Merge pull request #1241 from akohlmey/collected-small-fixes

Collected small changes and updates for stable release

doc/src/Build_extras.txt

@@ -735,66 +735,69 @@ from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
 :link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
 
 PLUMED can be linked into MD codes in three different modes: static,
-shared, and runtime.  With the "static" mode, all the code that PLUMED requires
-is linked statically into LAMMPS. LAMMPS is then fully
-independent from the PLUMED installation, but you have to
-rebuild/relink it in order to update the PLUMED code inside it.  With
-the "shared" linkage mode, LAMMPS is linked to a shared library
-that contains the PLUMED code.  This library should preferably be installed in a
-globally accessible location. When PLUMED is linked in this way the same library
-can be used by multiple MD packages.  Furthermore, the PLUMED library LAMMPS uses can be updated
-without the need for a recompile of LAMMPS for as
-long as the shared PLUMED library is ABI-compatible. 
+shared, and runtime.  With the "static" mode, all the code that PLUMED
+requires is linked statically into LAMMPS. LAMMPS is then fully
+independent from the PLUMED installation, but you have to rebuild/relink
+it in order to update the PLUMED code inside it.  With the "shared"
+linkage mode, LAMMPS is linked to a shared library that contains the
+PLUMED code.  This library should preferably be installed in a globally
+accessible location. When PLUMED is linked in this way the same library
+can be used by multiple MD packages.  Furthermore, the PLUMED library
+LAMMPS uses can be updated without the need for a recompile of LAMMPS
+for as long as the shared PLUMED library is ABI-compatible.
 
-The third linkage
-mode is "runtime" which allows the user to specify which PLUMED kernel should be used at runtime
-by using the PLUMED_KERNEL environment
-variable. This variable should point to the location of the libplumedKernel.so
-dynamical shared object, which is then loaded at runtime. This mode of linking is
-particularly convenient for doing PLUMED development and comparing
-multiple PLUMED versions as these sorts of comparisons can be done without recompiling the hosting MD
-code. All three linkage modes are supported by LAMMPS on selected
-operating systems (e.g. Linux) and using either CMake or traditional
-make build. The "static" mode should be the most portable, while the "runtime"
-mode support in LAMMPS makes the most assumptions about operating
-system and compiler environment. If one mode does not work, try a
-different one, switch to a different build system, consider
-a global PLUMED installation or consider downloading PLUMED during the LAMMPS build.
+The third linkage mode is "runtime" which allows the user to specify
+which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
+environment variable. This variable should point to the location of the
+libplumedKernel.so dynamical shared object, which is then loaded at
+runtime. This mode of linking is particularly convenient for doing
+PLUMED development and comparing multiple PLUMED versions as these sorts
+of comparisons can be done without recompiling the hosting MD code. All
+three linkage modes are supported by LAMMPS on selected operating
+systems (e.g. Linux) and using either CMake or traditional make
+build. The "static" mode should be the most portable, while the
+"runtime" mode support in LAMMPS makes the most assumptions about
+operating system and compiler environment. If one mode does not work,
+try a different one, switch to a different build system, consider a
+global PLUMED installation or consider downloading PLUMED during the
+LAMMPS build.
 
 [CMake build]:
 
-When the "-D PKG_USER-PLUMED" flag is included in the cmake command you must ensure that 
-GSL is installed in locations that are specified in your environment.  There
-are then two additional commands that control the manner in which PLUMED is obtained and linked
-into LAMMPS.
+When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
+must ensure that GSL is installed in locations that are specified in
+your environment.  There are then two additional commands that control
+the manner in which PLUMED is obtained and linked into LAMMPS.
 
 -D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
 -D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
 
 If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
-downloaded (the version of PLUMED that will be downloaded is hard-coded to a vetted version of
-PLUMED, usually a recent stable release version) and built inside the
-CMake build directory.  If DOWNLOAD_PLUMED is set to "no" (the default),
-CMake will try to detect and link to an installed version of PLUMED. 
-For this to work, the PLUMED library has to be installed into a
-location where the pkg-config tool can find it or the PKG_CONFIG_PATH
-environment variable has to be set up accordingly.  PLUMED should be installed 
-in such a location if you compile it using the default make; make install commands.
+downloaded (the version of PLUMED that will be downloaded is hard-coded
+to a vetted version of PLUMED, usually a recent stable release version)
+and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set
+to "no" (the default), CMake will try to detect and link to an installed
+version of PLUMED.  For this to work, the PLUMED library has to be
+installed into a location where the pkg-config tool can find it or the
+PKG_CONFIG_PATH environment variable has to be set up accordingly.
+PLUMED should be installed in such a location if you compile it using
+the default make; make install commands.
 
