ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'github/master' into adaptglok

Browse Source 
# Conflicts:
#	doc/src/min_modify.rst
This commit is contained in:
Axel Kohlmeyer
2020-01-31 12:24:59 -05:00
parent bb94303e73 56ff70de70
commit b524db88a3
38 changed files with 306 additions and 293 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
doc/src/Intro_features.rst
View File

@ -87,7 +87,7 @@ commands)
* water potentials: TIP3P, TIP4P, SPC
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim\_init, kim\_interactions, and kim\_query <kim_commands>` commands
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials

2
doc/src/Packages_details.rst
View File

@ -927,7 +927,7 @@ Also several computes which calculate properties of rigid bodies.
* src/RIGID: filenames -> commands
* :doc:`compute erotate/rigid <compute_erotate_rigid>`
* fix shake"_fix\_shake.html
* :doc:`fix shake <fix_shake>`
* :doc:`fix rattle <fix_shake>`
* :doc:`fix rigid/\* <fix_rigid>`
* examples/ASPHERE

6
doc/src/angle_cosine_buck6d.rst
View File

@ -46,9 +46,9 @@ internally.
Additional to the cosine term the *cosine/buck6d* angle style computes
the short range (vdW) interaction belonging to the
:doc:`pair\_buck6d <pair_buck6d_coul_gauss>` between the end atoms of the
:doc:`pair_style buck6d <pair_buck6d_coul_gauss>` between the end atoms of the
angle. For this reason this angle style only works in combination
with the :doc:`pair\_buck6d <pair_buck6d_coul_gauss>` styles and needs
with the :doc:`pair_style buck6d <pair_buck6d_coul_gauss>` styles and needs
the :doc:`special_bonds <special_bonds>` 1-3 interactions to be weighted
0.0 to prevent double counting.
@ -61,7 +61,7 @@ Restrictions
*cosine/buck6d* can only be used in combination with the
:doc:`pair\_buck6d <pair_buck6d_coul_gauss>` style and with a
:doc:`pair_style buck6d <pair_buck6d_coul_gauss>` style and with a
:doc:`special_bonds <special_bonds>` 0.0 weighting of 1-3 interactions.
This angle style can only be used if LAMMPS was built with the

2
doc/src/angle_cosine_shift.rst
View File

@ -83,6 +83,6 @@ Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`,
:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
**Default:** none

4
doc/src/angle_cosine_shift_exp.rst
View File

@ -94,7 +94,7 @@ Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`,
:doc:`angle\_cosine\_shift <angle_cosine_shift>`,
:doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`
:doc:`angle_style cosine/shift <angle_cosine_shift>`,
:doc:`dihedral_style cosine/shift/exp <dihedral_cosine_shift_exp>`
**Default:** none

2
doc/src/bond_harmonic_shift_cut.rst
View File

@ -86,6 +86,6 @@ Related commands
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_harmonic <bond_harmonic>`,
:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
:doc:`bond_style harmonic/shift <bond_harmonic_shift>`
**Default:** none

2
doc/src/compute_fep.rst
View File

@ -301,7 +301,7 @@ Related commands
""""""""""""""""
:doc:`fix adapt/fep <fix_adapt_fep>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`pair\_fep\_soft <pair_fep_soft>`
:doc:`pair_style .../soft <pair_fep_soft>`
Default
"""""""

25
doc/src/compute_hma.rst
View File

@ -54,19 +54,22 @@ effects, smaller timestep inaccuracy, faster equilibration and shorter
decorrelation time.
HMA should not be used if atoms are expected to diffuse. It is also
restricted to simulations in the NVT ensemble. While this compute may be
used with any potential in LAMMPS, it will provide inaccurate results
restricted to simulations in the NVT ensemble. While this compute may
be used with any potential in LAMMPS, it will provide inaccurate results
for potentials that do not go to 0 at the truncation distance;
:doc:`pair\_lj\_smooth\_linear <pair_lj_smooth_linear>` and Ewald summation should
work fine, while :doc:`pair_lj <pair_lj>` will perform poorly unless
the potential is shifted (via :doc:`pair_modify <pair_modify>` shift) or the cutoff is large. Furthermore, computation of the heat capacity with
this compute is restricted to those that implement the single\_hessian method
in Pair. Implementing single\_hessian in additional pair styles is simple.
Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
buffalo.edu) if your desired pair style does not have this method. This is
the list of pair styles that currently implement pair\_hessian:
:doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>` and Ewald
summation should work fine, while :doc:`pair_style lj/cut <pair_lj>`
will perform poorly unless the potential is shifted (via
:doc:`pair_modify <pair_modify>` shift) or the cutoff is large.
Furthermore, computation of the heat capacity with this compute is
restricted to those that implement the *single\_hessian* method in Pair.
Implementing *single\_hessian* in additional pair styles is simple.
Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke
(kofke at buffalo.edu) if your desired pair style does not have this
method. This is the list of pair styles that currently implement
*single\_hessian*:
* :doc:`lj\_smooth\_linear <pair_lj_smooth_linear>`
* :doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>`
In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble

2
doc/src/dihedral_cosine_shift_exp.rst
View File

@ -92,7 +92,7 @@ Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
**Default:** none

2
doc/src/fix_adapt_fep.rst
View File

@ -319,7 +319,7 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
Default
"""""""

