parameterizations for the following elements: C, H, O, N.
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.. note::
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We do not distribute a wide variety of ReaxFF force field files
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with LAMMPS. Adri van Duin's group at PSU is the central repository
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for this kind of data as they are continuously deriving and updating
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parameterizations for different classes of materials. You can submit
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a contact request at the Materials Computation Center (MCC) website
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`https://www.mri.psu.edu/materials-computation-center/connect-mcc <https://www.mri.psu.edu/materials-computation-center/connect-mcc>`_,
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describing the material(s) you are interested in modeling with ReaxFF.
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They can tell
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you what is currently available or what it would take to create a
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suitable ReaxFF parameterization.
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The format of these files is identical to that used originally by van
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Duin. We have tested the accuracy of *pair_style reax* potential
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against the original ReaxFF code for the systems mentioned above. You
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can use other ffield files for specific chemical systems that may be
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available elsewhere (but note that their accuracy may not have been
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tested).
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The *hbcut*\ , *hbnewflag*\ , *tripflag*\ , and *precision* settings are
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optional arguments. If none are provided, default settings are used:
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*hbcut* = 6 (which is Angstroms in real units), *hbnewflag* = 1 (use
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new hbond function style), *tripflag* = 1 (apply stabilization to all
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triple bonds), and *precision* = 1.0e-6 (one part in 10^6). If you
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wish to override any of these defaults, then all of the settings must
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be specified.
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Two examples using *pair_style reax* are provided in the examples/reax
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sub-directory, along with corresponding examples for
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:doc:`pair_style reax/c <pair_reax_c>`. Note that while the energy and force
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calculated by both of these pair styles match very closely, the
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contributions due to the valence angles differ slightly due to
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the fact that with *pair_style reax/c* the default value of *thb_cutoff_sq*
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is 0.00001, while for *pair_style reax* it is hard-coded to be 0.001.
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Use of this pair style requires that a charge be defined for every
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atom since the *reax* pair style performs a charge equilibration (QEq)
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calculation. See the :doc:`atom_style <atom_style>` and
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:doc:`read_data <read_data>` commands for details on how to specify
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charges.
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The thermo variable *evdwl* stores the sum of all the ReaxFF potential
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energy contributions, with the exception of the Coulombic and charge
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equilibration contributions which are stored in the thermo variable
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*ecoul*\ . The output of these quantities is controlled by the
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:doc:`thermo <thermo>` command.
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This pair style tallies a breakdown of the total ReaxFF potential
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energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 14.
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The 14 values correspond to the following sub-categories (the variable
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names in italics match those used in the ReaxFF FORTRAN library):
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1. *eb* = bond energy
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2. *ea* = atom energy
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3. *elp* = lone-pair energy
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4. *emol* = molecule energy (always 0.0)
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5. *ev* = valence angle energy
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6. *epen* = double-bond valence angle penalty
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7. *ecoa* = valence angle conjugation energy
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8. *ehb* = hydrogen bond energy
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9. *et* = torsion energy
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10. *eco* = conjugation energy
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11. *ew* = van der Waals energy
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12. *ep* = Coulomb energy
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13. *efi* = electric field energy (always 0.0)
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14. *eqeq* = charge equilibration energy
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To print these quantities to the log file (with descriptive column
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headings) the following commands could be included in an input script:
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.. parsed-literal::
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compute reax all pair reax
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variable eb equal c_reax[1]
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variable ea equal c_reax[2]
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...
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variable eqeq equal c_reax[14]
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thermo_style custom step temp epair v_eb v_ea ... v_eqeq
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Only a single pair_coeff command is used with the *reax* style which
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specifies a ReaxFF potential file with parameters for all needed
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elements. These are mapped to LAMMPS atom types by specifying N
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additional arguments after the filename in the pair_coeff command,
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where N is the number of LAMMPS atom types:
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* filename
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* N indices = mapping of ReaxFF elements to atom types
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The specification of the filename and the mapping of LAMMPS atom types
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recognized by the ReaxFF is done differently than for other LAMMPS
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potentials, due to the non-portable difficulty of passing character
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strings (e.g. filename, element names) between C++ and Fortran.
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The filename has to be "ffield.reax" and it has to exist in the
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directory you are running LAMMPS in. This means you cannot prepend a
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path to the file in the potentials dir. Rather, you should copy that
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file into the directory you are running from. If you wish to use
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another ReaxFF potential file, then name it "ffield.reax" and put it
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in the directory you run from.
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In the ReaxFF potential file, near the top, after the general
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parameters, is the atomic parameters section that contains element
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names, each with a couple dozen numeric parameters. If there are M
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elements specified in the *ffield* file, think of these as numbered 1
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to M. Each of the N indices you specify for the N atom types of LAMMPS
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atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
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be mapped to whatever element you specify as the first index value,
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etc. If a mapping value is specified as NULL, the mapping is not
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performed. This can be used when a ReaxFF potential is used as part
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of the *hybrid* pair style. The NULL values are placeholders for atom
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types that will be used with other potentials.
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.. note::
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Currently the reax pair style cannot be used as part of the
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*hybrid* pair style. Some additional changes still need to be made to
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enable this.
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As an example, say your LAMMPS simulation has 4 atom types and the
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elements are ordered as C, H, O, N in the *ffield* file. If you want
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the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
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H, you would use the following pair_coeff command:
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.. parsed-literal::
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pair_coeff * * ffield.reax 1 1 4 2
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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This pair style does not support the :doc:`pair_modify <pair_modify>`
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mix, shift, table, and tail options.
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This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*\ , *middle*\ , *outer* keywords.
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Restrictions
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""""""""""""
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The ReaxFF potential files provided with LAMMPS in the potentials
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directory are parameterized for real :doc:`units <units>`. You can use
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the ReaxFF potential with any LAMMPS units, but you would need to
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create your own potential file with coefficients listed in the
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appropriate units if your simulation doesn't use "real" units.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style reax/c <pair_reax_c>`,
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:doc:`fix_reax_bonds <fix_reax_bonds>`
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Default
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"""""""
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The keyword defaults are *hbcut* = 6, *hbnewflag* = 1, *tripflag* = 1,
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*precision* = 1.0e-6.
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----------
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.. _Chenoweth_2008:
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**(Chenoweth_2008)** Chenoweth, van Duin and Goddard,
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Journal of Physical Chemistry A, 112, 1040-1053 (2008).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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