remove MSCG package from LAMMPS distribution
This commit is contained in:
Axel Kohlmeyer
@ -278,7 +278,6 @@ set(STANDARD_PACKAGES
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MOLECULE
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MOLFILE
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MPIIO
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MSCG
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NETCDF
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ORIENT
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PERI
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@ -440,7 +439,7 @@ if(BUILD_OMP)
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target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
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endif()
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if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
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if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
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enable_language(C)
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if (NOT USE_INTERNAL_LINALG)
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find_package(LAPACK)
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@ -520,7 +519,7 @@ else()
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endif()
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foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
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PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM MSCG COMPRESS ML-PACE LEPTON)
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PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
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if(PKG_${PKG_WITH_INCL})
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include(Packages/${PKG_WITH_INCL})
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endif()
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@ -1,28 +0,0 @@
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find_package(GSL REQUIRED)
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find_package(MSCG QUIET)
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if(MSGC_FOUND)
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set(DOWNLOAD_MSCG_DEFAULT OFF)
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else()
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set(DOWNLOAD_MSCG_DEFAULT ON)
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endif()
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option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
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if(DOWNLOAD_MSCG)
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set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
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set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
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mark_as_advanced(MSCG_URL)
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mark_as_advanced(MSCG_MD5)
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include(ExternalCMakeProject)
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ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
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# set include and link library
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target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
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target_link_libraries(lammps PRIVATE mscg)
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else()
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find_package(MSCG)
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if(NOT MSCG_FOUND)
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message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIR, or set DOWNLOAD_MSCG=ON to download it")
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endif()
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target_link_libraries(lammps PRIVATE MSCG::MSCG)
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endif()
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target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})
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@ -64,7 +64,6 @@ set(ALL_PACKAGES
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MOLECULE
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MOLFILE
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MPIIO
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MSCG
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NETCDF
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OPENMP
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OPT
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@ -66,7 +66,6 @@ set(ALL_PACKAGES
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MOLECULE
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MOLFILE
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MPIIO
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MSCG
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NETCDF
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OPENMP
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OPT
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@ -9,7 +9,6 @@ endforeach()
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set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
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set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
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set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
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set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
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set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
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set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)
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@ -20,7 +20,6 @@ set(PACKAGES_WITH_LIB
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ML-QUIP
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MOLFILE
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MPIIO
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MSCG
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NETCDF
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PLUMED
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PYTHON
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@ -52,7 +52,6 @@ This is the list of packages that may require additional steps.
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* :ref:`ML-POD <ml-pod>`
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* :ref:`ML-QUIP <ml-quip>`
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* :ref:`MOLFILE <molfile>`
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* :ref:`MSCG <mscg>`
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* :ref:`NETCDF <netcdf>`
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* :ref:`OPENMP <openmp>`
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* :ref:`OPT <opt>`
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@ -921,59 +920,6 @@ Python version 3.6 or later.
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----------
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.. _mscg:
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MSCG package
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-----------------------
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To build with this package, you must download and build the MS-CG
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library. Building the MS-CG library requires that the GSL
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(GNU Scientific Library) headers and libraries are installed on your
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machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for
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more details.
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.. tabs::
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.. tab:: CMake build
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.. code-block:: bash
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-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
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-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
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-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location)
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If ``DOWNLOAD_MSCG`` is set, the MSCG library will be downloaded
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and built inside the CMake build directory. If the MSCG library
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is already on your system (in a location CMake cannot find it),
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``MSCG_LIBRARY`` is the filename (plus path) of the MSCG library
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file, not the directory the library file is in.
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``MSCG_INCLUDE_DIR`` is the directory the MSCG include file is in.
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.. tab:: Traditional make
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You can download and build the MS-CG library manually if you
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prefer; follow the instructions in ``lib/mscg/README``\ . You can
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also do it in one step from the ``lammps/src`` dir, using a
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command like these, which simply invokes the
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``lib/mscg/Install.py`` script with the specified args:
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.. code-block:: bash
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make lib-mscg # print help message
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make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
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# with the settings compatible with "make serial"
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make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
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# with the settings compatible with "make mpi"
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make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
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Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
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will be created in ``lib/mscg`` to point to the MS-CG
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``src/installation`` dir. When LAMMPS is built in src it will use
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these links. You should not need to edit the
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``lib/mscg/Makefile.lammps`` file.
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----------
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.. _opt:
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OPT package
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@ -55,7 +55,6 @@ packages:
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* :ref:`ML-POD <ml-pod>`
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* :ref:`ML-QUIP <ml-quip>`
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* :ref:`MOLFILE <molfile>`
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* :ref:`MSCG <mscg>`
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* :ref:`NETCDF <netcdf>`
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* :ref:`OPENMP <openmp>`
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* :ref:`OPT <opt>`
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@ -116,7 +116,6 @@ OPT.
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* :doc:`momentum (k) <fix_momentum>`
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* :doc:`momentum/chunk <fix_momentum>`
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* :doc:`move <fix_move>`
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* :doc:`mscg <fix_mscg>`
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* :doc:`msst <fix_msst>`
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* :doc:`mvv/dpd <fix_mvv_dpd>`
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* :doc:`mvv/edpd <fix_mvv_dpd>`
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@ -85,6 +85,16 @@ The same functionality is available through
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:doc:`bond style mesocnt <bond_mesocnt>` and
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:doc:`angle style mesocnt <angle_mesocnt>`.
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MSCG package
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------------
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.. deprecated:: TBD
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The MSCG package has been removed from LAMMPS since it was unmaintained
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for many years and instead superseded by the `OpenMSCG software
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<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
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University of Chicago, which can be used independent from LAMMPS.
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REAX package
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------------
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@ -104,8 +104,6 @@ Lowercase directories
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+-------------+------------------------------------------------------------------+
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| min | energy minimization of 2d LJ melt |
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+-------------+------------------------------------------------------------------+
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| mscg | parameterize a multi-scale coarse-graining (MSCG) model |
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+-------------+------------------------------------------------------------------+
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| msst | MSST shock dynamics |
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+-------------+------------------------------------------------------------------+
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| multi | multi neighboring for systems with large interaction disparities |
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@ -88,7 +88,6 @@ page gives those details.
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* :ref:`MOLECULE <PKG-MOLECULE>`
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* :ref:`MOLFILE <PKG-MOLFILE>`
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* :ref:`MPIIO <PKG-MPIIO>`
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* :ref:`MSCG <PKG-MSCG>`
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* :ref:`NETCDF <PKG-NETCDF>`
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* :ref:`OPENMP <PKG-OPENMP>`
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* :ref:`OPT <PKG-OPT>`
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@ -2066,38 +2065,6 @@ The MPIIO package requires that LAMMPS is build in :ref:`MPI parallel mode <seri
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----------
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.. _PKG-MSCG:
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MSCG package
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------------
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**Contents:**
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A :doc:`fix mscg <fix_mscg>` command which can parameterize a
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Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library <mscg-home_>`_.
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.. _mscg-home: https://github.com/uchicago-voth/MSCG-release
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To use this package you must have the MS-CG library available on your
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system.
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**Authors:** The fix was written by Lauren Abbott (Sandia). The MS-CG
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library was developed by Jacob Wagner in Greg Voth's group at the
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University of Chicago.
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**Install:**
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This package has :ref:`specific installation instructions <mscg>` on the :doc:`Build extras <Build_extras>` page.
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**Supporting info:**
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* src/MSCG: filenames -> commands
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* src/MSCG/README
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* lib/mscg/README
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* examples/mscg
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----------
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.. _PKG-NETCDF:
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NETCDF package
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@ -338,11 +338,6 @@ whether an extra library is needed to build and use the package:
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- :doc:`dump <dump>`
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- n/a
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- no
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* - :ref:`MSCG <PKG-MSCG>`
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- multi-scale coarse-graining wrapper
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- :doc:`fix mscg <fix_mscg>`
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- mscg
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- ext
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* - :ref:`NETCDF <PKG-NETCDF>`
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- dump output via NetCDF
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- :doc:`dump netcdf <dump_netcdf>`
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@ -268,7 +268,6 @@ accelerated styles exist.
