forked from lijiext/lammps
remove meam and reax from documentation
This commit is contained in:
Axel Kohlmeyer
parent
dedc6cf20c
commit
e86b933862
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@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
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"OPT"_#opt,
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"POEMS"_#poems,
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"PYTHON"_#python,
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"REAX"_#reax,
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"VORONOI"_#voronoi,
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"USER-ATC"_#user-atc,
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"USER-AWPMD"_#user-awpmd,
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@ -536,45 +535,6 @@ build fails.
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:line
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REAX package :h4,link(reax)
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NOTE: the use of the REAX package and its "pair_style
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reax"_pair_reax.html command is discouraged, as it is no longer
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maintained. Please use the USER-REAXC package and its "pair_style
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reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
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enabled variant (pair_style reax/c/kk), which has a more robust memory
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management. See the "pair_style reax/c"_pair_reaxc.html doc page for
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details.
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[CMake build]:
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No additional settings are needed besides "-D PKG_REAX=yes".
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[Traditional make]:
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Before building LAMMPS, you must build the REAX library in lib/reax.
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You can do this manually if you prefer; follow the instructions in
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lib/reax/README. You can also do it in one step from the lammps/src
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dir, using a command like these, which simply invoke the
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lib/reax/Install.py script with the specified args:
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make lib-reax # print help message
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make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
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make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
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make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
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The build should produce two files: lib/reax/libreax.a and
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lib/reax/Makefile.lammps. The latter is copied from an existing
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Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
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Fortran (REAX library). Typically the two compilers used for LAMMPS
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and the REAX library need to be consistent (e.g. both Intel or both
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GNU compilers). If necessary, you can edit/create a new
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lib/reax/Makefile.machine file for your system, which should define an
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EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
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file.
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:line
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VORONOI package :h4,link(voronoi)
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To build with this package, you must download and build the "Voro++
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@ -621,8 +581,8 @@ The USER-ATC package requires the MANYBODY package also be installed.
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[CMake build]:
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No additional settings are needed besides "-D PKG_REAX=yes" and "-D
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PKG_MANYBODY=yes".
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No additional settings are needed besides "-D PKG_USER-ATC=yes"
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and "-D PKG_MANYBODY=yes".
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[Traditional make]:
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@ -47,7 +47,6 @@ packages:
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"OPT"_Build_extras.html#opt,
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"POEMS"_Build_extras.html#poems,
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"PYTHON"_Build_extras.html#python,
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"REAX"_Build_extras.html#reax,
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"VORONOI"_Build_extras.html#voronoi,
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"USER-ATC"_Build_extras.html#user-atc,
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"USER-AWPMD"_Build_extras.html#user-awpmd,
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@ -169,8 +169,7 @@ OPT.
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"qmmm"_fix_qmmm.html,
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"qtb"_fix_qtb.html,
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"rattle"_fix_shake.html,
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"reax/bonds"_fix_reax_bonds.html,
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"reax/c/bonds (k)"_fix_reax_bonds.html,
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"reax/c/bonds (k)"_fix_reaxc_bonds.html,
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"reax/c/species (k)"_fix_reaxc_species.html,
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"recenter"_fix_recenter.html,
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"restrain"_fix_restrain.html,
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@ -160,8 +160,7 @@ OPT.
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"lubricateU/poly"_pair_lubricateU.html,
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"mdpd"_pair_meso.html,
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"mdpd/rhosum"_pair_meso.html,
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"meam"_pair_meam.html,
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"meam/c"_pair_meam.html,
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"meam/c"_pair_meamc.html,
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"meam/spline (o)"_pair_meam_spline.html,
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"meam/sw/spline"_pair_meam_sw_spline.html,
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"mgpt"_pair_mgpt.html,
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@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
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needed to run in parallel.
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The LAMMPS binaries contain all optional packages included in the
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source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
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and USER-QMMM. The serial version also does not include the MPIIO and
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source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
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The serial version also does not include the MPIIO and
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USER-LB packages. GPU support is provided for OpenCL.
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The installer site also has instructions on how to run LAMMPS under
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@ -45,7 +45,6 @@ as contained in the file name.
