Merge branch 'develop' into colvars-update

doc/src/Build_development.rst

@@ -153,7 +153,12 @@ development headers to compile (if those are not found locally a recent
 version of that library will be downloaded and compiled along with
 LAMMPS and the test programs) and will download and compile a specific
 version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
-test framework that is used to implement the tests.
+test framework that is used to implement the tests.  Those unit tests
+may be combined with memory access and leak checking with valgrind
+(see below for how to enable it).  In that case, running so-called
+death tests will create a lot of false positives and thus they can be
+disabled by configuring compilation with the additional setting
+``-D SKIP_DEATH_TESTS=on``.
 
 .. admonition:: Software version and LAMMPS configuration requirements
    :class: note

doc/src/Howto_lammps_gui.rst

@@ -98,10 +98,26 @@ get access to the other included executables.
 Linux on x86\_64
 ^^^^^^^^^^^^^^^^
 
-After downloading and unpacking the
+For Linux with x86\_64 CPU there are currently two variants. The first
+is compiled on Ubuntu 20.04LTS, is using some wrapper scripts, and
+should be compatible with more recent Linux distributions.  After
+downloading and unpacking the
 ``LAMMPS-Linux-x86_64-GUI-<version>.tar.gz`` package.  You can switch
 into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
 
+The second variant uses `flatpak <https://www.flatpak.org>`_ and
+requires the flatpak management and runtime software to be installed.
+After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``
+flatpak bundle, you can install it with ``flatpak install --user
+LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``.  After installation,
+LAMMPS-GUI should be integrated into your desktop environment under
+"Applications > Science" but also can be launched from the console with
+``flatpak run org.lammps.lammps-gui``.  The flatpak bundle also includes
+the console LAMMPS executable ``lmp`` which can be launched to run
+simulations with, for example: ``flatpak run --command=lmp
+org.lammps.lammps-gui -in in.melt``.
+
+
 Compiling from Source
 ^^^^^^^^^^^^^^^^^^^^^
 
@@ -400,10 +416,16 @@ Otherwise the default sequence of colors of the :doc:`dump image
 <dump_image>` command is assigned to the different atom types and the
 diameters are all the same.
 
-.. image:: JPG/lammps-gui-image.png
+.. figure:: JPG/lammps-gui-image.png
    :align: center
    :scale: 50%
 
+   Visualization of LAMMPS "peptide" example
+
+.. versionchanged:: 1.6
+
+   Buttons for toggling shininess and re-centering were added.
+
 The default image size, some default image quality settings, the view
 style and some colors can be changed in the ``Preferences`` dialog
 window.  From the image viewer window further adjustments can be made:
@@ -442,6 +464,12 @@ Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
 dialog will pop up asking whether to cancel the exit operation, or to
 save or not save the buffer contents to a file.
 
+.. versionadded:: 1.6
+
+The editor has an auto-save mode that can be enabled or disabled in the
+``Preferences`` dialog.  In auto-save mode, the editor buffer is
+automatically saved before running LAMMPS or before exiting LAMMPS-GUI.
+
 Context Specific Word Completion
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -471,11 +499,12 @@ Line Reformatting
 The editor supports reformatting lines according to the syntax in order
 to have consistently aligned lines.  This primarily means adding
 whitespace padding to commands, type specifiers, IDs and names.  This
-reformatting is performed by default when hitting the 'Enter' key to
+reformatting is performed manually by hitting the 'Tab' key.  It is
-start a new line.  This feature can be turned on or off in the
+also possible to have this done automatically when hitting the 'Enter'
-``Preferences`` dialog, but it can still be manually performed by
+key to start a new line.  This feature can be turned on or off in the
-hitting the 'TAB' key.  The amount of padding can be adjusted in the
+``Preferences`` dialog for ``Editor Settings`` with the
-``Preferences`` dialog for the *Editor*.
+"Reformat with 'Enter'" checkbox. The amount of padding for multiple
+categories can be adjusted in the same dialog.
 
 Internally this functionality is achieved by splitting the line into
 "words" and then putting it back together with padding added where the
@@ -696,13 +725,15 @@ General Settings:
   log) of the application can be set.
 - *Select Text Font:* Opens a font selection dialog where the type and
   size for the text editor and log font of the application can be set.
-- *GUI update interval:* Allows to set the time interval between GUI
+- *GUI update interval:* Allows to set the time interval between GUI and
-  and data updates during a LAMMPS run in milliseconds. The default is
+  data updates during a LAMMPS run in milliseconds. The default is to
-  to update the GUI every 10 milliseconds. This is good for most cases.
+  update the GUI every 10 milliseconds. This is good for many cases.
-  For LAMMPS runs that run *very* fast, however, data may be missed and
+  Set this to 100 milliseconds or more if LAMMPS-GUI consumes too many
-  through lowering this interval, this can be corrected. However, this
+  resources during a run.  For LAMMPS runs that run *very* fast (for
-  will make the GUI use more resources, which may be a problem on some
+  example in tutorial examples), however, data may be missed and through
-  computers with slower CPUs and a small number of CPU cores. This
+  lowering this interval, this can be corrected.  However, this will
+  make the GUI use more resources, which may be a problem on some
+  computers with slower CPUs and a small number of CPU cores.  This
   setting may be changed to a value between 1 and 1000 milliseconds.
 
 Accelerators:
@@ -719,18 +750,23 @@ Snapshot Image:
 ^^^^^^^^^^^^^^^
 
 This tab allows setting defaults for the snapshot images displayed in
-the ``Image Viewer`` window, such as its dimensions and the zoom
+the ``Image Viewer`` window, such as its dimensions and the zoom factor
-factor applied.  The *Antialias* switch will render images with twice
+applied.  The *Antialias* switch will render images with twice the
-the number of pixels for width and height and then smoothly scale the
+number of pixels for width and height and then smoothly scale the image
-image back to the requested size.  This produces higher quality images
+back to the requested size.  This produces higher quality images with
-with smoother edges at the expense of requiring more CPU time to
+smoother edges at the expense of requiring more CPU time to render the
-render the image.  The *HQ Image mode* option turns on screen space
+image.  The *HQ Image mode* option turns on screen space ambient
-ambient occlusion (SSAO) mode when rendering images.  This is also
+occlusion (SSAO) mode when rendering images.  This is also more time
-more time consuming, but produces a more 'spatial' representation of
+consuming, but produces a more 'spatial' representation of the system
-the system shading of atoms by their depth.  The *VDW Style* checkbox
+shading of atoms by their depth.  The *Shiny Image mode* option will
-selects whether atoms are represented by space filling spheres when
+render objects with a shiny surface when enabled.  Otherwise the
-checked or by smaller spheres and sticks.  Finally there are a couple
+surfaces will be matted.  The *Show Box* option selects whether the
-of drop down lists to select the background and box colors.
+system box is drawn as a colored set of sticks.  Similarly, the *Show
+Axes* option selects whether a representation of the three system axes
+will be drawn as colored sticks. The *VDW Style* checkbox selects
+whether atoms are represented by space filling spheres when checked or
+by smaller spheres and sticks.  Finally there are a couple of drop down
+lists to select the background and box colors.
 
 Editor Settings:
 ^^^^^^^^^^^^^^^^
@@ -741,9 +777,11 @@ ranges, IDs (e.g. for fixes), and names (e.g. for groups).  The value
 set is the minimum width for the text element and it can be chosen in
 the range between 1 and 32.
 
-The two settings which follow enable or disable the automatic
+The three settings which follow enable or disable the automatic
-reformatting when hitting the 'Enter' key and the automatic display of
+reformatting when hitting the 'Enter' key, the automatic display of
-the completion pop-up window.
+the completion pop-up window, and whether auto-save mode is enabled.
+In auto-save mode the editor buffer is saved before a run or before
+exiting LAMMPS-GUI.
 
 -----------
 

doc/src/Tools.rst

@@ -92,7 +92,7 @@ Miscellaneous tools
    * :ref:`emacs <emacs>`
    * :ref:`i-PI <ipi>`
    * :ref:`kate <kate>`
-   * :ref:`LAMMPS GUI <lammps_gui>`
+   * :ref:`LAMMPS-GUI <lammps_gui>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`Offline build tool <offline>`
    * :ref:`singularity/apptainer <singularity_tool>`
@@ -524,6 +524,7 @@ The LAMMPS-GUI has been successfully compiled and tested on:
 - Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
+- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.40, Qt version 6.7
 - Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
 
 .. _lammps_gui_install:
@@ -532,14 +533,28 @@ The LAMMPS-GUI has been successfully compiled and tested on:
 Pre-compiled executables
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pre-compiled LAMMPS executable packages that include the GUI are currently
+Pre-compiled LAMMPS executable packages that include the GUI are
-available from https://download.lammps.org/static or
+currently available from https://download.lammps.org/static or
-https://github.com/lammps/lammps/releases.  You can unpack the archives
+https://github.com/lammps/lammps/releases.  For Windows, you need to
-(or mount the macOS disk image) and run the GUI directly in place. The
+download and then run the application installer.  For macOS you download
-folder may also be moved around and added to the ``PATH`` environment
+and mount the disk image and then drag the application bundle to the
-variable so the executables will be found automatically.  The LAMMPS-GUI
+Applications folder.  For Linux (x86_64) you currently have two
-executable is called ``lammps-gui`` and either takes no arguments or
+options: 1) you can download the tar.gz archive, unpack it and run the
-attempts to load the first argument as LAMMPS input file.
+GUI directly in place.  The ``LAMMPS_GUI`` folder may also be moved
+around and added to the ``PATH`` environment variable so the executables
+will be found automatically.  2) you can download the `Flatpak file
+<https://www.flatpak.org/>`_ and then install it locally with the
+*flatpak* command: ``flatpak install --user
+LAMMPS-Linux-x86_64-GUI-<version>.flatpak`` and run it with ``flatpak
+run org.lammps.lammps-gui``.  The flatpak bundle also includes the
+command line version of LAMMPS and some LAMMPS tools like msi2lmp.  The
+can be launched by using the ``--command`` flag. For example to run
+LAMMPS directly on the ``in.lj`` benchmark input you would type in the
+``bench`` folder: ``flatpak run --command=lmp -in in.lj`` The flatpak
+version should also appear in the applications menu of standard desktop
+environments.  The LAMMPS-GUI executable is called ``lammps-gui`` and
+either takes no arguments or attempts to load the first argument as
+LAMMPS input file.
 
 .. _lammps_gui_compilation:
 
@@ -1107,13 +1122,13 @@ necessary development headers and libraries are present.
 
 .. code-block:: bash
 
-   -D WITH_SWIG=on         # to enable building any SWIG wrapper
+   -D WITH_SWIG=on          # to enable building any SWIG wrapper
-   -D BUILD_SWIG_JAVA=on   # to enable building the Java wrapper
+   -D BUILD_SWIG_JAVA=on    # to enable building the Java wrapper
-   -D BUILD_SWIG_LUA=on    # to enable building the Lua wrapper
+   -D BUILD_SWIG_LUA=on     # to enable building the Lua wrapper
-   -D BUILD_SWIG_PERL5=on  # to enable building the Perl 5.x wrapper
+   -D BUILD_SWIG_PERL5=on   # to enable building the Perl 5.x wrapper
-   -D BUILD_SWIG_PYTHON=on # to enable building the Python wrapper
+   -D BUILD_SWIG_PYTHON=on  # to enable building the Python wrapper
-   -D BUILD_SWIG_RUBY=on   # to enable building the Ruby wrapper
+   -D BUILD_SWIG_RUBY=on    # to enable building the Ruby wrapper
-   -D BUILD_SWIG_TCL=on    # to enable building the Tcl wrapper
+   -D BUILD_SWIG_TCL=on     # to enable building the Tcl wrapper
 
 
 Manual building allows a little more flexibility. E.g. one can choose

doc/src/dump_image.rst

@@ -111,10 +111,10 @@ Syntax
   .. parsed-literal::
 
        *acolor* args = type color
-         type = atom type or range of types (see below)
+         type = atom type (numeric or type label) or range of numeric types (see below)
          color = name of color or color1/color2/...
        *adiam* args = type diam
-         type = atom type or range of types (see below)
+         type = atom type (numeric or type label) or range of numeric types (see below)
          diam = diameter of atoms of that type (distance units)
        *amap* args = lo hi style delta N entry1 entry2 ... entryN
          lo = number or *min* = lower bound of range of color map
@@ -139,10 +139,10 @@ Syntax
        *backcolor* arg = color
          color = name of color for background
        *bcolor* args = type color
-         type = bond type or range of types (see below)
+         type = bond type (numeric or type label) or range of numeric types (see below)
          color = name of color or color1/color2/...
        *bdiam* args = type diam
-         type = bond type or range of types (see below)
+         type = bond type (numeric or type label) or range of numeric types (see below)
          diam = diameter of bonds of that type (distance units)
        *bitrate* arg = rate
          rate = target bitrate for movie in kbps
@@ -169,6 +169,9 @@ Examples
 
    dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
 
+   labelmap atom 1 C 2 H 3 O 4 N
+   dump_modify 1 acolor C gray acolor H white acolor O red acolor N blue
+
 Description
 """""""""""
 
@@ -739,15 +742,15 @@ The *acolor* keyword can be used with the dump image command, when its
 atom color setting is *type*, to set the color that atoms of each type
 will be drawn in the image.
 
-The specified *type* should be an integer from 1 to Ntypes = the
+The specified *type* should be a type label or integer from 1 to Ntypes
-number of atom types.  A wildcard asterisk can be used in place of or
+= the number of atom types.  For numeric types, a wildcard asterisk can
-in conjunction with the *type* argument to specify a range of atom
+be used in place of or in conjunction with the *type* argument to
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+specify a range of atom types.  This takes the form "\*" or "\*n" or
-the number of atom types, then an asterisk with no numeric values
+"n\*" or "m\*n". If N = the number of atom types, then an asterisk with
-means all types from 1 to N.  A leading asterisk means all types from
+no numeric values means all types from 1 to N.  A leading asterisk
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+means all types from 1 to n (inclusive).  A trailing asterisk means all
-(inclusive).  A middle asterisk means all types from m to n
+types from n to N (inclusive).  A middle asterisk means all types from
-(inclusive).
+m to n (inclusive).
 
 The specified *color* can be a single color which is any of the 140
 pre-defined colors (see below) or a color name defined by the
@@ -761,11 +764,12 @@ fashion to each of the specified atom types.
 
 The *adiam* keyword can be used with the dump image command, when its
 atom diameter setting is *type*, to set the size that atoms of each
-type will be drawn in the image.  The specified *type* should be an
+type will be drawn in the image.  The specified *type* should be a type
-integer from 1 to Ntypes.  As with the *acolor* keyword, a wildcard
+label or integer from 1 to Ntypes.  As with the *acolor* keyword, a
-asterisk can be used as part of the *type* argument to specify a range
+wildcard asterisk can be used as part of the *type* argument to specify
-of atom types.  The specified *diam* is the size in whatever distance
+a range of numeric atom types.  The specified *diam* is the size in
-:doc:`units <units>` the input script is using, e.g. Angstroms.
+whatever distance :doc:`units <units>` the input script is using, e.g.
+Angstroms.
 
 ----------
 
@@ -908,14 +912,15 @@ The *bcolor* keyword can be used with the dump image command, with its
 *bond* keyword, when its color setting is *type*, to set the color
 that bonds of each type will be drawn in the image.
 
-The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
+The specified *type* should be a type label or integer from 1 to
-is the number of bond types.  A wildcard asterisk can be used in place of or
+:math:`N`, where :math:`N` is the number of bond types.  For numeric
-in conjunction with the *type* argument to specify a range of bond
+types, a wildcard asterisk can be used in place of or in conjunction
-types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N`
+with the *type* argument to specify a range of bond types.  This takes
-is the number of bond types, then an asterisk with no numerical values
+the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is the number
-means all types from 1 to :math:`N`.  A leading asterisk means all types from
+of bond types, then an asterisk with no numerical values means all
-1 to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
+types from 1 to :math:`N`.  A leading asterisk means all types from 1
-(inclusive).  A middle asterisk means all types from m to n
+to n (inclusive).  A trailing asterisk means all types from m to
+:math:`N` (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
 The specified *color* can be a single color which is any of the 140
@@ -931,11 +936,11 @@ of the specified bond types.
 The *bdiam* keyword can be used with the dump image command, with its
 *bond* keyword, when its *diam* setting is *type*, to set the diameter
 that bonds of each type will be drawn in the image.  The specified
-*type* should be an integer from 1 to Nbondtypes.  As with the
+*type* should be a type label or integer from 1 to Nbondtypes.  As with
-*bcolor* keyword, a wildcard asterisk can be used as part of the
+the *bcolor* keyword, a wildcard asterisk can be used as part of the
-*type* argument to specify a range of bond types.  The specified
+*type* argument to specify a range of numeric bond types.  The
-*diam* is the size in whatever distance :doc:`units <units>` you are
+specified *diam* is the size in whatever distance :doc:`units <units>`
-using (e.g., Angstroms).
+you are using (e.g., Angstroms).
 
 ----------
 

doc/utils/sphinx-config/false_positives.txt

@@ -1186,6 +1186,7 @@ flaglog
 flagN
 flagVF
 flang
+flatpak
 fld
 floralwhite
 Florez

python/lammps/core.py

@@ -342,8 +342,8 @@ class lammps(object):
     if self.has_mpi_support:
       try:
         from mpi4py import __version__ as mpi4py_version
-        # tested to work with mpi4py versions 2 and 3
+        # tested to work with mpi4py versions 2, 3, and 4
-        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
+        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3','4']
       except ImportError:
         # ignore failing import
         pass
@@ -369,7 +369,7 @@ class lammps(object):
         if not self.has_mpi_support:
           raise Exception('LAMMPS not compiled with real MPI library')
         if not self.has_mpi4py:
-          raise Exception('Python mpi4py version is not 2 or 3')
+          raise Exception('Python mpi4py version is not 2, 3, or 4')
         if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int):
           MPI_Comm = c_int
         else:

src/GRANULAR/fix_add_heat.cpp

@@ -142,7 +142,7 @@ void FixAddHeat::post_force(int /*vflag*/)
       if (mask[i] & groupbit)
         heatflow[i] = 0.0;
 
-  double vtmp, dt;
+  double vtmp = 0.0;
   if (vstyle == CONSTANT) vtmp = value;
   if (vstyle == EQUAL) vtmp = input->variable->compute_equal(var);
   for (int i = 0; i < atom->nlocal; i++) {

src/KSPACE/pppm_dipole.cpp

@@ -613,8 +613,7 @@ void PPPMDipole::allocate()
   memory->create2d_offset(rho1d,3,-order/2,order/2,"pppm_dipole:rho1d");
   memory->create2d_offset(drho1d,3,-order/2,order/2,"pppm_dipole:drho1d");
   memory->create2d_offset(rho_coeff,order,(1-order)/2,order/2,"pppm_dipole:rho_coeff");
-  memory->create2d_offset(drho_coeff,order,(1-order)/2,order/2,
+  memory->create2d_offset(drho_coeff,order,(1-order)/2,order/2,"pppm_dipole:drho_coeff");
-                          "pppm_dipole:drho_coeff");
 
   // create 2 FFTs and a Remap
   // 1st FFT keeps data in FFT decomposition
@@ -669,8 +668,23 @@ void PPPMDipole::deallocate()
   memory->destroy(densityy_fft_dipole);
   memory->destroy(densityz_fft_dipole);
 
+  memory->destroy(density_fft);
+  memory->destroy(greensfn);
+  memory->destroy(work1);
+  memory->destroy(work2);
   memory->destroy(work3);
   memory->destroy(work4);
+  memory->destroy(vg);
+
+  memory->destroy1d_offset(fkx,nxlo_fft);
+  memory->destroy1d_offset(fky,nylo_fft);
+  memory->destroy1d_offset(fkz,nzlo_fft);
+
+  memory->destroy(gf_b);
+  memory->destroy2d_offset(rho1d,-order_allocated/2);
+  memory->destroy2d_offset(drho1d,-order_allocated/2);
+  memory->destroy2d_offset(rho_coeff,(1-order_allocated)/2);
+  memory->destroy2d_offset(drho_coeff,(1-order_allocated)/2);
 
   delete fft1;
   delete fft2;
@@ -678,6 +692,7 @@ void PPPMDipole::deallocate()
 
   fft1 = fft2 = nullptr;
   remap = nullptr;
+  gf_b = nullptr;
 }
 
 /* ----------------------------------------------------------------------

src/ML-POD/fitpod_command.cpp

@@ -1492,8 +1492,6 @@ void FitPOD::environment_cluster_calculation(const datastruct &data)
           &beta, A, &Mdesc);
     MPI_Allreduce(MPI_IN_PLACE, A, Mdesc * Mdesc, MPI_DOUBLE, MPI_SUM, world);
 
-    //if (comm->me == 0) print_matrix("A", Mdesc, Mdesc, A, Mdesc);
-
     if ((comm->me == 0) && (save == 1))
       savematrix2binfile(data.filenametag + "_covariance_matrix_elem" + std::to_string(elem + 1) +
                              ".bin",

src/ML-POD/pair_pod.cpp

@@ -77,6 +77,7 @@ PairPOD::PairPOD(LAMMPS *lmp) : Pair(lmp), fastpodptr(nullptr)
   abfx = nullptr;
   abfy = nullptr;
   abfz = nullptr;
+  abftm = nullptr;
   sumU = nullptr;
   forcecoeff = nullptr;
   Centroids = nullptr;
@@ -88,6 +89,7 @@ PairPOD::PairPOD(LAMMPS *lmp) : Pair(lmp), fastpodptr(nullptr)
   pdd = nullptr;
   coefficients = nullptr;
   pn3 = nullptr;
+  pq3 = nullptr;
   pc3 = nullptr;
   pa4 = nullptr;
   pb4 = nullptr;
@@ -124,6 +126,7 @@ PairPOD::~PairPOD()
   memory->destroy(abfx);
   memory->destroy(abfy);
   memory->destroy(abfz);
+  memory->destroy(abftm);
   memory->destroy(sumU);
   memory->destroy(forcecoeff);
   memory->destroy(Centroids);
@@ -135,6 +138,7 @@ PairPOD::~PairPOD()
   memory->destroy(pdd);
   memory->destroy(coefficients);
   memory->destroy(pn3);
+  memory->destroy(pq3);
   memory->destroy(pc3);
   memory->destroy(pa4);
   memory->destroy(pb4);
@@ -568,14 +572,18 @@ void PairPOD::copy_data_from_pod_class()
   besselparams[1] = fastpodptr->besselparams[1];
   besselparams[2] = fastpodptr->besselparams[2];
 
+  memory->destroy(abftm);
   memory->create(abftm, 4*K3, "abftm");
+  memory->destroy(elemindex);
   memory->create(elemindex, nelements*nelements, "elemindex");
   for (int i=0; i<nelements*nelements; i++) elemindex[i] = fastpodptr->elemindex[i];
 
+  memory->destroy(Phi);
   memory->create(Phi, ns * ns, "pair_pod:Phi");
   for (int i=0; i<ns*ns; i++)
     Phi[i] = fastpodptr->Phi[i];
 
+  memory->destroy(coefficients);
   memory->create(coefficients, nCoeffPerElement * nelements, "pair_pod:coefficients");
   for (int i=0; i<nCoeffPerElement * nelements; i++)
     coefficients[i] = fastpodptr->coeff[i];
@@ -590,11 +598,17 @@ void PairPOD::copy_data_from_pod_class()
       Centroids[i] = fastpodptr->Centroids[i];
   }
 
+  memory->destroy(pn3);
   memory->create(pn3, nabf3+1, "pn3"); // array stores the number of monomials for each degree
+  memory->destroy(pq3);
   memory->create(pq3, K3*2, "pq3"); // array needed for the recursive computation of the angular basis functions
+  memory->destroy(pc3);
   memory->create(pc3, K3, "pc3");   // array needed for the computation of the three-body descriptors
+  memory->destroy(pa4);
   memory->create(pa4, nabf4+1, "pa4"); // this array is a subset of the array {0, 1, 4, 10, 19, 29, 47, 74, 89, 119, 155, 209, 230, 275, 335, 425, 533, 561, 624, 714, 849, 949, 1129, 1345}
+  memory->destroy(pb4);
   memory->create(pb4, Q4*3, "pb4"); // array stores the indices of the monomials needed for the computation of the angular basis functions
+  memory->destroy(pc4);
   memory->create(pc4, Q4, "pc4");   // array of monomial coefficients needed for the computation of the four-body descriptors
   for (int i=0; i<nabf3+1; i++) pn3[i] = fastpodptr->pn3[i];
   for (int i=0; i<K3; i++) pc3[i] = fastpodptr->pc3[i];
@@ -890,7 +904,7 @@ void PairPOD::angularbasis(double *tm, double *tmu, double *tmv, double *tmw, in
       double tmvm = abfy[mj];
       double tmwm = abfz[mj];
 
-      double tmn, tmun, tmvn, tmwn;
+      double tmn = 0.0, tmun = 0.0, tmvn = 0.0, tmwn = 0.0;
       // Calculate angular basis function and its derivatives using recursion relation
       if (d==1) {
         tmn = tmm*u;

src/MOLECULE/fix_cmap.cpp

@@ -593,7 +593,6 @@ void FixCMAP::post_force(int vflag)
         vcmap[5] = (vb12y*f1[2])+(vb32y*f3[2])+((vb43y+vb32y)*f4[2])+
           ((vb54y+vb43y+vb32y)*f5[2]);
         ev_tally(nlist,list,5.0,E,vcmap);
-        //ev_tally(5,list,nlocal,newton_bond,E,vcmap);
       }
   }
 }

src/MOLECULE/pair_lj_cut_tip4p_cut.cpp

@@ -38,14 +38,18 @@ using namespace MathConst;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJCutTIP4PCut::PairLJCutTIP4PCut(LAMMPS *lmp) : Pair(lmp)
+PairLJCutTIP4PCut::PairLJCutTIP4PCut(LAMMPS *lmp) :
+    Pair(lmp), cut_lj(nullptr), cut_ljsq(nullptr), epsilon(nullptr), sigma(nullptr), lj1(nullptr),
+    lj2(nullptr), lj3(nullptr), lj4(nullptr), offset(nullptr), hneigh(nullptr), newsite(nullptr)
+
 {
   single_enable = 0;
   writedata = 1;
 
   nmax = 0;
-  hneigh = nullptr;
+
-  newsite = nullptr;
+  typeH = typeO = typeA = typeB = -1;
+  alpha = qdist = 0.0;
 
   // TIP4P cannot compute virial as F dot r
   // due to finding bonded H atoms which are not near O atom

src/QEQ/fix_qeq.cpp

@@ -763,11 +763,12 @@ void FixQEq::read_file(char *file)
       chi[n] = eta[n] = gamma[n] = zeta[n] = zcore[n] = 0.0;
     }
 
+    FILE *fp = nullptr;
     try {
       int nlo,nhi;
       double val;
 
-      FILE *fp = utils::open_potential(file,lmp,nullptr);
+      fp = utils::open_potential(file,lmp,nullptr);
       if (fp == nullptr)
         throw qeq_parser_error(fmt::format("Cannot open fix qeq parameter file {}: {}",
                                            file,utils::getsyserror()));
@@ -798,7 +799,7 @@ void FixQEq::read_file(char *file)
         for (int n=nlo; n <= nhi; ++n) setflag[n] = 1;
       }
     } catch (EOFException &) {
-      ; // catch and ignore to exit loop
+      fclose(fp);
     } catch (std::exception &e) {
       error->one(FLERR,e.what());
     }

src/QEQ/fix_qeq_point.cpp

@@ -54,6 +54,7 @@ void FixQEqPoint::init()
   neighbor->add_request(this, NeighConst::REQ_FULL);
 
   int ntypes = atom->ntypes;
+  memory->destroy(shld);
   memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding");
 }
 

src/QEQ/fix_qeq_shielded.cpp

@@ -56,6 +56,7 @@ void FixQEqShielded::init()
   neighbor->add_request(this, NeighConst::REQ_FULL);
 
   const int ntypes = atom->ntypes;
+  memory->destroy(shld);
   memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding");
 
   init_shielding();

src/bond.cpp

@@ -36,12 +36,13 @@ int Bond::instance_total = 0;
    a particular bond style can override this
 ------------------------------------------------------------------------- */
 
-Bond::Bond(LAMMPS *_lmp) : Pointers(_lmp)
+Bond::Bond(LAMMPS *_lmp) :
+    Pointers(_lmp), setflag(nullptr), virial{0.0, 0.0, 0.0, 0.0, 0.0, 0.0}, eatom(nullptr),
+    vatom(nullptr), svector(nullptr)
 {
   instance_me = instance_total++;
 
   energy = 0.0;
-  virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
   writedata = 1;
   reinitflag = 1;
 
@@ -53,12 +54,8 @@ Bond::Bond(LAMMPS *_lmp) : Pointers(_lmp)
   partial_flag = 0;
 
   single_extra = 0;
-  svector = nullptr;
 
   maxeatom = maxvatom = 0;
-  eatom = nullptr;
-  vatom = nullptr;
-  setflag = nullptr;
 
   execution_space = Host;
   datamask_read = ALL_MASK;

src/dump_image.cpp

@@ -1536,7 +1536,7 @@ int DumpImage::modify_param(int narg, char **arg)
   if (strcmp(arg[0],"acolor") == 0) {
     if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
     int nlo,nhi;
-    utils::bounds(FLERR,arg[1],1,atom->ntypes,nlo,nhi,error);
+    utils::bounds_typelabel(FLERR,arg[1],1,atom->ntypes,nlo,nhi,lmp,Atom::ATOM);
 
     // get list of colors
     // assign colors in round-robin fashion to types
@@ -1557,7 +1557,7 @@ int DumpImage::modify_param(int narg, char **arg)
   if (strcmp(arg[0],"adiam") == 0) {
     if (narg < 3) error->all(FLERR,"Illegal dump_modify command");
     int nlo,nhi;
-    utils::bounds(FLERR,arg[1],1,atom->ntypes,nlo,nhi,error);
+    utils::bounds_typelabel(FLERR,arg[1],1,atom->ntypes,nlo,nhi,lmp,Atom::ATOM);
     double diam = utils::numeric(FLERR,arg[2],false,lmp);
     if (diam <= 0.0) error->all(FLERR,"Illegal dump_modify command");
     for (int i = nlo; i <= nhi; i++) diamtype[i] = diam;
@@ -1588,7 +1588,7 @@ int DumpImage::modify_param(int narg, char **arg)
     if (atom->nbondtypes == 0)
       error->all(FLERR,"Dump modify bcolor not allowed with no bond types");
     int nlo,nhi;
-    utils::bounds(FLERR,arg[1],1,atom->nbondtypes,nlo,nhi,error);
+    utils::bounds_typelabel(FLERR,arg[1],1,atom->nbondtypes,nlo,nhi,lmp,Atom::BOND);
 
     // process list of ncount colornames separated by '/'
     // assign colors in round-robin fashion to bond types
@@ -1611,7 +1611,7 @@ int DumpImage::modify_param(int narg, char **arg)
     if (atom->nbondtypes == 0)
       error->all(FLERR,"Dump modify bdiam not allowed with no bond types");
     int nlo,nhi;
-    utils::bounds(FLERR,arg[1],1,atom->nbondtypes,nlo,nhi,error);
+    utils::bounds_typelabel(FLERR,arg[1],1,atom->nbondtypes,nlo,nhi,lmp,Atom::BOND);
     double diam = utils::numeric(FLERR,arg[2],false,lmp);
     if (diam <= 0.0) error->all(FLERR,"Illegal dump_modify command");
     for (int i = nlo; i <= nhi; i++) bdiamtype[i] = diam;

src/library.cpp

@@ -54,6 +54,7 @@
 #include "universe.h"
 #include "update.h"
 #include "variable.h"
+#include "version.h"
 
 #include <cstring>
 
@@ -1391,6 +1392,11 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name)
   if (strcmp(name,"respa_levels") == 0) return LAMMPS_INT;
   if (strcmp(name,"respa_dt") == 0) return LAMMPS_DOUBLE;
 
+  if (strcmp(name,"git_commit") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"git_branch") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"git_descriptor") == 0) return LAMMPS_STRING;
+  if (strcmp(name,"lammps_version") == 0) return LAMMPS_STRING;
+
   if (strcmp(name,"boxlo") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"boxhi") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"sublo") == 0) return LAMMPS_DOUBLE;
@@ -1547,6 +1553,56 @@ report the "native" data type.  The following tables are provided:
 
 .. _extract_box_settings:
 
+**Timestep settings**
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Name
+     - Type
+     - Length
+     - Description
+   * - dt
+     - double
+     - 1
+     - length of the time step. See :doc:`timestep`.
+   * - ntimestep
+     - bigint
+     - 1
+     - current time step number. See :doc:`reset_timestep`.
+   * - atime
+     - double
+     - 1
+     - accumulated simulation time in time units.
+
+**Git revision and version settings**
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Name
+     - Type
+     - Length
+     - Description
+   * - git_commit
+     - const char \*
+     - 1
+     - Git commit hash for the LAMMPS version.
+   * - git_branch
+     - const char \*
+     - 1
+     - Git branch for the LAMMPS version.
+   * - git_descriptor
+     - const char \*
+     - 1
+     - Combined descriptor for the git revision
+   * - lammps_version
+     - const char \*
+     - 1
+     - LAMMPS version string.
+
 **Simulation box settings**
 
 .. list-table::
@@ -1557,18 +1613,6 @@ report the "native" data type.  The following tables are provided:
      - Type
      - Length
      - Description
-   * - boxlo
-     - double
-     - 3
-     - lower box boundaries. See :doc:`create_box`.
-   * - boxhi
-     - double
-     - 3
-     - upper box boundaries. See :doc:`create_box`.
-   * - boxxlo
-     - double
-     - 1
-     - lower box boundary in x-direction. See :doc:`create_box`.
    * - boxxhi
      - double
      - 1
@@ -1866,6 +1910,12 @@ void *lammps_extract_global(void *handle, const char *name)
     if (strcmp(name,"respa_levels") == 0) return (void *) &respa->nlevels;
     if (strcmp(name,"respa_dt") == 0) return (void *) respa->step;
   }
+
+  if (strcmp(name,"git_commit") == 0) return (void *)LAMMPS::git_commit;
+  if (strcmp(name,"git_branch") == 0) return (void  *)LAMMPS::git_branch;
+  if (strcmp(name,"git_descriptor") == 0) return (void *)LAMMPS::git_descriptor;
+  if (strcmp(name,"lammps_version") == 0) return (void *)LAMMPS_VERSION;
+
   if (strcmp(name,"boxlo") == 0) return (void *) lmp->domain->boxlo;
   if (strcmp(name,"boxhi") == 0) return (void *) lmp->domain->boxhi;
   if (strcmp(name,"sublo") == 0) return (void *) lmp->domain->sublo;
@@ -1877,6 +1927,7 @@ void *lammps_extract_global(void *handle, const char *name)
     if (strcmp(name,"subhi_lambda") == 0)
       return (void *) lmp->domain->subhi_lamda;
   }
+
   if (strcmp(name,"boxxlo") == 0) return (void *) &lmp->domain->boxlo[0];
   if (strcmp(name,"boxxhi") == 0) return (void *) &lmp->domain->boxhi[0];
   if (strcmp(name,"boxylo") == 0) return (void *) &lmp->domain->boxlo[1];

src/pair.cpp

@@ -53,14 +53,15 @@ int Pair::instance_total = 0;
 /* ---------------------------------------------------------------------- */
 
 Pair::Pair(LAMMPS *lmp) :
-    Pointers(lmp), eatom(nullptr), vatom(nullptr), cvatom(nullptr), cutsq(nullptr),
+    Pointers(lmp), virial{0.0, 0.0, 0.0, 0.0, 0.0, 0.0}, eatom(nullptr), vatom(nullptr),
-    setflag(nullptr), cutghost(nullptr), rtable(nullptr), drtable(nullptr), ftable(nullptr),
+    cvatom(nullptr), cutsq(nullptr), setflag(nullptr), cutghost(nullptr), rtable(nullptr),
-    dftable(nullptr), ctable(nullptr), dctable(nullptr), etable(nullptr), detable(nullptr),
+    drtable(nullptr), ftable(nullptr), dftable(nullptr), ctable(nullptr), dctable(nullptr),
-    ptable(nullptr), dptable(nullptr), vtable(nullptr), dvtable(nullptr), rdisptable(nullptr),
+    etable(nullptr), detable(nullptr), ptable(nullptr), dptable(nullptr), vtable(nullptr),
-    drdisptable(nullptr), fdisptable(nullptr), dfdisptable(nullptr), edisptable(nullptr),
+    dvtable(nullptr), rdisptable(nullptr), drdisptable(nullptr), fdisptable(nullptr),
-    dedisptable(nullptr), pvector(nullptr), svector(nullptr), list(nullptr), listhalf(nullptr),
+    dfdisptable(nullptr), edisptable(nullptr), dedisptable(nullptr), pvector(nullptr),
-    listfull(nullptr), list_tally_compute(nullptr), elements(nullptr), elem1param(nullptr),
+    svector(nullptr), list(nullptr), listhalf(nullptr), listfull(nullptr),
-    elem2param(nullptr), elem3param(nullptr), map(nullptr)
+    list_tally_compute(nullptr), elements(nullptr), elem1param(nullptr), elem2param(nullptr),
+    elem3param(nullptr), map(nullptr)
 {
   instance_me = instance_total++;
 

src/update.cpp

@@ -63,6 +63,7 @@ Update::Update(LAMMPS *lmp) :
   restrict_output = 0;
   setupflag = 0;
   multireplica = 0;
+  nsteps = 0;
 
   eflag_global = vflag_global = -1;
   eflag_atom = vflag_atom = 0;

src/write_dump.cpp

@@ -50,16 +50,25 @@ void WriteDump::command(int narg, char **arg)
   int dumpfreq = MAX(1, update->nsteps);
   dumpfreq += update->ntimestep % dumpfreq;
 
+  std::string dump_id = "WRITE_DUMP";
   auto dumpargs = new char *[modindex + 2];
-  dumpargs[0] = (char *) "WRITE_DUMP";                      // dump id
+  dumpargs[0] = (char *) dump_id.c_str();                   // dump id
   dumpargs[1] = arg[0];                                     // group
   dumpargs[2] = arg[1];                                     // dump style
   dumpargs[3] = utils::strdup(std::to_string(dumpfreq));    // dump frequency
 
   for (int i = 2; i < modindex; ++i) dumpargs[i + 2] = arg[i];
 
-  Dump *dump = output->add_dump(modindex + 2, dumpargs);
+  auto *dump = output->add_dump(modindex + 2, dumpargs);
-  if (modindex < narg) dump->modify_params(narg - modindex - 1, &arg[modindex + 1]);
+
+  try {
+    if (modindex < narg) dump->modify_params(narg - modindex - 1, &arg[modindex + 1]);
+  } catch (LAMMPSException &e) {
+    // delete dump after error and then rethrow the exception to avoid re-use of dump-ID error
+    dump = output->get_dump_by_id(dump_id);
+    if (dump) output->delete_dump(dump_id);
+    throw e;
+  }
 
   // write out one frame and then delete the dump again
   // set multifile_override for DumpImage so that filename needs no "*"
@@ -74,7 +83,7 @@ void WriteDump::command(int narg, char **arg)
 
   // delete the Dump instance and local storage
 
-  output->delete_dump(dumpargs[0]);
+  output->delete_dump(dump_id);
   delete[] dumpargs[3];
   delete[] dumpargs;
 }

tools/lammps-gui/CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.16)
 
-project(lammps-gui VERSION 1.6.5 LANGUAGES CXX)
+project(lammps-gui VERSION 1.6.6 LANGUAGES CXX)
 
 set(CMAKE_AUTOUIC ON)
 set(CMAKE_AUTOMOC ON)
@@ -198,6 +198,27 @@ if(BUILD_OMP)
   target_link_libraries(lammps-gui PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+# build LAMMPS-GUI and LAMMPS as flatpak, if tools are installed
+find_program(FLATPAK_COMMAND flatpak DOC "Path to flatpak command")
+find_program(FLATPAK_BUILDER flatpak-builder DOC "Path to flatpak-builder command")
+if(FLATPAK_COMMAND AND FLATPAK_BUILDER)
+  file(STRINGS ${LAMMPS_DIR}/src/version.h line REGEX LAMMPS_VERSION)
+  string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z][A-Za-z][A-Za-z])[A-Za-z]* ([0-9]+)\""
+                       "\\1\\2\\3" LAMMPS_RELEASE "${line}")
+  add_custom_target(flatpak
+    COMMAND ${FLATPAK_BUILDER} --force-clean --verbose --ccache --repo=repo --user --default-branch=${LAMMPS_RELEASE}
+                   --install-deps-from=flathub flatpak-build ${LAMMPS_DIR}/tools/lammps-gui/org.lammps.lammps-gui.yml
+    COMMAND ${FLATPAK_COMMAND} build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose
+                                      repo LAMMPS_GUI-Linux-amd64.flatpak org.lammps.lammps-gui ${LAMMPS_RELEASE}
+    COMMENT "Create Flatpak bundle file of LAMMPS-GUI and LAMMPS"
+    BYPRODUCT LAMMPS-Linux-amd64.flatpak
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  )
+else()
+  add_custom_target(flatpak
+    COMMAND ${CMAKE_COMMAND} -E echo "The flatpak and flatpak-builder commands required to build a LAMMPS-GUI flatpak bundle were not found. Skipping.")
+endif()
+
 # when compiling on macOS, create an "app bundle"
 if(APPLE)
   set_target_properties(lammps-gui PROPERTIES
@@ -284,6 +305,7 @@ elseif((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
 elseif((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND NOT LAMMPS_GUI_USE_PLUGIN)
   install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-gui.desktop DESTINATION ${CMAKE_INSTALL_DATADIR}/applications/)
+  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-gui.appdata.xml DESTINATION ${CMAKE_INSTALL_DATADIR}/appdata/)
   install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-input.xml DESTINATION ${CMAKE_INSTALL_DATADIR}/mime/packages/)
   install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-input.xml DESTINATION ${CMAKE_INSTALL_DATADIR}/mime/text/x-application-lammps.xml)
   install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/icons/hicolor DESTINATION ${CMAKE_INSTALL_DATADIR}/icons/)
@@ -307,10 +329,11 @@ elseif((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND NOT LAMMPS_GUI_USE_PLUGIN)
       message(WARNING "Unresolved dependencies detected: ${_u_deps}")
     endif() ]]
   )
+
   add_custom_target(tgz
     COMMAND ${LAMMPS_DIR}/cmake/packaging/build_linux_tgz.sh
     DEPENDS lammps-gui
-    COMMENT "Create compressed tar file of LAMMPS with dependent libraries and wrapper"
+    COMMENT "Create compressed tar file of LAMMPS-GUI with dependent libraries and wrapper"
     BYPRODUCT LAMMPS-Linux-amd64.tar.gz
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
   )

tools/lammps-gui/TODO.md

@@ -4,7 +4,12 @@ LAMMPS-GUI TODO list:
 
 - figure out how widgets can be resized to fraction of available screen size.
 - figure out stacking order of frames and whether it can be more flexible
-- bundle LAMMPS tutorial input files
+- figure out how to avoid corrupted cached thermo data while reading it.
+- implement a timed "Auto-Save" feature that saves after some idle time.  set timeout in Editor preferences.
+- bundle or download? LAMMPS tutorial input files
+- add a "Colors" menu to the image viewer to adjust color settings for the
+  current image (unlike the defaults in the perferences). Support color by
+  property (e.g. scan computes or fixes with per-atom data), define colormaps etc.
 
 - implement indenting regions for (nested) loops?
 - implement data file manager GUI with the following features:

tools/lammps-gui/codeeditor.cpp

@@ -14,6 +14,7 @@
 #include "codeeditor.h"
 #include "fileviewer.h"
 #include "lammpsgui.h"
+#include "lammpswrapper.h"
 #include "linenumberarea.h"
 
 #include <QAbstractItemView>
@@ -146,6 +147,7 @@ CodeEditor::CodeEditor(QWidget *parent) :
 {
     help_action = new QShortcut(QKeySequence::fromString("Ctrl+?"), parent);
     connect(help_action, &QShortcut::activated, this, &CodeEditor::get_help);
+    docver = "";
 
     // set up completer class (without a model currently)
 #define COMPLETER_SETUP(completer)                                                            \
@@ -1159,12 +1161,30 @@ void CodeEditor::insertCompletedCommand(const QString &completion)
     setTextCursor(cursor);
 }
 
+void CodeEditor::setDocver()
+{
+    LammpsWrapper *lammps = &qobject_cast<LammpsGui *>(parent())->lammps;
+    docver                = "/";
+    if (lammps) {
+        QString git_branch = (const char *)lammps->extract_global("git_branch");
+        if ((git_branch == "stable") || (git_branch == "maintenance")) {
+            docver = "/stable/";
+        } else if (git_branch == "release") {
+            docver = "/";
+        } else {
+            docver = "/latest/";
+        }
+    }
+}
+
 void CodeEditor::get_help()
 {
     QString page, help;
     find_help(page, help);
+    if (docver.isEmpty()) setDocver();
     if (!page.isEmpty())
-        QDesktopServices::openUrl(QUrl(QString("https://docs.lammps.org/%1").arg(page)));
+        QDesktopServices::openUrl(
+            QUrl(QString("https://docs.lammps.org%1%2").arg(docver).arg(page)));
 }
 
 void CodeEditor::find_help(QString &page, QString &help)
@@ -1215,8 +1235,9 @@ void CodeEditor::find_help(QString &page, QString &help)
 void CodeEditor::open_help()
 {
     auto *act = qobject_cast<QAction *>(sender());
+    if (docver.isEmpty()) setDocver();
     QDesktopServices::openUrl(
-        QUrl(QString("https://docs.lammps.org/%1").arg(act->data().toString())));
+        QUrl(QString("https://docs.lammps.org%1%2").arg(docver).arg(act->data().toString())));
 }
 
 void CodeEditor::open_url()

tools/lammps-gui/codeeditor.h

@@ -79,6 +79,7 @@ protected:
     void dropEvent(QDropEvent *event) override;
     void contextMenuEvent(QContextMenuEvent *event) override;
     void keyPressEvent(QKeyEvent *event) override;
+    void setDocver();
 
 private slots:
     void updateLineNumberAreaWidth(int newBlockCount);
@@ -107,6 +108,7 @@ private:
     int highlight;
     bool reformat_on_return;
     bool automatic_completion;
+    QString docver;
 
     QMap<QString, QString> cmd_map;
     QMap<QString, QString> fix_map;

tools/lammps-gui/fileviewer.cpp

@@ -16,6 +16,7 @@
 #include "lammpsgui.h"
 
 #include <QApplication>
+#include <QEvent>
 #include <QFile>
 #include <QFileInfo>
 #include <QIcon>

tools/lammps-gui/help_index.table

@@ -20,6 +20,8 @@ angle_cosine_shift_exp.html angle_style cosine/shift/exp
 angle_cosine_shift_exp.html angle_style cosine/shift/exp/omp
 angle_cosine_shift.html angle_style cosine/shift
 angle_cosine_shift.html angle_style cosine/shift/omp
+angle_cosine_squared_restricted.html angle_style cosine/squared/restricted
+angle_cosine_squared_restricted.html angle_style cosine/squared/restricted/omp
 angle_cosine_squared.html angle_style cosine/squared
 angle_cosine_squared.html angle_style cosine/squared/omp
 angle_cross.html angle_style cross
@@ -35,6 +37,7 @@ angle_harmonic.html angle_style harmonic/intel
 angle_harmonic.html angle_style harmonic/kk
 angle_harmonic.html angle_style harmonic/omp
 angle_hybrid.html angle_style hybrid
+angle_hybrid.html angle_style hybrid/kk
 angle_lepton.html angle_style lepton
 angle_lepton.html angle_style lepton/omp
 angle_mesocnt.html angle_style mesocnt
@@ -43,6 +46,7 @@ angle_none.html angle_style none
 angle_quartic.html angle_style quartic
 angle_quartic.html angle_style quartic/omp
 angle_spica.html angle_style spica
+angle_spica.html angle_style spica/kk
 angle_spica.html angle_style spica/omp
 angle_style.html angle_style
 angle_table.html angle_style table
@@ -150,6 +154,7 @@ bond_harmonic_shift_cut.html bond_style harmonic/shift/cut/omp
 bond_harmonic_shift.html bond_style harmonic/shift
 bond_harmonic_shift.html bond_style harmonic/shift/omp
 bond_hybrid.html bond_style hybrid
+bond_hybrid.html bond_style hybrid/kk
 bond_lepton.html bond_style lepton
 bond_lepton.html bond_style lepton/omp
 bond_mesocnt.html bond_style mesocnt
@@ -164,6 +169,7 @@ bond_oxdna.html bond_style oxdna/fene
 bond_oxdna.html bond_style oxrna2/fene
 bond_quartic.html bond_style quartic
 bond_quartic.html bond_style quartic/omp
+bond_rheo_shell.html bond_style rheo/shell
 bond_special.html bond_style special
 bond_style.html bond_style
 bond_table.html bond_style table
@@ -260,6 +266,10 @@ compute_pair.html compute pair
 compute_pe_atom.html compute pe/atom
 compute_pe.html compute pe
 compute_plasticity_atom.html compute plasticity/atom
+compute_pod_atom.html compute pod/atom
+compute_pod_atom.html compute podd/atom
+compute_pod_atom.html compute pod/global
+compute_pod_atom.html compute pod/local
 compute_pressure_alchemy.html compute pressure/alchemy
 compute_pressure.html compute pressure
 compute_pressure_uef.html compute pressure/uef
@@ -275,6 +285,7 @@ compute_reaxff_atom.html compute reaxff/atom/kk
 compute_reduce_chunk.html compute reduce/chunk
 compute_reduce.html compute reduce
 compute_reduce.html compute reduce/region
+compute_rheo_property_atom.html compute rheo/property/atom
 compute_rigid_local.html compute rigid/local
 compute.html compute
 compute_saed.html compute saed
@@ -360,6 +371,7 @@ delete_bonds.html delete_bonds
 dielectric.html dielectric
 dihedral_charmm.html dihedral_style charmm
 dihedral_charmm.html dihedral_style charmmfsw
+dihedral_charmm.html dihedral_style charmmfsw/kk
 dihedral_charmm.html dihedral_style charmm/intel
 dihedral_charmm.html dihedral_style charmm/kk
 dihedral_charmm.html dihedral_style charmm/omp
@@ -369,6 +381,7 @@ dihedral_class2.html dihedral_style class2/omp
 dihedral_coeff.html dihedral_coeff
 dihedral_cosine_shift_exp.html dihedral_style cosine/shift/exp
 dihedral_cosine_shift_exp.html dihedral_style cosine/shift/exp/omp
+dihedral_cosine_squared_restricted.html dihedral_style cosine/squared/restricted
 dihedral_fourier.html dihedral_style fourier
 dihedral_fourier.html dihedral_style fourier/intel
 dihedral_fourier.html dihedral_style fourier/omp
@@ -379,6 +392,7 @@ dihedral_harmonic.html dihedral_style harmonic/omp
 dihedral_helix.html dihedral_style helix
 dihedral_helix.html dihedral_style helix/omp
 dihedral_hybrid.html dihedral_style hybrid
+dihedral_hybrid.html dihedral_style hybrid/kk
 dihedral_lepton.html dihedral_style lepton
 dihedral_lepton.html dihedral_style lepton/omp
 dihedral_multi_harmonic.html dihedral_style multi/harmonic
@@ -443,6 +457,7 @@ fix_acks2_reaxff.html fix acks2/reaxff/kk
 fix_adapt_fep.html fix adapt/fep
 fix_adapt.html fix adapt
 fix_addforce.html fix addforce
+fix_add_heat.html fix add/heat
 fix_addtorque.html fix addtorque
 fix_alchemy.html fix alchemy
 fix_amoeba_bitorsion.html fix amoeba/bitorsion
@@ -475,6 +490,7 @@ fix_cmap.html fix cmap
 fix_colvars.html fix colvars
 fix_controller.html fix controller
 fix_damping_cundall.html fix damping/cundall
+fix_deform_pressure.html fix deform/pressure
 fix_deform.html fix deform
 fix_deform.html fix deform/kk
 fix_deposit.html fix deposit
@@ -667,6 +683,11 @@ fix_reaxff_species.html fix reaxff/species
 fix_reaxff_species.html fix reaxff/species/kk
 fix_recenter.html fix recenter
 fix_restrain.html fix restrain
+fix_rheo_oxidation.html fix rheo/oxidation
+fix_rheo_pressure.html fix rheo/pressure
+fix_rheo.html fix rheo
+fix_rheo_thermal.html fix rheo/thermal
+fix_rheo_viscosity.html fix rheo/viscosity
 fix_rhok.html fix rhok
 fix_rigid_meso.html fix rigid/meso
 fix_rigid.html fix rigid
@@ -741,6 +762,8 @@ fix_wall_body_polygon.html fix wall/body/polygon
 fix_wall_body_polyhedron.html fix wall/body/polyhedron
 fix_wall_ees.html fix wall/ees
 fix_wall_ees.html fix wall/region/ees
+fix_wall_flow.html fix wall/flow
+fix_wall_flow.html fix wall/flow/kk
 fix_wall_gran_region.html fix wall/gran/region
 fix_wall_gran.html fix wall/gran
 fix_wall_gran.html fix wall/gran/kk
@@ -784,6 +807,7 @@ improper_harmonic.html improper_style harmonic/intel
 improper_harmonic.html improper_style harmonic/kk
 improper_harmonic.html improper_style harmonic/omp
 improper_hybrid.html improper_style hybrid
+improper_hybrid.html improper_style hybrid/kk
 improper_inversion_harmonic.html improper_style inversion/harmonic
 improper_none.html improper_style none
 improper_ring.html improper_style ring
@@ -937,6 +961,7 @@ pair_charmm.html pair_style lj/charmm/coul/msm
 pair_charmm.html pair_style lj/charmm/coul/msm/omp
 pair_charmm.html pair_style lj/charmmfsw/coul/charmmfsh
 pair_charmm.html pair_style lj/charmmfsw/coul/long
+pair_charmm.html pair_style lj/charmmfsw/coul/long/kk
 pair_class2.html pair_style lj/class2
 pair_class2.html pair_style lj/class2/coul/cut
 pair_class2.html pair_style lj/class2/coul/cut/kk
@@ -1024,6 +1049,8 @@ pair_dipole.html pair_style lj/long/dipole/long
 pair_dipole.html pair_style lj/sf/dipole/sf
 pair_dipole.html pair_style lj/sf/dipole/sf/gpu
 pair_dipole.html pair_style lj/sf/dipole/sf/omp
+pair_dpd_coul_slater_long.html pair_style dpd/coul/slater/long
+pair_dpd_coul_slater_long.html pair_style dpd/coul/slater/long/gpu
 pair_dpd_ext.html pair_style dpd/ext
 pair_dpd_ext.html pair_style dpd/ext/kk
 pair_dpd_ext.html pair_style dpd/ext/omp
@@ -1132,9 +1159,14 @@ pair_hbond_dreiding.html pair_style hbond/dreiding/morse/omp
 pair_hdnnp.html pair_style hdnnp
 pair_hybrid.html pair_style hybrid
 pair_hybrid.html pair_style hybrid/kk
+pair_hybrid.html pair_style hybrid/molecular
+pair_hybrid.html pair_style hybrid/molecular/omp
+pair_hybrid.html pair_style hybrid/omp
 pair_hybrid.html pair_style hybrid/overlay
 pair_hybrid.html pair_style hybrid/overlay/kk
+pair_hybrid.html pair_style hybrid/overlay/omp
 pair_hybrid.html pair_style hybrid/scaled
+pair_hybrid.html pair_style hybrid/scaled/omp
 pair_ilp_graphene_hbn.html pair_style ilp/graphene/hbn
 pair_ilp_graphene_hbn.html pair_style ilp/graphene/hbn/opt
 pair_ilp_tmd.html pair_style ilp/tmd
@@ -1292,6 +1324,8 @@ pair_pace.html pair_style pace
 pair_pace.html pair_style pace/extrapolation
 pair_pace.html pair_style pace/extrapolation/kk
 pair_pace.html pair_style pace/kk
+pair_pedone.html pair_style pedone
+pair_pedone.html pair_style pedone/omp
 pair_peri.html pair_style peri/eps
 pair_peri.html pair_style peri/lps
 pair_peri.html pair_style peri/lps/omp
@@ -1299,6 +1333,7 @@ pair_peri.html pair_style peri/pmb
 pair_peri.html pair_style peri/pmb/omp
 pair_peri.html pair_style peri/ves
 pair_pod.html pair_style pod
+pair_pod.html pair_style pod/kk
 pair_polymorphic.html pair_style polymorphic
 pair_python.html pair_style python
 pair_quip.html pair_style quip
@@ -1306,9 +1341,13 @@ pair_rann.html pair_style rann
 pair_reaxff.html pair_style reaxff
 pair_reaxff.html pair_style reaxff/kk
 pair_reaxff.html pair_style reaxff/omp
+pair_rebomos.html pair_style rebomos
+pair_rebomos.html pair_style rebomos/omp
 pair_resquared.html pair_style resquared
 pair_resquared.html pair_style resquared/gpu
 pair_resquared.html pair_style resquared/omp
+pair_rheo.html pair_style rheo
+pair_rheo_solid.html pair_style rheo/solid
 pair_saip_metal.html pair_style saip/metal
 pair_saip_metal.html pair_style saip/metal/opt
 pair_sdpd_taitwater_isothermal.html pair_style sdpd/taitwater/isothermal
@@ -1324,6 +1363,7 @@ pair_snap.html pair_style snap/intel
 pair_snap.html pair_style snap/kk
 pair_soft.html pair_style soft
 pair_soft.html pair_style soft/gpu
+pair_soft.html pair_style soft/kk
 pair_soft.html pair_style soft/omp
 pair_sph_heatconduction.html pair_style sph/heatconduction
 pair_sph_heatconduction.html pair_style sph/heatconduction/gpu
@@ -1337,6 +1377,7 @@ pair_sph_taitwater.html pair_style sph/taitwater/gpu
 pair_spica.html pair_style lj/spica
 pair_spica.html pair_style lj/spica/coul/long
 pair_spica.html pair_style lj/spica/coul/long/gpu
+pair_spica.html pair_style lj/spica/coul/long/kk
 pair_spica.html pair_style lj/spica/coul/long/omp
 pair_spica.html pair_style lj/spica/coul/msm
 pair_spica.html pair_style lj/spica/coul/msm/omp
@@ -1390,6 +1431,8 @@ pair_thole.html pair_style thole
 pair_threebody_table.html pair_style threebody/table
 pair_tracker.html pair_style tracker
 pair_tri_lj.html pair_style tri/lj
+pair_uf3.html pair_style uf3
+pair_uf3.html pair_style uf3/kk
 pair_ufm.html pair_style ufm
 pair_ufm.html pair_style ufm/gpu
 pair_ufm.html pair_style ufm/omp

tools/lammps-gui/imageviewer.cpp

@@ -23,7 +23,9 @@
 #include <QFile>
 #include <QFileDialog>
 #include <QFileInfo>
+#include <QFontMetrics>
 #include <QGuiApplication>
+#include <QHBoxLayout>
 #include <QIcon>
 #include <QImage>
 #include <QImageReader>
@@ -150,9 +152,11 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
 
     QSettings settings;
 
-    vdwfactor = 0.5;
+    vdwfactor   = 0.5;
-    auto pix  = QPixmap(":/icons/emblem-photos.png");
+    shinyfactor = 0.6;
+    auto pix    = QPixmap(":/icons/emblem-photos.png");
     xcenter = ycenter = zcenter = 0.5;
+    auto bsize = QFontMetrics(QApplication::font()).size(Qt::TextSingleLine, "Height:  200");
 
     auto *renderstatus = new QLabel(QString());
     renderstatus->setPixmap(pix.scaled(22, 22, Qt::KeepAspectRatio));
@@ -166,19 +170,23 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
     xval->setValue(settings.value("xsize", "800").toInt());
     xval->setObjectName("xsize");
     xval->setToolTip("Set rendered image width");
+    xval->setMinimumSize(bsize);
     auto *yval = new QSpinBox;
     yval->setRange(100, 10000);
     yval->setStepType(QAbstractSpinBox::AdaptiveDecimalStepType);
     yval->setValue(settings.value("ysize", "600").toInt());
     yval->setObjectName("ysize");
     yval->setToolTip("Set rendered image height");
+    yval->setMinimumSize(bsize);
     settings.endGroup();
     connect(xval, &QAbstractSpinBox::editingFinished, this, &ImageViewer::edit_size);
     connect(yval, &QAbstractSpinBox::editingFinished, this, &ImageViewer::edit_size);
 
     // workaround for incorrect highlight bug on macOS
-    auto *dummy = new QPushButton(QIcon(), "");
+    auto *dummy1 = new QPushButton(QIcon(), "");
-    dummy->hide();
+    dummy1->hide();
+    auto *dummy2 = new QPushButton(QIcon(), "");
+    dummy2->hide();
 
     auto *dossao = new QPushButton(QIcon(":/icons/hd-img.png"), "");
     dossao->setCheckable(true);
@@ -188,6 +196,10 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
     doanti->setCheckable(true);
     doanti->setToolTip("Toggle anti-aliasing");
     doanti->setObjectName("antialias");
+    auto *doshiny = new QPushButton(QIcon(":/icons/image-shiny.png"), "");
+    doshiny->setCheckable(true);
+    doshiny->setToolTip("Toggle shininess");
+    doshiny->setObjectName("shiny");
     auto *dovdw = new QPushButton(QIcon(":/icons/vdw-style.png"), "");
     dovdw->setCheckable(true);
     dovdw->setToolTip("Toggle VDW style representation");
@@ -229,32 +241,41 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
         combo->addItem(gname);
     }
 
-    auto *menuLayout = new QHBoxLayout;
+    auto *menuLayout   = new QHBoxLayout;
+    auto *buttonLayout = new QHBoxLayout;
+    auto *topLayout    = new QVBoxLayout;
+    topLayout->addLayout(menuLayout);
+    topLayout->addLayout(buttonLayout);
+
     menuLayout->addWidget(menuBar);
     menuLayout->addWidget(renderstatus);
     menuLayout->addWidget(new QLabel(" Width: "));
     menuLayout->addWidget(xval);
     menuLayout->addWidget(new QLabel(" Height: "));
     menuLayout->addWidget(yval);
-    menuLayout->addWidget(dummy);
+    menuLayout->addWidget(dummy1);
-    menuLayout->addWidget(dossao);
-    menuLayout->addWidget(doanti);
-    menuLayout->addWidget(dovdw);
-    menuLayout->addWidget(dobox);
-    menuLayout->addWidget(doaxes);
-    menuLayout->addWidget(zoomin);
-    menuLayout->addWidget(zoomout);
-    menuLayout->addWidget(rotleft);
-    menuLayout->addWidget(rotright);
-    menuLayout->addWidget(rotup);
-    menuLayout->addWidget(rotdown);
-    menuLayout->addWidget(recenter);
-    menuLayout->addWidget(reset);
     menuLayout->addWidget(new QLabel(" Group: "));
     menuLayout->addWidget(combo);
+    buttonLayout->addWidget(dummy2);
+    buttonLayout->addWidget(dossao);
+    buttonLayout->addWidget(doanti);
+    buttonLayout->addWidget(doshiny);
+    buttonLayout->addWidget(dovdw);
+    buttonLayout->addWidget(dobox);
+    buttonLayout->addWidget(doaxes);
+    buttonLayout->addWidget(zoomin);
+    buttonLayout->addWidget(zoomout);
+    buttonLayout->addWidget(rotleft);
+    buttonLayout->addWidget(rotright);
+    buttonLayout->addWidget(rotup);
+    buttonLayout->addWidget(rotdown);
+    buttonLayout->addWidget(recenter);
+    buttonLayout->addWidget(reset);
+    buttonLayout->addStretch(1);
 
     connect(dossao, &QPushButton::released, this, &ImageViewer::toggle_ssao);
     connect(doanti, &QPushButton::released, this, &ImageViewer::toggle_anti);
+    connect(doshiny, &QPushButton::released, this, &ImageViewer::toggle_shiny);
     connect(dovdw, &QPushButton::released, this, &ImageViewer::toggle_vdw);
     connect(dobox, &QPushButton::released, this, &ImageViewer::toggle_box);
     connect(doaxes, &QPushButton::released, this, &ImageViewer::toggle_axes);
@@ -268,7 +289,7 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
     connect(reset, &QPushButton::released, this, &ImageViewer::reset_view);
     connect(combo, SIGNAL(currentIndexChanged(int)), this, SLOT(change_group(int)));
 
-    mainLayout->addLayout(menuLayout);
+    mainLayout->addLayout(topLayout);
     mainLayout->addWidget(scrollArea);
     setWindowIcon(QIcon(":/icons/lammps-icon-128x128.png"));
     setWindowTitle(QString("LAMMPS-GUI - Image Viewer - ") + QFileInfo(fileName).fileName());
@@ -278,6 +299,7 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
     // layout has not yet be established, so we need to fix up some pushbutton
     // properties directly since lookup in reset_view() will have failed
     dobox->setChecked(showbox);
+    doshiny->setChecked(shinyfactor > 0.4);
     dovdw->setChecked(vdwfactor > 1.0);
     dovdw->setEnabled(useelements || usediameter || usesigma);
     doaxes->setChecked(showaxes);
@@ -296,16 +318,17 @@ void ImageViewer::reset_view()
 {
     QSettings settings;
     settings.beginGroup("snapshot");
-    xsize     = settings.value("xsize", "800").toInt();
+    xsize       = settings.value("xsize", "800").toInt();
-    ysize     = settings.value("ysize", "600").toInt();
+    ysize       = settings.value("ysize", "600").toInt();
-    zoom      = settings.value("zoom", 1.0).toDouble();
+    zoom        = settings.value("zoom", 1.0).toDouble();
-    hrot      = settings.value("hrot", 60).toInt();
+    hrot        = settings.value("hrot", 60).toInt();
-    vrot      = settings.value("vrot", 30).toInt();
+    vrot        = settings.value("vrot", 30).toInt();
-    vdwfactor = settings.value("vdwstyle", false).toBool() ? 1.6 : 0.5;
+    shinyfactor = settings.value("shinystyle", true).toBool() ? 0.6 : 0.2;
-    showbox   = settings.value("box", true).toBool();
+    vdwfactor   = settings.value("vdwstyle", false).toBool() ? 1.6 : 0.5;
-    showaxes  = settings.value("axes", false).toBool();
+    showbox     = settings.value("box", true).toBool();
-    usessao   = settings.value("ssao", false).toBool();
+    showaxes    = settings.value("axes", false).toBool();
-    antialias = settings.value("antialias", false).toBool();
+    usessao     = settings.value("ssao", false).toBool();
+    antialias   = settings.value("antialias", false).toBool();
     xcenter = ycenter = zcenter = 0.5;
     settings.endGroup();
 
@@ -320,6 +343,8 @@ void ImageViewer::reset_view()
     if (button) button->setChecked(usessao);
     button = findChild<QPushButton *>("antialias");
     if (button) button->setChecked(antialias);
+    button = findChild<QPushButton *>("shiny");
+    if (button) button->setChecked(shinyfactor > 0.4);
     button = findChild<QPushButton *>("vdw");
     if (button) button->setChecked(vdwfactor > 1.0);
     button = findChild<QPushButton *>("box");
@@ -358,6 +383,17 @@ void ImageViewer::toggle_anti()
     createImage();
 }
 
+void ImageViewer::toggle_shiny()
+{
+    auto *button = qobject_cast<QPushButton *>(sender());
+    if (shinyfactor > 0.4)
+        shinyfactor = 0.2;
+    else
+        shinyfactor = 0.6;
+    button->setChecked(shinyfactor > 0.4);
+    createImage();
+}
+
 void ImageViewer::toggle_vdw()
 {
     auto *button = qobject_cast<QPushButton *>(sender());
@@ -508,12 +544,14 @@ void ImageViewer::createImage()
     // use Lennard-Jones sigma for radius, if available
     usesigma               = false;
     const char *pair_style = (const char *)lammps->extract_global("pair_style");
-    if (!useelements && pair_style && (strncmp(pair_style, "lj/", 3) == 0)) {
+    if (!useelements && !usediameter && pair_style && (strncmp(pair_style, "lj/", 3) == 0)) {
         double **sigma = (double **)lammps->extract_pair("sigma");
         if (sigma) {
             usesigma = true;
-            for (int i = 1; i <= ntypes; ++i)
+            for (int i = 1; i <= ntypes; ++i) {
-                adiams += QString("adiam %1 %2 ").arg(i).arg(vdwfactor * sigma[i][i]);
+                if (sigma[i][i] > 0.0)
+                    adiams += QString("adiam %1 %2 ").arg(i).arg(vdwfactor * sigma[i][i]);
+            }
         }
     }
     // adjust pushbutton state and clear adiams string to disable VDW display, if needed
@@ -526,17 +564,20 @@ void ImageViewer::createImage()
         if (button) button->setEnabled(false);
     }
 
+    // color
     if (useelements)
         dumpcmd += blank + "element";
     else
         dumpcmd += blank + settings.value("color", "type").toString();
+
+    // diameter
     if (usediameter && (vdwfactor > 1.0))
         dumpcmd += blank + "diameter";
     else
         dumpcmd += blank + settings.value("diameter", "type").toString();
     dumpcmd += QString(" size %1 %2").arg(xsize).arg(ysize);
     dumpcmd += QString(" zoom %1").arg(zoom);
-    dumpcmd += " shiny 0.5 ";
+    dumpcmd += QString(" shiny %1 ").arg(shinyfactor);
     dumpcmd += QString(" fsaa %1").arg(antialias ? "yes" : "no");
     if (nbondtypes > 0) {
         if (vdwfactor > 1.0)

tools/lammps-gui/imageviewer.h

@@ -46,6 +46,7 @@ private slots:
     void reset_view();
     void toggle_ssao();
     void toggle_anti();
+    void toggle_shiny();
     void toggle_vdw();
     void toggle_box();
     void toggle_axes();
@@ -90,7 +91,7 @@ private:
     QString last_dump_cmd;
     int xsize, ysize;
     int hrot, vrot;
-    double zoom, vdwfactor;
+    double zoom, vdwfactor, shinyfactor;
     double xcenter, ycenter, zcenter;
     bool showbox, showaxes, antialias, usessao, useelements, usediameter, usesigma;
 };

tools/lammps-gui/lammps-gui.appdata.xml

@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<component type="desktop">
+  <id>lammps-gui.desktop</id>
+  <metadata_license>CC-BY-3.0</metadata_license>
+  <project_license>GPL-2.0</project_license>
+  <name>LAMMPS-GUI</name>
+  <summary>
+    Graphical interface to edit, run, plot, and visualize simulations with the LAMMPS MD code
+  </summary>
+
+  <description>
+    <p>LAMMPS-GUI is an editor customized for editing input files for the LAMMPS MD simulation software.  It also includes LAMMPS and thus can run it directly from the GUI.  Furthermore it has facilities to create or view and animate snapshot images, monitor and plot thermodynamic properties and show the console output of the running simulation.</p>
+  </description>
+  <screenshots>
+    <screenshot type="default">
+      <image>https://docs.lammps.org/_images/lammps-gui-main.png</image>
+      <caption>LAMMPS-GUI main editor window</caption>
+    </screenshot>
+    <screenshot>
+      <image>https://docs.lammps.org/_images/lammps-gui-log.png</image>
+      <caption>LAMMPS-GUI output window</caption>
+    </screenshot>
+    <screenshot>
+      <image>https://docs.lammps.org/_images/lammps-gui-chart.png</image>
+      <caption>LAMMPS-GUI chart window</caption>
+    </screenshot>
+    <screenshot>
+      <image>https://docs.lammps.org/_images/lammps-gui-slideshow.png</image>
+      <caption>LAMMPS-GUI slideshow window</caption>
+    </screenshot>
+    <screenshot>
+      <image>https://docs.lammps.org/_images/lammps-gui-image.png</image>
+      <caption>LAMMPS-GUI snapshot image window</caption>
+    </screenshot>
+  </screenshots>
+
+  <url type="homepage">https://www.lammps.org/</url>
+  <url type="bugtracker">https://github.com/lammps/lammps/issues</url>
+  <url type="help">https://docs.lammps.org/stable/</url>
+
+  <update_contact>packages@lammps.org</update_contact>
+  <developer_name>Axel Kohlmeyer</developer_name>
+  <project_group>LAMMPS</project_group>
+  <keywords>
+    <keyword>Molecular Dynamics</keyword>
+    <keyword>Physics</keyword>
+    <keyword>Editor</keyword>
+    <keyword>N-body</keyword>
+  </keywords>
+
+  <provides>
+    <binary>lammps-gui</binary>
+    <binary>lmp</binary>
+  </provides>
+
+  <releases>
+    <release version="1.6.6" timestamp="1722581799">
+      <description>
+        First version packaged in flatpak format
+      </description>
+    </release>
+  </releases>
+</component>

tools/lammps-gui/lammpsgui.cpp

@@ -29,6 +29,7 @@
 #include <QClipboard>
 #include <QCoreApplication>
 #include <QDesktopServices>
+#include <QEvent>
 #include <QFileDialog>
 #include <QFileInfo>
 #include <QFont>
@@ -47,6 +48,7 @@
 #include <QTimer>
 #include <QUrl>
 
+#include <algorithm>
 #include <cstdint>
 #include <cstdlib>
 #include <cstring>
@@ -74,6 +76,7 @@ LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
     qRegisterMetaTypeStreamOperators<QList<QString>>("QList<QString>");
 #endif
 
+    docver = "";
     ui->setupUi(this);
     this->setCentralWidget(ui->textEdit);
     highlighter = new Highlighter(ui->textEdit->document());
@@ -137,8 +140,8 @@ LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
     // check and initialize nthreads setting. Default is to use max if there
     // is no preference but do not override OMP_NUM_THREADS
 #if defined(_OPENMP)
-    // use maximum number of available threads unless OMP_NUM_THREADS was set
+    // use up to 16 available threads unless OMP_NUM_THREADS was set
-    int nthreads = settings.value("nthreads", omp_get_max_threads()).toInt();
+    int nthreads = settings.value("nthreads", std::min(omp_get_max_threads(), 16)).toInt();
     if (!qEnvironmentVariableIsSet("OMP_NUM_THREADS")) {
         qputenv("OMP_NUM_THREADS", std::to_string(nthreads).c_str());
     }
@@ -152,6 +155,8 @@ LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
     lammps_args.push_back(mystrdup("-log"));
     lammps_args.push_back(mystrdup("none"));
 
+    installEventFilter(this);
+
     setWindowIcon(QIcon(":/icons/lammps-icon-128x128.png"));
 
     QFont all_font("Arial", -1);
@@ -355,7 +360,7 @@ LammpsGui::LammpsGui(QWidget *parent, const char *filename) :
 #undef ADD_STYLES
 
     settings.beginGroup("reformat");
-    ui->textEdit->setReformatOnReturn(settings.value("return", true).toBool());
+    ui->textEdit->setReformatOnReturn(settings.value("return", false).toBool());
     ui->textEdit->setAutoComplete(settings.value("automatic", true).toBool());
     settings.endGroup();
 }
@@ -713,6 +718,7 @@ void LammpsGui::quit()
     lammpsstatus->hide();
     lammps.finalize();
 
+    autoSave();
     if (ui->textEdit->document()->isModified()) {
         QMessageBox msg;
         msg.setWindowTitle("Unsaved Changes");
@@ -1002,6 +1008,7 @@ void LammpsGui::do_run(bool use_buffer)
         return;
     }
 
+    autoSave();
     if (!use_buffer && ui->textEdit->document()->isModified()) {
         QMessageBox msg;
         msg.setWindowTitle("Unsaved Changes");
@@ -1217,6 +1224,35 @@ void LammpsGui::view_variables()
     }
 }
 
+void LammpsGui::setDocver()
+{
+    QString git_branch = (const char *)lammps.extract_global("git_branch");
+    if ((git_branch == "stable") || (git_branch == "maintenance")) {
+        docver = "/stable/";
+    } else if (git_branch == "release") {
+        docver = "/";
+    } else {
+        docver = "/latest/";
+    }
+}
+
+void LammpsGui::autoSave()
+{
+    // no need to auto-save, if the document has no name or is not modified.
+    QString fileName = current_file;
+    if (fileName.isEmpty()) return;
+    if (!ui->textEdit->document()->isModified()) return;
+
+    // check preference
+    bool autosave = false;
+    QSettings settings;
+    settings.beginGroup("reformat");
+    autosave = settings.value("autosave", false).toBool();
+    settings.endGroup();
+
+    if (autosave) write_file(fileName);
+}
+
 void LammpsGui::about()
 {
     std::string version = "This is LAMMPS-GUI version " LAMMPS_GUI_VERSION;
@@ -1328,7 +1364,8 @@ void LammpsGui::help()
 
 void LammpsGui::manual()
 {
-    QDesktopServices::openUrl(QUrl("https://docs.lammps.org/"));
+    if (docver.isEmpty()) setDocver();
+    QDesktopServices::openUrl(QUrl(QString("https://docs.lammps.org%1").arg(docver)));
 }
 
 void LammpsGui::tutorial()
@@ -1338,7 +1375,9 @@ void LammpsGui::tutorial()
 
 void LammpsGui::howto()
 {
-    QDesktopServices::openUrl(QUrl("https://docs.lammps.org/Howto_lammps_gui.html"));
+    if (docver.isEmpty()) setDocver();
+    QDesktopServices::openUrl(
+        QUrl(QString("https://docs.lammps.org%1Howto_lammps_gui.html").arg(docver)));
 }
 
 void LammpsGui::defaults()
@@ -1395,7 +1434,7 @@ void LammpsGui::preferences()
         }
         if (imagewindow) imagewindow->createImage();
         settings.beginGroup("reformat");
-        ui->textEdit->setReformatOnReturn(settings.value("return", true).toBool());
+        ui->textEdit->setReformatOnReturn(settings.value("return", false).toBool());
         ui->textEdit->setAutoComplete(settings.value("automatic", true).toBool());
         settings.endGroup();
     }
@@ -1488,6 +1527,13 @@ void LammpsGui::start_lammps()
     }
 }
 
+bool LammpsGui::eventFilter(QObject *watched, QEvent *event)
+{
+    if (event->type() == QEvent::Close) {
+        autoSave();
+    }
+    return QWidget::eventFilter(watched, event);
+}
 // Local Variables:
 // c-basic-offset: 4
 // End:

tools/lammps-gui/lammpsgui.h

@@ -16,6 +16,7 @@
 
 #include <QMainWindow>
 
+#include <QEvent>
 #include <QGridLayout>
 #include <QList>
 #include <QPair>
@@ -69,6 +70,9 @@ protected:
     void do_run(bool use_buffer);
     void start_lammps();
     void run_done();
+    void setDocver();
+    void autoSave();
+    bool eventFilter(QObject *watched, QEvent *event) override;
 
 public slots:
     void quit();
@@ -132,6 +136,7 @@ private:
 
     LammpsWrapper lammps;
     LammpsRunner *runner;
+    QString docver;
     std::string plugin_path;
     bool is_running;
     int run_counter;

tools/lammps-gui/lammpsgui.qrc

@@ -42,6 +42,7 @@
     <file>icons/help-browser.png</file>
     <file>icons/help-faq.png</file>
     <file>icons/help-tutorial.png</file>
+    <file>icons/image-shiny.png</file>
     <file>icons/image-x-generic.png</file>
     <file>icons/media-playback-start-2.png</file>
     <file>icons/media-playlist-repeat.png</file>

tools/lammps-gui/org.lammps.lammps-gui.yml

@@ -0,0 +1,111 @@
+id: org.lammps.lammps-gui
+runtime: org.kde.Platform
+runtime-version: "5.15-23.08"
+sdk: org.kde.Sdk
+command: lammps-gui
+finish-args:
+  - --share=ipc
+  - --socket=fallback-x11
+  - --socket=wayland
+  - --filesystem=host
+build-options:
+  build-args:
+    - --share=network
+rename-icon: lammps
+rename-desktop-file: lammps-gui.desktop
+rename-appdata-file: lammps-gui.appdata.xml
+rename-mime-file: lammps-input.xml
+modules:
+  - name: lammps-gui
+    buildsystem: cmake-ninja
+    builddir: true
+    subdir: cmake
+    config-opts:
+      - -D PKG_AMOEBA=yes
+      - -D PKG_ASPHERE=yes
+      - -D PKG_AWPMD=yes
+      - -D PKG_BOCS=yes
+      - -D PKG_BODY=yes
+      - -D PKG_BPM=yes
+      - -D PKG_BROWNIAN=yes
+      - -D PKG_CG-DNA=yes
+      - -D PKG_CG-SPICA=yes
+      - -D PKG_CLASS2=yes
+      - -D PKG_COLLOID=yes
+      - -D PKG_COLVARS=yes
+      - -D PKG_COMPRESS=yes
+      - -D PKG_CORESHELL=yes
+      - -D PKG_DIELECTRIC=yes
+      - -D PKG_DIFFRACTION=yes
+      - -D PKG_DIPOLE=yes
+      - -D PKG_DPD-BASIC=yes
+      - -D PKG_DPD-MESO=yes
+      - -D PKG_DPD-REACT=yes
+      - -D PKG_DPD-SMOOTH=yes
+      - -D PKG_DRUDE=yes
+      - -D PKG_EFF=yes
+      - -D PKG_ELECTRODE=yes
+      - -D PKG_EXTRA-COMMAND=yes
+      - -D PKG_EXTRA-COMPUTE=yes
+      - -D PKG_EXTRA-DUMP=yes
+      - -D PKG_EXTRA-FIX=yes
+      - -D PKG_EXTRA-MOLECULE=yes
+      - -D PKG_EXTRA-PAIR=yes
+      - -D PKG_FEP=yes
+      - -D PKG_GRANULAR=yes
+      - -D PKG_GPU=yes
+      - -D GPU_API=opencl
+      - -D PKG_INTERLAYER=yes
+      - -D PKG_KSPACE=yes
+      - -D PKG_LEPTON=yes
+      - -D PKG_MACHDYN=yes
+      - -D PKG_MANYBODY=yes
+      - -D PKG_MANIFOLD=yes
+      - -D PKG_MC=yes
+      - -D PKG_MEAM=yes
+      - -D PKG_MESONT=yes
+      - -D PKG_MGPT=yes
+      - -D PKG_MISC=yes
+      - -D PKG_ML-IAP=yes
+      - -D PKG_ML-PACE=yes
+      - -D PKG_ML-POD=yes
+      - -D PKG_ML-RANN=yes
+      - -D PKG_ML-SNAP=yes
+      - -D PKG_ML-UF3=yes
+      - -D PKG_MOFFF=yes
+      - -D PKG_MOLECULE=yes
+      - -D PKG_OPENMP=yes
+      - -D PKG_OPT=yes
+      - -D PKG_ORIENT=yes
+      - -D PKG_PERI=yes
+      - -D PKG_PHONON=yes
+      - -D PKG_PLUGIN=yes
+      - -D PKG_POEMS=yes
+      - -D PKG_PTM=yes
+      - -D PKG_PYTHON=yes
+      - -D PKG_QEQ=yes
+      - -D PKG_QTB=yes
+      - -D PKG_REACTION=yes
+      - -D PKG_REAXFF=yes
+      - -D PKG_RIGID=yes
+      - -D PKG_SHOCK=yes
+      - -D PKG_SMTBQ=yes
+      - -D PKG_SPH=yes
+      - -D PKG_SPIN=yes
+      - -D PKG_SRD=yes
+      - -D PKG_TALLY=yes
+      - -D PKG_UEF=yes
+      - -D PKG_VORONOI=yes
+      - -D PKG_YAFF=yes
+      - -D BUILD_LAMMPS_GUI=yes
+      - -D BUILD_SHARED_LIBS=yes
+      - -D CMAKE_CXX_COMPILER=g++
+      - -D CMAKE_C_COMPILER=gcc
+      - -D CMAKE_Fortran_COMPILER=gfortran
+      - -D CMAKE_BUILD_TYPE=Release
+      - -D DOWNLOAD_POTENTIALS=no
+      - -D BUILD_TOOLS=yes
+    sources:
+      - type: git
+        url: https://github.com/akohlmey/lammps.git
+        branch: collected-small-changes

tools/lammps-gui/preferences.cpp

@@ -137,6 +137,8 @@ void Preferences::accept()
     if (box) settings->setValue("antialias", box->isChecked());
     box = tabWidget->findChild<QCheckBox *>("ssao");
     if (box) settings->setValue("ssao", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("shiny");
+    if (box) settings->setValue("shinystyle", box->isChecked());
     box = tabWidget->findChild<QCheckBox *>("box");
     if (box) settings->setValue("box", box->isChecked());
     box = tabWidget->findChild<QCheckBox *>("axes");
@@ -196,6 +198,8 @@ void Preferences::accept()
     if (box) settings->setValue("return", box->isChecked());
     box = tabWidget->findChild<QCheckBox *>("autoval");
     if (box) settings->setValue("automatic", box->isChecked());
+    box = tabWidget->findChild<QCheckBox *>("savval");
+    if (box) settings->setValue("autosave", box->isChecked());
     settings->endGroup();
 
     QDialog::accept();
@@ -444,6 +448,7 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     auto *zoom  = new QLabel("Zoom factor:");
     auto *anti  = new QLabel("Antialias:");
     auto *ssao  = new QLabel("HQ Image mode:");
+    auto *shiny = new QLabel("Shiny Image mode:");
     auto *bbox  = new QLabel("Show Box:");
     auto *axes  = new QLabel("Show Axes:");
     auto *vdw   = new QLabel("VDW Style:");
@@ -455,6 +460,7 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     auto *zval = new QLineEdit(settings->value("zoom", "1.0").toString());
     auto *aval = new QCheckBox;
     auto *sval = new QCheckBox;
+    auto *hval = new QCheckBox;
     auto *bval = new QCheckBox;
     auto *eval = new QCheckBox;
     auto *vval = new QCheckBox;
@@ -462,6 +468,8 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     sval->setObjectName("ssao");
     aval->setCheckState(settings->value("antialias", false).toBool() ? Qt::Checked : Qt::Unchecked);
     aval->setObjectName("anti");
+    hval->setCheckState(settings->value("shinystyle", true).toBool() ? Qt::Checked : Qt::Unchecked);
+    hval->setObjectName("shiny");
     bval->setCheckState(settings->value("box", true).toBool() ? Qt::Checked : Qt::Unchecked);
     bval->setObjectName("box");
     eval->setCheckState(settings->value("axes", false).toBool() ? Qt::Checked : Qt::Unchecked);
@@ -508,6 +516,8 @@ SnapshotTab::SnapshotTab(QSettings *_settings, QWidget *parent) :
     grid->addWidget(aval, i++, 1, Qt::AlignTop);
     grid->addWidget(ssao, i, 0, Qt::AlignTop);
     grid->addWidget(sval, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(shiny, i, 0, Qt::AlignTop);
+    grid->addWidget(hval, i++, 1, Qt::AlignVCenter);
     grid->addWidget(bbox, i, 0, Qt::AlignTop);
     grid->addWidget(bval, i++, 1, Qt::AlignVCenter);
     grid->addWidget(axes, i, 0, Qt::AlignTop);
@@ -536,29 +546,34 @@ EditorTab::EditorTab(QSettings *_settings, QWidget *parent) : QWidget(parent), s
     auto *namelbl  = new QLabel("Name width:");
     auto *retlbl   = new QLabel("Reformat with 'Enter':");
     auto *autolbl  = new QLabel("Automatic completion:");
+    auto *savlbl   = new QLabel("Auto-save on 'Run' and 'Quit':");
     auto *cmdval   = new QSpinBox;
     auto *typeval  = new QSpinBox;
     auto *idval    = new QSpinBox;
     auto *nameval  = new QSpinBox;
     auto *retval   = new QCheckBox;
     auto *autoval  = new QCheckBox;
+    auto *savval   = new QCheckBox;
+    cmdval->setObjectName("cmdval");
     cmdval->setRange(1, 32);
     cmdval->setValue(settings->value("command", "16").toInt());
-    cmdval->setObjectName("cmdval");
+    typeval->setObjectName("typeval");
     typeval->setRange(1, 32);
     typeval->setValue(settings->value("type", "4").toInt());
-    typeval->setObjectName("typeval");
+    idval->setObjectName("idval");
     idval->setRange(1, 32);
     idval->setValue(settings->value("id", "8").toInt());
-    idval->setObjectName("idval");
+    nameval->setObjectName("nameval");
     nameval->setRange(1, 32);
     nameval->setValue(settings->value("name", "8").toInt());
-    nameval->setObjectName("nameval");
-    retval->setCheckState(settings->value("return", true).toBool() ? Qt::Checked : Qt::Unchecked);
     retval->setObjectName("retval");
+    retval->setCheckState(settings->value("return", false).toBool() ? Qt::Checked : Qt::Unchecked);
+    autoval->setObjectName("autoval");
     autoval->setCheckState(settings->value("automatic", true).toBool() ? Qt::Checked
                                                                        : Qt::Unchecked);
-    autoval->setObjectName("autoval");
+    savval->setObjectName("savval");
+    savval->setCheckState(settings->value("autosave", false).toBool() ? Qt::Checked
+                                                                      : Qt::Unchecked);
     settings->endGroup();
 
     int i = 0;
@@ -575,6 +590,8 @@ EditorTab::EditorTab(QSettings *_settings, QWidget *parent) : QWidget(parent), s
     grid->addWidget(retval, i++, 1, Qt::AlignVCenter);
     grid->addWidget(autolbl, i, 0, Qt::AlignTop);
     grid->addWidget(autoval, i++, 1, Qt::AlignVCenter);
+    grid->addWidget(savlbl, i, 0, Qt::AlignTop);
+    grid->addWidget(savval, i++, 1, Qt::AlignVCenter);
 
     grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), i, 0);
     grid->addItem(new QSpacerItem(100, 100, QSizePolicy::Minimum, QSizePolicy::Expanding), i, 1);

tools/valgrind/MPICH.supp

@@ -39,3 +39,45 @@
    fun:PMPI_Init
    fun:main
 }
+{
+   MPICH_MPI_init4
+   Memcheck:Leak
+   match-leak-kinds: reachable
+   fun:calloc
+   fun:psmx3_recv_generic
+   ...
+   obj:*
+   ...
+   fun:MPIDI_Init.constprop.0
+   ...
+   fun:PMPI_Init
+   fun:main
+}
+{
+   MPICH_MPI_init5
+   Memcheck:Leak
+   match-leak-kinds: reachable
+   fun:calloc
+   obj:*
+   ...
+   fun: usdf_getinfo.lto_priv.0
+   ...
+   fun:MPID_Init.constprop.0
+   ...
+   fun:PMPI_Init
+   fun:main
+}
+{
+   MPICH_MPI_init6
+   Memcheck:Leak
+   match-leak-kinds: reachable
+   fun:malloc
+   fun:strdup
+   obj:*
+   ...
+   fun:MPID_Init.constprop.0
+   ...
+   obj:*
+   fun:PMPI_Init
+   fun:main
+}

tools/valgrind/OpenMP.supp

@@ -193,3 +193,13 @@
    fun:GOMP_parallel
 }
 
+{
+   gomp_realloc1
+   Memcheck:Leak
+   match-leak-kinds: reachable
+   fun:realloc
+   fun:gomp_realloc
+   fun:gomp_team_start
+   fun:GOMP_parallel
+}
+

unittest/CMakeLists.txt

@@ -28,6 +28,11 @@ add_library(GTest::GMock ALIAS gmock)
 add_library(GTest::GTestMain ALIAS gtest_main)
 add_library(GTest::GMockMain ALIAS gmock_main)
 
+option(SKIP_DEATH_TESTS "Do not run 'death tests' to reduce false positives in valgrind" OFF)
+mark_as_advanced(SKIP_DEATH_TESTS)
+if(SKIP_DEATH_TESTS)
+  add_compile_definitions(LAMMPS_SKIP_DEATH_TESTS)
+endif()
 # import
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
   add_compile_options(${_FLAG})

unittest/c-library/test_library_properties.cpp

@@ -547,13 +547,22 @@ TEST_F(LibraryProperties, neighlist)
     lammps_command(lmp, "run 0 post no");
     if (!verbose) ::testing::internal::GetCapturedStdout();
 
-    int nhisto =
+    void *ptr  = lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, 0);
-        *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 0, 0);
+    int nhisto = *(double *)ptr;
-    int nskip = *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 1, 0);
+    lammps_free(ptr);
-    double minval =
+
-        *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 2, 0);
+    ptr       = lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 1, 0);
-    double maxval =
+    int nskip = *(double *)ptr;
-        *(double *)lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 3, 0);
+    lammps_free(ptr);
+
+    ptr           = lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 2, 0);
+    double minval = *(double *)ptr;
+    lammps_free(ptr);
+
+    ptr           = lammps_extract_fix(lmp, "dist", LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR, 3, 0);
+    double maxval = *(double *)ptr;
+    lammps_free(ptr);
+
     // 21 pair distances counted, none skipped, smallest 1.0, largest 2.1
     EXPECT_EQ(nhisto, 21);
     EXPECT_EQ(nskip, 0);

unittest/testing/core.h

@@ -32,6 +32,12 @@ using LAMMPS_NS::LAMMPSException;
 
 using ::testing::ContainsRegex;
 
+#if defined(LAMMPS_SKIP_DEATH_TESTS)
+#define TEST_FAILURE(errmsg, ...)                             \
+    {                                                         \
+        ;                                                     \
+    }
+#else
 #define TEST_FAILURE(errmsg, ...)                             \
     {                                                         \
         ::testing::internal::CaptureStdout();                 \
@@ -39,6 +45,7 @@ using ::testing::ContainsRegex;
         auto mesg = ::testing::internal::GetCapturedStdout(); \
         ASSERT_THAT(mesg, ContainsRegex(errmsg));             \
     }
+#endif
 
 // whether to print verbose output (i.e. not capturing LAMMPS screen output).
 extern bool verbose;