Loading cmake/CMakeLists.txt +3 −3 Original line number Diff line number Diff line Loading @@ -134,9 +134,9 @@ 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/Errors_messages.rst +2 −2 Original line number Diff line number Diff line Loading @@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` *Bond/react: Atom affected by reaction too close to template edge* This means an atom which changes type or connectivity during the reaction is too close to an 'edge' atom defined in the superimpose reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. *Bond/react: Fix bond/react needs ghost atoms from farther away* This is because a processor needs to superimpose the entire unreacted This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm\_modify cutoff command can be used to extend the communication range. Loading doc/src/Packages_details.rst +34 −0 Original line number Diff line number Diff line Loading @@ -94,6 +94,7 @@ page gives those details. * :ref:`USER-QMMM <PKG-USER-QMMM>` * :ref:`USER-QTB <PKG-USER-QTB>` * :ref:`USER-QUIP <PKG-USER-QUIP>` * :ref:`USER-REACTION <PKG-USER-REACTION>` * :ref:`USER-REAXC <PKG-USER-REAXC>` * :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` * :ref:`USER-SDPD <PKG-USER-SDPD>` Loading Loading @@ -2180,6 +2181,39 @@ 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 doc/src/fix_bond_react.rst +24 −7 Original line number Diff line number Diff line Loading @@ -60,7 +60,7 @@ Syntax Examples """""""" For unabridged example scripts and files, see examples/USER/misc/bond\_react. For unabridged example scripts and files, see examples/USER/reaction. .. parsed-literal:: Loading Loading @@ -149,10 +149,9 @@ constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above (full examples can be found at examples/USER/misc/bond\_react). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. above (full examples can be found at examples/USER/reaction). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. .. note:: Loading Loading @@ -295,7 +294,7 @@ either 'none' or 'charges.' Further details are provided in the discussion of the 'update\_edges' keyword. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are three types of constraints available, as discussed below. there are four types of constraints available, as discussed below. A sample map file is given below: Loading Loading @@ -371,6 +370,24 @@ the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. The constraint of type 'dihedral' has the following syntax: .. parsed-literal:: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>` documentation for further details on convention. If *amin* is less than *amax*, these four atoms must form a dihedral angle greater than *amin* **and** less than *amax* for the reaction to occur. If *amin* is greater than *amax*, these four atoms must form a dihedral angle greater than *amin* **or** less than *amax* for the reaction to occur. Angles must be specified in degrees. Optionally, a second range of permissible angles *amin2*-*amax2* can be specified. The constraint of type 'arrhenius' imposes an additional reaction probability according to the temperature-dependent Arrhenius equation: Loading Loading @@ -516,7 +533,7 @@ Restrictions """""""""""" This fix is part of the USER-MISC package. It is only enabled if This fix is part of the USER-REACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. Loading Loading
cmake/CMakeLists.txt +3 −3 Original line number Diff line number Diff line Loading @@ -134,9 +134,9 @@ 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/Errors_messages.rst +2 −2 Original line number Diff line number Diff line Loading @@ -509,14 +509,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>` *Bond/react: Atom affected by reaction too close to template edge* This means an atom which changes type or connectivity during the reaction is too close to an 'edge' atom defined in the superimpose reaction is too close to an 'edge' atom defined in the map file. This could cause incorrect assignment of bonds, angle, etc. Generally, this means you must include more atoms in your templates, such that there are at least two atoms between each atom involved in the reaction and an edge atom. *Bond/react: Fix bond/react needs ghost atoms from farther away* This is because a processor needs to superimpose the entire unreacted This is because a processor needs to map the entire unreacted molecule template onto simulation atoms it knows about. The comm\_modify cutoff command can be used to extend the communication range. Loading
doc/src/Packages_details.rst +34 −0 Original line number Diff line number Diff line Loading @@ -94,6 +94,7 @@ page gives those details. * :ref:`USER-QMMM <PKG-USER-QMMM>` * :ref:`USER-QTB <PKG-USER-QTB>` * :ref:`USER-QUIP <PKG-USER-QUIP>` * :ref:`USER-REACTION <PKG-USER-REACTION>` * :ref:`USER-REAXC <PKG-USER-REAXC>` * :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` * :ref:`USER-SDPD <PKG-USER-SDPD>` Loading Loading @@ -2180,6 +2181,39 @@ 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
doc/src/fix_bond_react.rst +24 −7 Original line number Diff line number Diff line Loading @@ -60,7 +60,7 @@ Syntax Examples """""""" For unabridged example scripts and files, see examples/USER/misc/bond\_react. For unabridged example scripts and files, see examples/USER/reaction. .. parsed-literal:: Loading Loading @@ -149,10 +149,9 @@ constant-topology parts of your system separately. The dynamic group contains only atoms not involved in a reaction at a given timestep, and therefore should be used by a subsequent system-wide time integrator such as nvt, npt, or nve, as shown in the second example above (full examples can be found at examples/USER/misc/bond\_react). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. above (full examples can be found at examples/USER/reaction). The time integration command should be placed after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react. .. note:: Loading Loading @@ -295,7 +294,7 @@ either 'none' or 'charges.' Further details are provided in the discussion of the 'update\_edges' keyword. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are three types of constraints available, as discussed below. there are four types of constraints available, as discussed below. A sample map file is given below: Loading Loading @@ -371,6 +370,24 @@ the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. The constraint of type 'dihedral' has the following syntax: .. parsed-literal:: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>` documentation for further details on convention. If *amin* is less than *amax*, these four atoms must form a dihedral angle greater than *amin* **and** less than *amax* for the reaction to occur. If *amin* is greater than *amax*, these four atoms must form a dihedral angle greater than *amin* **or** less than *amax* for the reaction to occur. Angles must be specified in degrees. Optionally, a second range of permissible angles *amin2*-*amax2* can be specified. The constraint of type 'arrhenius' imposes an additional reaction probability according to the temperature-dependent Arrhenius equation: Loading Loading @@ -516,7 +533,7 @@ Restrictions """""""""""" This fix is part of the USER-MISC package. It is only enabled if This fix is part of the USER-REACTION package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. Loading
