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Merge branch 'lammps:develop' into fortran-fix-external

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hammondkd
2022-11-29 15:43:40 -06:00
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parent 5f9956405a a3e0cfa8f7
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1
doc/src/Commands_all.rst
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@ -31,7 +31,6 @@ table above.
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm_modify <comm_modify>`

1
doc/src/Commands_category.rst
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@ -25,7 +25,6 @@ Setup simulation box:
:columns: 4
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`create_box <create_box>`
* :doc:`dimension <dimension>`

17
doc/src/Commands_removed.rst
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@ -2,10 +2,11 @@ Removed commands and packages
=============================
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or replacements.
LAMMPS has special dummy styles implemented, that will stop LAMMPS and
print a suitable error message in most cases, when a style/command is used
that has been removed.
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
@ -17,6 +18,14 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
Box command
-----------
.. deprecated:: TBD
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids command
-----------------

5
doc/src/Howto_triclinic.rst
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@ -144,11 +144,6 @@ does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the :doc:`box <box>` command. Setting the *tilt*
keyword to *large* allows any tilt factors to be specified.
Box flips that may occur using the :doc:`fix deform <fix_deform>` or
:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
option with either of the commands.

2
doc/src/Run_options.rst
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@ -262,6 +262,8 @@ Disable generating a citation reminder (see above) at all.
**-nonbuf**
.. versionadded:: 15Sep2022
Turn off buffering for screen and logfile output. For performance
reasons, output to the screen and logfile is usually buffered, i.e.
output is only written to a file if its buffer - typically 4096 bytes -

18
doc/src/angle_gaussian.rst
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@ -25,23 +25,25 @@ The *gaussian* angle style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(\theta-\theta_{i})^2}{w_i^2}\right) \right)
This analytical form is a suitable potential for obtaining mesoscale
effective force fields which can reproduce target atomistic
distributions :ref:`(Milano) <Milano1>`.
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`T` temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`A_1` (> 0, radians)
* :math:`w_1` (> 0, radians)
* :math:`\theta_1` (degrees)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`A_n` (> 0, radians)
* :math:`w_n` (> 0, radians)
* :math:`\theta_n` (degrees)

25
doc/src/bond_gaussian.rst
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@ -25,33 +25,34 @@ The *gaussian* bond style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(r-r_{i})^2}{w_i^2}\right)\right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
This analytical form is a suitable potential for obtaining mesoscale
effective force fields which can reproduce target atomistic
distributions :ref:`(Milano) <Milano0>`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`T` temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`r_1` (length)
* :math:`A_1` (> 0, distance)
* :math:`w_1` (> 0, distance)
* :math:`r_1` (>= 0, distance)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`r_n` (length)
* :math:`A_n` (> 0, distance)
* :math:`w_n` (> 0, distance)
* :math:`r_n` (>= 0, distance)
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""

70
doc/src/box.rst
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@ -1,70 +0,0 @@
.. index:: box
box command
===========
Syntax
""""""
.. code-block:: LAMMPS
box keyword value ...
* one or more keyword/value pairs may be appended
* keyword = *tilt*
.. parsed-literal::
*tilt* value = *small* or *large*
Examples
""""""""
.. code-block:: LAMMPS
box tilt large
box tilt small
Description
"""""""""""
Set attributes of the simulation box.
For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword
allows simulation domains to be created with arbitrary tilt factors,
e.g. via the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` commands. Tilt factors determine how
skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` page for a discussion of triclinic
boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the first
dimension in the tilt factor (x for xz). If *tilt* is set to
*small*, which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt*
is set to *large*, then no limit is enforced. You can create
a box with any tilt factors you wish.
Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
Restrictions
""""""""""""
This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command.
Related commands
""""""""""""""""
none
Default
"""""""
The default value is tilt = small.

