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Merge pull request #2708 from akohlmey/refactor-reaxff-parser 

Refactoring and improving REAXFF and QEQ packages
This commit is contained in:
Axel Kohlmeyer 2021-07-22 23:04:09 -04:00 committed by GitHub
parent 9066495d78 d0a654097f
commit 320f7da91a
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GPG Key ID: 4AEE18F83AFDEB23
308 changed files with 15194 additions and 18022 deletions
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18
cmake/Modules/Packages/OPENMP.cmake
View File

@ -25,15 +25,15 @@
endif()
if(PKG_REAXFF)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_forces_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
${OPENMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
endif()
target_sources(lammps PRIVATE ${OPENMP_SOURCES})

6
doc/src/Commands_fix.rst
View File

@ -179,14 +179,14 @@ OPT.
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
* :doc:`qeq/reax (ko) <fix_qeq_reax>`
* :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
* :doc:`qeq/shielded <fix_qeq>`
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`rattle <fix_shake>`
* :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
* :doc:`reax/c/species (k) <fix_reaxc_species>`
* :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rhok <fix_rhok>`

2
doc/src/Commands_pair.rst
View File

@ -235,7 +235,7 @@ OPT.
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`rann <pair_rann>`
* :doc:`reax/c (ko) <pair_reaxc>`
* :doc:`reaxff (ko) <pair_reaxff>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

4
doc/src/Errors_warnings.rst
View File

@ -514,7 +514,7 @@ This will most likely cause errors in kinetic fluctuations.
will integrate the body motion, but it would be more efficient to use
fix rigid.
*Not using real units with pair reax*
*Not using real units with pair reaxff*
This is most likely an error, unless you have created your own ReaxFF
parameter file in a different set of units.
@ -805,5 +805,3 @@ This will most likely cause errors in kinetic fluctuations.
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.
*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
Self-explanatory.

8
doc/src/Packages_details.rst
View File

@ -2274,10 +2274,10 @@ for monitoring molecules as bonds are created and destroyed.
* src/REAXFF: filenames -> commands
* src/REAXFF/README
* :doc:`pair_style reax/c <pair_reaxc>`
* :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
* :doc:`fix reax/c/species <fix_reaxc_species>`
* examples/reax
* :doc:`pair_style reaxff <pair_reaxff>`
* :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
* :doc:`fix reaxff/species <fix_reaxff_species>`
* examples/reaxff
----------

2
doc/src/Packages_list.rst
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@ -370,7 +370,7 @@ whether an extra library is needed to build and use the package:
- no
* - :ref:`REAXFF <PKG-REAXFF>`
- ReaxFF potential (C/C++)
- :doc:`pair_style reaxc <pair_reaxc>`
- :doc:`pair_style reaxff <pair_reaxff>`
- reax
- no
* - :ref:`REPLICA <PKG-REPLICA>`

15
doc/src/Tools.rst
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@ -76,7 +76,6 @@ Post-processing tools
* :ref:`phonon <phonon>`
* :ref:`pymol_asphere <pymol>`
* :ref:`python <pythontools>`
* :ref:`reax <reax_tool>`
* :ref:`replica <replica>`
* :ref:`smd <smd>`
* :ref:`spin <spin>`
@ -947,20 +946,6 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
----------
.. _reax_tool:
reax tool
--------------------------
The reax sub-directory contains stand-alone codes that can
post-process the output of the :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
command from a LAMMPS simulation using :doc:`ReaxFF <pair_reaxc>`. See
the README.txt file for more info.
These tools were written by Aidan Thompson at Sandia.
----------
.. _smd:
smd tool

5
doc/src/compute_pair.rst
View File

@ -24,7 +24,7 @@ Examples
compute 1 all pair gauss
compute 1 all pair lj/cut/coul/cut ecoul
compute 1 all pair tersoff 2 epair
compute 1 all pair reax/c
compute 1 all pair reaxff
Description
"""""""""""
@ -64,7 +64,8 @@ is stored as a global scalar.
:doc:`pair_modify <pair_modify>` command.
Some pair styles tally additional quantities, e.g. a breakdown of
potential energy into 14 components is tallied by the :doc:`pair_style reax/c <pair_reaxc>` command. These values (1 or more)
potential energy into 14 components is tallied by the
:doc:`pair_style reaxff <pair_reaxff>` command. These values (1 or more)
are stored as a global vector by this compute. See the doc page for
:doc:`individual pair styles <pair_style>` for info on these values.

6
doc/src/fix.rst
View File

@ -322,14 +322,14 @@ accelerated styles exist.
* :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
* :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
* :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
* :doc:`qeq/reax <fix_qeq_reax>` - charge equilibration for ReaxFF potential
* :doc:`qeq/reaxff <fix_qeq_reaxff>` - charge equilibration for ReaxFF potential
* :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method
* :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
* :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
* :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
* :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
* :doc:`reax/c/bonds <fix_reaxc_bonds>` - write out ReaxFF bond information
* :doc:`reax/c/species <fix_reaxc_species>` - write out ReaxFF molecule information
* :doc:`reaxff/bonds <fix_reaxff_bonds>` - write out ReaxFF bond information
* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
* :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
* :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
* :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems

2
doc/src/fix_adapt.rst
View File

@ -186,7 +186,7 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>` | E0,R0,m,n,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`reax/c <pair_reaxc>` | chi, eta, gamma | type global |
| :doc:`reaxff <pair_reaxff>` | chi, eta, gamma | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`snap <pair_snap>` | scale | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+

2
doc/src/fix_gcmc.rst
View File

@ -374,7 +374,7 @@ in the context of NVT dynamics.
has been reached.
With some pair_styles, such as :doc:`Buckingham <pair_buck>`,
:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxc>`, two
:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxff>`, two
atoms placed close to each other may have an arbitrary large, negative
potential energy due to the functional form of the potential. While
these unphysical configurations are inaccessible to typical dynamical

41
doc/src/fix_qeq.rst
View File

@ -32,15 +32,16 @@ Syntax
* cutoff = global cutoff for charge-charge interactions (distance unit)
* tolerance = precision to which charges will be equilibrated
* maxiter = maximum iterations to perform charge equilibration
* qfile = a filename with QEq parameters or *coul/streitz* or *reax/c*
* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
* zero or more keyword/value pairs may be appended
* keyword = *alpha* or *qdamp* or *qstep*
* keyword = *alpha* or *qdamp* or *qstep* or *warn*
.. parsed-literal::
*alpha* value = Slater type orbital exponent (qeq/slater only)
*qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
*warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
Examples
""""""""
@ -90,19 +91,19 @@ on the current atom configuration), then remove the fix via the
The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
perform charge equilibration with the :doc:`COMB potential
<pair_comb>`. The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
<pair_comb>`. The :doc:`fix qeq/reaxff <fix_qeq_reaxff>` command can be
used to perform charge equilibration with the :doc:`ReaxFF force
field <pair_reaxc>`, although fix qeq/shielded yields the same
results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reax command will be
field <pair_reaxff>`, although fix qeq/shielded yields the same
results as fix qeq/reaxff if *Nevery*\ , *cutoff*\ , and *tolerance*
are the same. Eventually the fix qeq/reaxff command will be
deprecated.
The QEq method minimizes the electrostatic energy of the system (or
equalizes the derivative of energy with respect to charge of all the
atoms) by adjusting the partial charge on individual atoms based on
interactions with their neighbors within *cutoff*\ . It requires a few
parameters, in *metal* units, for each atom type which provided in a
file specified by *qfile*\ . The file has the following format
parameters in the appropriate units for each atom type which are read
from a file specified by *qfile*\ . The file has the following format
.. parsed-literal::
@ -112,7 +113,7 @@ file specified by *qfile*\ . The file has the following format
Ntype chi eta gamma zeta qcore
There have to be parameters given for every atom type. Wildcard entries
are possible using the same syntax as elsewhere in LAMMPS
are possible using the same type range syntax as for "coeff" commands
(i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
Empty lines or any text following the pound sign (#) are ignored.
Each line starts with the atom type followed by five parameters.
@ -126,6 +127,14 @@ entries per line are required.
* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
The fix qeq styles will print a warning if the charges are not
equilibrated within *tolerance* by *maxiter* steps, unless the
*warn* keyword is used with "no" as argument. This latter option
may be useful for testing and benchmarking purposes, as it allows
to use a fixed number of QEq iterations when *tolerance* is set
to a small enough value to always reach the *maxiter* limit. Turning
off warnings will avoid the excessive output in that case.
The *qeq/point* style describes partial charges on atoms as point
charges. Interaction between a pair of charged particles is 1/r,
which is the simplest description of the interaction between charges.
@ -141,11 +150,11 @@ interaction between a pair of charged particles. Interaction through
the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
field <vanDuin>` paper. The shielding accounts for charge overlap
between charged particles at small separation. This style is the same
as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
:doc:`pair_style reax/c <pair_reaxc>`. Only the *chi*\ , *eta*\ , and
as :doc:`fix qeq/reaxff <fix_qeq_reaxff>`, and can be used with
:doc:`pair_style reaxff <pair_reaxff>`. Only the *chi*\ , *eta*\ , and
*gamma* parameters from the *qfile* file are used. When using the string
*reax/c* as filename, these parameters are extracted directly from an
active *reax/c* pair style. This style solves partial charges on atoms
*reaxff* as filename, these parameters are extracted directly from an
active *reaxff* pair style. This style solves partial charges on atoms
via the matrix inversion method. A tolerance of 1.0e-6 is usually a
good number.
@ -221,15 +230,17 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
The qeq fixes are not compatible with the GPU and USER-INTEL packages.
Related commands
""""""""""""""""
:doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix qeq/comb <fix_qeq_comb>`
:doc:`fix qeq/reaxff <fix_qeq_reaxff>`, :doc:`fix qeq/comb <fix_qeq_comb>`
Default
"""""""
none
warn yes
----------

