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doc pages for virial contributions of fixes

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Plimpton
2021-01-26 09:26:31 -07:00
parent 6147b9c2ef
commit fc0936c778
14 changed files with 149 additions and 84 deletions
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28
doc/src/fix_addforce.rst
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@ -122,8 +122,8 @@ No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the global potential "energy" inferred by the added
force to the global potential energy of the system as part of
this fix to add the potential energy inferred by the added force to
the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
energy is a fictitious quantity but is needed so that the
@ -133,21 +133,23 @@ potential energy when atoms move in the direction of the added force.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
the global pressure of the system as part of :doc:`thermodynamic
output <thermo_style>`. The default setting for this fix is
:doc:`fix_modify virial no <fix_modify>`.
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix is adding its forces. Default is the outermost
level.
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above. The vector is the
total force on the group of atoms before the forces on individual
atoms are changed by the fix. The scalar and vector values calculated
by this fix are "extensive".
which can be accessed by various :doc:`output commands
<Howto_output>`. The scalar is the potential energy discussed above.
The vector is the total force on the group of atoms before the forces
on individual atoms are changed by the fix. The scalar and vector
values calculated by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

9
doc/src/fix_client_md.rst
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@ -80,10 +80,11 @@ the global potential energy of the system as part of
this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution computed by the external program to
the global pressure of the system as part of :doc:`thermodynamic
output <thermo_style>`. The default setting for this fix is
:doc:`fix_modify virial yes <fix_modify>`.
this fix to add the contribution computed by the server application to
the global pressure of the system via the :doc:`compute pressure
<compute_pressure>` command. This can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential

10
doc/src/fix_cmap.rst
View File

@ -109,10 +109,12 @@ default setting for this fix is :doc:`fix_modify energy yes
<fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the CMAP interactions between
atoms to the global prsesure of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial yes <fix_modify>`.
this fix to add the contribution due to the CMAP interactions to both
the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential

7
doc/src/fix_efield.rst
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@ -133,8 +133,11 @@ due to the electric field.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
the system's virial as part of :doc:`thermodynamic output
<thermo_style>`. The default is *virial no*
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` :doc:`compute stress/atom
<compute_stress_atom>` commands. The former can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA

8
doc/src/fix_external.rst
View File

@ -167,9 +167,11 @@ potential energy when atoms move in the direction of the added force.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution computed by the external program to
the global pressure of the system as part of :doc:`thermodynamic
output <thermo_style>`. The default setting for this fix is
:doc:`fix_modify virial yes <fix_modify>`.
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` :doc:`compute stress/atom
<compute_stress_atom>` commands. The former can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential

7
doc/src/fix_latte.rst
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@ -116,6 +116,13 @@ potential energy of the system as part of :doc:`thermodynamic output
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution compute by LATTE to the global
pressure of the system via the :doc:`compute pressure
<compute_pressure>` command. This can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution computed by LATTE to the global
pressure of the system as part of :doc:`thermodynamic output

19
doc/src/fix_lb_rigid_pc_sphere.rst
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@ -50,7 +50,8 @@ This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
created to be used in place of that fix, to integrate the equations of
motion of spherical rigid bodies when a lattice-Boltzmann fluid is
present with a user-specified value of the force-coupling constant.
The fix uses the integration algorithm described in :ref:`Mackay et al. <Mackay>` to update the positions, velocities, and orientations of
The fix uses the integration algorithm described in :ref:`Mackay et
al. <Mackay>` to update the positions, velocities, and orientations of
a set of spherical rigid bodies experiencing velocity dependent
hydrodynamic forces. The spherical bodies are assumed to rotate as
solid, uniform density spheres, with moments of inertia calculated
@ -88,9 +89,18 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about the *rigid* and *rigid/nve* fixes are written to
:doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`. The scalar value calculated by these
fixes is "intensive". The scalar is the current temperature of the
computes a global scalar which can be accessed by various :doc:`output
commands <Howto_output>`. The scalar value calculated by these fixes
is "intensive". The scalar is the current temperature of the
collection of rigid bodies. This is averaged over all rigid bodies
and their translational and rotational degrees of freedom. The
translational energy of a rigid body is 1/2 m v\^2, where m = total
@ -130,7 +140,8 @@ Restrictions
""""""""""""
This fix is part of the USER-LB package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this

7
doc/src/fix_plumed.rst
View File

@ -95,6 +95,13 @@ PLUMED to the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution from the biasing force to the global
pressure of the system via the :doc:`compute pressure
<compute_pressure>` command. This can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the PLUMED
energy mentioned above. The scalar value calculated by this fix is

42
doc/src/fix_poems.rst
View File

@ -39,14 +39,15 @@ useful for treating a large biomolecule as a collection of connected,
coarse-grained particles.
The coupling, associated motion constraints, and time integration is
performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS)` which computes the
constrained rigid-body motion of articulated (jointed) multibody
systems :ref:`(Anderson) <Anderson>`. POEMS was written and is distributed
by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
and other members of his group at Rensselaer Polytechnic Institute
(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
copyright information on POEMS and other details, please refer to the
documents in the poems directory distributed with LAMMPS.
performed by the software package `Parallelizable Open source
Efficient Multibody Software (POEMS)` which computes the constrained
rigid-body motion of articulated (jointed) multibody systems
:ref:`(Anderson) <Anderson>`. POEMS was written and is distributed by
Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, and
other members of his group at Rensselaer Polytechnic Institute (RPI).
Rudranarayan developed the LAMMPS/POEMS interface. For copyright
information on POEMS and other details, please refer to the documents
in the poems directory distributed with LAMMPS.
This fix updates the positions and velocities of the rigid atoms with
a constant-energy time integration, so you should not update the same
@ -107,7 +108,16 @@ off, and there is only a single fix poems defined.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces and torques
on atoms to both the global pressure and per-atom stress of the system
via the :doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *bodyforces* option is supported by
this fix style to set whether per-body forces and torques are computed
@ -115,16 +125,18 @@ early or late in a timestep, i.e. at the post-force stage or at the
final-integrate stage, respectively.
No global or per-atom quantities are stored by this fix for access by
various :doc:`output commands <Howto_output>`. No parameter of this fix
can be used with the *start/stop* keywords of the :doc:`run <run>`
command. This fix is not invoked during :doc:`energy minimization <minimize>`.
various :doc:`output commands <Howto_output>`. No parameter of this
fix can be used with the *start/stop* keywords of the :doc:`run <run>`
command. This fix is not invoked during :doc:`energy minimization
<minimize>`.
Restrictions
""""""""""""
This fix is part of the :ref:`POEMS <PKG-POEMS>` package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
built and linked with LAMMPS. See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the :ref:`POEMS <PKG-POEMS>` package. It is only
enabled if LAMMPS was built with that package, which also requires the
POEMS library be built and linked with LAMMPS. See the :doc:`Build
package <Build_package>` doc page for more info.
Related commands
""""""""""""""""

27
doc/src/fix_shake.rst
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@ -191,22 +191,29 @@ LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to keeping the constraints to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial yes*
No information about these fixes is written to :doc:`binary restart
files <restart>`.
No information about these fixes is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various :doc:`output commands <Howto_output>`. No parameter of these fixes can be used
with the *start/stop* keywords of the :doc:`run <run>` command. These
fixes are not invoked during :doc:`energy minimization <minimize>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
these fixes to add the contribution due to the added forces on atoms
to both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
No global or per-atom quantities are stored by these fixes for access
by various :doc:`output commands <Howto_output>`. No parameter of
these fixes can be used with the *start/stop* keywords of the
:doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
These fixes are part of the RIGID package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
For computational efficiency, there can only be one shake or rattle
fix defined in a simulation.

48
doc/src/fix_smd.rst
View File

@ -48,10 +48,12 @@ Description
"""""""""""
This fix implements several options of steered MD (SMD) as reviewed in
:ref:`(Izrailev) <Izrailev>`, which allows to induce conformational changes
in systems and to compute the potential of mean force (PMF) along the
assumed reaction coordinate :ref:`(Park) <Park>` based on Jarzynski's
equality :ref:`(Jarzynski) <Jarzynski>`. This fix borrows a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce <fix_setforce>`.
:ref:`(Izrailev) <Izrailev>`, which allows to induce conformational
changes in systems and to compute the potential of mean force (PMF)
along the assumed reaction coordinate :ref:`(Park) <Park>` based on
Jarzynski's equality :ref:`(Jarzynski) <Jarzynski>`. This fix borrows
a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce
<fix_setforce>`.
You can apply a moving spring force to a group of atoms (\ *tether*
style) or between two groups of atoms (\ *couple* style). The spring
@ -108,30 +110,36 @@ See the :doc:`read_restart <read_restart>` command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial no*
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by
this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix is adding its forces. Default is the outermost level.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
This fix computes a vector list of 7 quantities, which can be accessed
by various :doc:`output commands <Howto_output>`. The quantities in the
vector are in this order: the x-, y-, and z-component of the pulling
force, the total force in direction of the pull, the equilibrium
distance of the spring, the distance between the two reference points,
and finally the accumulated PMF (the sum of pulling forces times
displacement).
by various :doc:`output commands <Howto_output>`. The quantities in
the vector are in this order: the x-, y-, and z-component of the
pulling force, the total force in direction of the pull, the
equilibrium distance of the spring, the distance between the two
reference points, and finally the accumulated PMF (the sum of pulling
forces times displacement).
The force is the total force on the group of atoms by the spring. In
the case of the *couple* style, it is the force on the fix group
(group-ID) or the negative of the force on the second group (group-ID2).
The vector values calculated by this fix are "extensive".
(group-ID) or the negative of the force on the second group
(group-ID2). The vector values calculated by this fix are
"extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

8
doc/src/fix_wall.rst
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@ -342,8 +342,12 @@ for this fix is :doc:`fix_modify energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the interaction between atoms
and each wall to the system's virial as part of :doc:`thermodynamic
output <thermo_style>`. The default is *virial no*
and all the specified walls to both the global pressure and per-atom
stress of the system via the :doc:`compute pressure
<compute_pressure>` :doc:`compute stress/atom <compute_stress_atom>`
commands. The former can be accessed by :doc:`thermodynamic output
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA

5
doc/src/fix_wall_ees.rst
View File

@ -134,11 +134,6 @@ system as part of :doc:`thermodynamic output <thermo_style>`. The
default settings for thes fixes are :doc:`fix_modify energy no
<fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
these rixes to add the contribution due to the interaction between
atoms and each wall to the system's virial as part of
:doc:`thermodynamic output <thermo_style>`. The default is *virial no*
The :doc:`fix_modify <fix_modify>` *respa* option is supported by
these fixes. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the

8
doc/src/fix_wall_region.rst
View File

@ -202,8 +202,12 @@ this fix is :doc:`fix_modify energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the interaction between atoms
and each wall to the system's virial as part of :doc:`thermodynamic
output <thermo_style>`. The default is *virial no*
and the region wall to both the global pressure and per-atom stress of
the system via the :doc:`compute pressure <compute_pressure>`
:doc:`compute stress/atom <compute_stress_atom>` commands. The former
can be accessed by :doc:`thermodynamic output <thermo_style>`. The
default setting for this fix is :doc:`fix_modify virial no
<fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`