160
doc/src/fix_atc.rst
View File

@ -143,97 +143,97 @@ Related commands
After specifying this fix in your input script, several other :doc:`fix_modify <fix_modify>` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
fix\_modify commands for setup:
*fix\_modify* commands for setup:
* `fix\_modify AtC mesh create <USER/atc/man_mesh_create.html>`_
* `fix\_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature.html>`_
* `fix\_modify AtC mesh read <USER/atc/man_mesh_read.html>`_
* `fix\_modify AtC mesh write <USER/atc/man_mesh_write.html>`_
* `fix\_modify AtC mesh create\_nodeset <USER/atc/man_mesh_create_nodeset.html>`_
* `fix\_modify AtC mesh add\_to\_nodeset <USER/atc/man_mesh_add_to_nodeset.html>`_
* `fix\_modify AtC mesh create\_faceset box <USER/atc/man_mesh_create_faceset_box.html>`_
* `fix\_modify AtC mesh create\_faceset plane <USER/atc/man_mesh_create_faceset_plane.html>`_
* `fix\_modify AtC mesh create\_elementset <USER/atc/man_mesh_create_elementset.html>`_
* `fix\_modify AtC mesh delete\_elements <USER/atc/man_mesh_delete_elements.html>`_
* `fix\_modify AtC mesh nodeset\_to\_elementset <USER/atc/man_mesh_nodeset_to_elementset.html>`_
* `fix\_modify AtC boundary <USER/atc/man_boundary.html>`_
* `fix\_modify AtC internal\_quadrature <USER/atc/man_internal_quadrature.html>`_
* `fix\_modify AtC time\_integration (thermal) <USER/atc/man_thermal_time_integration.html>`_
* `fix\_modify AtC time\_integration (momentum) <USER/atc/man_momentum_time_integration.html>`_
* `fix\_modify AtC extrinsic electron\_integration <USER/atc/man_electron_integration.html>`_
* `fix\_modify AtC internal\_element\_set <USER/atc/man_internal_element_set.html>`_
* `fix\_modify AtC decomposition <USER/atc/man_decomposition.html>`_
* `fix_modify AtC mesh create <USER/atc/man_mesh_create.html>`_
* `fix_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature.html>`_
* `fix_modify AtC mesh read <USER/atc/man_mesh_read.html>`_
* `fix_modify AtC mesh write <USER/atc/man_mesh_write.html>`_
* `fix_modify AtC mesh create_nodeset <USER/atc/man_mesh_create_nodeset.html>`_
* `fix_modify AtC mesh add_to_nodeset <USER/atc/man_mesh_add_to_nodeset.html>`_
* `fix_modify AtC mesh create_faceset box <USER/atc/man_mesh_create_faceset_box.html>`_
* `fix_modify AtC mesh create_faceset plane <USER/atc/man_mesh_create_faceset_plane.html>`_
* `fix_modify AtC mesh create_elementset <USER/atc/man_mesh_create_elementset.html>`_
* `fix_modify AtC mesh delete_elements <USER/atc/man_mesh_delete_elements.html>`_
* `fix_modify AtC mesh nodeset_to_elementset <USER/atc/man_mesh_nodeset_to_elementset.html>`_
* `fix_modify AtC boundary <USER/atc/man_boundary.html>`_
* `fix_modify AtC internal_quadrature <USER/atc/man_internal_quadrature.html>`_
* `fix_modify AtC time_integration (thermal) <USER/atc/man_thermal_time_integration.html>`_
* `fix_modify AtC time_integration (momentum) <USER/atc/man_momentum_time_integration.html>`_
* `fix_modify AtC extrinsic electron_integration <USER/atc/man_electron_integration.html>`_
* `fix_modify AtC internal_element_set <USER/atc/man_internal_element_set.html>`_
* `fix_modify AtC decomposition <USER/atc/man_decomposition.html>`_
fix\_modify commands for boundary and initial conditions:
*fix\_modify* commands for boundary and initial conditions:
* `fix\_modify AtC initial <USER/atc/man_initial.html>`_
* `fix\_modify AtC fix <USER/atc/man_fix_nodes.html>`_
* `fix\_modify AtC unfix <USER/atc/man_unfix_nodes.html>`_
* `fix\_modify AtC fix\_flux <USER/atc/man_fix_flux.html>`_
* `fix\_modify AtC unfix\_flux <USER/atc/man_unfix_flux.html>`_
* `fix\_modify AtC source <USER/atc/man_source.html>`_
* `fix\_modify AtC remove\_source <USER/atc/man_remove_source.html>`_
* `fix_modify AtC initial <USER/atc/man_initial.html>`_
* `fix_modify AtC fix <USER/atc/man_fix_nodes.html>`_
* `fix_modify AtC unfix <USER/atc/man_unfix_nodes.html>`_
* `fix_modify AtC fix_flux <USER/atc/man_fix_flux.html>`_
* `fix_modify AtC unfix_flux <USER/atc/man_unfix_flux.html>`_
* `fix_modify AtC source <USER/atc/man_source.html>`_
* `fix_modify AtC remove_source <USER/atc/man_remove_source.html>`_
fix\_modify commands for control and filtering:
*fix\_modify* commands for control and filtering:
* `fix\_modify AtC control <USER/atc/man_control.html>`_
* `fix\_modify AtC control thermal <USER/atc/man_control_thermal.html>`_
* `fix\_modify AtC control thermal correction\_max\_iterations <USER/atc/man_control_thermal_correction_max_iterations.html>`_
* `fix\_modify AtC control momentum <USER/atc/man_control_momentum.html>`_
* `fix\_modify AtC control localized\_lambda <USER/atc/man_localized_lambda.html>`_
* `fix\_modify AtC control lumped\_lambda\_solve <USER/atc/man_lumped_lambda_solve.html>`_
* `fix\_modify AtC control mask\_direction <USER/atc/man_mask_direction.html>`_ control
* `fix\_modify AtC filter <USER/atc/man_time_filter.html>`_
* `fix\_modify AtC filter scale <USER/atc/man_filter_scale.html>`_
* `fix\_modify AtC filter type <USER/atc/man_filter_type.html>`_
* `fix\_modify AtC equilibrium\_start <USER/atc/man_equilibrium_start.html>`_
* `fix\_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
* `fix\_modify AtC poisson\_solver <USER/atc/man_poisson_solver.html>`_
* `fix_modify AtC control <USER/atc/man_control.html>`_
* `fix_modify AtC control thermal <USER/atc/man_control_thermal.html>`_
* `fix_modify AtC control thermal correction_max_iterations <USER/atc/man_control_thermal_correction_max_iterations.html>`_
* `fix_modify AtC control momentum <USER/atc/man_control_momentum.html>`_
* `fix_modify AtC control localized_lambda <USER/atc/man_localized_lambda.html>`_
* `fix_modify AtC control lumped_lambda_solve <USER/atc/man_lumped_lambda_solve.html>`_
* `fix_modify AtC control mask_direction <USER/atc/man_mask_direction.html>`_ control
* `fix_modify AtC filter <USER/atc/man_time_filter.html>`_
* `fix_modify AtC filter scale <USER/atc/man_filter_scale.html>`_
* `fix_modify AtC filter type <USER/atc/man_filter_type.html>`_
* `fix_modify AtC equilibrium_start <USER/atc/man_equilibrium_start.html>`_
* `fix_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
* `fix_modify AtC poisson_solver <USER/atc/man_poisson_solver.html>`_
fix\_modify commands for output:
*fix\_modify* commands for output:
* `fix\_modify AtC output <USER/atc/man_output.html>`_
* `fix\_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
* `fix\_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
* `fix\_modify AtC output boundary\_integral <USER/atc/man_boundary_integral.html>`_
* `fix\_modify AtC output contour\_integral <USER/atc/man_contour_integral.html>`_
* `fix\_modify AtC mesh output <USER/atc/man_mesh_output.html>`_
* `fix\_modify AtC write\_restart <USER/atc/man_write_restart.html>`_
* `fix\_modify AtC read\_restart <USER/atc/man_read_restart.html>`_
* `fix_modify AtC output <USER/atc/man_output.html>`_
* `fix_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
* `fix_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
* `fix_modify AtC output boundary_integral <USER/atc/man_boundary_integral.html>`_
* `fix_modify AtC output contour_integral <USER/atc/man_contour_integral.html>`_
* `fix_modify AtC mesh output <USER/atc/man_mesh_output.html>`_
* `fix_modify AtC write_restart <USER/atc/man_write_restart.html>`_
* `fix_modify AtC read_restart <USER/atc/man_read_restart.html>`_
fix\_modify commands for post-processing:
*fix\_modify* commands for post-processing:
* `fix\_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
* `fix\_modify AtC fields <USER/atc/man_hardy_fields.html>`_
* `fix\_modify AtC grdients <USER/atc/man_hardy_gradients.html>`_
* `fix\_modify AtC rates <USER/atc/man_hardy_rates.html>`_
* `fix\_modify AtC computes <USER/atc/man_hardy_computes.html>`_
* `fix\_modify AtC on\_the\_fly <USER/atc/man_hardy_on_the_fly.html>`_
* `fix\_modify AtC pair\_interactions/bond\_interactions <USER/atc/man_pair_interactions.html>`_
* `fix\_modify AtC sample\_frequency <USER/atc/man_sample_frequency.html>`_
* `fix\_modify AtC set <USER/atc/man_set.html>`_
* `fix_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
* `fix_modify AtC fields <USER/atc/man_hardy_fields.html>`_
* `fix_modify AtC grdients <USER/atc/man_hardy_gradients.html>`_
* `fix_modify AtC rates <USER/atc/man_hardy_rates.html>`_
* `fix_modify AtC computes <USER/atc/man_hardy_computes.html>`_
* `fix_modify AtC on_the_fly <USER/atc/man_hardy_on_the_fly.html>`_
* `fix_modify AtC pair_interactions/bond_interactions <USER/atc/man_pair_interactions.html>`_
* `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_
* `fix_modify AtC set <USER/atc/man_set.html>`_
miscellaneous fix\_modify commands:
miscellaneous *fix\_modify* commands:
* `fix\_modify AtC atom\_element\_map <USER/atc/man_atom_element_map.html>`_
* `fix\_modify AtC atom\_weight <USER/atc/man_atom_weight.html>`_
* `fix\_modify AtC write\_atom\_weights <USER/atc/man_write_atom_weights.html>`_
* `fix\_modify AtC reset\_time <USER/atc/man_reset_time.html>`_
* `fix\_modify AtC reset\_atomic\_reference\_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
* `fix\_modify AtC fe\_md\_boundary <USER/atc/man_fe_md_boundary.html>`_
* `fix\_modify AtC boundary\_faceset <USER/atc/man_boundary_faceset.html>`_
* `fix\_modify AtC consistent\_fe\_initialization <USER/atc/man_consistent_fe_initialization.html>`_
* `fix\_modify AtC mass\_matrix <USER/atc/man_mass_matrix.html>`_
* `fix\_modify AtC material <USER/atc/man_material.html>`_
* `fix\_modify AtC atomic\_charge <USER/atc/man_atomic_charge.html>`_
* `fix\_modify AtC source\_integration <USER/atc/man_source_integration.html>`_
* `fix\_modify AtC temperature\_definition <USER/atc/man_temperature_definition.html>`_
* `fix\_modify AtC track\_displacement <USER/atc/man_track_displacement.html>`_
* `fix\_modify AtC boundary\_dynamics <USER/atc/man_boundary_dynamics.html>`_
* `fix\_modify AtC add\_species <USER/atc/man_add_species.html>`_
* `fix\_modify AtC add\_molecule <USER/atc/man_add_molecule.html>`_
* `fix\_modify AtC remove\_species <USER/atc/man_remove_species.html>`_
* `fix\_modify AtC remove\_molecule <USER/atc/man_remove_molecule.html>`_
* `fix_modify AtC atom_element_map <USER/atc/man_atom_element_map.html>`_
* `fix_modify AtC atom_weight <USER/atc/man_atom_weight.html>`_
* `fix_modify AtC write_atom_weights <USER/atc/man_write_atom_weights.html>`_
* `fix_modify AtC reset_time <USER/atc/man_reset_time.html>`_
* `fix_modify AtC reset_atomic_reference_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
* `fix_modify AtC fe_md_boundary <USER/atc/man_fe_md_boundary.html>`_
* `fix_modify AtC boundary_faceset <USER/atc/man_boundary_faceset.html>`_
* `fix_modify AtC consistent_fe_initialization <USER/atc/man_consistent_fe_initialization.html>`_
* `fix_modify AtC mass_matrix <USER/atc/man_mass_matrix.html>`_
* `fix_modify AtC material <USER/atc/man_material.html>`_
* `fix_modify AtC atomic_charge <USER/atc/man_atomic_charge.html>`_
* `fix_modify AtC source_integration <USER/atc/man_source_integration.html>`_
* `fix_modify AtC temperature_definition <USER/atc/man_temperature_definition.html>`_
* `fix_modify AtC track_displacement <USER/atc/man_track_displacement.html>`_
* `fix_modify AtC boundary_dynamics <USER/atc/man_boundary_dynamics.html>`_
* `fix_modify AtC add_species <USER/atc/man_add_species.html>`_
* `fix_modify AtC add_molecule <USER/atc/man_add_molecule.html>`_
* `fix_modify AtC remove_species <USER/atc/man_remove_species.html>`_
* `fix_modify AtC remove_molecule <USER/atc/man_remove_molecule.html>`_
Note: a set of example input files with the attendant material files are included with this package

2
doc/src/fix_bond_react.rst
View File

@ -390,7 +390,7 @@ the activation energy (:doc:`units <units>` of energy), and *seed* is a
random number seed. The temperature is defined as the instantaneous
temperature averaged over all atoms in the reaction site, and is
calculated in the same manner as for example
:doc:`compute\_temp\_chunk <compute_temp_chunk>`. Currently, there are no
:doc:`compute temp/chunk <compute_temp_chunk>`. Currently, there are no
options for additional temperature averaging or velocity-biased
temperature calculations. A uniform random number between 0 and 1 is
generated using *seed*\ ; if this number is less than the result of the

6
doc/src/fix_nh_uef.rst
View File

@ -89,14 +89,14 @@ in the LAMMPS frame. Only when the positions and velocities are
updated is the system rotated to the flow frame, and it is rotated
back to the LAMMPS frame immediately afterwards. For this reason, all
vector-valued quantities (except for the tensors from
:doc:`compute\_pressure/uef <compute_pressure_uef>` and
:doc:`compute\_temp/uef <compute_temp_uef>`) will be computed in the
:doc:`compute pressure/uef <compute_pressure_uef>` and
:doc:`compute temp/uef <compute_temp_uef>`) will be computed in the
LAMMPS frame. Rotationally invariant scalar quantities like the
temperature and hydrostatic pressure are frame-invariant and will be
computed correctly. Additionally, the system is in the LAMMPS frame
during all of the output steps, and therefore trajectory files made
using the dump command will be in the LAMMPS frame unless the
:doc:`dump\_cfg/uef <dump_cfg_uef>` command is used.
:doc:`dump cfg/uef <dump_cfg_uef>` command is used.
----------

2
doc/src/fix_precession_spin.rst
View File

@ -85,7 +85,7 @@ function for the same parameters.
The temperature effects are accounted for by connecting the spin
:math:`i` to a thermal bath using a Langevin thermostat (see
:doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of
:doc:`fix langevin/spin <fix_langevin_spin>` for the definition of
this thermostat).
Style *anisotropy* is used to simulate an easy axis or an easy plane

17
doc/src/fix_wall_gran.rst
View File

@ -83,17 +83,18 @@ close enough to touch it.
The nature of the wall/particle interactions are determined by the
*fstyle* setting. It can be any of the styles defined by the
:doc:`pair_style gran/\* <pair_gran>` or the more general `pair\_style granular <pair_granular.html">`_ commands. Currently the options are
*hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and
*granular* with all the possible options of the associated
:doc:`pair_style gran/\* <pair_gran>` or the more general
:doc:`pair_style granular <pair_granular>` commands. Currently the
options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the
former, and *granular* with all the possible options of the associated
*pair\_coeff* command for the latter. The equation for the force
between the wall and particles touching it is the same as the
corresponding equation on the :doc:`pair_style gran/\* <pair_gran>` and
:doc:`pair\_style\_granular <pair_granular>` doc pages, in the limit of
one of the two particles going to infinite radius and mass (flat
wall). Specifically, delta = radius - r = overlap of particle with
wall, m\_eff = mass of particle, and the effective radius of contact =
RiRj/Ri+Rj is set to the radius of the particle.
:doc:`pair_style granular <pair_granular>` doc pages, in the limit of
one of the two particles going to infinite radius and mass (flat wall).
Specifically, delta = radius - r = overlap of particle with wall, m\_eff
= mass of particle, and the effective radius of contact = RiRj/Ri+Rj is
set to the radius of the particle.
The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag*
have the same meaning and units as those specified with the

13
doc/src/fix_wall_gran_region.rst
View File

@ -154,15 +154,16 @@ corresponding manner.
The nature of the wall/particle interactions are determined by the
*fstyle* setting. It can be any of the styles defined by the
:doc:`pair_style gran/\* <pair_gran>` or the more general `pair\_style granular <pair_granular.html">`_ commands. Currently the options are
*hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and
*granular* with all the possible options of the associated
:doc:`pair_style gran/\* <pair_gran>` or the more general
:doc:`pair_style granular <pair_granular>` commands. Currently the
options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the
former, and *granular* with all the possible options of the associated
*pair\_coeff* command for the latter. The equation for the force
between the wall and particles touching it is the same as the
corresponding equation on the :doc:`pair_style gran/\* <pair_gran>` and
:doc:`pair\_style\_granular <pair_granular>` doc pages, but the effective
radius is calculated using the radius of the particle and the radius
of curvature of the wall at the contact point.
:doc:`pair_style granular <pair_granular>` doc pages, but the effective
radius is calculated using the radius of the particle and the radius of
curvature of the wall at the contact point.
Specifically, delta = radius - r = overlap of particle with wall,
m\_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with

6
doc/src/min_modify.rst
View File

@ -121,7 +121,7 @@ quantities.
The choice of a line search algorithm for the *spin/cg* and
*spin/lbfgs* styles can be specified via the *line* keyword. The
*spin\_cubic* and *spin\_none* only make sense when one of those two
*spin\_cubic* and *spin\_none* keywords only make sense when one of those two
minimization styles is declared. The *spin\_cubic* performs the line
search based on a cubic interpolation of the energy along the search
direction. The *spin\_none* keyword deactivates the line search
@ -131,7 +131,7 @@ more robust if *spin\_cubic* line search is used.
The Newton *integrator* used for *fire* minimization can be selected
to be either the symplectic Euler (\ *eulerimplicit*\ ) or velocity
Verlet (\ *verlet*\ ). *tmax* define the maximum value for the
Verlet (\ *verlet*\ ). *tmax* defines the maximum value for the
adaptive timestep during a *fire* minimization. It is a multiplication
factor applied to the current :doc:`timestep <timestep>` (not in time
unit). For example, *tmax* = 4.0 with a :doc:`timestep <timestep>` of
@ -165,7 +165,7 @@ Restrictions
For magnetic GNEB calculations, only *spin\_none* value for *line*
keyword can be used when styles *spin/cg* and *spin/lbfgs* are
keyword can be used when minimization styles *spin/cg* and *spin/lbfgs* are
employed. See :doc:`neb/spin <neb_spin>` for more explanation.
Related commands

15
doc/src/min_spin.rst
View File

@ -70,14 +70,13 @@ discretization factor *discrete\_factor*.
By default, style *spin/cg* does not employ the line search procedure
and uses the adaptive time-step technique in the same way as style *spin*\ .
Style *spin/lbfgs* defines an orthogonal spin optimization
(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno
(L-BFGS) algorithm.
By default, style *spin/lbfgs* does not employ line search procedure.
If the line search procedure is not used then the discrete factor defines
the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*.
The default value for Kappa is 10.
The *spin\_cubic* line search can improve the convergence of the
Style *spin/lbfgs* defines an orthogonal spin optimization (OSO)
combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)
algorithm. By default, style *spin/lbfgs* does not employ line search
procedure. If the line search procedure is not used then the discrete
factor defines the maximum root mean squared rotation angle of spins by
equation *pi/(5\*Kappa)*. The default value for Kappa is 10. The
*spin\_cubic* line search option can improve the convergence of the
*spin/lbfgs* algorithm.
The :doc:`min_modify <min_modify>` command can be used to

5
doc/src/neb_spin.rst
View File

@ -389,8 +389,9 @@ This command can only be used if LAMMPS was built with the SPIN
package. See the :doc:`Build package <Build_package>` doc
page for more info.
For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
when styles *spin/cg* and *spin/lbfgs* are employed.
For magnetic GNEB calculations, only the *spin\_none* value for the
*line* keyword can be used when minimization styles *spin/cg* and
*spin/lbfgs* are employed.
----------

4
doc/src/pair_class2.rst
View File

@ -133,7 +133,7 @@ cutoff distance.
A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
free energy calculations, is part of the USER-FEP package and is documented with
the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
@ -203,7 +203,7 @@ LAMMPS was built with that package. See the :doc:`Build package <Build_package>
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
**Default:** none

2
doc/src/pair_coul.rst
View File

@ -392,7 +392,7 @@ info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
**Default:** none

6
doc/src/pair_fep_soft.rst
View File

@ -193,7 +193,7 @@ and Coulomb potentials modified by a soft core, with the functional form
The *lj/class2/soft* style is a 9-6 potential with the exponent of the
denominator of the first term in brackets taking the value 1.5 instead of 2
(other details differ, see the form of the potential in
:doc:`pair\_class2 <pair_class2>`).
:doc:`pair_style lj/class2 <pair_class2>`).
Coulomb interactions can also be damped with a soft core at short distance,
@ -255,14 +255,14 @@ optional cutoffs.
Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified
12-6 LJ potential used in CHARMM and documented in the
:doc:`pair\_lj\_charmm <pair_charmm>` style. In the soft version the parameters n,
:doc:`pair_style lj/charmm/coul/long <pair_charmm>` style. In the soft version the parameters n,
alpha\_LJ and alpha\_C are set in the :doc:`pair_style <pair_style>` command, before
the global cutoffs. The activation parameter lambda is introduced as an argument
of the :doc:`pair_coeff <pair_coeff>` command, after epsilon and sigma and
before the optional eps14 and sigma14.
Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in
:doc:`pair\_class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
:doc:`pair_style lj/class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
and alpha\_C are set in the :doc:`pair_style <pair_style>` command, before the
global cutoffs. The activation parameter lambda is introduced as an argument of
the the :doc:`pair_coeff <pair_coeff>` command, after epsilon and sigma and before

2
doc/src/pair_lj.rst
View File

@ -348,7 +348,7 @@ pair\_style command.
A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
free energy calculations, is part of the USER-FEP package and is documented with
the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.

2
doc/src/pair_lj_long.rst
View File

@ -180,7 +180,7 @@ specified in the pair\_style command.
A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
free energy calculations, is part of the USER-FEP package and is documented with
the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.

240
doc/src/pair_modify.rst
View File

@ -13,18 +13,14 @@ Syntax
* one or more keyword/value pairs may be listed
* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
or *tabinner/disp* or *tail* or *compute* or *nofdotr*
or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or
*compute/tally*
.. parsed-literal::
*pair* values = sub-style N *special* which wt1 wt2 wt3
or sub-style N *compute/tally* flag
*pair* value = sub-style N
sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
N = which instance of sub-style (only if sub-style is used multiple times)
*special* which wt1 wt2 wt3 = override *special_bonds* settings (optional)
which = *lj/coul* or *lj* or *coul*
w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
*compute/tally* flag = *yes* or *no*
N = which instance of sub-style (1 to M), only specify if sub-style is used multiple times
*mix* value = *geometric* or *arithmetic* or *sixthpower*
*shift* value = *yes* or *no*
*table* value = N
@ -37,8 +33,11 @@ Syntax
cutoff = inner cutoff at which to begin table (distance units)
*tail* value = *yes* or *no*
*compute* value = *yes* or *no*
*nofdotr*
*nofdotr* value = none
*special* values = which wt1 wt2 wt3
which = *lj/coul* or *lj* or *coul*
w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive
*compute/tally* value = *yes* or *no*
Examples
@ -53,47 +52,41 @@ Examples
pair_modify pair lj/cut compute no
pair_modify pair tersoff compute/tally no
pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5 special coul 0.0 0.0 0.8333333
Description
"""""""""""
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
Modify the parameters of the currently defined pair style. If the
pair style is :doc:`hybrid or hybrid/overlay <pair_hybrid>`, then the
specified parameters are by default modified for all the hybrid sub-styles.
If used, the *pair* keyword must appear first in the list of keywords.
It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. It means that all the
following parameters will only be modified for the specified
sub-style. If the sub-style is defined multiple times, then an
additional numeric argument *N* must also be specified, which is a
number from 1 to M where M is the number of times the sub-style was
listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra
number indicates which instance of the sub-style the remaining
keywords will be applied to. Note that if the *pair* keyword is not
used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the
specified keywords will be applied to all sub-styles.
.. note::
The *special* and *compute/tally* keywords can **only** be used in
conjunction with the *pair* keyword and must directly follow it.
*special* allows to override the
:doc:`special_bonds <special_bonds>` settings for the specified sub-style.
*compute/tally* allows to disable or enable registering
:doc:`compute \*/tally <compute_tally>` computes for a given sub-style.
More details are given below.
The behavior for hybrid pair styles can be changed by using the *pair*
keyword, which allows selection of a specific sub-style to apply all
remaining keywords to.
The *special* and *compute/tally* keywords can **only** be
used in conjunction with the *pair* keyword. See further details about
these 3 keywords below.
The *mix* keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J
must be set explicitly, either in the input script via the
"pair\_coeff" command or in the "Pair Coeffs" section of the :doc:`data file <read_data>`. For some pair styles it is not necessary to
specify coefficients when I != J, since a "mixing" rule will create
them from the I,I and J,J settings. The pair\_modify *mix* value
determines what formulas are used to compute the mixed coefficients.
In each case, the cutoff distance is mixed the same way as sigma.
:doc:`pair_coeff <pair_coeff>` command or in the "Pair Coeffs" section of the
:doc:`data file <read_data>`. For some pair styles it is not
necessary to specify coefficients when I != J, since a "mixing" rule
will create them from the I,I and J,J settings. The pair\_modify
*mix* value determines what formulas are used to compute the mixed
coefficients. In each case, the cutoff distance is mixed the same way
as sigma.
Note that not all pair styles support mixing. Also, some mix options
are not available for certain pair styles. See the doc page for
individual pair styles for those restrictions. Note also that the
:doc:`pair_coeff <pair_coeff>` command also can be to directly set
Note that not all pair styles support mixing and some mix options
are not available for certain pair styles. Also, there are additional
restrictions when using :doc:`pair style hybrid or hybrid/overlay <pair_hybrid>`.
See the doc page for individual pair styles for those restrictions. Note also that the
:doc:`pair_coeff <pair_coeff>` command also can be used to directly set
coefficients for a specific I != J pairing, in which case no mixing is
performed.
@ -135,10 +128,11 @@ see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2\^N is
pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear interpolation is
performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.
bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear
interpolation is performed between adjacent table values. In our
experiments with different table styles (lookup, linear, spline), this
method typically gave the best performance in terms of speed and
accuracy.
The choice of table length is a tradeoff in accuracy versus speed. A
larger N yields more accurate force computations, but requires more
@ -162,27 +156,28 @@ pairwise interactions are computed via table lookup for simulations
with "real" units, but some close pairs may be computed directly
(non-table) for simulations with "lj" units.
When the *tail* keyword is set to *yes*\ , certain pair styles will add
a long-range VanderWaals tail "correction" to the energy and pressure.
These corrections are bookkeeping terms which do not affect dynamics,
unless a constant-pressure simulation is being performed. See the doc
page for individual styles to see which support this option. These
corrections are included in the calculation and printing of
thermodynamic quantities (see the :doc:`thermo_style <thermo_style>`
command). Their effect will also be included in constant NPT or NPH
simulations where the pressure influences the simulation box
dimensions (e.g. the :doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`
commands). The formulas used for the long-range corrections come from
equation 5 of :ref:`(Sun) <Sun>`.
When the *tail* keyword is set to *yes*\ , certain pair styles will
add a long-range VanderWaals tail "correction" to the energy and
pressure. These corrections are bookkeeping terms which do not affect
dynamics, unless a constant-pressure simulation is being performed.
See the doc page for individual styles to see which support this
option. These corrections are included in the calculation and
printing of thermodynamic quantities (see the :doc:`thermo_style
<thermo_style>` command). Their effect will also be included in
constant NPT or NPH simulations where the pressure influences the
simulation box dimensions (e.g. the :doc:`fix npt <fix_nh>` and
:doc:`fix nph <fix_nh>` commands). The formulas used for the
long-range corrections come from equation 5 of :ref:`(Sun) <Sun>`.
.. note::
The tail correction terms are computed at the beginning of each
run, using the current atom counts of each atom type. If atoms are
deleted (or lost) or created during a simulation, e.g. via the :doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
re-computed. If you expect the counts to change dramatically, you can
break a run into a series of shorter runs so that the correction
factors are re-computed more frequently.
deleted (or lost) or created during a simulation, e.g. via the
:doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
re-computed. If you expect the counts to change dramatically, you
can break a run into a series of shorter runs so that the
correction factors are re-computed more frequently.
Several additional assumptions are inherent in using tail corrections,
including the following:
@ -191,26 +186,27 @@ including the following:
should not be used for systems that are non-liquid, 2d, have a slab
geometry (only 2d periodic), or inhomogeneous.
* G(r), the radial distribution function (rdf), is unity beyond the
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
LJ fluid), and it is probably a good idea to verify this assumption by
checking the rdf. The rdf is not exactly unity beyond the cutoff for
each pair of interaction types, so the tail correction is necessarily
an approximation.
cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for
an LJ fluid), and it is probably a good idea to verify this
assumption by checking the rdf. The rdf is not exactly unity beyond
the cutoff for each pair of interaction types, so the tail
correction is necessarily an approximation.
The tail corrections are computed at the beginning of each simulation
run. If the number of atoms changes during the run, e.g. due to atoms
leaving the simulation domain, or use of the :doc:`fix gcmc <fix_gcmc>`
command, then the corrections are not updated to reflect the changed
atom count. If this is a large effect in your simulation, you should
break the long run into several short runs, so that the correction
factors are re-computed multiple times.
The tail corrections are computed at the beginning of each
simulation run. If the number of atoms changes during the run,
e.g. due to atoms leaving the simulation domain, or use of the
:doc:`fix gcmc <fix_gcmc>` command, then the corrections are not
updated to reflect the changed atom count. If this is a large
effect in your simulation, you should break the long run into
several short runs, so that the correction factors are re-computed
multiple times.
* Thermophysical properties obtained from calculations with this option
enabled will not be thermodynamically consistent with the truncated
force-field that was used. In other words, atoms do not feel any LJ
pair interactions beyond the cutoff, but the energy and pressure
reported by the simulation include an estimated contribution from
those interactions.
* Thermophysical properties obtained from calculations with this
option enabled will not be thermodynamically consistent with the
truncated force-field that was used. In other words, atoms do not
feel any LJ pair interactions beyond the cutoff, but the energy and
pressure reported by the simulation include an estimated
contribution from those interactions.
The *compute* keyword allows pairwise computations to be turned off,
@ -225,53 +221,73 @@ a simulation with :doc:`pair_style hybrid <pair_hybrid>` with only a
subset of the hybrid sub-styles enabled. Second, this option allows
you to perform a simulation with only long-range interactions but no
short-range pairwise interactions. Doing this by simply not defining
a pair style will not work, because the
:doc:`kspace_style <kspace_style>` command requires a Kspace-compatible
pair style be defined.
a pair style will not work, because the :doc:`kspace_style
<kspace_style>` command requires a Kspace-compatible pair style be
defined.
The *nofdotr* keyword allows to disable an optimization that computes
the global stress tensor from the total forces and atom positions rather
than from summing forces between individual pairs of atoms.
the global stress tensor from the total forces and atom positions
rather than from summing forces between individual pairs of atoms.
----------
The *pair* keyword can only be used with the :doc:`hybrid and
hybrid/overlay <pair_hybrid>` pair styles. If used, it must appear
first in the list of keywords.
The *special* keyword allows to override the 1-2, 1-3, and 1-4
exclusion settings for individual sub-styles of a
:doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar
to the :doc:`special_bonds <special_bonds>` command, *which* and
wt1,wt2,wt3. The *which* argument can be *lj* to change the
Lennard-Jones settings, *coul* to change the Coulombic settings,
or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3
values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
1-3, and 1-4 bond topology neighbors, respectively. The *special*
keyword can only be used in conjunction with the *pair* keyword
and has to directly follow it. This option is not compatible with
pair styles from the GPU or the USER-INTEL package and attempting
it will cause an error.
Its meaning is that all the following parameters will only be modified
for the specified sub-style. If the sub-style is defined multiple
times, then an additional numeric argument *N* must also be specified,
which is a number from 1 to M where M is the number of times the
sub-style was listed in the :doc:`pair_style hybrid <pair_hybrid>`
command. The extra number indicates which instance of the sub-style
the remaining keywords will be applied to.
The *special* and *compute/tally* keywords can **only** be used in
conjunction with the *pair* keyword and they must directly follow it.
I.e. any other keyword, must appear after *pair*, *special*, and
*compute/tally*.
The *special* keyword overrides the global :doc:`special_bonds <special_bonds>`
1-2, 1-3, 1-4 exclusion settings (weights) for the sub-style selected
by the *pair* keyword.
Similar to the :doc:`special_bonds <special_bonds>` command, it takes
4 arguments. The *which* argument can be *lj* to change only the
non-Coulomb weights (e.g. Lennard-Jones or Buckingham), *coul* to change
only the Coulombic settings, or *lj/coul* to change both to the same
values. The *wt1,wt2,wt3* values are numeric weights from 0.0 to 1.0
inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively.
The *special* keyword can be used multiple times, e.g. to set the *lj*
and *coul* settings to different values.
.. note::
The global settings specified by the
:doc:`special_bonds <special_bonds>` command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
store the neighbor with no weighting applied. Thus only global values
different from exactly 0.0 or 1.0 can be overridden and an error is
generated if the requested setting is not compatible with the global
setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
usually a sufficient workaround in this case without causing a
significant error.
The *compute/tally* keyword takes exactly 1 argument (\ *no* or *yes*\ ),
and allows to selectively disable or enable processing of the various
:doc:`compute \*/tally <compute_tally>` styles for a given
:doc:`pair hybrid or hybrid/overlay <pair_hybrid>` sub-style.
The *special* keyword is not compatible with pair styles from the
GPU or the USER-INTEL package and attempting to use it will cause
an error.
.. note::
Any "pair\_modify pair compute/tally" command must be issued
Weights of exactly 0.0 or 1.0 in the :doc:`special_bonds <special_bonds>`
command have implications on the neighbor list construction, which
means that they cannot be overridden by using the *special* keyword.
One workaround for this restriction is to use the :doc:`special_bonds <special_bonds>`
command with weights like 1.0e-10 or 0.999999999 instead of 0.0 or 1.0,
respectively, which enables to reset each them to any value between 0.0
and 1.0 inclusively. Otherwise you can set **all** global weights to
an arbitrary number between 0.0 or 1.0, like 0.5, and then you have
to override **all** *special* settings for **all** sub-styles which use
the 1-2, 1-3, and 1-4 exclusion weights in their force/energy computation.
The *compute/tally* keyword disables or enables registering :doc:`compute
\*/tally <compute_tally>` computes for the sub-style specified by
the *pair* keyword. Use *no* to disable, or *yes* to enable.
.. note::
The "pair_modify pair compute/tally" command must be issued
**before** the corresponding compute style is defined.
@ -290,7 +306,7 @@ Related commands
""""""""""""""""
:doc:`pair_style <pair_style>`, :doc:`pair_style hybrid <pair_hybrid>`,
pair\_coeff"_pair\_coeff.html, :doc:`thermo_style <thermo_style>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`thermo_style <thermo_style>`,
:doc:`compute \*/tally <compute_tally>`
Default

4
doc/src/pair_morse.rst
View File

@ -95,7 +95,7 @@ the *morse* and *morse/smooth/linear* styles.
A version of the *morse* style with a soft core, *morse/soft*\ , suitable for use in
free energy calculations, is part of the USER-FEP package and is documented with
the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is only
the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is only
available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
@ -160,7 +160,7 @@ built with the USER-MISC package. See the :doc:`Build package <Build_package>`
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
**Default:** none

2
doc/src/pair_spin_exchange.rst
View File

@ -55,7 +55,7 @@ in :ref:`(Tranchida) <Tranchida3>`.
From this exchange interaction, each spin :math:`i` will be submitted
to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
such as:
.. math::

4
doc/src/pair_spin_magelec.rst
View File

@ -41,7 +41,7 @@ direction of a screened dielectric atomic polarization (in eV).
From this magneto-electric interaction, each spin i will be submitted
to a magnetic torque omega, and its associated atom can be submitted to a
force F for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
force F for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
such as:
.. image:: Eqs/pair_spin_me_forces.jpg
@ -68,7 +68,7 @@ Related commands
""""""""""""""""
:doc:`atom_style spin <atom_style>`, :doc:`pair_coeff <pair_coeff>`,
:doc:`pair\_spin\_exchange <pair_spin_exchange>`, :doc:`pair_eam <pair_eam>`,
:doc:`pair_style spin/exchange <pair_spin_exchange>`, :doc:`pair_eam <pair_eam>`,
**Default:** none

2
doc/src/pair_thole.rst
View File

@ -53,7 +53,7 @@ describes how to use the :doc:`thermalized Drude oscillator model <Howto_drude>`
discussed on the :doc:`Howto polarizable <Howto_polarizable>` doc page.
The *thole* pair style should be used as a sub-style within in the
:doc:`pair\_hybrid/overlay <pair_hybrid>` command, in conjunction with a
:doc:`pair_style hybrid/overlay <pair_hybrid>` command, in conjunction with a
main pair style including Coulomb interactions, i.e. any pair style
containing *coul/cut* or *coul/long* in its style name.