1
doc/src/commands_list.rst
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@ -13,7 +13,6 @@ Commands
bond_style
bond_write
boundary
box
change_box
clear
comm_modify

25
doc/src/create_box.rst
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@ -66,20 +66,21 @@ positive or negative values and are called "tilt factors" because they
are the amount of displacement applied to faces of an originally
orthogonal box to transform it into the parallelepiped.
By default, a *prism* region used with the create_box command must
have tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
By default, a *prism* region used with the create_box command must have
tilt factors :math:`(xy,xz,yz)` that do not skew the box more than half
the distance of the parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
box length is 10 and the :math:`xy` tilt factor must be between :math:`-5` and
:math:`5`. Similarly, both :math:`xz` and :math:`yz` must be between
:math:`-(x_\text{hi}-x_\text{lo})/2` and :math:`+(y_\text{hi}-y_\text{lo})/2`.
Note that this is not a limitation, since if the maximum tilt factor is 5 (as
in this example), then configurations with tilt :math:`= \dots, -15`,
:math:`-5`, :math:`5`, :math:`15`, :math:`25, \dots`
are all geometrically equivalent. If you wish to define a box with tilt
factors that exceed these limits, you can use the :doc:`box tilt <box>`
command, with a setting of *large*\ ; a setting of *small* is the
default.
box length is 10 and the :math:`xy` tilt factor must be between
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this example),
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
equivalent. Simulations with large tilt factors will run inefficiently,
since they require more ghost atoms and thus more communication. With
very large tilt factors, LAMMPS will eventually produce incorrect
trajectories and stop with errors due to lost atoms or similar.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and

2
doc/src/dump_image.rst
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@ -69,7 +69,7 @@ Syntax
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
*axes* values = axes length diam = draw xyz axes
axes = *yes* or *no = do or do not draw xyz axes lines next to simulation box
axes = *yes* or *no* = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
*subbox* values = lines diam = draw outline of processor sub-domains

2
doc/src/fix_bond_react.rst
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@ -640,7 +640,7 @@ specified by the *max_rxn* keyword.
.. versionadded:: TBD
The *rate_limit* keyword can enforce an upper limit on the overall
rate of the reaction. The number of reaction occurences is limited to
rate of the reaction. The number of reaction occurrences is limited to
Nlimit within an interval of Nsteps timesteps. No reactions are
permitted to occur within the first Nsteps timesteps of the first run
after reading a data file. Nlimit can be specified with an equal-style

97
doc/src/fix_nh_uef.rst
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@ -44,19 +44,23 @@ Examples
Description
"""""""""""
This fix can be used to simulate non-equilibrium molecular dynamics
(NEMD) under diagonal flow fields, including uniaxial and bi-axial
flow. Simulations under continuous extensional flow may be carried
out for an indefinite amount of time. It is an implementation of the
boundary conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
These fixes can be used to simulate non-equilibrium molecular dynamics
(NEMD) under diagonal flow fields, including uniaxial and bi-axial flow.
Simulations under continuous extensional flow may be carried out for an
indefinite amount of time. It is an implementation of the boundary
conditions from :ref:`(Dobson) <Dobson>`, and also uses numerical
lattice reduction as was proposed by :ref:`(Hunt) <Hunt>`. The lattice
reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is intended for
simulations of homogeneous flows, and integrates the SLLOD equations
of motion, originally proposed by Hoover and Ladd (see :ref:`(Evans and Morriss) <Sllod>`). Additional detail about this implementation can be
found in :ref:`(Nicholson and Rutledge) <Nicholson>`.
reduction algorithm is from :ref:`(Semaev) <Semaev>`. The fix is
intended for simulations of homogeneous flows, and integrates the SLLOD
equations of motion, originally proposed by Hoover and Ladd (see
:ref:`(Evans and Morriss) <Sllod>`). Additional detail about this
implementation can be found in :ref:`(Nicholson and Rutledge)
<Nicholson>`.
Note that NEMD simulations of a continuously strained system can be
performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>` commands.
performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod
<fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
commands.
The applied flow field is set by the *eps* keyword. The values
*edot_x* and *edot_y* correspond to the strain rates in the xx and yy
@ -73,11 +77,11 @@ to -(*edot_x* + *edot_y*).
The boundary conditions require a simulation box that does not have a
consistent alignment relative to the applied flow field. Since LAMMPS
utilizes an upper-triangular simulation box, it is not possible to
express the evolving simulation box in the same coordinate system as
the flow field. This fix keeps track of two coordinate systems: the
flow frame, and the upper triangular LAMMPS frame. The coordinate
systems are related to each other through the QR decomposition, as is
illustrated in the image below.
express the evolving simulation box in the same coordinate system as the
flow field. These fixes keep track of two coordinate systems: the flow
frame, and the upper triangular LAMMPS frame. The coordinate systems are
related to each other through the QR decomposition, as is illustrated in
the image below.
.. image:: JPG/uef_frames.jpg
:align: center
@ -99,12 +103,12 @@ using the dump command will be in the LAMMPS frame unless the
----------
Temperature control is achieved with the default Nose-Hoover style
thermostat documented in :doc:`fix npt <fix_nh>`. When this fix is
thermostat documented in :doc:`fix nvt <fix_nh>`. When this fix is
active, only the peculiar velocity of each atom is stored, defined as
the velocity relative to the streaming velocity. This is in contrast
to :doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame
velocity, and removes the contribution from the streaming velocity in
order to compute the temperature.
the velocity relative to the streaming velocity. This is in contrast to
:doc:`fix nvt/sllod <fix_nvt_sllod>`, which uses a lab-frame velocity,
and removes the contribution from the streaming velocity in order to
compute the temperature.
Pressure control is achieved using the default Nose-Hoover barostat
documented in :doc:`fix npt <fix_nh>`. There are two ways to control the
@ -156,8 +160,8 @@ The following commands will not work:
----------
These fix computes a temperature and pressure each timestep. To do
this, it creates its own computes of style "temp/uef" and
These fixes compute a temperature and pressure each timestep. To do
this, they create their own computes of style "temp/uef" and
"pressure/uef", as if one of these two sets of commands had been
issued:
@ -169,18 +173,19 @@ issued:
compute fix-ID_temp all temp/uef
compute fix-ID_press all pressure/uef fix-ID_temp
See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute pressure/uef <compute_pressure_uef>` commands for details. Note
that the IDs of the new computes are the fix-ID + underscore + "temp"
or fix_ID + underscore + "press".
See the :doc:`compute temp/uef <compute_temp_uef>` and :doc:`compute
pressure/uef <compute_pressure_uef>` commands for details. Note that
the IDs of the new computes are the fix-ID + underscore + "temp" or
fix_ID + underscore + "press".
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The fix writes the state of all the thermostat and barostat variables,
as well as the cumulative strain applied, 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.
as well as the cumulative strain applied, 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.
.. note::
@ -189,43 +194,41 @@ uninterrupted fashion.
not contain the cumulative applied strain, will this keyword be
necessary.
This fix can be used with the :doc:`fix_modify <fix_modify>` *temp* and
*press* options. The temperature and pressure computes used must be of
type *temp/uef* and *pressure/uef*\ .
These fixes can be used with the :doc:`fix_modify <fix_modify>` *temp*
and *press* options. The temperature and pressure computes used must be
of type *temp/uef* and *pressure/uef*\ .
This fix computes the same global scalar and vector quantities as :doc:`fix npt <fix_nh>`.
These fixes compute the same global scalar and vector quantities as
:doc:`fix nvt andnpt <fix_nh>`.
The fix is not invoked during :doc:`energy minimization <minimize>`.
These fixes are not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the UEF package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
These fixes are part of the UEF package. They are only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Due to requirements of the boundary conditions, when the *strain*
keyword is set to zero (or unset), the initial simulation box must be
cubic and have style triclinic. If the box is initially of type ortho,
use :doc:`change_box <change_box>` before invoking the fix.
.. note::
When resuming from restart files, you may need to use :doc:`box tilt
large <box>` since LAMMPS has internal criteria from lattice
reduction that are not the same as the criteria in the numerical
lattice reduction algorithm.
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix nvt/sllod <fix_nvt_sllod>`, :doc:`compute temp/uef <compute_temp_uef>`, :doc:`compute pressure/uef <compute_pressure_uef>`, :doc:`dump cfg/uef <dump_cfg_uef>`
:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, `fix nvt/sllod
:doc:<fix_nvt_sllod>`, `compute temp/uef <compute_temp_uef>`,
:doc::doc:`compute pressure/uef <compute_pressure_uef>`, `dump cfg/uef
:doc:<dump_cfg_uef>`
Default
"""""""
The default keyword values specific to this fix are exy = xyz, strain
= 0 0. The remaining defaults are the same as for :doc:`fix npt <fix_nh>`
except tchain = 1. The reason for this change is given in
The default keyword values specific to these fixes are exy = xyz, strain
= 0 0. The remaining defaults are the same as for :doc:`fix nvt or npt
<fix_nh>` except tchain = 1. The reason for this change is given in
:doc:`fix nvt/sllod <fix_nvt_sllod>`.
----------

2
doc/src/pair_ylz.rst
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@ -82,7 +82,7 @@ mixing as described below:
* :math:`\epsilon` = well depth (energy units)
* :math:`\sigma` = minimum effective particle radii (distance units)
* :math:`\zeta` = tune parameter for the slope of the attractive branch
* :math:`\zeta` = tuning parameter for the slope of the attractive branch
* :math:`\mu` = parameter related to bending rigidity
* :math:`\beta` = parameter related to the spontaneous curvature
* cutoff (distance units)

2
doc/src/python.rst
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@ -129,6 +129,8 @@ The first argument of the *python* command is either the *source*
keyword or the name of a Python function. This defines the mode
of the python command.
.. versionchanged:: TBD
If the *source* keyword is used, it is followed by either a file name or
the *here* keyword. No other keywords can be used. The *here* keyword
is followed by a string with python commands, either on a single line

24
doc/src/read_data.rst
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@ -340,16 +340,20 @@ and are called "tilt factors" because they are the amount of
displacement applied to faces of an originally orthogonal box to
transform it into the parallelepiped.
By default, the tilt factors (xy,xz,yz) can not skew the box more than
half the distance of the corresponding parallel box length. For
example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
xy tilt factor must be between -5 and 5. Similarly, both xz and yz
must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not
a limitation, since if the maximum tilt factor is 5 (as in this
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all geometrically equivalent. If you wish to define a box
with tilt factors that exceed these limits, you can use the :doc:`box tilt <box>` command, with a setting of *large*\ ; a setting of
*small* is the default.
The tilt factors (xy,xz,yz) should not skew the box more than half the
distance of the corresponding parallel box length. For example, if
:math:`x_\text{lo} = 2` and :math:`x_\text{hi} = 12`, then the :math:`x`
box length is 10 and the :math:`xy` tilt factor must be between
:math:`-5` and :math:`5`. Similarly, both :math:`xz` and :math:`yz`
must be between :math:`-(x_\text{hi}-x_\text{lo})/2` and
:math:`+(y_\text{hi}-y_\text{lo})/2`. Note that this is not a
limitation, since if the maximum tilt factor is 5 (as in this example),
then configurations with tilt :math:`= \dots, -15`, :math:`-5`,
:math:`5`, :math:`15`, :math:`25, \dots` are all geometrically
equivalent. Simulations with large tilt factors will run inefficiently,
since they require more ghost atoms and thus more communication. With
very large tilt factors, LAMMPS will eventually produce incorrect
trajectories and stop with errors due to lost atoms or similar.
See the :doc:`Howto triclinic <Howto_triclinic>` page for a
geometric description of triclinic boxes, as defined by LAMMPS, and