 The PLUMED_MODE setting determines the linkage mode for the PLUMED
-library.  The allowed values for this flag are "static" (default), "shared", or "runtime".
-For a discussion of PLUMED linkage modes, please see above.  When
-DOWNLOAD_PLUMED is enabled the static linkage mode is recommended.
+library.  The allowed values for this flag are "static" (default),
+"shared", or "runtime".  For a discussion of PLUMED linkage modes,
+please see above.  When DOWNLOAD_PLUMED is enabled the static linkage
+mode is recommended.
 
 [Traditional make]:
 
 PLUMED needs to be installed before the USER-PLUMED package is installed
-so that LAMMPS can find the right settings when compiling and linking the LAMMPS executable.
-You can either download and build PLUMED inside the LAMMPS plumed library folder or use
-a previously installed PLUMED library and point LAMMPS to its
-location. You also have to choose the linkage mode: "static" (default),
-"shared" or "runtime".  For a discussion of PLUMED linkage modes, please
-see above.
+so that LAMMPS can find the right settings when compiling and linking
+the LAMMPS executable.  You can either download and build PLUMED inside
+the LAMMPS plumed library folder or use a previously installed PLUMED
+library and point LAMMPS to its location. You also have to choose the
+linkage mode: "static" (default), "shared" or "runtime".  For a
+discussion of PLUMED linkage modes, please see above.
 
 Download/compilation/configuration of the plumed library can be done
 from the src folder through the following make args:
@@ -808,10 +811,10 @@ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installati
 
 Note that 2 symbolic (soft) links, "includelink" and "liblink" are
 created in lib/plumed that point to the location of the PLUMED build to
-use. A new file lib/plumed/Makefile.lammps is also created with
-settings suitable for LAMMPS to compile and link PLUMED using the desired
-linkage mode. After this step is completed, you can install the
-USER-PLUMED package and compile LAMMPS in the usual manner:
+use. A new file lib/plumed/Makefile.lammps is also created with settings
+suitable for LAMMPS to compile and link PLUMED using the desired linkage
+mode. After this step is completed, you can install the USER-PLUMED
+package and compile LAMMPS in the usual manner:
 
 make yes-user-plumed
 make machine :pre

doc/src/dump_modify.txt

@@ -461,10 +461,10 @@ last snapshot.  This can be accomplished with something the following
 commands:
 
 variable        Dhop equal 0.6
-variable        check atom "c_dsp[4] > v_Dhop"
+variable        check atom "c_dsp\[4\] > v_Dhop"
 compute         dsp all displace/atom refresh check
 dump            1 all custom 20 tmp.dump id type x y z
-dump_modify     1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
+dump_modify     1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre
 
 The "compute displace/atom"_compute_displace_atom.html command
 calculates the displacement of each atom from its reference position.

doc/src/fix_plumed.txt

@@ -32,11 +32,10 @@ enhance the sampling of phase space.
 
 The documentation included here only describes the fix plumed command
 itself.  This command is LAMMPS specific, whereas most of the
-functionality implemented in PLUMED will work with a range of
-MD codes, and when PLUMED is used as a stand alone code for analysis.
-The full "documentation for PLUMED"_plumeddocs is available online and
-included in the PLUMED source code.  The PLUMED library development is
-hosted at
+functionality implemented in PLUMED will work with a range of MD codes,
+and when PLUMED is used as a stand alone code for analysis.  The full
+"documentation for PLUMED"_plumeddocs is available online and included
+in the PLUMED source code.  The PLUMED library development is hosted at
 "https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
 A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
 
@@ -54,11 +53,12 @@ have been set.
 
 The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
 to PLUMED and there can only be one instance of the plumed fix at a
-time. The way the plumed fix is implemented ensures that the minimum amount of information
-required is communicated.  Furthermore, PLUMED supports multiple, completely independent
-collective variables, multiple independent biases and multiple
-independent forms of analysis.  There is thus really no restriction in
-functionality by only allowing only one plumed fix in the LAMMPS input.
+time. The way the plumed fix is implemented ensures that the minimum
+amount of information required is communicated.  Furthermore, PLUMED
+supports multiple, completely independent collective variables, multiple
+independent biases and multiple independent forms of analysis.  There is
+thus really no restriction in functionality by only allowing only one
+plumed fix in the LAMMPS input.
 
 The {plumedfile} keyword allows the user to specify the name of the
 PLUMED input file.  Instructions as to what should be included in a

doc/src/kspace_style.txt

@@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
     accuracy = desired relative error in forces
     smallq = cutoff for charges to be considered (optional) (charge units)
   {scafacos} values = method accuracy
-    method = fmm or p2nfft or ewald or direct
+    method = fmm or p2nfft or p3m or ewald or direct
     accuracy = desired relative error in forces :pre
 :ule
 
@@ -392,6 +392,8 @@ the same bond/angle/dihedral are weighted by the
 "special_bonds"_special_bonds.html command.  Likewise it does not
 support the "TIP4P water style" where a fictitious charge site is
 introduced in each water molecule.
+Finally, the methods {p3m} and {ewald} do not support computing the
+virial, so this contribution is not included.
 
 [Related commands:]