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Re: [lammps-users] ReaxFF form in Ashraf and van Duin (JPCA 2016, 10.1021/acs.jpca.6b12429)
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Re: [lammps-users] ReaxFF form in Ashraf and van Duin (JPCA 2016, 10.1021/acs.jpca.6b12429)


From: Ray Shan <rshan@...1795...>
Date: Fri, 11 Aug 2017 20:51:31 +0000

Hi Luca, Michal,

 

Indeed, removing Delta_boc from lines 152/153 in reaxc_valence_angles.cpp would reproduce the Ashraf_2017 paper for modified valence angle term, but simply removing this variable would break backward compatibility from all previous ReaxFF descriptions.

 

A better way to do this is to add a keyword, e.g. modval, in the pair_style reax/c argument – as shown in the attached pair_reaxc.html.  With the keyword set to yes, the valence angle takes the modified form. 

 

The attached tar ball contains all necessary changes, including the doc page, reax/c source code for the original, kokkos, and omp versions.  Untar it in the top level LAMMPS directory to include the changes.

 

Thanks,

Ray

 

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T. Ray Shan, Ph.D.   |   Support Scientist

MATERIALS DESIGN - San Diego, California, USA

Direct +1.760.495.4924, ext. 219 | www.materialsdesign.com

 

 

From: Luca Gelisio <luca.gelisio@...24...>
Date: Friday, August 11, 2017 at 8:50 AM
To: Giacomo Fiorin <giacomo.fiorin@...24...>
Cc: LAMMPS Users Mailing List <lammps-users@lists.sourceforge.net>
Subject: Re: [lammps-users] ReaxFF form in Ashraf and van Duin (JPCA 2016, 10.1021/acs.jpca.6b12429)

 

Hi Giacomo and Michal,

Yes, they've changed the valence angle term and I think Michal is right, that patch should be enough.

Thanks a lot,

luca

 

 

On Fri, Aug 11, 2017 at 4:08 PM, Giacomo Fiorin <giacomo.fiorin@...24...> wrote:

I see, thanks for the correction.

 

On Fri, Aug 11, 2017 at 9:57 AM, Michał Kański <michal.kanski@...2460...> wrote:

Hi Giacomo,

 

They’ve changed the valence angle term by removing the undercoordination term. See the equations 3 and 4 in the paper.

The modification isn’t big and I think one only needs to delete “workspace->Delta_boc[j]” from lines 152 and 153 in reaxc_valence_angles.cpp in order to introduce it. Someone with a larger experience with ReaxFF should confirm this though.

 

Michal

 

 

 

Od: Giacomo Fiorin
Wysłano: piątek, 11 sierpnia 2017 15:07

Do: Luca Gelisio
DW: LAMMPS Users Mailing List
Temat: Re: [lammps-users] ReaxFF form in Ashraf and van Duin (JPCA 2016, 10.1021/acs.jpca.6b12429)

 

Hi Luca, it looks like only the parameters set has been optimized, but the energy function is still the same.  Can you try running models with the force field file in the SI of this paper?

Giacomo

 

On Fri, Aug 11, 2017 at 8:14 AM, Luca Gelisio <luca.gelisio@...24...> wrote:

Dear LAMMPS users and developers,

 

According to LAMMPS reax/c webpage (http://lammps.sandia.gov/doc/pair_reaxc.html), the Reax version currently implemented in LAMMPS is the one reported in Chenoweth et al (JPCA 2008, 10.1021/acs.jpca.6b12429).

By chance, has someone already experimented with the version reported in Ashraf and van Duin (JPCA 2016, 10.1021/acs.jpca.6b12429)?

 

Thanks for any comment,

luca

 


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--

Giacomo Fiorin

Associate Professor of Research, Temple University, Philadelphia, PA

Contractor, National Institutes of Health, Bethesda, MD

 

Attachment: reaxc_modval.tar
Description: reaxc_modval.tar

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands

pair_style reax/c command

pair_style reax/c/kk command

pair_style reax/c/omp command

Syntax:

pair_style reax/c cfile keyword value 

Examples:

pair_style reax/c NULL modval yes
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100
pair_coeff * * ffield.reax C H O N 

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). 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 was initially implemented as a stand-alone C code and is now integrated into LAMMPS as a package.