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* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
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* :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
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* :doc:`move <fix_move>` - move atoms in a prescribed fashion
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* :doc:`mscg <fix_mscg>` - apply MSCG method for force-matching to generate coarse grain models
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* :doc:`msst <fix_msst>` - multi-scale shock technique (MSST) integration
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* :doc:`mvv/dpd <fix_mvv_dpd>` - DPD using the modified velocity-Verlet integration algorithm
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* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
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@ -1,141 +0,0 @@
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.. index:: fix mscg
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fix mscg command
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================
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID mscg N keyword args ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mscg = style name of this fix command
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* N = envoke this fix every this many timesteps
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* zero or more keyword/value pairs may be appended
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* keyword = *range* or *name* or *max*
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.. parsed-literal::
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*range* arg = *on* or *off*
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*on* = range finding functionality is performed
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*off* = force matching functionality is performed
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*name* args = name1 ... nameN
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name1,...,nameN = string names for each atom type (1-Ntype)
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*max* args = maxb maxa maxd
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maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all mscg 1
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fix 1 all mscg 1 range name A B
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fix 1 all mscg 1 max 4 8 20
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Description
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"""""""""""
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This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
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snapshots from a dump file to generate potentials for coarse-grained
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simulations from all-atom simulations, using a force-matching technique
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(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
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It makes use of the MS-CG library, written and maintained by Greg Voth's
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group at the University of Chicago, which is freely available on their
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`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
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See instructions on obtaining and installing the MS-CG library in the
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src/MSCG/README file, which must be done before you build LAMMPS with
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this fix command and use the command in a LAMMPS input script.
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An example script using this fix is provided the examples/mscg
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directory.
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The general workflow for using LAMMPS in conjunction with the MS-CG
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library to create a coarse-grained model and run coarse-grained
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simulations is as follows:
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1. Perform all-atom simulations on the system to be coarse grained.
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2. Generate a trajectory mapped to the coarse-grained model.
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3. Create input files for the MS-CG library.
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4. Run the range finder functionality of the MS-CG library.
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5. Run the force matching functionality of the MS-CG library.
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6. Check the results of the force matching.
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7. Run coarse-grained simulations using the new coarse-grained potentials.
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This fix can perform the range finding and force matching steps 4 and 5
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of the above workflow when used in conjunction with the :doc:`rerun
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<rerun>` command. It does not perform steps 1-3 and 6-7.
|
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Step 2 can be performed using a Python script (cgmap), which defines the
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coarse-grained model and converts a standard LAMMPS dump file for an
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all-atom simulation (step 1) into a LAMMPS dump file which has the
|
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positions of and forces on the coarse-grained beads. To use cgmap the
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following repositories need to be downloaded and installed.
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#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
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#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
|
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In step 3, an input file named "control.in" is needed by the MS-CG
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library which sets parameters for the range finding and force matching
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functionalities. See the examples/mscg/control.in file as an example.
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And see the documentation provided with the MS-CG library for more
|
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info on this file.
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When this fix is used to perform steps 4 and 5, the MS-CG library also
|
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produces additional output files. The range finder functionality
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(step 4) outputs files defining pair and bonded interaction ranges. The
|
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force matching functionality (step 5) outputs tabulated force files for
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every interaction in the system. Other diagnostic files can also be
|
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output depending on the parameters in the MS-CG library input script.
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Again, see the documentation provided with the MS-CG library for more
|
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info.
|
||||
|
||||
----------
|
||||
|
||||
The *range* keyword specifies which MS-CG library functionality should
|
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be invoked. If *on*, the step 4 range finder functionality is invoked.
|
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*off*, the step 5 force matching functionality is invoked.
|
||||
|
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If the *name* keyword is used, string names are defined to associate
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with the integer atom types in LAMMPS. *Ntype* names must be provided,
|
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one for each atom type (1-Ntype).
|
||||
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The *max* keyword specifies the maximum number of bonds, angles, and
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dihedrals a bead can have in the coarse-grained model.
|
||||
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Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the MSCG package. It is only enabled if LAMMPS was
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||||
built with that package. Building the MSCG package also requires
|
||||
external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
|
||||
pages for more info.
|
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Currently, the MS-CG library is not set up to run in parallel with MPI,
|
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so this fix can only be used in a serial LAMMPS build and run on a
|
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single processor.
|
||||
|
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Related commands
|
||||
""""""""""""""""
|
||||
|
||||
none
|
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|
||||
|
||||
Default
|
||||
"""""""
|
||||
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The default keyword settings are range off, max 4 12 36.
|
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|
||||
----------
|
||||
|
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.. _Izvekov:
|
||||
|
||||
**(Izvekov)** Izvekov, Voth, J Chem Phys 123, 134105 (2005).
|
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|
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.. _Noid:
|
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**(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
|
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Chem Phys 128, 134105 (2008).
|
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@ -91,7 +91,6 @@ mesh: create_atoms mesh command
|
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
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min: energy minimization of 2d LJ melt
|
||||
mliap: examples for using several bundled MLIAP potentials
|
||||
mscg: parameterize a multi-scale coarse-graining (MSCG) model
|
||||
msst: MSST shock dynamics
|
||||
nb3b: use of nonbonded 3-body harmonic pair style
|
||||
neb: nudged elastic band (NEB) calculation for barrier finding
|
||||
|
||||
@ -1,10 +0,0 @@
|
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Running this example requires that LAMMPS be built with the MSCG
|
||||
package and its fix mscg command. The fix uses the Multi-Scale
|
||||
Coarse-Graining (MS-CG) library, freely available at
|
||||
https://github.com/uchicago-voth/MSCG-release, to compute optimized
|
||||
coarse-grained force field parameters. The MS-CG library was
|
||||
developed by Jacob Wagner in Greg Voth's group at the University of
|
||||
Chicago.
|
||||
|
||||
See the lib/mscg/README file for instructions on how to download and
|
||||
install the MS-CG library for use with LAMMPS.
|
||||
@ -1,12 +0,0 @@
|
||||
block_size 1
|
||||
start_frame 1
|
||||
n_frames 19
|
||||
nonbonded_cutoff 10.0
|
||||
basis_type 0
|
||||
primary_output_style 0
|
||||
output_solution_flag 1
|
||||
output_spline_coeffs_flag 1
|
||||
pair_nonbonded_bspline_basis_order 6
|
||||
pair_nonbonded_basis_set_resolution 0.7
|
||||
pair_nonbonded_output_binwidth 0.1
|
||||
matrix_type 0
|
||||
File diff suppressed because it is too large
Load Diff
20180
examples/mscg/dump.meoh
20180
examples/mscg/dump.meoh
File diff suppressed because it is too large
Load Diff
@ -1,22 +0,0 @@
|
||||
units real
|
||||
atom_style full
|
||||
pair_style zero 10.0
|
||||
|
||||
read_data data.meoh
|
||||
pair_coeff * *
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step
|
||||
|
||||
# Test 1a: range finder functionality
|
||||
fix 1 all mscg 1 range on
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
print "TEST_1a mscg range finder"
|
||||
unfix 1
|
||||
|
||||
# Test 1b: force matching functionality
|
||||
fix 1 all mscg 1
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
print "TEST_1b mscg force matching"
|
||||
|
||||
print TEST_DONE
|
||||
@ -1,105 +0,0 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
pair_style zero 10.0
|
||||
|
||||
read_data data.meoh
|
||||
Reading data file ...