10
doc/src/rerun.rst
View File

@ -115,13 +115,13 @@ However if you specify a series of dump files in an incorrect order
(with respect to the timesteps they contain), you may skip large
numbers of snapshots
Note that the dump files specified as part of the *dump* keyword can
be parallel files, i.e. written as multiple files either per processor
Note that the dump files specified as part of the *dump* keyword can be
parallel files, i.e. written as multiple files either per processor
and/or per snapshot. If that is the case they will also be read in
parallel which can make the rerun command operate dramatically faster
for large systems. See the doc page for the `read\_dump <read_dump>`_ and
:doc:`dump <dump>` commands which describe how to read and write
parallel dump files.
for large systems. See the doc page for the :doc:`read_dump
<read_dump>` and :doc:`dump <dump>` commands which describe how to read
and write parallel dump files.
The *first*\ , *last*\ , *every*\ , *skip* keywords determine which
snapshots are read from the dump file(s). Snapshots are skipped until

6
doc/src/set.rst
View File

@ -359,9 +359,9 @@ particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_
of the particles is set to the 3 specified components.
Keyword *omega* sets the angular velocity of selected atoms. The
particles must be spheres as defined by the "atom\_style sphere"_
atom\_style.html command. The angular velocity vector of the particles
is set to the 3 specified components.
particles must be spheres as defined by the
:doc:`atom_style sphere <atom_style>` command. The angular velocity
vector of the particles is set to the 3 specified components.
Keyword *mass* sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the

2
doc/src/temper_grem.rst
View File

@ -14,7 +14,7 @@ Syntax
* N = total # of timesteps to run
* M = attempt a tempering swap every this many steps
* lambda = initial lambda for this ensemble
* fix-ID = ID of fix\_grem
* fix-ID = ID of *fix grem*
* thermostat-ID = ID of the thermostat that controls kinetic temperature
* seed1 = random # seed used to decide on adjacent temperature to partner with
* seed2 = random # seed for Boltzmann factor in Metropolis swap

4
src/USER-CGDNA/bond_oxdna_fene.cpp
View File

@ -221,7 +221,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
update->ntimestep,atom->tag[a],atom->tag[b],r);
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
if (rlogarg <= -8.0) error->one(FLERR,"Bad FENE bond");
}
fbond = -k[type]*rr0/rlogarg/Deltasq/r;
@ -421,7 +421,7 @@ double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/,
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
update->ntimestep,sqrt(rsq));
error->warning(FLERR,str,0);
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
if (rlogarg <= -8.0) error->one(FLERR,"Bad FENE bond");
}
double eng = -0.5 * k[type]*log(rlogarg);

2
src/kspace.cpp
View File

@ -286,7 +286,7 @@ void KSpace::qsum_qsq(int warning_flag)
double qsum_local(0.0), qsqsum_local(0.0);
#if defined(_OPENMP)
#pragma omp parallel for default(none) reduction(+:qsum_local,qsqsum_local)
#pragma omp parallel for default(shared) reduction(+:qsum_local,qsqsum_local)
#endif
for (int i = 0; i < nlocal; i++) {
qsum_local += q[i];

7
src/neighbor.cpp
View File

@ -402,13 +402,6 @@ void Neighbor::init()
}
}
// maxwt = max multiplicative factor on atom indices stored in neigh list
maxwt = 0;
if (special_flag[1] == 2) maxwt = 2;
if (special_flag[2] == 2) maxwt = 3;
if (special_flag[3] == 2) maxwt = 4;
// ------------------------------------------------------------------
// xhold array

1
src/neighbor.h
View File

@ -166,7 +166,6 @@ class Neighbor : protected Pointers {
int maxatom; // max size of atom-based NeighList arrays
int maxrequest; // max size of NeighRequest list
int maxwt; // max weighting factor applied + 1
// info for other Neigh classes: NBin,NStencil,NPair,NTopo

15
src/pair_hybrid.cpp
View File

@ -859,14 +859,17 @@ void PairHybrid::modify_params(int narg, char **arg)
iarg = 3;
}
// if 2nd keyword (after pair) is special:
// invoke modify_special() for the sub-style
// keywords "special" and "compute/tally" have to be listed directly
// after "pair" but can be given multiple times
again:
if (iarg < narg && strcmp(arg[iarg],"special") == 0) {
if (narg < iarg+5)
error->all(FLERR,"Illegal pair_modify special command");
modify_special(m,narg-iarg,&arg[iarg+1]);
iarg += 5;
goto again;
}
// if 2nd keyword (after pair) is compute/tally:
@ -881,11 +884,13 @@ void PairHybrid::modify_params(int narg, char **arg)
compute_tally[m] = 0;
} else error->all(FLERR,"Illegal pair_modify compute/tally command");
iarg += 2;
goto again;
}
// apply the remaining keywords to the base pair style itself and the
// sub-style except for "pair" and "special".
// the former is important for some keywords like "tail" or "compute"
// apply the remaining keywords to the base pair style itself and
// the sub-style except for "pair" and "special" or "compute/tally"
// and their arguments. the former is important for some keywords
// like "tail" or "compute"
if (narg-iarg > 0) {
Pair::modify_params(narg-iarg,&arg[iarg]);

9
src/random_mars.cpp
View File

@ -183,7 +183,7 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
int mode,index,oldindex,newvalue,nflip,which,niter;
int active[2],first[2],last[2];
int newactive[2],newfirst[2],newlast[2];
bigint nmark,nactive,nactiveall,nflipall,bnflip;
bigint nmark,nflipall;
bigint activeall[2],bsum[3],bsumall[3];
double thresh;
@ -210,15 +210,12 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
// choose to ADD or SUBTRACT from current nmark
// thresh = desired flips / size of active set
// nactive = size of current active set, only for debug output below
if (ntarget-nmark > 0) {
mode = ADD;
// nactive = active[mode];
thresh = 1.0 * (ntarget-nmark) / activeall[mode];
} else {
mode = SUBTRACT;
// nactive = active[mode];
thresh = 1.0 * (nmark-ntarget) / activeall[mode];
}
@ -278,12 +275,10 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
bsum[0] = nflip;
bsum[1] = active[0];
bsum[2] = active[1];
bsum[3] = nactive;
MPI_Allreduce(&bsum,&bsumall,4,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&bsum,&bsumall,3,MPI_LMP_BIGINT,MPI_SUM,world);
nflipall = bsumall[0];
activeall[0] = bsumall[1];
activeall[1] = bsumall[2];
nactiveall = bsumall[3];
if (mode == ADD) nmark += nflipall;
else if (mode == SUBTRACT) nmark -= nflipall;