Merge pull request lammps#3919 from akohlmey/collected-small-fixes

Collected small fixes and updates

doc/src/Build_basics.rst

@@ -488,8 +488,9 @@ using CMake or Make.
 
       .. code-block:: bash
 
-         -D BUILD_TOOLS=value         # yes or no (default)
-         -D BUILD_LAMMPS_SHELL=value  # yes or no (default)
+         -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
+         -D BUILD_LAMMPS_SHELL=value  # yes or no (default). Build lammps-shell
+         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build lammps-gui
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -503,7 +504,6 @@ using CMake or Make.
          make binary2txt       # build only binary2txt tool
          make chain            # build only chain tool
          make micelle2d        # build only micelle2d tool
-         make thermo_extract   # build only thermo_extract tool
 
          cd lammps/tools/lammps-shell
          make                  # build LAMMPS shell

doc/src/Build_extras.rst

@@ -886,6 +886,50 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
 
 ----------
 
+.. _machdyn:
+
+MACHDYN package
+-------------------------------
+
+To build with this package, you must download the Eigen3 library.
+Eigen3 is a template library, so you do not need to build it.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
+         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
+
+      If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
+      downloaded and inside the CMake build directory.  If the Eigen3
+      library is already on your system (in a location where CMake
+      cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
+      ``Eigen3`` include file is in.
+
+   .. tab:: Traditional make
+
+      You can download the Eigen3 library manually if you prefer; follow
+      the instructions in ``lib/machdyn/README``.  You can also do it in one
+      step from the ``lammps/src`` dir, using a command like these,
+      which simply invokes the ``lib/machdyn/Install.py`` script with the
+      specified args:
+
+      .. code-block:: bash
+
+         make lib-machdyn                         # print help message
+         make lib-machdyn args="-b"               # download to lib/machdyn/eigen3
+         make lib-machdyn args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+
+      Note that a symbolic (soft) link named ``includelink`` is created
+      in ``lib/machdyn`` to point to the Eigen dir.  When LAMMPS builds it
+      will use this link.  You should not need to edit the
+      ``lib/machdyn/Makefile.lammps`` file.
+
+----------
+
 .. _mliap:
 
 ML-IAP package
@@ -1431,6 +1475,55 @@ ML-POD package
 
 ----------
 
+.. _ml-quip:
+
+ML-QUIP package
+---------------------------------
+
+To build with this package, you must download and build the QUIP
+library.  It can be obtained from GitHub.  For support of GAP
+potentials, additional files with specific licensing conditions need
+to be downloaded and configured.  The automatic download will from
+within CMake will download the non-commercial use version.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
+         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
+
+      CMake will try to download and build the QUIP library from GitHub,
+      if it is not found on the local machine. This requires to have git
+      installed. It will use the same compilers and flags as used for
+      compiling LAMMPS.  Currently this is only supported for the GNU
+      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
+      want to use a previously compiled and installed QUIP library and
+      CMake cannot find it.
+
+      The QUIP library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the QUIP build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
+
+   .. tab:: Traditional make
+
+      The download/build procedure for the QUIP library, described in
+      ``lib/quip/README`` file requires setting two environment
+      variables, ``QUIP_ROOT`` and ``QUIP_ARCH``.  These are accessed by
+      the ``lib/quip/Makefile.lammps`` file which is used when you
+      compile and link LAMMPS with this package.  You should only need
+      to edit ``Makefile.lammps`` if the LAMMPS build can not use its
+      settings to successfully build on your system.
+
+----------
+
 .. _plumed:
 
