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Axel Kohlmeyer
2023-01-05 23:36:45 -05:00
parent c8a33aefd4 3bf527d070
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42
doc/src/Build_extras.rst
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@ -861,11 +861,11 @@ library.
.. code-block:: bash
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
make lib-latte # print help message
make lib-latte args="-b" # download and build in lib/latte/LATTE-master
make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
and ``filelink.o``, are created in ``lib/latte`` to point to
@ -1211,10 +1211,10 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU Fortran compiler
----------
@ -1262,10 +1262,10 @@ AWPMD package
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
----------
@ -1366,10 +1366,10 @@ This package depends on the KSPACE package.
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
@ -1450,10 +1450,10 @@ ML-POD package
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
The package itself is activated with ``make yes-ML-POD``.

2
doc/src/Commands_all.rst
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@ -24,6 +24,7 @@ table above.
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`angle_write <angle_write>`
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
@ -45,6 +46,7 @@ table above.
* :doc:`dielectric <dielectric>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`dihedral_write <dihedral_write>`
* :doc:`dimension <dimension>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`

24
doc/src/Packages_details.rst
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@ -2548,17 +2548,18 @@ REACTION package
**Contents:**
This package allows for complex bond topology changes (reactions)
during a running MD simulation, when using classical force fields.
Topology changes are defined in pre- and post-reaction molecule
templates and can include creation and deletion of bonds, angles,
dihedrals, impropers, atom types, bond types, angle types, dihedral
types, improper types, and/or atomic charges. Other options currently
available include reaction constraints (e.g. angle and Arrhenius
constraints), deletion of reaction byproducts or other small
molecules, and chiral-sensitive reactions.
This package implements the REACTER protocol, which allows for complex
bond topology changes (reactions) during a running MD simulation when
using classical force fields. Topology changes are defined in pre- and
post-reaction molecule templates and can include creation and deletion
of bonds, angles, dihedrals, impropers, atom types, bond types, angle
types, dihedral types, improper types, and/or atomic charges. Other
options currently available include reaction constraints (e.g., angle
and Arrhenius constraints), deletion of reaction byproducts or other
small molecules, creation of new atoms or molecules bonded to existing
atoms, and using LAMMPS variables for input parameters.
**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center.
**Author:** Jacob R. Gissinger (NASA Langley Research Center).
**Supporting info:**
@ -2568,7 +2569,8 @@ molecules, and chiral-sensitive reactions.
* examples/PACKAGES/reaction
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org
* `2021 LAMMPS Workshop <https://www.lammps.org/workshops/Aug21/talk/jacob-gissinger/>`_
* `REACTER website (reacter.org) <https://www.reacter.org/>`_
----------

11
doc/src/angle_table.rst
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@ -59,9 +59,12 @@ format of this file is described below.
----------
Suitable tables for use with this angle style can be created using the
Python code in the ``tools/tabulate`` folder of the LAMMPS source code
distribution.
Suitable tables for use with this angle style can be created by LAMMPS
itself from existing angle styles using the :doc:`angle_write
<angle_write>` command. This can be useful to have a template file for
testing the angle style settings and to build a compatible custom file.
Another option to generate tables is the Python code in the
``tools/tabulate`` folder of the LAMMPS source code distribution.
The format of a tabulated file is as follows (without the
parenthesized comments):
@ -154,7 +157,7 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_write <angle_write>`
Default
"""""""