|
||||
orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.007 seconds
|
||||
pair_coeff * *
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step
|
||||
|
||||
# Test 1a: range finder functionality
|
||||
fix 1 all mscg 1 range on
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
|
||||
Step
|
||||
0
|
||||
250
|
||||
500
|
||||
750
|
||||
1000
|
||||
1250
|
||||
1500
|
||||
1750
|
||||
2000
|
||||
2250
|
||||
2500
|
||||
2750
|
||||
3000
|
||||
3250
|
||||
3500
|
||||
3750
|
||||
4000
|
||||
4250
|
||||
4500
|
||||
Loop time of 0.245891 on 1 procs for 19 steps with 1000 atoms
|
||||
|
||||
print "TEST_1a mscg range finder"
|
||||
TEST_1a mscg range finder
|
||||
unfix 1
|
||||
|
||||
# Test 1b: force matching functionality
|
||||
fix 1 all mscg 1
|
||||
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
|
||||
Step
|
||||
0
|
||||
250
|
||||
500
|
||||
750
|
||||
1000
|
||||
1250
|
||||
1500
|
||||
1750
|
||||
2000
|
||||
2250
|
||||
2500
|
||||
2750
|
||||
3000
|
||||
3250
|
||||
3500
|
||||
3750
|
||||
4000
|
||||
4250
|
||||
4500
|
||||
Loop time of 0.433986 on 1 procs for 19 steps with 1000 atoms
|
||||
|
||||
print "TEST_1b mscg force matching"
|
||||
TEST_1b mscg force matching
|
||||
|
||||
print TEST_DONE
|
||||
TEST_DONE
|
||||
Total wall time: 0:00:00
|
||||
@ -1,71 +0,0 @@
|
||||
3.000000 9.109433117503674e+00
|
||||
3.100000 6.562933520937051e+00
|
||||
3.200000 3.803570347770783e+00
|
||||
3.300000 1.524835163098694e+00
|
||||
3.400000 3.680752991750511e-02
|
||||
3.500000 -6.369395346711866e-01
|
||||
3.600000 -6.624341032589213e-01
|
||||
3.700000 -2.983998819283989e-01
|
||||
3.800000 1.996942072449469e-01
|
||||
3.900000 6.507540486137935e-01
|
||||
4.000000 9.561503221901252e-01
|
||||
4.100000 1.082978861799261e+00
|
||||
4.200000 1.046366050930359e+00
|
||||
4.300000 8.917742185869113e-01
|
||||
4.400000 6.773070351372578e-01
|
||||
4.500000 4.561974686292022e-01
|
||||
4.600000 2.640422255436971e-01
|
||||
4.700000 1.180848207166380e-01
|
||||
4.800000 2.124502216672507e-02
|
||||
4.900000 -3.366915456585443e-02
|
||||
5.000000 -5.974945208074427e-02
|
||||
5.100000 -7.177537677873873e-02
|
||||
5.200000 -8.204929079011507e-02
|
||||
5.300000 -9.745573177789707e-02
|
||||
5.400000 -1.196283642109915e-01
|
||||
5.500000 -1.463411396781238e-01
|
||||
5.600000 -1.729465415853768e-01
|
||||
5.700000 -1.938138298537278e-01
|
||||
5.800000 -2.037672856165882e-01
|
||||
5.900000 -1.995060297815394e-01
|
||||
6.000000 -1.805447650094144e-01
|
||||
6.100000 -1.489384048916932e-01
|
||||
6.200000 -1.085276302304308e-01
|
||||
6.300000 -6.416601955090541e-02
|
||||
6.400000 -2.094717961426480e-02
|
||||
6.500000 1.656812406982645e-02
|
||||
6.600000 4.511482523443927e-02
|
||||
6.700000 6.322611594801032e-02
|
||||
6.800000 7.107524696431811e-02
|
||||
6.900000 7.005702917383723e-02
|
||||
7.000000 6.235932355899154e-02
|
||||
7.100000 5.053453114940768e-02
|
||||
7.200000 3.707108297716843e-02
|
||||
7.300000 2.397003518601587e-02
|
||||
7.400000 1.245439896007831e-02
|
||||
7.500000 3.015413982707119e-03
|
||||
7.600000 -4.408442264121739e-03
|
||||
7.700000 -1.024733994435217e-02
|
||||
7.800000 -1.511598231239246e-02
|
||||
7.900000 -1.962949115765983e-02
|
||||
8.000000 -2.422153184874873e-02
|
||||
8.100000 -2.902066868449916e-02
|
||||
8.200000 -3.387453677654857e-02
|
||||
8.300000 -3.843224513464188e-02
|
||||
8.400000 -4.222901944115068e-02
|
||||
8.500000 -4.477084482559266e-02
|
||||
8.600000 -4.561910863915099e-02
|
||||
8.700000 -4.447439067652353e-02
|
||||
8.800000 -4.123808661911404e-02
|
||||
8.900000 -3.601776131390161e-02
|
||||
9.000000 -2.911033476210515e-02
|
||||
9.100000 -2.098441550402311e-02
|
||||
9.200000 -1.226263400387303e-02
|
||||
9.300000 -3.703976034631109e-03
|
||||
9.400000 3.815231963949414e-03
|
||||
9.500000 9.355387087425532e-03
|
||||
9.600000 1.205664749783030e-02
|
||||
9.700000 1.131702059340882e-02
|
||||
9.800000 6.971799313021964e-03
|
||||
9.900000 -5.270015594498346e-04
|
||||
10.000000 -9.931209090702869e-03
|
||||
@ -1,104 +0,0 @@
|
||||
# Header information on force file
|
||||
|
||||
1_1
|
||||
N 99 R 0.200000 10.000000
|
||||
|
||||
1 0.200000 127.263594 80.411422
|
||||
2 0.300000 119.349776 77.864922
|
||||
3 0.400000 111.690609 75.318423
|
||||
4 0.500000 104.286092 72.771923
|
||||
5 0.600000 97.136225 70.225423
|
||||
6 0.700000 90.241007 67.678924
|
||||
7 0.800000 83.600440 65.132424
|
||||
8 0.900000 77.214522 62.585925
|
||||
9 1.000000 71.083255 60.039425
|
||||
10 1.100000 65.206637 57.492925
|
||||
11 1.200000 59.584670 54.946426
|
||||
12 1.300000 54.217352 52.399926
|
||||
13 1.400000 49.104684 49.853427
|
||||
14 1.500000 44.246667 47.306927
|
||||
15 1.600000 39.643299 44.760427
|
||||
16 1.700000 35.294581 42.213928
|
||||
17 1.800000 31.200513 39.667428
|
||||
18 1.900000 27.361096 37.120929
|
||||
19 2.000000 23.776328 34.574429
|
||||
20 2.100000 20.446210 32.027929
|
||||
21 2.200000 17.370742 29.481430
|
||||
22 2.300000 14.549924 26.934930
|
||||
23 2.400000 11.983756 24.388431
|
||||
24 2.500000 9.672238 21.841931
|
||||
25 2.600000 7.615370 19.295432
|
||||
26 2.700000 5.813151 16.748932
|
||||
27 2.800000 4.265583 14.202432
|
||||
28 2.900000 2.972665 11.655933
|
||||
29 3.000000 1.934397 9.109433
|
||||
30 3.100000 1.150778 6.562934
|
||||
31 3.200000 0.632453 3.803570
|
||||
32 3.300000 0.366033 1.524835
|
||||
33 3.400000 0.287951 0.036808
|
||||
34 3.500000 0.317957 -0.636940
|
||||
35 3.600000 0.382926 -0.662434
|
||||
36 3.700000 0.430968 -0.298400
|
||||
37 3.800000 0.435903 0.199694
|
||||
38 3.900000 0.393381 0.650754
|
||||
39 4.000000 0.313035 0.956150
|
||||
40 4.100000 0.211079 1.082979
|
||||
41 4.200000 0.104612 1.046366
|
||||
42 4.300000 0.007705 0.891774
|
||||
43 4.400000 -0.070749 0.677307
|
||||
44 4.500000 -0.127425 0.456197
|
||||
45 4.600000 -0.163437 0.264042
|
||||
46 4.700000 -0.182543 0.118085
|
||||
47 4.800000 -0.189509 0.021245
|
||||
48 4.900000 -0.188888 -0.033669
|
||||
49 5.000000 -0.184217 -0.059749
|
||||
50 5.100000 -0.177641 -0.071775
|
||||
51 5.200000 -0.169950 -0.082049
|
||||
52 5.300000 -0.160975 -0.097456
|
||||
53 5.400000 -0.150120 -0.119628
|
||||
54 5.500000 -0.136822 -0.146341
|
||||
55 5.600000 -0.120858 -0.172947
|
||||
56 5.700000 -0.102520 -0.193814
|
||||
57 5.800000 -0.082640 -0.203767
|
||||
58 5.900000 -0.062477 -0.199506
|
||||
59 6.000000 -0.043474 -0.180545
|
||||
60 6.100000 -0.027000 -0.148938
|
||||
61 6.200000 -0.014127 -0.108528
|
||||
62 6.300000 -0.005492 -0.064166
|
||||
63 6.400000 -0.001236 -0.020947
|
||||
64 6.500000 -0.001018 0.016568
|
||||
65 6.600000 -0.004102 0.045115
|
||||
66 6.700000 -0.009519 0.063226
|
||||
67 6.800000 -0.016234 0.071075
|
||||
68 6.900000 -0.023290 0.070057
|
||||
69 7.000000 -0.029911 0.062359
|
||||
70 7.100000 -0.035556 0.050535
|
||||
71 7.200000 -0.039936 0.037071
|
||||
72 7.300000 -0.042988 0.023970
|
||||
