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Merge branch 'develop' into pair_style_tutorial

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This commit is contained in:
Axel Kohlmeyer
2023-03-17 05:42:08 -04:00
parent 5dc9a570fa fce1f8e0af
commit aca8bc4ea9
226 changed files with 15065 additions and 8745 deletions
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32
cmake/CMakeLists.txt
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@ -841,8 +841,7 @@ if(BUILD_SHARED_LIBS)
set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
COMMENT "Installing LAMMPS Python module")
else()
@ -856,35 +855,6 @@ else()
${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
endif()
###############################################################################
# Add LAMMPS python module to "install" target. This is taylored for building
# LAMMPS for package managers and with different prefix settings.
# This requires either a shared library or that the PYTHON package is included.
###############################################################################
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
file(COPY ${LAMMPS_SOURCE_DIR}/version.h DESTINATION ${CMAKE_BINARY_DIR}/python/src)
file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
endif()
endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)

12
cmake/Modules/Packages/GPU.cmake
View File

@ -177,8 +177,6 @@ if(GPU_API STREQUAL "CUDA")
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
endif()
target_link_libraries(lammps PRIVATE gpu)
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@ -251,12 +249,12 @@ elseif(GPU_API STREQUAL "OPENCL")
else()
target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
endif()
target_link_libraries(lammps PRIVATE gpu)
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
add_dependencies(ocl_get_devices OpenCL::OpenCL)
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
@ -475,10 +473,14 @@ elseif(GPU_API STREQUAL "HIP")
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
endif()
target_link_libraries(lammps PRIVATE gpu)
endif()
if(BUILD_OMP)
find_package(OpenMP COMPONENTS CXX REQUIRED)
target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX)
endif()
target_link_libraries(lammps PRIVATE gpu)
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
# detect styles which have a GPU version
RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)

4
cmake/Modules/Packages/MSCG.cmake
View File

@ -7,8 +7,8 @@ else()
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)

4
cmake/Modules/Packages/PLUMED.cmake
View File

@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

3
cmake/Modules/StyleHeaderUtils.cmake
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@ -104,6 +104,7 @@ function(RegisterStyles search_path)
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
@ -127,6 +128,7 @@ function(RegisterStylesExt search_path extension sources)
FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS ${extension} DIHEDRAL ${sources})
FindStyleHeadersExt(${search_path} DUMP_CLASS ${extension} DUMP ${sources})
FindStyleHeadersExt(${search_path} FIX_CLASS ${extension} FIX ${sources})
FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension} GRAN_SUB_MOD ${sources})
FindStyleHeadersExt(${search_path} IMPROPER_CLASS ${extension} IMPROPER ${sources})
FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension} INTEGRATE ${sources})
FindStyleHeadersExt(${search_path} KSPACE_CLASS ${extension} KSPACE ${sources})
@ -151,6 +153,7 @@ function(GenerateStyleHeaders output_path)
GenerateStyleHeader(${output_path} DIHEDRAL dihedral ) # force
GenerateStyleHeader(${output_path} DUMP dump ) # output write_dump
GenerateStyleHeader(${output_path} FIX fix ) # modify
GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
GenerateStyleHeader(${output_path} IMPROPER improper ) # force
GenerateStyleHeader(${output_path} INTEGRATE integrate ) # update
GenerateStyleHeader(${output_path} KSPACE kspace ) # force

32
doc/github-development-workflow.md
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@ -123,7 +123,7 @@ request is merged. The template for pull requests includes a header
where connections between pull requests and issues can be listed, and
thus where this comment should be placed.
## Milestones and Release Planning
## Release Planning
LAMMPS uses a continuous release development model with incremental
changes, i.e. significant effort is made -- including automated pre-merge
@ -132,24 +132,28 @@ broken. These tests are run after every update to a pull request. More
extensive and time-consuming tests (including regression testing) are
performed after code is merged to the "develop" branch. There are feature
releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
developers feel, that a sufficient number of changes has been included
developers feel, that a sufficient number of changes have been included
and all post-merge testing has been successful. These feature releases are
marked with a `patch_<version date>` tag and the "release" branch
follows only these versions with fast-forward merges. While "develop" may
be temporarily broken through issues only detected by the post-merge tests,
The "release" branch is always supposed to be of production quality.
About once each year, there is a "stable" release of LAMMPS.
These have seen additional, manual testing and review of
results from testing with instrumented code and static code analysis.
Also, the last few feature releases before a stable release are "release
candidate" versions which only contain bug fixes, feature additions to
peripheral functionality, and documentation updates. In between stable
releases, bug fixes and infrastructure updates are back-ported from the
"develop" branch to the "maintenance" branch and occasionally merged
into "stable" and published as update releases.
About once each year, there is a "stable" release of LAMMPS. These have
seen additional, manual testing and review of results from testing with
instrumented code and static code analysis. Also, the last few feature
releases before a stable release are "release candidate" versions which
only contain bug fixes, feature additions to peripheral functionality,
and documentation updates. In between stable releases, bug fixes and
infrastructure updates are back-ported from the "develop" branch to the
"maintenance" branch and occasionally merged into "stable" and published
as update releases.
## Project Management
For release planning and the information of code contributors, issues
and pull requests being actively worked on are assigned a "milestone",
which corresponds to the next stable release or the stable release after
that, with a tentative release date.
and pull requests are being managed with GitHub Project Boards. There
are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports,
and LAMMPS Pull Requests. Each board is organized in columns where
submissions are categorized. Within each column the entries are
(manually) sorted according their priority.

6
doc/src/Build_extras.rst
View File

@ -181,6 +181,9 @@ way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
The GPU library has some multi-thread support using OpenMP. If LAMMPS is built
with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@ -278,6 +281,9 @@ To support the CUDA multiprocessor server you can set the define
the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
to empty.
The GPU library has some multi-thread support using OpenMP. You need to add
the compiler flag that enables OpenMP to the ``CUDR_OPTS`` Makefile variable.
If the library build is successful, 3 files should be created:
``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS

1
doc/src/Commands_bond.rst
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@ -42,6 +42,7 @@ OPT.
* :doc:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/restrain <bond_harmonic_restrain>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`lepton (o) <bond_lepton>`

2
doc/src/Commands_compute.rst
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@ -52,6 +52,8 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`dilatation/atom <compute_dilatation_atom>`
* :doc:`dipole <compute_dipole>`
* :doc:`dipole/chunk <compute_dipole_chunk>`
* :doc:`dipole/tip4p <compute_dipole>`
* :doc:`dipole/tip4p/chunk <compute_dipole_chunk>`
* :doc:`displace/atom <compute_displace_atom>`
* :doc:`dpd <compute_dpd>`
* :doc:`dpd/atom <compute_dpd_atom>`

2
doc/src/Commands_fix.rst
View File

@ -70,6 +70,7 @@ OPT.
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode>`
* :doc:`electrode/conq (i) <fix_electrode>`
@ -93,6 +94,7 @@ OPT.
* :doc:`grem <fix_grem>`
* :doc:`halt <fix_halt>`
* :doc:`heat <fix_heat>`
* :doc:`heat/flow <fix_heat_flow>`
* :doc:`hyper/global <fix_hyper_global>`
* :doc:`hyper/local <fix_hyper_local>`
* :doc:`imd <fix_imd>`

25
doc/src/Developer_notes.rst
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@ -11,6 +11,7 @@ Available topics are:
- `Reading and parsing of text and text files`_
- `Requesting and accessing neighbor lists`_
- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
- `KSpace PPPM FFT grids`_
@ -216,6 +217,30 @@ command:
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are multiple ways to manage per-atom data within LAMMPS. Often
the per-atom storage is only used locally and managed by the class that
uses it. If the data has to persist between multiple time steps and
migrate with atoms when they move from sub-domain to sub-domain or
across periodic boundaries, then using a custom atom style, or :doc:`fix
property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
possible options.
- Using the atom style is usually the most programming effort and mostly
needed when the per-atom data is an integral part of the model like a
per-atom charge or diameter and thus should be part of the Atoms
section of a :doc:`data file <read_data>`.
- Fix property/atom is useful if the data is optional or should be
entered by the user, or accessed as a (named) custom property. In this
case the fix should be entered as part of the input (and not
internally) which allows to enter and store its content with data files.
- Fix STORE/ATOM should be used when the data should be accessed internally
only and thus the fix can be created internally.
Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

29
doc/src/Developer_updating.rst
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@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
@ -385,6 +386,34 @@ New:
This change is **required** or else the code will not compile.
Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: TBD
The available functionality of the internal fix to store per-atom
properties was expanded to enable storing data with ghost atoms and to
support binary restart files. With those changes, the fix was renamed
to fix STORE/ATOM and the number and order of (required) arguments has
changed.
Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
New syntax: ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
Since this is an internal fix, there is no user visible change.
Use Output::get_dump_by_id() instead of Output::find_dump()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

12
doc/src/Howto_granular.rst
View File

@ -43,6 +43,15 @@ The fix style *freeze* zeroes both the force and torque of frozen
atoms, and should be used for granular system instead of the fix style
*setforce*\ .
To model heat conduction, one must add the temperature and heatflow
atom variables with:
* :doc:`fix property/atom <fix_property_atom>`
a temperature integration fix
* :doc:`fix heat/flow <fix_heat_flow>`
and a heat conduction option defined in both
* :doc:`pair_style granular <pair_granular>`
* :doc:`fix wall/gran <fix_wall_gran>`
For computational efficiency, you can eliminate needless pairwise
computations between frozen atoms by using this command:
@ -55,3 +64,6 @@ computations between frozen atoms by using this command:
will be the same as in 3d. If you wish to model granular particles in
2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
doc page, where 2d simulations are discussed.
To add custom granular contact models, see the
:doc:`modifying granular sub-models page <Modify_gran_sub_mod>`.

2
doc/src/Install_linux.rst
View File

@ -172,7 +172,7 @@ Pre-built EPEL Linux executable
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS (and KIM) packages for stable releases are available
in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedoraproject.org/wiki/EPEL>`_
in the `Extra Packages for Enterprise Linux (EPEL) repository <https://docs.fedoraproject.org/en-US/epel/>`_
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
and compatible Linux distributions. Names of packages, executable,
and content are the same as described above for Fedora Linux.

1
doc/src/Modify.rst
View File

@ -34,5 +34,6 @@ style requirements and recommendations <Modify_style>`.
Modify_min
Modify_region
Modify_body
Modify_gran_sub_mod
Modify_thermo
Modify_variable

177
doc/src/Modify_gran_sub_mod.rst Normal file
View File

@ -0,0 +1,177 @@
Granular Sub-Model styles
===============================
In granular models, particles are spheres with a finite radius and rotational
degrees of freedom as further described in the
:doc:`Howto granular page <Howto_granular>`. Interactions between pair of
particles or particles and walls may therefore depend on many different modes
of motion as described in :doc:`pair granular <pair_granular>` and
:doc:`fix wall/gran <fix_wall_gran>`. In both cases, the exchange of forces,
torques, and heat flow between two types of bodies is defined using a
GranularModel class. The GranularModel class organizes the details of an
interaction using a series of granular sub-models each of which describe a
particular interaction mode (e.g. normal forces or rolling friction). From a
parent GranSubMod class, several types of sub-model classes are derived:
* GranSubModNormal: normal force sub-model
* GranSubModDamping: normal damping sub-model
* GranSubModTangential: tangential forces and sliding friction sub-model
* GranSubModRolling: rolling friction sub-model
* GranSubModTwisting: twisting friction sub-model
* GranSubModHeat: heat conduction sub-model
For each type of sub-model, more classes are further derived, each describing a
specific implementation. For instance, from the GranSubModNormal class the
GranSubModNormalHooke, GranSubModNormalHertz, and GranSubModNormalJKR classes
are derived which calculate Hookean, Hertzian, or JKR normal forces,
respectively. This modular structure simplifies the addition of new granular
contact models as as one only needs to create a new GranSubMod class without
having to modify the more complex PairGranular, FixGranWall, and GranularModel
classes. Most GranSubMod methods are also already defined by the parent classes
so new contact models typically only require edits to a few relevant methods
(e.g. methods that define coefficients and calculate forces).
Each GranSubMod class has a pointer to both the LAMMPS class and the GranularModel
class which owns it, ``lmp`` and ``gm``, respectively. The GranularModel class
includes several public variables that describe the geometry/dynamics of the
contact such as
.. list-table::
* - ``xi`` and ``xj``
- Positions of the two contacting bodies
* - ``vi`` and ``vj``
- Velocities of the two contacting bodies
* - ``omegai`` and ``omegaj``
- Angular velocities of the two contacting bodies
* - ``dx`` and ``nx``
- The displacement and normalized displacement vectors
* - ``r``, ``rsq``, and ``rinv``
- The distance, distance squared, and inverse distance
* - ``radsum``
- The sum of particle radii
* - ``vr``, ``vn``, and ``vt``
- The relative velocity vector and its normal and tangential components
* - ``wr``
- The relative rotational velocity
These quantities, among others, are calculated in the ``GranularModel->check_contact()``
and ``GranularModel->calculate_forces()`` methods which can be referred to for more
details.
To create a new GranSubMod class, it is recommended that one first looks at similar
GranSubMod classes. All GranSubMod classes share several general methods which may
need to be defined
.. list-table::
* - ``GranSubMod->mix_coeff()``
- Optional method to define how coefficients are mixed for different atom types. By default, coefficients are mixed using a geometric mean.
* - ``GranSubMod->coeffs_to_local()``
- Parses coefficients to define local variables. Run once at model construction.
* - ``GranSubMod->init()``
- Optional method to define local variables after other GranSubMod types were created. For instance, this method may be used by a tangential model that derives parameters from the normal model.
There are also several type-specific methods
.. list-table::
* - ``GranSubModNormal->touch()``
- Optional method to test when particles are in contact. By default, this is when particles overlap.
* - ``GranSubModNormal->pulloff_distance()``
- Optional method to return the distance at which particles stop interacting. By default, this is when particles no longer overlap.
* - ``GranSubModNormal->calculate_area()``
- Optional method to return the surface area of the contact. By default, this returns the geometric cross section.
* - ``GranSubModNormal->set_fncrit()``
- Optional method that defines the critical force to break the contact used by some tangential, rolling, and twisting sub-models. By default, this is the current total normal force including damping.
* - ``GranSubModNormal->calculate_forces()``
- Required method that returns the normal contact force
* - ``GranSubModDamping->calculate_forces()``
- Required method that returns the normal damping force
* - ``GranSubModTangential->calculate_forces()``
- Required method that calculates tangential forces/torques
* - ``GranSubModTwisting->calculate_forces()``
- Required method that calculates twisting friction forces/torques
* - ``GranSubModRolling->calculate_forces()``
- Required method that calculates rolling friction forces/torques
* - ``GranSubModHeat->calculate_heat()``
- Required method that returns the rate of heat flow
As an example, say one wanted to create a new normal force option that consisted
of a Hookean force with a piecewise stiffness. This could be done by adding a new
set of files ``gran_sub_mod_custom.h``:
.. code-block:: c++
#ifdef GranSubMod_CLASS
// clang-format off
GranSubModStyle(hooke/piecewise,
GranSubModNormalHookePiecewise,
NORMAL);
// clang-format on
#else
#ifndef GRAN_SUB_MOD_CUSTOM_H_
#define GRAN_SUB_MOD_CUSTOM_H_
#include "gran_sub_mod.h"
#include "gran_sub_mod_normal.h"
namespace LAMMPS_NS {
namespace Granular_NS {
class GranSubModNormalHookePiecewise : public GranSubModNormal {
public:
GranSubModNormalHookePiecewise(class GranularModel *, class LAMMPS *);
void coeffs_to_local() override;
double calculate_forces();
protected:
double k1, k2, delta_switch;
};
} // namespace Granular_NS
} // namespace LAMMPS_NS
#endif /*GRAN_SUB_MOD_CUSTOM_H_ */
#endif /*GRAN_SUB_MOD_CLASS_H_ */
and ``gran_sub_mod_custom.cpp``
.. code-block:: c++
#include "gran_sub_mod_custom.h"
#include "gran_sub_mod_normal.h"
#include "granular_model.h"
using namespace LAMMPS_NS;
using namespace Granular_NS;
GranSubModNormalHookePiecewise::GranSubModNormalHookePiecewise(GranularModel *gm, LAMMPS *lmp) : GranSubModNormal(gm, lmp)
{
num_coeffs = 4;
}
/* ---------------------------------------------------------------------- */
void GranSubModNormalHookePiecewise::coeffs_to_local()
{
k1 = coeffs[0];
k2 = coeffs[1];
damp = coeffs[2];
delta_switch = coeffs[3];
}
/* ---------------------------------------------------------------------- */
double GranSubModNormalHookePiecewise::calculate_forces()
{
double Fne;
if (gm->delta >= delta_switch) {
Fne = k1 * delta_switch + k2 * (gm->delta - delta_switch);
} else {
Fne = k1 * gm->delta;
}
return Fne;
}

141
doc/src/Python_install.rst
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@ -27,124 +27,19 @@ interpreter can find it and installing the LAMMPS shared library into a
folder that the dynamic loader searches or inside of the installed
``lammps`` package folder. There are multiple ways to achieve this.
#. Do a full LAMMPS installation of libraries, executables, selected
headers, documentation (if enabled), and supporting files (only
available via CMake), which can also be either system-wide or into
user specific folders.
#. Install both components into a Python ``site-packages`` folder, either
system-wide or in the corresponding user-specific folder. This way no
additional environment variables need to be set, but the shared
library is otherwise not accessible.
#. Do an installation into a virtual environment. This can either be an
installation of the Python package only or a full installation of LAMMPS.
#. Do an installation into a virtual environment.
#. Leave the files where they are in the source/development tree and
adjust some environment variables.
.. tabs::
.. tab:: Full install (CMake-only)
:ref:`Build the LAMMPS executable and library <library>` with
``-DBUILD_SHARED_LIBS=on``, ``-DLAMMPS_EXCEPTIONS=on`` and
``-DPKG_PYTHON=on`` (The first option is required, the other two
are optional by recommended). The exact file name of the shared
library depends on the platform (Unix/Linux, macOS, Windows) and
the build configuration being used. The installation base folder
is already set by default to the ``$HOME/.local`` directory, but
it can be changed to a custom location defined by the
``CMAKE_INSTALL_PREFIX`` CMake variable. This uses a folder
called ``build`` to store files generated during compilation.
.. code-block:: bash
# create build folder
mkdir build
cd build
# configure LAMMPS compilation
cmake -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
# compile LAMMPS
cmake --build .
# install LAMMPS into $HOME/.local
cmake --install .
This leads to an installation to the following locations:
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$HOME/.local/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$HOME/.local/bin/`` | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
For a system-wide installation you need to set
``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
``/usr/local``); the default is ``${HOME}/.local``. The
installation step for a system folder installation (**not** the
configuration/compilation) needs to be done with superuser
privilege, e.g. by using ``sudo cmake --install .``. The
installation folders will then be changed to (assuming ``/usr`` as
prefix):
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=========================================================+=============================================================+
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/`` (32bit) | |
| | * ``/usr/lib64/`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``/usr/bin/`` | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``/usr/share/lammps/potentials/`` | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
To be able to use the "user" installation you have to ensure that
the folder containing the LAMMPS shared library is either included
in a path searched by the shared linker (e.g. like
``/usr/lib64/``) or part of the ``LD_LIBRARY_PATH`` environment
variable (or ``DYLD_LIBRARY_PATH`` on macOS). Otherwise you will
get an error when trying to create a LAMMPS object through the
Python module.
.. code-block:: bash
# Unix/Linux
export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH
# macOS
export DYLD_LIBRARY_PATH=$HOME/.local/lib:$DYLD_LIBRARY_PATH
If you plan to use the LAMMPS executable (e.g., ``lmp``), you may
also need to adjust the ``PATH`` environment variable (but many
newer Linux distributions already have ``$HOME/.local/bin``
included). Example:
.. code-block:: bash
export PATH=$HOME/.local/bin:$PATH
To make those changes permanent, you can add the commands to your
``$HOME/.bashrc`` file. For a system-wide installation is is not
necessary due to files installed in system folders that are loaded
automatically when a login shell is started.
.. tab:: Python package only
.. tab:: Python package
Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
:doc:`traditional make <Build_make>` procedure in :ref:`shared
@ -272,38 +167,6 @@ folder that the dynamic loader searches or inside of the installed
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
If you do a full installation (CMake only) with "install", this
leads to the following installation locations:
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+========================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
In that case you need to modify the ``$HOME/myenv/bin/activate``
script in a similar fashion you need to update your
``$HOME/.bashrc`` file to include the shared library and
executable locations in ``LD_LIBRARY_PATH`` (or
``DYLD_LIBRARY_PATH`` on macOS) and ``PATH``, respectively.
For example with:
.. code-block:: bash
# Unix/Linux
echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
# macOS
echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
.. tab:: In place usage
You can also :doc:`compile LAMMPS <Build>` as usual in

17
doc/src/atom_style.rst
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@ -161,15 +161,14 @@ and each stores a per-particle diameter and mass. If the diameter >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by use of the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
can be effectively treated as 2d discs for a 2d simulation if desired.
See also the :doc:`set density/disc <set>` command. The *sphere* and
*bpm/sphere* styles take an optional 0 or 1 argument. A value of 0
means the radius of each sphere is constant for the duration of the
simulation. A value of 1 means the radii may vary dynamically during
the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
command.
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`,
:doc:`fix npt/sphere <fix_npt_sphere>` commands for the *sphere* style,
spheres can be effectively treated as 2d discs for a 2d simulation if
desired. See also the :doc:`set density/disc <set>` command. These
styles take an optional 0 or 1 argument. A value of 0 means the
radius of each sphere is constant for the duration of the simulation.
A value of 1 means the radii may vary dynamically during the simulation,
e.g. due to use of the :doc:`fix adapt <fix_adapt>` command.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or

90
doc/src/bond_harmonic_restrain.rst Normal file
View File

@ -0,0 +1,90 @@
.. index:: bond_style harmonic/restrain
bond_style harmonic/restrain command
====================================
Syntax
""""""
.. code-block:: LAMMPS
bond_style harmonic/restrain
Examples
""""""""
.. code-block:: LAMMPS
bond_style harmonic
bond_coeff 5 80.0
Description
"""""""""""
.. versionadded:: TBD
The *harmonic/restrain* bond style uses the potential
.. math::
E = K (r - r_{t=0})^2
where :math:`r_{t=0}` is the distance between the bonded atoms at the
beginning of the first :doc:`run <run>` or :doc:`minimize <minimize>`
command after the bond style has been defined (*t=0*). Note that the
usual 1/2 factor is included in :math:`K`. This will effectively
restrain bonds to their initial length, whatever that is. This is where
this bond style differs from :doc:`bond style harmonic <bond_harmonic>`
where the bond length is set through the per bond type coefficients.
The following coefficient must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands
* :math:`K` (energy/distance\^2)
This bond style differs from other options to add harmonic restraints
like :doc:`fix restrain <fix_restrain>` or :doc:`pair style list
<pair_list>` or :doc:`fix colvars <fix_colvars>` in that it requires a
bond topology, and thus the defined bonds will trigger exclusion of
special neighbors from the neighbor list according to the
:doc:`special_bonds <special_bonds>` settings.
Restart info
""""""""""""
This bond style supports the :doc:`write_restart <write_restart>` and
:doc:`read_restart <read_restart>` commands. The state of the initial
bond lengths is stored with restart files and read back.
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
page for more info.
This bond style maintains internal data to determine the original bond
lengths :math:`r_{t=0}`. This information will be written to
:doc:`binary restart files <write_restart>` but **not** to :doc:`data
files <write_data>`. Thus, continuing a simulation is *only* possible
with :doc:`read_restart <read_restart>`. When using the :doc:`read_data
command <read_data>`, the reference bond lengths :math:`r_{t=0}` will be
re-initialized from the current geometry.
This bond style cannot be used with :doc:`fix shake or fix rattle
<fix_shake>`, with :doc:`fix filter/corotate <fix_filter_corotate>`, or
any :doc:`tip4p pair style <pair_lj_cut_tip4p>` since there is no specific
equilibrium distance for a given bond type.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`bond_harmonic <bond_harmonic>`,
:doc:`fix restrain <fix_restrain>`, :doc:`pair style list <pair_list>`
Default
"""""""
none

3
doc/src/bond_style.rst
View File

@ -10,7 +10,7 @@ Syntax
bond_style style args
* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
* args = none for any style except *hybrid*
@ -93,6 +93,7 @@ accelerated styles exist.
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
* :doc:`harmonic <bond_harmonic>` - harmonic bond
* :doc:`harmonic/restrain <bond_harmonic_restrain>` - harmonic bond to restrain to original bond distance
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
* :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
* :doc:`lepton <bond_lepton>` - bond potential from evaluating a string

2
doc/src/compute.rst
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@ -206,6 +206,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`dilatation/atom <compute_dilatation_atom>` - Peridynamic dilatation for each atom
* :doc:`dipole <compute_dipole>` - dipole vector and total dipole
* :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
* :doc:`dipole/tip4p <compute_dipole>` - dipole vector and total dipole with TIP4P pair style
* :doc:`dipole/tip4p/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk with TIP4P pair style
* :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
* :doc:`dpd <compute_dpd>` - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
* :doc:`dpd/atom <compute_dpd_atom>` - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature

45
doc/src/compute_dipole.rst
View File

@ -1,6 +1,10 @@
.. index:: compute dipole
.. index:: compute dipole/tip4p
compute dipole command
======================
compute dipole/tip4p command
============================
Syntax
@ -8,10 +12,10 @@ Syntax
.. code-block:: LAMMPS
compute ID group-ID dipole arg
compute ID group-ID style arg
* ID, group-ID are documented in :doc:`compute <compute>` command
* dipole = style name of this compute command
* style = *dipole* or *dipole/tip4p*
* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
Examples
@ -21,6 +25,7 @@ Examples
compute 1 fluid dipole
compute dw water dipole geometry
compute dw water dipole/tip4p
Description
"""""""""""
@ -28,13 +33,20 @@ Description
Define a computation that calculates the dipole vector and total dipole
for a group of atoms.
This compute calculates the x,y,z coordinates of the dipole vector
and the total dipole moment for the atoms in the compute group.
This includes all effects due to atoms passing through periodic boundaries.
For a group with a net charge the resulting dipole is made position independent
by subtracting the position vector of the center of mass or geometric center
times the net charge from the computed dipole vector. Both per-atom charges
and per-atom dipole moments, if present, contribute to the computed dipole.
These computes calculate the x,y,z coordinates of the dipole vector and
the total dipole moment for the atoms in the compute group. This
includes all effects due to atoms passing through periodic boundaries.
For a group with a net charge the resulting dipole is made position
independent by subtracting the position vector of the center of mass or
geometric center times the net charge from the computed dipole
vector. Both per-atom charges and per-atom dipole moments, if present,
contribute to the computed dipole.
.. versionadded:: TBD
Compute *dipole/tip4p* includes adjustments for the charge carrying
point M in molecules with TIP4P water geometry. The corresponding
parameters are extracted from the pair style.
.. note::
@ -49,10 +61,10 @@ and per-atom dipole moments, if present, contribute to the computed dipole.
Output info
"""""""""""
This compute calculations a global scalar containing the magnitude of
the computed dipole moment and a global vector of length 3 with the
dipole vector. See the :doc:`Howto output <Howto_output>` page for
an overview of LAMMPS output options.
These computes calculate a global scalar containing the magnitude of the
computed dipole moment and a global vector of length 3 with the dipole
vector. See the :doc:`Howto output <Howto_output>` page for an overview
of LAMMPS output options.
The computed values are "intensive". The array values will be in
dipole units (i.e., charge :doc:`units <units>` times distance
@ -60,7 +72,12 @@ dipole units (i.e., charge :doc:`units <units>` times distance
Restrictions
""""""""""""
none
Compute style *dipole/tip4p* is part of the EXTRA-COMPUTE package. It is
only enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` page for more info.
Compute style *dipole/tip4p* can only be used with tip4p pair styles.
Related commands
""""""""""""""""

47
doc/src/compute_dipole_chunk.rst
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@ -1,17 +1,21 @@
.. index:: compute dipole/chunk
.. index:: compute dipole/tip4p/chunk
compute dipole/chunk command
============================
compute dipole/tip4p/chunk command
==================================
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID dipole/chunk chunkID arg
compute ID group-ID style chunkID arg
* ID, group-ID are documented in :doc:`compute <compute>` command
* dipole/chunk = style name of this compute command
* style = *dipole/chunk* or *dipole/tip4p/chunk*
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
@ -38,13 +42,20 @@ or atoms in a spatial bin. See the :doc:`compute chunk/atom
details of how chunks can be defined and examples of how they can be
used to measure properties of a system.
This compute calculates the :math:`(x,y,z)` coordinates of the dipole vector
and the total dipole moment for each chunk, which includes all effects due
to atoms passing through periodic boundaries. For chunks with a net
charge the resulting dipole is made position independent by subtracting
the position vector of the center of mass or geometric center times the
net charge from the computed dipole vector. Both per-atom charges and
per-atom dipole moments, if present, contribute to the computed dipole.
These computes calculate the :math:`(x,y,z)` coordinates of the dipole
vector and the total dipole moment for each chunk, which includes all
effects due to atoms passing through periodic boundaries. For chunks
with a net charge the resulting dipole is made position independent by
subtracting the position vector of the center of mass or geometric
center times the net charge from the computed dipole vector. Both
per-atom charges and per-atom dipole moments, if present, contribute to
the computed dipole.
.. versionadded:: TBD
Compute *dipole/tip4p/chunk* includes adjustments for the charge
carrying point M in molecules with TIP4P water geometry. The
corresponding parameters are extracted from the pair style.
Note that only atoms in the specified group contribute to the
calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
@ -78,12 +89,12 @@ command, for example:
Output info
"""""""""""
This compute calculates a global array where the number of rows = the
These computes calculate a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified :doc:`compute
chunk/atom <compute_chunk_atom>` command. The number of columns is 4 for
the :math:`(x,y,z)` dipole vector components and the total dipole of each
chunk. These values can be accessed by any command that uses global
array values from a compute as input. See the :doc:`Howto output
chunk/atom <compute_chunk_atom>` command. The number of columns is 4
for the :math:`(x,y,z)` dipole vector components and the total dipole of
each chunk. These values can be accessed by any command that uses
global array values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in
@ -92,7 +103,13 @@ dipole units (i.e., charge :doc:`units <units>` times distance
Restrictions
""""""""""""
none
Compute style *dipole/tip4p/chunk* is part of the EXTRA-COMPUTE
package. It is only enabled if LAMMPS was built with that package. See
the :doc:`Build package <Build_package>` page for more info.
Compute style *dipole/tip4p/chunk* can only be used with tip4p pair
styles.
Related commands
""""""""""""""""

3
doc/src/dump.rst
View File

@ -111,6 +111,7 @@ Syntax
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
heatflow, temperature,
c_ID, c_ID[I], f_ID, f_ID[I], v_name,
i_name, d_name, i2_name[I], d2_name[I]
@ -137,6 +138,8 @@ Syntax
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
heatflow = rate of heat flow into particle
temperature = temperature of particle
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID

2
doc/src/fix.rst
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@ -222,6 +222,7 @@ accelerated styles exist.
* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
* :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
* :doc:`electrode/conp <fix_electrode>` - impose electric potential
* :doc:`electrode/conq <fix_electrode>` - impose total electric charge
@ -245,6 +246,7 @@ accelerated styles exist.
* :doc:`grem <fix_grem>` - implements the generalized replica exchange method
* :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
* :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
* :doc:`heat/flow <fix_heat_flow>` - plain time integration of heat flow with per-atom temperature updates
* :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
* :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol

96
doc/src/fix_efield.rst
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@ -1,17 +1,21 @@
.. index:: fix efield
.. index:: fix efield/tip4p
fix efield command
==================
fix efield/tip4p command
========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID efield ex ey ez keyword value ...
fix ID group-ID style ex ey ez keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* efield = style name of this fix command
* style = *efield* or *efield/tip4p*
* ex,ey,ez = E-field component values (electric field units)
* any of ex,ey,ez can be a variable (see below)
* zero or more keyword/value pairs may be appended to args
@ -31,27 +35,36 @@ Examples
fix kick external-field efield 1.0 0.0 0.0
fix kick external-field efield 0.0 0.0 v_oscillate
fix kick external-field efield/tip4p 1.0 0.0 0.0
Description
"""""""""""
Add a force F = qE to each charged atom in the group due to an
Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
external electric field being applied to the system. If the system
contains point-dipoles, also add a torque on the dipoles due to the
external electric field.
For charges, any of the 3 quantities defining the E-field components
can be specified as an equal-style or atom-style
:doc:`variable <variable>`, namely *ex*, *ey*, *ez*\ . If the value is a
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
its value used to determine the E-field component.
.. versionadded:: TBD
When the *efield/tip4p* style is used, the E-field will be applied to
the position of the virtual charge site M of a TIP4P molecule instead of
the oxygen position as it is defined by a corresponding :doc:`TIP4P pair
style <pair_lj_cut_tip4p>`. The forces on the M site due to the
external field are projected on the oxygen and hydrogen atoms of the
TIP4P molecules.
For charges, any of the 3 quantities defining the E-field components can
be specified as an equal-style or atom-style :doc:`variable <variable>`,
namely *ex*, *ey*, *ez*\ . If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case, the
variable will be evaluated each timestep, and its value used to
determine the E-field component.
For point-dipoles, equal-style variables can be used, but atom-style
variables are not currently supported, since they imply a spatial
gradient in the electric field which means additional terms with
gradients of the field are required for the force and torque on
dipoles.
gradients of the field are required for the force and torque on dipoles.
Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
@ -81,10 +94,18 @@ self-consistent minimization problem (see below).
The *energy* keyword is not allowed if the added field is a constant
vector (ex,ey,ez), with all components defined as numeric constants
and not as variables. This is because LAMMPS can compute the energy
for each charged particle directly as E = -x dot qE = -q (x\*ex + y\*ey
+ z\*ez), so that -Grad(E) = F. Similarly for point-dipole particles
the energy can be computed as E = -mu dot E = -(mux\*ex + muy\*ey +
muz\*ez).
for each charged particle directly as
.. math::
U_{efield} = -\vec{x} \cdot q\vec{E} = -q (x\cdot E_x + y\cdot E_y + z\cdot Ez),
so that :math:`-\nabla U_{efield} = \vec{F}`. Similarly for point-dipole particles
the energy can be computed as
.. math::
U_{efield} = -\vec{\mu} \cdot \vec{E} = -\mu_x\cdot E_x + \mu_y\cdot E_y + \mu_z\cdot E_z
The *energy* keyword is optional if the added force is defined with
one or more variables, and if you are performing dynamics via the
@ -120,29 +141,28 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy inferred by the added force due
to the electric field to the global potential energy of the system as
part of :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
Note that this energy is a fictitious quantity but is needed so that
the :doc:`minimize <minimize>` command can include the forces added by
this fix in a consistent manner. I.e. there is a decrease in
potential energy when atoms move in the direction of the added force
due to the electric field.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential energy inferred by the added force due to the
electric field to the global potential energy of the system as part of
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify energy no <fix_modify>`. Note that this
energy is a fictitious quantity but is needed so that the :doc:`minimize
<minimize>` command can include the forces added by this fix in a
consistent manner. I.e. there is a decrease in potential energy when
atoms move in the direction of the added force due to the electric
field.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to both the
global pressure and per-atom stress of the system via the :doc:`compute
pressure <compute_pressure>` and :doc:`compute stress/atom
<compute_stress_atom>` commands. The former can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix adding its forces. Default is the
outermost level.
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands
@ -169,7 +189,11 @@ the iteration count during the minimization.
Restrictions
""""""""""""
None
Fix style *efield/tip4p* is part of the EXTRA-FIX package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` page for more info.
Fix style *efield/tip4p* can only be used with tip4p pair styles.
Related commands
""""""""""""""""

70
doc/src/fix_heat_flow.rst Normal file
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@ -0,0 +1,70 @@
.. index:: fix heat/flow
fix heat/flow command
==========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID heat/flow style values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* heat/flow = style name of this fix command
* one style with corresponding value(s) needs to be listed
.. parsed-literal::
style = *constant* or *type*
*constant* = cp
cp = value of specifc heat (energy/(mass * temperature) units)
*type* = cp1 ... cpN
cpN = value of specifc heat for type N (energy/(mass * temperature) units)
*
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all heat/flow constant 1.0
fix 1 all heat/flow type 1.0 0.5
Description
"""""""""""
Perform plain time integration to update temperature for atoms in the
group each timestep. The specific heat of atoms can be defined using either
the *constant* or *type* keywords. For style *constant*, the specific heat
is a constant value *cp* for all atoms. For style *type*, *N* different values
of the specific heat are defined, one for each of the *N* types of atoms.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
No global or per-atom quantities are stored by this fix for access by various
:doc:`output commands <Howto_output>`. No parameter of this fix can be used
with the *start/stop* keywords of the :doc:`run <run>` command. This fix is
not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix requires that atoms store temperature and heat flow
as defined by the :doc:`fix property/atom <fix_property_atom>` command.
Related commands
""""""""""""""""
:doc:`pair granular <pair_granular>`, :doc:`fix property/atom <fix_property_atom>`
Default
"""""""
none

16
doc/src/fix_wall_gran.rst
View File

@ -46,7 +46,7 @@ Syntax
radius = cylinder radius (distance units)
* zero or more keyword/value pairs may be appended to args
* keyword = *wiggle* or *shear* or *contacts*
* keyword = *wiggle* or *shear* or *contacts* or *temperature*
.. parsed-literal::
@ -59,6 +59,8 @@ Syntax
vshear = magnitude of shear velocity (velocity units)
*contacts* value = none
generate contact information for each particle
*temperature* value = temperature
specify temperature of wall
Examples
@ -71,7 +73,7 @@ Examples
fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji heat 10 region myCone temperature 1.0
fix 6 all wall/gran hooke 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
Description
@ -177,6 +179,16 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
*vshear* < 0. In this case, *vshear* is the tangential velocity of
the wall at whatever *radius* has been defined.
The *temperature* keyword is used to assign a temperature to the wall.
The following value can either be a numeric value or an equal-style
:doc:`variable <variable>`. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case, the
variable will be evaluated each timestep, and its value used to determine
the temperature. This option must be used in conjunction with a heat
conduction model defined in :doc:`pair_style granular <pair_granular>`,
:doc:`fix property/atom <fix_property_atom>` to store temperature and a
heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
flow.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

15
doc/src/fix_wall_gran_region.rst
View File

@ -36,12 +36,14 @@ Syntax
* wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
* region-ID = region whose boundary will act as wall
* keyword = *contacts*
* keyword = *contacts* or *temperature*
.. parsed-literal::
*contacts* value = none
generate contact information for each particle
*temperature* value = temperature
specify temperature of wall
Examples
""""""""
@ -200,6 +202,17 @@ values for the 6 wall/particle coefficients than for particle/particle
interactions. E.g. if you wish to model the wall as a different
material.
The *temperature* keyword is used to assign a temperature to the wall.
The following value can either be a numeric value or an equal-style
:doc:`variable <variable>`. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case, the
variable will be evaluated each timestep, and its value used to determine
the temperature. This option must be used in conjunction with a heat
conduction model defined in :doc:`pair_style granular <pair_granular>`,
:doc:`fix property/atom <fix_property_atom>` to store temperature and a
heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
flow.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

5
doc/src/pair_gran.rst
View File

@ -279,6 +279,11 @@ statistically similar results. This is because the forces they
compute depend on atom velocities. See the
:doc:`read_restart <read_restart>` command for more details.
Accumulated values for individual contacts are saved to to restart
files but are not saved to data files. Therefore, forces may
differ significantly when a system is reloaded using A
:doc:`read_data <read_data>` command.
Related commands
""""""""""""""""

80
doc/src/pair_granular.rst
View File

@ -37,6 +37,9 @@ Examples
pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall
pair_style granular
pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 heat area 0.1
Description
"""""""""""
@ -223,16 +226,19 @@ for all models except *jkr*, for which it is given implicitly according
to :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`. For *damping viscoelastic*,
:math:`\eta_{n0}` is in units of 1/(\ *time*\ \*\ *distance*\ ).
The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`. Here, the damping coefficient specified as part of
the normal model is interpreted as a restitution coefficient
:math:`e`. The damping constant :math:`\eta_n` is given by:
The *tsuji* model is based on the work of :ref:`(Tsuji et al) <Tsuji1992>`.
Here, the damping coefficient specified as part of the normal model is interpreted
as a restitution coefficient :math:`e`. The damping constant :math:`\eta_n` is
given by:
.. math::
\eta_n = \alpha (m_{eff}k_n)^{1/2}
For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. The parameter :math:`\alpha` is related to the restitution
coefficient *e* according to:
For normal contact models based on material parameters, :math:`k_n = 4/3Ea`. This
damping model is not compatible with cohesive normal models such as *JKR* or *DMT*.
The parameter :math:`\alpha` is related to the restitution coefficient *e*
according to:
.. math::
@ -631,6 +637,34 @@ attractive force. This keyword cannot be used with the JKR or DMT models.
----------
The optional *heat* keyword enables heat conduction. The options currently
supported are:
1. *none*
2. *area* : :math:`k_{s}`
If the *heat* keyword is not specified, the model defaults to *none*.
For *heat* *area*, the heat
:math:`Q` conducted between two particles is given by
.. math::
Q = k_{s} a \Delta T
where :math:`\Delta T` is the difference in the two particles' temperature,
:math:`k_{s}` is a non-negative numeric value for the conductivity, and
:math:`a` is the area of the contact and depends on the normal force model.
Note that the option *none* must either be used in all or none of of the
*pair_coeff* calls. See :doc:`fix heat/flow <fix_heat_flow>` and
:doc:`fix property/atom <fix_property_atom>` for more information on this
option.
----------
The *granular* pair style can reproduce the behavior of the
*pair gran/\** styles with the appropriate settings (some very
minor differences can be expected due to corrections in
@ -641,7 +675,7 @@ is equivalent to *pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1*\ .
The second example is equivalent to
*pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
The third example is equivalent to
*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1*\ .
*pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1 limit_damping*\ .
----------
@ -733,22 +767,30 @@ These extra quantities can be accessed by the :doc:`compute pair/local <compute_
Restrictions
""""""""""""
All the granular pair styles are part of the GRANULAR package. It is
only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This pair style is part of the GRANULAR package. It is
only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the :doc:`atom_style <atom_style>`. They also
require a per-particle radius is stored. The *sphere* atom style does
all of this.
This pair style requires that atoms store per-particle radius,
torque, and angular velocity (omega) as defined by the
:doc:`atom_style sphere <atom_style>`.
This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>` command so that velocities are stored by ghost
atoms.
This pair style requires you to use the :doc:`comm_modify vel yes <comm_modify>`
command so that velocities are stored by ghost atoms.
These pair styles will not restart exactly when using the
:doc:`read_restart <read_restart>` command, though they should provide
statistically similar results. This is because the forces they
compute depend on atom velocities. See the
:doc:`read_restart <read_restart>` command for more details.
This pair style will not restart exactly when using the
:doc:`read_restart <read_restart>` command, though it should provide
statistically similar results. This is because the forces it
computes depend on atom velocities and the atom velocities have
been propagated half a timestep between the force computation and
when the restart is written, due to using Velocity Verlet time
integration. See the :doc:`read_restart <read_restart>` command
for more details.
Accumulated values for individual contacts are saved to restart
files but are not saved to data files. Therefore, forces may
differ significantly when a system is reloaded using the
:doc:`read_data <read_data>` command.
Related commands
""""""""""""""""

10
doc/src/set.rst
View File

@ -19,7 +19,7 @@ Syntax
*spin/electron* or *radius/electron* or
*quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
*theta* or *theta/random* or *angmom* or *omega* or
*mass* or *density* or *density/disc* or
*mass* or *density* or *density/disc* or *temperature* or
*volume* or *image* or *bond* or *angle* or *dihedral* or
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
@ -100,6 +100,8 @@ Syntax
value can be an atom-style variable (see below)
*density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
value can be an atom-style variable (see below)
*temperature* value = temperature for finite-size particles (temperature units)
value can be an atom-style variable (see below)
*volume* value = particle volume for Peridynamic particle (distance\^3 units)
value can be an atom-style variable (see below)
*image* nx ny nz
@ -429,6 +431,12 @@ assumed to be in mass/distance\^2 units).
If none of these cases are valid, then the mass is set to the density
value directly (the input density is assumed to be in mass units).
Keyword *temperature* sets the temperature of a finite-size particle.
Currently, only the GRANULAR package supports this attribute. The
temperature must be added using an instance of
:doc:`fix property/atom <fix_property_atom>` The values for the
temperature must be positive.
Keyword *volume* sets the volume of all selected particles. Currently,
only the :doc:`atom_style peri <atom_style>` command defines particles
with a volume attribute. Note that this command does not adjust the

3
doc/utils/requirements.txt
View File

@ -1,5 +1,6 @@
Sphinx<6.0.0
Sphinx < 7.0.0
sphinxcontrib-spelling
sphinxcontrib-jquery >=3.0.0
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs
breathe

1
doc/utils/sphinx-config/conf.py.in
View File

@ -47,6 +47,7 @@ extensions = [
'sphinx.ext.mathjax',
'sphinx.ext.imgmath',
'sphinx.ext.autodoc',
'sphinxcontrib.jquery',
'sphinxfortran.fortran_domain',
'sphinx_tabs.tabs',
'table_from_list',

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -1376,6 +1376,7 @@ hdnnp
HDNNP
Hearn
heatconduction
heatflow
Hebbeker
Hebenstreit
Hecht
@ -2473,6 +2474,7 @@ nodeless
nodeset
nodesets
Noehring
nofix
Noffset
noforce
noguess

484
examples/granregion/log.16Mar23.granregion.box.g++.1 Normal file
View File

@ -0,0 +1,484 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
Particle insertion: 48 every 566 steps, 100 by step 1133
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.5861 | 0.5861 | 0.5861 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
100 30 0.803783 0.803783 0.39507978 0.0029137134
200 30 1.1967995 1.1967995 0.5882574 0.0043383984
300 30 1.2814686 1.2814686 0.62987441 0.0046453238
400 30 0.82331082 0.82331082 0.41173176 0.0029845017
500 30 0.7708462 0.7708462 0.38777784 0.0043831147
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
600 64 0.51564897 0.51564897 0.26631577 0.0040059368
700 64 0.57239348 0.57239348 0.29566901 0.0045075987
800 64 0.61837087 0.61837087 0.32195387 0.0048123564
900 64 0.53061888 0.53061888 0.28564763 0.0055906552
1000 64 0.496299 0.496299 0.26801572 0.0061169128
1100 64 0.46068308 0.46068308 0.24699057 0.0055717699
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
1200 99 0.39206225 0.39206225 0.21356546 0.0066294211
1300 99 0.38624966 0.38624966 0.21345854 0.0049051051
1400 99 0.35615284 0.35615284 0.19785725 0.0046170772
1500 99 0.31486693 0.31486693 0.17429055 0.0064903432
1600 99 0.26369001 0.26369001 0.15095266 0.0045226847
1700 100 0.1925923 0.1925923 0.11308104 0.007362313
1800 100 0.13724978 0.13724978 0.083276845 0.0058136373
1900 100 0.077212636 0.077212636 0.053159386 0.0016509598
2000 100 0.065294031 0.065294031 0.04372752 0.0020346467
2100 100 0.057431398 0.057431398 0.037977068 0.0012681098
2200 100 0.059093045 0.059093045 0.037435193 0.00096610799
2300 100 0.03422338 0.03422338 0.025491304 0.00069886052
2400 100 0.020558284 0.020558284 0.016163009 0.0017260663
2500 100 0.015339709 0.015339709 0.012329236 0.00041308031
2600 100 0.012891354 0.012891354 0.009766054 0.00030356722
2700 100 0.0092634449 0.0092634449 0.0073580108 0.00077723051
2800 100 0.0073925841 0.0073925841 0.0059932218 0.00016466767
2900 100 0.0081228267 0.0081228267 0.006281761 0.00013828388
3000 100 0.0041833223 0.0041833223 0.0035147096 0.00013160599
3100 100 0.0035930775 0.0035930775 0.0030039922 0.00060639771
3200 100 0.0030824465 0.0030824465 0.0026541293 0.00047391014
3300 100 0.0035087522 0.0035087522 0.0027664508 0.00014080317
3400 100 0.0018537868 0.0018537868 0.0017099705 6.3326674e-05
3500 100 0.0015371228 0.0015371228 0.0014155433 0.00021612522
3600 100 0.001708556 0.001708556 0.0014369892 8.1034202e-05
3700 100 0.00095948652 0.00095948652 0.0009788528 3.4694023e-05
3800 100 0.00091875668 0.00091875668 0.00086805146 3.9373686e-05
3900 100 0.001557068 0.001557068 0.001159526 2.5178607e-05
4000 100 0.00062012451 0.00062012451 0.00066806922 5.6680551e-06
4100 100 0.00060940771 0.00060940771 0.00065614741 1.0137901e-05
4200 100 0.00059538437 0.00059538437 0.00064501521 7.3679744e-06
4300 100 0.00052946048 0.00052946048 0.00059353641 5.9225081e-06
4400 100 0.00051202281 0.00051202281 0.00057524772 3.6198435e-05
4500 100 0.00049986632 0.00049986632 0.00055754521 2.2275519e-05
4600 100 0.00048187334 0.00048187334 0.00053988815 2.2015243e-05
4700 100 0.00045261491 0.00045261491 0.00050298355 8.9681339e-05
4800 100 0.00034965427 0.00034965427 0.0004278781 1.0983535e-05
4900 100 0.00033555621 0.00033555621 0.00041435167 2.9266598e-05
5000 100 0.00031387148 0.00031387148 0.00039605781 2.5628425e-05
Loop time of 0.073938 on 1 procs for 5000 steps with 100 atoms
Performance: 29213677.752 tau/day, 67624.254 timesteps/s, 6.762 Matom-step/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0084547 | 0.0084547 | 0.0084547 | 0.0 | 11.43
Neigh | 0.011399 | 0.011399 | 0.011399 | 0.0 | 15.42
Comm | 0.00077205 | 0.00077205 | 0.00077205 | 0.0 | 1.04
Output | 0.00042663 | 0.00042663 | 0.00042663 | 0.0 | 0.58
Modify | 0.049692 | 0.049692 | 0.049692 | 0.0 | 67.21
Other | | 0.003194 | | | 4.32
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 164 ave 164 max 164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 164
Ave neighs/atom = 1.64
Neighbor list builds = 281
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Region properties for region container changed between runs, resetting its motion (src/GRANULAR/fix_wall_gran_region.cpp:101)
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00031387148 0.00031387148 0.00039605781 2.6174978e-05
5100 100 0.54537023 0.54537023 0.30042175 0.0087427352
5200 100 0.57210852 0.57210852 0.3192468 0.0098134067
5300 100 0.7168108 0.7168108 0.38577893 0.011004584
5400 100 0.78895524 0.78895524 0.41889428 0.013555713
5500 100 0.87797874 0.87797874 0.45689223 0.01565356
5600 100 0.95424379 0.95424379 0.48830429 0.014707858
5700 100 1.0046012 1.0046012 0.51054927 0.01469179
5800 100 1.0371453 1.0371453 0.5262568 0.015576788
5900 100 1.0545743 1.0545743 0.5361173 0.01589889
6000 100 1.0932949 1.0932949 0.55402214 0.017484573
6100 100 1.1148364 1.1148364 0.56241126 0.01721788
6200 100 1.1315267 1.1315267 0.57050887 0.017961246
6300 100 1.1506124 1.1506124 0.58009471 0.017159062
6400 100 1.1663328 1.1663328 0.5876586 0.017935311
6500 100 1.1821086 1.1821086 0.59595161 0.018005316
6600 100 1.2039397 1.2039397 0.60567523 0.021604661
6700 100 1.2269912 1.2269912 0.61770225 0.018907995
6800 100 1.2447034 1.2447034 0.62576519 0.020537655
6900 100 1.2625323 1.2625323 0.63486698 0.02010613
7000 100 1.2617127 1.2617127 0.63318163 0.019670429
7100 100 1.260715 1.260715 0.63311254 0.01981063
7200 100 1.2790404 1.2790404 0.64079 0.020218912
7300 100 1.2760228 1.2760228 0.6395331 0.021749952
7400 100 1.2799657 1.2799657 0.64139078 0.020472917
7500 100 1.2846472 1.2846472 0.64343076 0.020610029
7600 100 1.2883963 1.2883963 0.6449186 0.020748906
7700 100 1.2926891 1.2926891 0.64684538 0.020599574
7800 100 1.3033565 1.3033565 0.65126214 0.021822145
7900 100 1.3025797 1.3025797 0.65069472 0.02121384
8000 100 1.3052551 1.3052551 0.65209898 0.021398725
8100 100 1.3069868 1.3069868 0.65304899 0.021246465
8200 100 1.3091964 1.3091964 0.65438143 0.021222398
8300 100 1.3101277 1.3101277 0.65518554 0.021329556
8400 100 1.3117162 1.3117162 0.65551056 0.021468306
8500 100 1.3143892 1.3143892 0.65683087 0.021610874
8600 100 1.3164123 1.3164123 0.65789423 0.021564818
8700 100 1.3186854 1.3186854 0.65914031 0.021745193
8800 100 1.3216944 1.3216944 0.66041385 0.022178553
8900 100 1.3207558 1.3207558 0.65988071 0.021810027
9000 100 1.3213131 1.3213131 0.66020938 0.021890893
9100 100 1.3224905 1.3224905 0.66088289 0.021824994
9200 100 1.3240681 1.3240681 0.66183168 0.021784616
9300 100 1.3254174 1.3254174 0.66279883 0.021664485
9400 100 1.3326916 1.3326916 0.66633358 0.021979709
9500 100 1.3405062 1.3405062 0.66975745 0.022238702
9600 100 1.3363695 1.3363695 0.66742377 0.022104646
9700 100 1.3363391 1.3363391 0.6673032 0.022066628
9800 100 1.334875 1.334875 0.6665532 0.021902669
9900 100 1.3339805 1.3339805 0.66614358 0.022018971
10000 100 1.3337897 1.3337897 0.66609803 0.022184385
Loop time of 0.213875 on 1 procs for 5000 steps with 100 atoms
Performance: 10099379.673 tau/day, 23378.194 timesteps/s, 2.338 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031863 | 0.031863 | 0.031863 | 0.0 | 14.90
Neigh | 0.026844 | 0.026844 | 0.026844 | 0.0 | 12.55
Comm | 0.0011059 | 0.0011059 | 0.0011059 | 0.0 | 0.52
Output | 0.00072907 | 0.00072907 | 0.00072907 | 0.0 | 0.34
Modify | 0.14874 | 0.14874 | 0.14874 | 0.0 | 69.54
Other | | 0.004595 | | | 2.15
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 186 ave 186 max 186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 186
Ave neighs/atom = 1.86
Neighbor list builds = 626
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.3337897 1.3337897 0.66609803 0.022303323
10100 100 0.29960521 0.29960521 0.17535846 0.0099382421
10200 100 0.15737069 0.15737069 0.1024212 0.0045555648
10300 100 0.087501771 0.087501771 0.070895975 0.00093482858
10400 100 0.069967301 0.069967301 0.059253397 0.0008760803
10500 100 0.056137153 0.056137153 0.047810947 0.0009202993
10600 100 0.046835352 0.046835352 0.039400006 0.0011343063
10700 100 0.035422167 0.035422167 0.030746587 0.00081816474
10800 100 0.029180739 0.029180739 0.02627693 0.00039292712
10900 100 0.025094915 0.025094915 0.023244435 0.00044742245
11000 100 0.018014893 0.018014893 0.016862375 0.00017018411
11100 100 0.014549072 0.014549072 0.014551468 0.00020988549
11200 100 0.012586232 0.012586232 0.012569333 0.00019035396
11300 100 0.01003586 0.01003586 0.010253286 0.0004598214
11400 100 0.0067515743 0.0067515743 0.0069569741 0.00040592883
11500 100 0.0057834612 0.0057834612 0.0060790719 0.00013993531
11600 100 0.005496335 0.005496335 0.0056855922 0.00013419698
11700 100 0.0051524178 0.0051524178 0.0053354591 7.4388594e-05
11800 100 0.004911096 0.004911096 0.0051415984 0.00010665621
11900 100 0.004687138 0.004687138 0.0049520306 6.7492552e-05
12000 100 0.0041516495 0.0041516495 0.0044351666 4.3841199e-05
12100 100 0.0033948026 0.0033948026 0.0036851466 4.2010682e-05
12200 100 0.0029584231 0.0029584231 0.0031151054 5.1583068e-05
12300 100 0.0028401114 0.0028401114 0.0030094644 4.5499489e-05
12400 100 0.002650861 0.002650861 0.0027699066 0.00015370263
12500 100 0.0026018053 0.0026018053 0.0027178583 3.219734e-05
12600 100 0.0025788693 0.0025788693 0.0026939358 3.6615314e-05
12700 100 0.0024798907 0.0024798907 0.0026181033 3.0688648e-05
12800 100 0.0023930719 0.0023930719 0.0025491721 7.5200629e-05
12900 100 0.0022100795 0.0022100795 0.0024231125 2.3210159e-05
13000 100 0.0021267492 0.0021267492 0.0023312893 2.463758e-05
13100 100 0.0020732193 0.0020732193 0.0022673707 2.5656089e-05
13200 100 0.0020010659 0.0020010659 0.0021834293 2.4913608e-05
13300 100 0.0019645929 0.0019645929 0.0021311636 6.8209063e-05
13400 100 0.0019236711 0.0019236711 0.0020928899 2.3805429e-05
13500 100 0.001857137 0.001857137 0.0020387354 3.1316165e-05
13600 100 0.0018399111 0.0018399111 0.0020204586 2.27689e-05
13700 100 0.0016240252 0.0016240252 0.0017492695 0.00023180963
13800 100 0.0015856393 0.0015856393 0.0017164012 4.2480373e-05
13900 100 0.0014770352 0.0014770352 0.001571278 2.3192512e-05
14000 100 0.0013712974 0.0013712974 0.0014839763 4.7410142e-05
14100 100 0.0012396318 0.0012396318 0.0013778109 1.3867692e-05
14200 100 0.0011502319 0.0011502319 0.0012780584 0.00018410725
14300 100 0.0011020896 0.0011020896 0.0012348357 7.8122446e-05
14400 100 0.0010486644 0.0010486644 0.0011483239 0.00015074963
14500 100 0.00094167471 0.00094167471 0.0010033809 1.9550083e-05
14600 100 0.00080775791 0.00080775791 0.00087434944 4.6043659e-05
14700 100 0.00076176039 0.00076176039 0.00083462461 8.1916038e-05
14800 100 0.00073637901 0.00073637901 0.00081306941 9.1126903e-06
14900 100 0.00072682383 0.00072682383 0.00079396231 8.9944449e-06
15000 100 0.00070207518 0.00070207518 0.00077168127 2.2155171e-05
Loop time of 0.0756704 on 1 procs for 5000 steps with 100 atoms
Performance: 28544845.995 tau/day, 66076.032 timesteps/s, 6.608 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0079484 | 0.0079484 | 0.0079484 | 0.0 | 10.50
Neigh | 0.0043035 | 0.0043035 | 0.0043035 | 0.0 | 5.69
Comm | 0.00064796 | 0.00064796 | 0.00064796 | 0.0 | 0.86
Output | 0.00044137 | 0.00044137 | 0.00044137 | 0.0 | 0.58
Modify | 0.059329 | 0.059329 | 0.059329 | 0.0 | 78.40
Other | | 0.003 | | | 3.97
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 165 ave 165 max 165 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 165
Ave neighs/atom = 1.65
Neighbor list builds = 101
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00070207518 0.00070207518 0.00077168127 2.0192237e-05
15100 100 1.1160127 1.1160127 0.69939857 0.01822663
15200 100 1.2546016 1.2546016 0.78819474 0.017013321
15300 100 1.1930613 1.1930613 0.77429911 0.015607175
15400 100 1.3791371 1.3791371 0.87875984 0.018478669
15500 100 1.6063158 1.6063158 0.98587325 0.027330546
15600 100 1.7719925 1.7719925 1.0773314 0.025651867
15700 100 1.8053439 1.8053439 1.0934572 0.033790716
15800 100 1.959016 1.959016 1.1465659 0.033715025
15900 100 2.1365654 2.1365654 1.2217718 0.03009529
16000 100 2.2883378 2.2883378 1.2768504 0.030582689
16100 100 2.4384012 2.4384012 1.3513708 0.031435936
16200 100 2.3571308 2.3571308 1.29989 0.034824253
16300 100 2.4671092 2.4671092 1.3516798 0.032364282
16400 100 2.4411936 2.4411936 1.3385743 0.031890134
16500 100 2.4930545 2.4930545 1.3635435 0.032601452
16600 100 2.5771906 2.5771906 1.4113993 0.034547128
16700 100 2.723199 2.723199 1.4769168 0.036582811
16800 100 2.8616886 2.8616886 1.5379462 0.036224198
16900 100 2.9517942 2.9517942 1.5872824 0.038757052
17000 100 3.0150335 3.0150335 1.6337001 0.044031411
17100 100 3.2211536 3.2211536 1.7374532 0.041483093
17200 100 3.2509982 3.2509982 1.7512835 0.042718835
17300 100 3.262348 3.262348 1.7648674 0.049291835
17400 100 3.4050702 3.4050702 1.8352043 0.04435958
17500 100 3.5236051 3.5236051 1.9003369 0.045640904
17600 100 3.4005287 3.4005287 1.8404347 0.044832295
17700 100 3.3190992 3.3190992 1.8154147 0.046365998
17800 100 3.2981138 3.2981138 1.811389 0.04607132
17900 100 3.2839466 3.2839466 1.7863773 0.045628167
18000 100 3.1519747 3.1519747 1.7382103 0.041739193
18100 100 3.1205305 3.1205305 1.7101547 0.043511342
18200 100 3.2014874 3.2014874 1.746745 0.04452173
18300 100 3.2739622 3.2739622 1.7796276 0.041345823
18400 100 3.3157359 3.3157359 1.8158932 0.047414
18500 100 3.5592096 3.5592096 1.9307695 0.046458132
18600 100 3.6594352 3.6594352 1.9851626 0.046396953
18700 100 3.6392917 3.6392917 1.9701361 0.047272883
18800 100 3.8490892 3.8490892 2.0832481 0.052344106
18900 100 3.8465732 3.8465732 2.0790411 0.054203126
19000 100 4.010008 4.010008 2.1620722 0.054242542
19100 100 4.0417392 4.0417392 2.168506 0.066484948
19200 100 3.8791541 3.8791541 2.0791914 0.060788142
19300 100 4.1023603 4.1023603 2.1944127 0.056461298
19400 100 4.1294375 4.1294375 2.2009649 0.061099665
19500 100 3.9274112 3.9274112 2.0877398 0.066068401
19600 100 4.066229 4.066229 2.1678487 0.055961003
19700 100 3.9829257 3.9829257 2.1184329 0.061961838
19800 100 4.0303258 4.0303258 2.14544 0.053667616
19900 100 3.9385166 3.9385166 2.1074364 0.060804382
20000 100 3.8534401 3.8534401 2.0796496 0.057588336
Loop time of 0.167801 on 1 procs for 5000 steps with 100 atoms
Performance: 12872385.064 tau/day, 29797.188 timesteps/s, 2.980 Matom-step/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013849 | 0.013849 | 0.013849 | 0.0 | 8.25
Neigh | 0.038108 | 0.038108 | 0.038108 | 0.0 | 22.71
Comm | 0.0011352 | 0.0011352 | 0.0011352 | 0.0 | 0.68
Output | 0.00073125 | 0.00073125 | 0.00073125 | 0.0 | 0.44
Modify | 0.10927 | 0.10927 | 0.10927 | 0.0 | 65.12
Other | | 0.004703 | | | 2.80
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 157 ave 157 max 157 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157
Ave neighs/atom = 1.57
Neighbor list builds = 914
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.8534401 3.8534401 2.0796496 0.057176513
20100 100 1.2993548 1.2993548 0.81360425 0.016153186
20200 100 1.0761427 1.0761427 0.68479926 0.014383682
20300 100 0.95889127 0.95889127 0.61193887 0.01314653
20400 100 0.89684043 0.89684043 0.57475851 0.011106613
20500 100 0.85901565 0.85901565 0.54372093 0.015717834
20600 100 0.98438384 0.98438384 0.6079212 0.013965815
20700 100 1.1061789 1.1061789 0.66511277 0.013698526
20800 100 1.0615292 1.0615292 0.6269413 0.014496973
20900 100 0.92980037 0.92980037 0.54727184 0.014568574
21000 100 0.71248123 0.71248123 0.41945517 0.01199152
21100 100 0.34785801 0.34785801 0.21699877 0.0062324631
21200 100 0.2452514 0.2452514 0.15265503 0.0041094159
21300 100 0.22937209 0.22937209 0.13988978 0.0034016589
21400 100 0.17765021 0.17765021 0.11334596 0.0024169343
21500 100 0.11484505 0.11484505 0.078119393 0.0020987046
21600 100 0.077564645 0.077564645 0.056175123 0.002107237
21700 100 0.049571519 0.049571519 0.039920177 0.00099127481
21800 100 0.0403125 0.0403125 0.032827882 0.00074671903
21900 100 0.02735168 0.02735168 0.023877339 0.0018186225
22000 100 0.02218474 0.02218474 0.01893178 0.00061438633
22100 100 0.021701103 0.021701103 0.0179008 0.00068071664
22200 100 0.01777321 0.01777321 0.014521817 0.00045296506
22300 100 0.016056338 0.016056338 0.01280709 0.00038192299
22400 100 0.013344054 0.013344054 0.010788852 0.0002617289
22500 100 0.011625836 0.011625836 0.0094362641 0.00045947089
22600 100 0.0068875777 0.0068875777 0.0058858647 0.00028566999
22700 100 0.0054081662 0.0054081662 0.0049545239 0.00029291503
22800 100 0.0045080107 0.0045080107 0.0042362636 0.00015217816
22900 100 0.0038090552 0.0038090552 0.0036905284 0.00049430003
23000 100 0.003551951 0.003551951 0.0033639677 0.00022478393
23100 100 0.0033854012 0.0033854012 0.00317485 0.00015179604
23200 100 0.0032951003 0.0032951003 0.0029760374 0.00015363208
23300 100 0.0022995179 0.0022995179 0.0023224311 0.00018791799
23400 100 0.0020834178 0.0020834178 0.0021434342 0.00020683744
23500 100 0.0019221303 0.0019221303 0.0020227484 0.00018960984
23600 100 0.0018393381 0.0018393381 0.0019560681 0.00021375486
23700 100 0.0019027035 0.0019027035 0.0020047598 0.00010932204
23800 100 0.0023612063 0.0023612063 0.0021895633 6.7671176e-05
23900 100 0.0019570853 0.0019570853 0.0018847178 5.6761457e-05
24000 100 0.0013011744 0.0013011744 0.0013899106 3.8847148e-05
24100 100 0.001281115 0.001281115 0.0013737259 3.7559904e-05
24200 100 0.0012136262 0.0012136262 0.0013002937 6.8727546e-05
24300 100 0.0011789934 0.0011789934 0.0012399341 3.7633632e-05
24400 100 0.0011601514 0.0011601514 0.0012186534 4.0077907e-05
24500 100 0.0010660295 0.0010660295 0.0011419405 0.00015757237
24600 100 0.00098862453 0.00098862453 0.0010869455 4.5714503e-05
24700 100 0.00087647136 0.00087647136 0.00091405278 3.3129869e-05
24800 100 0.00063913046 0.00063913046 0.00072298864 3.5424308e-05
24900 100 0.00062195456 0.00062195456 0.00070527087 2.6201396e-05
25000 100 0.00057599538 0.00057599538 0.00065623226 2.0096103e-05
Loop time of 0.0771328 on 1 procs for 5000 steps with 100 atoms
Performance: 28003659.560 tau/day, 64823.286 timesteps/s, 6.482 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0090635 | 0.0090635 | 0.0090635 | 0.0 | 11.75
Neigh | 0.012028 | 0.012028 | 0.012028 | 0.0 | 15.59
Comm | 0.0008345 | 0.0008345 | 0.0008345 | 0.0 | 1.08
Output | 0.00038777 | 0.00038777 | 0.00038777 | 0.0 | 0.50
Modify | 0.051619 | 0.051619 | 0.051619 | 0.0 | 66.92
Other | | 0.0032 | | | 4.15
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 158
Ave neighs/atom = 1.58
Neighbor list builds = 310
Dangerous builds = 0
Total wall time: 0:00:00

484
examples/granregion/log.16Mar23.granregion.box.g++.4 Normal file
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@ -0,0 +1,484 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 2 by 2 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
Particle insertion: 48 every 566 steps, 100 by step 1133
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4843 | 0.4843 | 0.4843 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
100 30 0.803783 0.803783 0.39507978 0.0029137134
200 30 1.1967995 1.1967995 0.5882574 0.0043383984
300 30 1.2814686 1.2814686 0.62987441 0.0046453238
400 30 0.82331082 0.82331082 0.41173176 0.0029845017
500 30 0.7708462 0.7708462 0.38777784 0.0043831147
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
600 64 0.51564897 0.51564897 0.26631577 0.0040059368
700 64 0.57239348 0.57239348 0.29566901 0.0045075987
800 64 0.61837087 0.61837087 0.32195387 0.0048123564
900 64 0.53061888 0.53061888 0.28564763 0.0055906552
1000 64 0.496299 0.496299 0.26801572 0.0061169128
1100 64 0.46068308 0.46068308 0.24699057 0.0055717699
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
1200 99 0.39206225 0.39206225 0.21356546 0.0066294211
1300 99 0.38624966 0.38624966 0.21345854 0.0049051051
1400 99 0.35615284 0.35615284 0.19785725 0.0046170772
1500 99 0.31486693 0.31486693 0.17429055 0.0064903432
1600 99 0.26369001 0.26369001 0.15095266 0.0045226847
1700 100 0.1925923 0.1925923 0.11308104 0.007362313
1800 100 0.13724978 0.13724978 0.083276845 0.0058136373
1900 100 0.077212636 0.077212636 0.053159386 0.0016509598
2000 100 0.065294031 0.065294031 0.04372752 0.0020346467
2100 100 0.057431398 0.057431398 0.037977068 0.0012681098
2200 100 0.059093046 0.059093046 0.037435194 0.00096610935
2300 100 0.034223376 0.034223376 0.025491303 0.00069886041
2400 100 0.020558283 0.020558283 0.016163008 0.0017260646
2500 100 0.015339698 0.015339698 0.012329233 0.00041312351
2600 100 0.012891357 0.012891357 0.0097660566 0.00030356702
2700 100 0.0092631621 0.0092631621 0.0073576327 0.00077729311
2800 100 0.0073866488 0.0073866488 0.0060126175 0.00018677664
2900 100 0.0081122362 0.0081122362 0.0062557089 0.00013749542
3000 100 0.0042333757 0.0042333757 0.0035407672 0.00016515787
3100 100 0.0035433278 0.0035433278 0.0029683167 0.00033693479
3200 100 0.0030692964 0.0030692964 0.0026495167 0.00043739373
3300 100 0.0033703684 0.0033703684 0.0026931948 0.00014857157
3400 100 0.0018405709 0.0018405709 0.0016990035 6.0202278e-05
3500 100 0.0014788087 0.0014788087 0.0013889916 0.00016730937
3600 100 0.0015932961 0.0015932961 0.0013807898 0.0001418157
3700 100 0.00096238915 0.00096238915 0.00097931829 6.7974535e-05
3800 100 0.00093087985 0.00093087985 0.00087659377 0.0001504142
3900 100 0.0015825065 0.0015825065 0.0011708936 1.9583518e-05
4000 100 0.00062295367 0.00062295367 0.00067129665 3.9455653e-05
4100 100 0.00061259406 0.00061259406 0.00065710963 1.8540759e-05
4200 100 0.00059619666 0.00059619666 0.00064365219 7.3779336e-06
4300 100 0.00051191641 0.00051191641 0.00057870947 6.3349656e-06
4400 100 0.00050668587 0.00050668587 0.00057057233 6.2702376e-06
4500 100 0.00049474942 0.00049474942 0.00055151343 1.5746831e-05
4600 100 0.00049309932 0.00049309932 0.00054086323 6.1021041e-06
4700 100 0.00049263883 0.00049263883 0.00052677244 6.0964056e-06
4800 100 0.00041885021 0.00041885021 0.00047389202 9.5350789e-05
4900 100 0.00035596444 0.00035596444 0.00042522549 5.8036712e-05
5000 100 0.00032946897 0.00032946897 0.00040320773 6.5350005e-06
Loop time of 0.0763179 on 4 procs for 5000 steps with 100 atoms
Performance: 28302682.620 tau/day, 65515.469 timesteps/s, 6.552 Matom-step/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010572 | 0.0039588 | 0.0074661 | 4.6 | 5.19
Neigh | 0.0025868 | 0.0049885 | 0.0075283 | 3.4 | 6.54
Comm | 0.011862 | 0.014631 | 0.018383 | 2.0 | 19.17
Output | 0.0009702 | 0.0012326 | 0.0014234 | 0.5 | 1.62
Modify | 0.0019843 | 0.018558 | 0.036592 | 12.2 | 24.32
Other | | 0.03295 | | | 43.17
Nlocal: 25 ave 54 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 4.5 ave 10 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 40.5 ave 94 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 162
Ave neighs/atom = 1.62
Neighbor list builds = 281
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Region properties for region container changed between runs, resetting its motion (src/GRANULAR/fix_wall_gran_region.cpp:101)
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00032946897 0.00032946897 0.00040320773 6.050219e-06
5100 100 0.54371575 0.54371575 0.29836301 0.008148168
5200 100 0.60281896 0.60281896 0.33161676 0.0083772071
5300 100 0.70823011 0.70823011 0.38289657 0.0099694209
5400 100 0.78467127 0.78467127 0.4133495 0.010119104
5500 100 0.85741178 0.85741178 0.44761254 0.013013239
5600 100 0.93241573 0.93241573 0.47879351 0.017769592
5700 100 1.019104 1.019104 0.51644461 0.015312937
5800 100 1.0550014 1.0550014 0.53450507 0.017227797
5900 100 1.0910946 1.0910946 0.55272891 0.017469625
6000 100 1.1275288 1.1275288 0.56906788 0.018958103
6100 100 1.1545017 1.1545017 0.58324166 0.019220208
6200 100 1.1815817 1.1815817 0.59552677 0.019397271
6300 100 1.1963931 1.1963931 0.60251664 0.018382058
6400 100 1.2084652 1.2084652 0.60776713 0.020027986
6500 100 1.2217215 1.2217215 0.61406339 0.021750945
6600 100 1.2364016 1.2364016 0.62124174 0.021701243
6700 100 1.2739954 1.2739954 0.63930766 0.02025277
6800 100 1.3032733 1.3032733 0.65268105 0.021684843
6900 100 1.3226653 1.3226653 0.66168772 0.021187963
7000 100 1.3464995 1.3464995 0.67431153 0.022066117
7100 100 1.3250485 1.3250485 0.66342366 0.02109487
7200 100 1.3384316 1.3384316 0.67035095 0.021554113
7300 100 1.3280234 1.3280234 0.66553439 0.020829435
7400 100 1.3218971 1.3218971 0.66186263 0.020882591
7500 100 1.3293858 1.3293858 0.66506462 0.020897778
7600 100 1.3386019 1.3386019 0.66909392 0.020754479
7700 100 1.3465327 1.3465327 0.67316081 0.021231547
7800 100 1.3510586 1.3510586 0.67531764 0.021053475
7900 100 1.3508987 1.3508987 0.67535907 0.020769633
8000 100 1.3575635 1.3575635 0.67875993 0.022020776
8100 100 1.3655144 1.3655144 0.68258066 0.021016999
8200 100 1.375187 1.375187 0.68732222 0.021385146
8300 100 1.3799568 1.3799568 0.69000134 0.02114428
8400 100 1.3755871 1.3755871 0.68757909 0.022395102
8500 100 1.3708345 1.3708345 0.68509834 0.021603853
8600 100 1.3689806 1.3689806 0.68388935 0.022127839
8700 100 1.3697516 1.3697516 0.68411868 0.02165119
8800 100 1.3700522 1.3700522 0.68423671 0.021554001
8900 100 1.3705045 1.3705045 0.68451935 0.021470392
9000 100 1.3715107 1.3715107 0.68506443 0.021789844
9100 100 1.3707806 1.3707806 0.68467539 0.021451331
9200 100 1.371112 1.371112 0.68485975 0.021479203
9300 100 1.3716851 1.3716851 0.68516034 0.021515076
9400 100 1.3719031 1.3719031 0.68529221 0.021502802
9500 100 1.3726759 1.3726759 0.68544012 0.021585119
9600 100 1.3746583 1.3746583 0.68636924 0.02206073
9700 100 1.3761662 1.3761662 0.68716579 0.021533719
9800 100 1.3760157 1.3760157 0.687092 0.02163129
9900 100 1.3762626 1.3762626 0.68726404 0.021707045
10000 100 1.376303 1.376303 0.68735031 0.022306557
Loop time of 0.128472 on 4 procs for 5000 steps with 100 atoms
Performance: 16812995.511 tau/day, 38918.971 timesteps/s, 3.892 Matom-step/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012241 | 0.0085024 | 0.016023 | 7.8 | 6.62
Neigh | 0.0051137 | 0.0079745 | 0.011012 | 3.2 | 6.21
Comm | 0.0050448 | 0.009504 | 0.015048 | 4.6 | 7.40
Output | 0.00090309 | 0.0014765 | 0.0019648 | 1.2 | 1.15
Modify | 0.0072253 | 0.041211 | 0.076226 | 16.7 | 32.08
Other | | 0.0598 | | | 46.55
Nlocal: 25 ave 51 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 3.25 ave 7 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 46 ave 101 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 184
Ave neighs/atom = 1.84
Neighbor list builds = 628
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.376303 1.376303 0.68735031 0.022411506
10100 100 0.28192752 0.28192752 0.16298909 0.0041760951
10200 100 0.14576408 0.14576408 0.10117889 0.0058653094
10300 100 0.10070361 0.10070361 0.078060938 0.0041432979
10400 100 0.07455595 0.07455595 0.061163197 0.0029733745
10500 100 0.063531027 0.063531027 0.052515707 0.0015731241
10600 100 0.049259626 0.049259626 0.041321284 0.00073083104
10700 100 0.037377957 0.037377957 0.032017729 0.0022631642
10800 100 0.031849901 0.031849901 0.027079116 0.0014148618
10900 100 0.02795233 0.02795233 0.02461403 0.00037567522
11000 100 0.02597858 0.02597858 0.022516094 0.00054992645
11100 100 0.021812043 0.021812043 0.019276946 0.00043233309
11200 100 0.019318956 0.019318956 0.017224213 0.00035792964
11300 100 0.017760494 0.017760494 0.01578407 0.00056959435
11400 100 0.015485043 0.015485043 0.013703 0.00061308169
11500 100 0.015051781 0.015051781 0.012994991 0.00040607387
11600 100 0.012204953 0.012204953 0.01079191 0.00059482171
11700 100 0.011242847 0.011242847 0.0096811013 0.00018299476
11800 100 0.0089605707 0.0089605707 0.0075086629 0.0012779422
11900 100 0.0065544011 0.0065544011 0.0056480432 0.00039599272
12000 100 0.0048068901 0.0048068901 0.004185961 0.00022434097
12100 100 0.0045272524 0.0045272524 0.0039084556 7.8443821e-05
12200 100 0.0038926209 0.0038926209 0.0033949999 0.00011203445
12300 100 0.0034653 0.0034653 0.0030246557 0.00014999893
12400 100 0.0034031041 0.0034031041 0.0029879474 7.9628343e-05
12500 100 0.0032219984 0.0032219984 0.0028369239 6.1651251e-05
12600 100 0.0031148659 0.0031148659 0.0027543848 5.7332789e-05
12700 100 0.0027407824 0.0027407824 0.0024822578 5.150993e-05
12800 100 0.0026205294 0.0026205294 0.0023576698 8.896122e-05
12900 100 0.0025633289 0.0025633289 0.0023134486 7.0525939e-05
13000 100 0.0025434711 0.0025434711 0.0022833007 5.5638668e-05
13100 100 0.0025046562 0.0025046562 0.002227265 5.2772716e-05
13200 100 0.0023544645 0.0023544645 0.0021086805 0.00030775943
13300 100 0.0022163971 0.0022163971 0.0020107508 4.9204292e-05
13400 100 0.0021307794 0.0021307794 0.0019334987 4.8144132e-05
13500 100 0.0019891796 0.0019891796 0.0018128084 4.8532374e-05
13600 100 0.0018591538 0.0018591538 0.0016721703 4.4781385e-05
13700 100 0.001768055 0.001768055 0.001597222 1.6800418e-05
13800 100 0.001569014 0.001569014 0.0014331265 4.2982654e-05
13900 100 0.0013700893 0.0013700893 0.0012782771 4.8209662e-05
14000 100 0.0012398662 0.0012398662 0.0011606486 5.5766702e-05
14100 100 0.0011707267 0.0011707267 0.0010811523 3.4913501e-05
14200 100 0.0010483984 0.0010483984 0.0009831881 3.4742894e-05
14300 100 0.0010043196 0.0010043196 0.00092474592 3.4196115e-05
14400 100 0.00094238924 0.00094238924 0.00087181843 8.1414071e-05
14500 100 0.00093341457 0.00093341457 0.00086429224 3.3276909e-05
14600 100 0.00086042474 0.00086042474 0.00079524877 3.2260019e-05
14700 100 0.00080525469 0.00080525469 0.00075380989 2.8374703e-05
14800 100 0.00070848512 0.00070848512 0.0006762901 2.9937591e-05
14900 100 0.00060414588 0.00060414588 0.00058494979 2.5684401e-05
15000 100 0.00054251571 0.00054251571 0.00053643753 4.5496354e-05
Loop time of 0.0553238 on 4 procs for 5000 steps with 100 atoms
Performance: 39042861.362 tau/day, 90376.994 timesteps/s, 9.038 Matom-step/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00085556 | 0.0028667 | 0.0052429 | 3.6 | 5.18
Neigh | 0.00076731 | 0.0012173 | 0.0016987 | 1.3 | 2.20
Comm | 0.0016497 | 0.0060965 | 0.010792 | 5.7 | 11.02
Output | 0.00072675 | 0.00099509 | 0.0011615 | 0.0 | 1.80
Modify | 0.00064371 | 0.014719 | 0.030427 | 11.6 | 26.61
Other | | 0.02943 | | | 53.19
Nlocal: 25 ave 54 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 5 ave 11 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 40 ave 88 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 160
Ave neighs/atom = 1.6
Neighbor list builds = 97
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.609 | 5.672 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00054251571 0.00054251571 0.00053643753 4.3506263e-05
15100 100 1.1164435 1.1164435 0.7163854 0.017358175
15200 100 1.0384203 1.0384203 0.66790042 0.016095459
15300 100 1.0829984 1.0829984 0.712381 0.015915015
15400 100 1.4187366 1.4187366 0.89537718 0.023771032
15500 100 1.5397547 1.5397547 0.97895571 0.025145916
15600 100 1.7993339 1.7993339 1.1003794 0.026783317
15700 100 1.8858073 1.8858073 1.1481696 0.030802833
15800 100 1.9368129 1.9368129 1.1450129 0.032144729
15900 100 2.0379823 2.0379823 1.1738926 0.031969116
16000 100 2.0655671 2.0655671 1.187038 0.032395513
16100 100 2.1199141 2.1199141 1.2102937 0.028830059
16200 100 2.1819656 2.1819656 1.245147 0.029493813
16300 100 2.2451204 2.2451204 1.2726968 0.029915554
16400 100 2.1697892 2.1697892 1.2342734 0.027495983
16500 100 2.2689358 2.2689358 1.2710223 0.029516621
16600 100 2.3901976 2.3901976 1.3328992 0.030049751
16700 100 2.4731258 2.4731258 1.3763126 0.032663365
16800 100 2.5708338 2.5708338 1.4255635 0.032731991
16900 100 2.7232422 2.7232422 1.5006931 0.036649645
17000 100 2.901986 2.901986 1.5886643 0.037333791
17100 100 2.8787369 2.8787369 1.5752504 0.03582313
17200 100 3.1137189 3.1137189 1.6974538 0.041245422
17300 100 3.1805823 3.1805823 1.7370013 0.040766564
17400 100 3.3215703 3.3215703 1.8109954 0.044269306
17500 100 3.3767256 3.3767256 1.813696 0.048012575
17600 100 3.3618731 3.3618731 1.8004834 0.06103562
17700 100 3.2288285 3.2288285 1.7447885 0.042875761
17800 100 3.2545435 3.2545435 1.7617642 0.04661949
17900 100 3.1162969 3.1162969 1.6850561 0.040086156
18000 100 3.2053719 3.2053719 1.7132296 0.040657811
18100 100 3.2924625 3.2924625 1.7709303 0.048407939
18200 100 3.1682076 3.1682076 1.7136129 0.040996326
18300 100 3.2244534 3.2244534 1.7401102 0.043957312
18400 100 3.1470903 3.1470903 1.7171698 0.043123438
18500 100 3.2690021 3.2690021 1.7803818 0.042693323
18600 100 3.2566233 3.2566233 1.7670476 0.04776305
18700 100 3.384347 3.384347 1.8334885 0.04441225
18800 100 3.6479797 3.6479797 1.9565845 0.047454733
18900 100 3.6894531 3.6894531 1.9767079 0.053222159
19000 100 3.7867788 3.7867788 2.0265223 0.055923793
19100 100 3.9120999 3.9120999 2.0850815 0.053591707
19200 100 3.8255419 3.8255419 2.0517931 0.061034295
19300 100 3.764721 3.764721 2.0089969 0.068118255
19400 100 3.8604884 3.8604884 2.0640292 0.052825172
19500 100 3.7763823 3.7763823 2.0223758 0.054529616
19600 100 3.9158781 3.9158781 2.0873723 0.053130512
19700 100 3.6394071 3.6394071 1.9735106 0.047466529
19800 100 3.5409741 3.5409741 1.9335311 0.047317029
19900 100 3.5961407 3.5961407 1.954696 0.048093129
20000 100 3.4355899 3.4355899 1.8679902 0.0486077
Loop time of 0.107854 on 4 procs for 5000 steps with 100 atoms
Performance: 20026986.271 tau/day, 46358.765 timesteps/s, 4.636 Matom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0025992 | 0.0042158 | 0.0061269 | 1.9 | 3.91
Neigh | 0.0089595 | 0.011254 | 0.012853 | 1.3 | 10.43
Comm | 0.020408 | 0.022579 | 0.024669 | 1.4 | 20.94
Output | 0.0010271 | 0.0011457 | 0.0012268 | 0.2 | 1.06
Modify | 0.019454 | 0.032696 | 0.040003 | 4.4 | 30.31
Other | | 0.03596 | | | 33.34
Nlocal: 25 ave 36 max 16 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 5.5 ave 8 max 2 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 34.25 ave 48 max 19 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 137
Ave neighs/atom = 1.37
Neighbor list builds = 908
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.734 | 5.735 | 5.735 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.4355899 3.4355899 1.8679902 0.047866781
20100 100 1.1677914 1.1677914 0.70763342 0.015645481
20200 100 0.99137326 0.99137326 0.61064707 0.012080974
20300 100 0.84603548 0.84603548 0.52093267 0.012501649
20400 100 0.82813609 0.82813609 0.50585936 0.010248184
20500 100 0.86524293 0.86524293 0.5210492 0.011145216
20600 100 0.92229302 0.92229302 0.54567614 0.012838894
20700 100 0.93499886 0.93499886 0.55161401 0.011618713
20800 100 0.95831407 0.95831407 0.56173113 0.014502297
20900 100 0.88486451 0.88486451 0.51926962 0.013847246
21000 100 0.66876325 0.66876325 0.39313901 0.010224296
21100 100 0.46578708 0.46578708 0.28086455 0.0089121873
21200 100 0.21445902 0.21445902 0.14749113 0.0033665892
21300 100 0.12935011 0.12935011 0.09319765 0.002811107
21400 100 0.10572326 0.10572326 0.075154962 0.0034728629
21500 100 0.10952604 0.10952604 0.073864376 0.0017411404
21600 100 0.074321422 0.074321422 0.051368858 0.0037915268
21700 100 0.043324694 0.043324694 0.032954769 0.00092476658
21800 100 0.034911155 0.034911155 0.026843877 0.00061350592
21900 100 0.02261818 0.02261818 0.018357224 0.00049800957
22000 100 0.015096211 0.015096211 0.01390442 0.00059260194
22100 100 0.016119209 0.016119209 0.013990821 0.00038431756
22200 100 0.012184692 0.012184692 0.011062653 0.00030466184
22300 100 0.0090526001 0.0090526001 0.0080893293 0.00082507232
22400 100 0.007155528 0.007155528 0.0067365227 0.00094740021
22500 100 0.0057433117 0.0057433117 0.0057438575 0.00016706605
22600 100 0.0053029734 0.0053029734 0.0050429137 0.00018457156
22700 100 0.0041888319 0.0041888319 0.0039979907 0.00029467329
22800 100 0.0046486843 0.0046486843 0.0042259456 0.00019395675
22900 100 0.0046414295 0.0046414295 0.0040659744 0.00016025205
23000 100 0.0033983576 0.0033983576 0.0033431909 0.00039998961
23100 100 0.0031212625 0.0031212625 0.0031113361 0.00024783655
23200 100 0.0026724347 0.0026724347 0.0026905233 0.00026001445
23300 100 0.0029222876 0.0029222876 0.002946198 0.00012385327
23400 100 0.0023944825 0.0023944825 0.0021829995 0.00016185776
23500 100 0.0020384082 0.0020384082 0.0019106613 9.2139544e-05
23600 100 0.0019773679 0.0019773679 0.0018577006 8.9169073e-05
23700 100 0.0018850072 0.0018850072 0.0017715658 9.1301463e-05
23800 100 0.0020857322 0.0020857322 0.001864009 7.4633597e-05
23900 100 0.0017616498 0.0017616498 0.001680563 4.8547939e-05
24000 100 0.0017183254 0.0017183254 0.0016568629 6.56741e-05
24100 100 0.0014311732 0.0014311732 0.0013829993 6.0743962e-05
24200 100 0.0013434756 0.0013434756 0.001315682 0.00025727478
24300 100 0.0012855885 0.0012855885 0.0012558467 9.0130585e-05
24400 100 0.0012731213 0.0012731213 0.0012408428 8.2008231e-05
24500 100 0.0011333063 0.0011333063 0.001045815 8.8391061e-05
24600 100 0.0010560932 0.0010560932 0.00098304208 5.6725938e-05
24700 100 0.00097698038 0.00097698038 0.00092381967 7.1771848e-05
24800 100 0.00094316799 0.00094316799 0.00089343119 5.5558578e-05
24900 100 0.00082812377 0.00082812377 0.00076615512 5.8668812e-05
25000 100 0.00076097781 0.00076097781 0.00069462801 6.5742694e-05
Loop time of 0.0523621 on 4 procs for 5000 steps with 100 atoms
Performance: 41251226.669 tau/day, 95488.951 timesteps/s, 9.549 Matom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0011166 | 0.0029573 | 0.0049613 | 3.3 | 5.65
Neigh | 0.0026276 | 0.0033989 | 0.0041666 | 1.1 | 6.49
Comm | 0.0054479 | 0.0084136 | 0.01182 | 2.9 | 16.07
Output | 0.00070658 | 0.00092447 | 0.0010421 | 0.0 | 1.77
Modify | 0.0015069 | 0.012796 | 0.025273 | 9.9 | 24.44
Other | | 0.02387 | | | 45.59
Nlocal: 25 ave 55 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 6 ave 14 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 39.25 ave 88 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 157
Ave neighs/atom = 1.57
Neighbor list builds = 280
Dangerous builds = 0
Total wall time: 0:00:00

635
examples/granregion/log.16Mar23.granregion.funnel.g++.1 Normal file
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LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.5 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/multi/newtoff
stencil: full/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 3000 every 59965 steps, 2000 by step 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.648 | 6.648 | 6.648 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.52844331 2000 -0
2000 0.76085445 2000 -0
3000 0.99183068 2000 -0
4000 1.2193085 2000 -0
5000 1.4439617 2000 -0
6000 1.6703511 2000 -0
7000 1.9053408 2000 -0
8000 2.1323525 2000 -0
9000 2.3566342 2000 -0
10000 2.5829638 2000 -0
11000 2.8106202 2000 -0
12000 3.0371473 2000 -0
13000 3.2621782 2000 -0
14000 3.4860689 2000 -0
15000 3.7138322 2000 -0
16000 3.9424002 2000 -0
17000 4.1703584 2000 -0
18000 4.3973348 2000 -0
19000 4.6213358 2000 -0
20000 4.8547603 2000 -0
Loop time of 4.85478 on 1 procs for 20000 steps with 2000 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52375 | 0.52375 | 0.52375 | 0.0 | 10.79
Neigh | 0.070018 | 0.070018 | 0.070018 | 0.0 | 1.44
Comm | 0.011077 | 0.011077 | 0.011077 | 0.0 | 0.23
Output | 0.00071321 | 0.00071321 | 0.00071321 | 0.0 | 0.01
Modify | 4.1233 | 4.1233 | 4.1233 | 0.0 | 84.93
Other | | 0.126 | | | 2.59
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1607 ave 1607 max 1607 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1607
Ave neighs/atom = 0.8035
Neighbor list builds = 71
Dangerous builds = 0
unfix ins
run 150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6652.2957
21000 0.22761741 2000 6807.2201
22000 0.45508977 2000 6973.9359
23000 0.68132308 2000 7142.3648
24000 0.91084802 2000 7276.9717
25000 1.1397154 2000 7369.4191
26000 1.3724974 2000 7497.6526
27000 1.6037436 2000 7638.946
28000 1.8381254 2000 7780.0339
29000 2.0763695 2000 7881.8177
30000 2.3169444 2000 7967.2641
31000 2.5544704 2000 7994.9273
32000 2.7981688 2000 7937.0671
33000 3.0486439 2000 7774.0508
34000 3.3065315 2000 7591.1491
35000 3.5712927 2000 7357.5176
36000 3.8415508 2000 7147.2024
37000 4.1137466 2000 6979.1604
38000 4.3946186 2000 6813.2152
39000 4.6737386 2000 6660.2701
40000 4.9654287 2000 6502.8957
41000 5.2606376 2000 6324.3951
42000 5.5633065 2000 6132.7516
43000 5.8692745 2000 5913.1841
44000 6.1757115 2000 5732.2095
45000 6.4896845 2000 5508.8322
46000 6.8170163 2000 5306.8932
47000 7.1514543 2000 5152.0521
48000 7.4863157 2000 5028.2274
49000 7.8214974 2000 4896.102
50000 8.1600826 2000 4723.5189
51000 8.4984004 2000 4583.7526
52000 8.8500924 2000 4447.0187
53000 9.2046999 2000 4303.2307
54000 9.5724785 2000 4168.5251
55000 9.9479954 2000 4036.9704
56000 10.324666 2000 3901.1183
57000 10.708944 2000 3716.7071
58000 11.108887 2000 3473.5422
59000 11.515057 2000 3245.1223
60000 11.922119 2000 3039.7845
61000 12.331146 2000 2780.0187
62000 12.745147 2000 2577.3345
63000 13.169644 2000 2346.2488
64000 13.602869 2000 2116.7298
65000 14.044828 2000 1903.7828
66000 14.49159 2000 1631.1676
67000 14.953127 2000 1431.0198
68000 15.428874 2000 1212.875
69000 15.981012 2000 995.45046
70000 16.458356 2000 811.54766
71000 16.936094 2000 624.08622
72000 17.432306 2000 471.00862
73000 17.949423 2000 358.33486
74000 18.467878 2000 284.39416
75000 18.970599 2000 234.26671
76000 19.45957 2000 185.61836
77000 19.959792 2000 152.95918
78000 20.455734 2000 122.49023
79000 20.93849 2000 102.29396
80000 21.430632 2000 86.284684
81000 21.925932 2000 73.984781
82000 22.428573 2000 63.042918
83000 22.945552 2000 53.338428
84000 23.467102 2000 45.89585
85000 23.992243 2000 40.412826
86000 24.512956 2000 34.183381
87000 25.037944 2000 29.671524
88000 25.56622 2000 26.90414
89000 26.102251 2000 24.362631
90000 26.638165 2000 21.887341
91000 27.17863 2000 19.985662
92000 27.72662 2000 18.728162
93000 28.276842 2000 16.99941
94000 28.830281 2000 15.71941
95000 29.389744 2000 14.744057
96000 29.972451 2000 14.214918
97000 30.575245 2000 13.450182
98000 31.141552 2000 12.79222
99000 31.711177 2000 12.10595
100000 32.286609 2000 11.281863
101000 32.879692 2000 10.025419
102000 33.460265 2000 9.9574468
103000 34.040002 2000 9.4078117
104000 34.619096 2000 8.9079161
105000 35.199384 2000 8.6269302
106000 35.784782 2000 8.5512649
107000 36.37489 2000 8.4703948
108000 36.963891 2000 8.2747542
109000 37.551549 2000 8.2895118
110000 38.154561 2000 8.1785613
111000 38.749306 2000 7.8443234
112000 39.344241 2000 7.7436124
113000 39.938878 2000 7.8118604
114000 40.531935 2000 7.3806177
115000 41.130022 2000 7.0857235
116000 41.726772 2000 7.1346752
117000 42.322611 2000 7.0653751
118000 42.927287 2000 6.6314104
119000 43.524125 2000 6.2169614
120000 44.127912 2000 5.8988829
121000 44.724988 2000 5.4197277
122000 45.328051 2000 4.6381303
123000 45.93285 2000 4.4949206
124000 46.54149 2000 4.4261118
125000 47.301723 2000 4.4223703
126000 48.071689 2000 4.4858898
127000 48.834286 2000 4.3312536
128000 49.448737 2000 3.7124973
129000 50.169622 2000 3.5467396
130000 50.867494 2000 3.5104139
131000 51.585563 2000 3.5725612
132000 52.240372 2000 3.669455
133000 52.892134 2000 3.6168912
134000 53.50594 2000 3.3598517
135000 54.114565 2000 3.3743407
136000 54.725082 2000 3.1109764
137000 55.358218 2000 3.0720146
138000 55.977314 2000 3.1303776
139000 56.589791 2000 3.2052806
140000 57.212518 2000 2.8958882
141000 57.867102 2000 2.9931572
142000 58.690342 2000 3.0967832
143000 59.418639 2000 3.0576365
144000 60.035852 2000 3.2016943
145000 60.666569 2000 3.3817709
146000 61.368878 2000 3.4527239
147000 62.159309 2000 3.5928733
148000 62.879677 2000 3.7784682
149000 63.50784 2000 3.6587944
150000 64.129366 2000 3.7945669
151000 64.74324 2000 3.5551557
152000 65.360802 2000 3.6248848
153000 65.979475 2000 3.7361463
154000 66.593554 2000 3.8534319
155000 67.30899 2000 4.0101408
156000 68.295637 2000 3.7670652
157000 69.257704 2000 3.1487676
158000 70.085566 2000 2.980076
159000 70.914218 2000 3.0350592
160000 71.734553 2000 3.125389
161000 72.423913 2000 2.7516115
162000 73.264994 2000 2.413911
163000 74.126424 2000 2.297713
164000 75.050891 2000 2.3190806
165000 75.917063 2000 2.2868879
166000 76.783267 2000 2.1658547
167000 77.516683 2000 1.7511071
168000 78.319102 2000 1.4112478
169000 78.961239 2000 1.3623558
170000 79.578448 2000 1.3701579
Loop time of 79.5785 on 1 procs for 150000 steps with 2000 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 40.78 | 40.78 | 40.78 | 0.0 | 51.25
Neigh | 0.6504 | 0.6504 | 0.6504 | 0.0 | 0.82
Comm | 0.090848 | 0.090848 | 0.090848 | 0.0 | 0.11
Output | 0.0059597 | 0.0059597 | 0.0059597 | 0.0 | 0.01
Modify | 36.939 | 36.939 | 36.939 | 0.0 | 46.42
Other | | 1.112 | | | 1.40
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15308 ave 15308 max 15308 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15308
Ave neighs/atom = 7.654
Neighbor list builds = 367
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.69 | 12.69 | 12.69 Mbytes
Step CPU Atoms KinEng
170000 0 2000 1.3701579
171000 0.71457906 2000 2.3724823
172000 1.4067557 2000 3.5881441
173000 2.0500352 2000 5.3771633
174000 2.8020081 2000 7.5896471
175000 3.467807 2000 10.77251
176000 4.064748 2000 14.806868
177000 4.6769962 2000 19.607624
178000 5.26259 2000 25.426227
179000 5.8424937 2000 32.23584
180000 6.4222206 2000 39.930468
181000 6.9910375 2000 47.686304
182000 7.5601562 2000 56.506806
183000 8.1243537 2000 66.514326
184000 8.6871123 2000 77.554644
185000 9.3749051 2000 89.224002
186000 10.008412 2000 102.07846
187000 10.668269 2000 116.08141
188000 11.26663 2000 130.97964
189000 11.874542 2000 146.77806
190000 12.436262 2000 162.79858
191000 12.973297 2000 179.02052
192000 13.532286 2000 196.26683
193000 14.056018 2000 214.38928
194000 14.593726 2000 232.32068
195000 15.115478 2000 251.74644
196000 15.637308 2000 272.25231
197000 16.159144 2000 294.64075
198000 16.676958 2000 318.32895
199000 17.186114 2000 342.44005
200000 17.706244 2000 368.35469
201000 18.221731 2000 395.2465
202000 18.739505 2000 422.63599
203000 19.259645 2000 450.45248
204000 19.769875 2000 479.60812
205000 20.293972 2000 510.44155
206000 20.806658 2000 543.25751
207000 21.348998 2000 577.35928
208000 21.888691 2000 612.29718
209000 22.421596 2000 647.8951
210000 22.922782 2000 683.79409
211000 23.473165 2000 720.36556
212000 24.008952 2000 759.27331
213000 24.56155 2000 798.27302
214000 25.062386 2000 837.93849
215000 25.563743 2000 877.92945
216000 26.066188 2000 919.62532
217000 26.584605 2000 962.83509
218000 27.15076 2000 1008.5243
219000 27.651387 2000 1054.5769
220000 28.146147 2000 1103.1843
221000 28.644239 2000 1153.0349
222000 29.141899 2000 1204.5599
223000 29.636644 2000 1257.1367
224000 30.13786 2000 1308.6735
WARNING: Lost atoms: original 2000 current 1999 (src/thermo.cpp:487)
225000 30.638093 1999 1360.1205
226000 31.127956 1998 1404.8405
227000 31.620394 1996 1448.4869
228000 32.108597 1992 1491.8112
229000 32.592048 1985 1518.7013
230000 33.067462 1971 1507.6699
231000 33.552874 1965 1533.5096
232000 34.037763 1948 1489.4128
233000 34.531058 1933 1477.4536
234000 35.01451 1915 1425.8398
235000 35.495081 1904 1410.1451
236000 35.963357 1892 1401.7595
237000 36.428382 1880 1368.893
238000 36.890459 1868 1341.8885
239000 37.358838 1850 1286.7968
240000 37.828549 1833 1219.5123
241000 38.29428 1820 1173.3608
242000 38.750021 1806 1106.0727
243000 39.206425 1788 1035.912
244000 39.690492 1779 1021.6147
245000 40.138287 1767 969.40032
246000 40.582591 1757 939.12022
247000 41.02378 1739 840.9396
248000 41.472154 1730 822.06575
249000 41.916625 1719 762.11057
250000 42.365019 1707 708.50308
251000 42.804617 1700 692.12647
252000 43.257666 1697 694.5812
253000 43.777656 1686 652.36951
254000 44.244131 1682 662.95256
255000 44.667759 1677 637.34619
256000 45.111967 1672 630.71277
257000 45.550194 1669 641.87365
258000 45.985106 1665 635.862
259000 46.42582 1664 658.5339
260000 46.860965 1662 669.95468
261000 47.298309 1660 676.93495
262000 47.748236 1657 681.72646
263000 48.215018 1655 687.4078
264000 48.657973 1651 681.61352
265000 49.076584 1647 673.20622
266000 49.497823 1644 677.30073
267000 49.917789 1641 671.05897
268000 50.347112 1639 689.55776
269000 50.778062 1637 711.98809
270000 51.226034 1633 705.29974
Loop time of 51.2261 on 1 procs for 100000 steps with 1633 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.462 | 27.462 | 27.462 | 0.0 | 53.61
Neigh | 0.47887 | 0.47887 | 0.47887 | 0.0 | 0.93
Comm | 0.058496 | 0.058496 | 0.058496 | 0.0 | 0.11
Output | 0.0039167 | 0.0039167 | 0.0039167 | 0.0 | 0.01
Modify | 22.566 | 22.566 | 22.566 | 0.0 | 44.05
Other | | 0.6567 | | | 1.28
Nlocal: 1633 ave 1633 max 1633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11358 ave 11358 max 11358 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11358
Ave neighs/atom = 6.955297
Neighbor list builds = 244
Dangerous builds = 0
Total wall time: 0:02:15

635
examples/granregion/log.16Mar23.granregion.funnel.g++.4 Normal file
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@ -0,0 +1,635 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 4 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.5 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/multi/newtoff
stencil: full/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 3000 every 59965 steps, 2000 by step 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.049 | 6.049 | 6.049 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.55467905 2000 -0
2000 0.77825615 2000 -0
3000 0.99338813 2000 -0
4000 1.2048904 2000 -0
5000 1.4073987 2000 -0
6000 1.6070452 2000 -0
7000 1.8056594 2000 -0
8000 1.9907326 2000 -0
9000 2.1732359 2000 -0
10000 2.3525506 2000 -0
11000 2.4202338 2000 -0
12000 2.4883928 2000 -0
13000 2.5587335 2000 -0
14000 2.6327822 2000 -0
15000 2.7095893 2000 -0
16000 2.7909032 2000 -0
17000 2.8763781 2000 -0
18000 2.9671807 2000 -0
19000 3.05783 2000 -0
20000 3.1546642 2000 -0
Loop time of 3.1547 on 4 procs for 20000 steps with 2000 atoms
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.045592 | 0.12271 | 0.29398 | 28.5 | 3.89
Neigh | 0.011353 | 0.019401 | 0.032667 | 5.7 | 0.61
Comm | 0.043342 | 0.09899 | 0.1539 | 14.6 | 3.14
Output | 0.00097884 | 0.0019761 | 0.0024333 | 1.3 | 0.06
Modify | 0.8096 | 1.2822 | 2.26 | 50.7 | 40.65
Other | | 1.629 | | | 51.65
Nlocal: 500 ave 510 max 493 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 154 ave 227 max 79 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 415.5 ave 610 max 258 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1662
Ave neighs/atom = 0.831
Neighbor list builds = 71
Dangerous builds = 0
unfix ins
run 150000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.33 | 12.5 | 12.68 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6652.2957
21000 0.068149031 2000 6807.2201
22000 0.13906682 2000 6973.9359
23000 0.21167896 2000 7142.3648
24000 0.28828482 2000 7276.9717
25000 0.36895294 2000 7369.4191
26000 0.45705665 2000 7497.6526
27000 0.55283141 2000 7638.946
28000 0.65163553 2000 7780.0339
29000 0.75208427 2000 7881.8177
30000 0.85956458 2000 7967.2641
31000 0.94177635 2000 7994.9273
32000 1.0345834 2000 7937.0672
33000 1.1315152 2000 7774.0508
34000 1.2426423 2000 7591.1511
35000 1.3578344 2000 7357.5032
36000 1.4893311 2000 7147.3776
37000 1.6240315 2000 6980.0719
38000 1.7664339 2000 6813.0872
39000 1.91857 2000 6657.0694
40000 2.0835393 2000 6505.1356
41000 2.2038908 2000 6330.3106
42000 2.330345 2000 6148.0635
43000 2.4596185 2000 5933.4808
44000 2.5912876 2000 5759.5507
45000 2.7316375 2000 5510.4729
46000 2.8777238 2000 5332.8673
47000 3.0357893 2000 5164.4197
48000 3.1931582 2000 5027.4099
49000 3.341993 2000 4904.6999
50000 3.4914327 2000 4712.0967
51000 3.6880787 2000 4575.8693
52000 3.8868278 2000 4443.4894
53000 4.0538325 2000 4272.1666
54000 4.2275386 2000 4113.2811
55000 4.3935565 2000 3974.5981
56000 4.6008319 2000 3863.5272
57000 4.8305792 2000 3676.8918
58000 5.1085757 2000 3446.5177
59000 5.3025239 2000 3227.8857
60000 5.5061134 2000 2997.8151
61000 5.6771065 2000 2745.5998
62000 5.8533046 2000 2530.2536
63000 6.0266287 2000 2352.9283
64000 6.1975348 2000 2102.4916
65000 6.375875 2000 1906.3034
66000 6.6008814 2000 1683.179
67000 6.8728018 2000 1440.0663
68000 7.1104699 2000 1220.2743
69000 7.3660591 2000 1012.4596
70000 7.6208232 2000 796.99913
71000 7.8459169 2000 631.28788
72000 8.0433916 2000 459.93641
73000 8.2225178 2000 359.28959
74000 8.3982201 2000 286.19292
75000 8.5769976 2000 235.53259
76000 8.7541865 2000 187.55737
77000 9.0010462 2000 144.42323
78000 9.2721615 2000 116.12613
79000 9.4992863 2000 95.625301
80000 9.7368141 2000 82.645629
81000 9.9462546 2000 72.124657
82000 10.15281 2000 64.266704
83000 10.365519 2000 56.7285
84000 10.55069 2000 49.44393
85000 10.764107 2000 42.434733
86000 10.993211 2000 37.816266
87000 11.243268 2000 33.892006
88000 11.487204 2000 29.898596
89000 11.684173 2000 26.4401
90000 11.880908 2000 23.329056
91000 12.078366 2000 21.291141
92000 12.347446 2000 19.494401
93000 12.582632 2000 18.157646
94000 12.833491 2000 17.176709
95000 13.109452 2000 16.059418
96000 13.34541 2000 15.524934
97000 13.604566 2000 13.887097
98000 13.816696 2000 12.98846
99000 14.043128 2000 12.325347
100000 14.35998 2000 11.567779
101000 14.584033 2000 11.097346
102000 14.793606 2000 10.981696
103000 15.011832 2000 10.914661
104000 15.223053 2000 10.183009
105000 15.435892 2000 9.9825606
106000 15.651946 2000 9.5164341
107000 15.870696 2000 9.4270389
108000 16.237826 2000 9.2752131
109000 16.525601 2000 8.580319
110000 16.74452 2000 8.3138082
111000 16.991527 2000 7.826454
112000 17.322972 2000 7.5958866
113000 17.649386 2000 7.2760339
114000 17.967676 2000 7.2879075
115000 18.27941 2000 6.8298855
116000 18.619507 2000 6.6964815
117000 18.979092 2000 6.490952
118000 19.303215 2000 6.0204595
119000 19.683409 2000 5.9293145
120000 20.034873 2000 5.7244854
121000 20.329374 2000 5.4221021
122000 20.670529 2000 4.8227757
123000 20.970073 2000 4.7914829
124000 21.297132 2000 4.6895984
125000 21.524346 2000 4.4951309
126000 21.742931 2000 4.5186107
127000 21.983039 2000 4.5989696
128000 22.203881 2000 4.5578225
129000 22.428553 2000 4.2667783
130000 22.662049 2000 4.0855202
131000 22.893977 2000 4.129346
132000 23.134398 2000 4.1720282
133000 23.367561 2000 4.3178701
134000 23.614361 2000 4.1047803
135000 23.840139 2000 3.856834
136000 24.095293 2000 4.0099605
137000 24.320746 2000 4.1104868
138000 24.555868 2000 4.1538456
139000 24.798604 2000 4.3079797
140000 25.125474 2000 4.0655486
141000 25.360498 2000 4.1257388
142000 25.597535 2000 4.1180413
143000 25.824173 2000 4.2764691
144000 26.082826 2000 4.3992832
145000 26.307002 2000 4.0978942
146000 26.532413 2000 4.1776805
147000 26.759469 2000 4.2261665
148000 26.989405 2000 4.4049886
149000 27.215826 2000 4.5559941
150000 27.443235 2000 4.7449947
151000 27.670397 2000 4.962558
152000 27.901368 2000 4.8517188
153000 28.148201 2000 4.9263912
154000 28.379071 2000 4.6200149
155000 28.621063 2000 4.8289752
156000 28.870192 2000 5.043235
157000 29.105614 2000 5.2399981
158000 29.330537 2000 5.494424
159000 29.558095 2000 4.9215021
160000 29.785841 2000 4.8938104
161000 30.011182 2000 5.0832139
162000 30.23825 2000 5.2281894
163000 30.464829 2000 5.4710487
164000 30.719854 2000 5.7311326
165000 31.038065 2000 5.9048483
166000 31.340672 2000 6.1177544
167000 31.649901 2000 4.0749212
168000 31.928746 2000 4.0087545
169000 32.153717 2000 2.8333927
170000 32.380796 2000 2.6131424
Loop time of 32.3808 on 4 procs for 150000 steps with 2000 atoms
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.997 | 12.251 | 14.992 | 89.3 | 37.83
Neigh | 0.1358 | 0.20191 | 0.24331 | 9.0 | 0.62
Comm | 1.2102 | 2.0432 | 2.4992 | 36.1 | 6.31
Output | 0.0079578 | 0.012222 | 0.020149 | 4.4 | 0.04
Modify | 7.1333 | 9.974 | 12.03 | 56.2 | 30.80
Other | | 7.899 | | | 24.39
Nlocal: 500 ave 547 max 414 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 447.5 ave 678 max 201 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 4478.75 ave 5715 max 3358 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 17915
Ave neighs/atom = 8.9575
Neighbor list builds = 375
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.53 | 12.68 Mbytes
Step CPU Atoms KinEng
170000 0 2000 2.6131424
171000 0.22601136 2000 3.529459
172000 0.45221016 2000 4.7071494
173000 0.68427839 2000 6.3480095
174000 0.91114205 2000 8.8055429
175000 1.1431874 2000 12.020148
176000 1.3732197 2000 16.079961
177000 1.6051751 2000 20.911155
178000 1.8346523 2000 26.447901
179000 2.0762403 2000 32.277607
180000 2.3420473 2000 39.374754
181000 2.6328957 2000 46.824434
182000 2.8669203 2000 54.755937
183000 3.1047916 2000 63.957816
184000 3.3310346 2000 74.217343
185000 3.5685015 2000 85.472859
186000 3.7955114 2000 97.586962
187000 4.0326183 2000 110.39658
188000 4.267244 2000 123.54524
189000 4.4987867 2000 137.45798
190000 4.7358838 2000 151.81094
191000 4.9494874 2000 166.91945
192000 5.1552044 2000 182.93379
193000 5.3547002 2000 200.32195
194000 5.5590208 2000 218.31863
195000 5.7575332 2000 237.22122
196000 5.9520759 2000 255.12936
197000 6.1457469 2000 273.87347
198000 6.341216 2000 293.82126
199000 6.5397944 2000 315.13067
200000 6.7418645 2000 337.18517
201000 6.9368245 2000 359.48438
202000 7.1538903 2000 382.76229
203000 7.3864641 2000 408.60338
204000 7.6731476 2000 435.15421
205000 7.9053649 2000 462.53542
206000 8.1480905 2000 490.85791
207000 8.3856692 2000 519.80878
208000 8.6034715 2000 550.44978
209000 8.8046602 2000 581.78594
210000 9.0044136 2000 615.02491
211000 9.2216638 2000 649.34564
212000 9.4269046 2000 684.24357
213000 9.6587854 2000 720.72627
214000 9.8596293 2000 757.96901
215000 10.05877 2000 796.8493
216000 10.256066 2000 836.58839
217000 10.48718 2000 877.81823
218000 10.694787 2000 920.81077
219000 10.891455 2000 963.77552
220000 11.147269 2000 1007.6868
221000 11.400829 2000 1054.0654
222000 11.65238 2000 1102.4934
223000 11.846807 2000 1151.1348
224000 12.040148 2000 1200.6622
225000 12.229259 2000 1251.5126
WARNING: Lost atoms: original 2000 current 1999 (src/thermo.cpp:487)
226000 12.420863 1999 1299.6349
227000 12.635492 1997 1338.1126
228000 12.827738 1987 1354.6661
229000 13.016127 1980 1369.1412
230000 13.211511 1970 1369.1776
231000 13.404909 1963 1377.7863
232000 13.602332 1950 1362.1028
233000 13.796103 1938 1344.4535
234000 13.988442 1924 1318.1397
235000 14.185813 1907 1269.3181
236000 14.378388 1895 1242.269
237000 14.568867 1881 1188.0729
238000 14.75676 1868 1162.8778
239000 14.947894 1854 1111.9974
240000 15.160004 1840 1050.2813
241000 15.340495 1831 1024.5782
242000 15.523597 1816 980.07203
243000 15.725193 1807 973.84606
244000 15.902549 1796 936.95947
245000 16.081382 1790 916.53685
246000 16.261081 1780 893.82891
247000 16.451727 1770 853.09944
248000 16.628641 1755 804.73429
249000 16.804105 1749 773.19378
250000 16.978354 1738 734.78084
251000 17.152527 1725 668.92528
252000 17.328291 1717 651.36038
253000 17.512786 1706 595.48412
254000 17.695931 1699 564.79829
255000 17.874221 1695 558.19897
256000 18.050516 1693 568.02459
257000 18.228697 1692 584.97166
258000 18.400925 1689 574.19701
259000 18.576449 1687 583.36332
260000 18.754006 1684 577.56927
261000 18.946091 1681 582.0375
262000 19.182957 1679 583.29644
263000 19.394795 1676 575.09831
264000 19.604668 1673 575.78272
265000 19.81517 1672 595.66572
266000 20.046658 1670 610.84262
267000 20.332684 1665 588.36505
268000 20.573691 1662 593.44831
269000 20.800574 1660 600.31964
270000 21.058624 1656 588.46212
Loop time of 21.0587 on 4 procs for 100000 steps with 1656 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.8632 | 8.4037 | 11.541 | 97.3 | 39.91
Neigh | 0.13431 | 0.15665 | 0.17248 | 3.8 | 0.74
Comm | 0.70516 | 1.4552 | 1.9637 | 40.7 | 6.91
Output | 0.0030904 | 0.0079543 | 0.016722 | 5.9 | 0.04
Modify | 5.3661 | 6.1781 | 6.8249 | 22.0 | 29.34
Other | | 4.857 | | | 23.06
Nlocal: 414 ave 426 max 385 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 408 ave 634 max 183 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 3463 ave 4360 max 2354 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 13852
Ave neighs/atom = 8.3647343
Neighbor list builds = 255
Dangerous builds = 0
Total wall time: 0:00:56

634
examples/granregion/log.16Mar23.granregion.mixer.g++.1 Normal file
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@ -0,0 +1,634 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.6 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton
stencil: half/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
Particle insertion: 444 every 84653 steps, 1000 by step 169307
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
run 200000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.861 | 5.861 | 5.861 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.11477344 444 -0 0.015707963
2000 0.21604269 444 -0 0.031415927
3000 0.31421365 444 -0 0.04712389
4000 0.41095902 444 -0 0.062831853
5000 0.50703042 444 -0 0.078539816
6000 0.60585007 444 -0 0.09424778
7000 0.70232419 444 -0 0.10995574
8000 0.80002622 444 -0 0.12566371
9000 0.89464008 444 -0 0.14137167
10000 0.99260726 444 -0 0.15707963
11000 1.090675 444 -0 0.1727876
12000 1.1878107 444 -0 0.18849556
13000 1.2860401 444 -0 0.20420352
14000 1.3830433 444 -0 0.21991149
15000 1.4834023 444 -0 0.23561945
16000 1.5799984 444 -0 0.25132741
17000 1.6758091 444 -0 0.26703538
18000 1.7713554 444 -0 0.28274334
19000 1.8684734 444 -0 0.2984513
20000 1.9661563 444 -0 0.31415927
21000 2.0629748 444 -0 0.32986723
22000 2.1575594 444 -0 0.34557519
23000 2.2530422 444 -0 0.36128316
24000 2.3525179 444 -0 0.37699112
25000 2.4494323 444 -0 0.39269908
26000 2.5454666 444 -0 0.40840704
27000 2.6402269 444 -0 0.42411501
28000 2.7364338 444 -0 0.43982297
29000 2.8349 444 -0 0.45553093
30000 2.9327959 444 -0 0.4712389
31000 3.0304534 444 -0 0.48694686
32000 3.1315005 444 -0 0.50265482
33000 3.2290307 444 -0 0.51836279
34000 3.3243787 444 -0 0.53407075
35000 3.4232964 444 -0 0.54977871
36000 3.5235978 444 -0 0.56548668
37000 3.6214101 444 -0 0.58119464
38000 3.7179412 444 -0 0.5969026
39000 3.8159856 444 -0 0.61261057
40000 3.9121916 444 -0 0.62831853
41000 4.0080794 444 -0 0.64402649
42000 4.1087349 444 -0 0.65973446
43000 4.2059697 444 -0 0.67544242
44000 4.3043867 444 -0 0.69115038
45000 4.4014253 444 -0 0.70685835
46000 4.5000241 444 -0 0.72256631
47000 4.5970258 444 -0 0.73827427
48000 4.6929243 444 -0 0.75398224
49000 4.7894702 444 -0 0.7696902
50000 4.8858098 444 -0 0.78539816
51000 4.985063 444 -0 0.80110613
52000 5.0863877 444 -0 0.81681409
53000 5.181301 444 -0 0.83252205
54000 5.2819523 444 -0 0.84823002
55000 5.3895357 444 -0 0.86393798
56000 5.5225568 444 -0 0.87964594
57000 5.6473901 444 -0 0.89535391
58000 5.7786123 444 -0 0.91106187
59000 5.8932617 444 -0 0.92676983
60000 6.004952 444 -0 0.9424778
61000 6.1168028 444 -0 0.95818576
62000 6.2274784 444 -0 0.97389372
63000 6.341172 444 -0 0.98960169
64000 6.4565154 444 -0 1.0053096
65000 6.5684785 444 -0 1.0210176
66000 6.6836542 444 -0 1.0367256
67000 6.797745 444 -0 1.0524335
68000 6.9091592 444 -0 1.0681415
69000 7.0230958 444 -0 1.0838495
70000 7.140508 444 -0 1.0995574
71000 7.2547153 444 -0 1.1152654
72000 7.3698096 444 -0 1.1309734
73000 7.4846587 444 -0 1.1466813
74000 7.6005538 444 -0 1.1623893
75000 7.715498 444 -0 1.1780972
76000 7.8306339 444 -0 1.1938052
77000 7.9458861 444 -0 1.2095132
78000 8.0608796 444 -0 1.2252211
79000 8.1819612 444 -0 1.2409291
80000 8.3017939 444 -0 1.2566371
81000 8.4206794 444 -0 1.272345
82000 8.5396045 444 -0 1.288053
83000 8.6588178 444 -0 1.303761
84000 8.7939815 444 -0 1.3194689
85000 8.9999511 888 -0 1.3351769
86000 9.2762515 888 -0 1.3508848
87000 9.5497189 888 -0 1.3665928
88000 9.8025426 888 -0 1.3823008
89000 10.063005 888 -0 1.3980087
90000 10.343956 888 -0 1.4137167
91000 10.630004 888 -0 1.4294247
92000 10.865437 888 -0 1.4451326
93000 11.090302 888 -0 1.4608406
94000 11.306921 888 -0 1.4765485
95000 11.525442 888 -0 1.4922565
96000 11.786482 888 -0 1.5079645
97000 12.033336 888 -0 1.5236724
98000 12.258224 888 -0 1.5393804
99000 12.486583 888 -0 1.5550884
100000 12.70566 888 -0 1.5707963
101000 12.934051 888 -0 1.5865043
102000 13.194977 888 -0 1.6022123
103000 13.503561 888 -0 1.6179202
104000 13.737785 888 -0 1.6336282
105000 13.96388 888 -0 1.6493361
106000 14.190156 888 -0 1.6650441
107000 14.416346 888 -0 1.6807521
108000 14.642321 888 -0 1.69646
109000 14.877668 888 -0 1.712168
110000 15.114644 888 -0 1.727876
111000 15.354762 888 -0 1.7435839
112000 15.615795 888 -0 1.7592919
113000 15.854301 888 -0 1.7749998
114000 16.099855 888 -0 1.7907078
115000 16.344044 888 -0 1.8064158
116000 16.60829 888 -0 1.8221237
117000 16.847146 888 -0 1.8378317
118000 17.086787 888 -0 1.8535397
119000 17.324264 888 -0 1.8692476
120000 17.563913 888 -0 1.8849556
121000 17.798333 888 -0 1.9006636
122000 18.033339 888 -0 1.9163715
123000 18.275883 888 -0 1.9320795
124000 18.542879 888 -0 1.9477874
125000 18.790098 888 -0 1.9634954
126000 19.034113 888 -0 1.9792034
127000 19.286183 888 -0 1.9949113
128000 19.574764 888 -0 2.0106193
129000 19.832536 888 -0 2.0263273
130000 20.085705 888 -0 2.0420352
131000 20.327805 888 -0 2.0577432
132000 20.576476 888 -0 2.0734512
133000 20.82021 888 -0 2.0891591
134000 21.063425 888 -0 2.1048671
135000 21.304848 888 -0 2.120575
136000 21.554936 888 -0 2.136283
137000 21.797949 888 -0 2.151991
138000 22.041181 888 -0 2.1676989
139000 22.288509 888 -0 2.1834069
140000 22.539512 888 -0 2.1991149
141000 22.786046 888 -0 2.2148228
142000 23.052553 888 -0 2.2305308
143000 23.321282 888 -0 2.2462387
144000 23.619171 888 -0 2.2619467
145000 23.918581 888 -0 2.2776547
146000 24.200849 888 -0 2.2933626
147000 24.500127 888 -0 2.3090706
148000 24.756357 888 -0 2.3247786
149000 25.015262 888 -0 2.3404865
150000 25.271136 888 -0 2.3561945
151000 25.519846 888 -0 2.3719025
152000 25.780481 888 -0 2.3876104
153000 26.027917 888 -0 2.4033184
154000 26.277021 888 -0 2.4190263
155000 26.54158 888 -0 2.4347343
156000 26.828357 888 -0 2.4504423
157000 27.172993 888 -0 2.4661502
158000 27.454171 888 -0 2.4818582
159000 27.72964 888 -0 2.4975662
160000 28.007464 888 -0 2.5132741
161000 28.28268 888 -0 2.5289821
162000 28.561094 888 -0 2.54469
163000 28.839295 888 -0 2.560398
164000 29.117588 888 -0 2.576106
165000 29.394126 888 -0 2.5918139
166000 29.675102 888 -0 2.6075219
167000 29.951524 888 -0 2.6232299
168000 30.233181 888 -0 2.6389378
169000 30.516798 888 -0 2.6546458
170000 30.818897 1000 -0 2.6703538
171000 31.215403 1000 -0 2.6860617
172000 31.528362 1000 -0 2.7017697
173000 31.844759 1000 -0 2.7174776
174000 32.159787 1000 -0 2.7331856
175000 32.482605 1000 -0 2.7488936
176000 32.798004 1000 -0 2.7646015
177000 33.112668 1000 -0 2.7803095
178000 33.429501 1000 -0 2.7960175
179000 33.74646 1000 -0 2.8117254
180000 34.059172 1000 -0 2.8274334
181000 34.381226 1000 -0 2.8431414
182000 34.697465 1000 -0 2.8588493
183000 35.008892 1000 -0 2.8745573
184000 35.332856 1000 -0 2.8902652
185000 35.650733 1000 -0 2.9059732
186000 35.971328 1000 -0 2.9216812
187000 36.298046 1000 -0 2.9373891
188000 36.622634 1000 -0 2.9530971
189000 36.945728 1000 -0 2.9688051
190000 37.268801 1000 -0 2.984513
191000 37.592615 1000 -0 3.000221
192000 37.915197 1000 -0 3.0159289
193000 38.226138 1000 -0 3.0316369
194000 38.534735 1000 -0 3.0473449
195000 38.844711 1000 -0 3.0630528
196000 39.159518 1000 -0 3.0787608
197000 39.474235 1000 -0 3.0944688
198000 39.786609 1000 -0 3.1101767
199000 40.10213 1000 -0 3.1258847
200000 40.421226 1000 -0 3.1415927
Loop time of 40.4213 on 1 procs for 200000 steps with 1000 atoms
Performance: 20199.903 tau/day, 4947.886 timesteps/s, 4.948 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6681 | 3.6681 | 3.6681 | 0.0 | 9.07
Neigh | 0.050194 | 0.050194 | 0.050194 | 0.0 | 0.12
Comm | 0.53308 | 0.53308 | 0.53308 | 0.0 | 1.32
Output | 0.0071363 | 0.0071363 | 0.0071363 | 0.0 | 0.02
Modify | 35.563 | 35.563 | 35.563 | 0.0 | 87.98
Other | | 0.5999 | | | 1.48
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 197 ave 197 max 197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3812 ave 3812 max 3812 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3812
Ave neighs/atom = 3.812
Neighbor list builds = 205
Dangerous builds = 0
unfix ins
run 200000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 1.0188213 3.1415927
201000 0.31745969 1000 1.0237918 3.1573006
202000 0.6315036 1000 1.0177231 3.1730086
203000 0.9480314 1000 1.0127096 3.1887165
204000 1.2572431 1000 1.0084386 3.2044245
205000 1.5683429 1000 0.9957528 3.2201325
206000 1.8801922 1000 1.0003921 3.2358404
207000 2.1905883 1000 0.99358387 3.2515484
208000 2.4948426 1000 0.99103748 3.2672564
209000 2.8195665 1000 0.98488628 3.2829643
210000 3.1420952 1000 0.98305824 3.2986723
211000 3.4618849 1000 0.97185818 3.3143802
212000 3.7910078 1000 0.96191966 3.3300882
213000 4.1184009 1000 0.95953159 3.3457962
214000 4.4491355 1000 0.95307268 3.3615041
215000 4.7782398 1000 0.95612155 3.3772121
216000 5.1088177 1000 0.96582166 3.3929201
217000 5.4376503 1000 0.96124408 3.408628
218000 5.7707229 1000 0.95705813 3.424336
219000 6.1055922 1000 0.9660222 3.440044
220000 6.4418056 1000 0.97539486 3.4557519
221000 6.7755181 1000 0.97919396 3.4714599
222000 7.104521 1000 0.97448171 3.4871678
223000 7.4368025 1000 0.95742917 3.5028758
224000 7.7623405 1000 0.94218245 3.5185838
225000 8.0932682 1000 0.93056484 3.5342917
226000 8.4217598 1000 0.92009109 3.5499997
227000 8.747426 1000 0.90684871 3.5657077
228000 9.0818038 1000 0.91719046 3.5814156
229000 9.4125504 1000 0.92681746 3.5971236
230000 9.7439963 1000 0.9195493 3.6128316
231000 10.075499 1000 0.93275667 3.6285395
232000 10.404017 1000 0.9494565 3.6442475
233000 10.774786 1000 0.95036607 3.6599554
234000 11.158713 1000 0.9596283 3.6756634
235000 11.566878 1000 0.98314341 3.6913714
236000 11.977294 1000 0.98115865 3.7070793
237000 12.347191 1000 0.9723466 3.7227873
238000 12.686388 1000 0.95267817 3.7384953
239000 13.031631 1000 0.92661956 3.7542032
240000 13.451121 1000 0.92237207 3.7699112
241000 13.855031 1000 0.91301732 3.7856191
242000 14.272001 1000 0.90488754 3.8013271
243000 14.632631 1000 0.90430417 3.8170351
244000 14.97608 1000 0.90179051 3.832743
245000 15.419173 1000 0.89658897 3.848451
246000 15.903699 1000 0.89583335 3.864159
247000 16.312374 1000 0.89409138 3.8798669
248000 16.660472 1000 0.89948364 3.8955749
249000 17.063147 1000 0.90196936 3.9112829
250000 17.423622 1000 0.89616943 3.9269908
251000 17.76439 1000 0.87816303 3.9426988
252000 18.103828 1000 0.86705341 3.9584067
253000 18.454644 1000 0.84494344 3.9741147
254000 18.876297 1000 0.81541663 3.9898227
255000 19.264851 1000 0.80071805 4.0055306
256000 19.669757 1000 0.80290754 4.0212386
257000 20.066097 1000 0.80000385 4.0369466
258000 20.481516 1000 0.80379277 4.0526545
259000 20.851537 1000 0.81091684 4.0683625
260000 21.246226 1000 0.80124855 4.0840704
261000 21.586832 1000 0.79581606 4.0997784
262000 21.968726 1000 0.78415946 4.1154864
263000 22.388474 1000 0.78837276 4.1311943
264000 22.76238 1000 0.78962435 4.1469023
265000 23.13787 1000 0.79388706 4.1626103
266000 23.470742 1000 0.80484385 4.1783182
267000 23.801402 1000 0.79505699 4.1940262
268000 24.14266 1000 0.78663829 4.2097342
269000 24.545281 1000 0.77557297 4.2254421
270000 24.886776 1000 0.76992342 4.2411501
271000 25.218744 1000 0.75955867 4.256858
272000 25.549898 1000 0.76207709 4.272566
273000 25.882738 1000 0.76891185 4.288274
274000 26.212384 1000 0.77380617 4.3039819
275000 26.540612 1000 0.77349795 4.3196899
276000 26.869636 1000 0.77559636 4.3353979
277000 27.200449 1000 0.76806972 4.3511058
278000 27.548549 1000 0.76223861 4.3668138
279000 27.883681 1000 0.76306533 4.3825218
280000 28.221552 1000 0.76369569 4.3982297
281000 28.558479 1000 0.75945303 4.4139377
282000 28.892758 1000 0.75872312 4.4296456
283000 29.224927 1000 0.75354345 4.4453536
284000 29.565477 1000 0.74433058 4.4610616
285000 29.914679 1000 0.7349005 4.4767695
286000 30.265305 1000 0.73182808 4.4924775
287000 30.607982 1000 0.73334122 4.5081855
288000 30.94168 1000 0.73308623 4.5238934
289000 31.276062 1000 0.73620818 4.5396014
290000 31.614934 1000 0.73906492 4.5553093
291000 31.959782 1000 0.73921306 4.5710173
292000 32.296279 1000 0.73919766 4.5867253
293000 32.615262 1000 0.75148875 4.6024332
294000 32.93925 1000 0.76390126 4.6181412
295000 33.266316 1000 0.76421084 4.6338492
296000 33.591115 1000 0.78124272 4.6495571
297000 33.924279 1000 0.78526224 4.6652651
298000 34.256265 1000 0.78279226 4.6809731
299000 34.584382 1000 0.78390001 4.696681
300000 34.910629 1000 0.78017239 4.712389
301000 35.233205 1000 0.77432653 4.7280969
302000 35.55956 1000 0.7627792 4.7438049
303000 35.885484 1000 0.75222273 4.7595129
304000 36.205453 1000 0.73765921 4.7752208
305000 36.525101 1000 0.72338298 4.7909288
306000 36.845236 1000 0.71944975 4.8066368
307000 37.168044 1000 0.71547274 4.8223447
308000 37.491196 1000 0.71267737 4.8380527
309000 37.827079 1000 0.70506173 4.8537606
310000 38.168049 1000 0.70685173 4.8694686
311000 38.504282 1000 0.70327488 4.8851766
312000 38.846152 1000 0.69732519 4.9008845
313000 39.191958 1000 0.70137823 4.9165925
314000 39.532177 1000 0.70613806 4.9323005
315000 39.876728 1000 0.70981591 4.9480084
316000 40.225244 1000 0.72246602 4.9637164
317000 40.573681 1000 0.71946499 4.9794244
318000 40.918134 1000 0.73275857 4.9951323
319000 41.261914 1000 0.74357547 5.0108403
320000 41.607984 1000 0.74138038 5.0265482
321000 41.957822 1000 0.73285846 5.0422562
322000 42.30176 1000 0.72990718 5.0579642
323000 42.644077 1000 0.72024459 5.0736721
324000 42.985509 1000 0.71052943 5.0893801
325000 43.323921 1000 0.69560261 5.1050881
326000 43.664945 1000 0.69939398 5.120796
327000 44.004741 1000 0.71331291 5.136504
328000 44.347204 1000 0.72181082 5.152212
329000 44.689866 1000 0.72534262 5.1679199
330000 45.055673 1000 0.73874292 5.1836279
331000 45.400501 1000 0.74135464 5.1993358
332000 45.743289 1000 0.73578005 5.2150438
333000 46.087061 1000 0.72662516 5.2307518
334000 46.427231 1000 0.72030125 5.2464597
335000 46.767813 1000 0.72801784 5.2621677
336000 47.108619 1000 0.73020974 5.2778757
337000 47.44666 1000 0.7344527 5.2935836
338000 47.784653 1000 0.73826638 5.3092916
339000 48.124114 1000 0.74079395 5.3249995
340000 48.463953 1000 0.74030413 5.3407075
341000 48.804616 1000 0.74815855 5.3564155
342000 49.143226 1000 0.75762011 5.3721234
343000 49.482788 1000 0.76311094 5.3878314
344000 49.822597 1000 0.76394459 5.4035394
345000 50.162186 1000 0.75550163 5.4192473
346000 50.496689 1000 0.7594991 5.4349553
347000 50.831695 1000 0.76650932 5.4506633
348000 51.167201 1000 0.76750437 5.4663712
349000 51.501847 1000 0.77084248 5.4820792
350000 51.841805 1000 0.76487701 5.4977871
351000 52.179907 1000 0.76870148 5.5134951
352000 52.517605 1000 0.77597853 5.5292031
353000 52.850047 1000 0.77929348 5.544911
354000 53.182408 1000 0.7744937 5.560619
355000 53.512931 1000 0.76114616 5.576327
356000 53.845782 1000 0.75392687 5.5920349
357000 54.178336 1000 0.74858889 5.6077429
358000 54.514517 1000 0.75630978 5.6234508
359000 54.850783 1000 0.75781107 5.6391588
360000 55.183323 1000 0.75613713 5.6548668
361000 55.518704 1000 0.75250391 5.6705747
362000 55.851425 1000 0.75790051 5.6862827
363000 56.212376 1000 0.75283475 5.7019907
364000 56.542027 1000 0.7431151 5.7176986
365000 56.874325 1000 0.73274509 5.7334066
366000 57.208926 1000 0.72261631 5.7491146
367000 57.596495 1000 0.71279773 5.7648225
368000 58.007863 1000 0.70452113 5.7805305
369000 58.346944 1000 0.69777381 5.7962384
370000 58.686215 1000 0.69698007 5.8119464
371000 59.030366 1000 0.69322062 5.8276544
372000 59.368607 1000 0.67728454 5.8433623
373000 59.704376 1000 0.67335006 5.8590703
374000 60.044772 1000 0.66920493 5.8747783
375000 60.382875 1000 0.65614401 5.8904862
376000 60.72002 1000 0.65874131 5.9061942
377000 61.058554 1000 0.67072465 5.9219022
378000 61.400078 1000 0.68118419 5.9376101
379000 61.748931 1000 0.68481865 5.9533181
380000 62.098203 1000 0.68840839 5.969026
381000 62.444961 1000 0.69447162 5.984734
382000 62.797286 1000 0.69881397 6.000442
383000 63.154921 1000 0.69610171 6.0161499
384000 63.508448 1000 0.70059329 6.0318579
385000 63.857115 1000 0.71085103 6.0475659
386000 64.207915 1000 0.71532684 6.0632738
387000 64.561127 1000 0.72968624 6.0789818
388000 64.939826 1000 0.74729894 6.0946897
389000 65.284635 1000 0.76268063 6.1103977
390000 65.631752 1000 0.77170089 6.1261057
391000 65.981566 1000 0.77212462 6.1418136
392000 66.328406 1000 0.773784 6.1575216
393000 66.655905 1000 0.7731096 6.1732296
394000 66.993751 1000 0.77245259 6.1889375
395000 67.322842 1000 0.76912533 6.2046455
396000 67.647532 1000 0.76397972 6.2203535
397000 67.977448 1000 0.75736166 6.2360614
398000 68.310064 1000 0.75287599 6.2517694
399000 68.635966 1000 0.75354368 6.2674773
400000 68.963492 1000 0.75582397 6.2831853
Loop time of 68.9635 on 1 procs for 200000 steps with 1000 atoms
Performance: 11839.683 tau/day, 2900.084 timesteps/s, 2.900 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.238 | 11.238 | 11.238 | 0.0 | 16.30
Neigh | 0.077817 | 0.077817 | 0.077817 | 0.0 | 0.11
Comm | 1.5441 | 1.5441 | 1.5441 | 0.0 | 2.24
Output | 0.0082341 | 0.0082341 | 0.0082341 | 0.0 | 0.01
Modify | 55.304 | 55.304 | 55.304 | 0.0 | 80.19
Other | | 0.7909 | | | 1.15
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 278 ave 278 max 278 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5072 ave 5072 max 5072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5072
Ave neighs/atom = 5.072
Neighbor list builds = 166
Dangerous builds = 0
Total wall time: 0:01:49

