forked from lijiext/lammps
Merge pull request #1932 from akohlmey/atc-doc-to-rst
Convert AtC documentation html files to reStructuredText
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
68dc62c512
|
|
@ -262,8 +262,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
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enable_language(Fortran)
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file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
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add_library(linalg STATIC ${LAPACK_SOURCES})
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set(BLAS_LIBRARIES "${CMAKE_BINARY_DIR}/liblinalg.a")
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set(LAPACK_LIBRARIES "${CMAKE_BINARY_DIR}/liblinalg.a")
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set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
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set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
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else()
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list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
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endif()
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@ -344,7 +344,7 @@ include(Packages/COMPRESS)
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set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_TUNE_FLAGS}")
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if(CMAKE_Fortran_FLAGS)
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if(CMAKE_Fortran_COMPILER)
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set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${CMAKE_TUNE_FLAGS}")
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endif()
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########################################################################
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@ -22,6 +22,7 @@ endif()
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set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
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set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
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set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
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set(CMAKE_TUNE_FLAGS "" CACHE STRING "" FORCE)
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set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
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set(CMAKE_EXE_LINKER_FLAGS "--enable-stdcall-fixup" CACHE STRING "" FORCE)
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set(BUILD_TOOLS ON CACHE BOOL "" FORCE)
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set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")
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@ -76,13 +76,9 @@ html: $(ANCHORCHECK) $(MATHJAX)
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@rm -rf html/USER
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@rm -rf html/JPG
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@cp -r src/PDF html/PDF
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@cp -r src/USER html/USER
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@mkdir -p html/JPG
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@cp `grep -A2 '\.\. .*image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
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@rm -rf html/PDF/.[sg]*
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@rm -rf html/USER/.[sg]*
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@rm -rf html/USER/*/.[sg]*
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@rm -rf html/USER/*/*.[sg]*
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@mkdir -p html/_static/mathjax
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@cp -r $(MATHJAX)/es5 html/_static/mathjax/
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@echo "Build finished. The HTML pages are in doc/html."
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@ -151,11 +147,7 @@ pdf: $(ANCHORCHECK)
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@rm -rf latex/PDF
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@rm -rf latex/USER
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@cp -r src/PDF latex/PDF
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@cp -r src/USER latex/USER
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@rm -rf latex/PDF/.[sg]*
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@rm -rf latex/USER/.[sg]*
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@rm -rf latex/USER/*/.[sg]*
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@rm -rf latex/USER/*/*.[sg]*
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@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
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fetch:
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@ -31,7 +31,7 @@ platforms and particularly on Linux. However, alternate build tools
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(e.g. Ninja) and project files for Integrated Development Environments
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(IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
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selected via the ``-G`` command line flag. Further details about features
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and settings for CMake are in the `CMake online documentation <cmake_doc>`_
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and settings for CMake are in the `CMake online documentation <cmake_doc_>`_
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.. _cmake_doc: https://cmake.org/documentation/
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|
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@ -240,9 +240,11 @@ C-style interface, provided in src/library.cpp and src/library.h.
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See the :doc:`Python library <Python_library>` doc page for a
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description of the Python interface to LAMMPS, which wraps the C-style
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interface from a shared library through the ctypes python module.
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interface from a shared library through the `ctypes python module <ctypes_>`_.
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See the sample codes in examples/COUPLE/simple for examples of C++ and
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C and Fortran codes that invoke LAMMPS through its library interface.
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Other examples in the COUPLE directory use coupling ideas discussed on
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the :doc:`Howto couple <Howto_couple>` doc page.
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.. _ctypes: https://docs.python.org/3/library/ctypes.html
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@ -38,7 +38,7 @@ input script command that it was processing. Of course, LAMMPS cannot
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figure out your physics or numerical mistakes, like choosing too big a
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timestep, specifying erroneous force field coefficients, or putting 2
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atoms on top of each other! If you run into errors that LAMMPS
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doesn't catch that you think it should flag, please send an email to
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does not catch that you think it should flag, please send an email to
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the `developers <https://lammps.sandia.gov/authors.html>`_.
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If you get an error message about an invalid command in your input
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@ -96,13 +96,13 @@ cases:
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LAMMPS runs in the available memory a processor allows to be
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allocated. Most reasonable MD runs are compute limited, not memory
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limited, so this shouldn't be a bottleneck on most platforms. Almost
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limited, so this should not be a bottleneck on most platforms. Almost
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all large memory allocations in the code are done via C-style malloc's
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which will generate an error message if you run out of memory.
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Smaller chunks of memory are allocated via C++ "new" statements. If
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you are unlucky you could run out of memory just when one of these
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small requests is made, in which case the code will crash or hang (in
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parallel), since LAMMPS doesn't trap on those errors.
|
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parallel), since LAMMPS does not trap on those errors.
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|
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Illegal arithmetic can cause LAMMPS to run slow or crash. This is
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typically due to invalid physics and numerics that your simulation is
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|
|
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@ -2177,7 +2177,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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The command is accessing a vector added by the fix property/atom
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command, that does not exist.
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*Compute property/atom for atom property that isn't allocated*
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*Compute property/atom for atom property that is not allocated*
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Self-explanatory.
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*Compute property/atom integer vector does not exist*
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@ -2194,7 +2194,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Compute property/local does not (yet) work with atom_style template*
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Self-explanatory.
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*Compute property/local for property that isn't allocated*
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*Compute property/local for property that is not allocated*
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Self-explanatory.
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*Compute rdf requires a pair style be defined*
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@ -3100,7 +3100,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Dump_modify region ID does not exist*
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Self-explanatory.
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*Dumping an atom property that isn't allocated*
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*Dumping an atom property that is not allocated*
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The chosen atom style does not define the per-atom quantity being
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dumped.
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@ -3126,7 +3126,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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|
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*Energy was not tallied on needed timestep*
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You are using a thermo keyword that requires potentials to
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have tallied energy, but they didn't on this timestep. See the
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have tallied energy, but they did not on this timestep. See the
|
||||
variable doc page for ideas on how to make this work.
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|
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*Epsilon or sigma reference not set by pair style in PPPMDisp*
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@ -4145,7 +4145,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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Fixes that calculate global or local quantities cannot be used with
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fix store/state.
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*Fix store/state for atom property that isn't allocated*
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*Fix store/state for atom property that is not allocated*
|
||||
Self-explanatory.
|
||||
|
||||
*Fix store/state variable is not atom-style variable*
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||||
|
|
@ -4739,7 +4739,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
|
|||
|
||||
*Invalid LAMMPS restart file*
|
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The file does not appear to be a LAMMPS restart file since
|
||||
it doesn't contain the correct magic string at the beginning.
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||||
it does not contain the correct magic string at the beginning.
|
||||
|
||||
*Invalid Masses section in molecule file*
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Self-explanatory.
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||||
|
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@ -6427,7 +6427,7 @@ keyword to allow for additional bonds to be formed
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|||
|
||||
*Pair hybrid sub-style does not support single call*
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||||
You are attempting to invoke a single() call on a pair style
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||||
that doesn't support it.
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that does not support it.
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||||
|
||||
*Pair hybrid sub-style is not used*
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No pair_coeff command used a sub-style specified in the pair_style
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@ -6901,7 +6901,7 @@ keyword to allow for additional bonds to be formed
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|||
|
||||
*Per-atom energy was not tallied on needed timestep*
|
||||
You are using a thermo keyword that requires potentials to
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||||
have tallied energy, but they didn't on this timestep. See the
|
||||
have tallied energy, but they did not on this timestep. See the
|
||||
variable doc page for ideas on how to make this work.
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||||
|
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*Per-atom fix in equal-style variable formula*
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|
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@ -6909,7 +6909,7 @@ keyword to allow for additional bonds to be formed
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*Per-atom virial was not tallied on needed timestep*
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You are using a thermo keyword that requires potentials to have
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tallied the virial, but they didn't on this timestep. See the
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tallied the virial, but they did not on this timestep. See the
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variable doc page for ideas on how to make this work.
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*Per-processor system is too big*
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@ -7070,7 +7070,7 @@ keyword to allow for additional bonds to be formed
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It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
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integer.
