diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 56fcf548e6..039756e7ff 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -23,8 +23,8 @@ src/MLIAP/* @athomps src/SNAP/* @athomps src/SPIN/* @julient31 src/USER-BROWNIAN/* @samueljmcameron -src/USER-CGDNA/* @ohenrich -src/USER-CGSDK/* @akohlmey +src/CG-DNA/* @ohenrich +src/CG-SDK/* @akohlmey src/USER-COLVARS/* @giacomofiorin src/USER-DIELECTRIC/* @ndtrung81 src/USER-FEP/* @agiliopadua diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 5d8967adfa..6853477d34 100644 --- a/cmake/CMakeLists.txt +++ b/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 diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 2f22a09f2b..5521816a70 100644 --- a/cmake/presets/all_off.cmake +++ b/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 diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index ca714c3f0e..935cf7b538 100644 --- a/cmake/presets/all_on.cmake +++ b/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 diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 94aef93f29..d0d94b6b70 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/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 diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 4b7519923b..8abe396521 100644 --- a/cmake/presets/most.cmake +++ b/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) diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/CG-DNA.pdf similarity index 100% rename from doc/src/PDF/USER-CGDNA.pdf rename to doc/src/PDF/CG-DNA.pdf diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 9aca2d4da1..2e1419ae9c 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -70,8 +70,8 @@ page gives those details. * :ref:`USER-AWPMD ` * :ref:`USER-BOCS ` * :ref:`USER-BROWNIAN ` - * :ref:`USER-CGDNA ` - * :ref:`USER-CGSDK ` + * :ref:`CG-DNA ` + * :ref:`CG-SDK ` * :ref:`USER-COLVARS ` * :ref:`USER-DIELECTRIC ` * :ref:`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/USER-CGDNA/README +* src/CG-DNA: filenames -> commands +* /src/CG-DNA/README * :doc:`pair_style oxdna/\* ` * :doc:`pair_style oxdna2/\* ` * :doc:`pair_style 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/USER-CGSDK/README +* src/CG-SDK: filenames -> commands +* src/CG-SDK/README * :doc:`pair_style lj/sdk/\* ` * :doc:`angle_style sdk ` * examples/PACKAGES/cgsdk diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index ef6e79437c..33e8c8b7a9 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -41,9 +41,9 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-BROWNIAN ` | Brownian dynamics and self-propelled particles | :doc:`fix brownian `, :doc:`fix propel/self ` | USER/brownian | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | +| :ref:`CG-DNA ` | coarse-grained DNA force fields | src/CG-DNA/README | USER/cgdna | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | +| :ref:`CG-SDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 340a3e4de7..fe0cd3968b 100644 --- a/doc/src/angle_sdk.rst +++ b/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 ` doc +CG-SDK package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 33d23d4e7b..b2cc68fa22 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -86,7 +86,7 @@ Please cite :ref:`(Henrich) ` 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 `_. +`here `_. Please cite also the relevant oxDNA/oxRNA publications. These are :ref:`(Ouldridge) ` and :ref:`(Ouldridge-DPhil) ` 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 ` doc page for more info. Related commands diff --git a/doc/src/fix_nve_dot.rst b/doc/src/fix_nve_dot.rst index 4b8b420f63..26af6efb4b 100644 --- a/doc/src/fix_nve_dot.rst +++ b/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) `. -The preprint version of the article can be found `here `_. +The preprint version of the article can be found `here `_. ---------- @@ -46,7 +46,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -:ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. +:ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/fix_nve_dotc_langevin.rst b/doc/src/fix_nve_dotc_langevin.rst index d1dd948382..944767ff51 100644 --- a/doc/src/fix_nve_dotc_langevin.rst +++ b/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) `. -The preprint version of the article can be found `here `_. +The preprint version of the article can be found `here `_. ---------- @@ -130,7 +130,7 @@ Restrictions """""""""""" These pair styles can only be used if LAMMPS was built with the -:ref:`USER-CGDNA ` package and the MOLECULE and ASPHERE package. +:ref:`CG-DNA ` package and the MOLECULE and ASPHERE package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index a86bf4aaa5..b6b55a503b 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -99,7 +99,7 @@ Please cite :ref:`(Henrich) ` 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 `_. +`here `_. Please cite also the relevant oxDNA publications :ref:`(Ouldridge) `, :ref:`(Ouldridge-DPhil) ` @@ -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 ` doc page for more info. Related commands diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index 23c2d8c919..37739c3813 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -108,7 +108,7 @@ Please cite :ref:`(Henrich) ` 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 `_. +`here `_. Please cite also the relevant oxDNA2 publications :ref:`(Snodin) ` and :ref:`(Sulc) `. @@ -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 ` doc page for more info. Related commands diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 825e15e626..bd89f1fec0 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -109,7 +109,7 @@ Please cite :ref:`(Henrich) ` 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 `_. +`here `_. Please cite also the relevant oxRNA2 publications :ref:`(Sulc1) ` and :ref:`(Sulc2) `. @@ -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 ` doc page for more info. Related commands diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 541c53d37e..a89a833998 100644 --- a/doc/src/pair_sdk.rst +++ b/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 ` diff --git a/examples/PACKAGES/cgsdk/README b/examples/PACKAGES/cgsdk/README index 5d3a493779..09b9b0a8ea 100644 --- a/examples/PACKAGES/cgsdk/README +++ b/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. diff --git a/src/USER-CGDNA/Install.sh b/src/CG-DNA/Install.sh similarity index 100% rename from src/USER-CGDNA/Install.sh rename to src/CG-DNA/Install.sh diff --git a/src/USER-CGDNA/README.md b/src/CG-DNA/README.md similarity index 96% rename from src/USER-CGDNA/README.md rename to src/CG-DNA/README.md index 015c1db188..bd3799a060 100644 --- a/src/USER-CGDNA/README.md +++ b/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 diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/CG-DNA/bond_oxdna2_fene.cpp similarity index 100% rename from src/USER-CGDNA/bond_oxdna2_fene.cpp rename to src/CG-DNA/bond_oxdna2_fene.cpp diff --git a/src/USER-CGDNA/bond_oxdna2_fene.h b/src/CG-DNA/bond_oxdna2_fene.h similarity index 100% rename from src/USER-CGDNA/bond_oxdna2_fene.h rename to src/CG-DNA/bond_oxdna2_fene.h diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/CG-DNA/bond_oxdna_fene.cpp similarity index 100% rename from src/USER-CGDNA/bond_oxdna_fene.cpp rename to src/CG-DNA/bond_oxdna_fene.cpp diff --git a/src/USER-CGDNA/bond_oxdna_fene.h b/src/CG-DNA/bond_oxdna_fene.h similarity index 100% rename from src/USER-CGDNA/bond_oxdna_fene.h rename to src/CG-DNA/bond_oxdna_fene.h diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/CG-DNA/bond_oxrna2_fene.cpp similarity index 100% rename from src/USER-CGDNA/bond_oxrna2_fene.cpp rename to src/CG-DNA/bond_oxrna2_fene.cpp diff --git a/src/USER-CGDNA/bond_oxrna2_fene.h b/src/CG-DNA/bond_oxrna2_fene.h similarity index 100% rename from src/USER-CGDNA/bond_oxrna2_fene.h rename to src/CG-DNA/bond_oxrna2_fene.h diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/CG-DNA/fix_nve_dot.cpp similarity index 100% rename from src/USER-CGDNA/fix_nve_dot.cpp rename to src/CG-DNA/fix_nve_dot.cpp diff --git a/src/USER-CGDNA/fix_nve_dot.h b/src/CG-DNA/fix_nve_dot.h similarity index 100% rename from src/USER-CGDNA/fix_nve_dot.h rename to src/CG-DNA/fix_nve_dot.h diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/CG-DNA/fix_nve_dotc_langevin.cpp similarity index 100% rename from src/USER-CGDNA/fix_nve_dotc_langevin.cpp rename to src/CG-DNA/fix_nve_dotc_langevin.cpp diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.h b/src/CG-DNA/fix_nve_dotc_langevin.h similarity index 100% rename from src/USER-CGDNA/fix_nve_dotc_langevin.h rename to src/CG-DNA/fix_nve_dotc_langevin.h diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/CG-DNA/mf_oxdna.h similarity index 100% rename from src/USER-CGDNA/mf_oxdna.h rename to src/CG-DNA/mf_oxdna.h diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/CG-DNA/pair_oxdna2_coaxstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_coaxstk.cpp rename to src/CG-DNA/pair_oxdna2_coaxstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.h b/src/CG-DNA/pair_oxdna2_coaxstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_coaxstk.h rename to src/CG-DNA/pair_oxdna2_coaxstk.h diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/CG-DNA/pair_oxdna2_dh.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_dh.cpp rename to src/CG-DNA/pair_oxdna2_dh.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_dh.h b/src/CG-DNA/pair_oxdna2_dh.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_dh.h rename to src/CG-DNA/pair_oxdna2_dh.h diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/CG-DNA/pair_oxdna2_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_excv.cpp rename to src/CG-DNA/pair_oxdna2_excv.cpp diff --git a/src/USER-CGDNA/pair_oxdna2_excv.h b/src/CG-DNA/pair_oxdna2_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna2_excv.h rename to src/CG-DNA/pair_oxdna2_excv.h diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/CG-DNA/pair_oxdna_coaxstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_coaxstk.cpp rename to src/CG-DNA/pair_oxdna_coaxstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.h b/src/CG-DNA/pair_oxdna_coaxstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_coaxstk.h rename to src/CG-DNA/pair_oxdna_coaxstk.h diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/CG-DNA/pair_oxdna_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_excv.cpp rename to src/CG-DNA/pair_oxdna_excv.cpp diff --git a/src/USER-CGDNA/pair_oxdna_excv.h b/src/CG-DNA/pair_oxdna_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_excv.h rename to src/CG-DNA/pair_oxdna_excv.h diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/CG-DNA/pair_oxdna_hbond.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_hbond.cpp rename to src/CG-DNA/pair_oxdna_hbond.cpp diff --git a/src/USER-CGDNA/pair_oxdna_hbond.h b/src/CG-DNA/pair_oxdna_hbond.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_hbond.h rename to src/CG-DNA/pair_oxdna_hbond.h diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/CG-DNA/pair_oxdna_stk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_stk.cpp rename to src/CG-DNA/pair_oxdna_stk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_stk.h b/src/CG-DNA/pair_oxdna_stk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_stk.h rename to src/CG-DNA/pair_oxdna_stk.h diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/CG-DNA/pair_oxdna_xstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxdna_xstk.cpp rename to src/CG-DNA/pair_oxdna_xstk.cpp diff --git a/src/USER-CGDNA/pair_oxdna_xstk.h b/src/CG-DNA/pair_oxdna_xstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxdna_xstk.h rename to src/CG-DNA/pair_oxdna_xstk.h diff --git a/src/USER-CGDNA/pair_oxrna2_dh.cpp b/src/CG-DNA/pair_oxrna2_dh.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_dh.cpp rename to src/CG-DNA/pair_oxrna2_dh.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_dh.h b/src/CG-DNA/pair_oxrna2_dh.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_dh.h rename to src/CG-DNA/pair_oxrna2_dh.h diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/CG-DNA/pair_oxrna2_excv.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_excv.cpp rename to src/CG-DNA/pair_oxrna2_excv.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_excv.h b/src/CG-DNA/pair_oxrna2_excv.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_excv.h rename to src/CG-DNA/pair_oxrna2_excv.h diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.cpp b/src/CG-DNA/pair_oxrna2_hbond.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_hbond.cpp rename to src/CG-DNA/pair_oxrna2_hbond.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_hbond.h b/src/CG-DNA/pair_oxrna2_hbond.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_hbond.h rename to src/CG-DNA/pair_oxrna2_hbond.h diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/CG-DNA/pair_oxrna2_stk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_stk.cpp rename to src/CG-DNA/pair_oxrna2_stk.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_stk.h b/src/CG-DNA/pair_oxrna2_stk.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_stk.h rename to src/CG-DNA/pair_oxrna2_stk.h diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/CG-DNA/pair_oxrna2_xstk.cpp similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_xstk.cpp rename to src/CG-DNA/pair_oxrna2_xstk.cpp diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.h b/src/CG-DNA/pair_oxrna2_xstk.h similarity index 100% rename from src/USER-CGDNA/pair_oxrna2_xstk.h rename to src/CG-DNA/pair_oxrna2_xstk.h diff --git a/src/USER-CGSDK/Install.sh b/src/CG-SDK/Install.sh similarity index 100% rename from src/USER-CGSDK/Install.sh rename to src/CG-SDK/Install.sh diff --git a/src/USER-CGSDK/README b/src/CG-SDK/README similarity index 91% rename from src/USER-CGSDK/README rename to src/CG-SDK/README index 3d5cae9b20..c6bd90531e 100644 --- a/src/USER-CGSDK/README +++ b/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 diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/CG-SDK/angle_sdk.cpp similarity index 100% rename from src/USER-CGSDK/angle_sdk.cpp rename to src/CG-SDK/angle_sdk.cpp diff --git a/src/USER-CGSDK/angle_sdk.h b/src/CG-SDK/angle_sdk.h similarity index 100% rename from src/USER-CGSDK/angle_sdk.h rename to src/CG-SDK/angle_sdk.h diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/CG-SDK/lj_sdk_common.h similarity index 100% rename from src/USER-CGSDK/lj_sdk_common.h rename to src/CG-SDK/lj_sdk_common.h diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/CG-SDK/pair_lj_sdk.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk.cpp rename to src/CG-SDK/pair_lj_sdk.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/CG-SDK/pair_lj_sdk.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk.h rename to src/CG-SDK/pair_lj_sdk.h diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/CG-SDK/pair_lj_sdk_coul_long.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_long.cpp rename to src/CG-SDK/pair_lj_sdk_coul_long.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.h b/src/CG-SDK/pair_lj_sdk_coul_long.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_long.h rename to src/CG-SDK/pair_lj_sdk_coul_long.h diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/CG-SDK/pair_lj_sdk_coul_msm.cpp similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp rename to src/CG-SDK/pair_lj_sdk_coul_msm.cpp diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.h b/src/CG-SDK/pair_lj_sdk_coul_msm.h similarity index 100% rename from src/USER-CGSDK/pair_lj_sdk_coul_msm.h rename to src/CG-SDK/pair_lj_sdk_coul_msm.h diff --git a/src/Depend.sh b/src/Depend.sh index c97321a9ef..8598afc867 100755 --- a/src/Depend.sh +++ b/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 diff --git a/src/Makefile b/src/Makefile index dc28e28261..b8f03b324a 100644 --- a/src/Makefile +++ b/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 \ - user-cgsdk user-colvars user-dielectric user-diffraction user-dpd user-drude \ +PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs cg-dna \ + 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 \ diff --git a/src/USER-BROWNIAN/fix_brownian.cpp b/src/USER-BROWNIAN/fix_brownian.cpp index fc6b434080..b811ede721 100644 --- a/src/USER-BROWNIAN/fix_brownian.cpp +++ b/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) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_asphere.cpp b/src/USER-BROWNIAN/fix_brownian_asphere.cpp index ef0c246508..fccc6b5040 100644 --- a/src/USER-BROWNIAN/fix_brownian_asphere.cpp +++ b/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) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_base.cpp b/src/USER-BROWNIAN/fix_brownian_base.cpp index fd5d1f5df7..0fa928bebf 100644 --- a/src/USER-BROWNIAN/fix_brownian_base.cpp +++ b/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) ------------------------------------------------------------------------- */ diff --git a/src/USER-BROWNIAN/fix_brownian_sphere.cpp b/src/USER-BROWNIAN/fix_brownian_sphere.cpp index 4621be595f..cf835dcdc1 100644 --- a/src/USER-BROWNIAN/fix_brownian_sphere.cpp +++ b/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) ------------------------------------------------------------------------- */