634
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LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 2 by 2 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} multi
neighbor 0.6 multi
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Balancing ...
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton
stencil: half/multi/3d
bin: multi
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
Particle insertion: 444 every 84653 steps, 1000 by step 169307
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:895)
thermo_modify flush yes lost warn
run 200000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
@Article{Intveld08,
author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
title = {Accurate and Efficient Methods for Modeling Colloidal
Mixtures in an Explicit Solvent using Molecular Dynamics},
journal = {Comput.\ Phys.\ Commut.},
year = 2008,
volume = 179,
pages = {320--329}
}
@article{Shire2020,
author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
Detection Applied to Investigate the Quasi-Static Limit},
journal = {Computational Particle Mechanics},
year = {2020}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.816 | 5.816 | 5.816 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.069039547 444 -0 0.015707963
2000 0.12867095 444 -0 0.031415927
3000 0.18791426 444 -0 0.04712389
4000 0.24614388 444 -0 0.062831853
5000 0.30404486 444 -0 0.078539816
6000 0.36105446 444 -0 0.09424778
7000 0.41713358 444 -0 0.10995574
8000 0.47282802 444 -0 0.12566371
9000 0.52742586 444 -0 0.14137167
10000 0.58233488 444 -0 0.15707963
11000 0.62155506 444 -0 0.1727876
12000 0.6605457 444 -0 0.18849556
13000 0.69971591 444 -0 0.20420352
14000 0.73821845 444 -0 0.21991149
15000 0.77860211 444 -0 0.23561945
16000 0.8188072 444 -0 0.25132741
17000 0.85992964 444 -0 0.26703538
18000 0.9008443 444 -0 0.28274334
19000 0.94216466 444 -0 0.2984513
20000 0.98508697 444 -0 0.31415927
21000 1.0241468 444 -0 0.32986723
22000 1.0606191 444 -0 0.34557519
23000 1.0972735 444 -0 0.36128316
24000 1.134726 444 -0 0.37699112
25000 1.1723693 444 -0 0.39269908
26000 1.211349 444 -0 0.40840704
27000 1.250291 444 -0 0.42411501
28000 1.2906408 444 -0 0.43982297
29000 1.3307315 444 -0 0.45553093
30000 1.3704867 444 -0 0.4712389
31000 1.4064392 444 -0 0.48694686
32000 1.4426955 444 -0 0.50265482
33000 1.4789666 444 -0 0.51836279
34000 1.5163037 444 -0 0.53407075
35000 1.5534135 444 -0 0.54977871
36000 1.5907054 444 -0 0.56548668
37000 1.6296055 444 -0 0.58119464
38000 1.6690167 444 -0 0.5969026
39000 1.7082024 444 -0 0.61261057
40000 1.7476796 444 -0 0.62831853
41000 1.7847465 444 -0 0.64402649
42000 1.8216975 444 -0 0.65973446
43000 1.8594424 444 -0 0.67544242
44000 1.8975401 444 -0 0.69115038
45000 1.9361216 444 -0 0.70685835
46000 1.9764821 444 -0 0.72256631
47000 2.0221252 444 -0 0.73827427
48000 2.0635337 444 -0 0.75398224
49000 2.104472 444 -0 0.7696902
50000 2.1447842 444 -0 0.78539816
51000 2.1808558 444 -0 0.80110613
52000 2.2180542 444 -0 0.81681409
53000 2.2547243 444 -0 0.83252205
54000 2.2934546 444 -0 0.84823002
55000 2.3321909 444 -0 0.86393798
56000 2.3732179 444 -0 0.87964594
57000 2.4141133 444 -0 0.89535391
58000 2.455667 444 -0 0.91106187
59000 2.4983196 444 -0 0.92676983
60000 2.5415086 444 -0 0.9424778
61000 2.581342 444 -0 0.95818576
62000 2.6215029 444 -0 0.97389372
63000 2.6633884 444 -0 0.98960169
64000 2.7048848 444 -0 1.0053096
65000 2.7497607 444 -0 1.0210176
66000 2.7952373 444 -0 1.0367256
67000 2.8399748 444 -0 1.0524335
68000 2.8851806 444 -0 1.0681415
69000 2.9303317 444 -0 1.0838495
70000 2.9815632 444 -0 1.0995574
71000 3.0257986 444 -0 1.1152654
72000 3.068788 444 -0 1.1309734
73000 3.1130125 444 -0 1.1466813
74000 3.1558178 444 -0 1.1623893
75000 3.1993327 444 -0 1.1780972
76000 3.2444469 444 -0 1.1938052
77000 3.2901781 444 -0 1.2095132
78000 3.3356302 444 -0 1.2252211
79000 3.3814834 444 -0 1.2409291
80000 3.4290631 444 -0 1.2566371
81000 3.4715671 444 -0 1.272345
82000 3.5136342 444 -0 1.288053
83000 3.5566281 444 -0 1.303761
84000 3.6001405 444 -0 1.3194689
85000 3.6709788 888 -0 1.3351769
86000 3.7652387 888 -0 1.3508848
87000 3.8618109 888 -0 1.3665928
88000 3.9546406 888 -0 1.3823008
89000 4.0475587 888 -0 1.3980087
90000 4.1424919 888 -0 1.4137167
91000 4.2114594 888 -0 1.4294247
92000 4.2842588 888 -0 1.4451326
93000 4.3524161 888 -0 1.4608406
94000 4.4204131 888 -0 1.4765485
95000 4.4886628 888 -0 1.4922565
96000 4.5588224 888 -0 1.5079645
97000 4.6304943 888 -0 1.5236724
98000 4.7018695 888 -0 1.5393804
99000 4.774147 888 -0 1.5550884
100000 4.847776 888 -0 1.5707963
101000 4.9173562 888 -0 1.5865043
102000 4.9886499 888 -0 1.6022123
103000 5.0618801 888 -0 1.6179202
104000 5.1331411 888 -0 1.6336282
105000 5.205209 888 -0 1.6493361
106000 5.2795148 888 -0 1.6650441
107000 5.3523346 888 -0 1.6807521
108000 5.4263886 888 -0 1.69646
109000 5.5029416 888 -0 1.712168
110000 5.5807033 888 -0 1.727876
111000 5.6574852 888 -0 1.7435839
112000 5.7320356 888 -0 1.7592919
113000 5.8097178 888 -0 1.7749998
114000 5.8858974 888 -0 1.7907078
115000 5.9636528 888 -0 1.8064158
116000 6.0421783 888 -0 1.8221237
117000 6.12052 888 -0 1.8378317
118000 6.2016349 888 -0 1.8535397
119000 6.2834058 888 -0 1.8692476
120000 6.3644485 888 -0 1.8849556
121000 6.4398727 888 -0 1.9006636
122000 6.5152081 888 -0 1.9163715
123000 6.5916482 888 -0 1.9320795
124000 6.6694407 888 -0 1.9477874
125000 6.7474201 888 -0 1.9634954
126000 6.8270768 888 -0 1.9792034
127000 6.9060885 888 -0 1.9949113
128000 6.9847809 888 -0 2.0106193
129000 7.0660497 888 -0 2.0263273
130000 7.1468939 888 -0 2.0420352
131000 7.2275386 888 -0 2.0577432
132000 7.3103515 888 -0 2.0734512
133000 7.3904073 888 -0 2.0891591
134000 7.4711333 888 -0 2.1048671
135000 7.5529594 888 -0 2.120575
136000 7.6399017 888 -0 2.136283
137000 7.7263891 888 -0 2.151991
138000 7.815523 888 -0 2.1676989
139000 7.9041642 888 -0 2.1834069
140000 7.9950145 888 -0 2.1991149
141000 8.0776291 888 -0 2.2148228
142000 8.1584715 888 -0 2.2305308
143000 8.2409653 888 -0 2.2462387
144000 8.326064 888 -0 2.2619467
145000 8.4107211 888 -0 2.2776547
146000 8.4946153 888 -0 2.2933626
147000 8.5784663 888 -0 2.3090706
148000 8.6648861 888 -0 2.3247786
149000 8.7503472 888 -0 2.3404865
150000 8.8378801 888 -0 2.3561945
151000 8.9221381 888 -0 2.3719025
152000 9.0101516 888 -0 2.3876104
153000 9.0982387 888 -0 2.4033184
154000 9.1851912 888 -0 2.4190263
155000 9.2744741 888 -0 2.4347343
156000 9.3697509 888 -0 2.4504423
157000 9.4640354 888 -0 2.4661502
158000 9.5594845 888 -0 2.4818582
159000 9.6572972 888 -0 2.4975662
160000 9.7543656 888 -0 2.5132741
161000 9.8485073 888 -0 2.5289821
162000 9.9446493 888 -0 2.54469
163000 10.040013 888 -0 2.560398
164000 10.137116 888 -0 2.576106
165000 10.23506 888 -0 2.5918139
166000 10.335537 888 -0 2.6075219
167000 10.436607 888 -0 2.6232299
168000 10.537429 888 -0 2.6389378
169000 10.642458 888 -0 2.6546458
170000 10.74705 1000 -0 2.6703538
171000 10.857156 1000 -0 2.6860617
172000 10.965939 1000 -0 2.7017697
173000 11.076233 1000 -0 2.7174776
174000 11.184172 1000 -0 2.7331856
175000 11.293846 1000 -0 2.7488936
176000 11.402493 1000 -0 2.7646015
177000 11.513895 1000 -0 2.7803095
178000 11.625438 1000 -0 2.7960175
179000 11.738308 1000 -0 2.8117254
180000 11.854793 1000 -0 2.8274334
181000 11.968344 1000 -0 2.8431414
182000 12.082268 1000 -0 2.8588493
183000 12.196356 1000 -0 2.8745573
184000 12.313359 1000 -0 2.8902652
185000 12.429559 1000 -0 2.9059732
186000 12.545853 1000 -0 2.9216812
187000 12.661447 1000 -0 2.9373891
188000 12.777355 1000 -0 2.9530971
189000 12.894856 1000 -0 2.9688051
190000 13.0103 1000 -0 2.984513
191000 13.126221 1000 -0 3.000221
192000 13.241507 1000 -0 3.0159289
193000 13.356198 1000 -0 3.0316369
194000 13.468168 1000 -0 3.0473449
195000 13.582232 1000 -0 3.0630528
196000 13.700446 1000 -0 3.0787608
197000 13.816948 1000 -0 3.0944688
198000 13.934106 1000 -0 3.1101767
199000 14.053497 1000 -0 3.1258847
200000 14.171799 1000 -0 3.1415927
Loop time of 14.1719 on 4 procs for 200000 steps with 1000 atoms
Performance: 57614.644 tau/day, 14112.479 timesteps/s, 14.112 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46468 | 0.82686 | 1.2428 | 39.9 | 5.83
Neigh | 0.010644 | 0.013047 | 0.015567 | 2.0 | 0.09
Comm | 2.2447 | 2.716 | 3.2525 | 28.2 | 19.16
Output | 0.0040193 | 0.0057101 | 0.0084742 | 2.2 | 0.04
Modify | 7.9913 | 8.6193 | 9.394 | 20.9 | 60.82
Other | | 1.991 | | | 14.05
Nlocal: 250 ave 266 max 237 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 294 ave 335 max 253 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 960.25 ave 1454 max 492 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3841
Ave neighs/atom = 3.841
Neighbor list builds = 201
Dangerous builds = 0
unfix ins
run 200000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.87 | 11.89 | 11.9 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 1.0060272 3.1415927
201000 0.11023112 1000 1.0117513 3.1573006
202000 0.22297119 1000 1.0121624 3.1730086
203000 0.33090251 1000 1.0099707 3.1887165
204000 0.43921623 1000 1.0099624 3.2044245
205000 0.54813391 1000 1.009398 3.2201325
206000 0.6597641 1000 0.99686298 3.2358404
207000 0.76806828 1000 0.96520673 3.2515484
208000 0.88217705 1000 0.96521294 3.2672564
209000 0.99810181 1000 0.96501099 3.2829643
210000 1.1113988 1000 0.96426624 3.2986723
211000 1.2252752 1000 0.9564358 3.3143802
212000 1.3381064 1000 0.95482019 3.3300882
213000 1.4513852 1000 0.9446233 3.3457962
214000 1.5630713 1000 0.92461651 3.3615041
215000 1.6785702 1000 0.92106646 3.3772121
216000 1.7937182 1000 0.92058667 3.3929201
217000 1.9092992 1000 0.91797493 3.408628
218000 2.0251567 1000 0.91351081 3.424336
219000 2.1419482 1000 0.91991749 3.440044
220000 2.258391 1000 0.92943198 3.4557519
221000 2.3747328 1000 0.93176684 3.4714599
222000 2.4930355 1000 0.92625008 3.4871678
223000 2.6111794 1000 0.9216243 3.5028758
224000 2.729971 1000 0.92332955 3.5185838
225000 2.8489286 1000 0.91963985 3.5342917
226000 2.97003 1000 0.91913679 3.5499997
227000 3.0874646 1000 0.92381436 3.5657077
228000 3.2089543 1000 0.93085242 3.5814156
229000 3.3281962 1000 0.92872221 3.5971236
230000 3.4476271 1000 0.92536664 3.6128316
231000 3.5681706 1000 0.92953138 3.6285395
232000 3.6911427 1000 0.93937257 3.6442475
233000 3.8115833 1000 0.95916002 3.6599554
234000 3.9301977 1000 0.96652709 3.6756634
235000 4.0481963 1000 0.96753364 3.6913714
236000 4.1684171 1000 0.96096249 3.7070793
237000 4.2874672 1000 0.97028893 3.7227873
238000 4.4072896 1000 0.95323014 3.7384953
239000 4.5292898 1000 0.94143454 3.7542032
240000 4.6529563 1000 0.9334569 3.7699112
241000 4.7701737 1000 0.93340822 3.7856191
242000 4.8891772 1000 0.93517762 3.8013271
243000 5.0078759 1000 0.92632745 3.8170351
244000 5.1260291 1000 0.91858996 3.832743
245000 5.2472736 1000 0.90006015 3.848451
246000 5.363907 1000 0.8850116 3.864159
247000 5.4838317 1000 0.87807775 3.8798669
248000 5.6039445 1000 0.85981326 3.8955749
249000 5.7262584 1000 0.85764597 3.9112829
250000 5.8488174 1000 0.86748856 3.9269908
251000 5.9665578 1000 0.85889952 3.9426988
252000 6.084021 1000 0.84476495 3.9584067
253000 6.203987 1000 0.84094974 3.9741147
254000 6.3221073 1000 0.82638568 3.9898227
255000 6.441682 1000 0.81449512 4.0055306
256000 6.5625653 1000 0.80130582 4.0212386
257000 6.6860772 1000 0.79100139 4.0369466
258000 6.8117355 1000 0.78531082 4.0526545
259000 6.9379959 1000 0.7678277 4.0683625
260000 7.0606907 1000 0.74798797 4.0840704
261000 7.1846943 1000 0.73902576 4.0997784
262000 7.3084818 1000 0.73326104 4.1154864
263000 7.4304296 1000 0.7370234 4.1311943
264000 7.5536012 1000 0.73817854 4.1469023
265000 7.6792395 1000 0.74675482 4.1626103
266000 7.8061753 1000 0.7480056 4.1783182
267000 7.9331093 1000 0.748671 4.1940262
268000 8.0593048 1000 0.74430146 4.2097342
269000 8.1888555 1000 0.73246199 4.2254421
270000 8.3184687 1000 0.71666285 4.2411501
271000 8.4489277 1000 0.69699332 4.256858
272000 8.5822473 1000 0.69724726 4.272566
273000 8.7148666 1000 0.69752702 4.288274
274000 8.8426159 1000 0.69393439 4.3039819
275000 8.9746848 1000 0.67961922 4.3196899
276000 9.1020134 1000 0.67808365 4.3353979
277000 9.232486 1000 0.66241302 4.3511058
278000 9.3607588 1000 0.65559661 4.3668138
279000 9.4879578 1000 0.64949975 4.3825218
280000 9.6142148 1000 0.65351945 4.3982297
281000 9.7437802 1000 0.66566267 4.4139377
282000 9.87097 1000 0.68284419 4.4296456
283000 9.9975944 1000 0.68906456 4.4453536
284000 10.124724 1000 0.69474503 4.4610616
285000 10.25369 1000 0.71686298 4.4767695
286000 10.38212 1000 0.70966561 4.4924775
287000 10.513274 1000 0.70173402 4.5081855
288000 10.641359 1000 0.69841037 4.5238934
289000 10.765608 1000 0.68947449 4.5396014
290000 10.893738 1000 0.68391661 4.5553093
291000 11.018982 1000 0.69112115 4.5710173
292000 11.146639 1000 0.70208247 4.5867253
293000 11.269392 1000 0.70044553 4.6024332
294000 11.39243 1000 0.69973655 4.6181412
295000 11.517741 1000 0.70719661 4.6338492
296000 11.643013 1000 0.69961909 4.6495571
297000 11.771064 1000 0.7038606 4.6652651
298000 11.899855 1000 0.70651383 4.6809731
299000 12.024499 1000 0.72028817 4.696681
300000 12.151124 1000 0.72141372 4.712389
301000 12.278902 1000 0.73011344 4.7280969
302000 12.402615 1000 0.74750506 4.7438049
303000 12.524021 1000 0.74362139 4.7595129
304000 12.645914 1000 0.73643471 4.7752208
305000 12.766721 1000 0.73250587 4.7909288
306000 12.945373 1000 0.72450933 4.8066368
307000 13.084062 1000 0.71650682 4.8223447
308000 13.210593 1000 0.71012044 4.8380527
309000 13.339536 1000 0.7045498 4.8537606
310000 13.477512 1000 0.69904261 4.8694686
311000 13.617832 1000 0.69370407 4.8851766
312000 13.802532 1000 0.70012261 4.9008845
313000 13.9682 1000 0.69796658 4.9165925
314000 14.139079 1000 0.70673901 4.9323005
315000 14.290205 1000 0.70285296 4.9480084
316000 14.414474 1000 0.69917788 4.9637164
317000 14.541743 1000 0.69153454 4.9794244
318000 14.672817 1000 0.69630312 4.9951323
319000 14.800594 1000 0.70732059 5.0108403
320000 14.982014 1000 0.71069744 5.0265482
321000 15.126459 1000 0.70982909 5.0422562
322000 15.264165 1000 0.70514067 5.0579642
323000 15.391036 1000 0.70591206 5.0736721
324000 15.518096 1000 0.70992653 5.0893801
325000 15.644416 1000 0.70605327 5.1050881
326000 15.772686 1000 0.70492617 5.120796
327000 15.899812 1000 0.69711977 5.136504
328000 16.050906 1000 0.68791974 5.152212
329000 16.197987 1000 0.68350425 5.1679199
330000 16.346901 1000 0.67886559 5.1836279
331000 16.511885 1000 0.6838106 5.1993358
332000 16.666556 1000 0.68570448 5.2150438
333000 16.820557 1000 0.68347768 5.2307518
334000 16.972048 1000 0.67352858 5.2464597
335000 17.171176 1000 0.67154375 5.2621677
336000 17.380218 1000 0.67050288 5.2778757
337000 17.561848 1000 0.66093797 5.2935836
338000 17.746525 1000 0.65261747 5.3092916
339000 17.926411 1000 0.65084314 5.3249995
340000 18.105197 1000 0.65003008 5.3407075
341000 18.235972 1000 0.65397536 5.3564155
342000 18.389741 1000 0.67129271 5.3721234
343000 18.604032 1000 0.68934086 5.3878314
344000 18.788879 1000 0.71225704 5.4035394
345000 18.935273 1000 0.72645711 5.4192473
346000 19.136926 1000 0.73153889 5.4349553
347000 19.310095 1000 0.74047453 5.4506633
348000 19.476545 1000 0.74508084 5.4663712
349000 19.599138 1000 0.74030176 5.4820792
350000 19.753114 1000 0.72037009 5.4977871
351000 19.893497 1000 0.71009934 5.5134951
352000 20.020982 1000 0.69475509 5.5292031
353000 20.149857 1000 0.68883962 5.544911
354000 20.278476 1000 0.68764856 5.560619
355000 20.407747 1000 0.6853423 5.576327
356000 20.53591 1000 0.69528948 5.5920349
357000 20.668654 1000 0.70787069 5.6077429
358000 20.802835 1000 0.70110924 5.6234508
359000 20.950394 1000 0.69356484 5.6391588
360000 21.076061 1000 0.69727901 5.6548668
361000 21.224785 1000 0.69878093 5.6705747
362000 21.416947 1000 0.70063124 5.6862827
363000 21.632619 1000 0.68842038 5.7019907
364000 21.836231 1000 0.68478573 5.7176986
365000 21.963636 1000 0.68232032 5.7334066
366000 22.092926 1000 0.66971225 5.7491146
367000 22.219251 1000 0.67006227 5.7648225
368000 22.344723 1000 0.6694355 5.7805305
369000 22.470654 1000 0.66622377 5.7962384
370000 22.59941 1000 0.66501888 5.8119464
371000 22.732869 1000 0.66108622 5.8276544
372000 22.859824 1000 0.65989005 5.8433623
373000 22.989282 1000 0.65277032 5.8590703
374000 23.116089 1000 0.64599939 5.8747783
375000 23.243733 1000 0.64279675 5.8904862
376000 23.371971 1000 0.64321129 5.9061942
377000 23.505382 1000 0.65596736 5.9219022
378000 23.638755 1000 0.68055295 5.9376101
379000 23.770714 1000 0.71147476 5.9533181
380000 23.906376 1000 0.7478441 5.969026
381000 24.040685 1000 0.76216879 5.984734
382000 24.173446 1000 0.78574658 6.000442
383000 24.30114 1000 0.80947952 6.0161499
384000 24.426872 1000 0.81514681 6.0318579
385000 24.555905 1000 0.81469775 6.0475659
386000 24.684891 1000 0.80579609 6.0632738
387000 24.811946 1000 0.79952446 6.0789818
388000 24.940028 1000 0.78668384 6.0946897
389000 25.061479 1000 0.78375511 6.1103977
390000 25.18315 1000 0.78124583 6.1261057
391000 25.303012 1000 0.77072038 6.1418136
392000 25.423275 1000 0.75748297 6.1575216
393000 25.542996 1000 0.74703682 6.1732296
394000 25.661826 1000 0.74135384 6.1889375
395000 25.782254 1000 0.73344196 6.2046455
396000 25.903156 1000 0.72305463 6.2203535
397000 26.026207 1000 0.71221263 6.2360614
398000 26.145498 1000 0.70602241 6.2517694
399000 26.266146 1000 0.69822375 6.2674773
400000 26.387762 1000 0.69567985 6.2831853
Loop time of 26.3878 on 4 procs for 200000 steps with 1000 atoms
Performance: 30942.580 tau/day, 7579.263 timesteps/s, 7.579 Matom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6871 | 2.8172 | 3.925 | 64.8 | 10.68
Neigh | 0.017325 | 0.021917 | 0.026669 | 3.1 | 0.08
Comm | 4.7404 | 6.0917 | 7.4409 | 54.5 | 23.09
Output | 0.0043138 | 0.0065642 | 0.0087622 | 1.9 | 0.02
Modify | 13.258 | 14.716 | 16.132 | 35.6 | 55.77
Other | | 2.735 | | | 10.36
Nlocal: 250 ave 257 max 241 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 387.5 ave 477 max 299 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1233.5 ave 1523 max 917 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 4934
Ave neighs/atom = 4.934
Neighbor list builds = 168
Dangerous builds = 0
Total wall time: 0:00:40

475
examples/granregion/log.27Nov18.granregion.box.g++.1
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@ -1,475 +0,0 @@
LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 1 by 1 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
Particle insertion: 48 every 566 steps, 100 by step 1133
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.5855 | 0.5855 | 0.5855 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
100 21 0.54270729 0.54270729 0.26473526 0.0013567682
200 21 0.87606961 0.87606961 0.42735103 0.002190174
300 21 1.1428374 1.1428374 0.55748167 0.0028570936
400 21 1.3543103 1.3543103 0.66829516 0.0033857758
500 21 1.0677786 1.0677786 0.53582407 0.0045048164
600 56 0.6744286 0.6744286 0.3502938 0.0047464584
700 56 0.75569283 0.75569283 0.39779462 0.0051953882
800 56 0.61597505 0.61597505 0.32943642 0.0086022783
900 56 0.65260802 0.65260802 0.34474044 0.0059298996
1000 56 0.51624952 0.51624952 0.28326898 0.0067827337
1100 56 0.46050076 0.46050076 0.25656319 0.0061891094
1200 81 0.39112346 0.39112346 0.21690172 0.0086559316
1300 81 0.33302617 0.33302617 0.19109398 0.0033381104
1400 81 0.3933533 0.3933533 0.21221692 0.004135078
1500 81 0.35495297 0.35495297 0.19925984 0.0037374946
1600 81 0.34150606 0.34150606 0.19025811 0.0053492835
1700 100 0.2561647 0.2561647 0.14186278 0.0090767057
1800 100 0.21124278 0.21124278 0.12154878 0.0028545759
1900 100 0.21793955 0.21793955 0.12173867 0.0029049155
2000 100 0.25530858 0.25530858 0.13892272 0.0035528009
2100 100 0.24671808 0.24671808 0.13687783 0.0076812435
2200 100 0.22465216 0.22465216 0.12513603 0.0042528715
2300 100 0.19362854 0.19362854 0.10914305 0.0061173739
2400 100 0.061627608 0.061627608 0.045907717 0.0010422721
2500 100 0.052700901 0.052700901 0.038883014 0.0019341647
2600 100 0.037332018 0.037332018 0.028357146 0.0028364476
2700 100 0.033526602 0.033526602 0.024609055 0.00044524562
2800 100 0.0194148 0.0194148 0.014491377 0.00056526591
2900 100 0.012346108 0.012346108 0.009857017 0.00081855699
3000 100 0.0107344 0.0107344 0.008669364 0.00040371396
3100 100 0.0092678291 0.0092678291 0.0073003108 0.00033287397
3200 100 0.0085847001 0.0085847001 0.0064045591 0.00023253547
3300 100 0.0049475182 0.0049475182 0.0041173627 0.00019876269
3400 100 0.0030471097 0.0030471097 0.0026940466 0.00013462604
3500 100 0.0031188371 0.0031188371 0.002612223 0.00026148578
3600 100 0.0017616584 0.0017616584 0.0017464137 0.00019049724
3700 100 0.0015475923 0.0015475923 0.0015560356 0.00025062814
3800 100 0.0012547887 0.0012547887 0.0012622678 0.00014132236
3900 100 0.0010047282 0.0010047282 0.0010379262 9.7665594e-05
4000 100 0.00080895307 0.00080895307 0.00088263027 8.1278842e-05
4100 100 0.00079078739 0.00079078739 0.00085810727 8.1271694e-05
4200 100 0.00075192318 0.00075192318 0.00083085046 8.9352453e-05
4300 100 0.00063546457 0.00063546457 0.00073222177 8.9264255e-05
4400 100 0.00062398391 0.00062398391 0.00071312118 8.4200615e-05
4500 100 0.00056464934 0.00056464934 0.00066087801 9.2097641e-05
4600 100 0.00066951894 0.00066951894 0.00071633313 8.2457941e-05
4700 100 0.001128837 0.001128837 0.00095293877 0.00011716361
4800 100 0.00049580391 0.00049580391 0.00056710488 0.00010718794
4900 100 0.00054374371 0.00054374371 0.00058671699 5.6580257e-05
5000 100 0.00043016232 0.00043016232 0.00050264172 2.8640786e-05
Loop time of 0.0807264 on 1 procs for 5000 steps with 100 atoms
Performance: 26757050.955 tau/day, 61937.618 timesteps/s
97.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0089066 | 0.0089066 | 0.0089066 | 0.0 | 11.03
Neigh | 0.017107 | 0.017107 | 0.017107 | 0.0 | 21.19
Comm | 0.00091505 | 0.00091505 | 0.00091505 | 0.0 | 1.13
Output | 0.00051451 | 0.00051451 | 0.00051451 | 0.0 | 0.64
Modify | 0.047671 | 0.047671 | 0.047671 | 0.0 | 59.05
Other | | 0.005612 | | | 6.95
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 158
Ave neighs/atom = 1.58
Neighbor list builds = 310
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00043016232 0.00043016232 0.00050264172 2.8677624e-05
5100 100 0.56489668 0.56489668 0.31137762 0.011848041
5200 100 0.66068288 0.66068288 0.35915482 0.010199755
5300 100 0.74068022 0.74068022 0.39643217 0.010806409
5400 100 0.80913562 0.80913562 0.42748505 0.01190892
5500 100 0.89409135 0.89409135 0.46135116 0.013093474
5600 100 0.97585093 0.97585093 0.50021126 0.013588886
5700 100 1.0151954 1.0151954 0.5174624 0.01601347
5800 100 1.0452728 1.0452728 0.53122496 0.01879329
5900 100 1.0881689 1.0881689 0.55152229 0.017120714
6000 100 1.1133186 1.1133186 0.5638022 0.017284617
6100 100 1.1532099 1.1532099 0.58310076 0.017031384
6200 100 1.1798849 1.1798849 0.5959516 0.017971323
6300 100 1.19387 1.19387 0.60173877 0.020140984
6400 100 1.2126705 1.2126705 0.61086899 0.018426638
6500 100 1.2137646 1.2137646 0.61284198 0.019127381
6600 100 1.2339012 1.2339012 0.62199324 0.019378799
6700 100 1.2439326 1.2439326 0.62488425 0.021049447
6800 100 1.2489549 1.2489549 0.6278167 0.019552409
6900 100 1.2733303 1.2733303 0.63898149 0.020237284
7000 100 1.2835029 1.2835029 0.6440245 0.020798586
7100 100 1.2866111 1.2866111 0.64522896 0.020355019
7200 100 1.2886381 1.2886381 0.6467497 0.02062322
7300 100 1.2885085 1.2885085 0.64617988 0.020350755
7400 100 1.2912349 1.2912349 0.64691898 0.020197503
7500 100 1.2963062 1.2963062 0.64926335 0.020349791
7600 100 1.3016488 1.3016488 0.65150178 0.021001457
7700 100 1.3009311 1.3009311 0.65106234 0.021546471
7800 100 1.3016987 1.3016987 0.65143099 0.020994967
7900 100 1.3028811 1.3028811 0.65164558 0.022200425
8000 100 1.3087855 1.3087855 0.65439023 0.021310808
8100 100 1.3102001 1.3102001 0.65514941 0.021177764
8200 100 1.3133931 1.3133931 0.65681861 0.021591267
8300 100 1.3148898 1.3148898 0.65775353 0.021335384
8400 100 1.3160355 1.3160355 0.65845913 0.021238095
8500 100 1.3171797 1.3171797 0.65934185 0.021172983
8600 100 1.3176785 1.3176785 0.65964311 0.020747457
8700 100 1.3180425 1.3180425 0.66019624 0.021275913
8800 100 1.3287501 1.3287501 0.66444242 0.021832635
8900 100 1.3249847 1.3249847 0.6625848 0.021337451
9000 100 1.326216 1.326216 0.66297827 0.021470663
9100 100 1.3261662 1.3261662 0.66303852 0.021423573
9200 100 1.3312132 1.3312132 0.6653609 0.021385943
9300 100 1.3300976 1.3300976 0.66504574 0.021489888
9400 100 1.3377335 1.3377335 0.66820989 0.021565001
9500 100 1.3421956 1.3421956 0.67027168 0.022402346
9600 100 1.3464217 1.3464217 0.67228206 0.021991922
9700 100 1.3470623 1.3470623 0.67258349 0.022035729
9800 100 1.3446725 1.3446725 0.67135725 0.022295251
9900 100 1.343146 1.343146 0.67066672 0.022049041
10000 100 1.3435397 1.3435397 0.67093067 0.022451365
Loop time of 0.247549 on 1 procs for 5000 steps with 100 atoms
Performance: 8725560.044 tau/day, 20198.056 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031783 | 0.031783 | 0.031783 | 0.0 | 12.84
Neigh | 0.038383 | 0.038383 | 0.038383 | 0.0 | 15.51
Comm | 0.0012343 | 0.0012343 | 0.0012343 | 0.0 | 0.50
Output | 0.00056028 | 0.00056028 | 0.00056028 | 0.0 | 0.23
Modify | 0.1687 | 0.1687 | 0.1687 | 0.0 | 68.15
Other | | 0.00689 | | | 2.78
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 199 ave 199 max 199 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 199
Ave neighs/atom = 1.99
Neighbor list builds = 621
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.3435397 1.3435397 0.67093067 0.022411116
10100 100 0.31352763 0.31352763 0.18877908 0.01321582
10200 100 0.13367611 0.13367611 0.090010637 0.0074171016
10300 100 0.068195658 0.068195658 0.052632714 0.0019696287
10400 100 0.053814936 0.053814936 0.043037586 0.0017121584
10500 100 0.04032072 0.04032072 0.032944572 0.0011809154
10600 100 0.029178161 0.029178161 0.023951873 0.0007804529
10700 100 0.025978206 0.025978206 0.021045025 0.00099531465
10800 100 0.023205036 0.023205036 0.01898502 0.00040036401
10900 100 0.019994638 0.019994638 0.016451227 0.00027385559
11000 100 0.017838131 0.017838131 0.014730762 0.00040399762
11100 100 0.014863196 0.014863196 0.012314308 0.00019097464
11200 100 0.012131256 0.012131256 0.010102122 0.00018514926
11300 100 0.010881385 0.010881385 0.0090013541 0.00016579157
11400 100 0.0076519814 0.0076519814 0.0064604568 0.00035399997
11500 100 0.0067507315 0.0067507315 0.0057378868 0.00049116726
11600 100 0.0053146649 0.0053146649 0.0047005938 0.00019625233
11700 100 0.0044162463 0.0044162463 0.0039534657 0.00012548039
11800 100 0.0037025387 0.0037025387 0.0033604103 6.2969827e-05
11900 100 0.0032632211 0.0032632211 0.0030406641 8.1600622e-05
12000 100 0.0028944057 0.0028944057 0.0026875858 6.6435833e-05
12100 100 0.0027644728 0.0027644728 0.0025859762 5.5899271e-05
12200 100 0.002480367 0.002480367 0.0023685117 6.0201418e-05
12300 100 0.0024136475 0.0024136475 0.0023107986 4.4386874e-05
12400 100 0.0021911567 0.0021911567 0.0021413262 5.0213175e-05
12500 100 0.0019775905 0.0019775905 0.0019927698 0.00035250097
12600 100 0.0017410363 0.0017410363 0.001830428 5.7885177e-05
12700 100 0.0015749276 0.0015749276 0.0016816771 4.5530192e-05
12800 100 0.0015187705 0.0015187705 0.0016218625 4.0589413e-05
12900 100 0.0014778376 0.0014778376 0.001580232 4.0085455e-05
13000 100 0.0014693491 0.0014693491 0.0015681809 4.0407656e-05
13100 100 0.0014434495 0.0014434495 0.0015356278 5.7849212e-05
13200 100 0.0014121959 0.0014121959 0.0015058758 3.2720737e-05
13300 100 0.0012876041 0.0012876041 0.0013838998 3.7725702e-05
13400 100 0.0012304951 0.0012304951 0.0013373457 3.6784546e-05
13500 100 0.0011954303 0.0011954303 0.0012877627 3.6584963e-05
13600 100 0.0011028947 0.0011028947 0.0011955404 2.3767582e-05
13700 100 0.0010611762 0.0010611762 0.0011504675 3.485879e-05
13800 100 0.0010080835 0.0010080835 0.0010997919 3.7905404e-05
13900 100 0.00096495712 0.00096495712 0.0010530767 3.5273885e-05
14000 100 0.00094945029 0.00094945029 0.0010409175 3.3718395e-05
14100 100 0.00092386757 0.00092386757 0.0010217415 3.3313256e-05
14200 100 0.00088928389 0.00088928389 0.000983023 3.290941e-05
14300 100 0.00082696485 0.00082696485 0.00092690771 3.1651431e-05
14400 100 0.00081086188 0.00081086188 0.00091681096 3.1845632e-05
14500 100 0.00077732305 0.00077732305 0.00087592983 4.8087361e-05
14600 100 0.00073386005 0.00073386005 0.00082546873 3.0892065e-05
14700 100 0.00068701098 0.00068701098 0.00075953521 0.00010208859
14800 100 0.00065860451 0.00065860451 0.00073738846 2.9272912e-05
14900 100 0.00064706564 0.00064706564 0.00072748391 2.9817955e-05
15000 100 0.00064227996 0.00064227996 0.00070964586 3.2547768e-05
Loop time of 0.0840213 on 1 procs for 5000 steps with 100 atoms
Performance: 25707757.817 tau/day, 59508.699 timesteps/s
98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01004 | 0.01004 | 0.01004 | 0.0 | 11.95
Neigh | 0.0057366 | 0.0057366 | 0.0057366 | 0.0 | 6.83
Comm | 0.00086808 | 0.00086808 | 0.00086808 | 0.0 | 1.03
Output | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 0.59
Modify | 0.060893 | 0.060893 | 0.060893 | 0.0 | 72.47
Other | | 0.005989 | | | 7.13
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151 ave 151 max 151 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151
Ave neighs/atom = 1.51
Neighbor list builds = 92
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00064227996 0.00064227996 0.00070964586 3.2291286e-05
15100 100 0.81230775 0.81230775 0.53266834 0.010948517
15200 100 0.87957637 0.87957637 0.57559572 0.012401402
15300 100 1.0262431 1.0262431 0.66535656 0.015239294
15400 100 1.2863564 1.2863564 0.82026439 0.020115365
15500 100 1.4721549 1.4721549 0.92138954 0.022400442
15600 100 1.7140429 1.7140429 1.0103822 0.02558084
15700 100 1.8963287 1.8963287 1.0916756 0.032032318
15800 100 2.0741177 2.0741177 1.1706233 0.034251942
15900 100 2.1434733 2.1434733 1.2054242 0.030132271
16000 100 2.1409892 2.1409892 1.2019761 0.030914205
16100 100 2.2496058 2.2496058 1.2476438 0.030939743
16200 100 2.233356 2.233356 1.2499888 0.030097445
16300 100 2.2673491 2.2673491 1.272321 0.030968524
16400 100 2.3735648 2.3735648 1.3126117 0.034532377
16500 100 2.4510087 2.4510087 1.3588349 0.036685351
16600 100 2.497406 2.497406 1.3811443 0.032019982
16700 100 2.6800518 2.6800518 1.4661941 0.037455527
16800 100 2.8673997 2.8673997 1.5558303 0.03606532
16900 100 3.1229488 3.1229488 1.6918439 0.039753213
17000 100 3.117815 3.117815 1.6996841 0.046210837
17100 100 3.3336225 3.3336225 1.7834517 0.047865361
17200 100 3.1773164 3.1773164 1.7113961 0.047778334
17300 100 3.4336759 3.4336759 1.8343073 0.049673718
17400 100 3.3142326 3.3142326 1.7796613 0.055329946
17500 100 3.3205493 3.3205493 1.7853946 0.043558145
17600 100 3.2764553 3.2764553 1.7640702 0.051463316
17700 100 3.1909643 3.1909643 1.7407995 0.043248948
17800 100 3.1958324 3.1958324 1.735056 0.050123145
17900 100 3.2431806 3.2431806 1.7380638 0.050838878
18000 100 3.2967417 3.2967417 1.7705821 0.042176084
18100 100 3.4270672 3.4270672 1.8459819 0.043589925
18200 100 3.3638494 3.3638494 1.8159436 0.048949648
18300 100 3.3192279 3.3192279 1.8122198 0.043629595
18400 100 3.2627211 3.2627211 1.796316 0.045504529
18500 100 3.5669172 3.5669172 1.9257062 0.048460393
18600 100 3.5546411 3.5546411 1.9154318 0.046890968
18700 100 3.7288485 3.7288485 2.011106 0.046906531
18800 100 3.6800347 3.6800347 1.9936406 0.049985172
18900 100 3.7151898 3.7151898 2.007659 0.050394561
19000 100 3.9693368 3.9693368 2.1311549 0.053710204
19100 100 3.6907732 3.6907732 1.9939387 0.05480136
19200 100 3.8808777 3.8808777 2.0790125 0.055093552
19300 100 3.8422142 3.8422142 2.0756951 0.058090774
19400 100 3.7836875 3.7836875 2.0399805 0.06965907
19500 100 4.0480195 4.0480195 2.169214 0.053420651
19600 100 3.965917 3.965917 2.1245227 0.059077084
19700 100 3.8980869 3.8980869 2.0956306 0.050857062
19800 100 4.008079 4.008079 2.1501421 0.054938689
19900 100 3.7244506 3.7244506 2.0080877 0.055481507
20000 100 3.8146094 3.8146094 2.0541416 0.053187111
Loop time of 0.210396 on 1 procs for 5000 steps with 100 atoms
Performance: 10266363.999 tau/day, 23764.731 timesteps/s
98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013991 | 0.013991 | 0.013991 | 0.0 | 6.65
Neigh | 0.056947 | 0.056947 | 0.056947 | 0.0 | 27.07
Comm | 0.0013928 | 0.0013928 | 0.0013928 | 0.0 | 0.66
Output | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.26
Modify | 0.13027 | 0.13027 | 0.13027 | 0.0 | 61.92
Other | | 0.007249 | | | 3.45
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 144 ave 144 max 144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 144
Ave neighs/atom = 1.44
Neighbor list builds = 910
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.8146094 3.8146094 2.0541416 0.052956687
20100 100 1.3848453 1.3848453 0.82244153 0.017544632
20200 100 0.89469578 0.89469578 0.55929611 0.0111604
20300 100 0.83962013 0.83962013 0.52665461 0.010396174
20400 100 0.77264252 0.77264252 0.48961142 0.0095493901
20500 100 0.78613208 0.78613208 0.48683715 0.012166835
20600 100 0.88411633 0.88411633 0.52854942 0.011725323
20700 100 0.89833225 0.89833225 0.52549693 0.012193413
20800 100 0.90216089 0.90216089 0.51167019 0.014289685
20900 100 0.98665057 0.98665057 0.5468893 0.013794318
21000 100 0.7576342 0.7576342 0.42758791 0.011720156
21100 100 0.3821563 0.3821563 0.23426423 0.005324458
21200 100 0.17486973 0.17486973 0.12876582 0.0029726352
21300 100 0.17940562 0.17940562 0.12400155 0.0026179917
21400 100 0.15526876 0.15526876 0.10526802 0.002341177
21500 100 0.079493361 0.079493361 0.062289324 0.0017379534
21600 100 0.057299519 0.057299519 0.047939171 0.0020095941
21700 100 0.056900097 0.056900097 0.045799124 0.0017782068
21800 100 0.039847861 0.039847861 0.035138066 0.0018265057
21900 100 0.03919167 0.03919167 0.031815619 0.0012160098
22000 100 0.025499317 0.025499317 0.022126202 0.0010056809
22100 100 0.018956113 0.018956113 0.017843095 0.0016109368
22200 100 0.017337018 0.017337018 0.016063068 0.00042537508
22300 100 0.014785686 0.014785686 0.013007571 0.00049466367
22400 100 0.011754087 0.011754087 0.010399793 0.00042349151
22500 100 0.010362474 0.010362474 0.009077435 0.00025198478
22600 100 0.0089484896 0.0089484896 0.0079474121 0.00035239475
22700 100 0.0089936432 0.0089936432 0.0077908763 0.00018548371
22800 100 0.0068663718 0.0068663718 0.0064061667 0.00025641972
22900 100 0.0050272392 0.0050272392 0.0046676214 0.00040466013
23000 100 0.0049250142 0.0049250142 0.0044849467 0.00035704909
23100 100 0.0050508148 0.0050508148 0.0043117775 0.00030051828
23200 100 0.0037293467 0.0037293467 0.0033592517 0.00038108923
23300 100 0.0032823722 0.0032823722 0.0030511575 0.00040421775
23400 100 0.0026913866 0.0026913866 0.0025493429 9.2813733e-05
23500 100 0.0025590632 0.0025590632 0.0024466447 8.4695125e-05
23600 100 0.0025270441 0.0025270441 0.0024236554 8.4237376e-05
23700 100 0.0026406527 0.0026406527 0.0024501963 0.00015009901
23800 100 0.0024633391 0.0024633391 0.0023470594 3.8990761e-05
23900 100 0.0029505606 0.0029505606 0.0025122613 4.9810757e-05
24000 100 0.0019535519 0.0019535519 0.0019112421 3.5804751e-05
24100 100 0.0017505151 0.0017505151 0.001726233 2.380737e-05
24200 100 0.0015864857 0.0015864857 0.0015479949 1.963276e-05
24300 100 0.0014535898 0.0014535898 0.0014221262 3.6607862e-05
24400 100 0.0013744934 0.0013744934 0.0013523293 1.4522467e-05
24500 100 0.0013286378 0.0013286378 0.0013097089 3.2389792e-05
24600 100 0.0012093624 0.0012093624 0.0011617482 4.848694e-05
24700 100 0.0011817062 0.0011817062 0.0011409092 3.8898899e-05
24800 100 0.0011142524 0.0011142524 0.0010877723 1.4560662e-05
24900 100 0.0010941199 0.0010941199 0.0010614415 7.0209336e-05
25000 100 0.0010773559 0.0010773559 0.0010389783 1.3332279e-05
Loop time of 0.0912137 on 1 procs for 5000 steps with 100 atoms
Performance: 23680652.416 tau/day, 54816.325 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010053 | 0.010053 | 0.010053 | 0.0 | 11.02
Neigh | 0.017597 | 0.017597 | 0.017597 | 0.0 | 19.29
Comm | 0.00092912 | 0.00092912 | 0.00092912 | 0.0 | 1.02
Output | 0.00049806 | 0.00049806 | 0.00049806 | 0.0 | 0.55
Modify | 0.056085 | 0.056085 | 0.056085 | 0.0 | 61.49
Other | | 0.006052 | | | 6.63
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 143 ave 143 max 143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 143
Ave neighs/atom = 1.43
Neighbor list builds = 289
Dangerous builds = 0
Total wall time: 0:00:00