73 7.400000 -0.044809 0.012454
|
||||
74 7.500000 -0.045583 0.003015
|
||||
75 7.600000 -0.045513 -0.004408
|
||||
76 7.700000 -0.044781 -0.010247
|
||||
77 7.800000 -0.043512 -0.015116
|
||||
78 7.900000 -0.041775 -0.019629
|
||||
79 8.000000 -0.039583 -0.024222
|
||||
80 8.100000 -0.036920 -0.029021
|
||||
81 8.200000 -0.033776 -0.033875
|
||||
82 8.300000 -0.030160 -0.038432
|
||||
83 8.400000 -0.026127 -0.042229
|
||||
84 8.500000 -0.021777 -0.044771
|
||||
85 8.600000 -0.017258 -0.045619
|
||||
86 8.700000 -0.012753 -0.044474
|
||||
87 8.800000 -0.008467 -0.041238
|
||||
88 8.900000 -0.004605 -0.036018
|
||||
89 9.000000 -0.001348 -0.029110
|
||||
90 9.100000 0.001156 -0.020984
|
||||
91 9.200000 0.002819 -0.012263
|
||||
92 9.300000 0.003617 -0.003704
|
||||
93 9.400000 0.003612 0.003815
|
||||
94 9.500000 0.002953 0.009355
|
||||
95 9.600000 0.001882 0.012057
|
||||
96 9.700000 0.000714 0.011317
|
||||
97 9.800000 -0.000201 0.006972
|
||||
98 9.900000 -0.000523 -0.000527
|
||||
99 10.000000 0.000000 -0.009931
|
||||
@ -1,2 +0,0 @@
|
||||
n: 1 1 6 11 3.000000000000000e+00 1.000000000000000e+01
|
||||
9.109454054135307e+00 6.178334150703818e+00 -6.242976259059743e+00 4.778144787445235e+00 -1.082885612852992e+00 4.521835893850554e-01 -6.477047196208028e-01 2.947887062333265e-01 -4.195609079009661e-02 1.111775827831465e-02 -8.823466147380592e-02 -1.696076806027540e-02 3.192205281984208e-02 3.656991607866288e-03 -9.931306149957592e-03
|
||||
@ -1 +0,0 @@
|
||||
1 1 2.852369 10.000000 fm
|
||||
@ -1,17 +0,0 @@
|
||||
fm_matrix_rows:3000; fm_matrix_columns:15;
|
||||
Singular vector:
|
||||
2.307693e+00
|
||||
1.998418e+00
|
||||
1.400114e+00
|
||||
1.183608e+00
|
||||
9.718949e-01
|
||||
7.471241e-01
|
||||
5.277965e-01
|
||||
5.084369e-01
|
||||
3.510398e-01
|
||||
2.997000e-01
|
||||
2.142454e-01
|
||||
1.201800e-01
|
||||
7.143923e-02
|
||||
3.077326e-02
|
||||
1.835581e-02
|
||||
@ -1,2 +0,0 @@
|
||||
<EFBFBD>ٝ\
|
||||
8"@<40>!D:<3A><>@<40>v<EFBFBD><76><EFBFBD><EFBFBD><18>H<EFBFBD><48><EFBFBD><EFBFBD> @H3H<33>S<7F><53>Ԗ p<><70><EFBFBD>??<3F><>俀% s<><73><EFBFBD>?:y<><79>D{<7B><><EFBFBD>z<EFBFBD>A<EFBFBD>Ć?#Tg<54><67><EFBFBD><EFBFBD><EFBFBD>l#<23><>)^<5E><><EFBFBD><EFBFBD><EFBFBD>YX<>?K<>pkD<6B>m?<3F>
|
||||
@ -41,8 +41,6 @@ mdi hooks to the MDI library, used by MDI package
|
||||
from Taylor Barnes (MolSSI at Virginia Tech)
|
||||
molfile hooks to VMD molfile plugins, used by the MOLFILE package
|
||||
from Axel Kohlmeyer (Temple U) and the VMD development team
|
||||
mscg hooks to the MSCG library, used by fix_mscg command
|
||||
from Jacob Wagner and Greg Voth group (U Chicago)
|
||||
netcdf hooks to a NetCDF library installed on your system
|
||||
from Lars Pastewka (Karlsruhe Institute of Technology)
|
||||
plugin settings to load styles into LAMMPS from plugins
|
||||
|
||||
4
lib/mscg/.gitignore
vendored
4
lib/mscg/.gitignore
vendored
@ -1,4 +0,0 @@
|
||||
# files to ignore
|
||||
/liblink
|
||||
/includelink
|
||||
/MSCG-release-*
|
||||
@ -1,154 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
"""
|
||||
Install.py tool to download, unpack, build, and link to the MS-CG library
|
||||
used to automate the steps described in the README file in this dir
|
||||
"""
|
||||
|
||||
from __future__ import print_function
|
||||
import sys, os, subprocess, shutil, tarfile
|
||||
from argparse import ArgumentParser
|
||||
|
||||
sys.path.append('..')
|
||||
from install_helpers import fullpath, geturl, checkmd5sum, getfallback
|
||||
|
||||
parser = ArgumentParser(prog='Install.py',
|
||||
description="LAMMPS library build wrapper script")
|
||||
|
||||
# settings
|
||||
|
||||
version = "1.7.3.1"
|
||||
machine = "g++_simple"
|
||||
|
||||
# help message
|
||||
|
||||
HELP = """
|
||||
Syntax from src dir: make lib-mscg args="-p [path] -m [suffix] -v [version]"
|
||||
or: make lib-mscg args="-b -m [suffix]"
|
||||
Syntax from lib dir: python Install.py -p [path] -m [suffix] -v [version]
|
||||
Syntax from lib dir: python Install.py -b -m [suffix]
|
||||
|
||||
Example:
|
||||
|
||||
make lib-mscg args="-b -m serial " # download/build in lib/mscg/MSCG-release with settings compatible with "make serial"
|
||||
make lib-mscg args="-b -m mpi " # download/build in lib/mscg/MSCG-release with settings compatible with "make mpi"
|
||||
make lib-mscg args="-p /usr/local/mscg-release " # use existing MS-CG installation in /usr/local/mscg-release
|
||||
"""
|
||||
|
||||
# known checksums for different MSCG versions. used to validate the download.
|
||||
checksums = { \
|
||||
'1.7.3.1' : '8c45e269ee13f60b303edd7823866a91', \
|
||||
}
|
||||
|
||||
# parse and process arguments
|
||||
|
||||
pgroup = parser.add_mutually_exclusive_group()
|
||||
pgroup.add_argument("-b", "--build", action="store_true",
|
||||
help="download and build the MSCG library")
|
||||
pgroup.add_argument("-p", "--path",
|
||||
help="specify folder of existing MSCG installation")
|
||||
parser.add_argument("-v", "--version", default=version, choices=checksums.keys(),
|
||||
help="set version of MSCG to download and build (default: %s)" % version)
|
||||
parser.add_argument("-m", "--machine", default=machine, choices=['mpi', 'serial', 'g++_simple', 'intel_simple', 'lapack', 'mac'],
|
||||
help="set machine suffix specifies which src/Make/Makefile.suffix to use. (default: %s)" % machine)
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
# print help message and exit, if neither build nor path options are given
|
||||
if not args.build and not args.path:
|
||||
parser.print_help()
|
||||
sys.exit(HELP)
|
||||
|
||||
buildflag = args.build
|
||||
pathflag = args.path is not None
|
||||
mscgpath = args.path
|
||||
msuffix = args.machine
|
||||
mscgver = args.version
|
||||
|
||||
# settings
|
||||
|
||||
url = "https://github.com/uchicago-voth/MSCG-release/archive/%s.tar.gz" % mscgver
|
||||
tarname = "MS-CG-%s.tar.gz" % mscgver
|
||||
tardir = "MSCG-release-%s" % mscgver
|
||||
|
||||
homepath = fullpath('.')
|
||||
homedir = os.path.join(homepath, tardir)
|
||||
|
||||
if pathflag:
|
||||
if not os.path.isdir(mscgpath):
|
||||
sys.exit("MS-CG path %s does not exist" % mscgpath)
|
||||
homedir = fullpath(mscgpath)
|
||||
|
||||
# download and unpack MS-CG tarfile
|
||||
|
||||
if buildflag:
|
||||
print("Downloading MS-CG ...")
|
||||
tarname = os.path.join(homepath, tarname)
|
||||
fallback = getfallback('mscg', url)
|
||||
try:
|
||||
geturl(url, tarname)
|
||||
except:
|
||||
geturl(fallback, tarname)
|
||||
|
||||
# verify downloaded archive integrity via md5 checksum, if known.
|
||||
if mscgver in checksums:
|
||||
if not checkmd5sum(checksums[mscgver], tarname):
|
||||
print("Checksum did not match. Trying fallback URL", fallback)
|
||||
geturl(fallback, tarname)
|
||||
if not checkmd5sum(checksums[mscgver], tarname):
|
||||
sys.exit("Checksum for LATTE library does not match for fallback, too.")
|
||||
|
||||
print("Unpacking MS-CG tarfile ...")
