rename USER-CGDNA and USER-CGSDK to CG-DNA and CG-SDK

.github/CODEOWNERS

@@ -23,8 +23,8 @@ src/MLIAP/*           @athomps
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
 src/USER-BROWNIAN/*   @samueljmcameron
-src/USER-CGDNA/*      @ohenrich
+src/CG-DNA/*      @ohenrich
-src/USER-CGSDK/*      @akohlmey
+src/CG-SDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
 src/USER-DIELECTRIC/* @ndtrung81
 src/USER-FEP/*        @agiliopadua

cmake/CMakeLists.txt

@@ -141,7 +141,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE PERI POEMS
   PLUGIN QEQ REPLICA RIGID SHOCK SPIN ML-SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
+  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS CG-DNA USER-MESODPD CG-SDK
   USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
   USER-H5MD USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT
   USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB

cmake/presets/all_off.cmake

@@ -5,7 +5,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
   GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE
   MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN
   SRD VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
+  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
   USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
   USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP

cmake/presets/all_on.cmake

@@ -7,7 +7,7 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
   GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE
   MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN
   SRD VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
+  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS CG-DNA CG-SDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
   USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
   USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP

cmake/presets/mingw-cross.cmake

@@ -1,7 +1,7 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  GRANULAR KSPACE LATTE MANYBODY MC MISC ML-IAP MOLECULE OPT
                  PERI POEMS QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI
-                 USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
+                 USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN CG-DNA CG-SDK
                  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
                  USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
                  USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP

cmake/presets/most.cmake

@@ -5,7 +5,7 @@
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC ML-IAP MOLECULE OPT PERI
         PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI
-        USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+        USER-BROWNIAN USER-BOCS CG-DNA CG-SDK USER-COLVARS
         USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
         USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
         USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF USER-DIELECTRIC)

doc/src/Packages_details.rst

@@ -70,8 +70,8 @@ page gives those details.
    * :ref:`USER-AWPMD <PKG-USER-AWPMD>`
    * :ref:`USER-BOCS <PKG-USER-BOCS>`
    * :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
-   * :ref:`USER-CGDNA <PKG-USER-CGDNA>`
+   * :ref:`CG-DNA <PKG-CG-DNA>`
-   * :ref:`USER-CGSDK <PKG-USER-CGSDK>`
+   * :ref:`CG-SDK <PKG-CG-SDK>`
    * :ref:`USER-COLVARS <PKG-USER-COLVARS>`
    * :ref:`USER-DIELECTRIC <PKG-USER-DIELECTRIC>`
    * :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>`
@@ -1291,9 +1291,9 @@ Example inputs are in the examples/PACKAGES/brownian folder.
 
 ----------
 
-.. _PKG-USER-CGDNA:
+.. _PKG-CG-DNA:
 
-USER-CGDNA package
+CG-DNA package
 ------------------
 
 **Contents:**
@@ -1307,8 +1307,8 @@ rigid-body integrators with improved stability.
 
 **Supporting info:**
 
-* src/USER-CGDNA: filenames -> commands
+* src/CG-DNA: filenames -> commands
-* /src/USER-CGDNA/README
+* /src/CG-DNA/README
 * :doc:`pair_style oxdna/\* <pair_oxdna>`
 * :doc:`pair_style oxdna2/\* <pair_oxdna2>`
 * :doc:`pair_style oxrna2/\* <pair_oxrna2>`
@@ -1319,9 +1319,9 @@ rigid-body integrators with improved stability.
 
