diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a8b2a5661d..4dd079eaae 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -262,8 +262,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) enable_language(Fortran) file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) - set(BLAS_LIBRARIES "${CMAKE_BINARY_DIR}/liblinalg.a") - set(LAPACK_LIBRARIES "${CMAKE_BINARY_DIR}/liblinalg.a") + set(BLAS_LIBRARIES "$") + set(LAPACK_LIBRARIES "$") else() list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES}) endif() @@ -344,7 +344,7 @@ include(Packages/COMPRESS) set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_TUNE_FLAGS}") -if(CMAKE_Fortran_FLAGS) +if(CMAKE_Fortran_COMPILER) set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${CMAKE_TUNE_FLAGS}") endif() ######################################################################## diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 1285c3f262..a733142455 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -22,6 +22,7 @@ endif() set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE) -set(CMAKE_TUNE_FLAGS "" CACHE STRING "" FORCE) +set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE) +set(CMAKE_EXE_LINKER_FLAGS "--enable-stdcall-fixup" CACHE STRING "" FORCE) set(BUILD_TOOLS ON CACHE BOOL "" FORCE) set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer") diff --git a/doc/Makefile b/doc/Makefile index 1097d1e37c..ff56226e83 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -76,13 +76,9 @@ html: $(ANCHORCHECK) $(MATHJAX) @rm -rf html/USER @rm -rf html/JPG @cp -r src/PDF html/PDF - @cp -r src/USER html/USER @mkdir -p html/JPG @cp `grep -A2 '\.\. .*image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/ @rm -rf html/PDF/.[sg]* - @rm -rf html/USER/.[sg]* - @rm -rf html/USER/*/.[sg]* - @rm -rf html/USER/*/*.[sg]* @mkdir -p html/_static/mathjax @cp -r $(MATHJAX)/es5 html/_static/mathjax/ @echo "Build finished. The HTML pages are in doc/html." @@ -151,11 +147,7 @@ pdf: $(ANCHORCHECK) @rm -rf latex/PDF @rm -rf latex/USER @cp -r src/PDF latex/PDF - @cp -r src/USER latex/USER @rm -rf latex/PDF/.[sg]* - @rm -rf latex/USER/.[sg]* - @rm -rf latex/USER/*/.[sg]* - @rm -rf latex/USER/*/*.[sg]* @echo "Build finished. Manual.pdf and Developer.pdf are in this directory." fetch: diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 06e5a87594..7a60ffa437 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -31,7 +31,7 @@ platforms and particularly on Linux. However, alternate build tools (e.g. Ninja) and project files for Integrated Development Environments (IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is selected via the ``-G`` command line flag. Further details about features -and settings for CMake are in the `CMake online documentation `_ +and settings for CMake are in the `CMake online documentation `_ .. _cmake_doc: https://cmake.org/documentation/ diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index 64c890d8ec..b18dc49e38 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -240,9 +240,11 @@ C-style interface, provided in src/library.cpp and src/library.h. See the :doc:`Python library ` doc page for a description of the Python interface to LAMMPS, which wraps the C-style -interface from a shared library through the ctypes python module. +interface from a shared library through the `ctypes python module `_. See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS through its library interface. Other examples in the COUPLE directory use coupling ideas discussed on the :doc:`Howto couple ` doc page. + +.. _ctypes: https://docs.python.org/3/library/ctypes.html diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 603952a29d..34567db385 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -38,7 +38,7 @@ input script command that it was processing. Of course, LAMMPS cannot figure out your physics or numerical mistakes, like choosing too big a timestep, specifying erroneous force field coefficients, or putting 2 atoms on top of each other! If you run into errors that LAMMPS -doesn't catch that you think it should flag, please send an email to +does not catch that you think it should flag, please send an email to the `developers `_. If you get an error message about an invalid command in your input @@ -96,13 +96,13 @@ cases: LAMMPS runs in the available memory a processor allows to be allocated. Most reasonable MD runs are compute limited, not memory -limited, so this shouldn't be a bottleneck on most platforms. Almost +limited, so this should not be a bottleneck on most platforms. Almost all large memory allocations in the code are done via C-style malloc's which will generate an error message if you run out of memory. Smaller chunks of memory are allocated via C++ "new" statements. If you are unlucky you could run out of memory just when one of these small requests is made, in which case the code will crash or hang (in -parallel), since LAMMPS doesn't trap on those errors. +parallel), since LAMMPS does not trap on those errors. Illegal arithmetic can cause LAMMPS to run slow or crash. This is typically due to invalid physics and numerics that your simulation is diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 6ca3f9e51c..6970cb4a9a 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -2177,7 +2177,7 @@ Doc page with :doc:`WARNING messages ` The command is accessing a vector added by the fix property/atom command, that does not exist. -*Compute property/atom for atom property that isn't allocated* +*Compute property/atom for atom property that is not allocated* Self-explanatory. *Compute property/atom integer vector does not exist* @@ -2194,7 +2194,7 @@ Doc page with :doc:`WARNING messages ` *Compute property/local does not (yet) work with atom_style template* Self-explanatory. -*Compute property/local for property that isn't allocated* +*Compute property/local for property that is not allocated* Self-explanatory. *Compute rdf requires a pair style be defined* @@ -3100,7 +3100,7 @@ Doc page with :doc:`WARNING messages ` *Dump_modify region ID does not exist* Self-explanatory. -*Dumping an atom property that isn't allocated* +*Dumping an atom property that is not allocated* The chosen atom style does not define the per-atom quantity being dumped. @@ -3126,7 +3126,7 @@ Doc page with :doc:`WARNING messages ` *Energy was not tallied on needed timestep* You are using a thermo keyword that requires potentials to - 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. *Epsilon or sigma reference not set by pair style in PPPMDisp* @@ -4145,7 +4145,7 @@ Doc page with :doc:`WARNING messages ` Fixes that calculate global or local quantities cannot be used with fix store/state. -*Fix store/state for atom property that isn't allocated* +*Fix store/state for atom property that is not allocated* Self-explanatory. *Fix store/state variable is not atom-style variable* @@ -4739,7 +4739,7 @@ Doc page with :doc:`WARNING messages ` *Invalid LAMMPS restart file* The file does not appear to be a LAMMPS restart file since - it doesn't contain the correct magic string at the beginning. + it does not contain the correct magic string at the beginning. *Invalid Masses section in molecule file* Self-explanatory. @@ -6427,7 +6427,7 @@ keyword to allow for additional bonds to be formed *Pair hybrid sub-style does not support single call* You are attempting to invoke a single() call on a pair style - that doesn't support it. + that does not support it. *Pair hybrid sub-style is not used* No pair_coeff command used a sub-style specified in the pair_style @@ -6901,7 +6901,7 @@ keyword to allow for additional bonds to be formed *Per-atom energy was not tallied on needed timestep* You are using a thermo keyword that requires potentials to - 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. *Per-atom fix in equal-style variable formula* @@ -6909,7 +6909,7 @@ keyword to allow for additional bonds to be formed *Per-atom 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 + tallied the virial, but they did not on this timestep. See the variable doc page for ideas on how to make this work. *Per-processor system is too big* @@ -7070,7 +7070,7 @@ keyword to allow for additional bonds to be formed It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit integer. -*Read dump of atom property that isn't allocated* +*Read dump of atom property that is not allocated* Self-explanatory. *Read rerun dump file timestep > specified stop* @@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed creates one large file for all processors. *Restart file byte ordering is not recognized* - 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 contain a recognized byte-ordering flag at the beginning. *Restart file byte ordering is swapped* @@ -7701,7 +7701,7 @@ keyword to allow for additional bonds to be formed Keywords that refer to time (such as cpu, elapsed) do not make sense in between runs. -*Threshold for an atom property that isn't allocated* +*Threshold for an atom property that is not allocated* A dump threshold has been requested on a quantity that is not defined by the atom style used in this simulation. @@ -8355,7 +8355,7 @@ keyword to allow for additional bonds to be formed *Variable name must be alphanumeric or underscore characters* Self-explanatory. -*Variable uses atom property that isn't allocated* +*Variable uses atom property that is not allocated* Self-explanatory. *Velocity command before simulation box is defined* @@ -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. diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 55db356589..795af96e0a 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -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 diff --git a/doc/src/Howto_pylammps.rst b/doc/src/Howto_pylammps.rst index e1694e2062..96d9acd994 100644 --- a/doc/src/Howto_pylammps.rst +++ b/doc/src/Howto_pylammps.rst @@ -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 ` 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 `_. The ``lammps.py`` wrapper +is discussed on the :doc:`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 `_ into `Jupyter notebooks `_, +e.g. for embedded visualization output from :doc:`dump style 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 diff --git a/doc/src/Howto_viz.rst b/doc/src/Howto_viz.rst index 0ffdf08331..2eb009c185 100644 --- a/doc/src/Howto_viz.rst +++ b/doc/src/Howto_viz.rst @@ -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 `_ for details. Specifically, Pizza.py can convert -LAMMPS dump files into PDB, XYZ, `Ensight `_, and VTK formats. +LAMMPS dump files into PDB, XYZ, `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/ diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index f805c594c6..a9afb122ad 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -72,6 +72,7 @@ every LAMMPS command. angles dihedrals impropers + fix_modify_atc_commands Indices and tables ================== diff --git a/doc/src/Modify_overview.rst b/doc/src/Modify_overview.rst index 2deceae7db..3ec05c4ddd 100644 --- a/doc/src/Modify_overview.rst +++ b/doc/src/Modify_overview.rst @@ -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 diff --git a/doc/src/Python_shlib.rst b/doc/src/Python_shlib.rst index bd1d559359..0c86362e12 100644 --- a/doc/src/Python_shlib.rst +++ b/doc/src/Python_shlib.rst @@ -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 diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html deleted file mode 100644 index 4e7810aa61..0000000000 --- a/doc/src/USER/atc/man_add_molecule.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC add_molecule - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC add_molecule

-syntax

-

fix_modify_AtC add_molecule <small|large> <TAG> <GROUP_NAME>
-

-
    -
  • small|large = can be small if molecule size < cutoff radius, must be large otherwise
    -
    • -
  • <TAG> = tag for tracking a species
    -
    • -
  • <GROUP_NAME> = name of group that tracking will be applied to
    -
    • -
-

-examples

-

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

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html deleted file mode 100644 index a990ab626f..0000000000 --- a/doc/src/USER/atc/man_add_species.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC add_species - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC add_species

-syntax

-

fix_modify_AtC add_species <TAG> <group|type> <ID>
-

-
    -
  • <TAG> = tag for tracking a species
    -
    • -
  • group|type = LAMMPS defined group or type of atoms
    -
    • -
  • <ID> = name of group or type number
    -
    • -
-

-examples

-

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

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html deleted file mode 100644 index a5707d280e..0000000000 --- a/doc/src/USER/atc/man_atom_element_map.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC atom_element_map - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC atom_element_map

-syntax

-

fix_modify AtC atom_element_map <eulerian|lagrangian> <frequency>
-

-
    -
  • frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian
    • -
-

-examples

-

fix_modify atc atom_element_map eulerian 100

-

-description

-

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.

-

-restrictions

-

Cannot change map type after initialization.

-

-related

-

-default

-

lagrangian

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html deleted file mode 100644 index 350ab13b92..0000000000 --- a/doc/src/USER/atc/man_atom_weight.html +++ /dev/null @@ -1,59 +0,0 @@ - - - - -ATC: fix_modify AtC atom_weight - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC atom_weight

-syntax

-

fix_modify AtC atom_weight <method> <arguments>

-
    -
  • <method> =
    - value: atoms in specified group assigned 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
    - read_in: list of values for atoms are read-in from specified file
    -
    • -
-

-examples

-

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

-

Use of lattice option requires a lattice type and parameter is already specified.

-

-related

-

-default

-

lattice

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html deleted file mode 100644 index 17e854a37f..0000000000 --- a/doc/src/USER/atc/man_atomic_charge.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC atomic_charge - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC atomic_charge

-syntax

-

fix_modify AtC <include | omit> atomic_charge

-
    -
  • <include | omit> = switch to activiate/deactiviate inclusion of intrinsic atomic charge in ATC
    • -
-

-examples

-

fix_modify atc compute include atomic_charge

-

-description

-

Determines whether AtC tracks the total charge as a finite element field

-

-restrictions

-

Required for: electrostatics

-

-related

-

-default

-

if the atom charge is defined, default is on, otherwise default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html deleted file mode 100644 index c4448bc191..0000000000 --- a/doc/src/USER/atc/man_boundary.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC boundary - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC boundary

-syntax

-

fix_modify AtC boundary type <atom-type-id>

-
    -
  • <atom-type-id> = type id for atoms that represent a fictitious boundary internal to the FE mesh
    • -
-

-examples

-

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

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html deleted file mode 100644 index 335ff2d209..0000000000 --- a/doc/src/USER/atc/man_boundary_dynamics.html +++ /dev/null @@ -1,44 +0,0 @@ - - - - -ATC: fix_modify AtC boundary_dynamics - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC boundary_dynamics

-syntax

-

fix_modify AtC boundary_dynamics < on | damped_harmonic | prescribed | coupled | none > [args]
-

-

-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

-

-default

-

prescribed on

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html deleted file mode 100644 index 6c2fb84940..0000000000 --- a/doc/src/USER/atc/man_boundary_faceset.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC boundary_faceset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC boundary_faceset

-syntax

-

fix_modify AtC boundary_faceset <is | add> [args]

-

-examples

-

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

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html deleted file mode 100644 index c4b0d4865e..0000000000 --- a/doc/src/USER/atc/man_boundary_integral.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC output boundary_integral - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output boundary_integral

-syntax

-

fix_modify AtC output boundary_integral [field] faceset [name]

-
    -
  • field (string) : name of hardy field
    • -
  • name (string) : name of faceset
    • -
-

-examples

-

fix_modify AtC output boundary_integral stress faceset loop1
-

-

-description

-

Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html deleted file mode 100644 index baa306a1c8..0000000000 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC consistent_fe_initialization - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC consistent_fe_initialization

-syntax

-

fix_modify AtC consistent_fe_initialization <on | off>

-
    -
  • <on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field
    • -
-

-examples

-

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

-

-default

-

Default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html deleted file mode 100644 index 16f6d9abad..0000000000 --- a/doc/src/USER/atc/man_contour_integral.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC output contour_integral - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output contour_integral

-syntax

-

fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]>

-
    -
  • field (string) : name of hardy field
    • -
  • name (string) : name of faceset
    • -
  • axis (string) : x or y or z
    • -
-

-examples

-

fix_modify AtC output contour_integral stress faceset loop1
-

-

-description

-

Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html deleted file mode 100644 index e94a9a52ef..0000000000 --- a/doc/src/USER/atc/man_control.html +++ /dev/null @@ -1,70 +0,0 @@ - - - - -ATC: fix_modify AtC control - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control

-syntax

-

fix_modify AtC control <physics_type> <solution_parameter>

-


-

-
    -
  • physics_type (string) = thermal | momentum
    -
    • -
  • solution_parameter (string) = max_iterations | tolerance
    -
    • -
-

fix_modify AtC transfer <physics_type> control max_iterations <max_iterations>
-

-
    -
  • max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers
    -
    • -
-

fix_modify AtC transfer <physics_type> control tolerance <tolerance>
-

-
    -
  • tolerance (float) = relative tolerance to which matrix equations will be solved
    -
    • -
-

-examples

-

fix_modify AtC control thermal max_iterations 10
- fix_modify AtC control momentum tolerance 1.e-5
-

-

-description

-

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.

-

-restrictions

-

only for be used with specific controllers : thermal, momentum
- They are ignored if a lumped solution is requested

-

-related

-

-default

-

max_iterations is the number of rows in the matrix
- tolerance is 1.e-10

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html deleted file mode 100644 index e3074eae8f..0000000000 --- a/doc/src/USER/atc/man_control_momentum.html +++ /dev/null @@ -1,66 +0,0 @@ - - - - -ATC: fix_modify AtC control momentum - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control momentum

-syntax

-

fix_modify AtC control momentum none
-

-

fix_modify AtC control momentum rescale <frequency>
-

-
    -
  • frequency (int) = time step frequency for applying displacement and velocity rescaling
    -
    • -
-

fix_modify AtC control momentum glc_displacement
-

-

fix_modify AtC control momentum glc_velocity
-

-

fix_modify AtC control momentum hoover
-

-

fix_modify AtC control momentum flux [faceset face_set_id, interpolate]

-
    -
  • 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
    -
    • -
-

-examples

-

fix_modify AtC control momentum glc_velocity
- fix_modify AtC control momentum flux faceset bndy_faces
-

-

-description

-

-restrictions

-

only to be used with specific transfers : elastic
- rescale not valid with time filtering activated

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html deleted file mode 100644 index 8d32f1c4f9..0000000000 --- a/doc/src/USER/atc/man_control_thermal.html +++ /dev/null @@ -1,74 +0,0 @@ - - - - -ATC: fix_modify AtC control thermal - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control thermal

-syntax

-

fix_modify AtC control thermal <control_type> <optional_args>

-
    -
  • control_type (string) = none | rescale | hoover | flux
    -
    • -
-

fix_modify AtC control thermal rescale <frequency>
-

-
    -
  • frequency (int) = time step frequency for applying velocity rescaling
    -
    • -
-

fix_modify AtC control thermal hoover
-

-

fix_modify AtC control thermal flux <boundary_integration_type(optional)> <face_set_id(optional)>
-

-
    -
  • boundary_integration_type (string) = faceset | interpolate
    -
    • -
  • 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
    -
    • -
-

-examples

-

fix_modify AtC control thermal none
- fix_modify AtC control thermal rescale 10
- fix_modify AtC control thermal hoover
- fix_modify AtC control thermal flux
- fix_modify AtC control thermal flux faceset bndy_faces
-

-

-description

-

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.

-

-restrictions

-

only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux)
- rescale not valid with time filtering activated

-

-related

-

-default

-

none
- rescale frequency is 1
- flux boundary_integration_type is interpolate

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html deleted file mode 100644 index d28ec334f5..0000000000 --- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC control thermal correction_max_iterations - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control thermal correction_max_iterations

-syntax

-

fix_modify AtC control thermal correction_max_iterations <max_iterations>

-
    -
  • max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers
    -
    • -
-

-examples

-

fix_modify AtC control thermal correction_max_iterations 10
-

-

-description

-

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.

-

-restrictions

-

only for use with thermal physics using the fractional step method.

-

-related

-

-default

-

correction_max_iterations is 20

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html deleted file mode 100644 index 98eedafa6c..0000000000 --- a/doc/src/USER/atc/man_decomposition.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC decomposition - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC decomposition

-syntax

-

fix_modify AtC decomposition <type>

-
    -
  • <type> =
    - replicated_memory: nodal information replicated on each processor
    - distributed_memory: only owned nodal information on processor
    -
    • -
-

-examples

-

fix_modify atc decomposition distributed_memory
-

-

-description

-

Command for assigning the distribution of work and memory for parallel runs.

-

-restrictions

-

replicated_memory is appropriate for simulations were the number of nodes << number of atoms

-

-related

-

-default

-

replicated_memory

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html deleted file mode 100644 index 7cf40f6813..0000000000 --- a/doc/src/USER/atc/man_electron_integration.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC extrinsic electron_integration - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC extrinsic electron_integration

-syntax

-

fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)>
-

-
    -
  • integration_type (string) = explicit | implicit | steady
    -
    • -
  • num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration
    • -
-

-examples

-

fix_modify AtC extrinsic electron_integration implicit
- fix_modify AtC extrinsic electron_integration explicit 100
-

-

-description

-

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.

-

-restrictions

-

For use only with two_temperature type of AtC fix ( see fix atc command )
-

-

-default

-

implicit
- subcycle_steps = 1

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html deleted file mode 100644 index 8c81ce5925..0000000000 --- a/doc/src/USER/atc/man_equilibrium_start.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC equilibrium_start - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC equilibrium_start

-syntax

-

fix_modify AtC equilibrium_start <on|off>

-

-examples

-

fix_modify atc equilibrium_start on
-

-

-description

-

Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.

-

-restrictions

-

only needed before filtering is begun

-

-related

-

see fix_modify AtC filter

-

-default

-

on

-
-
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- - diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html deleted file mode 100644 index f4d1b01e88..0000000000 --- a/doc/src/USER/atc/man_extrinsic_exchange.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC extrinsic exchange - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC extrinsic exchange

-syntax

-

fix_modify AtC extrinsic exchange <on|off>

-

-examples

-

fix_modify AtC extrinsic exchange on
-

-

-description

-

Switches energy exchange between the MD system and electron system on and off

-

-restrictions

-

Only valid for use with two_temperature type of AtC fix.

-

-related

-

see fix atc command

-

-default

-

on

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html deleted file mode 100644 index e39ddd3cec..0000000000 --- a/doc/src/USER/atc/man_fe_md_boundary.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC fe_md_boundary - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fe_md_boundary

-syntax

-

fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args]

-

-examples

-

fix_modify atc fe_md_boundary interpolate
-

-

-description

-

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.

-

-restrictions

-

If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.

-

-related

-

see for how to specify the faceset name.

-

-default

-

Interpolate.

-
-
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- - diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html deleted file mode 100644 index 485b8c95a0..0000000000 --- a/doc/src/USER/atc/man_fem_mesh.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC fem create mesh - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- -

fix_modify AtC fem create mesh

-syntax

-fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
    -
  • nx ny nz = number of elements in x, y, z
  • region-id = id of region that is to be meshed
  • f p p = perioidicity flags for x, y, z
-

-examples

-

fix_modify AtC fem create mesh 10 1 1 feRegion p p p
-

-

-description

-

Creates a uniform mesh in a rectangular region

-

-restrictions

-

creates only uniform rectangular grids in a rectangular region

-

-related

-

-default

-none -
Generated on Mon Aug 17 09:35:16 2009 for ATC by  - -doxygen 1.3.9.1
- - diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html deleted file mode 100644 index e2190dea21..0000000000 --- a/doc/src/USER/atc/man_filter_scale.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC filter scale - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC filter scale

-syntax

-

fix_modify AtC filter scale <scale>
-

-
    -
  • scale (real) = characteristic time scale of the filter
    -
    • -
-

-examples

-

fix_modify AtC filter scale 10.0
-

-

-description

-

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

-

-restrictions

-

only for be used with specific transfers: thermal, two_temperature

-

-related

-

fix_modify AtC filter fix_modify AtC filter type

-

-default

-

0.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html deleted file mode 100644 index 0928139d7d..0000000000 --- a/doc/src/USER/atc/man_filter_type.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC filter type - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC filter type

-syntax

-

fix_modify AtC filter type <exponential | step | no_filter>
-

-

-examples

-

fix_modify AtC filter type exponential
-

-

-description

-

Specifies the type of time filter used.

-

-restrictions

-

only for be used with specific transfers: thermal, two_temperature

-

-related

-

fix_modify AtC filter fix_modify AtC filter scale

-

-default

-

No default.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html deleted file mode 100644 index 7c5afd645a..0000000000 --- a/doc/src/USER/atc/man_fix_atc.html +++ /dev/null @@ -1,252 +0,0 @@ - - - - -ATC: fix atc command - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix atc command

-syntax

-

fix <fixID> <group> atc <type> <parameter_file>

-
    -
  • fixID = name of fix
    • -
  • group = name of group fix is to be applied
    • -
  • type
    - = thermal : thermal coupling with fields: temperature
    - = two_temperature : electron-phonon coupling with field: temperature and electron_temperature
    - = hardy : on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
    - = field : on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
    -
    • -
  • parameter_file = name of the file with material parameters.
    - note: Neither hardy nor field requires a parameter file
    • -
-

-examples

-

fix AtC internal atc thermal Ar_thermal.dat
- fix AtC internal atc two_temperature Ar_ttm.mat
- fix AtC internal atc hardy
- fix AtC internal atc field
-

-

-description

-

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.

-

The following coupling example is typical, but non-exhaustive:
-

-

# ... commands to create and initialize the MD system
-

-

# initial fix to designate coupling type and group to apply it to
- # tag group physics material_file
- fix AtC internal atc thermal Ar_thermal.mat
-
- # create a uniform 12 x 2 x 2 mesh that covers region contain the group
- # nx ny nz region periodicity
- fix_modify AtC mesh create 12 2 2 mdRegion f p p
-
- # specify the control method for the type of coupling
- # physics control_type
- fix_modify AtC thermal control flux
-
- # specify the initial values for the empirical field "temperature"
- # field node_group value
- fix_modify AtC initial temperature all 30.
-
- # create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output atc_fe_output 100
-
-

-

run 1000
-

-

likewise for this post-processing example:
-

-

# ... commands to create and initialize the MD system
-

-

# initial fix to designate post-processing and the group to apply it to
- # no material file is allowed nor required
- fix AtC internal atc hardy
-
- # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
- fix AtC kernel quartic_sphere 10.0
-
- # create a uniform 1 x 1 x 1 mesh that covers region contain the group
- # with periodicity this effectively creates a system average
- fix_modify AtC mesh create 1 1 1 box p p p
-
- # change from default lagrangian map to eulerian
- # refreshed every 100 steps
- fix_modify AtC atom_element_map eulerian 100
-
- # start with no field defined
- # add mass density, potential energy density, stress and temperature
- fix_modify AtC fields add density energy stress temperature
-
- # create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output nvtFE 100 text
-

-

run 1000
-

-

the mesh's linear interpolation functions can be used as the localization function
- by using the field option:
-

-

fix AtC internal atc field
-
- fix_modify AtC mesh create 1 1 1 box p p p
-
- ...
-
-

-

Note coupling and post-processing can be combined in the same simulations using separate fixes.
- For detailed exposition of the theory and algorithms please see:
-

-
    -
  • Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, An atomistic-to-continuum coupling method for heat transfer in solids. Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
    -
    • -
  • Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, Calculation of stress in atomistic simulation. Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
    -
    • -
  • Zimmerman, JA; Jones, RE; Templeton, JA, A material frame approach for evaluating continuum variables in atomistic simulations. Journal of Computational Physics (2010), 229:2364.
    -
    • -
  • Templeton, JA; Jones, RE; Wagner, GJ, Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
    -
    • -
  • Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, Electron transport enhanced molecular dynamics for metals and semi-metals. International Journal for Numerical Methods in Engineering (2010), 83:940.
    -
    • -
  • Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. Journal of Chemical Theory and Computation (2011), 7:1736.
    -
    • -
  • Mandadapu, KK; Templeton, JA; Lee, JW, Polarization as a field variable from molecular dynamics simulations. Journal of Chemical Physics (2013), 139:054115.
    -
    • -
-

Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element method , Dover 2003, for the basics of FE simulation.

-

-restrictions

-

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.

-

Currently,

-
    -
  • the coupling is restricted to thermal physics
    • -
  • the FE computations are done in serial on each processor.
    • -
-

-related

-

fix_modify commands for setup:
-

- -

fix_modify commands for boundary and initial conditions:
-

- -

fix_modify commands for control and filtering:
-

- -

fix_modify commands for output:
-

- -

fix_modify commands for post-processing:
-

- -

miscellaneous fix_modify commands:
-

- -

Note: a set of example input files with the attendant material files are included with this package

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html deleted file mode 100644 index 31bd5619a3..0000000000 --- a/doc/src/USER/atc/man_fix_flux.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC fix_flux - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fix_flux

-syntax

-

fix_modify AtC fix_flux <field> <face_set> <value | function>

-
    -
  • <field> = field name valid for type of physics, temperature | electron_temperature
    • -
  • <face_set> = name of set of element faces
    • -
-

-examples

-

fix_modify atc fix_flux temperature faceSet 10.0
-

-

-description

-

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.

-

-restrictions

-

Only normal fluxes (Neumann data) can be prescribed.

-

-related

-

see fix_modify AtC unfix_flux

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html deleted file mode 100644 index 2245e32607..0000000000 --- a/doc/src/USER/atc/man_fix_nodes.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC fix - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fix

-syntax

-

fix_modify AtC fix <field> <nodeset> <constant | function>

-
    -
  • <field> = field name valid for type of physics
    • -
  • <nodeset> = name of set of nodes to apply boundary condition
    • -
  • <constant | function> = value or name of function followed by its parameters
    • -
-

-examples

-

fix_modify AtC fix temperature groupNAME 10.
- fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0
-

-

-description

-

Creates a constraint on the values of the specified field at specified nodes.

-

-restrictions

-

keyword 'all' reserved in nodeset name

-

-related

-

see fix_modify AtC unfix

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html deleted file mode 100644 index ec2dc3ccb9..0000000000 --- a/doc/src/USER/atc/man_hardy_computes.html +++ /dev/null @@ -1,65 +0,0 @@ - - - - -ATC: fix_modify AtC computes - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC computes

-syntax

-

fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number>
-

-
    -
  • 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
    -
    • -
  • per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS
    -
    • -
  • volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions
    -
    • -
-

-examples

-

compute virial all stress/atom
- fix_modify AtC computes add virial volume
- fix_modify AtC computes delete virial
-
- compute centrosymmetry all centro/atom
- fix_modify AtC computes add centrosymmetry number
-

-

-description

-

Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS
-

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )
- Per-atom compute must be specified before corresponding continuum field can be requested
-

-

-related

-

See manual page for compute

-

-default

-

No defaults exist for this command

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html deleted file mode 100644 index 483e5be6bd..0000000000 --- a/doc/src/USER/atc/man_hardy_fields.html +++ /dev/null @@ -1,81 +0,0 @@ - - - - -ATC: fix_modify AtC fields - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC fields

-syntax

-

fix_modify AtC fields <all | none>
- fix_modify AtC fields <add | delete> <list_of_fields>
-

-
    -
  • all | none (keyword) = output all or no fields
    -
    • -
  • add | delete (keyword) = add or delete the listed output fields
    -
    • -
  • fields (keyword) =
    - density : mass per unit volume
    - displacement : displacement vector
    - momentum : momentum per unit volume
    - velocity : defined by momentum divided by density
    - projected_velocity : simple kernel estimation of atomic velocities
    - temperature : temperature derived from the relative atomic kinetic energy (as done by )
    - kinetic_temperature : temperature derived from the full kinetic energy
    - number_density : simple kernel estimation of number of atoms per unit volume
    - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis
    - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis
    - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian
    - potential_energy : potential energy per unit volume
    - kinetic_energy : kinetic energy per unit volume
    - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume
    - internal_energy : total internal energy (potential + thermal) per unit volume
    - energy : total energy (potential + kinetic) per unit volume
    - number_density : number of atoms per unit volume
    - 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]
    - vacancy_concentration: volume fraction of vacancy content
    - type_concentration: volume fraction of a specific atom type
    -
    • -
-

-examples

-

fix_modify AtC fields add velocity temperature

-

-description

-

Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.
- fix_modify AtC fields none
- followed by
- fix_modify AtC fields add velocity temperature
- will only output the velocity and temperature fields.

-

-restrictions

-

Must be used with the hardy/field type of AtC fix, see fix atc command. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber.

-

-related

-

See fix_modify AtC gradients , fix_modify AtC rates and fix_modify AtC computes

-

-default

-

By default, no fields are output

-
-
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- - diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html deleted file mode 100644 index 1ecfade0ea..0000000000 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC gradients - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC gradients

-syntax

-

fix_modify AtC gradients <add | delete> <list_of_fields>
-

-
    -
  • add | delete (keyword) = add or delete the calculation of gradients for the listed output fields
    -
    • -
  • fields (keyword) =
    - gradients can be calculated for all fields listed in fix_modify AtC fields
    • -
-

-examples

-

fix_modify AtC gradients add temperature velocity stress
- fix_modify AtC gradients delete velocity
-

-

-description

-

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 fix_modify AtC atom_element_map )

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

No gradients are calculated by default

-
-
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- - diff --git a/doc/src/USER/atc/man_hardy_kernel.html b/doc/src/USER/atc/man_hardy_kernel.html deleted file mode 100644 index 620b9b1d36..0000000000 --- a/doc/src/USER/atc/man_hardy_kernel.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - -ATC: fix_modify AtC kernel - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC kernel

-syntax

-

fix_modify AtC kernel <type> <parameters>

-
    -
  • type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
    -
    • -
  • parameters :
    - step = radius (double)
    - cell = hx, hy, hz (double) or h (double)
    - cubic_bar = half-width (double)
    - cubic_cylinder = radius (double)
    - cubic_sphere = radius (double)
    - quartic_bar = half-width (double)
    - quartic_cylinder = radius (double)
    - quartic_sphere = radius (double)
    -
    • -
-

-examples

-

fix_modify AtC kernel cell 1.0 1.0 1.0
- fix_modify AtC kernel quartic_sphere 10.0

-

-description

-

-restrictions

-

Must be used with the hardy AtC fix
- For bar kernel types, half-width oriented along x-direction
- For cylinder kernel types, cylindrical axis is assumed to be in z-direction
- ( see fix atc command )

-

-related

-

-default

-

No default

-
-
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- - diff --git a/doc/src/USER/atc/man_hardy_on_the_fly.html b/doc/src/USER/atc/man_hardy_on_the_fly.html deleted file mode 100644 index 04d24ff029..0000000000 --- a/doc/src/USER/atc/man_hardy_on_the_fly.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - -ATC: fix_modify AtC on_the_fly - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC on_the_fly

-syntax

-

fix_modify AtC on_the_fly <bond | kernel> <optional on | off>
- - bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements
-

-
    -
  • on | off (keyword) = activate or discontinue on-the-fly mode
    -
    • -
-

-examples

-

fix_modify AtC on_the_fly bond on
- fix_modify AtC on_the_fly kernel
- fix_modify AtC on_the_fly kernel off
-

-

-description

-

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.
- on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag.
-

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

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.
-

-
-
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- - diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html deleted file mode 100644 index 8066543485..0000000000 --- a/doc/src/USER/atc/man_hardy_rates.html +++ /dev/null @@ -1,56 +0,0 @@ - - - - -ATC: fix_modify AtC rates - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC rates

-syntax

-

fix_modify AtC rates <add | delete> <list_of_fields>
-

-
    -
  • add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields
    -
    • -
  • fields (keyword) =
    - rates can be calculated for all fields listed in fix_modify AtC fields
    • -
-

-examples

-

fix_modify AtC rates add temperature velocity stress
- fix_modify AtC rates delete stress
-

-

-description

-

Requests calculation and output of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.
-

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

No rates are calculated by default

-
-
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- - diff --git a/doc/src/USER/atc/man_initial.html b/doc/src/USER/atc/man_initial.html deleted file mode 100644 index c8348c45ed..0000000000 --- a/doc/src/USER/atc/man_initial.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC initial - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC initial

-syntax

-

fix_modify AtC initial <field> <nodeset> <constant | function>

-
    -
  • <field> = field name valid for type of physics, temperature | electron_temperature
    • -
  • <nodeset> = name of set of nodes to apply initial condition
    • -
  • <constant | function> = value or name of function followed by its parameters
    • -
-

-examples

-

fix_modify atc initial temperature groupNAME 10.

-

-description

-

Sets the initial values for the specified field at the specified nodes.

-

-restrictions

-

keyword 'all' reserved in nodeset name

-

-default

-

none

-
-
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- - diff --git a/doc/src/USER/atc/man_internal_atom_integrate.html b/doc/src/USER/atc/man_internal_atom_integrate.html deleted file mode 100644 index f76607cc91..0000000000 --- a/doc/src/USER/atc/man_internal_atom_integrate.html +++ /dev/null @@ -1,38 +0,0 @@ - - - - -ATC: fix_modify AtC internal_atom_integrate - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC internal_atom_integrate

-syntax

-

fix_modify AtC internal_atom_integrate <on | off> fix_modify AtC internal_atom_integrate on

-

-description

-

Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms.

-

-default

-

on for coupling methods, off for post-processors off

-
-
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- - diff --git a/doc/src/USER/atc/man_internal_element_set.html b/doc/src/USER/atc/man_internal_element_set.html deleted file mode 100644 index a5d893f2a3..0000000000 --- a/doc/src/USER/atc/man_internal_element_set.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC internal_element_set - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC internal_element_set

-syntax

-

fix_modify AtC internal_element_set <element-set-name>

-
    -
  • <element-set-name> = name of element set defining internal region, or off
    • -
-

-examples

-

fix_modify AtC internal_element_set myElementSet fix_modify AtC internal_element_set off

-

-description

-

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.

-

-restrictions

-

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

-

-related

-

see atom_element_map_type and boundary

-

-default

-

off

-
-
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- - diff --git a/doc/src/USER/atc/man_internal_quadrature.html b/doc/src/USER/atc/man_internal_quadrature.html deleted file mode 100644 index 6af543cbae..0000000000 --- a/doc/src/USER/atc/man_internal_quadrature.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC internal_quadrature - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC internal_quadrature

-syntax

-

fix_modify atc internal_quadrature <on | off> [region]

-

-examples

-

fix_modify atc internal_quadrature off

-

-description

-

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.

-

-optional

-

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.