99
doc/src/angle_write.rst Normal file
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@ -0,0 +1,99 @@
.. index:: angle_write
angle_write command
===================
Syntax
""""""
.. code-block:: LAMMPS
angle_write atype N file keyword
* atype = angle type
* N = # of values
* file = name of file to write values to
* keyword = section name in file for this set of tabulated values
Examples
""""""""
.. code-block:: LAMMPS
angle_write 1 500 table.txt Harmonic_1
angle_write 3 1000 table.txt Harmonic_3
Description
"""""""""""
.. versionadded:: TBD
Write energy and force values to a file as a function of angle for the
currently defined angle potential. Force in this context means the
force with respect to the angle, not the force on individual atoms.
This is useful for plotting the potential function or otherwise
debugging its values. The resulting file can also be used as input for
use with :doc:`angle style table <angle_table>`.
If the file already exists, the table of values is appended to the end
of the file to allow multiple tables of energy and force to be included
in one file. The individual sections may be identified by the *keyword*.
The energy and force values are computed for angles ranging from 0
degrees to 180 degrees for 3 interacting atoms forming an angle type
atype, using the appropriate :doc:`angle_coeff <angle_coeff>`
coefficients. N evenly spaced angles are used.
For example, for N = 6, values are computed at :math:`\theta = 0, 36,
72, 108, 144, 180`.
The file is written in the format used as input for the
:doc:`angle_style table <angle_table>` option with *keyword* as the
section name. Each line written to the file lists an index number
(1-N), an angle (in degrees), an energy (in energy units), and a force
(in force units per radians^2). In case a new file is created, the
first line will be a comment with a "DATE:" and "UNITS:" tag with the
current date and :doc:`units <units>` settings. For subsequent
invocations of the *angle_write* command for the same file, data will be
appended and the current units settings will be compared to the data
from the header, if present. The *angle_write* will refuse to add a
table to an existing file if the units are not the same.
Restrictions
""""""""""""
All force field coefficients for angle and other kinds of interactions
must be set before this command can be invoked.
The table of the angle energy and force data data is created by using a
separate, internally created, new LAMMPS instance with a dummy system of
3 atoms for which the angle potential energy is computed after
transferring the angle style and coefficients and arranging the 3 atoms
into the corresponding geometries. The angle force is then determined
from the potential energies through numerical differentiation. As a
consequence of this approach, not all angle styles are compatible. The
following conditions must be met:
- The angle style must be able to write its coefficients to a data file.
This condition excludes for example :doc:`angle style hybrid <angle_hybrid>` and
:doc:`angle style table <angle_table>`.
- The potential function must not have any terms that depend on geometry
properties other than the angle. This condition excludes for example
:doc:`angle style class2 <angle_class2>` all angle types for
:doc:`angle style charmm <angle_charmm>` that have non-zero
Urey-Bradley terms. Please note that the *write_angle* command has no
way of checking for this condition, so the resulting tables may be
bogus if the requirement is not met. It is thus recommended to make
careful tests for any created tables.
Related commands
""""""""""""""""
:doc:`angle_style table <angle_table>`, :doc:`bond_write <bond_write>`,
:doc:`dihedral_write <dihedral_write>`, :doc:`angle_style <angle_style>`,
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none

2
doc/src/bond_write.rst
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@ -70,7 +70,7 @@ be specified even if the potential has a finite value at r = 0.0.
Related commands
""""""""""""""""
:doc:`bond_style table <bond_table>`,
:doc:`bond_style table <bond_table>`, `angle_write <angle_write>`,
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
Default

2
doc/src/commands_list.rst
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@ -6,6 +6,7 @@ Commands
angle_coeff
angle_style
angle_write
atom_modify
atom_style
balance
@ -27,6 +28,7 @@ Commands
dielectric
dihedral_coeff
dihedral_style
dihedral_write
dimension
displace_atoms
dump

101
doc/src/dihedral_write.rst Normal file
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@ -0,0 +1,101 @@
.. index:: dihedral_write
dihedral_write command
======================
Syntax
""""""
.. code-block:: LAMMPS
dihedral_write dtype N file keyword
* dtype = dihedral type
* N = # of values
* file = name of file to write values to
* keyword = section name in file for this set of tabulated values
Examples
""""""""
.. code-block:: LAMMPS
dihedral_write 1 500 table.txt Harmonic_1
dihedral_write 3 1000 table.txt Harmonic_3
Description
"""""""""""
.. versionadded:: TBD
Write energy and force values to a file as a function of the dihedral
angle for the currently defined dihedral potential. Force in this
context means the force with respect to the dihedral angle, not the
force on individual atoms. This is useful for plotting the potential
function or otherwise debugging its values. The resulting file can also
be used as input for use with :doc:`dihedral style table
<dihedral_table>`.
If the file already exists, the table of values is appended to the end
of the file to allow multiple tables of energy and force to be included
in one file. The individual sections may be identified by the *keyword*.
The energy and force values are computed for dihedrals ranging from 0
degrees to 360 degrees for 4 interacting atoms forming an dihedral type
dtype, using the appropriate :doc:`dihedral_coeff <dihedral_coeff>`
coefficients. N evenly spaced dihedrals are used. Since 0 and 360
degrees are the same dihedral angle, the latter entry is skipped.
For example, for N = 6, values would be computed at
:math:`\phi = 0, 60, 120, 180, 240, 300`.
The file is written in the format used as input for the
:doc:`dihedral_style table <dihedral_table>` option with *keyword* as
the section name. Each line written to the file lists an index number
(1-N), an dihedral angle (in degrees), an energy (in energy units), and
a force (in force units per radians^2). In case a new file is created,
the first line will be a comment with a "DATE:" and "UNITS:" tag with
the current date and :doc:`units <units>` settings. For subsequent
invocations of the *dihedral_write* command for the same file, data will
be appended and the current units settings will be compared to the data
from the header, if present. The *dihedral_write* will refuse to add a
table to an existing file if the units are not the same.
Restrictions
""""""""""""
All force field coefficients for dihedrals and other kinds of interactions
must be set before this command can be invoked.
The table of the dihedral energy and force data data is created by using a
separate, internally created, new LAMMPS instance with a dummy system of
4 atoms for which the dihedral potential energy is computed after
transferring the dihedral style and coefficients and arranging the 4 atoms
into the corresponding geometries. The dihedral force is then determined
from the potential energies through numerical differentiation. As a
consequence of this approach, not all dihedral styles are compatible. The
following conditions must be met:
- The dihedral style must be able to write its coefficients to a data file.
This condition excludes for example :doc:`dihedral style hybrid <dihedral_hybrid>` and
:doc:`dihedral style table <dihedral_table>`.
- The potential function must not have any terms that depend on geometry
properties other than the dihedral. This condition excludes for
example :doc:`dihedral style class2 <dihedral_class2>`. Please note
that the *write_dihedral* command has no way of checking for this
condition. It will check the style name against an internal list of
known to be incompatible styles. The resulting tables may be bogus
for unlisted dihedral styles if the requirement is not met. It is
thus recommended to make careful tests for any created tables.
Related commands
""""""""""""""""
:doc:`dihedral_style table <dihedral_table>`, :doc:`bond_write <bond_write>`,
:doc:`angle_write <angle_write>`, :doc:`dihedral_style <dihedral_style>`,
:doc:`dihedral_coeff <dihedral_coeff>`
Default
"""""""
none

40
doc/src/fix_bond_react.rst
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@ -123,6 +123,17 @@ using this fix is
(4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates
(5) fill a simulation box with molecules and run a simulation with fix bond/react.
.. note::
.. versionadded:: 15Sep2022
:doc:`Type labels <Howto_type_labels>` allow for molecule templates
and data files to use alphanumeric atom types that match those of
a force field. Input files that use type labels are inherently
compatible with each other and portable between different
simulations. Therefore, it is highly recommended to use type labels
to specify atom, bond, etc. types when using fix bond/react.
Only one 'fix bond/react' command can be used at a time. Multiple
reactions can be simultaneously applied by specifying multiple *react*
arguments to a single 'fix bond/react' command. This syntax is
@ -228,18 +239,18 @@ pairs are identified within the cutoff distance:
initiator partners, these two atoms are identified as the initiator atom
pair of the reaction site.
Note that it can be helpful to select
unique atom types for the initiator atoms: if an initiator atom pair
is identified, as described in the previous steps, but it does not
correspond to the same pair specified in the pre-reaction template, an
otherwise eligible reaction could be prevented from occurring. Once
this unique initiator atom pair is identified for each reaction, there
could be two or more reactions that involve the same atom on the same
time step. If this is the case, only one such reaction is permitted to
occur. This reaction is chosen randomly from all potential reactions
involving the overlapping atom. This capability allows, for example,
different reaction pathways to proceed from identical reaction sites
with user-specified probabilities.
Note that it can be helpful to select unique atom types for the
initiator atoms: if an initiator atom pair is identified, as described
in the previous steps, but it does not correspond to the same pair
specified in the pre-reaction template, an otherwise eligible reaction
could be prevented from occurring. Once this unique initiator atom
pair is identified for each reaction, there could be two or more
reactions that involve the same atom on the same time step. If this is
the case, only one such reaction is permitted to occur. This reaction
is chosen randomly from all potential reactions involving the
overlapping atom. This capability allows, for example, different
reaction pathways to proceed from identical reaction sites with
user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
@ -280,7 +291,10 @@ for a given simulation. All atom types in the pre-reacted template
must be the same as those of a potential reaction site in the
simulation. A detailed discussion of matching molecule template atom
types with the simulation is provided on the :doc:`molecule <molecule>`
command page.
command page. It is highly recommended to use :doc:`Type labels <Howto_type_labels>`
(added in version 15Sep2022) in both molecule templates and data
files, which automates the process of syncing atom types between
different input files.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It

9
doc/src/fix_pair.rst
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@ -1,7 +1,7 @@
.. index:: fix pair
fix pair command
=======================
================
Syntax
""""""
@ -47,7 +47,12 @@ These are example use cases:
The *N* argument determines how often the fix is invoked.
The *pstyle* argument is the name of the pair style. It can be a
sub-style used in a :doc:`pair_style hybrid <pair_hybrid>` command.
sub-style used in a :doc:`pair_style hybrid <pair_hybrid>` command. If
there are multiple sub-styles using the same pair style, then *pstyle*
should be specified as "style:N", where *N* is the number of the
instance of the pair style you wish monitor (e.g., the first or second).
For example, *pstyle* could be specified as "pace/extrapolation" or
"amoeba" or "eam:1" or "eam:2".
One or more *name/flag* pairs of arguments follow. Each *name* is a
per-atom quantity which the pair style must recognize as an extraction

6
doc/src/pair_pace.rst
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@ -1,6 +1,7 @@
.. index:: pair_style pace
.. index:: pair_style pace/kk
.. index:: pair_style pace/extrapolation
.. index:: pair_style pace/extrapolation/kk
pair_style pace command
=======================
@ -127,6 +128,9 @@ but not more often than every 20 steps.
On all other steps `pair_style pace recursive` will be used.
When using the pair style *pace/extrapolation* with the KOKKOS package on GPUs
product B-basis evaluator is always used and only *linear* ASI is supported.
----------
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
@ -186,4 +190,4 @@ recursive, chunksize = 4096,
.. _Lysogorskiy2022:
**(Lysogorskiy2022)** Lysogorskiy, Bochkarev, Mrovec, Drautz, TBS (2022).
**(Lysogorskiy2022)** Lysogorskiy, Bochkarev, Mrovec, Drautz, arXiv:2212.08716 (2022).

2
doc/utils/sphinx-config/false_positives.txt
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@ -174,6 +174,7 @@ attrac
Atw
Atwater
atwt
atype
augt
AuO
automagically
@ -828,6 +829,7 @@ dtemp
dtgrow
dtheta
dtshrink
dtype
du
dU
Ducastelle