Merge branch 'master' of https://github.com/lammps/lammps into kk_update_3.4.0

doc/src/Commands_pair.rst

@@ -87,6 +87,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (gio) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/ext <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (go) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`

doc/src/Developer_utils.rst

@@ -9,8 +9,8 @@ reading or writing to files with error checking or translation of
 strings into specific types of numbers with checking for validity.  This
 reduces redundant implementations and encourages consistent behavior.
 
-I/O with status check
-^^^^^^^^^^^^^^^^^^^^^
+I/O with status check and similar functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The the first two functions are wrappers around the corresponding C
 library calls ``fgets()`` or ``fread()``.  They will check if there
@@ -19,6 +19,14 @@ In that case, the functions will stop with an error message, indicating
 the name of the problematic file, if possible unless the *error* argument
 is a NULL pointer.
 
+The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
+but it will read in a whole line (i.e. until the end of line or end
+of file), but store only as many characters as will fit into the buffer
+including a final newline character and the terminating NULL byte.
+If the line in the file is longer it will thus be truncated in the buffer.
+This function is used by :cpp:func:`read_lines_from_file` to read individual
+lines but make certain they follow the size constraints.
+
 The :cpp:func:`read_lines_from_file` function will read the requested
 number of lines of a maximum length into a buffer and will return 0
 if successful or 1 if not. It also guarantees that all lines are
@@ -33,6 +41,9 @@ NULL character.
 .. doxygenfunction:: sfread
    :project: progguide
 
+.. doxygenfunction:: fgets_trunc
+   :project: progguide
+
 .. doxygenfunction:: read_lines_from_file
    :project: progguide
 
@@ -174,7 +185,10 @@ Argument processing
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
+   :project: progguide
+
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
 .. doxygenfunction:: getsyserror

doc/src/Howto_drude2.rst

@@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
 have to be modified to include the Drude dipoles and how to handle
 them.
 
+Example input scripts available: examples/USER/drude
+
 ----------
 
 **Overview of Drude induced dipoles**

doc/src/Library_config.rst

@@ -15,6 +15,8 @@ This section documents the following functions:
 - :cpp:func:`lammps_config_package_count`
 - :cpp:func:`lammps_config_package_name`
 - :cpp:func:`lammps_config_accelerator`
+- :cpp:func:`lammps_has_gpu_device`
+- :cpp:func:`lammps_gpu_device_info`
 - :cpp:func:`lammps_has_style`
 - :cpp:func:`lammps_style_count`
 - :cpp:func:`lammps_style_name`
@@ -132,6 +134,16 @@ approach.
 
 -----------------------
 
+.. doxygenfunction:: lammps_has_gpu_device
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_get_gpu_device_info
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_has_style
    :project: progguide
 

doc/src/Tools.rst

@@ -94,6 +94,7 @@ Miscellaneous tools
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
+   * :ref:`Offline build tool <offline>`
    * :ref:`singularity <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
@@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
 