-

-restrictions

-

-related

-

-default

-

on

-
-
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- - diff --git a/doc/src/USER/atc/man_kernel_function.html b/doc/src/USER/atc/man_kernel_function.html deleted file mode 100644 index cb02c05c23..0000000000 --- a/doc/src/USER/atc/man_kernel_function.html +++ /dev/null @@ -1,62 +0,0 @@ - - - - -ATC: fix_modify AtC kernel - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC kernel

-syntax

-

fix_modify AtC kernel <type> <parameters>

-
    -
  • type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere
    -
    • -
  • parameters :
    - step = radius (double)
    - cell = hx, hy, hz (double) or h (double)
    - cubic_bar = half-width (double)
    - cubic_cylinder = radius (double)
    - cubic_sphere = radius (double)
    - quartic_bar = half-width (double)
    - quartic_cylinder = radius (double)
    - quartic_sphere = radius (double)
    -
    • -
-

-examples

-

fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0

-

-description

-

-restrictions

-

Must be used with the hardy AtC fix
- For bar kernel types, half-width oriented along x-direction
- For cylinder kernel types, cylindrical axis is assumed to be in z-direction
- ( see fix atc command )

-

-related

-

-default

-

No default

-
-
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- - diff --git a/doc/src/USER/atc/man_localized_lambda.html b/doc/src/USER/atc/man_localized_lambda.html deleted file mode 100644 index 88442d63a1..0000000000 --- a/doc/src/USER/atc/man_localized_lambda.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC control localized_lambda - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control localized_lambda

-syntax

-

fix_modify AtC control localized_lambda <on|off>

-

-examples

-

fix_modify atc control localized_lambda on
-

-

-description

-

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.

-

-restrictions

-

-related

-

-default

-

Default is off.

-
-
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- - diff --git a/doc/src/USER/atc/man_lumped_lambda_solve.html b/doc/src/USER/atc/man_lumped_lambda_solve.html deleted file mode 100644 index 89aabebd3c..0000000000 --- a/doc/src/USER/atc/man_lumped_lambda_solve.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC control lumped_lambda_solve - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control lumped_lambda_solve

-syntax

-

fix_modify AtC control lumped_lambda_solve <on|off>

-

-examples

-

fix_modify atc control lumped_lambda_solve on
-

-

-description

-

Command to use or not use lumped matrix for lambda solve

-

-restrictions

-

-related

-

-default

-
-
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- - diff --git a/doc/src/USER/atc/man_mask_direction.html b/doc/src/USER/atc/man_mask_direction.html deleted file mode 100644 index ea5a6e357b..0000000000 --- a/doc/src/USER/atc/man_mask_direction.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC control mask_direction - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC control mask_direction

-syntax

-

fix_modify AtC control mask_direction <direction> <on|off>

-

-examples

-

fix_modify atc control mask_direction 0 on
-

-

-description

-

Command to mask out certain dimensions from the atomic regulator

-

-restrictions

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mass_matrix.html b/doc/src/USER/atc/man_mass_matrix.html deleted file mode 100644 index fd744e5bbf..0000000000 --- a/doc/src/USER/atc/man_mass_matrix.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mass_matrix - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mass_matrix

-syntax

-

fix_modify AtC mass_matrix <fe | md_fe>

-
    -
  • <fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region
    • -
-

-examples

-

fix_modify atc mass_matrix fe

-

-description

-

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.

-

-restrictions

-

Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate

-

-related

-

-default

-

Default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_material.html b/doc/src/USER/atc/man_material.html deleted file mode 100644 index 1646abc671..0000000000 --- a/doc/src/USER/atc/man_material.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC material - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC material

-syntax

-

fix_modify AtC material [elementset_name] [material_id]
-

-

-examples

-

fix_modify AtC material gap_region 2

-

-description

-

Sets the material model in elementset_name to be of type material_id.

-

-restrictions

-

The element set must already be created and the material must be specified in the material file given the the atc fix on construction

-

-related

-

-default

-

All elements default to the first material in the material file.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_add_to_nodeset.html b/doc/src/USER/atc/man_mesh_add_to_nodeset.html deleted file mode 100644 index c4976f699d..0000000000 --- a/doc/src/USER/atc/man_mesh_add_to_nodeset.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh add_to_nodeset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh add_to_nodeset

-syntax

-

fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

-
    -
  • <id> = id of FE nodeset to be added to
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added
    • -
-

-examples

-

fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12

-

-description

-

Command to add nodes to an already existing FE nodeset.

-

-restrictions

-

-related

-

-default

-

Coordinates are assumed to be in lattice units.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create.html b/doc/src/USER/atc/man_mesh_create.html deleted file mode 100644 index 98989bd015..0000000000 --- a/doc/src/USER/atc/man_mesh_create.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create

-syntax

-

fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
-

-
    -
  • nx ny nz = number of elements in x, y, z
    • -
  • region-id = id of region that is to be meshed
    • -
  • f p p = periodicity flags for x, y, z
    • -
-

-examples

-

fix_modify AtC mesh create 10 1 1 feRegion p p p
-

-

-description

-

Creates a uniform mesh in a rectangular region

-

-restrictions

-

Creates only uniform rectangular grids in a rectangular region

-

-related

-

fix_modify AtC mesh quadrature

-

-default

-

When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_elementset.html b/doc/src/USER/atc/man_mesh_create_elementset.html deleted file mode 100644 index 735d462b73..0000000000 --- a/doc/src/USER/atc/man_mesh_create_elementset.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_elementset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_elementset

-syntax

-

fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

-
    -
  • <id> = id to assign to the collection of FE element
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements
    • -
-

-examples

-

fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100

-

-description

-

Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations.

-

-restrictions

-

Only viable for rectangular grids.

-

-related

-

-default

-

Coordinates are assumed to be in lattice units.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_faceset_box.html b/doc/src/USER/atc/man_mesh_create_faceset_box.html deleted file mode 100644 index 0ae68435e5..0000000000 --- a/doc/src/USER/atc/man_mesh_create_faceset_box.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_faceset box - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_faceset box

-syntax

-

fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]

-
    -
  • <id> = id to assign to the collection of FE faces
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces
    • -
  • <in|out> = "in" gives inner faces to the box, "out" gives the outer faces to the box
    • -
  • units = option to specify real as opposed to lattice units
    • -
-

-examples

-

fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out

-

-description

-

Command to assign an id to a set of FE faces.

-

-restrictions

-

Only viable for rectangular grids.

-

-related

-

-default

-

The default options are units = lattice and the use of outer faces

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_faceset_plane.html b/doc/src/USER/atc/man_mesh_create_faceset_plane.html deleted file mode 100644 index cd78816bae..0000000000 --- a/doc/src/USER/atc/man_mesh_create_faceset_plane.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_faceset plane - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_faceset plane

-syntax

-

fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]

-
    -
  • <id> = id to assign to the collection of FE faces
    • -
  • <x|y|z> = coordinate directions that define plane on which faceset lies
    • -
  • <val1>,<lval2>,<uval2> = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]
    • -
  • units = option to specify real as opposed to lattice units
    • -
-

-examples

-

fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0

-

-description

-

Command to assign an id to a set of FE faces.

-

-restrictions

-

Only viable for rectangular grids.

-

-related

-

-default

-

The default option is units = lattice.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_create_nodeset.html b/doc/src/USER/atc/man_mesh_create_nodeset.html deleted file mode 100644 index 0e3624cf8a..0000000000 --- a/doc/src/USER/atc/man_mesh_create_nodeset.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh create_nodeset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh create_nodeset

-syntax

-

fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

-
    -
  • <id> = id to assign to the collection of FE nodes
    • -
  • <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes
    • -
-

-examples

-

fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12

-

-description

-

Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions.

-

-restrictions

-

-related

-

-default

-

Coordinates are assumed to be in lattice units.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_delete_elements.html b/doc/src/USER/atc/man_mesh_delete_elements.html deleted file mode 100644 index e39cc54d41..0000000000 --- a/doc/src/USER/atc/man_mesh_delete_elements.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC mesh delete_elements - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh delete_elements

-syntax

-

fix_modify AtC mesh delete_elements <element_set>

-
    -
  • <element_set> = name of an element set
    • -
-

-examples

-

fix_modify AtC delete_elements gap

-

-description

-

Deletes a group of elements from the mesh.

-

-restrictions

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html deleted file mode 100644 index 66b55a48fb..0000000000 --- a/doc/src/USER/atc/man_mesh_nodeset_to_elementset.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC mesh nodeset_to_elementset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh nodeset_to_elementset

-syntax

-

fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>

-
    -
  • <nodeset_id> = id of desired nodeset from which to create elementset
    • -
  • <elementset_id> = id to assign to the collection of FE element
    • -
  • <max/min> = flag to choose either the maximal or minimal elementset
    • -
-

-examples

-

fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min

-

-description

-

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

-

-restrictions

-

None.

-

-related

-

-default

-

Unless specified, the maximal element set is created

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_output.html b/doc/src/USER/atc/man_mesh_output.html deleted file mode 100644 index 1d2983afff..0000000000 --- a/doc/src/USER/atc/man_mesh_output.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC mesh output - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh output

-syntax

-

fix_modify AtC mesh output <file_prefix>

-

-examples

-

fix_modify AtC mesh output meshData
-

-

-description

-

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.

-

-restrictions

-

none

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_quadrature.html b/doc/src/USER/atc/man_mesh_quadrature.html deleted file mode 100644 index 821e50e4cf..0000000000 --- a/doc/src/USER/atc/man_mesh_quadrature.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC mesh quadrature - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh quadrature

-syntax

-

fix_modify AtC mesh quadrature <quad>

-
    -
  • 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
    • -
-

-examples

-

fix_modify AtC mesh quadrature face

-

-description

-

(Re-)assigns the quadrature style for the existing mesh.

-

-restrictions

-

-related

-

fix_modify AtC mesh create

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_read.html b/doc/src/USER/atc/man_mesh_read.html deleted file mode 100644 index 315180e1db..0000000000 --- a/doc/src/USER/atc/man_mesh_read.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC mesh read - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh read

-syntax

-

fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p>

-
    -
  • filename = name of file containing mesh to be read
    • -
  • f p p = periodicity flags for x, y, z
    • -
-

-examples

-

fix_modify AtC mesh read myComponent.mesh p p p
- fix_modify AtC mesh read myOtherComponent.exo

-

-description

-

Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed.

-

-restrictions

-

-related

-

-default

-

periodicity flags are false by default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_mesh_write.html b/doc/src/USER/atc/man_mesh_write.html deleted file mode 100644 index f709c02a84..0000000000 --- a/doc/src/USER/atc/man_mesh_write.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC mesh write - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC mesh write

-syntax

-

fix_modify AtC mesh write <filename>

-
    -
  • filename = name of file to write mesh
    • -
-

-examples

-

fix_modify AtC mesh write myMesh.mesh
-

-

-description

-

Writes a mesh to a text file.

-

-restrictions

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_momentum_time_integration.html b/doc/src/USER/atc/man_momentum_time_integration.html deleted file mode 100644 index ee0505847c..0000000000 --- a/doc/src/USER/atc/man_momentum_time_integration.html +++ /dev/null @@ -1,58 +0,0 @@ - - - - -ATC: fix_modify AtC time_integration (momentum) - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC time_integration (momentum)

-syntax

-

fix_modify AtC time_integration <descriptor>
-

-
    -
  • descriptor (string) = time integration type
    -
    • -
-

various time integration methods for the finite elements
-

-

-description

-

verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force
- 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
- gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power
-

-

-examples

-

fix_modify atc time_integration verlet
- fix_modify atc time_integration fractional_step
-

-

-description

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_output.html b/doc/src/USER/atc/man_output.html deleted file mode 100644 index d0a08fa0da..0000000000 --- a/doc/src/USER/atc/man_output.html +++ /dev/null @@ -1,61 +0,0 @@ - - - - -ATC: fix_modify AtC output - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output

-syntax

-

fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]

-
    -
  • filename_prefix (string) = prefix for data files
    • -
  • frequency (integer) = frequency of output in time-steps
    • -
  • options (keyword/s):
    - text = creates text output of index, step and nodal variable values for unique nodes
    - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes
    - binary = creates binary Ensight output
    - vector_components = outputs vectors as scalar components
    - tensor_components = outputs tensor as scalar components (use this for Paraview)
    -
    • -
-

-examples

-

fix_modify AtC output heatFE 100
- fix_modify AtC output hardyFE 1 text tensor_components
- fix_modify AtC output hardyFE 10 text binary tensor_components
- fix_modify AtC output index step
-

-

-description

-

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.

-

-restrictions

-

-related

-

see fix atc command

-

-default

-

no default format output indexed by time

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_output_elementset.html b/doc/src/USER/atc/man_output_elementset.html deleted file mode 100644 index 18afe0aa97..0000000000 --- a/doc/src/USER/atc/man_output_elementset.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC output elementset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output elementset

-syntax

-

fix_modify AtC output volume_integral <eset_name> <field> {`

-
    -
  • set_name (string) = name of elementset to be integrated over
    • -
  • fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset
    -
    • -
-

-examples

-

fix_modify AtC output eset1 mass_density
-

-

-description

-

Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file.

-

-restrictions

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_output_nodeset.html b/doc/src/USER/atc/man_output_nodeset.html deleted file mode 100644 index 7906c5fc52..0000000000 --- a/doc/src/USER/atc/man_output_nodeset.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - -ATC: fix_modify AtC output nodeset - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC output nodeset

-syntax

-

fix_modify AtC output nodeset <nodeset_name> <operation>

-
    -
  • nodeset_name (string) = name of nodeset to be operated on
    • -
  • operation (keyword/s):
    - sum = creates nodal sum over nodes in specified nodeset
    -
    • -
-

-examples

-

fix_modify AtC output nodeset nset1 sum
-

-

-description

-

Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file.

-

-restrictions

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_pair_interactions.html b/doc/src/USER/atc/man_pair_interactions.html deleted file mode 100644 index 3ec2eecc60..0000000000 --- a/doc/src/USER/atc/man_pair_interactions.html +++ /dev/null @@ -1,48 +0,0 @@ - - - - -ATC: fix_modify AtC pair_interactions/bond_interactions - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC pair_interactions/bond_interactions

-syntax

-

fix_modify AtC pair_interactions <on|off>
- fix_modify AtC bond_interactions <on|off>
-

-

-examples

-

fix_modify AtC bond_interactions on
-

-

-description

-

include bonds and/or pairs in the stress and heat flux computations

-

-restrictions

-

-related

-

-default

-

pair interactions: on, bond interactions: off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html deleted file mode 100644 index 3e22a51f3e..0000000000 --- a/doc/src/USER/atc/man_poisson_solver.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC poisson_solver - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC poisson_solver

-syntax

-

fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>

-
    -
  • nx ny nz = number of elements in x, y, z
    • -
  • region-id = id of region that is to be meshed
    • -
  • f p p = perioidicity flags for x, y, z
    • -
-

-examples

-

fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p

-

-description

-

Creates a uniform mesh in a rectangular region

-

-restrictions

-

creates only uniform rectangular grids in a rectangular region

-

-related

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html deleted file mode 100644 index d13151a12e..0000000000 --- a/doc/src/USER/atc/man_read_restart.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC read_restart - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC read_restart

-syntax

-

fix_modify AtC read_restart [file_name]
-

-

-examples

-

fix_modify AtC read_restart ATC_state
-

-

-description

-

Reads the current state of the fields from a named text-based restart file.

-

-restrictions

-

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.

-

-related

-

see write_restart fix_modify AtC write_restart

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html deleted file mode 100644 index 54e4e3419f..0000000000 --- a/doc/src/USER/atc/man_remove_molecule.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC remove_molecule - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC remove_molecule

-syntax

-

fix_modify_AtC remove_molecule <TAG>
-

-
    -
  • <TAG> = tag for tracking a molecule type
    -
    • -
-

-examples

-

fix_modify AtC remove_molecule water
-

-

-description

-

Removes tag designated for tracking a specified set of molecules.
-

-

-restrictions

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html deleted file mode 100644 index c15e0ca46d..0000000000 --- a/doc/src/USER/atc/man_remove_source.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC remove_source - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC remove_source

-syntax

-

fix_modify AtC remove_source <field> <element_set>

-
    -
  • <field> = field name valid for type of physics
    • -
  • <element_set> = name of set of elements
    • -
-

-examples

-

fix_modify atc remove_source temperature groupNAME

-

-description

-

Remove a domain source.

-

-restrictions

-

keyword 'all' reserved in element_set name

-

-related

-

see fix_modify AtC source

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html deleted file mode 100644 index ee063ce57f..0000000000 --- a/doc/src/USER/atc/man_remove_species.html +++ /dev/null @@ -1,52 +0,0 @@ - - - - -ATC: fix_modify AtC remove_species - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC remove_species

-syntax

-

fix_modify_AtC delete_species <TAG>
-

-
    -
  • <TAG> = tag for tracking a species
    -
    • -
-

-examples

-

fix_modify AtC remove_species gold
-

-

-description

-

Removes tag designated for tracking a specified species.
-

-

-restrictions

-

-related

-

-default

-

No defaults for this command.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html deleted file mode 100644 index 3c43861054..0000000000 --- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html +++ /dev/null @@ -1,47 +0,0 @@ - - - - -ATC: fix_modify AtC reset_atomic_reference_positions - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC reset_atomic_reference_positions

-syntax

-

fix_modify AtC reset_atomic_reference_positions

-

-examples

-

fix_modify atc reset_atomic_reference_positions

-

-description

-

Resets the atomic positions ATC uses to perform point to field operations. In can be used to use perfect lattice sites in ATC but a thermalized or deformed lattice in LAMMPS.

-

-restrictions

-

-

-related

-

-

-default

-

Default is off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html deleted file mode 100644 index 9607848e1a..0000000000 --- a/doc/src/USER/atc/man_reset_time.html +++ /dev/null @@ -1,63 +0,0 @@ - - - - -ATC: fix_modify AtC reset_time - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC reset_time

-syntax

-

fix_modify AtC reset_time

-

-examples

-

fix_modify atc reset_time 0.0
-

-

-description

-

Resets the simulation time counter.

-

-restrictions

-

-related

-

-default

-

-syntax

-

fix_modify AtC kernel_bandwidth

-

-examples

-

fix_modify atc reset_time 8
-

-

-description

-

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.

-

-restrictions

-

Only is used if kernel functions are being used.

-

-related

-

-default

-

Number of sample locations.

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html deleted file mode 100644 index 9a9a8e3a02..0000000000 --- a/doc/src/USER/atc/man_sample_frequency.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC sample_frequency - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC sample_frequency

-syntax

-

fix_modify AtC sample_frequency [freq]

-
    -
  • freq (int) : frequency to sample field in number of steps
    • -
-

-examples

-

fix_modify AtC sample_frequency 10

-

-description

-

Specifies a frequency at which fields are computed for the case where time filters are being applied.

-

-restrictions

-

Must be used with the hardy/field AtC fix ( see fix atc command ) and is only relevant when time filters are being used.

-

-related

-

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html deleted file mode 100644 index 55ad8d952b..0000000000 --- a/doc/src/USER/atc/man_set.html +++ /dev/null @@ -1,54 +0,0 @@ - - - - -ATC: fix_modify AtC set - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC set

-syntax

-

fix_modify AtC set reference_potential_energy <value_or_filename(optional)>

-
    -
  • value (double) : optional user specified zero point for PE in native LAMMPS energy units
    -
    • -
  • filename (string) : optional user specified string for file of nodal PE values to be read-in
    • -
-

-examples

-

fix_modify AtC set reference_potential_energy
- fix_modify AtC set reference_potential_energy -0.05
- fix_modify AtC set reference_potential_energy myPEvalues
-

-

-description

-

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.

-

-restrictions

-

Must be used with the hardy/field type of AtC fix ( see fix atc command )

-

-related

-

-default

-

Defaults to lammps zero point i.e. isolated atoms

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html deleted file mode 100644 index 78fb1652eb..0000000000 --- a/doc/src/USER/atc/man_source.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC source - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC source

-syntax

-

fix_modify AtC source <field> <element_set> <value | function>

-
    -
  • <field> = field name valid for type of physics
    • -
  • <element_set> = name of set of elements
    • -
-

-examples

-

fix_modify atc source temperature middle temporal_ramp 10. 0.

-

-description

-

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.

-

-restrictions

-

keyword 'all' reserved in element_set name

-

-related

-

see fix_modify AtC remove_source

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html deleted file mode 100644 index 3b261b7810..0000000000 --- a/doc/src/USER/atc/man_source_integration.html +++ /dev/null @@ -1,44 +0,0 @@ - - - - -ATC: fix_modify AtC source_integration - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC source_integration

-syntax

-

fix_modify AtC source_integration < fe | atom>

-

-examples

-

fix_modify atc source_integration atom

-

-description

-

-restrictions

-

-related

-

-default

-

Default is fe

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html deleted file mode 100644 index c317c06c00..0000000000 --- a/doc/src/USER/atc/man_temperature_definition.html +++ /dev/null @@ -1,45 +0,0 @@ - - - - -ATC: fix_modify AtC temperature_definition - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC temperature_definition

-syntax

-

fix_modify AtC temperature_definition <kinetic|total>

-

-examples

-

fix_modify atc temperature_definition kinetic
-

-

-description

-

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.

-

-restrictions

-

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.

-

-default

-

kinetic

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html deleted file mode 100644 index 830591921e..0000000000 --- a/doc/src/USER/atc/man_thermal_time_integration.html +++ /dev/null @@ -1,57 +0,0 @@ - - - - -ATC: fix_modify AtC time_integration (thermal) - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC time_integration (thermal)

-syntax

-

fix_modify AtC time_integration <descriptor>
-

-
    -
  • descriptor (string) = time integration type
    -
    • -
-

various time integration methods for the finite elements
-

-

-description

-

gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power
- 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
-

-

-examples

-

fix_modify atc time_integration gear
- fix_modify atc time_integration fractional_step
-

-

-description

-

-related

-

see fix atc command

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html deleted file mode 100644 index 5000fb079d..0000000000 --- a/doc/src/USER/atc/man_time_filter.html +++ /dev/null @@ -1,55 +0,0 @@ - - - - -ATC: fix_modify AtC filter - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC filter

-syntax

-

fix_modify AtC filter <on | off | equilibrate>
-

-
    -
  • on | off (keyword) = turns filter on or off
    -
    • -
  • equilibrate = runs dynamics without filtering but initializes filtered quantities
    • -
-

-examples

-

fix_modify atc transfer filter on
-

-

-description

-

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

-

-restrictions

-

only for be used with specific transfers: thermal, two_temperature

-

-related

-

fix_modify AtC filter scale
- fix_modify AtC equilibrium_start

-

-default

-

off

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html deleted file mode 100644 index 2c7cf26150..0000000000 --- a/doc/src/USER/atc/man_track_displacement.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - -ATC: fix_modify AtC track_displacement - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC track_displacement

-syntax

-

fix_modify AtC track_displacement <on/off>
-

-

-examples

-

fix_modify atc track_displacement on
-

-

-description

-

Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.

-

-restrictions

-

Some constitutive models require the displacement field

-

-default

-

on

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html deleted file mode 100644 index 551896431a..0000000000 --- a/doc/src/USER/atc/man_unfix_flux.html +++ /dev/null @@ -1,50 +0,0 @@ - - - - -ATC: fix_modify AtC unfix_flux - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC unfix_flux

-syntax

-

fix_modify AtC fix_flux <field> <face_set> <value | function>

-
    -
  • <field> = field name valid for type of physics, temperature | electron_temperature
    • -
  • <face_set> = name of set of element faces
    • -
-

-examples

-

fix_modify atc unfix_flux temperature faceSet
-

-

-description

-

Command for removing prescribed normal fluxes e.g. heat_flux, stress.

-

-restrictions

-

-related

-

see fix_modify AtC unfix_flux

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html deleted file mode 100644 index 4dfd9b3cfc..0000000000 --- a/doc/src/USER/atc/man_unfix_nodes.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC unfix - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC unfix

-syntax

-

fix_modify AtC unfix <field> <nodeset>

-
    -
  • <field> = field name valid for type of physics
    • -
  • <nodeset> = name of set of nodes
    • -
-

-examples

-

fix_modify AtC unfix temperature groupNAME

-

-description

-

Removes constraint on field values for specified nodes.

-

-restrictions

-

keyword 'all' reserved in nodeset name

-

-related

-

see fix_modify AtC fix

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html deleted file mode 100644 index 1722d74f67..0000000000 --- a/doc/src/USER/atc/man_write_atom_weights.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - -ATC: fix_modify AtC write_atom_weights - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC write_atom_weights

-syntax

-

fix_modify AtC write_atom_weights <filename> <frequency>

-
    -
  • <filename> = name of file that atomic weights are written to
    -
    • -
  • <frequency> = how often writes will occur
    -
    • -
-

-examples

-

fix_modify atc write_atom_weights atm_wt_file.txt 10
-

-

-description

-

Command for writing the values of atomic weights to a specified file.

-

-restrictions

-

-related

-

-default

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html deleted file mode 100644 index 74c6e2d289..0000000000 --- a/doc/src/USER/atc/man_write_restart.html +++ /dev/null @@ -1,49 +0,0 @@ - - - - -ATC: fix_modify AtC write_restart - - - - -
- LAMMPS Website     - LAMMPS Manual     - USER-AtC Manual     - Commands -
- -
- - - -
- - -

fix_modify AtC write_restart

-syntax

-

fix_modify AtC write_restart [file_name]
-

-

-examples

-

fix_modify AtC write_restart restart.mydata
-

-

-description

-

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.

-

-restrictions

-

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.