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"LATTE"_#PKG-LATTE,
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"MANYBODY"_#PKG-MANYBODY,
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"MC"_#PKG-MC,
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"MEAM"_#PKG-MEAM,
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"MESSAGE"_#PKG-MESSAGE,
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"MISC"_#PKG-MISC,
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"MOLECULE"_#PKG-MOLECULE,
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@ -533,37 +532,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
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:line
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MEAM package :link(PKG-MEAM),h4
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[Contents:]
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A pair style for the modified embedded atom (MEAM) potential.
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Please note that the use of the MEAM package is discouraged as
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it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
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which is a direct translation of the MEAM package to C++.
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USER-MEAMC contains additional optimizations making it run faster
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than MEAM on most machines, while providing the identical features
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and user interface.
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[Author:] Greg Wagner (Northwestern U) while at Sandia.
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[Install:]
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This package has "specific installation
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instructions"_Build_extras.html#gpu on the "Build
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extras"_Build_extras.html doc page.
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[Supporting info:]
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src/MEAM: filenames -> commands
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src/meam/README
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lib/meam/README
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"pair_style meam"_pair_meam.html
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examples/meam :ul
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:line
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MESSAGE package :link(PKG-MESSAGE),h4
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[Contents:]
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@ -1552,10 +1520,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
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[Contents:]
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A pair style for the modified embedded atom (MEAM) potential
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translated from the Fortran version in the "MEAM"_#PKG-MEAM package
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to plain C++. In contrast to the MEAM package, no library
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needs to be compiled and the pair style can be instantiated
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multiple times.
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translated from the Fortran version in the (obsolete) "MEAM" package
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to plain C++. The USER-MEAMC fully replaces the MEAM package, which
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has been removed from LAMMPS after the 12 December 2018 version.
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[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
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based on the Fortran version of Greg Wagner (Northwestern U) while at
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@ -1565,8 +1532,8 @@ Sandia.
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src/USER-MEAMC: filenames -> commands
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src/USER-MEAMC/README
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"pair_style meam/c"_pair_meam.html
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examples/meam :ul
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"pair_style meam/c"_pair_meamc.html
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examples/meamc :ul
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:line
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@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
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"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
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"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
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"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
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"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
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"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
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"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
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"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
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@ -53,7 +53,7 @@ Package, Description, Doc page, Example, Library
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"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
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"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
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"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
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"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
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"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
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"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
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"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
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"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
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@ -486,7 +486,7 @@ README for more info on Pizza.py and how to use these scripts.
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reax tool :h4,link(reax_tool)
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The reax sub-directory contains stand-alond codes that can
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post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
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post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
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command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
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the README.txt file for more info.
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@ -312,9 +312,8 @@ accelerated styles exist.
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"qmmm"_fix_qmmm.html -
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"qtb"_fix_qtb.html -
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"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
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"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
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"reax/c/bonds"_fix_reax_bonds.html -
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"reax/c/species"_fix_reaxc_species.html -
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"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
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"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
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"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
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"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
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"rhok"_fix_rhok.html -
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@ -6,13 +6,12 @@
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:line
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fix reax/bonds command :h3
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fix reax/c/bonds command :h3
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fix reax/c/bonds/kk command :h3
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[Syntax:]
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fix ID group-ID reax/bonds Nevery filename :pre
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fix ID group-ID reaxc/bonds Nevery filename :pre
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ID, group-ID are documented in "fix"_fix.html command
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reax/bonds = style name of this fix command
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@ -21,16 +20,14 @@ filename = name of output file :ul
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[Examples:]
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fix 1 all reax/bonds 100 bonds.tatb
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fix 1 all reax/c/bonds 100 bonds.reaxc :pre
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[Description:]
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Write out the bond information computed by the ReaxFF potential
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specified by "pair_style reax"_pair_reax.html or "pair_style
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reax/c"_pair_reaxc.html in the exact same format as the original
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stand-alone ReaxFF code of Adri van Duin. The bond information is
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written to {filename} on timesteps that are multiples of {Nevery},
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Write out the bond information computed by the ReaxFF potential specified
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by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
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original stand-alone ReaxFF code of Adri van Duin. The bond information
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is written to {filename} on timesteps that are multiples of {Nevery},
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including timestep 0. For time-averaged chemical species analysis,
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please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
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@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
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[Restrictions:]
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The fix reax/bonds command requires that the "pair_style
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reax"_pair_reax.html be invoked. This fix is part of the REAX
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package. It is only enabled if LAMMPS was built with that package,
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which also requires the REAX library be built and linked with LAMMPS.
