diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index a55e3e50cc..fddf3435f9 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -159,7 +159,6 @@ OPT. * :doc:`orient/fcc ` * :doc:`orient/eco ` * :doc:`pafi ` - * :doc:`pair/tracker ` * :doc:`phonon ` * :doc:`pimd ` * :doc:`planeforce ` @@ -223,7 +222,6 @@ OPT. * :doc:`spring/rg ` * :doc:`spring/self ` * :doc:`srd ` - * :doc:`store/local ` * :doc:`store/force ` * :doc:`store/state ` * :doc:`tdpd/source ` diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index c63034e766..0f1abcd7d7 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -23,6 +23,7 @@ General howto Howto_library Howto_couple Howto_mdi + Howto_bpm Howto_broken_bonds Settings howto diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index c4b6fc9398..06d70ef35d 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -1,5 +1,5 @@ Bonded particle models -=============== +====================== The BPM package implements bonded particle models which can be used to simulate mesoscale solids. Solids are constructed as a collection of @@ -21,7 +21,7 @@ pouring of extended, elastic bodies. ---------- Bonds can be created using a :doc:`read data ` or -:doc:`create bond ` command. Alternatively, a +:doc:`create bonds ` command. Alternatively, a :doc:`molecule ` template with bonds can be used with :doc:`fix deposit ` or :doc:`fix pour ` to create solid grains. @@ -98,7 +98,7 @@ to :doc:`fix nve/asphere `. To monitor the fracture of bonds in the system, all BPM bond styles have the ability to record instances of bond breakage to output using -the :doc:`dump local ` command. Additionally, one can use +the :doc:`dump local ` command. Additionally, one can use :doc:`compute nbond/atom ` to tally the current number of bonds per atom. @@ -118,7 +118,7 @@ following are currently compatible with BPM bond styles: * :doc:`fix bond/break ` * :doc:`fix bond/swap ` -Note :doc:`bond_create ` requires certain special_bonds settings. +Note :doc:`create_bonds ` requires certain special_bonds settings. To subtract pair interactions, one will need to switch between different special_bonds settings in the input script. An example is found in examples/bpm/impact. diff --git a/doc/src/Howto_broken_bonds.rst b/doc/src/Howto_broken_bonds.rst index bf82088dec..5e66d9528c 100755 --- a/doc/src/Howto_broken_bonds.rst +++ b/doc/src/Howto_broken_bonds.rst @@ -1,10 +1,10 @@ Broken Bonds -=============== +============ Typically, bond interactions persist for the duration of a simulation in LAMMPS. However, there are some exceptions that allow for bonds to break includung the :doc:`quartic bond style ` and the -bond styles in the :doc:`BPM package ` which contains the +bond styles in the :doc:`BPM package ` which contains the :doc:`bpm/spring ` and :doc:`bpm/rotational ` bond styles. In these cases, a bond can be broken if it is stretched beyond a user-defined threshold. @@ -26,7 +26,7 @@ two atoms is turned on, since they are no longer bonded. In the BPM package, one can either turn off all pair interactions between bonded particles or leave them on, overlaying pair forces on top of bond forces. To remove pair forces, the special bond list is dynamically -updated. More details can be found on the :doc:`Howto BPM ` +updated. More details can be found on the :doc:`Howto BPM ` page. Bonds can also be broken by fixes which change bond topology, including @@ -44,5 +44,5 @@ status of broken bonds or permanently delete them, e.g.: delete_bonds all stats delete_bonds all bond 0 remove -The compute :doc:`nbonds/atom ` can also be used +The compute :doc:`nbond/atom ` can also be used to tally the current number of bonds per atom, excluding broken bonds. \ No newline at end of file diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 2ccc28a340..bdc7279e6e 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -304,7 +304,7 @@ models for mesoscale simulations of solids and fracture. See the * :doc:`atom_style bpm/sphere ` * :doc:`bond_style bpm/rotational ` * :doc:`bond_style bpm/spring ` -* :doc:`compute nbonds/atom ` +* :doc:`compute nbond/atom ` * :doc:`fix nve/bpm/sphere ` * :doc:`pair_style bpm/spring ` * examples/bpm diff --git a/doc/src/bond_bpm_rotational.rst b/doc/src/bond_bpm_rotational.rst index 2a752217e3..b13d27dfbe 100644 --- a/doc/src/bond_bpm_rotational.rst +++ b/doc/src/bond_bpm_rotational.rst @@ -1,7 +1,7 @@ .. index:: bond_style bpm/rotational bond_style bpm/rotational command -========================== +================================= Syntax """""" @@ -71,7 +71,7 @@ particles which are proportional to angular bending and twisting displacements with stiffnesses of :math`k_b` and :math:`k_t', respectively. Details on the calculations of shear displacements and angular displacements can be found in :ref:`(Wang) ` and -:ref:`(Wang and Mora) `. +:ref:`(Wang and Mora) `. Bonds will break under sufficient stress. A breaking criteria is calculated @@ -154,7 +154,7 @@ timesteps. At the end of each interval, all of the saved accumulated data is deleted to make room for new data. Individual datum may therefore persist anywhere between *1* to *N* timesteps depending on when they are saved. This data can be accessed using the *fix_ID* and a -:doc:`dump local ` command. To ensure all data is output, +:doc:`dump local ` command. To ensure all data is output, the dump frequency should correspond to the same interval of *N* timesteps. A dump frequency of an integer multiple of *N* can be used to regularly output a sample of the accumulated data. diff --git a/doc/src/bond_bpm_spring.rst b/doc/src/bond_bpm_spring.rst index 4084aa760a..1d2f12701d 100644 --- a/doc/src/bond_bpm_spring.rst +++ b/doc/src/bond_bpm_spring.rst @@ -1,7 +1,7 @@ .. index:: bond_style bpm/spring bond_style bpm/spring command -========================== +============================= Syntax """""" @@ -118,7 +118,7 @@ timesteps. At the end of each interval, all of the saved accumulated data is deleted to make room for new data. Individual datum may therefore persist anywhere between *1* to *N* timesteps depending on when they are saved. This data can be accessed using the *fix_ID* and a -:doc:`dump local ` command. To ensure all data is output, +:doc:`dump local ` command. To ensure all data is output, the dump frequency should correspond to the same interval of *N* timesteps. A dump frequency of an integer multiple of *N* can be used to regularly output a sample of the accumulated data. diff --git a/doc/src/compute_nbond_atom.rst b/doc/src/compute_nbond_atom.rst index 8322f16330..e86986287f 100644 --- a/doc/src/compute_nbond_atom.rst +++ b/doc/src/compute_nbond_atom.rst @@ -1,7 +1,7 @@ .. index:: compute nbond/atom compute nbond/atom command -======================= +========================== Syntax """""" @@ -50,6 +50,3 @@ Default """"""" none - ----------- - diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 1f44651ef4..c65cd68a29 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -475,7 +475,7 @@ The *fileper* keyword is documented below with the *nfile* keyword. The *header* keyword toggles whether the dump file will include a header. Excluding a header will reduce the size of the dump file for data produced by :doc:`pair tracker ` or -:doc:`bpm bond styles ` which may not require the +:doc:`bpm bond styles ` which may not require the information typically written to the header. ---------- diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 425df36d3a..3b6ef044c8 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -365,7 +365,6 @@ accelerated styles exist. * :doc:`spring/rg ` - spring on radius of gyration of group of atoms * :doc:`spring/self ` - spring from each atom to its origin * :doc:`srd ` - stochastic rotation dynamics (SRD) -* :doc:`store/local ` - store local data for output * :doc:`store/force ` - store force on each atom * :doc:`store/state ` - store attributes for each atom * :doc:`tdpd/source ` - @@ -384,7 +383,6 @@ accelerated styles exist. * :doc:`ttm/grid ` - two-temperature model for electronic/atomic coupling (distributed grid) * :doc:`ttm/mod ` - enhanced two-temperature model with additional options * :doc:`tune/kspace ` - auto-tune KSpace parameters -* :doc:`update/special/bonds ` - update special bond lists for BPM bond styles that allow for bond breakage * :doc:`vector ` - accumulate a global vector every N timesteps * :doc:`viscosity ` - Muller-Plathe momentum exchange for viscosity calculation * :doc:`viscous ` - viscous damping for granular simulations diff --git a/doc/src/fix_nve_bpm_sphere.rst b/doc/src/fix_nve_bpm_sphere.rst index 0a320d8fca..861586ab2a 100644 --- a/doc/src/fix_nve_bpm_sphere.rst +++ b/doc/src/fix_nve_bpm_sphere.rst @@ -1,7 +1,7 @@ .. index:: fix nve/bpm/sphere fix nve/bpm/sphere command -====================== +========================== Syntax """""" @@ -38,7 +38,7 @@ ensemble. This fix differs from the :doc:`fix nve ` command, which assumes point particles and only updates their position and velocity. -It also differs from the :doc:`fix nve/sphere ` +It also differs from the :doc:`fix nve/sphere ` command which assumes finite-size spheroid particles which do not store a quaternion. It thus does not update a particle's orientation or quaternion. diff --git a/doc/src/pair_bpm_spring.rst b/doc/src/pair_bpm_spring.rst index ea5451b78d..9e6b5bb87b 100755 --- a/doc/src/pair_bpm_spring.rst +++ b/doc/src/pair_bpm_spring.rst @@ -1,7 +1,7 @@ .. index:: pair_style bpm/spring pair_style bpm/spring command -======================= +============================= Syntax """""" @@ -27,9 +27,9 @@ Style *bpm/spring* computes pairwise forces with the formula .. math:: F = k (r - r_c) - + where :math:`k` is a stiffness and :math:`r_c` is the cutoff length. -An additional damping force is also applied to interacting +An additional damping force is also applied to interacting particles. The force is proportional to the difference in the normal velocity of particles diff --git a/doc/src/pair_tracker.rst b/doc/src/pair_tracker.rst index d2dddd7d45..04967e952d 100644 --- a/doc/src/pair_tracker.rst +++ b/doc/src/pair_tracker.rst @@ -86,7 +86,7 @@ timesteps. At the end of each interval, all of the saved accumulated data is deleted to make room for new data. Individual datum may therefore persist anywhere between *1* to *N* timesteps depending on when they are saved. This data can be accessed using the *fix_ID* and a -:doc:`dump local ` command. To ensure all data is output, +:doc:`dump local ` command. To ensure all data is output, the dump frequency should correspond to the same interval of *N* timesteps. A dump frequency of an integer multiple of *N* can be used to regularly output a sample of the accumulated data. @@ -178,9 +178,6 @@ This fix is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -A corresponding :doc:`fix store_local ` must be -defined to use this pair style. - This pair style is currently incompatible with granular pair styles that extend beyond the contact (e.g. JKR and DMT). diff --git a/src/atom.cpp b/src/atom.cpp index 47583d137b..a923483c62 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -2618,7 +2618,7 @@ length of the data area, and a short description. - int - 1 - 1 if the particle is a body particle, 0 if not - * - quat + * - quat - double - 4 - four quaternion components of the particles