2
doc/src/fix_qeq_comb.rst
View File

@ -41,7 +41,7 @@ Perform charge equilibration (QeQ) in conjunction with the COMB
equilibration portion of the calculation using the so-called QEq
method, whereby the charge on each atom is adjusted to minimize the
energy of the system. This fix can only be used with the COMB
potential; see the :doc:`fix qeq/reax <fix_qeq_reax>` command for a QeQ
potential; see the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` command for a QeQ
calculation that can be used with any potential.
Only charges on the atoms in the specified group are equilibrated.

76
doc/src/fix_qeq_reax.rst → doc/src/fix_qeq_reaxff.rst
View File

@ -1,59 +1,61 @@
.. index:: fix qeq/reax
.. index:: fix qeq/reax/kk
.. index:: fix qeq/reax/omp
.. index:: fix qeq/reaxff
.. index:: fix qeq/reaxff/kk
.. index:: fix qeq/reaxff/omp
fix qeq/reax command
====================
fix qeq/reaxff command
======================
Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp*
Accelerator Variants: *qeq/reaxff/kk*, *qeq/reaxff/omp*
Syntax
""""""
.. parsed-literal::
fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args
fix ID group-ID qeq/reaxff Nevery cutlo cuthi tolerance params args
* ID, group-ID are documented in :doc:`fix <fix>` command
* qeq/reax = style name of this fix command
* qeq/reaxff = style name of this fix command
* Nevery = perform QEq every this many steps
* cutlo,cuthi = lo and hi cutoff for Taper radius
* tolerance = precision to which charges will be equilibrated
* params = reax/c or a filename
* params = reaxff or a filename
* one or more keywords or keyword/value pairs may be appended
.. parsed-literal::
keyword = *dual* or *maxiter*
*dual* = process S and T matrix in parallel (only for qeq/reax/omp)
keyword = *dual* or *maxiter* or *nowarn*
*dual* = process S and T matrix in parallel (only for qeq/reaxff/omp)
*maxiter* N = limit the number of iterations to *N*
*nowarn* = do not print a warning message if the maximum number of iterations was reached
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
Description
"""""""""""
Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe2>` and formulated in :ref:`(Nakano) <Nakano2>`. It is
typically used in conjunction with the ReaxFF force field model as
implemented in the :doc:`pair_style reax/c <pair_reaxc>` command, but
it can be used with any potential in LAMMPS, so long as it defines and
uses charges on each atom. The :doc:`fix qeq/comb <fix_qeq_comb>`
command should be used to perform charge equilibration with the :doc:`COMB potential <pair_comb>`. For more technical details about the
charge equilibration performed by fix qeq/reax, see the
Perform the charge equilibration (QEq) method as described in
:ref:`(Rappe and Goddard) <Rappe2>` and formulated in :ref:`(Nakano)
<Nakano2>`. It is typically used in conjunction with the ReaxFF force
field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. The :doc:`fix qeq/comb
<fix_qeq_comb>` command should be used to perform charge equilibration
with the :doc:`COMB potential <pair_comb>`. For more technical details
about the charge equilibration performed by fix qeq/reaxff, see the
:ref:`(Aktulga) <qeq-Aktulga>` paper.
The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It requires some parameters for each atom type.
If the *params* setting above is the word "reax/c", then these are
extracted from the :doc:`pair_style reax/c <pair_reaxc>` command and
If the *params* setting above is the word "reaxff", then these are
extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
the ReaxFF force field file it reads in. If a file name is specified
for *params*\ , then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
@ -74,17 +76,26 @@ of this fix are hard-coded to be A, eV, and electronic charge.
The optional *dual* keyword allows to perform the optimization
of the S and T matrices in parallel. This is only supported for
the *qeq/reax/omp* style. Otherwise they are processed separately.
the *qeq/reaxff/omp* style. Otherwise they are processed separately.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
The optional *nowarn* keyword silences the warning message printed
when the maximum number of iterations was reached. This can be
useful for comparing serial and parallel results where having the
same fixed number of QEq iterations is desired, which can be achieved
by using a very small tolerance and setting *maxiter* to the desired
number of iterations.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. No global scalar or vector or per-atom
quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`. No parameter of this fix can be used
with the *start/stop* keywords of the :doc:`run <run>` command.
No information about this fix is written to :doc:`binary restart files
<restart>`. This fix computes a global scalar (the number of
iterations) for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
This fix is invoked during :doc:`energy minimization <minimize>`.
@ -98,16 +109,17 @@ Restrictions
""""""""""""
This fix is part of the REAXFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
This fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
be used for periodic cell dimensions less than 10 angstroms.
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 angstroms.
Related commands
""""""""""""""""
:doc:`pair_style reax/c <pair_reaxc>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`
Default
"""""""

20
doc/src/fix_reaxc_bonds.rst → doc/src/fix_reaxff_bonds.rst
View File

@ -1,17 +1,17 @@
.. index:: fix reax/c/bonds
.. index:: fix reax/c/bonds/kk
.. index:: fix reaxff/bonds
.. index:: fix reaxff/bonds/kk
fix reax/c/bonds command
fix reaxff/bonds command
========================
Accelerator Variants: *reax/c/bonds/kk*
Accelerator Variants: *reaxff/bonds/kk*
Syntax
""""""
.. parsed-literal::
fix ID group-ID reaxc/bonds Nevery filename
fix ID group-ID reaxff/bonds Nevery filename
* ID, group-ID are documented in :doc:`fix <fix>` command
* reax/bonds = style name of this fix command
@ -23,17 +23,17 @@ Examples
.. code-block:: LAMMPS
fix 1 all reax/c/bonds 100 bonds.reaxc
fix 1 all reaxff/bonds 100 bonds.reaxff
Description
"""""""""""
Write out the bond information computed by the ReaxFF potential specified
by :doc:`pair_style reax/c <pair_reaxc>` in the exact same format as the
by :doc:`pair_style reaxff <pair_reaxff>` in the exact same format as the
original stand-alone ReaxFF code of Adri van Duin. The bond information
is written to *filename* on timesteps that are multiples of *Nevery*\ ,
including timestep 0. For time-averaged chemical species analysis,
please see the :doc:`fix reaxc/c/species <fix_reaxc_species>` command.
please see the :doc:`fix reaxff/species <fix_reaxff_species>` command.
The specified group-ID is ignored by this fix.
@ -76,7 +76,7 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
The fix reax/c/bonds command requires that the :doc:`pair_style reax/c <pair_reaxc>` is invoked. This fix is part of the
The fix reaxff/bonds command requires that the :doc:`pair_style reaxff <pair_reaxff>` is invoked. This fix is part of the
REAXFF package. It is only enabled if LAMMPS was built with that
package. See the :doc:`Build package <Build_package>` doc page for more
info.
@ -87,7 +87,7 @@ To write gzipped bond files, you must compile LAMMPS with the
Related commands
""""""""""""""""
:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/species <fix_reaxc_species>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/species <fix_reaxff_species>`
Default
"""""""