 ----------
 
-.. _PKG-USER-CGSDK:
+.. _PKG-CG-SDK:
 
-USER-CGSDK package
+CG-SDK package
 ------------------
 
 **Contents:**
@@ -1335,8 +1335,8 @@ acids.
 
 **Supporting info:**
 
-* src/USER-CGSDK: filenames -> commands
+* src/CG-SDK: filenames -> commands
-* src/USER-CGSDK/README
+* src/CG-SDK/README
 * :doc:`pair_style lj/sdk/\* <pair_sdk>`
 * :doc:`angle_style sdk <angle_sdk>`
 * examples/PACKAGES/cgsdk

doc/src/Packages_user.rst

@@ -41,9 +41,9 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`       | Brownian dynamics and self-propelled particles                  | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>`  | USER/brownian                                        | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`USER-CGDNA <PKG-USER-CGDNA>`             | coarse-grained DNA force fields                                 | src/USER-CGDNA/README                                                         | USER/cgdna                                           | no      |
+| :ref:`CG-DNA <PKG-CG-DNA>`             | coarse-grained DNA force fields                                 | src/CG-DNA/README                                                         | USER/cgdna                                           | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`USER-CGSDK <PKG-USER-CGSDK>`             | SDK coarse-graining model                                       | :doc:`pair_style lj/sdk <pair_sdk>`                                           | USER/cgsdk                                           | no      |
+| :ref:`CG-SDK <PKG-CG-SDK>`             | SDK coarse-graining model                                       | :doc:`pair_style lj/sdk <pair_sdk>`                                           | USER/cgsdk                                           | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-COLVARS <PKG-USER-COLVARS>`         | collective variables library                                    | :doc:`fix colvars <fix_colvars>`                                              | USER/colvars                                         | int     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+

doc/src/angle_sdk.rst

@@ -64,7 +64,7 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-USER-CGSDK package.  See the :doc:`Build package <Build_package>` doc
+CG-SDK package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 
 Related commands

doc/src/bond_oxdna.rst

@@ -86,7 +86,7 @@ Please cite :ref:`(Henrich) <Henrich0>` in any publication that uses
 this implementation.  The article contains general information
 on the model, its implementation and performance as well as the structure of
 the data and input file. The preprint version of the article can be found
-`here <PDF/USER-CGDNA.pdf>`_.
+`here <PDF/CG-DNA.pdf>`_.
 Please cite also the relevant oxDNA/oxRNA publications. These are
 :ref:`(Ouldridge) <Ouldridge0>` and
 :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil0>` for oxDNA,
@@ -101,7 +101,7 @@ Restrictions
 """"""""""""
 
 This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+CG-DNA package and the MOLECULE and ASPHERE package.  See the
 :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands

doc/src/fix_nve_dot.rst

@@ -38,7 +38,7 @@ The particles are always considered to have a finite size.
 
 An example input file can be found in /examples/PACKAGES/cgdna/examples/duplex1/.
 Further details of the implementation and stability of the integrator are contained in :ref:`(Henrich) <Henrich4>`.
-The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
+The preprint version of the article can be found `here <PDF/CG-DNA.pdf>`_.
 
 ----------
 
@@ -46,7 +46,7 @@ Restrictions
 """"""""""""
 
 These pair styles can only be used if LAMMPS was built with the
-:ref:`USER-CGDNA <PKG-USER-CGDNA>` package and the MOLECULE and ASPHERE package.
+:ref:`CG-DNA <PKG-CG-DNA>` package and the MOLECULE and ASPHERE package.
 See the :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands

doc/src/fix_nve_dotc_langevin.rst

@@ -122,7 +122,7 @@ rotational to the translational friction coefficient.
 
 An example input file can be found in examples/PACKAGES/cgdna/examples/duplex2/.
 Further details of the implementation and stability of the integrators are contained in :ref:`(Henrich) <Henrich5>`.
-The preprint version of the article can be found `here <PDF/USER-CGDNA.pdf>`_.
+The preprint version of the article can be found `here <PDF/CG-DNA.pdf>`_.
 
 ----------
 
@@ -130,7 +130,7 @@ Restrictions
 """"""""""""
 