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The fix reax/c/bonds command requires that the "pair_style
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reax/c"_pair_reaxc.html be invoked. This fix is part of the
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reax/c"_pair_reaxc.html is invoked. This fix is part of the
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USER-REAXC package. It is only enabled if LAMMPS was built with that
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package. See the "Build package"_Build_package.html doc page for more
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info.
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@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
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[Related commands:]
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"pair_style reax"_pair_reax.html, "pair_style
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reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
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"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
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[Default:] none
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@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
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[Restrictions:]
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The fix species currently only works with "pair_style
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The "fix reax/c/species" currently only works with "pair_style
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reax/c"_pair_reaxc.html and it requires that the "pair_style
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reax/c"_pair_reaxc.html be invoked. This fix is part of the
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USER-REAXC package. It is only enabled if LAMMPS was built with that
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@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
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[Related commands:]
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"pair_style reax/c"_pair_reaxc.html, "fix
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reax/bonds"_fix_reax_bonds.html
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"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
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[Default:]
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@ -135,7 +135,7 @@ Fixes :h1
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fix_qeq_reax
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fix_qmmm
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fix_qtb
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fix_reax_bonds
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fix_reaxc_bonds
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fix_reaxc_species
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fix_recenter
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fix_restrain
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@ -598,7 +598,7 @@ pair_lj_soft.html
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pair_lubricate.html
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pair_lubricateU.html
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pair_mdf.html
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pair_meam.html
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pair_meamc.html
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pair_meam_spline.html
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pair_meam_sw_spline.html
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pair_meso.html
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@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your
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model, then you should just list the sub-style once and use the
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pair_coeff command to assign parameters for the different type pairs.
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NOTE: There are two exceptions to this option to list an individual
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pair style multiple times. The first is for pair styles implemented
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as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
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reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
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This is because unlike a C++ class, they can not be instantiated
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multiple times, due to the manner in which they were coded in Fortran.
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The second is for GPU-enabled pair styles in the GPU package. This is
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b/c the GPU package also currently assumes that only one instance of a
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pair style is being used.
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NOTE: There is one exception to this option to list an individual
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pair style multiple times: GPU-enabled pair styles in the GPU package.
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This is because the GPU package currently assumes that only one
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instance of a pair style is being used.
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In the pair_coeff commands, the name of a pair style must be added
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after the I,J type specification, with the remaining coefficients
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@ -152,7 +152,7 @@ info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html
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"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html
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[Default:] none
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@ -116,7 +116,7 @@ info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html,
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"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html,
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"pair_style meam/spline"_pair_meam_spline.html
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[Default:] none
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@ -1,216 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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pair_style reax command :h3
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[Syntax:]
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pair_style reax hbcut hbnewflag tripflag precision :pre
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hbcut = hydrogen-bond cutoff (optional) (distance units)
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hbnewflag = use old or new hbond function style (0 or 1) (optional)
|
||||
tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
|
||||
precision = precision for charge equilibration (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style reax
|
||||
pair_style reax 10.0 0 1 1.0e-5
|
||||
pair_coeff * * ffield.reax 3 1 2 2
|
||||
pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {reax} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper:
|
||||
"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010.
|
||||
|
||||
WARNING: pair style reax is now deprecated and will soon be retired. Users
|
||||
should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
|
||||
differs from the {reax/c} style in the lo-level implementation details.
|
||||
The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
|
||||
LAMMPS requires that a file called ffield.reax be provided, containing
|
||||
the ReaxFF parameters for each atom type, bond type, etc. The format
|
||||
is identical to the ffield file used by van Duin and co-workers. The
|
||||
filename is required as an argument in the pair_coeff command. Any
|
||||
value other than "ffield.reax" will be rejected (see below).