57
doc/src/fix_reaxc_species.rst → doc/src/fix_reaxff_species.rst
View File

@ -1,20 +1,20 @@
.. index:: fix reax/c/species
.. index:: fix reax/c/species/kk
.. index:: fix reaxff/species
.. index:: fix reaxff/species/kk
fix reax/c/species command
fix reaxff/species command
==========================
Accelerator Variants: *reax/c/species/kk*
Accelerator Variants: *reaxff/species/kk*
Syntax
""""""
.. parsed-literal::
fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ...
fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* reax/c/species = style name of this command
* reaxff/species = style name of this command
* Nevery = sample bond-order every this many timesteps
* Nrepeat = # of bond-order samples used for calculating averages
* Nfreq = calculate average bond-order every this many timesteps
@ -37,15 +37,15 @@ Examples
.. code-block:: LAMMPS
fix 1 all reax/c/species 10 10 100 species.out
fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
fix 1 all reaxff/species 10 10 100 species.out
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
Description
"""""""""""
Write out the chemical species information computed by the ReaxFF
potential specified by :doc:`pair_style reax/c <pair_reaxc>`.
potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
Bond-order values (either averaged or instantaneous, depending on
value of *Nrepeat*\ ) are used to determine chemical bonds. Every
*Nfreq* timesteps, chemical species information is written to
@ -73,7 +73,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must
match the number of LAMMPS atom types and each symbol must consist of
1 or 2 alphanumeric characters. Normally, these symbols should be
chosen to match the chemical identity of each LAMMPS atom type, as
specified using the :doc:`reax/c pair_coeff <pair_reaxc>` command and
specified using the :doc:`reaxff pair_coeff <pair_reaxff>` command and
the ReaxFF force field file.
The optional keyword *position* writes center-of-mass positions of
@ -115,12 +115,12 @@ average bond-order for the species analysis output on timestep 100.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
This fix computes both a global vector of length 2 and a per-atom
vector, either of which can be accessed by various :doc:`output commands <Howto_output>`. The values in the global vector are
"intensive".
This fix computes both a global vector of length 2 and a per-atom vector,
either of which can be accessed by various :doc:`output commands <Howto_output>`.
The values in the global vector are "intensive".
The 2 values in the global vector are as follows:
@ -134,7 +134,8 @@ will be the same and will be equal to the smallest atom ID of
any atom in the molecule.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command.
This fix is not invoked during :doc:`energy minimization <minimize>`.
----------
@ -145,26 +146,20 @@ the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minim
Restrictions
""""""""""""
The "fix reax/c/species" currently only works with :doc:`pair_style reax/c <pair_reaxc>` and it requires that the :doc:`pair_style reax/c <pair_reaxc>` be invoked. This fix is part of the
REAXFF package. It is only enabled if LAMMPS was built with that
package. See the :doc:`Build package <Build_package>` doc page for more
info.
The "fix reaxff/species" requires that :doc:`pair_style reaxff <pair_reaxff>` is used.
This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that
package. See the :doc:`Build package <Build_package>` doc page for more info.
To write gzipped species files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
It should be possible to extend it to other reactive pair_styles (such as
:doc:`rebo <pair_airebo>`, :doc:`airebo <pair_airebo>`,
:doc:`comb <pair_comb>`, and :doc:`bop <pair_bop>`), but this has not yet been done.
To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option.
Related commands
""""""""""""""""
:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
Default
"""""""
The default values for bond-order cutoffs are 0.3 for all I-J pairs. The
default element symbols are C, H, O, N. Position files are not written
by default.
The default values for bond-order cutoffs are 0.3 for all I-J pairs.
The default element symbols are C, H, O, N.
Position files are not written by default.

4
doc/src/kim_commands.rst
View File

@ -372,9 +372,9 @@ the *kim interactions* command executes the following LAMMPS input commands:
.. code-block:: LAMMPS
pair_style reax/c lmp_control safezone 2.0 mincap 100
pair_style reaxff lmp_control safezone 2.0 mincap 100
pair_coeff * * ffield.reax.rdx C H N O
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
fix reaxqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq
.. note::

3
doc/src/package.rst
View File

@ -448,7 +448,8 @@ does not require atomic operations in the calculation of pair forces. For
that reason, *full* is the default setting for GPUs. However, when
running on CPUs, a *half* neighbor list is the default because it are
often faster, just as it is for non-accelerated pair styles. Similarly,
the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`.
the *neigh/qeq* keyword determines how neighbor lists are built for
:doc:`fix qeq/reaxff/kk <fix_qeq_reaxff>`.
If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
threads only over atoms. However, for small systems, this may not expose

118
doc/src/pair_reaxc.rst → doc/src/pair_reaxff.rst
View File

@ -1,18 +1,18 @@
.. index:: pair_style reax/c
.. index:: pair_style reax/c/kk
.. index:: pair_style reax/c/omp
.. index:: pair_style reaxff
.. index:: pair_style reaxff/kk
.. index:: pair_style reaxff/omp
pair_style reax/c command
pair_style reaxff command
=========================
Accelerator Variants: *reax/c/kk*, *reax/c/omp*
Accelerator Variants: *reaxff/kk*, *reaxff/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style reax/c cfile keyword value
pair_style reaxff cfile keyword value
* cfile = NULL or name of a control file
* zero or more keyword/value pairs may be appended
@ -20,7 +20,7 @@ Syntax
.. parsed-literal::
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff fix
*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
*safezone* = factor used for array allocation
@ -32,37 +32,38 @@ Examples
.. code-block:: LAMMPS
pair_style reax/c NULL
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_style reaxff NULL
pair_style reaxff controlfile checkqeq no
pair_style reaxff NULL lgvdw yes
pair_style reaxff 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
Style *reaxff* 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: :ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`. 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 :ref:`(Aktulga) <Aktulga>` paper. The *reax/c* style was initially
implemented as a stand-alone C code and is now integrated into LAMMPS
as a package.
supplemental information of the following paper:
:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`. The version integrated
into LAMMPS matches the version of ReaxFF From Summer 2010. For more
technical details about the pair reaxff implementation of ReaxFF, see
the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
implemented as a stand-alone C code and is now converted to C++ and
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
The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
is derived from the *reaxff* style. The Kokkos version can run on GPUs
and can also use OpenMP multithreading. For more information about the
Kokkos package, see :doc:`Packages details <Packages_details>` and
:doc:`Speed kokkos <Speed_kokkos>` doc pages. One important
consideration when using the *reax/c/kk* style is the choice of either
consideration when using the *reaxff/kk* style is the choice of either
half or full neighbor lists. This setting can be changed using the
Kokkos :doc:`package <package>` command.
The *reax/c* style differs from the (obsolete) "pair_style reax"
The *reaxff* style differs from the (obsolete) "pair_style reax"
command in the implementation details. The *reax* style was a
Fortran library, linked to LAMMPS. The *reax* style has been removed
from LAMMPS after the 12 December 2018 version.
@ -73,7 +74,7 @@ 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
Duin. We have tested the accuracy of *pair_style reaxff* 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
@ -102,10 +103,11 @@ control variable. The format of the control file is described below.
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.
code. If these are changed by setting control variables in the
control file, the results from LAMMPS and the serial code will
not agree.
Examples using *pair_style reax/c* are provided in the examples/reax
Examples using *pair_style reaxff* are provided in the examples/reax
sub-directory.
Use of this pair style requires that a charge be defined for every
@ -115,25 +117,28 @@ 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 :doc:`fix qeq/reax <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 :doc:`fix qeq/reax <fix_qeq_reax>` command for details.
Therefore, by default, LAMMPS requires that either the
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
:doc:`fix qeq/shielded <fix_qeq>` command be used with
*pair_style reaxff* when simulating a ReaxFF model, to equilibrate
the charges each timestep.
Using the keyword *checkqeq* with the value *no* turns off the check
for the QEq fixes, 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 :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
:doc:`fix qeq/shielded <fix_qeq>` command documentation for more 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 :ref:`(Liu) <Liu_2011>` 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
low-gradient correction of ReaxFF for long-range London Dispersion,
as described in the :ref:`(Liu) <Liu_2011>` paper. The bundled force
field file *ffield.reax.lg* is designed for this correction, and is
trained for several energetic materials (see "Liu"). When using *lgvdw yes*,
the 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.
or lg corrected pair styles, using the wrong ffield file generates an
error.
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
@ -144,7 +149,7 @@ discontinuities in the potential energy when the bonding of an atom
drops to zero.
Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used
for allocating reax/c arrays. Increasing these values can avoid memory
for allocating reaxff arrays. Increasing these values can avoid memory
problems, such as segmentation faults and bondchk failed errors, that
could occur under certain conditions. These keywords are not used by
the Kokkos version, which instead uses a more robust memory allocation
@ -158,7 +163,8 @@ equilibration contributions which are stored in the thermo variable
:doc:`thermo <thermo>` command.
This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 14.
energy into sub-categories, which can be accessed via the
:doc:`compute pair <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):
@ -183,14 +189,14 @@ headings) the following commands could be included in an input script:
.. code-block:: LAMMPS
compute reax all pair reax/c
compute reax all pair reaxff
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
Only a single pair_coeff command is used with the *reaxff* 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,
@ -209,7 +215,7 @@ 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
performed. This can be used when the *reaxff* 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.
@ -241,7 +247,7 @@ brief description of their use and default values.
*simulation_name*
Output files produced by *pair_style reax/c* carry
Output files produced by *pair_style reaxff* carry
this name + extensions specific to their contents. Partial energies
are reported with a ".pot" extension, while the trajectory file has
".trj" extension.
@ -286,8 +292,7 @@ brief description of their use and default values.
to be considered in three body interactions. (default value = 0.00001)
*write_freq*
Frequency of writes into the trajectory file. (default
value = 0)
Frequency of writes into the trajectory file. (default value = 0)
*traj_title*
Title of the trajectory - not the name of the trajectory file.
@ -315,7 +320,8 @@ Mixing, shift, table, tail correction, restart, rRESPA info
This pair style does not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
This pair style does not write its information to :doc:`binary restart files <restart>`,
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.
@ -333,18 +339,20 @@ Restrictions
""""""""""""
This pair style is part of the REAXFF package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.
The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real :doc:`units <units>`. You can use
the ReaxFF potential with any LAMMPS units, but you would need to
directory are parameterized for *real* :doc:`units <units>`. You can use
the ReaxFF pair style with any LAMMPS units, but you would need to
create your own potential file with coefficients listed in the
appropriate units if your simulation does not use "real" units.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`, :doc:`fix reax/c/species <fix_reaxc_species>`
:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix reaxff/bonds <fix_reaxff_bonds>`, :doc:`fix reaxff/species <fix_reaxff_species>`
Default
"""""""

2
doc/src/pair_style.rst
View File

@ -299,7 +299,7 @@ accelerated styles exist.
* :doc:`python <pair_python>` -
* :doc:`quip <pair_quip>` -
* :doc:`rann <pair_rann>` -
* :doc:`reax/c <pair_reaxc>` - ReaxFF potential in C
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions

55
doc/utils/check-styles.py
View File

@ -254,40 +254,27 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index)
skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c')
counter = 0
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",
command,'Command',suffix=False)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",
compute,'Compute',suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",
compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",
fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=True)
counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",
fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False)
counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",
pair,'Pair',skip=('meam/c','lj/sf'),suffix=True)
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",
pair,'Pair',skip=('meam/c','lj/sf'),suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",
bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",
bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",
angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",
angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",
dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",
dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",
improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",
improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",
kspace,'KSpace',suffix=True)
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=False)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",fix,'Fix',skip=skip_fix,suffix=True)
counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",fix,'Fix',skip=skip_fix,suffix=False)
counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair,'Pair',skip=skip_pair,suffix=True)
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
if counter:
print(f"Found {counter} issue(s) with style lists")
@ -295,13 +282,13 @@ if counter:
counter = 0
counter += check_style_index("compute", compute, index["compute"])
counter += check_style_index("fix", fix, index["fix"], skip=['python'])
counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf'])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
if counter:
print(f"Found {counter} issue(s) with style index")

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -2744,6 +2744,7 @@ reamin
reax
REAXFF
ReaxFF
reaxff
rebo
recursing
Ree

2
examples/README
View File

@ -103,7 +103,7 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script
qeq: use of QEQ package for charge equilibration
reax: RDX and TATB and several other models using ReaxFF
reaxff: RDX and TATB and several other models using ReaxFF
rerun: use of rerun and read_dump commands
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void

22
examples/qeq/buck.inc Normal file
View File

@ -0,0 +1,22 @@
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve

75
examples/qeq/in.qeq.buck
View File

@ -1,41 +1,68 @@
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
replicate 2 2 2
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
group type1 type 1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot
thermo 10
timestep 0.0001
include buck.inc
velocity all create 300.0 1281937
fix 1 all nve
run 0 post no
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
write_restart qeq.restart
run 100
clear
print "Using fix qeq/point"
read_restart qeq.restart
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/shielded"
read_restart qeq.restart
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/slater"
read_restart qeq.restart
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/dynamic"
read_restart qeq.restart
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
run 100
clear
print "Using fix qeq/fire"
read_restart qeq.restart
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
run 100

650
examples/qeq/log.20Apr21.qeq.buck.g++.1 Normal file
View File

@ -0,0 +1,650 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
read_data CPU = 0.009 seconds
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
velocity all create 300.0 1281937
run 0 post no
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.30705229
grid = 48 48 54
stencil order = 5
estimated absolute RMS force accuracy = 1.8909403e-05
estimated relative force accuracy = 1.3131854e-06
using double precision FFTW3
3d grid and FFT values/proc = 184525 124416
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Fix qeq CG convergence failed (4.357840257025601e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
WARNING: Fix qeq CG convergence failed (5.274094378414531e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
Per MPI rank memory allocation (min/avg/max) = 38.75 | 38.75 | 38.75 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10
Loop time of 1.66893e-06 on 1 procs for 0 steps with 1200 atoms
write_restart qeq.restart
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/point"
Using fix qeq/point
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/point, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3
10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8
20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8
30 -3568.22095 0.86767937 -0.43383969 0.000000000001 8
40 -3633.24956 0.87335551 -0.43667775 0.000000000000 8
50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8
60 -3784.36769 0.88402303 -0.44201151 -0.000000000000 8
70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8
80 -3965.29722 0.89431515 -0.44715757 -0.000000000001 8
90 -4048.36764 0.89698588 -0.44849294 0.000000000000 8
100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8
Loop time of 11.5935 on 1 procs for 100 steps with 1200 atoms
Performance: 0.075 ns/day, 322.041 hours/ns, 8.626 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8257 | 2.8257 | 2.8257 | 0.0 | 24.37
Kspace | 1.2136 | 1.2136 | 1.2136 | 0.0 | 10.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015541 | 0.015541 | 0.015541 | 0.0 | 0.13
Output | 0.0014489 | 0.0014489 | 0.0014489 | 0.0 | 0.01
Modify | 7.5351 | 7.5351 | 7.5351 | 0.0 | 64.99
Other | | 0.00206 | | | 0.02
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/shielded"
Using fix qeq/shielded
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1
40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 7.93936 on 1 procs for 100 steps with 1200 atoms
Performance: 0.109 ns/day, 220.538 hours/ns, 12.595 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8061 | 2.8061 | 2.8061 | 0.0 | 35.34
Kspace | 1.2176 | 1.2176 | 1.2176 | 0.0 | 15.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015528 | 0.015528 | 0.015528 | 0.0 | 0.20
Output | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 0.02
Modify | 3.8966 | 3.8966 | 3.8966 | 0.0 | 49.08
Other | | 0.002076 | | | 0.03
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/slater"
Using fix qeq/slater
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 24.69 | 24.69 | 24.69 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 -0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 0.000000000001 1
40 -2942.24129 0.76536939 -0.38268470 -0.000000000001 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000001 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 7.9652 on 1 procs for 100 steps with 1200 atoms
Performance: 0.108 ns/day, 221.256 hours/ns, 12.555 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.809 | 2.809 | 2.809 | 0.0 | 35.27
Kspace | 1.2214 | 1.2214 | 1.2214 | 0.0 | 15.33
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015635 | 0.015635 | 0.015635 | 0.0 | 0.20
Output | 0.0014393 | 0.0014393 | 0.0014393 | 0.0 | 0.02
Modify | 3.9157 | 3.9157 | 3.9157 | 0.0 | 49.16
Other | | 0.002091 | | | 0.03
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 735200.0 ave 735200 max 735200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/dynamic"
Using fix qeq/dynamic
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.38094 0.85231286 -0.42615643 0.000000000001 43
10 -3452.05217 0.85475894 -0.42737947 -0.000000000001 17
20 -3497.8643 0.85999180 -0.42999590 -0.000000000007 22
30 -3568.53169 0.86772479 -0.43386239 -0.000000000006 22
40 -3633.43753 0.87338291 -0.43669146 -0.000000000006 22
50 -3700.27953 0.87807632 -0.43903816 -0.000000000005 22
60 -3784.4004 0.88402822 -0.44201411 0.000000000002 17
70 -3877.73706 0.89012201 -0.44506100 0.000000000002 22
80 -3965.36111 0.89432486 -0.44716243 0.000000000008 17
90 -4048.57901 0.89701688 -0.44850844 -0.000000000004 22
100 -4118.62736 0.89718691 -0.44859346 -0.000000000026 17
Loop time of 18.5333 on 1 procs for 100 steps with 1200 atoms
Performance: 0.047 ns/day, 514.815 hours/ns, 5.396 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.8268 | 2.8268 | 2.8268 | 0.0 | 15.25
Kspace | 1.2138 | 1.2138 | 1.2138 | 0.0 | 6.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015407 | 0.015407 | 0.015407 | 0.0 | 0.08
Output | 0.0014303 | 0.0014303 | 0.0014303 | 0.0 | 0.01
Modify | 14.474 | 14.474 | 14.474 | 0.0 | 78.10
Other | | 0.001973 | | | 0.01
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/fire"
Using fix qeq/fire
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 1 by 1 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 42772 21870
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.87 | 17.87 | 17.87 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.06113 0.85226679 -0.42613339 0.000000000004 37
10 -3452.0494 0.85475813 -0.42737906 0.000000000001 10
20 -3497.83503 0.85998739 -0.42999370 0.000000000003 13
30 -3568.47507 0.86771599 -0.43385799 0.000000000004 13
40 -3633.35368 0.87337029 -0.43668514 0.000000000004 13
50 -3700.15601 0.87805847 -0.43902924 0.000000000005 13
60 -3784.32042 0.88401635 -0.44200818 0.000000000000 11
70 -3877.59818 0.89010162 -0.44505081 0.000000000000 13
80 -3965.28426 0.89431356 -0.44715678 0.000000000000 11
90 -4048.3338 0.89698069 -0.44849034 0.000000000001 13
100 -4118.63638 0.89718818 -0.44859409 0.000000000003 12
Loop time of 13.0492 on 1 procs for 100 steps with 1200 atoms
Performance: 0.066 ns/day, 362.479 hours/ns, 7.663 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7996 | 2.7996 | 2.7996 | 0.0 | 21.45
Kspace | 1.2141 | 1.2141 | 1.2141 | 0.0 | 9.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.015527 | 0.015527 | 0.015527 | 0.0 | 0.12
Output | 0.0014405 | 0.0014405 | 0.0014405 | 0.0 | 0.01
Modify | 9.0166 | 9.0166 | 9.0166 | 0.0 | 69.10
Other | | 0.001981 | | | 0.02
Nlocal: 1200.00 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100.00 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600.0 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00