|
||||
|
||||
if os.path.exists(os.path.join(homepath, tardir)):
|
||||
shutil.rmtree(os.path.join(homepath, tardir))
|
||||
|
||||
if tarfile.is_tarfile(tarname):
|
||||
tgz = tarfile.open(tarname)
|
||||
tgz.extractall(path=homepath)
|
||||
os.remove(tarname)
|
||||
else:
|
||||
sys.exit("File %s is not a supported archive", tarname)
|
||||
|
||||
if os.path.basename(homedir) != tardir:
|
||||
if os.path.exists(homedir):
|
||||
shutil.rmtree(homedir)
|
||||
os.rename(os.path.join(homepath, tardir), homedir)
|
||||
|
||||
# build MS-CG
|
||||
|
||||
if buildflag:
|
||||
print("Building MS-CG ...")
|
||||
mkf = "Makefile.%s" % msuffix
|
||||
mkp = os.path.join(homedir, 'src', 'Make', mkf)
|
||||
if os.path.exists(mkp):
|
||||
shutil.copyfile(mkp, os.path.join(homedir, 'src', mkf))
|
||||
elif os.path.exists("Makefile.%s" % msuffix):
|
||||
shutil.copyfile("Makefile.%s" % msuffix, os.path.join(homedir, 'src', mkf))
|
||||
else:
|
||||
sys.exit("Cannot find Makefile.%s" % msuffix)
|
||||
try:
|
||||
cmd = 'make -C %s -f Makefile.%s' % (os.path.join(homedir, 'src'), msuffix)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
print(txt.decode('UTF-8'))
|
||||
except subprocess.CalledProcessError as e:
|
||||
print("Make failed with:\n %s" % e.output.decode('UTF-8'))
|
||||
sys.exit(1)
|
||||
|
||||
if not os.path.exists("Makefile.lammps"):
|
||||
print("Creating Makefile.lammps")
|
||||
if os.path.exists("Makefile.lammps.%s" % msuffix):
|
||||
shutil.copyfile('Makefile.lammps.%s' % msuffix, 'Makefile.lammps')
|
||||
else:
|
||||
shutil.copyfile('Makefile.lammps.default', 'Makefile.lammps')
|
||||
else: print("Makefile.lammps exists. Please check its settings")
|
||||
|
||||
# create 2 links in lib/mscg to MS-CG src dir
|
||||
|
||||
print("Creating links to MS-CG include and lib files")
|
||||
if os.path.isfile("includelink") or os.path.islink("includelink"):
|
||||
os.remove("includelink")
|
||||
if os.path.isfile("liblink") or os.path.islink("liblink"):
|
||||
os.remove("liblink")
|
||||
os.symlink(os.path.join(homedir, 'src'), 'includelink')
|
||||
os.symlink(os.path.join(homedir, 'src'), 'liblink')
|
||||
@ -1,5 +0,0 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
mscg_SYSINC =
|
||||
mscg_SYSLIB = -lgsl -lgslcblas
|
||||
mscg_SYSPATH =
|
||||
@ -1,5 +0,0 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
mscg_SYSINC = -std=c++11
|
||||
mscg_SYSLIB = -lm -lgsl -llapack -lgslcblas
|
||||
mscg_SYSPATH =
|
||||
@ -1,5 +0,0 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
mscg_SYSINC =
|
||||
mscg_SYSLIB = -lgsl -lgslcblas
|
||||
mscg_SYSPATH =
|
||||
@ -1,5 +0,0 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
mscg_SYSINC =
|
||||
mscg_SYSLIB = -lgsl -lgslcblas
|
||||
mscg_SYSPATH =
|
||||
@ -1,104 +0,0 @@
|
||||
# This Makefile is meant for use after
|
||||
# module load gsl/2.2.1+gcc-6.1
|
||||
# module load gcc/6.1
|
||||
# It also requires LAPACK
|
||||
# Module names refer to those on any of RCC's clusters at UChicago.
|
||||
|
||||
# This makefile does NOT include GROMACS reading or MKL (sparse matrix)
|
||||
# It uses the gcc/g++ compiler (v4.9+) for C++11 support
|
||||
|
||||
# 1) Try this first (as it is the easiest)
|
||||
NO_GRO_LIBS = -lgsl -lgslcblas
|
||||
|
||||
# 2) If it does not find your libraries automatically, you can specify them manually
|
||||
# # A) Set the GSL_LIB to the location of your GSL library's lib directory (must be V2+)
|
||||
GSL_LIB = /software/gsl-2.2.1-el6-x86_64+gcc-6.1/lib
|
||||
# # B) Set the LAPACK_DIR to the location of your LAPACK library base directory
|
||||
LAPACK_LIB = $(HOME)/local/lapack-3.7.0
|
||||
# # C) Uncomment this next line and then run again (after cleaning up any object files)
|
||||
#NO_GRO_LIBS = -L$(GSL_LIB) -L$(LAPACK_LIB) -lgsl -lgslcblas -llapack -lm
|
||||
|
||||
OPT = -O2
|
||||
NO_GRO_LDFLAGS = $(OPT)
|
||||
NO_GRO_CFLAGS = $(OPT)
|
||||
DIMENSION = 3
|
||||
CC = mpicc
|
||||
|
||||
COMMON_SOURCE = control_input.h fm_output.h force_computation.h geometry.h interaction_hashing.h interaction_model.h matrix.h splines.h topology.h trajectory_input.h misc.h mscg.h
|
||||
NO_GRO_COMMON_OBJECTS = control_input.o fm_output.o force_computation.o geometry.o interaction_hashing.o interaction_model.o matrix.o splines.o topology.o trajectory_input_no_gro.o misc.o
|
||||
|
||||
# Target executables
|
||||
# The library for LAMMPS is lib_mscg.a
|
||||
libmscg.a: mscg.o $(NO_GRO_COMMON_OBJECTS)
|
||||
ar rvs libmscg.a *.o
|
||||
|
||||
newfm_no_gro.x: newfm.o $(NO_GRO_COMMON_OBJECTS)
|
||||
$(CC) $(NO_GRO_LDFLAGS) -o $@ newfm.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
|
||||
|
||||
combinefm_no_gro.x: combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS)
|
||||
$(CC) $(NO_GRO_LDFLAGS) -o $@ combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
|
||||
|
||||
rangefinder_no_gro.x: rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS)
|
||||
$(CC) $(NO_GRO_LDFLAGS) -o $@ rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
|
||||
|
||||
# Target objects
|
||||
|
||||
mscg.o: mscg.cpp $(COMMON_SOURCE) range_finding.o
|
||||
$(CC) $(NO_GRO_CFLAGS) -c mscg.cpp -o mscg.o $(NO_GRO_LIBS)
|
||||
|
||||
newfm.o: newfm.cpp $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c newfm.cpp
|
||||
|
||||
combinefm.o: combinefm.cpp batch_fm_combination.h $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c combinefm.cpp
|
||||
|
||||
rangefinder.o: rangefinder.cpp range_finding.h $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c rangefinder.cpp
|
||||
|
||||
scalarfm.o: scalarfm.cpp $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c scalarfm.cpp
|
||||
|
||||
batch_fm_combination.o: batch_fm_combination.cpp batch_fm_combination.h external_matrix_routines.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c batch_fm_combination.cpp
|
||||
|
||||
control_input.o: control_input.cpp control_input.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c control_input.cpp
|
||||
|
||||
geometry.o: geometry.cpp geometry.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c geometry.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
fm_output.o: fm_output.cpp fm_output.h force_computation.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c fm_output.cpp
|
||||
|
||||
force_computation.o: force_computation.cpp force_computation.h interaction_model.h matrix.h trajectory_input.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c force_computation.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
interaction_hashing.o: interaction_hashing.cpp interaction_hashing.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c interaction_hashing.cpp
|
||||
|
||||
interaction_model.o: interaction_model.cpp interaction_model.h control_input.h interaction_hashing.h topology.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c interaction_model.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
matrix.o: matrix.cpp matrix.h control_input.h external_matrix_routines.h interaction_model.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c matrix.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
misc.o: misc.cpp misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c misc.cpp
|
||||
|
||||
range_finding.o: range_finding.cpp range_finding.h force_computation.h interaction_model.h matrix.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c range_finding.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
splines.o: splines.cpp splines.h interaction_model.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c splines.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
topology.o: topology.cpp topology.h interaction_model.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c topology.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
trajectory_input_no_gro.o: trajectory_input.cpp trajectory_input.h control_input.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c trajectory_input.cpp -D"_exclude_gromacs=1" -o trajectory_input_no_gro.o
|
||||
|
||||
# Other convenient commands
|
||||
clean:
|
||||
rm *.[o]
