Merge pull request #4403 from akohlmey/collected-small-changes

Collected small changes and fixes

doc/doxygen/Doxyfile.in

@@ -2,7 +2,7 @@
 
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "LAMMPS Programmer's Guide"
-PROJECT_NUMBER         = "4 May 2022"
+PROJECT_NUMBER         = "19 November 2024"
 PROJECT_BRIEF          = "Documentation of the LAMMPS library interface and Python wrapper"
 PROJECT_LOGO           = lammps-logo.png
 CREATE_SUBDIRS         = NO

doc/src/Intro_authors.rst

@@ -8,6 +8,8 @@ send an email to all of them at this address: "developers at
 lammps.org".  General questions about LAMMPS should be posted in the
 `LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
 
+.. We need to keep this file in sync with https://www.lammps.org/authors.html
+
 .. raw:: latex
 
    \small
@@ -27,7 +29,7 @@ lammps.org".  General questions about LAMMPS should be posted in the
    * - `Steve Plimpton <sjp_>`_
      - SNL (retired)
      - sjplimp at gmail.com
-     - MD kernels, parallel algorithms & scalability, code structure and design
+     - original author, MD kernels, parallel algorithms & scalability, code structure and design
    * - `Aidan Thompson <at_>`_
      - SNL
      - athomps at sandia.gov

doc/src/Packages_details.rst

@@ -2789,14 +2789,15 @@ implements smoothed particle hydrodynamics (SPH) for liquids.  See the
 related :ref:`MACHDYN package <PKG-MACHDYN>` package for smooth Mach dynamics
 (SMD) for solids.
 
-This package contains ideal gas, Lennard-Jones equation of states,
-Tait, and full support for complete (i.e. internal-energy dependent)
-equations of state.  It allows for plain or Monaghans XSPH integration
-of the equations of motion.  It has options for density continuity or
-density summation to propagate the density field.  It has
-:doc:`set <set>` command options to set the internal energy and density
-of particles from the input script and allows the same quantities to
-be output with thermodynamic output or to dump files via the :doc:`compute property/atom <compute_property_atom>` command.
+This package contains ideal gas, Lennard-Jones equation of states, Tait,
+and full support for complete (i.e. internal-energy dependent) equations
+of state.  It allows for plain or Monaghans XSPH integration of the
+equations of motion.  It has options for density continuity or density
+summation to propagate the density field.  It has :doc:`set <set>`
+command options to set the internal energy and density of particles from
+the input script and allows the same quantities to be output with
+thermodynamic output or to dump files via the :doc:`compute
+property/atom <compute_property_atom>` command.
 
 **Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
 Dynamics, Ernst Mach Institute, Germany).
@@ -2809,6 +2810,17 @@ Dynamics, Ernst Mach Institute, Germany).
 * ``examples/PACKAGES/sph``
 * https://www.lammps.org/movies.html#sph
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
+.. note::
+
+   Please also note, that the :ref:`RHEO package <PKG-RHEO>` offers
+   similar functionality in a more modern and flexible implementation.
+
 ----------
 
 .. _PKG-SPIN:

doc/src/bond_bpm_rotational.rst

@@ -155,7 +155,7 @@ page on BPMs.
 If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
 The recommended bond communication distance no longer depends on bond failure
-coefficients (which are ignored) but instead corresponds to the typical heurestic
+coefficients (which are ignored) but instead corresponds to the typical heuristic
 maximum strain used by typical non-bpm bond styles. Similar behavior to *break no*
 can also be attained by setting arbitrarily high values for all four failure
 coefficients. One cannot use *break no* with *smooth yes*.

doc/src/bond_bpm_spring.rst

@@ -119,7 +119,7 @@ If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
 during a simulation run. This will prevent some unnecessary calculation.
 The recommended bond communication distance no longer depends on the value of
 :math:`\epsilon_c` (which is ignored) but instead corresponds to the typical
-heurestic maximum strain used by typical non-bpm bond styles. Similar behavior
+heuristic maximum strain used by typical non-bpm bond styles. Similar behavior
 to *break no* can also be attained by setting an arbitrarily high value of
 :math:`\epsilon_c`. One cannot use *break no* with *smooth yes*.
 

doc/src/compute_sph_e_atom.rst

@@ -33,6 +33,12 @@ particle.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 The value of the internal energy will be 0.0 for atoms not in the
 specified compute group.
 

doc/src/compute_sph_rho_atom.rst

@@ -32,6 +32,12 @@ kernel function interpolation using "pair style sph/rhosum".
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 The value of the SPH density will be 0.0 for atoms not in the
 specified compute group.
 

doc/src/compute_sph_t_atom.rst

@@ -37,6 +37,12 @@ particles, i.e. a Smooth-Particle Hydrodynamics particle.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 The value of the internal energy will be 0.0 for atoms not in the
 specified compute group.
 

doc/src/fix_rheo.rst

@@ -64,7 +64,7 @@ Description
 
 Perform time integration for RHEO particles, updating positions, velocities,
 and densities. For a detailed breakdown of the integration timestep and
-numerical details, see :ref:`(Palermo) <rheo_palermo>`. For an overview
+numerical details, see :ref:`(Palermo) <fix_rheo_palermo>`. For an overview
 and list of other features available in the RHEO package, see
 :doc:`the RHEO howto <Howto_rheo>`.
 
@@ -101,7 +101,7 @@ A modified form of Fickian particle shifting can be enabled with the
 more uniform spatial distribution. By default, shifting does not consider the
 type of a particle and therefore may be inappropriate in systems consisting
 of multiple atom types representing multiple fluid phases. However, two
-optional subarguments can follow the *shift* keyword, *exclude/type* and
+optional sub-arguments can follow the *shift* keyword, *exclude/type* and
 *scale/cross/type* to adjust shifting at fluid interfaces.
 
 The *exclude/type* option lets the user specify a list of atom types which
@@ -155,7 +155,7 @@ threshold for this classification is set by the numerical value of
 By default, RHEO integrates particles' densities using a mass diffusion
 equation. Alternatively, one can update densities every timestep by performing
 a kernel summation of the masses of neighboring particles by specifying the *rho/sum*
-keyword. Following this keyword, one may include the optional *self/mass* subargument
+keyword. Following this keyword, one may include the optional *self/mass* sub-argument
 which modifies the behavior of the density summation. Typically, the density
 :math:`\rho` of a particle is calculated as the sum over neighbors
 
@@ -218,11 +218,11 @@ Default
 
 ----------
 
-.. _rheo_palermo:
+.. _fix_rheo_palermo:
 
 **(Palermo)** Palermo, Wolf, Clemmer, O'Connor, Phys. Fluids, 36, 113337 (2024).
 
-.. _rheo_yang:
+.. _fix_rheo_yang:
 
 **(Yang)** Yang, Rakhsha, Hu, Negrut, J. Comp. Physics, 458, 111079 (2022).
 

doc/src/fix_sph.rst

@@ -32,6 +32,12 @@ Hydrodynamics.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_sph_stationary.rst

@@ -32,6 +32,12 @@ space.  SPH stands for Smoothed Particle Hydrodynamics.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_sph_heatconduction.rst

@@ -30,6 +30,12 @@ The transport model is the diffusion equation for the internal energy.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 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.

doc/src/pair_sph_idealgas.rst

@@ -36,6 +36,12 @@ particles from interpenetrating :ref:`(Monaghan) <ideal-Monoghan>`.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 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.

doc/src/pair_sph_lj.rst

@@ -34,6 +34,12 @@ interpenetrating :ref:`(Monaghan) <Monoghan>`.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 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.

doc/src/pair_sph_rhosum.rst

@@ -29,6 +29,12 @@ SPH particles by kernel function interpolation, every Nstep timesteps.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 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.

doc/src/pair_sph_taitwater.rst

@@ -41,6 +41,12 @@ prevent particles from interpenetrating :ref:`(Monaghan) <Monaghan>`.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 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.

doc/src/pair_sph_taitwater_morris.rst

@@ -37,6 +37,12 @@ This pair style also computes laminar viscosity :ref:`(Morris) <Morris>`.
 See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 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.

doc/src/set.rst

@@ -516,6 +516,12 @@ Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
 and density of smoothed particle hydrodynamics (SPH) particles.  See
 `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
 Keyword *smd/mass/density* sets the mass of all selected particles, but
 it is only applicable to the Smooth Mach Dynamics package MACHDYN.  It
 assumes that the particle volume has already been correctly set and

doc/utils/sphinx-config/false_positives.txt

@@ -2499,6 +2499,7 @@ neel
 Neel
 Neelov
 Negre
+Negrut
 nelem
 Nelement
 Nelements
@@ -3116,6 +3117,7 @@ Rafferty
 rahman
 Rahman
 Rajamanickam
+Rakhsha
 Ralf
 Raman
 ramped

examples/comb/README

@@ -20,5 +20,3 @@ Examples:
 4. in.comb.Cu2O.elastic: Cu2O crystal, qeq on, minimizes, then calculates
    elastic constants
 5. in.comb.HfO2: HfO2 polymorphs: Monoclinic HfO2 NVT @ 300K
-6. in.comb.CuaS: Metallic Cu and amorphous silica interface, qeq on,
-	five step NVE run

src/COLVARS/colvarproxy_lammps.cpp

@@ -204,7 +204,7 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
   double xtmp = pos2.x - pos1.x;
   double ytmp = pos2.y - pos1.y;
   double ztmp = pos2.z - pos1.z;
-  _lmp->domain->minimum_image(xtmp,ytmp,ztmp);
+  _lmp->domain->minimum_image_big(xtmp,ytmp,ztmp);
   return {xtmp, ytmp, ztmp};
 }
 

src/PHONON/fix_phonon.cpp

@@ -400,7 +400,7 @@ void FixPhonon::end_of_step()
       ndim = sysdim;
       for (i = 1; i < nucell; ++i) {
         for (idim = 0; idim < sysdim; ++idim) dist2orig[idim] = Rnow[idx][ndim++] - Rnow[idx][idim];
-        domain->minimum_image(dist2orig);
+        domain->minimum_image_big(dist2orig);
         for (idim = 0; idim < sysdim; ++idim) basis[i][idim] += dist2orig[idim];
       }
     }

src/REAXFF/fix_qtpie_reaxff.cpp

@@ -49,7 +49,6 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 
 static constexpr double CONV_TO_EV = 14.4;
-static constexpr double SMALL = 1.0e-14;
 static constexpr double QSUMSMALL = 0.00001;
 static constexpr double ANGSTROM_TO_BOHRRADIUS = 1.8897261259;
 
@@ -1101,7 +1100,6 @@ void FixQtpieReaxFF::calc_chi_eff()
   memset(&chi_eff[0],0,atom->nmax*sizeof(double));
 
   const auto x = (const double * const *)atom->x;
-  const int ntypes = atom->ntypes;
   const int *type = atom->type;
 
   double dist,overlap,sum_n,sum_d,expa,expb,chia,chib,phia,phib,p,m;

src/RIGID/fix_ehex.cpp

@@ -434,7 +434,7 @@ bool FixEHEX::check_cluster(tagint *shake_atom, int n, Region *region)
 
       // take into account pbc
 
-      domain->minimum_image(xtemp);
+      domain->minimum_image_big(xtemp);
 
       for (int k = 0; k < 3; k++) xcom[k] += mi * (x[lid[0]][k] + xtemp[k]);
     }

src/angle_zero.cpp

@@ -54,13 +54,13 @@ void AngleZero::compute(int eflag, int vflag)
 
 void AngleZero::settings(int narg, char **arg)
 {
-  if ((narg != 0) && (narg != 1)) error->all(FLERR, "Illegal angle_style command");
+  if (narg > 1) error->all(FLERR, "Too many angle_style zero keywords");
 
   if (narg == 1) {
     if (strcmp("nocoeff", arg[0]) == 0)
       coeffflag = 0;
     else
-      error->all(FLERR, "Illegal angle_style command");
+      error->all(FLERR, "Unknown angle_style zero keyword {}", arg[0]);
   }
 }
 

src/dump.cpp

@@ -73,6 +73,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) :
 
   clearstep = 0;
   sort_flag = 0;
+  sortcol = 0;
   balance_flag = 0;
   append_flag = 0;
   buffer_allow = 0;

src/fix_vector.cpp

@@ -114,9 +114,11 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
         error->all(FLERR, "Fix for fix {} vector not computed at compatible time", val.id);
 
       if (val.argindex == 0)
+        value = ifix->extscalar;
+      else if (ifix->extvector >= 0)
         value = ifix->extvector;
       else
-        value = ifix->extarray;
+        value = ifix->extlist[val.argindex - 1];
       val.val.f = ifix;
 
     } else if (val.which == ArgInfo::VARIABLE) {

src/library.cpp

@@ -519,7 +519,7 @@ must be freed with :cpp:func:`lammps_free` after use to avoid a memory leak.
 \endverbatim
  *
  * \param  handle  pointer to a previously created LAMMPS instance
- * \param  cmd     string with a single LAMMPS input line
+ * \param  line    string with a single LAMMPS input line
  * \return         string with expanded line */
 
 char *lammps_expand(void *handle, const char *line)

src/lmptype.h

@@ -287,7 +287,7 @@ struct multitype {
     int64_t b;
   } data;
 
-  multitype() : type(LAMMPS_NONE) { data.d = 0.0; }
+  multitype() noexcept : type(LAMMPS_NONE) { data.d = 0.0; }
   multitype(const multitype &) = default;
   multitype(multitype &&) = default;
   ~multitype() = default;

src/tokenizer.h

@@ -59,17 +59,21 @@ class TokenizerException : public std::exception {
   std::string message;
 
  public:
-  // remove unused default constructor
+  /** The default constructor is disabled */
   TokenizerException() = delete;
 
   /** Thrown during retrieving or skipping tokens
    *
    * \param   msg     String with error message
-   * \param  token  String of the token/word that caused the error */
+   * \param   token   String of the token or word that caused the error */
   explicit TokenizerException(const std::string &msg, const std::string &token);
 
   /** Retrieve message describing the thrown exception
-   * \return string with error message */
+   *
+   * This function provides the message that can be retrieved when the corresponding
+   * exception is caught.
+   *
+   * \return  String with error message */
   const char *what() const noexcept override { return message.c_str(); }
 };
 

src/utils.h

@@ -59,7 +59,7 @@ namespace utils {
 
   void missing_cmd_args(const std::string &file, int line, const std::string &cmd, Error *error);
 
-  /* Internal function handling the argument list for logmesg(). */
+  /*! Internal function handling the argument list for logmesg(). */
 
   void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args);
 
@@ -426,12 +426,11 @@ This functions adds the following case to :cpp:func:`utils::bounds() <LAMMPS_NS:
    * \param ref     per-grid reference from input script, e.g. "c_10:grid:data[2]"
    * \param nevery  frequency at which caller will access fix for per-grid info,
    *                ignored when reference is to a compute
+   * \param id     ID of Compute or Fix
+   * \param igrid  which grid is referenced (0 to N-1)
+   * \param idata  which data on grid is referenced (0 to N-1)
+   * \param index  which column of data is referenced (0 for vec, 1-N for array)
    * \param lmp     pointer to top-level LAMMPS class instance
-   * \param verify  check bounds for interaction type
-   * \return id     ID of Compute or Fix
-   * \return igrid  which grid is referenced (0 to N-1)
-   * \return idata  which data on grid is referenced (0 to N-1)
-   * \return index  which column of data is referenced (0 for vec, 1-N for array)
    * \return        ArgINFO::COMPUTE or FIX or UNKNOWN or NONE */
 
   int check_grid_reference(char *errstr, char *ref, int nevery, char *&id, int &igrid, int &idata,
@@ -442,7 +441,10 @@ This functions adds the following case to :cpp:func:`utils::bounds() <LAMMPS_NS:
    * Format of grid ID reference = id:gname:dname.
    * Return vector with the 3 sub-strings.
    *
-   * \param name = complete grid ID
+   * \param file     name of source file for error message
+   * \param line     line number in source file for error message
+   * \param name     complete grid ID
+   * \param error    pointer to Error class
    * \return std::vector<std::string> containing the 3 sub-strings  */
 
   std::vector<std::string> parse_grid_id(const char *file, int line, const std::string &name,

tools/lammps-gui/CMakeLists.txt

@@ -205,7 +205,7 @@ 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}")
-  set(FLATPAK_BUNDLE "LAMMPS_GUI-Linux-amd64-${LAMMPS_RELEASE}.flatpak")
+  set(FLATPAK_BUNDLE "LAMMPS-Linux-x86_64-GUI-${LAMMPS_RELEASE}.flatpak")
   add_custom_target(flatpak
     COMMAND ${FLATPAK_COMMAND} --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
     COMMAND ${FLATPAK_BUILDER} --force-clean --verbose --repo=${CMAKE_CURRENT_BINARY_DIR}/flatpak-repo

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

@@ -56,6 +56,9 @@
   <releases>
     <release version="1.6.11" timestamp="1725080055">
       <description>
+        move cursor to end of log buffer before inserting new text
+        remove empirical filter to remove outliers from corrupted data
+        change tutorial download URL to tutorial website
       </description>
     </release>
     <release version="1.6.10" timestamp="1724585189">

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

@@ -88,6 +88,7 @@ modules:
       - -D PKG_QTB=yes
       - -D PKG_REACTION=yes
       - -D PKG_REAXFF=yes
+      - -D PKG_RHEO=yes
       - -D PKG_RIGID=yes
       - -D PKG_SHOCK=yes
       - -D PKG_SMTBQ=yes