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Merge branch 'master' into fix-ttm-grid

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Axel Kohlmeyer
2021-08-26 16:57:19 -04:00
parent 16d73c86ba e3af1544f1
commit 892a18c3f6
674 changed files with 17960 additions and 15036 deletions
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77
doc/src/Build_development.rst
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@ -1,15 +1,15 @@
Development build options (CMake only)
======================================
Development build options
=========================
The CMake build procedure of LAMMPS offers a few extra options which are
The build procedures in LAMMPS offers a few extra options which are
useful during development, testing or debugging.
----------
.. _compilation:
Monitor compilation flags
-------------------------
Monitor compilation flags (CMake only)
--------------------------------------
Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
@ -30,8 +30,8 @@ variable VERBOSE set to 1:
.. _clang-tidy:
Enable static code analysis with clang-tidy
-------------------------------------------
Enable static code analysis with clang-tidy (CMake only)
--------------------------------------------------------
The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
static code analysis tool to diagnose (and potentially fix) typical
@ -52,8 +52,8 @@ significantly more time consuming than the compilation itself.
.. _iwyu_processing:
Report missing and unneeded '#include' statements
-------------------------------------------------
Report missing and unneeded '#include' statements (CMake only)
--------------------------------------------------------------
The conventions for how and when to use and order include statements in
LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
@ -86,8 +86,8 @@ on recording all commands required to do the compilation.
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
---------------------------------------------------------
Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in the code
@ -116,8 +116,8 @@ compilation and linking stages. This is done through setting the
.. _testing:
Code Coverage and Unit Testing
------------------------------
Code Coverage and Unit Testing (CMake only)
-------------------------------------------
The LAMMPS code is subject to multiple levels of automated testing
during development: integration testing (i.e. whether the code compiles
@ -464,7 +464,8 @@ Coding style utilities
To aid with enforcing some of the coding style conventions in LAMMPS
some additional build targets have been added. These require Python 3.5
or later and will only work on Unix-like operating and file systems.
or later and will only work properly on Unix-like operating and file systems.
The following options are available.
.. code-block:: bash
@ -476,17 +477,43 @@ The following options are available.
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
These should help to replace all TAB characters with blanks and remove
any trailing whitespace. Also all LAMMPS homepage URL references can be
updated to the location change from Sandia to the lammps.org domain.
And the permission check can remove executable permissions from non-executable
files (like source code).
Clang-format support
--------------------
For the code in the ``unittest`` and ``src`` trees we are transitioning
to use the `clang-format` tool to assist with having a consistent source
code style. The `clang-format` command bundled with Clang version 8.0
or later is required. The configuration is in files ``.clang-format``
in the respective folders. Since the modifications from `clang-format`
can be significant and - especially for "legacy style code" - also is
not always improving readability, a large number of files currently have
a ``// clang-format off`` at the top, which will disable the processing.
Over time, files will be refactored and updated to that `clang-format`
may be applied to them (at least in part).
code formatting style. The `clang-format` command bundled with Clang
version 8.0 or later is required. The configuration is in files called
``.clang-format`` in the respective folders. Since the modifications
from `clang-format` can be significant and - especially for "legacy
style code" - they are not always improving readability, a large number
of files currently have a ``// clang-format off`` at the top, which will
disable the processing. As of fall 2021 all files have been either
"protected" this way or are enabled for full or partial `clang-format`
processing. Over time, the "protected" files will be refactored and
updated so that `clang-format` may be applied to them as well.
If `clang-format` is available, the source code files in the ``unittest``
tree can be updated to conform to the formatting settings using
``make format-tests`` and the files in ``src`` with ``make format-src``.
It is recommended for all newly contributed files to use the clang-format
processing while writing the code or do the coding style processing
(including the scripts mentioned in the previous paragraph)
If `clang-format` is available, files can be updated individually with
commands like the following:
.. code-block:: bash
$ clang-format -i some_file.cpp
The following target are available for both, GNU make and CMake:
.. code-block:: bash
make format-src # apply clang-format to all files in src and the package folders
make format-tests # apply clang-format to all files in the unittest tree

2
doc/src/Commands_compute.rst
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@ -152,7 +152,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`temp/chunk <compute_temp_chunk>`
* :doc:`temp/com <compute_temp_com>`
* :doc:`temp/cs <compute_temp_cs>`
* :doc:`temp/deform <compute_temp_deform>`
* :doc:`temp/deform (k) <compute_temp_deform>`
* :doc:`temp/deform/eff <compute_temp_deform_eff>`
* :doc:`temp/drude <compute_temp_drude>`
* :doc:`temp/eff <compute_temp_eff>`

2
doc/src/Commands_fix.rst
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@ -148,7 +148,7 @@ OPT.
* :doc:`nvt/body <fix_nvt_body>`
* :doc:`nvt/eff <fix_nh_eff>`
* :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* :doc:`nvt/sllod (io) <fix_nvt_sllod>`
* :doc:`nvt/sllod (iko) <fix_nvt_sllod>`
* :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
* :doc:`nvt/sphere (o) <fix_nvt_sphere>`
* :doc:`nvt/uef <fix_nh_uef>`

1
doc/src/Commands_kspace.rst
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@ -24,6 +24,7 @@ OPT.
* :doc:`ewald (o) <kspace_style>`
* :doc:`ewald/disp <kspace_style>`
* :doc:`ewald/disp/dipole <kspace_style>`
* :doc:`ewald/dipole <kspace_style>`
* :doc:`ewald/dipole/spin <kspace_style>`
* :doc:`msm (o) <kspace_style>`

3
doc/src/angle_cosine_shift.rst
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@ -53,7 +53,8 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package.
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""

2
doc/src/angle_cosine_shift_exp.rst
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@ -64,7 +64,7 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/angle_fourier.rst
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@ -50,7 +50,7 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/angle_fourier_simple.rst
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@ -49,7 +49,7 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/angle_gaussian.rst
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@ -49,7 +49,7 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/angle_quartic.rst
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@ -57,7 +57,7 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/bond_gaussian.rst
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@ -50,7 +50,7 @@ Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/bond_harmonic_shift.rst
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@ -56,7 +56,7 @@ Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

2
doc/src/bond_harmonic_shift_cut.rst
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@ -54,7 +54,7 @@ Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

3
doc/src/compute_temp_deform.rst
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@ -1,8 +1,11 @@
.. index:: compute temp/deform
.. index:: compute temp/deform/kk
compute temp/deform command
===========================
Accelerator Variants: *temp/deform/kk*
Syntax
""""""

4
doc/src/dihedral_fourier.rst
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@ -54,8 +54,8 @@ or :doc:`read_restart <read_restart>` commands:
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
This dihedral 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.
Related commands

4
doc/src/dihedral_nharmonic.rst
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@ -50,8 +50,8 @@ or :doc:`read_restart <read_restart>` commands:
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
This dihedral 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.
Related commands

4
doc/src/dihedral_quadratic.rst
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@ -55,8 +55,8 @@ radian\^2.
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
This dihedral 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.
Related commands

2
doc/src/dihedral_spherical.rst
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@ -89,7 +89,7 @@ Restrictions
""""""""""""
This dihedral style can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands

7
doc/src/dihedral_table.rst
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@ -244,9 +244,10 @@ script after reading the restart file.
Restrictions
""""""""""""
These dihedral styles can only be used if LAMMPS was built with the
MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
The *table* dihedral style can only be used if LAMMPS was built with the
MOLECULE package. The *table/cut* dihedral 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.
Related commands
""""""""""""""""

6
doc/src/fix_bond_swap.rst
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@ -65,7 +65,7 @@ The second use case is a collection of polymer chains with some
fraction of their sites identified as "sticker" sites. Initially each
polymer chain is isolated from the others in a topological sense, and
there is an intra-chain bond between every pair of sticker sites on
the same chain. Over time, bonds swap so that inter-moleculer sticker
the same chain. Over time, bonds swap so that inter-molecular sticker
bonds are created. This models a vitrification-style process whereby
the polymer chains all become interconnected. For this use case, if
angles are defined they should not include bonds between sticker
@ -97,7 +97,7 @@ means that bond pairs which straddle processor boundaries are not
eligible for swapping on this step.
(3) The distances between 4 pairs of atoms -- (A1,A2), (B1,B2),
(A1,B2), (B1,A2) -- must all be less thann the specified *cutoff*\ .
(A1,B2), (B1,A2) -- must all be less than the specified *cutoff*\ .
(4) The molecule IDs of A1 and B1 must be the same (see below).
@ -116,7 +116,7 @@ Boltzmann constant, and T is the current temperature of the system.
IMPORTANT: Whether the swap is accepted or rejected, no other swaps
are attempted by this processor on this timestep. No other
eliglble 4-tuples of atoms are considered. This means that each
eligible 4-tuples of atoms are considered. This means that each
processor will perform either a single swap or none on timesteps
this fix is invoked.

3
doc/src/fix_nvt_sllod.rst
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@ -1,11 +1,12 @@
.. index:: fix nvt/sllod
.. index:: fix nvt/sllod/intel
.. index:: fix nvt/sllod/omp
.. index:: fix nvt/sllod/kk
fix nvt/sllod command
=====================
Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp*
Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp*, *nvt/sllod/kk*
Syntax
""""""

10
doc/src/kspace_style.rst
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@ -2,6 +2,7 @@
.. index:: kspace_style ewald/dipole
.. index:: kspace_style ewald/dipole/spin
.. index:: kspace_style ewald/disp
.. index:: kspace_style ewald/disp/dipole
.. index:: kspace_style ewald/omp
.. index:: kspace_style pppm
.. index:: kspace_style pppm/kk
@ -39,7 +40,7 @@ Syntax
kspace_style style value
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos*
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos*
.. parsed-literal::
@ -52,6 +53,8 @@ Syntax
accuracy = desired relative error in forces
*ewald/disp* value = accuracy
accuracy = desired relative error in forces
*ewald/disp/dipole* value = accuracy
accuracy = desired relative error in forces
*ewald/omp* value = accuracy
accuracy = desired relative error in forces
*pppm* value = accuracy
@ -156,6 +159,8 @@ matching keyword to the name of the KSpace style, as in this table:
+----------------------+-----------------------+
| tip4p/long | tip4p |
+----------------------+-----------------------+
| dipole/long | dipole |
+----------------------+-----------------------+
----------
@ -168,7 +173,8 @@ The *ewald/disp* style adds a long-range dispersion sum option for
but in a more efficient manner than the *ewald* style. The :math:`1/r^6`
capability means that Lennard-Jones or Buckingham potentials can be
used without a cutoff, i.e. they become full long-range potentials.
The *ewald/disp* style can also be used with point-dipoles, see
The *ewald/disp/dipole* style can also be used with point-dipoles, see
:ref:`(Toukmaji) <Toukmaji>`.
The *ewald/dipole* style adds long-range standard Ewald summations