-

-related

-

see read_restart fix_modify AtC read_restart

-

-default

-

none

-
-
Generated on 21 Aug 2013 for ATC by  - -doxygen 1.6.1
- - diff --git a/doc/src/atc_add_molecule.rst b/doc/src/atc_add_molecule.rst new file mode 100644 index 0000000000..dc0f0318ac --- /dev/null +++ b/doc/src/atc_add_molecule.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC add_molecule + +fix_modify AtC add_molecule command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify add_molecule + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC add_species ` +- :doc:`fix_modify AtC remove_species ` +- :doc:`fix_modify AtC remove_molecule ` + +Default +""""""" + +None. diff --git a/doc/src/atc_add_species.rst b/doc/src/atc_add_species.rst new file mode 100644 index 0000000000..0b39379e62 --- /dev/null +++ b/doc/src/atc_add_species.rst @@ -0,0 +1,49 @@ +.. index:: fix_modify AtC add_species + +fix_modify AtC add_species command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify add_species + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC add_molecule ` +- :doc:`fix_modify AtC remove_species ` +- :doc:`fix_modify AtC remove_molecule ` + +Default +""""""" + +None. diff --git a/doc/src/atc_atom_element_map.rst b/doc/src/atc_atom_element_map.rst new file mode 100644 index 0000000000..96895acc8e --- /dev/null +++ b/doc/src/atc_atom_element_map.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC atom_element_map + +fix_modify AtC atom_element_map command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify atom_element_map [] + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*lagrangian* diff --git a/doc/src/atc_atom_weight.rst b/doc/src/atc_atom_weight.rst new file mode 100644 index 0000000000..50e7ea146d --- /dev/null +++ b/doc/src/atc_atom_weight.rst @@ -0,0 +1,56 @@ +.. index:: fix_modify AtC atom_weight + +fix_modify AtC atom_weight command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify atom_weight + +* AtC fixID = ID of :doc:`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* : 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*\ : 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 ` + +Default +""""""" + +*lattice* + diff --git a/doc/src/atc_atomic_charge.rst b/doc/src/atc_atomic_charge.rst new file mode 100644 index 0000000000..4b3d34b815 --- /dev/null +++ b/doc/src/atc_atomic_charge.rst @@ -0,0 +1,43 @@ +.. index:: fix_modify AtC atomic_charge + +fix_modify AtC atomic_charge command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify atomic_charge + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +If the atom charge is defined, default is on, otherwise default is off. diff --git a/doc/src/atc_boundary_dynamics.rst b/doc/src/atc_boundary_dynamics.rst new file mode 100644 index 0000000000..696d091094 --- /dev/null +++ b/doc/src/atc_boundary_dynamics.rst @@ -0,0 +1,43 @@ +.. index:: fix_modify AtC boundary_dynamics + +fix_modify AtC boundary_dynamics command +======================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify boundary_dynamics + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*prescribed on* diff --git a/doc/src/atc_boundary_faceset.rst b/doc/src/atc_boundary_faceset.rst new file mode 100644 index 0000000000..c33239b833 --- /dev/null +++ b/doc/src/atc_boundary_faceset.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC boundary_faceset + +fix_modify AtC boundary_faceset command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify boundary_faceset + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC fe_md_boundary ` +- :doc:`fix_modify AtC mesh create_faceset box ` +- :doc:`fix_modify AtC mesh create_faceset plane ` + +Default +""""""" + +None. diff --git a/doc/src/atc_boundary_type.rst b/doc/src/atc_boundary_type.rst new file mode 100644 index 0000000000..26b40e5a12 --- /dev/null +++ b/doc/src/atc_boundary_type.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC boundary type + +fix_modify AtC boundary type command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify boundary type + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +None. diff --git a/doc/src/atc_consistent_fe_initialization.rst b/doc/src/atc_consistent_fe_initialization.rst new file mode 100644 index 0000000000..3241752262 --- /dev/null +++ b/doc/src/atc_consistent_fe_initialization.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC consistent_fe_initialization + +fix_modify AtC consistent_fe_initialization command +=================================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify consistent_fe_initialization + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +Default is *off* diff --git a/doc/src/atc_control_localized_lambda.rst b/doc/src/atc_control_localized_lambda.rst new file mode 100644 index 0000000000..eb286756b7 --- /dev/null +++ b/doc/src/atc_control_localized_lambda.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC control localized_lambda + +fix_modify AtC control localized_lambda command +=============================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify control localized_lambda + +* AtC fixID = ID of :doc:`fix atc ` instance +* control localized_lambda = name of the AtC sub-command +* *on* or *off* = Toggles state of localization algorithm + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC control localized_lambda on + +Description +""""""""""" + +Turns the localization algorithms *on* or *off* 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. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +off diff --git a/doc/src/atc_control_momentum.rst b/doc/src/atc_control_momentum.rst new file mode 100644 index 0000000000..7a9e88c721 --- /dev/null +++ b/doc/src/atc_control_momentum.rst @@ -0,0 +1,78 @@ +.. index:: fix_modify AtC control momentum + +fix_modify AtC control momentum command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify control + fix_modify AtC control momentum none + fix_modify AtC control momentum rescale + fix_modify AtC control momentum glc_displacement + fix_modify AtC control momentum glc_velocity + fix_modify AtC control momentum hoover + fix_modify AtC control momentum flux [faceset face_set_id, interpolate] + +* AtC fixID = ID of :doc:`fix atc ` instance +* control = name of the AtC sub-command +* physics_type = *thermal* or *momentum* +* solution_parameter = *max_iterations* or *tolerance* +* value = solution_parameter value +* momentum option = *none* or *rescale* or *glc_displacement* or *glc_velocity* *hoover* or *flux* +* frequency = time step frequency for applying displacement and velocity rescaling +* faceset_id = id of boundary face set (optional, only for *faceset*) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC control momentum none + fix_modify AtC control momentum flux faceset bndy_faces + fix_modify AtC control momentum glc_velocity + +Description +""""""""""" + +The general version of *control* 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. + +The *control momentum* version sets the momentum exchange mechanism 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. + +*correction_max_iterations* 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. + +Restrictions +"""""""""""" + +Only for be used with the specific controllers *thermal* or *momentum*. +They are ignored if a lumped solution is requested. + +*control momentum* is only for be used with specific transfers: elastic +*rescale* not valid with time filtering activated + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC control thermal ` + +Default +""""""" + +- *max_iterations* is the number of rows in the matrix. +- *tolerance* is 1.0e-10. diff --git a/doc/src/atc_control_thermal.rst b/doc/src/atc_control_thermal.rst new file mode 100644 index 0000000000..dc3f28f8eb --- /dev/null +++ b/doc/src/atc_control_thermal.rst @@ -0,0 +1,88 @@ +.. index:: fix_modify AtC control thermal + +fix_modify AtC control thermal command +====================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify control + fix_modify control thermal + fix_modify control thermal rescale + fix_modify control thermal flux + fix_modify control thermal correction_max_iterations + +* AtC fixID = ID of :doc:`fix atc ` instance +* control = name of the AtC sub-command +* physics_type = *thermal* or *momentum* +* solution_parameter = *max_iterations* or *tolerance* +* value = solution_parameter value +* thermal control_type = *none* or *rescale* or *hoover* or *flux* +* frequency = time step frequency for applying velocity rescaling +* boundary_integration_type = *faceset* or *interpolate* (optional) +* faceset_id = id of boundary face set (optional, only for *faceset*) +* correction_max_iterations = maximum number of iterations that will be used by iterative matrix solvers for *thermal* physics type + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC control thermal none + fix_modify AtC control thermal rescale 10 + fix_modify AtC control thermal hoover + fix_modify AtC control thermal flux + fix_modify AtC control thermal flux faceset bndy_faces + fix_modify AtC control thermal correction_max_iterations 10 + +Description +""""""""""" + +The general version of *control* 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. + +The *control thermal* version sets the energy exchange mechanism 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* allow the prescription of sources or fixed temperatures on the +atoms. + +*correction_max_iterations* 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. + +Restrictions +"""""""""""" + +Only for be used with the specific controllers *thermal* or *momentum*. +They are ignored if a lumped solution is requested. + +*control thermal* is only for be used with specific transfers: thermal (*rescale*\ , *hoover*\ , *flux*\ ), *two_temperature* (*flux*\ ). +*rescale* not valid with time filtering activated + +*correction_max_iterations* is only for use with *thermal* physics using +the fractional step method. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC control momentum ` + +Default +""""""" + +- *max_iterations* is the number of rows in the matrix. +- *tolerance* is 1.0e-10. +- *rescale* frequency is 1 +- *flux* boundary_integration_type is *interpolate* +- *correction_max_iterations* is 20 diff --git a/doc/src/atc_decomposition.rst b/doc/src/atc_decomposition.rst new file mode 100644 index 0000000000..50d11bf52f --- /dev/null +++ b/doc/src/atc_decomposition.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC decomposition + +fix_modify AtC decomposition command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify decomposition + +* AtC fixID = ID of :doc:`fix atc ` instance +* decomposition = name of the AtC sub-command +* type = *replicated_memory* or *distributed_memory* + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC decomposition distributed_memory + +Description +""""""""""" + +Command for assigning the distribution of work and memory for parallel +runs. With *replicated_memory* the nodal information is replicated on +each processor, and with *distributed_memory* only the owned nodal +information kept on each processor. The *replicated_memory* option +is most appropriate for simulations were the number of nodes is much +smaller than the number of atoms. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +replicated_memory diff --git a/doc/src/atc_electron_integration.rst b/doc/src/atc_electron_integration.rst new file mode 100644 index 0000000000..2f3fd9eee2 --- /dev/null +++ b/doc/src/atc_electron_integration.rst @@ -0,0 +1,49 @@ +.. index:: fix_modify AtC extrinsic electron_integration + +fix_modify AtC extrinsic electron_integration command +===================================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify extrinsic electron_integration [] + +* AtC fixID = ID of :doc:`fix atc ` instance +* extrinsic electron_integration = name of the AtC sub-command +* integration_type = *explicit* or *implicit* or *steady* +* num_subcycle_steps = number of subcycle steps for the electron time integration (optional) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC extrinsic electron_integration implicit + fix_modify AtC extrinsic electron_integration explicit 100 + +Description +""""""""""" + +Switches between integration schemes for the electron temperature. The +number of subcycling steps used to integrate the electron temperature for +one LAMMPS timestep can be manually adjusted to capture fast electron +dynamics. + +Restrictions +"""""""""""" + +For use only with the two_temperature type of the AtC fix (see +:doc:`fix atc ` command) + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +*implicit* and *subcycle_steps* = 1 diff --git a/doc/src/atc_equilibrium_start.rst b/doc/src/atc_equilibrium_start.rst new file mode 100644 index 0000000000..0068dc02c3 --- /dev/null +++ b/doc/src/atc_equilibrium_start.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC equilibrium_start + +fix_modify AtC equilibrium_start command +======================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify equilibrium_start + +* AtC fixID = ID of :doc:`fix atc ` instance +* equilibrium_start = name of the AtC sub-command +* *exponential* or *step* or *no_filter* = select type of filter + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC equilibrium_start on + +Description +""""""""""" + +Starts filtered calculations assuming they start in equilibrium, +i.e. perfect finite element force balance. + +Restrictions +"""""""""""" + +Only for use with these specific transfers: thermal, two_temperature + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC filter ` +- :doc:`fix_modify AtC filter scale ` + +Default +""""""" + +None. diff --git a/doc/src/atc_extrinsic_exchange.rst b/doc/src/atc_extrinsic_exchange.rst new file mode 100644 index 0000000000..03d794115b --- /dev/null +++ b/doc/src/atc_extrinsic_exchange.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC extrinsic exchange + +fix_modify AtC extrinsic exchange command +========================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify extrinsic exchange + +* AtC fixID = ID of :doc:`fix atc ` instance +* extrinsic exchange = name of the AtC sub-command +* *on* or *off* = set state of energy exchange + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC extrinsic exchange on + +Description +""""""""""" + +Switches energy exchange between the MD system and the electron system +on or off + +Restrictions +"""""""""""" + +For use only with the two_temperature type of the AtC fix (see +:doc:`fix atc ` command) + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +*on* diff --git a/doc/src/atc_fe_md_boundary.rst b/doc/src/atc_fe_md_boundary.rst new file mode 100644 index 0000000000..ad66bf6d49 --- /dev/null +++ b/doc/src/atc_fe_md_boundary.rst @@ -0,0 +1,52 @@ +.. index:: fix_modify AtC fe_md_boundary + +fix_modify AtC fe_md_boundary command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify fe_md_boundary + +* AtC fixID = ID of :doc:`fix atc ` instance +* fe_md_boundary = name of the AtC sub-command +* *faceset* or *interpolate* or *no_boundary* + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC fe_md_boundary interpolate + +Description +""""""""""" + +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. + + +Restrictions +"""""""""""" + +If *faceset* is used, all the AtC non-boundary atoms must lie within and +completely fill the domain enclosed by the faceset. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_faceset box ` +- :doc:`fix_modify AtC mesh create_faceset plane ` + +Default +""""""" + +*interpolate* diff --git a/doc/src/atc_filter_scale.rst b/doc/src/atc_filter_scale.rst new file mode 100644 index 0000000000..ce62a589eb --- /dev/null +++ b/doc/src/atc_filter_scale.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC filter scale + +fix_modify AtC filter scale command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify filter scale + +* AtC fixID = ID of :doc:`fix atc ` instance +* filter scale = name of the AtC sub-command +* scale = characteristic times scale of the filter + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC filter scale 10.0 + +Description +""""""""""" + +Sets the time scale for MD dynamics filter to construct a more +appropriate continuous field. + +Restrictions +"""""""""""" + +Only for use with these specific transfers: thermal, two_temperature + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC filter ` +- :doc:`fix_modify AtC filter type ` + +Default +""""""" + +0.0 diff --git a/doc/src/atc_filter_type.rst b/doc/src/atc_filter_type.rst new file mode 100644 index 0000000000..5e2da80755 --- /dev/null +++ b/doc/src/atc_filter_type.rst @@ -0,0 +1,43 @@ +.. index:: fix_modify AtC filter type + +fix_modify AtC filter type command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify filter type + +* AtC fixID = ID of :doc:`fix atc ` instance +* filter type = name of the AtC sub-command +* *exponential* or *step* or *no_filter* = select type of filter + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC filter type exponential + +Description +""""""""""" + +Specifies the type of time filter used. + +Restrictions +"""""""""""" + +Only for use with these specific transfers: thermal, two_temperature + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC filter ` +- :doc:`fix_modify AtC filter scale ` + +Default +""""""" + +None. diff --git a/doc/src/atc_fix.rst b/doc/src/atc_fix.rst new file mode 100644 index 0000000000..d3ba972508 --- /dev/null +++ b/doc/src/atc_fix.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC fix + +fix_modify AtC fix command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify fix + +* AtC fixID = ID of :doc:`fix atc ` instance +* fix = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* nodeset = name of set of nodes to apply boundary condition +* *constant* or *function* = value or name of function followed by its parameters + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC fix temperature groupNAME 10. + fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 + +Description +""""""""""" + +Creates a constraint on the values of the specified field at specified nodes. + +Restrictions +"""""""""""" + +The keyword *all* is reserved and thus not available as nodeset name. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC unfix ` + +Default +""""""" + +None. diff --git a/doc/src/atc_fix_flux.rst b/doc/src/atc_fix_flux.rst new file mode 100644 index 0000000000..12699e9163 --- /dev/null +++ b/doc/src/atc_fix_flux.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC fix_flux + +fix_modify AtC fix_flux command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify fix_flux + +* AtC fixID = ID of :doc:`fix atc ` instance +* fix_flux = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* face_set = name of set of element faces +* *value* or *function* = value or name of function followed by its parameters + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC fix_flux temperature faceSet 10.0 + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +Only normal fluxes (Neumann data) can be prescribed. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC unfix_flux ` + +Default +""""""" + +None. diff --git a/doc/src/atc_hardy_computes.rst b/doc/src/atc_hardy_computes.rst new file mode 100644 index 0000000000..609740fe99 --- /dev/null +++ b/doc/src/atc_hardy_computes.rst @@ -0,0 +1,54 @@ +.. index:: fix_modify AtC computes + +fix_modify AtC computes command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify computes + +* AtC fixID = ID of :doc:`fix atc ` instance +* computes = name of the AtC sub-command +* *add* or *delete* = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity +* per-atom compute-ID = ID of a per-atom compute; fields can be calculated for all per-atom computes available in LAMMPS +* *volume* or *number* = select whether the created field is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute virial all stress/atom + fix_modify AtC computes add virial volume + fix_modify AtC computes delete virial + + compute centrosymmetry all centro/atom + fix_modify AtC computes add centrosymmetry number + +Description +""""""""""" + +Calculates continuum fields corresponding to specified per-atom +:doc:`computes ` created by LAMMPS. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy `. The per-atom compute +must be specified before the corresponding continuum field can be +requested. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC fields ` +- :doc:`compute ` + +Default +""""""" + +None. diff --git a/doc/src/atc_hardy_fields.rst b/doc/src/atc_hardy_fields.rst new file mode 100644 index 0000000000..70f3360af8 --- /dev/null +++ b/doc/src/atc_hardy_fields.rst @@ -0,0 +1,86 @@ +.. index:: fix_modify AtC fields + +fix_modify AtC fields command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify fields + fix_modify fields + +* AtC fixID = ID of :doc:`fix atc ` instance +* fields = name of the AtC sub-command +* *all* or *none* = output all or no fields +* *add* or *delete* = add or delete the listed output fields +* list_of_fields = one or more of the fields listed below: + + - density : mass per unit volume + - displacement : displacement vector + - momentum : momentum per unit volume + - velocity : defined by momentum divided by density + - projected_velocity : simple kernel estimation of atomic velocities + - temperature : temperature derived from the relative atomic kinetic energy + - kinetic_temperature : temperature derived from the full kinetic energy + - number_density : simple kernel estimation of number of atoms per unit volume + - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis + - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis + - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian + - potential_energy : potential energy per unit volume + - kinetic_energy : kinetic energy per unit volume + - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume + - internal_energy : total internal energy (potential + thermal) per unit volume + - energy : total energy (potential + kinetic) per unit volume + - number_density : number of atoms per unit volume + - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_ + - vacancy_concentration : volume fraction of vacancy content + - type_concentration : volume fraction of a specific atom type + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC fields add velocity temperature + + +Description +""""""""""" + +Allows modification of the fields calculated and output by the AtC +transfer class. The commands are cumulative, e.g.: + +.. code-block:: LAMMPS + + fix_modify AtC fields none + fix_modify AtC fields add velocity temperature + +will only output the velocity and temperature fields. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy `. Currently, the stress +and heat flux formulas are only correct for central force potentials, +e.g. Lennard-Jones and EAM but not Stillinger-Weber. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC gradients ` +- :doc:`fix_modify AtC rates ` +- :doc:`fix_modify AtC computes ` + + +Default +""""""" + +By default, no fields are output. + +References +"""""""""" + +.. [Eshelby] J.D. Eshelby, 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] diff --git a/doc/src/atc_hardy_gradients.rst b/doc/src/atc_hardy_gradients.rst new file mode 100644 index 0000000000..36fad76afe --- /dev/null +++ b/doc/src/atc_hardy_gradients.rst @@ -0,0 +1,74 @@ +.. index:: fix_modify AtC gradients + +fix_modify AtC gradients command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify gradients + +* AtC fixID = ID of :doc:`fix atc ` instance +* gradients = name of the AtC sub-command +* *add* or *delete* = select whether to add or delete calculation of gradients for the listed output fields +* list_of_fields = one or more of the fields listed below: + + - density : mass per unit volume + - displacement : displacement vector + - momentum : momentum per unit volume + - velocity : defined by momentum divided by density + - projected_velocity : simple kernel estimation of atomic velocities + - temperature : temperature derived from the relative atomic kinetic energy + - kinetic_temperature : temperature derived from the full kinetic energy + - number_density : simple kernel estimation of number of atoms per unit volume + - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis + - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis + - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian + - potential_energy : potential energy per unit volume + - kinetic_energy : kinetic energy per unit volume + - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume + - internal_energy : total internal energy (potential + thermal) per unit volume + - energy : total energy (potential + kinetic) per unit volume + - number_density : number of atoms per unit volume + - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_ + - vacancy_concentration : volume fraction of vacancy content + - type_concentration : volume fraction of a specific atom type + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC gradients add temperature velocity stress + fix_modify AtC gradients delete velocity + + +Description +""""""""""" + +Requests calculation and output of gradients of the fields from the AtC +transfer class. These gradients will be with regard to spatial or +material coordinate for Eulerian or Lagrangian analysis, respectively, +as specified by :doc:`fix_modify AtC atom_element_map ` + + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy `. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC atom_element_map ` +- :doc:`fix_modify AtC fields ` +- :doc:`fix_modify AtC rates ` + +Default +""""""" + +None. diff --git a/doc/src/atc_hardy_kernel.rst b/doc/src/atc_hardy_kernel.rst new file mode 100644 index 0000000000..a52f2a9968 --- /dev/null +++ b/doc/src/atc_hardy_kernel.rst @@ -0,0 +1,64 @@ +.. index:: fix_modify AtC kernel + +fix_modify AtC kernel command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify kernel + +* AtC fixID = ID of :doc:`fix atc ` instance +* kernel = name of the AtC sub-command +* type = *step* or *cell* or *cubic_bar* or *cubic_cylinder* or + *cubic_sphere* or *quartic_bar* or *quartic_cylinder* or + *quartic_sphere* +* the following parameter(s) are required for each kernel: + + - *step* : + - *cell* : or + - *cubic_bar* : + - *cubic_cylinder* : + - *cubic_sphere* : + - *quartic_bar* : + - *quartic_cylinder* : + - *quartic_sphere* : + + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC kernel cell 1.0 1.0 1.0 + fix_modify AtC kernel quartic_sphere 10.0 + + +Description +""""""""""" + +Sets the localization kernel type and parameters for :doc:`fix atc hardy `. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy `. For bar kernel types, +half-width oriented along x-direction. For cylinder kernel types, +cylindrical axis is assumed to be in z-direction. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC fields ` +- :doc:`fix_modify AtC gradients ` +- :doc:`fix_modify AtC rates ` +- :doc:`fix_modify AtC computes ` + +Default +""""""" + +None. diff --git a/doc/src/atc_hardy_on_the_fly.rst b/doc/src/atc_hardy_on_the_fly.rst new file mode 100644 index 0000000000..fe7c688387 --- /dev/null +++ b/doc/src/atc_hardy_on_the_fly.rst @@ -0,0 +1,54 @@ +.. index:: fix_modify AtC on_the_fly + +fix_modify AtC on_the_fly command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify on_the_fly + +* AtC fixID = ID of :doc:`fix atc ` instance +* on_the_fly = name of the AtC sub-command +* *bond* or *kernel* = specifies on-the-fly calculation of *bond* or *kernel* matrix elements +* *on* or *off* = activate or discontinue on-the-fly mode + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC on_the_fly bond on + fix_modify AtC on_the_fly kernel + fix_modify AtC on_the_fly kernel off + +Description +""""""""""" + +Overrides normal mode of pre-calculating and storing bond pair-to-node a +nd kernel atom-to-node matrices. If activated, it will calculate elements +of these matrices during repeated calls of field computations +(i.e. "on-the-fly") and not store them for future use. The *on* flag is +optional - if omitted, on_the_fly will be activated for the specified +matrix. Can be deactivated using the *off* flag. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy `. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +By default, on-the-fly calculation is not active (i.e. off). However, +THE code does a memory allocation check to determine if it can store all +needed bond and kernel matrix elements. If this allocation fails, +on-the-fly will be activated. + diff --git a/doc/src/atc_hardy_rates.rst b/doc/src/atc_hardy_rates.rst new file mode 100644 index 0000000000..890ada0c47 --- /dev/null +++ b/doc/src/atc_hardy_rates.rst @@ -0,0 +1,74 @@ +.. index:: fix_modify AtC rates + +fix_modify AtC rates command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify rates + +* AtC fixID = ID of :doc:`fix atc ` instance +* rates = name of the AtC sub-command +* *add* or *delete* = select whether to add or delete calculation of rates for the listed output fields +* list_of_fields = one or more of the fields listed below: + + - density : mass per unit volume + - displacement : displacement vector + - momentum : momentum per unit volume + - velocity : defined by momentum divided by density + - projected_velocity : simple kernel estimation of atomic velocities + - temperature : temperature derived from the relative atomic kinetic energy + - kinetic_temperature : temperature derived from the full kinetic energy + - number_density : simple kernel estimation of number of atoms per unit volume + - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis + - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis + - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian + - potential_energy : potential energy per unit volume + - kinetic_energy : kinetic energy per unit volume + - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume + - internal_energy : total internal energy (potential + thermal) per unit volume + - energy : total energy (potential + kinetic) per unit volume + - number_density : number of atoms per unit volume + - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_ + - vacancy_concentration : volume fraction of vacancy content + - type_concentration : volume fraction of a specific atom type + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC rates add temperature velocity stress + fix_modify AtC rates delete stress + + +Description +""""""""""" + +Requests calculation and output of rates (time derivatives) of the +fields from the AtC transfer class. For Eulerian analysis (see +:doc:`fix_modify AtC atom_element_map `) these +rates are the partial time derivatives of the nodal fields, not the full +(material) time derivatives. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy `. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC atom_element_map ` +- :doc:`fix_modify AtC fields ` +- :doc:`fix_modify AtC fields ` + +Default +""""""" + +None. diff --git a/doc/src/atc_initial.rst b/doc/src/atc_initial.rst new file mode 100644 index 0000000000..7d62251c6c --- /dev/null +++ b/doc/src/atc_initial.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC initial + +fix_modify AtC initial command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify initial + +* AtC fixID = ID of :doc:`fix atc ` instance +* initial = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* nodeset = name of set of nodes to apply initial condition +* *constant* or *function* = value or name of function followed by its parameters + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC initial temperature groupNAME 10. + +Description +""""""""""" + +Sets the initial values for the specified field at the specified nodes. + +Restrictions +"""""""""""" + +The keyword *all* is reserved and thus not available as nodeset name. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_internal_element_set.rst b/doc/src/atc_internal_element_set.rst new file mode 100644 index 0000000000..4a376f55a3 --- /dev/null +++ b/doc/src/atc_internal_element_set.rst @@ -0,0 +1,52 @@ +.. index:: fix_modify AtC internal_element_set + +fix_modify AtC internal_element_set command +=========================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify internal_element_set + +* AtC fixID = ID of :doc:`fix atc ` instance +* internal_element_set = name of the AtC sub-command +* element_set_name = name of element set defining internal region, or *off* + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC internal_element_set myElementSet + fix_modify AtC internal_element_set off + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +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. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC atom_element_map ` +- :doc:`fix_modify AtC boundary type ` + +Default +""""""" + +*off* diff --git a/doc/src/atc_internal_quadrature.rst b/doc/src/atc_internal_quadrature.rst new file mode 100644 index 0000000000..b171914021 --- /dev/null +++ b/doc/src/atc_internal_quadrature.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC internal_quadrature + +fix_modify AtC internal_quadrature command +========================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify internal_quadrature [region] + +* AtC fixID = ID of :doc:`fix atc ` instance +* internal_quadrature = name of the AtC sub-command +* on or off = select whether internal quadrature is enabled or not +* region = treat finite elements as within MD region (optional) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC internal_quadrature off + +Description +""""""""""" + +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. + +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. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +on. diff --git a/doc/src/atc_kernel_bandwidth.rst b/doc/src/atc_kernel_bandwidth.rst new file mode 100644 index 0000000000..02707cfd30 --- /dev/null +++ b/doc/src/atc_kernel_bandwidth.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC kernel_bandwidth + +fix_modify AtC kernel_bandwidth command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify kernel_bandwidth + +* AtC fixID = ID of :doc:`fix atc ` instance +* kernel_bandwidth = name of the AtC sub-command +* value = new bandwidth value + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC kernel_bandwidth 8 + +Description +""""""""""" + +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. + + +Restrictions +"""""""""""" + +Only is used if kernel functions are being used. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +Number of sample locations. + diff --git a/doc/src/atc_lumped_lambda_solve.rst b/doc/src/atc_lumped_lambda_solve.rst new file mode 100644 index 0000000000..e777116da5 --- /dev/null +++ b/doc/src/atc_lumped_lambda_solve.rst @@ -0,0 +1,41 @@ +.. index:: fix_modify AtC control lumped_lambda_solve + +fix_modify AtC control lumped_lambda_solve command +================================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify control lumped_lambda_solve + +* AtC fixID = ID of :doc:`fix atc ` instance +* control lumped_lambda_solve = name of the AtC sub-command +* *on* or *off* = Toggles state of lumped matrix + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC control lumped_lambda_solve on + +Description +""""""""""" + +Command select whether to use or not use lumped matrix for lambda solve. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +off diff --git a/doc/src/atc_mask_direction.rst b/doc/src/atc_mask_direction.rst new file mode 100644 index 0000000000..ed5c605834 --- /dev/null +++ b/doc/src/atc_mask_direction.rst @@ -0,0 +1,38 @@ +.. index:: fix_modify AtC control mask_direction + +fix_modify AtC control mask_direction command +============================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify control mask_direction + +* AtC fixID = ID of :doc:`fix atc ` instance +* control mask_direction = name of the AtC sub-command +* direction = select direction +* *on* or *off* = Toggles state + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC control mask_direction 0 on + +Description +""""""""""" + +Command to mask out certain dimensions from the atomic regulator + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` + diff --git a/doc/src/atc_mass_matrix.rst b/doc/src/atc_mass_matrix.rst new file mode 100644 index 0000000000..eb586b933b --- /dev/null +++ b/doc/src/atc_mass_matrix.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC mass_matrix + +fix_modify AtC mass_matrix command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mass_matrix + +* AtC fixID = ID of :doc:`fix atc ` instance +* mass_matrix = name of the AtC sub-command +* *fe* or *md_fe* = activate/deactivate using the FE mass matrix in the MD region + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mass_matrix fe + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +Should not be used unless the FE region is contained within the MD +region, otherwise the method will be unstable and inaccurate. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +*md_fe* diff --git a/doc/src/atc_material.rst b/doc/src/atc_material.rst new file mode 100644 index 0000000000..471bffffb2 --- /dev/null +++ b/doc/src/atc_material.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC material + +fix_modify AtC material command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify material + +* AtC fixID = ID of :doc:`fix atc ` instance +* material = name of the AtC sub-command +* elementset_name = name of the elementset +* material_id = ID of the material + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC material gap_region 1 + +Description +""""""""""" + +Sets the material model in *elementset_name* to be of type *material_id*\ . + +Restrictions +"""""""""""" + +The element set must already be created and the material must be +specified in the material file given the the atc fix on construction + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +All elements default to the first material in the material file. diff --git a/doc/src/atc_mesh_add_to_nodeset.rst b/doc/src/atc_mesh_add_to_nodeset.rst new file mode 100644 index 0000000000..f9f6f575fe --- /dev/null +++ b/doc/src/atc_mesh_add_to_nodeset.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC mesh add_to_nodeset + +fix_modify AtC mesh add_to_nodeset command +========================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh add_to_nodeset + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create_nodeset = name of the AtC sub-command +* id = id to assign to the collection of FE nodes +* = coordinates of the bounding box that contains the desired nodes to be added + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh add_to_nodeset lbc -12.1 -11.9 -12 12 -12 12 + +Description +""""""""""" + +Command to add nodes to an already existing FE nodeset. + +Restrictions +"""""""""""" + +None + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_nodeset ` + + +Default +""""""" + +Coordinates are assumed to be in lattice units. diff --git a/doc/src/atc_mesh_create.rst b/doc/src/atc_mesh_create.rst new file mode 100644 index 0000000000..b17bb8ac0d --- /dev/null +++ b/doc/src/atc_mesh_create.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC mesh create + +fix_modify AtC mesh create command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh create + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create = name of the AtC sub-command +* nx ny nz = number of elements in x-, y-, and z-direction +* region-ID = ID of region that is to be meshed +* f or p = periodicity flags for x-, y-, and z-direction + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh create 10 1 1 feRegion p p p + +Description +""""""""""" + +Creates a uniform mesh in a rectangular region. + +Restrictions +"""""""""""" + +Creates only uniform rectangular grids in a rectangular region + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh quadrature ` + +Default +""""""" + +When created, the mesh defaults to gauss2 (2-point Gaussian) +quadrature. Use the :doc:`fix_modify AtC mesh quadrature +` command to change the quadrature style. diff --git a/doc/src/atc_mesh_create_elementset.rst b/doc/src/atc_mesh_create_elementset.rst new file mode 100644 index 0000000000..3cb406e7bc --- /dev/null +++ b/doc/src/atc_mesh_create_elementset.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC mesh create_elementset + +fix_modify AtC mesh create_elementset command +============================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh create_elementset + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create_elementset = name of the AtC sub-command +* id = id to assign to the collection of FE nodes +* = coordinates of the bounding box that contains only the desired elements + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 + +Description +""""""""""" + +Command to assign an id to a set of FE elements to be used subsequently +in defining material and mesh-based operations. + +Restrictions +"""""""""""" + +Only viable for rectangular grids. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh delete_elements ` +- :doc:`fix_modify AtC mesh nodeset_to_elementset ` + +Default +""""""" + +Coordinates are assumed to be in lattice units. diff --git a/doc/src/atc_mesh_create_faceset_box.rst b/doc/src/atc_mesh_create_faceset_box.rst new file mode 100644 index 0000000000..09b099d179 --- /dev/null +++ b/doc/src/atc_mesh_create_faceset_box.rst @@ -0,0 +1,49 @@ +.. index:: fix_modify AtC mesh create_faceset box + +fix_modify AtC mesh create_faceset box command +============================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh create_faceset box [units] + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create_faceset = name of the AtC sub-command +* id = id to assign to the collection of FE faces +* box = use bounding box to define FE faces +* = coordinates of the bounding box that is coincident with the desired FE faces +* = "in" gives inner faces to the box, "out" gives the outer faces to the box +* units = option to specify real as opposed to lattice units + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out + + +Description +""""""""""" + +Command to assign an id to a set of FE faces. + +Restrictions +"""""""""""" + +Only viable for rectangular grids. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_faceset plane ` + +Default +""""""" + +The default options are units = lattice and the use of outer faces. diff --git a/doc/src/atc_mesh_create_faceset_plane.rst b/doc/src/atc_mesh_create_faceset_plane.rst new file mode 100644 index 0000000000..035e584044 --- /dev/null +++ b/doc/src/atc_mesh_create_faceset_plane.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC mesh create_faceset plane + +fix_modify AtC mesh create_faceset plane command +================================================ + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh create_faceset plane [units] + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create_faceset = name of the AtC sub-command +* id = id to assign to the collection of FE faces +* plane = use plane to define faceset +* ,, = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2] +* units = option to specify real as opposed to lattice units + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 + + +Description +""""""""""" + +Command to assign an id to a set of FE faces. + +Restrictions +"""""""""""" + +Only viable for rectangular grids. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_faceset box ` + +Default +""""""" + +The default options are units = lattice. diff --git a/doc/src/atc_mesh_create_nodeset.rst b/doc/src/atc_mesh_create_nodeset.rst new file mode 100644 index 0000000000..a2f9d74d07 --- /dev/null +++ b/doc/src/atc_mesh_create_nodeset.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC mesh create_nodeset + +fix_modify AtC mesh create_nodeset command +========================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh create_nodeset + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create_nodeset = name of the AtC sub-command +* id = id to assign to the collection of FE nodes +* = coordinates of the bounding box that contains only the desired nodes + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 + +Description +""""""""""" + +Command to assign an id to a set of FE nodes to be used subsequently in +defining boundary conditions. + +Restrictions +"""""""""""" + +None + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh add_to_nodeset ` + +Default +""""""" + +Coordinates are assumed to be in lattice units. diff --git a/doc/src/atc_mesh_delete_elements.rst b/doc/src/atc_mesh_delete_elements.rst new file mode 100644 index 0000000000..9785f0adf6 --- /dev/null +++ b/doc/src/atc_mesh_delete_elements.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC mesh delete_elements + +fix_modify AtC mesh delete_elements command +============================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh delete_elements + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh create_elementset = name of the AtC sub-command +* id = id of the element set + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh delete_elements gap + +Description +""""""""""" + +Deletes a group of elements from the mesh. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_elementset ` +- :doc:`fix_modify AtC mesh nodeset_to_elementset ` + +Default +""""""" + +None. diff --git a/doc/src/atc_mesh_nodeset_to_elementset.rst b/doc/src/atc_mesh_nodeset_to_elementset.rst new file mode 100644 index 0000000000..d8721cc295 --- /dev/null +++ b/doc/src/atc_mesh_nodeset_to_elementset.rst @@ -0,0 +1,50 @@ +.. index:: fix_modify AtC mesh nodeset_to_elementset + +fix_modify AtC mesh nodeset_to_elementset command +================================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh nodeset_to_elementset + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh nodeset_to_elementset = name of the AtC sub-command +* nodeset_id = id of desired nodeset from which to create the elementset +* elementset_id = id to assign to the collection of FE elements +* = flag to choose either the maximal or minimal elementset + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min + + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create_elementset ` +- :doc:`fix_modify AtC mesh delete_elements ` + +Default +""""""" + +Unless specified, the maximal element set is created. diff --git a/doc/src/atc_mesh_output.rst b/doc/src/atc_mesh_output.rst new file mode 100644 index 0000000000..63756df98e --- /dev/null +++ b/doc/src/atc_mesh_output.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC mesh output + +fix_modify AtC mesh output command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh output + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh output = name of the AtC sub-command +* file_prefix = prefix of various generated output files + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh output meshData + + +Description +""""""""""" + +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 (EnSight, "gold" format) +output of mesh data. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_mesh_quadrature.rst b/doc/src/atc_mesh_quadrature.rst new file mode 100644 index 0000000000..0c9bd4b30f --- /dev/null +++ b/doc/src/atc_mesh_quadrature.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC mesh quadrature + +fix_modify AtC mesh quadrature command +====================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh quatrature + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh quadrature = name of the AtC sub-command +* quad = *nodal* or *gauss1* or *gauss2* or *gauss3* or *face* + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh quadrature face + +Description +""""""""""" + +(Re-)assigns the quadrature style for an existing mesh. When a mesh is +created its quadrature method defaults to gauss2. Use this call to +change it after the fact. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create ` + +Default +""""""" + +None. diff --git a/doc/src/atc_mesh_read.rst b/doc/src/atc_mesh_read.rst new file mode 100644 index 0000000000..9848e12b07 --- /dev/null +++ b/doc/src/atc_mesh_read.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC mesh read + +fix_modify AtC mesh read command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh read + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh read = name of the AtC sub-command +* filename = name of the file containing the mesh to be read +* f or p = periodicity flags for x-, y-, and z-direction (optional) + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh read myComponent.mesh p p p + fix_modify AtC mesh read myOtherComponent.exo + +Description +""""""""""" + +Reads a mesh from a text or exodus file, and assigns periodic boundary +conditions if needed. + +Restrictions +"""""""""""" + +None + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create ` +- :doc:`fix_modify AtC mesh write ` + +Default +""""""" + +Periodicity flags are set to false (f) by default. diff --git a/doc/src/atc_mesh_write.rst b/doc/src/atc_mesh_write.rst new file mode 100644 index 0000000000..dbb8f9c219 --- /dev/null +++ b/doc/src/atc_mesh_write.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC mesh write + +fix_modify AtC mesh write command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify mesh write + +* AtC fixID = ID of :doc:`fix atc ` instance +* mesh write = name of the AtC sub-command +* filename = name of the file containing the mesh to be write + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC mesh write myMesh.mesh + +Description +""""""""""" + +Writes a mesh to a text file. + +Restrictions +"""""""""""" + +None + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC mesh create ` +- :doc:`fix_modify AtC mesh read ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output.rst b/doc/src/atc_output.rst new file mode 100644 index 0000000000..3fb1491be1 --- /dev/null +++ b/doc/src/atc_output.rst @@ -0,0 +1,61 @@ +.. index:: fix_modify AtC output + +fix_modify AtC output command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output [text|full_text|binary|vector_components|tensor_components] + fix_modify output index [step|time] + +* AtC fixID = ID of :doc:`fix atc ` instance +* *output* or *output index* = name of the AtC sub-command +* filename_prefix = prefix for data files (for *output*) +* frequency = frequency of output in time-steps (for *output*) +* optional keywords for *output*: + + - text = creates text output of index, step and nodal variable values for unique nodes + - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes + - binary = creates binary EnSight output + - vector_components = outputs vectors as scalar components + - tensor_components = outputs tensor as scalar components (for use with ParaView) + +* *step* or *time* = index output by step or by time (for *output index*) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output heatFE 100 + fix_modify AtC output hardyFE 1 text tensor_components + fix_modify AtC output hardyFE 10 text binary tensor_components + fix_modify AtC output index step + + +Description +""""""""""" + +Creates text and/or binary (EnSight, "gold" format) output of nodal/mesh +data which is transfer/physics specific. Output indexing by step or time +is possible. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix atc command ` + +Default +""""""" + +No default format. Output indexed by time. diff --git a/doc/src/atc_output_boundary_integral.rst b/doc/src/atc_output_boundary_integral.rst new file mode 100644 index 0000000000..71a3e03ac2 --- /dev/null +++ b/doc/src/atc_output_boundary_integral.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC output boundary_integral + +fix_modify AtC output boundary_integral command +=============================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output boundary_integral faceset [name] + +* AtC fixID = ID of :doc:`fix atc ` instance +* output boundary_integral = name of the AtC sub-command +* fieldname = name of hardy field +* faceset = required keyword +* name= name of faceset + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output boundary_integral stress faceset loop1 + + +Description +""""""""""" + +Calculates a surface integral of the given field dotted with the outward +normal of the faces and puts output in the "GLOBALS" file. + +Restrictions +"""""""""""" + +Must be used with the hardy/field type of :doc:`fix atc ` + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output_contour_integral.rst b/doc/src/atc_output_contour_integral.rst new file mode 100644 index 0000000000..24678ef6cc --- /dev/null +++ b/doc/src/atc_output_contour_integral.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC output contour_integral + +fix_modify AtC output contour_integral command +============================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output contour_integral faceset [axis [x|y|z]] + +* AtC fixID = ID of :doc:`fix atc ` instance +* output contour_integral = name of the AtC sub-command +* fieldname = name of hardy field +* faceset = required keyword +* name = name of faceset +* *axis x* or *axis y* or *axis z* = (optional) + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output contour_integral stress faceset loop1 + + +Description +""""""""""" + +Calculates a surface integral of the given field dotted with the outward +normal of the faces and puts output in the "GLOBALS" file. + +Restrictions +"""""""""""" + +Must be used with the hardy/field type of :doc:`fix atc ` + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output_nodeset.rst b/doc/src/atc_output_nodeset.rst new file mode 100644 index 0000000000..eb12a2344e --- /dev/null +++ b/doc/src/atc_output_nodeset.rst @@ -0,0 +1,49 @@ +.. index:: fix_modify AtC output nodeset + +fix_modify AtC output nodeset command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output nodeset + +* AtC fixID = ID of :doc:`fix atc ` instance +* output nodeset = name of the AtC sub-command +* nodeset_name= name of nodeset to be operated on +* operation = *sum* + + * *sum* = creates nodal sum over nodes in specified nodeset + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output nodeset nset1 sum + + +Description +""""""""""" + +Performs operation over the nodes belonging to specified nodeset and +outputs resulting variable values to GLOBALS file. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix atc command ` + +Default +""""""" + +None. diff --git a/doc/src/atc_output_volume_integral.rst b/doc/src/atc_output_volume_integral.rst new file mode 100644 index 0000000000..464d43cbce --- /dev/null +++ b/doc/src/atc_output_volume_integral.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC output volume_integral + +fix_modify AtC output volume_integral command +============================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify output volume_integral + +* AtC fixID = ID of :doc:`fix atc ` instance +* output volume_integral = name of the AtC sub-command +* elementset_name= name of elementset to be integrated over +* fieldname = name of field to integrate + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC output volume_integral eset1 mass_density + + +Description +""""""""""" + +Performs volume integration of specified field over elementset and +outputs resulting variable values to GLOBALS file. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix atc command ` + +Default +""""""" + +None. diff --git a/doc/src/atc_pair_interactions.rst b/doc/src/atc_pair_interactions.rst new file mode 100644 index 0000000000..73ada09001 --- /dev/null +++ b/doc/src/atc_pair_interactions.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC pair_interactions + +fix_modify AtC pair_interactions command +======================================== + +fix_modify AtC bond_interactions command +======================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify pair_interactions + fix_modify bond_interactions + +* AtC fixID = ID of :doc:`fix atc ` instance +* *pair_interactions* or *bond_interactions* = name of the AtC sub-command +* *on* or *off* = activate or deactivate + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC pair_interactions off + fix_modify AtC bond_interactions on + +Description +""""""""""" + +Include bonds and/or pairs in stress and heat flux computations. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +*pair_interactions*\ : on, *bond_interactions*\ : off diff --git a/doc/src/atc_poisson_solver.rst b/doc/src/atc_poisson_solver.rst new file mode 100644 index 0000000000..d37f214b97 --- /dev/null +++ b/doc/src/atc_poisson_solver.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC poisson_solver + +fix_modify AtC poisson_solver command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify poisson_solver mesh create + +* AtC fixID = ID of :doc:`fix atc ` instance +* poisson_solver = name of the AtC sub-command +* *nx* *ny* *nz* = number of elements in x, y, and z +* region-id = id of region to be meshed +* *f* or *p* = periodicity flags for x, y, and z + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p + +Description +""""""""""" + +Creates a uniform mesh in a rectangular region. + +Restrictions +"""""""""""" + +Creates only uniform rectangular grids in rectangular regions. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_read_restart.rst b/doc/src/atc_read_restart.rst new file mode 100644 index 0000000000..11ba4519a4 --- /dev/null +++ b/doc/src/atc_read_restart.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC read_restart + +fix_modify AtC read_restart command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify read_restart + +* AtC fixID = ID of :doc:`fix atc ` instance +* read_restart = name of the AtC sub-command +* file_name = name of AtC restart file + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC read_restart restart.mydata.AtC + + +Description +""""""""""" + +Reads the current state of the AtC fields from a named text-based restart file. + +Restrictions +"""""""""""" + +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. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC write_restart ` + +Default +""""""" + +None. diff --git a/doc/src/atc_remove_molecule.rst b/doc/src/atc_remove_molecule.rst new file mode 100644 index 0000000000..a654cd5c1d --- /dev/null +++ b/doc/src/atc_remove_molecule.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC remove_molecule + +fix_modify AtC remove_molecule command +====================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify remove_molecule + +* AtC fixID = ID of :doc:`fix atc ` instance +* remove_molecule = name of the AtC sub-command +* tag = tag for tracking a molecule + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC remove_molecule water + +Description +""""""""""" + +Removes tag designated for tracking a specified set of molecules. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC add_species ` +- :doc:`fix_modify AtC add_molecule ` +- :doc:`fix_modify AtC remove_species ` + +Default +""""""" + +None. diff --git a/doc/src/atc_remove_source.rst b/doc/src/atc_remove_source.rst new file mode 100644 index 0000000000..d98b7933da --- /dev/null +++ b/doc/src/atc_remove_source.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC remove_source + +fix_modify AtC remove_source command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify remove_source + +* AtC fixID = ID of :doc:`fix atc ` instance +* remove_source = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* element_set = name of set of elements + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC remove_source temperature groupNAME + +Description +""""""""""" + +Remove a domain source. + +Restrictions +"""""""""""" + +The keyword *all* is reserved and thus not available as element_set name. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC source ` + +Default +""""""" + +None. diff --git a/doc/src/atc_remove_species.rst b/doc/src/atc_remove_species.rst new file mode 100644 index 0000000000..20e1f6a742 --- /dev/null +++ b/doc/src/atc_remove_species.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC remove_species + +fix_modify AtC remove_species command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify remove_species + +* AtC fixID = ID of :doc:`fix atc ` instance +* remove_species = name of the AtC sub-command +* tag = tag for tracking a species + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC remove_species gold + +Description +""""""""""" + +Removes tag designated for tracking a specified species. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC add_species ` +- :doc:`fix_modify AtC add_molecule ` +- :doc:`fix_modify AtC remove_molecule ` + +Default +""""""" + +None. diff --git a/doc/src/atc_reset_atomic_reference.rst b/doc/src/atc_reset_atomic_reference.rst new file mode 100644 index 0000000000..8f53cbfbe9 --- /dev/null +++ b/doc/src/atc_reset_atomic_reference.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC reset_atomic_reference_positions + +fix_modify AtC reset_atomic_reference_positions command +======================================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify reset_atomic_reference_positions + +* AtC fixID = ID of :doc:`fix atc ` instance +* reset_atomic_reference_positions = name of the AtC sub-command + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC reset_atomic_reference_positions + +Description +""""""""""" + +Resets the atomic positions ATC uses to perform point to field +operations. In can be used to use perfect lattice sites in ATC but a +thermalized or deformed lattice in LAMMPS. + + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None + diff --git a/doc/src/atc_reset_time.rst b/doc/src/atc_reset_time.rst new file mode 100644 index 0000000000..147a6ab910 --- /dev/null +++ b/doc/src/atc_reset_time.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC reset_time + +fix_modify AtC reset_time command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify reset_time + +* AtC fixID = ID of :doc:`fix atc ` instance +* reset_time = name of the AtC sub-command +* value = new time value + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC reset_time 0.0 + +Description +""""""""""" + +Resets the simulation time counter. + + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None + diff --git a/doc/src/atc_sample_frequency.rst b/doc/src/atc_sample_frequency.rst new file mode 100644 index 0000000000..5b0da6d9dd --- /dev/null +++ b/doc/src/atc_sample_frequency.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC sample_frequency + +fix_modify AtC sample_frequency command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify sample_frequency + +* AtC fixID = ID of :doc:`fix atc ` instance +* sample_frequency = name of the AtC sub-command +* freq = frequency to sample fields in number of steps + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC sample_frequency 10 + +Description +""""""""""" + +Specifies a frequency at which fields are computed for the case where +time filters are being applied. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy ` and is only relevant when time filters are being used. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. + diff --git a/doc/src/atc_set_reference_pe.rst b/doc/src/atc_set_reference_pe.rst new file mode 100644 index 0000000000..ff4d95526f --- /dev/null +++ b/doc/src/atc_set_reference_pe.rst @@ -0,0 +1,50 @@ +.. index:: fix_modify AtC set reference_potential_energy + +fix_modify AtC set reference_potential_energy command +===================================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify set reference_potential_energy [] + +* AtC fixID = ID of :doc:`fix atc ` instance +* set reference_potential_energy = name of the AtC sub-command +* value = optional user specified zero point for PE in native LAMMPS energy units +* filename = optional user specified string for file of nodal PE values to be read-in + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC set reference_potential_energy + fix_modify AtC set reference_potential_energy -0.05 + fix_modify AtC set reference_potential_energy myPEvalues + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +Must be used with :doc:`fix atc hardy ` or :doc:`fix atc field `. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +Defaults to the LAMMPS zero point i.e. isolated atoms. + diff --git a/doc/src/atc_source.rst b/doc/src/atc_source.rst new file mode 100644 index 0000000000..6df4b67d1c --- /dev/null +++ b/doc/src/atc_source.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC source + +fix_modify AtC source command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify source + +* AtC fixID = ID of :doc:`fix atc ` instance +* source = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* element_set = name of set of elements +* *value* or *function* = value or name of function followed by its parameters + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC source temperature middle temporal_ramp 10.0 0.0 + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +The keyword *all* is reserved and thus not available as element_set name. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC remove_source ` + +Default +""""""" + +None. diff --git a/doc/src/atc_source_integration.rst b/doc/src/atc_source_integration.rst new file mode 100644 index 0000000000..b10e6c7e2a --- /dev/null +++ b/doc/src/atc_source_integration.rst @@ -0,0 +1,42 @@ +.. index:: fix_modify AtC source_integration + +fix_modify AtC source_integration command +========================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify source_integration + +* AtC fixID = ID of :doc:`fix atc ` instance +* source_integration = name of the AtC sub-command +* *fe* or *atom* = (undocumented) + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC source_integration atom + +Description +""""""""""" + +(undocumented) + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +Default is *fe* diff --git a/doc/src/atc_temperature_definition.rst b/doc/src/atc_temperature_definition.rst new file mode 100644 index 0000000000..b5a27467ca --- /dev/null +++ b/doc/src/atc_temperature_definition.rst @@ -0,0 +1,48 @@ +.. index:: fix_modify AtC temperature_definition + +fix_modify AtC temperature_definition command +============================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify temperature_definition + +* AtC fixID = ID of :doc:`fix atc ` instance +* temperature_definition = name of the AtC sub-command +* *kinetic* or *total* = (undocumented) + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC temperature_definition kinetic + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +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. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +*kinetic* diff --git a/doc/src/atc_time_filter.rst b/doc/src/atc_time_filter.rst new file mode 100644 index 0000000000..0a97c83259 --- /dev/null +++ b/doc/src/atc_time_filter.rst @@ -0,0 +1,46 @@ +.. index:: fix_modify AtC filter + +fix_modify AtC filter command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify filter + +* AtC fixID = ID of :doc:`fix atc ` instance +* filter = name of the AtC sub-command +* *on* or *off* or *equilibrate* = Select state of filter + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC filter on + +Description +""""""""""" + +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. + +Restrictions +"""""""""""" + +Only for use with these specific transfers: thermal, two_temperature + +Related AtC commands +"""""""""""""""""""" +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC filter scale ` +- :doc:`fix_modify AtC equilibrium_start ` + +Default +""""""" + +off diff --git a/doc/src/atc_time_integration.rst b/doc/src/atc_time_integration.rst new file mode 100644 index 0000000000..580be0430c --- /dev/null +++ b/doc/src/atc_time_integration.rst @@ -0,0 +1,78 @@ +.. index:: fix_modify AtC time_integration + +fix_modify AtC time_integration command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify time_integration + +* AtC fixID = ID of :doc:`fix atc ` instance +* time_integration = name of the AtC sub-command +* descriptor = *gear* or *fractional_step* or *verlet* + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC time_integration fractional_step + + +Description +""""""""""" + +Command to select the thermal or momentum time integration. + +--------- + +Options for thermal time integration: + +*gear* + atomic velocity update with 2nd order Verlet, nodal temperature update + with 3rd or 4th order Gear, thermostats based on controlling power + +*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 + +--------- + +Options for momentum time integration: + +*verlet* + atomic velocity update with 2nd order Verlet, nodal temperature update + with 2nd order Verlet, kinetostats based on controlling force + +*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 + +*gear* + atomic velocity update with 2nd order Verlet, nodal temperature update + with 3rd or 4th order Gear, kinetostats based on controlling power. + +--------- + +Restrictions +"""""""""""" + +None. + + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. diff --git a/doc/src/atc_track_displacement.rst b/doc/src/atc_track_displacement.rst new file mode 100644 index 0000000000..043f42ea9c --- /dev/null +++ b/doc/src/atc_track_displacement.rst @@ -0,0 +1,43 @@ +.. index:: fix_modify AtC track_displacement + +fix_modify AtC track_displacement command +========================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify track_displacement + +* AtC fixID = ID of :doc:`fix atc ` instance +* track_displacement = name of the AtC sub-command +* *on* or *off* = (undocumented) + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC track_displacement on + +Description +""""""""""" + +Determines whether displacement is tracked or not. For solids problems +this is a useful quantity, but for fluids it is not relevant. + +Restrictions +"""""""""""" + +Some constitutive models require the displacement field. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +*on* diff --git a/doc/src/atc_unfix.rst b/doc/src/atc_unfix.rst new file mode 100644 index 0000000000..12ee37bbde --- /dev/null +++ b/doc/src/atc_unfix.rst @@ -0,0 +1,44 @@ +.. index:: fix_modify AtC unfix + +fix_modify AtC unfix command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify unfix + +* AtC fixID = ID of :doc:`fix atc ` instance +* unfix = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* nodeset = name of set of nodes to apply boundary condition + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC unfix temperature groupNAME + +Description +""""""""""" + +Removes constraint on field values for specified nodes. + +Restrictions +"""""""""""" + +The keyword *all* is reserved and thus not available as nodeset name. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC fix ` + +Default +""""""" + +None. diff --git a/doc/src/atc_unfix_flux.rst b/doc/src/atc_unfix_flux.rst new file mode 100644 index 0000000000..da9d1b4aba --- /dev/null +++ b/doc/src/atc_unfix_flux.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC unfix_flux + +fix_modify AtC unfix_flux command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify unfix_flux + +* AtC fixID = ID of :doc:`fix atc ` instance +* unfix_flux = name of the AtC sub-command +* field = field kind name valid for type of physics: *temperature* or *electron_temperature* +* face_set = name of set of element faces + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC unfix_flux temperature faceSet + +Description +""""""""""" + +Command for removing prescribed normal fluxes e.g. heat_flux, stress. + + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC fix_flux ` + +Default +""""""" + +None. diff --git a/doc/src/atc_write_atom_weights.rst b/doc/src/atc_write_atom_weights.rst new file mode 100644 index 0000000000..ecb69b5deb --- /dev/null +++ b/doc/src/atc_write_atom_weights.rst @@ -0,0 +1,45 @@ +.. index:: fix_modify AtC write_atom_weights + +fix_modify AtC write_atom_weights command +========================================= + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify write_atom_weights + +* AtC fixID = ID of :doc:`fix atc ` instance +* write_atom_weights = name of the AtC sub-command +* filename = name of file that atomic weights are written to +* frequency = how often writes will occur + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC write_atom_weights atm_wt_file.txt 10 + +Description +""""""""""" + +Command for writing the values of atomic weights to a specified file. + + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None + diff --git a/doc/src/atc_write_restart.rst b/doc/src/atc_write_restart.rst new file mode 100644 index 0000000000..e4f19dea10 --- /dev/null +++ b/doc/src/atc_write_restart.rst @@ -0,0 +1,47 @@ +.. index:: fix_modify AtC write_restart + +fix_modify AtC write_restart command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify write_restart + +* AtC fixID = ID of :doc:`fix atc ` instance +* write_restart = name of the AtC sub-command +* file_name = name of AtC restart file + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix_modify AtC write_restart restart.mydata.AtC + + +Description +""""""""""" + +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 otherwise similar LAMMPS command. + +Restrictions +"""""""""""" + +None. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` +- :doc:`fix_modify AtC read_restart ` + +Default +""""""" + +None. diff --git a/doc/src/compute_adf.rst b/doc/src/compute_adf.rst index c0d754d883..a9375fa038 100644 --- a/doc/src/compute_adf.rst +++ b/doc/src/compute_adf.rst @@ -209,7 +209,7 @@ atoms further away than that distance. If you want an ADF for larger distances, you can use the :doc:`rerun ` command to post-process a dump file and set the cutoff for the potential to be longer in the rerun script. Note that in the rerun context, the force cutoff is -arbitrary, since you aren't running dynamics and thus are not changing +arbitrary, since you are not running dynamics and thus are not changing your model. Related commands diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 5f426ffb51..0aedfe09aa 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -180,7 +180,7 @@ atoms further away than that distance. If you want an RDF for larger distances, you can use the :doc:`rerun ` command to post-process a dump file and set the cutoff for the potential to be longer in the rerun script. Note that in the rerun context, the force cutoff is -arbitrary, since you aren't running dynamics and thus are not changing +arbitrary, since you are not running dynamics and thus are not changing your model. The definition of g(r) used by LAMMPS is only appropriate for characterizing atoms that are uniformly distributed throughout the simulation cell. In such cases, the coordination number is still diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 2e0b079e09..b58489f868 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -200,7 +200,7 @@ not overlap, regardless of their relative orientations. optional keywords allowed by the :doc:`create_box ` command for extra bonds (angles,etc) or extra special neighbors. This is because by default, the :doc:`create_box ` command sets up a - non-molecular system which doesn't allow molecules to be added. + non-molecular system which does not allow molecules to be added. ---------- diff --git a/doc/src/dump.rst b/doc/src/dump.rst index c842d5fafe..36a20defb6 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -286,7 +286,7 @@ Style *custom* allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are listed above and will appear in the order specified. You cannot specify a quantity that is not defined for a particular simulation - -such as *q* for atom style *bond*\ , since that atom style doesn't +such as *q* for atom style *bond*\ , since that atom style does not assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the possible dump custom attributes diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 5f7f42b4be..75fff9d444 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -520,7 +520,7 @@ includes an initial snapshot with the reference position of all atoms. Note that only computes with a *refresh* option will work with dump_modify refresh. See individual compute doc pages for details. Currently, only compute displace/atom supports this option. Others -may be added at some point. If you use a compute that doesn't support +may be added at some point. If you use a compute that does not support refresh operations, LAMMPS will not complain; dump_modify refresh will simply do nothing. diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 6903275310..81a16b907a 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -18,8 +18,8 @@ Syntax *thermal* = thermal coupling with fields: temperature *two_temperature* = electron-phonon coupling with field: temperature and electron_temperature - *hardy* = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) - *field* = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) + *hardy* = on-the-fly post-processing using kernel localization functions + *field* = on-the-fly post-processing using mesh-based localization functions * parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file @@ -36,7 +36,12 @@ Examples Description """"""""""" -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. +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. .. image:: JPG/atc_nanotube.jpg :align: center @@ -115,119 +120,126 @@ Note coupling and post-processing can be combined in the same simulations using **Restart, fix_modify, output, run start/stop, minimize info:** -No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` options -relevant to this fix are listed below. No global scalar or vector or -per-atom quantities are stored by this fix for access by various -:doc:`output commands `. No parameter of this fix can be -used with the *start/stop* keywords of the :doc:`run ` command. -This fix is not invoked during :doc:`energy minimization `. +No information about this fix is written to :doc:`binary restart files +`. The :doc:`fix_modify ` options relevant to this +fix are listed below. No global scalar or vector or per-atom quantities +are stored by this fix for access by various :doc:`output commands +`. No parameter of this fix can be used with the +*start/stop* keywords of the :doc:`run ` command. This fix is not +invoked during :doc:`energy minimization `. Restrictions """""""""""" -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. In addition, currently: +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. In addition, currently: * the coupling is restricted to thermal physics * the FE computations are done in serial on each processor. +.. _atc_fix_modify: + Related commands """""""""""""""" -After specifying this fix in your input script, several other :doc:`fix_modify ` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. +After specifying this fix in your input script, several other +:doc:`fix_modify ` commands are used to setup the problem, +e.g. define the finite element mesh and prescribe initial and boundary +conditions. *fix_modify* commands for setup: -* `fix_modify AtC mesh create `_ -* `fix_modify AtC mesh quadrature `_ -* `fix_modify AtC mesh read `_ -* `fix_modify AtC mesh write `_ -* `fix_modify AtC mesh create_nodeset `_ -* `fix_modify AtC mesh add_to_nodeset `_ -* `fix_modify AtC mesh create_faceset box `_ -* `fix_modify AtC mesh create_faceset plane `_ -* `fix_modify AtC mesh create_elementset `_ -* `fix_modify AtC mesh delete_elements `_ -* `fix_modify AtC mesh nodeset_to_elementset `_ -* `fix_modify AtC boundary `_ -* `fix_modify AtC internal_quadrature `_ -* `fix_modify AtC time_integration (thermal) `_ -* `fix_modify AtC time_integration (momentum) `_ -* `fix_modify AtC extrinsic electron_integration `_ -* `fix_modify AtC internal_element_set `_ -* `fix_modify AtC decomposition `_ +* :doc:`fix_modify AtC mesh create ` +* :doc:`fix_modify AtC mesh quadrature ` +* :doc:`fix_modify AtC mesh read ` +* :doc:`fix_modify AtC mesh write ` +* :doc:`fix_modify AtC mesh create_nodeset ` +* :doc:`fix_modify AtC mesh add_to_nodeset ` +* :doc:`fix_modify AtC mesh create_faceset box ` +* :doc:`fix_modify AtC mesh create_faceset plane ` +* :doc:`fix_modify AtC mesh create_elementset ` +* :doc:`fix_modify AtC mesh delete_elements ` +* :doc:`fix_modify AtC mesh nodeset_to_elementset ` +* :doc:`fix_modify AtC boundary type ` +* :doc:`fix_modify AtC internal_quadrature ` +* :doc:`fix_modify AtC time_integration ` +* :doc:`fix_modify AtC extrinsic electron_integration ` +* :doc:`fix_modify AtC internal_element_set ` +* :doc:`fix_modify AtC decomposition ` *fix_modify* commands for boundary and initial conditions: -* `fix_modify AtC initial `_ -* `fix_modify AtC fix `_ -* `fix_modify AtC unfix `_ -* `fix_modify AtC fix_flux `_ -* `fix_modify AtC unfix_flux `_ -* `fix_modify AtC source `_ -* `fix_modify AtC remove_source `_ +* :doc:`fix_modify AtC initial ` +* :doc:`fix_modify AtC fix ` +* :doc:`fix_modify AtC unfix ` +* :doc:`fix_modify AtC fix_flux ` +* :doc:`fix_modify AtC unfix_flux ` +* :doc:`fix_modify AtC source ` +* :doc:`fix_modify AtC remove_source ` *fix_modify* commands for control and filtering: -* `fix_modify AtC control `_ -* `fix_modify AtC control thermal `_ -* `fix_modify AtC control thermal correction_max_iterations `_ -* `fix_modify AtC control momentum `_ -* `fix_modify AtC control localized_lambda `_ -* `fix_modify AtC control lumped_lambda_solve `_ -* `fix_modify AtC control mask_direction `_ control -* `fix_modify AtC filter `_ -* `fix_modify AtC filter scale `_ -* `fix_modify AtC filter type `_ -* `fix_modify AtC equilibrium_start `_ -* `fix_modify AtC extrinsic exchange `_ -* `fix_modify AtC poisson_solver `_ +* :doc:`fix_modify AtC control thermal ` +* :doc:`fix_modify AtC control momentum ` +* :doc:`fix_modify AtC control localized_lambda ` +* :doc:`fix_modify AtC control lumped_lambda_solve ` +* :doc:`fix_modify AtC control mask_direction ` +* :doc:`fix_modify AtC filter ` +* :doc:`fix_modify AtC filter scale ` +* :doc:`fix_modify AtC filter type ` +* :doc:`fix_modify AtC equilibrium_start ` +* :doc:`fix_modify AtC extrinsic exchange ` +* :doc:`fix_modify AtC poisson_solver ` *fix_modify* commands for output: -* `fix_modify AtC output `_ -* `fix_modify AtC output nodeset `_ -* `fix_modify AtC output elementset `_ -* `fix_modify AtC output boundary_integral `_ -* `fix_modify AtC output contour_integral `_ -* `fix_modify AtC mesh output `_ -* `fix_modify AtC write_restart `_ -* `fix_modify AtC read_restart `_ +* :doc:`fix_modify AtC output ` +* :doc:`fix_modify AtC output nodeset ` +* :doc:`fix_modify AtC output volume_integral ` +* :doc:`fix_modify AtC output boundary_integral ` +* :doc:`fix_modify AtC output contour_integral ` +* :doc:`fix_modify AtC mesh output ` +* :doc:`fix_modify AtC write_restart ` +* :doc:`fix_modify AtC read_restart ` *fix_modify* commands for post-processing: -* `fix_modify AtC kernel `_ -* `fix_modify AtC fields `_ -* `fix_modify AtC grdients `_ -* `fix_modify AtC rates `_ -* `fix_modify AtC computes `_ -* `fix_modify AtC on_the_fly `_ -* `fix_modify AtC pair_interactions/bond_interactions `_ -* `fix_modify AtC sample_frequency `_ -* `fix_modify AtC set `_ +* :doc:`fix_modify AtC kernel ` +* :doc:`fix_modify AtC fields ` +* :doc:`fix_modify AtC gradients ` +* :doc:`fix_modify AtC rates ` +* :doc:`fix_modify AtC computes ` +* :doc:`fix_modify AtC on_the_fly ` +* :doc:`fix_modify AtC pair/bond_interactions ` +* :doc:`fix_modify AtC sample_frequency ` +* :doc:`fix_modify AtC set ` miscellaneous *fix_modify* commands: -* `fix_modify AtC atom_element_map `_ -* `fix_modify AtC atom_weight `_ -* `fix_modify AtC write_atom_weights `_ -* `fix_modify AtC reset_time `_ -* `fix_modify AtC reset_atomic_reference_positions `_ -* `fix_modify AtC fe_md_boundary `_ -* `fix_modify AtC boundary_faceset `_ -* `fix_modify AtC consistent_fe_initialization `_ -* `fix_modify AtC mass_matrix `_ -* `fix_modify AtC material `_ -* `fix_modify AtC atomic_charge `_ -* `fix_modify AtC source_integration `_ -* `fix_modify AtC temperature_definition `_ -* `fix_modify AtC track_displacement `_ -* `fix_modify AtC boundary_dynamics `_ -* `fix_modify AtC add_species `_ -* `fix_modify AtC add_molecule `_ -* `fix_modify AtC remove_species `_ -* `fix_modify AtC remove_molecule `_ +* :doc:`fix_modify AtC atom_element_map ` +* :doc:`fix_modify AtC atom_weight ` +* :doc:`fix_modify AtC write_atom_weights ` +* :doc:`fix_modify AtC kernel_bandwidth ` +* :doc:`fix_modify AtC reset_time ` +* :doc:`fix_modify AtC reset_atomic_reference_positions ` +* :doc:`fix_modify AtC fe_md_boundary ` +* :doc:`fix_modify AtC boundary_faceset ` +* :doc:`fix_modify AtC consistent_fe_initialization ` +* :doc:`fix_modify AtC mass_matrix ` +* :doc:`fix_modify AtC material ` +* :doc:`fix_modify AtC atomic_charge ` +* :doc:`fix_modify AtC source_integration ` +* :doc:`fix_modify AtC temperature_definition ` +* :doc:`fix_modify AtC track_displacement ` +* :doc:`fix_modify AtC boundary_dynamics ` +* :doc:`fix_modify AtC add_species ` +* :doc:`fix_modify AtC add_molecule ` +* :doc:`fix_modify AtC remove_species ` +* :doc:`fix_modify AtC remove_molecule ` -Note: a set of example input files with the attendant material files are included with this package +Note: a set of example input files with the attendant material files are included in the ``examples/USER/atc`` folders. Default """"""" diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index a87fdadf83..2ad289e91e 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -108,7 +108,7 @@ non-zero molecule ID, but does not check for this at the time of swapping. If not using *semi-grand* this fix checks to ensure all atoms of the -given types have the same atomic charge. LAMMPS doesn't enforce this +given types have the same atomic charge. LAMMPS does not enforce this in general, but it is needed for this fix to simplify the swapping procedure. Successful swaps will swap the atom type and charge of the swapped atoms. Conversely, when using *semi-grand*\ , it is assumed that all the atom diff --git a/doc/src/fix_ehex.rst b/doc/src/fix_ehex.rst index 4e2ea3a73d..10622c8b3e 100644 --- a/doc/src/fix_ehex.rst +++ b/doc/src/fix_ehex.rst @@ -109,7 +109,7 @@ found in reference "(Wirnsberger)"#_Wirnsberger. This fix is different from a thermostat such as :doc:`fix nvt ` or :doc:`fix temp/rescale ` in that energy is -added/subtracted continually. Thus if there isn't another mechanism +added/subtracted continually. Thus if there is not another mechanism in place to counterbalance this effect, the entire system will heat or cool continuously. diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 3412daf63c..82a2b6e7f8 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -96,7 +96,7 @@ with optional time-dependence as well. Fix heat is different from a thermostat such as :doc:`fix nvt ` or :doc:`fix temp/rescale ` in that energy is -added/subtracted continually. Thus if there isn't another mechanism +added/subtracted continually. Thus if there is not another mechanism in place to counterbalance this effect, the entire system will heat or cool continuously. You can use multiple heat fixes so that the net energy change is 0.0 or use :doc:`fix viscous ` to drain diff --git a/doc/src/fix_modify_atc_commands.rst b/doc/src/fix_modify_atc_commands.rst new file mode 100644 index 0000000000..ec326b8bf4 --- /dev/null +++ b/doc/src/fix_modify_atc_commands.rst @@ -0,0 +1,8 @@ +fix_modify AtC commands +############################ + +.. toctree:: + :maxdepth: 1 + :glob: + + atc_* diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index b337a4e048..518b4d2302 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -45,7 +45,7 @@ Apply a spring force to a group of atoms or between two groups of atoms. This is useful for applying an umbrella force to a small molecule or lightly tethering a large group of atoms (e.g. all the solvent or a large molecule) to the center of the simulation box so -that it doesn't wander away over the course of a long simulation. It +that it does not wander away over the course of a long simulation. It can also be used to hold the centers of mass of two groups of atoms at a given distance or orientation with respect to each other. diff --git a/doc/src/if.rst b/doc/src/if.rst index fff561bd77..96a0eca42e 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -53,7 +53,7 @@ until one is found to be true, in which case its commands (f1, f2, ..., fN) are executed. If no Boolean expression is TRUE, then the commands associated with the else keyword, namely (e1, e2, ..., eN), are executed. The elif and else keywords and their associated -commands are optional. If they aren't specified and the initial +commands are optional. If they are not specified and the initial Boolean expression is FALSE, then no commands are executed. The syntax for Boolean expressions is described below. diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index 930b6cc5ce..aa00949990 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -124,7 +124,7 @@ a description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only white-space after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding -value(s) is read from the line. If it doesn't contain a header +value(s) is read from the line. If it does not contain a header keyword, the line begins the body of the file. The body of the file contains zero or more sections. The first line diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index 74b4572b95..2618953dd7 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -177,7 +177,7 @@ atom can have. LAMMPS can crash without an error message if the number of neighbors for a single particle is larger than the *page* setting, which means it is much, much larger than the *one* setting. This is - because LAMMPS doesn't error check these limits for every pairwise + because LAMMPS does not error check these limits for every pairwise interaction (too costly), but only after all the particle's neighbors have been found. This problem usually means something is very wrong with the way you have setup your problem (particle spacing, cutoff diff --git a/doc/src/package.rst b/doc/src/package.rst index 609216206d..a6a2353087 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -444,7 +444,7 @@ CPUs (i.e. the Kokkos CUDA back end is not enabled). A value of *full* uses a full neighbor lists and is the default when running on GPUs. This performs twice as much computation as the *half* option, however that is often a win because it is thread-safe and -doesn't require atomic operations in the calculation of pair forces. For +does not require atomic operations in the calculation of pair forces. For that reason, *full* is the default setting for GPUs. However, when running on CPUs, a *half* neighbor list is the default because it are often faster, just as it is for non-accelerated pair styles. Similarly, diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index 2023e655f4..e5a17658cf 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -119,7 +119,7 @@ The AGNI force field files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the AGNI potential with any LAMMPS units, but you would need to create your own AGNI potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index d7fc9a9c07..b6d1af2a79 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -246,7 +246,7 @@ The CH.airebo and CH.airebo-m potential files provided with LAMMPS You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units, but you would need to create your own AIREBO or AIREBO-M potential file with coefficients listed in the appropriate units, if your simulation -doesn't use "metal" units. +does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index a03bc3fffe..247f539ab5 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -196,7 +196,7 @@ with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the COMB potential with any LAMMPS units, but you would need to create your own COMB potential file with coefficients listed in the appropriate units if your simulation -doesn't use "metal" units. +does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index 1fa193777a..25a51c4de8 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -127,7 +127,7 @@ The *C.drip* parameter file provided with LAMMPS (see the "potentials" directory) is parameterized for metal :doc:`units `. You can use the DRIP potential with any LAMMPS units, but you would need to create your own custom parameter file with coefficients listed in the appropriate units, if your -simulation doesn't use "metal" units. +simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index 02f779bebf..5561e30919 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -174,7 +174,7 @@ The EDIP potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the EDIP potential with any LAMMPS units, but you would need to create your own EDIP potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index d2d1283618..7564252459 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -111,7 +111,7 @@ The Gao-Weber potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the GW potential with any LAMMPS units, but you would need to create your own GW potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index 4eb7a345ee..ef26556c69 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -84,7 +84,7 @@ The C.lcbop potential file provided with LAMMPS (see the potentials directory) is parameterized for metal :doc:`units `. You can use the LCBOP potential with any LAMMPS units, but you would need to create your own LCBOP potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index e40fbe60c1..1481b0bf4f 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -149,7 +149,7 @@ drops to zero. Optional keywords *safezone* and *mincap* are used for allocating reax/c arrays. Increasing these values can avoid memory problems, such as segmentation faults and bondchk failed errors, that could -occur under certain conditions. These keywords aren't used by the +occur under certain conditions. These keywords are not used by the Kokkos version, which instead uses a more robust memory allocation scheme that checks if the sizes of the arrays have been exceeded and automatically allocates more memory. @@ -341,7 +341,7 @@ The ReaxFF potential files provided with LAMMPS in the potentials directory are parameterized for real :doc:`units `. You can use the ReaxFF potential with any LAMMPS units, but you would need to create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "real" units. +appropriate units if your simulation does not use "real" units. Related commands """""""""""""""" diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index f7999c720a..b4fddc6867 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -222,7 +222,7 @@ The Stillinger-Weber potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the SW potential with any LAMMPS units, but you would need to create your own SW potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 7881c8ee70..050b1367f3 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -271,7 +271,7 @@ The Tersoff potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the Tersoff potential with any LAMMPS units, but you would need to create your own Tersoff potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 3d5bdbdaee..1761a0b9fb 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -209,7 +209,7 @@ The Tersoff/MOD potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the Tersoff/MOD potential with any LAMMPS units, but you would need to create your own Tersoff/MOD potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index fe86ef2cbb..57dc3db51e 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -286,7 +286,7 @@ The Tersoff/ZBL potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the Tersoff potential with any LAMMPS units, but you would need to create your own Tersoff potential file with coefficients -listed in the appropriate units if your simulation doesn't use "metal" +listed in the appropriate units if your simulation does not use "metal" units. Related commands diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 044709d65d..6fc5cfe015 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -245,7 +245,7 @@ The Vashishta potential files provided with LAMMPS (see the potentials directory) are parameterized for metal :doc:`units `. You can use the Vashishta potential with any LAMMPS units, but you would need to create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "metal" units. +appropriate units if your simulation does not use "metal" units. Related commands """""""""""""""" diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 2714cee4c1..642f930b9d 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -227,7 +227,7 @@ description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only white-space after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding -value(s) is read from the line. If it doesn't contain a header +value(s) is read from the line. If it does not contain a header keyword, the line begins the body of the file. The body of the file contains zero or more sections. The first line diff --git a/doc/src/read_restart.rst b/doc/src/read_restart.rst index ef77cef1af..90cc426b0d 100644 --- a/doc/src/read_restart.rst +++ b/doc/src/read_restart.rst @@ -92,7 +92,7 @@ value. The file with the largest timestep value is read in. Thus, this effectively means, read the latest restart file. It's useful if you want your script to continue a run from where it left off. See the :doc:`run ` command and its "upto" option for how to specify -the run command so it doesn't need to be changed either. +the run command so it does not need to be changed either. If a "%" character appears in the restart filename, LAMMPS expects a set of multiple files to exist. The :doc:`restart ` and diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst index 8463fd774b..16b036b449 100644 --- a/doc/src/rerun.rst +++ b/doc/src/rerun.rst @@ -55,7 +55,7 @@ initial simulation produced the dump file: * Compute the energy and forces of snapshots using a different potential. * Calculate one or more diagnostic quantities on the snapshots that - weren't computed in the initial run. These can also be computed with + were not computed in the initial run. These can also be computed with settings not used in the initial run, e.g. computing an RDF via the :doc:`compute rdf ` command with a longer cutoff than was used initially. diff --git a/doc/src/shell.rst b/doc/src/shell.rst index a7646a74d2..4eb2652c1a 100644 --- a/doc/src/shell.rst +++ b/doc/src/shell.rst @@ -8,9 +8,9 @@ Syntax .. parsed-literal:: - shell cmd args + shell command args -* cmd = *cd* or *mkdir* or *mv* or *rm* or *rmdir* or *putenv* or arbitrary command +* command = *cd* or *mkdir* or *mv* or *rm* or *rmdir* or *putenv* or arbitrary command .. parsed-literal:: @@ -62,30 +62,30 @@ With the exception of *cd*\ , all commands, including ones invoked via a system() call, are executed by only a single processor, so that files/directories are not being manipulated by multiple processors. -The *cd* cmd executes the Unix "cd" command to change the working +The *cd* command executes the Unix "cd" command to change the working directory. All subsequent LAMMPS commands that read/write files will use the new directory. All processors execute this command. -The *mkdir* cmd executes the Unix "mkdir" command to create one or +The *mkdir* command executes the Unix "mkdir" command to create one or more directories. -The *mv* cmd executes the Unix "mv" command to rename a file and/or +The *mv* command executes the Unix "mv" command to rename a file and/or move it to a new directory. -The *rm* cmd executes the Unix "rm" command to remove one or more +The *rm* command executes the Unix "rm" command to remove one or more files. -The *rmdir* cmd executes the Unix "rmdir" command to remove one or +The *rmdir* command executes the Unix "rmdir" command to remove one or more directories. A directory must be empty to be successfully removed. -The *putenv* cmd defines or updates an environment variable directly. +The *putenv* command defines or updates an environment variable directly. Since this command does not pass through the shell, no shell variable expansion or globbing is performed, only the usual substitution for LAMMPS variables defined with the :doc:`variable ` command is performed. The resulting string is then used literally. -Any other cmd is passed as-is to the shell along with its arguments as +Any other command is passed as-is to the shell along with its arguments as one string, invoked by the C-library system() call. For example, these lines in your input script: diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 9553504673..e63cf1f65a 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -259,6 +259,8 @@ Bogaerts Bogusz Bohrs Boltzman +BondAngle +BondBond bondchk bondmax bondtype @@ -390,6 +392,7 @@ cmake CMake cmap Cmax +cmd cmdlist Cmin cmm @@ -485,6 +488,7 @@ cstring cstyle csvr Ctypes +ctypes cuda Cuda CUDA @@ -745,6 +749,8 @@ electronegative electronegativity Eleftheriou ElementN +elementset +elementsets elif Elj Ellad @@ -770,6 +776,7 @@ engrot engtrans engvib enobonds +EnSight enthalpy enums envoke @@ -812,6 +819,8 @@ erotate Ertas ervel Espanol +Eshelby +eshelby eskm esu esub @@ -824,6 +833,8 @@ ethernet etol etot etotal +Eulerian +eulerian eulerimplicit Europhys ev @@ -844,6 +855,8 @@ extrema exy ey ez +faceset +facesets factorizable factorizations Fahrenberger @@ -861,6 +874,7 @@ fdotr fdt Fehlberg Fellinger +fe femtosecond femtoseconds fene @@ -884,6 +898,7 @@ fhg Fi Fichthorn Fickian +fieldname figshare Fij filelink @@ -1154,6 +1169,8 @@ Hugoniot Hura hux hwloc +hx +hy hydrophobicity hydrostatic hydrostatically @@ -1163,6 +1180,7 @@ hyperdynamics hyperradius hyperspherical hysteretic +hz Ibanez ibar ibm @@ -1381,6 +1399,7 @@ Khvostov Ki Kikugawa kim +kinetostats kJ kk Klahn @@ -1584,6 +1603,7 @@ lucy Luding Lussetti Lustig +lval lwsock lx ly @@ -1983,6 +2003,8 @@ Nocedal nocite nocoeff nodeless +nodeset +nodesets Noehring noforce Noid @@ -2161,6 +2183,7 @@ parameterizations parameterize parameterized params +ParaView parmin Parrinello Partay @@ -2252,6 +2275,7 @@ pN png Podhorszki Poiseuille +poisson Polak polarizabilities polarizability @@ -2336,6 +2360,7 @@ pymbar pymodule pymol pypar +pythonic Pyy pz Pz @@ -2759,6 +2784,8 @@ Stukowski Su subbox subcutoff +subcycle +subcycling Subramaniyan subscripted subscripting @@ -3026,6 +3053,7 @@ util utils utsa Uttormark +uval uvm uwo Uzdin @@ -3188,6 +3216,7 @@ xmax Xmax xmgrace xMIC +xmin xmovie Xmovie xmu @@ -3221,6 +3250,8 @@ yhi yi ylat ylo +ymax +ymin Yoshida ys ysu @@ -3254,6 +3285,8 @@ Ziegenhain Zj zlim zlo +zmax +zmin zmq zN zs