|
||||
|
||||
all: libmscg.a newfm_no_gro.x rangefinder_no_gro.x combinefm_no_gro.x
|
||||
@ -1,104 +0,0 @@
|
||||
# This Makefile is meant for use after
|
||||
# module load gsl/2.2.1+gcc-6.1
|
||||
# module load gcc/6.1
|
||||
# It also requires LAPACK
|
||||
# Module names refer to those on any of RCC's clusters at UChicago.
|
||||
|
||||
# This makefile does NOT include GROMACS reading or MKL (sparse matrix)
|
||||
# It uses the gcc/g++ compiler (v4.9+) for C++11 support
|
||||
|
||||
# 1) Try this first (as it is the easiest)
|
||||
NO_GRO_LIBS = -lgsl -lgslcblas
|
||||
|
||||
# 2) If it does not find your libraries automatically, you can specify them manually
|
||||
# # A) Set the GSL_LIB to the location of your GSL library's lib directory (must be V2+)
|
||||
GSL_LIB = /software/gsl-2.2.1-el6-x86_64+gcc-6.1/lib
|
||||
# # B) Set the LAPACK_DIR to the location of your LAPACK library base directory
|
||||
LAPACK_LIB = $(HOME)/local/lapack-3.7.0
|
||||
# # C) Uncomment this next line and then run again (after cleaning up any object files)
|
||||
#NO_GRO_LIBS = -L$(GSL_LIB) -L$(LAPACK_LIB) -lgsl -lgslcblas -llapack -lm
|
||||
|
||||
OPT = -O2
|
||||
NO_GRO_LDFLAGS = $(OPT)
|
||||
NO_GRO_CFLAGS = $(OPT)
|
||||
DIMENSION = 3
|
||||
CC = g++
|
||||
|
||||
COMMON_SOURCE = control_input.h fm_output.h force_computation.h geometry.h interaction_hashing.h interaction_model.h matrix.h splines.h topology.h trajectory_input.h misc.h mscg.h
|
||||
NO_GRO_COMMON_OBJECTS = control_input.o fm_output.o force_computation.o geometry.o interaction_hashing.o interaction_model.o matrix.o splines.o topology.o trajectory_input_no_gro.o misc.o
|
||||
|
||||
# Target executables
|
||||
# The library for LAMMPS is lib_mscg.a
|
||||
libmscg.a: mscg.o $(NO_GRO_COMMON_OBJECTS)
|
||||
ar rvs libmscg.a *.o
|
||||
|
||||
newfm_no_gro.x: newfm.o $(NO_GRO_COMMON_OBJECTS)
|
||||
$(CC) $(NO_GRO_LDFLAGS) -o $@ newfm.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
|
||||
|
||||
combinefm_no_gro.x: combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS)
|
||||
$(CC) $(NO_GRO_LDFLAGS) -o $@ combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
|
||||
|
||||
rangefinder_no_gro.x: rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS)
|
||||
$(CC) $(NO_GRO_LDFLAGS) -o $@ rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
|
||||
|
||||
# Target objects
|
||||
|
||||
mscg.o: mscg.cpp $(COMMON_SOURCE) range_finding.o
|
||||
$(CC) $(NO_GRO_CFLAGS) -c mscg.cpp -o mscg.o $(NO_GRO_LIBS)
|
||||
|
||||
newfm.o: newfm.cpp $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c newfm.cpp
|
||||
|
||||
combinefm.o: combinefm.cpp batch_fm_combination.h $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c combinefm.cpp
|
||||
|
||||
rangefinder.o: rangefinder.cpp range_finding.h $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c rangefinder.cpp
|
||||
|
||||
scalarfm.o: scalarfm.cpp $(COMMON_SOURCE)
|
||||
$(CC) $(NO_GRO_CFLAGS) -c scalarfm.cpp
|
||||
|
||||
batch_fm_combination.o: batch_fm_combination.cpp batch_fm_combination.h external_matrix_routines.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c batch_fm_combination.cpp
|
||||
|
||||
control_input.o: control_input.cpp control_input.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c control_input.cpp
|
||||
|
||||
geometry.o: geometry.cpp geometry.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c geometry.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
fm_output.o: fm_output.cpp fm_output.h force_computation.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c fm_output.cpp
|
||||
|
||||
force_computation.o: force_computation.cpp force_computation.h interaction_model.h matrix.h trajectory_input.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c force_computation.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
interaction_hashing.o: interaction_hashing.cpp interaction_hashing.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c interaction_hashing.cpp
|
||||
|
||||
interaction_model.o: interaction_model.cpp interaction_model.h control_input.h interaction_hashing.h topology.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c interaction_model.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
matrix.o: matrix.cpp matrix.h control_input.h external_matrix_routines.h interaction_model.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c matrix.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
misc.o: misc.cpp misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c misc.cpp
|
||||
|
||||
range_finding.o: range_finding.cpp range_finding.h force_computation.h interaction_model.h matrix.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c range_finding.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
splines.o: splines.cpp splines.h interaction_model.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c splines.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
topology.o: topology.cpp topology.h interaction_model.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c topology.cpp -DDIMENSION=$(DIMENSION)
|
||||
|
||||
trajectory_input_no_gro.o: trajectory_input.cpp trajectory_input.h control_input.h misc.h
|
||||
$(CC) $(NO_GRO_CFLAGS) -c trajectory_input.cpp -D"_exclude_gromacs=1" -o trajectory_input_no_gro.o
|
||||
|
||||
# Other convenient commands
|
||||
clean:
|
||||
rm *.[o]
|
||||
|
||||
all: libmscg.a newfm_no_gro.x rangefinder_no_gro.x combinefm_no_gro.x
|
||||
@ -1,69 +0,0 @@
|
||||
This directory contains links to the Multi-scale Coarse-graining
|
||||
(MS-CG) library which is required to use the MSCG package and its fix
|
||||
command in a LAMMPS input script.
|
||||
|
||||
The MS-CG library is available at
|
||||
https://github.com/uchicago-voth/MSCG-release and was developed by
|
||||
Jacob Wagner in Greg Voth's group at the University of Chicago.
|
||||
|
||||
This library requires a the GNU scientific library (GSL v 2.1+).
|
||||
|
||||
You can type "make lib-mscg" from the src directory to see help on how
|
||||
to download and build this library via make commands, or you can do
|
||||
the same thing by typing "python Install.py -m <machine>" from within this
|
||||
directory, or you can do it manually by following the instructions
|
||||
below.
|
||||
|
||||
-----------------
|
||||
|
||||
You must perform the following steps yourself.
|
||||
|
||||
1. Download MS-CG at https://github.com/uchicago-voth/MSCG-release
|
||||
either as a tarball or via SVN, and unpack the tarball either in
|
||||
this lib/mscg directory or somewhere else on your system.
|
||||
|
||||
2. Ensure that you have GSL installed and a compiler with support for C++11.
|
||||
|
||||
3. Compile MS-CG from within its home directory using your makefile of choice:
|
||||
% make -f Makefile.<machine> libmscg.a
|
||||
It is recommended that you start with Makefile.g++_simple for
|
||||
most machines. There are also two Makefile with settings matching
|
||||
the "mpi" and "serial" makefiles in the main LAMMPS folder.
|
||||
|
||||
4. There is no need to install MS-CG system-wide if you only wish
|
||||
to use it from LAMMPS.
|
||||
|
||||
5. Create two soft links in this dir (lib/mscg) to the MS-CG src
|
||||
directory. E.g if you built MS-CG in this dir:
|
||||
% ln -s src includelink
|
||||
% ln -s src liblink
|
||||
These links could instead be set to the include and lib
|
||||
directories created by a MS-CG install, e.g.
|
||||
% ln -s /usr/local/include includelink
|
||||
% ln -s /usr/local/lib liblink
|
||||
|
||||
6. Copy a suitable Makefile.lammps.<machine> to Makefile.lammps or
|
||||
copy Makefile.lammps.default to Makefile.lammps and edit as needed.
|
||||
|
||||
-----------------
|
||||
|
||||
When these steps are complete you can build LAMMPS with the MS-CG
|
||||
package installed:
|
||||
|
||||
% cd lammps/src
|
||||
% make yes-MSCG
|
||||
% make g++ (or whatever target you wish)
|
||||
|
||||
Note that if you download and unpack a new LAMMPS tarball, the
|
||||
"includelink" and "liblink" files will be lost and you will need to
|
||||
re-create them (step 4). If you built MS-CG in this directory (as
|
||||
opposed to somewhere else on your system) and did not install it
|
||||
somewhere else, you will also need to repeat steps 1,2,3.
|
||||
|
||||
The Makefile.lammps file in this directory is there for compatibility
|
||||
with the way other libraries under the lib dir are linked with by
|
||||
LAMMPS. MS-CG requires the GSL and LAPACK libraries as listed in
|
||||
Makefile.lammps. If they are not in default locations where your
|
||||
LD_LIBRARY_PATH environment settings can find them, then you should
|
||||
add the approrpriate -L paths to the mscg_SYSPATH variable in
|
||||
Makefile.lammps.
|
||||
@ -1,63 +0,0 @@
|
||||
# Install/unInstall package files in LAMMPS
|
||||
# mode = 0/1/2 for uninstall/install/update
|
||||
|
||||
mode=$1
|
||||
|
||||
# arg1 = file, arg2 = file it depends on
|
||||
|
||||
action () {
|
||||
if (test $mode = 0) then
|
||||
rm -f ../$1
|
||||
elif (! cmp -s $1 ../$1) then
|
||||
if (test -z "$2" || test -e ../$2) then
|
||||
cp $1 ..
|
||||
if (test $mode = 2) then
|
||||
echo " updating src/$1"
|
||||
fi
|
||||
fi
|
||||
elif (test -n "$2") then
|
||||
if (test ! -e ../$2) then
|
||||
rm -f ../$1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
# all package files with no dependencies
|
||||
|
||||
for file in *.cpp *.h; do
|
||||
test -f ${file} && action $file
|
||||
done
|
||||
|
||||
# edit 2 Makefile.package files to include/exclude package info
|
||||
|
||||
if (test $1 = 1) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*mscg[^ \t]* //' ../Makefile.package
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/mscg/includelink |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mscg/liblink |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-lmscg |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(mscg_SYSINC) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(mscg_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(mscg_SYSPATH) |' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings
|
||||
# multiline form needed for BSD sed on Macs
|
||||
sed -i -e '4 i \
|
||||
include ..\/..\/lib\/mscg\/Makefile.lammps
|
||||
' ../Makefile.package.settings
|
||||
fi
|
||||
|
||||
elif (test $1 = 0) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*mscg[^ \t]* //' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^[ \t]*include.*mscg.*$/d' ../Makefile.package.settings
|
||||
fi
|
||||
|
||||
fi
|
||||
@ -1,18 +0,0 @@
|
||||
The MSCG package adds a fix mscg command, which carries out
|
||||
multi-scale coarse-graining for the parameterization of coarse-grained
|
||||
(CG) interactions.
|
||||
|
||||
It uses the Multi-Scale Coarse-Graining (MS-CG) library, available at
|
||||
https://github.com/uchicago-voth/MSCG-release. The MSCG library was
|
||||
developed by Jacob Wagner in Greg Voth's group at the University of
|
||||
Chicago.
|
||||
|
||||
The library can be downloaded and built in lib/mscg or elsewhere on
|
||||
your system, which must be done before building LAMMPS with this
|
||||
package. Details of the download, build, and install process for MSCG
|
||||
are given in the lib/mscg/README file. Also see the LAMMPS manual for
|
||||
general information on building LAMMPS with external libraries. The
|
||||
settings in the Makefile.lammps file in lib/mscg must be correct for
|
||||
LAMMPS to build correctly with this package installed.
|
||||
|
||||
There are example scripts for using this package in examples/mscg.
|
||||
@ -1,329 +0,0 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Lauren Abbott (Sandia)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_mscg.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "input.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
#include "region.h"
|
||||
#include "update.h"
|
||||
#include "variable.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
#include "mscg.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMSCG::FixMSCG(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal fix mscg command");
|
||||
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
|
||||
if (nevery <= 0) error->all(FLERR,"Illegal fix mscg command");
|
||||
|
||||
me = comm->me;
|
||||
nprocs = comm->nprocs;
|
||||
if (nprocs > 1) error->all(FLERR,"Fix mscg does not yet support parallel use via MPI");
|
||||
|
||||
if (sizeof(tagint) != sizeof(smallint))
|
||||
error->all(FLERR,"Fix mscg must be used with 32-bit atom IDs");
|
||||
|
||||
// initialize
|
||||
|
||||
int natoms = atom->natoms;
|
||||
int ntypes = atom->ntypes;
|
||||
|
||||
max_partners_bond = 4;
|
||||
max_partners_angle = 12;
|
||||
max_partners_dihedral = 36;
|
||||
nframes = n_frames = block_size = 0;
|
||||
range_flag = 0;
|
||||
name_flag = 0;
|
||||
f = nullptr;
|
||||
|
||||
type_names = new char*[natoms];
|
||||
for (int i = 0; i < natoms; i++) type_names[i] = new char[24];
|
||||
|
||||
// parse remaining arguments
|
||||
|
||||
int iarg = 4;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"range") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mscg command");
|
||||
range_flag = utils::logical(FLERR, arg[iarg+1], false, lmp);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"name") == 0) {
|
||||
if (iarg+ntypes+1 > narg)
|
||||
error->all(FLERR,"Illegal fix mscg command");
|
||||
name_flag = 1;
|
||||
for (int i = 0; i < ntypes; i++) {
|
||||
iarg += 1;
|
||||
delete[] type_names[i];
|
||||
type_names[i] = utils::strdup(arg[iarg]);
|
||||
}
|
||||
iarg += 1;
|
||||
} else if (strcmp(arg[iarg],"max") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix mscg command");
|
||||
max_partners_bond = utils::inumeric(FLERR,arg[iarg+1],false, lmp);
|
||||
max_partners_angle = utils::inumeric(FLERR,arg[iarg+2],false, lmp);
|
||||
max_partners_dihedral = utils::inumeric(FLERR,arg[iarg+3],false, lmp);
|
||||
iarg += 4;
|
||||
} else error->all(FLERR,"Illegal fix mscg command");
|
||||
}
|
||||
|
||||
if (name_flag == 0) {
|
||||
for (int i = 0; i < natoms; i++) {
|
||||
delete[] type_names[i];
|
||||
type_names[i] = utils::strdup(std::to_string(i+1));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMSCG::~FixMSCG()
|
||||
{
|
||||
int natoms = atom->natoms;
|
||||
for (int i = 0; i < natoms; i++) delete[] type_names[i];
|
||||
delete[] type_names;
|
||||
memory->destroy(f);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixMSCG::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= END_OF_STEP;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMSCG::post_constructor()
|
||||
{
|
||||
if (domain->triclinic == 1)
|
||||
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
|
||||
|
||||
// topology information
|
||||
// sort by atom id to send to mscg lib
|
||||
|
||||
int natoms = atom->natoms;
|
||||
int nlocal = atom->nlocal;
|
||||
tagint *tag = atom->tag;
|
||||
int *type = atom->type;
|
||||
int *num_bond = atom->num_bond;
|
||||
tagint **bond_atom = atom->bond_atom;
|
||||
int *num_angle = atom->num_angle;
|
||||
tagint **angle_atom1 = atom->angle_atom1;
|
||||
tagint **angle_atom3 = atom->angle_atom3;
|
||||
int *num_dihedral = atom->num_dihedral;
|
||||
tagint **dihedral_atom1 = atom->dihedral_atom1;
|
||||
tagint **dihedral_atom3 = atom->dihedral_atom3;
|
||||
tagint **dihedral_atom4 = atom->dihedral_atom4;
|
||||
double *prd_half = domain->prd_half;
|
||||
int i,ii,j,jj,jnum,k,l;
|
||||
|
||||
n_cg_sites = natoms;
|
||||
n_cg_types = atom->ntypes;
|
||||
|
||||
memory->grow(f,nlocal,3,"fix_mscg:f");
|
||||
f1d = new double[n_cg_sites*3]();
|
||||
x1d = new double[n_cg_sites*3]();
|
||||
cg_site_types = new int[n_cg_sites]();
|
||||
n_partners_bond = new unsigned[n_cg_sites]();
|
||||
n_partners_angle = new unsigned[n_cg_sites]();
|
||||
n_partners_dihedral = new unsigned[n_cg_sites]();
|
||||
partners_bond = new unsigned*[n_cg_sites];
|
||||
for (i = 0; i < n_cg_sites; i++)
|
||||
partners_bond[i] = new unsigned[1*max_partners_bond]();
|
||||
partners_angle = new unsigned*[n_cg_sites];
|
||||
for (i = 0; i < n_cg_sites; i++)
|
||||
partners_angle[i] = new unsigned[2*max_partners_angle]();
|
||||
partners_dihedral = new unsigned*[n_cg_sites];
|
||||
for (i = 0; i < n_cg_sites; i++)
|
||||
partners_dihedral[i] = new unsigned[3*max_partners_dihedral]();
|
||||
|
||||
for (i = 0; i < 3; i++)
|
||||
box_half_lengths[i] = prd_half[i];
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
cg_site_types[i] = 0;
|
||||
n_partners_bond[i] = 0;
|
||||
n_partners_angle[i] = 0;
|
||||
n_partners_dihedral[i] = 0;
|
||||
}
|
||||
|
||||
for (ii = 0; ii < nlocal; ii++) {
|
||||
i = tag[ii];
|
||||
cg_site_types[i-1] = type[ii];
|
||||
|
||||
jnum = num_bond[ii];
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = bond_atom[ii][jj];
|
||||
if (n_partners_bond[i-1] >= max_partners_bond ||
|
||||
n_partners_bond[j-1] >= max_partners_bond)
|
||||
error->all(FLERR,"Bond list overflow, boost fix_mscg max");
|
||||
partners_bond[i-1][n_partners_bond[i-1]] = j-1;
|
||||
partners_bond[j-1][n_partners_bond[j-1]] = i-1;
|
||||
n_partners_bond[i-1]++;
|
||||
n_partners_bond[j-1]++;
|
||||
}
|
||||
|
||||
jnum = num_angle[ii];
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = angle_atom1[ii][jj];
|
||||
k = angle_atom3[ii][jj];
|
||||
if (n_partners_angle[j-1] >= max_partners_angle ||
|
||||
n_partners_angle[k-1] >= max_partners_angle)
|
||||
error->all(FLERR,"Angle list overflow, boost fix_mscg max");
|
||||
partners_angle[j-1][n_partners_angle[j-1]*2] = i-1;
|
||||
partners_angle[j-1][n_partners_angle[j-1]*2+1] = k-1;
|
||||
partners_angle[k-1][n_partners_angle[k-1]*2] = i-1;
|
||||
partners_angle[k-1][n_partners_angle[k-1]*2+1] = j-1;
|
||||
n_partners_angle[j-1]++;
|
||||
n_partners_angle[k-1]++;
|
||||
}
|
||||
|
||||
jnum = num_dihedral[ii];
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = dihedral_atom1[ii][jj];
|
||||
k = dihedral_atom3[ii][jj];
|
||||
l = dihedral_atom4[ii][jj];
|
||||
if (n_partners_dihedral[j-1] >= max_partners_dihedral ||
|
||||
n_partners_dihedral[l-1] >= max_partners_dihedral)
|
||||
error->all(FLERR,"Dihedral list overflow, boost fix_mscg max");
|
||||
partners_dihedral[j-1][n_partners_dihedral[j-1]*3] = i-1;
|
||||
partners_dihedral[j-1][n_partners_dihedral[j-1]*3+1] = k-1;
|
||||
partners_dihedral[j-1][n_partners_dihedral[j-1]*3+2] = l-1;
|
||||
partners_dihedral[l-1][n_partners_dihedral[l-1]*3] = k-1;
|
||||
partners_dihedral[l-1][n_partners_dihedral[l-1]*3+1] = i-1;
|
||||
partners_dihedral[l-1][n_partners_dihedral[l-1]*3+2] = j-1;
|
||||
n_partners_dihedral[j-1]++;
|
||||
n_partners_dihedral[l-1]++;
|
||||
}
|
||||
}
|
||||
|
||||
// pass topology data to mscg code and run startup
|
||||
|
||||
fprintf(screen,"Initializing MSCG with topology data ...\n");
|
||||
if (range_flag)
|
||||
mscg_struct = rangefinder_startup_part1(mscg_struct);
|
||||
else
|
||||
mscg_struct = mscg_startup_part1(mscg_struct);
|
||||
|
||||
n_frames = get_n_frames(mscg_struct);
|
||||
block_size = get_block_size(mscg_struct);
|
||||
|
||||
mscg_struct =
|
||||
setup_topology_and_frame(mscg_struct,n_cg_sites,n_cg_types,type_names,
|
||||
cg_site_types,box_half_lengths);
|
||||
mscg_struct =
|
||||
set_bond_topology(mscg_struct,partners_bond,n_partners_bond);
|
||||
mscg_struct =
|
||||
set_angle_topology(mscg_struct,partners_angle,n_partners_angle);
|
||||
mscg_struct =
|
||||
set_dihedral_topology(mscg_struct,partners_dihedral,n_partners_dihedral);
|
||||
mscg_struct =
|
||||
generate_exclusion_topology(mscg_struct);
|
||||
|
||||
if (range_flag)
|
||||
mscg_struct = rangefinder_startup_part2(mscg_struct);
|
||||
else
|
||||
mscg_struct = mscg_startup_part2(mscg_struct);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMSCG::init()
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
double **force = atom->f;
|
||||
int i;
|
||||
|
||||
// forces are reset to 0 before pre_force, saved here
|
||||
// init called for each frame of dump in rerun command
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
f[i][0] = force[i][0];
|
||||
f[i][1] = force[i][1];
|
||||
f[i][2] = force[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMSCG::end_of_step()
|
||||
{
|
||||
if (domain->triclinic == 1)
|
||||
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
tagint *tag = atom->tag;
|
||||
double **x = atom->x;
|
||||
int i,ii,j;
|
||||
|
||||
// trajectory information
|
||||
|
||||
for (ii = 0; ii < nlocal; ii++) {
|
||||
i = tag[ii];
|
||||
for (j = 0; j < 3; j++) {
|
||||
x1d[(i-1)*3+j] = x[ii][j];
|
||||
f1d[(i-1)*3+j] = f[ii][j];
|
||||
}
|
||||
}
|
||||
|
||||
// pass x,f to mscg to update matrix
|
||||
|
||||
nframes++;
|
||||
if (range_flag)
|
||||
mscg_struct = rangefinder_process_frame(mscg_struct,x1d,f1d);
|
||||
else
|
||||
mscg_struct = mscg_process_frame(mscg_struct,x1d,f1d);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMSCG::post_run()
|
||||
{
|
||||
// call mscg to solve matrix and generate output
|
||||
|
||||
fprintf(screen,"Finalizing MSCG ...\n");
|
||||
|
||||
if (nframes != n_frames)
|
||||
error->warning(FLERR,"Fix mscg n_frames is inconsistent with control.in");
|
||||
if (nframes % block_size != 0)
|
||||
error->warning(FLERR,"Fix mscg n_frames is not divisible by block_size in control.in");
|
||||
|
||||
if (range_flag)
|
||||
rangefinder_solve_and_output(mscg_struct);
|
||||
else
|
||||
mscg_solve_and_output(mscg_struct);
|
||||
}
|
||||
@ -1,52 +0,0 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(mscg,FixMSCG);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_MSCG_H
|
||||
#define LMP_FIX_MSCG_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixMSCG : public Fix {
|
||||
public:
|
||||
FixMSCG(class LAMMPS *, int, char **);
|
||||
~FixMSCG() override;
|
||||
int setmask() override;
|
||||
void post_constructor() override;
|
||||
void init() override;
|
||||
void end_of_step() override;
|
||||
void post_run() override;
|
||||
|
||||
private:
|
||||
int range_flag, name_flag, me, nprocs;
|
||||
int nframes, n_frames, block_size, n_cg_sites, n_cg_types, *cg_site_types;
|
||||
int max_partners_bond, max_partners_angle, max_partners_dihedral;
|
||||
unsigned *n_partners_bond, *n_partners_angle, *n_partners_dihedral;
|
||||
unsigned **partners_bond, **partners_angle, **partners_dihedral;
|
||||
double *x1d, *f1d, **f;
|
||||
double box_half_lengths[3];
|
||||
char **type_names;
|
||||
void *mscg_struct;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -107,7 +107,6 @@ PACKAGE = \
|
||||
molecule \
|
||||
molfile \
|
||||
mpiio \
|
||||
mscg \
|
||||
netcdf \
|
||||
openmp \
|
||||
opt \
|
||||
@ -214,7 +213,6 @@ PACKLIB = \
|
||||
kokkos \
|
||||
lepton \
|
||||
mpiio \
|
||||
mscg \
|
||||
poems \
|
||||
python \
|
||||
voronoi \
|
||||
@ -252,7 +250,6 @@ PACKEXT = \
|
||||
ml-pace \
|
||||
ml-quip \
|
||||
molfile \
|
||||
mscg \
|
||||
netcdf \
|
||||
plumed \
|
||||
qmmm \
|
||||
|
||||
@ -51,6 +51,9 @@ FixDeprecated::FixDeprecated(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg,
|
||||
} else if (my_style == "client/md") {
|
||||
if (lmp->comm->me == 0)
|
||||
utils::logmesg(lmp, "\nThe MESSAGE package has been replaced by the MDI package.\n\n");
|
||||
} else if (my_style == "mscg") {
|
||||
if (lmp->comm->me == 0)
|
||||
utils::logmesg(lmp, "\nThe MSCG package has been removed from LAMMPS.\n\n");
|
||||
}
|
||||
error->all(FLERR, "This fix style is no longer available");
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user