Merge branch 'master' into dielectric-updates

# Conflicts:
#	src/DIELECTRIC/Install.sh
#	src/DIELECTRIC/pppm_disp_dielectric.cpp
#	src/DIELECTRIC/pppm_disp_dielectric.h

src/.gitignore

@@ -70,8 +70,8 @@
 
 /meam*.h
 /meam*.cpp
-/pair_meamc.cpp
-/pair_meamc.h
+/pair_meam.cpp
+/pair_meam.h
 
 /compute_mliap.cpp
 /compute_mliap.h
@@ -1431,6 +1431,10 @@
 /pair_thole.h
 /pair_buck_mdf.cpp
 /pair_buck_mdf.h
+/pair_dpd.cpp
+/pair_dpd.h
+/pair_dpd_tstat.cpp
+/pair_dpd_tstat.h
 /pair_dpd_ext.cpp
 /pair_dpd_ext.h
 /pair_dpd_ext_tstat.cpp

src/ADIOS/Install.sh

@@ -72,7 +72,7 @@ adios_SYSLIB=${ADIOS2_LIB}
       sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings
       # multiline form needed for BSD sed on Macs
       sed -i -e '4 i \
-include ../USER-ADIOS/Makefile.lammps
+include ../ADIOS/Makefile.lammps
 ' ../Makefile.package.settings
     fi
   fi

src/ADIOS/README

@@ -8,7 +8,7 @@ Configure LAMMPS with CMake
         ADIOS2_DIR
     to the ADIOS 2.x installation path
  b. use the cmake option
-       -D PKG_USER-ADIOS=yes
+       -D PKG_ADIOS=yes
 
 The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory);
 If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket.

src/ATC/Install.sh

@@ -31,7 +31,7 @@ action () {
 
 if (test $1 = 1) then
   if (test ! -e ../pair_eam.cpp) then
-    echo "Must install MANYBODY package with USER-ATC"
+    echo "Must install MANYBODY package with ATC"
     exit 1
   fi
 fi
@@ -54,9 +54,9 @@ if (test $1 = 1) then
 #   sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/atc |' ../Makefile.package
 #   sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/atc$(LIBSOBJDIR) |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-latc |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(user-atc_SYSINC) |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-atc_SYSLIB) |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-atc_SYSPATH) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(atc_SYSINC) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(atc_SYSLIB) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(atc_SYSPATH) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then

src/ATC/README

@@ -7,7 +7,7 @@ See the doc page for the fix atc command to get started.  At the
 bottom of the doc page are many links to additional documentation
 contained in the doc/USER/atc directory.
 
-There are example scripts for using this package in examples/USER/atc.
+There are example scripts for using this package in examples/PACKAGES/atc.
 
 This package uses an external library in lib/atc which must be
 compiled before making LAMMPS.  See the lib/atc/README file and the

src/ATC/fix_atc.cpp

@@ -37,7 +37,7 @@ using namespace FixConst;
 using std::string;
 
 #ifdef LAMMPS_BIGBIG
-#error "The USER-ATC package is not compatible with -DLAMMPS_BIGBIG"
+#error "The ATC package is not compatible with -DLAMMPS_BIGBIG"
 #endif
 
 // main page of doxygen documentation

src/AWPMD/Install.sh

@@ -41,8 +41,8 @@ if (test $1 = 1) then
     sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/awpmd/ivutils/include -I../../lib/awpmd/systems/interact |' ../Makefile.package
     sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/awpmd |' ../Makefile.package
     sed -i -e 's|^PKG_LIB =[ \t]*|&-lawpmd |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(user-awpmd_SYSPATH) |' ../Makefile.package
-    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(user-awpmd_SYSLIB) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(awpmd_SYSPATH) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(awpmd_SYSLIB) |' ../Makefile.package
   fi
 
   if (test -e ../Makefile.package.settings) then

src/AWPMD/README

@@ -4,7 +4,7 @@ Wave Packet Molecular Dynamics (AWPMD) method.
 See the doc page for the pair_style awpmd/cut command to get started.
 
 There are example scripts for using this package in
-examples/USER/awpmd.
+examples/PACKAGES/awpmd.
 
 This package uses an external library in lib/awpmd which must be
 compiled before making LAMMPS.  See the lib/awpmd/README file and the

src/BOCS/README

@@ -7,7 +7,7 @@ molecular liquids," J. Chem. Phys. 143, 243148 (2015).
 
 doi: 10.1063/1.4937383
 
-The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+The BOCS user package for LAMMPS is part of the BOCS software package:
 https://github.com/noid-group/BOCS
 
 See the following reference for information about the entire package:
@@ -16,4 +16,4 @@ Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
 "BOCS: Bottom-Up Open-Source Coarse-Graining Software."
 J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
 
-Example inputs are in the examples/USER/bocs folder.
+Example inputs are in the examples/PACKAGES/bocs folder.

src/BOCS/compute_pressure_bocs.cpp

@@ -11,7 +11,7 @@
 
    See the README file in the top-level LAMMPS directory.
 -------------------------------------------------------------------------
-   USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+   BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
    from The Pennsylvania State University
 ------------------------------------------------------------------------- */
 

src/BOCS/compute_pressure_bocs.h

@@ -10,7 +10,7 @@
 
    See the README file in the top-level LAMMPS directory.
 -------------------------------------------------------------------------
-   USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+   BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
    from The Pennsylvania State University
 ------------------------------------------------------------------------- */
 

src/BOCS/fix_bocs.cpp

@@ -11,7 +11,7 @@
 
    See the README file in the top-level LAMMPS directory.
 -------------------------------------------------------------------------
-   USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+   BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
    from The Pennsylvania State University
 ------------------------------------------------------------------------- */
 