650
examples/qeq/log.20Apr21.qeq.buck.g++.4 Normal file
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@ -0,0 +1,650 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# a pair style using charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
read_data CPU = 0.009 seconds
#replicate 2 2 2
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
fix 2 all qeq/shielded 1 10 1.0e-20 10 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
velocity all create 300.0 1281937
run 0 post no
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.30705229
grid = 48 48 54
stencil order = 5
estimated absolute RMS force accuracy = 1.8909403e-05
estimated relative force accuracy = 1.3131854e-06
using double precision FFTW3
3d grid and FFT values/proc = 57970 32256
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
WARNING: Fix qeq CG convergence failed (4.299911728887494e-19) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
WARNING: Fix qeq CG convergence failed (5.273380778822746e-18) after 10 iterations at step 0 (src/QEQ/fix_qeq.cpp:410)
Per MPI rank memory allocation (min/avg/max) = 14.97 | 15.02 | 15.08 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00327 0.76536977 -0.38268489 0.000000000000 10
Loop time of 3.33786e-06 on 4 procs for 0 steps with 1200 atoms
write_restart qeq.restart
System init for write_restart ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/point"
Using fix qeq/point
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/point, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.17988 0.85228288 -0.42614144 -0.000000000000 3
10 -3452.03328 0.85475605 -0.42737803 -0.000000000000 8
20 -3497.57515 0.85994936 -0.42997468 0.000000000000 8
30 -3568.22095 0.86767937 -0.43383969 0.000000000000 8
40 -3633.24956 0.87335551 -0.43667775 -0.000000000000 8
50 -3700.10219 0.87805056 -0.43902528 0.000000000000 8
60 -3784.36769 0.88402303 -0.44201151 0.000000000000 8
70 -3877.51378 0.89008950 -0.44504475 0.000000000000 8
80 -3965.29722 0.89431515 -0.44715757 0.000000000000 8
90 -4048.36764 0.89698588 -0.44849294 -0.000000000000 8
100 -4118.65809 0.89719102 -0.44859551 0.000000000000 8
Loop time of 3.30911 on 4 procs for 100 steps with 1200 atoms
Performance: 0.261 ns/day, 91.920 hours/ns, 30.220 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67613 | 0.68904 | 0.71562 | 1.9 | 20.82
Kspace | 0.36056 | 0.3881 | 0.39892 | 2.6 | 11.73
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013339 | 0.017982 | 0.019974 | 2.0 | 0.54
Output | 0.0006721 | 0.00099713 | 0.0019572 | 0.0 | 0.03
Modify | 2.2109 | 2.211 | 2.211 | 0.0 | 66.81
Other | | 0.002041 | | | 0.06
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/shielded"
Using fix qeq/shielded
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.006 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1
40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 2.25559 on 4 procs for 100 steps with 1200 atoms
Performance: 0.383 ns/day, 62.655 hours/ns, 44.334 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67442 | 0.69181 | 0.70907 | 2.0 | 30.67
Kspace | 0.39381 | 0.41151 | 0.43023 | 2.6 | 18.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012851 | 0.01426 | 0.015146 | 0.7 | 0.63
Output | 0.00066686 | 0.00098681 | 0.0019395 | 0.0 | 0.04
Modify | 1.1349 | 1.135 | 1.135 | 0.0 | 50.32
Other | | 0.002035 | | | 0.09
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/slater"
Using fix qeq/slater
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.012 seconds
fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.10 | 11.14 | 11.16 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -2879.00309 0.76536977 -0.38268489 0.000000000000 3
10 -2882.50998 0.76536972 -0.38268486 0.000000000000 2
20 -2893.89472 0.76536950 -0.38268475 -0.000000000000 2
30 -2913.6181 0.76536875 -0.38268438 -0.000000000000 1
40 -2942.24129 0.76536939 -0.38268470 0.000000000000 1
50 -2980.18817 0.76536780 -0.38268390 0.000000000000 2
60 -3027.60957 0.76536804 -0.38268402 -0.000000000000 2
70 -3084.12552 0.76536573 -0.38268287 0.000000000000 2
80 -3148.8697 0.76536550 -0.38268275 0.000000000000 1
90 -3220.43086 0.76536380 -0.38268190 0.000000000000 2
100 -3297.0618 0.76536251 -0.38268126 0.000000000000 2
Loop time of 2.39249 on 4 procs for 100 steps with 1200 atoms
Performance: 0.361 ns/day, 66.458 hours/ns, 41.797 timesteps/s
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.6751 | 0.70301 | 0.71919 | 2.1 | 29.38
Kspace | 0.45569 | 0.47315 | 0.49885 | 2.6 | 19.78
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012967 | 0.018681 | 0.020909 | 2.4 | 0.78
Output | 0.00066733 | 0.00099397 | 0.0019579 | 0.0 | 0.04
Modify | 1.1945 | 1.1946 | 1.1947 | 0.0 | 49.93
Other | | 0.002046 | | | 0.09
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 91900 max 91900 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 183800.0 ave 183800 max 183800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 735200
Ave neighs/atom = 612.66667
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/dynamic"
Using fix qeq/dynamic
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.002 seconds
fix 2 all qeq/dynamic 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/dynamic, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.38094 0.85231286 -0.42615643 -0.000000000001 43
10 -3452.05217 0.85475894 -0.42737947 -0.000000000003 17
20 -3497.8643 0.85999180 -0.42999590 0.000000000000 22
30 -3568.53169 0.86772479 -0.43386239 -0.000000000000 22
40 -3633.43753 0.87338291 -0.43669146 0.000000000006 22
50 -3700.27953 0.87807632 -0.43903816 0.000000000003 22
60 -3784.4004 0.88402822 -0.44201411 0.000000000009 17
70 -3877.73706 0.89012201 -0.44506100 0.000000000010 22
80 -3965.36111 0.89432486 -0.44716243 0.000000000011 17
90 -4048.57901 0.89701688 -0.44850844 0.000000000012 22
100 -4118.62736 0.89718691 -0.44859346 0.000000000013 17
Loop time of 5.27704 on 4 procs for 100 steps with 1200 atoms
Performance: 0.164 ns/day, 146.584 hours/ns, 18.950 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68437 | 0.69096 | 0.69826 | 0.7 | 13.09
Kspace | 0.38484 | 0.38941 | 0.39524 | 0.7 | 7.38
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012609 | 0.01529 | 0.016842 | 1.3 | 0.29
Output | 0.00067735 | 0.0010006 | 0.0019588 | 1.7 | 0.02
Modify | 4.1783 | 4.1783 | 4.1784 | 0.0 | 79.18
Other | | 0.002027 | | | 0.04
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
clear
using 1 OpenMP thread(s) per MPI task
print "Using fix qeq/fire"
Using fix qeq/fire
read_restart qeq.restart
Reading restart file ...
restart file = 8 Apr 2021, LAMMPS = 8 Apr 2021
restoring atom style charge from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (25.158320 25.158320 28.020256)
1 by 2 by 2 MPI processor grid
restoring pair style buck/coul/long from restart
1200 atoms
read_restart CPU = 0.001 seconds
fix 2 all qeq/fire 1 10 1.0e-3 100 param.qeq2
include buck.inc
kspace_style pppm 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
variable nqeq equal f_2
thermo_style custom step pe c_q1 c_q2 v_qtot v_nqeq
thermo 10
thermo_modify format line "%4d %12.9g %12.8f %12.8f %16.12f %6.0f"
timestep 0.0001
fix 1 all nve
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
G vector (1/distance) = 0.27644401
grid = 27 27 30
stencil order = 5
estimated absolute RMS force accuracy = 1.4502702e-05
estimated relative force accuracy = 1.0071569e-06
using double precision FFTW3
3d grid and FFT values/proc = 14960 5832
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 4 4 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.195 | 9.246 | 9.278 Mbytes
Step PotEng c_q1 c_q2 v_qtot v_nqeq
0 -3432.05316 0.85226679 -0.42613339 0.000000000001 37
10 -3452.04937 0.85475813 -0.42737906 0.000000000001 10
20 -3497.83659 0.85998739 -0.42999370 0.000000000002 13
30 -3568.47793 0.86771599 -0.43385799 0.000000000002 13
40 -3633.35326 0.87337029 -0.43668514 0.000000000002 13
50 -3700.16079 0.87805847 -0.43902924 0.000000000000 13
60 -3784.31906 0.88401635 -0.44200818 -0.000000000001 11
70 -3877.60163 0.89010162 -0.44505081 -0.000000000000 13
80 -3965.28179 0.89431356 -0.44715678 0.000000000001 11
90 -4048.33861 0.89698069 -0.44849034 0.000000000001 13
100 -4118.63861 0.89718818 -0.44859409 0.000000000002 12
Loop time of 3.88026 on 4 procs for 100 steps with 1200 atoms
Performance: 0.223 ns/day, 107.785 hours/ns, 25.771 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.68424 | 0.69912 | 0.73572 | 2.5 | 18.02
Kspace | 0.38093 | 0.41715 | 0.43168 | 3.2 | 10.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012711 | 0.013318 | 0.014003 | 0.4 | 0.34
Output | 0.00066566 | 0.00098735 | 0.0019317 | 0.0 | 0.03
Modify | 2.7477 | 2.7477 | 2.7477 | 0.0 | 70.81
Other | | 0.002004 | | | 0.05
Nlocal: 300.000 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875.00 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900.0 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.33333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:17

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examples/qeq/log.27Nov18.qeq.buck.g++.1
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 1 by 1 MPI processor grid
9600 atoms
Time spent = 0.00114894 secs
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 8 8 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes
Step PotEng c_q1 c_q2 v_qtot S/CPU
0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0
10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877
20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179
30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643
40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341
50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127
60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762
70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546
80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079
90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419
100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001
Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms
Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48
Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01
Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00
Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11
Other | | 0.007197 | | | 0.00
Nlocal: 9600 ave 9600 max 9600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22125 ave 22125 max 22125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.9408e+06 ave 2.9408e+06 max 2.9408e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:01

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examples/qeq/log.27Nov18.qeq.buck.g++.4
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 2 by 2 MPI processor grid
9600 atoms
Time spent = 0.000675201 secs
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5, bins = 8 8 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair buck/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix qeq/fire, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes
Step PotEng c_q1 c_q2 v_qtot S/CPU
0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0
10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312
20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316
30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335
40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139
50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263
60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722
70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406
80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813
90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145
100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486
Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms
Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22
Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75
Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00
Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03
Other | | 0.01409 | | | 0.03
Nlocal: 2400 ave 2400 max 2400 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 11550 ave 11550 max 11550 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 735200 ave 740758 max 729642 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:49

1
examples/qeq/param.qeq1
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@ -1,3 +1,4 @@
# UNITS: real
1 5.3200 14.8732 1.0206 0.0 0.0
2 5.8678 14.0000 0.9000 0.0 0.0
3 8.5000 17.9978 1.0503 0.0 0.0

1
examples/qeq/param.qeq2
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@ -1,2 +1,3 @@
# UNITS: metal
1 0.00000 7.25028 0.01 0.772871 0.000000
2 11.26882 15.37920 0.01 0.243072 0.000000

52
examples/reax/in.reaxc.rdx
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# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

52
examples/reax/in.reaxc.rdx-shielded
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# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

55
examples/reax/in.reaxc.tatb
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# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25

55
examples/reax/in.reaxc.tatb-shielded
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# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25

116
examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1
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LAMMPS (4 Jan 2019)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.54 | 15.54 | 15.54 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79939 0 168.88404
10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512
30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749
40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085
50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995
60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414
70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648
80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464
90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914
100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951
Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms
Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.59308 | 0.59308 | 0.59308 | 0.0 | 90.21
Neigh | 0.020665 | 0.020665 | 0.020665 | 0.0 | 3.14
Comm | 0.0015757 | 0.0015757 | 0.0015757 | 0.0 | 0.24
Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.06
Modify | 0.04156 | 0.04156 | 0.04156 | 0.0 | 6.32
Other | | 0.000154 | | | 0.02
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1306 ave 1306 max 1306 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1306
Ave neighs/atom = 62.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