The reax/c/kk style is a Kokkos version of the ReaxFF potential that is derived from the reax/c style. The Kokkos version can run on GPUs and can also use OpenMP multithreading. For more information about the Kokkos package, see Section 4 and Section 5.3.3. One important consideration when using the reax/c/kk style is the choice of either half or full neighbor lists. This setting can be changed using the Kokkos package command.

The reax/c style differs from the pair_style reax 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.

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).

NOTE: We do not distribute a wide variety of ReaxFF force field files with LAMMPS. Adri van Duin's group at PSU is the central repository for this kind of data as they are continuously deriving and updating parameterizations for different classes of materials. You can submit a contact request at the Materials Computation Center (MCC) website https://www.mri.psu.edu/materials-computation-center/connect-mcc, describing the material(s) you are interested in modeling with ReaxFF. They can tell you what is currently available or what it would take to create a suitable ReaxFF parameterization.

The cfile setting can be specified as NULL, in which case default settings are used. A control file can be specified which defines values of control variables. Some control variables are global parameters for the ReaxFF potential. Others define certain performance and output settings. Each line in the control file specifies the value for a control variable. The format of the control file is described below.

NOTE: The LAMMPS default values for the ReaxFF global parameters correspond to those used by Adri van Duin's stand-alone serial code. If these are changed by setting control variables in the control file, the results from LAMMPS and the serial code will not agree.

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

Use of this pair style requires that a charge be defined for every atom. See the atom_style and read_data 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 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 command for details.

Using the optional keyword lgvdw with the value yes turns on the low-gradient correction of the ReaxFF/C for long-range London Dispersion, as described in the (Liu) paper. Force field file ffield.reax.lg is designed for this correction, and is trained for several energetic materials (see "Liu"). When using lg-correction, recommended value for parameter thb is 0.01, which can be set in the control file. Note: Force field files are different for the original or lg corrected pair styles, using wrong ffield file generates an error message.

Using the optional keyword enobonds with the value yes, the energy of atoms with no bonds (i.e. isolated atoms) is included in the total potential energy and the per-atom energy of that atom. If the value no is specified then the energy of atoms with no bonds is set to zero. The latter behavior is usual not desired, as it causes discontinuities in the potential energy when the bonding of an atom drops to zero.

Optional keywords safezone and mincap are used for allocating reax/c arrays. Increasing these values can avoid memory problems, such as segmentation faults and bondchk failed errors, that could occur under certain conditions. These keywords aren't used by the Kokkos version, which instead uses a more robust memory allocation scheme that checks if the sizes of the arrays have been exceeded and automatically allocates more memory.

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 command.

Using the optional keyword modval with the value yes turns on the modified valence angle term, as described in the (Ashraf) paper. This formalism removes the angle under- coordination contribution from the valence angle term, which provides a better description for the non-linear HCO molecule.

This pair style tallies a breakdown of the total ReaxFF potential energy into sub-categories, which can be accessed via the compute pair 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):

  1. eb = bond energy
  2. ea = atom energy
  3. elp = lone-pair energy
  4. emol = molecule energy (always 0.0)
  5. ev = valence angle energy
  6. epen = double-bond valence angle penalty
  7. ecoa = valence angle conjugation energy
  8. ehb = hydrogen bond energy
  9. et = torsion energy
  10. eco = conjugation energy
  11. ew = van der Waals energy
  12. ep = Coulomb energy
  13. efi = electric field energy (always 0.0)
  14. eqeq = charge equilibration energy

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 

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:

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.

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 C C N H 

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

variable_name value 

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 = 5.0)

hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen bond interactions.(default value = 7.5. A value of 0.0 turns off hydrogen bonds)

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)

thb_cutoff_sq: cutoff value for the strength of bond order products to be considered in three body interactions. (default value = 0.00001)

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)


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

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

This pair style does not write its information to binary restart files, 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 command. It does not support the inner, middle, outer keywords.


Styles with a gpu, intel, kk, 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 5 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 GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Making LAMMPS 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 when you invoke LAMMPS, or you can use the suffix command in your input script.

See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.


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 for more info.

The ReaxFF potential files provided with LAMMPS in the potentials directory are parameterized for real units. 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.

Related commands:

pair_coeff, fix qeq/reax, fix reax/c/bonds, fix reax/c/species, pair_style reax

Default:

The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2, mincap = 50, modval = no.


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

(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).

(Liu) L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).

(Ashraf) C. Ashraf, A. C.T. van Duin, Journal of Physical Chemistry A, 121, 1051-1068 (2017).