 These pair styles can only be used if LAMMPS was built with the
-:ref:`USER-CGDNA <PKG-USER-CGDNA>` package and the MOLECULE and ASPHERE package.
+:ref:`CG-DNA <PKG-CG-DNA>` package and the MOLECULE and ASPHERE package.
 See the :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands

doc/src/pair_oxdna.rst

@@ -99,7 +99,7 @@ Please cite :ref:`(Henrich) <Henrich1>` in any publication that uses
 this implementation.  The article contains general information
 on the model, its implementation and performance as well as the structure of
 the data and input file. The preprint version of the article can be found
-`here <PDF/USER-CGDNA.pdf>`_.
+`here <PDF/CG-DNA.pdf>`_.
 Please cite also the relevant oxDNA publications
 :ref:`(Ouldridge) <Ouldridge1>`,
 :ref:`(Ouldridge-DPhil) <Ouldridge-DPhil1>`
@@ -111,7 +111,7 @@ Restrictions
 """"""""""""
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+CG-DNA package and the MOLECULE and ASPHERE package.  See the
 :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands

doc/src/pair_oxdna2.rst

@@ -108,7 +108,7 @@ Please cite :ref:`(Henrich) <Henrich2>` in any publication that uses
 this implementation.  The article contains general information
 on the model, its implementation and performance as well as the structure of
 the data and input file. The preprint version of the article can be found
-`here <PDF/USER-CGDNA.pdf>`_.
+`here <PDF/CG-DNA.pdf>`_.
 Please cite also the relevant oxDNA2 publications
 :ref:`(Snodin) <Snodin2>` and :ref:`(Sulc) <Sulc2>`.
 
@@ -118,7 +118,7 @@ Restrictions
 """"""""""""
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+CG-DNA package and the MOLECULE and ASPHERE package.  See the
 :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands

doc/src/pair_oxrna2.rst

@@ -109,7 +109,7 @@ Please cite :ref:`(Henrich) <Henrich3>` in any publication that uses
 this implementation.  The article contains general information
 on the model, its implementation and performance as well as the structure of
 the data and input file. The preprint version of the article can be found
-`here <PDF/USER-CGDNA.pdf>`_.
+`here <PDF/CG-DNA.pdf>`_.
 Please cite also the relevant oxRNA2 publications
 :ref:`(Sulc1) <Sulc31>` and :ref:`(Sulc2) <Sulc32>`.
 
@@ -119,7 +119,7 @@ Restrictions
 """"""""""""
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
+CG-DNA package and the MOLECULE and ASPHERE package.  See the
 :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands

doc/src/pair_sdk.rst

@@ -148,7 +148,7 @@ the use of the *inner*\ , *middle*\ , and *outer* keywords of the :doc:`run_styl
 Restrictions
 """"""""""""
 
-All of the lj/sdk pair styles are part of the USER-CGSDK package.  The
+All of the lj/sdk pair styles are part of the CG-SDK package.  The
 *lj/sdk/coul/long* style also requires the KSPACE package to be built
 (which is enabled by default).  They are only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`

examples/PACKAGES/cgsdk/README

@@ -1,4 +1,4 @@
-LAMMPS USER-CGSDK example problems
+LAMMPS CG-SDK example problems
 
 Each of these sub-directories contains a sample problem for the SDK
 coarse grained MD potentials that you can run with LAMMPS.

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/Depend.sh

@@ -48,7 +48,7 @@ depend () {
 if (test $1 = "ASPHERE") then
   depend GPU
   depend USER-OMP
-  depend USER-CGDNA
+  depend CG-DNA
   depend USER-INTEL
 fi
 
@@ -121,7 +121,7 @@ if (test $1 = "ML-SNAP") then
   depend ML-IAP
 fi
 
-if (test $1 = "USER-CGSDK") then
+if (test $1 = "CG-SDK") then
   depend GPU
   depend KOKKOS
   depend USER-OMP

src/Makefile

@@ -51,8 +51,8 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  ml-iap molecule mpiio mscg opt peri plugin poems \
 	  python qeq replica rigid shock ml-snap spin srd voronoi
 
-PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \
+PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs cg-dna \
-	   user-cgsdk user-colvars user-dielectric user-diffraction user-dpd user-drude \
+	   cg-sdk user-colvars user-dielectric user-diffraction user-dpd user-drude \
 	   user-eff user-fep user-h5md user-hdnnp user-intel user-lb user-manifold \
 	   user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \
 	   user-mofff user-molfile user-netcdf user-omp user-phonon \

src/USER-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/USER-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/USER-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/USER-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)
 ------------------------------------------------------------------------- */