116
examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4
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LAMMPS (4 Jan 2019)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.62 | 12.08 | 13.84 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452
10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929
30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706
40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076
50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999
60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412
70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967
80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525
90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126
100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944
Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms
Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s
93.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.53395 | 0.5352 | 0.53805 | 0.2 | 84.37
Neigh | 0.0088253 | 0.012023 | 0.016203 | 2.4 | 1.90
Comm | 0.0051677 | 0.0081 | 0.0093861 | 1.9 | 1.28
Output | 0.00049353 | 0.00054371 | 0.00058222 | 0.0 | 0.09
Modify | 0.074155 | 0.078299 | 0.081472 | 0.9 | 12.34
Other | | 0.0001715 | | | 0.03
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 326.5 ave 927 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1306
Ave neighs/atom = 62.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

114
examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1
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LAMMPS (4 Jan 2019)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 169.6 | 169.6 | 169.6 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274
5 0.61603942 -44761.698 -44760.994 8934.628 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691
10 2.3525549 -44763.227 -44760.541 12288.614 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9684 0 6381.7061
15 4.9013311 -44766.36 -44760.764 17716.982 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2449 0 6370.4111
20 7.8294673 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5142 0 6355.2654
25 10.697904 -44772.904 -44760.691 34232.821 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3541 0 6336.8349
Loop time of 7.80985 on 1 procs for 25 steps with 384 atoms
Performance: 0.017 ns/day, 1388.418 hours/ns, 3.201 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.003 | 5.003 | 5.003 | 0.0 | 64.06
Neigh | 1.1164 | 1.1164 | 1.1164 | 0.0 | 14.29
Comm | 0.0065806 | 0.0065806 | 0.0065806 | 0.0 | 0.08
Output | 0.00029969 | 0.00029969 | 0.00029969 | 0.0 | 0.00
Modify | 1.6831 | 1.6831 | 1.6831 | 0.0 | 21.55
Other | | 0.0004976 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 336304 ave 336304 max 336304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.792
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:08

114
examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4
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LAMMPS (4 Jan 2019)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
5 0.61603968 -44761.698 -44760.994 8934.6336 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
10 2.3525543 -44763.227 -44760.541 12288.588 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9756 0 6381.7133
15 4.9013233 -44766.36 -44760.764 17716.934 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2627 0 6370.4289
20 7.8294615 -44769.686 -44760.747 25205.586 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4958 0 6355.2471
25 10.697919 -44772.904 -44760.691 34232.898 -61069.308 490.25887 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3285 0 6336.8093
Loop time of 4.34178 on 4 procs for 25 steps with 384 atoms
Performance: 0.031 ns/day, 771.872 hours/ns, 5.758 timesteps/s
96.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1756 | 3.1763 | 3.1771 | 0.0 | 73.16
Neigh | 0.58917 | 0.59661 | 0.6035 | 0.9 | 13.74
Comm | 0.0088837 | 0.010178 | 0.011116 | 0.8 | 0.23
Output | 0.00036407 | 0.0019013 | 0.003552 | 2.7 | 0.04
Modify | 0.54882 | 0.55637 | 0.56413 | 0.8 | 12.81
Other | | 0.0004123 | | | 0.01
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 84076 ave 84076 max 84076 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.792
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

115
examples/reax/log.8March18.reaxc.rdx.g++.1
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LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.28 | 15.28 | 15.28 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79937 0 168.88402
10 1288.6114 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43322 0 107.75935
20 538.95849 -1942.7037 -1910.5731 -10725.658 -2803.7395 7.9078331 0.077926702 0 81.610043 0.22951937 -57.557104 0 30.331203 -10.178049 878.99015 -159.69092 0 89.315159
30 463.09542 -1933.5765 -1905.9685 -33255.507 -2749.8591 -8.0154628 0.027628767 0 81.627403 0.11972403 -50.262284 0 20.82032 -9.6327022 851.88722 -149.495 0 79.205731
40 885.49449 -1958.9126 -1906.1228 -4814.7123 -2795.644 9.1506221 0.1374749 0 70.948046 0.24360579 -57.8627 0 19.076515 -11.141211 873.73892 -159.9939 0 92.434059
50 861.1646 -1954.4599 -1903.1206 -1896.7387 -2784.8446 3.8269113 0.1579328 0 79.851775 3.3492107 -78.066127 0 32.628975 -7.9565255 872.81826 -190.98565 0 114.75994
60 1167.785 -1971.8432 -1902.2243 -3482.6975 -2705.8638 -17.121582 0.22749067 0 44.507705 7.856069 -74.788959 0 16.256519 -4.6046602 835.8308 -188.33691 0 114.19414
70 1439.9947 -1989.3024 -1903.4554 23845.067 -2890.7896 31.958874 0.26671735 0 85.758608 3.1803486 -71.002907 0 24.357106 -10.311315 905.86799 -175.38482 0 106.79659
80 502.40024 -1930.7547 -1900.8035 -20356.557 -2703.8096 -18.663105 0.11286226 0 99.803799 2.0329394 -76.171387 0 19.236609 -6.2786041 826.47358 -166.03157 0 92.539694
90 749.09267 -1946.9834 -1902.3254 17798.812 -2863.7586 42.068927 0.24338042 0 96.18195 0.96181754 -69.955528 0 24.61541 -11.58277 903.68895 -190.13838 0 120.69139
100 1109.7046 -1968.5875 -1902.4311 -4490.6736 -2755.8953 -7.1235173 0.21757663 0 61.806405 7.0825933 -75.645487 0 20.114745 -6.2371664 863.56285 -198.56939 0 122.09923
Loop time of 0.395195 on 1 procs for 100 steps with 21 atoms
Performance: 21.863 ns/day, 1.098 hours/ns, 253.039 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3722 | 0.3722 | 0.3722 | 0.0 | 94.18
Neigh | 0.0098455 | 0.0098455 | 0.0098455 | 0.0 | 2.49
Comm | 0.00047445 | 0.00047445 | 0.00047445 | 0.0 | 0.12
Output | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.09
Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 3.08
Other | | 0.0001521 | | | 0.04
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.1905
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

115
examples/reax/log.8March18.reaxc.rdx.g++.4
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@ -1,115 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.37 | 11.76 | 13.34 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79988 0 168.88453
10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252286 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
20 538.95818 -1942.7037 -1910.5731 -10725.623 -2803.7394 7.9078307 0.077926702 0 81.61005 0.22951942 -57.557107 0 30.331206 -10.178049 878.9901 -159.68951 0 89.313749
30 463.09514 -1933.5765 -1905.9685 -33255.525 -2749.859 -8.0154737 0.027628797 0 81.627408 0.11972402 -50.262283 0 20.82031 -9.6327021 851.88715 -149.49499 0 79.205724
40 885.49412 -1958.9125 -1906.1227 -4814.6606 -2795.6439 9.150622 0.13747487 0 70.948029 0.24360517 -57.862679 0 19.076509 -11.141214 873.7389 -159.99392 0 92.434078
50 861.16393 -1954.46 -1903.1207 -1896.7323 -2784.8449 3.8270197 0.1579328 0 79.851743 3.3492115 -78.066132 0 32.628992 -7.9565379 872.81841 -190.98568 0 114.75996
60 1167.7846 -1971.8432 -1902.2243 -3482.8111 -2705.8633 -17.121657 0.2274907 0 44.507681 7.8560366 -74.788989 0 16.256493 -4.6046537 835.8305 -188.33687 0 114.1941
70 1439.9942 -1989.3023 -1903.4554 23845.444 -2890.7894 31.958784 0.26671721 0 85.758586 3.1803655 -71.002918 0 24.357158 -10.311304 905.86792 -175.38481 0 106.79657
80 502.3975 -1930.7546 -1900.8036 -20356.439 -2703.8105 -18.662812 0.11286123 0 99.80391 2.0329293 -76.171334 0 19.236803 -6.2786439 826.47397 -166.03141 0 92.539551
90 749.09048 -1946.9837 -1902.3258 17798.718 -2863.7582 42.068719 0.24338057 0 96.181773 0.96183581 -69.955529 0 24.615414 -11.582758 903.68862 -190.1384 0 120.69139
100 1109.6999 -1968.5875 -1902.4314 -4490.3728 -2755.8964 -7.1231468 0.21757685 0 61.806149 7.0826648 -75.645428 0 20.115002 -6.2371958 863.56343 -198.56957 0 122.09942
Loop time of 0.329552 on 4 procs for 100 steps with 21 atoms
Performance: 26.217 ns/day, 0.915 hours/ns, 303.443 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26372 | 0.26499 | 0.26754 | 0.3 | 80.41
Neigh | 0.0045478 | 0.0062494 | 0.0076699 | 1.5 | 1.90
Comm | 0.0041637 | 0.0064691 | 0.0080271 | 1.8 | 1.96
Output | 0.00054169 | 0.00056636 | 0.00060368 | 0.0 | 0.17
Modify | 0.049433 | 0.051134 | 0.05311 | 0.6 | 15.52
Other | | 0.000141 | | | 0.04
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.9048
Neighbor list builds = 10
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

113
examples/reax/log.8March18.reaxc.tatb.g++.1
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@ -1,113 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 176.7 | 176.7 | 176.7 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275
5 0.61603968 -44761.698 -44760.994 8934.6347 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
10 2.3525551 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9768 0 6381.7146
15 4.9013279 -44766.36 -44760.764 17717.01 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2375 0 6370.4038
20 7.8294645 -44769.686 -44760.747 25205.624 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4889 0 6355.2402
25 10.697904 -44772.904 -44760.691 34232.965 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3125 0 6336.7934
Loop time of 4.72562 on 1 procs for 25 steps with 384 atoms
Performance: 0.029 ns/day, 840.110 hours/ns, 5.290 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.775 | 3.775 | 3.775 | 0.0 | 79.88
Neigh | 0.47047 | 0.47047 | 0.47047 | 0.0 | 9.96
Comm | 0.0025151 | 0.0025151 | 0.0025151 | 0.0 | 0.05
Output | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.01
Modify | 0.47676 | 0.47676 | 0.47676 | 0.0 | 10.09
Other | | 0.0005293 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

113
examples/reax/log.8March18.reaxc.tatb.g++.4
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@ -1,113 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 5 4 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 118 | 118 | 118 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
10 2.3525544 -44763.227 -44760.541 12288.587 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9764 0 6381.7141
15 4.9013311 -44766.36 -44760.764 17716.955 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2558 0 6370.4221
20 7.8294715 -44769.686 -44760.747 25205.613 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4906 0 6355.2419
25 10.697924 -44772.904 -44760.691 34232.794 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91376 -1582.3261 253.82253 -653.53183 18791.975 -8684.3641 0 6336.8449
Loop time of 2.84068 on 4 procs for 25 steps with 384 atoms
Performance: 0.048 ns/day, 505.009 hours/ns, 8.801 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3253 | 2.328 | 2.3305 | 0.2 | 81.95
Neigh | 0.2589 | 0.26458 | 0.26897 | 0.7 | 9.31
Comm | 0.0094428 | 0.012062 | 0.014872 | 2.3 | 0.42
Output | 0.00043392 | 0.0042209 | 0.0054941 | 3.4 | 0.15
Modify | 0.22563 | 0.23134 | 0.23579 | 0.8 | 8.14
Other | | 0.0005122 | | | 0.02
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.771
Neighbor list builds = 5
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

0
examples/reax/AB/README → examples/reaxff/AB/README
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0
examples/reax/AB/data.AB → examples/reaxff/AB/data.AB
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examples/reax/AB/ffield.reax.AB → examples/reaxff/AB/ffield.reax.AB
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examples/reax/AB/in.AB → examples/reaxff/AB/in.AB
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0
examples/reax/AB/lmp_control → examples/reaxff/AB/lmp_control
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examples/reax/AB/log.8Mar18.AB.g++.1 → examples/reaxff/AB/log.8Mar18.AB.g++.1
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examples/reax/AB/log.8Mar18.AB.g++.4 → examples/reaxff/AB/log.8Mar18.AB.g++.4
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examples/reax/AB/param.qeq → examples/reaxff/AB/param.qeq
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examples/reax/AuO/README → examples/reaxff/AuO/README
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examples/reax/AuO/data.AuO → examples/reaxff/AuO/data.AuO
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examples/reax/AuO/ffield.reax.AuO → examples/reaxff/AuO/ffield.reax.AuO
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examples/reax/AuO/in.AuO → examples/reaxff/AuO/in.AuO
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examples/reax/AuO/lmp_control → examples/reaxff/AuO/lmp_control
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examples/reax/AuO/log.8Mar18.AuO.g++.1 → examples/reaxff/AuO/log.8Mar18.AuO.g++.1
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examples/reax/AuO/log.8Mar18.AuO.g++.4 → examples/reaxff/AuO/log.8Mar18.AuO.g++.4
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examples/reax/AuO/param.qeq → examples/reaxff/AuO/param.qeq
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examples/reax/CHO/README → examples/reaxff/CHO/README
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examples/reax/CHO/data.CHO → examples/reaxff/CHO/data.CHO
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examples/reax/CHO/ffield.reax.cho → examples/reaxff/CHO/ffield.reax.cho
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examples/reax/CHO/in.CHO → examples/reaxff/CHO/in.CHO
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examples/reax/CHO/log.8Mar18.CHO.g++.4 → examples/reaxff/CHO/log.8Mar18.CHO.g++.4
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examples/reax/FC/README → examples/reaxff/FC/README
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examples/reax/FC/ffield.reax.FC → examples/reaxff/FC/ffield.reax.FC
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examples/reax/FC/log.8Mar18.FC.g++.4 → examples/reaxff/FC/log.8Mar18.FC.g++.4
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examples/reax/FeOH3/README → examples/reaxff/FeOH3/README
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examples/reax/FeOH3/data.FeOH3 → examples/reaxff/FeOH3/data.FeOH3
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examples/reax/FeOH3/ffield.reax.Fe_O_C_H → examples/reaxff/FeOH3/ffield.reax.Fe_O_C_H
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examples/reax/FeOH3/in.FeOH3 → examples/reaxff/FeOH3/in.FeOH3
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examples/reax/FeOH3/lmp_control → examples/reaxff/FeOH3/lmp_control
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examples/reax/FeOH3/log.5Oct16.FeOH3.g++.1 → examples/reaxff/FeOH3/log.5Oct16.FeOH3.g++.1
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examples/reax/FeOH3/param.qeq → examples/reaxff/FeOH3/param.qeq
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examples/reax/HNS/README.txt → examples/reaxff/HNS/README.txt
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examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 → examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.1
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examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 → examples/reaxff/HNS/log.8Mar18.reaxc.hns.g++.4
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examples/reax/RDX/README → examples/reaxff/RDX/README
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examples/reax/RDX/data.RDX → examples/reaxff/RDX/data.RDX
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examples/reax/RDX/ffield.reax.rdx → examples/reaxff/RDX/ffield.reax.rdx
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examples/reax/RDX/in.RDX → examples/reaxff/RDX/in.RDX
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examples/reax/RDX/lmp_control → examples/reaxff/RDX/lmp_control
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examples/reax/RDX/log.8Mar18.RDX.g++.1 → examples/reaxff/RDX/log.8Mar18.RDX.g++.1
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examples/reax/RDX/log.8Mar18.RDX.g++.4 → examples/reaxff/RDX/log.8Mar18.RDX.g++.4
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examples/reax/RDX/param.qeq → examples/reaxff/RDX/param.qeq
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examples/reax/README → examples/reaxff/README
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examples/reax/VOH/README → examples/reaxff/VOH/README
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examples/reax/VOH/data.VOH → examples/reaxff/VOH/data.VOH
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examples/reax/VOH/ffield.reax.V_O_C_H → examples/reaxff/VOH/ffield.reax.V_O_C_H
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examples/reax/VOH/in.VOH → examples/reaxff/VOH/in.VOH
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