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doc/compute_angle.rst deleted 100644 → 0
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.. index:: compute angle
compute angle command
=====================
Syntax
""""""
.. parsed-literal::
compute ID group-ID angle
* ID, group-ID are documented in :doc:`compute <compute>` command
* angle = style name of this compute command
Examples
""""""""
.. parsed-literal::
compute 1 all angle
Description
"""""""""""
Define a computation that extracts the angle energy calculated by each
of the angle sub-styles used in the "angle_style
hybrid" angle_hybrid.html command. These values are made accessible
for output or further processing by other commands. The group
specified for this command is ignored.
This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if you want to know the portion of the total
energy contributed by one or more of the hybrid sub-styles.
**Output info:**
This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
:doc:`units <units>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
doc/compute_dihedral.rst deleted 100644 → 0
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.. index:: compute dihedral
compute dihedral command
========================
Syntax
""""""
.. parsed-literal::
compute ID group-ID dihedral
* ID, group-ID are documented in :doc:`compute <compute>` command
* dihedral = style name of this compute command
Examples
""""""""
.. parsed-literal::
compute 1 all dihedral
Description
"""""""""""
Define a computation that extracts the dihedral energy calculated by
each of the dihedral sub-styles used in the :doc:`dihedral_style hybrid <dihedral_hybrid>` command. These values are made
accessible for output or further processing by other commands. The
group specified for this command is ignored.
This compute is useful when using :doc:`dihedral_style hybrid <dihedral_hybrid>` if you want to know the portion of the
total energy contributed by one or more of the hybrid sub-styles.
**Output info:**
This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`dihedral_style hybrid <dihedral_style>` command. which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
:doc:`units <units>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
doc/compute_improper.rst deleted 100644 → 0
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.. index:: compute improper
compute improper command
========================
Syntax
""""""
.. parsed-literal::
compute ID group-ID improper
* ID, group-ID are documented in :doc:`compute <compute>` command
* improper = style name of this compute command
Examples
""""""""
.. parsed-literal::
compute 1 all improper
Description
"""""""""""
Define a computation that extracts the improper energy calculated by
each of the improper sub-styles used in the :doc:`improper_style hybrid <improper_hybrid>` command. These values are made
accessible for output or further processing by other commands. The
group specified for this command is ignored.
This compute is useful when using :doc:`improper_style hybrid <improper_hybrid>` if you want to know the portion of the
total energy contributed by one or more of the hybrid sub-styles.
**Output info:**
This compute calculates a global vector of length N where N is the
number of sub_styles defined by the :doc:`improper_style hybrid <improper_style>` command. which can be accessed by indices
1-N. These values can be used by any command that uses global scalar
or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
options.
The vector values are "extensive" and will be in energy
:doc:`units <units>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
doc/fix_shardlow.rst deleted 100644 → 0
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.. index:: fix shardlow
fix shardlow command
====================
Syntax
""""""
.. parsed-literal::
fix ID group-ID shardlow
* ID, group-ID are documented in :doc:`fix <fix>` command
* shardlow = style name of this fix command
Examples
""""""""
.. parsed-literal::
fix 1 all shardlow
Description
"""""""""""
Specifies that the Shardlow splitting algorithm (SSA) is to be used to
integrate the DPD equations of motion. The SSA splits the integration
into a stochastic and deterministic integration step. The fix
*shardlow* performs the stochastic integration step and must be used
in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nph>`). The stochastic
integration of the dissipative and random forces is performed prior to
the deterministic integration of the conservative force. Further
details regarding the method are provided in :ref:`(Lisal) <Lisal>` and
:ref:`(Larentzos) <Larentzos>`.
The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt <pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command to properly initialize the
fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
necessary).
Note that numerous variants of DPD can be specified by choosing an
appropriate combination of the integrator and :doc:`pair_style dpd/fdt <pair_style>` command. DPD under isothermal conditions can
be specified by using fix *shardlow*, fix *nve* and pair_style
*dpd/fdt*. DPD under isoenergetic conditions can be specified by
using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*. DPD
under isobaric conditions can be specified by using fix shardlow, fix
*nph* and pair_style *dpd/fdt*. DPD under isoenthalpic conditions can
be specified by using fix shardlow, fix *nph* and pair_style
*dpd/fdt/energy*. Examples of each DPD variant are provided in the
examples/USER/dpd directory.
----------
Restrictions
""""""""""""
This fix is only available if LAMMPS is built with the USER-DPD
package. See the :ref:`Making LAMMPS <start_3>` section
for more info.
This fix is currently limited to orthogonal simulation cell
geometries.
This fix must be used with an additional fix that specifies time
integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.
The Shardlow splitting algorithm requires the sizes of the sub-domain
lengths to be larger than twice the cutoff+skin. Generally, the
domain decomposition is dependant on the number of processors
requested.
Related commands
""""""""""""""""
:doc:`pair_style dpd/fdt <pair_dpd_fdt>`, :doc:`fix eos/cv <fix_eos_cv>`
**Default:** none
----------
.. _Lisal:
**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
particle dynamics as isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.",
J. Chem. Phys., 135, 204105 (2011).
.. _Larentzos:
**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
Dissipative Particle Dynamics Using Shardlow-Like Splitting
Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).
.. _Larentzos:
**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
Laboratory, Aberdeen Proving Ground, MD (2014).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
doc/fix_smd.rst deleted 100644 → 0
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.. index:: fix smd
fix smd command
===============
Syntax
""""""
.. parsed-literal::
fix ID group-ID smd type values keyword values
* ID, group-ID are documented in :doc:`fix <fix>` command
* smd = style name of this fix command
* mode = *cvel* or *cfor* to select constant velocity or constant force SMD
.. parsed-literal::
*cvel* values = K vel
K = spring constant (force/distance units)
vel = velocity of pulling (distance/time units)
*cfor* values = force
force = pulling force (force units)
* keyword = *tether* or *couple*
.. parsed-literal::
*tether* values = x y z R0
x,y,z = point to which spring is tethered
R0 = distance of end of spring from tether point (distance units)
*couple* values = group-ID2 x y z R0
group-ID2 = 2nd group to couple to fix group with a spring
x,y,z = direction of spring, automatically computed with 'auto'
R0 = distance of end of spring (distance units)
Examples
""""""""
.. parsed-literal::
fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0
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>`.
You can apply a moving spring force to a group of atoms (*tether*
style) or between two groups of atoms (*couple* style). The spring
can then be used in either constant velocity (*cvel*) mode or in
constant force (*cfor*) mode to induce transitions in your systems.
When running in *tether* style, you may need some way to fix some
other part of the system (e.g. via :doc:`fix spring/self <fix_spring_self>`)
The *tether* style attaches a spring between a point at a distance of
R0 away from a fixed point *x,y,z* and the center of mass of the fix
group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
applied to each atom in the group where *K* is the spring constant, Mi
is the mass of the atom, and M is the total mass of all atoms in the
group. Note that *K* thus represents the total force on the group of
atoms, not a per-atom force.
In *cvel* mode the distance R is incremented or decremented
monotonously according to the pulling (or pushing) velocity.
In *cfor* mode a constant force is added and the actual distance
in direction of the spring is recorded.
The *couple* style links two groups of atoms together. The first
group is the fix group; the second is specified by group-ID2. The
groups are coupled together by a spring that is at equilibrium when
the two groups are displaced by a vector in direction *x,y,z* with
respect to each other and at a distance R0 from that displacement.
Note that *x,y,z* only provides a direction and will be internally
normalized. But since it represents the *absolute* displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the *auto* parameter. In this case the direction is
recomputed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
in each of the two groups.
For both the *tether* and *couple* styles, any of the x,y,z values can
be specified as NULL which means do not include that dimension in the
distance calculation or force application.
For constant velocity pulling (*cvel* mode), the running integral
over the pulling force in direction of the spring is recorded and
can then later be used to compute the potential of mean force (PMF)
by averaging over multiple independent trajectories along the same
pulling path.
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The fix stores the direction of the spring, current pulling target
distance and the running PMF to :doc:`binary restart files <restart>`.
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.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix.
This fix computes a vector list of 7 quantities, which can be accessed
by various :ref:`output commands <howto_15>`. 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 2nd 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>`.
Restrictions
""""""""""""
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""
:doc:`fix drag <fix_drag>`, :doc:`fix spring <fix_spring>`,
:doc:`fix spring/self <fix_spring_self>`,
:doc:`fix spring/rg <fix_spring_rg>`
**Default:** none
----------
.. _Israilev:
**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
**(Park)**
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
**(Jarzynski)**
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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