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*Read dump of atom property that isn't allocated*
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*Read dump of atom property that is not allocated*
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Self-explanatory.
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*Read rerun dump file timestep > specified stop*
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@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed
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creates one large file for all processors.
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*Restart file byte ordering is not recognized*
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The file does not appear to be a LAMMPS restart file since it doesn't
|
||||
The file does not appear to be a LAMMPS restart file since it does not
|
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contain a recognized byte-ordering flag at the beginning.
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*Restart file byte ordering is swapped*
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|
|
@ -7701,7 +7701,7 @@ keyword to allow for additional bonds to be formed
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Keywords that refer to time (such as cpu, elapsed) do not
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make sense in between runs.
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||||
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*Threshold for an atom property that isn't allocated*
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*Threshold for an atom property that is not allocated*
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A dump threshold has been requested on a quantity that is
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not defined by the atom style used in this simulation.
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||||
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|
|
@ -8355,7 +8355,7 @@ keyword to allow for additional bonds to be formed
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|||
*Variable name must be alphanumeric or underscore characters*
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Self-explanatory.
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||||
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||||
*Variable uses atom property that isn't allocated*
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*Variable uses atom property that is not allocated*
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||||
Self-explanatory.
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||||
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||||
*Velocity command before simulation box is defined*
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||||
|
|
@ -8396,7 +8396,7 @@ keyword to allow for additional bonds to be formed
|
|||
|
||||
*Virial was not tallied on needed timestep*
|
||||
You are using a thermo keyword that requires potentials to
|
||||
have tallied the virial, but they didn't on this timestep. See the
|
||||
have tallied the virial, but they did not on this timestep. See the
|
||||
variable doc page for ideas on how to make this work.
|
||||
|
||||
*Voro++ error: narea and neigh have a different size*
|
||||
|
|
@ -8423,7 +8423,7 @@ keyword to allow for additional bonds to be formed
|
|||
This is because LAMMPS does not compute the Lennard-Jones interactions
|
||||
with these particles for efficiency reasons.
|
||||
|
||||
*World variable count doesn't match # of partitions*
|
||||
*World variable count does not match # of partitions*
|
||||
A world-style variable must specify a number of values equal to the
|
||||
number of processor partitions.
|
||||
|
||||
|
|
|
|||
|
|
@ -360,7 +360,7 @@ It looks something like this:
|
|||
.. image:: JPG/tutorial_reverse_pull_request.png
|
||||
:align: center
|
||||
|
||||
For some reason, the highlighted button didn't work in my case, but I
|
||||
For some reason, the highlighted button did not work in my case, but I
|
||||
can go to my own repository and merge the pull request from there:
|
||||
|
||||
.. image:: JPG/tutorial_reverse_pull_request2.png
|
||||
|
|
|
|||
|
|
@ -6,19 +6,23 @@ PyLammps Tutorial
|
|||
Overview
|
||||
--------
|
||||
|
||||
PyLammps is a Python wrapper class which can be created on its own or
|
||||
use an existing lammps Python object. It creates a simpler,
|
||||
Python-like interface to common LAMMPS functionality, in contrast to
|
||||
the lammps.py wrapper on the C-style LAMMPS library interface which is
|
||||
written using Python ctypes. The lammps.py wrapper is discussed on
|
||||
the :doc:`Python library <Python_library>` doc page.
|
||||
``PyLammps`` is a Python wrapper class for LAMMPS which can be created
|
||||
on its own or use an existing lammps Python object. It creates a simpler,
|
||||
more "pythonic" interface to common LAMMPS functionality, in contrast to
|
||||
the ``lammps.py`` wrapper for the C-style LAMMPS library interface which
|
||||
is written using `Python ctypes <ctypes_>`_. The ``lammps.py`` wrapper
|
||||
is discussed on the :doc:`Python library <Python_library>` doc page.
|
||||
|
||||
Unlike the flat ctypes interface, PyLammps exposes a discoverable API.
|
||||
It no longer requires knowledge of the underlying C++ code
|
||||
implementation. Finally, the IPyLammps wrapper builds on top of
|
||||
PyLammps and adds some additional features for IPython integration
|
||||
into IPython notebooks, e.g. for embedded visualization output from
|
||||
dump/image.
|
||||
Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable
|
||||
API. It no longer requires knowledge of the underlying C++ code
|
||||
implementation. Finally, the ``IPyLammps`` wrapper builds on top of
|
||||
``PyLammps`` and adds some additional features for
|
||||
`IPython integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_,
|
||||
e.g. for embedded visualization output from :doc:`dump style image <dump_image>`.
|
||||
|
||||
.. _ctypes: https://docs.python.org/3/library/ctypes.html
|
||||
.. _ipython: https://ipython.org/
|
||||
.. _jupyter: https://jupyter.org/
|
||||
|
||||
Comparison of lammps and PyLammps interfaces
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
|
@ -26,7 +30,7 @@ Comparison of lammps and PyLammps interfaces
|
|||
lammps.lammps
|
||||
"""""""""""""
|
||||
|
||||
* uses C-Types
|
||||
* uses ``ctypes``
|
||||
* direct memory access to native C++ data
|
||||
* provides functions to send and receive data to LAMMPS
|
||||
* requires knowledge of how LAMMPS internally works (C pointers, etc)
|
||||
|
|
@ -34,7 +38,7 @@ lammps.lammps
|
|||
lammps.PyLammps
|
||||
"""""""""""""""
|
||||
|
||||
* higher-level abstraction built on top of original C-Types interface
|
||||
* higher-level abstraction built on top of original ctypes interface
|
||||
* manipulation of Python objects
|
||||
* communication with LAMMPS is hidden from API user
|
||||
* shorter, more concise Python
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ A Python-based toolkit distributed by our group can read native LAMMPS
|
|||
dump files, including custom dump files with additional columns of
|
||||
user-specified atom information, and convert them to various formats
|
||||
or pipe them into visualization software directly. See the `Pizza.py WWW site <pizza_>`_ for details. Specifically, Pizza.py can convert
|
||||
LAMMPS dump files into PDB, XYZ, `Ensight <ensight_>`_, and VTK formats.
|
||||
LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
|
||||
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
|
||||
RasMol visualization programs. Pizza.py has tools that do interactive
|
||||
3d OpenGL visualization and one that creates SVG images of dump file
|
||||
|
|
@ -27,6 +27,6 @@ snapshots.
|
|||
|
||||
.. _pizza: https://pizza.sandia.gov
|
||||
|
||||
.. _ensight: https://daac.hpc.mil/software/EnSight/
|
||||
.. _ensight: https://www.ansys.com/products/fluids/ansys-ensight
|
||||
|
||||
.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
|
||||
|
|
|
|||
|
|
@ -72,6 +72,7 @@ every LAMMPS command.
|
|||
angles
|
||||
dihedrals
|
||||
impropers
|
||||
fix_modify_atc_commands
|
||||
|
||||
Indices and tables
|
||||
==================
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@ src directory and re-building LAMMPS.
|
|||
|
||||
The advantage of C++ and its object-orientation is that all the code
|
||||
and variables needed to define the new feature are in the 2 files you
|
||||
write, and thus shouldn't make the rest of LAMMPS more complex or
|
||||
write, and thus should not make the rest of LAMMPS more complex or
|
||||
cause side-effect bugs.
|
||||
|
||||
Here is a concrete example. Suppose you write 2 files pair_foo.cpp
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@ CMAKE_INSTALL_PREFIX.
|
|||
make install
|
||||
|
||||
This will also install the Python module into your virtualenv. Since virtualenv
|
||||
doesn't change your LD_LIBRARY_PATH, you still need to add its lib64 folder to
|
||||
does not change your LD_LIBRARY_PATH, you still need to add its lib64 folder to
|
||||
it, which contains the installed liblammps.so.