475
examples/granregion/log.27Nov18.granregion.box.g++.4
View File

@ -1,475 +0,0 @@
LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# pouring spheres into container box
units lj
atom_style sphere
boundary f f f
dimension 3
comm_modify vel yes
region box block -10 10 -10 10 -10 10 units box
create_box 2 box
Created orthogonal box = (-10 -10 -10) to (10 10 10)
1 by 2 by 2 MPI processor grid
pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1
pair_coeff * * gran/hooke
region container block -6 6 -6 6 -6 6 units box
fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 2 all nve/sphere
fix 3 all gravity 1.0 vector 0 0 -1
region slab block -2 2 -2 2 -2 2 units box
fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore
Particle insertion: 48 every 566 steps, 100 by step 1133
timestep 0.005
compute 1 all temp
compute_modify 1 dynamic/dof yes
compute 2 all temp/sphere
compute_modify 2 dynamic/dof yes
thermo 100
thermo_style custom step atoms temp c_1 c_2 press
thermo_modify lost ignore
compute_modify thermo_temp dynamic/dof yes
#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03
#dump_modify 2 pad 5
run 5000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 31 31 31
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke, perpetual
attributes: half, newton on, size
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.4834 | 0.4834 | 0.4834 Mbytes
Step Atoms Temp c_1 c_2 Press
0 0 0 0 0 0
100 21 0.54270729 0.54270729 0.26473526 0.0013567682
200 21 0.87606961 0.87606961 0.42735103 0.002190174
300 21 1.1428374 1.1428374 0.55748167 0.0028570936
400 21 1.3543103 1.3543103 0.66829516 0.0033857758
500 21 1.0677786 1.0677786 0.53582407 0.0045048164
600 56 0.6744286 0.6744286 0.3502938 0.0047464584
700 56 0.75569283 0.75569283 0.39779462 0.0051953882
800 56 0.61597505 0.61597505 0.32943642 0.0086022783
900 56 0.65260802 0.65260802 0.34474044 0.0059298996
1000 56 0.51624952 0.51624952 0.28326898 0.0067827337
1100 56 0.46050076 0.46050076 0.25656319 0.0061891094
1200 81 0.39112346 0.39112346 0.21690172 0.0086559316
1300 81 0.33302617 0.33302617 0.19109398 0.0033381104
1400 81 0.3933533 0.3933533 0.21221692 0.004135078
1500 81 0.35495297 0.35495297 0.19925984 0.0037374946
1600 81 0.34150606 0.34150606 0.19025811 0.0053492835
1700 100 0.2561647 0.2561647 0.14186278 0.0090767057
1800 100 0.21124278 0.21124278 0.12154878 0.002854576
1900 100 0.21793955 0.21793955 0.12173867 0.0029049175
2000 100 0.25530858 0.25530858 0.13892272 0.0035528022
2100 100 0.24671805 0.24671805 0.13687782 0.0076812357
2200 100 0.22465212 0.22465212 0.12513612 0.0042526344
2300 100 0.19362805 0.19362805 0.10914275 0.0061175383
2400 100 0.061626039 0.061626039 0.045905953 0.0010393593
2500 100 0.052690575 0.052690575 0.038879745 0.0018543933
2600 100 0.037256691 0.037256691 0.02833916 0.0027683815
2700 100 0.033416362 0.033416362 0.024551243 0.00046725913
2800 100 0.019617758 0.019617758 0.014619416 0.00064550316
2900 100 0.012313874 0.012313874 0.0098188153 0.00033470181
3000 100 0.010948455 0.010948455 0.0087981878 0.00034401243
3100 100 0.009359431 0.009359431 0.0073642412 0.00045497356
3200 100 0.008129885 0.008129885 0.0061460516 0.00029944201
3300 100 0.0050682533 0.0050682533 0.0042692811 0.00026543293
3400 100 0.0031539312 0.0031539312 0.0027256511 0.00012475748
3500 100 0.0023621311 0.0023621311 0.0021691817 0.0001186392
3600 100 0.0018305354 0.0018305354 0.0018004128 0.00015926282
3700 100 0.0016522492 0.0016522492 0.0017231072 0.0002193159
3800 100 0.0011715102 0.0011715102 0.0012739973 0.0001747857
3900 100 0.0010607606 0.0010607606 0.0010974725 0.00012476088
4000 100 0.00087570802 0.00087570802 0.00095828935 6.5544103e-05
4100 100 0.00078598203 0.00078598203 0.00088068743 9.4560761e-05
4200 100 0.00088317454 0.00088317454 0.00092784605 8.1108122e-05
4300 100 0.0015013254 0.0015013254 0.0012069505 8.8289686e-05
4400 100 0.00070054041 0.00070054041 0.00079451193 5.195712e-05
4500 100 0.00096259073 0.00096259073 0.00091232511 3.4895669e-05
4600 100 0.00056641848 0.00056641848 0.00069083146 3.9657253e-05
4700 100 0.0005455099 0.0005455099 0.00064816699 2.8131762e-05
4800 100 0.00048254366 0.00048254366 0.00057192255 4.7914432e-05
4900 100 0.00037108125 0.00037108125 0.00048035333 6.4711817e-05
5000 100 0.00031290399 0.00031290399 0.00042398478 4.6025975e-05
Loop time of 0.075416 on 4 procs for 5000 steps with 100 atoms
Performance: 28641126.336 tau/day, 66298.904 timesteps/s
93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0022948 | 0.0041364 | 0.0061705 | 2.8 | 5.48
Neigh | 0.0043123 | 0.0057145 | 0.0070784 | 1.8 | 7.58
Comm | 0.014259 | 0.018658 | 0.024313 | 3.3 | 24.74
Output | 0.0011525 | 0.001404 | 0.0015383 | 0.4 | 1.86
Modify | 0.0030508 | 0.014543 | 0.026602 | 9.5 | 19.28
Other | | 0.03096 | | | 41.05
Nlocal: 25 ave 51 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5.5 ave 12 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 39.75 ave 84 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 159
Ave neighs/atom = 1.59
Neighbor list builds = 310
Dangerous builds = 0
region container delete
variable theta equal (step-5000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
Step Atoms Temp c_1 c_2 Press
5000 100 0.00031290399 0.00031290399 0.00042398478 4.4282259e-05
5100 100 0.62661084 0.62661084 0.33840611 0.012020153
5200 100 0.67371678 0.67371678 0.36218522 0.0093514044
5300 100 0.75892331 0.75892331 0.4000747 0.010693252
5400 100 0.86207426 0.86207426 0.44630388 0.013540097
5500 100 0.96205334 0.96205334 0.49432848 0.017375079
5600 100 1.0261194 1.0261194 0.52203912 0.016045333
5700 100 1.0584366 1.0584366 0.53794336 0.018621676
5800 100 1.0881674 1.0881674 0.55300469 0.01930602
5900 100 1.1214233 1.1214233 0.56613492 0.021141141
6000 100 1.1666836 1.1666836 0.58759377 0.017655361
6100 100 1.1785775 1.1785775 0.59365148 0.01829443
6200 100 1.2092305 1.2092305 0.60798809 0.018752443
6300 100 1.2331787 1.2331787 0.62003386 0.020291021
6400 100 1.2561616 1.2561616 0.63143643 0.019899235
6500 100 1.284432 1.284432 0.6460504 0.02083284
6600 100 1.2678801 1.2678801 0.63882384 0.019456553
6700 100 1.2662641 1.2662641 0.63676836 0.020235578
6800 100 1.2785484 1.2785484 0.64129093 0.020335162
6900 100 1.2916608 1.2916608 0.64764298 0.020154225
7000 100 1.2907774 1.2907774 0.64724849 0.020550885
7100 100 1.3074473 1.3074473 0.65460147 0.020847362
7200 100 1.3124592 1.3124592 0.65641332 0.020897348
7300 100 1.3206191 1.3206191 0.66011491 0.021444077
7400 100 1.3273988 1.3273988 0.66350669 0.02129418
7500 100 1.3343911 1.3343911 0.66707269 0.021337376
7600 100 1.3368998 1.3368998 0.66869327 0.021415901
7700 100 1.330658 1.330658 0.66535295 0.021500761
7800 100 1.330801 1.330801 0.66555123 0.022806058
7900 100 1.3392828 1.3392828 0.66926796 0.02194009
8000 100 1.3432728 1.3432728 0.67142337 0.022393719
8100 100 1.3411612 1.3411612 0.66989302 0.022366895
8200 100 1.3427451 1.3427451 0.67054285 0.021966329
8300 100 1.3418147 1.3418147 0.67023132 0.022513459
8400 100 1.346493 1.346493 0.67247837 0.022705366
8500 100 1.3513958 1.3513958 0.6749092 0.022834077
8600 100 1.3520297 1.3520297 0.67506261 0.023227676
8700 100 1.3517157 1.3517157 0.67485073 0.023043414
8800 100 1.3530071 1.3530071 0.67547212 0.022933766
8900 100 1.3550454 1.3550454 0.67657277 0.022744182
9000 100 1.3554069 1.3554069 0.67673505 0.022802134
9100 100 1.3556675 1.3556675 0.67698335 0.022868449
9200 100 1.3534709 1.3534709 0.67600677 0.022537792
9300 100 1.3525103 1.3525103 0.67569499 0.022687849
9400 100 1.3612673 1.3612673 0.67967213 0.022703588
9500 100 1.3649439 1.3649439 0.68147385 0.023498539
9600 100 1.3629376 1.3629376 0.68063814 0.023515579
9700 100 1.3648924 1.3648924 0.68137104 0.023641856
9800 100 1.3662063 1.3662063 0.68196538 0.023576884
9900 100 1.3689695 1.3689695 0.68326751 0.023572622
10000 100 1.3701139 1.3701139 0.68383343 0.023720885
Loop time of 0.174251 on 4 procs for 5000 steps with 100 atoms
Performance: 12395939.906 tau/day, 28694.305 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0024631 | 0.010709 | 0.020461 | 8.0 | 6.15
Neigh | 0.0078361 | 0.012368 | 0.016955 | 4.0 | 7.10
Comm | 0.0059071 | 0.013641 | 0.023547 | 6.6 | 7.83
Output | 0.0011749 | 0.0021775 | 0.0030091 | 1.4 | 1.25
Modify | 0.015055 | 0.055709 | 0.097013 | 17.2 | 31.97
Other | | 0.07965 | | | 45.71
Nlocal: 25 ave 51 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4.5 ave 10 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 49.25 ave 101 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 197
Ave neighs/atom = 1.97
Neighbor list builds = 627
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
Step Atoms Temp c_1 c_2 Press
10000 100 1.3701139 1.3701139 0.68383343 0.023895921
10100 100 0.25960098 0.25960098 0.15183967 0.0049554084
10200 100 0.15017576 0.15017576 0.10081112 0.0045433238
10300 100 0.10129671 0.10129671 0.078049099 0.0014012658
10400 100 0.06742425 0.06742425 0.055603816 0.0010184792
10500 100 0.053446366 0.053446366 0.045338293 0.00089291689
10600 100 0.041898231 0.041898231 0.036081995 0.00060703885
10700 100 0.03580041 0.03580041 0.031118724 0.00067731964
10800 100 0.030933755 0.030933755 0.026372348 0.00039362325
10900 100 0.027278004 0.027278004 0.022868898 0.0003680788
11000 100 0.021566952 0.021566952 0.017994879 0.0013056062
11100 100 0.019143625 0.019143625 0.015833865 0.00050998112
11200 100 0.015659868 0.015659868 0.013119379 0.00012755696
11300 100 0.013554605 0.013554605 0.01147808 0.00027393437
11400 100 0.01204033 0.01204033 0.010273026 0.00033430792
11500 100 0.010958991 0.010958991 0.0093924566 0.00049023273
11600 100 0.01012553 0.01012553 0.0084556996 0.00021457333
11700 100 0.0083584131 0.0083584131 0.0071118766 7.7149089e-05
11800 100 0.007044883 0.007044883 0.0058675523 0.00036165381
11900 100 0.0059875106 0.0059875106 0.0050610372 7.4095443e-05
12000 100 0.0045180275 0.0045180275 0.0039006565 0.00014607704
12100 100 0.0036631356 0.0036631356 0.0031154279 7.031064e-05
12200 100 0.0034443424 0.0034443424 0.0029190637 0.00020974475
12300 100 0.0030853504 0.0030853504 0.0026315266 3.4873541e-05
12400 100 0.0025451749 0.0025451749 0.0022290833 0.00041551536
12500 100 0.0021624857 0.0021624857 0.0019127734 2.6760761e-05
12600 100 0.0020637862 0.0020637862 0.0018186641 4.9446655e-05
12700 100 0.0019889538 0.0019889538 0.0017604689 3.326943e-05
12800 100 0.0018706349 0.0018706349 0.0016669237 2.3327318e-05
12900 100 0.0017472824 0.0017472824 0.001579469 8.816765e-05
13000 100 0.0016034824 0.0016034824 0.0014549852 3.5407524e-05
13100 100 0.00151798 0.00151798 0.0013826659 1.8754149e-05
13200 100 0.0013049781 0.0013049781 0.0012137907 0.00015263775
13300 100 0.0012270536 0.0012270536 0.0011590841 4.77636e-06
13400 100 0.0011395128 0.0011395128 0.0010860297 2.5606328e-05
13500 100 0.0010858414 0.0010858414 0.0010486713 5.8563931e-05
13600 100 0.0010474389 0.0010474389 0.001015904 1.4319658e-05
13700 100 0.00099241549 0.00099241549 0.00097825038 1.2281142e-05
13800 100 0.00084449252 0.00084449252 0.00084141963 1.0451215e-05
13900 100 0.00084004792 0.00084004792 0.00083755495 3.7174162e-05
14000 100 0.00082183505 0.00082183505 0.00082027058 1.0170209e-05
14100 100 0.00082377076 0.00082377076 0.00080489795 1.181976e-05
14200 100 0.00076903208 0.00076903208 0.00076216608 4.4590341e-05
14300 100 0.00075173269 0.00075173269 0.00074828209 2.2134371e-05
14400 100 0.00074379148 0.00074379148 0.00074072001 1.5746014e-05
14500 100 0.00072454029 0.00072454029 0.0007174429 8.9830398e-06
14600 100 0.00072372648 0.00072372648 0.00071678769 9.1111512e-06
14700 100 0.00071541587 0.00071541587 0.00070893868 7.8446375e-05
14800 100 0.0006820307 0.0006820307 0.00066675502 8.4401299e-06
14900 100 0.00067050627 0.00067050627 0.00065751846 0.0001228548
15000 100 0.00064977132 0.00064977132 0.00062305247 7.8887775e-06
Loop time of 0.0746691 on 4 procs for 5000 steps with 100 atoms
Performance: 28927619.905 tau/day, 66962.083 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0021737 | 0.0042608 | 0.0063519 | 3.2 | 5.71
Neigh | 0.0012126 | 0.0019009 | 0.0026193 | 1.6 | 2.55
Comm | 0.0023425 | 0.0092477 | 0.016876 | 7.2 | 12.38
Output | 0.0010619 | 0.0017995 | 0.0030522 | 1.8 | 2.41
Modify | 0.00097013 | 0.017151 | 0.03415 | 12.3 | 22.97
Other | | 0.04031 | | | 53.98
Nlocal: 25 ave 55 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 3.75 ave 9 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 42.5 ave 88 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 170
Ave neighs/atom = 1.7
Neighbor list builds = 97
Dangerous builds = 0
region container delete
variable theta equal (step-15000)*(4.0*PI/5000)
region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes
Step Atoms Temp c_1 c_2 Press
15000 100 0.00064977132 0.00064977132 0.00062305247 7.9405607e-06
15100 100 1.0123899 1.0123899 0.66185504 0.014587215
15200 100 1.0332828 1.0332828 0.67443308 0.014002815
15300 100 1.0804076 1.0804076 0.72450056 0.016985272
15400 100 1.2868163 1.2868163 0.8708132 0.022190597
15500 100 1.5180471 1.5180471 0.99613124 0.026761866
15600 100 1.5422016 1.5422016 1.0021746 0.024490139
15700 100 1.7142241 1.7142241 1.0611146 0.0301368
15800 100 1.8747057 1.8747057 1.1207858 0.027612699
15900 100 1.9294819 1.9294819 1.1289025 0.027270228
16000 100 1.953275 1.953275 1.1264475 0.031568811
16100 100 2.0434228 2.0434228 1.1665365 0.026358952
16200 100 2.2129393 2.2129393 1.2448327 0.029613382
16300 100 2.2558224 2.2558224 1.2373264 0.028306021
16400 100 2.367398 2.367398 1.293448 0.029659303
16500 100 2.4221549 2.4221549 1.3198966 0.032541712
16600 100 2.510283 2.510283 1.3618001 0.034740544
16700 100 2.6776293 2.6776293 1.4508262 0.034556341
16800 100 2.8095841 2.8095841 1.5190571 0.035183782
16900 100 2.8485646 2.8485646 1.5344387 0.037153336
17000 100 3.0298285 3.0298285 1.6321623 0.040745906
17100 100 3.0218054 3.0218054 1.6187189 0.042082135
17200 100 3.1981705 3.1981705 1.7090597 0.041770208
17300 100 3.3178559 3.3178559 1.7723201 0.044604756
17400 100 3.3940903 3.3940903 1.8229846 0.049231759
17500 100 3.3274817 3.3274817 1.7870996 0.051649102
17600 100 3.3204358 3.3204358 1.791527 0.043875639
17700 100 3.2185649 3.2185649 1.7480866 0.049941218
17800 100 3.2507826 3.2507826 1.7727758 0.048622479
17900 100 3.2432767 3.2432767 1.7796296 0.044343902
18000 100 3.0841272 3.0841272 1.6978832 0.045344433
18100 100 3.0953909 3.0953909 1.699898 0.040070963
18200 100 3.1405704 3.1405704 1.7316463 0.042528194
18300 100 3.1904871 3.1904871 1.7555188 0.041141165
18400 100 3.3256779 3.3256779 1.8243767 0.043908318
18500 100 3.5161823 3.5161823 1.9150861 0.045165166
18600 100 3.5668273 3.5668273 1.9217975 0.048127705
18700 100 3.6648305 3.6648305 1.9685241 0.051205352
18800 100 3.9000502 3.9000502 2.0886668 0.05262835
18900 100 4.0217758 4.0217758 2.1465498 0.054502839
19000 100 3.8431174 3.8431174 2.0581611 0.054852333
19100 100 4.1721454 4.1721454 2.2221193 0.053831555
19200 100 3.9061181 3.9061181 2.096323 0.058077678
19300 100 4.0191085 4.0191085 2.1408069 0.05475437
19400 100 3.8840871 3.8840871 2.0887677 0.061905092
19500 100 3.8388062 3.8388062 2.0567095 0.051076414
19600 100 3.6331742 3.6331742 1.9574769 0.04748008
19700 100 3.6996954 3.6996954 1.9887285 0.053305043
19800 100 3.8649872 3.8649872 2.0827424 0.060484008
19900 100 3.8305733 3.8305733 2.0700281 0.052926584
20000 100 3.7948463 3.7948463 2.0657301 0.048516953
Loop time of 0.156359 on 4 procs for 5000 steps with 100 atoms
Performance: 13814330.011 tau/day, 31977.616 timesteps/s
94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0040646 | 0.0058124 | 0.0074518 | 1.6 | 3.72
Neigh | 0.014813 | 0.018389 | 0.020829 | 1.6 | 11.76
Comm | 0.031892 | 0.034103 | 0.036658 | 1.0 | 21.81
Output | 0.0013497 | 0.0019822 | 0.003484 | 2.0 | 1.27
Modify | 0.031006 | 0.046878 | 0.056364 | 4.5 | 29.98
Other | | 0.0492 | | | 31.46
Nlocal: 25 ave 37 max 10 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 3.75 ave 6 max 2 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 36.25 ave 57 max 9 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 145
Ave neighs/atom = 1.45
Neighbor list builds = 921
Dangerous builds = 0
region container delete
region container block -6 6 -6 6 -6 6 units box
run 5000
Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.734 | 5.734 Mbytes
Step Atoms Temp c_1 c_2 Press
20000 100 3.7948463 3.7948463 2.0657301 0.048381317
20100 100 1.1359931 1.1359931 0.70170151 0.015300556
20200 100 0.87354617 0.87354617 0.55969299 0.012181983
20300 100 0.84424484 0.84424484 0.52849351 0.017724782
20400 100 0.82422562 0.82422562 0.50175766 0.0098154181
20500 100 0.83731289 0.83731289 0.49814627 0.010465327
20600 100 0.93125924 0.93125924 0.53803834 0.011624902
20700 100 1.0810919 1.0810919 0.60974741 0.01425935
20800 100 1.0646343 1.0646343 0.60037545 0.013418132
20900 100 1.0608055 1.0608055 0.58353908 0.015119612
21000 100 0.68173094 0.68173094 0.3941588 0.0099947535
21100 100 0.35407592 0.35407592 0.21306735 0.0043859494
21200 100 0.19247432 0.19247432 0.12989264 0.0031808422
21300 100 0.13493768 0.13493768 0.093987634 0.0025990872
21400 100 0.085735857 0.085735857 0.062091707 0.001434207
21500 100 0.074307566 0.074307566 0.05224051 0.0022163094
21600 100 0.069932382 0.069932382 0.045388838 0.0020296572
21700 100 0.041749712 0.041749712 0.031422931 0.001211155
21800 100 0.03378055 0.03378055 0.026248846 0.0020596463
21900 100 0.030608528 0.030608528 0.022868294 0.0016282878
22000 100 0.025632448 0.025632448 0.019606402 0.0011659657
22100 100 0.013785062 0.013785062 0.011561769 0.00069006322
22200 100 0.013139066 0.013139066 0.010559726 0.00038424576
22300 100 0.01455318 0.01455318 0.011094558 0.00054735929
22400 100 0.0096885414 0.0096885414 0.008012617 0.00055875777
22500 100 0.0081193116 0.0081193116 0.006802973 0.00052914932
22600 100 0.0057159621 0.0057159621 0.0048680253 0.00054864875
22700 100 0.0052344376 0.0052344376 0.0045511708 0.00026333033
22800 100 0.0054554177 0.0054554177 0.0045005479 0.0002085972
22900 100 0.0039455776 0.0039455776 0.0035287888 0.00022514017
23000 100 0.0042620461 0.0042620461 0.0035747729 0.00020030999
23100 100 0.0035303095 0.0035303095 0.0031995108 0.00016007298
23200 100 0.0029747457 0.0029747457 0.0027095904 0.00029775807
23300 100 0.0032404433 0.0032404433 0.002769389 0.00019627995
23400 100 0.0024965262 0.0024965262 0.0022343473 0.00018870133
23500 100 0.00251617 0.00251617 0.0022533604 0.0002661237
23600 100 0.0025923653 0.0025923653 0.0022887204 0.00018475201
23700 100 0.0023016545 0.0023016545 0.0019829032 0.00014888334
23800 100 0.0028358441 0.0028358441 0.0021790504 0.00064613131
23900 100 0.0016682403 0.0016682403 0.0014930521 8.8407075e-05
24000 100 0.0016341577 0.0016341577 0.0014597606 0.00011262081
24100 100 0.0015433636 0.0015433636 0.0013981581 8.364568e-05
24200 100 0.0015033978 0.0015033978 0.0013582013 8.4539006e-05
24300 100 0.0014513098 0.0014513098 0.0012943981 0.00010546194
24400 100 0.0013293352 0.0013293352 0.001206366 8.4967509e-05
24500 100 0.0013732518 0.0013732518 0.001202532 0.00014787559
24600 100 0.00091890041 0.00091890041 0.00084499923 0.00010080638
24700 100 0.00083467915 0.00083467915 0.00077071316 5.3934025e-05
24800 100 0.00080701934 0.00080701934 0.0007477161 5.3982095e-05
24900 100 0.00080620771 0.00080620771 0.0007471026 5.3581294e-05
25000 100 0.00080568604 0.00080568604 0.00074625735 5.3574637e-05
Loop time of 0.0792506 on 4 procs for 5000 steps with 100 atoms
Performance: 27255302.560 tau/day, 63090.978 timesteps/s
95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0023611 | 0.0047854 | 0.0077851 | 3.4 | 6.04
Neigh | 0.0042653 | 0.005571 | 0.0067258 | 1.5 | 7.03
Comm | 0.0077977 | 0.013373 | 0.019515 | 4.4 | 16.87
Output | 0.0010924 | 0.0017727 | 0.0030222 | 1.8 | 2.24
Modify | 0.0023608 | 0.015964 | 0.030545 | 10.5 | 20.14
Other | | 0.03778 | | | 47.68
Nlocal: 25 ave 50 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5 ave 10 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 35.75 ave 78 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 143
Ave neighs/atom = 1.43
Neighbor list builds = 287
Dangerous builds = 0
Total wall time: 0:00:00

601
examples/granregion/log.27Nov18.granregion.funnel.g++.1
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@ -1,601 +0,0 @@
LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} bin
neighbor 0.5 bin
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 3000 every 59965 steps, 2000 by step 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.63593698 2000 -0
2000 1.0282419 2000 -0
3000 1.4184453 2000 -0
4000 1.8055785 2000 -0
5000 2.1941335 2000 -0
6000 2.5804653 2000 -0
7000 2.9660621 2000 -0
8000 3.3506265 2000 -0
9000 3.7344413 2000 -0
10000 4.1212304 2000 -0
11000 4.5044594 2000 -0
12000 4.8875456 2000 -0
13000 5.2698007 2000 -0
14000 5.6527214 2000 -0
15000 6.0349295 2000 -0
16000 6.4172938 2000 -0
17000 6.8001184 2000 -0
18000 7.1826644 2000 -0
19000 7.5654378 2000 -0
20000 7.9511659 2000 -0
Loop time of 7.95118 on 1 procs for 20000 steps with 2000 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.6189 | 0.6189 | 0.6189 | 0.0 | 7.78
Neigh | 0.09361 | 0.09361 | 0.09361 | 0.0 | 1.18
Comm | 0.016098 | 0.016098 | 0.016098 | 0.0 | 0.20
Output | 0.00048828 | 0.00048828 | 0.00048828 | 0.0 | 0.01
Modify | 6.9973 | 6.9973 | 6.9973 | 0.0 | 88.00
Other | | 0.2248 | | | 2.83
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1537 ave 1537 max 1537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1537
Ave neighs/atom = 0.7685
Neighbor list builds = 69
Dangerous builds = 0
unfix ins
run 150000
Per MPI rank memory allocation (min/avg/max) = 12.77 | 12.77 | 12.77 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6443.7665
21000 0.3826313 2000 6572.3531
22000 0.76688981 2000 6723.8376
23000 1.1534231 2000 6853.1812
24000 1.5391715 2000 6976.0209
25000 1.9263508 2000 7096.9955
26000 2.3168406 2000 7215.5795
27000 2.7065961 2000 7349.2382
28000 3.096664 2000 7471.8719
29000 3.4905531 2000 7574.8228
30000 3.8877606 2000 7659.3836
31000 4.2839894 2000 7703.6856
32000 4.6859732 2000 7644.279
33000 5.0932801 2000 7526.6944
34000 5.5045564 2000 7370.0821
35000 5.9206297 2000 7193.0457
36000 6.343729 2000 6990.9899
37000 6.7719142 2000 6849.2841
38000 7.2016783 2000 6701.7433
39000 7.6354482 2000 6538.9557
40000 8.078445 2000 6381.9346
41000 8.5191586 2000 6217.5253
42000 8.9630713 2000 6093.5344
43000 9.4097741 2000 5943.0479
44000 9.8652256 2000 5841.0782
45000 10.331057 2000 5652.8319
46000 10.803253 2000 5476.1466
47000 11.278766 2000 5267.7855
48000 11.759121 2000 5131.4036
49000 12.248896 2000 4972.7696
50000 12.747719 2000 4867.0868
51000 13.246704 2000 4681.897
52000 13.757842 2000 4506.8185
53000 14.276078 2000 4346.8045
54000 14.795933 2000 4193.8194
55000 15.311241 2000 4058.2049
56000 15.828737 2000 3879.0325
57000 16.359453 2000 3696.3154
58000 16.905406 2000 3504.0399
59000 17.460454 2000 3284.6522
60000 18.027276 2000 3061.0727
61000 18.586931 2000 2874.2926
62000 19.158563 2000 2653.0722
63000 19.738442 2000 2437.4941
64000 20.331411 2000 2124.1876
65000 20.936204 2000 1864.5661
66000 21.547443 2000 1610.2335
67000 22.166888 2000 1390.0428
68000 22.789106 2000 1163.7679
69000 23.416016 2000 933.0928
70000 24.038879 2000 745.66667
71000 24.663115 2000 605.58458
72000 25.294193 2000 444.31183
73000 25.932019 2000 357.19162
74000 26.568184 2000 291.16762
75000 27.203393 2000 230.58362
76000 27.836079 2000 197.59502
77000 28.467344 2000 166.55702
78000 29.099997 2000 139.89052
79000 29.741694 2000 117.1145
80000 30.388097 2000 100.12353
81000 31.036193 2000 85.233155
82000 31.688463 2000 71.145302
83000 32.343411 2000 61.545348
84000 32.999346 2000 54.099358
85000 33.652976 2000 46.922028
86000 34.306931 2000 41.606645
87000 34.967787 2000 37.462793
88000 35.633721 2000 33.698298
89000 36.310035 2000 29.340455
90000 36.995441 2000 26.072122
91000 37.67904 2000 23.20848
92000 38.367699 2000 21.015862
93000 39.058641 2000 20.134175
94000 39.749342 2000 19.196075
95000 40.442651 2000 18.285127
96000 41.140177 2000 17.476411
97000 41.840761 2000 16.55882
98000 42.543845 2000 15.444541
99000 43.256415 2000 14.41642
100000 43.97382 2000 13.818738
101000 44.684596 2000 12.878373
102000 45.401082 2000 12.11804
103000 46.120936 2000 11.016885
104000 46.83935 2000 10.531044
105000 47.559419 2000 10.46735
106000 48.286016 2000 10.246007
107000 49.012266 2000 9.6423041
108000 49.74013 2000 9.3948808
109000 50.471961 2000 9.5178141
110000 51.206152 2000 9.4143884
111000 51.939123 2000 9.5058226
112000 52.673443 2000 9.6911516
113000 53.410485 2000 9.7756849
114000 54.152537 2000 9.3876232
115000 54.891784 2000 8.6725333
116000 55.631474 2000 8.6691065
117000 56.371762 2000 8.0156055
118000 57.110131 2000 7.9150786
119000 57.8533 2000 7.5310892
120000 58.599064 2000 7.2940498
121000 59.340753 2000 6.8347898
122000 60.084676 2000 6.696484
123000 60.826952 2000 6.7799146
124000 61.569413 2000 6.7901567
125000 62.316334 2000 6.7532108
126000 63.061374 2000 6.762162
127000 63.806385 2000 6.6317366
128000 64.555969 2000 6.8246399
129000 65.308131 2000 6.9130358
130000 66.060967 2000 7.1750566
131000 66.809725 2000 6.9507379
132000 67.559796 2000 6.7987445
133000 68.314249 2000 6.8535775
134000 69.065513 2000 7.0255144
135000 69.817604 2000 6.7381064
136000 70.572079 2000 6.5567748
137000 71.324444 2000 6.2655395
138000 72.079147 2000 6.1923013
139000 72.831323 2000 6.0958081
140000 73.59117 2000 5.9185709
141000 74.343753 2000 5.9151241
142000 75.096509 2000 5.4743035
143000 75.852151 2000 5.438642
144000 76.605005 2000 4.6646664
145000 77.357571 2000 4.6899837
146000 78.113125 2000 4.5357917
147000 78.867751 2000 4.5993842
148000 79.625344 2000 4.7076884
149000 80.37992 2000 4.8306642
150000 81.143175 2000 4.8282147
151000 81.899326 2000 4.546308
152000 82.658645 2000 4.6700755
153000 83.41837 2000 4.7557633
154000 84.17509 2000 4.9004538
155000 84.934161 2000 5.0552949
156000 85.695466 2000 4.0672495
157000 86.453115 2000 3.5819543
158000 87.212663 2000 3.3533477
159000 87.967768 2000 3.3281001
160000 88.729631 2000 3.0831743
161000 89.498983 2000 3.0519269
162000 90.259424 2000 3.0951675
163000 91.019656 2000 2.9868352
164000 91.776359 2000 2.9195788
165000 92.536374 2000 2.5637813
166000 93.296332 2000 2.5553272
167000 94.05653 2000 2.0752912
168000 94.814559 2000 1.9689845
169000 95.576005 2000 1.9117916
170000 96.337863 2000 1.8568914
Loop time of 96.3379 on 1 procs for 150000 steps with 2000 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 37.121 | 37.121 | 37.121 | 0.0 | 38.53
Neigh | 0.8454 | 0.8454 | 0.8454 | 0.0 | 0.88
Comm | 0.11506 | 0.11506 | 0.11506 | 0.0 | 0.12
Output | 0.004431 | 0.004431 | 0.004431 | 0.0 | 0.00
Modify | 56.517 | 56.517 | 56.517 | 0.0 | 58.67
Other | | 1.735 | | | 1.80
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15524 ave 15524 max 15524 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15524
Ave neighs/atom = 7.762
Neighbor list builds = 388
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes
Step CPU Atoms KinEng
170000 0 2000 1.8568914
171000 0.75704765 2000 2.4011583
172000 1.5101345 2000 3.176628
173000 2.2556529 2000 4.5364486
174000 2.9946566 2000 6.5494125
175000 3.7253478 2000 9.1934319
176000 4.4570525 2000 12.25765
177000 5.1876664 2000 15.799657
178000 5.9178619 2000 19.982558
179000 6.6439464 2000 24.927165
180000 7.3749168 2000 30.428362
181000 8.1011977 2000 36.74232
182000 8.8207343 2000 43.820448
183000 9.5397925 2000 50.903222
184000 10.253098 2000 59.425781
185000 10.965505 2000 69.143119
186000 11.673319 2000 79.210705
187000 12.373966 2000 90.411346
188000 13.075475 2000 102.35389
189000 13.770632 2000 114.93888
190000 14.469445 2000 128.63341
191000 15.158381 2000 143.44526
192000 15.846267 2000 159.04574
193000 16.527754 2000 174.3114
194000 17.204808 2000 190.42123
195000 17.881059 2000 207.70459
196000 18.556555 2000 224.90931
197000 19.229818 2000 242.64914
198000 19.905086 2000 261.48312
199000 20.578518 2000 281.28308
200000 21.25632 2000 302.95108
201000 21.921347 2000 325.95534
202000 22.583873 2000 350.6874
203000 23.244724 2000 376.31773
204000 23.904842 2000 404.21947
205000 24.562788 2000 432.96116
206000 25.217762 2000 462.4113
207000 25.875814 2000 491.91207
208000 26.531285 2000 522.15395
209000 27.184766 2000 553.1024
210000 27.842961 2000 585.7133
211000 28.489339 2000 619.96357
212000 29.139612 2000 653.96189
213000 29.783866 2000 689.8027
214000 30.426881 2000 727.28401
215000 31.06706 2000 766.40354
216000 31.706399 2000 805.65433
217000 32.343033 2000 845.40981
218000 32.989384 2000 884.24637
219000 33.633664 2000 923.5998
220000 34.285172 2000 965.01779
221000 34.931959 2000 1009.1763
222000 35.571624 2000 1054.7789
223000 36.207868 2000 1101.9922
224000 36.836062 2000 1151.1205
225000 37.464514 2000 1201.3979
226000 38.09746 2000 1252.4054
227000 38.732507 1999 1296.6784
228000 39.371367 1997 1342.3466
229000 40.012553 1992 1368.8559
230000 40.652111 1977 1360.2259
231000 41.275478 1965 1340.3793
232000 41.892734 1953 1318.8318
233000 42.50588 1938 1295.5667
234000 43.121427 1924 1270.0641
235000 43.740727 1914 1258.296
236000 44.359241 1902 1224.3945
237000 44.979463 1899 1248.3905
238000 45.597358 1885 1206.9229
239000 46.210114 1875 1195.5429
240000 46.818148 1861 1142.6591
241000 47.411079 1851 1131.5523
242000 48.002522 1841 1116.8741
243000 48.594254 1830 1099.9978
244000 49.191798 1822 1078.6068
245000 49.791332 1814 1072.1498
246000 50.389728 1803 1020.7842
247000 50.984212 1794 1000.1936
248000 51.571047 1781 942.02462
249000 52.149428 1772 916.83697
250000 52.726202 1758 825.10751
251000 53.29913 1748 789.06351
252000 53.871912 1739 753.92258
253000 54.441009 1729 697.83686
254000 55.010203 1718 648.98541
255000 55.573602 1710 620.38129
256000 56.134709 1705 622.43466
257000 56.701827 1700 595.79102
258000 57.264463 1698 608.49223
259000 57.827817 1695 614.0119
260000 58.398994 1690 601.50438
261000 58.964611 1687 608.5892
262000 59.526765 1683 597.07884
263000 60.082729 1682 618.65041
264000 60.640105 1678 615.47784
265000 61.195717 1675 605.27658
266000 61.751087 1671 583.69853
267000 62.305546 1669 600.11043
268000 62.86105 1666 598.79807
269000 63.417551 1663 588.40338
270000 63.974486 1660 579.59387
Loop time of 63.9745 on 1 procs for 100000 steps with 1660 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 26.514 | 26.514 | 26.514 | 0.0 | 41.44
Neigh | 0.60324 | 0.60324 | 0.60324 | 0.0 | 0.94
Comm | 0.075881 | 0.075881 | 0.075881 | 0.0 | 0.12
Output | 0.0029137 | 0.0029137 | 0.0029137 | 0.0 | 0.00
Modify | 35.686 | 35.686 | 35.686 | 0.0 | 55.78
Other | | 1.092 | | | 1.71
Nlocal: 1660 ave 1660 max 1660 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11681 ave 11681 max 11681 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11681
Ave neighs/atom = 7.03675
Neighbor list builds = 249
Dangerous builds = 0
Total wall time: 0:02:48

601
examples/granregion/log.27Nov18.granregion.funnel.g++.4
View File

@ -1,601 +0,0 @@
LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
# pour particles into cone-shaped funnel, settle them, let them run out bottom
variable name string funnel_pour
thermo_modify flush yes
units si
variable PI equal 3.141592653589
variable seed equal 14314
###############################################
# Geometry-related parameters
###############################################
variable xlo equal 10
variable xhi equal 40
variable ylo equal 10
variable yhi equal 40
variable zlo equal -20
variable zhi equal 50
variable xc equal 25
variable yc equal 25
variable zconehi equal 50
variable zconelo equal 10
variable zcyllo equal 0
variable radconelo equal 2
variable radconehi equal 20
################################################
# Particle sizes
################################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable skin equal ${rhi}
variable skin equal 0.5
###############################################
# Granular contact parameters
###############################################
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable density equal 1.0
variable EYoung equal 10^5
variable Poisson equal 2.0/7.0
variable GShear equal ${EYoung}/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+${Poisson}))
variable GShear equal 100000/(2*(1+0.285714285714286))
variable gravity equal 1.0
variable reff equal 0.5*(${rhi}+${rlo})
variable reff equal 0.5*(0.5+${rlo})
variable reff equal 0.5*(0.5+0.25)
variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*${PI}*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3
variable meff equal 1*4.0/3.0*3.141592653589*0.375^3
variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo}
variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25
variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi}
variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5
## Typical way to set kn, kt, etc.:
variable kn equal 4.0*${GShear}/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson}))
variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286))
variable kt equal 4.0*${GShear}/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-${Poisson})
variable kt equal 4.0*38888.8888888889/(2-0.285714285714286)
variable a equal (-2.0*log(${coeffRes})/${PI})^2
variable a equal (-2.0*log(0.1)/${PI})^2
variable a equal (-2.0*log(0.1)/3.141592653589)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 903.503751814138*0.5
variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0)
variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0)
variable dt equal ${tcol}*0.05
variable dt equal 0.00210943016014969*0.05
timestep ${dt}
timestep 0.000105471508007485
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton off
atom_style sphere
boundary p p f
region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi}
region boxreg block 10 40 10 40 ${zlo} ${zhi}
region boxreg block 10 40 10 40 -20 ${zhi}
region boxreg block 10 40 10 40 -20 50
create_box 1 boxreg
Created orthogonal box = (10 10 -20) to (40 40 50)
1 by 1 by 4 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1
pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1
pair_coeff * *
neighbor ${skin} bin
neighbor 0.5 bin
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 30, bins = 1 1 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
# insertion region for fix/pour
region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box
region insreg cylinder z 25 ${yc} 10 30 50 side in units box
region insreg cylinder z 25 25 10 30 50 side in units box
# define cone and cylinder regions - see lammps doc on region command
# note new open options
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 2
region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open
region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2
region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2
region hopreg union 2 conereg cylreg
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density}
fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 3000 every 59965 steps, 2000 by step 1
#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
thermo_modify flush yes lost warn
# Initial run to fill up the cone
run 20000
Per MPI rank memory allocation (min/avg/max) = 6.05 | 6.05 | 6.05 Mbytes
Step CPU Atoms KinEng
0 0 0 -0
1000 0.63366675 2000 -0
2000 1.0221362 2000 -0
3000 1.3905275 2000 -0
4000 1.7514329 2000 -0
5000 2.1040537 2000 -0
6000 2.4468088 2000 -0
7000 2.7853072 2000 -0
8000 3.1109948 2000 -0
9000 3.4281557 2000 -0
10000 3.7435207 2000 -0
11000 3.8612552 2000 -0
12000 3.9786677 2000 -0
13000 4.0988154 2000 -0
14000 4.2249811 2000 -0
15000 4.3562138 2000 -0
16000 4.4940333 2000 -0
17000 4.6394637 2000 -0
18000 4.7909062 2000 -0
19000 4.9482198 2000 -0
20000 5.1116607 2000 -0
Loop time of 5.11176 on 4 procs for 20000 steps with 2000 atoms
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.050997 | 0.14884 | 0.36048 | 32.0 | 2.91
Neigh | 0.01374 | 0.025199 | 0.043743 | 7.0 | 0.49
Comm | 0.063387 | 0.1781 | 0.29748 | 22.6 | 3.48
Output | 0.0016627 | 0.0060938 | 0.015082 | 6.8 | 0.12
Modify | 1.1198 | 1.987 | 3.7195 | 72.6 | 38.87
Other | | 2.767 | | | 54.12
Nlocal: 500 ave 505 max 493 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 159.25 ave 254 max 71 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 397.5 ave 616 max 214 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 1590
Ave neighs/atom = 0.795
Neighbor list builds = 69
Dangerous builds = 0
unfix ins
run 150000
Per MPI rank memory allocation (min/avg/max) = 12.37 | 12.51 | 12.7 Mbytes
Step CPU Atoms KinEng
20000 0 2000 6443.7665
21000 0.11261106 2000 6572.3531
22000 0.23091817 2000 6723.8376
23000 0.35577631 2000 6853.1812
24000 0.48790455 2000 6976.0209
25000 0.63509274 2000 7096.9955
26000 0.78251743 2000 7215.5795
27000 0.93707466 2000 7349.2382
28000 1.1032445 2000 7471.8719
29000 1.2721858 2000 7574.8228
30000 1.449265 2000 7659.3836
31000 1.5742557 2000 7703.6856
32000 1.7076068 2000 7644.279
33000 1.8527873 2000 7526.6944
34000 2.009855 2000 7370.0821
35000 2.1766446 2000 7193.0459
36000 2.3557482 2000 6990.9912
37000 2.5468907 2000 6849.286
38000 2.7480681 2000 6701.7548
39000 2.9574037 2000 6538.6915
40000 3.1807711 2000 6382.3209
41000 3.3486595 2000 6216.424
42000 3.5162592 2000 6091.29
43000 3.687057 2000 5945.3256
44000 3.8662596 2000 5840.875
45000 4.0557241 2000 5649.763
46000 4.2541051 2000 5476.2837
47000 4.4571214 2000 5277.0701
48000 4.6628008 2000 5123.9796
49000 4.8686502 2000 4968.3344
50000 5.0788848 2000 4869.5754
51000 5.2552598 2000 4704.8517
52000 5.4428713 2000 4522.8978
53000 5.6520596 2000 4393.8047
54000 5.8613031 2000 4235.438
55000 6.0776098 2000 4082.3073
56000 6.2998042 2000 3901.0483
57000 6.5321434 2000 3718.0882
58000 6.7745438 2000 3504.621
59000 7.0237701 2000 3285.7484
60000 7.2791855 2000 3047.3386
61000 7.489058 2000 2875.4032
62000 7.7044094 2000 2647.83
63000 7.9194827 2000 2396.5343
64000 8.1429474 2000 2107.2113
65000 8.3745618 2000 1858.1977
66000 8.610673 2000 1615.8096
67000 8.8505244 2000 1416.5065
68000 9.0955915 2000 1206.8534
69000 9.3609676 2000 953.93974
70000 9.6382594 2000 766.9148
71000 9.8719468 2000 611.45063
72000 10.095534 2000 464.94805
73000 10.317962 2000 364.31415
74000 10.547287 2000 298.77524
75000 10.764052 2000 245.73022
76000 10.978769 2000 207.8035
77000 11.199921 2000 179.1305
78000 11.410296 2000 151.21032
79000 11.624499 2000 124.49675
80000 11.849562 2000 106.71504
81000 12.077449 2000 93.299034
82000 12.306904 2000 81.220408
83000 12.539016 2000 67.383955
84000 12.773108 2000 57.287165
85000 13.009487 2000 49.255887
86000 13.252544 2000 44.082536
87000 13.502564 2000 40.193574
88000 13.747198 2000 36.903867
89000 13.993028 2000 33.55332
90000 14.240036 2000 30.730912
91000 14.472719 2000 28.650574
92000 14.708542 2000 26.377609
93000 14.948106 2000 24.433165
94000 15.186653 2000 22.933076
95000 15.428022 2000 22.31788
96000 15.676323 2000 20.829124
97000 15.916326 2000 19.401354
98000 16.160197 2000 18.943699
99000 16.404796 2000 17.690599
100000 16.659731 2000 17.215943
101000 16.904498 2000 15.948087
102000 17.150993 2000 15.140324
103000 17.39584 2000 14.885674
104000 17.643707 2000 14.414752
105000 17.889343 2000 14.270676
106000 18.136159 2000 13.943799
107000 18.383653 2000 13.840145
108000 18.630952 2000 12.826341
109000 18.878218 2000 12.209012
110000 19.125558 2000 11.916194
111000 19.3726 2000 11.970849
112000 19.621494 2000 11.56909
113000 19.869978 2000 11.390562
114000 20.123402 2000 11.276545
115000 20.370963 2000 11.171298
116000 20.619975 2000 11.686225
117000 20.869585 2000 11.379805
118000 21.118875 2000 10.539511
119000 21.36837 2000 10.064595
120000 21.629511 2000 10.003722
121000 21.877867 2000 9.6974586
122000 22.127922 2000 9.7156209
123000 22.378215 2000 9.615256
124000 22.630463 2000 8.8979008
125000 22.882154 2000 8.2220003
126000 23.135763 2000 8.3153866
127000 23.392389 2000 8.0945497
128000 23.645521 2000 7.8942467
129000 23.89965 2000 7.4794776
130000 24.153195 2000 7.3635341
131000 24.406239 2000 7.5757743
132000 24.66016 2000 7.7047492
133000 24.914093 2000 8.0142133
134000 25.173429 2000 8.1716714
135000 25.433318 2000 7.7803343
136000 25.692997 2000 6.3545482
137000 25.947787 2000 6.313769
138000 26.200427 2000 6.4948596
139000 26.452514 2000 6.6183259
140000 26.714963 2000 6.7922281
141000 26.968235 2000 7.0752448
142000 27.220962 2000 7.2328717
143000 27.474819 2000 7.626453
144000 27.728029 2000 7.4576787
145000 27.981958 2000 7.124435
146000 28.236591 2000 7.2581589
147000 28.489842 2000 7.0622049
148000 28.744432 2000 7.1672801
149000 28.998739 2000 7.3248363
150000 29.253511 2000 7.0092266
151000 29.50567 2000 6.8124438
152000 29.759836 2000 6.9808705
153000 30.015359 2000 7.1516731
154000 30.275488 2000 6.6245443
155000 30.533407 2000 5.5867165
156000 30.788683 2000 5.318949
157000 31.043126 2000 5.1195805
158000 31.297011 2000 5.2045485
159000 31.551327 2000 5.24992
160000 31.807728 2000 5.3270577
161000 32.061371 2000 4.995281
162000 32.315467 2000 5.0755874
163000 32.57628 2000 5.0788135
164000 32.83119 2000 4.5917317
165000 33.085634 2000 4.6255452
166000 33.344148 2000 4.2563299
167000 33.599342 2000 3.3808566
168000 33.853488 2000 3.218931
169000 34.121464 2000 3.0839289
170000 34.378727 2000 3.0358838
Loop time of 34.3788 on 4 procs for 150000 steps with 2000 atoms
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.5861 | 10.058 | 12.152 | 68.4 | 29.26
Neigh | 0.17612 | 0.25274 | 0.30005 | 9.2 | 0.74
Comm | 1.5024 | 2.6626 | 3.4174 | 44.9 | 7.74
Output | 0.006542 | 0.019532 | 0.046425 | 11.5 | 0.06
Modify | 11.945 | 14.674 | 16.29 | 42.7 | 42.68
Other | | 6.711 | | | 19.52
Nlocal: 500 ave 508 max 489 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 446.75 ave 708 max 191 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 4498 ave 5441 max 3786 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 17992
Ave neighs/atom = 8.996
Neighbor list builds = 403
Dangerous builds = 0
# remove "plug" - need to redefine cylinder region & union
region cylreg delete
region hopreg delete
region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open
region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2
region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2
region hopreg union 2 cylreg conereg
unfix hopper3
fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg
fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg
run 100000
Per MPI rank memory allocation (min/avg/max) = 13.68 | 15.35 | 16.59 Mbytes
Step CPU Atoms KinEng
170000 0 2000 3.0358838
171000 0.25455499 2000 3.7725185
172000 0.50768304 2000 4.727285
173000 0.76122355 2000 5.9840449
174000 1.0141416 2000 8.0335022
175000 1.2750733 2000 10.177259
176000 1.5277736 2000 13.655163
177000 1.7810826 2000 17.987975
178000 2.0348532 2000 23.266471
179000 2.2915859 2000 29.266364
180000 2.547174 2000 35.84089
181000 2.8009758 2000 43.130989
182000 3.0531759 2000 51.177142
183000 3.3130636 2000 60.031831
184000 3.5651338 2000 69.52374
185000 3.8185399 2000 79.941907
186000 4.070199 2000 91.195382
187000 4.3204038 2000 102.1696
188000 4.5699775 2000 112.73657
189000 4.8184452 2000 123.57252
190000 5.0653601 2000 135.59942
191000 5.3119307 2000 147.37757
192000 5.5574484 2000 159.12931
193000 5.8029084 2000 170.90271
194000 6.0463562 2000 185.71189
195000 6.2883332 2000 201.83733
196000 6.5281694 2000 218.30785
197000 6.7682493 2000 236.05694
198000 7.0084231 2000 255.23099
199000 7.2519951 2000 273.94566
200000 7.5010133 2000 293.91107
201000 7.7396591 2000 316.52142
202000 7.9784184 2000 340.91391
203000 8.224021 2000 364.81801
204000 8.4597676 2000 390.06478
205000 8.6934731 2000 415.90918
206000 8.9342225 2000 441.0995
207000 9.1714027 2000 467.40314
208000 9.4081488 2000 494.93631
209000 9.6457636 2000 524.70539
210000 9.8831718 2000 556.52058
211000 10.118018 2000 589.36821
212000 10.3541 2000 622.6887
213000 10.587226 2000 657.05888
214000 10.820744 2000 691.14292
215000 11.055785 2000 726.94959
216000 11.298702 2000 762.92802
217000 11.534793 2000 801.23648
218000 11.769849 2000 841.1559
219000 12.000917 2000 882.4342
220000 12.232812 2000 924.8466
221000 12.461166 2000 968.86229
222000 12.698451 2000 1013.1381
223000 12.930287 2000 1058.2988
224000 13.172862 2000 1105.2911
225000 13.405001 2000 1152.8617
226000 13.633187 1999 1197.6777
227000 13.857126 1998 1243.1211
228000 14.079622 1992 1262.1402
229000 14.303362 1987 1281.9162
230000 14.530392 1973 1264.0674
231000 14.756486 1964 1277.8347
232000 14.984495 1953 1266.7926
233000 15.213102 1940 1244.0038
234000 15.441666 1925 1206.4472
235000 15.667547 1914 1193.33
236000 15.895047 1901 1160.4096
237000 16.120833 1890 1141.6816
238000 16.346628 1883 1149.1584
239000 16.573303 1877 1141.7514
240000 16.801035 1871 1146.8662
241000 17.024775 1866 1152.561
242000 17.248651 1858 1148.2529
243000 17.47241 1847 1114.7239
244000 17.70222 1832 1070.9996
245000 17.926477 1824 1066.7549
246000 18.157588 1813 1027.1865
247000 18.378868 1804 1011.5024
248000 18.599988 1797 993.10451
249000 18.819007 1787 951.89778
250000 19.044634 1777 926.30475
251000 19.254408 1764 875.07091
252000 19.465788 1755 824.89358
253000 19.676327 1742 742.51957
254000 19.887648 1731 708.30958
255000 20.094912 1722 690.09761
256000 20.299963 1713 638.00218
257000 20.506153 1705 596.86839
258000 20.713994 1701 583.71937
259000 20.919755 1691 549.0049
260000 21.123122 1688 549.4278
261000 21.332215 1684 535.35719
262000 21.533673 1682 546.74031
263000 21.737042 1678 532.69324
264000 21.941306 1676 537.89254
265000 22.15135 1676 559.50898
266000 22.358371 1670 540.21452
267000 22.563236 1668 557.19857
268000 22.764648 1665 569.52869
269000 22.96391 1658 543.77057
270000 23.172415 1656 550.23716
Loop time of 23.1725 on 4 procs for 100000 steps with 1656 atoms
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3849 | 7.3002 | 10.192 | 91.3 | 31.50
Neigh | 0.14271 | 0.16781 | 0.19054 | 4.5 | 0.72
Comm | 1.086 | 1.9721 | 2.6157 | 42.7 | 8.51
Output | 0.0018437 | 0.013918 | 0.041359 | 13.5 | 0.06
Modify | 8.6598 | 9.3198 | 9.8874 | 16.6 | 40.22
Other | | 4.399 | | | 18.98
Nlocal: 414 ave 454 max 385 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 395.25 ave 645 max 157 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 3498.5 ave 4524 max 2034 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 13994
Ave neighs/atom = 8.45048
Neighbor list builds = 240
Dangerous builds = 0
Total wall time: 0:01:02

602
examples/granregion/log.27Nov18.granregion.mixer.g++.1
View File

@ -1,602 +0,0 @@
LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 1 by 1 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} bin
neighbor 0.6 bin
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
Particle insertion: 444 every 84653 steps, 1000 by step 169307
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
thermo_modify flush yes lost warn
run 200000
Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.15327144 444 -0 0.015707963
2000 0.30070925 444 -0 0.031415927
3000 0.44653535 444 -0 0.04712389
4000 0.59226131 444 -0 0.062831853
5000 0.73794818 444 -0 0.078539816
6000 0.88327622 444 -0 0.09424778
7000 1.0286083 444 -0 0.10995574
8000 1.1740625 444 -0 0.12566371
9000 1.3224797 444 -0 0.14137167
10000 1.4717772 444 -0 0.15707963
11000 1.6204555 444 -0 0.1727876
12000 1.7690799 444 -0 0.18849556
13000 1.918304 444 -0 0.20420352
14000 2.0670426 444 -0 0.21991149
15000 2.2157068 444 -0 0.23561945
16000 2.3642888 444 -0 0.25132741
17000 2.5129776 444 -0 0.26703538
18000 2.6614521 444 -0 0.28274334
19000 2.8100598 444 -0 0.2984513
20000 2.9591351 444 -0 0.31415927
21000 3.1073661 444 -0 0.32986723
22000 3.2557554 444 -0 0.34557519
23000 3.4041324 444 -0 0.36128316
24000 3.5526814 444 -0 0.37699112
25000 3.700824 444 -0 0.39269908
26000 3.8496137 444 -0 0.40840704
27000 3.9986103 444 -0 0.42411501
28000 4.1475384 444 -0 0.43982297
29000 4.2963772 444 -0 0.45553093
30000 4.4454341 444 -0 0.4712389
31000 4.5942066 444 -0 0.48694686
32000 4.7434044 444 -0 0.50265482
33000 4.893549 444 -0 0.51836279
34000 5.0427935 444 -0 0.53407075
35000 5.1920972 444 -0 0.54977871
36000 5.3411844 444 -0 0.56548668
37000 5.4904606 444 -0 0.58119464
38000 5.6397707 444 -0 0.5969026
39000 5.7900345 444 -0 0.61261057
40000 5.9405882 444 -0 0.62831853
41000 6.089345 444 -0 0.64402649
42000 6.2388933 444 -0 0.65973446
43000 6.3888056 444 -0 0.67544242
44000 6.5379841 444 -0 0.69115038
45000 6.6875141 444 -0 0.70685835
46000 6.8370855 444 -0 0.72256631
47000 6.9866009 444 -0 0.73827427
48000 7.1364653 444 -0 0.75398224
49000 7.2859883 444 -0 0.7696902
50000 7.4368248 444 -0 0.78539816
51000 7.5870779 444 -0 0.80110613
52000 7.7370813 444 -0 0.81681409
53000 7.8879561 444 -0 0.83252205
54000 8.0383027 444 -0 0.84823002
55000 8.1916294 444 -0 0.86393798
56000 8.3458471 444 -0 0.87964594
57000 8.5010631 444 -0 0.89535391
58000 8.6560545 444 -0 0.91106187
59000 8.8110209 444 -0 0.92676983
60000 8.9674675 444 -0 0.9424778
61000 9.1231239 444 -0 0.95818576
62000 9.2785382 444 -0 0.97389372
63000 9.4343674 444 -0 0.98960169
64000 9.5911541 444 -0 1.0053096
65000 9.7477772 444 -0 1.0210176
66000 9.9050307 444 -0 1.0367256
67000 10.063978 444 -0 1.0524335
68000 10.221835 444 -0 1.0681415
69000 10.37944 444 -0 1.0838495
70000 10.537409 444 -0 1.0995574
71000 10.695649 444 -0 1.1152654
72000 10.85453 444 -0 1.1309734
73000 11.013438 444 -0 1.1466813
74000 11.172689 444 -0 1.1623893
75000 11.332172 444 -0 1.1780972
76000 11.492824 444 -0 1.1938052
77000 11.653915 444 -0 1.2095132
78000 11.815798 444 -0 1.2252211
79000 11.97868 444 -0 1.2409291
80000 12.141392 444 -0 1.2566371
81000 12.30536 444 -0 1.272345
82000 12.468797 444 -0 1.288053
83000 12.633028 444 -0 1.303761
84000 12.797936 444 -0 1.3194689
85000 13.019726 888 -0 1.3351769
86000 13.333436 888 -0 1.3508848
87000 13.648179 888 -0 1.3665928
88000 13.962435 888 -0 1.3823008
89000 14.276158 888 -0 1.3980087
90000 14.590669 888 -0 1.4137167
91000 14.904268 888 -0 1.4294247
92000 15.216788 888 -0 1.4451326
93000 15.529868 888 -0 1.4608406
94000 15.843157 888 -0 1.4765485
95000 16.156564 888 -0 1.4922565
96000 16.469569 888 -0 1.5079645
97000 16.784048 888 -0 1.5236724
98000 17.100451 888 -0 1.5393804
99000 17.416338 888 -0 1.5550884
100000 17.733482 888 -0 1.5707963
101000 18.052522 888 -0 1.5865043
102000 18.371428 888 -0 1.6022123
103000 18.690222 888 -0 1.6179202
104000 19.009665 888 -0 1.6336282
105000 19.328189 888 -0 1.6493361
106000 19.647804 888 -0 1.6650441
107000 19.96805 888 -0 1.6807521
108000 20.286857 888 -0 1.69646
109000 20.607965 888 -0 1.712168
110000 20.931749 888 -0 1.727876
111000 21.251903 888 -0 1.7435839
112000 21.572158 888 -0 1.7592919
113000 21.892612 888 -0 1.7749998
114000 22.214408 888 -0 1.7907078
115000 22.535498 888 -0 1.8064158
116000 22.856752 888 -0 1.8221237
117000 23.178885 888 -0 1.8378317
118000 23.501127 888 -0 1.8535397
119000 23.8241 888 -0 1.8692476
120000 24.147258 888 -0 1.8849556
121000 24.472969 888 -0 1.9006636
122000 24.799108 888 -0 1.9163715
123000 25.125275 888 -0 1.9320795
124000 25.453866 888 -0 1.9477874
125000 25.784766 888 -0 1.9634954
126000 26.117013 888 -0 1.9792034
127000 26.448734 888 -0 1.9949113
128000 26.780032 888 -0 2.0106193
129000 27.113678 888 -0 2.0263273
130000 27.450001 888 -0 2.0420352
131000 27.782047 888 -0 2.0577432
132000 28.114287 888 -0 2.0734512
133000 28.446648 888 -0 2.0891591
134000 28.780438 888 -0 2.1048671
135000 29.116443 888 -0 2.120575
136000 29.451848 888 -0 2.136283
137000 29.787778 888 -0 2.151991
138000 30.12804 888 -0 2.1676989
139000 30.46814 888 -0 2.1834069
140000 30.808946 888 -0 2.1991149
141000 31.147584 888 -0 2.2148228
142000 31.486475 888 -0 2.2305308
143000 31.826754 888 -0 2.2462387
144000 32.165796 888 -0 2.2619467
145000 32.506074 888 -0 2.2776547
146000 32.847604 888 -0 2.2933626
147000 33.188988 888 -0 2.3090706
148000 33.532869 888 -0 2.3247786
149000 33.876629 888 -0 2.3404865
150000 34.221172 888 -0 2.3561945
151000 34.562559 888 -0 2.3719025
152000 34.904679 888 -0 2.3876104
153000 35.247727 888 -0 2.4033184
154000 35.591228 888 -0 2.4190263
155000 35.949192 888 -0 2.4347343
156000 36.320157 888 -0 2.4504423
157000 36.693571 888 -0 2.4661502
158000 37.069463 888 -0 2.4818582
159000 37.44221 888 -0 2.4975662
160000 37.81863 888 -0 2.5132741
161000 38.195121 888 -0 2.5289821
162000 38.573424 888 -0 2.54469
163000 38.950044 888 -0 2.560398
164000 39.331977 888 -0 2.576106
165000 39.714367 888 -0 2.5918139
166000 40.097099 888 -0 2.6075219
167000 40.477443 888 -0 2.6232299
168000 40.860404 888 -0 2.6389378
169000 41.244357 888 -0 2.6546458
170000 41.658126 1000 -0 2.6703538
171000 42.082517 1000 -0 2.6860617
172000 42.507502 1000 -0 2.7017697
173000 42.93363 1000 -0 2.7174776
174000 43.361133 1000 -0 2.7331856
175000 43.792381 1000 -0 2.7488936
176000 44.223827 1000 -0 2.7646015
177000 44.656581 1000 -0 2.7803095
178000 45.087615 1000 -0 2.7960175
179000 45.521129 1000 -0 2.8117254
180000 45.957808 1000 -0 2.8274334
181000 46.391451 1000 -0 2.8431414
182000 46.825486 1000 -0 2.8588493
183000 47.26091 1000 -0 2.8745573
184000 47.694263 1000 -0 2.8902652
185000 48.123312 1000 -0 2.9059732
186000 48.554081 1000 -0 2.9216812
187000 48.982617 1000 -0 2.9373891
188000 49.414355 1000 -0 2.9530971
189000 49.84753 1000 -0 2.9688051
190000 50.284462 1000 -0 2.984513
191000 50.71899 1000 -0 3.000221
192000 51.157278 1000 -0 3.0159289
193000 51.586171 1000 -0 3.0316369
194000 52.011691 1000 -0 3.0473449
195000 52.437732 1000 -0 3.0630528
196000 52.863703 1000 -0 3.0787608
197000 53.290403 1000 -0 3.0944688
198000 53.7191 1000 -0 3.1101767
199000 54.147195 1000 -0 3.1258847
200000 54.575967 1000 -0 3.1415927
Loop time of 54.576 on 1 procs for 200000 steps with 1000 atoms
Performance: 14960.907 tau/day, 3664.615 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7989 | 3.7989 | 3.7989 | 0.0 | 6.96
Neigh | 0.067629 | 0.067629 | 0.067629 | 0.0 | 0.12
Comm | 0.63734 | 0.63734 | 0.63734 | 0.0 | 1.17
Output | 0.0049303 | 0.0049303 | 0.0049303 | 0.0 | 0.01
Modify | 49.1 | 49.1 | 49.1 | 0.0 | 89.97
Other | | 0.9668 | | | 1.77
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 196 ave 196 max 196 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3910 ave 3910 max 3910 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3910
Ave neighs/atom = 3.91
Neighbor list builds = 219
Dangerous builds = 0
unfix ins
run 200000
Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 0.93873133 3.1415927
201000 0.4261198 1000 0.93239566 3.1573006
202000 0.84928846 1000 0.90333835 3.1730086
203000 1.2720087 1000 0.89351493 3.1887165
204000 1.6929317 1000 0.87648478 3.2044245
205000 2.114043 1000 0.86818482 3.2201325
206000 2.5357664 1000 0.86033251 3.2358404
207000 2.9579847 1000 0.85442625 3.2515484
208000 3.3812878 1000 0.8517451 3.2672564
209000 3.8124611 1000 0.84406987 3.2829643
210000 4.2440236 1000 0.83964642 3.2986723
211000 4.6781921 1000 0.82994066 3.3143802
212000 5.1116509 1000 0.82908369 3.3300882
213000 5.5468135 1000 0.83115482 3.3457962
214000 5.9802556 1000 0.82680518 3.3615041
215000 6.4107294 1000 0.8223909 3.3772121
216000 6.8419023 1000 0.81872537 3.3929201
217000 7.2763367 1000 0.82446065 3.408628
218000 7.7160695 1000 0.82278874 3.424336
219000 8.1540956 1000 0.83017397 3.440044
220000 8.5917952 1000 0.82232305 3.4557519
221000 9.0296218 1000 0.82584132 3.4714599
222000 9.4719794 1000 0.82143909 3.4871678
223000 9.9180939 1000 0.82925587 3.5028758
224000 10.361852 1000 0.84546265 3.5185838
225000 10.803539 1000 0.84436452 3.5342917
226000 11.248456 1000 0.84849375 3.5499997
227000 11.695092 1000 0.8409057 3.5657077
228000 12.136044 1000 0.83139305 3.5814156
229000 12.579807 1000 0.83098473 3.5971236
230000 13.02219 1000 0.81335147 3.6128316
231000 13.463863 1000 0.78946649 3.6285395
232000 13.906293 1000 0.78807613 3.6442475
233000 14.348807 1000 0.79086655 3.6599554
234000 14.793175 1000 0.79358862 3.6756634
235000 15.238316 1000 0.79444252 3.6913714
236000 15.683342 1000 0.79392156 3.7070793
237000 16.12611 1000 0.80416034 3.7227873
238000 16.5711 1000 0.80365093 3.7384953
239000 17.014355 1000 0.80860323 3.7542032
240000 17.454467 1000 0.80245788 3.7699112
241000 17.89162 1000 0.79602568 3.7856191
242000 18.330859 1000 0.79023692 3.8013271
243000 18.769301 1000 0.79066782 3.8170351
244000 19.211293 1000 0.77671368 3.832743
245000 19.651443 1000 0.77121874 3.848451
246000 20.092102 1000 0.74658977 3.864159
247000 20.532732 1000 0.73825017 3.8798669
248000 20.975646 1000 0.7187986 3.8955749
249000 21.418807 1000 0.71707058 3.9112829
250000 21.862497 1000 0.72983635 3.9269908
251000 22.311832 1000 0.7355358 3.9426988
252000 22.75883 1000 0.74427811 3.9584067
253000 23.203455 1000 0.74968093 3.9741147
254000 23.651472 1000 0.75350303 3.9898227
255000 24.102152 1000 0.75617916 4.0055306
256000 24.554236 1000 0.74949839 4.0212386
257000 25.008718 1000 0.73534118 4.0369466
258000 25.461913 1000 0.73761942 4.0526545
259000 25.916674 1000 0.75485851 4.0683625
260000 26.373941 1000 0.77147511 4.0840704
261000 26.832072 1000 0.76658917 4.0997784
262000 27.28741 1000 0.76441563 4.1154864
263000 27.742157 1000 0.74449444 4.1311943
264000 28.192718 1000 0.7403314 4.1469023
265000 28.642541 1000 0.74262656 4.1626103
266000 29.09406 1000 0.74117022 4.1783182
267000 29.547747 1000 0.73877643 4.1940262
268000 29.998243 1000 0.75062626 4.2097342
269000 30.449751 1000 0.74649396 4.2254421
270000 30.901232 1000 0.75371324 4.2411501
271000 31.354755 1000 0.75254842 4.256858
272000 31.810717 1000 0.74245946 4.272566
273000 32.265754 1000 0.73056023 4.288274
274000 32.719719 1000 0.72004393 4.3039819
275000 33.173929 1000 0.70665742 4.3196899
276000 33.628581 1000 0.69417262 4.3353979
277000 34.080936 1000 0.67343474 4.3511058
278000 34.532053 1000 0.66922758 4.3668138
279000 34.985569 1000 0.66239909 4.3825218
280000 35.443496 1000 0.66406486 4.3982297
281000 35.901536 1000 0.67123654 4.4139377
282000 36.357765 1000 0.67660885 4.4296456
283000 36.811956 1000 0.6809288 4.4453536
284000 37.266937 1000 0.69561154 4.4610616
285000 37.720866 1000 0.70874512 4.4767695
286000 38.177032 1000 0.72957833 4.4924775
287000 38.633109 1000 0.72891066 4.5081855
288000 39.086933 1000 0.72673285 4.5238934
289000 39.538699 1000 0.72583062 4.5396014
290000 39.991294 1000 0.7209406 4.5553093
291000 40.437987 1000 0.70642559 4.5710173
292000 40.885753 1000 0.69074151 4.5867253
293000 41.326601 1000 0.68041469 4.6024332
294000 41.763719 1000 0.6712034 4.6181412
295000 42.198532 1000 0.66140336 4.6338492
296000 42.635139 1000 0.65458145 4.6495571
297000 43.071132 1000 0.63884999 4.6652651
298000 43.507309 1000 0.63182296 4.6809731
299000 43.943936 1000 0.6324286 4.696681
300000 44.383148 1000 0.62640427 4.712389
301000 44.819379 1000 0.62138494 4.7280969
302000 45.260834 1000 0.62902694 4.7438049
303000 45.705719 1000 0.63308052 4.7595129
304000 46.14622 1000 0.63266845 4.7752208
305000 46.586693 1000 0.63464534 4.7909288
306000 47.028768 1000 0.62941378 4.8066368
307000 47.470183 1000 0.62801025 4.8223447
308000 47.914518 1000 0.62291875 4.8380527
309000 48.365654 1000 0.62529494 4.8537606
310000 48.817185 1000 0.62504442 4.8694686
311000 49.269423 1000 0.63074915 4.8851766
312000 49.722869 1000 0.64292914 4.9008845
313000 50.175859 1000 0.65319818 4.9165925
314000 50.630132 1000 0.66755513 4.9323005
315000 51.084836 1000 0.67585436 4.9480084
316000 51.539391 1000 0.67676226 4.9637164
317000 51.995233 1000 0.67394312 4.9794244
318000 52.453581 1000 0.67299959 4.9951323
319000 52.906322 1000 0.68074615 5.0108403
320000 53.362206 1000 0.67696004 5.0265482
321000 53.813824 1000 0.67899008 5.0422562
322000 54.264433 1000 0.67901671 5.0579642
323000 54.715627 1000 0.67620354 5.0736721
324000 55.168 1000 0.67165541 5.0893801
325000 55.620891 1000 0.67820953 5.1050881
326000 56.073685 1000 0.67490808 5.120796
327000 56.526012 1000 0.67238149 5.136504
328000 56.977525 1000 0.66885914 5.152212
329000 57.431088 1000 0.66876389 5.1679199
330000 57.886694 1000 0.66879597 5.1836279
331000 58.338381 1000 0.66577546 5.1993358
332000 58.791084 1000 0.6602875 5.2150438
333000 59.242965 1000 0.65879422 5.2307518
334000 59.698559 1000 0.6581474 5.2464597
335000 60.153261 1000 0.6521249 5.2621677
336000 60.605605 1000 0.63371979 5.2778757
337000 61.059824 1000 0.62373279 5.2935836
338000 61.510606 1000 0.6212013 5.3092916
339000 61.962049 1000 0.62303395 5.3249995
340000 62.413564 1000 0.63183785 5.3407075
341000 62.86366 1000 0.64387158 5.3564155
342000 63.317623 1000 0.65045982 5.3721234
343000 63.772034 1000 0.65401192 5.3878314
344000 64.225206 1000 0.65181077 5.4035394
345000 64.681317 1000 0.64098248 5.4192473
346000 65.136483 1000 0.63163559 5.4349553
347000 65.588996 1000 0.64182161 5.4506633
348000 66.042215 1000 0.65528889 5.4663712
349000 66.501687 1000 0.66603277 5.4820792
350000 66.960896 1000 0.67362185 5.4977871
351000 67.417316 1000 0.68867905 5.5134951
352000 67.876742 1000 0.6907547 5.5292031
353000 68.336836 1000 0.69043981 5.544911
354000 68.797396 1000 0.68676964 5.560619
355000 69.255062 1000 0.68019369 5.576327
356000 69.711663 1000 0.66189875 5.5920349
357000 70.172728 1000 0.65275709 5.6077429
358000 70.632655 1000 0.64560617 5.6234508
359000 71.091165 1000 0.63865266 5.6391588
360000 71.548341 1000 0.6366388 5.6548668
361000 72.006137 1000 0.63619567 5.6705747
362000 72.466621 1000 0.63986167 5.6862827
363000 72.928505 1000 0.656198 5.7019907
364000 73.391876 1000 0.66522563 5.7176986
365000 73.852366 1000 0.67330205 5.7334066
366000 74.317924 1000 0.67997811 5.7491146
367000 74.781431 1000 0.67734915 5.7648225
368000 75.24363 1000 0.66811078 5.7805305
369000 75.704319 1000 0.67232161 5.7962384
370000 76.165294 1000 0.67262944 5.8119464
371000 76.624971 1000 0.68614241 5.8276544
372000 77.085918 1000 0.70293842 5.8433623
373000 77.544679 1000 0.71889856 5.8590703
374000 78.007103 1000 0.7170296 5.8747783
375000 78.468913 1000 0.71258031 5.8904862
376000 78.93354 1000 0.70758873 5.9061942
377000 79.39396 1000 0.69486822 5.9219022
378000 79.850685 1000 0.68311194 5.9376101
379000 80.307228 1000 0.67317549 5.9533181
380000 80.767418 1000 0.67691049 5.969026
381000 81.227579 1000 0.69231691 5.984734
382000 81.686924 1000 0.69998609 6.000442
383000 82.145783 1000 0.69328258 6.0161499
384000 82.604827 1000 0.69903908 6.0318579
385000 83.056443 1000 0.69455744 6.0475659
386000 83.507131 1000 0.68865933 6.0632738
387000 83.95695 1000 0.68630439 6.0789818
388000 84.404079 1000 0.6800564 6.0946897
389000 84.851053 1000 0.66747339 6.1103977
390000 85.298614 1000 0.65695883 6.1261057
391000 85.744507 1000 0.65659359 6.1418136
392000 86.191348 1000 0.65933663 6.1575216
393000 86.632782 1000 0.65170236 6.1732296
394000 87.074105 1000 0.65631817 6.1889375
395000 87.5177 1000 0.66205838 6.2046455
396000 87.963111 1000 0.65512694 6.2203535
397000 88.408348 1000 0.65266011 6.2360614
398000 88.854042 1000 0.64593806 6.2517694
399000 89.298754 1000 0.64940473 6.2674773
400000 89.745445 1000 0.66033435 6.2831853
Loop time of 89.7455 on 1 procs for 200000 steps with 1000 atoms
Performance: 9098.023 tau/day, 2228.525 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.924 | 10.924 | 10.924 | 0.0 | 12.17
Neigh | 0.10266 | 0.10266 | 0.10266 | 0.0 | 0.11
Comm | 1.9424 | 1.9424 | 1.9424 | 0.0 | 2.16
Output | 0.0056458 | 0.0056458 | 0.0056458 | 0.0 | 0.01
Modify | 75.442 | 75.442 | 75.442 | 0.0 | 84.06
Other | | 1.329 | | | 1.48
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 272 ave 272 max 272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4933 ave 4933 max 4933 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4933
Ave neighs/atom = 4.933
Neighbor list builds = 171
Dangerous builds = 0
Total wall time: 0:02:24

602
examples/granregion/log.27Nov18.granregion.mixer.g++.4
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@ -1,602 +0,0 @@
LAMMPS (27 Nov 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
variable name string mixer
thermo_modify flush yes
variable seed equal 14314
###############################################
# Particle parameters
################################################
variable rlo equal 0.3
variable rhi equal 0.6
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.3
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.6
variable skin equal ${rhi}
variable skin equal 0.6
variable coeffRes equal 0.1
variable coeffFric equal 0.5
variable kn equal 10^5
variable kt equal 0.2*${kn}
variable kt equal 0.2*100000
variable gravity equal 1.0
variable density equal 1.0
variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo}
variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3
variable a equal (-2.0*log(${coeffRes})/PI)^2
variable a equal (-2.0*log(0.1)/PI)^2
variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a))
variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351))
variable gamma_t equal ${gamma_n}*0.5
variable gamma_t equal 806.699778405191*0.5
variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0)
variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0)
variable dt equal ${tcol}*0.02
variable dt equal 0.00236257621510454*0.02
timestep ${dt}
timestep 4.72515243020908e-05
###############################################
variable dumpfreq equal 1000
variable logfreq equal 1000
newton on
atom_style sphere
boundary p p f
region boxreg block 0 20 0 20 0 20
create_box 1 boxreg
Created orthogonal box = (0 0 0) to (20 20 20)
1 by 2 by 2 MPI processor grid
pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1
pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1
pair_coeff * *
neighbor ${skin} bin
neighbor 0.6 bin
thermo ${logfreq}
thermo 1000
comm_style brick
comm_modify mode multi group all vel yes
balance 1.1 shift xyz 20 1.1
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 20, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
fix bal all balance 10000 1.1 shift xyz 20 1.01
####################### Options specific to pouring #########################
region insreg cylinder z 10 10 8 10 18 side in units box
region cylreg cylinder z 10 10 10 0 20 side in units box
variable theta equal (step/400000)*2*PI
region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box
region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box
region mixer intersect 3 cylreg b1 b2 side in
fix grav all gravity ${gravity} vector 0 0 -1
fix grav all gravity 1 vector 0 0 -1
fix 1 all nve/sphere
fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer
fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer
fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density}
fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1
Particle insertion: 444 every 84653 steps, 1000 by step 169307
#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z
#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0
#dump_modify 2 pad 6
thermo_style custom step cpu atoms ke v_theta
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705)
thermo_modify flush yes lost warn
run 200000
Per MPI rank memory allocation (min/avg/max) = 5.817 | 5.817 | 5.817 Mbytes
Step CPU Atoms KinEng v_theta
0 0 0 -0 0
1000 0.096722603 444 -0 0.015707963
2000 0.18796778 444 -0 0.031415927
3000 0.27916241 444 -0 0.04712389
4000 0.37111688 444 -0 0.062831853
5000 0.46224833 444 -0 0.078539816
6000 0.55190682 444 -0 0.09424778
7000 0.64120579 444 -0 0.10995574
8000 0.73025131 444 -0 0.12566371
9000 0.82121348 444 -0 0.14137167
10000 0.91006637 444 -0 0.15707963
11000 0.97034311 444 -0 0.1727876
12000 1.030247 444 -0 0.18849556
13000 1.0894752 444 -0 0.20420352
14000 1.1483686 444 -0 0.21991149
15000 1.2138393 444 -0 0.23561945
16000 1.2744856 444 -0 0.25132741
17000 1.3361425 444 -0 0.26703538
18000 1.3998857 444 -0 0.28274334
19000 1.4625463 444 -0 0.2984513
20000 1.5255082 444 -0 0.31415927
21000 1.5845048 444 -0 0.32986723
22000 1.6437175 444 -0 0.34557519
23000 1.7022173 444 -0 0.36128316
24000 1.7614172 444 -0 0.37699112
25000 1.8209105 444 -0 0.39269908
26000 1.8818901 444 -0 0.40840704
27000 1.9439991 444 -0 0.42411501
28000 2.0067189 444 -0 0.43982297
29000 2.0697014 444 -0 0.45553093
30000 2.1327429 444 -0 0.4712389
31000 2.1904151 444 -0 0.48694686
32000 2.2478669 444 -0 0.50265482
33000 2.3062997 444 -0 0.51836279
34000 2.3723967 444 -0 0.53407075
35000 2.4331915 444 -0 0.54977871
36000 2.4937904 444 -0 0.56548668
37000 2.5550685 444 -0 0.58119464
38000 2.6170652 444 -0 0.5969026
39000 2.6789875 444 -0 0.61261057
40000 2.7414019 444 -0 0.62831853
41000 2.799027 444 -0 0.64402649
42000 2.8570235 444 -0 0.65973446
43000 2.9140713 444 -0 0.67544242
44000 2.9702985 444 -0 0.69115038
45000 3.0274565 444 -0 0.70685835
46000 3.0860338 444 -0 0.72256631
47000 3.1450455 444 -0 0.73827427
48000 3.2057948 444 -0 0.75398224
49000 3.267339 444 -0 0.7696902
50000 3.3300545 444 -0 0.78539816
51000 3.3942592 444 -0 0.80110613
52000 3.4522727 444 -0 0.81681409
53000 3.5117693 444 -0 0.83252205
54000 3.5717957 444 -0 0.84823002
55000 3.6338761 444 -0 0.86393798
56000 3.7006576 444 -0 0.87964594
57000 3.7648654 444 -0 0.89535391
58000 3.829128 444 -0 0.91106187
59000 3.8930187 444 -0 0.92676983
60000 3.9581499 444 -0 0.9424778
61000 4.0213017 444 -0 0.95818576
62000 4.0822632 444 -0 0.97389372
63000 4.1443422 444 -0 0.98960169
64000 4.2072315 444 -0 1.0053096
65000 4.2711387 444 -0 1.0210176
66000 4.3361402 444 -0 1.0367256
67000 4.4031398 444 -0 1.0524335
68000 4.4698064 444 -0 1.0681415
69000 4.5374978 444 -0 1.0838495
70000 4.6051283 444 -0 1.0995574
71000 4.6694169 444 -0 1.1152654
72000 4.7335079 444 -0 1.1309734
73000 4.7967482 444 -0 1.1466813
74000 4.8603547 444 -0 1.1623893
75000 4.9250085 444 -0 1.1780972
76000 4.9909372 444 -0 1.1938052
77000 5.0578024 444 -0 1.2095132
78000 5.1250138 444 -0 1.2252211
79000 5.1929755 444 -0 1.2409291
80000 5.2627637 444 -0 1.2566371
81000 5.3280981 444 -0 1.272345
82000 5.3957336 444 -0 1.288053
83000 5.4648135 444 -0 1.303761
84000 5.5368683 444 -0 1.3194689
85000 5.6352935 888 -0 1.3351769
86000 5.7708502 888 -0 1.3508848
87000 5.9051492 888 -0 1.3665928
88000 6.0384896 888 -0 1.3823008
89000 6.1714747 888 -0 1.3980087
90000 6.3042989 888 -0 1.4137167
91000 6.4114611 888 -0 1.4294247
92000 6.5164247 888 -0 1.4451326
93000 6.6219602 888 -0 1.4608406
94000 6.728405 888 -0 1.4765485
95000 6.8411646 888 -0 1.4922565
96000 6.9479821 888 -0 1.5079645
97000 7.0569239 888 -0 1.5236724
98000 7.1673372 888 -0 1.5393804
99000 7.2778809 888 -0 1.5550884
100000 7.398834 888 -0 1.5707963
101000 7.5066864 888 -0 1.5865043
102000 7.6158357 888 -0 1.6022123
103000 7.725111 888 -0 1.6179202
104000 7.8344197 888 -0 1.6336282
105000 7.9532022 888 -0 1.6493361
106000 8.0643187 888 -0 1.6650441
107000 8.1765473 888 -0 1.6807521
108000 8.2890661 888 -0 1.69646
109000 8.4048562 888 -0 1.712168
110000 8.5208168 888 -0 1.727876
111000 8.6303153 888 -0 1.7435839
112000 8.7401052 888 -0 1.7592919
113000 8.8518219 888 -0 1.7749998
114000 8.9638157 888 -0 1.7907078
115000 9.0766122 888 -0 1.8064158
116000 9.1908746 888 -0 1.8221237
117000 9.306145 888 -0 1.8378317
118000 9.4229569 888 -0 1.8535397
119000 9.5407412 888 -0 1.8692476
120000 9.6574531 888 -0 1.8849556
121000 9.7683234 888 -0 1.9006636
122000 9.8812008 888 -0 1.9163715
123000 9.9952521 888 -0 1.9320795
124000 10.111879 888 -0 1.9477874
125000 10.228812 888 -0 1.9634954
126000 10.347842 888 -0 1.9792034
127000 10.47052 888 -0 1.9949113
128000 10.593136 888 -0 2.0106193
129000 10.718124 888 -0 2.0263273
130000 10.844211 888 -0 2.0420352
131000 10.959177 888 -0 2.0577432
132000 11.075781 888 -0 2.0734512
133000 11.191418 888 -0 2.0891591
134000 11.313376 888 -0 2.1048671
135000 11.432321 888 -0 2.120575
136000 11.551893 888 -0 2.136283
137000 11.672695 888 -0 2.151991
138000 11.793487 888 -0 2.1676989
139000 11.914089 888 -0 2.1834069
140000 12.037441 888 -0 2.1991149
141000 12.161974 888 -0 2.2148228
142000 12.286641 888 -0 2.2305308
143000 12.414012 888 -0 2.2462387
144000 12.540939 888 -0 2.2619467
145000 12.66985 888 -0 2.2776547
146000 12.79975 888 -0 2.2933626
147000 12.932702 888 -0 2.3090706
148000 13.066088 888 -0 2.3247786
149000 13.200814 888 -0 2.3404865
150000 13.33565 888 -0 2.3561945
151000 13.465995 888 -0 2.3719025
152000 13.586622 888 -0 2.3876104
153000 13.711423 888 -0 2.4033184
154000 13.835058 888 -0 2.4190263
155000 13.967661 888 -0 2.4347343
156000 14.100609 888 -0 2.4504423
157000 14.234485 888 -0 2.4661502
158000 14.373325 888 -0 2.4818582
159000 14.510608 888 -0 2.4975662
160000 14.651416 888 -0 2.5132741
161000 14.785767 888 -0 2.5289821
162000 14.921569 888 -0 2.54469
163000 15.058895 888 -0 2.560398
164000 15.198786 888 -0 2.576106
165000 15.341662 888 -0 2.5918139
166000 15.487128 888 -0 2.6075219
167000 15.649383 888 -0 2.6232299
168000 15.795388 888 -0 2.6389378
169000 15.942671 888 -0 2.6546458
170000 16.091824 1000 -0 2.6703538
171000 16.239863 1000 -0 2.6860617
172000 16.391118 1000 -0 2.7017697
173000 16.5417 1000 -0 2.7174776
174000 16.69479 1000 -0 2.7331856
175000 16.847412 1000 -0 2.7488936
176000 17.000374 1000 -0 2.7646015
177000 17.15471 1000 -0 2.7803095
178000 17.31284 1000 -0 2.7960175
179000 17.46991 1000 -0 2.8117254
180000 17.629018 1000 -0 2.8274334
181000 17.787736 1000 -0 2.8431414
182000 17.946197 1000 -0 2.8588493
183000 18.105271 1000 -0 2.8745573
184000 18.263731 1000 -0 2.8902652
185000 18.433277 1000 -0 2.9059732
186000 18.594456 1000 -0 2.9216812
187000 18.755532 1000 -0 2.9373891
188000 18.918447 1000 -0 2.9530971
189000 19.080359 1000 -0 2.9688051
190000 19.243927 1000 -0 2.984513
191000 19.395044 1000 -0 3.000221
192000 19.546837 1000 -0 3.0159289
193000 19.695827 1000 -0 3.0316369
194000 19.843856 1000 -0 3.0473449
195000 19.993821 1000 -0 3.0630528
196000 20.145787 1000 -0 3.0787608
197000 20.298114 1000 -0 3.0944688
198000 20.45074 1000 -0 3.1101767
199000 20.607595 1000 -0 3.1258847
200000 20.760979 1000 -0 3.1415927
Loop time of 20.7611 on 4 procs for 200000 steps with 1000 atoms
Performance: 39328.699 tau/day, 9633.409 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.57172 | 0.93292 | 1.2995 | 37.1 | 4.49
Neigh | 0.015648 | 0.018747 | 0.02175 | 2.1 | 0.09
Comm | 3.17 | 3.6151 | 4.0856 | 23.0 | 17.41
Output | 0.0051017 | 0.012686 | 0.033359 | 10.6 | 0.06
Modify | 12.36 | 13.269 | 14.095 | 21.8 | 63.91
Other | | 2.912 | | | 14.03
Nlocal: 250 ave 270 max 230 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 297 ave 337 max 234 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 982.5 ave 1580 max 496 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 3930
Ave neighs/atom = 3.93
Neighbor list builds = 218
Dangerous builds = 0
unfix ins
run 200000
Per MPI rank memory allocation (min/avg/max) = 12 | 12.19 | 12.35 Mbytes
Step CPU Atoms KinEng v_theta
200000 0 1000 0.89289812 3.1415927
201000 0.15554476 1000 0.90162438 3.1573006
202000 0.31118774 1000 0.89175077 3.1730086
203000 0.47266722 1000 0.88068523 3.1887165
204000 0.64758801 1000 0.88775074 3.2044245
205000 0.85137105 1000 0.89009449 3.2201325
206000 1.0712745 1000 0.89031724 3.2358404
207000 1.3620427 1000 0.90901476 3.2515484
208000 1.6051998 1000 0.91977358 3.2672564
209000 1.7975032 1000 0.92044257 3.2829643
210000 1.9654117 1000 0.90550844 3.2986723
211000 2.1186137 1000 0.90179135 3.3143802
212000 2.2714169 1000 0.90474936 3.3300882
213000 2.4236252 1000 0.9011002 3.3457962
214000 2.5737655 1000 0.89619815 3.3615041
215000 2.7326233 1000 0.89129064 3.3772121
216000 2.8794787 1000 0.88785486 3.3929201
217000 3.0264313 1000 0.89448821 3.408628
218000 3.1743443 1000 0.89323746 3.424336
219000 3.3225086 1000 0.88176869 3.440044
220000 3.4717121 1000 0.86989815 3.4557519
221000 3.6229391 1000 0.85900389 3.4714599
222000 3.7768724 1000 0.85440461 3.4871678
223000 3.9287963 1000 0.8604449 3.5028758
224000 4.082505 1000 0.84537374 3.5185838
225000 4.234731 1000 0.84526488 3.5342917
226000 4.3872988 1000 0.85877362 3.5499997
227000 4.5396216 1000 0.86762074 3.5657077
228000 4.7092509 1000 0.86460359 3.5814156
229000 4.8631954 1000 0.85409682 3.5971236
230000 5.0194352 1000 0.83902718 3.6128316
231000 5.1765387 1000 0.83908755 3.6285395
232000 5.3335299 1000 0.83178808 3.6442475
233000 5.4917257 1000 0.83369584 3.6599554
234000 5.654233 1000 0.8530074 3.6756634
235000 5.8163757 1000 0.86385009 3.6913714
236000 5.9791231 1000 0.86453337 3.7070793
237000 6.1401029 1000 0.86137572 3.7227873
238000 6.300632 1000 0.8656285 3.7384953
239000 6.4597898 1000 0.85993724 3.7542032
240000 6.6216707 1000 0.8484153 3.7699112
241000 6.7793672 1000 0.84624799 3.7856191
242000 6.939244 1000 0.83739227 3.8013271
243000 7.1013088 1000 0.83026469 3.8170351
244000 7.267416 1000 0.81060567 3.832743
245000 7.4318523 1000 0.81081038 3.848451
246000 7.6077905 1000 0.80857771 3.864159
247000 7.7763391 1000 0.80353315 3.8798669
248000 7.9485247 1000 0.80191903 3.8955749
249000 8.1208956 1000 0.79865102 3.9112829
250000 8.2921841 1000 0.79407385 3.9269908
251000 8.4614651 1000 0.7880275 3.9426988
252000 8.6266186 1000 0.79212521 3.9584067
253000 8.7913449 1000 0.78976714 3.9741147
254000 8.9596558 1000 0.79720779 3.9898227
255000 9.1278918 1000 0.79329363 4.0055306
256000 9.3016815 1000 0.80851295 4.0212386
257000 9.4701304 1000 0.82322071 4.0369466
258000 9.6399531 1000 0.83042211 4.0526545
259000 9.8090186 1000 0.82773068 4.0683625
260000 9.9798045 1000 0.8246773 4.0840704
261000 10.148952 1000 0.81374287 4.0997784
262000 10.318855 1000 0.79936963 4.1154864
263000 10.496092 1000 0.78124408 4.1311943
264000 10.671031 1000 0.77790646 4.1469023
265000 10.843052 1000 0.77212005 4.1626103
266000 11.01867 1000 0.77977752 4.1783182
267000 11.192151 1000 0.79237542 4.1940262
268000 11.362491 1000 0.80631398 4.2097342
269000 11.53223 1000 0.82380407 4.2254421
270000 11.7123 1000 0.82477127 4.2411501
271000 11.883593 1000 0.81655074 4.256858
272000 12.052348 1000 0.80678676 4.272566
273000 12.220196 1000 0.79162789 4.288274
274000 12.395164 1000 0.78896081 4.3039819
275000 12.569757 1000 0.77904648 4.3196899
276000 12.748754 1000 0.78252999 4.3353979
277000 12.91648 1000 0.78293295 4.3511058
278000 13.086087 1000 0.78311337 4.3668138
279000 13.260159 1000 0.77657634 4.3825218
280000 13.428503 1000 0.76835711 4.3982297
281000 13.596094 1000 0.75586438 4.4139377
282000 13.763325 1000 0.74600306 4.4296456
283000 13.932867 1000 0.73228762 4.4453536
284000 14.098865 1000 0.72344939 4.4610616
285000 14.269317 1000 0.72160289 4.4767695
286000 14.441196 1000 0.71321619 4.4924775
287000 14.614458 1000 0.72631772 4.5081855
288000 14.783358 1000 0.74390396 4.5238934
289000 14.953564 1000 0.77320352 4.5396014
290000 15.12428 1000 0.77249469 4.5553093
291000 15.283974 1000 0.7583723 4.5710173
292000 15.449553 1000 0.74568347 4.5867253
293000 15.611965 1000 0.74108034 4.6024332
294000 15.770807 1000 0.72706174 4.6181412
295000 15.927151 1000 0.71122597 4.6338492
296000 16.086734 1000 0.70272297 4.6495571
297000 16.245418 1000 0.6945394 4.6652651
298000 16.406617 1000 0.69541258 4.6809731
299000 16.568989 1000 0.71696092 4.696681
300000 16.754911 1000 0.72939561 4.712389
301000 16.919453 1000 0.73621801 4.7280969
302000 17.07794 1000 0.72052605 4.7438049
303000 17.234397 1000 0.71057318 4.7595129
304000 17.39014 1000 0.70014814 4.7752208
305000 17.550789 1000 0.68855925 4.7909288
306000 17.718802 1000 0.68665019 4.8066368
307000 17.874036 1000 0.6831349 4.8223447
308000 18.029367 1000 0.67929468 4.8380527
309000 18.188065 1000 0.67833006 4.8537606
310000 18.348243 1000 0.67764037 4.8694686
311000 18.512475 1000 0.68271978 4.8851766
312000 18.676519 1000 0.69021026 4.9008845
313000 18.836426 1000 0.68795473 4.9165925
314000 18.997681 1000 0.68308892 4.9323005
315000 19.158794 1000 0.68086977 4.9480084
316000 19.318186 1000 0.67879169 4.9637164
317000 19.479364 1000 0.68128526 4.9794244
318000 19.645085 1000 0.68718719 4.9951323
319000 19.806831 1000 0.68419901 5.0108403
320000 19.97005 1000 0.68045269 5.0265482
321000 20.130643 1000 0.68430036 5.0422562
322000 20.291637 1000 0.68195368 5.0579642
323000 20.457605 1000 0.67964011 5.0736721
324000 20.621699 1000 0.67681293 5.0893801
325000 20.78525 1000 0.67601868 5.1050881
326000 20.950321 1000 0.67600265 5.120796
327000 21.11346 1000 0.68484094 5.136504
328000 21.276964 1000 0.68526189 5.152212
329000 21.440971 1000 0.67602072 5.1679199
330000 21.609791 1000 0.68222852 5.1836279
331000 21.773574 1000 0.68825647 5.1993358
332000 21.93854 1000 0.68168415 5.2150438
333000 22.102281 1000 0.67460357 5.2307518
334000 22.265741 1000 0.67747925 5.2464597
335000 22.436954 1000 0.681763 5.2621677
336000 22.614367 1000 0.67611867 5.2778757
337000 22.779064 1000 0.66903217 5.2935836
338000 22.945739 1000 0.6684293 5.3092916
339000 23.111375 1000 0.66465194 5.3249995
340000 23.278674 1000 0.66226848 5.3407075
341000 23.444642 1000 0.66407188 5.3564155
342000 23.614615 1000 0.65762812 5.3721234
343000 23.785007 1000 0.66936507 5.3878314
344000 23.956265 1000 0.67424224 5.4035394
345000 24.129057 1000 0.684271 5.4192473
346000 24.303073 1000 0.68294352 5.4349553
347000 24.475812 1000 0.69795697 5.4506633
348000 24.652771 1000 0.69818863 5.4663712
349000 24.830973 1000 0.69578798 5.4820792
350000 25.00923 1000 0.69377251 5.4977871
351000 25.185421 1000 0.69638202 5.5134951
352000 25.363647 1000 0.70115823 5.5292031
353000 25.540517 1000 0.70891635 5.544911
354000 25.718709 1000 0.70876639 5.560619
355000 25.893633 1000 0.71130235 5.576327
356000 26.068423 1000 0.69380913 5.5920349
357000 26.243801 1000 0.67934899 5.6077429
358000 26.418883 1000 0.67024516 5.6234508
359000 26.594722 1000 0.66145645 5.6391588
360000 26.770322 1000 0.65335546 5.6548668
361000 26.946396 1000 0.65495192 5.6705747
362000 27.12296 1000 0.64973833 5.6862827
363000 27.298461 1000 0.64532381 5.7019907
364000 27.473586 1000 0.64282855 5.7176986
365000 27.653872 1000 0.64451862 5.7334066
366000 27.830317 1000 0.64366439 5.7491146
367000 28.007037 1000 0.64395479 5.7648225
368000 28.184079 1000 0.65827587 5.7805305
369000 28.376009 1000 0.66311341 5.7962384
370000 28.557287 1000 0.66165026 5.8119464
371000 28.736569 1000 0.66878374 5.8276544
372000 28.91063 1000 0.66944548 5.8433623
373000 29.084648 1000 0.66061945 5.8590703
374000 29.258649 1000 0.65320954 5.8747783
375000 29.433156 1000 0.64641195 5.8904862
376000 29.611781 1000 0.64631388 5.9061942
377000 29.78531 1000 0.64232398 5.9219022
378000 29.955917 1000 0.63805257 5.9376101
379000 30.126378 1000 0.63666047 5.9533181
380000 30.297285 1000 0.63651856 5.969026
381000 30.471635 1000 0.6377374 5.984734
382000 30.644813 1000 0.64750107 6.000442
383000 30.816208 1000 0.65655138 6.0161499
384000 30.986444 1000 0.65408935 6.0318579
385000 31.156501 1000 0.64437236 6.0475659
386000 31.327665 1000 0.63862174 6.0632738
387000 31.49731 1000 0.64133807 6.0789818
388000 31.682031 1000 0.64174374 6.0946897
389000 31.85148 1000 0.64480071 6.1103977
390000 32.020336 1000 0.64982943 6.1261057
391000 32.187634 1000 0.6461109 6.1418136
392000 32.357282 1000 0.64044412 6.1575216
393000 32.527796 1000 0.64662995 6.1732296
394000 32.704323 1000 0.65330527 6.1889375
395000 32.880643 1000 0.66026265 6.2046455
396000 33.048614 1000 0.6718969 6.2203535
397000 33.222059 1000 0.66481385 6.2360614
398000 33.391738 1000 0.66685494 6.2517694
399000 33.560431 1000 0.6612594 6.2674773
400000 33.729715 1000 0.65289572 6.2831853
Loop time of 33.7298 on 4 procs for 200000 steps with 1000 atoms
Performance: 24207.249 tau/day, 5929.470 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6748 | 2.6848 | 3.6646 | 58.4 | 7.96
Neigh | 0.021206 | 0.026438 | 0.03191 | 3.1 | 0.08
Comm | 6.133 | 7.3745 | 8.6652 | 45.0 | 21.86
Output | 0.0053763 | 0.016101 | 0.044719 | 13.0 | 0.05
Modify | 18.26 | 20.115 | 22.413 | 39.2 | 59.64
Other | | 3.513 | | | 10.42
Nlocal: 250 ave 266 max 230 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 401.5 ave 476 max 325 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1264 ave 1634 max 895 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 5056
Ave neighs/atom = 5.056
Neighbor list builds = 160
Dangerous builds = 0
Total wall time: 0:00:54

2
examples/granular/in.pour.drum
View File

@ -44,7 +44,7 @@ change_box all boundary p p f
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
variable theta equal 0

84
examples/granular/in.pour.heat Normal file
View File

@ -0,0 +1,84 @@
# pour one types of particles into cylinder and oscillate
# temperature of the bottom plate
variable name string heat_plate
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 10
variable boxy equal 10
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_height equal 30
variable xc equal 0.5*${boxx}
variable yc equal 0.5*${boxx}
variable zc equal 0.5*${boxz}
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dhi equal 2.0*${rhi}
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable dens equal 1.0
variable skin equal 0.4*${rhi}
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
create_box 2 boxreg
change_box all boundary p p f
pair_style granular
pair_coeff * * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji heat area 5.0
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
fix 0 all property/atom temperature heatflow
fix 1 all balance 100 1.0 shift xy 5 1.1
fix 2 all nve/sphere
fix 3 all heat/flow constant 1.0
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 1000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
comm_modify vel yes
neighbor ${skin} bin
neigh_modify delay 0 every 1 check yes
variable oscillate equal 1.0*sin(step*0.0001)
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji heat area 5.0 region bottom_wall temperature v_oscillate
thermo_style custom step atoms ke pxx pyy pzz
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 1000 ${name}.dump id type radius mass x y z temperature heatflow
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
group delgroup dynamic all var zmax every 10000
run 100000

272
examples/granular/log.15Sep22.pour.drum.g++.1 Normal file
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@ -0,0 +1,272 @@
LAMMPS (15 Sep 2022)
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
# This simulates a rotating drum powder characterization experiment.
variable name string rotating_drum_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_rad equal 30*0.5
variable drum_height equal 20
variable xc equal 0.5*${boxx}
variable xc equal 0.5*30
variable yc equal 0.5*${boxx}
variable yc equal 0.5*30
variable zc equal 0.5*${boxz}
variable zc equal 0.5*50
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*0.5
variable dens equal 1.0
variable skin equal 0.4*${rhi}
variable skin equal 0.4*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (30 30 50)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
variable theta equal 0
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 20 ${boxz}
region insreg cylinder z 15 15 14.45 20 50
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
variable zmax atom z+c_1>0.5*20
group delgroup dynamic all var zmax every 10000
dynamic group delgroup defined
run 2000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 50 50 84
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.08 | 16.08 | 16.08 Mbytes
Step Atoms KinEng v_theta
0 0 -0 0
100 4000 -0 0
200 4000 -0 0
300 4000 -0 0
400 4000 -0 0
500 4000 -0 0
600 4000 -0 0
700 4000 -0 0
800 4000 -0 0
900 4000 -0 0
1000 4000 -0 0
1100 4000 -0 0
1200 4000 -0 0
1300 4000 -0 0
1400 4000 -0 0
1500 4000 -0 0
1600 4000 -0 0
1700 4000 -0 0
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 2.81549 on 1 procs for 2000 steps with 4000 atoms
Performance: 61374.657 tau/day, 710.355 timesteps/s, 2.841 Matom-step/s
98.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.35362 | 0.35362 | 0.35362 | 0.0 | 12.56
Neigh | 1.0852 | 1.0852 | 1.0852 | 0.0 | 38.54
Comm | 0.041891 | 0.041891 | 0.041891 | 0.0 | 1.49
Output | 0.00059151 | 0.00059151 | 0.00059151 | 0.0 | 0.02
Modify | 1.2814 | 1.2814 | 1.2814 | 0.0 | 45.51
Other | | 0.0528 | | | 1.88
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 179 ave 179 max 179 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7019 ave 7019 max 7019 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7019
Ave neighs/atom = 1.75475
Neighbor list builds = 1000
Dangerous builds = 0
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
Deleted 0 atoms, new total = 4000
#Add top lid
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 22.42 | 22.42 | 22.42 Mbytes
Step Atoms KinEng v_theta
2000 4000 59.969827 0
2100 4000 47.251389 0.031415927
2200 4000 33.726755 0.062831853
2300 4000 24.212479 0.09424778
2400 4000 17.366268 0.12566371
2500 4000 18.502318 0.15707963
2600 4000 17.44981 0.18849556
2700 4000 16.068315 0.21991149
2800 4000 14.252644 0.25132741
2900 4000 11.544019 0.28274334
3000 4000 9.0353662 0.31415927
3100 4000 6.9955912 0.34557519
3200 4000 5.955137 0.37699112
3300 4000 5.8947849 0.40840704
3400 4000 6.0544729 0.43982297
3500 4000 6.5326359 0.4712389
3600 4000 6.6047764 0.50265482
3700 4000 6.7073614 0.53407075
3800 4000 6.7367804 0.56548668
3900 4000 6.6178006 0.5969026
4000 4000 6.3834858 0.62831853
4100 4000 5.8660652 0.65973446
4200 4000 5.308513 0.69115038
4300 4000 4.7270842 0.72256631
4400 4000 4.1920733 0.75398224
4500 4000 3.7068814 0.78539816
4600 4000 3.3259615 0.81681409
4700 4000 2.9339231 0.84823002
4800 4000 2.670752 0.87964594
4900 4000 2.4509115 0.91106187
5000 4000 2.2609335 0.9424778
Loop time of 9.82178 on 1 procs for 3000 steps with 4000 atoms
Performance: 26390.330 tau/day, 305.444 timesteps/s, 1.222 Matom-step/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2932 | 3.2932 | 3.2932 | 0.0 | 33.53
Neigh | 2.2872 | 2.2872 | 2.2872 | 0.0 | 23.29
Comm | 0.067117 | 0.067117 | 0.067117 | 0.0 | 0.68
Output | 0.00093425 | 0.00093425 | 0.00093425 | 0.0 | 0.01
Modify | 4.0986 | 4.0986 | 4.0986 | 0.0 | 41.73
Other | | 0.07476 | | | 0.76
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 363 ave 363 max 363 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13089 ave 13089 max 13089 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13089
Ave neighs/atom = 3.27225
Neighbor list builds = 1247
Dangerous builds = 130
Total wall time: 0:00:12

272
examples/granular/log.15Sep22.pour.drum.g++.4 Normal file
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LAMMPS (15 Sep 2022)
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
# This simulates a rotating drum powder characterization experiment.
variable name string rotating_drum_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_rad equal 30*0.5
variable drum_height equal 20
variable xc equal 0.5*${boxx}
variable xc equal 0.5*30
variable yc equal 0.5*${boxx}
variable yc equal 0.5*30
variable zc equal 0.5*${boxz}
variable zc equal 0.5*50
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*0.5
variable dens equal 1.0
variable skin equal 0.4*${rhi}
variable skin equal 0.4*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (30 30 50)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
variable theta equal 0
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 20 ${boxz}
region insreg cylinder z 15 15 14.45 20 50
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
variable zmax atom z+c_1>0.5*20
group delgroup dynamic all var zmax every 10000
dynamic group delgroup defined
run 2000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 50 50 84
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.3 | 15.3 | 15.3 Mbytes
Step Atoms KinEng v_theta
0 0 -0 0
100 4000 -0 0
200 4000 -0 0
300 4000 -0 0
400 4000 -0 0
500 4000 -0 0
600 4000 -0 0
700 4000 -0 0
800 4000 -0 0
900 4000 -0 0
1000 4000 -0 0
1100 4000 -0 0
1200 4000 -0 0
1300 4000 -0 0
1400 4000 -0 0
1500 4000 -0 0
1600 4000 -0 0
1700 4000 -0 0
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 0.744926 on 4 procs for 2000 steps with 4000 atoms
Performance: 231969.322 tau/day, 2684.830 timesteps/s, 10.739 Matom-step/s
98.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.064917 | 0.069813 | 0.074844 | 1.7 | 9.37
Neigh | 0.15075 | 0.15915 | 0.1692 | 1.9 | 21.36
Comm | 0.11223 | 0.11821 | 0.12247 | 1.1 | 15.87
Output | 0.00030739 | 0.00036898 | 0.00046777 | 0.0 | 0.05
Modify | 0.36068 | 0.36657 | 0.37031 | 0.7 | 49.21
Other | | 0.03082 | | | 4.14
Nlocal: 1000 ave 1010 max 990 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 285 ave 287 max 283 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 1714.25 ave 1764 max 1651 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 6857
Ave neighs/atom = 1.71425
Neighbor list builds = 1000
Dangerous builds = 0
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
Deleted 0 atoms, new total = 4000
#Add top lid
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 21.6 | 21.6 | 21.6 Mbytes
Step Atoms KinEng v_theta
2000 4000 60.10546 0
2100 4000 47.274123 0.031415927
2200 4000 33.475582 0.062831853
2300 4000 24.083669 0.09424778
2400 4000 17.36351 0.12566371
2500 4000 18.576501 0.15707963
2600 4000 17.39 0.18849556
2700 4000 15.789254 0.21991149
2800 4000 14.08156 0.25132741
2900 4000 11.636681 0.28274334
3000 4000 8.9897685 0.31415927
3100 4000 7.0703519 0.34557519
3200 4000 6.0741809 0.37699112
3300 4000 5.8286097 0.40840704
3400 4000 6.059001 0.43982297
3500 4000 6.4310861 0.4712389
3600 4000 6.3957528 0.50265482
3700 4000 6.4858292 0.53407075
3800 4000 6.4685962 0.56548668
3900 4000 6.3469676 0.5969026
4000 4000 6.2808022 0.62831853
4100 4000 5.957048 0.65973446
4200 4000 5.5378951 0.69115038
4300 4000 4.8523264 0.72256631
4400 4000 4.2485239 0.75398224
4500 4000 3.7587486 0.78539816
4600 4000 3.327008 0.81681409
4700 4000 2.9421013 0.84823002
4800 4000 2.75247 0.87964594
4900 4000 2.5306332 0.91106187
5000 4000 2.352504 0.9424778
Loop time of 2.48704 on 4 procs for 3000 steps with 4000 atoms
Performance: 104220.238 tau/day, 1206.253 timesteps/s, 4.825 Matom-step/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.51605 | 0.70407 | 0.86299 | 14.7 | 28.31
Neigh | 0.3522 | 0.42808 | 0.50041 | 8.0 | 17.21
Comm | 0.17318 | 0.42324 | 0.7046 | 29.0 | 17.02
Output | 0.00079725 | 0.0013956 | 0.002092 | 1.3 | 0.06
Modify | 0.68507 | 0.79676 | 0.90954 | 8.9 | 32.04
Other | | 0.1335 | | | 5.37
Nlocal: 1000 ave 1330 max 670 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 525.5 ave 781 max 417 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 3243.75 ave 4460 max 2012 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 12975
Ave neighs/atom = 3.24375
Neighbor list builds = 1299
Dangerous builds = 129
Total wall time: 0:00:03

195
examples/granular/log.15Sep22.pour.flatwall.g++.1 Normal file
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LAMMPS (15 Sep 2022)
# pour two types of particles (cohesive and non-cohesive) on flat wall
variable name string pour_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable xc1 equal 0.3*${boxx}
variable xc1 equal 0.3*20
variable xc2 equal 0.7*${boxx}
variable xc2 equal 0.7*20
variable yc equal 0.5*${boxy}
variable yc equal 0.5*20
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable dens equal 1.0
variable skin equal 0.3*${rhi}
variable skin equal 0.3*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (20 20 30)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 30
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 30
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.15
ghost atom cutoff = 1.15
binsize = 0.575, bins = 35 35 53
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.27 | 15.27 | 15.27 Mbytes
Step Atoms KinEng
0 0 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
WARNING: Less insertions than requested (../fix_pour.cpp:681)
100 926 -0
200 926 -0
300 926 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
WARNING: Less insertions than requested (../fix_pour.cpp:681)
400 1498 -0
500 1498 -0
600 1498 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
WARNING: Less insertions than requested (../fix_pour.cpp:681)
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 10.7721 on 1 procs for 5000 steps with 3000 atoms
Performance: 40103.467 tau/day, 464.160 timesteps/s, 1.392 Matom-step/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.1117 | 8.1117 | 8.1117 | 0.0 | 75.30
Neigh | 1.2885 | 1.2885 | 1.2885 | 0.0 | 11.96
Comm | 0.059888 | 0.059888 | 0.059888 | 0.0 | 0.56
Output | 0.0011158 | 0.0011158 | 0.0011158 | 0.0 | 0.01
Modify | 1.2436 | 1.2436 | 1.2436 | 0.0 | 11.54
Other | | 0.06727 | | | 0.62
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 471 ave 471 max 471 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 16713 ave 16713 max 16713 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 16713
Ave neighs/atom = 5.571
Neighbor list builds = 1102
Dangerous builds = 0
Total wall time: 0:00:10

195
examples/granular/log.15Sep22.pour.flatwall.g++.4 Normal file
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LAMMPS (15 Sep 2022)
# pour two types of particles (cohesive and non-cohesive) on flat wall
variable name string pour_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable xc1 equal 0.3*${boxx}
variable xc1 equal 0.3*20
variable xc2 equal 0.7*${boxx}
variable xc2 equal 0.7*20
variable yc equal 0.5*${boxy}
variable yc equal 0.5*20
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable dens equal 1.0
variable skin equal 0.3*${rhi}
variable skin equal 0.3*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0 0 0) to (20 20 30)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 30
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 30
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.15
ghost atom cutoff = 1.15
binsize = 0.575, bins = 35 35 53
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.04 | 15.04 | 15.04 Mbytes
Step Atoms KinEng
0 0 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
WARNING: Less insertions than requested (../fix_pour.cpp:681)
100 926 -0
200 926 -0
300 926 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
WARNING: Less insertions than requested (../fix_pour.cpp:681)
400 1498 -0
500 1498 -0
600 1498 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
WARNING: Less insertions than requested (../fix_pour.cpp:681)
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
WARNING: Less insertions than requested (../fix_pour.cpp:681)
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 4.06277 on 4 procs for 5000 steps with 3000 atoms
Performance: 106331.276 tau/day, 1230.686 timesteps/s, 3.692 Matom-step/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85426 | 1.7801 | 2.7631 | 64.4 | 43.82
Neigh | 0.18775 | 0.25657 | 0.3279 | 11.5 | 6.32
Comm | 0.23605 | 1.3334 | 2.3703 | 81.6 | 32.82
Output | 0.00059456 | 0.0008165 | 0.0012002 | 0.0 | 0.02
Modify | 0.59336 | 0.64066 | 0.6864 | 4.3 | 15.77
Other | | 0.05122 | | | 1.26
Nlocal: 750 ave 1032 max 463 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 426.5 ave 482 max 375 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 4164.25 ave 6310 max 1941 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 16657
Ave neighs/atom = 5.5523333
Neighbor list builds = 1114
Dangerous builds = 0
Total wall time: 0:00:04

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examples/granular/log.29Oct20.pour.drum.g++.1
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@ -1,271 +0,0 @@
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
# This simulates a rotating drum powder characterization experiment.
variable name string rotating_drum_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_rad equal 30*0.5
variable drum_height equal 20
variable xc equal 0.5*${boxx}
variable xc equal 0.5*30
variable yc equal 0.5*${boxx}
variable yc equal 0.5*30
variable zc equal 0.5*${boxz}
variable zc equal 0.5*50
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*0.5
variable dens equal 1.0
variable skin equal 0.4*${rhi}
variable skin equal 0.4*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
variable theta equal 0
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 20 ${boxz}
region insreg cylinder z 15 15 14.45 20 50
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
variable zmax atom z+c_1>0.5*20
group delgroup dynamic all var zmax every 10000
dynamic group delgroup defined
run 2000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 50 50 84
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.03 | 13.03 | 13.03 Mbytes
Step Atoms KinEng v_theta
0 0 -0 0
100 4000 -0 0
200 4000 -0 0
300 4000 -0 0
400 4000 -0 0
500 4000 -0 0
600 4000 -0 0
700 4000 -0 0
800 4000 -0 0
900 4000 -0 0
1000 4000 -0 0
1100 4000 -0 0
1200 4000 -0 0
1300 4000 -0 0
1400 4000 -0 0
1500 4000 -0 0
1600 4000 -0 0
1700 4000 -0 0
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 10.5178 on 1 procs for 2000 steps with 4000 atoms
Performance: 16429.309 tau/day, 190.154 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0701 | 1.0701 | 1.0701 | 0.0 | 10.17
Neigh | 4.2135 | 4.2135 | 4.2135 | 0.0 | 40.06
Comm | 0.38276 | 0.38276 | 0.38276 | 0.0 | 3.64
Output | 0.0013647 | 0.0013647 | 0.0013647 | 0.0 | 0.01
Modify | 4.7076 | 4.7076 | 4.7076 | 0.0 | 44.76
Other | | 0.1424 | | | 1.35
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 171.000 ave 171 max 171 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8093.00 ave 8093 max 8093 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8093
Ave neighs/atom = 2.0232500
Neighbor list builds = 1004
Dangerous builds = 4
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
Deleted 0 atoms, new total = 4000
#Add top lid
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Per MPI rank memory allocation (min/avg/max) = 19.37 | 19.37 | 19.37 Mbytes
Step Atoms KinEng v_theta
2000 4000 65.647582 0
2100 4000 105.60001 0.031415927
2200 4000 112.27573 0.062831853
2300 4000 92.758671 0.09424778
2400 4000 88.925835 0.12566371
2500 4000 81.369163 0.15707963
2600 4000 32.046943 0.18849556
2700 4000 4.1926368 0.21991149
2800 4000 3.9933453 0.25132741
2900 4000 4.5062193 0.28274334
3000 4000 5.3409521 0.31415927
3100 4000 6.0165991 0.34557519
3200 4000 6.606767 0.37699112
3300 4000 7.3997751 0.40840704
3400 4000 8.1098807 0.43982297
3500 4000 8.6552424 0.4712389
3600 4000 9.8445204 0.50265482
3700 4000 10.098753 0.53407075
3800 4000 10.039489 0.56548668
3900 4000 9.6376278 0.5969026
4000 4000 9.2598836 0.62831853
4100 4000 8.7116037 0.65973446
4200 4000 8.1274117 0.69115038
4300 4000 7.1487627 0.72256631
4400 4000 6.2253778 0.75398224
4500 4000 5.3061398 0.78539816
4600 4000 4.4319316 0.81681409
4700 4000 4.205607 0.84823002
4800 4000 3.2112987 0.87964594
4900 4000 2.6449777 0.91106187
5000 4000 2.3475497 0.9424778
Loop time of 32.4926 on 1 procs for 3000 steps with 4000 atoms
Performance: 7977.205 tau/day, 92.329 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0124 | 8.0124 | 8.0124 | 0.0 | 24.66
Neigh | 10.993 | 10.993 | 10.993 | 0.0 | 33.83
Comm | 0.86697 | 0.86697 | 0.86697 | 0.0 | 2.67
Output | 0.0021827 | 0.0021827 | 0.0021827 | 0.0 | 0.01
Modify | 12.367 | 12.367 | 12.367 | 0.0 | 38.06
Other | | 0.2515 | | | 0.77
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 318.000 ave 318 max 318 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14807.0 ave 14807 max 14807 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14807
Ave neighs/atom = 3.7017500
Neighbor list builds = 2189
Dangerous builds = 1536
Total wall time: 0:00:43

271
examples/granular/log.29Oct20.pour.drum.g++.4
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@ -1,271 +0,0 @@
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) into cylinder
# 'turn' cylinder by changing direction of gravity, then rotate it.
# This simulates a rotating drum powder characterization experiment.
variable name string rotating_drum_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 30
variable boxy equal 30
variable boxz equal 50
variable drum_rad equal ${boxx}*0.5
variable drum_rad equal 30*0.5
variable drum_height equal 20
variable xc equal 0.5*${boxx}
variable xc equal 0.5*30
variable yc equal 0.5*${boxx}
variable yc equal 0.5*30
variable zc equal 0.5*${boxz}
variable zc equal 0.5*50
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*${rhi}
variable cyl_rad_inner equal 15-1.1*0.5
variable dens equal 1.0
variable skin equal 0.4*${rhi}
variable skin equal 0.4*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 ${boxy} 0 ${boxz}
region boxreg block 0 30 0 30 0 ${boxz}
region boxreg block 0 30 0 30 0 50
create_box 2 boxreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (30.000000 30.000000 50.000000)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
variable theta equal 0
region curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
region curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
region bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
region bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
region insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
region insreg cylinder z 15 15 14.45 20 ${boxz}
region insreg cylinder z 15 15 14.45 20 50
fix 0 all balance 100 1.0 shift xy 5 1.1
fix 1 all nve/sphere
fix grav all gravity 10 vector 0 0 -1
fix ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
fix ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
Particle insertion: 9396 every 490 steps, 2000 by step 1
comm_modify vel yes
neighbor ${skin} bin
neighbor 0.2 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
fix 4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
thermo_style custom step atoms ke v_theta
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
#For removal later
compute 1 all property/atom radius
variable zmax atom z+c_1>0.5*${drum_height}
variable zmax atom z+c_1>0.5*20
group delgroup dynamic all var zmax every 10000
dynamic group delgroup defined
run 2000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 50 50 84
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes
Step Atoms KinEng v_theta
0 0 -0 0
100 4000 -0 0
200 4000 -0 0
300 4000 -0 0
400 4000 -0 0
500 4000 -0 0
600 4000 -0 0
700 4000 -0 0
800 4000 -0 0
900 4000 -0 0
1000 4000 -0 0
1100 4000 -0 0
1200 4000 -0 0
1300 4000 -0 0
1400 4000 -0 0
1500 4000 -0 0
1600 4000 -0 0
1700 4000 -0 0
1800 4000 -0 0
1900 4000 -0 0
2000 4000 -0 0
Loop time of 3.86825 on 4 procs for 2000 steps with 4000 atoms
Performance: 44671.398 tau/day, 517.030 timesteps/s
96.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26114 | 0.27918 | 0.28728 | 2.0 | 7.22
Neigh | 1.2044 | 1.2414 | 1.3105 | 3.7 | 32.09
Comm | 0.38592 | 0.47065 | 0.51052 | 7.4 | 12.17
Output | 0.0007236 | 0.0013456 | 0.0024846 | 1.8 | 0.03
Modify | 1.6217 | 1.6723 | 1.7801 | 5.0 | 43.23
Other | | 0.2034 | | | 5.26
Nlocal: 1000.00 ave 1012 max 988 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 269.250 ave 278 max 256 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 2060.50 ave 2156 max 1921 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8242
Ave neighs/atom = 2.0605000
Neighbor list builds = 1004
Dangerous builds = 4
#Remove any particles that are above z > 0.5*drum_height
delete_atoms group delgroup
Deleted 0 atoms, new total = 4000
#Add top lid
region top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
region top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
fix 5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
# 'Turn' drum by switching the direction of gravity
unfix grav
unfix ins1
unfix ins2
fix grav all gravity 10 vector 0 -1 0
variable theta equal 2*PI*elapsed/20000.0
run 3000
Per MPI rank memory allocation (min/avg/max) = 18.55 | 18.55 | 18.55 Mbytes
Step Atoms KinEng v_theta
2000 4000 65.819213 0
2100 4000 105.02389 0.031415927
2200 4000 112.02469 0.062831853
2300 4000 92.271262 0.09424778
2400 4000 89.369506 0.12566371
2500 4000 80.910925 0.15707963
2600 4000 31.620722 0.18849556
2700 4000 4.3019937 0.21991149
2800 4000 3.9913967 0.25132741
2900 4000 4.5203726 0.28274334
3000 4000 5.484886 0.31415927
3100 4000 6.1085958 0.34557519
3200 4000 6.7085635 0.37699112
3300 4000 7.4787777 0.40840704
3400 4000 8.2116413 0.43982297
3500 4000 8.7979302 0.4712389
3600 4000 9.871649 0.50265482
3700 4000 10.012426 0.53407075
3800 4000 9.9067754 0.56548668
3900 4000 9.725458 0.5969026
4000 4000 9.3350056 0.62831853
4100 4000 8.8337295 0.65973446
4200 4000 8.2712493 0.69115038
4300 4000 6.9609934 0.72256631
4400 4000 6.0120294 0.75398224
4500 4000 5.0490036 0.78539816
4600 4000 4.2796544 0.81681409
4700 4000 4.1736483 0.84823002
4800 4000 3.0860106 0.87964594
4900 4000 2.6670909 0.91106187
5000 4000 2.2901814 0.9424778
Loop time of 10.7627 on 4 procs for 3000 steps with 4000 atoms
Performance: 24083.252 tau/day, 278.741 timesteps/s
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6731 | 2.0701 | 2.3327 | 18.9 | 19.23
Neigh | 2.7389 | 3.1706 | 3.5146 | 15.7 | 29.46
Comm | 0.93507 | 1.5441 | 2.1182 | 39.1 | 14.35
Output | 0.0021682 | 0.0044412 | 0.006026 | 2.2 | 0.04
Modify | 3.0031 | 3.4223 | 3.9262 | 18.3 | 31.80
Other | | 0.5511 | | | 5.12
Nlocal: 1000.00 ave 1277 max 723 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 569.750 ave 809 max 454 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 3690.50 ave 4937 max 2426 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 14762
Ave neighs/atom = 3.6905000
Neighbor list builds = 2187
Dangerous builds = 1610
Total wall time: 0:00:14

188
examples/granular/log.29Oct20.pour.flatwall.g++.1
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@ -1,188 +0,0 @@
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) on flat wall
variable name string pour_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable xc1 equal 0.3*${boxx}
variable xc1 equal 0.3*20
variable xc2 equal 0.7*${boxx}
variable xc2 equal 0.7*20
variable yc equal 0.5*${boxy}
variable yc equal 0.5*20
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable dens equal 1.0
variable skin equal 0.3*${rhi}
variable skin equal 0.3*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
1 by 1 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 30
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 30
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.15
ghost atom cutoff = 1.15
binsize = 0.575, bins = 35 35 53
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
Step Atoms KinEng
0 0 -0
100 926 -0
200 926 -0
300 926 -0
400 1498 -0
500 1498 -0
600 1498 -0
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 24.3889 on 1 procs for 5000 steps with 3000 atoms
Performance: 17713.003 tau/day, 205.012 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.362 | 14.362 | 14.362 | 0.0 | 58.89
Neigh | 3.3483 | 3.3483 | 3.3483 | 0.0 | 13.73
Comm | 0.42893 | 0.42893 | 0.42893 | 0.0 | 1.76
Output | 0.0025065 | 0.0025065 | 0.0025065 | 0.0 | 0.01
Modify | 6.059 | 6.059 | 6.059 | 0.0 | 24.84
Other | | 0.1876 | | | 0.77
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 462.000 ave 462 max 462 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 17694.0 ave 17694 max 17694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17694
Ave neighs/atom = 5.8980000
Neighbor list builds = 1133
Dangerous builds = 0
Total wall time: 0:00:24

188
examples/granular/log.29Oct20.pour.flatwall.g++.4
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@ -1,188 +0,0 @@
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# pour two types of particles (cohesive and non-cohesive) on flat wall
variable name string pour_two_types
atom_style sphere
units lj
###############################################
# Geometry-related parameters
###############################################
variable boxx equal 20
variable boxy equal 20
variable boxz equal 30
variable xc1 equal 0.3*${boxx}
variable xc1 equal 0.3*20
variable xc2 equal 0.7*${boxx}
variable xc2 equal 0.7*20
variable yc equal 0.5*${boxy}
variable yc equal 0.5*20
###############################################
# Particle-related parameters
###############################################
variable rlo equal 0.25
variable rhi equal 0.5
variable dlo equal 2.0*${rlo}
variable dlo equal 2.0*0.25
variable dhi equal 2.0*${rhi}
variable dhi equal 2.0*0.5
variable dens equal 1.0
variable skin equal 0.3*${rhi}
variable skin equal 0.3*0.5
#############
processors * * 1
region boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 ${boxy} 0 ${boxz}
region boxreg block 0 20 0 20 0 ${boxz}
region boxreg block 0 20 0 20 0 30
create_box 2 boxreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (20.000000 20.000000 30.000000)
2 by 2 by 1 MPI processor grid
change_box all boundary p p f
Changing box ...
pair_style granular
pair_coeff 1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
comm_modify vel yes
region insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 ${boxz}
region insreg1 cylinder z 6 10 5 15 30
region insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 ${boxz}
region insreg2 cylinder z 14 10 5 15 30
fix 1 all nve/sphere
fix grav all gravity 10.0 vector 0 0 -1
fix ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
fix ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
fix ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
fix ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
Particle insertion: 562 every 346 steps, 1500 by step 693
neighbor ${skin} bin
neighbor 0.15 bin
neigh_modify delay 0 every 1 check yes
fix 3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
thermo_style custom step atoms ke
thermo_modify lost warn
thermo 100
timestep 0.001
#dump 1 all custom 100 ${name}.dump id type radius mass x y z
run 5000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.15
ghost atom cutoff = 1.15
binsize = 0.575, bins = 35 35 53
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
Step Atoms KinEng
0 0 -0
100 926 -0
200 926 -0
300 926 -0
400 1498 -0
500 1498 -0
600 1498 -0
700 2275 -0
800 2275 -0
900 2275 -0
1000 2275 -0
1100 2954 -0
1200 2954 -0
1300 2954 -0
1400 3000 -0
1500 3000 -0
1600 3000 -0
1700 3000 -0
1800 3000 -0
1900 3000 -0
2000 3000 -0
2100 3000 -0
2200 3000 -0
2300 3000 -0
2400 3000 -0
2500 3000 -0
2600 3000 -0
2700 3000 -0
2800 3000 -0
2900 3000 -0
3000 3000 -0
3100 3000 -0
3200 3000 -0
3300 3000 -0
3400 3000 -0
3500 3000 -0
3600 3000 -0
3700 3000 -0
3800 3000 -0
3900 3000 -0
4000 3000 -0
4100 3000 -0
4200 3000 -0
4300 3000 -0
4400 3000 -0
4500 3000 -0
4600 3000 -0
4700 3000 -0
4800 3000 -0
4900 3000 -0
5000 3000 -0
Loop time of 12.1982 on 4 procs for 5000 steps with 3000 atoms
Performance: 35414.923 tau/day, 409.895 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7141 | 3.8131 | 6.2143 | 107.3 | 31.26
Neigh | 0.77648 | 0.96585 | 1.1892 | 18.3 | 7.92
Comm | 0.7427 | 3.5566 | 5.9731 | 128.4 | 29.16
Output | 0.0067544 | 0.0086352 | 0.011408 | 1.8 | 0.07
Modify | 3.3476 | 3.5826 | 3.8235 | 11.5 | 29.37
Other | | 0.2715 | | | 2.23
Nlocal: 750.000 ave 1033 max 463 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 435.000 ave 492 max 378 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4434.50 ave 7028 max 1967 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 17738
Ave neighs/atom = 5.9126667
Neighbor list builds = 1139
Dangerous builds = 0
Total wall time: 0:00:12

105
examples/mscg/log.16Mar23.g++.1 Normal file
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@ -0,0 +1,105 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
pair_style zero 10.0
read_data data.meoh
Reading data file ...
orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
pair_coeff * *
thermo 1
thermo_style custom step
# Test 1a: range finder functionality
fix 1 all mscg 1 range on
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
Step
0
250
500
750
1000
1250
1500
1750
2000
2250
2500
2750
3000
3250
3500
3750
4000
4250
4500
Loop time of 0.245891 on 1 procs for 19 steps with 1000 atoms
print "TEST_1a mscg range finder"
TEST_1a mscg range finder
unfix 1
# Test 1b: force matching functionality
fix 1 all mscg 1
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.045 | 6.045 | 6.045 Mbytes
Step
0
250
500
750
1000
1250
1500
1750
2000
2250
2500
2750
3000
3250
3500
3750
4000
4250
4500
Loop time of 0.433986 on 1 procs for 19 steps with 1000 atoms
print "TEST_1b mscg force matching"
TEST_1b mscg force matching
print TEST_DONE
TEST_DONE
Total wall time: 0:00:00

145
examples/mscg/log.31Mar17.g++.1
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@ -1,145 +0,0 @@
LAMMPS (13 Apr 2017)
units real
atom_style full
pair_style zero 10.0
read_data data.meoh
orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_coeff * *
thermo 1
thermo_style custom step
# Test 1a: range finder functionality
fix 1 all mscg 1 range on
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair zero, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
Step
0
250
500
750
1000
1250
1500
1750
2000
2250
2500
2750
3000
3250
3500
3750
4000
4250
4500
Loop time of 0.581537 on 1 procs for 19 steps with 1000 atoms
Performance: 2.823 ns/day, 8.502 hours/ns, 32.672 timesteps/s
99.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.5815 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2934 ave 2934 max 2934 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 50654 ave 50654 max 50654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 50654
Ave neighs/atom = 50.654
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
print "TEST_1a mscg range finder"
TEST_1a mscg range finder
unfix 1
# Test 1b: force matching functionality
fix 1 all mscg 1
rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
Step
0
250
500
750
1000
1250
1500
1750
2000
2250
2500
2750
3000
3250
3500
3750
4000
4250
4500
Loop time of 0.841917 on 1 procs for 19 steps with 1000 atoms
Performance: 1.950 ns/day, 12.309 hours/ns, 22.568 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.8419 | | |100.00
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2934 ave 2934 max 2934 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 50654 ave 50654 max 50654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 50654
Ave neighs/atom = 50.654
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
print "TEST_1b mscg force matching"
TEST_1b mscg force matching
print TEST_DONE
TEST_DONE
Total wall time: 0:00:01

71
examples/mscg/output_16Mar23/1_1.dat Normal file
View File

@ -0,0 +1,71 @@
3.000000 9.109433117503674e+00
3.100000 6.562933520937051e+00
3.200000 3.803570347770783e+00
3.300000 1.524835163098694e+00
3.400000 3.680752991750511e-02
3.500000 -6.369395346711866e-01
3.600000 -6.624341032589213e-01
3.700000 -2.983998819283989e-01
3.800000 1.996942072449469e-01
3.900000 6.507540486137935e-01
4.000000 9.561503221901252e-01
4.100000 1.082978861799261e+00
4.200000 1.046366050930359e+00
4.300000 8.917742185869113e-01
4.400000 6.773070351372578e-01
4.500000 4.561974686292022e-01
4.600000 2.640422255436971e-01
4.700000 1.180848207166380e-01
4.800000 2.124502216672507e-02
4.900000 -3.366915456585443e-02
5.000000 -5.974945208074427e-02
5.100000 -7.177537677873873e-02
5.200000 -8.204929079011507e-02
5.300000 -9.745573177789707e-02
5.400000 -1.196283642109915e-01
5.500000 -1.463411396781238e-01
5.600000 -1.729465415853768e-01
5.700000 -1.938138298537278e-01
5.800000 -2.037672856165882e-01
5.900000 -1.995060297815394e-01
6.000000 -1.805447650094144e-01
6.100000 -1.489384048916932e-01
6.200000 -1.085276302304308e-01
6.300000 -6.416601955090541e-02
6.400000 -2.094717961426480e-02
6.500000 1.656812406982645e-02
6.600000 4.511482523443927e-02
6.700000 6.322611594801032e-02
6.800000 7.107524696431811e-02
6.900000 7.005702917383723e-02
7.000000 6.235932355899154e-02
7.100000 5.053453114940768e-02
7.200000 3.707108297716843e-02
7.300000 2.397003518601587e-02
7.400000 1.245439896007831e-02
7.500000 3.015413982707119e-03
7.600000 -4.408442264121739e-03
7.700000 -1.024733994435217e-02
7.800000 -1.511598231239246e-02
7.900000 -1.962949115765983e-02
8.000000 -2.422153184874873e-02
8.100000 -2.902066868449916e-02
8.200000 -3.387453677654857e-02
8.300000 -3.843224513464188e-02
8.400000 -4.222901944115068e-02
8.500000 -4.477084482559266e-02
8.600000 -4.561910863915099e-02
8.700000 -4.447439067652353e-02
8.800000 -4.123808661911404e-02
8.900000 -3.601776131390161e-02
9.000000 -2.911033476210515e-02
9.100000 -2.098441550402311e-02
9.200000 -1.226263400387303e-02
9.300000 -3.703976034631109e-03
9.400000 3.815231963949414e-03
9.500000 9.355387087425532e-03
9.600000 1.205664749783030e-02
9.700000 1.131702059340882e-02
9.800000 6.971799313021964e-03
9.900000 -5.270015594498346e-04
10.000000 -9.931209090702869e-03

104
examples/mscg/output_16Mar23/1_1.table Normal file
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@ -0,0 +1,104 @@
# Header information on force file
1_1
N 99 R 0.200000 10.000000
1 0.200000 127.263594 80.411422
2 0.300000 119.349776 77.864922
3 0.400000 111.690609 75.318423
4 0.500000 104.286092 72.771923
5 0.600000 97.136225 70.225423
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13 1.400000 49.104684 49.853427
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90 9.100000 0.001156 -0.020984
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97 9.800000 -0.000201 0.006972
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99 10.000000 0.000000 -0.009931

2
examples/mscg/output_16Mar23/b-spline.out Normal file
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@ -0,0 +1,2 @@
n: 1 1 6 11 3.000000000000000e+00 1.000000000000000e+01
9.109454054135307e+00 6.178334150703818e+00 -6.242976259059743e+00 4.778144787445235e+00 -1.082885612852992e+00 4.521835893850554e-01 -6.477047196208028e-01 2.947887062333265e-01 -4.195609079009661e-02 1.111775827831465e-02 -8.823466147380592e-02 -1.696076806027540e-02 3.192205281984208e-02 3.656991607866288e-03 -9.931306149957592e-03

0
examples/mscg/output_9Jan17/rmin.in → examples/mscg/output_16Mar23/rmin.in
View File

0
examples/mscg/output_9Jan17/rmin_b.in → examples/mscg/output_16Mar23/rmin_b.in
View File

17
examples/mscg/output_16Mar23/sol_info.out Normal file
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@ -0,0 +1,17 @@
fm_matrix_rows:3000; fm_matrix_columns:15;
Singular vector:
2.307693e+00
1.998418e+00
1.400114e+00
1.183608e+00
9.718949e-01
7.471241e-01
5.277965e-01
5.084369e-01
3.510398e-01
2.997000e-01
2.142454e-01
1.201800e-01
7.143923e-02
3.077326e-02
1.835581e-02

2
examples/mscg/output_16Mar23/x.out Normal file
View File

@ -0,0 +1,2 @@
<EFBFBD>ٝ\
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77
examples/mscg/output_9Jan17/1_1.dat
View File

@ -1,77 +0,0 @@
2.500000 5.670970817963099e+02
2.600000 2.404059283529051e+02
2.700000 9.157060823529977e+01
2.800000 3.428273061369140e+01
2.900000 1.619868149395266e+01
3.000000 1.039607214301755e+01
3.100000 6.830187514267188e+00
3.200000 3.861970842349535e+00
3.300000 1.645948643278161e+00
3.400000 2.395428971623918e-01
3.500000 -4.276763637833773e-01
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3.800000 2.402697744243800e-01
3.900000 6.956064296165573e-01
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4.200000 1.209501102128581e+00
4.300000 1.076304670380924e+00
4.400000 8.575891319958883e-01
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4.600000 3.807992942746473e-01
4.700000 1.995994191469442e-01
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82
examples/mscg/output_9Jan17/1_1.table
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@ -1,82 +0,0 @@
# Header information on force file
1_1
N 77 R 2.500000 10.100000
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2 2.600000 29.053372 240.405928
3 2.700000 12.454545 91.570608
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8 3.200000 0.912149 3.861971
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2
examples/mscg/output_9Jan17/b-spline.out
View File

@ -1,2 +0,0 @@
n: 1 1 6 12 2.400000000000002e+00 1.010000000000000e+01
1.200460787805587e+03 2.169623423326193e+01 2.388396964379328e+01 -1.197754948555067e+01 6.472482422420378e+00 -1.483711824891365e+00 7.768139601662113e-01 -7.869494711740244e-01 4.830820182054661e-01 -1.892989444995645e-01 1.021275453070386e-01 -1.637649039972671e-01 5.570978712841167e-02 7.637188693695119e-03 -4.109175461195019e-03 -5.352186189455146e-02

18
examples/mscg/output_9Jan17/sol_info.out
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@ -1,18 +0,0 @@
fm_matrix_rows:3000; fm_matrix_columns:16;
Singular vector:
2.442317e+00
2.105009e+00
1.433251e+00
1.184602e+00
9.739627e-01
6.944898e-01
5.376709e-01
4.616070e-01
3.257062e-01
2.683729e-01
1.530153e-01
9.336288e-02
5.042150e-02
2.126912e-02
1.446682e-02
4.167763e-05

1
examples/mscg/output_9Jan17/x.out
View File

@ -1 +0,0 @@
<EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD>@47h<<3C>5@<40><><EFBFBD><EFBFBD>K<EFBFBD>7@<40>R<EFBFBD>]<5D><>'<27><><EFBFBD><EFBFBD>n<EFBFBD><6E>@݌I<DD8C>H<EFBFBD><48><EFBFBD><19>?<3F><><EFBFBD><EFBFBD>?r<>I<EFBFBD><49>.<2E><><11>^<5E><><EFBFBD><EFBFBD>?W<57><7F><EFBFBD>:ȿ(O<1D>%<25>?<3F>Ns<4E>?<3F>Ŀ<EFBFBD>:<3A>C<EFBFBD><43><EFBFBD>?<3F><><EFBFBD>:,H?<3F>}<7D>c<EFBFBD><63>p<EFBFBD><70><EFBFBD><EFBFBD><EFBFBD>7g<37><67>

125
examples/pour/log.16Mar23.pour.2d.g++.1 Normal file
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@ -0,0 +1,125 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
comm_modify vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: full/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.805 | 5.805 | 5.805 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 224 202.80417 0 5000
2000 224 373.00249 0 5000
3000 224 599.26757 0 5000
4000 448 1078.4787 0 5000
5000 448 1589.4845 0 5000
6000 448 1743.8281 26.918824 5000
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
7000 669 1818.5075 88.370238 5000
8000 669 1850.1368 105.77613 5000
9000 669 1757.9791 107.52328 5000
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
10000 886 1792.8816 79.515458 5000
11000 886 1639.0751 64.104708 5000
12000 886 1541.1208 55.91813 5000
13000 1000 1462.8753 69.093182 5000
14000 1000 1277.8754 48.097953 5000
15000 1000 1144.6235 50.637004 5000
16000 1000 847.34312 43.242219 5000
17000 1000 574.34264 41.336666 5000
18000 1000 383.60272 32.744393 5000
19000 1000 174.44969 31.691706 5000
20000 1000 44.566368 14.781893 5000
21000 1000 22.655785 9.8501131 5000
22000 1000 17.403069 6.4074514 5000
23000 1000 13.892292 4.8987582 5000
24000 1000 11.699592 4.0659436 5000
25000 1000 9.6606627 3.6642658 5000
Loop time of 2.84114 on 1 procs for 25000 steps with 1000 atoms
Performance: 760257.044 tau/day, 8799.271 timesteps/s, 8.799 Matom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.092 | 1.092 | 1.092 | 0.0 | 38.44
Neigh | 0.30793 | 0.30793 | 0.30793 | 0.0 | 10.84
Comm | 0.012168 | 0.012168 | 0.012168 | 0.0 | 0.43
Output | 0.00076223 | 0.00076223 | 0.00076223 | 0.0 | 0.03
Modify | 1.3179 | 1.3179 | 1.3179 | 0.0 | 46.38
Other | | 0.1104 | | | 3.89
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2344 ave 2344 max 2344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2344
Ave neighs/atom = 2.344
Neighbor list builds = 2097
Dangerous builds = 0
Total wall time: 0:00:02

125
examples/pour/log.16Mar23.pour.2d.g++.4 Normal file
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@ -0,0 +1,125 @@
LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
comm_modify vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: full/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.77 | 5.77 | 5.77 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 224 202.80417 0 5000
2000 224 373.00249 0 5000
3000 224 599.26757 0 5000
4000 448 1078.4787 0 5000
5000 448 1589.4845 0 5000
6000 448 1743.8281 26.918824 5000
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
7000 669 1818.5075 88.370238 5000
8000 669 1850.1368 105.77613 5000
9000 669 1757.9791 107.52328 5000
WARNING: Fewer insertions than requested (src/GRANULAR/fix_pour.cpp:681)
10000 886 1792.8816 79.515458 5000
11000 886 1639.0751 64.104716 5000
12000 886 1541.1046 55.902437 5000
13000 1000 1461.0291 68.011357 5000
14000 1000 1286.1144 48.551003 5000
15000 1000 1155.6137 55.503871 5000
16000 1000 833.49034 46.163926 5000
17000 1000 581.69308 43.140124 5000
18000 1000 369.375 37.675729 5000
19000 1000 188.74424 31.66369 5000
20000 1000 48.73107 23.067611 5000
21000 1000 27.652985 14.176945 5000
22000 1000 22.545416 9.6960211 5000
23000 1000 17.575825 6.6345699 5000
24000 1000 12.464163 4.9073459 5000
25000 1000 9.9507487 3.1967219 5000
Loop time of 0.793403 on 4 procs for 25000 steps with 1000 atoms
Performance: 2722450.224 tau/day, 31509.841 timesteps/s, 31.510 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2392 | 0.24458 | 0.25441 | 1.2 | 30.83
Neigh | 0.075663 | 0.07738 | 0.078869 | 0.4 | 9.75
Comm | 0.037752 | 0.045698 | 0.049012 | 2.2 | 5.76
Output | 0.00063359 | 0.0006788 | 0.00078796 | 0.0 | 0.09
Modify | 0.30883 | 0.3111 | 0.31377 | 0.3 | 39.21
Other | | 0.114 | | | 14.36
Nlocal: 250 ave 254 max 244 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 19.75 ave 28 max 11 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 600 ave 624 max 569 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 2400
Ave neighs/atom = 2.4
Neighbor list builds = 2138
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
comm_modify vel yes cutoff 2.5
fix prop all property/atom mol ghost yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
Read molecule template object:
1 molecules
0 fragments
5 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
fix 3 all rigid/small molecule mol object
create bodies CPU = 0.000 seconds
0 rigid bodies with 0 atoms
2.236068 = max distance from body owner to body atom
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 all enforce2d
compute 1 all erotate/sphere
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic/dof yes
thermo 1000
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Gravity may not be correctly applied to rigid bodies if they consist of overlapped particles (src/RIGID/fix_rigid_small.cpp:554)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 2.5
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: full/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.811 | 5.811 | 5.811 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 130 248.65568 0.002050506 5000
2000 130 452.01354 0.0020557556 5000
3000 130 720.36849 0.0021462148 5000
4000 260 1281.7126 0.0021462148 5000
5000 260 1875.9602 0.0021462148 5000
6000 260 1742.7747 2.0692779 5000
7000 390 1860.2142 1.7515066 5000
8000 390 1853.6219 2.3354959 5000
9000 390 1749.6466 5.1516327 5000
10000 520 1860.4314 4.2186838 5000
11000 520 1636.9411 4.006706 5000
12000 520 1454.1835 4.3341069 5000
13000 650 1881.6358 3.9606372 5000
14000 650 1648.6494 3.8239413 5000
15000 650 1463.0973 2.9363979 5000
16000 780 1571.0119 3.9061213 5000
17000 780 1472.941 2.0289533 5000
18000 780 1370.5265 3.1038747 5000
19000 910 1433.6728 2.7600498 5000
20000 910 1375.3634 2.964893 5000
21000 910 1184.8059 2.5050961 5000
22000 1040 1312.0948 1.844008 5000
23000 1040 1181.4208 1.7766375 5000
24000 1040 1263.1226 2.1430511 5000
25000 1170 1152.9064 2.4175531 5000
Loop time of 3.37143 on 1 procs for 25000 steps with 1170 atoms
Performance: 640677.536 tau/day, 7415.249 timesteps/s, 8.676 Matom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.91106 | 0.91106 | 0.91106 | 0.0 | 27.02
Neigh | 0.19015 | 0.19015 | 0.19015 | 0.0 | 5.64
Comm | 0.016916 | 0.016916 | 0.016916 | 0.0 | 0.50
Output | 0.0011065 | 0.0011065 | 0.0011065 | 0.0 | 0.03
Modify | 2.1372 | 2.1372 | 2.1372 | 0.0 | 63.39
Other | | 0.115 | | | 3.41
Nlocal: 1170 ave 1170 max 1170 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1685 ave 1685 max 1685 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1685
Ave neighs/atom = 1.4401709
Neighbor list builds = 1707
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
comm_modify vel yes cutoff 2.5
fix prop all property/atom mol ghost yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
Read molecule template object:
1 molecules
0 fragments
5 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
fix 3 all rigid/small molecule mol object
create bodies CPU = 0.000 seconds
0 rigid bodies with 0 atoms
2.236068 = max distance from body owner to body atom
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 all enforce2d
compute 1 all erotate/sphere
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic/dof yes
thermo 1000
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Gravity may not be correctly applied to rigid bodies if they consist of overlapped particles (src/RIGID/fix_rigid_small.cpp:554)
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 2.5
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: full/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.773 | 5.773 | 5.773 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 130 248.65568 0.002050506 5000
2000 130 452.01354 0.0020557556 5000
3000 130 720.36849 0.0021462148 5000
4000 260 1281.7126 0.0021462148 5000
5000 260 1875.9602 0.0021462148 5000
6000 260 1742.7747 2.0692779 5000
7000 390 1860.2142 1.7515066 5000
8000 390 1853.6219 2.3354959 5000
9000 390 1749.6466 5.1516327 5000
10000 520 1860.4314 4.2186838 5000
11000 520 1636.9411 4.006706 5000
12000 520 1454.1835 4.3341069 5000
13000 650 1881.6358 3.9606372 5000
14000 650 1648.6494 3.8239413 5000
15000 650 1463.0973 2.9363979 5000
16000 780 1571.0119 3.9061213 5000
17000 780 1472.941 2.0289532 5000
18000 780 1370.5265 3.1038747 5000
19000 910 1433.6728 2.7600454 5000
20000 910 1375.3629 2.9649297 5000
21000 910 1184.8017 2.5049255 5000
22000 1040 1312.0653 1.8441521 5000
23000 1040 1181.5473 1.7693597 5000
24000 1040 1263.4442 2.1476891 5000
25000 1170 1152.2404 2.4292153 5000
Loop time of 1.59966 on 4 procs for 25000 steps with 1170 atoms
Performance: 1350285.365 tau/day, 15628.303 timesteps/s, 18.285 Matom-step/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.23769 | 0.30075 | 0.35002 | 7.5 | 18.80
Neigh | 0.048877 | 0.062647 | 0.073072 | 3.7 | 3.92
Comm | 0.075225 | 0.087826 | 0.096819 | 2.9 | 5.49
Output | 0.0010015 | 0.0011427 | 0.0015053 | 0.6 | 0.07
Modify | 0.97758 | 0.99506 | 1.0071 | 1.1 | 62.20
Other | | 0.1522 | | | 9.52
Nlocal: 292.5 ave 314 max 274 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 44.5 ave 67 max 23 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 430 ave 452 max 393 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Total # of neighbors = 1720
Ave neighs/atom = 1.4700855
Neighbor list builds = 1707
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 34 34 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.956 | 5.956 | 5.956 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 6600
1000 402 753.1301 0 6600
2000 402 1389.6785 0 6600
3000 402 1439.3007 16.360577 6600
4000 804 1694.9311 52.966189 6600
5000 804 1564.7533 67.202593 6600
6000 804 1303.6937 65.31424 6600
7000 1206 1590.3342 63.948699 6600
8000 1206 1489.2483 54.736993 6600
9000 1206 1234.442 56.141183 6600
10000 1608 1314.3588 49.189129 6600
11000 1608 1238.0609 42.558653 6600
12000 1608 1143.6455 41.554747 6600
13000 2010 1229.989 49.661038 6600
14000 2010 1176.3015 40.982761 6600
15000 2010 1011.4718 45.872673 6600
16000 2412 1128.8326 47.405058 6600
17000 2412 1035.4314 40.22595 6600
18000 2412 873.87039 40.07875 6600
19000 2814 967.91799 41.49685 6600
20000 2814 928.0341 39.924344 6600
21000 2814 820.35467 37.621246 6600
22000 2814 549.00702 41.541324 6600
23000 3000 441.94025 41.467527 6600
24000 3000 339.91044 25.849093 6600
25000 3000 243.91083 20.921917 6600
Loop time of 8.07068 on 1 procs for 25000 steps with 3000 atoms
Performance: 267635.587 tau/day, 3097.634 timesteps/s, 9.293 Matom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.6682 | 4.6682 | 4.6682 | 0.0 | 57.84
Neigh | 1.0497 | 1.0497 | 1.0497 | 0.0 | 13.01
Comm | 0.16028 | 0.16028 | 0.16028 | 0.0 | 1.99
Output | 0.00076244 | 0.00076244 | 0.00076244 | 0.0 | 0.01
Modify | 2.0196 | 2.0196 | 2.0196 | 0.0 | 25.02
Other | | 0.172 | | | 2.13
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 667 ave 667 max 667 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13503 ave 13503 max 13503 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13503
Ave neighs/atom = 4.501
Neighbor list builds = 1150
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 10.64 | 10.64 | 10.64 Mbytes
Step Atoms KinEng c_1 Volume
25000 3000 243.91083 20.921917 6600
26000 3000 111.73212 19.181089 6600
27000 3000 175.53659 12.143401 6600
28000 3000 315.95861 12.721047 6600
29000 3000 516.24386 15.103525 6600
30000 3000 779.3423 19.057186 6600
31000 3000 1118.6219 21.320808 6600
32000 3000 1512.8878 25.012099 6600
33000 3000 1969.247 30.402739 6600
34000 3000 2499.318 37.297539 6600
35000 3000 3074.9401 45.925996 6600
36000 3000 3768.2108 39.734162 6600
37000 3000 4400.6971 44.337674 6600
38000 3000 5178.4457 63.168989 6600
39000 3000 6028.928 56.570416 6600
40000 3000 6947.424 67.360376 6600
41000 3000 7896.0016 69.368604 6600
42000 3000 8977.9347 66.242546 6600
43000 3000 10026.618 55.776273 6600
44000 3000 11106.873 69.943396 6600
45000 3000 12264.363 79.440158 6600
46000 3000 13562.635 67.026549 6600
47000 3000 14796.806 70.121289 6600
48000 3000 16254.182 70.690438 6600
49000 3000 17711.386 63.668043 6600
50000 3000 19144.269 66.708659 6600
Loop time of 17.582 on 1 procs for 25000 steps with 3000 atoms
Performance: 122853.050 tau/day, 1421.910 timesteps/s, 4.266 Matom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.641 | 11.641 | 11.641 | 0.0 | 66.21
Neigh | 1.7715 | 1.7715 | 1.7715 | 0.0 | 10.08
Comm | 0.38219 | 0.38219 | 0.38219 | 0.0 | 2.17
Output | 0.0010728 | 0.0010728 | 0.0010728 | 0.0 | 0.01
Modify | 3.4549 | 3.4549 | 3.4549 | 0.0 | 19.65
Other | | 0.3309 | | | 1.88
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 748 ave 748 max 748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14117 ave 14117 max 14117 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14117
Ave neighs/atom = 4.7056667
Neighbor list builds = 848
Dangerous builds = 0
Total wall time: 0:00:25

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LAMMPS (8 Feb 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 34 34 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.831 | 5.831 | 5.831 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 6600
1000 402 753.1301 0 6600
2000 402 1389.6785 0 6600
3000 402 1439.3007 16.360577 6600
4000 804 1694.9311 52.966189 6600
5000 804 1564.7533 67.202593 6600
6000 804 1303.6937 65.31424 6600
7000 1206 1590.3342 63.948699 6600
8000 1206 1489.2483 54.736993 6600
9000 1206 1234.442 56.141183 6600
10000 1608 1314.3588 49.189127 6600
11000 1608 1237.9823 42.555046 6600
12000 1608 1142.8729 41.96142 6600
13000 2010 1230.1948 49.194135 6600
14000 2010 1178.1648 39.43872 6600
15000 2010 1031.6441 46.416609 6600
16000 2412 1109.7641 45.866965 6600
17000 2412 1047.232 38.618366 6600
18000 2412 888.02373 41.307438 6600
19000 2814 965.06339 40.889834 6600
20000 2814 922.71203 40.04001 6600
21000 2814 815.9575 38.366756 6600
22000 2814 570.89153 37.83039 6600
23000 3000 428.71007 37.62527 6600
24000 3000 341.87262 24.030639 6600
25000 3000 243.78921 22.003596 6600
Loop time of 2.70972 on 4 procs for 25000 steps with 3000 atoms
Performance: 797131.262 tau/day, 9226.056 timesteps/s, 27.678 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2559 | 1.2759 | 1.2886 | 1.2 | 47.09
Neigh | 0.29364 | 0.29822 | 0.30487 | 0.8 | 11.01
Comm | 0.24161 | 0.25182 | 0.26235 | 1.5 | 9.29
Output | 0.00076819 | 0.00084565 | 0.00098501 | 0.0 | 0.03
Modify | 0.59267 | 0.61574 | 0.63388 | 2.3 | 22.72
Other | | 0.2672 | | | 9.86
Nlocal: 750 ave 759 max 734 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 381.75 ave 392 max 367 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3569.75 ave 3651 max 3448 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 14279
Ave neighs/atom = 4.7596667
Neighbor list builds = 1151
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 10.43 | 10.43 | 10.43 Mbytes
Step Atoms KinEng c_1 Volume
25000 3000 243.78921 22.003596 6600
26000 3000 119.4338 18.414134 6600
27000 3000 172.50337 12.019175 6600
28000 3000 316.78411 12.871972 6600
29000 3000 524.47221 16.004598 6600
30000 3000 812.57656 20.096736 6600
31000 3000 1181.7814 28.226314 6600
32000 3000 1612.855 28.279192 6600
33000 3000 2075.6364 29.358829 6600
34000 3000 2634.5344 36.312508 6600
35000 3000 3213.2814 43.992962 6600
36000 3000 3900.499 38.674908 6600
37000 3000 4594.329 46.025242 6600
38000 3000 5367.8353 46.404081 6600
39000 3000 6180.9788 56.484589 6600
40000 3000 7111.5267 51.165038 6600
41000 3000 7998.6331 65.039037 6600
42000 3000 9037.3716 69.653749 6600
43000 3000 10148.985 65.082635 6600
44000 3000 11242.901 62.787818 6600
45000 3000 12445.247 64.68269 6600
46000 3000 13773.582 59.313484 6600
47000 3000 15000.566 54.417728 6600
48000 3000 16312.814 60.23943 6600
49000 3000 17730.721 60.028021 6600
50000 3000 19221.273 62.659312 6600
Loop time of 5.52345 on 4 procs for 25000 steps with 3000 atoms
Performance: 391059.670 tau/day, 4526.154 timesteps/s, 13.578 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1235 | 3.1506 | 3.1758 | 1.1 | 57.04
Neigh | 0.47171 | 0.47561 | 0.48174 | 0.5 | 8.61
Comm | 0.39363 | 0.39957 | 0.4049 | 0.6 | 7.23
Output | 0.0010759 | 0.0011654 | 0.0012802 | 0.2 | 0.02
Modify | 0.93409 | 0.95091 | 0.96521 | 1.2 | 17.22
Other | | 0.5456 | | | 9.88
Nlocal: 750 ave 759 max 744 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 404.75 ave 411 max 402 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 3694.75 ave 3722 max 3672 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 14779
Ave neighs/atom = 4.9263333
Neighbor list builds = 856
Dangerous builds = 0
Total wall time: 0:00:08

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
comm_modify vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.804 | 5.804 | 5.804 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 224 201.77464 0 5000
2000 224 372.42868 0 5000
3000 224 599.60221 0 5000
4000 448 1084.3752 0 5000
5000 448 1592.4543 0 5000
6000 448 1763.3153 37.274939 5000
7000 672 1805.206 89.331853 5000
8000 672 1778.0015 111.58381 5000
9000 672 1592.6805 97.550311 5000
10000 896 1631.962 76.905078 5000
11000 896 1590.1527 68.644552 5000
12000 896 1564.4707 60.119562 5000
13000 1000 1490.072 56.982972 5000
14000 1000 1266.4669 57.579371 5000
15000 1000 1034.1055 46.079374 5000
16000 1000 748.70283 43.933154 5000
17000 1000 462.65166 37.522016 5000
18000 1000 327.40481 29.450285 5000
19000 1000 223.24319 31.981144 5000
20000 1000 54.792042 23.449101 5000
21000 1000 25.805484 16.352528 5000
22000 1000 20.617765 11.756965 5000
23000 1000 16.115382 7.9435503 5000
24000 1000 11.971003 5.9411126 5000
25000 1000 10.404117 4.3811155 5000
Loop time of 2.72875 on 1 procs for 25000 steps with 1000 atoms
Performance: 791570.958 tau/day, 9161.701 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.95597 | 0.95597 | 0.95597 | 0.0 | 35.03
Neigh | 0.38475 | 0.38475 | 0.38475 | 0.0 | 14.10
Comm | 0.010862 | 0.010862 | 0.010862 | 0.0 | 0.40
Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.02
Modify | 1.2364 | 1.2364 | 1.2364 | 0.0 | 45.31
Other | | 0.1402 | | | 5.14
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2374 ave 2374 max 2374 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2374
Ave neighs/atom = 2.374
Neighbor list builds = 2089
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
comm_modify vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.77 | 5.77 | 5.77 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 224 201.77464 0 5000
2000 224 372.42868 0 5000
3000 224 599.60221 0 5000
4000 448 1084.3752 0 5000
5000 448 1592.4543 0 5000
6000 448 1763.3153 37.274939 5000
7000 672 1805.206 89.331853 5000
8000 672 1778.0015 111.58381 5000
9000 672 1592.6805 97.550311 5000
10000 896 1630.8521 79.742572 5000
11000 896 1593.1588 67.633788 5000
12000 896 1562.2084 65.097236 5000
13000 1000 1504.1203 63.468934 5000
14000 1000 1266.5724 55.837334 5000
15000 1000 1041.8665 48.938774 5000
16000 1000 766.27305 43.846151 5000
17000 1000 466.30103 43.206188 5000
18000 1000 320.50154 26.84775 5000
19000 1000 207.91453 29.183522 5000
20000 1000 52.447982 19.30378 5000
21000 1000 22.027641 10.395933 5000
22000 1000 15.395099 6.7003289 5000
23000 1000 11.97674 5.2548063 5000
24000 1000 7.8974699 3.7396899 5000
25000 1000 6.1288038 2.2056805 5000
Loop time of 0.901039 on 4 procs for 25000 steps with 1000 atoms
Performance: 2397232.992 tau/day, 27745.752 timesteps/s
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21557 | 0.22754 | 0.23651 | 1.9 | 25.25
Neigh | 0.098304 | 0.10178 | 0.10595 | 1.0 | 11.30
Comm | 0.051792 | 0.066485 | 0.079589 | 3.8 | 7.38
Output | 0.00052619 | 0.00061941 | 0.00082016 | 0.0 | 0.07
Modify | 0.31782 | 0.32767 | 0.33815 | 1.5 | 36.37
Other | | 0.1769 | | | 19.64
Nlocal: 250 ave 267 max 232 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 18 ave 23 max 14 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 606 ave 664 max 559 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 2424
Ave neighs/atom = 2.424
Neighbor list builds = 2060
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
comm_modify vel yes cutoff 2.5
fix prop all property/atom mol ghost yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
Read molecule object:
5 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 all enforce2d
compute 1 all erotate/sphere
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic/dof yes
thermo 1000
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 2.5
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.81 | 5.81 | 5.81 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 130 259.24123 2.3772821e-30 5000
2000 130 465.39775 9.5010246e-30 5000
3000 130 736.55426 2.1365791e-29 5000
4000 260 1274.295 6.045774e-05 5000
5000 260 1855.4991 0.0021687846 5000
6000 260 1743.415 1.9678991 5000
7000 390 1675.8228 2.0085353 5000
8000 390 1845.2936 2.678293 5000
9000 390 1747.0301 2.5461774 5000
10000 520 2204.3744 1.3847146 5000
11000 520 1872.5943 6.5018283 5000
12000 520 1448.8705 3.2789997 5000
13000 650 1687.7845 2.4723994 5000
14000 650 1534.5832 1.7381523 5000
15000 650 1517.5812 2.4425352 5000
16000 780 1681.4276 3.5245463 5000
17000 780 1660.4845 3.5652485 5000
18000 780 1400.1788 4.1717202 5000
19000 910 1525.4386 3.2537276 5000
20000 910 1326.4257 3.5226044 5000
21000 910 1125.4321 3.1564949 5000
22000 1040 1262.0253 1.6097601 5000
23000 1040 1042.7 3.1078701 5000
24000 1040 1167.4717 1.4954047 5000
25000 1170 1214.9087 2.4525535 5000
Loop time of 3.36515 on 1 procs for 25000 steps with 1170 atoms
Performance: 641872.369 tau/day, 7429.078 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.73922 | 0.73922 | 0.73922 | 0.0 | 21.97
Neigh | 0.22808 | 0.22808 | 0.22808 | 0.0 | 6.78
Comm | 0.013331 | 0.013331 | 0.013331 | 0.0 | 0.40
Output | 0.00082207 | 0.00082207 | 0.00082207 | 0.0 | 0.02
Modify | 2.2694 | 2.2694 | 2.2694 | 0.0 | 67.44
Other | | 0.1143 | | | 3.40
Nlocal: 1170 ave 1170 max 1170 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1699 ave 1699 max 1699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1699
Ave neighs/atom = 1.45214
Neighbor list builds = 1715
Dangerous builds = 0
Total wall time: 0:00:03

142
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
comm_modify vel yes cutoff 2.5
fix prop all property/atom mol ghost yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
Read molecule object:
5 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# ensure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 all enforce2d
compute 1 all erotate/sphere
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic/dof yes
thermo 1000
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 2.5
binsize = 0.6, bins = 167 84 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.773 | 5.773 | 5.773 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 5000
1000 130 259.24123 2.3773387e-30 5000
2000 130 465.39775 9.5010816e-30 5000
3000 130 736.55426 2.1365846e-29 5000
4000 260 1274.295 6.045774e-05 5000
5000 260 1855.4991 0.0021687846 5000
6000 260 1743.415 1.9678991 5000
7000 390 1675.8228 2.0085353 5000
8000 390 1845.2936 2.678293 5000
9000 390 1747.0301 2.5461774 5000
10000 520 2204.3744 1.3847146 5000
11000 520 1872.5943 6.5018283 5000
12000 520 1448.8705 3.2789997 5000
13000 650 1687.7845 2.4723994 5000
14000 650 1534.5832 1.7381523 5000
15000 650 1517.5812 2.4425352 5000
16000 780 1680.8761 3.5506853 5000
17000 780 1661.6046 3.6673972 5000
18000 780 1391.3201 4.1075002 5000
19000 910 1526.6687 3.410537 5000
20000 910 1387.6908 2.7370047 5000
21000 910 1056.6723 2.5690119 5000
22000 1040 1226.7461 1.2299974 5000
23000 1040 1106.7165 3.1057108 5000
24000 1040 1161.9203 2.0994962 5000
25000 1170 1187.5093 2.9596172 5000
Loop time of 1.4211 on 4 procs for 25000 steps with 1170 atoms
Performance: 1519946.444 tau/day, 17591.973 timesteps/s
94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19053 | 0.21869 | 0.23582 | 3.7 | 15.39
Neigh | 0.06394 | 0.066575 | 0.070017 | 0.9 | 4.68
Comm | 0.055579 | 0.070079 | 0.080658 | 3.4 | 4.93
Output | 0.0012593 | 0.0031545 | 0.0088205 | 5.8 | 0.22
Modify | 0.89034 | 0.9006 | 0.91315 | 0.9 | 63.37
Other | | 0.162 | | | 11.40
Nlocal: 292.5 ave 296 max 285 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Nghost: 44 ave 60 max 21 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 433.25 ave 449 max 418 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 1733
Ave neighs/atom = 1.4812
Neighbor list builds = 1708
Dangerous builds = 0
Total wall time: 0:00:01

175
examples/pour/log.27Nov18.pour.g++.1
View File

@ -1,175 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 34 34 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.955 | 5.955 | 5.955 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 6600
1000 402 768.04606 0 6600
2000 402 1407.1714 0 6600
3000 402 1373.819 15.59952 6600
4000 804 1737.1399 39.311164 6600
5000 804 1571.3184 67.501382 6600
6000 804 1318.6439 77.636174 6600
7000 1206 1522.1986 68.863683 6600
8000 1206 1387.2223 64.067846 6600
9000 1206 1265.9044 51.726525 6600
10000 1608 1460.3212 48.844763 6600
11000 1608 1310.2001 53.532609 6600
12000 1608 1134.4592 48.567743 6600
13000 2010 1182.5037 45.620614 6600
14000 2010 1192.4303 39.066935 6600
15000 2010 967.05968 42.363789 6600
16000 2412 1119.8304 39.217157 6600
17000 2412 1063.7921 45.71714 6600
18000 2412 855.28326 42.745948 6600
19000 2814 970.7019 40.155896 6600
20000 2814 923.94347 34.590568 6600
21000 2814 793.75092 36.707509 6600
22000 2814 543.4546 37.669131 6600
23000 3000 446.47658 39.719019 6600
24000 3000 331.57201 24.034747 6600
25000 3000 239.90493 18.457205 6600
Loop time of 8.66761 on 1 procs for 25000 steps with 3000 atoms
Performance: 249203.592 tau/day, 2884.301 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5311 | 4.5311 | 4.5311 | 0.0 | 52.28
Neigh | 1.4556 | 1.4556 | 1.4556 | 0.0 | 16.79
Comm | 0.2322 | 0.2322 | 0.2322 | 0.0 | 2.68
Output | 0.00084257 | 0.00084257 | 0.00084257 | 0.0 | 0.01
Modify | 2.1642 | 2.1642 | 2.1642 | 0.0 | 24.97
Other | | 0.2837 | | | 3.27
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 658 ave 658 max 658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13479 ave 13479 max 13479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13479
Ave neighs/atom = 4.493
Neighbor list builds = 1149
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Per MPI rank memory allocation (min/avg/max) = 13.24 | 13.24 | 13.24 Mbytes
Step Atoms KinEng c_1 Volume
25000 3000 239.90493 18.457205 6600
26000 3000 86.453151 19.990229 6600
27000 3000 104.03763 12.243926 6600
28000 3000 187.74939 11.703132 6600
29000 3000 316.59921 14.610301 6600
30000 3000 520.76149 18.82089 6600
31000 3000 821.71283 25.266473 6600
32000 3000 1153.8578 30.714985 6600
33000 3000 1520.1476 38.247011 6600
34000 3000 2006.3144 44.480026 6600
35000 3000 2556.4751 55.768118 6600
36000 3000 3160.9914 63.728696 6600
37000 3000 3877.5537 71.484742 6600
38000 3000 4675.4987 79.37485 6600
39000 3000 5479.8489 94.281786 6600
40000 3000 6350.6439 106.39353 6600
41000 3000 7245.0837 113.40306 6600
42000 3000 8227.1726 129.62268 6600
43000 3000 9422.0189 144.63991 6600
44000 3000 10616.036 149.84326 6600
45000 3000 11908.182 169.96204 6600
46000 3000 13257.313 184.73533 6600
47000 3000 14765.4 201.20237 6600
48000 3000 16184.643 202.00907 6600
49000 3000 17573.204 215.30429 6600
50000 3000 19117.749 232.28939 6600
Loop time of 16.4345 on 1 procs for 25000 steps with 3000 atoms
Performance: 131430.508 tau/day, 1521.186 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.893 | 9.893 | 9.893 | 0.0 | 60.20
Neigh | 2.1448 | 2.1448 | 2.1448 | 0.0 | 13.05
Comm | 0.47991 | 0.47991 | 0.47991 | 0.0 | 2.92
Output | 0.0011523 | 0.0011523 | 0.0011523 | 0.0 | 0.01
Modify | 3.4635 | 3.4635 | 3.4635 | 0.0 | 21.07
Other | | 0.4522 | | | 2.75
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 742 ave 742 max 742 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13997 ave 13997 max 13997 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13997
Ave neighs/atom = 4.66567
Neighbor list builds = 836
Dangerous builds = 0
Total wall time: 0:00:25

175
examples/pour/log.27Nov18.pour.g++.4
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@ -1,175 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6, bins = 34 34 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.83 | 5.83 | 5.83 Mbytes
Step Atoms KinEng c_1 Volume
0 0 -0 0 6600
1000 402 768.04606 0 6600
2000 402 1407.1714 0 6600
3000 402 1373.819 15.59952 6600
4000 804 1737.1399 39.311164 6600
5000 804 1571.3184 67.501382 6600
6000 804 1318.6439 77.636174 6600
7000 1206 1521.8348 69.010381 6600
8000 1206 1391.0761 64.407583 6600
9000 1206 1264.98 50.32567 6600
10000 1608 1462.7175 49.903609 6600
11000 1608 1317.5878 52.401196 6600
12000 1608 1120.9416 46.067058 6600
13000 2010 1200.1517 49.662302 6600
14000 2010 1180.2805 38.850379 6600
15000 2010 970.23519 39.121533 6600
16000 2412 1101.3888 44.051087 6600
17000 2412 1054.4967 43.489619 6600
18000 2412 850.25959 42.296696 6600
19000 2814 959.68841 42.757546 6600
20000 2814 933.72206 42.668586 6600
21000 2814 779.2842 42.116934 6600
22000 2814 537.68477 35.113909 6600
23000 3000 456.26221 36.394458 6600
24000 3000 334.38331 26.256087 6600
25000 3000 233.7217 18.768345 6600
Loop time of 2.79912 on 4 procs for 25000 steps with 3000 atoms
Performance: 771671.423 tau/day, 8931.382 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0916 | 1.1431 | 1.1982 | 4.0 | 40.84
Neigh | 0.37439 | 0.39186 | 0.41149 | 2.6 | 14.00
Comm | 0.32241 | 0.32795 | 0.33831 | 1.1 | 11.72
Output | 0.00068283 | 0.0029467 | 0.0094671 | 6.9 | 0.11
Modify | 0.5813 | 0.5952 | 0.60947 | 1.5 | 21.26
Other | | 0.3381 | | | 12.08
Nlocal: 750 ave 765 max 730 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 390.75 ave 393 max 385 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 3548 ave 3643 max 3454 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 14192
Ave neighs/atom = 4.73067
Neighbor list builds = 1152
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.39 | 13.06 Mbytes
Step Atoms KinEng c_1 Volume
25000 3000 233.7217 18.768345 6600
26000 3000 80.58756 21.114703 6600
27000 3000 112.90794 11.760837 6600
28000 3000 211.68857 11.667711 6600
29000 3000 368.27114 15.483397 6600
30000 3000 611.33941 21.023859 6600
31000 3000 902.04662 29.663904 6600
32000 3000 1188.6213 31.996848 6600
33000 3000 1626.3144 38.244424 6600
34000 3000 2068.1939 45.793779 6600
35000 3000 2654.4292 55.900641 6600
36000 3000 3212.0662 64.492942 6600
37000 3000 3942.9079 73.557353 6600
38000 3000 4710.2169 84.24051 6600
39000 3000 5513.597 93.737814 6600
40000 3000 6367.338 112.43633 6600
41000 3000 7417.7889 130.70338 6600
42000 3000 8428.2678 124.66302 6600
43000 3000 9498.0121 136.37107 6600
44000 3000 10680.269 149.21074 6600
45000 3000 11852.03 154.67802 6600
46000 3000 12896.699 167.10324 6600
47000 3000 14218.465 196.70386 6600
48000 3000 15555.796 204.40316 6600
49000 3000 16694.338 208.98934 6600
50000 3000 17936.665 192.19442 6600
Loop time of 5.65089 on 4 procs for 25000 steps with 3000 atoms
Performance: 382240.368 tau/day, 4424.078 timesteps/s
94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5656 | 2.5853 | 2.6068 | 0.9 | 45.75
Neigh | 0.57736 | 0.59939 | 0.61824 | 1.9 | 10.61
Comm | 0.58146 | 0.63908 | 0.70461 | 5.5 | 11.31
Output | 0.00081015 | 0.002184 | 0.0061922 | 5.0 | 0.04
Modify | 0.91975 | 0.93371 | 0.95875 | 1.5 | 16.52
Other | | 0.8912 | | | 15.77
Nlocal: 750 ave 758 max 741 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 404 ave 417 max 395 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 3603.75 ave 3695 max 3528 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 14415
Ave neighs/atom = 4.805
Neighbor list builds = 827
Dangerous builds = 0
Total wall time: 0:00:08

28
lib/plumed/Install.py
View File

@ -17,17 +17,17 @@ parser = ArgumentParser(prog='Install.py',
# settings
version = "2.8.1"
version = "2.8.2"
mode = "static"
# help message
HELP = """
Syntax from src dir: make lib-plumed args="-b"
or: make lib-plumed args="-b -v 2.4.3"
or: make lib-plumed args="-b -v 2.8.2"
or: make lib-plumed args="-p /usr/local/plumed2 -m shared"
Syntax from lib dir: python Install.py -b -v 2.4.3
Syntax from lib dir: python Install.py -b -v 2.8.2
or: python Install.py -b
or: python Install.py -p /usr/local/plumed2 -m shared
@ -37,30 +37,14 @@ make lib-plumed args="-b" # download/build in lib/plumed/plumed2
make lib-plumed args="-p $HOME/plumed2 -m shared" # use existing Plumed2 installation in $HOME/plumed2
"""
# known checksums for different PLUMED versions. used to validate the download.
# known checksums for different PLUMED versions. used to validate downloads.
checksums = { \
'2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \
'2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \
'2.4.4' : '71ed465bdc7c2059e282dbda8d564e71', \
'2.5.0' : '6224cd089493661e19ceacccd35cf911', \
'2.5.1' : 'c2a7b519e32197a120cdf47e0f194f81', \
'2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
'2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
'2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \
'2.5.7' : '1ca36226fdb8110b1009aa61d615d4e5', \
'2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \
'2.6.1' : '89a9a450fc6025299fe16af235957163', \
'2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \
'2.6.5' : 'b67356f027e5c2747823b0422c3b0ec2', \
'2.6.6' : '6b470dcdce04c221ea42d8500b03c49b', \
'2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \
'2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \
'2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \
'2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \
'2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \
'2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \
'2.8.0' : '489b23daba70da78cf0506cbc31689c6', \
'2.7.6' : 'fb8c0ec10f97a9353eb123a5c4c35aa6', \
'2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
'2.8.2' : '599092b6a0aa6fff992612537ad98994', \
}
# parse and process arguments

12
python/install.py
View File

@ -59,10 +59,14 @@ olddir = os.path.abspath('.')
os.chdir(os.path.dirname(args.package))
# remove any wheel files left over from previous calls
print("Purging existing wheels...")
for wheel in glob.glob('lammps-*.whl'):
print("deleting " + wheel)
os.remove(wheel)
if os.path.isdir(os.path.join(olddir,"build")):
print("Cleaning old build directory")
shutil.rmtree(os.path.join(olddir,"build"))
#print("Purging existing wheels...")
#for wheel in glob.glob('lammps-*.whl'):
# print("deleting " + wheel)
# os.remove(wheel)
# copy shared object to the current folder so that
# it will show up in the installation at the expected location

3
python/lammps/core.py
View File

@ -814,7 +814,8 @@ class lammps(object):
# set length of vector for items that are not a scalar
vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3,
'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3 }
'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3,
'special_lj':4, 'special_coul':4 }
if name in vec_dict:
veclen = vec_dict[name]
elif name == 'respa_dt':

28
src/.gitignore vendored
View File

@ -462,8 +462,6 @@
/atom_vec_full.h
/atom_vec_full_hars.cpp
/atom_vec_full_hars.h
/atom_vec_granular.cpp
/atom_vec_granular.h
/atom_vec_molecular.cpp
/atom_vec_molecular.h
/atom_vec_oxdna.cpp
@ -492,6 +490,8 @@
/bond_gromos.h
/bond_harmonic.cpp
/bond_harmonic.h
/bond_harmonic_restrain.cpp
/bond_harmonic_restrain.h
/bond_harmonic_shift.cpp
/bond_harmonic_shift.h
/bond_harmonic_shift_cut.cpp
@ -534,6 +534,10 @@
/compute_damage_atom.h
/compute_dilatation_atom.cpp
/compute_dilatation_atom.h
/compute_dipole_tip4p.cpp
/compute_dipole_tip4p.h
/compute_dipole_tip4p_chunk.cpp
/compute_dipole_tip4p_chunk.h
/compute_dpd.cpp
/compute_dpd.h
/compute_dpd_atom.cpp
@ -752,6 +756,8 @@
/fix_damping_cundall.h
/fix_dpd_energy.cpp
/fix_dpd_energy.h
/fix_efield_tip4p.cpp
/fix_efield_tip4p.h
/fix_electron_stopping.cpp
/fix_electron_stopping.h
/fix_electron_stopping_fit.cpp
@ -1565,6 +1571,8 @@
/fix_srp.h
/fix_srp_react.cpp
/fix_srp_react.h
/fix_heat_flow.cpp
/fix_heat_flow.h
/fix_tfmc.cpp
/fix_tfmc.h
/fix_ttm.cpp
@ -1573,6 +1581,22 @@
/fix_ttm_grid.h
/fix_ttm_mod.cpp
/fix_ttm_mod.h
/granular_model.cpp
/granular_model.h
/gran_sub_mod_normal.cpp
/gran_sub_mod_normal.h
/gran_sub_mod_damping.cpp
/gran_sub_mod_damping.h
/gran_sub_mod_tangential.cpp
/gran_sub_mod_tangential.h
/gran_sub_mod_twisting.cpp
/gran_sub_mod_twisting.h
/gran_sub_mod_rolling.cpp
/gran_sub_mod_rolling.h
/gran_sub_mod_heat.cpp
/gran_sub_mod_heat.h
/gran_sub_mod.cpp
/gran_sub_mod.h
/pair_born_coul_long_cs.cpp
/pair_born_coul_long_cs.h
/pair_born_coul_dsf_cs.cpp

2
src/AMOEBA/amoeba_induce.cpp
View File

@ -19,7 +19,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "math_const.h"
#include "math_special.h"
#include "my_page.h"

2
src/AMOEBA/amoeba_utils.cpp
View File

@ -17,7 +17,7 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "neigh_list.h"
#include <cmath>

4
src/AMOEBA/improper_amoeba.cpp
View File

@ -36,6 +36,10 @@ using namespace MathConst;
ImproperAmoeba::ImproperAmoeba(LAMMPS *lmp) : Improper(lmp)
{
writedata = 1;
// the second atom in the quadruplet is the atom of symmetry
symmatoms[1] = 1;
}
/* ---------------------------------------------------------------------- */

26
src/AMOEBA/pair_amoeba.cpp
View File

@ -20,7 +20,7 @@
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "math_special.h"
@ -861,8 +861,8 @@ void PairAmoeba::init_style()
Fix *myfix;
if (first_flag) {
id_pole = utils::strdup("AMOEBA_pole");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
fixpole = dynamic_cast<FixStorePeratom *>(myfix);
myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM 13 0 0 1",id_pole,group->names[0]));
fixpole = dynamic_cast<FixStoreAtom *>(myfix);
}
// creation of per-atom storage
@ -873,14 +873,14 @@ void PairAmoeba::init_style()
if (first_flag && use_pred) {
id_udalt = utils::strdup("AMOEBA_udalt");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
id_udalt, group->names[0], maxualt));
fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
id_upalt = utils::strdup("AMOEBA_upalt");
myfix = modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 {} 3",
myfix = modify->add_fix(fmt::format("{} {} STORE/ATOM {} 3 0 1",
id_upalt, group->names[0], maxualt));
fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
}
// create pages for storing pairwise data:
@ -995,21 +995,21 @@ void PairAmoeba::init_style()
if (id_pole) {
myfix = modify->get_fix_by_id(id_pole);
if (!myfix)
error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_pole);
fixpole = dynamic_cast<FixStorePeratom *>(myfix);
error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_pole);
fixpole = dynamic_cast<FixStoreAtom *>(myfix);
}
if (id_udalt) {
myfix = modify->get_fix_by_id(id_udalt);
if (!myfix)
error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_udalt);
fixudalt = dynamic_cast<FixStorePeratom *>(myfix);
error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_udalt);
fixudalt = dynamic_cast<FixStoreAtom *>(myfix);
myfix = modify->get_fix_by_id(id_upalt);
if (!myfix)
error->all(FLERR,"Could not find internal pair amoeba fix STORE/PERATOM id {}", id_upalt);
fixupalt = dynamic_cast<FixStorePeratom *>(myfix);
error->all(FLERR,"Could not find internal pair amoeba fix STORE/ATOM id {}", id_upalt);
fixupalt = dynamic_cast<FixStoreAtom *>(myfix);
}
// assign hydrogen neighbors (redID) to each owned atom

6
src/AMOEBA/pair_amoeba.h
View File

@ -166,9 +166,9 @@ class PairAmoeba : public Pair {
int *amgroup; // AMOEBA polarization group, 1 to Ngroup
char *id_pole, *id_udalt, *id_upalt;
class FixStorePeratom *fixpole; // stores pole = multipole components
class FixStorePeratom *fixudalt; // stores udalt = induced dipole history
class FixStorePeratom *fixupalt; // stores upalt = induced dipole history
class FixStoreAtom *fixpole; // stores pole = multipole components
class FixStoreAtom *fixudalt; // stores udalt = induced dipole history
class FixStoreAtom *fixupalt; // stores upalt = induced dipole history
// static per-type properties defined in force-field file

4
src/CLASS2/improper_class2.cpp
View File

@ -39,6 +39,10 @@ using namespace MathConst;
ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp)
{
writedata = 1;
// the second atom in the quadruplet is the atom of symmetry
symmatoms[1] = 1;
}
/* ---------------------------------------------------------------------- */

5
src/COLVARS/ndx_group.cpp
View File

@ -81,6 +81,8 @@ void Ndx2Group::command(int narg, char **arg)
if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
if (atom->tag_enable == 0)
error->all(FLERR,"Must have atom IDs for ndx2group command");
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,"Must have an atom map for ndx2group command");
if (comm->me == 0) {
fp = fopen(arg[0], "r");
if (fp == nullptr)
@ -153,11 +155,12 @@ void Ndx2Group::command(int narg, char **arg)
MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
// read tags for atoms in group and broadcast
std::vector<tagint> tags = read_section(fp,name);
std::vector<tagint> tags = read_section(fp,next);
num = tags.size();
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
create(name,tags);
name = next;
}
} else {
MPI_Bcast(&len,1,MPI_INT,0,world);

6
src/CORESHELL/compute_temp_cs.cpp
View File

@ -24,7 +24,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fix_store_peratom.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "memory.h"
@ -67,8 +67,8 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
// id = compute-ID + COMPUTE_STORE, fix group = compute group
id_fix = utils::strdup(id + std::string("_COMPUTE_STORE"));
fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 0 1", id_fix, group->names[igroup])));
fix = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 0", id_fix, group->names[igroup])));
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called

2
src/CORESHELL/compute_temp_cs.h
View File

@ -54,7 +54,7 @@ class ComputeTempCS : public Compute {
double **vint;
char *id_fix;
class FixStorePeratom *fix;
class FixStoreAtom *fix;
void dof_compute();
void vcm_pairs();

220
src/EXTRA-COMPUTE/compute_dipole_tip4p.cpp Normal file
View File

@ -0,0 +1,220 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "compute_dipole_tip4p.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
enum { MASSCENTER, GEOMCENTER };
/* ---------------------------------------------------------------------- */
ComputeDipoleTIP4P::ComputeDipoleTIP4P(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if ((narg < 3) || (narg > 4)) error->all(FLERR, "Illegal compute dipole/tip4p command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
extscalar = 0;
extvector = 0;
vector = new double[size_vector];
vector[0] = vector[1] = vector[2] = 0.0;
usecenter = MASSCENTER;
if (narg == 4) {
if (utils::strmatch(arg[3], "^geom"))
usecenter = GEOMCENTER;
else if (strcmp(arg[3], "mass") == 0)
usecenter = MASSCENTER;
else
error->all(FLERR, "Illegal compute dipole/tip4p command");
}
}
/* ---------------------------------------------------------------------- */
ComputeDipoleTIP4P::~ComputeDipoleTIP4P()
{
delete[] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeDipoleTIP4P::init()
{
if (!force->pair) error->all(FLERR, "Pair style must be defined for compute dipole/ti4p");
int itmp;
double *p_qdist = (double *) force->pair->extract("qdist", itmp);
int *p_typeO = (int *) force->pair->extract("typeO", itmp);
int *p_typeH = (int *) force->pair->extract("typeH", itmp);
int *p_typeA = (int *) force->pair->extract("typeA", itmp);
int *p_typeB = (int *) force->pair->extract("typeB", itmp);
if (!p_qdist || !p_typeO || !p_typeH || !p_typeA || !p_typeB)
error->all(FLERR, "Pair style is incompatible with compute dipole/tip4p");
typeO = *p_typeO;
typeH = *p_typeH;
int typeA = *p_typeA;
int typeB = *p_typeB;
if (!force->angle || !force->bond || !force->angle->setflag || !force->bond->setflag)
error->all(FLERR, "Bond and angle potentials must be defined for compute dipole/tip4p");
if ((typeA < 1) || (typeA > atom->nangletypes) || (force->angle->setflag[typeA] == 0))
error->all(FLERR, "Bad TIP4P angle type for compute dipole/tip4p");
if ((typeB < 1) || (typeB > atom->nbondtypes) || (force->bond->setflag[typeB] == 0))
error->all(FLERR, "Bad TIP4P bond type for compute dipole/tip4p");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = *p_qdist / (cos(0.5 * theta) * blen);
}
/* ---------------------------------------------------------------------- */
void ComputeDipoleTIP4P::compute_vector()
{
invoked_vector = update->ntimestep;
const auto x = atom->x;
const auto mask = atom->mask;
const auto type = atom->type;
const auto image = atom->image;
const auto mass = atom->mass;
const auto rmass = atom->rmass;
const auto q = atom->q;
const auto mu = atom->mu;
const auto nlocal = atom->nlocal;
double dipole[3] = {0.0, 0.0, 0.0};
double comproc[3] = {0.0, 0.0, 0.0};
double com[3] = {0.0, 0.0, 0.0};
double masstotal = 0.0;
double chrgtotal = 0.0;
double massproc = 0.0;
double chrgproc = 0.0;
double unwrap[3], xM[3];
double *xi;
for (int i = 0; i < nlocal; ++i) {
if (mask[i] & groupbit) {
double massone = 1.0; // for usecenter == GEOMCENTER
if (usecenter == MASSCENTER) {
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
}
massproc += massone;
if (atom->q_flag) chrgproc += q[i];
domain->unmap(x[i], image[i], unwrap);
comproc[0] += unwrap[0] * massone;
comproc[1] += unwrap[1] * massone;
comproc[2] += unwrap[2] * massone;
}
}
MPI_Allreduce(&massproc, &masstotal, 1, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(&chrgproc, &chrgtotal, 1, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(comproc, com, 3, MPI_DOUBLE, MPI_SUM, world);
if (masstotal > 0.0) {
com[0] /= masstotal;
com[1] /= masstotal;
com[2] /= masstotal;
}
// compute dipole moment
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (type[i] == typeO) {
find_M(i, xM);
xi = xM;
} else {
xi = x[i];
}
domain->unmap(xi, image[i], unwrap);
if (atom->q_flag) {
dipole[0] += q[i] * unwrap[0];
dipole[1] += q[i] * unwrap[1];
dipole[2] += q[i] * unwrap[2];
}
if (atom->mu_flag) {
dipole[0] += mu[i][0];
dipole[1] += mu[i][1];
dipole[2] += mu[i][2];
}
}
}
MPI_Allreduce(dipole, vector, 3, MPI_DOUBLE, MPI_SUM, world);
// correct for position dependence with a net charged group
vector[0] -= chrgtotal * com[0];
vector[1] -= chrgtotal * com[1];
vector[2] -= chrgtotal * com[2];
}
/* ---------------------------------------------------------------------- */
double ComputeDipoleTIP4P::compute_scalar()
{
if (invoked_vector != update->ntimestep) compute_vector();
invoked_scalar = update->ntimestep;
scalar = sqrt(vector[0] * vector[0] + vector[1] * vector[1] + vector[2] * vector[2]);
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeDipoleTIP4P::find_M(int i, double *xM)
{
double **x = atom->x;
int iH1 = atom->map(atom->tag[i] + 1);
int iH2 = atom->map(atom->tag[i] + 2);
if ((iH1 == -1) || (iH2 == -1)) error->one(FLERR, "TIP4P hydrogen is missing");
if ((atom->type[iH1] != typeH) || (atom->type[iH2] != typeH))
error->one(FLERR, "TIP4P hydrogen has incorrect atom type");
// set iH1,iH2 to index of closest image to O
iH1 = domain->closest_image(i, iH1);
iH2 = domain->closest_image(i, iH2);
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
}

46
src/EXTRA-COMPUTE/compute_dipole_tip4p.h Normal file
View File

@ -0,0 +1,46 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
// clang-format off
ComputeStyle(dipole/tip4p,ComputeDipoleTIP4P);
// clang-format on
#else
#ifndef LMP_COMPUTE_DIPOLE_TIP4P_H
#define LMP_COMPUTE_DIPOLE_TIP4P_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeDipoleTIP4P : public Compute {
public:
ComputeDipoleTIP4P(class LAMMPS *, int, char **);
~ComputeDipoleTIP4P() override;
void init() override;
void compute_vector() override;
double compute_scalar() override;
private:
int usecenter;
int typeO, typeH;
double alpha;
void find_M(int i, double *xM);
};
} // namespace LAMMPS_NS
#endif
#endif

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