@@ -43,7 +43,7 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 
 static const char cite_user_bocs_package[] =
-  "USER-BOCS package:\n\n"
+  "BOCS package:\n\n"
   "@Article{Dunn2018,\n"
   " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n"
   " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n"

src/BOCS/fix_bocs.h

@@ -10,7 +10,7 @@
 
    See the README file in the top-level LAMMPS directory.
 -------------------------------------------------------------------------
-   USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+   BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
    from The Pennsylvania State University
 ------------------------------------------------------------------------- */
 

src/BROWNIAN/fix_brownian.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
+   Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
 
    Contributing author: Sam Cameron (University of Bristol)
 ------------------------------------------------------------------------- */

src/BROWNIAN/fix_brownian_asphere.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
+   Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
 
    Contributing author: Sam Cameron (University of Bristol)
 ------------------------------------------------------------------------- */

src/BROWNIAN/fix_brownian_base.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
+   Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
 
    Contributing author: Sam Cameron (University of Bristol)
 ------------------------------------------------------------------------- */

src/BROWNIAN/fix_brownian_sphere.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
+   Originally modified from CG-DNA/fix_nve_dotc_langevin.cpp.
 
    Contributing author: Sam Cameron (University of Bristol)
 ------------------------------------------------------------------------- */

src/CG-DNA/README.md

@@ -40,13 +40,13 @@ gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
 144114 (2015).
 
 Example input and data files can be found in
-/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
+examples/PACKAGES/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
 Python setup tools which create single straight or helical DNA or RNA
 strands as well as DNA or RNA duplexes or arrays of duplexes can be
-found in /examples/USER/cgdna/util/. A technical report with more
+found in examples/PACKAGES/cgdna/util/. A technical report with more
 general information on the model, its implementation and performance
 as well as the structure of the data and input file can be found
-in /doc/src/PDF/USER-CGDNA.pdf.
+in doc/src/PDF/CG-DNA.pdf.
 
 IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
 with the MOLECULE and ASPHERE packages.  These should be included in

src/CG-SDK/README

@@ -1,8 +1,9 @@
-This package implements 3 commands which can be used in a LAMMPS input
+This package implements 4 commands which can be used in a LAMMPS input
 script:
 
 pair_style lj/sdk
 pair_style lj/sdk/coul/long
+pair_style lj/sdk/coul/msm
 angle_style sdk
 
 These styles allow coarse grained MD simulations with the
@@ -13,7 +14,7 @@ lipids and charged amino acids.
 See the doc pages for these commands for details.
 
 There are example scripts for using this package in
-examples/USER/cgsdk
+examples/PACKAGES/cgsdk
 
 This is the second generation implementation reducing the the clutter
 of the previous version. For many systems with long range

src/COLVARS/README

@@ -13,7 +13,7 @@ on building LAMMPS with external libraries.  The settings in the
 Makefile.lammps file in that directory must be correct for LAMMPS to
 build correctly with this package installed.
 
-The files in the USER-COLVARS package folder implement an interface
+The files in the COLVARS package folder implement an interface
 between LAMMPS and Colvars, originally written by Axel Kohlmeyer
 (akohlmey@gmail.com) and maintained by Giacomo Fiorin
 (giacomo.fiorin@gmail.com).
@@ -36,7 +36,7 @@ which also includes citations to the articles documenting the various
 methods that make use Colvars.
 
 There are also example scripts for using this package in the folder
-examples/USER/colvars, as well as the GitHub page for Colvars.
+examples/PACKAGES/colvars, as well as the GitHub page for Colvars.
 
 Please contact Giacomo Fiorin (giacomo.fiorin@gmail.com) for questions
 regarding this package.

src/DIELECTRIC/Install.sh

@@ -31,7 +31,7 @@ action () {
 
 if (test $1 = 1) then
   if (test ! -e ../pppm.cpp) then
-    echo "Must install KSPACE package with USER-DIELECTRIC"
+    echo "Must install KSPACE package with DIELECTRIC package"
     exit 1
   fi
 fi

src/DIELECTRIC/README

@@ -1,4 +1,4 @@
-The USER-DIELECTRIC package provides several solvers for computing surface induced charges
+The DIELECTRIC package provides several solvers for computing surface induced charges
 at the interface between two media with different dielectric constants:
 
   * the boundary element solver using the GMRES algorithm (fix polarize/bem/gmres),
@@ -10,7 +10,7 @@ or mobile (for example, dielectric colloids in a solvent).
 
 See the header of the source files for more details on the references of the methods.
 
-The USER-DIELECTRIC package was created by Trung Nguyen while at Northwestern.
+The DIELECTRIC package was created by Trung Nguyen while at Northwestern.
 Questions can be addressed to Trung Nguyen (ndactrung@gmail.com).
 
 * Citation
@@ -23,6 +23,6 @@ Molecular Dynamics simulation", Computer Physics Communications 241, 80--91 (201
 
 * Examples
 
-Example input scripts and data files can be found under examples/USER/dielectric:
+Example input scripts and data files can be found under examples/PACKAGES/dielectric:
 
 mpirun -np 8 ../../../src/lmp_mpi -in in.confined

src/DIELECTRIC/atom_vec_dielectric.cpp

@@ -20,7 +20,7 @@
 using namespace LAMMPS_NS;
 
 static const char cite_user_dielectric_package[] =
-  "USER-DIELECTRIC package:\n\n"
+  "DIELECTRIC package:\n\n"
   "@Article{TrungCPC19,\n"
   " author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
   " Francisco J. Solis, Monica Olvera de la Cruz,\n"