|
||||
|
||||
.. code-block:: bash
|
||||
|
|
|
|||
|
|
@ -1,57 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml">
|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC add_molecule</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify_AtC add_molecule <small|large> <TAG> <GROUP_NAME> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>small|large = can be small if molecule size < cutoff radius, must be large otherwise <br/>
|
||||
</li>
|
||||
<li><TAG> = tag for tracking a species <br/>
|
||||
</li>
|
||||
<li><GROUP_NAME> = name of group that tracking will be applied to <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> group WATERGROUP type 1 2 </code> <br/>
|
||||
<code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Associates a tag with all molecules corresponding to a specified group. <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No defaults for this command. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
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|
||||
|
|
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|
|||
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||||
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|
||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC add_species</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify_AtC add_species <TAG> <group|type> <ID> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><TAG> = tag for tracking a species <br/>
|
||||
</li>
|
||||
<li>group|type = LAMMPS defined group or type of atoms <br/>
|
||||
</li>
|
||||
<li><ID> = name of group or type number <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
|
||||
<code> group GOLDGROUP type 1 </code> <br/>
|
||||
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No defaults for this command. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
</html>
|
||||
|
|
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|
|||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC atom_element_map</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC atom_element_map <eulerian|lagrangian> <frequency> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Cannot change map type after initialization. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>lagrangian </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
||||
|
|
@ -1,59 +0,0 @@
|
|||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC atom_weight</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC atom_weight <method> <arguments></p>
|
||||
<ul>
|
||||
<li><method> = <br/>
|
||||
value: atoms in specified group assigned constant value given <br/>
|
||||
lattice: volume per atom for specified lattice type (e.g. fcc) and parameter <br/>
|
||||
element: element volume divided among atoms within element <br/>
|
||||
region: volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions. <br/>
|
||||
group: volume per atom determined based on the atom count in a group and its volume<br/>
|
||||
read_in: list of values for atoms are read-in from specified file <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
|
||||
<code> fix_modify atc atom_weight lattice </code> <br/>
|
||||
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>lattice </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
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|
|||
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||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC atomic_charge</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC <include | omit> atomic_charge</p>
|
||||
<ul>
|
||||
<li><include | omit> = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc compute include atomic_charge </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Determines whether AtC tracks the total charge as a finite element field </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Required for: electrostatics </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>if the atom charge is defined, default is on, otherwise default is off </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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|
||||
|
|
@ -1,46 +0,0 @@
|
|||
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|
||||
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|
||||
<title>ATC: fix_modify AtC boundary</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC boundary type <atom-type-id></p>
|
||||
<ul>
|
||||
<li><atom-type-id> = type id for atoms that represent a fictitious boundary internal to the FE mesh </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to define the atoms that represent the fictitious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
||||
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|
||||
|
|
@ -1,44 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
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|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
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|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC boundary_dynamics < on | damped_harmonic | prescribed | coupled | none > [args] <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>prescribed on </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
||||
|
|
@ -1,45 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC boundary_faceset</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
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|
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||||
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||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC boundary_faceset <is | add> [args] </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p>fix_modify AtC boundary_faceset is obndy </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>This is only valid when fe_md_boundary is set to faceset. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
||||
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|
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||||
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|
||||
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|
||||
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|
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<a href="../../Manual.html">LAMMPS Manual</a>
|
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|
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|
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||||
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<!-- Generated by Doxygen 1.6.1 -->
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||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
|
||||
<ul>
|
||||
<li>field (string) : name of hardy field</li>
|
||||
<li>name (string) : name of faceset </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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|
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|
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|
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<title>ATC: fix_modify AtC consistent_fe_initialization</title>
|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
||||
<!-- Generated by Doxygen 1.6.1 -->
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC consistent_fe_initialization <on | off></p>
|
||||
<ul>
|
||||
<li><on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Default is off </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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|
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|
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|
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<title>ATC: fix_modify AtC output contour_integral</title>
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|
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|
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|
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<a href="../../Manual.html">LAMMPS Manual</a>
|
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<a href="../../fix_atc.html">USER-AtC Manual</a>
|
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|
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||||
<hr>
|
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]></p>
|
||||
<ul>
|
||||
<li>field (string) : name of hardy field</li>
|
||||
<li>name (string) : name of faceset</li>
|
||||
<li>axis (string) : x or y or z </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
||||
|
|
@ -1,70 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>ATC: fix_modify AtC control</title>
|
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|
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<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
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|
||||
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|
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<a href="../../Manual.html">LAMMPS Manual</a>
|
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|
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|
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|
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||||
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<!-- Generated by Doxygen 1.6.1 -->
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_control">fix_modify AtC control </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control <physics_type> <solution_parameter> </p>
|
||||
<p><br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>physics_type (string) = thermal | momentum<br/>
|
||||
</li>
|
||||
<li>solution_parameter (string) = max_iterations | tolerance<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>fix_modify AtC transfer <physics_type> control max_iterations <max_iterations><br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>fix_modify AtC transfer <physics_type> control tolerance <tolerance> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
|
||||
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only for be used with specific controllers : thermal, momentum <br/>
|
||||
They are ignored if a lumped solution is requested </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>max_iterations is the number of rows in the matrix<br/>
|
||||
tolerance is 1.e-10 </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
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|
||||
|
|
@ -1,66 +0,0 @@
|
|||
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|
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
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|
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<!-- Generated by Doxygen 1.6.1 -->
|
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control momentum none <br/>
|
||||
</p>
|
||||
<p>fix_modify AtC control momentum rescale <frequency><br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>frequency (int) = time step frequency for applying displacement and velocity rescaling <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>fix_modify AtC control momentum glc_displacement <br/>
|
||||
</p>
|
||||
<p>fix_modify AtC control momentum glc_velocity <br/>
|
||||
</p>
|
||||
<p>fix_modify AtC control momentum hoover <br/>
|
||||
</p>
|
||||
<p>fix_modify AtC control momentum flux [faceset face_set_id, interpolate]</p>
|
||||
<ul>
|
||||
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p>fix_modify AtC control momentum glc_velocity <br/>
|
||||
fix_modify AtC control momentum flux faceset bndy_faces <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only to be used with specific transfers : elastic <br/>
|
||||
rescale not valid with time filtering activated </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
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<a href="http://www.doxygen.org/index.html">
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<title>ATC: fix_modify AtC control thermal</title>
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|
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|
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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||||
|
||||
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|
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|
||||
|
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<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control thermal <control_type> <optional_args></p>
|
||||
<ul>
|
||||
<li>control_type (string) = none | rescale | hoover | flux<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>fix_modify AtC control thermal rescale <frequency> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>frequency (int) = time step frequency for applying velocity rescaling <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>fix_modify AtC control thermal hoover <br/>
|
||||
</p>
|
||||
<p>fix_modify AtC control thermal flux <boundary_integration_type(optional)> <face_set_id(optional)><br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>boundary_integration_type (string) = faceset | interpolate<br/>
|
||||
</li>
|
||||
<li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC control thermal none </code> <br/>
|
||||
<code> fix_modify AtC control thermal rescale 10 </code> <br/>
|
||||
<code> fix_modify AtC control thermal hoover </code> <br/>
|
||||
<code> fix_modify AtC control thermal flux </code> <br/>
|
||||
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
|
||||
rescale not valid with time filtering activated </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none<br/>
|
||||
rescale frequency is 1<br/>
|
||||
flux boundary_integration_type is interpolate </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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<title>ATC: fix_modify AtC control thermal correction_max_iterations</title>
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||||
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|
||||
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||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
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||||
|
||||
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|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control thermal correction_max_iterations <max_iterations></p>
|
||||
<ul>
|
||||
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only for use with thermal physics using the fractional step method. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>correction_max_iterations is 20 </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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|
||||
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||||
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||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
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|
||||
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||||
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||||
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|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC decomposition <type></p>
|
||||
<ul>
|
||||
<li><type> = <br/>
|
||||
replicated_memory: nodal information replicated on each processor <br/>
|
||||
distributed_memory: only owned nodal information on processor <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command for assigning the distribution of work and memory for parallel runs. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>replicated_memory is appropriate for simulations were the number of nodes << number of atoms </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>replicated_memory </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC extrinsic electron_integration</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
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|
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|
||||
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|
||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>integration_type (string) = explicit | implicit | steady <br/>
|
||||
</li>
|
||||
<li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
|
||||
<code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>implicit<br/>
|
||||
subcycle_steps = 1 </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
||||
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|
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|||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC equilibrium_start</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
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|
||||
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|
||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC equilibrium_start <on|off></p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc equilibrium_start on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only needed before filtering is begun</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>on </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
</html>
|
||||
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|
@ -1,48 +0,0 @@
|
|||
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|
||||
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|
||||
<title>ATC: fix_modify AtC extrinsic exchange</title>
|
||||
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|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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||||
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||||
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|
||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC extrinsic exchange <on|off></p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC extrinsic exchange on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Switches energy exchange between the MD system and electron system on and off</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Only valid for use with two_temperature type of AtC fix.</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>on </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC fe_md_boundary</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
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||||
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||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args] </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see for how to specify the faceset name. </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Interpolate. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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</html>
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||||
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||||
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<title>ATC: fix_modify AtC fem create mesh</title>
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||||
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|
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||||
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||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
<h3><a class="anchor" id="man_fem_mesh">fix_modify AtC fem create mesh</a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p><ul>
|
||||
<li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Creates a uniform mesh in a rectangular region</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>creates only uniform rectangular grids in a rectangular region</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
none
|
||||
<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
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||||
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||||
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address>
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<title>ATC: fix_modify AtC filter scale</title>
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|
||||
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|
||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC filter scale <scale> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>scale (real) = characteristic time scale of the filter <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC filter scale 10.0 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only for be used with specific transfers: thermal, two_temperature</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>0. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<!-- Generated by Doxygen 1.6.1 -->
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||||
|
||||
|
||||
<h3><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC filter type <exponential | step | no_filter> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC filter type exponential </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Specifies the type of time filter used. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only for be used with specific transfers: thermal, two_temperature</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No default. </p>
|
||||
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|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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|
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<!-- Generated by Doxygen 1.6.1 -->
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<div class="contents">
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||||
|
||||
|
||||
<h3><a class="anchor" id="man_fix_atc">fix atc command </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix <fixID> <group> atc <type> <parameter_file></p>
|
||||
<ul>
|
||||
<li>fixID = name of fix</li>
|
||||
<li>group = name of group fix is to be applied</li>
|
||||
<li>type<br/>
|
||||
= thermal : thermal coupling with fields: temperature <br/>
|
||||
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature <br/>
|
||||
= hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) <br/>
|
||||
= field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) <br/>
|
||||
</li>
|
||||
<li>parameter_file = name of the file with material parameters. <br/>
|
||||
note: Neither hardy nor field requires a parameter file </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/>
|
||||
<code> fix AtC internal atc two_temperature Ar_ttm.mat </code> <br/>
|
||||
<code> fix AtC internal atc hardy </code> <br/>
|
||||
<code> fix AtC internal atc field </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
|
||||
<p>The following coupling example is typical, but non-exhaustive:<br/>
|
||||
</p>
|
||||
<p><code> # ... commands to create and initialize the MD system <br/>
|
||||
</code></p>
|
||||
<p><code> # initial fix to designate coupling type and group to apply it to <br/>
|
||||
# tag group physics material_file <br/>
|
||||
fix AtC internal atc thermal Ar_thermal.mat<br/>
|
||||
<br/>
|
||||
# create a uniform 12 x 2 x 2 mesh that covers region contain the group <br/>
|
||||
# nx ny nz region periodicity <br/>
|
||||
fix_modify AtC mesh create 12 2 2 mdRegion f p p<br/>
|
||||
<br/>
|
||||
# specify the control method for the type of coupling <br/>
|
||||
# physics control_type <br/>
|
||||
fix_modify AtC thermal control flux <br/>
|
||||
<br/>
|
||||
# specify the initial values for the empirical field "temperature" <br/>
|
||||
# field node_group value <br/>
|
||||
fix_modify AtC initial temperature all 30.<br/>
|
||||
<br/>
|
||||
# create an output stream for nodal fields <br/>
|
||||
# filename output_frequency <br/>
|
||||
fix_modify AtC output atc_fe_output 100<br/>
|
||||
<br/>
|
||||
</code></p>
|
||||
<p><code> run 1000 <br/>
|
||||
</code></p>
|
||||
<p>likewise for this post-processing example: <br/>
|
||||
</p>
|
||||
<p><code> # ... commands to create and initialize the MD system <br/>
|
||||
</code></p>
|
||||
<p><code> # initial fix to designate post-processing and the group to apply it to <br/>
|
||||
# no material file is allowed nor required <br/>
|
||||
fix AtC internal atc hardy <br/>
|
||||
<br/>
|
||||
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function <br/>
|
||||
fix AtC kernel quartic_sphere 10.0 <br/>
|
||||
<br/>
|
||||
# create a uniform 1 x 1 x 1 mesh that covers region contain the group <br/>
|
||||
# with periodicity this effectively creates a system average <br/>
|
||||
fix_modify AtC mesh create 1 1 1 box p p p <br/>
|
||||
<br/>
|
||||
# change from default lagrangian map to eulerian <br/>
|
||||
# refreshed every 100 steps <br/>
|
||||
fix_modify AtC atom_element_map eulerian 100 <br/>
|
||||
<br/>
|
||||
# start with no field defined <br/>
|
||||
# add mass density, potential energy density, stress and temperature <br/>
|
||||
fix_modify AtC fields add density energy stress temperature <br/>
|
||||
<br/>
|
||||
# create an output stream for nodal fields <br/>
|
||||
# filename output_frequency <br/>
|
||||
fix_modify AtC output nvtFE 100 text <br/>
|
||||
</code></p>
|
||||
<p><code> run 1000 <br/>
|
||||
</code></p>
|
||||
<p>the mesh's linear interpolation functions can be used as the localization function <br/>
|
||||
by using the field option: <br/>
|
||||
</p>
|
||||
<p><code> fix AtC internal atc field <br/>
|
||||
<br/>
|
||||
fix_modify AtC mesh create 1 1 1 box p p p <br/>
|
||||
<br/>
|
||||
... <br/>
|
||||
<br/>
|
||||
</code></p>
|
||||
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes. <br/>
|
||||
For detailed exposition of the theory and algorithms please see:<br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/>
|
||||
</li>
|
||||
<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/>
|
||||
</li>
|
||||
<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/>
|
||||
</li>
|
||||
<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/>
|
||||
</li>
|
||||
<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/>
|
||||
</li>
|
||||
<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/>
|
||||
</li>
|
||||
<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
|
||||
<p>Currently,</p>
|
||||
<ul>
|
||||
<li>the coupling is restricted to thermal physics</li>
|
||||
<li>the FE computations are done in serial on each processor.</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>fix_modify commands for setup: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a></li>
|
||||
<li><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li>
|
||||
<li><a class="el" href="man_mesh_read.html">fix_modify AtC mesh read</a></li>
|
||||
<li><a class="el" href="man_mesh_write.html">fix_modify AtC mesh write</a></li>
|
||||
<li><a class="el" href="man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li>
|
||||
<li><a class="el" href="man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li>
|
||||
<li><a class="el" href="man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li>
|
||||
<li><a class="el" href="man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li>
|
||||
<li><a class="el" href="man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li>
|
||||
<li><a class="el" href="man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li>
|
||||
<li><a class="el" href="man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li>
|
||||
<li><a class="el" href="man_boundary.html">fix_modify AtC boundary</a></li>
|
||||
<li><a class="el" href="man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li>
|
||||
<li><a class="el" href="man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li>
|
||||
<li><a class="el" href="man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li>
|
||||
<li><a class="el" href="man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li>
|
||||
<li><a class="el" href="man_internal_element_set.html">fix_modify AtC internal_element_set</a></li>
|
||||
<li><a class="el" href="man_decomposition.html">fix_modify AtC decomposition</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for boundary and initial conditions:<br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="man_initial.html">fix_modify AtC initial</a></li>
|
||||
<li><a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a></li>
|
||||
<li><a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a></li>
|
||||
<li><a class="el" href="man_fix_flux.html">fix_modify AtC fix_flux</a></li>
|
||||
<li><a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a></li>
|
||||
<li><a class="el" href="man_source.html">fix_modify AtC source</a></li>
|
||||
<li><a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for control and filtering: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="man_control.html">fix_modify AtC control</a></li>
|
||||
<li><a class="el" href="man_control_thermal.html">fix_modify AtC control thermal</a></li>
|
||||
<li><a class="el" href="man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li>
|
||||
<li><a class="el" href="man_control_momentum.html">fix_modify AtC control momentum</a></li>
|
||||
<li><a class="el" href="man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li>
|
||||
<li><a class="el" href="man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li>
|
||||
<li><a class="el" href="man_mask_direction.html">fix_modify AtC control mask_direction</a></li>
|
||||
<li><a class="el" href="man_time_filter.html">fix_modify AtC filter</a></li>
|
||||
<li><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></li>
|
||||
<li><a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></li>
|
||||
<li><a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li>
|
||||
<li><a class="el" href="man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li>
|
||||
<li><a class="el" href="man_poisson_solver.html">fix_modify AtC poisson_solver</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for output: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="man_output.html">fix_modify AtC output</a></li>
|
||||
<li><a class="el" href="man_output_nodeset.html">fix_modify AtC output nodeset</a></li>
|
||||
<li><a class="el" href="man_output_elementset.html">fix_modify AtC output elementset</a></li>
|
||||
<li><a class="el" href="man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li>
|
||||
<li><a class="el" href="man_contour_integral.html">fix_modify AtC output contour_integral</a></li>
|
||||
<li><a class="el" href="man_mesh_output.html">fix_modify AtC mesh output</a></li>
|
||||
<li><a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a></li>
|
||||
<li><a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a></li>
|
||||
</ul>
|
||||
<p>fix_modify commands for post-processing: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="man_hardy_kernel.html">fix_modify AtC kernel</a></li>
|
||||
<li><a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
|
||||
<li><a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a></li>
|
||||
<li><a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a></li>
|
||||
<li><a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a></li>
|
||||
<li><a class="el" href="man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li>
|
||||
<li><a class="el" href="man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li>
|
||||
<li><a class="el" href="man_sample_frequency.html">fix_modify AtC sample_frequency</a></li>
|
||||
<li><a class="el" href="man_set.html">fix_modify AtC set</a></li>
|
||||
</ul>
|
||||
<p>miscellaneous fix_modify commands: <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a></li>
|
||||