 ----------
 
+.. _offline:
+
+Scripts for building LAMMPS when offline
+----------------------------------------
+
+In some situations it might be necessary to build LAMMPS on a system
+without direct internet access. The scripts in ``tools/offline`` folder
+allow you to pre-load external dependencies for both the documentation
+build and for building LAMMPS with CMake.
+
+It does so by
+
+ #. downloading necessary ``pip`` packages,
+ #. cloning ``git`` repositories
+ #. downloading tarballs
+
+to a designated cache folder.
+
+As of April 2021, all of these downloads make up around 600MB. By
+default, the offline scripts will download everything into the
+``$HOME/.cache/lammps`` folder, but this can be changed by setting the
+``LAMMPS_CACHING_DIR`` environment variable.
+
+Once the caches have been initialized, they can be used for building the
+LAMMPS documentation or compiling LAMMPS using CMake on an offline
+system.
+
+The ``use_caches.sh`` script must be sourced into the current shell
+to initialize the offline build environment. Note that it must use
+the same ``LAMMPS_CACHING_DIR``. This script does the following:
+
+ #. Set up environment variables that modify the behavior of both,
+    ``pip`` and ``git``
+ #. Start a simple local HTTP server using Python to host files for CMake
+
+Afterwards, it will print out instruction on how to modify the CMake
+command line to make sure it uses the local HTTP server.
+
+To undo the environment changes and shutdown the local HTTP server,
+run the ``deactivate_caches`` command.
+
+Examples
+^^^^^^^^
+
+For all of the examples below, you first need to create the cache, which
+requires an internet connection.
+
+.. code-block:: bash
+
+   ./tools/offline/init_caches.sh
+
+Afterwards, you can disconnect or copy the contents of the
+``LAMMPS_CACHING_DIR`` folder to an offline system.
+
+Documentation Build
+^^^^^^^^^^^^^^^^^^^
+
+The documentation build will create a new virtual environment that
+typically first installs dependencies from ``pip``. With the offline
+environment loaded, these installations will instead grab the necessary
+packages from your local cache.
+
+.. code-block:: bash
+
+   # if LAMMPS_CACHING_DIR is different from default, make sure to set it first
+   # export LAMMPS_CACHING_DIR=path/to/folder
+   source tools/offline/use_caches.sh
+   cd doc/
+   make html
+
+   deactivate_caches
+
+CMake Build
+^^^^^^^^^^^
+
+When compiling certain packages with external dependencies, the CMake
+build system will download necessary files or sources from the web. For
+more flexibility the CMake configuration allows users to specify the URL
+of each of these dependencies.  What the ``init_caches.sh`` script does
+is create a CMake "preset" file, which sets the URLs for all of the known
+dependencies and redirects the download to the local cache.
+
+.. code-block:: bash
+
+   # if LAMMPS_CACHING_DIR is different from default, make sure to set it first
+   # export LAMMPS_CACHING_DIR=path/to/folder
+   source tools/offline/use_caches.sh
+
+   mkdir build
+   cd build
+   cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
+   make -j 8
+
+   deactivate_caches
+
+----------
+
 .. _phonon:
 
 phonon tool

doc/src/compute_fep.rst

@@ -48,6 +48,8 @@ Examples
    compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
    compute 1 all fep 300 atom charge 2 v_delta
 
+Example input scripts available: examples/USER/fep
+
 Description
 """""""""""
 

doc/src/compute_temp_drude.rst

@@ -20,6 +20,8 @@ Examples
 
    compute TDRUDE all temp/drude
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/fix_adapt_fep.rst

@@ -56,6 +56,9 @@ Examples
    fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
    fix 1 all adapt/fep 10 atom diameter 1 v_size
 
+
+Example input scripts available: examples/USER/fep
+
 Description
 """""""""""
 

doc/src/fix_drude.rst

@@ -22,6 +22,8 @@ Examples
    fix 1 all drude 1 1 0 1 0 2 2 2
    fix 1 all drude C C N C N D D D
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/fix_drude_transform.rst

@@ -25,6 +25,8 @@ Examples
    fix 3 all drude/transform/direct
    fix 1 all drude/transform/inverse
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/fix_langevin_drude.rst

@@ -35,6 +35,8 @@ Examples
    fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
    fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/fix_tgnh_drude.rst

@@ -62,6 +62,8 @@ Examples
    fix 2 jello tgnpt/drude temp 300.0 300.0 100.0 1.0 20.0 tri 5.0 5.0 1000.0
    fix 2 ice tgnpt/drude temp 250.0 250.0 100.0 1.0 20.0 x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/pair_coul_tt.rst

@@ -29,6 +29,7 @@ Examples
    pair_coeff 1 2  coul/tt 4.0 1.0 4 12.0
    pair_coeff 1 3* coul/tt 4.5 1.0 4
 
+Example input scripts available: examples/USER/drude
 
 Description
 """""""""""