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
documented in potentials/README.reax. The default ffield.reax
|
||||
contains parameterizations for the following elements: C, H, O, N.
|
||||
|
||||
NOTE: We do not distribute a wide variety of ReaxFF force field files
|
||||
with LAMMPS. Adri van Duin's group at PSU is the central repository
|
||||
for this kind of data as they are continuously deriving and updating
|
||||
parameterizations for different classes of materials. You can submit
|
||||
a contact request at the Materials Computation Center (MCC) website
|
||||
"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
|
||||
describing the material(s) you are interested in modeling with ReaxFF.
|
||||
They can tell
|
||||
you what is currently available or what it would take to create a
|
||||
suitable ReaxFF parameterization.
|
||||
|
||||
The format of these files is identical to that used originally by van
|
||||
Duin. We have tested the accuracy of {pair_style reax} potential
|
||||
against the original ReaxFF code for the systems mentioned above. You
|
||||
can use other ffield files for specific chemical systems that may be
|
||||
available elsewhere (but note that their accuracy may not have been
|
||||
tested).
|
||||
|
||||
The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are
|
||||
optional arguments. If none are provided, default settings are used:
|
||||
{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use
|
||||
new hbond function style), {tripflag} = 1 (apply stabilization to all
|
||||
triple bonds), and {precision} = 1.0e-6 (one part in 10^6). If you
|
||||
wish to override any of these defaults, then all of the settings must
|
||||
be specified.
|
||||
|
||||
Two examples using {pair_style reax} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
|
||||
calculated by both of these pair styles match very closely, the
|
||||
contributions due to the valence angles differ slightly due to
|
||||
the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
|
||||
is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom since the {reax} pair style performs a charge equilibration (QEq)
|
||||
calculation. See the "atom_style"_atom_style.html and
|
||||
"read_data"_read_data.html commands for details on how to specify
|
||||
charges.
|
||||
|
||||
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
|
||||
energy contributions, with the exception of the Coulombic and charge
|
||||
equilibration contributions which are stored in the thermo variable
|
||||
{ecoul}. The output of these quantities is controlled by the
|
||||
"thermo"_thermo.html command.
|
||||
|
||||
This pair style tallies a breakdown of the total ReaxFF potential
|
||||
energy into sub-categories, which can be accessed via the "compute
|
||||
pair"_compute_pair.html command as a vector of values of length 14.
|
||||
The 14 values correspond to the following sub-categories (the variable
|
||||
names in italics match those used in the ReaxFF FORTRAN library):
|
||||
|
||||
{eb} = bond energy
|
||||
{ea} = atom energy
|
||||
{elp} = lone-pair energy
|
||||
{emol} = molecule energy (always 0.0)
|
||||
{ev} = valence angle energy
|
||||
{epen} = double-bond valence angle penalty
|
||||
{ecoa} = valence angle conjugation energy
|
||||
{ehb} = hydrogen bond energy
|
||||
{et} = torsion energy
|
||||
{eco} = conjugation energy
|
||||
{ew} = van der Waals energy
|
||||
{ep} = Coulomb energy
|
||||
{efi} = electric field energy (always 0.0)
|
||||
{eqeq} = charge equilibration energy :ol
|
||||
|
||||
To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:
|
||||
|
||||
compute reax all pair reax
|
||||
variable eb equal c_reax\[1\]
|
||||
variable ea equal c_reax\[2\]
|
||||
...
|
||||
variable eqeq equal c_reax\[14\]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
|
||||
|
||||
Only a single pair_coeff command is used with the {reax} style which
|
||||
specifies a ReaxFF potential file with parameters for all needed
|
||||
elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
N indices = mapping of ReaxFF elements to atom types :ul
|
||||
|
||||
The specification of the filename and the mapping of LAMMPS atom types
|
||||
recognized by the ReaxFF is done differently than for other LAMMPS
|
||||
potentials, due to the non-portable difficulty of passing character
|
||||
strings (e.g. filename, element names) between C++ and Fortran.
|
||||
|
||||
The filename has to be "ffield.reax" and it has to exist in the
|
||||
directory you are running LAMMPS in. This means you cannot prepend a
|
||||
path to the file in the potentials dir. Rather, you should copy that
|
||||
file into the directory you are running from. If you wish to use
|
||||
another ReaxFF potential file, then name it "ffield.reax" and put it
|
||||
in the directory you run from.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
names, each with a couple dozen numeric parameters. If there are M
|
||||
elements specified in the {ffield} file, think of these as numbered 1
|
||||
to M. Each of the N indices you specify for the N atom types of LAMMPS
|
||||
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
|
||||
be mapped to whatever element you specify as the first index value,
|
||||
etc. If a mapping value is specified as NULL, the mapping is not
|
||||
performed. This can be used when a ReaxFF potential is used as part
|
||||
of the {hybrid} pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.
|
||||
|
||||
NOTE: Currently the reax pair style cannot be used as part of the
|
||||
{hybrid} pair style. Some additional changes still need to be made to
|
||||
enable this.
|
||||
|
||||
As an example, say your LAMMPS simulation has 4 atom types and the
|
||||
elements are ordered as C, H, O, N in the {ffield} file. If you want
|
||||
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
|
||||
H, you would use the following pair_coeff command:
|
||||
|
||||
pair_coeff * * ffield.reax 1 1 4 2 :pre
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
mix, shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The ReaxFF potential files provided with LAMMPS in the potentials
|
||||
directory are parameterized for real "units"_units.html. You can use
|
||||
the ReaxFF potential with any LAMMPS units, but you would need to
|
||||
create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "real" units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
|
||||
"fix_reax_bonds"_fix_reax_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1,
|
||||
{precision} = 1.0e-6.
|
||||
|
||||
:line
|
||||
|
||||
:link(Chenoweth_20081)
|
||||
[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
|
||||
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
|
||||
|
|
@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre
|
|||
Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper: "(Chenoweth et al.,
|
||||
2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches
|
||||
|
|
@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either
|
|||
half or full neighbor lists. This setting can be changed using the
|
||||
Kokkos "package"_package.html command.
|
||||
|
||||
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
|
||||
command in the lo-level implementation details. The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
The {reax/c} 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.
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
|
|
@ -338,8 +337,7 @@ appropriate units if your simulation doesn't use "real" units.
|
|||
|
||||
"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
|
||||
reax/c/bonds"_fix_reax_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html, "pair_style
|
||||
reax"_pair_reax.html
|
||||
reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -226,8 +226,7 @@ accelerated styles exist.
|
|||
"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
|
||||
"mdpd"_pair_meso.html - mDPD particle interactions
|
||||
"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
|
||||
"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
|
||||
"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
|
||||
"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
|
||||
"meam/spline"_pair_meam_spline.html - splined version of MEAM
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
|
||||
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
|
||||
|
|
@ -260,7 +259,6 @@ accelerated styles exist.
|
|||
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
|
||||
"python"_pair_python.html -
|
||||
"quip"_pair_quip.html -
|
||||
"reax"_pair_reax.html - ReaxFF potential in Fortran
|
||||
"reax/c"_pair_reaxc.html - ReaxFF potential in C
|
||||
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
|
||||
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
|
||||
|
|
|
|||
|
|
@ -63,7 +63,7 @@ Pair Styles :h1
|
|||
pair_lubricate
|
||||
pair_lubricateU
|
||||
pair_mdf
|
||||
pair_meam
|
||||
pair_meamc
|
||||
pair_meam_spline
|
||||
pair_meam_sw_spline
|
||||
pair_meso
|
||||
|
|
@ -82,7 +82,6 @@ Pair Styles :h1
|
|||
pair_polymorphic
|
||||
pair_python
|
||||
pair_quip
|
||||
pair_reax
|
||||
pair_reaxc
|
||||
pair_resquared
|
||||
pair_sdk
|
||||
|
|
|
|||
|
|
@ -4,19 +4,7 @@
|
|||
The programs in this folder can be used to analyze the
|
||||
output of simulations using the ReaxFF potentials;
|
||||
|
||||
mol_fra.c: reads the output of fix reax/bonds
|
||||
and identifies fragments
|
||||
Compile it using a C compiler
|
||||
To test, run it with Cutoff.dic and bonds.reax
|
||||
Contact: Aidan Thompson
|
||||
|
||||
bondConnectCheck.f90: reads the output of fix reax/bonds.
|
||||
Does not do fragment analysis.
|
||||
Compile it using FORTRAN compiler
|
||||
To test, run it with bonds.reax
|
||||
Contact: Paul Liangliang Huang <lhuang4@ncsu.edu>
|
||||
|
||||
reaxc_bond.pl: reads the bonding information in the
|
||||
.trj file produced by pair_style reax/c and
|
||||
outputs molecule counts for each frame.
|
||||
outputs molecule counts for each frame.
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue