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

Merge pull request #3370 from lammps/doc-pair-dipole

Browse Source 
Edits to pair dipole doc page
This commit is contained in:
Axel Kohlmeyer
2022-08-03 12:47:08 -04:00
committed by GitHub
parent 67e0621806 1eaa807bbf
commit 7a5fa964b4
5 changed files with 134 additions and 99 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
doc/src/Commands_parse.rst
View File

@ -123,14 +123,15 @@ LAMMPS:
.. _six:
6. If you want text with spaces to be treated as a single argument, it
can be enclosed in either single or double or triple quotes. A long
single argument enclosed in single or double quotes can span multiple
lines if the "&" character is used, as described above. When the
lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are
not needed. For example:
can be enclosed in either single (') or double (") or triple (""")
quotes. A long single argument enclosed in single or double quotes
can span multiple lines if the "&" character is used, as described
in :ref:`1 <one>` above. When the lines are concatenated together
by LAMMPS (and the "&" characters and line breaks removed), the
combined text will become a single line. If you want multiple lines
of an argument to retain their line breaks, the text can be enclosed
in triple quotes, in which case "&" characters are not needed and do
not function as line continuation character. For example:
.. code-block:: LAMMPS
@ -144,8 +145,9 @@ LAMMPS:
System temperature = $t
"""
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
In each of these cases, the single, double, or triple quotes are
removed and the enclosed text stored internally as a single
argument.
See the :doc:`dump modify format <dump_modify>`, :doc:`print
<print>`, :doc:`if <if>`, and :doc:`python <python>` commands for

18
doc/src/fix_npt_sphere.rst
View File

@ -22,7 +22,7 @@ Syntax
*disc* value = none = treat particles as 2d discs, not spheres
* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
* NOTE: additional thermostat and barostat and dipole related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
Examples
""""""""
@ -33,6 +33,7 @@ Examples
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 update dipole
fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
Description
@ -61,8 +62,9 @@ The only difference between discs and spheres in this context is their
moment of inertia, as used in the time integration.
Additional parameters affecting the thermostat and barostat are
specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command. See, for example, discussion of the *temp*,
*iso*, *aniso*, and *dilate* keywords.
specified by keywords and values documented with the :doc:`fix npt
<fix_nh>` command. See, for example, discussion of the *temp*, *iso*,
*aniso*, and *dilate* keywords.
The particles in the fix group are the only ones whose velocities and
positions are updated by the velocity/position update portion of the
@ -87,8 +89,10 @@ this, the fix creates its own computes of style "temp/sphere" and
compute fix-ID_temp all temp/sphere
compute fix-ID_press all pressure fix-ID_temp
See the :doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute pressure <compute_pressure>` commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
See the :doc:`compute temp/sphere <compute_temp_sphere>` and
:doc:`compute pressure <compute_pressure>` commands for details. Note
that the IDs of the new computes are the fix-ID + underscore + "temp"
or fix_ID
+ underscore + "press", and the group for the new computes is "all"
since pressure is computed for the entire system.
@ -170,7 +174,9 @@ defined by the :doc:`dimension <dimension>` keyword.
Related commands
""""""""""""""""
:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`, :doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere <fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
:doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere
<fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
Default
"""""""

13
doc/src/fix_nve_sphere.rst
View File

@ -51,7 +51,8 @@ If the *update* keyword is used with the *dipole* value, then the
orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole <atom_style>` command.
e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole
<atom_style>` command.
The default dipole orientation integrator can be changed to the
Dullweber-Leimkuhler-McLachlan integration scheme
@ -75,11 +76,13 @@ moment of inertia, as used in the time integration.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. 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>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

21
doc/src/fix_nvt_sphere.rst
View File

@ -22,7 +22,7 @@ Syntax
*disc* value = none = treat particles as 2d discs, not spheres
* additional thermostat related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
* NOTE: additional thermostat and dipole related keyword/value pairs from the :doc:`fix nvt <fix_nh>` command can be appended
Examples
""""""""
@ -32,6 +32,7 @@ Examples
fix 1 all nvt/sphere temp 300.0 300.0 100.0
fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc
fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2
fix 1 all nvt/sphere temp 300.0 300.0 100.0 update dipole
Description
"""""""""""
@ -77,13 +78,13 @@ underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
:doc:`compute_modify <compute_modify>` command or print this temperature
during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
It also means that changing attributes of *thermo_temp* will have no
effect on this fix.
the :doc:`thermo_style <thermo_style>` command) with ID =
*thermo_temp*. This means you can change the attributes of this fix's
temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
<compute_modify>` command or print this temperature during
thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
command using the appropriate compute-ID. It also means that changing
attributes of *thermo_temp* will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with :doc:`compute commands <compute>` that remove a "bias" from the
@ -148,7 +149,9 @@ defined by the :doc:`dimension <dimension>` keyword.
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`, :doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix npt_sphere <fix_npt_sphere>`, :doc:`fix_modify <fix_modify>`
:doc:`fix nvt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
:doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix npt_sphere
<fix_npt_sphere>`, :doc:`fix_modify <fix_modify>`
Default
"""""""

159
doc/src/pair_dipole.rst
View File

@ -78,12 +78,12 @@ Examples
Description
"""""""""""
Style *lj/cut/dipole/cut* computes interactions between pairs of particles
that each have a charge and/or a point dipole moment. In addition to
the usual Lennard-Jones interaction between the particles (Elj) the
charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole (Epp)
interactions are computed by these formulas for the energy (E), force
(F), and torque (T) between particles I and J.
Style *lj/cut/dipole/cut* computes interactions between pairs of
particles that each have a charge and/or a point dipole moment. In
addition to the usual Lennard-Jones interaction between the particles
(Elj) the charge-charge (Eqq), charge-dipole (Eqp), and dipole-dipole
(Epp) interactions are computed by these formulas for the energy (E),
force (F), and torque (T) between particles I and J.
.. math::
@ -112,18 +112,18 @@ interactions are computed by these formulas for the energy (E), force
\frac{3}{r^5} (\vec{p_i} \bullet \vec{r})
(\vec{p_j} \times \vec{r})
where :math:`q_i` and :math:`q_j` are the charges on the two particles,
:math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole moment vectors of
the two particles, r is their separation distance, and the vector r =
Ri - Rj is the separation vector between the two particles. Note that
Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as
symmetric forces, and Tij != -Tji since the torques do not act
symmetrically. These formulas are discussed in :ref:`(Allen) <Allen2>`
and in :ref:`(Toukmaji) <Toukmaji2>`.
where :math:`q_i` and :math:`q_j` are the charges on the two
particles, :math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole
moment vectors of the two particles, r is their separation distance,
and the vector r = Ri - Rj is the separation vector between the two
particles. Note that Eqq and Fqq are simply Coulombic energy and
force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
torques do not act symmetrically. These formulas are discussed in
:ref:`(Allen) <Allen2>` and in :ref:`(Toukmaji) <Toukmaji2>`.
Also note, that in the code, all of these terms (except Elj) have a
:math:`C/\epsilon` prefactor, the same as the Coulombic term in the LJ +
Coulombic pair styles discussed :doc:`here <pair_lj>`. C is an
:math:`C/\epsilon` prefactor, the same as the Coulombic term in the
LJ + Coulombic pair styles discussed :doc:`here <pair_lj>`. C is an
energy-conversion constant and epsilon is the dielectric constant
which can be set by the :doc:`dielectric <dielectric>` command. The
same is true of the equations that follow for other dipole pair
@ -135,11 +135,11 @@ moment. In general, a shifted-force potential is a (slightly) modified
potential containing extra terms that make both the energy and its
derivative go to zero at the cutoff distance; this removes
(cutoff-related) problems in energy conservation and any numerical
instability in the equations of motion :ref:`(Allen) <Allen2>`. Shifted-force
interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq),
charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
potentials are computed by these formulas for the energy (E), force
(F), and torque (T) between particles I and J:
instability in the equations of motion :ref:`(Allen)
<Allen2>`. Shifted-force interactions for the Lennard-Jones (E_LJ),
charge-charge (Eqq), charge-dipole (Eqp), dipole-charge (Epq) and
dipole-dipole (Epp) potentials are computed by these formulas for the
energy (E), force (F), and torque (T) between particles I and J:
.. math::
@ -207,65 +207,52 @@ potentials are computed by these formulas for the energy (E), force
where :math:`\epsilon` and :math:`\sigma` are the standard LJ
parameters, :math:`r_c` is the cutoff, :math:`q_i` and :math:`q_j` are
the charges on the two particles, :math:`\vec{p_i}` and
:math:`\vec{p_j}` are the dipole moment vectors of the two particles, r
is their separation distance, and the vector r = Ri - Rj is the
separation vector between the two particles. Note that Eqq and Fqq are
simply Coulombic energy and force, Fij = -Fji as symmetric forces, and
Tij != -Tji since the torques do not act symmetrically. The
:math:`\vec{p_j}` are the dipole moment vectors of the two particles,
r is their separation distance, and the vector r = Ri - Rj is the
separation vector between the two particles. Note that Eqq and Fqq
are simply Coulombic energy and force, Fij = -Fji as symmetric forces,
and Tij != -Tji since the torques do not act symmetrically. The
shifted-force formula for the Lennard-Jones potential is reported in
:ref:`(Stoddard) <Stoddard>`. The original (non-shifted) formulas for
the electrostatic potentials, forces and torques can be found in
:ref:`(Price) <Price2>`. The shifted-force electrostatic potentials have
been obtained by applying equation 5.13 of :ref:`(Allen) <Allen2>`. The
formulas for the corresponding forces and torques have been obtained by
applying the 'chain rule' as in appendix C.3 of :ref:`(Allen) <Allen2>`.
:ref:`(Price) <Price2>`. The shifted-force electrostatic potentials
have been obtained by applying equation 5.13 of :ref:`(Allen)
<Allen2>`. The formulas for the corresponding forces and torques have
been obtained by applying the 'chain rule' as in appendix C.3 of
:ref:`(Allen) <Allen2>`.
If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
they are used as cutoffs for the LJ and Coulombic (q,p) terms
respectively. This pair style also supports an optional *scale* keyword
as part of a pair_coeff statement, where the interactions can be
scaled according to this factor. This scale factor is also made available
for use with fix adapt.
respectively. This pair style also supports an optional *scale*
keyword as part of a pair_coeff statement, where the interactions can
be scaled according to this factor. This scale factor is also made
available for use with fix adapt.
Style *lj/cut/dipole/long* computes long-range point-dipole
interactions as discussed in :ref:`(Toukmaji) <Toukmaji2>`. Dipole-dipole,
dipole-charge, and charge-charge interactions are all supported, along
with the standard 12/6 Lennard-Jones interactions, which are computed
with a cutoff. A :doc:`kspace_style <kspace_style>` must be defined to
use this pair style. Currently, only :doc:`kspace_style ewald/disp <kspace_style>` support long-range point-dipole
interactions.
Style *lj/cut/dipole/long* computes the short-range portion of
point-dipole interactions as discussed in :ref:`(Toukmaji)
<Toukmaji2>`. Dipole-dipole, dipole-charge, and charge-charge
interactions are all supported, along with the standard 12/6
Lennard-Jones interactions, which are computed with a cutoff. A
:doc:`kspace_style <kspace_style>` must be defined to use this pair
style. If only dipoles (not point charges) are included in the model,
the kspace style can be one of these 3 options, all of which compute
the long-range portion of dipole-dipole interactions. If the model
includes point charges only the first of these kspace styles can be
used:
Style *lj/long/dipole/long* also computes point-dipole interactions as
discussed in :ref:`(Toukmaji) <Toukmaji2>`. Long-range dipole-dipole,
dipole-charge, and charge-charge interactions are all supported, along
with the standard 12/6 Lennard-Jones interactions. LJ interactions
can be cutoff or long-ranged.
* :doc:`kspace_style ewald/disp <kspace_style>`
* :doc:`kspace_style ewald/dipole <kspace_style>`
* :doc:`kspace_style pppm/dipole <kspace_style>`
For style *lj/long/dipole/long*, if *flag_lj* is set to *long*, no
cutoff is used on the LJ 1/r\^6 dispersion term. The long-range
portion is calculated by using the :doc:`kspace_style ewald_disp <kspace_style>` command. The specified LJ cutoff then
determines which portion of the LJ interactions are computed directly
by the pair potential versus which part is computed in reciprocal
space via the Kspace style. If *flag_lj* is set to *cut*, the LJ
interactions are simply cutoff, as with :doc:`pair_style lj/cut <pair_lj>`. If *flag_lj* is set to *off*, LJ interactions
are not computed at all.
Style *lj/long/dipole/long* has the same functionality as style
*lj/cut/dipole/long*, except it also has an option to compute 12/6
Lennard-Jones interactions for use with a long-range dispersion kspace
style. This is done by setting its *flag_lj* argument to *long*. For
long-range LJ interactions, the doc:`kspace_style ewald/disp
<kspace_style>` command must be used.
If *flag_coul* is set to *long*, no cutoff is used on the Coulombic or
dipole interactions. The long-range portion is calculated by using
*ewald_disp* of the :doc:`kspace_style <kspace_style>` command. If
*flag_coul* is set to *off*, Coulombic and dipole interactions are not
computed at all.
Atoms with dipole moments should be integrated using the :doc:`fix nve/sphere update dipole <fix_nve_sphere>` or the :doc:`fix nvt/sphere update dipole <fix_nvt_sphere>` command to rotate the
dipole moments. The *omega* option on the :doc:`fix langevin <fix_langevin>` command can be used to thermostat the
rotational motion. The :doc:`compute temp/sphere <compute_temp_sphere>`
command can be used to monitor the temperature, since it includes
rotational degrees of freedom. The :doc:`atom_style hybrid dipole sphere <atom_style>` command should be used since
it defines the point dipoles and their rotational state.
The magnitude and orientation of the dipole moment for each particle
can be defined by the :doc:`set <set>` command or in the "Atoms" section
of the data file read in by the :doc:`read_data <read_data>` command.
----------
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -287,6 +274,40 @@ type pair.
----------
Note that for systems using these pair styles, typically particles
should be able to exert torque on each other via their dipole moments
so that the particle and its dipole moment can rotate. This requires
they not be point particles, but finite-size spheres. Thus you should
use a command like :doc:`atom_style hybrid sphere dipole <atom_style>`
to use particles with both attributes.
The magnitude and orientation of the dipole moment for each particle
can be defined by the :doc:`set <set>` command or in the "Atoms"
section of the data file read in by the :doc:`read_data <read_data>`
command.
Rotating finite-size particles have 6 degrees of freedom (DOFs),
translation and rotational. You can use the :doc:`compute temp/sphere
<compute_temp_sphere>` command to monitor a temperature which includes
all these DOFs.
Finite-size particles with dipole moments should be integrated using
one of these options:
* :doc:`fix nve/sphere update dipole <fix_nve_sphere>`
* :doc:`fix nve/sphere update dipole <fix_nve_sphere>` plus :doc:`fix langevin omega yes <fix_langevin>`
* :doc:`fix nvt/sphere update dipole <fix_nvt_sphere>`
* :doc:`fix npt/sphere update dipole <fix_npt_sphere>`
In all cases the "update dipole" setting insures the dipole moments
are also rotated when the finite-size spheres rotate. The 2nd and 3rd
bullets perform thermostatting; in the case of a Langevin thermostat
the "omega yes" option also thermostats the rotational degrees of
freedom (if desired). The 4th bullet performs thermostatting and
barostatting.
----------
.. include:: accel_styles.rst
----------