 PLUMED package
@@ -1952,55 +2045,6 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
-.. _ml-quip:
-
-ML-QUIP package
----------------------------------
-
-To build with this package, you must download and build the QUIP
-library.  It can be obtained from GitHub.  For support of GAP
-potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  The automatic download will from
-within CMake will download the non-commercial use version.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
-         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
-         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
-
-      CMake will try to download and build the QUIP library from GitHub,
-      if it is not found on the local machine. This requires to have git
-      installed. It will use the same compilers and flags as used for
-      compiling LAMMPS.  Currently this is only supported for the GNU
-      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
-      want to use a previously compiled and installed QUIP library and
-      CMake cannot find it.
-
-      The QUIP library requires LAPACK (and BLAS) and CMake can identify
-      their locations and pass that info to the QUIP build script. But
-      on some systems this triggers a (current) limitation of CMake and
-      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
-      those cases to use the bundled linear algebra library and work around
-      the limitation.
-
-   .. tab:: Traditional make
-
-      The download/build procedure for the QUIP library, described in
-      ``lib/quip/README`` file requires setting two environment
-      variables, ``QUIP_ROOT`` and ``QUIP_ARCH``.  These are accessed by
-      the ``lib/quip/Makefile.lammps`` file which is used when you
-      compile and link LAMMPS with this package.  You should only need
-      to edit ``Makefile.lammps`` if the LAMMPS build can not use its
-      settings to successfully build on your system.
-
-----------
-
 .. _scafacos:
 
 SCAFACOS package
@@ -2048,50 +2092,6 @@ To build with this package, you must download and build the
 
 ----------
 
-.. _machdyn:
-
-MACHDYN package
--------------------------------
-
-To build with this package, you must download the Eigen3 library.
-Eigen3 is a template library, so you do not need to build it.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
-         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
-
-      If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
-      downloaded and inside the CMake build directory.  If the Eigen3
-      library is already on your system (in a location where CMake
-      cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
-      ``Eigen3`` include file is in.
-
-   .. tab:: Traditional make
-
-      You can download the Eigen3 library manually if you prefer; follow
-      the instructions in ``lib/smd/README``.  You can also do it in one
-      step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/smd/Install.py`` script with the
-      specified args:
-
-      .. code-block:: bash
-
-         make lib-smd                         # print help message
-         make lib-smd args="-b"               # download to lib/smd/eigen3
-         make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
-
-      Note that a symbolic (soft) link named ``includelink`` is created
-      in ``lib/smd`` to point to the Eigen dir.  When LAMMPS builds it
-      will use this link.  You should not need to edit the
-      ``lib/smd/Makefile.lammps`` file.
-
-----------
-
 .. _vtk:
 
 VTK package

doc/src/Howto_lammps_gui.rst

@@ -528,6 +528,13 @@ 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
+  and data updates during a LAMMPS run in milliseconds. The default is
+  to update the GUI every 100 milliseconds. This is good for most cases.
+  For LAMMPS runs that run very fast, however, data may be missed and
+  through 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. The default value is 100 milliseconds.
 
 Accelerators:
 ^^^^^^^^^^^^^

doc/src/fix_plumed.rst

@@ -24,7 +24,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
+   fix pl all plumed plumedfile plumed.dat outfile p.log
 
 Description
 """""""""""

lib/machdyn/Install.py

@@ -31,17 +31,17 @@
 # help message
 
 HELP = """
-Syntax from src dir: make lib-smd args="-b"
-                 or: make lib-smd args="-p /usr/include/eigen3"
+Syntax from src dir: make lib-machdyn args="-b"
+                 or: make lib-machdyn args="-p /usr/include/eigen3"
 
 Syntax from lib dir: python Install.py -b
                  or: python Install.py -p /usr/include/eigen3"
                  or: python Install.py -v 3.4.0 -b
 
 Example:
 
-make lib-smd args="-b"   # download/build in default lib/smd/eigen-eigen-*
-make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
+make lib-machdyn args="-b"   # download/build in default lib/machdyn/eigen-eigen-*
+make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
 """
 
 pgroup = parser.add_mutually_exclusive_group()
@@ -105,7 +105,7 @@
   edir = os.path.join(homepath, "eigen-%s" % version)
   os.rename(edir, eigenpath)
 
-# create link in lib/smd to Eigen src dir
+# create link in lib/machdyn to Eigen src dir
 
 print("Creating link to Eigen include folder")
 if os.path.isfile("includelink") or os.path.islink("includelink"):

lib/machdyn/README

@@ -4,21 +4,21 @@ to use the MACHDYN package in a LAMMPS input script.
 The Eigen library is available at http://eigen.tuxfamily.org.  It's
 a general C++ template library for linear algebra.
 
-You can type "make lib-smd" from the src directory to see help on how
+You can type "make lib-machdyn" from the src directory to see help on how
 to download build this library via make commands, or you can do the
 same thing by typing "python Install.py" from within this directory,
 or you can do it manually by following the instructions below.
 
 Instructions:
 
 1.  Download the Eigen tarball at http://eigen.tuxfamily.org and
-    unpack the tarball either in this /lib/smd directory or somewhere
+    unpack the tarball either in this lib/machdyn directory or somewhere
     else on your system.  It should unpack with into a directory with
     a name similar to eigen-eigen-bdd17ee3b1b3.  You can rename
     the directory to just "eigen" if you wish.  Note that Eigen is a
     template library, so you do not have to build it.
 
-2.  Create a soft link in this dir (lib/smd)
+2.  Create a soft link in this dir (lib/machdyn)
     to the eigen directory.  E.g if you unpacked Eigen in this dir:
       % ln -s eigen-eigen-bdd17ee3b1b3 includelink
     If you unpacked Eigen somewhere else and renamed

src/BODY/fix_wall_body_polyhedron.cpp

@@ -17,18 +17,20 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_body_polyhedron.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polyhedron.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/KOKKOS/Install.sh

@@ -96,8 +96,8 @@ action compute_coord_atom_kokkos.cpp
 action compute_coord_atom_kokkos.h
 action compute_erotate_sphere_kokkos.cpp
 action compute_erotate_sphere_kokkos.h
-action compute_local_comp_atom_kokkos.cpp compute_local_comp_atom.cpp
-action compute_local_comp_atom_kokkos.h compute_local_comp_atom.h
+action compute_composition_atom_kokkos.cpp compute_composition_atom.cpp
+action compute_composition_atom_kokkos.h compute_composition_atom.h
 action compute_orientorder_atom_kokkos.cpp
 action compute_orientorder_atom_kokkos.h
 action compute_temp_deform_kokkos.cpp

src/KSPACE/ewald_disp.cpp

@@ -1129,8 +1129,6 @@ void EwaldDisp::compute_energy_peratom()
 
 /* ---------------------------------------------------------------------- */
 
-#define swap(a, b) { register double t = a; a= b; b = t; }
-
 void EwaldDisp::compute_virial()
 {
   memset(virial, 0, 6*sizeof(double));

src/MANYBODY/pair_airebo.cpp

@@ -59,6 +59,7 @@ PairAIREBO::PairAIREBO(LAMMPS *lmp)
   nextra = 3;
   pvector = new double[nextra];
 
+  trim_flag = 0; // workaround
   maxlocal = 0;
   REBO_numneigh = nullptr;
   REBO_firstneigh = nullptr;

src/read_restart.cpp

@@ -801,7 +801,7 @@ void ReadRestart::header()
       int itmp = read_int();
       if (atom->map_user == Atom::MAP_NONE) atom->map_style = itmp;
     } else if (flag == ATOM_MAP_USER) {
-      int itmp = read_int();  // ignored
+      read_int();  // ignored
     } else if (flag == ATOM_SORTFREQ) {
       atom->sortfreq = read_int();
     } else if (flag == ATOM_SORTBIN) {

tools/Makefile

@@ -16,15 +16,11 @@ chain:	chain.o
 micelle2d:	micelle2d.o
 	ifort micelle2d.o -o micelle2d
 
-thermo_extract:	thermo_extract.o
-	gcc -g thermo_extract.o -o thermo_extract
-
 stl_bin2txt:	stl_bin2txt.o
 	g++ -g stl_bin2txt.o -o stl_bin2txt
 
 clean:
 	rm binary2txt chain micelle2d
-	rm thermo_extract
 	rm *.o
 
 #

tools/lammps-gui/CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.16)
 
-project(lammps-gui VERSION 1.5.3 LANGUAGES CXX)
+project(lammps-gui VERSION 1.5.4 LANGUAGES CXX)
 
 set(CMAKE_AUTOUIC ON)
 set(CMAKE_AUTOMOC ON)