doc/src/pair_dpd_ext.rst

@@ -0,0 +1,138 @@
+.. index:: pair_style dpd/ext
+.. index:: pair_style dpd/ext/tstat
+
+pair_style dpd/ext command
+==========================
+
+pair_style dpd/ext/tstat command
+================================
+
+Syntax
+""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style dpd/ext T cutoff seed
+   pair_style dpd/ext/tstat Tstart Tstop cutoff seed
+
+* T = temperature (temperature units)
+* Tstart,Tstop = desired temperature at start/end of run (temperature units)
+* cutoff = global cutoff for DPD interactions (distance units)
+* seed = random # seed (positive integer)
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   pair_style dpd/ext 1.0 2.5 34387
+   pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2
+   pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2
+
+   pair_style dpd/ext/tstat 1.0 1.0 2.5 34387
+   pair_coeff 1 1 4.5 4.5 0.5 0.5 1.2
+   pair_coeff 1 2 4.5 4.5 0.5 0.5 1.2
+
+Description
+"""""""""""
+
+The style *dpd/ext* computes an extended force field for dissipative particle dynamics (DPD) following the exposition in :ref:`(Groot) <Groot>`, :ref:`(Junghans) <Junghans>`.
+
+Style *dpd/ext/tstat* invokes an extended DPD thermostat on pairwise interactions, equivalent to the non-conservative portion of the extended DPD force field. To use *dpd/ext/tstat* as a thermostat for another pair style, use the :doc:`pair_style hybrid/overlay <pair_hybrid>` command to compute both the desired pair interaction and the thermostat for each pair of particles.
+
+For the style *dpd/ext*\ , the force on atom I due to atom J is given as a sum
+of 3 terms
+
+.. math::
+
+   \mathbf{f}  = & f^C + f^D + f^R \qquad \qquad r < r_c \\
+   f^C      = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\
+   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\
+   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
+   w(r)     = & 1 - r/r_c \\
+
+where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D` is a dissipative force, and :math:`\mathbf{f}^R` is a random force. :math:`A_{ij}` is the maximum repulsion between the two atoms, :math:`\hat{\mathbf{r}}_{ij}` is a unit vector in the direction :math:`\mathbf{r}_i - \mathbf{r}_j`, :math:`\mathbf{v}_{ij} = \mathbf{v}_i - \mathbf{v}_j` is the vector difference in velocities of the two atoms, :math:`\alpha` and :math:`\mathbf{\xi}_{ij}` are Gaussian random numbers with zero mean and unit variance, :math:`\Delta t` is the timestep, :math:`w (r) = 1 - r / r_c` is a weight function for the conservative interactions that varies between 0 and 1, :math:`r_c` is the corresponding cutoff, :math:`w_{\alpha} ( r ) = ( 1 - r / \bar{r}_c )^{s_{\alpha}}`, :math:`\alpha \equiv ( \parallel, \perp )`, are weight functions with coefficients :math:`s_\alpha` that vary between 0 and 1, :math:`\bar{r}_c` is the corresponding cutoff, :math:`\mathbf{I}` is the unit matrix, :math:`\sigma_{\alpha} = \sqrt{2 k T \gamma_{\alpha}}`, where :math:`k` is the Boltzmann constant and :math:`T` is the temperature in the pair\_style command.
+
+For the style *dpd/ext/tstat*\ , the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
+
+For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
+
+For the style *dpd/ext/tstat*, the force on atom I due to atom J is the same as the above equation, except that the conservative :math:`\mathbf{f}^C` term is dropped. Also, during the run, T is set each timestep to a ramped value from Tstart to Tstop.
+
+For the style *dpd/ext*\ , the pairwise energy associated with style *dpd/ext* is only due to the conservative force term :math:`\mathbf{f}^C`, and is shifted to be zero at the cutoff distance :math:`r_c`. The pairwise virial is calculated using all three terms. There is no pairwise energy for style *dpd/ext/tstat*, but the last two terms of the formula contribute the virial.
+
+For the style *dpd/ext*, the following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in the examples above:
+
+* A (force units)
+* :math:`\gamma_{\perp}` (force/velocity units)
+* :math:`\gamma_{\parallel}` (force/velocity units)
+* :math:`s_{\perp}` (unitless)
+* :math:`s_{\parallel}` (unitless)
+* :math:`r_c` (distance units)
+
+The last coefficient is optional. If not specified, the global DPD cutoff is used. Note that :math:`\sigma`'s are set equal to :math:`\sqrt{2 k T \gamma}`, where :math:`T` is the temperature set by the :doc:`pair_style <pair_style>` command so it does not need to be specified.
+
+
+For the style *dpd/ext/tstat*, the coefficients defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command is the same, except that A is not included.
+
+.. note::
+
+ If you are modeling DPD polymer chains, you may want to use the :doc:`pair_style srp <pair_srp>` command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other.
+
+.. note::
+
+ The virial calculation for pressure when using this pair style includes all the components of force listed above, including the random force.
+
+----------
+
+
+**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
+
+The style *dpd/ext* does not support mixing. Thus, coefficients for all I,J pairs must be specified explicitly.
+
+The pair styles do not support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction. Note that as discussed above, the energy due to the conservative :math:`\mathbf{f}^C` term is already shifted to be zero at the cutoff distance :math:`r_c`.
+
+The :doc:`pair_modify <pair_modify>` table option is not relevant for the style *dpd/ext*.
+
+The style *dpd/ext* does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
+
+The pair styles can only be used via the pair keyword of the :doc:`run_style respa <run_style>` command. They do not support the *inner*\ , *middle*\ , and *outer*\  keywords.
+
+The style *dpd/ext/tstat* can ramp its target temperature over multiple runs, using the start and stop keywords of the :doc:`run <run>` command. See the :doc:`run <run>` command for details of how to do this.
+
+----------
+
+
+Restrictions
+""""""""""""
+
+The default frequency for rebuilding neighbor lists is every 10 steps (see the :doc:`neigh_modify <neigh_modify>` command). This may be too infrequent for style *dpd/ext* simulations since particles move rapidly and can overlap by large amounts. If this setting yields a non-zero number of \say{dangerous} reneighborings (printed at the end of a simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change.
+
+The pair styles require to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost atoms.
+
+The pair styles will not restart exactly when using the :doc:`read_restart <read_restart>` command, though they should provide statistically similar results. This is because the forces they compute depend on atom velocities. See the :doc:`read_restart <read_restart>` command for more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`pair_style srp <pair_srp>`
+
+**Default:** none
+
+
+----------
+
+
+.. _Groot:
+
+
+
+**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+
+.. _Junghans:
+
+
+
+**(Junghans)** Junghans, Praprotnik and Kremer, Soft Matter 4, 156, 1119-1128 (2008).

doc/src/pair_fep_soft.rst

@@ -182,6 +182,8 @@ Examples
    pair_coeff * * 100.0 2.0 1.5 1.0
    pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
 
+Example input scripts available: examples/USER/fep
+
 Description
 """""""""""
 

doc/src/pair_hybrid.rst

@@ -257,7 +257,7 @@ then overrides them with 0.0 only for CHARMM:
 .. code-block:: LAMMPS
 
    special_bonds amber
-   pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+   pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
    pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
 
 The this input achieves the same effect:
@@ -265,7 +265,7 @@ The this input achieves the same effect:
 .. code-block:: LAMMPS
 
    special_bonds 0.0 0.0 0.1
-   pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+   pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
    pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
    pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
    pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
@@ -279,7 +279,7 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
 .. code-block:: LAMMPS
 
    special_bonds lj/coul 1e-20 1e-20 0.5
-   pair_hybrid tersoff lj/cut/coul/long 12.0
+   pair_style hybrid tersoff lj/cut/coul/long 12.0
    pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
 
 For use with the various :doc:`compute \*/tally <compute_tally>`
@@ -417,7 +417,11 @@ assigned automatically to the sub-style defined for both I,I and J,J and
 its coefficients generated by the mixing rule used by that sub-style.
 For the *hybrid/overlay* and *hybrid/scaled* style, there is an
 additional requirement that both the I,I and J,J pairs are assigned to a
-single sub-style.  See the :doc:`pair_modify <pair_modify>` command for
+single sub-style.  If this requirement is not met, no I,J coeffs will be
+generated, even if the sub-styles support mixing, and I,J pair
+coefficients must be explicitly defined.
+
+See the :doc:`pair_modify <pair_modify>` command for
 details of mixing rules.  See the See the doc page for the sub-style to
 see if allows for mixing.
 

doc/src/pair_style.rst

@@ -150,6 +150,8 @@ accelerated styles exist.
 * :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
 * :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
 * :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
+* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
+* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting  with generalized force field
 * :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
 * :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
 * :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting

doc/src/pair_thole.rst

@@ -42,6 +42,8 @@ Examples
 
    pair_style lj/cut/thole/long 2.6 12.0
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/read_data.rst

@@ -223,6 +223,9 @@ The structure of the data file is important, though many settings and
 sections are optional or can come in any order.  See the examples
 directory for sample data files for different problems.
 
+The file will be read line by line, but there is a limit of 254
+characters per line and characters beyond that limit will be ignored.
+
 A data file has a header and a body.  The header appears first.  The
 first line of the header is always skipped; it typically contains a
 description of the file.  Then lines are read one at a time.  Lines

doc/src/thermo_modify.rst

@@ -11,12 +11,13 @@ Syntax
    thermo_modify keyword value ...
 
 * one or more keyword/value pairs may be listed
-* keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*
+* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press*
 
   .. parsed-literal::
 
        *lost* value = *error* or *warn* or *ignore*
        *lost/bond* value = *error* or *warn* or *ignore*
+       *warn* value = *ignore* or *reset* or *default* or a number
        *norm* value = *yes* or *no*
        *flush* value = *yes* or *no*
        *line* value = *one* or *multi*
@@ -75,6 +76,43 @@ are drifting out of the box through a fixed boundary condition (see
 the :doc:`boundary <boundary>` command).  In this case one atom may be
 deleted before the rest of the molecule is, on a later timestep.
 
+The *warn* keyword allows you to control whether LAMMPS will print
+warning messages and how many of them.  Most warning messages are only
+printed by MPI rank 0.  They are usually pointing out important issues
+that should be investigated, but LAMMPS cannot determine for
+certain whether they are an indication of an error.
+
+Some warning messages are printed during a run (or immediately before)
+each time a specific MPI rank encounters the issue, e.g. bonds that are
+stretched too far or dihedrals in extreme configurations. These number
+of these can quickly blow up the size of the log file and screen output.
+Thus a limit of 100 warning messages is applied by default.  The warning
+count is applied to the entire input unless reset with a ``thermo_modify
+warn reset`` command.  If there are more warnings than the limit, LAMMPS
+will print one final warning that it will not print any additional
+warning messages.
+
+.. note::
+
+   The warning limit is enforced on either the per-processor count or
+   the total count across all processors. For efficiency reasons,
+   however, the total count is only updated at steps with thermodynamic
+   output. Thus when running on a large number of processors in
+   parallel, the total number of warnings printed can be significantly
+   larger than the given limit.
+
+Any number after the keyword *warn* will change the warning limit
+accordingly.  With the value *ignore* all warnings will be suppressed,
+with the value *always* no limit will be applied and warnings will
+always be printed, with the value *reset* the internal warning counter
+will be reset to zero, and with the value *default*, the counter is
+reset and the limit set to 100.  An example usage of either *reset* or
+*default* would be to re-enable warnings that were disabled or have
+reached the limit during equilibration, where the warnings would be
+acceptable while the system is still adjusting, but then change
+to all warnings for the production run, where they would indicate
+problems that would require a closer look at what is causing them.
+
 The *norm* keyword determines whether various thermodynamic output
 values are normalized by the number of atoms or not, depending on
 whether it is set to *yes* or *no*\ .  Different unit styles have
@@ -183,9 +221,9 @@ Related commands
 Default
 """""""
 
-The option defaults are lost = error, norm = yes for unit style of
-*lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no,
-and temp/press = compute IDs defined by thermo_style.
+The option defaults are lost = error, warn = 100, norm = yes for unit
+style of *lj*\ , norm = no for unit style of *real* and *metal*\ ,
+flush = no, and temp/press = compute IDs defined by thermo_style.
 
 The defaults for the line and format options depend on the thermo
 style.  For styles "one" and "custom", the line and format defaults

doc/src/variable.rst

@@ -363,12 +363,14 @@ variable, as discussed below.
 
 The rules for formatting the file are as follows.  Each time a set of
 per-atom values is read, a non-blank line is searched for in the file.
-A comment character "#" can be used anywhere on a line; text starting
-with the comment character is stripped.  Blank lines are skipped.  The
-first "word" of a non-blank line, delimited by white-space, is read as
-the count N of per-atom lines to immediately follow.  N can be the
-total number of atoms in the system, or only a subset.  The next N
-lines have the following format
+The file is read line by line but only up to 254 characters are used.
+The rest are ignored.  A comment character "#" can be used anywhere
+on a line and all text following and the "#" character are ignored;
+text starting with the comment character is stripped.  Blank lines
+are skipped.  The first "word" of a non-blank line, delimited by
+white-space, is read as the count N of per-atom lines to immediately
+follow.  N can be the total number of atoms in the system, or only a
+subset.  The next N lines have the following format
 
 .. parsed-literal::
 

doc/utils/requirements.txt

@@ -4,3 +4,4 @@ git+git://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx_tabs
 breathe
 Pygments
+six

doc/utils/sphinx-config/false_positives.txt

@@ -1024,6 +1024,7 @@ fmag
 fmass
 fmm
 fmt
+fmtlib
 fmx
 fmy
 fmz
@@ -2542,6 +2543,7 @@ ppn
 pppm
 prd
 Prakash
+Praprotnik
 pre
 Pre
 prec