<li><a class="el" href="man_atom_weight.html">fix_modify AtC atom_weight</a></li>
|
||||
<li><a class="el" href="man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li>
|
||||
<li><a class="el" href="man_reset_time.html">fix_modify AtC reset_time</a></li>
|
||||
<li><a class="el" href="man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li>
|
||||
<li><a class="el" href="man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li>
|
||||
<li><a class="el" href="man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li>
|
||||
<li><a class="el" href="man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li>
|
||||
<li><a class="el" href="man_mass_matrix.html">fix_modify AtC mass_matrix</a></li>
|
||||
<li><a class="el" href="man_material.html">fix_modify AtC material</a></li>
|
||||
<li><a class="el" href="man_atomic_charge.html">fix_modify AtC atomic_charge</a></li>
|
||||
<li><a class="el" href="man_source_integration.html">fix_modify AtC source_integration</a></li>
|
||||
<li><a class="el" href="man_temperature_definition.html">fix_modify AtC temperature_definition</a></li>
|
||||
<li><a class="el" href="man_track_displacement.html">fix_modify AtC track_displacement</a></li>
|
||||
<li><a class="el" href="man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li>
|
||||
<li><a class="el" href="man_add_species.html">fix_modify AtC add_species</a></li>
|
||||
<li><a class="el" href="man_add_molecule.html">fix_modify AtC add_molecule</a></li>
|
||||
<li><a class="el" href="man_remove_species.html">fix_modify AtC remove_species</a></li>
|
||||
<li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
|
||||
</ul>
|
||||
<p>Note: a set of example input files with the attendant material files are included with this package </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
||||
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|
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
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|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC fix_flux <field> <face_set> <value | function></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
|
||||
<li><face_set> = name of set of element faces </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Only normal fluxes (Neumann data) can be prescribed. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
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||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC fix <field> <nodeset> <constant | function></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics</li>
|
||||
<li><nodeset> = name of set of nodes to apply boundary condition</li>
|
||||
<li><constant | function> = value or name of function followed by its parameters </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/>
|
||||
<code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Creates a constraint on the values of the specified field at specified nodes. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>keyword 'all' reserved in nodeset name </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,65 +0,0 @@
|
|||
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|
||||
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|
||||
<title>ATC: fix_modify AtC computes</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br/>
|
||||
</li>
|
||||
<li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br/>
|
||||
</li>
|
||||
<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> compute virial all stress/atom </code> <br/>
|
||||
<code> fix_modify AtC computes add virial volume </code> <br/>
|
||||
<code> fix_modify AtC computes delete virial </code> <br/>
|
||||
<br/>
|
||||
<code> compute centrosymmetry all centro/atom </code> <br/>
|
||||
<code> fix_modify AtC computes add centrosymmetry number </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
|
||||
Per-atom compute must be specified before corresponding continuum field can be requested <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>See manual page for compute </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No defaults exist for this command </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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|
||||
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|
@ -1,81 +0,0 @@
|
|||
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||||
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|
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC fields <all | none> <br/>
|
||||
fix_modify AtC fields <add | delete> <list_of_fields> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>all | none (keyword) = output all or no fields <br/>
|
||||
</li>
|
||||
<li>add | delete (keyword) = add or delete the listed output fields <br/>
|
||||
</li>
|
||||
<li>fields (keyword) = <br/>
|
||||
density : mass per unit volume <br/>
|
||||
displacement : displacement vector <br/>
|
||||
momentum : momentum per unit volume <br/>
|
||||
velocity : defined by momentum divided by density <br/>
|
||||
projected_velocity : simple kernel estimation of atomic velocities <br/>
|
||||
temperature : temperature derived from the relative atomic kinetic energy (as done by ) <br/>
|
||||
kinetic_temperature : temperature derived from the full kinetic energy <br/>
|
||||
number_density : simple kernel estimation of number of atoms per unit volume <br/>
|
||||
stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br/>
|
||||
transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br/>
|
||||
heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br/>
|
||||
potential_energy : potential energy per unit volume <br/>
|
||||
kinetic_energy : kinetic energy per unit volume <br/>
|
||||
thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume <br/>
|
||||
internal_energy : total internal energy (potential + thermal) per unit volume <br/>
|
||||
energy : total energy (potential + kinetic) per unit volume <br/>
|
||||
number_density : number of atoms per unit volume <br/>
|
||||
eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335] <br/>
|
||||
vacancy_concentration: volume fraction of vacancy content <br/>
|
||||
type_concentration: volume fraction of a specific atom type <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC fields add velocity temperature </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
|
||||
<code> fix_modify AtC fields none </code> <br/>
|
||||
followed by <br/>
|
||||
<code> fix_modify AtC fields add velocity temperature </code> <br/>
|
||||
will only output the velocity and temperature fields. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="../../fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>By default, no fields are output </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
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|
||||
|
|
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|
|||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC gradients <add | delete> <list_of_fields> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>add | delete (keyword) = add or delete the calculation of gradients for the listed output fields <br/>
|
||||
</li>
|
||||
<li>fields (keyword) = <br/>
|
||||
gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
|
||||
<code> fix_modify AtC gradients delete velocity </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Requests calculation and output of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No gradients are calculated by default </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
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|
||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
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||||
|
||||
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|
||||
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC kernel <type> <parameters></p>
|
||||
<ul>
|
||||
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
|
||||
</li>
|
||||
<li>parameters :<br/>
|
||||
step = radius (double) <br/>
|
||||
cell = hx, hy, hz (double) or h (double) <br/>
|
||||
cubic_bar = half-width (double) <br/>
|
||||
cubic_cylinder = radius (double) <br/>
|
||||
cubic_sphere = radius (double) <br/>
|
||||
quartic_bar = half-width (double) <br/>
|
||||
quartic_cylinder = radius (double) <br/>
|
||||
quartic_sphere = radius (double) <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/>
|
||||
<code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy AtC fix <br/>
|
||||
For bar kernel types, half-width oriented along x-direction <br/>
|
||||
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
|
||||
( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No default </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
<title>ATC: fix_modify AtC on_the_fly</title>
|
||||
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|
||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
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<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC on_the_fly <bond | kernel> <optional on | off> <br/>
|
||||
- bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC on_the_fly bond on </code> <br/>
|
||||
<code> fix_modify AtC on_the_fly kernel </code> <br/>
|
||||
<code> fix_modify AtC on_the_fly kernel off </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
|
||||
on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
|
||||
</p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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||||
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||||
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||||
<title>ATC: fix_modify AtC rates</title>
|
||||
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|
||||
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|
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<a href="../../Manual.html">LAMMPS Manual</a>
|
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|
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|
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|
||||
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|
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC rates <add | delete> <list_of_fields> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields <br/>
|
||||
</li>
|
||||
<li>fields (keyword) = <br/>
|
||||
rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
|
||||
<code> fix_modify AtC rates delete stress </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Requests calculation and output of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No rates are calculated by default </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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||||
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|
||||
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|
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|
|||
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||||
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||||
<title>ATC: fix_modify AtC initial</title>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
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|
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<a href="../../Commands_all.html">Commands</a>
|
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|
||||
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|
||||
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_initial">fix_modify AtC initial </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC initial <field> <nodeset> <constant | function></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
|
||||
<li><nodeset> = name of set of nodes to apply initial condition</li>
|
||||
<li><constant | function> = value or name of function followed by its parameters </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets the initial values for the specified field at the specified nodes. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>keyword 'all' reserved in nodeset name </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
||||
|
|
@ -1,38 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC internal_atom_integrate</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC internal_atom_integrate <on | off> <code> fix_modify AtC internal_atom_integrate on </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>on for coupling methods, off for post-processors off </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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||||
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
||||
|
|
@ -1,50 +0,0 @@
|
|||
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||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC internal_element_set</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
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|
||||
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|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
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|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC internal_element_set <element-set-name></p>
|
||||
<ul>
|
||||
<li><element-set-name> = name of element set defining internal region, or off </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see atom_element_map_type and boundary </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>off </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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|
||||
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|
||||
|
|
@ -1,48 +0,0 @@
|
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC internal_quadrature</title>
|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
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||||
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|
||||
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|
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<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify atc internal_quadrature <on | off> [region] </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc internal_quadrature off </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
|
||||
<h4><a class="anchor" id="optional">
|
||||
optional</a></h4>
|
||||
<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
<h3><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC kernel <type> <parameters></p>
|
||||
<ul>
|
||||
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
|
||||
</li>
|
||||
<li>parameters :<br/>
|
||||
step = radius (double) <br/>
|
||||
cell = hx, hy, hz (double) or h (double) <br/>
|
||||
cubic_bar = half-width (double) <br/>
|
||||
cubic_cylinder = radius (double) <br/>
|
||||
cubic_sphere = radius (double) <br/>
|
||||
quartic_bar = half-width (double) <br/>
|
||||
quartic_cylinder = radius (double) <br/>
|
||||
quartic_sphere = radius (double) <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy AtC fix <br/>
|
||||
For bar kernel types, half-width oriented along x-direction <br/>
|
||||
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
|
||||
( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No default </p>
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||||
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||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<title>ATC: fix_modify AtC control localized_lambda</title>
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<!-- Generated by Doxygen 1.6.1 -->
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control localized_lambda <on|off> </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc control localized_lambda on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Default is off. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<title>ATC: fix_modify AtC control lumped_lambda_solve</title>
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||||
<h3><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control lumped_lambda_solve <on|off> </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to use or not use lumped matrix for lambda solve </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
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|
||||
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|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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<title>ATC: fix_modify AtC control mask_direction</title>
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<!-- Generated by Doxygen 1.6.1 -->
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|
||||
|
||||
<h3><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC control mask_direction <direction> <on|off> </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc control mask_direction 0 on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to mask out certain dimensions from the atomic regulator </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
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|
||||
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<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<title>ATC: fix_modify AtC mass_matrix</title>
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<!-- Generated by Doxygen 1.6.1 -->
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||||
|
||||
<h3><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mass_matrix <fe | md_fe></p>
|
||||
<ul>
|
||||
<li><fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc mass_matrix fe </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Default is off </p>
|
||||
</div>
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<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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<h3><a class="anchor" id="man_material">fix_modify AtC material </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC material [elementset_name] [material_id] <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC material gap_region 2</code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets the material model in elementset_name to be of type material_id. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>All elements default to the first material in the material file. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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||||
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||||
<h3><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax></p>
|
||||
<ul>
|
||||
<li><id> = id of FE nodeset to be added to</li>
|
||||
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to add nodes to an already existing FE nodeset. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Coordinates are assumed to be in lattice units. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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|
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<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
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|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>nx ny nz = number of elements in x, y, z</li>
|
||||
<li>region-id = id of region that is to be meshed</li>
|
||||
<li>f p p = periodicity flags for x, y, z </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Creates a uniform mesh in a rectangular region </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Creates only uniform rectangular grids in a rectangular region </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>ATC: fix_modify AtC mesh create_elementset</title>
|
||||
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|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
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|
||||
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|
||||
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|
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|
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|
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<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax></p>
|
||||
<ul>
|
||||
<li><id> = id to assign to the collection of FE element</li>
|
||||
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Only viable for rectangular grids. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Coordinates are assumed to be in lattice units. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh create_faceset box</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]</p>
|
||||
<ul>
|
||||
<li><id> = id to assign to the collection of FE faces</li>
|
||||
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces</li>
|
||||
<li><in|out> = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
|
||||
<li>units = option to specify real as opposed to lattice units </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to assign an id to a set of FE faces. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Only viable for rectangular grids. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>The default options are units = lattice and the use of outer faces </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,52 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh create_faceset plane</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
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|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]</p>
|
||||
<ul>
|
||||
<li><id> = id to assign to the collection of FE faces</li>
|
||||
<li><x|y|z> = coordinate directions that define plane on which faceset lies</li>
|
||||
<li><val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
|
||||
<li>units = option to specify real as opposed to lattice units </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to assign an id to a set of FE faces. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Only viable for rectangular grids. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>The default option is units = lattice. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,49 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh create_nodeset</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax></p>
|
||||
<ul>
|
||||
<li><id> = id to assign to the collection of FE nodes</li>
|
||||
<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Coordinates are assumed to be in lattice units. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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|
||||
|
|
@ -1,48 +0,0 @@
|
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh delete_elements</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
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||||
<center>
|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
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|
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<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
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||||
|
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<!-- Generated by Doxygen 1.6.1 -->
|
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh delete_elements <element_set></p>
|
||||
<ul>
|
||||
<li><element_set> = name of an element set </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC delete_elements gap </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Deletes a group of elements from the mesh. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
||||
|
|
@ -1,51 +0,0 @@
|
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<title>ATC: fix_modify AtC mesh nodeset_to_elementset</title>
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|
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
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|
||||
<hr>
|
||||
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||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min></p>
|
||||
<ul>
|
||||
<li><nodeset_id> = id of desired nodeset from which to create elementset</li>
|
||||
<li><elementset_id> = id to assign to the collection of FE element</li>
|
||||
<li><max/min> = flag to choose either the maximal or minimal elementset </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>None. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Unless specified, the maximal element set is created </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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</body>
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</html>
|
||||
|
|
@ -1,47 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<title>ATC: fix_modify AtC mesh output</title>
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|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh output <file_prefix> </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh output meshData </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>none </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
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|
||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh quadrature</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh quadrature <quad></p>
|
||||
<ul>
|
||||
<li>quad = one of <nodal|gauss1|gauss2|gauss3|face> --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh quadrature face </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>(Re-)assigns the quadrature style for the existing mesh. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
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|
||||
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|
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh read</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
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|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p></p>
|
||||
<ul>
|
||||
<li>filename = name of file containing mesh to be read</li>
|
||||
<li>f p p = periodicity flags for x, y, z </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
|
||||
<code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>periodicity flags are false by default </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
</html>
|
||||
|
|
@ -1,48 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC mesh write</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC mesh write <filename></p>
|
||||
<ul>
|
||||
<li>filename = name of file to write mesh </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Writes a mesh to a text file. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,58 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC time_integration (momentum)</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC time_integration <descriptor> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>descriptor (string) = time integration type <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>various time integration methods for the finite elements<br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
|
||||
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
|
||||
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc time_integration verlet </code> <br/>
|
||||
<code> fix_modify atc time_integration fractional_step </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,61 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
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<title>ATC: fix_modify AtC output</title>
|
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<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_output">fix_modify AtC output </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
|
||||
<ul>
|
||||
<li>filename_prefix (string) = prefix for data files</li>
|
||||
<li>frequency (integer) = frequency of output in time-steps</li>
|
||||
<li>options (keyword/s): <br/>
|
||||
text = creates text output of index, step and nodal variable values for unique nodes <br/>
|
||||
full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes <br/>
|
||||
binary = creates binary Ensight output <br/>
|
||||
vector_components = outputs vectors as scalar components <br/>
|
||||
tensor_components = outputs tensor as scalar components (use this for Paraview)<br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC output heatFE 100 </code> <br/>
|
||||
<code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
|
||||
<code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
|
||||
<code> fix_modify AtC output index step </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>no default format output indexed by time </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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|
||||
|
|
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|
|||
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||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
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<title>ATC: fix_modify AtC output elementset</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
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||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC output volume_integral <eset_name> <field> {`</p>
|
||||
<ul>
|
||||
<li>set_name (string) = name of elementset to be integrated over</li>
|
||||
<li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC output eset1 mass_density </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
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</body>
|
||||
</html>
|
||||
|
|
@ -1,53 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
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<title>ATC: fix_modify AtC output nodeset</title>
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC output nodeset <nodeset_name> <operation></p>
|
||||
<ul>
|
||||
<li>nodeset_name (string) = name of nodeset to be operated on</li>
|
||||
<li>operation (keyword/s): <br/>
|
||||
sum = creates nodal sum over nodes in specified nodeset <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
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|
|||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC pair_interactions/bond_interactions</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC pair_interactions <on|off> <br/>
|
||||
fix_modify AtC bond_interactions <on|off> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC bond_interactions on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>include bonds and/or pairs in the stress and heat flux computations </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>pair interactions: on, bond interactions: off </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
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|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC poisson_solver</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p></p>
|
||||
<ul>
|
||||
<li>nx ny nz = number of elements in x, y, z</li>
|
||||
<li>region-id = id of region that is to be meshed</li>
|
||||
<li>f p p = perioidicity flags for x, y, z </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Creates a uniform mesh in a rectangular region </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>creates only uniform rectangular grids in a rectangular region </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,49 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC read_restart</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC read_restart [file_name] <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC read_restart ATC_state </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Reads the current state of the fields from a named text-based restart file. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,52 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC remove_molecule</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify_AtC remove_molecule <TAG> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><TAG> = tag for tracking a molecule type <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC remove_molecule water </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Removes tag designated for tracking a specified set of molecules. <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No defaults for this command. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,50 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC remove_source</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC remove_source <field> <element_set></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics</li>
|
||||
<li><element_set> = name of set of elements </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc remove_source temperature groupNAME </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Remove a domain source. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>keyword 'all' reserved in element_set name </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
||||
</html>
|
||||
|
|
@ -1,52 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC remove_species</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify_AtC delete_species <TAG> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li><TAG> = tag for tracking a species <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC remove_species gold </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Removes tag designated for tracking a specified species. <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>No defaults for this command. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
</html>
|
||||
|
|
@ -1,47 +0,0 @@
|
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC reset_atomic_reference_positions</title>
|
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|
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC reset_atomic_reference_positions </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc reset_atomic_reference_positions </code></p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p><code> </code></p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><code> </code></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p><code> Default is off </code></p>
|
||||
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|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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||||
<title>ATC: fix_modify AtC reset_time</title>
|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
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||||
|
||||
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|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC reset_time </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc reset_time 0.0 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Resets the simulation time counter. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC kernel_bandwidth </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc reset_time 8 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Only is used if kernel functions are being used. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Number of sample locations. </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
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<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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|
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||||
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|
||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
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|
||||
|
||||
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|
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|
||||
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|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC sample_frequency [freq]</p>
|
||||
<ul>
|
||||
<li>freq (int) : frequency to sample field in number of steps </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC sample_frequency 10 </code></p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><code> </code></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p><code> none </code></p>
|
||||
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|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
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||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
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||||
|
||||
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|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_set">fix_modify AtC set </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC set reference_potential_energy <value_or_filename(optional)></p>
|
||||
<ul>
|
||||
<li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
|
||||
</li>
|
||||
<li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC set reference_potential_energy </code> <br/>
|
||||
<code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
|
||||
<code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Defaults to lammps zero point i.e. isolated atoms </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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|
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
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|
||||
|
||||
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|
||||
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||||
|
||||
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|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_source">fix_modify AtC source </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC source <field> <element_set> <value | function></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics</li>
|
||||
<li><element_set> = name of set of elements </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>keyword 'all' reserved in element_set name </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,44 +0,0 @@
|
|||
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||||
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||||
<title>ATC: fix_modify AtC source_integration</title>
|
||||
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|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
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|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC source_integration < fe | atom> </p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc source_integration atom </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>Default is fe </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
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||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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||||
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||||
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|
||||
|
|
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||||
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|
||||
<title>ATC: fix_modify AtC temperature_definition</title>
|
||||
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|
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||||
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||||
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|
||||
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|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC temperature_definition <kinetic|total></p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc temperature_definition kinetic </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>kinetic </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
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||||
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|
||||
|
|
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|
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||||
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|
||||
<title>ATC: fix_modify AtC time_integration (thermal)</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
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|
||||
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||||
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||||
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|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
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|
||||
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|
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|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
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|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC time_integration <descriptor> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>descriptor (string) = time integration type <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<p>various time integration methods for the finite elements<br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/>
|
||||
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc time_integration gear </code> <br/>
|
||||
<code> fix_modify atc time_integration fractional_step </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
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|
||||
|
|
@ -1,55 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC filter</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC filter <on | off | equilibrate> <br/>
|
||||
</p>
|
||||
<ul>
|
||||
<li>on | off (keyword) = turns filter on or off<br/>
|
||||
</li>
|
||||
<li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc transfer filter on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics</p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>only for be used with specific transfers: thermal, two_temperature</p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a> <br/>
|
||||
<a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>off </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
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|
||||
|
|
@ -1,46 +0,0 @@
|
|||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC track_displacement</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC track_displacement <on/off> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc track_displacement on </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>Some constitutive models require the displacement field </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>on </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,50 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC unfix_flux</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC fix_flux <field> <face_set> <value | function></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
|
||||
<li><face_set> = name of set of element faces </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command for removing prescribed normal fluxes e.g. heat_flux, stress. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
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|
||||
</html>
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
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|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC unfix</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC unfix <field> <nodeset></p>
|
||||
<ul>
|
||||
<li><field> = field name valid for type of physics</li>
|
||||
<li><nodeset> = name of set of nodes </li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC unfix temperature groupNAME </code> </p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Removes constraint on field values for specified nodes. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>keyword 'all' reserved in nodeset name </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see <a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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||||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC write_atom_weights</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC write_atom_weights <filename> <frequency></p>
|
||||
<ul>
|
||||
<li><filename> = name of file that atomic weights are written to <br/>
|
||||
</li>
|
||||
<li><frequency> = how often writes will occur <br/>
|
||||
</li>
|
||||
</ul>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Command for writing the values of atomic weights to a specified file. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -1,49 +0,0 @@
|
|||
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
||||
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|
||||
<head>
|
||||
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
|
||||
<title>ATC: fix_modify AtC write_restart</title>
|
||||
<link href="tabs.css" rel="stylesheet" type="text/css"/>
|
||||
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
|
||||
</head>
|
||||
<body>
|
||||
<center>
|
||||
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
|
||||
<a href="../../Manual.html">LAMMPS Manual</a>
|
||||
<a href="../../fix_atc.html">USER-AtC Manual</a>
|
||||
<a href="../../Commands_all.html">Commands</a>
|
||||
</center>
|
||||
|
||||
<hr>
|
||||
|
||||
|
||||
<!-- Generated by Doxygen 1.6.1 -->
|
||||
<div class="contents">
|
||||
|
||||
|
||||
<h3><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h3><h4><a class="anchor" id="syntax">
|
||||
syntax</a></h4>
|
||||
<p>fix_modify AtC write_restart [file_name] <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="examples">
|
||||
examples</a></h4>
|
||||
<p><code> fix_modify AtC write_restart restart.mydata </code> <br/>
|
||||
</p>
|
||||
<h4><a class="anchor" id="description">
|
||||
description</a></h4>
|
||||
<p>Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. </p>
|
||||
<h4><a class="anchor" id="restrictions">
|
||||
restrictions</a></h4>
|
||||
<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
|
||||
<h4><a class="anchor" id="related">
|
||||
related</a></h4>
|
||||
<p>see read_restart <a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a> </p>
|
||||
<h4><a class="anchor" id="default">
|
||||
default</a></h4>
|
||||
<p>none </p>
|
||||
</div>
|
||||
<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
|
||||
<a href="http://www.doxygen.org/index.html">
|
||||
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
|
||||
</body>
|
||||
</html>
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
.. index:: fix_modify AtC add_molecule
|
||||
|
||||
fix_modify AtC add_molecule command
|
||||
===================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> add_molecule <small|large> <tag> <group-ID>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* add_molecule = name of the AtC sub-command
|
||||
* *small* or *large* = can be *small* if molecule size < cutoff radius, must be *large* otherwise
|
||||
* tag = tag for tracking a molecule
|
||||
* *group-ID* = LAMMPS defined group-ID
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
group WATERGROUP type 1 2
|
||||
fix_modify AtC add_molecule small water WATERGROUP
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Associates a tag with all molecules corresponding to a specified group.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
None.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
- :doc:`fix_modify AtC add_species <atc_add_species>`
|
||||
- :doc:`fix_modify AtC remove_species <atc_remove_species>`
|
||||
- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
None.
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
.. index:: fix_modify AtC add_species
|
||||
|
||||
fix_modify AtC add_species command
|
||||
==================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> add_species <tag> <group|type> <ID>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* add_species = name of the AtC sub-command
|
||||
* tag = tag for tracking a species
|
||||
* *group* or *type* = LAMMPS defined group or type of atoms
|
||||
* ID = name of group or type number
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC add_species gold type 1
|
||||
group GOLDGROUP type 1
|
||||
fix_modify AtC add_species gold group GOLDGROUP
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Associates a tag with all atoms of a specified type or within a specified group.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
None.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
|
||||
- :doc:`fix_modify AtC remove_species <atc_remove_species>`
|
||||
- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
None.
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
.. index:: fix_modify AtC atom_element_map
|
||||
|
||||
fix_modify AtC atom_element_map command
|
||||
=======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> atom_element_map <eulerian|lagrangian> [<frequency>]
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* atom_element_map = name of the AtC sub-command
|
||||
* *eulerian* or *lagrangian* = frame of reference
|
||||
* frequency = frequency of updating atom-to-continuum maps based on the current configuration - (only for eulerian)
|
||||
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC atom_element_map eulerian 100
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Changes frame of reference from *eulerian* to *lagrangian* or vice versa
|
||||
and sets the frequency for which the map from atoms to elements is
|
||||
reformed and all the attendant data is recalculated.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Cannot change map type after initialization.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
*lagrangian*
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
.. index:: fix_modify AtC atom_weight
|
||||
|
||||
fix_modify AtC atom_weight command
|
||||
==================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> atom_weight <method> <args>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* atom_weight = name of the AtC sub-command
|
||||
* method = *constant* or *lattice* or *element* or *region* or *group* or *read_in*
|
||||
|
||||
- *constant* <group-ID> <value>: atoms in specified group are assigned the constant value given
|
||||
- *lattice*\ : volume per atom for specified lattice type (e.g. fcc) and parameter
|
||||
- *element*\ : element volume divided among atoms within element
|
||||
- *region*\ : volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions.
|
||||
- *group*\ : volume per atom determined based on the atom count in a group and its volume
|
||||
- *node*\ : (undocumented)
|
||||
- *node_element*\ : (undocumented)
|
||||
- *read_in*\ <filename>: list of values for atoms are read-in from specified file
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC atom_weight constant myatoms 11.8
|
||||
fix_modify AtC atom_weight lattice
|
||||
fix_modify AtC atom_weight read-in atm_wt_file.txt
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Command for assigning the value of atomic weights used for atomic
|
||||
integration in atom-continuum coupled simulations.
|
||||
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
The use of the lattice option requires a lattice type and parameter is already specified.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
*lattice*
|
||||
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
.. index:: fix_modify AtC atomic_charge
|
||||
|
||||
fix_modify AtC atomic_charge command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> <include|omit> atomic_charge
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* *include* or *omit* = switch to activate/deactivate inclusion of intrinsic atomic charge in ATC
|
||||
* atomic_charge = name of the AtC sub-command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC include atomic_charge
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Determines whether AtC tracks the total charge as a finite element
|
||||
field.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Required for: *electrostatics*
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
If the atom charge is defined, default is on, otherwise default is off.
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
.. index:: fix_modify AtC boundary_dynamics
|
||||
|
||||
fix_modify AtC boundary_dynamics command
|
||||
========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> boundary_dynamics <on|damped_harmonic|prescribed|coupled|none>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* boundary_dynamics = name of the AtC sub-command
|
||||
* *on* or *damped_harmonic* *prescribed* *coupled* *none*
|
||||
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Sets different schemes for controlling boundary atoms. *on* will integrate
|
||||
the boundary atoms using the velocity-verlet algorithm. *damped_harmonic*
|
||||
uses a mass/spring/dashpot for the boundary atoms with added arguments
|
||||
of the damping and spring constants followed by the ratio of the
|
||||
boundary type mass to the desired mass. *prescribed* forces the boundary
|
||||
atoms to follow the finite element displacement. *coupled* does the same.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Boundary atoms must be specified. When using swaps between internal and
|
||||
boundary atoms, the initial configuration must have already correctly
|
||||
partitioned the two.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
*prescribed on*
|
||||
|
|
@ -0,0 +1,47 @@
|
|||
.. index:: fix_modify AtC boundary_faceset
|
||||
|
||||
fix_modify AtC boundary_faceset command
|
||||
=======================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> boundary_faceset <is|add> <faceset_name>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* boundary_faceset = name of the AtC sub-command
|
||||
* *is* or *add* = select whether to select or add a faceset
|
||||
* faceset_name = name of the faceset
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC boundary_faceset is obndy
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command species the faceset name when using a faceset to compute
|
||||
the MD/FE boundary fluxes. The faceset must already exist.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This is only valid when *fe_md_boundary* is set to *faceset*\ .
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
- :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
|
||||
- :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
|
||||
- :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
None.
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
.. index:: fix_modify AtC boundary type
|
||||
|
||||
fix_modify AtC boundary type command
|
||||
====================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> boundary type <atom-type-id>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* boundary type = name of the AtC sub-command
|
||||
* atom-type-id = type id for atoms that represent a fictitious boundary internal to the FE mesh
|
||||
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC boundary type ghost_atoms
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Command to define the atoms that represent the fictitious boundary
|
||||
internal to the FE mesh. For fully overlapped MD/FE domains with
|
||||
periodic boundary conditions no boundary atoms should be defined.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
None.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
None.
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
.. index:: fix_modify AtC consistent_fe_initialization
|
||||
|
||||
fix_modify AtC consistent_fe_initialization command
|
||||
===================================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix_modify <AtC fixID> consistent_fe_initialization <on|off>
|
||||
|
||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
|
||||
* consistent_fe_initialization = name of the AtC sub-command
|
||||
* *on* or *off* = switch to activate/deactivate the initial setting of the FE intrinsic field to match the projected MD field
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix_modify AtC consistent_fe_initialization on
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Determines whether AtC initializes FE intrinsic fields (e.g.,
|
||||
temperature) to match the projected MD values. This is particularly
|
||||
useful for fully overlapping simulations.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Can be used with: *thermal*, *two_temperature*.
|
||||
Cannot be used with time filtering on.
|
||||
Does not include boundary nodes.
|
||||
|
||||
Related AtC commands
|
||||
""""""""""""""""""""
|
||||
|
||||
- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
Default is *off*
|
||||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue