Loading cmake/CMakeLists.txt +3 −3 Original line number Diff line number Diff line Loading @@ -132,9 +132,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) Loading doc/src/Packages_details.rst +48 −15 Original line number Diff line number Diff line Loading @@ -38,21 +38,21 @@ page gives those details. | :ref:`SRD <PKG-SRD>` | :ref:`VORONOI <PKG-VORONOI>` | | | | | +------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+ +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-ADIOS <PKG-USER-ADIOS>` | :ref:`USER-ATC <PKG-USER-ATC>` | :ref:`USER-AWPMD <PKG-USER-AWPMD>` | :ref:`USER-BOCS <PKG-USER-BOCS>` | :ref:`USER-CGDNA <PKG-USER-CGDNA>` | :ref:`USER-CGSDK <PKG-USER-CGSDK>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-COLVARS <PKG-USER-COLVARS>` | :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | :ref:`USER-DPD <PKG-USER-DPD>` | :ref:`USER-DRUDE <PKG-USER-DRUDE>` | :ref:`USER-EFF <PKG-USER-EFF>` | :ref:`USER-FEP <PKG-USER-FEP>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-H5MD <PKG-USER-H5MD>` | :ref:`USER-INTEL <PKG-USER-INTEL>` | :ref:`USER-LB <PKG-USER-LB>` | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | :ref:`USER-MEAMC <PKG-USER-MEAMC>` | :ref:`USER-MESO <PKG-USER-MESO>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-MGPT <PKG-USER-MGPT>` | :ref:`USER-MISC <PKG-USER-MISC>` | :ref:`USER-MOFFF <PKG-USER-MOFFF>` | :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | :ref:`USER-NETCDF <PKG-USER-NETCDF>` | :ref:`USER-OMP <PKG-USER-OMP>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-PHONON <PKG-USER-PHONON>` | :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`USER-PTM <PKG-USER-PTM>` | :ref:`USER-QMMM <PKG-USER-QMMM>` | :ref:`USER-QTB <PKG-USER-QTB>` | :ref:`USER-QUIP <PKG-USER-QUIP>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-REAXC <PKG-USER-REAXC>` | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | :ref:`USER-SDPD <PKG-USER-SDPD>` | :ref:`USER-SMD <PKG-USER-SMD>` | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | :ref:`USER-SPH <PKG-USER-SPH>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-TALLY <PKG-USER-TALLY>` | :ref:`USER-UEF <PKG-USER-UEF>` | :ref:`USER-VTK <PKG-USER-VTK>` | :ref:`USER-YAFF <PKG-USER-YAFF>` | | | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-REACTION <PKG-USER-REACTION>` | :ref:`USER-REAXC <PKG-USER-REAXC>` | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | :ref:`USER-SDPD <PKG-USER-SDPD>` | :ref:`USER-SMD <PKG-USER-SMD>` | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-SPH <PKG-USER-SPH>` | :ref:`USER-TALLY <PKG-USER-TALLY>` | :ref:`USER-UEF <PKG-USER-UEF>` | :ref:`USER-VTK <PKG-USER-VTK>` | :ref:`USER-YAFF <PKG-USER-YAFF>` | | +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ ---------- Loading Loading @@ -2111,6 +2111,39 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d ---------- .. _PKG-USER-REACTION: USER-REACTION package ------------------ **Contents:** This package allows for complex bond topology changes (reactions) during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. Other options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions. **Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. **Supporting info:** * src/USER-REACTION: filenames -> commands * src/USER-REACTION/README * :doc:`fix bond/react <fix_bond_react>` * examples/USER/reaction * `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_ * `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_ * disarmmd.org ---------- .. _PKG-USER-REAXC: USER-REAXC package Loading doc/src/Packages_user.rst +2 −0 Original line number Diff line number Diff line Loading @@ -91,6 +91,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair\_style quip <pair_quip>` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair\_style reaxc <pair_reaxc>` | reax | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace\_style scafacos <kspace_style>` | USER/scafacos | ext | Loading src/Makefile +1 −1 Original line number Diff line number Diff line Loading @@ -63,7 +63,7 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ Loading Loading
cmake/CMakeLists.txt +3 −3 Original line number Diff line number Diff line Loading @@ -132,9 +132,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) Loading
doc/src/Packages_details.rst +48 −15 Original line number Diff line number Diff line Loading @@ -38,21 +38,21 @@ page gives those details. | :ref:`SRD <PKG-SRD>` | :ref:`VORONOI <PKG-VORONOI>` | | | | | +------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+ +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-ADIOS <PKG-USER-ADIOS>` | :ref:`USER-ATC <PKG-USER-ATC>` | :ref:`USER-AWPMD <PKG-USER-AWPMD>` | :ref:`USER-BOCS <PKG-USER-BOCS>` | :ref:`USER-CGDNA <PKG-USER-CGDNA>` | :ref:`USER-CGSDK <PKG-USER-CGSDK>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-COLVARS <PKG-USER-COLVARS>` | :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | :ref:`USER-DPD <PKG-USER-DPD>` | :ref:`USER-DRUDE <PKG-USER-DRUDE>` | :ref:`USER-EFF <PKG-USER-EFF>` | :ref:`USER-FEP <PKG-USER-FEP>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-H5MD <PKG-USER-H5MD>` | :ref:`USER-INTEL <PKG-USER-INTEL>` | :ref:`USER-LB <PKG-USER-LB>` | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | :ref:`USER-MEAMC <PKG-USER-MEAMC>` | :ref:`USER-MESO <PKG-USER-MESO>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-MGPT <PKG-USER-MGPT>` | :ref:`USER-MISC <PKG-USER-MISC>` | :ref:`USER-MOFFF <PKG-USER-MOFFF>` | :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | :ref:`USER-NETCDF <PKG-USER-NETCDF>` | :ref:`USER-OMP <PKG-USER-OMP>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-PHONON <PKG-USER-PHONON>` | :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`USER-PTM <PKG-USER-PTM>` | :ref:`USER-QMMM <PKG-USER-QMMM>` | :ref:`USER-QTB <PKG-USER-QTB>` | :ref:`USER-QUIP <PKG-USER-QUIP>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-REAXC <PKG-USER-REAXC>` | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | :ref:`USER-SDPD <PKG-USER-SDPD>` | :ref:`USER-SMD <PKG-USER-SMD>` | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | :ref:`USER-SPH <PKG-USER-SPH>` | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-TALLY <PKG-USER-TALLY>` | :ref:`USER-UEF <PKG-USER-UEF>` | :ref:`USER-VTK <PKG-USER-VTK>` | :ref:`USER-YAFF <PKG-USER-YAFF>` | | | +----------------------------------------+------------------------------------------------+------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-REACTION <PKG-USER-REACTION>` | :ref:`USER-REAXC <PKG-USER-REAXC>` | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | :ref:`USER-SDPD <PKG-USER-SDPD>` | :ref:`USER-SMD <PKG-USER-SMD>` | :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ | :ref:`USER-SPH <PKG-USER-SPH>` | :ref:`USER-TALLY <PKG-USER-TALLY>` | :ref:`USER-UEF <PKG-USER-UEF>` | :ref:`USER-VTK <PKG-USER-VTK>` | :ref:`USER-YAFF <PKG-USER-YAFF>` | | +------------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------+--------------------------------------+------------------------------------+ ---------- Loading Loading @@ -2111,6 +2111,39 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d ---------- .. _PKG-USER-REACTION: USER-REACTION package ------------------ **Contents:** This package allows for complex bond topology changes (reactions) during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. Other options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions. **Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. **Supporting info:** * src/USER-REACTION: filenames -> commands * src/USER-REACTION/README * :doc:`fix bond/react <fix_bond_react>` * examples/USER/reaction * `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_ * `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_ * disarmmd.org ---------- .. _PKG-USER-REAXC: USER-REAXC package Loading
doc/src/Packages_user.rst +2 −0 Original line number Diff line number Diff line Loading @@ -91,6 +91,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair\_style quip <pair_quip>` | USER/quip | ext | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair\_style reaxc <pair_reaxc>` | reax | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ | :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace\_style scafacos <kspace_style>` | USER/scafacos | ext | Loading
src/Makefile +1 −1 Original line number Diff line number Diff line Loading @@ -63,7 +63,7 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ Loading
